Breast Invasive Carcinoma: PARADIGM pathway analysis of mRNA expression and copy number data
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
Overview
Introduction

PAthway Representation and Analysis by Direct Inference on Graphical Models (PARADIGM) predicts the activity of a diverse set of molecular concepts such as genes, complexes, and processes. The predicted activities are called Inferred Pathway Levels (IPLs) and are derived from a probabilistic belief propagation strategy that incorporates multimodal data such as copy number and gene expression estimates with a concept's pathway context.

Summary

There were 51 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
Signaling events regulated by Ret tyrosine kinase 98
Signaling events mediated by Stem cell factor receptor (c-Kit) 90
Endothelins 76
IGF1 pathway 72
FOXM1 transcription factor network 69
Plasma membrane estrogen receptor signaling 67
EGFR-dependent Endothelin signaling events 66
Syndecan-1-mediated signaling events 65
Osteopontin-mediated events 64
IL4-mediated signaling events 63
Results

The following list describes the columns found in Table 2.

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

  • Avg.Num.Perturbations = Average number of samples with perturbations across the pathway concepts determined by a background permutation model (>2 standard deviations away from the permuted distribution)

  • Total.Perturbations = Total number of perturbed concepts across all samples (>2 standard deviations away from the permuted distribution)

  • Num.Entities = Number of concepts that belong to the pathway

  • Min.Mean.Truth = Minimum IPL for concepts in the pathway among real samples

  • Max.Mean.Truth = Maximum IPL for concepts in the pathway among real samples

  • Min.Mean.Within = Minimum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Max.Mean.Within = Maximum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Min.Mean.Any = Minimum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes)

  • Max.Mean.Any = Maximum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes).

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway.

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Signaling events regulated by Ret tyrosine kinase 98 8115 82 -0.16 0.036 1000 -1000 -0.034 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 90 7057 78 -0.31 0.13 1000 -1000 -0.034 -1000
Endothelins 76 7360 96 -0.18 0.035 1000 -1000 -0.025 -1000
IGF1 pathway 72 4149 57 -0.079 0.052 1000 -1000 -0.022 -1000
FOXM1 transcription factor network 69 3540 51 -0.44 0.034 1000 -1000 -0.075 -1000
Plasma membrane estrogen receptor signaling 67 5827 86 -0.22 0.21 1000 -1000 -0.034 -1000
EGFR-dependent Endothelin signaling events 66 1391 21 -0.072 0.048 1000 -1000 -0.016 -1000
Syndecan-1-mediated signaling events 65 2226 34 -0.13 0.042 1000 -1000 -0.012 -1000
Osteopontin-mediated events 64 2446 38 -0.14 0.04 1000 -1000 -0.025 -1000
IL4-mediated signaling events 63 5745 91 -0.53 0.43 1000 -1000 -0.066 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 58 4006 68 -0.35 0.15 1000 -1000 -0.054 -1000
HIF-1-alpha transcription factor network 57 4399 76 -0.18 0.05 1000 -1000 -0.02 -1000
Glucocorticoid receptor regulatory network 55 6341 114 -0.39 0.19 1000 -1000 -0.038 -1000
Signaling events mediated by the Hedgehog family 54 2820 52 -0.096 0.052 1000 -1000 -0.014 -1000
Fc-epsilon receptor I signaling in mast cells 51 4975 97 -0.098 0.036 1000 -1000 -0.055 -1000
Thromboxane A2 receptor signaling 49 5227 105 -0.11 0.062 1000 -1000 -0.026 -1000
Wnt signaling 49 344 7 -0.067 0.03 1000 -1000 -0.005 -1000
IL23-mediated signaling events 49 2969 60 -0.2 0.036 1000 -1000 -0.033 -1000
TCR signaling in naïve CD8+ T cells 46 4361 93 -0.072 0.048 1000 -1000 -0.032 -1000
Nongenotropic Androgen signaling 46 2408 52 -0.12 0.063 1000 -1000 -0.017 -1000
Stabilization and expansion of the E-cadherin adherens junction 46 3437 74 -0.095 0.059 1000 -1000 -0.044 -1000
IL12-mediated signaling events 45 3992 87 -0.26 0.043 1000 -1000 -0.033 -1000
IL27-mediated signaling events 44 2292 51 -0.2 0.099 1000 -1000 -0.05 -1000
IL6-mediated signaling events 44 3315 75 -0.14 0.038 1000 -1000 -0.034 -1000
Noncanonical Wnt signaling pathway 43 1143 26 -0.067 0.036 1000 -1000 -0.036 -1000
FAS signaling pathway (CD95) 42 1991 47 -0.1 0.049 1000 -1000 -0.031 -1000
Syndecan-4-mediated signaling events 40 2680 67 -0.061 0.087 1000 -1000 -0.028 -1000
E-cadherin signaling in keratinocytes 40 1758 43 -0.062 0.036 1000 -1000 -0.013 -1000
Signaling mediated by p38-gamma and p38-delta 39 585 15 -0.056 0.033 1000 -1000 -0.026 -1000
Arf6 signaling events 38 2356 62 -0.069 0.079 1000 -1000 -0.006 -1000
LPA receptor mediated events 38 3964 102 -0.077 0.036 1000 -1000 -0.037 -1000
Ephrin B reverse signaling 36 1730 48 -0.12 0.073 1000 -1000 -0.037 -1000
IL2 signaling events mediated by PI3K 35 2074 58 -0.23 0.036 1000 -1000 -0.039 -1000
E-cadherin signaling in the nascent adherens junction 34 2605 76 -0.082 0.056 1000 -1000 -0.043 -1000
E-cadherin signaling events 34 173 5 -0.011 0.028 1000 -1000 0.024 -1000
ErbB4 signaling events 33 2316 69 -0.1 0.059 1000 -1000 -0.022 -1000
TCGA08_p53 33 234 7 -0.028 0.026 1000 -1000 -0.006 -1000
Signaling events mediated by PTP1B 32 2483 76 -0.091 0.062 1000 -1000 -0.038 -1000
Canonical Wnt signaling pathway 32 1672 51 -0.15 0.09 1000 -1000 -0.035 -1000
Coregulation of Androgen receptor activity 31 2370 76 -0.15 0.054 1000 -1000 -0.011 -1000
PLK2 and PLK4 events 31 93 3 -0.013 0.03 1000 -1000 0.001 -1000
Syndecan-2-mediated signaling events 31 2167 69 -0.019 0.048 1000 -1000 -0.032 -1000
Integrins in angiogenesis 30 2561 84 -0.12 0.06 1000 -1000 -0.024 -1000
amb2 Integrin signaling 29 2415 82 -0.049 0.047 1000 -1000 -0.015 -1000
Caspase cascade in apoptosis 28 2117 74 -0.066 0.047 1000 -1000 -0.024 -1000
Cellular roles of Anthrax toxin 28 1122 39 -0.074 0.035 1000 -1000 -0.017 -1000
TCGA08_retinoblastoma 28 230 8 -0.011 0.024 1000 -1000 -0.009 -1000
Regulation of nuclear SMAD2/3 signaling 27 3708 136 -0.19 0.067 1000 -1000 -0.034 -1000
Reelin signaling pathway 27 1526 56 -0.068 0.07 1000 -1000 -0.021 -1000
BCR signaling pathway 27 2715 99 -0.1 0.065 1000 -1000 -0.039 -1000
Visual signal transduction: Rods 27 1429 52 -0.064 0.067 1000 -1000 -0.017 -1000
BMP receptor signaling 26 2185 81 -0.11 0.067 1000 -1000 -0.022 -1000
Nectin adhesion pathway 26 1685 63 -0.047 0.054 1000 -1000 -0.032 -1000
IL1-mediated signaling events 26 1628 62 -0.028 0.075 1000 -1000 -0.029 -1000
Aurora B signaling 26 1747 67 -0.062 0.053 1000 -1000 -0.027 -1000
mTOR signaling pathway 25 1369 53 -0.068 0.045 1000 -1000 -0.031 -1000
VEGFR1 specific signals 25 1439 56 -0.028 0.036 1000 -1000 -0.026 -1000
PDGFR-alpha signaling pathway 24 1058 44 -0.14 0.05 1000 -1000 -0.024 -1000
Arf6 downstream pathway 23 1020 43 -0.047 0.048 1000 -1000 -0.033 -1000
IFN-gamma pathway 23 1618 68 -0.061 0.059 1000 -1000 -0.038 -1000
PLK1 signaling events 22 1889 85 -0.074 0.052 1000 -1000 -0.032 -1000
Visual signal transduction: Cones 21 816 38 -0.023 0.051 1000 -1000 0 -1000
FOXA2 and FOXA3 transcription factor networks 21 966 46 -0.2 0.043 1000 -1000 -0.044 -1000
Glypican 1 network 21 1046 48 -0.025 0.049 1000 -1000 -0.022 -1000
Ceramide signaling pathway 21 1631 76 -0.069 0.069 1000 -1000 -0.026 -1000
S1P1 pathway 21 777 36 -0.034 0.036 1000 -1000 -0.024 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 21 976 45 -0.041 0.055 1000 -1000 -0.024 -1000
Insulin Pathway 21 1594 74 -0.063 0.081 1000 -1000 -0.021 -1000
Presenilin action in Notch and Wnt signaling 20 1267 61 -0.2 0.071 1000 -1000 -0.032 -1000
TRAIL signaling pathway 20 985 48 -0.022 0.037 1000 -1000 -0.021 -1000
ceramide signaling pathway 20 1011 49 -0.057 0.049 1000 -1000 -0.02 -1000
EPHB forward signaling 20 1708 85 -0.047 0.11 1000 -1000 -0.045 -1000
Calcium signaling in the CD4+ TCR pathway 20 648 31 -0.035 0.045 1000 -1000 -0.036 -1000
Class I PI3K signaling events 20 1521 73 -0.061 0.045 1000 -1000 -0.026 -1000
Regulation of Telomerase 20 2059 102 -0.15 0.063 1000 -1000 -0.025 -1000
PDGFR-beta signaling pathway 19 1932 97 -0.065 0.067 1000 -1000 -0.025 -1000
ErbB2/ErbB3 signaling events 18 1199 65 -0.045 0.048 1000 -1000 -0.045 -1000
EPO signaling pathway 18 1023 55 -0.11 0.046 1000 -1000 -0.016 -1000
RXR and RAR heterodimerization with other nuclear receptor 18 968 52 -0.057 0.063 1000 -1000 -0.02 -1000
Syndecan-3-mediated signaling events 17 601 35 -0.031 0.069 1000 -1000 -0.02 -1000
p75(NTR)-mediated signaling 16 2044 125 -0.045 0.086 1000 -1000 -0.037 -1000
Atypical NF-kappaB pathway 16 507 31 -0.017 0.036 1000 -1000 -0.007 -1000
Ras signaling in the CD4+ TCR pathway 16 282 17 -0.002 0.05 1000 -1000 -0.013 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 15 821 54 -0.035 0.05 1000 -1000 -0.016 -1000
Hedgehog signaling events mediated by Gli proteins 15 985 65 -0.022 0.076 1000 -1000 -0.037 -1000
LPA4-mediated signaling events 14 175 12 -0.029 0.021 1000 -1000 -0.019 -1000
HIF-2-alpha transcription factor network 14 627 43 -0.1 0.11 1000 -1000 -0.034 -1000
Regulation of p38-alpha and p38-beta 14 773 54 -0.018 0.073 1000 -1000 -0.017 -1000
Neurotrophic factor-mediated Trk receptor signaling 14 1740 120 -0.077 0.09 1000 -1000 -0.031 -1000
Regulation of Androgen receptor activity 14 1029 70 -0.14 0.048 1000 -1000 -0.028 -1000
Aurora A signaling 13 790 60 -0.007 0.05 1000 -1000 -0.007 -1000
Signaling mediated by p38-alpha and p38-beta 13 594 44 -0.055 0.056 1000 -1000 -0.007 -1000
Glypican 2 network 13 54 4 0 0.014 1000 -1000 0 -1000
Signaling events mediated by VEGFR1 and VEGFR2 13 1669 125 -0.025 0.045 1000 -1000 -0.017 -1000
IL2 signaling events mediated by STAT5 13 291 22 -0.024 0.037 1000 -1000 -0.021 -1000
S1P3 pathway 13 547 42 -0.016 0.044 1000 -1000 -0.012 -1000
p38 MAPK signaling pathway 13 585 44 -0.051 0.058 1000 -1000 -0.017 -1000
Sphingosine 1-phosphate (S1P) pathway 12 363 28 -0.009 0.044 1000 -1000 -0.007 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 12 1067 85 -0.14 0.064 1000 -1000 -0.034 -1000
FoxO family signaling 12 802 64 -0.092 0.049 1000 -1000 -0.035 -1000
Retinoic acid receptors-mediated signaling 12 746 58 -0.071 0.068 1000 -1000 -0.036 -1000
Paxillin-independent events mediated by a4b1 and a4b7 11 425 37 -0.024 0.073 1000 -1000 -0.02 -1000
S1P5 pathway 11 198 17 -0.001 0.035 1000 -1000 -0.005 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 11 914 83 -0.057 0.069 1000 -1000 -0.015 -1000
TCGA08_rtk_signaling 11 288 26 -0.026 0.043 1000 -1000 -0.014 -1000
Angiopoietin receptor Tie2-mediated signaling 11 1034 88 -0.063 0.063 1000 -1000 -0.053 -1000
S1P4 pathway 11 296 25 -0.009 0.044 1000 -1000 -0.015 -1000
Nephrin/Neph1 signaling in the kidney podocyte 10 360 34 -0.039 0.076 1000 -1000 -0.029 -1000
Paxillin-dependent events mediated by a4b1 10 379 36 -0.061 0.064 1000 -1000 -0.035 -1000
Effects of Botulinum toxin 10 268 26 -0.062 0.051 1000 -1000 -0.002 -1000
Signaling events mediated by PRL 10 347 34 -0.038 0.051 1000 -1000 -0.024 -1000
BARD1 signaling events 9 564 57 -0.048 0.07 1000 -1000 -0.044 -1000
a4b1 and a4b7 Integrin signaling 9 49 5 0.021 0.042 1000 -1000 0.02 -1000
Signaling events mediated by HDAC Class III 9 398 40 -0.064 0.065 1000 -1000 -0.039 -1000
Class IB PI3K non-lipid kinase events 9 27 3 -0.026 0.026 1000 -1000 -0.025 -1000
Signaling events mediated by HDAC Class II 8 635 75 -0.089 0.076 1000 -1000 -0.025 -1000
Class I PI3K signaling events mediated by Akt 8 586 68 -0.053 0.076 1000 -1000 -0.021 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 8 293 33 -0.015 0.072 1000 -1000 -0.022 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 6 138 23 0 0.055 1000 -1000 -0.013 -1000
Ephrin A reverse signaling 6 44 7 0 0.042 1000 -1000 0 -1000
JNK signaling in the CD4+ TCR pathway 6 118 17 -0.01 0.08 1000 -1000 -0.016 -1000
Insulin-mediated glucose transport 6 221 32 0 0.042 1000 -1000 -0.014 -1000
Arf6 trafficking events 6 488 71 -0.041 0.043 1000 -1000 -0.027 -1000
Canonical NF-kappaB pathway 5 197 39 0 0.074 1000 -1000 -0.015 -1000
Alternative NF-kappaB pathway 5 77 13 0 0.082 1000 -1000 0 -1000
Circadian rhythm pathway 4 101 22 -0.01 0.067 1000 -1000 -0.018 -1000
Signaling events mediated by HDAC Class I 4 434 104 -0.047 0.081 1000 -1000 -0.03 -1000
Arf1 pathway 4 240 54 -0.001 0.062 1000 -1000 -0.01 -1000
Aurora C signaling 3 22 7 0 0.054 1000 -1000 -0.008 -1000
Rapid glucocorticoid signaling 2 55 20 -0.001 0.044 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 21 27 0 0.081 1000 -1000 -0.019 -1000
Total 3449 213033 7203 -11 8 131000 -131000 -3.2 -131000
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.038 0.13 -10000 0 -0.52 30 30
Crk/p130 Cas/Paxillin -0.13 0.16 -10000 0 -0.32 171 171
JUN -0.13 0.18 0.19 2 -0.4 113 115
HRAS 0.032 0.036 -10000 0 -0.42 3 3
RET51/GFRalpha1/GDNF/GRB10 -0.1 0.2 -10000 0 -0.31 228 228
RAP1A 0.031 0.045 -10000 0 -0.42 5 5
FRS2 0.033 0.022 -10000 0 -0.42 1 1
RAP1A/GDP 0.023 0.032 -10000 0 -0.3 5 5
RET51/GFRalpha1/GDNF/DOK1 -0.097 0.21 -10000 0 -0.32 220 220
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.036 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.023 -10000 0 -0.42 1 1
RET9/GFRalpha1/GDNF/Enigma -0.041 0.14 -10000 0 -0.23 171 171
RHOA 0.026 0.061 -10000 0 -0.42 9 9
RAP1A/GTP -0.093 0.18 -10000 0 -0.28 221 221
GRB7 0.024 0.058 -10000 0 -0.42 8 8
RET51/GFRalpha1/GDNF -0.092 0.2 -10000 0 -0.31 217 217
MAPKKK cascade -0.11 0.19 -10000 0 -0.32 206 206
BCAR1 0.03 0.014 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.064 0.17 -10000 0 -0.28 181 181
lamellipodium assembly -0.11 0.16 -10000 0 -0.3 174 174
RET51/GFRalpha1/GDNF/SHC -0.08 0.18 -10000 0 -0.29 195 195
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
RET9/GFRalpha1/GDNF/SHC -0.028 0.12 -10000 0 -0.23 123 123
RET9/GFRalpha1/GDNF/Shank3 -0.042 0.14 -10000 0 -0.23 174 174
MAPK3 -0.11 0.15 0.24 3 -0.38 90 93
DOK1 0.027 0.061 -10000 0 -0.42 9 9
DOK6 0.005 0.11 -10000 0 -0.42 31 31
PXN 0.036 0.004 -10000 0 -10000 0 0
neurite development -0.11 0.16 0.28 2 -0.37 102 104
DOK5 0.012 0.089 -10000 0 -0.42 20 20
GFRA1 -0.13 0.21 -10000 0 -0.42 177 177
MAPK8 -0.12 0.18 -10000 0 -0.3 220 220
HRAS/GTP -0.11 0.22 -10000 0 -0.35 217 217
tube development -0.03 0.14 0.22 24 -0.22 163 187
MAPK1 -0.12 0.16 0.24 3 -0.3 171 174
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.053 0.12 -10000 0 -0.22 157 157
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
SRC 0.033 0.029 -10000 0 -0.42 2 2
PDLIM7 0.035 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.093 0.21 -10000 0 -0.32 220 220
SHC1 0.028 0.025 -10000 0 -0.42 1 1
RET51/GFRalpha1/GDNF/Dok4 -0.1 0.2 -10000 0 -0.31 220 220
RET51/GFRalpha1/GDNF/Dok5 -0.1 0.2 -10000 0 -0.32 213 213
PRKCA 0.032 0.012 -10000 0 -10000 0 0
HRAS/GDP 0.024 0.025 -10000 0 -0.3 3 3
CREB1 -0.086 0.17 -10000 0 -0.33 148 148
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.039 0.11 -10000 0 -0.23 115 115
RET51/GFRalpha1/GDNF/Grb7 -0.095 0.2 -10000 0 -0.32 211 211
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.095 0.2 -10000 0 -0.42 137 137
DOK4 0.028 0.032 -10000 0 -0.42 2 2
JNK cascade -0.13 0.17 0.19 2 -0.4 113 115
RET9/GFRalpha1/GDNF/FRS2 -0.042 0.14 -10000 0 -0.23 169 169
SHANK3 0.035 0.029 -10000 0 -0.42 2 2
RASA1 0.029 0.05 -10000 0 -0.42 6 6
NCK1 0.034 0.021 -10000 0 -0.42 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.036 0.1 -10000 0 -0.22 114 114
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.1 0.18 -10000 0 -0.3 205 205
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.12 0.19 -10000 0 -0.31 221 221
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.11 0.19 -10000 0 -0.34 181 181
PI3K -0.16 0.25 0.24 5 -0.45 174 179
SOS1 0.035 0.021 -10000 0 -0.42 1 1
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.028 0.14 -10000 0 -0.22 163 163
GRB10 0.023 0.075 -10000 0 -0.42 14 14
activation of MAPKK activity -0.081 0.15 -10000 0 -0.27 167 167
RET51/GFRalpha1/GDNF/FRS2 -0.095 0.2 -10000 0 -0.31 216 216
GAB1 0.027 0.061 -10000 0 -0.42 9 9
IRS1 -0.014 0.14 -10000 0 -0.42 54 54
IRS2 0.008 0.099 -10000 0 -0.42 25 25
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.12 0.2 -10000 0 -0.35 186 186
RET51/GFRalpha1/GDNF/PKC alpha -0.089 0.2 -10000 0 -0.32 200 200
GRB2 0.033 0.011 -10000 0 -10000 0 0
PRKACA 0.036 0.005 -10000 0 -10000 0 0
GDNF 0.032 0.036 -10000 0 -0.42 3 3
RAC1 0.035 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.12 0.23 -10000 0 -0.35 226 226
Rac1/GTP -0.12 0.2 0.21 4 -0.36 174 178
RET9/GFRalpha1/GDNF -0.06 0.14 -10000 0 -0.25 172 172
GFRalpha1/GDNF -0.074 0.16 -10000 0 -0.3 172 172
Signaling events mediated by Stem cell factor receptor (c-Kit)

Figure S2.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S2.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.12 0.19 0.38 1 -0.41 133 134
CRKL -0.13 0.2 -10000 0 -0.43 138 138
HRAS -0.077 0.17 -10000 0 -0.36 94 94
mol:PIP3 -0.088 0.2 0.28 2 -0.41 101 103
SPRED1 0.02 0.08 -10000 0 -0.42 16 16
SPRED2 0.02 0.082 -10000 0 -0.42 17 17
GAB1 -0.14 0.21 -10000 0 -0.44 138 138
FOXO3 -0.1 0.2 -10000 0 -0.39 132 132
AKT1 -0.11 0.22 -10000 0 -0.42 132 132
BAD -0.1 0.2 -10000 0 -0.39 130 130
megakaryocyte differentiation -0.13 0.21 -10000 0 -0.44 135 135
GSK3B -0.1 0.2 0.34 1 -0.4 128 129
RAF1 -0.056 0.15 0.26 4 -0.3 85 89
SHC1 0.028 0.025 -10000 0 -0.42 1 1
STAT3 -0.12 0.2 -10000 0 -0.43 133 133
STAT1 -0.31 0.48 -10000 0 -0.88 185 185
HRAS/SPRED1 -0.054 0.16 0.26 1 -0.32 90 91
cell proliferation -0.13 0.21 -10000 0 -0.43 136 136
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
TEC 0.031 0.045 -10000 0 -0.42 5 5
RPS6KB1 -0.13 0.22 -10000 0 -0.45 135 135
HRAS/SPRED2 -0.053 0.16 0.26 1 -0.31 91 92
LYN/TEC/p62DOK -0.092 0.22 -10000 0 -0.42 125 125
MAPK3 -0.034 0.12 0.24 8 -0.25 33 41
STAP1 -0.13 0.21 -10000 0 -0.44 135 135
GRAP2 0.032 0.023 -10000 0 -0.42 1 1
JAK2 -0.26 0.41 -10000 0 -0.74 188 188
STAT1 (dimer) -0.3 0.46 -10000 0 -0.86 185 185
mol:Gleevec 0.005 0.008 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.099 0.22 -10000 0 -0.42 126 126
actin filament polymerization -0.13 0.21 -10000 0 -0.43 135 135
LYN 0.03 0.014 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.19 0.3 -10000 0 -0.55 183 183
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
CBL/CRKL/GRB2 -0.1 0.2 -10000 0 -0.4 125 125
PI3K -0.1 0.23 -10000 0 -0.45 126 126
PTEN 0.027 0.061 -10000 0 -0.42 9 9
SCF/KIT/EPO/EPOR -0.3 0.53 -10000 0 -1.2 121 121
MAPK8 -0.13 0.21 -10000 0 -0.44 136 136
STAT3 (dimer) -0.12 0.2 -10000 0 -0.42 133 133
positive regulation of transcription -0.025 0.1 0.23 8 -0.21 30 38
mol:GDP -0.083 0.17 -10000 0 -0.37 92 92
PIK3C2B -0.12 0.2 -10000 0 -0.41 128 128
CBL/CRKL -0.12 0.2 -10000 0 -0.41 135 135
FER -0.13 0.21 -10000 0 -0.44 134 134
SH2B3 -0.13 0.21 -10000 0 -0.44 135 135
PDPK1 -0.07 0.19 0.31 12 -0.39 91 103
SNAI2 -0.14 0.22 -10000 0 -0.46 137 137
positive regulation of cell proliferation -0.22 0.36 -10000 0 -0.69 164 164
KITLG -0.051 0.16 -10000 0 -0.44 72 72
cell motility -0.22 0.36 -10000 0 -0.69 164 164
PTPN6 0.038 0.032 -10000 0 -0.41 2 2
EPOR -0.068 0.18 -10000 0 -1 5 5
STAT5A (dimer) -0.19 0.3 -10000 0 -0.58 168 168
SOCS1 0.032 0.023 -10000 0 -0.42 1 1
cell migration 0.13 0.21 0.44 135 -10000 0 135
SOS1 0.035 0.021 -10000 0 -0.42 1 1
EPO 0.012 0.029 -10000 0 -10000 0 0
VAV1 0.019 0.082 -10000 0 -0.42 17 17
GRB10 -0.14 0.21 -10000 0 -0.45 136 136
PTPN11 0.041 0.009 -10000 0 -10000 0 0
SCF/KIT -0.14 0.22 -10000 0 -0.46 135 135
GO:0007205 0.007 0.011 -10000 0 -10000 0 0
MAP2K1 -0.042 0.13 0.24 6 -0.25 73 79
CBL 0.032 0.012 -10000 0 -10000 0 0
KIT -0.27 0.53 -10000 0 -1.3 101 101
MAP2K2 -0.043 0.13 0.27 7 -0.25 75 82
SHC/Grb2/SOS1 -0.08 0.2 -10000 0 -0.42 96 96
STAT5A -0.2 0.32 -10000 0 -0.6 164 164
GRB2 0.033 0.011 -10000 0 -10000 0 0
response to radiation -0.14 0.22 -10000 0 -0.45 138 138
SHC/GRAP2 0.038 0.032 -10000 0 -0.3 2 2
PTPRO -0.14 0.21 -10000 0 -0.45 134 134
SH2B2 -0.13 0.21 -10000 0 -0.44 135 135
DOK1 0.027 0.061 -10000 0 -0.42 9 9
MATK -0.13 0.21 -10000 0 -0.44 135 135
CREBBP -0.008 0.08 -10000 0 -0.18 16 16
BCL2 -0.3 0.56 -10000 0 -1.3 113 113
Endothelins

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
AKT1 -0.011 0.19 0.27 72 -0.32 101 173
PTK2B 0.028 0.015 -10000 0 -10000 0 0
mol:Ca2+ -0.056 0.26 -10000 0 -0.69 48 48
EDN1 -0.01 0.19 0.23 66 -0.43 65 131
EDN3 -0.011 0.12 -10000 0 -0.42 38 38
EDN2 -0.054 0.18 -10000 0 -0.42 93 93
HRAS/GDP -0.065 0.23 0.28 4 -0.46 99 103
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.059 0.2 0.19 3 -0.39 103 106
ADCY4 -0.011 0.17 0.26 8 -0.4 43 51
ADCY5 -0.015 0.16 0.23 5 -0.38 45 50
ADCY6 -0.01 0.16 0.26 6 -0.38 45 51
ADCY7 -0.013 0.16 0.27 4 -0.4 39 43
ADCY1 -0.009 0.16 0.25 7 -0.38 43 50
ADCY2 -0.026 0.17 0.26 5 -0.41 55 60
ADCY3 -0.01 0.16 0.26 9 -0.38 46 55
ADCY8 -0.006 0.14 0.26 4 -0.36 38 42
ADCY9 -0.013 0.16 0.24 8 -0.38 45 53
arachidonic acid secretion -0.089 0.26 0.28 1 -0.5 111 112
ETB receptor/Endothelin-1/Gq/GTP -0.05 0.16 -10000 0 -0.32 105 105
GNAO1 0.03 0.014 -10000 0 -10000 0 0
HRAS 0.032 0.036 -10000 0 -0.42 3 3
ETA receptor/Endothelin-1/G12/GTP 0.03 0.21 0.37 72 -0.3 93 165
ETA receptor/Endothelin-1/Gs/GTP 0.025 0.2 0.35 71 -0.3 90 161
mol:GTP -0.001 0.006 -10000 0 -10000 0 0
COL3A1 -0.016 0.21 0.27 72 -0.5 49 121
EDNRB 0.003 0.097 -10000 0 -0.36 26 26
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.008 0.2 0.27 69 -0.44 51 120
CYSLTR1 -0.025 0.23 0.27 71 -0.51 61 132
SLC9A1 -0.004 0.13 0.19 72 -0.28 46 118
mol:GDP -0.081 0.24 0.27 5 -0.48 104 109
SLC9A3 -0.12 0.35 -10000 0 -0.7 110 110
RAF1 -0.094 0.24 -10000 0 -0.49 110 110
JUN -0.098 0.36 -10000 0 -0.93 64 64
JAK2 -0.008 0.19 0.27 73 -0.32 95 168
mol:IP3 -0.074 0.21 0.23 1 -0.43 99 100
ETA receptor/Endothelin-1 0.014 0.25 0.42 72 -0.37 103 175
PLCB1 -0.023 0.14 -10000 0 -0.42 59 59
PLCB2 0.032 0.023 -10000 0 -0.43 1 1
ETA receptor/Endothelin-3 0 0.15 -10000 0 -0.32 72 72
FOS -0.14 0.36 -10000 0 -0.89 83 83
Gai/GDP -0.11 0.32 -10000 0 -0.72 101 101
CRK 0.032 0.023 -10000 0 -0.42 1 1
mol:Ca ++ -0.089 0.27 0.27 4 -0.5 112 116
BCAR1 0.03 0.014 -10000 0 -10000 0 0
PRKCB1 -0.077 0.22 0.26 12 -0.44 103 115
GNAQ -0.001 0.007 -10000 0 -10000 0 0
GNAZ 0.023 0.07 -10000 0 -0.42 12 12
GNAL 0.031 0.036 -10000 0 -0.42 3 3
Gs family/GDP -0.064 0.22 0.26 4 -0.45 95 99
ETA receptor/Endothelin-1/Gq/GTP -0.041 0.2 0.2 61 -0.38 91 152
MAPK14 -0.068 0.17 0.23 1 -0.36 92 93
TRPC6 -0.061 0.28 -10000 0 -0.74 48 48
GNAI2 0.028 0.054 -10000 0 -0.42 7 7
GNAI3 0.035 0.006 -10000 0 -10000 0 0
GNAI1 0.017 0.087 -10000 0 -0.42 19 19
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.067 0.18 -10000 0 -0.36 103 103
ETB receptor/Endothelin-2 -0.04 0.15 -10000 0 -0.31 111 111
ETB receptor/Endothelin-3 -0.009 0.11 -10000 0 -0.31 54 54
ETB receptor/Endothelin-1 -0.012 0.17 -10000 0 -0.32 96 96
MAPK3 -0.14 0.34 -10000 0 -0.78 93 93
MAPK1 -0.14 0.34 -10000 0 -0.79 94 94
Rac1/GDP -0.062 0.23 0.28 5 -0.46 95 100
cAMP biosynthetic process -0.004 0.17 0.26 21 -0.4 44 65
MAPK8 -0.072 0.3 -10000 0 -0.67 74 74
SRC 0.033 0.03 -10000 0 -0.42 2 2
ETB receptor/Endothelin-1/Gi/GTP -0.043 0.15 -10000 0 -0.34 82 82
p130Cas/CRK/Src/PYK2 -0.1 0.26 -10000 0 -0.55 100 100
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.062 0.23 0.28 5 -0.46 94 99
COL1A2 -0.074 0.3 0.39 1 -0.6 95 96
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.031 0.18 -10000 0 -0.32 123 123
mol:DAG -0.074 0.21 0.23 1 -0.43 99 100
MAP2K2 -0.11 0.28 0.33 1 -0.59 105 106
MAP2K1 -0.11 0.28 0.3 2 -0.59 106 108
EDNRA 0.016 0.17 0.23 72 -0.38 58 130
positive regulation of muscle contraction -0.012 0.17 0.23 73 -0.29 92 165
Gq family/GDP -0.058 0.22 -10000 0 -0.45 87 87
HRAS/GTP -0.08 0.23 -10000 0 -0.46 100 100
PRKCH -0.075 0.21 0.23 4 -0.43 99 103
RAC1 0.035 0.006 -10000 0 -10000 0 0
PRKCA -0.061 0.21 0.24 22 -0.43 89 111
PRKCB -0.074 0.2 0.22 1 -0.42 101 102
PRKCE -0.076 0.2 0.22 1 -0.42 97 98
PRKCD -0.075 0.2 0.22 1 -0.44 90 91
PRKCG -0.079 0.21 0.22 1 -0.43 97 98
regulation of vascular smooth muscle contraction -0.18 0.42 -10000 0 -1.1 83 83
PRKCQ -0.069 0.2 0.23 7 -0.42 94 101
PLA2G4A -0.099 0.28 -10000 0 -0.55 111 111
GNA14 -0.012 0.13 -10000 0 -0.42 43 43
GNA15 0.026 0.048 -10000 0 -0.42 5 5
GNA12 0.035 0.007 -10000 0 -10000 0 0
GNA11 0.029 0.039 -10000 0 -0.42 3 3
Rac1/GTP 0.03 0.21 0.37 72 -0.3 96 168
MMP1 -0.17 0.35 0.24 8 -0.78 120 128
IGF1 pathway

Figure S4.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S4.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.036 0.005 -10000 0 -10000 0 0
PTK2 0.028 0.016 -10000 0 -10000 0 0
CRKL -0.071 0.15 0.17 2 -0.3 136 138
GRB2/SOS1/SHC 0.052 0.036 -10000 0 -0.26 1 1
HRAS 0.032 0.036 -10000 0 -0.42 3 3
IRS1/Crk -0.064 0.16 -10000 0 -0.29 142 142
IGF-1R heterotetramer/IGF1/PTP1B -0.036 0.16 -10000 0 -0.29 132 132
AKT1 -0.077 0.14 0.17 14 -0.28 125 139
BAD -0.075 0.13 0.16 14 -0.27 121 135
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.068 0.15 0.17 2 -0.3 130 132
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.06 0.16 -10000 0 -0.3 142 142
RAF1 -0.037 0.14 0.29 4 -0.48 15 19
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.025 0.17 -10000 0 -0.29 129 129
YWHAZ 0.027 0.016 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.063 0.17 -10000 0 -0.3 151 151
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
RPS6KB1 -0.071 0.13 0.17 12 -0.29 107 119
GNB2L1 0.034 0.035 -10000 0 -0.42 3 3
positive regulation of MAPKKK cascade -0.023 0.14 0.3 10 -0.4 14 24
PXN 0.036 0.004 -10000 0 -10000 0 0
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.048 0.023 -10000 0 -0.3 1 1
HRAS/GTP -0.04 0.13 -10000 0 -0.26 113 113
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.003 0.13 -10000 0 -0.24 103 103
IGF-1R heterotetramer -0.061 0.18 -10000 0 -0.46 84 84
IGF-1R heterotetramer/IGF1/IRS/Nck -0.043 0.17 -10000 0 -0.29 142 142
Crk/p130 Cas/Paxillin -0.039 0.16 -10000 0 -0.28 138 138
IGF1R -0.061 0.18 -10000 0 -0.46 84 84
IGF1 -0.06 0.18 -10000 0 -0.46 78 78
IRS2/Crk -0.071 0.16 0.17 2 -0.29 150 152
PI3K -0.038 0.17 -10000 0 -0.29 145 145
apoptosis 0.05 0.11 0.31 46 -0.3 4 50
HRAS/GDP 0.024 0.025 -10000 0 -0.3 3 3
PRKCD -0.062 0.18 0.21 1 -0.37 99 100
RAF1/14-3-3 E -0.018 0.13 0.29 4 -0.42 14 18
BAD/14-3-3 -0.053 0.12 0.31 4 -0.33 46 50
PRKCZ -0.075 0.14 0.16 14 -0.27 135 149
Crk/p130 Cas/Paxillin/FAK1 -0.031 0.13 -10000 0 -0.34 44 44
PTPN1 0.03 0.031 -10000 0 -0.42 2 2
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.075 0.18 -10000 0 -0.35 130 130
BCAR1 0.03 0.014 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.018 0.14 -10000 0 -0.26 122 122
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.035 0.021 -10000 0 -0.42 1 1
IRS1/NCK2 -0.054 0.16 -10000 0 -0.29 142 142
GRB10 0.023 0.075 -10000 0 -0.42 14 14
PTPN11 -0.072 0.15 0.17 2 -0.29 142 144
IRS1 -0.075 0.16 -10000 0 -0.3 151 151
IRS2 -0.079 0.16 0.17 2 -0.31 142 144
IGF-1R heterotetramer/IGF1 -0.072 0.19 -10000 0 -0.37 139 139
GRB2 0.033 0.011 -10000 0 -10000 0 0
PDPK1 -0.075 0.14 0.18 14 -0.28 135 149
YWHAE 0.032 0.012 -10000 0 -10000 0 0
PRKD1 -0.071 0.2 0.21 5 -0.37 125 130
SHC1 0.028 0.025 -10000 0 -0.42 1 1
FOXM1 transcription factor network

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
NFATC3 -0.24 0.52 -9999 0 -1.2 84 84
PLK1 0.017 0.098 -9999 0 -1.1 3 3
BIRC5 -0.087 0.39 -9999 0 -1.4 41 41
HSPA1B -0.25 0.52 -9999 0 -1.1 97 97
MAP2K1 0.005 0.057 -9999 0 -10000 0 0
BRCA2 -0.27 0.54 -9999 0 -1.2 90 90
FOXM1 -0.39 0.86 -9999 0 -1.8 94 94
XRCC1 -0.24 0.52 -9999 0 -1.2 82 82
FOXM1B/p19 -0.3 0.58 -9999 0 -1.3 94 94
Cyclin D1/CDK4 -0.29 0.53 -9999 0 -1 136 136
CDC2 -0.27 0.56 -9999 0 -1.3 85 85
TGFA -0.28 0.5 -9999 0 -1 110 110
SKP2 -0.24 0.52 -9999 0 -1.2 79 79
CCNE1 0.024 0.05 -9999 0 -0.43 5 5
CKS1B -0.22 0.53 -9999 0 -1.2 81 81
RB1 -0.15 0.4 -9999 0 -1 65 65
FOXM1C/SP1 -0.3 0.62 -9999 0 -1.4 100 100
AURKB -0.08 0.31 -9999 0 -0.91 57 57
CENPF -0.23 0.56 -9999 0 -1.2 84 84
CDK4 0.016 0.037 -9999 0 -10000 0 0
MYC -0.23 0.45 -9999 0 -1 90 90
CHEK2 0.001 0.066 -9999 0 -0.45 3 3
ONECUT1 -0.28 0.52 -9999 0 -1.1 102 102
CDKN2A 0.014 0.075 -9999 0 -0.42 14 14
LAMA4 -0.25 0.53 -9999 0 -1.2 84 84
FOXM1B/HNF6 -0.35 0.65 -9999 0 -1.4 103 103
FOS -0.33 0.6 -9999 0 -1.2 131 131
SP1 0.034 0.024 -9999 0 -0.42 1 1
CDC25B -0.25 0.52 -9999 0 -1.2 84 84
response to radiation -0.004 0.032 -9999 0 -10000 0 0
CENPB -0.24 0.52 -9999 0 -1.2 84 84
CENPA -0.27 0.55 -9999 0 -1.2 91 91
NEK2 -0.26 0.58 -9999 0 -1.2 100 100
HIST1H2BA -0.25 0.52 -9999 0 -1.2 86 86
CCNA2 0.005 0.11 -9999 0 -0.43 28 28
EP300 0.032 0.03 -9999 0 -0.42 2 2
CCNB1/CDK1 -0.32 0.65 -9999 0 -1.5 84 84
CCNB2 -0.26 0.53 -9999 0 -1.2 86 86
CCNB1 -0.27 0.57 -9999 0 -1.3 86 86
ETV5 -0.25 0.53 -9999 0 -1.2 84 84
ESR1 -0.44 0.65 -9999 0 -1.2 206 206
CCND1 -0.32 0.52 -9999 0 -1.1 137 137
GSK3A 0.008 0.052 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.022 0.11 -9999 0 -0.33 29 29
CDK2 0.03 0.034 -9999 0 -0.43 2 2
G2/M transition of mitotic cell cycle -0.006 0.036 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.27 0.57 -9999 0 -1.3 95 95
GAS1 -0.32 0.59 -9999 0 -1.3 115 115
MMP2 -0.28 0.57 -9999 0 -1.3 97 97
RB1/FOXM1C -0.3 0.55 -9999 0 -1.1 129 129
CREBBP 0.033 0.011 -9999 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.007 0.13 -10000 0 -0.22 134 134
ER alpha/Gai/GDP/Gbeta gamma -0.12 0.21 -10000 0 -0.36 160 160
AKT1 -0.22 0.37 -10000 0 -0.74 167 167
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.22 0.38 -10000 0 -0.75 167 167
mol:Ca2+ -0.071 0.15 -10000 0 -0.42 59 59
IGF1R -0.042 0.17 -10000 0 -0.42 84 84
E2/ER alpha (dimer)/Striatin -0.037 0.13 -10000 0 -0.25 135 135
SHC1 0.028 0.025 -10000 0 -0.42 1 1
apoptosis 0.21 0.35 0.7 167 -10000 0 167
RhoA/GTP -0.038 0.11 -10000 0 -0.21 127 127
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.1 0.2 -10000 0 -0.38 152 152
regulation of stress fiber formation 0.038 0.1 0.31 8 -0.26 3 11
E2/ERA-ERB (dimer) -0.037 0.13 -10000 0 -0.25 132 132
KRAS 0.028 0.054 -10000 0 -0.42 7 7
G13/GTP -0.032 0.12 -10000 0 -0.23 124 124
pseudopodium formation -0.038 0.1 0.26 3 -0.31 8 11
E2/ER alpha (dimer)/PELP1 -0.038 0.13 -10000 0 -0.25 131 131
GRB2 0.033 0.011 -10000 0 -10000 0 0
GNG2 0.034 0.021 -10000 0 -0.42 1 1
GNAO1 0.03 0.014 -10000 0 -10000 0 0
HRAS 0.032 0.036 -10000 0 -0.42 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.14 0.23 -10000 0 -0.44 164 164
E2/ER beta (dimer) 0.026 0.005 -10000 0 -10000 0 0
mol:GDP -0.075 0.17 -10000 0 -0.34 133 133
mol:NADP -0.14 0.23 -10000 0 -0.44 164 164
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
mol:IP3 -0.072 0.15 -10000 0 -0.44 58 58
IGF-1R heterotetramer -0.042 0.17 -10000 0 -0.42 84 84
PLCB1 -0.072 0.16 -10000 0 -0.45 59 59
PLCB2 -0.051 0.15 -10000 0 -0.45 51 51
IGF1 -0.038 0.16 -10000 0 -0.42 78 78
mol:L-citrulline -0.14 0.23 -10000 0 -0.44 164 164
RHOA 0.026 0.061 -10000 0 -0.42 9 9
Gai/GDP -0.099 0.27 -10000 0 -0.62 102 102
JNK cascade 0.026 0.005 -10000 0 -10000 0 0
BCAR1 0.03 0.014 -10000 0 -10000 0 0
ESR2 0.035 0.007 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -10000 0 0
ESR1 -0.089 0.2 -10000 0 -0.42 132 132
Gq family/GDP/Gbeta gamma -0.015 0.17 -10000 0 -0.69 22 22
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.034 0.13 -10000 0 -0.57 7 7
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.089 0.19 0.27 1 -0.37 123 124
GNAZ 0.023 0.07 -10000 0 -0.42 12 12
E2/ER alpha (dimer) -0.062 0.14 -10000 0 -0.3 132 132
STRN 0.031 0.045 -10000 0 -0.42 5 5
GNAL 0.031 0.036 -10000 0 -0.42 3 3
PELP1 0.033 0.011 -10000 0 -10000 0 0
MAPK11 0.016 0.006 -10000 0 -10000 0 0
GNAI2 0.028 0.054 -10000 0 -0.42 7 7
GNAI3 0.035 0.006 -10000 0 -10000 0 0
GNAI1 0.017 0.087 -10000 0 -0.42 19 19
HBEGF -0.11 0.2 0.32 5 -0.47 65 70
cAMP biosynthetic process -0.028 0.1 -10000 0 -0.2 129 129
SRC -0.11 0.2 0.25 1 -0.35 159 160
PI3K 0.036 0.065 -10000 0 -0.3 17 17
GNB1 0.032 0.045 -10000 0 -0.42 5 5
G13/GDP/Gbeta gamma -0.049 0.16 -10000 0 -0.33 113 113
SOS1 0.035 0.021 -10000 0 -0.42 1 1
IGF-1R heterotetramer/IGF1 -0.13 0.19 -10000 0 -0.39 148 148
Gs family/GTP -0.022 0.11 -10000 0 -0.21 129 129
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.053 0.054 -10000 0 -0.23 15 15
vasodilation -0.13 0.22 0.24 1 -0.42 164 165
mol:DAG -0.072 0.15 -10000 0 -0.44 58 58
Gs family/GDP/Gbeta gamma -0.064 0.15 -10000 0 -0.32 109 109
MSN -0.042 0.11 0.26 3 -0.33 8 11
Gq family/GTP -0.052 0.15 -10000 0 -0.44 57 57
mol:PI-3-4-5-P3 -0.21 0.36 -10000 0 -0.72 167 167
NRAS 0.029 0.054 -10000 0 -0.42 7 7
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.13 0.22 0.42 164 -0.24 1 165
GRB2/SOS1 0.048 0.023 -10000 0 -0.3 1 1
RhoA/GDP -0.061 0.17 -10000 0 -0.35 113 113
NOS3 -0.14 0.24 -10000 0 -0.47 164 164
GNA11 0.033 0.036 -10000 0 -0.42 3 3
MAPKKK cascade -0.15 0.26 0.28 1 -0.52 159 160
E2/ER alpha (dimer)/PELP1/Src -0.11 0.21 0.27 2 -0.39 155 157
ruffle organization -0.038 0.1 0.26 3 -0.31 8 11
ROCK2 -0.039 0.12 0.28 3 -0.34 9 12
GNA14 -0.009 0.13 -10000 0 -0.42 43 43
GNA15 0.03 0.046 -10000 0 -0.42 5 5
GNA13 0.029 0.037 -10000 0 -0.42 3 3
MMP9 -0.12 0.2 0.35 7 -0.35 153 160
MMP2 -0.11 0.19 0.26 4 -0.35 146 150
EGFR-dependent Endothelin 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
HRAS 0.032 0.036 -10000 0 -0.42 3 3
EGFR -0.015 0.13 -10000 0 -0.42 49 49
EGF/EGFR -0.072 0.18 -10000 0 -0.27 199 199
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.001 0.13 -10000 0 -0.23 104 104
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA -0.002 0.12 -10000 0 -0.42 41 41
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.069 0.19 -10000 0 -0.42 110 110
EGF/EGFR dimer/SHC -0.029 0.14 -10000 0 -0.26 120 120
mol:GDP -0.005 0.12 -10000 0 -0.23 104 104
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.038 0.16 -10000 0 -0.42 77 77
GRB2/SOS1 0.048 0.023 -10000 0 -0.3 1 1
HRAS/GTP -0.017 0.11 -10000 0 -0.21 106 106
SHC1 0.028 0.025 -10000 0 -0.42 1 1
HRAS/GDP -0.007 0.12 -10000 0 -0.22 106 106
FRAP1 -0.017 0.14 0.23 40 -0.23 74 114
EGF/EGFR dimer -0.061 0.16 -10000 0 -0.3 152 152
SOS1 0.035 0.021 -10000 0 -0.42 1 1
GRB2 0.033 0.011 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.029 0.16 -10000 0 -0.33 103 103
Syndecan-1-mediated signaling events

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
TGFB1 0.035 0.021 -10000 0 -0.42 1 1
CCL5 -0.014 0.14 -10000 0 -0.42 52 52
SDCBP 0.023 0.058 -10000 0 -0.42 8 8
FGFR/FGF2/Syndecan-1 -0.11 0.23 0.22 6 -0.39 154 160
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 -0.11 0.22 -10000 0 -0.5 92 92
Syndecan-1/Syntenin -0.1 0.22 0.26 1 -0.48 94 95
MAPK3 -0.097 0.2 0.24 1 -0.46 90 91
HGF/MET 0.042 0.055 -10000 0 -0.3 12 12
TGFB1/TGF beta receptor Type II 0.035 0.021 -10000 0 -0.42 1 1
BSG 0.035 0.008 -10000 0 -10000 0 0
keratinocyte migration -0.11 0.22 -10000 0 -0.49 92 92
Syndecan-1/RANTES -0.13 0.24 0.26 1 -0.5 115 116
Syndecan-1/CD147 -0.096 0.23 0.27 1 -0.49 93 94
Syndecan-1/Syntenin/PIP2 -0.1 0.21 0.25 1 -0.47 94 95
LAMA5 0.027 0.05 -10000 0 -0.42 6 6
positive regulation of cell-cell adhesion -0.099 0.2 0.24 1 -0.45 94 95
MMP7 -0.032 0.15 -10000 0 -0.42 68 68
HGF 0.028 0.057 -10000 0 -0.42 8 8
Syndecan-1/CASK -0.12 0.21 -10000 0 -0.49 98 98
Syndecan-1/HGF/MET -0.1 0.23 0.27 1 -0.49 96 97
regulation of cell adhesion -0.1 0.19 0.23 1 -0.44 90 91
HPSE 0.015 0.091 -10000 0 -0.42 21 21
positive regulation of cell migration -0.11 0.23 0.22 6 -0.39 154 160
SDC1 -0.11 0.23 0.28 1 -0.4 155 156
Syndecan-1/Collagen -0.11 0.23 0.22 6 -0.39 154 160
PPIB 0.033 0.03 -10000 0 -0.42 2 2
MET 0.03 0.041 -10000 0 -0.42 4 4
PRKACA 0.036 0.005 -10000 0 -10000 0 0
MMP9 -0.013 0.14 -10000 0 -0.42 52 52
MAPK1 -0.1 0.21 0.24 1 -0.46 93 94
homophilic cell adhesion -0.12 0.22 0.22 6 -0.52 92 98
MMP1 -0.074 0.18 -10000 0 -0.42 107 107
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.037 0.15 0.36 1 -0.27 129 130
NF kappa B1 p50/RelA/I kappa B alpha -0.034 0.17 0.33 1 -0.43 46 47
alphaV/beta3 Integrin/Osteopontin/Src -0.043 0.16 -10000 0 -0.32 124 124
AP1 -0.085 0.23 -10000 0 -0.48 90 90
ILK -0.046 0.14 0.38 1 -0.26 118 119
bone resorption -0.053 0.14 -10000 0 -0.34 46 46
PTK2B 0.028 0.015 -10000 0 -10000 0 0
PYK2/p130Cas -0.027 0.16 -10000 0 -0.27 113 113
ITGAV 0.018 0.082 -10000 0 -0.43 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.04 0.064 -10000 0 -0.3 17 17
alphaV/beta3 Integrin/Osteopontin -0.022 0.16 -10000 0 -0.28 125 125
MAP3K1 -0.059 0.14 0.38 1 -0.27 142 143
JUN -0.001 0.12 -10000 0 -0.42 39 39
MAPK3 -0.059 0.14 0.27 3 -0.37 53 56
MAPK1 -0.064 0.15 0.27 3 -0.34 74 77
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
NFKB1 0.036 0.005 -10000 0 -10000 0 0
MAPK8 -0.064 0.13 0.22 8 -0.26 134 142
ITGB3 0.024 0.051 -10000 0 -0.43 5 5
NFKBIA -0.068 0.16 0.35 3 -0.42 59 62
FOS -0.031 0.15 -10000 0 -0.42 66 66
CD44 0.022 0.075 -10000 0 -0.42 14 14
CHUK 0.026 0.067 -10000 0 -0.42 11 11
PLAU -0.14 0.36 -10000 0 -1.2 53 53
NF kappa B1 p50/RelA -0.022 0.19 -10000 0 -0.45 56 56
BCAR1 0.03 0.014 -10000 0 -10000 0 0
RELA 0.035 0.006 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.031 0.081 -10000 0 -0.32 20 20
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.06 0.15 0.26 3 -0.28 146 149
VAV3 -0.099 0.15 0.22 7 -0.27 199 206
MAP3K14 -0.049 0.14 0.39 1 -0.27 127 128
ROCK2 0.033 0.035 -10000 0 -0.42 3 3
SPP1 -0.076 0.19 -10000 0 -0.42 115 115
RAC1 0.035 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.082 0.15 -10000 0 -0.25 187 187
MMP2 -0.1 0.19 -10000 0 -0.45 88 88
IL4-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
BCL2L1 -0.37 0.64 -10000 0 -1.3 125 125
STAT6 (cleaved dimer) -0.38 0.65 -10000 0 -1.3 140 140
IGHG1 -0.083 0.24 -10000 0 -0.71 14 14
IGHG3 -0.36 0.61 -10000 0 -1.2 140 140
AKT1 -0.12 0.32 -10000 0 -0.84 38 38
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.066 0.26 -10000 0 -0.86 21 21
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.14 0.36 -10000 0 -0.87 52 52
THY1 -0.38 0.66 -10000 0 -1.3 133 133
MYB -0.055 0.18 -10000 0 -0.42 97 97
HMGA1 0.034 0.029 -10000 0 -0.42 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.14 0.35 -10000 0 -0.69 76 76
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.12 0.33 -10000 0 -0.98 28 28
SP1 0.023 0.052 -10000 0 -0.21 5 5
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.019 0.056 -10000 0 -0.42 4 4
STAT6 (dimer)/ETS1 -0.37 0.64 -10000 0 -1.3 135 135
SOCS1 -0.2 0.39 -10000 0 -0.77 112 112
SOCS3 -0.12 0.32 -10000 0 -0.99 22 22
FCER2 -0.23 0.46 -10000 0 -0.98 78 78
PARP14 0.03 0.051 -10000 0 -0.42 6 6
CCL17 -0.43 0.71 -10000 0 -1.4 150 150
GRB2 0.033 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.076 0.26 -10000 0 -0.74 26 26
T cell proliferation -0.38 0.67 -10000 0 -1.4 130 130
IL4R/JAK1 -0.37 0.65 -10000 0 -1.3 126 126
EGR2 -0.41 0.7 -10000 0 -1.4 137 137
JAK2 -0.005 0.07 -10000 0 -0.46 2 2
JAK3 0.039 0.014 -10000 0 -10000 0 0
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
JAK1 0.018 0.048 -10000 0 -0.41 3 3
COL1A2 -0.22 0.54 -10000 0 -1.5 72 72
CCL26 -0.37 0.64 -10000 0 -1.3 126 126
IL4R -0.4 0.71 -10000 0 -1.5 124 124
PTPN6 0.022 0.045 -10000 0 -0.41 2 2
IL13RA2 -0.41 0.68 -10000 0 -1.4 138 138
IL13RA1 -0.009 0.087 -10000 0 -0.46 8 8
IRF4 -0.005 0.16 -10000 0 -1 5 5
ARG1 -0.066 0.26 -10000 0 -1.1 17 17
CBL -0.14 0.32 -10000 0 -0.66 74 74
GTF3A 0.024 0.046 -10000 0 -0.17 2 2
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
IL13RA1/JAK2 -0.001 0.1 -10000 0 -0.36 8 8
IRF4/BCL6 -0.005 0.16 -10000 0 -0.97 5 5
CD40LG 0.039 0.038 -10000 0 -0.42 3 3
MAPK14 -0.14 0.33 -10000 0 -0.72 61 61
mitosis -0.11 0.31 -10000 0 -0.78 38 38
STAT6 -0.48 0.88 -10000 0 -1.7 138 138
SPI1 0.033 0.051 -10000 0 -0.33 8 8
RPS6KB1 -0.093 0.3 -10000 0 -0.78 33 33
STAT6 (dimer) -0.48 0.88 -10000 0 -1.7 138 138
STAT6 (dimer)/PARP14 -0.42 0.73 -10000 0 -1.4 139 139
mast cell activation 0.005 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.14 0.34 -10000 0 -0.83 51 51
FRAP1 -0.12 0.32 -10000 0 -0.84 38 38
LTA -0.37 0.64 -10000 0 -1.3 120 120
FES 0.03 0.046 -10000 0 -0.42 5 5
T-helper 1 cell differentiation 0.43 0.78 1.5 138 -10000 0 138
CCL11 -0.4 0.66 -10000 0 -1.3 139 139
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.1 0.31 -10000 0 -0.88 29 29
IL2RG 0.034 0.042 -10000 0 -0.41 4 4
IL10 -0.33 0.65 -10000 0 -1.3 118 118
IRS1 -0.014 0.14 -10000 0 -0.42 54 54
IRS2 0.008 0.099 -10000 0 -0.42 25 25
IL4 -0.063 0.29 -10000 0 -1.3 18 18
IL5 -0.37 0.64 -10000 0 -1.3 123 123
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.26 0.51 -10000 0 -0.95 131 131
COL1A1 -0.26 0.59 -10000 0 -1.4 90 90
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.39 0.69 -10000 0 -1.5 115 115
IL2R gamma/JAK3 0.054 0.035 -10000 0 -0.29 4 4
TFF3 -0.53 0.76 -10000 0 -1.4 193 193
ALOX15 -0.38 0.65 -10000 0 -1.4 122 122
MYBL1 -0.011 0.13 -10000 0 -0.42 43 43
T-helper 2 cell differentiation -0.28 0.52 -10000 0 -1 130 130
SHC1 0.028 0.025 -10000 0 -0.42 1 1
CEBPB 0.029 0.056 -10000 0 -0.28 13 13
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.13 0.34 -10000 0 -0.83 45 45
mol:PI-3-4-5-P3 -0.12 0.33 -10000 0 -0.84 38 38
PI3K -0.13 0.35 -10000 0 -0.93 37 37
DOK2 0.009 0.086 -10000 0 -0.42 19 19
ETS1 0.015 0.043 -10000 0 -0.38 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.062 0.25 -10000 0 -0.68 23 23
ITGB3 -0.37 0.65 -10000 0 -1.3 124 124
PIGR -0.46 0.77 -10000 0 -1.4 170 170
IGHE 0.011 0.088 0.18 57 -0.22 10 67
MAPKKK cascade -0.06 0.24 -10000 0 -0.67 23 23
BCL6 0.018 0.085 -10000 0 -0.42 18 18
OPRM1 -0.37 0.64 -10000 0 -1.3 120 120
RETNLB -0.37 0.64 -10000 0 -1.3 121 121
SELP -0.43 0.75 -10000 0 -1.4 151 151
AICDA -0.36 0.62 -10000 0 -1.3 126 126
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.034 0.034 -10000 0 -0.26 4 4
NFATC2 -0.052 0.21 -10000 0 -0.53 47 47
NFATC3 -0.018 0.12 -10000 0 -0.26 72 72
CD40LG -0.19 0.38 -10000 0 -0.77 122 122
ITCH 0.013 0.071 -10000 0 -0.22 42 42
CBLB 0.014 0.07 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.14 0.33 -10000 0 -0.81 69 69
JUNB 0.032 0.041 -10000 0 -0.42 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.022 0.087 -10000 0 -0.26 44 44
T cell anergy -0.016 0.12 0.26 2 -0.36 45 47
TLE4 -0.045 0.17 -10000 0 -0.48 42 42
Jun/NFAT1-c-4/p21SNFT -0.17 0.4 -10000 0 -0.81 114 114
AP-1/NFAT1-c-4 -0.19 0.46 -10000 0 -0.89 112 112
IKZF1 -0.039 0.14 -10000 0 -0.36 47 47
T-helper 2 cell differentiation -0.17 0.3 -10000 0 -0.8 66 66
AP-1/NFAT1 -0.045 0.2 -10000 0 -0.4 82 82
CALM1 0.028 0.058 -10000 0 -0.16 42 42
EGR2 -0.23 0.49 -10000 0 -1.2 82 82
EGR3 -0.29 0.55 -10000 0 -1.2 121 121
NFAT1/FOXP3 -0.018 0.16 -10000 0 -0.4 41 41
EGR1 -0.038 0.16 -10000 0 -0.42 76 76
JUN -0.003 0.12 -10000 0 -0.42 39 39
EGR4 0 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.005 0.046 -10000 0 -0.15 45 45
GBP3 -0.089 0.25 -10000 0 -0.64 73 73
FOSL1 0.035 0.007 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 -0.16 0.4 -10000 0 -0.79 114 114
DGKA -0.04 0.16 -10000 0 -0.44 39 39
CREM 0.034 0.007 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.18 0.41 -10000 0 -0.83 116 116
CTLA4 -0.027 0.14 -10000 0 -0.4 29 29
NFAT1-c-4 (dimer)/EGR1 -0.2 0.43 -10000 0 -0.86 126 126
NFAT1-c-4 (dimer)/EGR4 -0.17 0.39 -10000 0 -0.8 120 120
FOS -0.034 0.15 -10000 0 -0.42 66 66
IFNG -0.19 0.43 -10000 0 -1 87 87
T cell activation -0.1 0.26 -10000 0 -0.73 36 36
MAF 0.015 0.078 -10000 0 -0.42 15 15
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.15 0.34 0.82 66 -10000 0 66
TNF -0.2 0.38 -10000 0 -0.77 130 130
FASLG -0.35 0.65 -10000 0 -1.2 155 155
TBX21 -0.044 0.17 -10000 0 -0.43 84 84
BATF3 0 0.001 -10000 0 -10000 0 0
PRKCQ 0.021 0.061 -10000 0 -0.3 12 12
PTPN1 -0.038 0.15 -10000 0 -0.41 39 39
NFAT1-c-4/ICER1 -0.17 0.4 -10000 0 -0.81 114 114
GATA3 -0.047 0.18 -10000 0 -0.42 91 91
T-helper 1 cell differentiation -0.19 0.41 -10000 0 -0.96 87 87
IL2RA -0.14 0.33 -10000 0 -0.77 76 76
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.035 0.14 -10000 0 -0.46 20 20
E2F1 0.033 0.054 -10000 0 -0.42 7 7
PPARG 0.012 0.093 -10000 0 -0.42 22 22
SLC3A2 -0.035 0.14 -10000 0 -0.41 32 32
IRF4 0.031 0.031 -10000 0 -0.42 2 2
PTGS2 -0.18 0.36 -10000 0 -0.78 107 107
CSF2 -0.19 0.38 -10000 0 -0.78 117 117
JunB/Fra1/NFAT1-c-4 -0.15 0.39 -10000 0 -0.79 114 114
IL4 -0.18 0.32 -10000 0 -0.84 65 65
IL5 -0.19 0.38 -10000 0 -0.78 116 116
IL2 -0.1 0.27 -10000 0 -0.77 32 32
IL3 -0.013 0.14 -10000 0 -0.85 10 10
RNF128 -0.016 0.16 -10000 0 -0.52 44 44
NFATC1 -0.15 0.34 -10000 0 -0.82 66 66
CDK4 0.1 0.22 0.56 42 -10000 0 42
PTPRK -0.069 0.22 -10000 0 -0.6 61 61
IL8 -0.2 0.39 -10000 0 -0.8 114 114
POU2F1 0.034 0.017 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.055 0.35 -10000 0 -0.72 76 76
HDAC7 0 0.003 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.008 0.35 -10000 0 -0.69 60 60
SMAD4 0.029 0.054 -10000 0 -0.42 7 7
ID2 -0.056 0.36 -10000 0 -0.72 76 76
AP1 -0.033 0.16 -10000 0 -0.35 88 88
ABCG2 -0.057 0.36 -10000 0 -0.72 78 78
HIF1A -0.023 0.16 -10000 0 -0.47 48 48
TFF3 -0.1 0.37 -10000 0 -0.74 88 88
GATA2 0.018 0.054 -10000 0 -0.42 5 5
AKT1 0.012 0.09 -10000 0 -0.21 17 17
response to hypoxia -0.007 0.066 -10000 0 -0.14 35 35
MCL1 -0.058 0.35 -10000 0 -0.72 76 76
NDRG1 -0.065 0.33 -10000 0 -0.74 66 66
SERPINE1 -0.063 0.36 -10000 0 -0.72 80 80
FECH -0.062 0.36 -10000 0 -0.72 81 81
FURIN -0.057 0.35 -10000 0 -0.71 80 80
NCOA2 0.026 0.047 -10000 0 -0.42 5 5
EP300 0.008 0.11 -10000 0 -0.27 34 34
HMOX1 -0.066 0.36 -10000 0 -0.72 81 81
BHLHE40 -0.077 0.34 -10000 0 -0.68 86 86
BHLHE41 -0.077 0.34 -10000 0 -0.68 86 86
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.05 0.17 -10000 0 -0.33 44 44
ENG -0.007 0.13 -10000 0 -0.32 35 35
JUN -0.009 0.12 -10000 0 -0.43 39 39
RORA -0.064 0.36 -10000 0 -0.73 78 78
ABCB1 -0.029 0.24 -10000 0 -0.94 28 28
TFRC -0.072 0.36 -10000 0 -0.73 83 83
CXCR4 -0.067 0.37 -10000 0 -0.74 83 83
TF -0.056 0.35 -10000 0 -0.72 76 76
CITED2 -0.059 0.35 -10000 0 -0.72 76 76
HIF1A/ARNT -0.035 0.43 -10000 0 -0.88 61 61
LDHA 0.01 0.19 -10000 0 -0.94 14 14
ETS1 -0.065 0.35 -10000 0 -0.72 77 77
PGK1 -0.053 0.36 -10000 0 -0.72 77 77
NOS2 -0.077 0.34 -10000 0 -0.68 86 86
ITGB2 -0.064 0.36 -10000 0 -0.74 79 79
ALDOA -0.05 0.35 -10000 0 -0.73 71 71
Cbp/p300/CITED2 -0.057 0.36 -10000 0 -0.78 66 66
FOS -0.038 0.15 -10000 0 -0.42 66 66
HK2 -0.054 0.36 -10000 0 -0.72 76 76
SP1 0.035 0.039 -10000 0 -0.18 8 8
GCK 0.013 0.18 -10000 0 -1.1 5 5
HK1 -0.053 0.35 -10000 0 -0.72 76 76
NPM1 -0.052 0.35 -10000 0 -0.71 76 76
EGLN1 -0.065 0.33 -10000 0 -0.72 72 72
CREB1 0.039 0.027 -10000 0 -0.42 1 1
PGM1 -0.059 0.35 -10000 0 -0.72 77 77
SMAD3 0.027 0.061 -10000 0 -0.42 9 9
EDN1 -0.18 0.48 -10000 0 -1.2 88 88
IGFBP1 -0.053 0.35 -10000 0 -0.71 78 78
VEGFA -0.042 0.27 0.44 1 -0.58 67 68
HIF1A/JAB1 0.003 0.12 -10000 0 -0.34 43 43
CP -0.12 0.38 -10000 0 -0.76 92 92
CXCL12 -0.071 0.38 -10000 0 -0.74 86 86
COPS5 0.027 0.043 -10000 0 -0.42 4 4
SMAD3/SMAD4 0.041 0.063 -10000 0 -0.3 16 16
BNIP3 -0.06 0.36 -10000 0 -0.7 84 84
EGLN3 -0.08 0.38 -10000 0 -0.76 84 84
CA9 -0.06 0.35 -10000 0 -0.71 78 78
TERT -0.056 0.35 -10000 0 -0.72 76 76
ENO1 -0.056 0.35 -10000 0 -0.72 75 75
PFKL -0.056 0.36 -10000 0 -0.73 75 75
NCOA1 0.032 0.045 -10000 0 -0.42 5 5
ADM -0.08 0.38 -10000 0 -0.75 88 88
ARNT 0.015 0.078 -10000 0 -10000 0 0
HNF4A 0.035 0.033 -10000 0 -0.42 2 2
ADFP -0.064 0.37 -10000 0 -0.74 82 82
SLC2A1 -0.03 0.29 -10000 0 -0.59 63 63
LEP -0.072 0.36 -10000 0 -0.73 79 79
HIF1A/ARNT/Cbp/p300 -0.022 0.35 -10000 0 -0.7 63 63
EPO -0.027 0.28 -10000 0 -0.69 43 43
CREBBP 0.017 0.098 -10000 0 -0.25 24 24
HIF1A/ARNT/Cbp/p300/HDAC7 -0.021 0.34 -10000 0 -0.68 61 61
PFKFB3 -0.058 0.35 -10000 0 -0.73 75 75
NT5E -0.059 0.36 -10000 0 -0.74 75 75
Glucocorticoid receptor regulatory network

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
PCK2 0.054 0.15 0.3 18 -0.83 8 26
SMARCC2 0.036 0.005 -10000 0 -10000 0 0
SMARCC1 0.033 0.03 -10000 0 -0.42 2 2
TBX21 -0.15 0.28 0.36 1 -0.72 89 90
SUMO2 0.029 0.02 -10000 0 -10000 0 0
STAT1 (dimer) 0.021 0.091 -10000 0 -0.38 23 23
FKBP4 0.03 0.046 -10000 0 -0.42 5 5
FKBP5 -0.003 0.12 -10000 0 -0.42 41 41
GR alpha/HSP90/FKBP51/HSP90 0.061 0.14 0.28 70 -0.26 21 91
PRL -0.035 0.13 -10000 0 -1.4 1 1
cortisol/GR alpha (dimer)/TIF2 0.14 0.24 0.53 109 -0.43 1 110
RELA -0.02 0.11 -10000 0 -0.21 78 78
FGG 0.14 0.23 0.47 121 -0.4 2 123
GR beta/TIF2 0.07 0.14 0.32 69 -0.31 8 77
IFNG -0.26 0.41 -10000 0 -0.83 136 136
apoptosis -0.003 0.17 0.51 4 -0.5 11 15
CREB1 0.038 0.042 -10000 0 -0.37 5 5
histone acetylation -0.025 0.11 0.31 4 -0.32 34 38
BGLAP -0.047 0.14 -10000 0 -0.5 14 14
GR/PKAc 0.11 0.12 0.32 55 -0.26 14 69
NF kappa B1 p50/RelA -0.039 0.19 -10000 0 -0.32 129 129
SMARCD1 0.036 0.004 -10000 0 -10000 0 0
MDM2 0.072 0.1 0.24 106 -10000 0 106
GATA3 -0.039 0.18 -10000 0 -0.41 91 91
AKT1 0.03 0.036 0.19 8 -0.43 2 10
CSF2 -0.05 0.13 -10000 0 -1.1 3 3
GSK3B 0.03 0.02 -10000 0 -10000 0 0
NR1I3 0.029 0.18 0.57 4 -0.61 8 12
CSN2 0.12 0.19 0.39 126 -0.37 5 131
BRG1/BAF155/BAF170/BAF60A 0.083 0.037 -10000 0 -0.23 3 3
NFATC1 0.023 0.09 -10000 0 -0.4 21 21
POU2F1 0.033 0.021 -10000 0 -0.25 1 1
CDKN1A -0.047 0.26 -10000 0 -1.5 14 14
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.001 0.006 -10000 0 -10000 0 0
SFN 0.012 0.099 -10000 0 -0.42 25 25
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.07 0.14 0.3 51 -0.25 32 83
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.079 0.31 0.48 3 -0.78 78 81
JUN -0.15 0.23 0.37 4 -0.45 150 154
IL4 -0.087 0.19 -10000 0 -0.62 27 27
CDK5R1 0.033 0.01 -10000 0 -10000 0 0
PRKACA 0.036 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.097 0.21 0.21 70 -0.37 149 219
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.086 0.13 0.3 58 -0.24 27 85
cortisol/GR alpha (monomer) 0.19 0.31 0.61 142 -0.44 2 144
NCOA2 0.025 0.047 -10000 0 -0.42 5 5
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.081 0.16 -10000 0 -0.43 73 73
AP-1/NFAT1-c-4 -0.27 0.37 -10000 0 -0.7 183 183
AFP -0.12 0.19 -10000 0 -0.64 18 18
SUV420H1 0.033 0.022 -10000 0 -0.42 1 1
IRF1 0.095 0.21 0.41 67 -0.68 14 81
TP53 0.014 0.13 -10000 0 -0.46 32 32
PPP5C 0.032 0.041 -10000 0 -0.42 4 4
KRT17 -0.38 0.56 -10000 0 -1.2 147 147
KRT14 -0.26 0.49 -10000 0 -1.3 93 93
TBP 0.04 0.019 -10000 0 -0.28 1 1
CREBBP 0.066 0.096 0.28 79 -10000 0 79
HDAC1 0.03 0.021 -10000 0 -0.42 1 1
HDAC2 0.031 0.023 -10000 0 -0.42 1 1
AP-1 -0.27 0.38 -10000 0 -0.71 183 183
MAPK14 0.033 0.014 -10000 0 -10000 0 0
MAPK10 0.009 0.089 -10000 0 -0.42 20 20
MAPK11 0.028 0.02 -10000 0 -10000 0 0
KRT5 -0.39 0.57 -10000 0 -1.2 150 150
interleukin-1 receptor activity -0.001 0.007 -10000 0 -10000 0 0
NCOA1 0.032 0.048 -10000 0 -0.37 6 6
STAT1 0.021 0.091 -10000 0 -0.38 23 23
CGA -0.071 0.17 -10000 0 -0.52 34 34
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.081 0.16 0.38 80 -0.39 2 82
MAPK3 0.027 0.028 -10000 0 -0.42 1 1
MAPK1 0.03 0.025 -10000 0 -0.42 1 1
ICAM1 -0.16 0.3 0.33 1 -0.63 110 111
NFKB1 -0.021 0.11 -10000 0 -0.2 93 93
MAPK8 -0.11 0.2 0.56 2 -0.38 133 135
MAPK9 0.016 0.085 -10000 0 -0.42 18 18
cortisol/GR alpha (dimer) -0.005 0.18 0.52 4 -0.52 11 15
BAX -0.01 0.1 -10000 0 -10000 0 0
POMC -0.091 0.2 0.62 1 -1.4 4 5
EP300 0.066 0.099 0.28 84 -0.43 2 86
cortisol/GR alpha (dimer)/p53 0.12 0.25 0.53 104 -0.42 1 105
proteasomal ubiquitin-dependent protein catabolic process 0.053 0.11 0.26 78 -10000 0 78
SGK1 0.08 0.14 0.33 94 -0.33 4 98
IL13 -0.22 0.26 -10000 0 -0.72 60 60
IL6 -0.2 0.38 -10000 0 -0.9 92 92
PRKACG 0.034 0.029 -10000 0 -0.42 2 2
IL5 -0.18 0.22 -10000 0 -0.62 48 48
IL2 -0.22 0.33 -10000 0 -0.72 121 121
CDK5 0.034 0.008 -10000 0 -10000 0 0
PRKACB 0.008 0.099 -10000 0 -0.42 25 25
HSP90AA1 0 0 -10000 0 -10000 0 0
IL8 -0.18 0.34 -10000 0 -0.83 87 87
CDK5R1/CDK5 0.047 0.018 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.001 0.18 -10000 0 -0.33 66 66
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.16 0.24 0.5 137 -0.4 1 138
SMARCA4 0.035 0.021 -10000 0 -0.42 1 1
chromatin remodeling 0.11 0.16 0.34 129 -0.26 1 130
NF kappa B1 p50/RelA/Cbp 0.026 0.18 0.35 40 -0.34 40 80
JUN (dimer) -0.15 0.23 0.37 4 -0.45 150 154
YWHAH 0.031 0.036 -10000 0 -0.42 3 3
VIPR1 -0.1 0.21 -10000 0 -0.51 79 79
NR3C1 0.12 0.21 0.42 122 -0.41 8 130
NR4A1 0.037 0.045 -10000 0 -0.44 4 4
TIF2/SUV420H1 0.037 0.046 -10000 0 -0.35 5 5
MAPKKK cascade -0.003 0.17 0.51 4 -0.5 11 15
cortisol/GR alpha (dimer)/Src-1 0.18 0.26 0.53 141 -0.36 1 142
PBX1 0.02 0.077 -10000 0 -0.4 15 15
POU1F1 0.04 0.025 -10000 0 -0.33 2 2
SELE -0.23 0.42 -10000 0 -0.92 126 126
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.11 0.16 0.34 129 -0.26 1 130
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.16 0.24 0.5 137 -0.4 1 138
mol:cortisol 0.11 0.18 0.35 144 -10000 0 144
MMP1 -0.37 0.54 -10000 0 -1.1 158 158
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.04 0.19 -10000 0 -0.58 53 53
IHH 0.017 0.088 -10000 0 -0.32 19 19
SHH Np/Cholesterol/GAS1 -0.027 0.11 -10000 0 -0.24 101 101
LRPAP1 0.035 0.007 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.027 0.1 0.23 101 -10000 0 101
SMO/beta Arrestin2 -0.022 0.17 -10000 0 -0.42 56 56
SMO -0.038 0.16 -10000 0 -0.36 88 88
AKT1 -0.015 0.16 -10000 0 -0.53 30 30
ARRB2 0.033 0.011 -10000 0 -10000 0 0
BOC 0.014 0.093 -10000 0 -0.42 22 22
ADRBK1 0.034 0.01 -10000 0 -10000 0 0
heart looping -0.034 0.16 -10000 0 -0.36 88 88
STIL -0.006 0.14 0.2 77 -0.23 98 175
DHH N/PTCH2 0.052 0.011 -10000 0 -10000 0 0
DHH N/PTCH1 -0.001 0.12 -10000 0 -0.29 69 69
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
DHH 0.036 0.005 -10000 0 -10000 0 0
PTHLH -0.064 0.25 -10000 0 -0.73 56 56
determination of left/right symmetry -0.034 0.16 -10000 0 -0.36 88 88
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
skeletal system development -0.063 0.25 -10000 0 -0.72 56 56
IHH N/Hhip 0.035 0.065 -10000 0 -0.29 12 12
DHH N/Hhip 0.049 0.029 -10000 0 -0.3 3 3
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.034 0.16 -10000 0 -0.36 88 88
pancreas development 0.032 0.036 -10000 0 -0.42 3 3
HHAT -0.017 0.13 -10000 0 -0.42 50 50
PI3K 0.036 0.065 -10000 0 -0.3 17 17
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.03 0.16 -10000 0 -0.42 71 71
somite specification -0.034 0.16 -10000 0 -0.36 88 88
SHH Np/Cholesterol/PTCH1 -0.031 0.11 -10000 0 -0.23 102 102
SHH Np/Cholesterol/PTCH2 0.003 0.074 -10000 0 -0.23 44 44
SHH Np/Cholesterol/Megalin -0.055 0.14 -10000 0 -0.27 133 133
SHH -0.016 0.09 -10000 0 -0.3 46 46
catabolic process -0.025 0.12 -10000 0 -0.32 70 70
SMO/Vitamin D3 -0.019 0.15 0.2 42 -0.33 63 105
SHH Np/Cholesterol/Hhip 0.002 0.075 -10000 0 -0.23 45 45
LRP2 -0.096 0.2 -10000 0 -0.42 144 144
receptor-mediated endocytosis -0.071 0.18 -10000 0 -0.36 98 98
SHH Np/Cholesterol/BOC -0.007 0.085 -10000 0 -0.23 63 63
SHH Np/Cholesterol/CDO -0.007 0.083 -10000 0 -0.24 56 56
mesenchymal cell differentiation -0.001 0.074 0.23 45 -10000 0 45
mol:Vitamin D3 -0.007 0.13 0.2 62 -0.24 102 164
IHH N/PTCH2 0.037 0.06 -10000 0 -0.27 10 10
CDON 0.021 0.067 -10000 0 -0.42 11 11
IHH N/PTCH1 -0.005 0.13 -10000 0 -0.33 70 70
Megalin/LRPAP1 -0.049 0.16 -10000 0 -0.3 144 144
PTCH2 0.035 0.006 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.007 0.07 -10000 0 -0.23 46 46
PTCH1 -0.025 0.12 -10000 0 -0.32 70 70
HHIP 0.032 0.036 -10000 0 -0.42 3 3
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.029 0.05 -10000 0 -0.42 6 6
LAT2 -0.049 0.14 -10000 0 -0.31 87 87
AP1 -0.06 0.21 0.29 1 -0.45 77 78
mol:PIP3 -0.025 0.19 0.3 20 -0.36 81 101
IKBKB 0.011 0.13 0.25 51 -0.24 44 95
AKT1 0.014 0.18 0.33 75 -0.35 27 102
IKBKG -0.008 0.12 0.22 18 -0.24 47 65
MS4A2 -0.076 0.19 -10000 0 -0.41 120 120
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
MAP3K1 -0.04 0.16 0.25 7 -0.38 63 70
mol:Ca2+ -0.013 0.16 0.26 25 -0.28 78 103
LYN 0.032 0.017 -10000 0 -10000 0 0
CBLB -0.047 0.14 -10000 0 -0.31 83 83
SHC1 0.028 0.025 -10000 0 -0.42 1 1
RasGAP/p62DOK 0.035 0.092 -10000 0 -0.24 46 46
positive regulation of cell migration -0.005 0.063 -10000 0 -0.3 23 23
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.004 0.18 0.32 71 -0.3 60 131
PTPN13 -0.07 0.2 -10000 0 -0.6 33 33
PTPN11 0.033 0.024 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.004 0.15 0.33 16 -0.32 28 44
SYK 0.006 0.12 -10000 0 -0.42 34 34
GRB2 0.033 0.011 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.056 0.16 -10000 0 -0.36 87 87
LAT -0.045 0.13 -10000 0 -0.3 82 82
PAK2 -0.035 0.17 0.25 9 -0.4 55 64
NFATC2 -0.012 0.066 -10000 0 -0.59 4 4
HRAS -0.036 0.18 0.26 9 -0.37 80 89
GAB2 0.031 0.013 -10000 0 -10000 0 0
PLA2G1B 0.013 0.11 -10000 0 -0.94 5 5
Fc epsilon R1 -0.029 0.16 -10000 0 -0.3 109 109
Antigen/IgE/Fc epsilon R1 -0.024 0.14 -10000 0 -0.27 109 109
mol:GDP -0.051 0.18 0.25 1 -0.44 62 63
JUN -0.001 0.12 -10000 0 -0.42 39 39
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
FOS -0.031 0.15 -10000 0 -0.42 66 66
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.044 0.14 -10000 0 -0.31 88 88
CHUK -0.011 0.12 0.2 25 -0.24 51 76
KLRG1 -0.038 0.12 0.16 2 -0.26 91 93
VAV1 -0.051 0.14 -10000 0 -0.32 88 88
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.045 0.13 -10000 0 -0.31 81 81
negative regulation of mast cell degranulation -0.041 0.11 -10000 0 -0.25 82 82
BTK -0.057 0.18 -10000 0 -0.5 52 52
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.063 0.18 -10000 0 -0.35 114 114
GAB2/PI3K/SHP2 -0.052 0.1 -10000 0 -0.29 57 57
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.048 0.13 -10000 0 -0.26 108 108
RAF1 0.014 0.11 -10000 0 -1 5 5
Fc epsilon R1/FcgammaRIIB/SHIP -0.024 0.16 -10000 0 -0.29 116 116
FCER1G 0.032 0.019 -10000 0 -10000 0 0
FCER1A -0.023 0.14 -10000 0 -0.43 56 56
Antigen/IgE/Fc epsilon R1/Fyn -0.016 0.14 -10000 0 -0.26 108 108
MAPK3 0.013 0.11 -10000 0 -0.97 5 5
MAPK1 0.008 0.11 -10000 0 -0.94 5 5
NFKB1 0.036 0.005 -10000 0 -10000 0 0
MAPK8 -0.041 0.22 -10000 0 -0.65 44 44
DUSP1 0.003 0.11 -10000 0 -0.42 34 34
NF-kappa-B/RelA 0.012 0.084 0.16 30 -0.15 39 69
actin cytoskeleton reorganization -0.044 0.18 -10000 0 -0.62 19 19
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.028 0.18 0.26 1 -0.34 86 87
FER -0.046 0.13 -10000 0 -0.31 83 83
RELA 0.035 0.006 -10000 0 -10000 0 0
ITK -0.032 0.11 -10000 0 -0.39 40 40
SOS1 0.035 0.021 -10000 0 -0.42 1 1
PLCG1 -0.042 0.19 0.27 4 -0.46 56 60
cytokine secretion -0.003 0.051 -10000 0 -0.12 22 22
SPHK1 -0.054 0.14 -10000 0 -0.31 93 93
PTK2 -0.046 0.19 -10000 0 -0.68 18 18
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.057 0.17 -10000 0 -0.38 88 88
EDG1 -0.005 0.064 -10000 0 -0.3 23 23
mol:DAG -0.03 0.19 0.29 14 -0.36 86 100
MAP2K2 0.008 0.11 -10000 0 -0.97 5 5
MAP2K1 0.01 0.11 -10000 0 -0.96 5 5
MAP2K7 0.035 0.021 -10000 0 -0.42 1 1
KLRG1/SHP2 -0.024 0.12 0.21 3 -0.34 37 40
MAP2K4 -0.098 0.36 -10000 0 -0.92 76 76
Fc epsilon R1/FcgammaRIIB -0.026 0.17 -10000 0 -0.31 116 116
mol:Choline -0.003 0.18 0.32 71 -0.3 60 131
SHC/Grb2/SOS1 -0.011 0.14 -10000 0 -0.3 72 72
FYN 0.027 0.054 -10000 0 -0.42 7 7
DOK1 0.027 0.061 -10000 0 -0.42 9 9
PXN -0.045 0.18 -10000 0 -0.61 18 18
HCLS1 -0.05 0.14 -10000 0 -0.32 87 87
PRKCB -0.016 0.15 0.24 25 -0.28 84 109
FCGR2B 0.001 0.11 -10000 0 -0.42 30 30
IGHE 0.001 0.008 -10000 0 -10000 0 0
KLRG1/SHIP -0.042 0.12 -10000 0 -0.26 82 82
LCP2 0.024 0.067 -10000 0 -0.42 11 11
PLA2G4A -0.052 0.14 -10000 0 -0.32 90 90
RASA1 0.029 0.05 -10000 0 -0.42 6 6
mol:Phosphatidic acid -0.003 0.18 0.32 71 -0.3 60 131
IKK complex 0.01 0.11 0.23 44 -0.2 34 78
WIPF1 0 0 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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
TGM2 0.017 0.085 -10000 0 -0.42 18 18
GNB1/GNG2 -0.05 0.08 -10000 0 -0.18 127 127
AKT1 -0.013 0.13 0.23 5 -0.21 102 107
EGF -0.069 0.19 -10000 0 -0.42 110 110
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.016 0.063 0.25 5 -0.26 3 8
mol:Ca2+ -0.035 0.17 -10000 0 -0.3 132 132
LYN 0.015 0.057 0.26 4 -0.28 2 6
RhoA/GTP -0.014 0.075 -10000 0 -0.13 116 116
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.055 0.19 -10000 0 -0.35 132 132
GNG2 0.034 0.021 -10000 0 -0.42 1 1
ARRB2 0.033 0.011 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.012 0.14 -10000 0 -0.46 32 32
G beta5/gamma2 -0.053 0.11 -10000 0 -0.24 126 126
PRKCH -0.051 0.2 0.3 3 -0.36 129 132
DNM1 0.033 0.035 -10000 0 -0.42 3 3
TXA2/TP beta/beta Arrestin3 0.028 0.027 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR 0.028 0.054 -10000 0 -0.42 7 7
G12 family/GTP -0.048 0.16 -10000 0 -0.3 118 118
ADRBK1 0.034 0.01 -10000 0 -10000 0 0
ADRBK2 0.024 0.067 -10000 0 -0.42 11 11
RhoA/GTP/ROCK1 0.041 0.04 -10000 0 -0.25 8 8
mol:GDP 0.022 0.14 0.42 32 -0.23 2 34
mol:NADP 0.035 0.007 -10000 0 -10000 0 0
RAB11A 0.034 0.021 -10000 0 -0.42 1 1
PRKG1 0.035 0.006 -10000 0 -10000 0 0
mol:IP3 -0.052 0.21 -10000 0 -0.38 132 132
cell morphogenesis 0.04 0.039 -10000 0 -0.25 8 8
PLCB2 -0.086 0.27 -10000 0 -0.52 132 132
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.007 0.058 0.25 4 -0.24 4 8
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.01 0.075 0.25 5 -0.32 8 13
RHOA 0.026 0.061 -10000 0 -0.42 9 9
PTGIR 0.033 0.029 -10000 0 -0.42 2 2
PRKCB1 -0.055 0.21 -10000 0 -0.4 121 121
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.035 0.007 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.087 0.27 -10000 0 -0.52 131 131
LCK -0.005 0.09 0.25 5 -0.29 15 20
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.049 0.047 0.23 1 -0.2 9 10
TXA2-R family/G12 family/GDP/G beta/gamma 0.036 0.093 -10000 0 -0.45 14 14
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.044 0.047 0.23 1 -0.2 9 10
MAPK14 -0.032 0.13 0.22 3 -0.24 127 130
TGM2/GTP -0.062 0.23 -10000 0 -0.42 129 129
MAPK11 -0.034 0.13 0.25 3 -0.23 128 131
ARHGEF1 -0.011 0.11 0.24 4 -0.18 112 116
GNAI2 0.028 0.054 -10000 0 -0.42 7 7
JNK cascade -0.054 0.21 -10000 0 -0.38 131 131
RAB11/GDP 0.034 0.021 -10000 0 -0.42 1 1
ICAM1 -0.036 0.16 -10000 0 -0.3 129 129
cAMP biosynthetic process -0.049 0.19 -10000 0 -0.34 132 132
Gq family/GTP/EBP50 -0.021 0.096 -10000 0 -0.23 78 78
actin cytoskeleton reorganization 0.04 0.039 -10000 0 -0.25 8 8
SRC 0.015 0.064 0.25 5 -0.27 2 7
GNB5 0.025 0.067 -10000 0 -0.42 11 11
GNB1 0.032 0.045 -10000 0 -0.42 5 5
EGF/EGFR -0.034 0.11 0.23 6 -0.3 40 46
VCAM1 -0.041 0.17 -10000 0 -0.31 129 129
TP beta/Gq family/GDP/G beta5/gamma2 -0.012 0.14 -10000 0 -0.46 32 32
platelet activation -0.04 0.17 0.31 1 -0.3 130 131
PGI2/IP 0.025 0.021 -10000 0 -0.3 2 2
PRKACA 0.019 0.035 -10000 0 -0.23 9 9
Gq family/GDP/G beta5/gamma2 -0.007 0.12 -10000 0 -0.41 30 30
TXA2/TP beta/beta Arrestin2 0.009 0.066 -10000 0 -0.44 6 6
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.008 0.029 -10000 0 -0.21 8 8
mol:DAG -0.064 0.23 -10000 0 -0.43 129 129
EGFR -0.015 0.13 -10000 0 -0.42 49 49
TXA2/TP alpha -0.074 0.25 -10000 0 -0.47 131 131
Gq family/GTP -0.016 0.077 0.22 2 -0.22 57 59
YES1 0.014 0.068 0.25 5 -0.28 6 11
GNAI2/GTP 0.022 0.052 -10000 0 -0.21 17 17
PGD2/DP 0.02 0.038 -10000 0 -0.3 7 7
SLC9A3R1 -0.009 0.13 -10000 0 -0.42 46 46
FYN 0.011 0.067 0.25 4 -0.26 8 12
mol:NO 0.035 0.007 -10000 0 -10000 0 0
GNA15 0.03 0.046 -10000 0 -0.42 5 5
PGK/cGMP 0.046 0.012 -10000 0 -10000 0 0
RhoA/GDP 0.026 0.06 -10000 0 -0.41 9 9
TP alpha/TGM2/GDP/G beta/gamma 0.056 0.075 0.28 2 -0.33 5 7
NOS3 0.035 0.007 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
PRKCA -0.04 0.19 0.3 4 -0.35 115 119
PRKCB -0.052 0.19 -10000 0 -0.36 130 130
PRKCE -0.052 0.2 0.29 2 -0.36 128 130
PRKCD -0.059 0.2 -10000 0 -0.39 128 128
PRKCG -0.058 0.21 -10000 0 -0.39 130 130
muscle contraction -0.081 0.25 -10000 0 -0.48 131 131
PRKCZ -0.046 0.18 -10000 0 -0.34 131 131
ARR3 0.036 0.002 -10000 0 -10000 0 0
TXA2/TP beta 0.042 0.056 0.28 1 -0.2 15 16
PRKCQ -0.048 0.2 0.3 2 -0.37 125 127
MAPKKK cascade -0.07 0.24 -10000 0 -0.45 131 131
SELE -0.055 0.19 -10000 0 -0.37 129 129
TP beta/GNAI2/GDP/G beta/gamma 0.062 0.067 0.28 2 -0.23 16 18
ROCK1 0.036 0.006 -10000 0 -10000 0 0
GNA14 -0.009 0.13 -10000 0 -0.42 43 43
chemotaxis -0.11 0.31 -10000 0 -0.61 129 129
GNA12 0.035 0.007 -10000 0 -10000 0 0
GNA13 0.029 0.037 -10000 0 -0.42 3 3
GNA11 0.033 0.036 -10000 0 -0.42 3 3
Rac1/GTP 0.026 0.005 -10000 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.067 0.15 -9999 0 -0.29 136 136
FZD6 -0.028 0.14 -9999 0 -0.42 60 60
WNT6 0.03 0.031 -9999 0 -0.42 2 2
WNT4 -0.019 0.14 -9999 0 -0.42 58 58
FZD3 0.007 0.095 -9999 0 -0.42 23 23
WNT5A -0.025 0.15 -9999 0 -0.42 63 63
WNT11 0.027 0.032 -9999 0 -0.42 2 2
IL23-mediated signaling events

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
CCL2 -0.16 0.54 -10000 0 -1.2 83 83
IL23A -0.13 0.49 -10000 0 -1.2 68 68
NF kappa B1 p50/RelA/I kappa B alpha -0.099 0.48 -10000 0 -1.1 73 73
positive regulation of T cell mediated cytotoxicity -0.14 0.52 -10000 0 -1.1 86 86
ITGA3 -0.13 0.48 -10000 0 -1.1 78 78
IL17F -0.049 0.33 0.47 5 -0.69 70 75
IL12B 0.02 0.075 -10000 0 -0.44 6 6
STAT1 (dimer) -0.14 0.5 -10000 0 -1.1 81 81
CD4 -0.1 0.45 -10000 0 -1 68 68
IL23 -0.12 0.47 -10000 0 -1.1 70 70
IL23R -0.001 0.22 -10000 0 -1.3 11 11
IL1B -0.15 0.53 -10000 0 -1.3 77 77
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.077 0.46 -10000 0 -1.1 60 60
TYK2 0.02 0.046 -10000 0 -10000 0 0
STAT4 0.01 0.1 -10000 0 -0.42 27 27
STAT3 0.029 0.032 -10000 0 -0.42 2 2
IL18RAP -0.022 0.15 -10000 0 -0.42 58 58
IL12RB1 0.02 0.046 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
IL12Rbeta1/TYK2 0.031 0.059 -10000 0 -10000 0 0
IL23R/JAK2 0.012 0.22 -10000 0 -1.2 11 11
positive regulation of chronic inflammatory response -0.14 0.52 -10000 0 -1.1 86 86
natural killer cell activation 0 0.012 0.081 7 -10000 0 7
JAK2 0.023 0.063 -10000 0 -0.46 2 2
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
NFKB1 0.036 0.007 -10000 0 -10000 0 0
RELA 0.036 0.007 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.11 0.45 -10000 0 -1 70 70
ALOX12B -0.11 0.45 -10000 0 -1.1 69 69
CXCL1 -0.17 0.55 -10000 0 -1.2 98 98
T cell proliferation -0.14 0.52 -10000 0 -1.1 86 86
NFKBIA 0.034 0.03 -10000 0 -0.42 2 2
IL17A -0.027 0.26 -10000 0 -0.53 70 70
PI3K -0.12 0.49 -10000 0 -1.1 75 75
IFNG -0.006 0.05 0.14 6 -0.13 46 52
STAT3 (dimer) -0.12 0.46 -10000 0 -1 74 74
IL18R1 0.015 0.09 -10000 0 -0.42 20 20
IL23/IL23R/JAK2/TYK2/SOCS3 -0.035 0.29 0.51 1 -0.65 53 54
IL18/IL18R -0.009 0.16 -10000 0 -0.34 84 84
macrophage activation -0.006 0.021 -10000 0 -0.044 60 60
TNF -0.13 0.48 -10000 0 -1.1 72 72
STAT3/STAT4 -0.13 0.49 -10000 0 -1.1 77 77
STAT4 (dimer) -0.14 0.52 -10000 0 -1.2 78 78
IL18 -0.001 0.11 -10000 0 -0.42 32 32
IL19 -0.077 0.46 -10000 0 -1.1 60 60
STAT5A (dimer) -0.14 0.49 -10000 0 -1.1 79 79
STAT1 0.02 0.075 -10000 0 -0.42 14 14
SOCS3 0.028 0.046 -10000 0 -0.42 5 5
CXCL9 -0.2 0.58 -10000 0 -1.2 109 109
MPO -0.097 0.45 -10000 0 -1 67 67
positive regulation of humoral immune response -0.14 0.52 -10000 0 -1.1 86 86
IL23/IL23R/JAK2/TYK2 -0.15 0.56 -10000 0 -1.2 84 84
IL6 -0.17 0.56 -10000 0 -1.2 91 91
STAT5A 0.027 0.037 -10000 0 -0.42 3 3
IL2 0.029 0.039 -10000 0 -0.42 3 3
positive regulation of tyrosine phosphorylation of STAT protein 0 0.012 0.081 7 -10000 0 7
CD3E -0.11 0.45 -10000 0 -1.1 67 67
keratinocyte proliferation -0.14 0.52 -10000 0 -1.1 86 86
NOS2 -0.11 0.45 -10000 0 -0.95 89 89
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.004 0.17 0.24 39 -0.34 68 107
FYN -0.038 0.2 0.28 5 -0.42 76 81
LAT/GRAP2/SLP76 -0.021 0.17 0.24 8 -0.37 71 79
IKBKB 0.03 0.014 -10000 0 -10000 0 0
AKT1 -0.026 0.15 0.25 14 -0.31 79 93
B2M 0.026 0.062 -10000 0 -0.43 9 9
IKBKG 0 0.055 0.13 19 -0.13 25 44
MAP3K8 0.004 0.11 -10000 0 -0.42 32 32
mol:Ca2+ -0.017 0.021 0.093 2 -0.056 75 77
integrin-mediated signaling pathway 0.03 0.048 -10000 0 -0.25 12 12
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.052 0.2 0.26 2 -0.43 84 86
TRPV6 -0.028 0.22 1.2 9 -0.62 1 10
CD28 0 0.12 -10000 0 -0.42 37 37
SHC1 -0.022 0.2 0.24 46 -0.38 86 132
receptor internalization -0.069 0.2 0.17 1 -0.4 124 125
PRF1 -0.054 0.22 -10000 0 -0.85 24 24
KRAS 0.028 0.054 -10000 0 -0.42 7 7
GRB2 0.033 0.011 -10000 0 -10000 0 0
COT/AKT1 -0.015 0.14 0.25 11 -0.28 69 80
LAT -0.042 0.19 0.24 13 -0.38 95 108
EntrezGene:6955 0 0.002 -10000 0 -0.016 7 7
CD3D 0.016 0.077 -10000 0 -0.43 14 14
CD3E 0.032 0.015 -10000 0 -10000 0 0
CD3G -0.021 0.14 -10000 0 -0.42 54 54
RASGRP2 -0.001 0.043 0.078 1 -0.17 27 28
RASGRP1 -0.043 0.17 0.32 2 -0.36 80 82
HLA-A 0.018 0.086 -10000 0 -0.43 18 18
RASSF5 0.019 0.064 -10000 0 -0.42 10 10
RAP1A/GTP/RAPL 0.03 0.048 -10000 0 -0.25 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.067 0.14 32 -0.12 30 62
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.022 0.071 -10000 0 -0.18 53 53
PRKCA -0.01 0.09 0.17 18 -0.21 49 67
GRAP2 0.032 0.023 -10000 0 -0.42 1 1
mol:IP3 -0.022 0.14 0.21 30 -0.31 67 97
EntrezGene:6957 0 0.003 0.011 2 -0.021 7 9
TCR/CD3/MHC I/CD8 -0.031 0.14 -10000 0 -0.32 77 77
ORAI1 0.007 0.16 0.59 1 -1 9 10
CSK -0.045 0.18 0.26 2 -0.4 83 85
B7 family/CD28 -0.027 0.22 0.29 1 -0.47 75 76
CHUK 0.026 0.067 -10000 0 -0.42 11 11
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.06 0.21 0.26 1 -0.42 104 105
PTPN6 -0.053 0.19 0.24 4 -0.4 89 93
VAV1 -0.059 0.2 0.26 2 -0.4 102 104
Monovalent TCR/CD3 -0.018 0.11 -10000 0 -0.3 61 61
CBL 0.032 0.012 -10000 0 -10000 0 0
LCK -0.046 0.21 0.26 5 -0.45 81 86
PAG1 -0.031 0.19 0.23 15 -0.4 82 97
RAP1A 0.031 0.045 -10000 0 -0.42 5 5
TCR/CD3/MHC I/CD8/LCK -0.062 0.21 0.28 1 -0.42 104 105
CD80 0.034 0.022 -10000 0 -0.42 1 1
CD86 0.017 0.09 -10000 0 -0.42 20 20
PDK1/CARD11/BCL10/MALT1 -0.013 0.09 -10000 0 -0.22 54 54
HRAS 0.032 0.036 -10000 0 -0.42 3 3
GO:0035030 -0.052 0.17 0.25 1 -0.4 75 76
CD8A 0 0.003 0.011 2 -0.018 7 9
CD8B 0 0.004 0.011 3 -0.013 21 24
PTPRC 0.006 0.095 -10000 0 -0.42 23 23
PDK1/PKC theta -0.028 0.18 0.32 18 -0.38 74 92
CSK/PAG1 -0.025 0.18 0.23 12 -0.41 68 80
SOS1 0.035 0.021 -10000 0 -0.42 1 1
peptide-MHC class I 0.033 0.088 -10000 0 -0.36 23 23
GRAP2/SLP76 -0.034 0.2 0.29 1 -0.4 89 90
STIM1 0.008 0.11 1.3 3 -10000 0 3
RAS family/GTP 0.013 0.085 0.18 5 -0.18 33 38
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.072 0.21 0.17 1 -0.41 123 124
mol:DAG -0.042 0.11 0.11 2 -0.26 81 83
RAP1A/GDP 0.011 0.034 0.077 15 -0.073 14 29
PLCG1 0.034 0.008 -10000 0 -10000 0 0
CD247 0 0.002 -10000 0 -0.016 7 7
cytotoxic T cell degranulation -0.051 0.21 -10000 0 -0.79 25 25
RAP1A/GTP 0 0.018 -10000 0 -0.065 31 31
mol:PI-3-4-5-P3 -0.04 0.17 0.25 2 -0.37 83 85
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.021 0.18 0.23 28 -0.38 67 95
NRAS 0.029 0.054 -10000 0 -0.42 7 7
ZAP70 0.034 0.022 -10000 0 -0.42 1 1
GRB2/SOS1 0.048 0.023 -10000 0 -0.3 1 1
LAT/GRAP2/SLP76/VAV1 -0.031 0.17 0.24 3 -0.39 69 72
MALT1 0.031 0.041 -10000 0 -0.42 4 4
TRAF6 0.035 0.021 -10000 0 -0.42 1 1
CD8 heterodimer 0.001 0.006 0.02 3 -0.021 12 15
CARD11 0.028 0.054 -10000 0 -0.42 7 7
PRKCB -0.033 0.077 0.11 2 -0.19 82 84
PRKCE -0.012 0.097 0.17 15 -0.22 53 68
PRKCQ -0.045 0.19 0.29 3 -0.42 82 85
LCP2 0.024 0.067 -10000 0 -0.42 11 11
BCL10 0.035 0.008 -10000 0 -10000 0 0
regulation of survival gene product expression -0.019 0.13 0.23 15 -0.28 73 88
IKK complex 0.013 0.061 0.16 33 -0.1 18 51
RAS family/GDP -0.004 0.015 -10000 0 -0.047 22 22
MAP3K14 -0.014 0.1 0.2 14 -0.22 64 78
PDPK1 -0.021 0.14 0.28 18 -0.32 65 83
TCR/CD3/MHC I/CD8/Fyn -0.061 0.2 -10000 0 -0.43 95 95
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.007 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.006 0.12 -10000 0 -0.24 102 102
regulation of S phase of mitotic cell cycle -0.026 0.11 -10000 0 -0.23 100 100
GNAO1 0.03 0.014 -10000 0 -10000 0 0
HRAS 0.032 0.036 -10000 0 -0.42 3 3
SHBG/T-DHT 0.022 0.008 -10000 0 -10000 0 0
PELP1 0.032 0.011 -10000 0 -10000 0 0
AKT1 0.007 0.019 -10000 0 -0.3 2 2
MAP2K1 -0.056 0.097 0.18 13 -0.22 86 99
T-DHT/AR -0.037 0.13 -10000 0 -0.3 99 99
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.006 73 73
GNAI2 0.028 0.054 -10000 0 -0.42 7 7
GNAI3 0.035 0.006 -10000 0 -10000 0 0
GNAI1 0.017 0.087 -10000 0 -0.42 19 19
mol:GDP -0.073 0.15 -10000 0 -0.37 99 99
cell proliferation -0.075 0.17 0.29 2 -0.43 77 79
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
FOS -0.12 0.28 -10000 0 -0.79 73 73
mol:Ca2+ -0.009 0.024 -10000 0 -0.062 58 58
MAPK3 -0.06 0.14 0.28 3 -0.33 69 72
MAPK1 -0.045 0.13 0.21 1 -0.35 46 47
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
mol:IP3 0 0.002 -10000 0 -0.004 71 71
cAMP biosynthetic process 0.003 0.017 -10000 0 -10000 0 0
GNG2 0.034 0.021 -10000 0 -0.42 1 1
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 71 71
HRAS/GTP -0.006 0.12 -10000 0 -0.22 99 99
actin cytoskeleton reorganization 0.039 0.051 -10000 0 -0.21 17 17
SRC 0.033 0.03 -10000 0 -0.42 2 2
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 71 71
PI3K 0.033 0.056 -10000 0 -0.25 17 17
apoptosis 0.063 0.17 0.43 77 -10000 0 77
T-DHT/AR/PELP1 -0.015 0.12 -10000 0 -0.25 99 99
HRAS/GDP -0.052 0.16 -10000 0 -0.36 101 101
CREB1 -0.069 0.18 -10000 0 -0.46 77 77
RAC1-CDC42/GTP 0.05 0.056 -10000 0 -0.21 17 17
AR -0.054 0.18 -10000 0 -0.42 99 99
GNB1 0.032 0.045 -10000 0 -0.42 5 5
RAF1 -0.035 0.1 0.22 5 -0.22 95 100
RAC1-CDC42/GDP -0.03 0.16 -10000 0 -0.35 98 98
T-DHT/AR/PELP1/Src 0.001 0.12 -10000 0 -0.23 98 98
MAP2K2 -0.057 0.098 0.18 15 -0.23 86 101
T-DHT/AR/PELP1/Src/PI3K -0.027 0.11 -10000 0 -0.24 100 100
GNAZ 0.023 0.07 -10000 0 -0.42 12 12
SHBG 0.032 0.012 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.037 0.13 -10000 0 -0.41 36 36
mol:T-DHT 0 0.001 0.002 2 -0.003 41 43
RAC1 0.035 0.006 -10000 0 -10000 0 0
GNRH1 0.006 0.014 -10000 0 -0.3 1 1
Gi family/GTP -0.028 0.084 -10000 0 -0.23 46 46
CDC42 0.035 0.008 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.013 0.083 -10000 0 -0.21 68 68
epithelial cell differentiation 0.026 0.094 -10000 0 -0.22 57 57
CYFIP2 -0.006 0.13 -10000 0 -0.42 45 45
ENAH -0.028 0.075 0.3 2 -0.31 8 10
EGFR -0.015 0.13 -10000 0 -0.42 49 49
EPHA2 0.032 0.036 -10000 0 -0.42 3 3
MYO6 -0.036 0.077 0.18 7 -0.22 67 74
CTNNB1 0.025 0.067 -10000 0 -0.42 11 11
ABI1/Sra1/Nap1 0.041 0.09 -10000 0 -0.26 40 40
AQP5 -0.095 0.17 -10000 0 -0.45 83 83
CTNND1 0.034 0.022 -10000 0 -0.42 1 1
mol:PI-4-5-P2 -0.032 0.07 0.18 6 -0.21 58 64
regulation of calcium-dependent cell-cell adhesion -0.032 0.069 0.18 5 -0.21 61 66
EGF -0.069 0.19 -10000 0 -0.42 110 110
NCKAP1 0.035 0.021 -10000 0 -0.42 1 1
AQP3 -0.094 0.17 -10000 0 -0.45 84 84
cortical microtubule organization 0.026 0.094 -10000 0 -0.22 57 57
GO:0000145 -0.033 0.065 0.16 6 -0.2 58 64
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.031 0.097 -10000 0 -0.22 57 57
MLLT4 0.02 0.078 -10000 0 -0.42 15 15
ARF6/GDP -0.041 0.067 -10000 0 -0.22 56 56
ARF6 0.034 0.029 -10000 0 -0.42 2 2
Ephrin A1/EPHA2/NCK1/GIT1 0.053 0.072 -10000 0 -0.23 20 20
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.026 0.093 -10000 0 -0.37 14 14
PVRL2 0.026 0.064 -10000 0 -0.42 10 10
ZYX -0.034 0.074 0.18 8 -0.21 64 72
ARF6/GTP 0.059 0.077 -10000 0 -0.24 20 20
CDH1 -0.011 0.13 -10000 0 -0.42 45 45
EGFR/EGFR/EGF/EGF -0.057 0.14 -10000 0 -0.22 191 191
RhoA/GDP 0.023 0.099 -10000 0 -0.22 64 64
actin cytoskeleton organization -0.04 0.074 0.16 7 -0.21 70 77
IGF-1R heterotetramer -0.042 0.17 -10000 0 -0.42 84 84
GIT1 0.034 0.022 -10000 0 -0.42 1 1
IGF1R -0.042 0.17 -10000 0 -0.42 84 84
IGF1 -0.038 0.16 -10000 0 -0.42 78 78
DIAPH1 0.002 0.2 -10000 0 -0.59 37 37
Wnt receptor signaling pathway -0.026 0.094 0.22 57 -10000 0 57
RHOA 0.026 0.061 -10000 0 -0.42 9 9
RhoA/GTP -0.043 0.068 -10000 0 -0.22 60 60
CTNNA1 0.035 0.021 -10000 0 -0.42 1 1
VCL -0.041 0.075 0.17 7 -0.22 70 77
EFNA1 0.014 0.08 -10000 0 -0.42 16 16
LPP -0.038 0.071 0.17 8 -0.21 57 65
Ephrin A1/EPHA2 0.01 0.092 -10000 0 -0.22 57 57
SEC6/SEC8 -0.048 0.069 -10000 0 -0.21 72 72
MGAT3 -0.032 0.07 0.18 5 -0.21 61 66
HGF/MET 0.016 0.093 -10000 0 -0.21 66 66
HGF 0.028 0.057 -10000 0 -0.42 8 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.013 0.084 -10000 0 -0.22 68 68
actin cable formation 0.016 0.11 0.28 9 -0.31 8 17
KIAA1543 -0.037 0.07 0.17 7 -0.22 58 65
KIFC3 -0.031 0.068 0.18 6 -0.21 52 58
NCK1 0.034 0.021 -10000 0 -0.42 1 1
EXOC3 0.036 0.002 -10000 0 -10000 0 0
ACTN1 -0.034 0.075 0.18 8 -0.21 65 73
NCK1/GIT1 0.049 0.025 -10000 0 -0.29 2 2
mol:GDP 0.026 0.094 -10000 0 -0.22 57 57
EXOC4 0.034 0.021 -10000 0 -0.42 1 1
STX4 -0.034 0.062 -10000 0 -0.21 57 57
PIP5K1C -0.032 0.071 0.18 6 -0.21 58 64
LIMA1 0 0 -10000 0 -10000 0 0
ABI1 0.035 0.008 -10000 0 -10000 0 0
ROCK1 -0.009 0.1 0.3 5 -0.32 7 12
adherens junction assembly -0.044 0.12 0.27 1 -0.48 15 16
IGF-1R heterotetramer/IGF1 -0.055 0.15 -10000 0 -0.24 175 175
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.076 -10000 0 -0.3 24 24
MET 0.03 0.041 -10000 0 -0.42 4 4
PLEKHA7 -0.031 0.07 0.18 8 -0.21 57 65
mol:GTP 0.051 0.071 -10000 0 -0.23 20 20
establishment of epithelial cell apical/basal polarity -0.044 0.072 0.14 13 -0.2 64 77
cortical actin cytoskeleton stabilization -0.013 0.083 -10000 0 -0.21 68 68
regulation of cell-cell adhesion -0.04 0.074 0.16 7 -0.21 70 77
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.013 0.084 -10000 0 -0.22 68 68
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.003 0.1 -10000 0 -0.33 19 19
TBX21 -0.26 0.57 -10000 0 -1.3 101 101
B2M 0.024 0.063 -10000 0 -0.42 9 9
TYK2 0.014 0.043 -10000 0 -10000 0 0
IL12RB1 0.013 0.043 -10000 0 -10000 0 0
GADD45B -0.18 0.44 -10000 0 -1.1 85 85
IL12RB2 -0.01 0.1 -10000 0 -0.43 26 26
GADD45G -0.17 0.43 -10000 0 -1 89 89
natural killer cell activation -0.005 0.022 -10000 0 -0.04 109 109
RELB 0.029 0.05 -10000 0 -0.42 6 6
RELA 0.035 0.006 -10000 0 -10000 0 0
IL18 0 0.11 -10000 0 -0.42 32 32
IL2RA 0.004 0.11 -10000 0 -0.42 31 31
IFNG -0.007 0.12 -10000 0 -0.42 38 38
STAT3 (dimer) -0.14 0.37 -10000 0 -0.79 101 101
HLA-DRB5 0.016 0.077 -10000 0 -0.42 14 14
FASLG -0.18 0.5 -10000 0 -1.1 89 89
NF kappa B2 p52/RelB -0.16 0.44 -10000 0 -0.94 100 100
CD4 0.028 0.021 -10000 0 -10000 0 0
SOCS1 0.032 0.023 -10000 0 -0.42 1 1
EntrezGene:6955 -0.003 0.012 -10000 0 -0.03 65 65
CD3D 0.008 0.078 -10000 0 -0.43 14 14
CD3E 0.024 0.026 -10000 0 -10000 0 0
CD3G -0.028 0.14 -10000 0 -0.43 54 54
IL12Rbeta2/JAK2 0.004 0.096 -10000 0 -0.33 26 26
CCL3 -0.17 0.43 -10000 0 -1 86 86
CCL4 -0.18 0.45 -10000 0 -1 93 93
HLA-A 0.017 0.086 -10000 0 -0.42 18 18
IL18/IL18R -0.001 0.16 -10000 0 -0.34 84 84
NOS2 -0.18 0.43 -10000 0 -0.87 114 114
IL12/IL12R/TYK2/JAK2/SPHK2 -0.008 0.11 -10000 0 -0.34 20 20
IL1R1 -0.22 0.5 -10000 0 -1.1 103 103
IL4 0.034 0.052 -10000 0 -0.42 5 5
JAK2 0.011 0.051 -10000 0 -0.46 2 2
EntrezGene:6957 -0.003 0.012 -10000 0 -0.032 55 55
TCR/CD3/MHC I/CD8 -0.073 0.28 -10000 0 -0.85 44 44
RAB7A -0.13 0.34 -10000 0 -0.76 99 99
lysosomal transport -0.12 0.32 -10000 0 -0.71 100 100
FOS -0.24 0.5 -10000 0 -1.1 105 105
STAT4 (dimer) -0.15 0.42 -10000 0 -0.89 101 101
STAT5A (dimer) -0.18 0.44 -10000 0 -0.96 100 100
GZMA -0.17 0.42 -10000 0 -0.92 102 102
GZMB -0.26 0.56 -10000 0 -1.3 103 103
HLX 0 0 -10000 0 -10000 0 0
LCK -0.21 0.5 -10000 0 -1.1 106 106
TCR/CD3/MHC II/CD4 -0.058 0.17 -10000 0 -0.45 62 62
IL2/IL2R 0.043 0.11 -10000 0 -0.29 46 46
MAPK14 -0.18 0.44 -10000 0 -0.99 97 97
CCR5 -0.16 0.4 -10000 0 -0.82 113 113
IL1B -0.021 0.13 -10000 0 -0.44 40 40
STAT6 -0.055 0.2 -10000 0 -0.59 35 35
STAT4 0.01 0.1 -10000 0 -0.42 27 27
STAT3 0.028 0.031 -10000 0 -0.42 2 2
STAT1 0.02 0.075 -10000 0 -0.42 14 14
NFKB1 0.036 0.005 -10000 0 -10000 0 0
NFKB2 0.035 0.021 -10000 0 -0.42 1 1
IL12B 0.01 0.063 -10000 0 -0.42 6 6
CD8A 0 0.008 -10000 0 -0.038 19 19
CD8B -0.001 0.009 -10000 0 -0.044 20 20
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.003 0.1 0.32 19 -10000 0 19
IL2RB 0.011 0.097 -10000 0 -0.42 24 24
proteasomal ubiquitin-dependent protein catabolic process -0.13 0.37 -10000 0 -0.79 101 101
IL2RG 0.031 0.041 -10000 0 -0.42 4 4
IL12 0.015 0.076 -10000 0 -0.33 10 10
STAT5A 0.027 0.037 -10000 0 -0.42 3 3
CD247 -0.002 0.011 -10000 0 -0.029 54 54
IL2 0.032 0.036 -10000 0 -0.42 3 3
SPHK2 0.035 0.007 -10000 0 -10000 0 0
FRAP1 0.035 0.007 -10000 0 -10000 0 0
IL12A 0.006 0.059 -10000 0 -0.42 5 5
IL12/IL12R/TYK2/JAK2 -0.21 0.53 -10000 0 -1.1 103 103
MAP2K3 -0.18 0.46 -10000 0 -1 102 102
RIPK2 0.028 0.015 -10000 0 -10000 0 0
MAP2K6 -0.18 0.45 -10000 0 -1 95 95
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.019 0.064 -10000 0 -0.42 9 9
IL18RAP -0.021 0.15 -10000 0 -0.43 58 58
IL12Rbeta1/TYK2 0.027 0.056 -10000 0 -10000 0 0
EOMES -0.048 0.28 -10000 0 -1.2 27 27
STAT1 (dimer) -0.15 0.38 -10000 0 -0.8 108 108
T cell proliferation -0.11 0.3 -10000 0 -0.62 109 109
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.016 0.091 -10000 0 -0.43 20 20
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.11 0.33 -10000 0 -0.67 110 110
ATF2 -0.16 0.4 -10000 0 -0.89 97 97
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.035 0.021 -10000 0 -0.42 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.099 0.24 0.61 68 -0.53 2 70
IL27/IL27R/JAK1 -0.088 0.34 0.89 2 -1.1 37 39
TBX21 -0.096 0.3 0.64 20 -0.58 96 116
IL12B 0.026 0.052 -10000 0 -0.42 6 6
IL12A 0.003 0.031 -10000 0 -0.3 5 5
IL6ST -0.05 0.16 -10000 0 -0.4 87 87
IL27RA/JAK1 -0.063 0.33 0.44 2 -1.2 35 37
IL27 -0.036 0.16 -10000 0 -0.42 73 73
TYK2 0.029 0.029 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.013 0.087 0.2 13 -0.25 54 67
T-helper 2 cell differentiation 0.099 0.24 0.61 68 -0.53 2 70
T cell proliferation during immune response 0.099 0.24 0.61 68 -0.53 2 70
MAPKKK cascade -0.099 0.24 0.53 2 -0.61 68 70
STAT3 0.028 0.031 -10000 0 -0.42 2 2
STAT2 0.036 0.005 -10000 0 -10000 0 0
STAT1 0.022 0.077 -10000 0 -0.42 14 14
IL12RB1 0.036 0.005 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.081 0.29 0.68 19 -0.6 76 95
IL27/IL27R/JAK2/TYK2 -0.1 0.25 0.53 2 -0.62 68 70
positive regulation of T cell mediated cytotoxicity -0.099 0.24 0.53 2 -0.61 68 70
STAT1 (dimer) -0.1 0.39 0.57 30 -0.91 64 94
JAK2 0.024 0.038 -10000 0 -0.43 2 2
JAK1 0.035 0.036 -10000 0 -0.39 3 3
STAT2 (dimer) -0.084 0.24 0.47 2 -0.59 68 70
T cell proliferation -0.11 0.25 0.48 2 -0.6 75 77
IL12/IL12R/TYK2/JAK2 0.001 0.2 -10000 0 -0.92 17 17
IL17A -0.013 0.087 0.2 13 -0.24 55 68
mast cell activation 0.099 0.24 0.61 68 -0.53 2 70
IFNG -0.01 0.05 0.13 6 -0.12 53 59
T cell differentiation -0.005 0.01 0.026 10 -0.023 91 101
STAT3 (dimer) -0.075 0.24 0.47 2 -0.59 64 66
STAT5A (dimer) -0.076 0.24 0.47 2 -0.6 64 66
STAT4 (dimer) -0.094 0.26 0.47 2 -0.59 76 78
STAT4 0.01 0.1 -10000 0 -0.42 27 27
T cell activation -0.002 0.032 0.12 32 -10000 0 32
IL27R/JAK2/TYK2 -0.08 0.32 -10000 0 -1.1 36 36
GATA3 -0.2 0.52 0.82 9 -1.3 91 100
IL18 -0.013 0.074 -10000 0 -0.3 32 32
positive regulation of mast cell cytokine production -0.073 0.23 0.46 2 -0.57 64 66
IL27/EBI3 -0.008 0.13 0.22 6 -0.31 76 82
IL27RA -0.091 0.33 -10000 0 -1.3 35 35
IL6 -0.018 0.14 -10000 0 -0.42 52 52
STAT5A 0.027 0.037 -10000 0 -0.42 3 3
monocyte differentiation 0 0.002 -10000 0 -0.013 1 1
IL2 0.022 0.15 0.47 35 -1.2 3 38
IL1B -0.017 0.082 -10000 0 -0.3 40 40
EBI3 0.026 0.053 0.16 1 -0.43 5 6
TNF 0.002 0.041 -10000 0 -0.3 9 9
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.075 0.28 -10000 0 -0.72 53 53
CRP -0.044 0.3 0.57 3 -0.75 45 48
cell cycle arrest -0.095 0.34 0.46 2 -0.78 71 73
TIMP1 -0.069 0.3 -10000 0 -0.77 54 54
IL6ST -0.049 0.17 -10000 0 -0.42 88 88
Rac1/GDP -0.05 0.19 0.28 1 -0.41 67 68
AP1 0.013 0.18 -10000 0 -0.47 34 34
GAB2 0.033 0.014 -10000 0 -10000 0 0
TNFSF11 -0.14 0.4 -10000 0 -0.95 84 84
HSP90B1 0 0.12 -10000 0 -0.83 8 8
GAB1 0.028 0.061 -10000 0 -0.42 9 9
MAPK14 -0.045 0.17 -10000 0 -0.52 32 32
AKT1 0.03 0.081 0.28 1 -0.36 9 10
FOXO1 0.037 0.08 0.26 1 -0.34 9 10
MAP2K6 -0.05 0.16 0.24 1 -0.42 55 56
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.061 0.21 0.33 2 -0.46 72 74
MITF -0.054 0.17 0.24 1 -0.4 65 66
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.036 0.005 -10000 0 -10000 0 0
A2M -0.053 0.33 -10000 0 -1.3 32 32
CEBPB 0.027 0.05 -10000 0 -0.42 6 6
GRB2/SOS1/GAB family/SHP2 0.005 0.12 0.3 1 -0.41 21 22
STAT3 -0.11 0.37 0.5 1 -0.85 71 72
STAT1 -0.01 0.17 -10000 0 -0.88 17 17
CEBPD -0.097 0.37 0.59 1 -0.89 70 71
PIK3CA 0.034 0.022 -10000 0 -0.42 1 1
PI3K 0.038 0.066 -10000 0 -0.3 17 17
JUN -0.001 0.12 -10000 0 -0.42 39 39
PIAS3/MITF -0.045 0.17 -10000 0 -0.4 59 59
MAPK11 -0.044 0.16 -10000 0 -0.52 32 32
STAT3 (dimer)/FOXO1 -0.052 0.28 0.44 3 -0.6 66 69
GRB2/SOS1/GAB family -0.017 0.17 0.3 1 -0.43 37 38
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.062 0.17 -10000 0 -0.38 75 75
GRB2 0.034 0.011 -10000 0 -10000 0 0
JAK2 0.032 0.03 -10000 0 -0.42 2 2
LBP -0.031 0.23 0.45 1 -0.58 45 46
PIK3R1 0.02 0.08 -10000 0 -0.42 16 16
JAK1 0.031 0.039 -10000 0 -0.42 3 3
MYC -0.067 0.37 0.59 2 -0.9 61 63
FGG -0.076 0.29 -10000 0 -0.74 51 51
macrophage differentiation -0.095 0.34 0.46 2 -0.78 71 73
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.023 0.16 -10000 0 -0.25 132 132
JUNB -0.075 0.28 -10000 0 -0.71 53 53
FOS -0.031 0.15 -10000 0 -0.42 66 66
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.06 0.17 0.27 1 -0.4 71 72
STAT1/PIAS1 -0.046 0.19 0.3 2 -0.41 68 70
GRB2/SOS1/GAB family/SHP2/PI3K 0.031 0.081 -10000 0 -0.34 12 12
STAT3 (dimer) -0.1 0.36 0.49 1 -0.83 71 72
PRKCD -0.072 0.24 0.35 2 -0.54 74 76
IL6R 0.021 0.06 -10000 0 -0.43 8 8
SOCS3 -0.042 0.19 0.43 1 -0.79 16 17
gp130 (dimer)/JAK1/JAK1/LMO4 -0.027 0.15 -10000 0 -0.26 135 135
Rac1/GTP -0.053 0.2 0.28 1 -0.43 72 73
HCK 0.018 0.087 -10000 0 -0.42 19 19
MAPKKK cascade 0.021 0.14 -10000 0 -0.5 25 25
bone resorption -0.13 0.37 -10000 0 -0.87 85 85
IRF1 -0.09 0.32 0.46 1 -0.77 65 66
mol:GDP -0.056 0.18 0.24 1 -0.4 70 71
SOS1 0.036 0.022 -10000 0 -0.42 1 1
VAV1 -0.057 0.18 0.24 1 -0.41 70 71
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.043 0.18 -10000 0 -0.54 36 36
PTPN11 0.016 0.091 -10000 0 -1.1 3 3
IL6/IL6RA 0.004 0.1 -10000 0 -0.3 46 46
gp130 (dimer)/TYK2/TYK2/LMO4 -0.022 0.14 -10000 0 -0.25 133 133
gp130 (dimer)/JAK2/JAK2/LMO4 -0.024 0.15 -10000 0 -0.26 134 134
IL6 -0.021 0.14 -10000 0 -0.42 52 52
PIAS3 0.035 0.006 -10000 0 -10000 0 0
PTPRE 0.02 0.07 -10000 0 -0.41 12 12
PIAS1 0.035 0.007 -10000 0 -10000 0 0
RAC1 0.036 0.006 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.053 0.13 0.23 1 -0.3 79 80
LMO4 -0.019 0.14 -10000 0 -0.42 53 53
STAT3 (dimer)/PIAS3 -0.09 0.34 0.46 1 -0.78 68 69
MCL1 0.038 0.094 -10000 0 -0.78 2 2
Noncanonical Wnt signaling pathway

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
NFATC2 0.03 0.036 -10000 0 -0.42 3 3
GNB1/GNG2 -0.048 0.17 -10000 0 -0.38 63 63
mol:DAG -0.056 0.15 -10000 0 -0.35 58 58
PLCG1 -0.059 0.15 0.2 3 -0.36 59 62
YES1 -0.066 0.15 -10000 0 -0.41 54 54
FZD3 0.007 0.095 -10000 0 -0.42 23 23
FZD6 -0.028 0.14 -10000 0 -0.42 60 60
G protein -0.035 0.17 0.29 10 -0.38 54 64
MAP3K7 -0.057 0.12 0.24 2 -0.32 52 54
mol:Ca2+ -0.054 0.14 -10000 0 -0.34 58 58
mol:IP3 -0.056 0.15 -10000 0 -0.35 58 58
NLK -0.036 0.25 -10000 0 -0.82 45 45
GNB1 0.032 0.045 -10000 0 -0.42 5 5
CAMK2A -0.056 0.14 0.25 2 -0.34 54 56
MAP3K7IP1 0.034 0.009 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.067 0.15 -10000 0 -0.29 136 136
CSNK1A1 0.036 0.006 -10000 0 -10000 0 0
GNAS -0.064 0.14 -10000 0 -0.39 52 52
GO:0007205 -0.059 0.14 0.26 2 -0.36 55 57
WNT6 0.03 0.031 -10000 0 -0.42 2 2
WNT4 -0.019 0.14 -10000 0 -0.42 58 58
NFAT1/CK1 alpha -0.047 0.16 0.29 2 -0.38 52 54
GNG2 0.034 0.021 -10000 0 -0.42 1 1
WNT5A -0.025 0.15 -10000 0 -0.42 63 63
WNT11 0.027 0.032 -10000 0 -0.42 2 2
CDC42 -0.062 0.15 0.19 2 -0.39 53 55
FAS signaling pathway (CD95)

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
SPTAN1 0.024 0.082 0.2 75 -10000 0 75
RFC1 0.021 0.074 0.19 67 -10000 0 67
PRKDC 0.044 0.1 0.22 111 -0.23 1 112
RIPK1 0.036 0.008 -10000 0 -10000 0 0
CASP7 -0.007 0.14 -10000 0 -0.68 18 18
FASLG/FAS/FADD/FAF1 0.003 0.091 0.2 37 -0.26 28 65
MAP2K4 -0.025 0.17 0.44 2 -0.44 47 49
mol:ceramide -0.013 0.11 -10000 0 -0.35 35 35
GSN 0.019 0.086 0.19 73 -0.23 8 81
FASLG/FAS/FADD/FAF1/Caspase 8 0.006 0.11 0.23 3 -0.31 32 35
FAS 0.003 0.11 -10000 0 -0.42 29 29
BID -0.017 0.053 0.26 12 -0.27 7 19
MAP3K1 -0.009 0.14 0.3 4 -0.48 21 25
MAP3K7 0.033 0.011 -10000 0 -10000 0 0
RB1 0.019 0.071 0.19 62 -0.23 1 63
CFLAR 0.032 0.046 -10000 0 -0.42 5 5
HGF/MET 0.016 0.12 -10000 0 -0.26 77 77
ARHGDIB 0.016 0.09 0.2 70 -0.25 13 83
FADD 0.025 0.021 -10000 0 -10000 0 0
actin filament polymerization -0.018 0.087 0.24 10 -0.19 73 83
NFKB1 0.004 0.1 -10000 0 -0.68 7 7
MAPK8 -0.044 0.21 0.51 2 -0.5 68 70
DFFA 0.023 0.078 0.19 71 -10000 0 71
DNA fragmentation during apoptosis 0.022 0.08 0.19 71 -10000 0 71
FAS/FADD/MET 0.034 0.077 -10000 0 -0.26 27 27
CFLAR/RIP1 0.049 0.038 -10000 0 -0.3 5 5
FAIM3 0.015 0.078 -10000 0 -0.42 15 15
FAF1 0.028 0.03 -10000 0 -0.42 1 1
PARP1 0.028 0.098 0.22 79 -0.24 3 82
DFFB 0.022 0.08 0.19 76 -0.2 1 77
CHUK -0.008 0.11 -10000 0 -0.58 10 10
FASLG -0.011 0.12 -10000 0 -0.42 36 36
FAS/FADD 0.02 0.077 -10000 0 -0.3 23 23
HGF 0.028 0.057 -10000 0 -0.42 8 8
LMNA 0.024 0.1 0.35 25 -0.22 6 31
CASP6 0.02 0.081 0.19 69 -0.23 3 72
CASP10 0.03 0.02 -10000 0 -10000 0 0
CASP3 0.032 0.092 0.23 81 -0.22 6 87
PTPN13 -0.03 0.16 -10000 0 -0.42 72 72
CASP8 -0.013 0.057 0.33 13 -10000 0 13
IL6 -0.1 0.41 -10000 0 -1.2 59 59
MET 0.03 0.041 -10000 0 -0.42 4 4
ICAD/CAD 0.018 0.073 0.32 5 -10000 0 5
FASLG/FAS/FADD/FAF1/Caspase 10 -0.014 0.11 -10000 0 -0.36 35 35
activation of caspase activity by cytochrome c -0.017 0.053 0.26 12 -0.27 7 19
PAK2 0.021 0.077 0.19 71 -10000 0 71
BCL2 -0.056 0.18 -10000 0 -0.42 99 99
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.027 0.18 -10000 0 -0.46 62 62
Syndecan-4/Syndesmos -0.033 0.2 -10000 0 -0.49 61 61
positive regulation of JNK cascade -0.045 0.22 -10000 0 -0.48 76 76
Syndecan-4/ADAM12 -0.051 0.23 -10000 0 -0.5 85 85
CCL5 -0.014 0.14 -10000 0 -0.42 52 52
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
DNM2 0.036 0.005 -10000 0 -10000 0 0
ITGA5 0.034 0.029 -10000 0 -0.42 2 2
SDCBP 0.023 0.058 -10000 0 -0.42 8 8
PLG 0.022 0.04 -10000 0 -0.4 2 2
ADAM12 -0.014 0.14 -10000 0 -0.42 53 53
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.028 0.046 -10000 0 -0.42 5 5
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.032 0.019 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.033 0.21 -10000 0 -0.5 66 66
Syndecan-4/CXCL12/CXCR4 -0.048 0.23 -10000 0 -0.52 76 76
Syndecan-4/Laminin alpha3 -0.055 0.22 -10000 0 -0.51 68 68
MDK 0.018 0.085 -10000 0 -0.42 18 18
Syndecan-4/FZD7 -0.049 0.22 -10000 0 -0.5 77 77
Syndecan-4/Midkine -0.039 0.21 -10000 0 -0.5 67 67
FZD7 -0.006 0.13 -10000 0 -0.42 43 43
Syndecan-4/FGFR1/FGF -0.033 0.2 -10000 0 -0.47 64 64
THBS1 0.001 0.12 -10000 0 -0.42 37 37
integrin-mediated signaling pathway -0.04 0.21 -10000 0 -0.48 75 75
positive regulation of MAPKKK cascade -0.045 0.22 -10000 0 -0.48 76 76
Syndecan-4/TACI -0.034 0.21 -10000 0 -0.5 66 66
CXCR4 0.007 0.11 -10000 0 -0.42 30 30
cell adhesion 0.012 0.1 0.2 46 -0.27 41 87
Syndecan-4/Dynamin -0.031 0.21 -10000 0 -0.5 66 66
Syndecan-4/TSP1 -0.045 0.22 -10000 0 -0.49 75 75
Syndecan-4/GIPC -0.031 0.21 -10000 0 -0.49 66 66
Syndecan-4/RANTES -0.053 0.22 -10000 0 -0.51 70 70
ITGB1 0.032 0.036 -10000 0 -0.42 3 3
LAMA1 0.034 0.009 -10000 0 -10000 0 0
LAMA3 -0.019 0.14 -10000 0 -0.42 58 58
RAC1 0.035 0.006 -10000 0 -10000 0 0
PRKCA 0.087 0.26 0.8 57 -10000 0 57
Syndecan-4/alpha-Actinin -0.034 0.22 -10000 0 -0.51 67 67
TFPI 0.034 0.008 -10000 0 -10000 0 0
F2 0.031 0.024 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.048 0.037 -10000 0 -0.3 5 5
positive regulation of cell adhesion -0.061 0.2 -10000 0 -0.5 68 68
ACTN1 0.027 0.061 -10000 0 -0.42 9 9
TNC 0.004 0.11 -10000 0 -0.42 31 31
Syndecan-4/CXCL12 -0.049 0.22 -10000 0 -0.5 76 76
FGF6 0.027 0.057 -10000 0 -0.42 8 8
RHOA 0.026 0.061 -10000 0 -0.42 9 9
CXCL12 -0.008 0.13 -10000 0 -0.42 47 47
TNFRSF13B 0.032 0.012 -10000 0 -10000 0 0
FGF2 -0.001 0.11 -10000 0 -0.42 34 34
FGFR1 0.02 0.064 -10000 0 -0.42 10 10
Syndecan-4/PI-4-5-P2 -0.058 0.19 -10000 0 -0.49 66 66
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.019 0.13 -10000 0 -0.4 51 51
cell migration -0.015 0.015 -10000 0 -10000 0 0
PRKCD 0.024 0.039 -10000 0 -0.39 2 2
vasculogenesis -0.043 0.21 -10000 0 -0.47 75 75
SDC4 -0.057 0.21 -10000 0 -0.52 66 66
Syndecan-4/Tenascin C -0.043 0.22 -10000 0 -0.5 75 75
Syndecan-4/PI-4-5-P2/PKC alpha -0.026 0.016 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.034 0.2 -10000 0 -0.5 61 61
MMP9 -0.013 0.14 -10000 0 -0.42 52 52
Rac1/GTP 0.012 0.1 0.2 46 -0.28 41 87
cytoskeleton organization -0.031 0.19 -10000 0 -0.48 61 61
GIPC1 0.033 0.035 -10000 0 -0.42 3 3
Syndecan-4/TFPI -0.034 0.21 -10000 0 -0.5 66 66
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.012 0.089 0.22 2 -0.26 26 28
adherens junction organization -0.045 0.13 -10000 0 -0.28 86 86
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.013 0.11 0.27 4 -0.27 29 33
FMN1 -0.036 0.12 -10000 0 -0.26 88 88
mol:IP3 -0.016 0.076 -10000 0 -0.23 25 25
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.035 0.13 -10000 0 -0.27 88 88
CTNNB1 0.026 0.067 -10000 0 -0.42 11 11
AKT1 -0.017 0.093 0.19 2 -0.25 28 30
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.062 0.19 -10000 0 -0.43 73 73
CTNND1 0.035 0.022 -10000 0 -0.42 1 1
mol:PI-4-5-P2 -0.032 0.12 0.22 1 -0.25 80 81
VASP -0.039 0.12 -10000 0 -0.27 83 83
ZYX -0.038 0.12 -10000 0 -0.27 84 84
JUB -0.047 0.13 -10000 0 -0.28 88 88
EGFR(dimer) -0.041 0.14 0.23 1 -0.27 105 106
E-cadherin/beta catenin-gamma catenin 0.015 0.099 -10000 0 -0.24 58 58
mol:PI-3-4-5-P3 -0.001 0.11 0.23 2 -0.25 29 31
PIK3CA 0.034 0.022 -10000 0 -0.42 1 1
PI3K -0.001 0.11 0.23 2 -0.26 29 31
FYN -0.017 0.092 0.22 2 -0.29 25 27
mol:Ca2+ -0.015 0.074 -10000 0 -0.22 25 25
JUP 0.03 0.042 -10000 0 -0.42 4 4
PIK3R1 0.02 0.08 -10000 0 -0.42 16 16
mol:DAG -0.016 0.076 -10000 0 -0.23 25 25
CDH1 -0.011 0.13 -10000 0 -0.42 45 45
RhoA/GDP -0.016 0.11 0.26 3 -0.27 35 38
establishment of polarity of embryonic epithelium -0.037 0.12 0.22 1 -0.26 83 84
SRC 0.033 0.029 -10000 0 -0.42 2 2
RAC1 0.035 0.006 -10000 0 -10000 0 0
RHOA 0.026 0.061 -10000 0 -0.42 9 9
EGFR -0.015 0.13 -10000 0 -0.42 49 49
CASR -0.013 0.078 0.22 2 -0.23 22 24
RhoA/GTP -0.001 0.09 0.21 2 -0.22 28 30
AKT2 -0.016 0.093 0.19 2 -0.25 28 30
actin cable formation -0.037 0.12 0.2 6 -0.26 83 89
apoptosis 0.009 0.099 0.26 29 -0.24 5 34
CTNNA1 0.036 0.022 -10000 0 -0.43 1 1
mol:GDP -0.03 0.1 0.22 2 -0.26 38 40
PIP5K1A -0.034 0.12 -10000 0 -0.26 80 80
PLCG1 -0.016 0.077 -10000 0 -0.23 25 25
Rac1/GTP -0.03 0.14 -10000 0 -0.3 55 55
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.016 0.036 -10000 0 -0.26 11 11
SNTA1 0.032 0.041 -10000 0 -0.42 4 4
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.022 0.05 -10000 0 -0.26 22 22
MAPK12 0.004 0.085 0.21 41 -0.23 34 75
CCND1 -0.056 0.16 -10000 0 -0.42 81 81
p38 gamma/SNTA1 0.026 0.09 0.21 47 -0.22 39 86
MAP2K3 0.032 0.023 -10000 0 -0.42 1 1
PKN1 0.033 0.035 -10000 0 -0.42 3 3
G2/M transition checkpoint 0.004 0.084 0.21 41 -0.23 34 75
MAP2K6 0.013 0.096 0.24 46 -0.24 34 80
MAPT -0.054 0.13 0.27 6 -0.28 104 110
MAPK13 0.006 0.052 -10000 0 -0.3 14 14
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.005 0.064 -10000 0 -0.29 23 23
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.015 0.032 -10000 0 -0.25 6 6
ARNO/beta Arrestin1-2 0.014 0.069 -10000 0 -0.2 40 40
EGFR -0.015 0.13 -10000 0 -0.42 49 49
EPHA2 0.032 0.036 -10000 0 -0.42 3 3
USP6 0.032 0.012 -10000 0 -10000 0 0
IQSEC1 0.034 0.021 -10000 0 -0.42 1 1
EGFR/EGFR/EGF/EGF -0.061 0.16 -10000 0 -0.3 152 152
ARRB2 0.011 0.043 -10000 0 -0.3 9 9
mol:GTP 0.006 0.02 0.11 5 -0.11 2 7
ARRB1 0.027 0.05 -10000 0 -0.42 6 6
FBXO8 0.035 0.007 -10000 0 -10000 0 0
TSHR 0.029 0.05 -10000 0 -0.42 6 6
EGF -0.069 0.19 -10000 0 -0.42 110 110
somatostatin receptor activity 0 0 0 2 -0.001 78 80
ARAP2 0 0 0 3 0 76 79
mol:GDP -0.029 0.1 0.14 1 -0.25 59 60
mol:PI-3-4-5-P3 0 0 0 3 0 77 80
ITGA2B 0.034 0.01 -10000 0 -10000 0 0
ARF6 0.033 0.029 -10000 0 -0.42 2 2
Ephrin A1/EPHA2/NCK1/GIT1 0.053 0.072 -10000 0 -0.23 20 20
ADAP1 0 0 0 4 0 44 48
KIF13B 0.022 0.051 -10000 0 -0.42 6 6
HGF/MET 0.042 0.055 -10000 0 -0.3 12 12
PXN 0.036 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.034 0.1 0.16 3 -0.23 80 83
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.035 0.15 -10000 0 -0.26 151 151
ADRB2 0.003 0.11 -10000 0 -0.42 33 33
receptor agonist activity 0 0 0 3 0 61 64
actin filament binding 0 0 0 2 0 79 81
SRC 0.033 0.029 -10000 0 -0.42 2 2
ITGB3 0.029 0.046 -10000 0 -0.42 5 5
GNAQ 0 0 0.001 5 -0.001 57 62
EFA6/PI-4-5-P2 0 0 0.001 5 -0.001 50 55
ARF6/GDP 0.004 0.075 0.2 2 -0.26 16 18
ARF6/GDP/GULP/ACAP1 -0.017 0.13 -10000 0 -0.27 72 72
alphaIIb/beta3 Integrin/paxillin/GIT1 0.079 0.043 -10000 0 -0.23 5 5
ACAP1 0 0 0 2 0 2 4
ACAP2 0 0 0 4 0 78 82
LHCGR/beta Arrestin2 0.018 0.06 -10000 0 -0.38 9 9
EFNA1 0.014 0.08 -10000 0 -0.42 16 16
HGF 0.028 0.057 -10000 0 -0.42 8 8
CYTH3 0 0 0.001 4 -0.001 69 73
CYTH2 -0.001 0.002 -10000 0 -0.004 83 83
NCK1 0.034 0.021 -10000 0 -0.42 1 1
fibronectin binding 0 0 0 4 0 52 56
endosomal lumen acidification 0 0 0 3 0 65 68
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0 0.12 -10000 0 -0.42 39 39
GNAQ/ARNO -0.001 0.003 0.007 6 -0.006 53 59
mol:Phosphatidic acid 0 0 0 4 0 78 82
PIP3-E 0.029 0.037 -10000 0 -0.42 3 3
MET 0.03 0.041 -10000 0 -0.42 4 4
GNA14 -0.009 0.13 -10000 0 -0.42 43 43
GNA15 0.03 0.046 -10000 0 -0.42 5 5
GIT1 0.034 0.022 -10000 0 -0.42 1 1
mol:PI-4-5-P2 0 0 0.001 3 -0.001 55 58
GNA11 0.033 0.036 -10000 0 -0.42 3 3
LHCGR 0.027 0.061 -10000 0 -0.42 9 9
AGTR1 -0.047 0.16 -10000 0 -0.42 80 80
desensitization of G-protein coupled receptor protein signaling pathway 0.018 0.06 -10000 0 -0.38 9 9
IPCEF1/ARNO -0.024 0.12 -10000 0 -0.2 150 150
alphaIIb/beta3 Integrin 0.046 0.035 -10000 0 -0.3 4 4
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.031 0.072 -10000 0 -0.19 45 45
NF kappa B1 p50/RelA/I kappa B alpha 0.021 0.095 0.27 6 -0.3 9 15
AP1 -0.034 0.12 -10000 0 -0.25 101 101
mol:PIP3 -0.031 0.091 -10000 0 -0.22 88 88
AKT1 -0.005 0.1 0.25 3 -0.31 26 29
PTK2B -0.042 0.1 0.14 1 -0.22 110 111
RHOA -0.015 0.1 -10000 0 -0.32 35 35
PIK3CB 0.031 0.045 -10000 0 -0.42 5 5
mol:Ca2+ -0.01 0.091 0.19 41 -0.2 53 94
MAGI3 0.013 0.099 -10000 0 -0.42 25 25
RELA 0.035 0.006 -10000 0 -10000 0 0
apoptosis 0.003 0.054 -10000 0 -0.18 39 39
HRAS/GDP 0.024 0.025 -10000 0 -0.3 3 3
positive regulation of microtubule depolymerization -0.075 0.12 0.18 3 -0.24 125 128
NF kappa B1 p50/RelA -0.02 0.082 -10000 0 -0.22 53 53
endothelial cell migration -0.01 0.12 -10000 0 -0.51 27 27
ADCY4 -0.016 0.089 -10000 0 -0.28 41 41
ADCY5 -0.016 0.086 -10000 0 -0.28 37 37
ADCY6 -0.014 0.083 -10000 0 -0.26 41 41
ADCY7 -0.015 0.089 -10000 0 -0.29 36 36
ADCY1 -0.014 0.084 -10000 0 -0.26 42 42
ADCY2 -0.026 0.1 -10000 0 -0.31 44 44
ADCY3 -0.015 0.085 -10000 0 -0.27 38 38
ADCY8 -0.013 0.075 -10000 0 -0.25 37 37
ADCY9 -0.016 0.081 -10000 0 -0.24 48 48
GSK3B -0.042 0.098 0.16 1 -0.22 97 98
arachidonic acid secretion -0.018 0.09 -10000 0 -0.27 48 48
GNG2 0.034 0.021 -10000 0 -0.42 1 1
TRIP6 0.009 0.071 -10000 0 -0.36 17 17
GNAO1 0.006 0.055 -10000 0 -0.22 27 27
HRAS 0.032 0.036 -10000 0 -0.42 3 3
NFKBIA -0.008 0.091 0.26 6 -0.27 17 23
GAB1 0.027 0.061 -10000 0 -0.42 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.022 0.2 -10000 0 -0.92 22 22
JUN -0.001 0.12 -10000 0 -0.42 39 39
LPA/LPA2/NHERF2 -0.004 0.077 -10000 0 -0.19 64 64
TIAM1 0 0.23 -10000 0 -1.1 22 22
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
mol:IP3 -0.009 0.09 0.19 41 -0.21 50 91
PLCB3 0.01 0.09 0.19 46 -0.23 42 88
FOS -0.031 0.15 -10000 0 -0.42 66 66
positive regulation of mitosis -0.018 0.09 -10000 0 -0.27 48 48
LPA/LPA1-2-3 -0.007 0.05 -10000 0 -0.17 42 42
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.03 0.014 -10000 0 -10000 0 0
stress fiber formation -0.006 0.082 -10000 0 -0.27 23 23
GNAZ -0.001 0.072 -10000 0 -0.21 49 49
EGFR/PI3K-beta/Gab1 -0.023 0.098 -10000 0 -0.22 88 88
positive regulation of dendritic cell cytokine production -0.007 0.05 -10000 0 -0.17 42 42
LPA/LPA2/MAGI-3 0.005 0.065 -10000 0 -0.17 50 50
ARHGEF1 0.027 0.077 0.19 54 -0.21 22 76
GNAI2 0.001 0.069 -10000 0 -0.21 45 45
GNAI3 0.006 0.058 -10000 0 -0.19 38 38
GNAI1 -0.005 0.082 -10000 0 -0.24 51 51
LPA/LPA3 -0.005 0.025 -10000 0 -0.086 42 42
LPA/LPA2 -0.004 0.025 -10000 0 -0.085 42 42
LPA/LPA1 -0.01 0.067 -10000 0 -0.22 42 42
HB-EGF/EGFR -0.026 0.13 -10000 0 -0.28 91 91
HBEGF -0.02 0.099 -10000 0 -0.3 56 56
mol:DAG -0.009 0.09 0.19 41 -0.21 50 91
cAMP biosynthetic process -0.02 0.09 0.19 5 -0.27 40 45
NFKB1 0.036 0.005 -10000 0 -10000 0 0
SRC 0.033 0.029 -10000 0 -0.42 2 2
GNB1 0.032 0.045 -10000 0 -0.42 5 5
LYN 0.005 0.094 0.22 27 -0.23 19 46
GNAQ -0.004 0.02 -10000 0 -0.07 42 42
LPAR2 0 0.001 -10000 0 -10000 0 0
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 -0.008 0.039 -10000 0 -0.13 42 42
IL8 -0.072 0.18 -10000 0 -0.43 80 80
PTK2 0.011 0.042 -10000 0 -0.16 26 26
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
CASP3 0.003 0.054 -10000 0 -0.18 39 39
EGFR -0.015 0.13 -10000 0 -0.42 49 49
PLCG1 -0.002 0.042 -10000 0 -0.12 47 47
PLD2 0.01 0.053 -10000 0 -0.17 38 38
G12/G13 0.03 0.063 -10000 0 -0.22 23 23
PI3K-beta -0.019 0.1 -10000 0 -0.34 28 28
cell migration 0.008 0.068 -10000 0 -0.26 22 22
SLC9A3R2 -0.004 0.12 -10000 0 -0.42 40 40
PXN -0.007 0.083 -10000 0 -0.28 23 23
HRAS/GTP -0.019 0.092 -10000 0 -0.27 48 48
RAC1 0.035 0.006 -10000 0 -10000 0 0
MMP9 -0.013 0.14 -10000 0 -0.42 52 52
PRKCE 0.03 0.05 -10000 0 -0.42 6 6
PRKCD -0.011 0.088 0.18 41 -0.21 40 81
Gi(beta/gamma) -0.009 0.088 -10000 0 -0.26 43 43
mol:LPA -0.008 0.039 -10000 0 -0.13 42 42
TRIP6/p130 Cas/FAK1/Paxillin 0.009 0.081 -10000 0 -0.28 18 18
MAPKKK cascade -0.018 0.09 -10000 0 -0.27 48 48
contractile ring contraction involved in cytokinesis -0.016 0.1 -10000 0 -0.32 37 37
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.014 0.074 -10000 0 -0.24 44 44
GNA15 0.007 0.035 -10000 0 -0.11 28 28
GNA12 0.035 0.007 -10000 0 -10000 0 0
GNA13 0.029 0.037 -10000 0 -0.42 3 3
MAPT -0.077 0.12 0.18 3 -0.25 125 128
GNA11 0.008 0.03 -10000 0 -0.097 28 28
Rac1/GTP 0.021 0.22 -10000 0 -0.98 22 22
MMP2 -0.01 0.12 -10000 0 -0.52 27 27
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.017 0.08 -10000 0 -0.42 16 16
EPHB2 0.033 0.03 -10000 0 -0.42 2 2
EFNB1 0.015 0.029 -10000 0 -0.3 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.073 0.065 -10000 0 -0.23 17 17
Ephrin B2/EPHB1-2 0.044 0.067 -10000 0 -0.24 23 23
neuron projection morphogenesis 0.048 0.056 -10000 0 -0.22 17 17
Ephrin B1/EPHB1-2/Tiam1 0.064 0.064 -10000 0 -0.24 17 17
DNM1 0.034 0.035 -10000 0 -0.42 3 3
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.082 0.21 -10000 0 -0.55 79 79
YES1 -0.11 0.3 -10000 0 -0.8 79 79
Ephrin B1/EPHB1-2/NCK2 0.069 0.051 -10000 0 -0.22 12 12
PI3K -0.049 0.23 -10000 0 -0.56 79 79
mol:GDP 0.062 0.063 -10000 0 -0.24 17 17
ITGA2B 0.034 0.01 -10000 0 -10000 0 0
endothelial cell proliferation 0.02 0.081 -10000 0 -0.26 35 35
FYN -0.11 0.3 -10000 0 -0.8 79 79
MAP3K7 -0.082 0.22 -10000 0 -0.59 76 76
FGR -0.1 0.3 -10000 0 -0.78 79 79
TIAM1 0.028 0.057 -10000 0 -0.42 8 8
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
RGS3 0.036 0.005 -10000 0 -10000 0 0
cell adhesion -0.057 0.21 -10000 0 -0.53 78 78
LYN -0.1 0.3 -10000 0 -0.79 79 79
Ephrin B1/EPHB1-2/Src Family Kinases -0.1 0.28 -10000 0 -0.74 79 79
Ephrin B1/EPHB1-2 -0.089 0.24 -10000 0 -0.64 78 78
SRC -0.1 0.3 -10000 0 -0.79 79 79
ITGB3 0.029 0.046 -10000 0 -0.42 5 5
EPHB1 0.027 0.05 -10000 0 -0.42 6 6
EPHB4 0.016 0.091 -10000 0 -0.42 21 21
RAC1 0.035 0.006 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.021 0.081 -10000 0 -0.26 35 35
alphaIIb/beta3 Integrin 0.046 0.035 -10000 0 -0.3 4 4
BLK -0.12 0.3 -10000 0 -0.8 79 79
HCK -0.11 0.3 -10000 0 -0.79 79 79
regulation of stress fiber formation -0.067 0.05 0.22 12 -10000 0 12
MAPK8 -0.08 0.2 -10000 0 -0.53 79 79
Ephrin B1/EPHB1-2/RGS3 0.069 0.051 -10000 0 -0.22 12 12
endothelial cell migration -0.079 0.19 -10000 0 -0.51 75 75
NCK2 0.036 0.005 -10000 0 -10000 0 0
PTPN13 -0.046 0.2 -10000 0 -0.54 72 72
regulation of focal adhesion formation -0.067 0.05 0.22 12 -10000 0 12
chemotaxis -0.066 0.05 0.22 12 -10000 0 12
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
Rac1/GTP 0.062 0.061 -10000 0 -0.23 17 17
angiogenesis -0.09 0.23 -10000 0 -0.63 79 79
LCK -0.12 0.3 -10000 0 -0.8 79 79
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.015 0.12 -10000 0 -0.44 22 22
UGCG -0.09 0.27 -10000 0 -0.73 73 73
AKT1/mTOR/p70S6K/Hsp90/TERT -0.062 0.19 0.31 1 -0.37 101 102
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.088 0.26 -10000 0 -0.71 74 74
mol:DAG -0.006 0.029 0.17 12 -10000 0 12
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.079 0.23 0.34 1 -0.43 121 122
FRAP1 -0.1 0.26 0.36 1 -0.49 124 125
FOXO3 -0.049 0.21 0.32 2 -0.47 62 64
AKT1 -0.054 0.22 0.33 2 -0.51 62 64
GAB2 0.029 0.015 -10000 0 -10000 0 0
SMPD1 -0.005 0.13 -10000 0 -0.68 16 16
SGMS1 -0.004 0.035 0.058 2 -0.076 54 56
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP -0.008 0.048 -10000 0 -0.25 17 17
CALM1 0.035 0.007 -10000 0 -10000 0 0
cell proliferation -0.041 0.19 0.28 3 -0.37 95 98
EIF3A 0 0 -10000 0 -10000 0 0
PI3K 0.034 0.066 -10000 0 -0.3 17 17
RPS6KB1 -0.043 0.16 -10000 0 -0.87 12 12
mol:sphingomyelin -0.006 0.029 0.17 12 -10000 0 12
natural killer cell activation -0.002 0.004 -10000 0 -0.014 20 20
JAK3 0.035 0.008 -10000 0 -10000 0 0
PIK3R1 0.018 0.08 -10000 0 -0.42 16 16
JAK1 0.032 0.036 -10000 0 -0.42 3 3
NFKB1 0.036 0.005 -10000 0 -10000 0 0
MYC -0.027 0.29 0.49 2 -0.95 35 37
MYB -0.23 0.5 -10000 0 -1.2 104 104
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.021 0.15 -10000 0 -0.36 54 54
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.025 0.16 -10000 0 -0.81 11 11
mol:PI-3-4-5-P3 -0.02 0.15 -10000 0 -0.35 53 53
Rac1/GDP 0.008 0.051 -10000 0 -0.23 17 17
T cell proliferation -0.018 0.14 0.29 3 -0.34 49 52
SHC1 0.026 0.026 -10000 0 -0.42 1 1
RAC1 0.035 0.006 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.01 0.028 -10000 0 -0.065 103 103
PRKCZ -0.021 0.15 -10000 0 -0.35 49 49
NF kappa B1 p50/RelA -0.069 0.24 0.36 1 -0.44 113 114
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.013 0.13 -10000 0 -0.42 33 33
HSP90AA1 0 0 -10000 0 -10000 0 0
RELA 0.035 0.006 -10000 0 -10000 0 0
IL2RA 0.002 0.11 -10000 0 -0.42 31 31
IL2RB 0.011 0.097 -10000 0 -0.42 24 24
TERT 0.032 0.03 -10000 0 -0.42 2 2
E2F1 -0.072 0.2 -10000 0 -0.43 113 113
SOS1 0.032 0.023 -10000 0 -0.43 1 1
RPS6 0.034 0.022 -10000 0 -0.42 1 1
mol:cAMP 0.004 0.013 0.031 100 -10000 0 100
PTPN11 0.032 0.012 -10000 0 -10000 0 0
IL2RG 0.029 0.042 -10000 0 -0.42 4 4
actin cytoskeleton organization -0.018 0.14 0.29 3 -0.34 49 52
GRB2 0.031 0.013 -10000 0 -10000 0 0
IL2 0.031 0.037 -10000 0 -0.42 3 3
PIK3CA 0.032 0.024 -10000 0 -0.42 1 1
Rac1/GTP 0.033 0.064 -10000 0 -0.22 17 17
LCK -0.019 0.14 -10000 0 -0.42 54 54
BCL2 -0.18 0.38 -10000 0 -0.82 118 118
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.07 0.16 -10000 0 -0.41 66 66
KLHL20 -0.025 0.09 0.25 1 -0.25 17 18
CYFIP2 -0.006 0.13 -10000 0 -0.42 45 45
Rac1/GDP -0.035 0.12 0.27 4 -0.26 60 64
ENAH -0.065 0.16 -10000 0 -0.41 63 63
AP1M1 0.035 0.021 -10000 0 -0.42 1 1
RAP1B 0.033 0.03 -10000 0 -0.42 2 2
RAP1A 0.031 0.045 -10000 0 -0.42 5 5
CTNNB1 0.025 0.067 -10000 0 -0.42 11 11
CDC42/GTP -0.013 0.083 -10000 0 -0.23 13 13
ABI1/Sra1/Nap1 -0.046 0.054 -10000 0 -0.16 37 37
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.03 0.1 -10000 0 -0.23 58 58
RAPGEF1 -0.073 0.15 -10000 0 -0.36 79 79
CTNND1 0.034 0.022 -10000 0 -0.42 1 1
regulation of calcium-dependent cell-cell adhesion -0.074 0.18 -10000 0 -0.35 144 144
CRK -0.069 0.16 -10000 0 -0.39 81 81
E-cadherin/gamma catenin/alpha catenin 0.018 0.098 -10000 0 -0.26 49 49
alphaE/beta7 Integrin 0.044 0.039 -10000 0 -0.3 5 5
IQGAP1 0.035 0.008 -10000 0 -10000 0 0
NCKAP1 0.035 0.021 -10000 0 -0.42 1 1
Rap1/GTP/I-afadin 0.047 0.064 -10000 0 -0.23 22 22
DLG1 -0.082 0.18 -10000 0 -0.4 88 88
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.031 0.056 -10000 0 -0.15 63 63
MLLT4 0.02 0.078 -10000 0 -0.42 15 15
ARF6/GTP/NME1/Tiam1 0.056 0.045 -10000 0 -0.24 9 9
PI3K -0.036 0.074 -10000 0 -0.19 62 62
ARF6 0.033 0.029 -10000 0 -0.42 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.004 0.1 -10000 0 -0.3 48 48
TIAM1 0.028 0.057 -10000 0 -0.42 8 8
E-cadherin(dimer)/Ca2+ 0.03 0.097 -10000 0 -0.22 57 57
AKT1 -0.024 0.053 0.17 3 -0.17 5 8
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
CDH1 -0.012 0.13 -10000 0 -0.42 45 45
RhoA/GDP -0.036 0.12 0.27 4 -0.27 63 67
actin cytoskeleton organization -0.017 0.068 0.18 2 -0.18 17 19
CDC42/GDP -0.033 0.12 0.27 4 -0.26 60 64
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.01 0.077 -10000 0 -0.22 56 56
ITGB7 0.036 0.005 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.033 0.1 -10000 0 -0.23 57 57
E-cadherin/Ca2+/beta catenin/alpha catenin 0.018 0.087 -10000 0 -0.22 56 56
mol:GDP -0.054 0.12 0.27 4 -0.3 64 68
CDC42/GTP/IQGAP1 0.045 0.014 -10000 0 -10000 0 0
JUP 0.028 0.042 -10000 0 -0.42 4 4
p120 catenin/RhoA/GDP -0.031 0.13 0.28 3 -0.28 62 65
RAC1/GTP/IQGAP1 0.046 0.013 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.049 0.033 -10000 0 -0.3 4 4
RHOA 0.026 0.061 -10000 0 -0.42 9 9
CDC42 0.035 0.008 -10000 0 -10000 0 0
CTNNA1 0.035 0.021 -10000 0 -0.42 1 1
positive regulation of S phase of mitotic cell cycle -0.03 0.077 0.15 1 -0.18 80 81
NME1 0.033 0.01 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.08 0.18 -10000 0 -0.4 83 83
regulation of cell-cell adhesion -0.018 0.069 -10000 0 -0.17 57 57
WASF2 -0.016 0.042 0.12 2 -0.11 8 10
Rap1/GTP -0.015 0.091 0.25 1 -0.25 13 14
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.036 0.1 -10000 0 -0.23 53 53
CCND1 -0.038 0.094 0.17 1 -0.23 80 81
VAV2 -0.068 0.18 -10000 0 -0.53 14 14
RAP1/GDP -0.02 0.1 0.26 1 -0.26 18 19
adherens junction assembly -0.078 0.17 -10000 0 -0.39 85 85
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.035 0.008 -10000 0 -10000 0 0
PIP5K1C 0.033 0.036 -10000 0 -0.42 3 3
regulation of heterotypic cell-cell adhesion 0.028 0.11 -10000 0 -0.22 62 62
E-cadherin/beta catenin -0.024 0.1 -10000 0 -0.29 63 63
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.081 0.18 -10000 0 -0.4 87 87
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
Rac1/GTP -0.076 0.13 -10000 0 -0.38 31 31
E-cadherin/beta catenin/alpha catenin 0.02 0.1 -10000 0 -0.25 56 56
ITGAE 0.028 0.046 -10000 0 -0.42 5 5
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.076 0.19 -10000 0 -0.36 144 144
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.014 0.1 -9999 0 -0.26 58 58
E-cadherin/beta catenin 0.004 0.11 -9999 0 -0.3 55 55
CTNNB1 0.025 0.067 -9999 0 -0.42 11 11
JUP 0.028 0.042 -9999 0 -0.42 4 4
CDH1 -0.011 0.13 -9999 0 -0.42 45 45
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.06 0.29 -10000 0 -0.92 46 46
epithelial cell differentiation -0.027 0.25 -10000 0 -0.72 48 48
ITCH 0.035 0.039 -10000 0 -10000 0 0
WWP1 -0.087 0.39 -10000 0 -1.4 42 42
FYN 0.027 0.054 -10000 0 -0.42 7 7
EGFR -0.015 0.13 -10000 0 -0.42 49 49
PRL 0.034 0.022 -10000 0 -0.42 1 1
neuron projection morphogenesis -0.019 0.21 0.32 10 -0.64 43 53
PTPRZ1 0.023 0.061 -10000 0 -0.42 9 9
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.028 0.22 -10000 0 -0.71 43 43
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.064 0.25 -10000 0 -0.87 43 43
ADAM17 0.036 0.037 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.079 0.3 -10000 0 -1 45 45
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.062 0.29 -10000 0 -0.9 47 47
NCOR1 0.032 0.012 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.054 0.25 -10000 0 -0.82 43 43
GRIN2B -0.062 0.22 0.25 1 -0.75 43 44
ErbB4/ErbB2/betacellulin -0.069 0.26 -10000 0 -0.72 56 56
STAT1 0.02 0.075 -10000 0 -0.42 14 14
HBEGF 0.029 0.05 -10000 0 -0.42 6 6
PRLR -0.001 0.12 -10000 0 -0.42 40 40
E4ICDs/ETO2 -0.1 0.32 -10000 0 -0.84 62 62
axon guidance -0.068 0.28 -10000 0 -0.91 45 45
NEDD4 0.025 0.076 -10000 0 -0.31 17 17
Prolactin receptor/Prolactin receptor/Prolactin 0.022 0.094 -10000 0 -0.3 39 39
CBFA2T3 -0.047 0.16 -10000 0 -0.42 81 81
ErbB4/ErbB2/HBEGF -0.05 0.26 -10000 0 -0.78 49 49
MAPK3 -0.016 0.22 0.35 8 -0.66 43 51
STAT1 (dimer) -0.064 0.29 -10000 0 -0.9 47 47
MAPK1 -0.016 0.22 0.35 8 -0.66 43 51
JAK2 0.032 0.03 -10000 0 -0.42 2 2
ErbB4/ErbB2/neuregulin 1 beta -0.063 0.25 -10000 0 -0.77 50 50
NRG1 0.013 0.021 -10000 0 -10000 0 0
NRG3 0.028 0.054 -10000 0 -0.42 7 7
NRG2 0.025 0.061 -10000 0 -0.42 9 9
NRG4 0.033 0.022 -10000 0 -0.42 1 1
heart development -0.068 0.28 -10000 0 -0.91 45 45
neural crest cell migration -0.062 0.25 -10000 0 -0.75 50 50
ERBB2 0.006 0.058 -10000 0 -0.3 15 15
WWOX/E4ICDs -0.071 0.28 -10000 0 -0.92 46 46
SHC1 0.028 0.025 -10000 0 -0.42 1 1
ErbB4/EGFR/neuregulin 4 -0.065 0.28 -10000 0 -0.84 48 48
apoptosis 0.059 0.28 0.84 49 -10000 0 49
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.062 0.29 -10000 0 -0.92 46 46
ErbB4/ErbB2/epiregulin -0.053 0.26 -10000 0 -0.77 50 50
ErbB4/ErbB4/betacellulin/betacellulin -0.079 0.29 -10000 0 -0.85 53 53
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.031 0.28 -10000 0 -0.72 57 57
MDM2 -0.068 0.29 0.29 13 -0.92 45 58
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.044 0.23 -10000 0 -0.77 43 43
STAT5A -0.041 0.28 0.33 8 -0.89 43 51
ErbB4/EGFR/neuregulin 1 beta -0.07 0.25 -10000 0 -0.79 46 46
DLG4 0.032 0.012 -10000 0 -10000 0 0
GRB2/SHC 0.038 0.029 -10000 0 -0.3 1 1
E4ICDs/TAB2/NCoR1 -0.048 0.28 -10000 0 -0.86 46 46
STAT5A (dimer) -0.019 0.28 -10000 0 -0.81 48 48
MAP3K7IP2 0.032 0.03 -10000 0 -0.42 2 2
STAT5B (dimer) -0.045 0.28 -10000 0 -0.87 46 46
LRIG1 0.006 0.11 -10000 0 -0.42 31 31
EREG 0.025 0.051 -10000 0 -0.42 6 6
BTC -0.009 0.13 -10000 0 -0.42 47 47
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.07 0.28 -10000 0 -0.92 45 45
ERBB4 -0.08 0.3 -10000 0 -1 45 45
STAT5B 0.03 0.024 -10000 0 -0.42 1 1
YAP1 -0.024 0.15 -10000 0 -0.41 48 48
GRB2 0.033 0.011 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.048 0.26 -10000 0 -0.76 50 50
glial cell differentiation 0.047 0.27 0.85 46 -10000 0 46
WWOX 0.027 0.016 -10000 0 -10000 0 0
cell proliferation -0.077 0.26 0.34 1 -0.8 48 49
TCGA08_p53

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
CDKN2A -0.002 0.05 -10000 0 -0.3 14 14
TP53 -0.025 0.091 0.26 1 -0.26 58 59
Senescence -0.028 0.093 0.25 1 -0.25 66 67
Apoptosis -0.028 0.093 0.25 1 -0.25 66 67
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.004 0.061 0.26 25 -10000 0 25
MDM4 0.026 0.032 -10000 0 -0.42 2 2
Signaling events mediated by PTP1B

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
PDGFRB 0.028 0.057 -10000 0 -0.42 8 8
Jak2/Leptin Receptor -0.035 0.14 -10000 0 -0.37 48 48
PTP1B/AKT1 -0.045 0.14 0.26 3 -0.31 71 74
FYN 0.027 0.054 -10000 0 -0.42 7 7
p210 bcr-abl/PTP1B -0.062 0.14 0.28 3 -0.33 73 76
EGFR -0.024 0.14 -10000 0 -0.43 49 49
EGF/EGFR -0.091 0.18 0.29 2 -0.32 157 159
CSF1 0.034 0.021 -10000 0 -0.42 1 1
AKT1 0.033 0.03 -10000 0 -0.43 2 2
INSR 0.034 0.029 -10000 0 -0.42 2 2
PTP1B/N-cadherin -0.056 0.15 0.3 2 -0.35 69 71
Insulin Receptor/Insulin -0.008 0.13 0.31 2 -0.33 39 41
HCK 0.018 0.087 -10000 0 -0.42 19 19
CRK 0.032 0.023 -10000 0 -0.42 1 1
TYK2 -0.061 0.14 0.3 4 -0.34 63 67
EGF -0.073 0.19 -10000 0 -0.43 110 110
YES1 0.029 0.05 -10000 0 -0.42 6 6
CAV1 -0.071 0.15 0.27 3 -0.34 80 83
TXN 0.033 0.007 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.056 0.16 0.3 2 -0.33 88 90
cell migration 0.062 0.14 0.33 73 -0.28 3 76
STAT3 0.028 0.032 -10000 0 -0.42 2 2
PRLR 0.001 0.12 -10000 0 -0.4 42 42
ITGA2B 0.033 0.01 -10000 0 -10000 0 0
CSF1R 0.035 0.006 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.028 0.098 -10000 0 -0.3 41 41
FGR 0.035 0.008 -10000 0 -10000 0 0
PTP1B/p130 Cas -0.045 0.14 0.3 1 -0.32 70 71
Crk/p130 Cas -0.038 0.14 0.3 1 -0.32 64 65
DOK1 -0.054 0.14 0.26 3 -0.38 52 55
JAK2 -0.043 0.14 -10000 0 -0.38 47 47
Jak2/Leptin Receptor/Leptin -0.038 0.14 0.25 1 -0.37 43 44
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
PTPN1 -0.062 0.14 0.28 3 -0.34 73 76
LYN 0.03 0.014 -10000 0 -10000 0 0
CDH2 0.013 0.091 -10000 0 -0.42 21 21
SRC -0.003 0.12 -10000 0 -0.63 14 14
ITGB3 0.028 0.046 -10000 0 -0.42 5 5
CAT1/PTP1B -0.085 0.2 0.32 2 -0.44 85 87
CAPN1 0.025 0.065 -10000 0 -0.43 10 10
CSK 0.034 0.022 -10000 0 -0.42 1 1
PI3K -0.003 0.14 0.28 2 -0.34 43 45
mol:H2O2 -0.001 0.006 -10000 0 -10000 0 0
STAT3 (dimer) -0.033 0.14 0.23 1 -0.36 39 40
negative regulation of transcription -0.042 0.14 -10000 0 -0.38 47 47
FCGR2A 0.018 0.07 -10000 0 -0.42 12 12
FER 0.032 0.022 -10000 0 -0.43 1 1
alphaIIb/beta3 Integrin 0.044 0.035 -10000 0 -0.31 4 4
BLK 0.022 0.038 -10000 0 -0.42 3 3
Insulin Receptor/Insulin/Shc 0.053 0.04 -10000 0 -0.26 3 3
RHOA 0.025 0.062 -10000 0 -0.43 9 9
LEPR 0.026 0.058 -10000 0 -0.42 8 8
BCAR1 0.03 0.014 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.033 0.01 -10000 0 -10000 0 0
mol:NADPH -0.002 0.004 -10000 0 -10000 0 0
TRPV6 -0.068 0.21 0.26 1 -0.48 79 80
PRL 0.036 0.026 -10000 0 -0.26 3 3
SOCS3 0.006 0.19 -10000 0 -1.3 10 10
SPRY2 0.005 0.11 -10000 0 -0.43 29 29
Insulin Receptor/Insulin/IRS1 0.032 0.11 -10000 0 -0.27 55 55
CSF1/CSF1R -0.035 0.15 0.3 2 -0.33 61 63
Ras protein signal transduction 0.055 0.17 0.62 39 -10000 0 39
IRS1 -0.014 0.14 -10000 0 -0.42 54 54
INS 0.034 0.022 -10000 0 -0.43 1 1
LEP 0.001 0.11 -10000 0 -0.42 32 32
STAT5B -0.052 0.14 0.23 3 -0.32 68 71
STAT5A -0.054 0.14 0.23 3 -0.33 69 72
GRB2 0.033 0.011 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.05 0.15 0.3 2 -0.34 73 75
CSN2 0.022 0.11 -10000 0 -1.4 2 2
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
LAT -0.009 0.12 -10000 0 -0.53 19 19
YBX1 0.037 0.043 -10000 0 -0.38 5 5
LCK -0.017 0.14 -10000 0 -0.42 54 54
SHC1 0.028 0.025 -10000 0 -0.42 1 1
NOX4 -0.023 0.15 -10000 0 -0.43 58 58
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.053 0.052 0.23 21 -0.42 1 22
AES 0.052 0.042 0.21 16 -10000 0 16
FBXW11 0.033 0.029 -10000 0 -0.42 2 2
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.04 0.055 -10000 0 -0.3 12 12
SMAD4 0.029 0.054 -10000 0 -0.42 7 7
DKK2 0.006 0.11 -10000 0 -0.42 31 31
TLE1 0.022 0.12 0.22 21 -0.42 33 54
MACF1 0.035 0.021 -10000 0 -0.42 1 1
CTNNB1 -0.003 0.1 0.28 3 -0.38 10 13
WIF1 0.03 0.014 -10000 0 -10000 0 0
beta catenin/RanBP3 0.073 0.21 0.41 115 -0.36 7 122
KREMEN2 -0.09 0.19 -10000 0 -0.42 129 129
DKK1 -0.027 0.14 -10000 0 -0.42 60 60
beta catenin/beta TrCP1 0.011 0.11 0.29 3 -0.37 10 13
FZD1 0.028 0.057 -10000 0 -0.42 8 8
AXIN2 -0.047 0.4 0.6 52 -1.2 34 86
AXIN1 0.037 0.002 -10000 0 -10000 0 0
RAN 0.036 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.044 0.066 -10000 0 -0.59 4 4
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.008 0.17 0.33 5 -0.54 26 31
Axin1/APC/GSK3 0.033 0.051 0.32 1 -0.31 1 2
Axin1/APC/GSK3/beta catenin/Macf1 0.021 0.081 0.33 3 -0.36 5 8
HNF1A 0.017 0.045 0.18 22 -10000 0 22
CTBP1 0.05 0.046 0.23 18 -10000 0 18
MYC 0.028 0.47 0.59 111 -1.3 37 148
RANBP3 0.036 0.007 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.044 0.15 -10000 0 -0.26 154 154
NKD1 0.027 0.037 -10000 0 -0.42 3 3
TCF4 0.031 0.1 0.22 19 -0.4 22 41
TCF3 0.048 0.052 0.22 18 -0.42 2 20
WNT1/LRP6/FZD1/Axin1 0.076 0.058 -10000 0 -0.23 13 13
Ran/GTP 0.028 0.006 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.09 0.26 0.51 109 -0.46 13 122
LEF1 0.038 0.085 0.23 19 -0.4 13 32
DVL1 0.03 0.049 -10000 0 -0.27 4 4
CSNK2A1 0.035 0.006 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.045 0.19 -10000 0 -0.55 36 36
DKK1/LRP6/Kremen 2 -0.06 0.16 -10000 0 -0.27 169 169
LRP6 0.029 0.046 -10000 0 -0.42 5 5
CSNK1A1 0.053 0.048 0.24 19 -10000 0 19
NLK 0.029 0.026 -10000 0 -0.43 1 1
CCND1 -0.15 0.6 0.58 75 -1.4 87 162
WNT1 0.035 0.021 -10000 0 -0.42 1 1
GSK3A 0.036 0.005 -10000 0 -10000 0 0
GSK3B 0.036 0.005 -10000 0 -10000 0 0
FRAT1 0.029 0.054 -10000 0 -0.42 7 7
PPP2R5D 0.028 0.065 0.24 1 -0.3 13 14
APC -0.012 0.059 0.2 19 -0.22 17 36
WNT1/LRP6/FZD1 0.022 0.051 -10000 0 -0.24 7 7
CREBBP 0.048 0.044 0.22 17 -10000 0 17
Coregulation of Androgen receptor activity

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
NRIP1 -0.009 0.14 -9999 0 -0.42 51 51
SVIL 0.022 0.078 -9999 0 -0.42 15 15
ZNF318 0.033 0.006 -9999 0 -10000 0 0
JMJD2C 0.04 0.011 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 -0.036 0.12 -9999 0 -0.25 106 106
CARM1 0.035 0.021 -9999 0 -0.42 1 1
PRDX1 0.033 0.036 -9999 0 -0.42 3 3
PELP1 0.032 0.011 -9999 0 -10000 0 0
CTNNB1 0.026 0.067 -9999 0 -0.42 11 11
AKT1 0.032 0.03 -9999 0 -0.42 2 2
PTK2B 0.028 0.016 -9999 0 -10000 0 0
MED1 -0.001 0 -9999 0 -10000 0 0
MAK 0.025 0.046 -9999 0 -0.42 5 5
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.037 0.005 -9999 0 -10000 0 0
GSN 0.023 0.078 -9999 0 -0.42 15 15
NCOA2 0.025 0.047 -9999 0 -0.42 5 5
NCOA6 0.037 0.007 -9999 0 -10000 0 0
DNA-PK 0.054 0.036 -9999 0 -0.26 2 2
NCOA4 0.03 0.05 -9999 0 -0.42 6 6
PIAS3 0.036 0.006 -9999 0 -10000 0 0
cell proliferation -0.014 0.097 -9999 0 -0.56 13 13
XRCC5 0.035 0.004 -9999 0 -10000 0 0
UBE3A 0.036 0.029 -9999 0 -0.42 2 2
T-DHT/AR/SNURF -0.051 0.12 -9999 0 -0.25 112 112
FHL2 -0.11 0.31 -9999 0 -0.91 63 63
RANBP9 0.036 0.008 -9999 0 -10000 0 0
JMJD1A 0.01 0.072 -9999 0 -0.15 86 86
CDK6 0.025 0.058 -9999 0 -0.42 8 8
TGFB1I1 0.018 0.085 -9999 0 -0.42 18 18
T-DHT/AR/CyclinD1 -0.073 0.17 -9999 0 -0.33 133 133
XRCC6 0.033 0.009 -9999 0 -10000 0 0
T-DHT/AR -0.062 0.14 -9999 0 -0.22 210 210
CTDSP1 0.034 0.029 -9999 0 -0.42 2 2
CTDSP2 0.032 0.029 -9999 0 -0.42 2 2
BRCA1 0.023 0.07 -9999 0 -0.42 12 12
TCF4 0.014 0.093 -9999 0 -0.42 22 22
CDKN2A 0.015 0.075 -9999 0 -0.42 14 14
SRF 0.018 0.061 -9999 0 -0.14 60 60
NKX3-1 -0.047 0.1 -9999 0 -0.23 99 99
KLK3 0.021 0.054 -9999 0 -10000 0 0
TMF1 0.035 0.008 -9999 0 -10000 0 0
HNRNPA1 -0.001 0 -9999 0 -10000 0 0
AOF2 0.036 0.008 -9999 0 -10000 0 0
APPL1 0.004 0.02 -9999 0 -0.3 2 2
T-DHT/AR/Caspase 8 -0.038 0.13 -9999 0 -0.25 111 111
AR -0.077 0.18 -9999 0 -0.43 100 100
UBA3 0 0 -9999 0 -10000 0 0
PATZ1 -0.001 0 -9999 0 -10000 0 0
PAWR 0.024 0.072 -9999 0 -0.42 13 13
PRKDC 0.029 0.031 -9999 0 -0.42 2 2
PA2G4 0.035 0.005 -9999 0 -10000 0 0
UBE2I 0.032 0.011 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.031 0.11 -9999 0 -0.23 106 106
RPS6KA3 0.034 0.041 -9999 0 -0.42 4 4
T-DHT/AR/ARA70 -0.041 0.13 -9999 0 -0.26 115 115
LATS2 0.024 0.061 -9999 0 -0.42 9 9
T-DHT/AR/PRX1 -0.035 0.12 -9999 0 -0.23 112 112
Cyclin D3/CDK11 p58 0.026 0.005 -9999 0 -10000 0 0
VAV3 -0.038 0.17 -9999 0 -0.42 81 81
KLK2 -0.012 0.087 -9999 0 -0.38 15 15
CASP8 0.036 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.021 0.12 -9999 0 -0.23 97 97
TMPRSS2 -0.15 0.35 -9999 0 -0.87 91 91
CCND1 -0.041 0.16 -9999 0 -0.42 79 79
PIAS1 0.037 0.007 -9999 0 -10000 0 0
mol:T-DHT -0.013 0.03 -9999 0 -0.064 116 116
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.035 0.036 -9999 0 -0.42 3 3
T-DHT/AR/CDK6 -0.04 0.13 -9999 0 -0.25 114 114
CMTM2 0.029 0.025 -9999 0 -0.42 1 1
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 -0.013 0.03 -9999 0 -0.065 116 116
CCND3 0.035 0.007 -9999 0 -10000 0 0
TGIF1 -0.001 0 -9999 0 -10000 0 0
FKBP4 0.031 0.046 -9999 0 -0.42 5 5
PLK2 and PLK4 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
PLK2 -0.005 0.12 -9999 0 -0.42 41 41
PLK4 0.03 0.05 -9999 0 -0.42 6 6
regulation of centriole replication -0.013 0.091 -9999 0 -0.3 46 46
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.006 0.11 -10000 0 -0.3 52 52
EPHB2 0.032 0.03 -10000 0 -0.42 2 2
Syndecan-2/TACI 0.011 0.064 -10000 0 -0.24 28 28
LAMA1 0.034 0.009 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 0.019 0.14 -10000 0 -0.25 86 86
HRAS 0.032 0.036 -10000 0 -0.42 3 3
Syndecan-2/CASK -0.005 0.057 -10000 0 -0.24 28 28
ITGA5 0.034 0.029 -10000 0 -0.42 2 2
BAX -0.008 0.052 -10000 0 -10000 0 0
EPB41 0.034 0.021 -10000 0 -0.42 1 1
positive regulation of cell-cell adhesion 0.008 0.065 -10000 0 -0.23 33 33
LAMA3 -0.019 0.14 -10000 0 -0.42 58 58
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.013 0.095 -10000 0 -0.42 23 23
Syndecan-2/MMP2 0 0.089 -10000 0 -0.29 40 40
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.015 0.1 -10000 0 -0.3 48 48
dendrite morphogenesis 0.012 0.065 -10000 0 -0.24 29 29
Syndecan-2/GM-CSF 0.011 0.066 -10000 0 -0.24 30 30
determination of left/right symmetry -0.005 0.069 -10000 0 -0.29 28 28
Syndecan-2/PKC delta 0.012 0.067 -10000 0 -0.24 30 30
GNB2L1 0.034 0.035 -10000 0 -0.42 3 3
MAPK3 0.033 0.09 0.2 82 -0.22 27 109
MAPK1 0.037 0.095 0.2 94 -0.22 29 123
Syndecan-2/RACK1 0.025 0.067 -10000 0 -0.22 31 31
NF1 0.032 0.03 -10000 0 -0.42 2 2
FGFR/FGF/Syndecan-2 -0.005 0.069 -10000 0 -0.29 28 28
ITGA2 -0.01 0.13 -10000 0 -0.42 48 48
MAPK8 -0.005 0.059 -10000 0 -0.24 29 29
Syndecan-2/alpha2/beta1 Integrin 0.043 0.11 -10000 0 -0.24 50 50
Syndecan-2/Kininogen 0.013 0.065 -10000 0 -0.25 28 28
ITGB1 0.032 0.036 -10000 0 -0.42 3 3
SRC 0.037 0.093 0.19 96 -0.22 29 125
Syndecan-2/CASK/Protein 4.1 0.012 0.059 -10000 0 -0.22 29 29
extracellular matrix organization 0.013 0.065 -10000 0 -0.24 28 28
actin cytoskeleton reorganization -0.006 0.1 -10000 0 -0.3 52 52
Syndecan-2/Caveolin-2/Ras 0.016 0.092 -10000 0 -0.27 41 41
Syndecan-2/Laminin alpha3 -0.013 0.1 -10000 0 -0.26 68 68
Syndecan-2/RasGAP 0.034 0.075 -10000 0 -0.21 35 35
alpha5/beta1 Integrin 0.048 0.037 -10000 0 -0.3 5 5
PRKCD 0.033 0.03 -10000 0 -0.42 2 2
Syndecan-2 dimer 0.012 0.066 -10000 0 -0.24 29 29
GO:0007205 0.003 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.019 0.067 0.2 1 -0.21 33 34
RHOA 0.026 0.061 -10000 0 -0.42 9 9
SDCBP 0.023 0.058 -10000 0 -0.42 8 8
TNFRSF13B 0.032 0.012 -10000 0 -10000 0 0
RASA1 0.029 0.05 -10000 0 -0.42 6 6
alpha2/beta1 Integrin 0.015 0.1 -10000 0 -0.3 48 48
Syndecan-2/Synbindin 0.011 0.064 -10000 0 -0.24 28 28
TGFB1 0.035 0.021 -10000 0 -0.42 1 1
CASP3 0.034 0.093 0.2 88 -0.22 29 117
FN1 -0.01 0.14 -10000 0 -0.42 50 50
Syndecan-2/IL8 -0.007 0.094 -10000 0 -0.27 53 53
SDC2 -0.005 0.069 -10000 0 -0.29 28 28
KNG1 0.035 0.008 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.011 0.067 -10000 0 -0.25 30 30
TRAPPC4 0.032 0.012 -10000 0 -10000 0 0
CSF2 0.031 0.036 -10000 0 -0.42 3 3
Syndecan-2/TGFB1 0.013 0.065 -10000 0 -0.25 28 28
Syndecan-2/Syntenin/PI-4-5-P2 0.009 0.065 -10000 0 -0.23 33 33
Syndecan-2/Ezrin 0.009 0.064 -10000 0 -0.22 34 34
PRKACA 0.036 0.095 0.2 93 -0.22 30 123
angiogenesis -0.007 0.094 -10000 0 -0.27 53 53
MMP2 0.005 0.1 -10000 0 -0.42 27 27
IL8 -0.004 0.12 -10000 0 -0.42 37 37
calcineurin-NFAT signaling pathway 0.011 0.064 -10000 0 -0.24 28 28
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.025 0.025 -10000 0 -0.3 3 3
alphaV beta3 Integrin 0.031 0.1 -10000 0 -0.26 51 51
PTK2 0.01 0.12 0.36 5 -0.42 18 23
IGF1R -0.042 0.17 -10000 0 -0.42 84 84
PI4KB 0 0 -10000 0 -10000 0 0
MFGE8 0.017 0.085 -10000 0 -0.42 18 18
SRC 0.033 0.029 -10000 0 -0.42 2 2
CDKN1B -0.008 0.12 -10000 0 -0.46 29 29
VEGFA 0 0 -10000 0 -10000 0 0
ILK 0.015 0.063 -10000 0 -0.48 5 5
ROCK1 0.036 0.006 -10000 0 -10000 0 0
AKT1 0.002 0.073 0.21 3 -0.42 8 11
PTK2B 0.006 0.059 0.21 9 -0.24 20 29
alphaV/beta3 Integrin/JAM-A 0.058 0.1 -10000 0 -0.23 42 42
CBL 0.032 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.051 0.073 -10000 0 -0.27 23 23
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.037 0.19 -10000 0 -0.31 151 151
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.006 0.07 -10000 0 -0.23 27 27
alphaV/beta3 Integrin/Syndecan-1 0.029 0.11 -10000 0 -0.27 56 56
PI4KA 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.079 0.21 -10000 0 -0.33 183 183
PI4 Kinase 0 0 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
alphaV/beta3 Integrin/Osteopontin -0.019 0.15 -10000 0 -0.27 124 124
RPS6KB1 -0.12 0.17 0.52 1 -0.44 78 79
TLN1 0.035 0.021 -10000 0 -0.42 1 1
MAPK3 -0.045 0.19 -10000 0 -0.56 50 50
GPR124 0.017 0.073 -10000 0 -0.42 13 13
MAPK1 -0.049 0.2 -10000 0 -0.55 57 57
PXN 0.036 0.004 -10000 0 -10000 0 0
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
alphaV/beta3 Integrin/Tumstatin 0.053 0.073 -10000 0 -0.28 21 21
cell adhesion 0.024 0.1 -10000 0 -0.27 47 47
ANGPTL3 0.031 0.041 -10000 0 -0.42 4 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.044 0.029 -10000 0 -0.25 4 4
IGF-1R heterotetramer -0.042 0.17 -10000 0 -0.42 84 84
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
TGFBR2 0.033 0.036 -10000 0 -0.42 3 3
ITGB3 0.029 0.046 -10000 0 -0.42 5 5
IGF1 -0.038 0.16 -10000 0 -0.42 78 78
RAC1 0.035 0.006 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.035 0.086 -10000 0 -0.3 26 26
apoptosis 0.022 0.077 -10000 0 -0.42 15 15
CD47 0.019 0.085 -10000 0 -0.42 18 18
alphaV/beta3 Integrin/CD47 0.042 0.089 -10000 0 -0.26 37 37
VCL 0.035 0.021 -10000 0 -0.42 1 1
alphaV/beta3 Integrin/Del1 -0.009 0.14 -10000 0 -0.28 104 104
CSF1 0.034 0.021 -10000 0 -0.42 1 1
PIK3C2A 0.011 0.08 -10000 0 -0.54 8 8
PI4 Kinase/Pyk2 0.004 0.075 -10000 0 -0.21 50 50
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.051 0.067 -10000 0 -0.25 20 20
FAK1/Vinculin 0.026 0.12 0.35 5 -0.34 18 23
alphaV beta3/Integrin/ppsTEM5 0.035 0.086 -10000 0 -0.3 26 26
RHOA 0.026 0.061 -10000 0 -0.42 9 9
VTN 0.035 0.008 -10000 0 -10000 0 0
BCAR1 0.03 0.014 -10000 0 -10000 0 0
FGF2 -0.001 0.11 -10000 0 -0.42 34 34
F11R -0.005 0.072 -10000 0 -0.3 28 28
alphaV/beta3 Integrin/Lactadherin 0.044 0.092 -10000 0 -0.31 27 27
alphaV/beta3 Integrin/TGFBR2 0.052 0.071 -10000 0 -0.27 21 21
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.06 0.066 -10000 0 -0.23 15 15
HSP90AA1 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.051 0.063 -10000 0 -0.24 20 20
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.01 0.14 -10000 0 -0.42 50 50
alphaV/beta3 Integrin/Pyk2 0.035 0.065 -10000 0 -0.24 20 20
SDC1 -0.003 0.13 -10000 0 -0.42 42 42
VAV3 -0.05 0.087 0.18 1 -0.24 83 84
PTPN11 0.036 0.004 -10000 0 -10000 0 0
IRS1 -0.014 0.14 -10000 0 -0.42 54 54
FAK1/Paxillin 0.025 0.12 0.35 5 -0.34 18 23
cell migration 0.019 0.11 0.32 6 -0.31 18 24
ITGAV 0.022 0.078 -10000 0 -0.42 15 15
PI3K 0.058 0.11 -10000 0 -0.22 50 50
SPP1 -0.073 0.19 -10000 0 -0.42 115 115
KDR 0.033 0.035 -10000 0 -0.42 3 3
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.022 0.077 -10000 0 -0.42 15 15
COL4A3 0.033 0.036 -10000 0 -0.42 3 3
angiogenesis -0.036 0.2 -10000 0 -0.56 52 52
Rac1/GTP -0.012 0.097 -10000 0 -0.22 86 86
EDIL3 -0.056 0.18 -10000 0 -0.42 97 97
cell proliferation 0.052 0.071 -10000 0 -0.27 21 21
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.018 0.11 -10000 0 -0.3 44 44
alphaM/beta2 Integrin/GPIbA 0.035 0.084 -10000 0 -0.29 22 22
alphaM/beta2 Integrin/proMMP-9 0.01 0.12 -10000 0 -0.29 61 61
PLAUR 0.009 0.11 -10000 0 -0.42 29 29
HMGB1 0.025 0.031 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.037 0.087 -10000 0 -0.3 23 23
AGER 0.025 0.037 -10000 0 -0.42 1 1
RAP1A 0.031 0.045 -10000 0 -0.42 5 5
SELPLG 0.025 0.07 -10000 0 -0.42 12 12
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.043 0.12 -10000 0 -0.24 62 62
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.013 0.14 -10000 0 -0.42 52 52
CYR61 -0.004 0.12 -10000 0 -0.42 40 40
TLN1 0.035 0.021 -10000 0 -0.42 1 1
Rap1/GTP 0.011 0.13 -10000 0 -0.36 35 35
RHOA 0.026 0.061 -10000 0 -0.42 9 9
P-selectin oligomer -0.039 0.16 -10000 0 -0.42 73 73
MYH2 -0.016 0.14 0.23 1 -0.42 33 34
MST1R -0.005 0.13 -10000 0 -0.42 44 44
leukocyte activation during inflammatory response 0.041 0.079 -10000 0 -0.25 23 23
APOB 0.036 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.005 0.1 -10000 0 -0.42 27 27
JAM3 0.014 0.087 -10000 0 -0.42 19 19
GP1BA 0.03 0.014 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CTGF 0.018 0.12 -10000 0 -0.32 45 45
alphaM/beta2 Integrin -0.01 0.13 -10000 0 -0.38 37 37
JAM3 homodimer 0.014 0.087 -10000 0 -0.42 19 19
ICAM2 0.027 0.046 -10000 0 -0.42 5 5
ICAM1 0.018 0.085 -10000 0 -0.42 18 18
phagocytosis triggered by activation of immune response cell surface activating receptor -0.009 0.13 -10000 0 -0.38 37 37
cell adhesion 0.034 0.083 -10000 0 -0.29 22 22
NFKB1 0 0.15 0.39 1 -0.36 53 54
THY1 0.015 0.085 -10000 0 -0.42 18 18
RhoA/GDP 0.02 0.043 -10000 0 -0.3 9 9
Lipoprotein(a) 0.045 0.019 -10000 0 -0.25 1 1
alphaM/beta2 Integrin/LRP/tPA 0.016 0.12 -10000 0 -0.26 61 61
IL6 -0.049 0.23 0.36 2 -0.6 65 67
ITGB2 0.006 0.098 -10000 0 -0.44 21 21
elevation of cytosolic calcium ion concentration 0.015 0.15 -10000 0 -0.35 61 61
alphaM/beta2 Integrin/JAM2/JAM3 0.026 0.13 -10000 0 -0.31 48 48
JAM2 0.012 0.099 -10000 0 -0.42 25 25
alphaM/beta2 Integrin/ICAM1 0.04 0.13 -10000 0 -0.27 64 64
alphaM/beta2 Integrin/uPA/Plg 0.026 0.13 -10000 0 -0.28 58 58
RhoA/GTP -0.03 0.14 -10000 0 -0.44 38 38
positive regulation of phagocytosis 0.004 0.14 -10000 0 -0.41 36 36
Ron/MSP 0.02 0.1 -10000 0 -0.3 44 44
alphaM/beta2 Integrin/uPAR/uPA 0.017 0.15 -10000 0 -0.35 61 61
alphaM/beta2 Integrin/uPAR 0.024 0.11 -10000 0 -0.33 39 39
PLAU -0.013 0.14 -10000 0 -0.42 52 52
PLAT -0.021 0.14 -10000 0 -0.42 51 51
actin filament polymerization -0.013 0.14 0.24 3 -0.4 33 36
MST1 0.034 0.008 -10000 0 -10000 0 0
alphaM/beta2 Integrin/lipoprotein(a) 0.047 0.083 -10000 0 -0.25 23 23
TNF -0.015 0.16 0.35 2 -0.41 51 53
RAP1B 0.033 0.03 -10000 0 -0.42 2 2
alphaM/beta2 Integrin/uPA 0.013 0.13 -10000 0 -0.31 56 56
fibrinolysis 0.024 0.12 -10000 0 -0.28 58 58
HCK 0.018 0.087 -10000 0 -0.42 19 19
dendritic cell antigen processing and presentation -0.009 0.13 -10000 0 -0.38 37 37
VTN 0.035 0.008 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 0.019 0.12 -10000 0 -0.29 48 48
LPA 0.033 0.022 -10000 0 -0.42 1 1
LRP1 0.035 0.021 -10000 0 -0.42 1 1
cell migration -0.011 0.13 -10000 0 -0.28 76 76
FN1 -0.01 0.14 -10000 0 -0.42 50 50
alphaM/beta2 Integrin/Thy1 0.024 0.1 -10000 0 -0.29 38 38
MPO 0.032 0.013 -10000 0 -10000 0 0
KNG1 0.035 0.008 -10000 0 -10000 0 0
RAP1/GDP 0.041 0.037 -10000 0 -0.25 7 7
ROCK1 -0.019 0.14 -10000 0 -0.42 37 37
ELA2 0.035 0.008 -10000 0 -10000 0 0
PLG 0.032 0.03 -10000 0 -0.42 2 2
CTGF 0.002 0.11 -10000 0 -0.42 34 34
alphaM/beta2 Integrin/Hck 0.03 0.11 -10000 0 -0.37 28 28
ITGAM 0.022 0.053 -10000 0 -0.43 5 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.003 0.14 -10000 0 -0.28 77 77
HP 0.027 0.037 -10000 0 -0.42 3 3
leukocyte adhesion 0 0.15 -10000 0 -0.39 44 44
SELP -0.039 0.16 -10000 0 -0.42 73 73
Caspase cascade in apoptosis

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
TOP1 -0.005 0.11 0.23 2 -0.46 10 12
ACTA1 -0.016 0.12 0.22 14 -0.31 41 55
NUMA1 -0.014 0.12 0.22 1 -0.42 16 17
SPTAN1 -0.021 0.12 0.24 8 -0.31 47 55
LIMK1 -0.033 0.13 0.23 4 -0.33 49 53
BIRC3 -0.008 0.12 -10000 0 -0.42 40 40
BIRC2 0.032 0.012 -10000 0 -10000 0 0
BAX 0.035 0.007 -10000 0 -10000 0 0
CASP10 -0.048 0.091 -10000 0 -0.26 75 75
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 -0.011 0.12 0.26 1 -0.49 12 13
DIABLO 0.036 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes -0.02 0.12 0.24 8 -0.3 47 55
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.03 0.05 -10000 0 -0.42 6 6
GSN -0.028 0.12 0.24 7 -0.32 51 58
MADD 0.036 0.005 -10000 0 -10000 0 0
TFAP2A -0.003 0.16 -10000 0 -0.58 33 33
BID -0.022 0.069 -10000 0 -0.17 82 82
MAP3K1 -0.034 0.14 -10000 0 -0.42 51 51
TRADD 0.03 0.014 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.047 0.037 -10000 0 -0.3 5 5
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.03 0.13 0.3 6 -0.33 51 57
CASP9 0.034 0.022 -10000 0 -0.42 1 1
DNA repair -0.022 0.069 0.25 12 -0.17 22 34
neuron apoptosis -0.031 0.2 -10000 0 -0.67 41 41
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.018 0.12 0.25 1 -0.3 48 49
APAF1 0.032 0.041 -10000 0 -0.42 4 4
CASP6 -0.014 0.15 -10000 0 -0.79 15 15
TRAF2 0.034 0.029 -10000 0 -0.42 2 2
ICAD/CAD -0.024 0.11 0.23 5 -0.31 45 50
CASP7 0.031 0.1 0.25 45 -0.34 12 57
KRT18 -0.066 0.22 -10000 0 -0.57 73 73
apoptosis -0.016 0.12 0.26 4 -0.37 24 28
DFFA -0.023 0.12 0.23 5 -0.31 46 51
DFFB -0.023 0.12 0.24 4 -0.31 48 52
PARP1 0.022 0.07 0.17 22 -0.25 12 34
actin filament polymerization 0.033 0.13 0.32 46 -0.29 7 53
TNF 0.026 0.061 -10000 0 -0.42 9 9
CYCS -0.008 0.057 0.15 3 -0.21 10 13
SATB1 -0.028 0.16 -10000 0 -0.71 16 16
SLK -0.023 0.12 0.23 5 -0.31 46 51
p15 BID/BAX -0.002 0.077 -10000 0 -0.25 13 13
CASP2 -0.016 0.1 0.22 4 -0.32 29 33
JNK cascade 0.034 0.14 0.42 51 -10000 0 51
CASP3 -0.021 0.12 0.22 8 -0.32 50 58
LMNB2 -0.009 0.12 0.25 1 -0.4 25 26
RIPK1 0.035 0.007 -10000 0 -10000 0 0
CASP4 0.023 0.061 -10000 0 -0.42 9 9
Mammalian IAPs/DIABLO 0.034 0.082 -10000 0 -0.23 39 39
negative regulation of DNA binding -0.002 0.16 -10000 0 -0.57 33 33
stress fiber formation -0.022 0.12 0.23 5 -0.3 46 51
GZMB -0.033 0.12 -10000 0 -0.31 75 75
CASP1 -0.008 0.1 -10000 0 -0.36 32 32
LMNB1 -0.06 0.16 0.25 1 -0.39 46 47
APP -0.031 0.2 -10000 0 -0.68 41 41
TNFRSF1A 0.033 0.022 -10000 0 -0.42 1 1
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.009 0.001 -10000 0 -10000 0 0
VIM -0.012 0.13 0.25 5 -0.38 25 30
LMNA -0.008 0.099 0.25 1 -0.32 20 21
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.016 0.11 -10000 0 -0.34 32 32
LRDD 0.035 0.008 -10000 0 -10000 0 0
SREBF1 -0.036 0.13 0.25 3 -0.33 45 48
APAF-1/Caspase 9 0.016 0.11 -10000 0 -0.64 12 12
nuclear fragmentation during apoptosis -0.013 0.12 0.22 1 -0.42 16 17
CFL2 -0.034 0.13 0.29 7 -0.33 46 53
GAS2 -0.031 0.13 0.24 6 -0.32 52 58
positive regulation of apoptosis -0.028 0.12 0.26 1 -0.36 29 30
PRF1 0.027 0.054 -10000 0 -0.42 7 7
Cellular roles of Anthrax toxin

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
ANTXR1 0.006 0.11 -10000 0 -0.42 32 32
ANTXR2 0.022 0.078 -10000 0 -0.42 15 15
negative regulation of myeloid dendritic cell antigen processing and presentation -0.006 0.017 -10000 0 -0.063 40 40
monocyte activation -0.017 0.12 -10000 0 -0.37 56 56
MAP2K2 0.004 0.1 -10000 0 -0.63 12 12
MAP2K1 -0.009 0.015 -10000 0 -0.089 5 5
MAP2K7 -0.009 0.018 -10000 0 -0.11 7 7
MAP2K6 -0.013 0.041 0.13 3 -0.22 15 18
CYAA -0.025 0.066 -10000 0 -0.24 40 40
MAP2K4 -0.008 0.018 -10000 0 -0.12 5 5
IL1B -0.026 0.07 0.16 2 -0.21 54 56
Channel 0.021 0.085 -10000 0 -0.26 40 40
NLRP1 -0.006 0.016 -10000 0 -0.058 40 40
CALM1 0.035 0.007 -10000 0 -10000 0 0
negative regulation of phagocytosis 0 0.074 -10000 0 -0.43 13 13
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.006 0.017 0.063 40 -10000 0 40
MAPK3 -0.007 0.023 0.13 6 -0.11 6 12
MAPK1 -0.009 0.018 -10000 0 -0.11 7 7
PGR -0.074 0.1 -10000 0 -0.22 169 169
PA/Cellular Receptors 0.021 0.093 -10000 0 -0.28 40 40
apoptosis -0.006 0.017 -10000 0 -0.063 40 40
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.021 0.081 -10000 0 -0.24 40 40
macrophage activation 0.001 0.051 0.17 35 -0.2 2 37
TNF 0.026 0.061 -10000 0 -0.42 9 9
VCAM1 -0.018 0.13 -10000 0 -0.37 56 56
platelet activation 0 0.074 -10000 0 -0.43 13 13
MAPKKK cascade 0.001 0.032 0.12 6 -0.12 5 11
IL18 -0.02 0.064 0.14 1 -0.24 34 35
negative regulation of macrophage activation -0.006 0.017 -10000 0 -0.063 40 40
LEF -0.006 0.017 -10000 0 -0.063 40 40
CASP1 -0.008 0.031 -10000 0 -0.085 61 61
mol:cAMP 0 0.075 -10000 0 -0.44 13 13
necrosis -0.006 0.017 -10000 0 -0.063 40 40
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.021 0.08 -10000 0 -0.24 40 40
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B 0.021 0.068 -10000 0 -0.39 12 12
CDKN2C 0.024 0.064 -10000 0 -0.39 11 11
CDKN2A 0.019 0.071 -10000 0 -0.39 14 14
CCND2 0.003 0.047 0.18 27 -0.13 2 29
RB1 -0.011 0.062 0.24 2 -0.21 38 40
CDK4 0.007 0.057 0.22 30 -10000 0 30
CDK6 0.004 0.058 0.21 28 -0.17 6 34
G1/S progression 0.018 0.073 0.2 57 -0.26 3 60
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.035 0.036 -10000 0 -0.41 2 2
HSPA8 0.018 0.073 -10000 0 -0.42 13 13
SMAD3/SMAD4/ER alpha -0.034 0.18 -10000 0 -0.29 135 135
AKT1 0.03 0.038 -10000 0 -0.13 16 16
GSC -0.19 0.49 -10000 0 -1.4 74 74
NKX2-5 0.028 0.022 -10000 0 -10000 0 0
muscle cell differentiation 0.012 0.17 0.39 53 -10000 0 53
SMAD2-3/SMAD4/SP1 0.022 0.18 -10000 0 -0.36 58 58
SMAD4 -0.004 0.097 -10000 0 -0.27 34 34
CBFB 0.03 0.014 -10000 0 -10000 0 0
SAP18 0.033 0.01 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.062 0.049 -10000 0 -0.23 4 4
SMAD3/SMAD4/VDR 0.059 0.12 -10000 0 -0.26 29 29
MYC -0.001 0.1 -10000 0 -0.41 29 29
CDKN2B -0.1 0.32 -10000 0 -1.1 35 35
AP1 -0.03 0.18 -10000 0 -0.43 69 69
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.007 0.099 -10000 0 -0.34 21 21
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.007 0.092 -10000 0 -0.27 45 45
SP3 0.028 0.03 -10000 0 -10000 0 0
CREB1 0.035 0.021 -10000 0 -0.42 1 1
FOXH1 0.013 0.059 -10000 0 -0.19 9 9
SMAD3/SMAD4/GR 0.027 0.12 -10000 0 -0.28 41 41
GATA3 -0.044 0.17 -10000 0 -0.41 91 91
SKI/SIN3/HDAC complex/NCoR1 0.015 0.073 -10000 0 -0.3 14 14
MEF2C/TIF2 -0.014 0.13 0.33 1 -0.37 39 40
endothelial cell migration 0.005 0.24 1.1 21 -10000 0 21
MAX 0.035 0.011 -10000 0 -10000 0 0
RBBP7 0.034 0.029 -10000 0 -0.42 2 2
RBBP4 0.034 0.021 -10000 0 -0.42 1 1
RUNX2 0.031 0.041 -10000 0 -0.42 4 4
RUNX3 -0.01 0.13 -10000 0 -0.42 46 46
RUNX1 0.008 0.11 -10000 0 -0.42 29 29
CTBP1 0.035 0.008 -10000 0 -10000 0 0
NR3C1 0.024 0.072 -10000 0 -0.42 13 13
VDR 0.02 0.082 -10000 0 -0.42 17 17
CDKN1A -0.042 0.24 -10000 0 -1.3 15 15
KAT2B 0.001 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.015 0.14 -10000 0 -0.28 81 81
DCP1A 0.034 0.022 -10000 0 -0.42 1 1
SKI 0.036 0.002 -10000 0 -10000 0 0
SERPINE1 -0.006 0.25 -10000 0 -1.1 21 21
SMAD3/SMAD4/ATF2 0.034 0.11 -10000 0 -0.27 30 30
SMAD3/SMAD4/ATF3 0.015 0.12 -10000 0 -0.3 43 43
SAP30 0.03 0.046 -10000 0 -0.42 5 5
Cbp/p300/PIAS3 0.067 0.051 0.22 2 -0.26 1 3
JUN -0.043 0.18 -10000 0 -0.44 65 65
SMAD3/SMAD4/IRF7 0.032 0.12 -10000 0 -0.28 41 41
TFE3 0.033 0.035 -10000 0 -0.14 11 11
COL1A2 -0.076 0.33 -10000 0 -0.88 68 68
mesenchymal cell differentiation -0.03 0.11 0.29 31 -10000 0 31
DLX1 0.033 0.011 -10000 0 -10000 0 0
TCF3 0.033 0.03 -10000 0 -0.42 2 2
FOS -0.038 0.16 -10000 0 -0.45 66 66
SMAD3/SMAD4/Max 0.033 0.11 -10000 0 -0.27 30 30
Cbp/p300/SNIP1 0.06 0.045 -10000 0 -0.26 4 4
ZBTB17 0.035 0.013 -10000 0 -10000 0 0
LAMC1 -0.007 0.11 -10000 0 -0.41 24 24
TGIF2/HDAC complex/SMAD3/SMAD4 0.028 0.11 -10000 0 -0.27 37 37
IRF7 0.028 0.059 -10000 0 -0.3 13 13
ESR1 -0.082 0.19 -10000 0 -0.41 132 132
HNF4A 0.033 0.03 -10000 0 -0.42 2 2
MEF2C -0.03 0.14 0.34 3 -0.39 43 46
SMAD2-3/SMAD4 0.018 0.13 -10000 0 -0.28 44 44
Cbp/p300/Src-1 0.062 0.049 -10000 0 -0.23 5 5
IGHV3OR16-13 -0.003 0.065 -10000 0 -0.44 8 8
TGIF2/HDAC complex 0.029 0.05 -10000 0 -0.42 6 6
CREBBP 0.034 0.019 -10000 0 -10000 0 0
SKIL 0.028 0.05 -10000 0 -0.42 6 6
HDAC1 0.034 0.021 -10000 0 -0.42 1 1
HDAC2 0.032 0.023 -10000 0 -0.42 1 1
SNIP1 0.032 0.036 -10000 0 -0.42 3 3
GCN5L2 0.031 0.029 -10000 0 -0.42 1 1
SMAD3/SMAD4/TFE3 0.04 0.12 -10000 0 -0.31 36 36
MSG1/HSC70 0.032 0.062 -10000 0 -0.3 15 15
SMAD2 0.011 0.059 -10000 0 -0.15 12 12
SMAD3 0.01 0.091 -10000 0 -0.32 21 21
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.001 0.079 -10000 0 -0.24 28 28
SMAD2/SMAD2/SMAD4 -0.001 0.063 0.26 4 -0.24 13 17
NCOR1 0.032 0.012 -10000 0 -10000 0 0
NCOA2 0.025 0.047 -10000 0 -0.42 5 5
NCOA1 0.031 0.045 -10000 0 -0.42 5 5
MYOD/E2A 0.032 0.077 -10000 0 -0.3 25 25
SMAD2-3/SMAD4/SP1/MIZ-1 0.035 0.18 -10000 0 -0.35 55 55
IFNB1 -0.005 0.096 0.36 1 -0.3 29 30
SMAD3/SMAD4/MEF2C -0.003 0.17 -10000 0 -0.42 44 44
CITED1 0.029 0.031 -10000 0 -0.42 2 2
SMAD2-3/SMAD4/ARC105 0.021 0.12 -10000 0 -0.24 44 44
RBL1 0.033 0.022 -10000 0 -0.42 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.004 0.12 -10000 0 -0.41 33 33
RUNX1-3/PEBPB2 0.013 0.12 -10000 0 -0.26 70 70
SMAD7 -0.041 0.21 -10000 0 -0.52 55 55
MYC/MIZ-1 0.016 0.082 0.19 5 -0.29 29 34
SMAD3/SMAD4 0.04 0.13 0.31 43 -0.39 19 62
IL10 -0.034 0.12 -10000 0 -0.28 83 83
PIASy/HDAC complex 0.024 0.043 -10000 0 -0.42 3 3
PIAS3 0.036 0.011 -10000 0 -10000 0 0
CDK2 0.035 0.033 -10000 0 -0.42 2 2
IL5 -0.035 0.13 -10000 0 -0.31 58 58
CDK4 0.038 0.017 -10000 0 -10000 0 0
PIAS4 0.024 0.043 -10000 0 -0.42 3 3
ATF3 0.011 0.084 -10000 0 -0.42 18 18
SMAD3/SMAD4/SP1 0.014 0.17 -10000 0 -0.35 60 60
FOXG1 -0.001 0.003 -10000 0 -10000 0 0
FOXO3 0.006 0.03 -10000 0 -0.15 10 10
FOXO1 0.006 0.029 -10000 0 -0.14 10 10
FOXO4 0.006 0.029 -10000 0 -0.14 10 10
heart looping -0.029 0.14 0.34 3 -0.38 43 46
CEBPB 0.025 0.053 -10000 0 -0.42 6 6
SMAD3/SMAD4/DLX1 0.033 0.11 -10000 0 -0.26 31 31
MYOD1 0.014 0.095 -10000 0 -0.42 23 23
SMAD3/SMAD4/HNF4 0.032 0.11 -10000 0 -0.28 27 27
SMAD3/SMAD4/GATA3 -0.011 0.17 -10000 0 -0.3 105 105
SnoN/SIN3/HDAC complex/NCoR1 0.028 0.05 -10000 0 -0.42 6 6
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.017 0.15 -10000 0 -0.28 78 78
SMAD3/SMAD4/SP1-3 0.029 0.18 -10000 0 -0.39 54 54
MED15 0 0 -10000 0 -10000 0 0
SP1 0.009 0.076 -10000 0 -0.19 38 38
SIN3B 0.035 0.005 -10000 0 -10000 0 0
SIN3A 0.035 0.007 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.032 0.15 -10000 0 -0.27 87 87
ITGB5 -0.045 0.18 -10000 0 -0.5 58 58
TGIF/SIN3/HDAC complex/CtBP 0.018 0.061 -10000 0 -0.29 9 9
SMAD3/SMAD4/AR -0.023 0.18 -10000 0 -0.31 113 113
AR -0.053 0.18 -10000 0 -0.42 99 99
negative regulation of cell growth 0.012 0.099 -10000 0 -0.34 20 20
SMAD3/SMAD4/MYOD 0.018 0.12 -10000 0 -0.26 54 54
E2F5 0.011 0.087 -10000 0 -0.42 19 19
E2F4 0.03 0.014 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.045 0.13 -10000 0 -0.25 46 46
SMAD2-3/SMAD4/FOXO1-3a-4 -0.004 0.1 -10000 0 -0.29 43 43
TFDP1 0.032 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.007 0.2 -10000 0 -0.44 66 66
SMAD3/SMAD4/RUNX2 0.031 0.11 -10000 0 -0.29 31 31
TGIF2 0.029 0.05 -10000 0 -0.42 6 6
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 0.036 0.003 -10000 0 -10000 0 0
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.048 0.017 -10000 0 -10000 0 0
VLDLR -0.007 0.12 -10000 0 -0.42 42 42
CRKL 0.031 0.041 -10000 0 -0.42 4 4
LRPAP1 0.035 0.007 -10000 0 -10000 0 0
FYN 0.027 0.054 -10000 0 -0.42 7 7
ITGA3 0.023 0.07 -10000 0 -0.42 12 12
RELN/VLDLR/Fyn 0.027 0.1 -10000 0 -0.27 51 51
MAPK8IP1/MKK7/MAP3K11/JNK1 0.07 0.07 -10000 0 -0.22 15 15
AKT1 -0.017 0.088 -10000 0 -0.23 57 57
MAP2K7 0.035 0.021 -10000 0 -0.42 1 1
RAPGEF1 0.036 0.004 -10000 0 -10000 0 0
DAB1 0.035 0.007 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.039 0.081 -10000 0 -0.23 40 40
LRPAP1/LRP8 0.024 0.089 -10000 0 -0.3 35 35
RELN/LRP8/DAB1/Fyn 0.045 0.09 -10000 0 -0.22 46 46
DAB1/alpha3/beta1 Integrin 0.016 0.12 -10000 0 -0.22 85 85
long-term memory 0.049 0.1 -10000 0 -0.22 55 55
DAB1/LIS1 0.032 0.12 -10000 0 -0.22 80 80
DAB1/CRLK/C3G 0.021 0.11 -10000 0 -0.22 80 80
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
DAB1/NCK2 0.039 0.12 -10000 0 -0.22 80 80
ARHGEF2 0.022 0.055 -10000 0 -0.42 7 7
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.033 0.011 -10000 0 -10000 0 0
CDK5R1 0.033 0.01 -10000 0 -10000 0 0
RELN 0.03 0.046 -10000 0 -0.42 5 5
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
RELN/LRP8/Fyn 0.031 0.096 -10000 0 -0.26 46 46
GRIN2A/RELN/LRP8/DAB1/Fyn 0.056 0.094 -10000 0 -0.22 41 41
MAPK8 0.033 0.035 -10000 0 -0.42 3 3
RELN/VLDLR/DAB1 0.032 0.088 -10000 0 -0.23 46 46
ITGB1 0.032 0.036 -10000 0 -0.42 3 3
MAP1B -0.027 0.12 0.32 5 -0.25 96 101
RELN/LRP8 0.039 0.089 -10000 0 -0.25 40 40
GRIN2B/RELN/LRP8/DAB1/Fyn 0.047 0.11 -10000 0 -0.23 61 61
PI3K 0.036 0.065 -10000 0 -0.3 17 17
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.04 0.059 -10000 0 -0.32 12 12
RAP1A -0.042 0.097 0.34 7 -0.43 3 10
PAFAH1B1 0.032 0.023 -10000 0 -0.42 1 1
MAPK8IP1 0.034 0.029 -10000 0 -0.42 2 2
CRLK/C3G 0.047 0.034 -10000 0 -0.3 4 4
GRIN2B 0.018 0.082 -10000 0 -0.42 17 17
NCK2 0.036 0.005 -10000 0 -10000 0 0
neuron differentiation 0.018 0.083 -10000 0 -0.32 9 9
neuron adhesion -0.041 0.11 0.35 7 -0.39 6 13
LRP8 -0.001 0.12 -10000 0 -0.42 35 35
GSK3B -0.015 0.092 0.19 5 -0.41 10 15
RELN/VLDLR/DAB1/Fyn 0.039 0.097 -10000 0 -0.23 51 51
MAP3K11 0.034 0.029 -10000 0 -0.42 2 2
RELN/VLDLR/DAB1/P13K -0.007 0.095 -10000 0 -0.24 60 60
CDK5 0.035 0.007 -10000 0 -10000 0 0
MAPT -0.068 0.18 0.77 6 -0.38 96 102
neuron migration -0.024 0.12 0.31 10 -0.34 17 27
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.017 0.082 -10000 0 -0.32 9 9
RELN/VLDLR 0.025 0.12 -10000 0 -0.24 80 80
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.021 0.16 0.26 4 -0.42 45 49
IKBKB 0.017 0.092 0.33 2 -0.28 7 9
AKT1 0.024 0.11 0.24 42 -0.22 22 64
IKBKG 0.027 0.079 0.25 4 -0.28 6 10
CALM1 -0.01 0.13 0.25 5 -0.37 37 42
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
MAP3K1 -0.02 0.18 0.3 3 -0.47 46 49
MAP3K7 0.033 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.011 0.14 0.26 5 -0.38 40 45
DOK1 0.027 0.061 -10000 0 -0.42 9 9
AP-1 -0.018 0.1 0.21 2 -0.24 48 50
LYN 0.03 0.014 -10000 0 -10000 0 0
BLNK 0.013 0.099 -10000 0 -0.42 25 25
SHC1 0.028 0.025 -10000 0 -0.42 1 1
BCR complex 0.025 0.074 -10000 0 -0.3 23 23
CD22 -0.018 0.12 0.26 1 -0.44 30 31
CAMK2G -0.009 0.12 0.24 7 -0.39 28 35
CSNK2A1 0.035 0.006 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.004 0.077 -10000 0 -0.24 36 36
GO:0007205 -0.011 0.14 0.26 5 -0.38 40 45
SYK 0.005 0.11 -10000 0 -0.42 34 34
ELK1 -0.012 0.13 0.25 5 -0.37 39 44
NFATC1 0.022 0.13 0.27 19 -0.36 29 48
B-cell antigen/BCR complex 0.025 0.074 -10000 0 -0.3 23 23
PAG1/CSK 0.035 0.051 -10000 0 -0.3 9 9
NFKBIB 0.027 0.05 0.15 7 -0.12 21 28
HRAS 0.003 0.12 0.24 17 -0.3 43 60
NFKBIA 0.028 0.05 0.15 7 -0.12 20 27
NF-kappa-B/RelA/I kappa B beta 0.032 0.045 0.16 7 -10000 0 7
RasGAP/Csk 0.038 0.1 -10000 0 -0.26 35 35
mol:GDP -0.01 0.14 0.26 5 -0.37 40 45
PTEN 0.027 0.061 -10000 0 -0.42 9 9
CD79B 0.007 0.094 -10000 0 -0.42 23 23
NF-kappa-B/RelA/I kappa B alpha 0.032 0.044 0.16 7 -10000 0 7
GRB2 0.033 0.011 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.01 0.18 0.32 4 -0.46 48 52
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
mol:IP3 -0.012 0.14 0.27 4 -0.39 40 44
CSK 0.034 0.022 -10000 0 -0.42 1 1
FOS -0.036 0.14 0.24 4 -0.36 51 55
CHUK 0.016 0.1 0.24 5 -0.32 21 26
IBTK 0.032 0.03 -10000 0 -0.42 2 2
CARD11/BCL10/MALT1/TAK1 0.01 0.13 0.26 2 -0.38 29 31
PTPN6 -0.01 0.12 0.25 1 -0.43 29 30
RELA 0.036 0.006 -10000 0 -10000 0 0
BCL2A1 0.023 0.035 0.14 3 -0.1 1 4
VAV2 0 0.14 0.26 2 -0.48 29 31
ubiquitin-dependent protein catabolic process 0.03 0.05 0.16 7 -0.12 21 28
BTK -0.012 0.19 -10000 0 -1.1 15 15
CD19 -0.017 0.12 0.26 1 -0.43 31 32
MAP4K1 0.035 0.007 -10000 0 -10000 0 0
CD72 0.009 0.1 -10000 0 -0.42 27 27
PAG1 0.02 0.061 -10000 0 -0.42 9 9
MAPK14 -0.015 0.16 0.3 2 -0.41 42 44
SH3BP5 0.021 0.078 -10000 0 -0.42 15 15
PIK3AP1 -0.02 0.15 0.28 4 -0.42 43 47
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.02 0.16 -10000 0 -0.46 43 43
RAF1 0.003 0.12 0.24 14 -0.31 32 46
RasGAP/p62DOK/SHIP 0.026 0.099 -10000 0 -0.26 40 40
CD79A 0.031 0.023 -10000 0 -0.42 1 1
re-entry into mitotic cell cycle -0.018 0.1 0.21 2 -0.24 49 51
RASA1 0.029 0.05 -10000 0 -0.42 6 6
MAPK3 0.012 0.1 0.23 26 -0.3 17 43
MAPK1 0.002 0.1 0.26 8 -0.31 19 27
CD72/SHP1 0.018 0.16 0.3 16 -0.44 33 49
NFKB1 0.036 0.005 -10000 0 -10000 0 0
MAPK8 -0.016 0.16 0.28 7 -0.4 44 51
actin cytoskeleton organization 0.019 0.14 0.3 13 -0.44 27 40
NF-kappa-B/RelA 0.065 0.087 0.29 6 -0.27 3 9
Calcineurin 0.004 0.13 0.25 1 -0.37 28 29
PI3K -0.025 0.11 -10000 0 -0.35 36 36
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.011 0.15 0.27 6 -0.42 41 47
SOS1 0.035 0.021 -10000 0 -0.42 1 1
Bam32/HPK1 -0.065 0.31 -10000 0 -0.74 77 77
DAPP1 -0.1 0.34 -10000 0 -0.84 77 77
cytokine secretion 0.023 0.13 0.26 23 -0.34 29 52
mol:DAG -0.012 0.14 0.27 4 -0.39 40 44
PLCG2 0.02 0.055 -10000 0 -0.42 7 7
MAP2K1 0.002 0.11 0.24 13 -0.32 24 37
B-cell antigen/BCR complex/FcgammaRIIB 0.02 0.094 -10000 0 -0.29 34 34
mol:PI-3-4-5-P3 0 0.11 0.23 27 -0.29 28 55
ETS1 -0.009 0.11 0.23 7 -0.37 27 34
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.033 0.12 -10000 0 -0.26 55 55
B-cell antigen/BCR complex/LYN -0.013 0.12 0.27 1 -0.44 32 33
MALT1 0.031 0.041 -10000 0 -0.42 4 4
TRAF6 0.035 0.021 -10000 0 -0.42 1 1
RAC1 0.008 0.14 0.3 9 -0.46 27 36
B-cell antigen/BCR complex/LYN/SYK -0.002 0.14 -10000 0 -0.45 30 30
CARD11 -0.013 0.14 0.26 7 -0.38 42 49
FCGR2B 0.001 0.11 -10000 0 -0.42 30 30
PPP3CA 0.027 0.061 -10000 0 -0.42 9 9
BCL10 0.034 0.008 -10000 0 -10000 0 0
IKK complex 0.024 0.05 0.16 19 -0.13 2 21
PTPRC 0.007 0.094 -10000 0 -0.42 23 23
PDPK1 0.005 0.085 0.2 29 -0.22 16 45
PPP3CB 0.035 0.021 -10000 0 -0.42 1 1
PPP3CC 0.024 0.043 -10000 0 -0.42 4 4
POU2F2 0.025 0.032 0.13 5 -0.1 1 6
Visual signal transduction: Rods

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
mol:K + 0.03 0.046 -10000 0 -0.42 5 5
GNAT1/GTP 0.024 0.025 -10000 0 -0.3 3 3
Metarhodopsin II/Arrestin 0.009 0.094 -10000 0 -0.25 57 57
PDE6G/GNAT1/GTP 0.042 0.028 -10000 0 -0.25 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.032 0.036 -10000 0 -0.42 3 3
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel -0.015 0.12 -10000 0 -0.22 123 123
mol:Na + 0.025 0.098 -10000 0 -0.24 48 48
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.007 0.12 -10000 0 -0.27 73 73
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.037 0.11 -10000 0 -0.25 48 48
CNGB1 0.03 0.014 -10000 0 -10000 0 0
RDH5 0.033 0.011 -10000 0 -10000 0 0
SAG -0.024 0.14 -10000 0 -0.42 58 58
mol:Ca2+ -0.034 0.087 0.33 6 -0.39 10 16
Na + (4 Units) 0.016 0.093 -10000 0 -0.24 47 47
RGS9 0.017 0.07 -10000 0 -0.42 12 12
GNB1/GNGT1 0.036 0.062 -10000 0 -0.3 16 16
GNAT1/GDP 0.018 0.11 -10000 0 -0.23 76 76
GUCY2D 0.032 0.012 -10000 0 -10000 0 0
GNGT1 0.017 0.067 -10000 0 -0.42 11 11
GUCY2F 0.027 0.064 -10000 0 -0.42 10 10
GNB5 0.025 0.067 -10000 0 -0.42 11 11
mol:GMP (4 units) -0.02 0.1 -10000 0 -0.22 105 105
mol:11-cis-retinal 0.033 0.01 -10000 0 -10000 0 0
mol:cGMP 0.048 0.084 -10000 0 -0.26 29 29
GNB1 0.032 0.045 -10000 0 -0.42 5 5
Rhodopsin 0.051 0.011 -10000 0 -10000 0 0
SLC24A1 0.03 0.046 -10000 0 -0.42 5 5
CNGA1 0.004 0.1 -10000 0 -0.42 28 28
Metarhodopsin II 0.023 0.004 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.064 0.077 -10000 0 -0.25 23 23
RGS9BP -0.023 0.15 -10000 0 -0.42 61 61
Metarhodopsin II/Transducin 0.015 0.047 -10000 0 -0.21 20 20
GCAP Family/Ca ++ 0.051 0.068 -10000 0 -0.25 23 23
PDE6A/B -0.027 0.15 -10000 0 -0.3 112 112
mol:Pi 0.006 0.12 -10000 0 -0.27 73 73
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.05 0.058 -10000 0 -0.23 19 19
PDE6B -0.064 0.19 -10000 0 -0.42 111 111
PDE6A 0.033 0.029 -10000 0 -0.42 2 2
PDE6G 0.034 0.01 -10000 0 -10000 0 0
RHO 0.036 0.006 -10000 0 -10000 0 0
PDE6 -0.015 0.15 -10000 0 -0.24 139 139
GUCA1A 0.022 0.075 -10000 0 -0.42 14 14
GC2/GCAP Family 0.067 0.09 -10000 0 -0.28 29 29
GUCA1C 0.026 0.064 -10000 0 -0.42 10 10
GUCA1B 0.034 0.021 -10000 0 -0.42 1 1
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS 0.045 0.1 -9999 0 -0.24 49 49
SMAD6-7/SMURF1 0.067 0.025 -9999 0 -0.26 1 1
NOG 0.029 0.037 -9999 0 -0.42 3 3
SMAD9 -0.029 0.16 -9999 0 -0.45 55 55
SMAD4 0.029 0.054 -9999 0 -0.42 7 7
SMAD5 -0.026 0.12 -9999 0 -0.38 26 26
BMP7/USAG1 -0.063 0.16 -9999 0 -0.31 139 139
SMAD5/SKI -0.014 0.13 -9999 0 -0.38 29 29
SMAD1 0.012 0.07 -9999 0 -0.32 6 6
BMP2 0.021 0.073 -9999 0 -0.42 13 13
SMAD1/SMAD1/SMAD4 0.033 0.077 -9999 0 -0.32 2 2
BMPR1A 0.031 0.045 -9999 0 -0.42 5 5
BMPR1B -0.004 0.11 -9999 0 -0.42 30 30
BMPR1A-1B/BAMBI -0.02 0.14 -9999 0 -0.26 120 120
AHSG 0.034 0.008 -9999 0 -10000 0 0
CER1 0.034 0.009 -9999 0 -10000 0 0
BMP2-4/CER1 0.016 0.12 -9999 0 -0.26 71 71
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.015 0.12 -9999 0 -0.36 30 30
BMP2-4 (homodimer) -0.006 0.13 -9999 0 -0.31 74 74
RGMB 0.028 0.057 -9999 0 -0.42 8 8
BMP6/BMPR2/BMPR1A-1B 0.051 0.091 -9999 0 -0.24 41 41
RGMA 0.019 0.073 -9999 0 -0.42 13 13
SMURF1 0.036 0.006 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.03 0.12 -9999 0 -0.36 32 32
BMP2-4/USAG1 -0.075 0.18 -9999 0 -0.29 189 189
SMAD6/SMURF1/SMAD5 -0.013 0.13 -9999 0 -0.38 28 28
SOSTDC1 -0.11 0.2 -9999 0 -0.42 151 151
BMP7/BMPR2/BMPR1A-1B 0.041 0.095 -9999 0 -0.24 45 45
SKI 0.036 0.002 -9999 0 -10000 0 0
BMP6 (homodimer) 0.027 0.05 -9999 0 -0.42 6 6
HFE2 0.026 0.064 -9999 0 -0.42 10 10
ZFYVE16 0.034 0.022 -9999 0 -0.42 1 1
MAP3K7 0.033 0.011 -9999 0 -10000 0 0
BMP2-4/CHRD 0.014 0.12 -9999 0 -0.28 70 70
SMAD5/SMAD5/SMAD4 -0.017 0.13 -9999 0 -0.38 30 30
MAPK1 0.033 0.022 -9999 0 -0.42 1 1
TAK1/TAB family 0.012 0.13 -9999 0 -0.36 24 24
BMP7 (homodimer) 0.016 0.072 -9999 0 -0.42 13 13
NUP214 0.035 0.021 -9999 0 -0.42 1 1
BMP6/FETUA 0.044 0.041 -9999 0 -0.3 6 6
SMAD1/SKI 0.027 0.08 -9999 0 -0.31 8 8
SMAD6 0.035 0.008 -9999 0 -10000 0 0
CTDSP2 0.034 0.029 -9999 0 -0.42 2 2
BMP2-4/FETUA 0.017 0.12 -9999 0 -0.26 69 69
MAP3K7IP1 0.034 0.009 -9999 0 -10000 0 0
GREM1 -0.002 0.12 -9999 0 -0.42 40 40
BMPR2 (homodimer) 0.034 0.029 -9999 0 -0.42 2 2
GADD34/PP1CA 0.06 0.039 -9999 0 -0.26 4 4
BMPR1A-1B (homodimer) 0.02 0.087 -9999 0 -0.3 34 34
CHRDL1 0.03 0.037 -9999 0 -0.42 3 3
ENDOFIN/SMAD1 0.026 0.08 -9999 0 -0.31 7 7
SMAD6-7/SMURF1/SMAD1 0.055 0.086 -9999 0 -0.31 5 5
SMAD6/SMURF1 0.036 0.006 -9999 0 -10000 0 0
BAMBI -0.054 0.17 -9999 0 -0.42 93 93
SMURF2 0.028 0.042 -9999 0 -0.42 4 4
BMP2-4/CHRDL1 0.014 0.12 -9999 0 -0.27 75 75
BMP2-4/GREM1 -0.009 0.15 -9999 0 -0.29 101 101
SMAD7 0.034 0.021 -9999 0 -0.42 1 1
SMAD8A/SMAD8A/SMAD4 -0.023 0.17 -9999 0 -0.44 59 59
SMAD1/SMAD6 0.026 0.08 -9999 0 -0.33 6 6
TAK1/SMAD6 0.048 0.017 -9999 0 -10000 0 0
BMP7 0.016 0.073 -9999 0 -0.42 13 13
BMP6 0.027 0.05 -9999 0 -0.42 6 6
MAP3K7IP2 0.032 0.03 -9999 0 -0.42 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.018 0.11 -9999 0 -0.33 36 36
PPM1A 0.034 0.021 -9999 0 -0.42 1 1
SMAD1/SMURF2 0.022 0.076 -9999 0 -0.32 6 6
SMAD7/SMURF1 0.05 0.02 -9999 0 -0.3 1 1
CTDSPL 0.029 0.054 -9999 0 -0.42 7 7
PPP1CA 0.031 0.03 -9999 0 -0.42 2 2
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.034 0.029 -9999 0 -0.42 2 2
PPP1R15A 0.034 0.021 -9999 0 -0.42 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.034 0.14 -9999 0 -0.41 36 36
CHRD 0.029 0.046 -9999 0 -0.42 5 5
BMPR2 0.034 0.029 -9999 0 -0.42 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.03 0.12 -9999 0 -0.38 31 31
BMP4 -0.028 0.15 -9999 0 -0.42 65 65
FST 0.023 0.064 -9999 0 -0.42 10 10
BMP2-4/NOG 0.012 0.12 -9999 0 -0.26 72 72
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.052 0.097 -9999 0 -0.23 45 45
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.028 0.057 -10000 0 -0.42 8 8
alphaV beta3 Integrin 0.036 0.071 -10000 0 -0.31 19 19
PTK2 -0.025 0.14 -10000 0 -0.43 36 36
positive regulation of JNK cascade -0.002 0.13 -10000 0 -0.32 44 44
CDC42/GDP 0.009 0.17 -10000 0 -0.42 44 44
Rac1/GDP 0.01 0.16 -10000 0 -0.41 45 45
RAP1B 0.033 0.03 -10000 0 -0.42 2 2
RAP1A 0.031 0.045 -10000 0 -0.42 5 5
CTNNB1 0.025 0.067 -10000 0 -0.42 11 11
CDC42/GTP 0 0.16 -10000 0 -0.4 42 42
nectin-3/I-afadin 0.022 0.098 -10000 0 -0.32 35 35
RAPGEF1 -0.016 0.16 -10000 0 -0.44 48 48
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.021 0.18 -10000 0 -0.47 61 61
PDGFB-D/PDGFRB 0.028 0.057 -10000 0 -0.42 8 8
TLN1 -0.015 0.074 0.19 4 -0.34 16 20
Rap1/GTP -0.006 0.12 -10000 0 -0.33 45 45
IQGAP1 0.035 0.008 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.047 0.064 -10000 0 -0.23 22 22
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.022 0.098 -10000 0 -0.32 35 35
PVR 0.031 0.041 -10000 0 -0.42 4 4
Necl-5(dimer) 0.031 0.041 -10000 0 -0.42 4 4
mol:GDP -0.012 0.19 -10000 0 -0.51 45 45
MLLT4 0.02 0.078 -10000 0 -0.42 15 15
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
PI3K 0.054 0.12 -10000 0 -0.28 47 47
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.033 0.064 -10000 0 -0.3 16 16
positive regulation of lamellipodium assembly 0.005 0.12 -10000 0 -0.32 43 43
PVRL1 0.03 0.024 -10000 0 -0.42 1 1
PVRL3 0.013 0.097 -10000 0 -0.42 24 24
PVRL2 0.026 0.064 -10000 0 -0.42 10 10
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
CDH1 -0.011 0.13 -10000 0 -0.42 45 45
CLDN1 -0.047 0.17 -10000 0 -0.42 86 86
JAM-A/CLDN1 0.002 0.14 -10000 0 -0.27 87 87
SRC -0.035 0.2 -10000 0 -0.51 64 64
ITGB3 0.029 0.046 -10000 0 -0.42 5 5
nectin-1(dimer)/I-afadin/I-afadin 0.033 0.064 -10000 0 -0.3 16 16
FARP2 -0.017 0.2 -10000 0 -0.53 44 44
RAC1 0.035 0.006 -10000 0 -10000 0 0
CTNNA1 0.035 0.021 -10000 0 -0.42 1 1
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.038 0.097 -10000 0 -0.28 38 38
nectin-1/I-afadin 0.033 0.064 -10000 0 -0.3 16 16
nectin-2/I-afadin 0.032 0.076 -10000 0 -0.3 24 24
RAC1/GTP/IQGAP1/filamentous actin 0.046 0.013 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.035 0.093 -10000 0 -0.28 36 36
CDC42/GTP/IQGAP1/filamentous actin 0.045 0.014 -10000 0 -10000 0 0
F11R 0.026 0.038 -10000 0 -0.42 3 3
positive regulation of filopodium formation -0.002 0.13 -10000 0 -0.32 44 44
alphaV/beta3 Integrin/Talin 0.008 0.11 0.27 1 -0.39 19 20
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.076 -10000 0 -0.3 24 24
nectin-2(dimer)/I-afadin/I-afadin 0.032 0.076 -10000 0 -0.3 24 24
PIP5K1C -0.011 0.077 -10000 0 -0.36 16 16
VAV2 -0.006 0.19 -10000 0 -0.51 39 39
RAP1/GDP 0.01 0.16 -10000 0 -0.39 44 44
ITGAV 0.022 0.078 -10000 0 -0.42 15 15
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.035 0.1 -10000 0 -0.28 42 42
nectin-3(dimer)/I-afadin/I-afadin 0.022 0.098 -10000 0 -0.32 35 35
Rac1/GTP 0.008 0.15 -10000 0 -0.39 43 43
PTPRM -0.006 0.089 -10000 0 -0.27 40 40
E-cadherin/beta catenin/alpha catenin 0.025 0.12 -10000 0 -0.22 78 78
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.035 0.008 -10000 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.026 0.004 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0.032 0.03 -10000 0 -0.42 2 2
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.01 0.11 -10000 0 -0.33 39 39
IRAK/TOLLIP 0.041 0.017 0.18 5 -10000 0 5
IKBKB 0.03 0.014 -10000 0 -10000 0 0
IKBKG 0.036 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.026 0.09 -10000 0 -0.3 35 35
IL1A 0.032 0.041 -10000 0 -0.42 4 4
IL1B -0.023 0.11 -10000 0 -0.34 53 53
IRAK/TRAF6/p62/Atypical PKCs 0.059 0.05 -10000 0 -0.21 12 12
IL1R2 0.004 0.11 -10000 0 -0.42 31 31
IL1R1 -0.005 0.13 -10000 0 -0.42 43 43
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.022 0.12 -10000 0 -0.4 29 29
TOLLIP 0.035 0.007 -10000 0 -10000 0 0
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.031 0.013 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.06 0.034 -10000 0 -0.26 2 2
IKK complex/ELKS 0.025 0.079 0.27 1 -0.32 9 10
JUN -0.028 0.068 0.16 17 -0.23 23 40
MAP3K7 0.033 0.011 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.006 0.15 -10000 0 -0.28 94 94
IL1 alpha/IL1R1/IL1RAP/MYD88 0.052 0.098 -10000 0 -0.23 50 50
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.063 0.1 -10000 0 -0.22 53 53
IL1 beta fragment/IL1R1/IL1RAP -0.011 0.14 -10000 0 -0.29 87 87
NFKB1 0.036 0.005 -10000 0 -10000 0 0
MAPK8 -0.014 0.059 0.18 25 -0.25 4 29
IRAK1 0.018 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.003 0.13 -10000 0 -0.32 73 73
IRAK4 0.033 0.035 -10000 0 -0.42 3 3
PRKCI 0.025 0.064 -10000 0 -0.42 10 10
TRAF6 0.035 0.021 -10000 0 -0.42 1 1
PI3K 0.036 0.065 -10000 0 -0.3 17 17
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.018 0.13 -10000 0 -0.38 39 39
CHUK 0.026 0.067 -10000 0 -0.42 11 11
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.011 0.14 -10000 0 -0.29 87 87
IL1 beta/IL1R2 -0.019 0.13 -10000 0 -0.3 85 85
IRAK/TRAF6/TAK1/TAB1/TAB2 0.075 0.045 -10000 0 -0.21 3 3
NF kappa B1 p50/RelA -0.004 0.13 -10000 0 -0.26 91 91
IRAK3 0.027 0.046 -10000 0 -0.42 5 5
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.001 0.13 -10000 0 -0.27 88 88
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.009 0.084 -10000 0 -0.23 53 53
IL1 alpha/IL1R1/IL1RAP 0.038 0.095 -10000 0 -0.26 46 46
RELA 0.035 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0.034 0.009 -10000 0 -10000 0 0
SQSTM1 0.034 0.021 -10000 0 -0.42 1 1
MYD88 0.031 0.041 -10000 0 -0.42 4 4
IRAK/TRAF6/MEKK3 0.053 0.03 -10000 0 -0.22 1 1
IL1RAP 0.033 0.022 -10000 0 -0.42 1 1
UBE2N 0.035 0.006 -10000 0 -10000 0 0
IRAK/TRAF6 -0.015 0.11 -10000 0 -0.24 86 86
CASP1 0.002 0.11 -10000 0 -0.42 30 30
IL1RN/IL1R2 0.003 0.12 -10000 0 -0.32 62 62
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.003 0.14 -10000 0 -0.28 88 88
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.003 0.11 -10000 0 -0.32 45 45
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
IL1RN 0.001 0.12 -10000 0 -0.42 37 37
TRAF6/TAK1/TAB1/TAB2 0.071 0.043 -10000 0 -0.21 3 3
MAP2K6 -0.01 0.057 0.18 22 -0.39 1 23
Aurora B 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
Condensin I complex -0.007 0.034 -10000 0 -0.097 60 60
STMN1 0.005 0.051 -10000 0 -0.34 10 10
Aurora B/RasGAP/Survivin 0.028 0.1 -10000 0 -0.28 43 43
Chromosomal passenger complex/Cul3 protein complex -0.044 0.12 -10000 0 -0.37 36 36
BIRC5 -0.004 0.12 -10000 0 -0.44 38 38
DES -0.062 0.26 -10000 0 -0.68 72 72
Aurora C/Aurora B/INCENP 0.053 0.049 -10000 0 -0.24 10 10
Aurora B/TACC1 0.023 0.064 -10000 0 -0.25 23 23
Aurora B/PP2A 0.045 0.034 -10000 0 -0.31 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.009 0.022 -10000 0 -0.18 6 6
mitotic metaphase/anaphase transition 0.001 0.006 0.012 76 -0.01 2 78
NDC80 0.005 0.025 -10000 0 -0.31 3 3
Cul3 protein complex 0.015 0.12 -10000 0 -0.26 76 76
KIF2C -0.056 0.21 -10000 0 -0.65 50 50
PEBP1 -0.001 0.004 0.01 2 -0.014 38 40
KIF20A 0.004 0.12 -10000 0 -0.42 35 35
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.04 0.051 -10000 0 -0.31 9 9
SEPT1 0.031 0.023 -10000 0 -0.42 1 1
SMC2 0 0 -10000 0 -10000 0 0
SMC4 0 0 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.044 0.18 -10000 0 -0.51 60 60
PSMA3 0.035 0.006 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.004 0.009 53 -0.009 7 60
H3F3B 0.014 0.028 -10000 0 -0.29 4 4
AURKB 0.03 0.04 -10000 0 -0.45 3 3
AURKC 0.034 0.021 -10000 0 -0.42 1 1
CDCA8 0.017 0.085 -10000 0 -0.44 16 16
cytokinesis -0.045 0.23 -10000 0 -0.64 50 50
Aurora B/Septin1 -0.026 0.22 -10000 0 -0.59 47 47
AURKA 0 0.004 0.009 53 -0.009 7 60
INCENP 0.025 0.053 -10000 0 -0.44 6 6
KLHL13 -0.034 0.16 -10000 0 -0.42 73 73
BUB1 -0.012 0.14 -10000 0 -0.42 52 52
hSgo1/Aurora B/Survivin 0.025 0.12 -10000 0 -0.34 39 39
EVI5 0.031 0.041 -10000 0 -0.42 4 4
RhoA/GTP -0.021 0.22 -10000 0 -0.55 53 53
SGOL1 0.02 0.08 -10000 0 -0.42 16 16
CENPA -0.039 0.15 -10000 0 -0.31 82 82
NCAPG 0 0 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.045 0.034 -10000 0 -0.31 3 3
NCAPD2 0 0 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.044 0.043 -10000 0 -0.31 6 6
RHOA 0.026 0.061 -10000 0 -0.42 9 9
NCAPH 0 0 -10000 0 -10000 0 0
NPM1 -0.02 0.12 -10000 0 -0.32 57 57
RASA1 0.029 0.05 -10000 0 -0.42 6 6
KLHL9 0.032 0.03 -10000 0 -0.42 2 2
mitotic prometaphase -0.001 0.004 0.01 2 -0.014 38 40
proteasomal ubiquitin-dependent protein catabolic process 0.045 0.034 -10000 0 -0.31 3 3
PPP1CC 0.033 0.035 -10000 0 -0.42 3 3
Centraspindlin -0.03 0.23 -10000 0 -0.6 53 53
RhoA/GDP 0.02 0.043 -10000 0 -0.3 9 9
NSUN2 -0.017 0.11 -10000 0 -0.3 57 57
MYLK 0.006 0.059 -10000 0 -0.3 17 17
KIF23 0.006 0.11 -10000 0 -0.43 30 30
VIM -0.006 0.072 -10000 0 -0.3 27 27
RACGAP1 0.02 0.085 -10000 0 -0.43 17 17
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.022 0.13 -10000 0 -0.34 58 58
Chromosomal passenger complex -0.048 0.18 -10000 0 -0.46 59 59
Chromosomal passenger complex/EVI5 0.04 0.13 -10000 0 -0.33 48 48
TACC1 0.011 0.089 -10000 0 -0.42 20 20
PPP2R5D 0.035 0.006 -10000 0 -10000 0 0
CUL3 0.032 0.041 -10000 0 -0.42 4 4
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
mTOR signaling pathway

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
GBL 0.032 0.023 -10000 0 -0.42 1 1
MKNK1 0.035 0.006 -10000 0 -10000 0 0
mol:PIP3 -0.024 0.1 0.26 5 -0.26 65 70
FRAP1 -0.008 0.11 -10000 0 -0.52 13 13
AKT1 -0.025 0.096 0.17 27 -0.25 60 87
INSR 0.034 0.029 -10000 0 -0.42 2 2
Insulin Receptor/Insulin 0.045 0.026 -10000 0 -0.25 3 3
mol:GTP 0.011 0.097 0.23 6 -0.21 54 60
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.006 0.051 -10000 0 -0.2 11 11
TSC2 0.032 0.023 -10000 0 -0.42 1 1
RHEB/GDP 0.004 0.081 -10000 0 -0.2 50 50
TSC1 0.036 0.005 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.009 0.11 -10000 0 -0.3 65 65
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.011 0.068 -10000 0 -0.24 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0 0.092 0.3 1 -0.34 14 15
MAP3K5 -0.015 0.086 0.19 7 -0.25 51 58
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
apoptosis -0.015 0.086 0.19 7 -0.25 51 58
mol:LY294002 0 0 0.001 2 -0.001 62 64
EIF4B -0.002 0.085 0.28 2 -0.3 14 16
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.012 0.082 0.26 1 -0.28 14 15
eIF4E/eIF4G1/eIF4A1 0.002 0.075 -10000 0 -0.31 14 14
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.002 0.12 -10000 0 -0.27 76 76
mTOR/RHEB/GTP/Raptor/GBL 0.01 0.061 0.22 3 -0.21 11 14
FKBP1A 0.035 0.007 -10000 0 -10000 0 0
RHEB/GTP 0.02 0.091 0.27 2 -0.27 12 14
mol:Amino Acids 0 0 0.001 2 -0.001 62 64
FKBP12/Rapamycin 0.026 0.006 -10000 0 -10000 0 0
PDPK1 -0.033 0.094 0.17 23 -0.26 60 83
EIF4E 0.036 0.005 -10000 0 -10000 0 0
ASK1/PP5C -0.035 0.22 -10000 0 -0.59 57 57
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.017 0.054 -10000 0 -0.38 1 1
TSC1/TSC2 0.013 0.1 0.25 6 -0.23 54 60
tumor necrosis factor receptor activity 0 0 0.001 62 -0.001 2 64
RPS6 0.034 0.022 -10000 0 -0.42 1 1
PPP5C 0.032 0.041 -10000 0 -0.42 4 4
EIF4G1 0.031 0.041 -10000 0 -0.42 4 4
IRS1 -0.031 0.11 -10000 0 -0.32 65 65
INS 0.034 0.021 -10000 0 -0.42 1 1
PTEN 0.027 0.06 -10000 0 -0.42 9 9
PDK2 -0.032 0.1 0.17 27 -0.26 66 93
EIF4EBP1 -0.068 0.32 -10000 0 -1.2 38 38
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
PPP2R5D -0.007 0.1 -10000 0 -0.46 13 13
peptide biosynthetic process 0.017 0.03 0.19 5 -0.23 5 10
RHEB 0.035 0.007 -10000 0 -10000 0 0
EIF4A1 0.032 0.012 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 17 -0.003 4 21
EEF2 0.017 0.03 0.19 5 -0.23 5 10
eIF4E/4E-BP1 -0.048 0.3 -10000 0 -1.1 38 38
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.003 0.12 -10000 0 -0.31 52 52
VEGFR1 homodimer/NRP1 -0.017 0.11 -10000 0 -0.31 52 52
mol:DAG -0.009 0.11 -10000 0 -0.3 43 43
VEGFR1 homodimer/NRP1/VEGFR 121 -0.015 0.098 -10000 0 -0.28 52 52
CaM/Ca2+ 0.009 0.11 -10000 0 -0.54 9 9
HIF1A -0.006 0.14 -10000 0 -0.41 53 53
GAB1 0.027 0.061 -10000 0 -0.42 9 9
AKT1 -0.016 0.11 0.33 1 -0.43 16 17
PLCG1 -0.009 0.11 -10000 0 -0.3 43 43
NOS3 0 0.11 0.48 1 -0.46 17 18
CBL 0.032 0.012 -10000 0 -10000 0 0
mol:NO 0.002 0.11 0.36 3 -0.45 17 20
FLT1 -0.015 0.12 -10000 0 -0.37 47 47
PGF 0.031 0.041 -10000 0 -0.42 4 4
VEGFR1 homodimer/NRP2/VEGFR121 0.002 0.11 -10000 0 -0.29 52 52
CALM1 0.035 0.007 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
eNOS/Hsp90 -0.004 0.11 -10000 0 -0.43 17 17
endothelial cell proliferation -0.002 0.12 0.3 8 -0.46 14 22
mol:Ca2+ -0.009 0.11 -10000 0 -0.3 43 43
MAPK3 -0.024 0.083 0.35 1 -0.48 10 11
MAPK1 -0.028 0.086 0.35 1 -0.49 9 10
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
PLGF homodimer 0.031 0.041 -10000 0 -0.42 4 4
PRKACA 0.036 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.027 0.054 -10000 0 -0.42 7 7
VEGFA homodimer 0 0 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer -0.017 0.11 -10000 0 -0.31 52 52
platelet activating factor biosynthetic process -0.005 0.1 0.33 5 -0.45 10 15
PI3K 0.026 0.13 -10000 0 -0.27 67 67
PRKCA -0.027 0.093 0.21 9 -0.53 9 18
PRKCB -0.028 0.095 0.18 15 -0.53 9 24
VEGFR1 homodimer/PLGF homodimer 0.002 0.12 -10000 0 -0.31 55 55
VEGFA 0 0 -10000 0 -10000 0 0
VEGFB 0.034 0.021 -10000 0 -0.42 1 1
mol:IP3 -0.009 0.11 -10000 0 -0.3 43 43
RASA1 -0.013 0.11 -10000 0 -0.3 49 49
NRP2 0.034 0.021 -10000 0 -0.42 1 1
VEGFR1 homodimer -0.015 0.12 -10000 0 -0.37 47 47
VEGFB homodimer 0.034 0.021 -10000 0 -0.42 1 1
NCK1 0.034 0.021 -10000 0 -0.42 1 1
eNOS/Caveolin-1 0.015 0.12 0.36 3 -0.46 18 21
PTPN11 0.036 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.024 0.13 -10000 0 -0.27 67 67
mol:L-citrulline 0.002 0.11 0.36 3 -0.45 17 20
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.016 0.11 -10000 0 -0.27 48 48
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.002 0.11 -10000 0 -0.28 53 53
CD2AP 0.035 0.007 -10000 0 -10000 0 0
PI3K/GAB1 0.032 0.14 -10000 0 -0.26 68 68
PDPK1 -0.007 0.11 0.35 2 -0.46 12 14
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.003 0.11 -10000 0 -0.28 52 52
mol:NADP 0.002 0.11 0.36 3 -0.45 17 20
HSP90AA1 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.015 0.1 -10000 0 -0.27 48 48
VEGFR1 homodimer/NRP2 0.003 0.12 -10000 0 -0.32 52 52
PDGFR-alpha signaling pathway

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
PDGFRA -0.004 0.11 -10000 0 -0.44 29 29
PDGF/PDGFRA/CRKL 0.02 0.088 -10000 0 -0.3 32 32
positive regulation of JUN kinase activity 0.048 0.073 -10000 0 -0.23 22 22
CRKL 0.031 0.041 -10000 0 -0.42 4 4
PDGF/PDGFRA/Caveolin-3 0.022 0.086 -10000 0 -0.3 30 30
AP1 -0.14 0.3 -10000 0 -0.81 78 78
mol:IP3 -0.014 0.08 -10000 0 -0.32 27 27
PLCG1 -0.014 0.08 -10000 0 -0.32 27 27
PDGF/PDGFRA/alphaV Integrin 0.014 0.1 -10000 0 -0.32 42 42
RAPGEF1 0.036 0.004 -10000 0 -10000 0 0
CRK 0.032 0.023 -10000 0 -0.42 1 1
mol:Ca2+ -0.014 0.08 -10000 0 -0.32 27 27
CAV3 0.034 0.021 -10000 0 -0.42 1 1
CAV1 0.027 0.054 -10000 0 -0.42 7 7
SHC/Grb2/SOS1 0.05 0.074 -10000 0 -0.23 22 22
PDGF/PDGFRA/Shf 0.022 0.086 -10000 0 -0.3 30 30
FOS -0.14 0.3 0.31 2 -0.8 78 80
JUN -0.053 0.083 -10000 0 -0.34 36 36
oligodendrocyte development 0.014 0.1 -10000 0 -0.32 42 42
GRB2 0.033 0.011 -10000 0 -10000 0 0
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
mol:DAG -0.014 0.08 -10000 0 -0.32 27 27
PDGF/PDGFRA -0.004 0.11 -10000 0 -0.44 29 29
actin cytoskeleton reorganization 0.02 0.09 -10000 0 -0.3 33 33
SRF 0.018 0.012 -10000 0 -10000 0 0
SHC1 0.028 0.025 -10000 0 -0.42 1 1
PI3K 0.034 0.099 -10000 0 -0.28 40 40
PDGF/PDGFRA/Crk/C3G 0.044 0.079 -10000 0 -0.25 30 30
JAK1 -0.01 0.079 -10000 0 -0.31 30 30
ELK1/SRF -0.026 0.071 0.15 24 -0.26 30 54
SHB 0.031 0.046 -10000 0 -0.42 5 5
SHF 0.033 0.022 -10000 0 -0.42 1 1
CSNK2A1 0.04 0.021 -10000 0 -10000 0 0
GO:0007205 -0.023 0.084 -10000 0 -0.35 28 28
SOS1 0.035 0.021 -10000 0 -0.42 1 1
Ras protein signal transduction 0.048 0.073 -10000 0 -0.23 22 22
PDGF/PDGFRA/SHB 0.02 0.09 -10000 0 -0.3 33 33
PDGF/PDGFRA/Caveolin-1 0.017 0.097 -10000 0 -0.33 33 33
ITGAV 0.022 0.078 -10000 0 -0.42 15 15
ELK1 -0.036 0.08 0.24 2 -0.32 30 32
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
PDGF/PDGFRA/Crk 0.019 0.085 -10000 0 -0.3 30 30
JAK-STAT cascade -0.01 0.079 -10000 0 -0.31 30 30
cell proliferation 0.022 0.086 -10000 0 -0.3 30 30
Arf6 downstream pathway

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
PLAUR -0.029 0.23 -10000 0 -0.98 28 28
regulation of axonogenesis -0.001 0.058 0.29 12 -10000 0 12
myoblast fusion -0.006 0.11 0.4 31 -10000 0 31
mol:GTP 0.01 0.066 -10000 0 -0.23 34 34
regulation of calcium-dependent cell-cell adhesion -0.047 0.082 0.24 33 -10000 0 33
ARF1/GTP 0.024 0.056 -10000 0 -0.19 24 24
mol:GM1 0 0.047 -10000 0 -0.18 30 30
mol:Choline -0.001 0.057 -10000 0 -0.22 27 27
lamellipodium assembly -0.007 0.12 -10000 0 -0.45 34 34
MAPK3 0.009 0.085 -10000 0 -0.33 29 29
ARF6/GTP/NME1/Tiam1 0.048 0.082 -10000 0 -0.24 33 33
ARF1 0.027 0.025 -10000 0 -0.42 1 1
ARF6/GDP 0.006 0.11 -10000 0 -0.4 31 31
ARF1/GDP 0.008 0.099 -10000 0 -0.36 29 29
ARF6 0.031 0.056 -10000 0 -0.32 5 5
RAB11A 0.034 0.021 -10000 0 -0.42 1 1
TIAM1 0.025 0.06 -10000 0 -0.42 8 8
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.009 0.086 -10000 0 -0.34 28 28
actin filament bundle formation -0.016 0.11 0.37 34 -10000 0 34
KALRN 0.001 0.082 -10000 0 -0.31 31 31
RAB11FIP3/RAB11A 0.047 0.043 -10000 0 -0.3 7 7
RhoA/GDP 0.017 0.11 -10000 0 -0.37 34 34
NME1 0.031 0.02 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.11 -10000 0 -0.37 33 33
substrate adhesion-dependent cell spreading 0.01 0.066 -10000 0 -0.23 34 34
cortical actin cytoskeleton organization -0.007 0.13 -10000 0 -0.46 34 34
RAC1 0.035 0.006 -10000 0 -10000 0 0
liver development 0.01 0.066 -10000 0 -0.23 34 34
ARF6/GTP 0.01 0.066 -10000 0 -0.23 34 34
RhoA/GTP 0.025 0.071 -10000 0 -0.21 38 38
mol:GDP -0.009 0.1 -10000 0 -0.4 32 32
ARF6/GTP/RAB11FIP3/RAB11A 0.048 0.067 -10000 0 -0.18 34 34
RHOA 0.026 0.061 -10000 0 -0.42 9 9
PLD1 0.007 0.068 -10000 0 -0.23 32 32
RAB11FIP3 0.031 0.049 -10000 0 -0.42 6 6
tube morphogenesis -0.007 0.12 -10000 0 -0.45 34 34
ruffle organization 0.001 0.058 -10000 0 -0.29 12 12
regulation of epithelial cell migration 0.01 0.066 -10000 0 -0.23 34 34
PLD2 0.012 0.052 -10000 0 -0.2 23 23
PIP5K1A 0.001 0.058 -10000 0 -0.3 12 12
mol:Phosphatidic acid -0.001 0.057 -10000 0 -0.22 27 27
Rac1/GTP -0.007 0.13 -10000 0 -0.46 34 34
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.045 0.086 -10000 0 -0.22 39 39
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.031 0.041 -10000 0 -0.42 4 4
STAT1 (dimer)/Cbp/p300 0.035 0.1 0.31 2 -0.27 28 30
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.052 0.051 -10000 0 -0.26 4 4
antigen processing and presentation of peptide antigen via MHC class I -0.016 0.093 -10000 0 -0.25 48 48
CaM/Ca2+ 0.047 0.085 -10000 0 -0.21 39 39
RAP1A 0.031 0.045 -10000 0 -0.42 5 5
STAT1 (dimer)/SHP2 0.017 0.095 0.28 3 -0.24 47 50
AKT1 -0.01 0.093 0.28 11 -0.23 24 35
MAP2K1 -0.022 0.081 0.27 3 -0.22 44 47
MAP3K11 0.005 0.079 0.26 5 -0.21 41 46
IFNGR1 0.03 0.022 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.005 0.13 -10000 0 -0.43 22 22
Rap1/GTP 0.001 0.067 -10000 0 -0.26 12 12
CRKL/C3G 0.047 0.034 -10000 0 -0.3 4 4
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.059 0.093 -10000 0 -0.22 39 39
CEBPB -0.016 0.16 0.41 1 -0.51 30 31
STAT3 0.028 0.031 -10000 0 -0.42 2 2
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.054 0.13 -10000 0 -0.84 6 6
STAT1 -0.002 0.09 0.29 3 -0.24 47 50
CALM1 0.035 0.007 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.007 0.12 -10000 0 -0.42 38 38
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
STAT1 (dimer)/PIAS1 0.017 0.093 0.29 3 -0.23 46 49
CEBPB/PTGES2/Cbp/p300 0.005 0.11 -10000 0 -0.33 31 31
mol:Ca2+ 0.042 0.083 -10000 0 -0.21 39 39
MAPK3 -0.015 0.14 -10000 0 -0.69 10 10
STAT1 (dimer) -0.011 0.13 -10000 0 -0.34 47 47
MAPK1 -0.044 0.2 0.4 1 -0.72 33 34
JAK2 0.028 0.036 -10000 0 -0.42 2 2
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
JAK1 0.029 0.04 -10000 0 -0.41 3 3
CAMK2D 0.022 0.075 -10000 0 -0.42 14 14
DAPK1 -0.007 0.13 0.35 1 -0.53 17 18
SMAD7 -0.001 0.058 0.16 8 -0.16 20 28
CBL/CRKL/C3G 0.034 0.084 0.3 2 -0.21 25 27
PI3K 0.036 0.095 -10000 0 -0.22 48 48
IFNG -0.007 0.12 -10000 0 -0.42 38 38
apoptosis -0.061 0.18 0.31 1 -0.42 86 87
CAMK2G 0.036 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.028 0.031 -10000 0 -0.42 2 2
CAMK2A 0.035 0.021 -10000 0 -0.42 1 1
CAMK2B -0.012 0.13 -10000 0 -0.42 47 47
FRAP1 -0.016 0.085 0.28 9 -0.26 10 19
PRKCD -0.011 0.092 0.29 10 -0.27 12 22
RAP1B 0.033 0.03 -10000 0 -0.42 2 2
negative regulation of cell growth -0.016 0.093 -10000 0 -0.25 48 48
PTPN2 0.035 0.008 -10000 0 -10000 0 0
EP300 0.032 0.03 -10000 0 -0.42 2 2
IRF1 -0.006 0.1 0.29 8 -0.42 15 23
STAT1 (dimer)/PIASy 0.013 0.094 0.29 3 -0.23 47 50
SOCS1 0.018 0.13 -10000 0 -1.1 6 6
mol:GDP 0.031 0.079 0.28 2 -0.21 25 27
CASP1 -0.012 0.083 0.16 7 -0.24 42 49
PTGES2 0.036 0.005 -10000 0 -10000 0 0
IRF9 0 0.049 0.12 4 -0.15 19 23
mol:PI-3-4-5-P3 0.021 0.086 -10000 0 -0.21 48 48
RAP1/GDP 0.025 0.08 -10000 0 -0.29 9 9
CBL 0.004 0.073 0.29 2 -0.2 39 41
MAP3K1 -0.005 0.089 0.26 5 -0.22 57 62
PIAS1 0.035 0.007 -10000 0 -10000 0 0
PIAS4 0.032 0.036 -10000 0 -0.42 3 3
antigen processing and presentation of peptide antigen via MHC class II -0.016 0.093 -10000 0 -0.25 48 48
PTPN11 0.008 0.08 0.29 4 -0.21 39 43
CREBBP 0.033 0.011 -10000 0 -10000 0 0
RAPGEF1 0.036 0.004 -10000 0 -10000 0 0
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.001 0.047 0.2 23 -0.12 5 28
BUB1B -0.019 0.097 -10000 0 -0.32 38 38
PLK1 0.003 0.033 0.091 10 -0.09 19 29
PLK1S1 0.002 0.019 0.053 11 -0.048 20 31
KIF2A 0.003 0.03 0.08 10 -0.081 19 29
regulation of mitotic centrosome separation 0.003 0.033 0.09 10 -0.089 19 29
GOLGA2 0.036 0.005 -10000 0 -10000 0 0
Hec1/SPC24 -0.008 0.019 -10000 0 -0.071 26 26
WEE1 -0.006 0.094 -10000 0 -0.35 27 27
cytokinesis -0.022 0.14 0.16 1 -0.39 50 51
PP2A-alpha B56 -0.036 0.28 -10000 0 -0.7 72 72
AURKA 0.002 0.02 0.06 11 -0.05 12 23
PICH/PLK1 -0.018 0.095 -10000 0 -0.33 35 35
CENPE -0.012 0.068 0.2 3 -0.25 31 34
RhoA/GTP 0.02 0.043 -10000 0 -0.3 9 9
positive regulation of microtubule depolymerization 0.003 0.03 0.08 10 -0.08 19 29
PPP2CA 0.031 0.045 -10000 0 -0.42 5 5
FZR1 0.035 0.006 -10000 0 -10000 0 0
TPX2 -0.008 0.078 -10000 0 -0.27 39 39
PAK1 0.014 0.086 -10000 0 -0.43 18 18
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.033 0.029 -10000 0 -0.42 2 2
CLSPN 0.004 0.057 -10000 0 -0.28 18 18
GORASP1 0.034 0.022 -10000 0 -0.42 1 1
metaphase 0.002 0.006 0.019 46 -10000 0 46
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.002 0.019 0.053 11 -0.048 20 31
G2 phase of mitotic cell cycle -0.001 0.002 0.011 2 -10000 0 2
STAG2 0.036 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.007 0.11 -10000 0 -0.51 20 20
spindle elongation 0.003 0.033 0.09 10 -0.089 19 29
ODF2 0.036 0.005 -10000 0 -10000 0 0
BUB1 -0.074 0.29 -10000 0 -0.75 74 74
TPT1 -0.009 0.063 -10000 0 -0.19 52 52
CDC25C -0.014 0.11 -10000 0 -0.36 42 42
CDC25B 0.028 0.045 -10000 0 -0.44 4 4
SGOL1 0.001 0.047 0.12 5 -0.2 23 28
RHOA 0.026 0.061 -10000 0 -0.42 9 9
CCNB1/CDK1 0.028 0.13 -10000 0 -0.37 41 41
CDC14B 0.005 0.024 -10000 0 -0.3 3 3
CDC20 0.017 0.087 -10000 0 -0.42 19 19
PLK1/PBIP1 -0.005 0.056 0.087 3 -0.21 28 31
mitosis 0 0.003 0.013 10 -10000 0 10
FBXO5 -0.003 0.05 0.13 9 -0.2 10 19
CDC2 0.014 0.097 -10000 0 -0.44 22 22
NDC80 0 0 -10000 0 -10000 0 0
metaphase plate congression 0.004 0.054 -10000 0 -0.25 20 20
ERCC6L -0.013 0.11 -10000 0 -0.35 41 41
NLP/gamma Tubulin 0.007 0.028 0.072 15 -0.083 10 25
microtubule cytoskeleton organization -0.009 0.063 -10000 0 -0.19 52 52
G2/M transition DNA damage checkpoint 0 0.003 0.011 19 -10000 0 19
PPP1R12A 0.036 0.005 -10000 0 -10000 0 0
interphase 0 0.003 0.011 19 -10000 0 19
PLK1/PRC1-2 0.014 0.11 -10000 0 -0.33 42 42
GRASP65/GM130/RAB1/GTP/PLK1 0.05 0.048 -10000 0 -0.19 2 2
RAB1A 0.035 0.021 -10000 0 -0.42 1 1
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.003 0.025 0.069 13 -0.069 13 26
mitotic prometaphase -0.001 0.004 0.018 20 -10000 0 20
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.054 -10000 0 -0.28 7 7
microtubule-based process 0.006 0.078 0.12 2 -0.22 44 46
Golgi organization 0.003 0.033 0.09 10 -0.089 19 29
Cohesin/SA2 0.021 0.035 -10000 0 -0.11 1 1
PPP1CB/MYPT1 0.052 0.009 -10000 0 -10000 0 0
KIF20A 0.003 0.12 -10000 0 -0.42 35 35
APC/C/CDC20 0.013 0.064 0.12 1 -0.25 20 21
PPP2R1A 0.035 0.007 -10000 0 -10000 0 0
chromosome segregation -0.005 0.055 0.086 3 -0.21 28 31
PRC1 0.009 0.1 -10000 0 -0.42 27 27
ECT2 0.004 0.072 0.21 29 -0.22 17 46
C13orf34 0.003 0.028 0.074 13 -0.077 16 29
NUDC 0.004 0.054 -10000 0 -0.25 20 20
regulation of attachment of spindle microtubules to kinetochore -0.018 0.096 -10000 0 -0.32 38 38
spindle assembly 0.01 0.035 0.088 22 -0.082 12 34
spindle stabilization 0.002 0.019 0.053 11 -0.047 20 31
APC/C/HCDH1 0.03 0.023 -10000 0 -0.25 3 3
MKLP2/PLK1 0.006 0.078 0.12 2 -0.22 44 46
CCNB1 0.011 0.1 -10000 0 -0.44 25 25
PPP1CB 0.036 0.005 -10000 0 -10000 0 0
BTRC 0.034 0.022 -10000 0 -0.42 1 1
ROCK2 0.007 0.059 -10000 0 -0.33 8 8
TUBG1 0.009 0.04 -10000 0 -0.18 16 16
G2/M transition of mitotic cell cycle -0.022 0.11 -10000 0 -0.37 40 40
MLF1IP -0.009 0.069 -10000 0 -0.3 27 27
INCENP 0.028 0.051 -10000 0 -0.43 6 6
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.047 0.055 -10000 0 -0.23 16 16
RGS9BP -0.023 0.15 -10000 0 -0.42 61 61
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.024 0.061 -10000 0 -0.26 19 19
mol:ADP 0.008 0.019 -10000 0 -0.3 2 2
GNAT2 0.019 0.085 -10000 0 -0.42 18 18
RGS9-1/Gbeta5/R9AP 0.007 0.12 -10000 0 -0.27 73 73
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.026 0.076 -10000 0 -0.27 30 30
GRK7 0.034 0.029 -10000 0 -0.42 2 2
CNGB3 0.022 0.051 -10000 0 -0.42 6 6
Cone Metarhodopsin II/X-Arrestin 0.027 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.04 0.089 0.2 91 -0.24 20 111
Cone PDE6 0.02 0.13 -10000 0 -0.24 84 84
Cone Metarhodopsin II 0.022 0.016 -10000 0 -0.22 2 2
Na + (4 Units) 0.038 0.064 -10000 0 -0.24 20 20
GNAT2/GDP 0.011 0.12 -10000 0 -0.24 85 85
GNB5 0.025 0.067 -10000 0 -0.42 11 11
mol:GMP (4 units) 0.005 0.078 0.19 16 -0.25 34 50
Cone Transducin 0.051 0.059 -10000 0 -0.24 16 16
SLC24A2 0.032 0.036 -10000 0 -0.42 3 3
GNB3/GNGT2 0.048 0.023 -10000 0 -0.3 1 1
GNB3 0.034 0.009 -10000 0 -10000 0 0
GNAT2/GTP 0.015 0.06 -10000 0 -0.3 18 18
CNGA3 0.018 0.078 -10000 0 -0.42 15 15
ARR3 0.036 0.002 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.025 0.061 -10000 0 -0.26 19 19
mol:Pi 0.006 0.12 -10000 0 -0.27 73 73
Cone CNG Channel 0.034 0.099 -10000 0 -0.25 44 44
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.032 0.036 -10000 0 -0.42 3 3
RGS9 0.017 0.07 -10000 0 -0.42 12 12
PDE6C 0.03 0.05 -10000 0 -0.42 6 6
GNGT2 0.033 0.03 -10000 0 -0.42 2 2
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.021 0.075 -10000 0 -0.42 14 14
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.031 0.24 -10000 0 -0.76 23 23
PCK1 0.019 0.17 -10000 0 -0.99 5 5
HNF4A -0.01 0.25 -10000 0 -0.78 20 20
KCNJ11 -0.053 0.34 -10000 0 -0.98 44 44
AKT1 -0.001 0.17 -10000 0 -0.41 22 22
response to starvation 0.004 0.002 -10000 0 -10000 0 0
DLK1 -0.023 0.27 0.63 1 -0.81 21 22
NKX2-1 0.038 0.13 0.36 4 -0.35 6 10
ACADM -0.032 0.26 -10000 0 -0.78 27 27
TAT -0.004 0.15 -10000 0 -0.6 3 3
CEBPB 0.031 0.051 -10000 0 -0.42 6 6
CEBPA 0.03 0.07 -10000 0 -0.42 12 12
TTR -0.03 0.28 0.57 1 -0.71 45 46
PKLR 0.013 0.25 -10000 0 -0.72 21 21
APOA1 -0.028 0.28 -10000 0 -0.88 22 22
CPT1C -0.031 0.27 -10000 0 -0.82 29 29
ALAS1 0.011 0.18 -10000 0 -1.1 4 4
TFRC -0.042 0.36 -10000 0 -1.2 37 37
FOXF1 0.027 0.025 -10000 0 -0.42 1 1
NF1 0.037 0.035 -10000 0 -0.37 3 3
HNF1A (dimer) 0.008 0.02 -10000 0 -0.21 4 4
CPT1A -0.023 0.27 0.56 1 -0.86 24 25
HMGCS1 -0.021 0.24 -10000 0 -0.74 23 23
NR3C1 0.034 0.074 -10000 0 -0.4 14 14
CPT1B -0.024 0.24 -10000 0 -0.75 22 22
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.035 0.021 -10000 0 -0.42 1 1
GCK -0.025 0.25 -10000 0 -0.76 24 24
CREB1 0.042 0.029 -10000 0 -0.24 4 4
IGFBP1 0.01 0.14 -10000 0 -1.3 1 1
PDX1 0.006 0.15 -10000 0 -0.37 23 23
UCP2 -0.052 0.31 -10000 0 -0.87 44 44
ALDOB -0.024 0.26 -10000 0 -0.8 22 22
AFP -0.024 0.12 -10000 0 -0.56 6 6
BDH1 -0.034 0.26 -10000 0 -0.77 31 31
HADH -0.024 0.26 -10000 0 -0.77 25 25
F2 -0.01 0.28 -10000 0 -0.86 22 22
HNF1A 0.008 0.02 -10000 0 -0.21 4 4
G6PC 0.04 0.091 -10000 0 -1.3 1 1
SLC2A2 0.003 0.2 -10000 0 -0.88 7 7
INS 0.024 0.024 0.2 2 -0.43 1 3
FOXA1 -0.037 0.18 -10000 0 -0.4 97 97
FOXA3 0.043 0.077 -10000 0 -0.23 24 24
FOXA2 -0.011 0.32 -10000 0 -0.88 24 24
ABCC8 -0.2 0.48 -10000 0 -0.9 151 151
ALB -0.03 0.15 -10000 0 -0.95 7 7
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.019 0.11 -10000 0 -0.27 53 53
fibroblast growth factor receptor signaling pathway 0.018 0.1 -10000 0 -0.27 53 53
LAMA1 0.034 0.009 -10000 0 -10000 0 0
PRNP 0.028 0.057 -10000 0 -0.42 8 8
GPC1/SLIT2 0.013 0.11 -10000 0 -0.31 52 52
SMAD2 0.005 0.064 0.19 6 -0.24 29 35
GPC1/PrPc/Cu2+ 0.03 0.069 -10000 0 -0.26 26 26
GPC1/Laminin alpha1 0.036 0.068 -10000 0 -0.3 19 19
TDGF1 0.034 0.008 -10000 0 -10000 0 0
CRIPTO/GPC1 0.037 0.068 -10000 0 -0.3 19 19
APP/GPC1 0.016 0.1 -10000 0 -0.3 47 47
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.005 0.06 -10000 0 -0.26 25 25
FLT1 0.026 0.058 -10000 0 -0.42 8 8
GPC1/TGFB/TGFBR1/TGFBR2 0.049 0.081 -10000 0 -0.26 30 30
SERPINC1 0.028 0.025 -10000 0 -0.42 1 1
FYN 0.005 0.057 -10000 0 -0.26 23 23
FGR 0.009 0.053 -10000 0 -0.26 19 19
positive regulation of MAPKKK cascade -0.025 0.12 -10000 0 -0.34 43 43
SLIT2 0.003 0.12 -10000 0 -0.42 35 35
GPC1/NRG 0.028 0.068 -10000 0 -0.3 19 19
NRG1 0.028 0.015 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.027 0.07 -10000 0 -0.26 26 26
LYN 0.009 0.045 -10000 0 -0.25 14 14
mol:Spermine -0.003 0.058 -10000 0 -0.3 19 19
cell growth 0.018 0.1 -10000 0 -0.27 53 53
BMP signaling pathway -0.018 0.087 0.42 19 -10000 0 19
SRC 0.008 0.055 -10000 0 -0.27 19 19
TGFBR1 0.027 0.061 -10000 0 -0.42 9 9
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.013 0.08 -10000 0 -0.42 16 16
GPC1 0.018 0.087 -10000 0 -0.42 19 19
TGFBR1 (dimer) 0.027 0.06 -10000 0 -0.42 9 9
VEGFA 0 0 -10000 0 -10000 0 0
BLK 0.006 0.046 -10000 0 -0.25 15 15
HCK 0.001 0.068 -10000 0 -0.26 33 33
FGF2 -0.001 0.11 -10000 0 -0.42 34 34
FGFR1 0.02 0.064 -10000 0 -0.42 10 10
VEGFR1 homodimer 0.026 0.057 -10000 0 -0.42 8 8
TGFBR2 0.033 0.036 -10000 0 -0.42 3 3
cell death 0.016 0.1 -10000 0 -0.3 47 47
ATIII/GPC1 0.03 0.065 -10000 0 -0.3 17 17
PLA2G2A/GPC1 0.022 0.09 -10000 0 -0.3 34 34
LCK -0.019 0.095 -10000 0 -0.26 68 68
neuron differentiation 0.028 0.068 -10000 0 -0.3 19 19
PrPc/Cu2+ 0.021 0.04 -10000 0 -0.3 8 8
APP 0.008 0.11 -10000 0 -0.42 29 29
TGFBR2 (dimer) 0.033 0.036 -10000 0 -0.42 3 3
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.007 0.054 -10000 0 -0.3 15 15
MAP4K4 -0.024 0.11 0.22 3 -0.3 42 45
BAG4 0.028 0.025 -10000 0 -0.42 1 1
PKC zeta/ceramide -0.008 0.048 0.12 3 -0.22 14 17
NFKBIA 0.033 0.03 -10000 0 -0.42 2 2
BIRC3 -0.008 0.12 -10000 0 -0.42 40 40
BAX 0.011 0.034 -10000 0 -0.37 2 2
RIPK1 0.035 0.007 -10000 0 -10000 0 0
AKT1 0.002 0.082 0.66 7 -0.39 2 9
BAD -0.011 0.05 0.17 3 -0.23 13 16
SMPD1 0.007 0.065 0.18 3 -0.23 17 20
RB1 -0.015 0.057 0.19 1 -0.23 21 22
FADD/Caspase 8 0.011 0.12 0.22 54 -0.34 21 75
MAP2K4 -0.022 0.064 0.19 2 -0.22 35 37
NSMAF 0.027 0.042 -10000 0 -0.42 4 4
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.009 0.054 0.19 8 -0.23 11 19
EGF -0.069 0.19 -10000 0 -0.42 110 110
mol:ceramide -0.008 0.052 0.13 10 -0.23 14 24
MADD 0.036 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.005 0.075 -10000 0 -0.31 28 28
ASAH1 0.009 0.088 -10000 0 -0.42 20 20
negative regulation of cell cycle -0.015 0.057 0.18 2 -0.23 21 23
cell proliferation -0.011 0.092 0.24 1 -0.22 29 30
BID -0.013 0.14 -10000 0 -0.68 14 14
MAP3K1 -0.02 0.066 0.21 1 -0.22 37 38
EIF2A -0.014 0.064 0.2 11 -0.22 23 34
TRADD 0.03 0.014 -10000 0 -10000 0 0
CRADD 0.03 0.05 -10000 0 -0.42 6 6
MAPK3 -0.007 0.053 0.2 4 -0.23 10 14
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.011 0.061 0.2 4 -0.26 10 14
Cathepsin D/ceramide 0.006 0.06 0.15 1 -0.22 19 20
FADD 0.007 0.11 0.22 53 -0.3 26 79
KSR1 -0.009 0.051 0.19 3 -0.23 12 15
MAPK8 -0.012 0.06 -10000 0 -0.21 23 23
PRKRA -0.009 0.051 0.19 3 -0.23 13 16
PDGFA 0.021 0.082 -10000 0 -0.42 17 17
TRAF2 0.034 0.029 -10000 0 -0.42 2 2
IGF1 -0.038 0.16 -10000 0 -0.42 78 78
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.008 0.052 0.13 10 -0.23 14 24
CTSD 0.029 0.046 -10000 0 -0.42 5 5
regulation of nitric oxide biosynthetic process 0.051 0.012 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.011 0.098 0.25 1 -0.24 29 30
PRKCD 0.033 0.03 -10000 0 -0.42 2 2
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.005 0.075 -10000 0 -0.31 28 28
RelA/NF kappa B1 0.051 0.012 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.024 0.072 -10000 0 -0.42 13 13
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.013 0.1 -10000 0 -0.36 26 26
TNFR1A/BAG4/TNF-alpha 0.048 0.047 -10000 0 -0.25 6 6
mol:Sphingosine-1-phosphate 0.007 0.054 -10000 0 -0.3 15 15
MAP2K1 -0.01 0.053 0.2 4 -0.23 9 13
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.035 0.006 -10000 0 -10000 0 0
CYCS 0.031 0.07 0.16 65 -0.21 4 69
TNFRSF1A 0.033 0.022 -10000 0 -0.42 1 1
NFKB1 0.036 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.039 0.028 -10000 0 -0.3 1 1
EIF2AK2 -0.017 0.06 0.17 5 -0.22 26 31
TNF-alpha/TNFR1A/FAN 0.051 0.05 -10000 0 -0.25 8 8
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.01 0.091 -10000 0 -0.36 16 16
MAP2K2 -0.011 0.054 0.18 10 -0.22 11 21
SMPD3 -0.026 0.12 0.19 1 -0.3 74 75
TNF 0.026 0.061 -10000 0 -0.42 9 9
PKC zeta/PAR4 0.018 0.051 -10000 0 -0.3 13 13
mol:PHOSPHOCHOLINE 0.037 0.095 0.21 103 -0.19 5 108
NF kappa B1/RelA/I kappa B alpha 0.069 0.057 -10000 0 -0.22 15 15
AIFM1 0.027 0.066 0.16 66 -0.17 8 74
BCL2 -0.057 0.18 -10000 0 -0.42 99 99
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.02 0.071 -10000 0 -0.29 24 24
PDGFRB 0.029 0.058 -10000 0 -0.43 8 8
SPHK1 -0.034 0.2 -10000 0 -0.76 35 35
mol:S1P -0.019 0.19 -10000 0 -0.65 35 35
S1P1/S1P/Gi -0.018 0.16 -10000 0 -0.5 32 32
GNAO1 0.031 0.015 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 0 0.14 0.33 1 -0.49 23 24
PLCG1 -0.016 0.14 0.3 1 -0.48 28 29
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.029 0.058 -10000 0 -0.43 8 8
GNAI2 0.029 0.055 -10000 0 -0.42 7 7
GNAI3 0.036 0.008 -10000 0 -10000 0 0
GNAI1 0.018 0.088 -10000 0 -0.42 19 19
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.001 0.12 -10000 0 -0.52 23 23
S1P1/S1P -0.01 0.17 0.25 1 -0.46 53 54
negative regulation of cAMP metabolic process -0.017 0.15 -10000 0 -0.48 32 32
MAPK3 -0.011 0.16 0.31 8 -0.54 26 34
calcium-dependent phospholipase C activity 0 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.043 -10000 0 -0.3 9 9
KDR 0.029 0.058 -10000 0 -0.22 21 21
PLCB2 -0.009 0.15 0.24 1 -0.42 49 50
RAC1 0.035 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.017 0.14 -10000 0 -0.38 54 54
receptor internalization -0.009 0.16 0.24 1 -0.42 54 55
PTGS2 -0.011 0.16 -10000 0 -0.74 15 15
Rac1/GTP -0.013 0.14 -10000 0 -0.38 52 52
RHOA 0.026 0.061 -10000 0 -0.42 9 9
VEGFA -0.003 0.033 -10000 0 -0.15 24 24
negative regulation of T cell proliferation -0.017 0.15 -10000 0 -0.48 32 32
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.024 0.07 -10000 0 -0.42 12 12
MAPK1 -0.019 0.15 -10000 0 -0.54 27 27
S1P1/S1P/PDGFB-D/PDGFRB 0.009 0.18 0.3 1 -0.45 48 49
ABCC1 0.03 0.042 -10000 0 -0.42 4 4
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.028 0.025 -10000 0 -0.42 1 1
Caspase 8 (4 units) 0.029 0.13 -10000 0 -0.4 23 23
NEF -0.011 0.049 -10000 0 -0.17 45 45
NFKBIA 0.022 0.05 -10000 0 -0.46 2 2
BIRC3 -0.012 0.14 -10000 0 -0.46 39 39
CYCS -0.005 0.12 0.19 4 -0.33 40 44
RIPK1 0.035 0.007 -10000 0 -10000 0 0
CD247 -0.011 0.049 -10000 0 -0.17 45 45
MAP2K7 0.004 0.18 -10000 0 -0.81 14 14
protein ubiquitination -0.015 0.12 0.22 2 -0.36 25 27
CRADD 0.03 0.05 -10000 0 -0.42 6 6
DAXX 0.036 0.006 -10000 0 -10000 0 0
FAS 0.008 0.11 -10000 0 -0.42 29 29
BID -0.006 0.12 -10000 0 -0.3 57 57
NF-kappa-B/RelA/I kappa B alpha 0.042 0.099 -10000 0 -0.26 39 39
TRADD 0.03 0.014 -10000 0 -10000 0 0
MAP3K5 0.012 0.095 -10000 0 -0.42 23 23
CFLAR 0.031 0.045 -10000 0 -0.42 5 5
FADD 0.029 0.014 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.042 0.1 -10000 0 -0.26 39 39
MAPK8 0.003 0.16 0.42 1 -0.72 14 15
APAF1 0.032 0.041 -10000 0 -0.42 4 4
TRAF1 0.035 0.021 -10000 0 -0.42 1 1
TRAF2 0.034 0.029 -10000 0 -0.42 2 2
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.002 0.13 -10000 0 -0.31 54 54
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.014 0.14 -10000 0 -0.4 34 34
CHUK -0.019 0.13 0.22 1 -0.39 25 26
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.055 0.095 -10000 0 -0.24 35 35
TCRz/NEF -0.017 0.083 -10000 0 -0.28 45 45
TNF 0.026 0.061 -10000 0 -0.42 9 9
FASLG -0.022 0.14 -10000 0 -0.52 36 36
NFKB1 0.023 0.041 -10000 0 -0.14 3 3
TNFR1A/BAG4/TNF-alpha 0.048 0.047 -10000 0 -0.25 6 6
CASP6 0.022 0.16 -10000 0 -0.53 24 24
CASP7 -0.041 0.2 0.29 1 -0.47 68 69
RELA 0.023 0.042 -10000 0 -0.14 3 3
CASP2 0.035 0.008 -10000 0 -10000 0 0
CASP3 -0.04 0.19 -10000 0 -0.47 63 63
TNFRSF1A 0.033 0.022 -10000 0 -0.42 1 1
TNFR1A/BAG4 0.039 0.028 -10000 0 -0.3 1 1
CASP8 0.036 0.004 -10000 0 -10000 0 0
CASP9 0.034 0.022 -10000 0 -0.42 1 1
MAP3K14 -0.013 0.13 0.24 2 -0.4 29 31
APAF-1/Caspase 9 -0.014 0.14 0.2 1 -0.34 56 57
BCL2 -0.031 0.16 0.58 1 -0.59 17 18
Insulin 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
CBL/APS/CAP 0.012 0.11 -10000 0 -0.22 76 76
TC10/GTP 0.029 0.068 -10000 0 -0.21 34 34
Insulin Receptor/Insulin/IRS1/Shp2 0.054 0.11 -10000 0 -0.25 55 55
HRAS 0.032 0.036 -10000 0 -0.42 3 3
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 -0.063 0.18 -10000 0 -0.42 98 98
FOXO3 -0.014 0.022 -10000 0 -0.096 2 2
AKT1 -0.045 0.13 0.31 7 -0.36 18 25
INSR 0.037 0.031 -10000 0 -0.42 2 2
Insulin Receptor/Insulin 0.081 0.06 -10000 0 -0.3 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.023 0.075 -10000 0 -0.42 14 14
SORBS1 0.007 0.11 -10000 0 -0.42 29 29
CRK 0.032 0.023 -10000 0 -0.42 1 1
PTPN1 0.005 0.038 -10000 0 -0.3 5 5
CAV1 -0.008 0.083 0.17 8 -0.23 58 66
CBL/APS/CAP/Crk-II/C3G 0.052 0.075 -10000 0 -0.22 30 30
Insulin Receptor/Insulin/IRS1/NCK2 0.054 0.11 -10000 0 -0.25 53 53
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.028 0.1 -10000 0 -0.22 66 66
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.019 0.08 -10000 0 -0.42 6 6
RPS6KB1 -0.04 0.11 0.28 7 -0.34 16 23
PARD6A 0.021 0.061 -10000 0 -0.42 9 9
CBL 0.032 0.012 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.007 0.11 -10000 0 -0.67 12 12
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.004 0.12 0.28 3 -0.28 31 34
HRAS/GTP -0.001 0.063 -10000 0 -0.2 40 40
Insulin Receptor 0.037 0.031 -10000 0 -0.42 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.049 0.1 -10000 0 -0.23 42 42
PRKCI 0.004 0.11 -10000 0 -0.46 24 24
Insulin Receptor/Insulin/GRB14/PDK1 -0.036 0.12 -10000 0 -0.23 135 135
SHC1 0.028 0.025 -10000 0 -0.42 1 1
negative regulation of MAPKKK cascade 0.046 0.11 -10000 0 -0.6 12 12
PI3K 0.04 0.11 -10000 0 -0.23 66 66
NCK2 0.036 0.005 -10000 0 -10000 0 0
RHOQ 0.031 0.045 -10000 0 -0.42 5 5
mol:H2O2 0 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.024 0.025 -10000 0 -0.3 3 3
AKT2 -0.046 0.13 0.33 6 -0.36 17 23
PRKCZ -0.008 0.084 -10000 0 -0.42 17 17
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.001 0.069 0.16 6 -0.21 44 50
F2RL2 -0.02 0.14 -10000 0 -0.42 58 58
TRIP10 0.032 0.041 -10000 0 -0.42 4 4
Insulin Receptor/Insulin/Shc 0.054 0.041 -10000 0 -0.22 3 3
TC10/GTP/CIP4/Exocyst 0.042 0.041 -10000 0 -0.25 9 9
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.075 0.06 -10000 0 -0.22 4 4
RAPGEF1 0.036 0.004 -10000 0 -10000 0 0
RASA1 0.029 0.05 -10000 0 -0.42 6 6
NCK1 0.034 0.021 -10000 0 -0.42 1 1
CBL/APS/CAP/Crk-II 0.039 0.072 -10000 0 -0.23 30 30
TC10/GDP 0.023 0.032 -10000 0 -0.3 5 5
Insulin Receptor/Insulin/SHC/GRB10 0.063 0.066 -10000 0 -0.23 13 13
INPP5D -0.03 0.07 -10000 0 -0.22 55 55
SOS1 0.035 0.021 -10000 0 -0.42 1 1
SGK1 -0.008 0.01 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.036 0.004 -10000 0 -10000 0 0
IRS1 -0.014 0.14 -10000 0 -0.42 54 54
p62DOK/RasGAP 0.046 0.11 -10000 0 -0.61 12 12
INS 0.037 0.024 -10000 0 -0.42 1 1
mol:PI-3-4-P2 -0.03 0.069 -10000 0 -0.22 55 55
GRB2 0.033 0.011 -10000 0 -10000 0 0
EIF4EBP1 -0.049 0.1 0.24 4 -0.33 18 22
PTPRA 0.038 0.013 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
TC10/GTP/CIP4 0.042 0.041 -10000 0 -0.25 9 9
PDPK1 0.032 0.023 -10000 0 -0.42 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.006 0.077 -10000 0 -0.22 39 39
Insulin Receptor/Insulin/IRS1 0.035 0.1 -10000 0 -0.24 55 55
Insulin Receptor/Insulin/IRS3 0.054 0.034 -10000 0 -0.3 3 3
Par3/Par6 0.023 0.11 -10000 0 -0.23 69 69
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.041 0.11 -10000 0 -0.46 18 18
HDAC1 0.04 0.028 -10000 0 -0.42 1 1
AES 0.037 0.009 -10000 0 -10000 0 0
FBXW11 0.033 0.029 -10000 0 -0.42 2 2
DTX1 0.033 0.035 -10000 0 -0.42 3 3
LRP6/FZD1 0.041 0.055 -10000 0 -0.3 12 12
TLE1 0.006 0.11 -10000 0 -0.42 33 33
AP1 -0.025 0.11 -10000 0 -0.28 62 62
NCSTN 0.028 0.025 -10000 0 -0.42 1 1
ADAM10 0.033 0.03 -10000 0 -0.42 2 2
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.037 0.15 -10000 0 -0.68 9 9
NICD/RBPSUH 0.005 0.097 -10000 0 -0.46 18 18
WIF1 0.03 0.014 -10000 0 -10000 0 0
NOTCH1 0.014 0.099 -10000 0 -0.48 18 18
PSENEN 0.035 0.006 -10000 0 -10000 0 0
KREMEN2 -0.09 0.19 -10000 0 -0.42 129 129
DKK1 -0.027 0.14 -10000 0 -0.42 60 60
beta catenin/beta TrCP1 0.012 0.1 0.28 1 -0.35 16 17
APH1B 0.025 0.067 -10000 0 -0.42 11 11
APH1A 0.031 0.036 -10000 0 -0.42 3 3
AXIN1 0.015 0.053 0.26 1 -0.39 2 3
CtBP/CBP/TCF1/TLE1/AES 0.027 0.089 0.29 3 -0.24 26 29
PSEN1 0.032 0.041 -10000 0 -0.42 4 4
FOS -0.031 0.15 -10000 0 -0.42 66 66
JUN -0.001 0.12 -10000 0 -0.42 39 39
MAP3K7 0.036 0.014 -10000 0 -10000 0 0
CTNNB1 -0.004 0.097 0.26 2 -0.37 15 17
MAPK3 0.032 0.023 -10000 0 -0.42 1 1
DKK2/LRP6/Kremen 2 -0.044 0.15 -10000 0 -0.26 154 154
HNF1A 0.002 0.006 -10000 0 -10000 0 0
CTBP1 0.036 0.01 -10000 0 -10000 0 0
MYC -0.083 0.35 -10000 0 -1.3 35 35
NKD1 0.028 0.038 -10000 0 -0.42 3 3
FZD1 0.028 0.057 -10000 0 -0.42 8 8
NOTCH1 precursor/Deltex homolog 1 0.042 0.11 -10000 0 -0.47 18 18
apoptosis -0.025 0.11 -10000 0 -0.28 63 63
Delta 1/NOTCHprecursor 0.04 0.11 -10000 0 -0.46 18 18
DLL1 0.034 0.01 -10000 0 -10000 0 0
PPARD 0.006 0.11 -10000 0 -0.9 6 6
Gamma Secretase 0.069 0.068 -10000 0 -0.22 13 13
APC -0.001 0.1 -10000 0 -0.45 18 18
DVL1 0.025 0.028 -10000 0 -0.26 2 2
CSNK2A1 0.035 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0.037 0.012 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.061 0.16 -10000 0 -0.27 169 169
LRP6 0.029 0.046 -10000 0 -0.42 5 5
CSNK1A1 0.035 0.006 -10000 0 -10000 0 0
NLK 0.029 0.025 -10000 0 -0.24 1 1
CCND1 -0.2 0.5 -10000 0 -1.3 84 84
WNT1 0.035 0.021 -10000 0 -0.42 1 1
Axin1/APC/beta catenin 0.021 0.1 0.34 2 -0.45 9 11
DKK2 0.006 0.11 -10000 0 -0.42 31 31
NOTCH1 precursor/DVL1 0.037 0.1 -10000 0 -0.53 10 10
GSK3B 0.036 0.005 -10000 0 -10000 0 0
FRAT1 0.03 0.054 -10000 0 -0.42 7 7
NOTCH/Deltex homolog 1 0.043 0.11 -10000 0 -0.47 18 18
PPP2R5D 0.012 0.068 0.23 3 -0.32 17 20
MAPK1 0.033 0.022 -10000 0 -0.42 1 1
WNT1/LRP6/FZD1 0.071 0.058 -10000 0 -0.23 13 13
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.026 0.02 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.007 0.13 -10000 0 -0.42 45 45
positive regulation of NF-kappaB transcription factor activity 0.01 0.097 -10000 0 -0.29 45 45
MAP2K4 -0.009 0.1 -10000 0 -0.36 25 25
IKBKB 0.03 0.014 -10000 0 -10000 0 0
TNFRSF10B 0.027 0.016 -10000 0 -10000 0 0
TNFRSF10A 0.023 0.047 -10000 0 -0.42 5 5
SMPD1 -0.006 0.071 -10000 0 -0.21 44 44
IKBKG 0.036 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.028 0.016 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.009 0.099 -10000 0 -0.3 45 45
TRAIL/TRAILR3 0.008 0.097 -10000 0 -0.29 46 46
TRAIL/TRAILR1 0.007 0.1 -10000 0 -0.31 47 47
TRAIL/TRAILR4 0.01 0.097 -10000 0 -0.29 45 45
TRAIL/TRAILR1/DAP3/GTP 0.02 0.08 -10000 0 -0.24 36 36
IKK complex 0.013 0.092 -10000 0 -0.4 14 14
RIPK1 0.035 0.007 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.021 0.018 -10000 0 -0.3 1 1
MAPK3 -0.01 0.085 -10000 0 -0.3 40 40
MAP3K1 -0.006 0.11 -10000 0 -0.38 26 26
TRAILR4 (trimer) 0.027 0.016 -10000 0 -10000 0 0
TRADD 0.03 0.014 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.023 0.047 -10000 0 -0.42 5 5
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.002 0.085 -10000 0 -0.29 34 34
CFLAR 0.031 0.045 -10000 0 -0.42 5 5
MAPK1 -0.009 0.083 -10000 0 -0.3 38 38
TRAIL/TRAILR1/FADD/TRADD/RIP 0.035 0.09 -10000 0 -0.23 33 33
mol:ceramide -0.006 0.071 -10000 0 -0.21 44 44
FADD 0.029 0.014 -10000 0 -10000 0 0
MAPK8 -0.022 0.11 -10000 0 -0.35 30 30
TRAF2 0.034 0.029 -10000 0 -0.42 2 2
TRAILR3 (trimer) 0.024 0.026 -10000 0 -0.42 1 1
CHUK 0.026 0.067 -10000 0 -0.42 11 11
TRAIL/TRAILR1/FADD 0.023 0.087 -10000 0 -0.26 34 34
DAP3 0.028 0.025 -10000 0 -0.42 1 1
CASP10 0.014 0.083 0.33 4 -0.29 18 22
JNK cascade 0.01 0.097 -10000 0 -0.29 45 45
TRAIL (trimer) -0.007 0.13 -10000 0 -0.42 45 45
TNFRSF10C 0.024 0.026 -10000 0 -0.42 1 1
TRAIL/TRAILR1/DAP3/GTP/FADD 0.027 0.075 -10000 0 -0.22 27 27
TRAIL/TRAILR2/FADD 0.025 0.083 -10000 0 -0.26 33 33
cell death -0.006 0.071 -10000 0 -0.21 44 44
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.001 0.083 -10000 0 -0.28 33 33
TRAILR2 (trimer) 0.027 0.016 -10000 0 -10000 0 0
CASP8 0.025 0.043 -10000 0 -0.66 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.037 0.086 -10000 0 -0.22 32 32
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.035 0.15 0.23 1 -0.41 41 42
BAG4 0.028 0.025 -10000 0 -0.42 1 1
BAD -0.007 0.049 0.19 2 -0.16 20 22
NFKBIA 0.033 0.03 -10000 0 -0.42 2 2
BIRC3 -0.008 0.12 -10000 0 -0.42 40 40
BAX -0.003 0.056 0.19 10 -0.16 15 25
EnzymeConsortium:3.1.4.12 -0.006 0.034 0.075 4 -0.092 36 40
IKBKB -0.016 0.14 0.28 3 -0.41 29 32
MAP2K2 -0.008 0.055 0.19 12 -0.2 9 21
MAP2K1 -0.007 0.051 0.19 10 -0.19 5 15
SMPD1 -0.006 0.041 -10000 0 -0.15 19 19
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.004 0.15 0.3 5 -0.4 30 35
MAP2K4 -0.015 0.057 0.18 1 -0.19 21 22
protein ubiquitination -0.032 0.14 0.25 1 -0.4 36 37
EnzymeConsortium:2.7.1.37 -0.011 0.056 0.2 9 -0.2 8 17
response to UV 0 0.001 0.002 12 -0.002 6 18
RAF1 -0.007 0.052 0.2 8 -0.19 6 14
CRADD 0.03 0.05 -10000 0 -0.42 6 6
mol:ceramide -0.006 0.05 0.11 2 -0.15 27 29
I-kappa-B-alpha/RELA/p50/ubiquitin 0.044 0.023 -10000 0 -0.25 2 2
MADD 0.036 0.005 -10000 0 -10000 0 0
MAP3K1 -0.016 0.06 -10000 0 -0.18 35 35
TRADD 0.03 0.014 -10000 0 -10000 0 0
RELA/p50 0.035 0.006 -10000 0 -10000 0 0
MAPK3 -0.004 0.055 0.2 8 -0.19 4 12
MAPK1 -0.007 0.062 0.2 8 -0.2 13 21
p50/RELA/I-kappa-B-alpha 0.049 0.026 -10000 0 -0.3 2 2
FADD -0.001 0.15 0.22 51 -0.4 31 82
KSR1 -0.007 0.05 0.19 3 -0.17 13 16
MAPK8 -0.019 0.058 0.21 3 -0.21 11 14
TRAF2 0.034 0.029 -10000 0 -0.42 2 2
response to radiation 0 0 0.002 3 -10000 0 3
CHUK -0.042 0.14 -10000 0 -0.4 42 42
TNF R/SODD 0.039 0.028 -10000 0 -0.3 1 1
TNF 0.026 0.061 -10000 0 -0.42 9 9
CYCS 0.015 0.069 0.16 28 -0.16 11 39
IKBKG -0.039 0.14 -10000 0 -0.4 37 37
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.03 0.15 -10000 0 -0.42 39 39
RELA 0.035 0.006 -10000 0 -10000 0 0
RIPK1 0.035 0.008 -10000 0 -10000 0 0
AIFM1 0.012 0.067 0.15 30 -0.16 15 45
TNF/TNF R/SODD 0.048 0.047 -10000 0 -0.25 6 6
TNFRSF1A 0.033 0.022 -10000 0 -0.42 1 1
response to heat 0 0 0.002 3 -10000 0 3
CASP8 0.011 0.12 -10000 0 -0.63 16 16
NSMAF -0.011 0.14 0.27 1 -0.42 29 30
response to hydrogen peroxide 0 0.001 0.002 12 -0.002 6 18
BCL2 -0.057 0.18 -10000 0 -0.42 99 99
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.04 0.038 -10000 0 -0.25 7 7
cell-cell adhesion 0.036 0.06 0.22 44 -10000 0 44
Ephrin B/EPHB2/RasGAP 0.069 0.081 -10000 0 -0.24 23 23
ITSN1 0.034 0.029 -10000 0 -0.42 2 2
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
SHC1 0.028 0.025 -10000 0 -0.42 1 1
Ephrin B1/EPHB3 0.035 0.058 -10000 0 -0.25 19 19
Ephrin B1/EPHB1 0.042 0.036 -10000 0 -0.25 7 7
HRAS/GDP -0.001 0.11 -10000 0 -0.28 40 40
Ephrin B/EPHB1/GRB7 0.063 0.084 -10000 0 -0.22 30 30
Endophilin/SYNJ1 -0.012 0.053 0.18 14 -0.21 20 34
KRAS 0.028 0.054 -10000 0 -0.42 7 7
Ephrin B/EPHB1/Src 0.07 0.079 -10000 0 -0.24 22 22
endothelial cell migration 0.032 0.094 -10000 0 -0.24 48 48
GRB2 0.033 0.011 -10000 0 -10000 0 0
GRB7 0.024 0.058 -10000 0 -0.42 8 8
PAK1 -0.02 0.067 0.29 2 -0.22 29 31
HRAS 0.032 0.036 -10000 0 -0.42 3 3
RRAS -0.015 0.057 0.18 13 -0.22 24 37
DNM1 0.033 0.035 -10000 0 -0.42 3 3
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.012 0.058 0.18 16 -0.22 19 35
lamellipodium assembly -0.036 0.06 -10000 0 -0.22 44 44
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.016 0.069 -10000 0 -0.31 12 12
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
EPHB2 0.032 0.03 -10000 0 -0.42 2 2
EPHB3 0.018 0.085 -10000 0 -0.42 18 18
EPHB1 0.026 0.05 -10000 0 -0.42 6 6
EPHB4 0.016 0.091 -10000 0 -0.42 21 21
mol:GDP -0.018 0.09 -10000 0 -0.33 25 25
Ephrin B/EPHB2 0.058 0.064 -10000 0 -0.22 19 19
Ephrin B/EPHB3 0.048 0.081 -10000 0 -0.23 32 32
JNK cascade -0.014 0.059 0.26 9 -0.23 18 27
Ephrin B/EPHB1 0.056 0.068 -10000 0 -0.22 22 22
RAP1/GDP -0.005 0.11 -10000 0 -0.28 39 39
EFNB2 0.017 0.08 -10000 0 -0.42 16 16
EFNB3 0.032 0.012 -10000 0 -10000 0 0
EFNB1 0.035 0.021 -10000 0 -0.42 1 1
Ephrin B2/EPHB1-2 0.044 0.067 -10000 0 -0.24 23 23
RAP1B 0.033 0.03 -10000 0 -0.42 2 2
RAP1A 0.031 0.045 -10000 0 -0.42 5 5
CDC42/GTP 0.036 0.091 -10000 0 -0.26 23 23
Rap1/GTP 0.015 0.069 -10000 0 -0.24 25 25
axon guidance 0.039 0.038 -10000 0 -0.25 7 7
MAPK3 0.025 0.072 0.2 20 -0.39 6 26
MAPK1 0.016 0.066 0.24 2 -0.39 6 8
Rac1/GDP -0.017 0.1 -10000 0 -0.29 38 38
actin cytoskeleton reorganization -0.023 0.076 -10000 0 -0.24 30 30
CDC42/GDP -0.016 0.1 -10000 0 -0.29 36 36
PI3K 0.038 0.098 -10000 0 -0.24 48 48
EFNA5 0.03 0.046 -10000 0 -0.42 5 5
Ephrin B2/EPHB4 0.02 0.081 -10000 0 -0.26 35 35
Ephrin B/EPHB2/Intersectin/N-WASP 0.011 0.074 -10000 0 -0.24 29 29
CDC42 0.035 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.008 0.067 -10000 0 -0.22 32 32
PTK2 0.11 0.23 0.55 112 -10000 0 112
MAP4K4 -0.015 0.059 0.27 9 -0.23 18 27
SRC 0.033 0.029 -10000 0 -0.42 2 2
KALRN 0.034 0.022 -10000 0 -0.42 1 1
Intersectin/N-WASP 0.045 0.048 -10000 0 -0.3 9 9
neuron projection morphogenesis -0.013 0.084 0.26 2 -0.3 15 17
MAP2K1 0.01 0.063 0.21 1 -0.41 6 7
WASL 0.029 0.054 -10000 0 -0.42 7 7
Ephrin B1/EPHB1-2/NCK1 0.079 0.05 -10000 0 -0.23 10 10
cell migration 0.027 0.093 0.25 4 -0.39 9 13
NRAS 0.029 0.054 -10000 0 -0.42 7 7
SYNJ1 -0.012 0.053 0.18 14 -0.21 20 34
PXN 0.036 0.004 -10000 0 -10000 0 0
TF -0.017 0.05 0.17 14 -0.21 16 30
HRAS/GTP 0.042 0.075 -10000 0 -0.22 30 30
Ephrin B1/EPHB1-2 0.058 0.042 -10000 0 -0.23 9 9
cell adhesion mediated by integrin 0.011 0.059 0.22 16 -0.21 12 28
RAC1 0.035 0.006 -10000 0 -10000 0 0
mol:GTP 0.048 0.075 -10000 0 -0.22 28 28
RAC1-CDC42/GTP -0.033 0.061 -10000 0 -0.24 27 27
RASA1 0.029 0.05 -10000 0 -0.42 6 6
RAC1-CDC42/GDP -0.003 0.11 -10000 0 -0.28 36 36
ruffle organization -0.03 0.076 -10000 0 -0.4 5 5
NCK1 0.034 0.021 -10000 0 -0.42 1 1
receptor internalization -0.019 0.051 0.17 13 -0.21 18 31
Ephrin B/EPHB2/KALRN 0.073 0.074 -10000 0 -0.23 19 19
ROCK1 0.018 0.06 0.19 23 -0.23 19 42
RAS family/GDP -0.047 0.07 -10000 0 -0.26 29 29
Rac1/GTP 0 0.076 -10000 0 -0.23 44 44
Ephrin B/EPHB1/Src/Paxillin 0.014 0.075 -10000 0 -0.27 23 23
Calcium signaling in the CD4+ TCR 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
NFATC1 0.008 0.055 -10000 0 -0.26 15 15
NFATC2 0.014 0.035 -10000 0 -0.27 3 3
NFATC3 0.016 0.026 -10000 0 -10000 0 0
CD40LG -0.019 0.18 0.38 3 -0.44 52 55
PTGS2 -0.022 0.17 0.38 3 -0.44 46 49
JUNB 0.032 0.041 -10000 0 -0.42 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.025 -10000 0 -0.11 1 1
CaM/Ca2+ 0.021 0.025 -10000 0 -0.11 1 1
CALM1 0.033 0.019 -10000 0 -10000 0 0
JUN -0.002 0.12 -10000 0 -0.42 39 39
mol:Ca2+ -0.001 0.009 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.023 0.01 -10000 0 -10000 0 0
FOSL1 0.035 0.007 -10000 0 -10000 0 0
CREM 0.035 0.007 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.016 0.12 -10000 0 -0.32 28 28
FOS -0.033 0.15 -10000 0 -0.42 66 66
IFNG -0.035 0.2 0.38 3 -0.5 59 62
AP-1/NFAT1-c-4 0.003 0.22 -10000 0 -0.5 53 53
FASLG -0.031 0.2 0.38 3 -0.52 52 55
NFAT1-c-4/ICER1 0.028 0.08 0.23 2 -0.24 14 16
IL2RA -0.029 0.2 0.38 3 -0.48 58 61
FKBP12/FK506 0.026 0.005 -10000 0 -10000 0 0
CSF2 -0.019 0.18 0.38 3 -0.44 51 54
JunB/Fra1/NFAT1-c-4 0.045 0.092 -10000 0 -0.28 9 9
IL4 -0.019 0.18 0.38 3 -0.44 53 56
IL2 0.009 0.15 -10000 0 -1 10 10
IL3 0.02 0.12 -10000 0 -0.71 11 11
FKBP1A 0.035 0.007 -10000 0 -10000 0 0
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.034 0.017 -10000 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.018 0.059 0.19 12 -0.2 19 31
DAPP1 -0.04 0.16 -10000 0 -0.4 61 61
Src family/SYK family/BLNK-LAT/BTK-ITK -0.061 0.23 -10000 0 -0.56 65 65
mol:DAG -0.017 0.092 0.21 5 -0.23 46 51
HRAS 0.031 0.038 -10000 0 -0.42 3 3
RAP1A 0.03 0.047 -10000 0 -0.42 5 5
ARF5/GDP -0.004 0.11 -10000 0 -0.32 30 30
PLCG2 0.02 0.055 -10000 0 -0.42 7 7
PLCG1 0.034 0.008 -10000 0 -10000 0 0
ARF5 0.034 0.021 -10000 0 -0.42 1 1
mol:GTP -0.018 0.06 0.19 14 -0.21 19 33
ARF1/GTP -0.009 0.052 0.23 7 -0.2 16 23
RHOA 0.026 0.061 -10000 0 -0.42 9 9
YES1 0.029 0.05 -10000 0 -0.42 6 6
RAP1A/GTP -0.017 0.061 0.18 28 -0.21 19 47
ADAP1 -0.018 0.056 0.18 13 -0.2 19 32
ARAP3 -0.018 0.06 0.19 14 -0.21 19 33
INPPL1 0.031 0.036 -10000 0 -0.42 3 3
PREX1 -0.036 0.16 -10000 0 -0.42 75 75
ARHGEF6 0.015 0.093 -10000 0 -0.42 22 22
ARHGEF7 0.032 0.011 -10000 0 -10000 0 0
ARF1 0.027 0.025 -10000 0 -0.42 1 1
NRAS 0.028 0.054 -10000 0 -0.41 7 7
FYN 0.027 0.054 -10000 0 -0.42 7 7
ARF6 0.034 0.029 -10000 0 -0.42 2 2
FGR 0.035 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.009 0.05 0.15 8 -0.12 33 41
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.028 0.057 -10000 0 -0.42 8 8
ZAP70 0.033 0.022 -10000 0 -0.42 1 1
mol:IP3 -0.016 0.067 0.18 8 -0.17 37 45
LYN 0.03 0.014 -10000 0 -10000 0 0
ARF1/GDP -0.002 0.1 -10000 0 -0.33 24 24
RhoA/GDP 0.012 0.091 0.23 6 -0.27 21 27
PDK1/Src/Hsp90 0.042 0.025 -10000 0 -0.25 2 2
BLNK 0.013 0.099 -10000 0 -0.42 25 25
actin cytoskeleton reorganization -0.021 0.11 0.23 5 -0.37 19 24
SRC 0.033 0.029 -10000 0 -0.42 2 2
PLEKHA2 -0.009 0.022 -10000 0 -0.25 4 4
RAC1 0.035 0.006 -10000 0 -10000 0 0
PTEN 0.027 0.059 -10000 0 -0.4 9 9
HSP90AA1 0 0 -10000 0 -10000 0 0
ARF6/GTP -0.019 0.059 0.2 13 -0.2 19 32
RhoA/GTP -0.022 0.067 0.17 27 -0.24 23 50
Src family/SYK family/BLNK-LAT -0.027 0.16 -10000 0 -0.46 47 47
BLK 0.022 0.038 -10000 0 -0.42 3 3
PDPK1 0.032 0.023 -10000 0 -0.42 1 1
CYTH1 -0.018 0.056 0.18 13 -0.2 19 32
HCK 0.018 0.087 -10000 0 -0.42 19 19
CYTH3 -0.018 0.056 0.18 13 -0.2 19 32
CYTH2 -0.018 0.056 0.18 13 -0.2 19 32
KRAS 0.027 0.055 -10000 0 -0.42 7 7
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.006 0.038 0.21 3 -0.19 3 6
SGK1 0.008 0.039 0.17 7 -0.2 3 10
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.02 0.11 -10000 0 -0.34 29 29
SOS1 0.035 0.021 -10000 0 -0.42 1 1
SYK 0.005 0.11 -10000 0 -0.42 34 34
ARF6/GDP -0.003 0.075 0.22 6 -0.26 12 18
mol:PI-3-4-5-P3 -0.018 0.06 0.22 11 -0.21 19 30
ARAP3/RAP1A/GTP -0.017 0.061 0.18 28 -0.21 19 47
VAV1 0.019 0.082 -10000 0 -0.42 17 17
mol:PI-3-4-P2 0.006 0.023 -10000 0 -0.3 3 3
RAS family/GTP/PI3K Class I 0.045 0.064 0.22 7 -0.21 19 26
PLEKHA1 -0.011 0.029 -10000 0 -0.25 7 7
Rac1/GDP -0.003 0.11 -10000 0 -0.33 28 28
LAT 0.03 0.031 -10000 0 -0.42 2 2
Rac1/GTP -0.018 0.12 -10000 0 -0.35 36 36
ITK -0.032 0.073 0.19 11 -0.22 46 57
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.028 0.12 0.25 4 -0.31 50 54
LCK -0.017 0.14 -10000 0 -0.42 54 54
BTK -0.025 0.068 0.19 12 -0.23 29 41
Regulation of Telomerase

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
Telomerase catalytic core complex -0.072 0.23 -10000 0 -0.62 42 42
RAD9A 0.034 0.01 -10000 0 -10000 0 0
AP1 -0.025 0.15 -10000 0 -0.34 88 88
IFNAR2 0.028 0.03 -10000 0 -0.43 1 1
AKT1 -0.034 0.11 -10000 0 -0.19 133 133
ER alpha/Oestrogen -0.063 0.14 -10000 0 -0.3 132 132
NFX1/SIN3/HDAC complex 0.012 0.072 -10000 0 -0.34 13 13
EGF -0.069 0.19 -10000 0 -0.42 110 110
SMG5 0 0 -10000 0 -10000 0 0
SMG6 0 0 -10000 0 -10000 0 0
SP3/HDAC2 0.039 0.037 -10000 0 -0.3 1 1
TERT/c-Abl -0.061 0.22 -10000 0 -0.58 43 43
SAP18 0.033 0.01 -10000 0 -10000 0 0
MRN complex 0.048 0.044 -10000 0 -0.26 4 4
WT1 -0.025 0.14 -10000 0 -0.42 54 54
WRN 0.027 0.025 -10000 0 -0.42 1 1
SP1 0.026 0.033 -10000 0 -0.43 1 1
SP3 0.035 0.007 -10000 0 -10000 0 0
TERF2IP 0.03 0.014 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.046 0.21 -10000 0 -0.53 45 45
Mad/Max 0.048 0.019 -10000 0 -10000 0 0
TERT -0.075 0.24 -10000 0 -0.66 39 39
CCND1 -0.15 0.44 -10000 0 -1.1 86 86
MAX 0.034 0.009 -10000 0 -10000 0 0
RBBP7 0.034 0.029 -10000 0 -0.42 2 2
RBBP4 0.034 0.021 -10000 0 -0.42 1 1
TERF2 0.027 0.031 -10000 0 -0.36 2 2
PTGES3 0.035 0.021 -10000 0 -0.42 1 1
SIN3A 0.035 0.007 -10000 0 -10000 0 0
Telomerase/911 0.021 0.069 -10000 0 -0.46 5 5
CDKN1B -0.028 0.14 -10000 0 -0.37 66 66
RAD1 0.033 0.029 -10000 0 -0.42 2 2
XRCC5 0.036 0.005 -10000 0 -10000 0 0
XRCC6 0.034 0.009 -10000 0 -10000 0 0
SAP30 0.03 0.046 -10000 0 -0.42 5 5
TRF2/PARP2 0.043 0.032 -10000 0 -0.28 2 2
UBE3A 0.034 0.029 -10000 0 -0.42 2 2
JUN -0.002 0.12 -10000 0 -0.42 39 39
E6 -0.001 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.02 0.027 -10000 0 -0.3 2 2
FOS -0.032 0.15 -10000 0 -0.42 66 66
IFN-gamma/IRF1 0.001 0.12 -10000 0 -0.3 70 70
PARP2 0.036 0.002 -10000 0 -10000 0 0
BLM 0.012 0.097 -10000 0 -0.42 24 24
Telomerase 0.012 0.044 0.18 1 -10000 0 1
IRF1 0.016 0.083 -10000 0 -0.26 34 34
ESR1 -0.089 0.2 -10000 0 -0.42 132 132
KU/TER 0.05 0.015 -10000 0 -10000 0 0
ATM/TRF2 0.036 0.035 -10000 0 -0.18 2 2
ubiquitin-dependent protein catabolic process 0.023 0.06 -10000 0 -0.27 11 11
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.025 0.056 -10000 0 -0.28 7 7
HDAC1 0.034 0.021 -10000 0 -0.42 1 1
HDAC2 0.025 0.032 -10000 0 -0.42 1 1
ATM 0.02 0.025 0.19 2 -10000 0 2
SMAD3 0.011 0.044 -10000 0 -0.3 10 10
ABL1 0.036 0.005 -10000 0 -10000 0 0
MXD1 0.035 0.007 -10000 0 -10000 0 0
MRE11A 0.031 0.013 -10000 0 -10000 0 0
HUS1 0.035 0.006 -10000 0 -10000 0 0
RPS6KB1 0.031 0.013 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.058 0.23 -10000 0 -0.57 54 54
NR2F2 -0.01 0.14 -10000 0 -0.42 49 49
MAPK3 0.008 0.032 -10000 0 -0.3 4 4
MAPK1 0.008 0.032 -10000 0 -0.3 4 4
TGFB1/TGF beta receptor Type II 0.035 0.021 -10000 0 -0.42 1 1
NFKB1 0.036 0.005 -10000 0 -10000 0 0
HNRNPC 0 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.02 0.025 0.19 2 -10000 0 2
NBN 0.028 0.025 -10000 0 -0.42 1 1
EGFR -0.015 0.13 -10000 0 -0.42 49 49
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.063 0.16 -10000 0 -0.31 152 152
MYC -0.002 0.1 -10000 0 -0.42 29 29
IL2 0.024 0.043 -10000 0 -0.42 3 3
KU 0.05 0.015 -10000 0 -10000 0 0
RAD50 0.032 0.041 -10000 0 -0.42 4 4
HSP90AA1 0 0 -10000 0 -10000 0 0
TGFB1 0.035 0.021 -10000 0 -0.42 1 1
TRF2/BLM 0.026 0.073 -10000 0 -0.28 25 25
FRAP1 0.035 0.007 -10000 0 -10000 0 0
KU/TERT -0.049 0.23 -10000 0 -0.59 42 42
SP1/HDAC2 0.038 0.043 -10000 0 -0.3 2 2
PINX1 0.028 0.015 -10000 0 -10000 0 0
Telomerase/EST1A -0.059 0.2 -10000 0 -0.51 49 49
Smad3/Myc 0.006 0.074 -10000 0 -0.25 35 35
911 complex 0.063 0.032 -10000 0 -0.26 2 2
IFNG -0.014 0.12 -10000 0 -0.33 60 60
Telomerase/PinX1 -0.057 0.2 -10000 0 -0.53 43 43
Telomerase/AKT1/mTOR/p70S6K -0.006 0.1 -10000 0 -0.42 16 16
SIN3B 0.036 0.005 -10000 0 -10000 0 0
YWHAE 0.032 0.012 -10000 0 -10000 0 0
Telomerase/EST1B -0.059 0.2 -10000 0 -0.51 49 49
response to DNA damage stimulus -0.001 0.033 0.13 1 -0.1 35 36
MRN complex/TRF2/Rap1 0.059 0.061 -10000 0 -0.25 5 5
TRF2/WRN 0.034 0.036 -10000 0 -0.28 3 3
Telomerase/hnRNP C1/C2 -0.059 0.2 -10000 0 -0.51 49 49
E2F1 0.021 0.057 -10000 0 -0.42 7 7
ZNFX1 0 0.001 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL 0.036 0.006 -10000 0 -10000 0 0
DKC1 0.036 0.003 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

Figure S76.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S76.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.014 0.15 0.28 2 -0.45 25 27
PDGFB-D/PDGFRB/SLAP 0.031 0.056 -10000 0 -0.3 11 11
PDGFB-D/PDGFRB/APS/CBL 0.037 0.041 -10000 0 -0.25 8 8
AKT1 -0.01 0.14 0.34 21 -0.39 11 32
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.004 0.14 0.28 1 -0.5 20 21
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
FGR 0.004 0.11 0.31 4 -0.43 21 25
mol:Ca2+ 0.006 0.13 0.26 2 -0.5 20 22
MYC 0.01 0.24 0.36 9 -0.72 40 49
SHC1 0.028 0.025 -10000 0 -0.42 1 1
HRAS/GDP 0.034 0.064 0.19 1 -0.22 16 17
LRP1/PDGFRB/PDGFB 0.058 0.06 -10000 0 -0.29 12 12
GRB10 0.023 0.075 -10000 0 -0.42 14 14
PTPN11 0.036 0.004 -10000 0 -10000 0 0
GO:0007205 0.005 0.13 -10000 0 -0.51 20 20
PTEN 0.027 0.061 -10000 0 -0.42 9 9
GRB2 0.033 0.011 -10000 0 -10000 0 0
GRB7 0.024 0.058 -10000 0 -0.42 8 8
PDGFB-D/PDGFRB/SHP2 0.047 0.046 -10000 0 -0.3 8 8
PDGFB-D/PDGFRB/GRB10 0.036 0.073 -10000 0 -0.3 22 22
cell cycle arrest 0.031 0.055 -10000 0 -0.3 11 11
HRAS 0.032 0.036 -10000 0 -0.42 3 3
HIF1A -0.025 0.13 0.32 19 -0.34 17 36
GAB1 -0.004 0.14 0.32 1 -0.49 25 26
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.005 0.14 0.3 4 -0.45 23 27
PDGFB-D/PDGFRB 0.052 0.055 -10000 0 -0.27 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.045 0.053 -10000 0 -0.3 11 11
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.01 0.15 0.3 1 -0.42 28 29
positive regulation of MAPKKK cascade 0.046 0.046 -10000 0 -0.3 8 8
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
mol:IP3 0.005 0.13 -10000 0 -0.51 20 20
E5 -0.001 0.002 -10000 0 -10000 0 0
CSK 0.034 0.022 -10000 0 -0.42 1 1
PDGFB-D/PDGFRB/GRB7 0.036 0.064 -10000 0 -0.3 16 16
SHB 0.031 0.046 -10000 0 -0.42 5 5
BLK -0.065 0.2 0.3 2 -0.43 96 98
PTPN2 0.034 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.045 0.046 -10000 0 -0.3 8 8
BCAR1 0.03 0.014 -10000 0 -10000 0 0
VAV2 -0.007 0.16 0.29 1 -0.48 30 31
CBL 0.032 0.012 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.042 0.058 -10000 0 -0.3 13 13
LCK -0.051 0.21 0.33 1 -0.56 63 64
PDGFRB 0.028 0.059 -10000 0 -0.43 8 8
ACP1 0.034 0.035 -10000 0 -0.42 3 3
HCK -0.003 0.14 0.32 4 -0.53 26 30
ABL1 -0.007 0.13 0.26 1 -0.44 26 27
PDGFB-D/PDGFRB/CBL -0.011 0.16 -10000 0 -0.55 27 27
PTPN1 0.03 0.031 -10000 0 -0.42 2 2
SNX15 0.035 0.007 -10000 0 -10000 0 0
STAT3 0.028 0.031 -10000 0 -0.42 2 2
STAT1 0.02 0.075 -10000 0 -0.42 14 14
cell proliferation 0.016 0.22 0.35 10 -0.64 40 50
SLA 0.022 0.047 -10000 0 -0.42 5 5
actin cytoskeleton reorganization 0.039 0.071 0.35 4 -0.22 8 12
SRC 0.013 0.094 0.3 5 -0.56 5 10
PI3K -0.038 0.095 -10000 0 -0.24 82 82
PDGFB-D/PDGFRB/GRB7/SHC 0.042 0.062 -10000 0 -0.26 15 15
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.004 0.14 0.28 1 -0.52 20 21
LYN 0.015 0.079 0.31 3 -0.36 9 12
LRP1 0.035 0.021 -10000 0 -0.42 1 1
SOS1 0.035 0.021 -10000 0 -0.42 1 1
STAT5B 0.03 0.024 -10000 0 -0.42 1 1
STAT5A 0.027 0.037 -10000 0 -0.42 3 3
NCK1-2/p130 Cas 0.067 0.068 -10000 0 -0.22 9 9
SPHK1 0.006 0.11 -10000 0 -0.42 30 30
EDG1 0.013 0.096 -10000 0 -0.42 23 23
mol:DAG 0.005 0.13 -10000 0 -0.51 20 20
PLCG1 0.005 0.14 -10000 0 -0.53 20 20
NHERF/PDGFRB 0.002 0.13 -10000 0 -0.28 80 80
YES1 -0.004 0.14 0.3 4 -0.48 28 32
cell migration 0.001 0.13 -10000 0 -0.28 80 80
SHC/Grb2/SOS1 0.06 0.068 -10000 0 -0.23 9 9
SLC9A3R2 -0.004 0.12 -10000 0 -0.42 40 40
SLC9A3R1 -0.009 0.13 -10000 0 -0.42 46 46
NHERF1-2/PDGFRB/PTEN 0.011 0.14 -10000 0 -0.27 86 86
FYN -0.013 0.16 0.31 2 -0.55 29 31
DOK1 0.021 0.071 0.2 38 -0.24 15 53
HRAS/GTP 0.024 0.025 -10000 0 -0.3 3 3
PDGFB 0.029 0.046 -10000 0 -0.42 5 5
RAC1 -0.022 0.2 0.29 1 -0.55 44 45
PRKCD 0.022 0.068 0.2 25 -0.26 10 35
FER 0.024 0.069 0.2 36 -0.24 10 46
MAPKKK cascade 0.043 0.11 0.34 23 -0.22 8 31
RASA1 0.021 0.072 0.2 33 -0.24 14 47
NCK1 0.034 0.021 -10000 0 -0.42 1 1
NCK2 0.036 0.005 -10000 0 -10000 0 0
p62DOK/Csk 0.042 0.065 0.34 2 -0.22 16 18
PDGFB-D/PDGFRB/SHB 0.042 0.058 -10000 0 -0.31 13 13
chemotaxis -0.006 0.13 0.26 1 -0.43 26 27
STAT1-3-5/STAT1-3-5 0.049 0.075 -10000 0 -0.22 24 24
Bovine Papilomavirus E5/PDGFRB 0.019 0.042 -10000 0 -0.3 8 8
PTPRJ 0.031 0.046 -10000 0 -0.42 5 5
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.009 0.017 -10000 0 -0.26 2 2
RAS family/GTP 0.03 0.11 0.25 1 -0.3 19 20
NFATC4 -0.03 0.068 0.23 1 -0.26 14 15
ERBB2IP 0.034 0.022 -10000 0 -0.42 1 1
HSP90 (dimer) 0 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.003 0.087 -10000 0 -0.26 36 36
JUN 0.008 0.074 0.2 2 -10000 0 2
HRAS 0.032 0.036 -10000 0 -0.42 3 3
DOCK7 -0.034 0.077 0.26 1 -0.27 28 29
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.02 0.089 -10000 0 -0.27 34 34
AKT1 0.003 0.021 -10000 0 -0.3 2 2
BAD -0.01 0.019 -10000 0 -0.25 3 3
MAPK10 -0.024 0.061 0.2 7 -0.21 15 22
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.002 0.094 -10000 0 -0.28 36 36
RAF1 0.011 0.11 0.27 12 -0.3 21 33
ErbB2/ErbB3/neuregulin 2 0.011 0.093 -10000 0 -0.27 45 45
STAT3 0.005 0.18 -10000 0 -0.88 19 19
cell migration -0.018 0.064 0.23 8 -0.21 10 18
mol:PI-3-4-5-P3 -0.001 0.001 -10000 0 -10000 0 0
cell proliferation -0.043 0.25 -10000 0 -0.64 54 54
FOS -0.045 0.21 0.31 1 -0.44 104 105
NRAS 0.029 0.054 -10000 0 -0.42 7 7
mol:Ca2+ -0.003 0.087 -10000 0 -0.26 36 36
MAPK3 -0.018 0.2 0.35 1 -0.52 47 48
MAPK1 -0.03 0.21 0.35 2 -0.55 49 51
JAK2 -0.032 0.078 0.26 1 -0.26 29 30
NF2 0.01 0.046 -10000 0 -0.68 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.002 0.072 0.18 3 -0.27 26 29
NRG1 0.028 0.015 -10000 0 -10000 0 0
GRB2/SOS1 0.048 0.023 -10000 0 -0.3 1 1
MAPK8 -0.019 0.098 0.22 2 -0.28 30 32
MAPK9 -0.023 0.058 0.2 6 -0.2 10 16
ERBB2 -0.03 0.055 0.6 1 -0.32 13 14
ERBB3 0.006 0.11 -10000 0 -0.42 32 32
SHC1 0.028 0.025 -10000 0 -0.42 1 1
RAC1 0.035 0.006 -10000 0 -10000 0 0
apoptosis 0.005 0.03 0.26 3 -0.21 4 7
STAT3 (dimer) 0.005 0.17 -10000 0 -0.86 19 19
RNF41 -0.013 0.016 -10000 0 -0.24 2 2
FRAP1 -0.009 0.012 -10000 0 -0.26 1 1
RAC1-CDC42/GTP -0.015 0.06 -10000 0 -0.2 28 28
ErbB2/ErbB2/HSP90 (dimer) -0.025 0.04 -10000 0 -0.26 13 13
CHRNA1 -0.004 0.16 0.33 1 -0.44 30 31
myelination -0.023 0.083 0.26 12 -0.32 7 19
PPP3CB -0.034 0.072 0.24 1 -0.25 30 31
KRAS 0.028 0.054 -10000 0 -0.42 7 7
RAC1-CDC42/GDP 0.039 0.096 0.25 1 -0.24 26 27
NRG2 0.025 0.061 -10000 0 -0.42 9 9
mol:GDP 0.002 0.072 0.18 3 -0.26 26 29
SOS1 0.035 0.021 -10000 0 -0.42 1 1
MAP2K2 -0.001 0.11 0.26 10 -0.32 25 35
SRC 0.033 0.029 -10000 0 -0.42 2 2
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.035 0.076 0.26 1 -0.26 29 30
MAP2K1 -0.029 0.21 -10000 0 -0.6 34 34
heart morphogenesis -0.003 0.087 -10000 0 -0.26 36 36
RAS family/GDP 0.041 0.11 0.26 1 -0.29 18 19
GRB2 0.033 0.011 -10000 0 -10000 0 0
PRKACA 0.014 0.054 -10000 0 -0.67 3 3
CHRNE 0.009 0.018 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
activation of caspase activity -0.003 0.021 0.3 2 -10000 0 2
nervous system development -0.003 0.087 -10000 0 -0.26 36 36
CDC42 0.035 0.008 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.003 0.14 -10000 0 -0.42 2 2
CRKL 0 0.076 0.24 5 -0.23 11 16
mol:DAG 0.019 0.08 0.25 2 -10000 0 2
HRAS 0.023 0.099 0.26 20 -10000 0 20
MAPK8 0.037 0.073 0.2 58 -0.25 2 60
RAP1A 0.001 0.077 0.24 5 -0.23 12 17
GAB1 0 0.076 0.23 4 -0.23 13 17
MAPK14 0.037 0.071 0.2 54 -10000 0 54
EPO 0.023 0.027 -10000 0 -10000 0 0
PLCG1 0.019 0.081 0.25 2 -10000 0 2
EPOR/TRPC2/IP3 Receptors 0.026 0.028 -10000 0 -10000 0 0
RAPGEF1 0.036 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.046 0.052 -10000 0 -0.27 4 4
GAB1/SHC/GRB2/SOS1 0.029 0.075 0.29 1 -0.2 7 8
EPO/EPOR (dimer) 0.037 0.039 -10000 0 -10000 0 0
IRS2 -0.009 0.087 0.21 10 -0.25 30 40
STAT1 -0.003 0.13 0.26 2 -0.27 78 80
STAT5B 0.021 0.081 0.26 1 -0.24 3 4
cell proliferation 0.014 0.079 0.19 76 -0.24 2 78
GAB1/SHIP/PIK3R1/SHP2/SHC 0.009 0.074 -10000 0 -0.21 22 22
TEC 0.001 0.076 0.21 8 -0.22 12 20
SOCS3 0.028 0.046 -10000 0 -0.42 5 5
STAT1 (dimer) -0.001 0.13 0.26 2 -0.27 79 81
JAK2 0.028 0.036 -10000 0 -0.44 2 2
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
EPO/EPOR (dimer)/JAK2 0.036 0.089 0.22 7 -0.17 41 48
EPO/EPOR 0.037 0.039 -10000 0 -10000 0 0
LYN 0.021 0.027 -10000 0 -10000 0 0
TEC/VAV2 0.016 0.081 0.29 2 -0.22 12 14
elevation of cytosolic calcium ion concentration 0.026 0.028 -10000 0 -10000 0 0
SHC1 0.028 0.025 -10000 0 -0.42 1 1
EPO/EPOR (dimer)/LYN 0.044 0.053 -10000 0 -10000 0 0
mol:IP3 0.019 0.08 0.25 2 -10000 0 2
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.005 0.095 0.29 1 -0.23 44 45
SH2B3 -0.003 0.009 -10000 0 -10000 0 0
NFKB1 0.038 0.072 0.2 56 -10000 0 56
EPO/EPOR (dimer)/JAK2/SOCS3 0.023 0.035 -10000 0 -0.21 6 6
PTPN6 -0.002 0.068 0.17 9 -0.18 28 37
TEC/VAV2/GRB2 0.028 0.084 0.3 2 -0.21 9 11
EPOR 0.026 0.028 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.028 0.076 0.3 1 -0.2 7 8
SOS1 0.035 0.021 -10000 0 -0.42 1 1
PLCG2 0.02 0.055 -10000 0 -0.42 7 7
CRKL/CBL/C3G 0.021 0.085 0.3 1 -0.23 10 11
VAV2 0.003 0.074 0.21 9 -0.23 8 17
CBL 0 0.071 0.23 4 -0.24 7 11
SHC/Grb2/SOS1 0.015 0.063 -10000 0 -0.2 4 4
STAT5A 0.019 0.082 0.26 1 -0.25 4 5
GRB2 0.033 0.011 -10000 0 -10000 0 0
STAT5 (dimer) 0.018 0.12 0.28 1 -0.31 44 45
LYN/PLCgamma2 0.03 0.043 -10000 0 -0.3 6 6
PTPN11 0.036 0.004 -10000 0 -10000 0 0
BTK -0.003 0.083 0.2 12 -0.24 21 33
BCL2 -0.11 0.33 -10000 0 -0.73 105 105
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.027 0.1 0.9 1 -0.78 1 2
VDR 0.02 0.082 -10000 0 -0.42 17 17
FAM120B 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.004 0.1 -10000 0 -0.27 49 49
RXRs/LXRs/DNA/Oxysterols 0.013 0.16 -10000 0 -0.4 56 56
MED1 0 0 -10000 0 -10000 0 0
mol:9cRA -0.001 0.019 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.004 0.092 -10000 0 -0.24 48 48
RXRs/NUR77 0.055 0.08 -10000 0 -0.25 11 11
RXRs/PPAR 0.009 0.076 -10000 0 -0.26 27 27
NCOR2 0.036 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.015 0.058 -10000 0 -0.3 17 17
RARs/VDR/DNA/Vit D3 0.053 0.083 -10000 0 -0.23 35 35
RARA 0.03 0.042 -10000 0 -0.42 4 4
NCOA1 0.031 0.045 -10000 0 -0.42 5 5
VDR/VDR/DNA 0.02 0.082 -10000 0 -0.42 17 17
RARs/RARs/DNA/9cRA 0.041 0.063 -10000 0 -0.22 23 23
RARG 0.036 0.005 -10000 0 -10000 0 0
RPS6KB1 0.054 0.15 0.54 42 -10000 0 42
RARs/THRs/DNA/SMRT 0.005 0.09 -10000 0 -0.24 47 47
THRA 0.02 0.075 -10000 0 -0.42 14 14
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.015 0.058 -10000 0 -0.3 17 17
RXRs/PPAR/9cRA/PGJ2/DNA 0.039 0.083 -10000 0 -0.24 16 16
NR1H4 0.035 0.021 -10000 0 -0.42 1 1
RXRs/LXRs/DNA 0.059 0.11 -10000 0 -0.25 14 14
NR1H2 0.029 0.031 -10000 0 -10000 0 0
NR1H3 0.026 0.052 -10000 0 -0.43 4 4
RXRs/VDR/DNA/Vit D3 0.044 0.084 -10000 0 -0.24 19 19
NR4A1 0.034 0.021 -10000 0 -0.42 1 1
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.026 0.063 -10000 0 -0.21 16 16
RXRG 0.017 0.06 -10000 0 -0.43 7 7
RXR alpha/CCPG 0.021 0.029 -10000 0 -0.31 2 2
RXRA 0.028 0.042 -10000 0 -0.44 2 2
RXRB 0.027 0.044 -10000 0 -0.26 4 4
THRB 0.024 0.07 -10000 0 -0.42 12 12
PPARG 0.012 0.093 -10000 0 -0.42 22 22
PPARD 0.036 0.006 -10000 0 -10000 0 0
TNF -0.001 0.19 -10000 0 -0.76 19 19
mol:Oxysterols -0.001 0.017 -10000 0 -10000 0 0
cholesterol transport 0.014 0.16 -10000 0 -0.4 56 56
PPARA 0.032 0.03 -10000 0 -0.42 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.015 0.089 -10000 0 -0.42 20 20
RXRs/NUR77/BCL2 -0.02 0.097 -10000 0 -0.22 84 84
SREBF1 -0.045 0.29 -10000 0 -0.94 45 45
RXRs/RXRs/DNA/9cRA 0.04 0.083 -10000 0 -0.24 16 16
ABCA1 -0.007 0.22 -10000 0 -0.9 19 19
RARs/THRs 0.063 0.1 -10000 0 -0.24 45 45
RXRs/FXR 0.056 0.081 -10000 0 -0.25 12 12
BCL2 -0.057 0.18 -10000 0 -0.42 99 99
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.027 0.032 -9999 0 -0.42 2 2
Syndecan-3/Src/Cortactin 0.007 0.15 -9999 0 -0.47 28 28
Syndecan-3/Neurocan -0.018 0.12 -9999 0 -0.48 30 30
POMC 0.032 0.036 -9999 0 -0.42 3 3
EGFR -0.015 0.13 -9999 0 -0.42 49 49
Syndecan-3/EGFR -0.011 0.15 -9999 0 -0.51 31 31
AGRP 0.029 0.025 -9999 0 -0.42 1 1
NCSTN 0.028 0.025 -9999 0 -0.42 1 1
PSENEN 0.035 0.006 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.025 0.067 -9999 0 -0.42 11 11
APH1A 0.031 0.036 -9999 0 -0.42 3 3
NCAN 0 0 -9999 0 -10000 0 0
long-term memory 0.018 0.12 -9999 0 -0.46 26 26
Syndecan-3/IL8 -0.007 0.14 -9999 0 -0.52 30 30
PSEN1 0.032 0.041 -9999 0 -0.42 4 4
Src/Cortactin 0.039 0.038 -9999 0 -0.3 4 4
FYN 0.027 0.054 -9999 0 -0.42 7 7
limb bud formation -0.015 0.12 -9999 0 -0.53 26 26
MC4R 0.034 0.022 -9999 0 -0.42 1 1
SRC 0.033 0.029 -9999 0 -0.42 2 2
PTN -0.029 0.15 -9999 0 -0.42 65 65
FGFR/FGF/Syndecan-3 -0.015 0.12 -9999 0 -0.53 26 26
neuron projection morphogenesis -0.031 0.12 -9999 0 -0.48 25 25
Syndecan-3/AgRP 0.009 0.13 -9999 0 -0.48 29 29
Syndecan-3/AgRP/MC4R 0.024 0.13 -9999 0 -0.5 25 25
Fyn/Cortactin 0.035 0.044 -9999 0 -0.3 6 6
SDC3 -0.016 0.12 -9999 0 -0.54 26 26
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.006 0.14 -9999 0 -0.51 30 30
IL8 -0.004 0.12 -9999 0 -0.42 37 37
Syndecan-3/Fyn/Cortactin 0.019 0.13 -9999 0 -0.47 26 26
Syndecan-3/CASK -0.018 0.12 -9999 0 -0.48 30 30
alpha-MSH/MC4R 0.047 0.034 -9999 0 -0.3 4 4
Gamma Secretase 0.069 0.069 -9999 0 -0.22 13 13
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.047 0.04 -10000 0 -0.3 6 6
Necdin/E2F1 0.013 0.11 -10000 0 -0.31 54 54
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.031 0.11 -10000 0 -0.23 70 70
NGF (dimer)/p75(NTR)/BEX1 0.038 0.035 -10000 0 -0.25 6 6
NT-4/5 (dimer)/p75(NTR) 0.022 0.026 -10000 0 -0.3 3 3
IKBKB 0.03 0.014 -10000 0 -10000 0 0
AKT1 0.021 0.069 0.19 43 -0.22 20 63
IKBKG 0.036 0 -10000 0 -10000 0 0
BDNF 0.031 0.024 -10000 0 -0.42 1 1
MGDIs/NGR/p75(NTR)/LINGO1 0.034 0.049 -10000 0 -0.25 13 13
FURIN 0.027 0.057 -10000 0 -0.42 8 8
proBDNF (dimer)/p75(NTR)/Sortilin 0.058 0.047 -10000 0 -0.25 9 9
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.026 0.054 -10000 0 -0.22 17 17
proBDNF (dimer) 0.031 0.024 -10000 0 -0.42 1 1
NTRK1 0.026 0.032 -10000 0 -0.42 2 2
RTN4R 0.024 0.067 -10000 0 -0.42 11 11
neuron apoptosis -0.008 0.1 0.28 1 -0.44 10 11
IRAK1 0.036 0.004 -10000 0 -10000 0 0
SHC1 0.012 0.022 -10000 0 -0.25 3 3
ARHGDIA 0.033 0.022 -10000 0 -0.42 1 1
RhoA/GTP 0.02 0.043 -10000 0 -0.3 9 9
Gamma Secretase 0.069 0.069 -10000 0 -0.22 13 13
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.04 0.083 -10000 0 -0.24 38 38
MAGEH1 0.006 0.11 -10000 0 -0.42 34 34
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.03 0.097 -10000 0 -0.24 54 54
Mammalian IAPs/DIABLO 0.034 0.082 -10000 0 -0.23 39 39
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.015 0.095 -10000 0 -0.42 23 23
APP 0.008 0.11 -10000 0 -0.42 29 29
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.034 0.029 -10000 0 -0.42 2 2
RhoA/GDP/RHOGDI 0.038 0.045 0.18 4 -0.21 12 16
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.01 0.05 0.2 18 -0.21 9 27
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.021 0.031 -10000 0 -0.21 6 6
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.042 0.03 -10000 0 -0.25 4 4
NCSTN 0.028 0.025 -10000 0 -0.42 1 1
mol:GTP 0.025 0.068 -10000 0 -0.25 28 28
PSENEN 0.035 0.006 -10000 0 -10000 0 0
mol:ceramide 0.016 0.044 0.19 13 -0.23 10 23
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.013 0.036 -10000 0 -0.18 14 14
p75(NTR)/beta APP 0.026 0.084 -10000 0 -0.3 30 30
BEX1 0.027 0.037 -10000 0 -0.42 3 3
mol:GDP -0.006 0.019 -10000 0 -0.25 3 3
NGF (dimer) 0.008 0.11 -10000 0 -0.23 76 76
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.049 0.054 -10000 0 -0.23 14 14
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
RAC1/GTP 0.037 0.023 -10000 0 -0.21 3 3
MYD88 0.031 0.041 -10000 0 -0.42 4 4
CHUK 0.026 0.067 -10000 0 -0.42 11 11
NGF (dimer)/p75(NTR)/PKA 0.025 0.069 -10000 0 -0.25 28 28
RHOB -0.011 0.14 -10000 0 -0.42 52 52
RHOA 0.026 0.061 -10000 0 -0.42 9 9
MAGE-G1/E2F1 0.045 0.043 -10000 0 -0.3 7 7
NT3 (dimer) 0.023 0.058 -10000 0 -0.42 8 8
TP53 -0.019 0.066 0.35 1 -0.23 17 18
PRDM4 0.02 0.046 0.19 18 -0.23 9 27
BDNF (dimer) -0.018 0.16 -10000 0 -0.31 110 110
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
SORT1 0.03 0.05 -10000 0 -0.42 6 6
activation of caspase activity 0.025 0.11 -10000 0 -0.23 70 70
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.057 0.044 -10000 0 -0.23 9 9
RHOC 0.033 0.036 -10000 0 -0.42 3 3
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.016 0.079 0.22 1 -0.29 13 14
DIABLO 0.036 0.004 -10000 0 -10000 0 0
SMPD2 0.016 0.045 0.19 13 -0.23 10 23
APH1B 0.025 0.067 -10000 0 -0.42 11 11
APH1A 0.031 0.036 -10000 0 -0.42 3 3
proNGF (dimer)/p75(NTR)/Sortilin 0.039 0.041 -10000 0 -0.25 9 9
PSEN1 0.032 0.041 -10000 0 -0.42 4 4
APAF-1/Pro-Caspase 9 0.047 0.037 -10000 0 -0.3 5 5
NT3 (dimer)/p75(NTR) 0.037 0.053 -10000 0 -0.3 11 11
MAPK8 -0.01 0.066 -10000 0 -0.27 7 7
MAPK9 -0.015 0.078 -10000 0 -0.32 11 11
APAF1 0.032 0.041 -10000 0 -0.42 4 4
NTF3 0.023 0.058 -10000 0 -0.42 8 8
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.012 0.14 -10000 0 -0.42 53 53
RAC1/GDP 0.026 0.004 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.018 0.11 -10000 0 -0.22 85 85
p75 CTF/Sortilin/TRAF6/NRIF 0.082 0.047 -10000 0 -0.23 8 8
RhoA-B-C/GTP 0.024 0.068 -10000 0 -0.25 28 28
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.086 0.059 -10000 0 -0.22 12 12
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.074 0.052 -10000 0 -0.23 10 10
PRKACB 0.008 0.099 -10000 0 -0.42 25 25
proBDNF (dimer)/p75 ECD 0.048 0.02 -10000 0 -0.3 1 1
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.008 0.12 -10000 0 -0.42 40 40
BIRC2 0.032 0.012 -10000 0 -10000 0 0
neuron projection morphogenesis -0.038 0.08 0.13 2 -0.26 38 40
BAD -0.02 0.079 -10000 0 -0.29 10 10
RIPK2 0.028 0.015 -10000 0 -10000 0 0
NGFR 0.03 0.036 -10000 0 -0.42 3 3
CYCS 0.005 0.064 0.19 13 -0.22 32 45
ADAM17 0.036 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.048 0.04 -10000 0 -0.23 4 4
BCL2L11 -0.019 0.079 -10000 0 -0.29 10 10
BDNF (dimer)/p75(NTR) 0.044 0.034 -10000 0 -0.3 4 4
PI3K 0.046 0.061 -10000 0 -0.23 19 19
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.056 0.045 -10000 0 -0.23 9 9
NDNL2 0.035 0.008 -10000 0 -10000 0 0
YWHAE 0.032 0.012 -10000 0 -10000 0 0
PRKCI 0.025 0.064 -10000 0 -0.42 10 10
NGF (dimer)/p75(NTR) 0.022 0.026 -10000 0 -0.3 3 3
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.045 0.074 -10000 0 -0.23 32 32
TRAF6 0.035 0.021 -10000 0 -0.42 1 1
RAC1 0.035 0.006 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.032 0.03 -10000 0 -0.42 2 2
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.018 0.046 0.16 3 -0.24 14 17
SQSTM1 0.034 0.021 -10000 0 -0.42 1 1
NGFRAP1 -0.025 0.16 -10000 0 -0.42 68 68
CASP3 -0.018 0.077 -10000 0 -0.27 10 10
E2F1 0.029 0.054 -10000 0 -0.42 7 7
CASP9 0.034 0.022 -10000 0 -0.42 1 1
IKK complex 0.042 0.064 -10000 0 -0.31 1 1
NGF (dimer)/TRKA 0.019 0.023 -10000 0 -0.3 2 2
MMP7 -0.032 0.15 -10000 0 -0.42 68 68
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.07 0.051 -10000 0 -0.22 11 11
MMP3 -0.045 0.16 -10000 0 -0.42 81 81
APAF-1/Caspase 9 -0.04 0.065 -10000 0 -0.19 66 66
Atypical NF-kappaB pathway

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
BCL3/RelA 0.045 0.048 -10000 0 -0.3 9 9
FBXW11 0.033 0.029 -10000 0 -0.42 2 2
NF kappa B1 p50/c-Rel 0.026 0.039 -10000 0 -0.25 8 8
NF kappa B1 p50/RelA/I kappa B alpha 0.003 0.1 0.2 1 -0.35 19 20
NFKBIA -0.016 0.1 -10000 0 -0.24 75 75
MAPK14 0.036 0.005 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.029 0.024 -10000 0 -0.24 2 2
ARRB2 0.017 0.006 -10000 0 -10000 0 0
REL 0.025 0.07 -10000 0 -0.42 12 12
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.026 0.039 -10000 0 -0.25 8 8
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.031 0.017 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
NF kappa B1 p50 dimer 0.023 0.021 0.26 3 -10000 0 3
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
NFKB1 0.014 0.007 -10000 0 -10000 0 0
RELA 0.035 0.006 -10000 0 -10000 0 0
positive regulation of anti-apoptosis -0.004 0.1 -10000 0 -0.25 52 52
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.003 0.1 -10000 0 -0.35 20 20
SRC 0.033 0.029 -10000 0 -0.42 2 2
PI3K 0.036 0.065 -10000 0 -0.3 17 17
NF kappa B1 p50/RelA -0.003 0.099 -10000 0 -0.25 50 50
IKBKB 0.03 0.014 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.029 -10000 0 -0.42 2 2
SYK 0.005 0.11 -10000 0 -0.42 34 34
I kappa B alpha/PIK3R1 -0.008 0.12 -10000 0 -0.24 83 83
cell death 0.003 0.099 -10000 0 -0.33 20 20
NF kappa B1 p105/c-Rel 0.026 0.039 -10000 0 -0.25 8 8
LCK -0.017 0.14 -10000 0 -0.42 54 54
BCL3 0.027 0.061 -10000 0 -0.42 9 9
Ras signaling in the CD4+ TCR 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
ERK1-2/ELK1 0.018 0.14 -9999 0 -0.4 21 21
MAP3K8 0.003 0.11 -9999 0 -0.42 32 32
FOS 0.021 0.097 -9999 0 -0.42 7 7
PRKCA 0.025 0.022 -9999 0 -10000 0 0
PTPN7 0.02 0.032 -9999 0 -0.44 1 1
HRAS 0.032 0.036 -9999 0 -0.42 3 3
PRKCB -0.002 0.006 -9999 0 -0.017 73 73
NRAS 0.029 0.054 -9999 0 -0.42 7 7
RAS family/GTP 0.05 0.055 -9999 0 -0.23 15 15
MAPK3 0.028 0.067 -9999 0 -0.44 6 6
MAP2K1 0.009 0.064 -9999 0 -0.23 9 9
ELK1 0.025 0.038 -9999 0 -0.42 2 2
BRAF 0.006 0.047 -9999 0 -0.35 7 7
mol:GTP -0.001 0.002 -9999 0 -0.005 73 73
MAPK1 0.013 0.099 -9999 0 -0.41 18 18
RAF1 0.01 0.023 -9999 0 -0.24 1 1
KRAS 0.028 0.054 -9999 0 -0.42 7 7
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.035 0.006 -10000 0 -10000 0 0
VLDLR -0.007 0.12 -10000 0 -0.42 42 42
LRPAP1 0.035 0.007 -10000 0 -10000 0 0
NUDC 0.035 0.007 -10000 0 -10000 0 0
RELN/LRP8 0.039 0.089 -10000 0 -0.25 40 40
CaM/Ca2+ 0.026 0.005 -10000 0 -10000 0 0
KATNA1 0.033 0.01 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.001 0.073 0.19 10 -0.23 40 50
IQGAP1/CaM 0.05 0.015 -10000 0 -10000 0 0
DAB1 0.035 0.007 -10000 0 -10000 0 0
IQGAP1 0.035 0.008 -10000 0 -10000 0 0
PLA2G7 -0.035 0.16 -10000 0 -0.42 74 74
CALM1 0.035 0.007 -10000 0 -10000 0 0
DYNLT1 0.034 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.024 0.089 -10000 0 -0.3 35 35
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0 0 -10000 0 -10000 0 0
CDK5R1 0.033 0.01 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.011 0.012 -10000 0 -0.25 1 1
CDK5R2 0.036 0.005 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.033 0.097 -10000 0 -0.26 46 46
YWHAE 0.032 0.012 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.016 0.07 0.33 1 -0.24 4 5
MAP1B -0.009 0.064 -10000 0 -0.26 30 30
RAC1 0.016 0.007 -10000 0 -10000 0 0
p35/CDK5 0.008 0.067 0.2 2 -0.21 38 40
RELN 0.03 0.046 -10000 0 -0.42 5 5
PAFAH/LIS1 -0.01 0.1 -10000 0 -0.25 74 74
LIS1/CLIP170 0.011 0.012 -10000 0 -0.25 1 1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.018 0.068 -10000 0 -0.23 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.009 0.1 -10000 0 -0.26 61 61
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.002 0.062 0.33 1 -0.26 4 5
LIS1/IQGAP1 0.034 0.014 -10000 0 -10000 0 0
RHOA 0.008 0.056 -10000 0 -0.4 9 9
PAFAH1B1 0.014 0.015 -10000 0 -0.3 1 1
PAFAH1B3 0.03 0.054 -10000 0 -0.42 7 7
PAFAH1B2 0.031 0.013 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.015 0.061 -10000 0 -0.18 29 29
NDEL1/Katanin 60/Dynein heavy chain 0.023 0.08 0.37 2 -0.25 4 6
LRP8 -0.001 0.12 -10000 0 -0.42 35 35
NDEL1/Katanin 60 0.009 0.072 0.33 1 -0.25 4 5
P39/CDK5 0.009 0.068 0.2 2 -0.21 40 42
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.033 0.019 -10000 0 -0.26 1 1
CDK5 -0.026 0.063 0.18 9 -0.22 40 49
PPP2R5D 0.035 0.006 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.009 0.011 -10000 0 -0.21 1 1
CSNK2A1 0.035 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.035 0.091 -10000 0 -0.23 46 46
RELN/VLDLR 0.025 0.12 -10000 0 -0.24 80 80
CDC42 0.016 0.007 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.035 0.021 -10000 0 -0.42 1 1
HDAC2 0.032 0.023 -10000 0 -0.42 1 1
GNB1/GNG2 0.034 0.1 -10000 0 -0.26 53 53
forebrain development -0.005 0.14 -10000 0 -0.56 18 18
GNAO1 0.03 0.014 -10000 0 -10000 0 0
SMO/beta Arrestin2 0.014 0.1 -10000 0 -0.3 48 48
SMO -0.01 0.13 -10000 0 -0.42 48 48
ARRB2 0.033 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.005 0.15 -10000 0 -0.4 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
GSK3B 0.036 0.005 -10000 0 -10000 0 0
GNAI2 0.028 0.054 -10000 0 -0.42 7 7
SIN3/HDAC complex 0.076 0.045 -10000 0 -0.23 5 5
GNAI1 0.017 0.087 -10000 0 -0.42 19 19
XPO1 0.037 0.005 -10000 0 -10000 0 0
GLI1/Su(fu) -0.02 0.17 -10000 0 -0.56 27 27
SAP30 0.03 0.046 -10000 0 -0.42 5 5
mol:GDP -0.01 0.13 -10000 0 -0.42 48 48
MIM/GLI2A 0.002 0.11 -10000 0 -0.42 31 31
IFT88 0.021 0.075 -10000 0 -0.42 14 14
GNAI3 0.036 0.006 -10000 0 -10000 0 0
GLI2 0.014 0.079 -10000 0 -0.33 15 15
GLI3 -0.008 0.15 0.24 3 -0.4 33 36
CSNK1D 0.034 0.009 -10000 0 -10000 0 0
CSNK1E 0.034 0.009 -10000 0 -10000 0 0
SAP18 0.034 0.01 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.021 0.075 -10000 0 -0.42 14 14
GNG2 0.034 0.021 -10000 0 -0.42 1 1
Gi family/GTP -0.017 0.12 -10000 0 -0.3 54 54
SIN3B 0.036 0.005 -10000 0 -10000 0 0
SIN3A 0.035 0.007 -10000 0 -10000 0 0
GLI3/Su(fu) -0.006 0.14 -10000 0 -0.4 41 41
GLI2/Su(fu) 0.004 0.11 -10000 0 -0.4 17 17
FOXA2 -0.022 0.2 -10000 0 -0.7 35 35
neural tube patterning -0.005 0.14 -10000 0 -0.56 18 18
SPOP 0.033 0.022 -10000 0 -0.42 1 1
Su(fu)/PIAS1 0.009 0.091 -10000 0 -0.32 16 16
GNB1 0.032 0.045 -10000 0 -0.42 5 5
CSNK1G2 0.033 0.029 -10000 0 -0.42 2 2
CSNK1G3 0.035 0.007 -10000 0 -10000 0 0
MTSS1 0.002 0.11 -10000 0 -0.42 31 31
embryonic limb morphogenesis -0.005 0.14 -10000 0 -0.56 18 18
SUFU -0.001 0.084 -10000 0 -0.35 16 16
LGALS3 -0.009 0.14 -10000 0 -0.42 49 49
catabolic process 0.015 0.15 -10000 0 -0.47 22 22
GLI3A/CBP 0.035 0.042 -10000 0 -0.33 6 6
KIF3A 0.029 0.054 -10000 0 -0.42 7 7
GLI1 -0.006 0.14 -10000 0 -0.58 18 18
RAB23 0.03 0.046 -10000 0 -0.42 5 5
CSNK1A1 0.036 0.006 -10000 0 -10000 0 0
IFT172 0.033 0.035 -10000 0 -0.42 3 3
RBBP7 0.034 0.029 -10000 0 -0.42 2 2
Su(fu)/Galectin3 -0.014 0.12 -10000 0 -0.3 57 57
GNAZ 0.023 0.07 -10000 0 -0.42 12 12
RBBP4 0.035 0.021 -10000 0 -0.42 1 1
CSNK1G1 0.035 0.007 -10000 0 -10000 0 0
PIAS1 0.035 0.007 -10000 0 -10000 0 0
PRKACA 0.036 0.005 -10000 0 -10000 0 0
GLI2/SPOP 0.028 0.082 -10000 0 -0.32 14 14
STK36 0.021 0.082 -10000 0 -0.42 17 17
Gi family/GNB1/GNG2/GDP -0.021 0.12 -10000 0 -0.38 37 37
PTCH1 -0.004 0.13 -10000 0 -0.51 18 18
MIM/GLI1 -0.001 0.14 -10000 0 -0.54 16 16
CREBBP 0.035 0.042 -10000 0 -0.33 6 6
Su(fu)/SIN3/HDAC complex 0.009 0.097 -10000 0 -0.4 18 18
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.015 0.039 -10000 0 -0.25 13 13
ADCY5 -0.013 0.039 -10000 0 -0.25 13 13
ADCY6 -0.012 0.026 -10000 0 -0.25 6 6
ADCY7 -0.009 0.024 -10000 0 -0.25 5 5
ADCY1 -0.011 0.024 -10000 0 -0.25 5 5
ADCY2 -0.029 0.071 -10000 0 -0.26 44 44
ADCY3 -0.014 0.036 -10000 0 -0.25 11 11
ADCY8 -0.008 0.022 -10000 0 -0.25 4 4
PRKCE 0.005 0.033 -10000 0 -0.3 6 6
ADCY9 -0.016 0.045 -10000 0 -0.27 15 15
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.021 0.086 0.2 44 -0.26 9 53
HIF-2-alpha transcription factor network

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
MMP14 -0.007 0.28 -10000 0 -1 34 34
oxygen homeostasis 0.005 0.01 -10000 0 -10000 0 0
TCEB2 0.033 0.011 -10000 0 -10000 0 0
TCEB1 0.028 0.025 -10000 0 -0.42 1 1
VHL/Elongin B/Elongin C/HIF2A 0.054 0.11 -10000 0 -0.33 11 11
EPO 0.072 0.18 -10000 0 -0.52 16 16
FIH (dimer) 0.037 0.02 -10000 0 -10000 0 0
APEX1 0.035 0.028 -10000 0 -10000 0 0
SERPINE1 0.056 0.2 -10000 0 -0.55 27 27
FLT1 -0.043 0.28 -10000 0 -0.8 48 48
ADORA2A 0.044 0.18 0.35 1 -0.53 24 25
germ cell development 0.064 0.18 -10000 0 -0.53 19 19
SLC11A2 0.065 0.19 -10000 0 -0.56 20 20
BHLHE40 0.053 0.18 -10000 0 -0.53 21 21
HIF1AN 0.038 0.02 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.073 0.15 0.33 1 -0.4 16 17
ETS1 0.037 0.033 -10000 0 -0.42 1 1
CITED2 0.016 0.18 -10000 0 -0.84 16 16
KDR -0.015 0.24 -10000 0 -0.76 32 32
PGK1 0.066 0.19 -10000 0 -0.54 20 20
SIRT1 0.036 0.006 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.11 0.23 -10000 0 -0.62 20 20
EPAS1 0.027 0.12 -10000 0 -0.33 24 24
SP1 0.033 0.039 -10000 0 -0.42 1 1
ABCG2 0.061 0.2 -10000 0 -0.58 21 21
EFNA1 0.032 0.19 -10000 0 -0.52 32 32
FXN 0.052 0.18 -10000 0 -0.53 19 19
POU5F1 0.064 0.19 -10000 0 -0.55 19 19
neuron apoptosis -0.1 0.22 0.6 20 -10000 0 20
EP300 0.032 0.03 -10000 0 -0.42 2 2
EGLN3 -0.012 0.14 -10000 0 -0.42 52 52
EGLN2 0.034 0.045 -10000 0 -0.41 4 4
EGLN1 0.023 0.057 -10000 0 -0.42 7 7
VHL/Elongin B/Elongin C 0.054 0.036 -10000 0 -0.26 1 1
VHL 0.035 0.007 -10000 0 -10000 0 0
ARNT 0.035 0.027 -10000 0 -10000 0 0
SLC2A1 0.046 0.18 -10000 0 -0.52 23 23
TWIST1 0.038 0.21 -10000 0 -0.58 35 35
ELK1 0.039 0.032 -10000 0 -0.32 3 3
HIF2A/ARNT/Cbp/p300 0.071 0.15 0.34 1 -0.41 14 15
VEGFA 0.053 0.18 -10000 0 -0.53 21 21
CREBBP 0.033 0.011 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.041 0.019 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.035 0.007 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.018 0.078 -10000 0 -0.42 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.029 0.024 -10000 0 -0.42 1 1
RAC1-CDC42/GTP/PAK family 0.002 0.065 -10000 0 -0.21 39 39
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.029 0.05 -10000 0 -0.42 6 6
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.031 0.013 -10000 0 -10000 0 0
FYN 0.027 0.054 -10000 0 -0.42 7 7
MAP3K12 0.036 0.004 -10000 0 -10000 0 0
FGR 0.035 0.008 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.005 0.14 0.21 4 -0.33 55 59
PRKG1 0.035 0.006 -10000 0 -10000 0 0
DUSP8 0.02 0.08 -10000 0 -0.42 16 16
PGK/cGMP/p38 alpha -0.009 0.14 0.2 2 -0.31 59 61
apoptosis -0.005 0.14 0.2 4 -0.32 55 59
RAL/GTP 0.045 0.028 -10000 0 -0.25 4 4
LYN 0.03 0.014 -10000 0 -10000 0 0
DUSP1 0.003 0.11 -10000 0 -0.42 34 34
PAK1 0.015 0.085 -10000 0 -0.42 18 18
SRC 0.033 0.029 -10000 0 -0.42 2 2
RAC1/OSM/MEKK3/MKK3 0.073 0.041 -10000 0 -0.23 1 1
TRAF6 0.035 0.021 -10000 0 -0.42 1 1
RAC1 0.035 0.006 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.035 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.046 0.013 -10000 0 -10000 0 0
MAPK11 -0.014 0.14 0.24 3 -0.38 41 44
BLK 0.022 0.038 -10000 0 -0.42 3 3
HCK 0.018 0.087 -10000 0 -0.42 19 19
MAP2K3 0.032 0.023 -10000 0 -0.42 1 1
DUSP16 0.03 0.046 -10000 0 -0.42 5 5
DUSP10 0.013 0.082 -10000 0 -0.42 17 17
TRAF6/MEKK3 0.039 0.021 -10000 0 -0.23 1 1
MAP3K7IP1 0.034 0.009 -10000 0 -10000 0 0
MAPK14 -0.018 0.14 0.21 5 -0.34 59 64
positive regulation of innate immune response -0.018 0.17 0.26 5 -0.42 50 55
LCK -0.017 0.14 -10000 0 -0.42 54 54
p38alpha-beta/MKP7 -0.007 0.17 0.27 5 -0.4 51 56
p38alpha-beta/MKP5 -0.013 0.16 0.27 4 -0.4 49 53
PGK/cGMP 0.026 0.004 -10000 0 -10000 0 0
PAK2 0.036 0 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.018 0.17 0.28 3 -0.41 53 56
CDC42 0.035 0.008 -10000 0 -10000 0 0
RALB 0.032 0.041 -10000 0 -0.42 4 4
RALA 0.035 0.007 -10000 0 -10000 0 0
PAK3 0.016 0.085 -10000 0 -0.42 18 18
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.031 0.041 -10000 0 -0.42 4 4
RAS family/GTP/Tiam1 0.011 0.068 -10000 0 -0.28 19 19
NT3 (dimer)/TRKC 0.039 0.046 -10000 0 -0.3 8 8
NT3 (dimer)/TRKB 0.046 0.071 -10000 0 -0.26 22 22
SHC/Grb2/SOS1/GAB1/PI3K 0.016 0.05 -10000 0 -0.2 20 20
RAPGEF1 0.036 0.004 -10000 0 -10000 0 0
BDNF 0.031 0.024 -10000 0 -0.42 1 1
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
DYNLT1 0.034 0.01 -10000 0 -10000 0 0
NTRK1 0.026 0.032 -10000 0 -0.42 2 2
NTRK2 0.02 0.078 -10000 0 -0.42 15 15
NTRK3 0.031 0.013 -10000 0 -10000 0 0
NT-4/5 (dimer)/TRKB 0.033 0.055 -10000 0 -0.25 17 17
neuron apoptosis 0.002 0.14 0.31 55 -0.28 2 57
SHC 2-3/Grb2 -0.003 0.15 0.29 2 -0.33 55 57
SHC1 0.028 0.025 -10000 0 -0.42 1 1
SHC2 -0.036 0.18 0.24 1 -0.44 76 77
SHC3 0.018 0.11 0.25 3 -0.41 20 23
STAT3 (dimer) -0.016 0.13 -10000 0 -0.34 69 69
NT3 (dimer)/TRKA 0.042 0.055 -10000 0 -0.25 11 11
RIN/GDP 0.068 0.084 0.24 27 -0.25 7 34
GIPC1 0.033 0.035 -10000 0 -0.42 3 3
KRAS 0.028 0.054 -10000 0 -0.42 7 7
DNAJA3 0.007 0.057 0.21 18 -0.26 5 23
RIN/GTP 0.025 0.021 -10000 0 -0.3 2 2
CCND1 -0.077 0.24 -10000 0 -0.69 67 67
MAGED1 0.015 0.095 -10000 0 -0.42 23 23
PTPN11 0.036 0.004 -10000 0 -10000 0 0
RICS 0.023 0.061 -10000 0 -0.42 9 9
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.052 0.036 -10000 0 -0.26 1 1
GRB2 0.033 0.011 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.033 0.033 -10000 0 -0.25 4 4
TRKA/NEDD4-2 0.021 0.08 -10000 0 -0.3 27 27
ELMO1 0.035 0.006 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.041 0.039 -10000 0 -0.25 8 8
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.032 0.036 -10000 0 -0.42 3 3
DOCK1 0.028 0.057 -10000 0 -0.42 8 8
GAB2 0.031 0.013 -10000 0 -10000 0 0
RIT2 0.033 0.029 -10000 0 -0.42 2 2
RIT1 0.027 0.032 -10000 0 -0.42 2 2
FRS2 0.033 0.022 -10000 0 -0.42 1 1
DNM1 0.033 0.035 -10000 0 -0.42 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.023 -10000 0 -0.42 1 1
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.043 0.068 0.23 21 -0.25 5 26
mol:GDP 0.071 0.11 0.29 26 -0.36 8 34
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.026 0.005 -10000 0 -10000 0 0
RIT1/GDP 0.041 0.071 0.24 8 -0.24 6 14
TIAM1 0.028 0.057 -10000 0 -0.42 8 8
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
BDNF (dimer)/TRKB 0.052 0.064 -10000 0 -0.25 19 19
KIDINS220/CRKL/C3G 0.047 0.034 -10000 0 -0.3 4 4
SHC/RasGAP 0.037 0.044 -10000 0 -0.3 6 6
FRS2 family/SHP2 0.067 0.025 -10000 0 -0.26 1 1
SHC/GRB2/SOS1/GAB1 0.061 0.054 -10000 0 -0.23 6 6
RIT1/GTP 0.02 0.023 -10000 0 -0.3 2 2
NT3 (dimer) 0.023 0.058 -10000 0 -0.42 8 8
RAP1/GDP 0.048 0.067 0.18 17 -0.23 6 23
KIDINS220/CRKL 0.031 0.041 -10000 0 -0.42 4 4
BDNF (dimer) 0.031 0.024 -10000 0 -0.42 1 1
ubiquitin-dependent protein catabolic process 0.02 0.068 -10000 0 -0.25 27 27
Schwann cell development -0.007 0.013 -10000 0 -10000 0 0
EHD4 0.031 0.041 -10000 0 -0.42 4 4
FRS2 family/GRB2/SOS1 0.077 0.041 -10000 0 -0.44 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.025 0.06 -10000 0 -0.25 5 5
RAP1B 0.033 0.03 -10000 0 -0.42 2 2
RAP1A 0.031 0.045 -10000 0 -0.42 5 5
CDC42/GTP 0.043 0.07 -10000 0 -0.21 27 27
ABL1 0.036 0.005 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.048 0.023 -10000 0 -0.3 1 1
Rap1/GTP 0.023 0.092 -10000 0 -0.38 11 11
STAT3 -0.016 0.13 -10000 0 -0.34 69 69
axon guidance 0.026 0.061 -10000 0 -0.21 27 27
MAPK3 0.05 0.077 0.19 101 -0.23 5 106
MAPK1 0.051 0.077 0.19 103 -0.23 5 108
CDC42/GDP 0.069 0.085 0.24 30 -0.24 7 37
NTF3 0.023 0.058 -10000 0 -0.42 8 8
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.035 0.031 -10000 0 -0.25 3 3
PI3K 0.036 0.065 -10000 0 -0.3 17 17
FRS3 0.035 0.007 -10000 0 -10000 0 0
FAIM 0.035 0.021 -10000 0 -0.42 1 1
GAB1 0.027 0.061 -10000 0 -0.42 9 9
RASGRF1 0.008 0.062 0.22 19 -0.23 8 27
SOS1 0.035 0.021 -10000 0 -0.42 1 1
MCF2L 0.013 0.037 -10000 0 -0.25 9 9
RGS19 0.031 0.031 -10000 0 -0.42 2 2
CDC42 0.035 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.068 0.098 0.32 3 -0.37 8 11
Rac1/GDP 0.068 0.086 0.24 29 -0.25 7 36
NGF (dimer)/TRKA/GRIT 0.026 0.047 -10000 0 -0.25 11 11
neuron projection morphogenesis -0.005 0.2 0.44 2 -0.84 18 20
NGF (dimer)/TRKA/NEDD4-2 0.02 0.068 -10000 0 -0.25 27 27
MAP2K1 0.035 0.1 0.2 129 -0.22 6 135
NGFR 0.03 0.036 -10000 0 -0.42 3 3
NGF (dimer)/TRKA/GIPC/GAIP 0.019 0.038 -10000 0 -0.26 7 7
RAS family/GTP/PI3K 0.012 0.065 -10000 0 -0.24 28 28
FRS2 family/SHP2/GRB2/SOS1 0.09 0.047 -10000 0 -0.42 1 1
NRAS 0.029 0.054 -10000 0 -0.42 7 7
GRB2/SOS1 0.048 0.023 -10000 0 -0.3 1 1
PRKCI 0.025 0.064 -10000 0 -0.42 10 10
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.005 0.061 -10000 0 -0.42 6 6
RASA1 0.029 0.05 -10000 0 -0.42 6 6
TRKA/c-Abl 0.04 0.031 -10000 0 -0.3 2 2
SQSTM1 0.034 0.021 -10000 0 -0.42 1 1
BDNF (dimer)/TRKB/GIPC 0.068 0.065 -10000 0 -0.23 18 18
NGF (dimer)/TRKA/p62/Atypical PKCs 0.041 0.047 -10000 0 -0.22 10 10
MATK 0.031 0.03 -10000 0 -0.42 2 2
NEDD4L 0.007 0.11 -10000 0 -0.42 31 31
RAS family/GDP -0.012 0.036 -10000 0 -0.17 13 13
NGF (dimer)/TRKA 0.011 0.058 0.23 17 -0.27 5 22
Rac1/GTP 0 0.052 -10000 0 -0.21 15 15
FRS2 family/SHP2/CRK family 0.082 0.055 -10000 0 -0.22 6 6
Regulation of Androgen receptor activity

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
HDAC1 0.016 0.015 -10000 0 -0.3 1 1
SMARCC1 0.003 0.12 -10000 0 -1.1 5 5
REL 0.024 0.07 -10000 0 -0.42 12 12
HDAC7 -0.036 0.1 0.21 2 -0.32 35 37
JUN -0.001 0.12 -10000 0 -0.42 39 39
EP300 0.032 0.03 -10000 0 -0.42 2 2
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 0 0.058 -10000 0 -0.31 15 15
FOXO1 0 0 -10000 0 -10000 0 0
T-DHT/AR -0.007 0.13 0.27 1 -0.33 35 36
MAP2K6 0.011 0.08 -10000 0 -0.43 15 15
BRM/BAF57 0.048 0.024 -10000 0 -0.3 1 1
MAP2K4 0.023 0.031 -10000 0 -0.42 1 1
SMARCA2 0.034 0.022 -10000 0 -0.42 1 1
PDE9A -0.001 0.12 -10000 0 -0.99 5 5
NCOA2 0.025 0.047 -10000 0 -0.42 5 5
CEBPA 0.024 0.07 -10000 0 -0.42 12 12
EHMT2 0.036 0.005 -10000 0 -10000 0 0
cell proliferation 0.027 0.13 0.32 15 -0.35 13 28
NR0B1 0.03 0.036 -10000 0 -0.42 3 3
EGR1 -0.037 0.16 -10000 0 -0.42 76 76
RXRs/9cRA 0.048 0.051 -10000 0 -0.23 11 11
AR/RACK1/Src 0.003 0.1 0.28 5 -0.28 20 25
AR/GR -0.026 0.12 0.23 2 -0.24 89 91
GNB2L1 0.034 0.035 -10000 0 -0.42 3 3
PKN1 0.033 0.035 -10000 0 -0.42 3 3
RCHY1 0.022 0.075 -10000 0 -0.42 14 14
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 0.007 0.033 -10000 0 -0.31 3 3
T-DHT/AR/TIF2/CARM1 0.01 0.092 0.36 1 -0.3 11 12
SRC -0.01 0.074 0.19 37 -0.24 18 55
NR3C1 0.024 0.072 -10000 0 -0.42 13 13
KLK3 -0.016 0.093 -10000 0 -0.42 1 1
APPBP2 0.025 0.024 -10000 0 -10000 0 0
TRIM24 0.036 0.008 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.032 0.07 0.15 1 -0.27 23 24
TMPRSS2 -0.14 0.38 -10000 0 -0.94 88 88
RXRG 0.022 0.055 -10000 0 -0.42 7 7
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.034 0.029 -10000 0 -0.42 2 2
RXRB 0.034 0.029 -10000 0 -0.42 2 2
CARM1 0.035 0.021 -10000 0 -0.42 1 1
NR2C2 0.035 0.008 -10000 0 -10000 0 0
KLK2 0.011 0.075 0.31 3 -0.3 3 6
AR -0.032 0.11 0.19 1 -0.24 92 93
SENP1 0.036 0.006 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
MDM2 0.033 0.008 -10000 0 -10000 0 0
SRY 0.024 0.07 -10000 0 -0.42 12 12
GATA2 0.029 0.046 -10000 0 -0.42 5 5
MYST2 0.032 0.03 -10000 0 -0.42 2 2
HOXB13 0.024 0.018 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.001 0.1 0.29 5 -0.28 22 27
positive regulation of transcription 0.029 0.046 -10000 0 -0.42 5 5
DNAJA1 0.024 0.042 -10000 0 -0.42 3 3
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.052 -10000 0 -0.29 14 14
NCOA1 0.036 0.054 -10000 0 -0.33 9 9
SPDEF -0.044 0.18 -10000 0 -0.42 90 90
T-DHT/AR/TIF2 0.014 0.078 0.24 8 -0.3 6 14
T-DHT/AR/Hsp90 -0.032 0.07 0.15 1 -0.27 23 24
GSK3B 0.036 0.005 -10000 0 -10000 0 0
NR2C1 0.03 0.05 -10000 0 -0.42 6 6
mol:T-DHT -0.008 0.072 0.21 30 -0.26 14 44
SIRT1 0.036 0.006 -10000 0 -10000 0 0
ZMIZ2 -0.001 0 -10000 0 -10000 0 0
POU2F1 0.017 0.055 -10000 0 -0.18 2 2
T-DHT/AR/DAX-1 -0.007 0.098 0.3 2 -0.29 22 24
CREBBP 0.033 0.011 -10000 0 -10000 0 0
SMARCE1 0.034 0.01 -10000 0 -10000 0 0
Aurora A signaling

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
Aurora A/GADD45A 0.032 0.055 -10000 0 -0.24 15 15
BIRC5 -0.002 0.12 -10000 0 -0.42 38 38
NFKBIA 0.018 0.051 0.25 15 -0.25 2 17
CPEB1 0.03 0.046 -10000 0 -0.42 5 5
AKT1 0.014 0.041 0.25 7 -0.25 2 9
NDEL1 0.032 0.012 -10000 0 -10000 0 0
Aurora A/BRCA1 0.028 0.047 -10000 0 -0.23 12 12
NDEL1/TACC3 0.042 0.049 -10000 0 -0.16 17 17
GADD45A 0.019 0.08 -10000 0 -0.42 16 16
GSK3B 0.039 0.016 -10000 0 -10000 0 0
PAK1/Aurora A 0.028 0.06 -10000 0 -0.24 18 18
MDM2 0.034 0.009 -10000 0 -10000 0 0
JUB 0.003 0.12 -10000 0 -0.42 35 35
TPX2 -0.007 0.083 -10000 0 -0.3 37 37
TP53 -0.004 0.093 -10000 0 -0.28 28 28
DLG7 -0.006 0.06 0.25 5 -0.18 39 44
AURKAIP1 0 0 -10000 0 -10000 0 0
ARHGEF7 0.032 0.011 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.045 0.052 -10000 0 -0.17 17 17
G2/M transition of mitotic cell cycle 0.028 0.047 -10000 0 -0.22 12 12
AURKA 0.024 0.035 -10000 0 -10000 0 0
AURKB 0.001 0.06 -10000 0 -0.18 43 43
CDC25B 0.014 0.048 -10000 0 -0.29 5 5
G2/M transition checkpoint 0.018 0.069 -10000 0 -0.22 35 35
mRNA polyadenylation 0.033 0.035 -10000 0 -0.2 5 5
Aurora A/CPEB 0.033 0.035 -10000 0 -0.2 5 5
Aurora A/TACC1/TRAP/chTOG 0.05 0.078 -10000 0 -0.23 23 23
BRCA1 0.022 0.07 -10000 0 -0.42 12 12
centrosome duplication 0.028 0.06 -10000 0 -0.24 18 18
regulation of centrosome cycle 0.041 0.048 -10000 0 -0.16 17 17
spindle assembly 0.048 0.076 -10000 0 -0.23 23 23
TDRD7 0.027 0.064 -10000 0 -0.42 10 10
Aurora A/RasGAP/Survivin 0.034 0.08 -10000 0 -0.21 27 27
CENPA -0.005 0.084 -10000 0 -0.27 43 43
Aurora A/PP2A 0.042 0.029 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.001 0.044 0.17 5 -0.24 1 6
negative regulation of DNA binding -0.006 0.097 -10000 0 -0.29 29 29
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.046 0.024 -10000 0 -0.3 1 1
RASA1 0.029 0.05 -10000 0 -0.42 6 6
Ajuba/Aurora A 0.019 0.069 -10000 0 -0.22 35 35
mitotic prometaphase 0.004 0.024 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.035 -10000 0 -10000 0 0
TACC1 0.011 0.089 -10000 0 -0.42 20 20
TACC3 0.017 0.087 -10000 0 -0.42 19 19
Aurora A/Antizyme1 0.037 0.025 -10000 0 -10000 0 0
Aurora A/RasGAP 0.038 0.042 -10000 0 -0.25 6 6
OAZ1 0.035 0.006 -10000 0 -10000 0 0
RAN 0.036 0.005 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.039 0.016 -10000 0 -10000 0 0
GIT1 0.034 0.022 -10000 0 -0.42 1 1
GIT1/beta-PIX/PAK1 0.044 0.068 -10000 0 -0.27 18 18
Importin alpha/Importin beta/TPX2 -0.007 0.082 -10000 0 -0.3 37 37
PPP2R5D 0.035 0.006 -10000 0 -10000 0 0
Aurora A/TPX2 0.008 0.052 -10000 0 -0.2 8 8
PAK1 0.015 0.085 -10000 0 -0.42 18 18
CKAP5 0.036 0.006 -10000 0 -10000 0 0
Signaling mediated by 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
PTGS2 0.014 0.097 -10000 0 -1 4 4
MKNK1 0.035 0.006 -10000 0 -10000 0 0
MAPK14 0.031 0.049 -10000 0 -0.3 4 4
ATF2/c-Jun -0.022 0.16 -10000 0 -0.54 40 40
MAPK11 0.03 0.048 -10000 0 -0.3 4 4
MITF 0.02 0.053 -10000 0 -0.33 8 8
MAPKAPK5 0.023 0.043 -10000 0 -0.33 4 4
KRT8 0.011 0.073 -10000 0 -0.28 25 25
MAPKAPK3 0.035 0.008 -10000 0 -10000 0 0
MAPKAPK2 0.025 0.043 -10000 0 -0.42 4 4
p38alpha-beta/CK2 0.041 0.065 -10000 0 -0.43 4 4
CEBPB 0.019 0.054 -10000 0 -0.32 9 9
SLC9A1 0.023 0.043 -10000 0 -0.33 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.017 0.07 0.23 1 -0.3 9 10
p38alpha-beta/MNK1 0.056 0.06 -10000 0 -0.36 3 3
JUN -0.025 0.16 -10000 0 -0.54 40 40
PPARGC1A 0.016 0.068 -10000 0 -0.34 13 13
USF1 0.013 0.057 -10000 0 -0.29 13 13
RAB5/GDP/GDI1 0.024 0.053 -10000 0 -0.23 5 5
NOS2 0.016 0.042 -10000 0 -0.34 4 4
DDIT3 0.023 0.045 -10000 0 -0.32 5 5
RAB5A 0.036 0.006 -10000 0 -10000 0 0
HSPB1 -0.012 0.084 0.28 2 -0.26 48 50
p38alpha-beta/HBP1 0.053 0.068 -10000 0 -0.31 7 7
CREB1 0.015 0.061 -10000 0 -0.29 10 10
RAB5/GDP 0.026 0.004 -10000 0 -10000 0 0
EIF4E 0.016 0.045 0.24 2 -0.32 3 5
RPS6KA4 0.022 0.048 -10000 0 -0.36 5 5
PLA2G4A 0.001 0.064 -10000 0 -0.28 20 20
GDI1 0.023 0.045 -10000 0 -0.32 5 5
TP53 0 0.061 -10000 0 -0.33 9 9
RPS6KA5 0.009 0.075 -10000 0 -0.28 27 27
ESR1 -0.055 0.14 -10000 0 -0.28 132 132
HBP1 0.033 0.036 -10000 0 -0.42 3 3
MEF2C 0.01 0.08 -10000 0 -0.32 24 24
MEF2A 0.022 0.045 -10000 0 -0.32 5 5
EIF4EBP1 0.01 0.066 -10000 0 -0.3 14 14
KRT19 -0.002 0.09 -10000 0 -0.28 43 43
ELK4 0.018 0.041 -10000 0 -0.31 4 4
ATF6 0.018 0.044 -10000 0 -0.32 5 5
ATF1 0.016 0.062 -10000 0 -0.27 13 13
p38alpha-beta/MAPKAPK2 0.042 0.069 -10000 0 -0.35 6 6
p38alpha-beta/MAPKAPK3 0.054 0.063 -10000 0 -0.35 4 4
Glypican 2 network

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
MDK 0.018 0.085 -9999 0 -0.42 18 18
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine 0.014 0.06 -9999 0 -0.3 18 18
neuron projection morphogenesis 0.014 0.06 -9999 0 -0.3 18 18
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.036 0.071 -10000 0 -0.31 19 19
AKT1 0.011 0.12 0.32 1 -0.39 22 23
PTK2B 0 0.089 0.36 1 -0.48 8 9
VEGFR2 homodimer/Frs2 0.029 0.078 -10000 0 -0.38 13 13
CAV1 0.027 0.054 -10000 0 -0.42 7 7
CALM1 0.035 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.027 0.082 -10000 0 -0.43 9 9
endothelial cell proliferation 0.034 0.12 0.32 11 -0.44 8 19
mol:Ca2+ 0.005 0.097 -10000 0 -0.46 10 10
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.045 0.085 -10000 0 -0.46 8 8
RP11-342D11.1 -0.01 0.096 -10000 0 -0.31 33 33
CDH5 0.027 0.037 -10000 0 -0.42 3 3
VEGFA homodimer 0.037 0.087 -10000 0 -0.23 44 44
SHC1 0.028 0.025 -10000 0 -0.42 1 1
SHC2 -0.025 0.15 -10000 0 -0.42 66 66
HRAS/GDP 0.02 0.09 -10000 0 -0.41 9 9
SH2D2A -0.001 0.11 -10000 0 -0.42 30 30
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.035 0.11 -10000 0 -0.43 14 14
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.005 0.1 -10000 0 -0.28 40 40
VEGFR1 homodimer 0.026 0.057 -10000 0 -0.42 8 8
SHC/GRB2/SOS1 0.043 0.1 -10000 0 -0.44 9 9
GRB10 -0.003 0.12 -10000 0 -0.5 20 20
PTPN11 0.036 0.004 -10000 0 -10000 0 0
GRB2 0.033 0.011 -10000 0 -10000 0 0
PAK1 0.015 0.085 -10000 0 -0.42 18 18
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.042 0.1 -10000 0 -0.44 11 11
HRAS 0.032 0.036 -10000 0 -0.42 3 3
VEGF/Rho/ROCK1/Integrin Complex 0.004 0.1 -10000 0 -0.34 25 25
HIF1A -0.007 0.13 -10000 0 -0.42 46 46
FRS2 0.033 0.022 -10000 0 -0.42 1 1
oxygen and reactive oxygen species metabolic process 0.043 0.084 -10000 0 -0.45 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.035 0.006 -10000 0 -10000 0 0
Nck/Pak 0.032 0.068 -10000 0 -0.3 19 19
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.021 0.095 -10000 0 -0.38 17 17
mol:GDP 0.031 0.096 -10000 0 -0.43 9 9
mol:NADP 0.019 0.1 -10000 0 -0.4 12 12
eNOS/Hsp90 0.017 0.097 -10000 0 -0.38 12 12
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
mol:IP3 0.004 0.098 -10000 0 -0.47 10 10
HIF1A/ARNT 0.02 0.1 -10000 0 -0.3 44 44
SHB 0.031 0.046 -10000 0 -0.42 5 5
VEGFA -0.001 0.015 -10000 0 -10000 0 0
VEGFC 0.022 0.075 -10000 0 -0.42 14 14
FAK1/Vinculin 0.015 0.12 0.34 2 -0.45 13 15
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.026 0.061 -10000 0 -0.42 9 9
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.034 0.1 -10000 0 -0.48 9 9
PTPN6 0.032 0.03 -10000 0 -0.42 2 2
EPAS1 0.028 0.077 -10000 0 -0.4 14 14
mol:L-citrulline 0.019 0.1 -10000 0 -0.4 12 12
ITGAV 0.022 0.078 -10000 0 -0.42 15 15
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.042 0.081 -10000 0 -0.45 7 7
VEGFR2 homodimer/VEGFA homodimer 0.023 0.11 -10000 0 -0.33 34 34
VEGFR2/3 heterodimer 0.03 0.078 -10000 0 -0.38 13 13
VEGFB 0.034 0.021 -10000 0 -0.42 1 1
MAPK11 -0.014 0.11 0.26 2 -0.44 16 18
VEGFR2 homodimer 0.012 0.084 -10000 0 -0.44 13 13
FLT1 0.026 0.058 -10000 0 -0.42 8 8
NEDD4 0.021 0.071 -10000 0 -0.42 11 11
MAPK3 0.003 0.095 0.27 7 -0.4 9 16
MAPK1 -0.002 0.095 0.25 6 -0.43 9 15
VEGFA145/NRP2 0.023 0.023 -10000 0 -0.32 1 1
VEGFR1/2 heterodimer 0.024 0.089 -10000 0 -0.37 18 18
KDR 0.012 0.084 -10000 0 -0.44 13 13
VEGFA165/NRP1/VEGFR2 homodimer 0.024 0.11 -10000 0 -0.31 32 32
SRC 0.033 0.029 -10000 0 -0.42 2 2
platelet activating factor biosynthetic process 0.003 0.099 0.27 6 -0.41 10 16
PI3K 0.005 0.13 -10000 0 -0.47 16 16
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.027 0.083 -10000 0 -0.37 14 14
FES 0.001 0.11 -10000 0 -0.51 10 10
GAB1 0.016 0.12 -10000 0 -0.4 25 25
VEGFR2 homodimer/VEGFA homodimer/Src 0.027 0.081 -10000 0 -0.34 15 15
CTNNB1 0.025 0.067 -10000 0 -0.42 11 11
SOS1 0.035 0.021 -10000 0 -0.42 1 1
ARNT 0.035 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.031 0.11 -10000 0 -0.39 15 15
VEGFR2 homodimer/VEGFA homodimer/Yes 0.023 0.088 -10000 0 -0.34 18 18
PI3K/GAB1 0.02 0.14 0.28 1 -0.41 23 24
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.042 0.098 -10000 0 -0.41 8 8
PRKACA 0.036 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.04 0.099 -10000 0 -0.35 22 22
HSP90AA1 0 0 -10000 0 -10000 0 0
CDC42 0.004 0.1 -10000 0 -0.32 31 31
actin cytoskeleton reorganization 0.004 0.1 -10000 0 -0.28 40 40
PTK2 -0.006 0.1 -10000 0 -0.51 12 12
EDG1 -0.006 0.14 -10000 0 -0.52 27 27
mol:DAG 0.004 0.098 -10000 0 -0.47 10 10
CaM/Ca2+ 0.021 0.096 -10000 0 -0.45 9 9
MAP2K3 -0.011 0.098 -10000 0 -0.45 12 12
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.016 0.13 -10000 0 -0.51 20 20
PLCG1 0.004 0.099 -10000 0 -0.47 10 10
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.04 0.088 -10000 0 -0.42 9 9
IQGAP1 0.035 0.008 -10000 0 -10000 0 0
YES1 0.029 0.05 -10000 0 -0.42 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.028 0.083 -10000 0 -0.38 13 13
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.027 0.082 -10000 0 -0.45 9 9
cell migration 0.017 0.1 0.3 3 -0.47 9 12
mol:PI-3-4-5-P3 0.006 0.12 -10000 0 -0.44 16 16
FYN 0.027 0.054 -10000 0 -0.42 7 7
VEGFB/NRP1 0.009 0.1 -10000 0 -0.47 10 10
mol:NO 0.019 0.1 -10000 0 -0.4 12 12
PXN 0.036 0.004 -10000 0 -10000 0 0
HRAS/GTP 0.004 0.082 -10000 0 -0.41 9 9
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.005 0.13 -10000 0 -0.51 20 20
VHL 0.035 0.007 -10000 0 -10000 0 0
ITGB3 0.029 0.046 -10000 0 -0.42 5 5
NOS3 0.018 0.11 -10000 0 -0.46 12 12
VEGFR2 homodimer/VEGFA homodimer/Sck -0.005 0.12 -10000 0 -0.27 70 70
RAC1 0.035 0.006 -10000 0 -10000 0 0
PRKCA -0.006 0.084 -10000 0 -0.47 7 7
PRKCB -0.009 0.089 -10000 0 -0.44 10 10
VCL 0.035 0.021 -10000 0 -0.42 1 1
VEGFA165/NRP1 -0.007 0.095 -10000 0 -0.3 34 34
VEGFR1/2 heterodimer/VEGFA homodimer 0.021 0.092 -10000 0 -0.36 18 18
VEGFA165/NRP2 0.023 0.023 -10000 0 -0.32 1 1
MAPKKK cascade 0.032 0.12 0.34 3 -0.44 16 19
NRP2 0.034 0.021 -10000 0 -0.42 1 1
VEGFC homodimer 0.022 0.075 -10000 0 -0.42 14 14
NCK1 0.034 0.021 -10000 0 -0.42 1 1
ROCK1 0.036 0.006 -10000 0 -10000 0 0
FAK1/Paxillin 0.015 0.12 0.34 2 -0.46 13 15
MAP3K13 0.001 0.11 -10000 0 -0.47 12 12
PDPK1 -0.002 0.1 0.26 2 -0.39 15 17
IL2 signaling events mediated by STAT5

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
GAB2 0.032 0.013 -9999 0 -10000 0 0
ELF1 0.014 0.096 -9999 0 -0.34 33 33
CCNA2 0.009 0.1 -9999 0 -0.42 28 28
PIK3CA 0.034 0.022 -9999 0 -0.42 1 1
JAK3 0.036 0.005 -9999 0 -10000 0 0
PIK3R1 0.02 0.08 -9999 0 -0.42 16 16
JAK1 0.033 0.036 -9999 0 -0.42 3 3
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.022 0.14 -9999 0 -0.4 25 25
SHC1 0.028 0.025 -9999 0 -0.42 1 1
SP1 0.032 0.073 -9999 0 -0.37 15 15
IL2RA -0.024 0.17 -9999 0 -0.61 36 36
IL2RB 0.012 0.097 -9999 0 -0.42 24 24
SOS1 0.035 0.021 -9999 0 -0.42 1 1
IL2RG 0.031 0.041 -9999 0 -0.42 4 4
G1/S transition of mitotic cell cycle -0.02 0.19 -9999 0 -0.75 22 22
PTPN11 0.037 0.004 -9999 0 -10000 0 0
CCND2 0.005 0.11 -9999 0 -0.68 13 13
LCK -0.017 0.14 -9999 0 -0.42 54 54
GRB2 0.034 0.011 -9999 0 -10000 0 0
IL2 0.033 0.036 -9999 0 -0.42 3 3
CDK6 0.025 0.058 -9999 0 -0.42 8 8
CCND3 0.025 0.13 -9999 0 -0.44 4 4
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.028 0.057 -10000 0 -0.42 8 8
mol:S1P 0.001 0.002 -10000 0 -0.025 3 3
S1P1/S1P/Gi -0.016 0.11 -10000 0 -0.3 43 43
GNAO1 0.031 0.015 -10000 0 -10000 0 0
S1P/S1P3/G12/G13 0.039 0.028 -10000 0 -0.23 3 3
AKT1 0.003 0.12 -10000 0 -0.46 29 29
AKT3 -0.004 0.12 -10000 0 -0.57 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.028 0.057 -10000 0 -0.42 8 8
GNAI2 0.029 0.054 -10000 0 -0.42 7 7
GNAI3 0.036 0.008 -10000 0 -10000 0 0
GNAI1 0.018 0.087 -10000 0 -0.42 19 19
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.001 0.002 -10000 0 -0.03 3 3
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0.013 0.095 -10000 0 -0.42 23 23
mol:Ca2+ 0.006 0.083 -10000 0 -0.3 22 22
MAPK3 -0.002 0.074 -10000 0 -0.3 16 16
MAPK1 0 0.076 -10000 0 -0.3 19 19
JAK2 -0.014 0.1 0.22 1 -0.35 27 28
CXCR4 -0.013 0.1 -10000 0 -0.35 26 26
FLT1 0.027 0.058 -10000 0 -0.42 8 8
RhoA/GDP 0.02 0.043 -10000 0 -0.3 9 9
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
SRC -0.004 0.081 -10000 0 -0.33 17 17
S1P/S1P3/Gi 0.006 0.083 -10000 0 -0.31 22 22
RAC1 0.035 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.005 0.096 -10000 0 -0.3 22 22
VEGFA 0.002 0.003 -10000 0 -0.04 3 3
S1P/S1P2/Gi 0.004 0.08 -10000 0 -0.24 40 40
VEGFR1 homodimer/VEGFA homodimer 0.024 0.042 -10000 0 -0.3 8 8
RHOA 0.026 0.061 -10000 0 -0.42 9 9
S1P/S1P3/Gq -0.006 0.079 -10000 0 -0.23 49 49
GNAQ 0 0 -10000 0 -10000 0 0
GNAZ 0.024 0.07 -10000 0 -0.42 12 12
G12/G13 0.044 0.033 -10000 0 -0.3 3 3
GNA14 -0.009 0.13 -10000 0 -0.42 43 43
GNA15 0.03 0.046 -10000 0 -0.42 5 5
GNA12 0.035 0.007 -10000 0 -10000 0 0
GNA13 0.029 0.037 -10000 0 -0.42 3 3
GNA11 0.033 0.036 -10000 0 -0.42 3 3
Rac1/GTP 0.008 0.092 -10000 0 -0.3 20 20
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.014 0.058 -10000 0 -0.2 27 27
TRAF2/ASK1 0.029 0.066 -10000 0 -0.25 25 25
ATM 0.031 0.013 -10000 0 -10000 0 0
MAP2K3 -0.051 0.16 0.28 2 -0.41 60 62
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.042 0.14 0.29 1 -0.36 52 53
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.027 0.064 -10000 0 -0.42 10 10
TXN 0.009 0.002 -10000 0 -10000 0 0
CALM1 0.035 0.007 -10000 0 -10000 0 0
GADD45A 0.019 0.08 -10000 0 -0.42 16 16
GADD45B 0.025 0.067 -10000 0 -0.42 11 11
MAP3K1 0.01 0.099 -10000 0 -0.42 25 25
MAP3K6 0.034 0.022 -10000 0 -0.42 1 1
MAP3K7 0.033 0.011 -10000 0 -10000 0 0
MAP3K4 0.034 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.032 0.075 -10000 0 -0.3 24 24
TAK1/TAB family 0.014 0.037 -10000 0 -0.26 6 6
RAC1/OSM/MEKK3 0.058 0.027 -10000 0 -10000 0 0
TRAF2 0.034 0.029 -10000 0 -0.42 2 2
RAC1/OSM/MEKK3/MKK3 -0.019 0.14 -10000 0 -0.32 49 49
TRAF6 0.016 0.024 -10000 0 -0.28 3 3
RAC1 0.035 0.006 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.012 0.13 -10000 0 -0.42 47 47
CCM2 0.035 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.015 0.086 -10000 0 -0.25 47 47
MAPK11 0.033 0.01 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.018 0.1 -10000 0 -0.23 68 68
OSM/MEKK3 0.045 0.02 -10000 0 -10000 0 0
TAOK1 0.012 0.033 -10000 0 -0.29 6 6
TAOK2 0.015 0.008 -10000 0 -10000 0 0
TAOK3 0.016 0.015 -10000 0 -0.29 1 1
MAP3K7IP1 0.034 0.009 -10000 0 -10000 0 0
MAPK14 0.036 0.005 -10000 0 -10000 0 0
MAP3K7IP2 0.032 0.03 -10000 0 -0.42 2 2
MAP3K5 0.012 0.095 -10000 0 -0.42 23 23
MAP3K10 0.023 0.075 -10000 0 -0.42 14 14
MAP3K3 0.031 0.013 -10000 0 -10000 0 0
TRX/ASK1 0.016 0.06 -10000 0 -0.21 30 30
GADD45/MTK1/MTK1 0.054 0.082 -10000 0 -0.23 33 33
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 0.035 0.007 -9999 0 -10000 0 0
SPHK1 0.005 0.11 -9999 0 -0.42 30 30
GNAI2 0.028 0.054 -9999 0 -0.42 7 7
mol:S1P 0.002 0.065 -9999 0 -0.27 25 25
GNAO1 0.03 0.014 -9999 0 -10000 0 0
mol:Sphinganine-1-P -0.003 0.074 -9999 0 -0.3 29 29
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.041 0.07 -9999 0 -0.22 23 23
GNAI3 0.035 0.006 -9999 0 -10000 0 0
G12/G13 0.044 0.033 -9999 0 -0.3 3 3
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0.013 0.095 -9999 0 -0.42 23 23
S1P1/S1P 0.024 0.088 -9999 0 -0.25 37 37
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
GNAI1 0.017 0.087 -9999 0 -0.42 19 19
S1P/S1P5/G12 0.029 0.066 -9999 0 -0.22 24 24
S1P/S1P3/Gq -0.001 0.095 -9999 0 -0.26 48 48
S1P/S1P4/Gi 0.002 0.094 -9999 0 -0.32 25 25
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.023 0.07 -9999 0 -0.42 12 12
GNA14 -0.009 0.13 -9999 0 -0.42 43 43
GNA15 0.03 0.046 -9999 0 -0.42 5 5
GNA12 0.035 0.007 -9999 0 -10000 0 0
GNA13 0.029 0.037 -9999 0 -0.42 3 3
GNA11 0.033 0.036 -9999 0 -0.42 3 3
ABCC1 0.029 0.042 -9999 0 -0.42 4 4
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.046 0.034 -10000 0 -0.3 4 4
CRKL 0.006 0.1 0.3 2 -0.46 15 17
mol:PIP3 0.011 0.054 0.39 9 -10000 0 9
AKT1 0.022 0.078 0.34 9 -10000 0 9
PTK2B 0.028 0.015 -10000 0 -10000 0 0
RAPGEF1 0.004 0.097 0.32 1 -0.44 15 16
RANBP10 0.03 0.014 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
HGF/MET/SHIP2 0.054 0.059 -10000 0 -0.26 15 15
MAP3K5 0 0.11 0.29 1 -0.43 17 18
HGF/MET/CIN85/CBL/ENDOPHILINS 0.064 0.073 -10000 0 -0.25 20 20
AP1 -0.022 0.13 -10000 0 -0.3 88 88
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.028 0.025 -10000 0 -0.42 1 1
apoptosis -0.14 0.34 -10000 0 -0.77 109 109
STAT3 (dimer) 0.01 0.07 -10000 0 -0.31 7 7
GAB1/CRKL/SHP2/PI3K 0.042 0.12 0.34 1 -0.41 17 18
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.024 0.097 -10000 0 -0.43 14 14
PTPN11 0.036 0.004 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.034 0.008 -10000 0 -10000 0 0
PTEN 0.027 0.061 -10000 0 -0.42 9 9
ELK1 -0.001 0.072 0.28 15 -10000 0 15
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.015 0.046 -10000 0 -0.21 5 5
PAK1 0.028 0.099 0.38 12 -10000 0 12
HGF/MET/RANBP10 0.05 0.055 -10000 0 -0.25 12 12
HRAS 0.014 0.1 -10000 0 -0.48 14 14
DOCK1 0.003 0.1 0.31 2 -0.44 15 17
GAB1 0.008 0.1 -10000 0 -0.48 15 15
CRK 0.005 0.098 -10000 0 -0.45 15 15
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.1 -10000 0 -0.46 15 15
JUN -0.001 0.12 -10000 0 -0.42 39 39
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.007 0.042 -10000 0 -0.2 17 17
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
cell morphogenesis 0.007 0.1 0.28 10 -0.34 9 19
GRB2/SHC 0.034 0.052 -10000 0 -0.21 7 7
FOS -0.031 0.15 -10000 0 -0.42 66 66
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility -0.001 0.072 0.28 15 -10000 0 15
HGF/MET/MUC20 0.039 0.047 -10000 0 -0.25 12 12
cell migration 0.034 0.051 -10000 0 -0.21 7 7
GRB2 0.033 0.011 -10000 0 -10000 0 0
CBL 0.032 0.012 -10000 0 -10000 0 0
MET/RANBP10 0.039 0.037 -10000 0 -0.29 4 4
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.015 0.054 -10000 0 -0.23 15 15
MET/MUC20 0.022 0.029 -10000 0 -0.3 4 4
RAP1B 0.008 0.099 0.27 8 -0.43 13 21
RAP1A 0.001 0.097 0.31 1 -0.43 16 17
HGF/MET/RANBP9 0.059 0.053 -10000 0 -0.26 12 12
RAF1 0.017 0.1 -10000 0 -0.45 14 14
STAT3 0.009 0.069 -10000 0 -0.31 7 7
cell proliferation 0.042 0.1 0.27 18 -0.33 9 27
RPS6KB1 0.01 0.048 -10000 0 -0.29 10 10
MAPK3 -0.017 0.082 0.68 5 -10000 0 5
MAPK1 0.007 0.15 0.63 27 -10000 0 27
RANBP9 0.035 0.007 -10000 0 -10000 0 0
MAPK8 0.01 0.11 0.29 1 -0.4 18 19
SRC 0.009 0.063 -10000 0 -0.26 6 6
PI3K 0.033 0.074 -10000 0 -0.23 23 23
MET/Glomulin 0.021 0.037 -10000 0 -0.24 5 5
SOS1 0.035 0.021 -10000 0 -0.42 1 1
MAP2K1 0.015 0.096 -10000 0 -0.43 13 13
MET 0.03 0.041 -10000 0 -0.42 4 4
MAP4K1 0.008 0.11 0.31 1 -0.46 15 16
PTK2 0.028 0.016 -10000 0 -10000 0 0
MAP2K2 0.014 0.098 -10000 0 -0.42 15 15
BAD 0.017 0.074 0.38 4 -10000 0 4
MAP2K4 -0.001 0.1 0.28 1 -0.39 17 18
SHP2/GRB2/SOS1/GAB1 0.044 0.098 -10000 0 -0.38 16 16
INPPL1 0.031 0.036 -10000 0 -0.42 3 3
PXN 0.036 0.004 -10000 0 -10000 0 0
SH3KBP1 0.027 0.064 -10000 0 -0.42 10 10
HGS 0 0.04 -10000 0 -0.18 20 20
PLCgamma1/PKC 0.025 0.006 -10000 0 -10000 0 0
HGF 0.028 0.057 -10000 0 -0.42 8 8
RASA1 0.029 0.05 -10000 0 -0.42 6 6
NCK1 0.034 0.021 -10000 0 -0.42 1 1
PTPRJ 0.031 0.046 -10000 0 -0.42 5 5
NCK/PLCgamma1 0.047 0.056 -10000 0 -0.19 16 16
PDPK1 0.027 0.08 0.33 10 -10000 0 10
HGF/MET/SHIP 0.039 0.047 -10000 0 -0.25 12 12
FoxO family signaling

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
G6PC 0.041 0.096 0.36 3 -1.3 1 4
PLK1 0.01 0.2 -10000 0 -0.77 13 13
CDKN1B 0.042 0.17 -10000 0 -0.45 31 31
FOXO3 -0.005 0.22 -10000 0 -0.76 19 19
KAT2B 0.001 0.019 -10000 0 -0.043 59 59
FOXO1/SIRT1 0.044 0.054 -10000 0 -0.26 4 4
CAT -0.008 0.23 -10000 0 -0.99 13 13
CTNNB1 0.025 0.067 -10000 0 -0.42 11 11
AKT1 0.029 0.046 -10000 0 -0.41 2 2
FOXO1 0.026 0.053 0.24 1 -0.28 4 5
MAPK10 0.008 0.06 0.2 9 -0.21 24 33
mol:GTP 0 0.002 -10000 0 -10000 0 0
FOXO4 0.017 0.097 0.28 1 -0.32 19 20
response to oxidative stress 0.004 0.02 -10000 0 -0.053 22 22
FOXO3A/SIRT1 0.021 0.19 -10000 0 -0.59 23 23
XPO1 0.036 0.005 -10000 0 -10000 0 0
EP300 0.034 0.031 -10000 0 -0.42 2 2
BCL2L11 0.029 0.086 -10000 0 -1.2 2 2
FOXO1/SKP2 0.042 0.049 0.21 1 -0.27 3 4
mol:GDP 0.004 0.02 -10000 0 -0.053 22 22
RAN 0.036 0.005 -10000 0 -10000 0 0
GADD45A 0.012 0.22 -10000 0 -0.78 28 28
YWHAQ 0.034 0.029 -10000 0 -0.42 2 2
FOXO1/14-3-3 family 0.038 0.12 -10000 0 -0.42 15 15
MST1 0.028 0.036 -10000 0 -10000 0 0
CSNK1D 0.034 0.009 -10000 0 -10000 0 0
CSNK1E 0.034 0.009 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.009 0.13 -10000 0 -0.4 27 27
YWHAB 0.035 0.008 -10000 0 -10000 0 0
MAPK8 0.018 0.044 0.2 10 -0.21 7 17
MAPK9 0.01 0.058 0.2 8 -0.22 22 30
YWHAG 0.036 0.005 -10000 0 -10000 0 0
YWHAE 0.032 0.012 -10000 0 -10000 0 0
YWHAZ 0.027 0.016 -10000 0 -10000 0 0
SIRT1 0.036 0.02 -10000 0 -10000 0 0
SOD2 0.031 0.16 -10000 0 -0.64 12 12
RBL2 -0.076 0.31 -10000 0 -0.74 72 72
RAL/GDP 0.046 0.037 -10000 0 -0.24 4 4
CHUK 0.019 0.074 -10000 0 -0.42 11 11
Ran/GTP 0.026 0.01 -10000 0 -10000 0 0
CSNK1G2 0.033 0.029 -10000 0 -0.42 2 2
RAL/GTP 0.046 0.038 -10000 0 -0.22 4 4
CSNK1G1 0.035 0.007 -10000 0 -10000 0 0
FASLG -0.092 0.4 -10000 0 -1.4 45 45
SKP2 0.034 0.009 -10000 0 -10000 0 0
USP7 0.033 0.012 -10000 0 -10000 0 0
IKBKB 0.023 0.035 -10000 0 -10000 0 0
CCNB1 -0.051 0.33 -10000 0 -1.1 37 37
FOXO1-3a-4/beta catenin 0.039 0.16 0.42 1 -0.41 27 28
proteasomal ubiquitin-dependent protein catabolic process 0.042 0.049 0.21 1 -0.27 3 4
CSNK1A1 0.036 0.006 -10000 0 -10000 0 0
SGK1 0.001 0.019 -10000 0 -0.043 59 59
CSNK1G3 0.035 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.049 0.013 -10000 0 -10000 0 0
ZFAND5 0.018 0.084 0.26 1 -0.26 19 20
SFN 0.012 0.099 -10000 0 -0.42 25 25
CDK2 0.036 0.03 -10000 0 -0.42 2 2
FOXO3A/14-3-3 0.016 0.12 -10000 0 -0.39 22 22
CREBBP 0.035 0.013 -10000 0 -10000 0 0
FBXO32 0.023 0.3 -10000 0 -1.2 20 20
BCL6 -0.007 0.27 -10000 0 -1.2 20 20
RALB 0.033 0.041 -10000 0 -0.42 4 4
RALA 0.036 0.007 -10000 0 -10000 0 0
YWHAH 0.031 0.036 -10000 0 -0.42 3 3
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.035 0.021 -10000 0 -0.42 1 1
HDAC3 0.036 0.006 -10000 0 -10000 0 0
VDR 0.02 0.082 -10000 0 -0.42 17 17
Cbp/p300/PCAF 0.041 0.026 -10000 0 -0.24 2 2
EP300 0.032 0.03 -10000 0 -0.42 2 2
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.014 0.057 0.19 1 -0.31 4 5
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.036 0.005 -10000 0 -10000 0 0
AKT1 0.028 0.092 0.21 56 -0.23 15 71
RAR alpha/9cRA/Cyclin H 0.045 0.1 0.26 1 -0.36 6 7
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.018 0.065 -10000 0 -0.27 9 9
CDC2 0.01 0.094 -10000 0 -0.42 22 22
response to UV -0.002 0.008 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.031 0.06 -10000 0 -0.25 11 11
NCOR2 0.036 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.015 0.058 -10000 0 -0.3 17 17
RXRs/RARs/NRIP1/9cRA -0.003 0.19 -10000 0 -0.53 52 52
NCOA2 0.025 0.047 -10000 0 -0.42 5 5
NCOA3 0.032 0.03 -10000 0 -0.42 2 2
NCOA1 0.031 0.045 -10000 0 -0.42 5 5
VDR/VDR/DNA 0.02 0.082 -10000 0 -0.42 17 17
RARG 0.031 0.018 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.047 0.01 -10000 0 -10000 0 0
MAPK3 0.027 0.029 -10000 0 -0.42 1 1
MAPK1 0.033 0.022 -10000 0 -0.42 1 1
MAPK8 0.027 0.041 -10000 0 -0.42 3 3
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.027 0.13 -10000 0 -0.41 13 13
RARA 0.011 0.044 -10000 0 -0.23 10 10
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.015 0.055 -10000 0 -0.33 3 3
PRKCA 0.024 0.032 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.008 0.2 -10000 0 -0.57 51 51
RXRG 0.011 0.045 -10000 0 -0.3 6 6
RXRA 0.017 0.09 -10000 0 -0.32 8 8
RXRB 0.017 0.037 -10000 0 -0.28 2 2
VDR/Vit D3/DNA 0.015 0.058 -10000 0 -0.3 17 17
RBP1 -0.028 0.15 -10000 0 -0.42 67 67
CRBP1/9-cic-RA -0.018 0.11 -10000 0 -0.3 67 67
RARB 0.011 0.09 -10000 0 -0.42 20 20
PRKCG 0.029 0.032 -10000 0 -10000 0 0
MNAT1 0.035 0.007 -10000 0 -10000 0 0
RAR alpha/RXRs 0.004 0.14 0.42 1 -0.41 18 19
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.03 0.11 0.27 1 -0.36 11 12
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.074 0.23 1 -0.29 6 7
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.008 0.2 -10000 0 -0.58 51 51
positive regulation of DNA binding 0.033 0.095 -10000 0 -0.32 7 7
NRIP1 -0.071 0.38 -10000 0 -1.2 51 51
RXRs/RARs 0.011 0.16 -10000 0 -0.42 47 47
RXRs/RXRs/DNA/9cRA -0.008 0.11 -10000 0 -0.33 31 31
PRKACA 0.036 0.005 -10000 0 -10000 0 0
CDK7 0.034 0.008 -10000 0 -10000 0 0
TFIIH 0.068 0.024 -10000 0 -0.24 1 1
RAR alpha/9cRA 0.066 0.066 -10000 0 -0.22 4 4
CCNH 0.034 0.022 -10000 0 -0.42 1 1
CREBBP 0.033 0.011 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.065 0.028 -10000 0 -0.2 1 1
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.015 0.063 -10000 0 -0.33 14 14
CRKL 0.031 0.041 -10000 0 -0.42 4 4
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
DOCK1 0.028 0.057 -10000 0 -0.42 8 8
ITGA4 0.021 0.078 -10000 0 -0.42 15 15
alpha4/beta7 Integrin/MAdCAM1 0.069 0.075 -10000 0 -0.25 22 22
EPO 0.03 0.014 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.042 0.061 -10000 0 -0.3 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.023 -10000 0 -0.42 1 1
alpha4/beta1 Integrin 0.039 0.069 -10000 0 -0.33 16 16
EPO/EPOR (dimer) 0.048 0.014 -10000 0 -10000 0 0
lamellipodium assembly 0.013 0.084 -10000 0 -0.34 15 15
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
PI3K 0.036 0.065 -10000 0 -0.3 17 17
ARF6 0.034 0.029 -10000 0 -0.42 2 2
JAK2 0.024 0.049 -10000 0 -0.25 14 14
PXN 0.036 0.004 -10000 0 -10000 0 0
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
MADCAM1 0.034 0.008 -10000 0 -10000 0 0
cell adhesion 0.066 0.074 -10000 0 -0.25 22 22
CRKL/CBL 0.043 0.037 -10000 0 -0.3 4 4
ITGB1 0.032 0.036 -10000 0 -0.42 3 3
SRC 0.001 0.087 -10000 0 -0.27 39 39
ITGB7 0.036 0.005 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.04 0.1 -10000 0 -0.3 37 37
p130Cas/Crk/Dock1 0.018 0.088 -10000 0 -0.24 39 39
VCAM1 0.009 0.1 -10000 0 -0.42 28 28
RHOA 0.026 0.061 -10000 0 -0.42 9 9
alpha4/beta1 Integrin/Paxillin/GIT1 0.073 0.068 -10000 0 -0.26 17 17
BCAR1 -0.024 0.075 0.18 16 -0.25 35 51
EPOR 0.036 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.032 0.012 -10000 0 -10000 0 0
GIT1 0.034 0.022 -10000 0 -0.42 1 1
Rac1/GTP 0.013 0.086 -10000 0 -0.35 15 15
S1P5 pathway

Figure S103.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S103.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.001 0.09 0.25 31 -10000 0 31
GNAI2 0.028 0.054 -10000 0 -0.42 7 7
S1P/S1P5/G12 0.024 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.014 -10000 0 -10000 0 0
RhoA/GTP -0.001 0.092 -10000 0 -0.25 31 31
negative regulation of cAMP metabolic process 0 0.076 -10000 0 -0.24 40 40
GNAZ 0.023 0.07 -10000 0 -0.42 12 12
GNAI3 0.035 0.006 -10000 0 -10000 0 0
GNA12 0.035 0.007 -10000 0 -10000 0 0
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0 0.077 -10000 0 -0.24 40 40
RhoA/GDP 0.02 0.043 -10000 0 -0.3 9 9
RHOA 0.026 0.061 -10000 0 -0.42 9 9
GNAI1 0.017 0.087 -10000 0 -0.42 19 19
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.036 0.004 -10000 0 -10000 0 0
NFATC1 0.02 0.09 0.3 2 -0.39 7 9
NFATC2 0.018 0.049 0.16 1 -0.19 7 8
NFATC3 0.013 0.007 -10000 0 -10000 0 0
YWHAE 0.032 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.019 0.09 0.21 4 -0.36 10 14
Exportin 1/Ran/NUP214 0.069 0.023 -10000 0 -0.26 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.043 0.087 -10000 0 -0.38 6 6
BCL2/BAX -0.018 0.14 -10000 0 -0.3 95 95
CaM/Ca2+/Calcineurin A alpha-beta B1 0.027 0.006 -10000 0 -10000 0 0
CaM/Ca2+ 0.027 0.006 -10000 0 -10000 0 0
BAX 0.035 0.007 -10000 0 -10000 0 0
MAPK14 0.036 0.005 -10000 0 -10000 0 0
BAD 0.034 0.021 -10000 0 -0.42 1 1
CABIN1/MEF2D 0.03 0.082 -10000 0 -0.38 6 6
Calcineurin A alpha-beta B1/BCL2 -0.057 0.18 -10000 0 -0.42 99 99
FKBP8 0.036 0.006 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.03 0.081 0.38 6 -10000 0 6
KPNB1 0.03 0.046 -10000 0 -0.42 5 5
KPNA2 0.025 0.058 -10000 0 -0.42 8 8
XPO1 0.036 0.005 -10000 0 -10000 0 0
SFN 0.012 0.099 -10000 0 -0.42 25 25
MAP3K8 0.004 0.11 -10000 0 -0.42 32 32
NFAT4/CK1 alpha 0.017 0.056 -10000 0 -0.21 23 23
MEF2D/NFAT1/Cbp/p300 0.056 0.065 -10000 0 -0.22 3 3
CABIN1 0.019 0.089 0.21 4 -0.37 9 13
CALM1 0.035 0.007 -10000 0 -10000 0 0
RAN 0.036 0.005 -10000 0 -10000 0 0
MAP3K1 0.01 0.099 -10000 0 -0.42 25 25
CAMK4 0.032 0.036 -10000 0 -0.42 3 3
mol:Ca2+ 0.001 0.001 -10000 0 -10000 0 0
MAPK3 0.032 0.023 -10000 0 -0.42 1 1
YWHAH 0.031 0.036 -10000 0 -0.42 3 3
Calcineurin A alpha-beta B1/AKAP79/PKA 0.025 0.091 -10000 0 -0.3 36 36
YWHAB 0.035 0.008 -10000 0 -10000 0 0
MAPK8 0.033 0.035 -10000 0 -0.42 3 3
MAPK9 0.019 0.085 -10000 0 -0.42 18 18
YWHAG 0.036 0.005 -10000 0 -10000 0 0
FKBP1A 0.035 0.007 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.031 0.09 0.32 1 -0.35 7 8
PRKCH 0.03 0.046 -10000 0 -0.42 5 5
CABIN1/Cbp/p300 0.046 0.029 -10000 0 -0.29 2 2
CASP3 0.035 0.008 -10000 0 -10000 0 0
PIM1 0.035 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.024 0.005 -10000 0 -10000 0 0
apoptosis 0.003 0.049 -10000 0 -0.29 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.029 0.06 -10000 0 -0.25 3 3
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.03 0.05 -10000 0 -0.42 6 6
JNK2/NFAT4 -0.002 0.08 -10000 0 -0.16 102 102
BAD/BCL-XL 0.051 0.019 -10000 0 -0.3 1 1
PRKCD 0.033 0.03 -10000 0 -0.42 2 2
NUP214 0.035 0.021 -10000 0 -0.42 1 1
PRKCZ 0 0 -10000 0 -10000 0 0
PRKCA 0.032 0.012 -10000 0 -10000 0 0
PRKCG 0.036 0 -10000 0 -10000 0 0
PRKCQ 0.025 0.054 -10000 0 -0.42 7 7
FKBP38/BCL2 -0.019 0.14 -10000 0 -0.3 97 97
EP300 0.033 0.03 -10000 0 -0.42 2 2
PRKCB1 0.003 0.11 -10000 0 -0.42 30 30
CSNK2A1 0.035 0.006 -10000 0 -10000 0 0
NFATc/JNK1 0.037 0.094 0.31 2 -0.37 7 9
CaM/Ca2+/FKBP38 0.047 0.012 -10000 0 -10000 0 0
FKBP12/FK506 0.026 0.005 -10000 0 -10000 0 0
CSNK1A1 0.018 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.045 0.026 -10000 0 -0.25 3 3
NFATc/ERK1 0.033 0.091 0.31 2 -0.39 6 8
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.05 0.097 -10000 0 -0.32 12 12
NR4A1 0.062 0.078 0.23 12 -0.43 1 13
GSK3B 0.036 0.005 -10000 0 -10000 0 0
positive T cell selection 0.013 0.007 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.021 0.036 -10000 0 -0.21 1 1
RCH1/ KPNB1 0.038 0.056 -10000 0 -0.3 12 12
YWHAQ 0.034 0.029 -10000 0 -0.42 2 2
PRKACA 0.036 0.005 -10000 0 -10000 0 0
AKAP5 0 0.12 -10000 0 -0.42 37 37
MEF2D 0.029 0.015 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.027 0.016 -10000 0 -10000 0 0
NFATc/p38 alpha 0.037 0.092 0.33 1 -0.37 7 8
CREBBP 0.033 0.011 -10000 0 -10000 0 0
BCL2 -0.057 0.18 -10000 0 -0.42 99 99
TCGA08_rtk_signaling

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
PDGFRA 0.009 0.11 -10000 0 -0.42 29 29
HRAS 0.032 0.036 -10000 0 -0.42 3 3
EGFR -0.015 0.13 -10000 0 -0.42 49 49
AKT 0.027 0.084 0.24 4 -0.24 19 23
FOXO3 0 0 -10000 0 -10000 0 0
AKT1 0.033 0.03 -10000 0 -0.42 2 2
FOXO1 0 0 -10000 0 -10000 0 0
AKT3 0.025 0.032 -10000 0 -0.42 2 2
FOXO4 0 0 -10000 0 -10000 0 0
MET 0.03 0.041 -10000 0 -0.42 4 4
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
PIK3CB 0.031 0.045 -10000 0 -0.42 5 5
NRAS 0.029 0.054 -10000 0 -0.42 7 7
PIK3CG 0.023 0.072 -10000 0 -0.42 13 13
PIK3R3 0.025 0.067 -10000 0 -0.42 11 11
PIK3R2 0.036 0.004 -10000 0 -10000 0 0
NF1 0.032 0.03 -10000 0 -0.42 2 2
RAS -0.002 0.079 0.17 3 -0.29 22 25
ERBB2 0.017 0.078 -10000 0 -0.42 15 15
proliferation/survival/translation -0.026 0.058 0.22 10 -0.18 5 15
PI3K 0.004 0.084 0.21 5 -0.23 35 40
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
KRAS 0.028 0.054 -10000 0 -0.42 7 7
FOXO 0.043 0.04 0.18 10 -10000 0 10
AKT2 0.036 0.005 -10000 0 -10000 0 0
PTEN 0.027 0.061 -10000 0 -0.42 9 9
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.024 0.17 -10000 0 -0.83 12 12
NCK1/PAK1/Dok-R -0.028 0.076 -10000 0 -0.42 11 11
NCK1/Dok-R 0.031 0.15 -10000 0 -0.86 9 9
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
mol:beta2-estradiol -0.007 0.015 0.31 1 -10000 0 1
RELA 0.035 0.006 -10000 0 -10000 0 0
SHC1 0.028 0.025 -10000 0 -0.42 1 1
Rac/GDP 0.026 0.004 -10000 0 -10000 0 0
F2 0.011 0.025 -10000 0 -10000 0 0
TNIP2 0.033 0.03 -10000 0 -0.42 2 2
NF kappa B/RelA 0.063 0.14 -10000 0 -0.79 9 9
FN1 -0.01 0.14 -10000 0 -0.42 50 50
PLD2 0.021 0.13 -10000 0 -0.85 9 9
PTPN11 0.036 0.004 -10000 0 -10000 0 0
GRB14 -0.063 0.18 -10000 0 -0.42 98 98
ELK1 0.024 0.13 -10000 0 -0.78 10 10
GRB7 0.024 0.058 -10000 0 -0.42 8 8
PAK1 0.015 0.085 -10000 0 -0.42 18 18
Tie2/Ang1/alpha5/beta1 Integrin 0.04 0.17 -10000 0 -0.88 9 9
CDKN1A 0.001 0.19 -10000 0 -0.74 25 25
ITGA5 0.034 0.029 -10000 0 -0.42 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.028 0.15 -10000 0 -0.86 9 9
CRK 0.032 0.023 -10000 0 -0.42 1 1
mol:NO 0.027 0.13 -10000 0 -0.58 13 13
PLG 0.019 0.13 -10000 0 -0.85 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.017 0.15 -10000 0 -0.8 11 11
GRB2 0.033 0.011 -10000 0 -10000 0 0
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
ANGPT2 -0.055 0.21 -10000 0 -0.78 21 21
BMX 0.009 0.15 -10000 0 -0.94 10 10
ANGPT1 0.015 0.035 -10000 0 -10000 0 0
tube development -0.003 0.17 -10000 0 -0.7 16 16
ANGPT4 0.035 0.022 -10000 0 -0.42 1 1
response to hypoxia 0 0.01 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.009 0.16 -10000 0 -0.88 9 9
alpha5/beta1 Integrin 0.048 0.037 -10000 0 -0.3 5 5
FGF2 -0.001 0.11 -10000 0 -0.42 34 34
STAT5A (dimer) -0.001 0.2 -10000 0 -0.79 21 21
mol:L-citrulline 0.027 0.13 -10000 0 -0.58 13 13
AGTR1 -0.046 0.16 -10000 0 -0.42 80 80
MAPK14 0.019 0.18 -10000 0 -1.1 11 11
Tie2/SHP2 0.011 0.17 -10000 0 -0.85 12 12
TEK 0.005 0.17 -10000 0 -0.96 11 11
RPS6KB1 0.036 0.16 -10000 0 -0.82 11 11
Angiotensin II/AT1 -0.03 0.12 -10000 0 -0.29 80 80
Tie2/Ang1/GRB2 0.034 0.14 -10000 0 -0.85 9 9
MAPK3 0.026 0.13 -10000 0 -0.78 9 9
MAPK1 0.016 0.12 -10000 0 -0.8 9 9
Tie2/Ang1/GRB7 0.03 0.14 -10000 0 -0.85 9 9
NFKB1 0.036 0.005 -10000 0 -10000 0 0
MAPK8 0.02 0.13 -10000 0 -0.85 9 9
PI3K 0.021 0.18 -10000 0 -0.96 12 12
FES 0.014 0.19 -10000 0 -1 13 13
Crk/Dok-R 0.03 0.15 -10000 0 -0.86 9 9
Tie2/Ang1/ABIN2 0.035 0.14 -10000 0 -0.86 9 9
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.026 0.15 -10000 0 -0.72 13 13
STAT5A 0.028 0.037 -10000 0 -0.42 3 3
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.055 0.17 -10000 0 -0.81 10 10
Tie2/Ang2 -0.012 0.21 -10000 0 -0.99 15 15
Tie2/Ang1 0.026 0.14 -10000 0 -0.9 9 9
FOXO1 0.026 0.16 -10000 0 -0.72 14 14
ELF1 0.034 0.053 -10000 0 -0.41 6 6
ELF2 0.027 0.13 -10000 0 -0.85 9 9
mol:Choline 0.02 0.12 -10000 0 -0.82 9 9
cell migration -0.013 0.052 -10000 0 -0.22 14 14
FYN -0.007 0.19 -10000 0 -0.85 14 14
DOK2 0.009 0.086 -10000 0 -0.42 19 19
negative regulation of cell cycle 0.005 0.18 -10000 0 -0.66 25 25
ETS1 0.035 0.028 -10000 0 -0.43 1 1
PXN 0.055 0.15 -10000 0 -0.65 11 11
ITGB1 0.032 0.036 -10000 0 -0.42 3 3
NOS3 0.024 0.14 -10000 0 -0.68 12 12
RAC1 0.035 0.006 -10000 0 -10000 0 0
TNF 0.033 0.065 -10000 0 -0.41 10 10
MAPKKK cascade 0.02 0.12 -10000 0 -0.82 9 9
RASA1 0.029 0.05 -10000 0 -0.42 6 6
Tie2/Ang1/Shc 0.028 0.14 -10000 0 -0.9 8 8
NCK1 0.034 0.021 -10000 0 -0.42 1 1
vasculogenesis 0.028 0.12 -10000 0 -0.52 13 13
mol:Phosphatidic acid 0.02 0.12 -10000 0 -0.82 9 9
mol:Angiotensin II 0.001 0.002 -10000 0 -10000 0 0
mol:NADP 0.027 0.13 -10000 0 -0.58 13 13
Rac1/GTP 0.034 0.16 -10000 0 -0.73 13 13
MMP2 0.011 0.14 -10000 0 -0.97 8 8
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.014 -10000 0 -10000 0 0
CDC42/GTP 0.003 0.087 -10000 0 -0.27 21 21
PLCG1 -0.009 0.074 -10000 0 -0.28 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.028 0.054 -10000 0 -0.42 7 7
GNAI3 0.035 0.006 -10000 0 -10000 0 0
G12/G13 0.044 0.033 -10000 0 -0.3 3 3
cell migration 0.002 0.085 -10000 0 -0.26 21 21
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.006 0.07 -10000 0 -0.29 15 15
MAPK1 -0.005 0.07 -10000 0 -0.28 19 19
S1P/S1P5/Gi 0 0.077 -10000 0 -0.24 40 40
GNAI1 0.017 0.087 -10000 0 -0.42 19 19
CDC42/GDP 0.026 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.024 0.005 -10000 0 -10000 0 0
RHOA 0.033 0.07 0.19 63 -0.24 11 74
S1P/S1P4/Gi 0 0.077 -10000 0 -0.24 40 40
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.023 0.07 -10000 0 -0.42 12 12
S1P/S1P4/G12/G13 0.038 0.027 -10000 0 -0.23 3 3
GNA12 0.035 0.007 -10000 0 -10000 0 0
GNA13 0.029 0.037 -10000 0 -0.42 3 3
CDC42 0.035 0.008 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.039 0.051 0.3 7 -10000 0 7
KIRREL 0.025 0.057 -10000 0 -0.43 7 7
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.04 0.051 -10000 0 -0.31 7 7
PLCG1 0.034 0.008 -10000 0 -10000 0 0
ARRB2 0.033 0.011 -10000 0 -10000 0 0
WASL 0.029 0.054 -10000 0 -0.42 7 7
Nephrin/NEPH1/podocin/CD2AP 0.065 0.059 -10000 0 -0.24 7 7
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.022 0.045 -10000 0 -0.21 13 13
FYN 0.057 0.1 0.28 66 -0.21 13 79
mol:Ca2+ 0.059 0.057 -10000 0 -0.23 7 7
mol:DAG 0.06 0.058 -10000 0 -0.24 7 7
NPHS2 0.03 0.03 -10000 0 -0.43 1 1
mol:IP3 0.06 0.058 -10000 0 -0.24 7 7
regulation of endocytosis 0.046 0.057 -10000 0 -0.2 12 12
Nephrin/NEPH1/podocin/Cholesterol 0.049 0.049 -10000 0 -0.23 7 7
establishment of cell polarity 0.039 0.051 -10000 0 -0.3 7 7
Nephrin/NEPH1/podocin/NCK1-2 0.076 0.065 -10000 0 -0.22 8 8
Nephrin/NEPH1/beta Arrestin2 0.051 0.06 -10000 0 -0.2 12 12
NPHS1 0.041 0.03 -10000 0 -0.38 1 1
Nephrin/NEPH1/podocin 0.048 0.057 -10000 0 -0.21 13 13
TJP1 0.032 0.036 -10000 0 -0.42 3 3
NCK1 0.034 0.021 -10000 0 -0.42 1 1
NCK2 0.036 0.005 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.061 0.059 -10000 0 -0.24 7 7
CD2AP 0.035 0.007 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.061 0.059 -10000 0 -0.24 7 7
GRB2 0.033 0.011 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.057 0.1 0.28 67 -0.22 11 78
cytoskeleton organization 0.023 0.069 0.23 31 -0.25 7 38
Nephrin/NEPH1 0.035 0.037 -10000 0 -0.21 7 7
Nephrin/NEPH1/ZO-1 0.051 0.056 -10000 0 -0.25 10 10
Paxillin-dependent events mediated by a4b1

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
CRKL 0.031 0.041 -10000 0 -0.42 4 4
Rac1/GDP 0.035 0.013 -10000 0 -10000 0 0
DOCK1 0.028 0.057 -10000 0 -0.42 8 8
ITGA4 0.021 0.078 -10000 0 -0.42 15 15
RAC1 0.035 0.006 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.042 0.061 -10000 0 -0.3 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.023 -10000 0 -0.42 1 1
alpha4/beta1 Integrin 0.058 0.065 -10000 0 -0.28 16 16
alpha4/beta7 Integrin/Paxillin 0.049 0.051 -10000 0 -0.23 15 15
lamellipodium assembly -0.013 0.13 -10000 0 -0.43 32 32
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
PI3K 0.036 0.065 -10000 0 -0.3 17 17
ARF6 0.034 0.029 -10000 0 -0.42 2 2
TLN1 0.035 0.021 -10000 0 -0.42 1 1
PXN 0.017 0.003 -10000 0 -10000 0 0
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
ARF6/GTP 0.059 0.064 -10000 0 -0.23 19 19
cell adhesion 0.062 0.063 -10000 0 -0.24 17 17
CRKL/CBL 0.043 0.037 -10000 0 -0.3 4 4
alpha4/beta1 Integrin/Paxillin 0.046 0.059 -10000 0 -0.26 16 16
ITGB1 0.032 0.036 -10000 0 -0.42 3 3
ITGB7 0.036 0.005 -10000 0 -10000 0 0
ARF6/GDP 0.033 0.031 -10000 0 -0.41 2 2
alpha4/beta1 Integrin/Paxillin/VCAM1 0.049 0.094 -10000 0 -0.26 37 37
p130Cas/Crk/Dock1 0.05 0.052 -10000 0 -0.25 9 9
VCAM1 0.009 0.1 -10000 0 -0.42 28 28
alpha4/beta1 Integrin/Paxillin/Talin 0.064 0.064 -10000 0 -0.25 17 17
alpha4/beta1 Integrin/Paxillin/GIT1 0.063 0.064 -10000 0 -0.24 17 17
BCAR1 0.03 0.014 -10000 0 -10000 0 0
mol:GDP -0.061 0.063 0.24 17 -10000 0 17
CBL 0.032 0.012 -10000 0 -10000 0 0
PRKACA 0.036 0.005 -10000 0 -10000 0 0
GIT1 0.034 0.022 -10000 0 -0.42 1 1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.064 0.064 -10000 0 -0.25 17 17
Rac1/GTP -0.017 0.14 -10000 0 -0.48 32 32
Effects of Botulinum toxin

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
STX1A 0.009 0.002 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.046 0.027 -10000 0 -0.29 2 2
STXBP1 0.036 0.005 -10000 0 -10000 0 0
ACh/CHRNA1 0.016 0.044 -10000 0 -0.24 7 7
RAB3GAP2/RIMS1/UNC13B 0.051 0.04 -10000 0 -0.25 3 3
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 0.012 -10000 0 -10000 0 0
mol:ACh -0.005 0.029 0.076 9 -0.11 18 27
RAB3GAP2 0.028 0.025 -10000 0 -0.42 1 1
STX1A/SNAP25/VAMP2 0.034 0.057 -10000 0 -0.18 3 3
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.016 0.044 -10000 0 -0.24 7 7
UNC13B 0.033 0.03 -10000 0 -0.42 2 2
CHRNA1 0.031 0.05 -10000 0 -0.42 6 6
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.042 0.11 -10000 0 -0.27 96 96
SNAP25 -0.001 0.043 -10000 0 -0.26 14 14
VAMP2 0.005 0.011 -10000 0 -0.23 1 1
SYT1 -0.062 0.17 -10000 0 -0.42 96 96
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.032 0.007 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.034 0.057 -10000 0 -0.18 3 3
Signaling events mediated by PRL

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
CCNE1 0.027 0.046 -10000 0 -0.42 5 5
mol:Halofuginone 0.004 0.009 -10000 0 -0.19 1 1
ITGA1 0.022 0.075 -10000 0 -0.42 14 14
CDKN1A -0.005 0.12 -10000 0 -0.45 27 27
PRL-3/alpha Tubulin 0.02 0.018 -10000 0 -0.3 1 1
mol:Ca2+ -0.036 0.081 0.34 1 -0.31 38 39
AGT -0.022 0.14 -10000 0 -0.42 52 52
CCNA2 -0.038 0.097 -10000 0 -0.52 3 3
TUBA1B 0 0 -10000 0 -10000 0 0
EGR1 -0.028 0.11 -10000 0 -0.29 77 77
CDK2/Cyclin E1 0.021 0.13 -10000 0 -0.45 21 21
MAPK3 0.012 0.016 -10000 0 -0.3 1 1
PRL-2 /Rab GGTase beta 0.047 0.04 -10000 0 -0.3 6 6
MAPK1 0.012 0.016 -10000 0 -0.3 1 1
PTP4A1 -0.028 0.085 -10000 0 -0.48 3 3
PTP4A3 0.027 0.025 -10000 0 -0.42 1 1
PTP4A2 0.03 0.05 -10000 0 -0.42 6 6
ITGB1 0.011 0.025 -10000 0 -0.3 3 3
SRC 0.033 0.029 -10000 0 -0.42 2 2
RAC1 0.013 0.059 -10000 0 -0.44 5 5
Rab GGTase beta/Rab GGTase alpha 0.051 0.013 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.001 0.098 0.37 1 -0.46 3 4
RABGGTA 0.035 0.007 -10000 0 -10000 0 0
BCAR1 -0.017 0.021 0.34 1 -10000 0 1
RHOC 0.01 0.071 -10000 0 -0.41 10 10
RHOA 0.001 0.092 -10000 0 -0.38 22 22
cell motility 0.012 0.087 0.35 1 -0.38 10 11
PRL-1/alpha Tubulin -0.028 0.079 -10000 0 -0.45 3 3
PRL-3/alpha1 Integrin 0.032 0.06 -10000 0 -0.32 12 12
ROCK1 0.017 0.082 0.35 1 -0.39 9 10
RABGGTB 0.035 0.007 -10000 0 -10000 0 0
CDK2 0.034 0.029 -10000 0 -0.42 2 2
mitosis -0.028 0.084 -10000 0 -0.48 3 3
ATF5 0.034 0.022 -10000 0 -0.42 1 1
BARD1 signaling events

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
BARD1/CSTF1 0.045 0.036 -10000 0 -0.3 4 4
ATM 0.031 0.013 -10000 0 -10000 0 0
UBE2D3 0.036 0.006 -10000 0 -10000 0 0
PRKDC 0.029 0.031 -10000 0 -0.42 2 2
ATR 0.036 0.006 -10000 0 -10000 0 0
UBE2L3 0.034 0.008 -10000 0 -10000 0 0
FANCD2 0.023 0.011 -10000 0 -10000 0 0
protein ubiquitination 0.06 0.073 -10000 0 -0.23 20 20
XRCC5 0.036 0.005 -10000 0 -10000 0 0
XRCC6 0.034 0.009 -10000 0 -10000 0 0
M/R/N Complex 0.048 0.044 -10000 0 -0.26 4 4
MRE11A 0.031 0.013 -10000 0 -10000 0 0
DNA-PK 0.056 0.037 -10000 0 -0.26 2 2
FA complex/FANCD2/Ubiquitin 0.003 0.093 -10000 0 -0.4 11 11
FANCF 0.032 0.041 -10000 0 -0.42 4 4
BRCA1 0.022 0.07 -10000 0 -0.42 12 12
CCNE1 0.027 0.046 -10000 0 -0.42 5 5
CDK2/Cyclin E1 0.044 0.045 -10000 0 -0.34 6 6
FANCG 0.035 0.006 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.037 0.062 -10000 0 -0.3 15 15
FANCE 0.032 0.036 -10000 0 -0.42 3 3
FANCC 0.035 0.021 -10000 0 -0.42 1 1
NBN 0.028 0.025 -10000 0 -0.42 1 1
FANCA 0.016 0.064 -10000 0 -0.42 10 10
DNA repair -0.015 0.11 0.28 4 -0.35 16 20
BRCA1/BARD1/ubiquitin 0.037 0.062 -10000 0 -0.3 15 15
BARD1/DNA-PK 0.07 0.05 -10000 0 -0.23 5 5
FANCL 0.036 0.006 -10000 0 -10000 0 0
mRNA polyadenylation -0.045 0.035 0.3 4 -10000 0 4
BRCA1/BARD1/CTIP/M/R/N Complex 0.017 0.08 -10000 0 -0.29 8 8
BRCA1/BACH1/BARD1/TopBP1 0.055 0.06 -10000 0 -0.26 15 15
BRCA1/BARD1/P53 0.05 0.091 -10000 0 -0.25 35 35
BARD1/CSTF1/BRCA1 0.049 0.06 -10000 0 -0.26 14 14
BRCA1/BACH1 0.021 0.07 -10000 0 -0.42 12 12
BARD1 0.033 0.035 -10000 0 -0.42 3 3
PCNA 0.03 0.046 -10000 0 -0.42 5 5
BRCA1/BARD1/UbcH5C 0.054 0.06 -10000 0 -0.26 15 15
BRCA1/BARD1/UbcH7 0.052 0.059 -10000 0 -0.26 14 14
BRCA1/BARD1/RAD51/PCNA 0.038 0.11 -10000 0 -0.24 59 59
BARD1/DNA-PK/P53 0.059 0.085 -10000 0 -0.22 29 29
BRCA1/BARD1/Ubiquitin 0.037 0.062 -10000 0 -0.3 15 15
BRCA1/BARD1/CTIP 0.034 0.061 -10000 0 -0.23 21 21
FA complex 0.02 0.056 -10000 0 -0.23 13 13
BARD1/EWS 0.047 0.031 -10000 0 -0.3 3 3
RBBP8 0.008 0.042 -10000 0 -0.3 9 9
TP53 0.008 0.1 -10000 0 -0.42 26 26
TOPBP1 0.036 0.006 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.048 0.089 0.24 35 -10000 0 35
BRCA1/BARD1 0.066 0.077 -10000 0 -0.23 20 20
CSTF1 0.032 0.023 -10000 0 -0.42 1 1
BARD1/EWS-Fli1 0.025 0.025 -10000 0 -0.3 3 3
CDK2 0.034 0.029 -10000 0 -0.42 2 2
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.006 0.13 -10000 0 -0.42 44 44
RAD50 0.032 0.041 -10000 0 -0.42 4 4
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.037 0.062 -10000 0 -0.3 15 15
EWSR1 0.034 0.009 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin 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
ITGB1 0.032 0.036 -9999 0 -0.42 3 3
ITGB7 0.036 0.005 -9999 0 -10000 0 0
ITGA4 0.021 0.078 -9999 0 -0.42 15 15
alpha4/beta7 Integrin 0.042 0.061 -9999 0 -0.3 15 15
alpha4/beta1 Integrin 0.039 0.069 -9999 0 -0.33 16 16
Signaling events mediated by HDAC Class III

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
EP300 0.032 0.03 -10000 0 -0.42 2 2
HDAC4 0.034 0.021 -10000 0 -0.42 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.005 0.017 -10000 0 -0.11 8 8
CDKN1A -0.018 0.097 0.4 1 -0.56 14 15
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.035 0.007 -10000 0 -10000 0 0
FOXO3 -0.006 0.023 0.35 2 -10000 0 2
FOXO1 0 0 -10000 0 -10000 0 0
FOXO4 0.01 0.023 -10000 0 -0.33 2 2
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.034 0.009 -10000 0 -10000 0 0
TAT 0.027 0.016 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.005 0.064 -10000 0 -0.3 23 23
PPARGC1A 0.024 0.064 -10000 0 -0.42 10 10
FHL2 -0.022 0.15 -10000 0 -0.42 61 61
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.048 0.019 -10000 0 -10000 0 0
HIST2H4A -0.005 0.017 0.11 8 -10000 0 8
SIRT1/FOXO3a 0.029 0.038 0.26 4 -0.2 2 6
SIRT1 0.035 0.019 0.21 4 -10000 0 4
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.054 0.037 -10000 0 -0.26 1 1
SIRT1/Histone H1b 0.021 0.077 -10000 0 -0.22 33 33
apoptosis -0.064 0.025 -10000 0 -10000 0 0
SIRT1/PGC1A 0.038 0.045 -10000 0 -0.25 10 10
p53/SIRT1 0.026 0.077 0.4 4 -0.3 21 25
SIRT1/FOXO4 0.031 0.045 -10000 0 -0.2 6 6
FOXO1/FHL2/SIRT1 0.011 0.087 -10000 0 -0.22 59 59
HIST1H1E 0 0.066 -10000 0 -0.25 31 31
SIRT1/p300 0.047 0.028 -10000 0 -0.27 2 2
muscle cell differentiation -0.009 0.06 0.25 23 -0.16 6 29
TP53 0.01 0.095 0.21 4 -0.42 22 26
KU70/SIRT1/BAX 0.065 0.025 -10000 0 -10000 0 0
CREBBP 0.033 0.011 -10000 0 -10000 0 0
MEF2D 0.029 0.015 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.041 0.024 -10000 0 -10000 0 0
ACSS2 0.015 0.02 0.19 4 -10000 0 4
SIRT1/PCAF/MYOD 0.01 0.061 0.16 7 -0.25 23 30
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.026 0.061 0.42 9 -10000 0 9
PI3K Class IB/PDE3B 0.026 0.061 -10000 0 -0.42 9 9
PDE3B 0.026 0.061 -10000 0 -0.42 9 9
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.075 0.048 -10000 0 -0.23 6 6
HDAC3 0.036 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.012 0.009 -10000 0 -0.19 1 1
GATA1/HDAC4 0.052 0.019 -10000 0 -0.3 1 1
GATA1/HDAC5 0.049 0.021 -10000 0 -0.3 1 1
GATA2/HDAC5 0.044 0.041 -10000 0 -0.3 6 6
HDAC5/BCL6/BCoR 0.048 0.075 -10000 0 -0.26 26 26
HDAC9 0.033 0.022 -10000 0 -0.42 1 1
Glucocorticoid receptor/Hsp90/HDAC6 0.04 0.048 -10000 0 -0.25 13 13
HDAC4/ANKRA2 0.04 0.059 -10000 0 -0.3 14 14
HDAC5/YWHAB 0.047 0.023 -10000 0 -0.3 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.016 0.011 -10000 0 -0.17 1 1
GATA2 0.029 0.046 -10000 0 -0.42 5 5
HDAC4/RFXANK 0.051 0.02 -10000 0 -0.3 1 1
BCOR 0.028 0.06 -10000 0 -0.42 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.032 0.03 -10000 0 -0.42 2 2
HDAC5 0.033 0.022 -10000 0 -0.42 1 1
GNB1/GNG2 0.048 0.039 -10000 0 -0.3 6 6
Histones 0.009 0.069 -10000 0 -0.37 4 4
ADRBK1 0.034 0.01 -10000 0 -10000 0 0
HDAC4 0.034 0.021 -10000 0 -0.42 1 1
XPO1 0.036 0.005 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.039 0.058 -10000 0 -0.3 13 13
HDAC4/Ubc9 0.046 0.024 -10000 0 -0.3 1 1
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.046 0.024 -10000 0 -0.3 1 1
TUBA1B 0 0 -10000 0 -10000 0 0
HDAC6 0.036 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0.048 0.022 -10000 0 -0.3 1 1
CAMK4 0.032 0.036 -10000 0 -0.42 3 3
Tubulin/HDAC6 0.037 0.055 -10000 0 -0.25 17 17
SUMO1 0.036 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.035 0.008 -10000 0 -10000 0 0
GATA1 0.036 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.032 0.012 -10000 0 -10000 0 0
NR3C1 0.024 0.072 -10000 0 -0.42 13 13
SUMO1/HDAC4 0.052 0.042 -10000 0 -0.19 1 1
SRF 0.035 0.007 -10000 0 -10000 0 0
HDAC4/YWHAB 0.049 0.021 -10000 0 -0.3 1 1
Tubulin 0.015 0.058 -10000 0 -0.3 17 17
HDAC4/14-3-3 E 0.047 0.023 -10000 0 -0.29 1 1
GNB1 0.032 0.045 -10000 0 -0.42 5 5
RANGAP1 0.033 0.022 -10000 0 -0.42 1 1
BCL6/BCoR 0.032 0.08 -10000 0 -0.3 27 27
HDAC4/HDAC3/SMRT (N-CoR2) 0.069 0.023 -10000 0 -0.26 1 1
HDAC4/SRF 0.064 0.036 -10000 0 -0.26 4 4
HDAC4/ER alpha -0.046 0.15 -10000 0 -0.3 133 133
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.009 0.068 -10000 0 -0.37 4 4
cell motility 0.036 0.055 -10000 0 -0.25 17 17
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.032 0.011 -10000 0 -10000 0 0
HDAC7/HDAC3 0.026 0.004 -10000 0 -10000 0 0
BCL6 0.018 0.085 -10000 0 -0.42 18 18
HDAC4/CaMK II delta B 0.034 0.021 -10000 0 -0.42 1 1
Hsp90/HDAC6 0.027 0 -10000 0 -10000 0 0
ESR1 -0.089 0.2 -10000 0 -0.42 132 132
HDAC6/HDAC11 0.035 0.077 -10000 0 -0.3 25 25
Ran/GTP/Exportin 1 0.054 0.041 -10000 0 -10000 0 0
NPC 0.021 0.003 -10000 0 -10000 0 0
MEF2C 0.015 0.091 -10000 0 -0.42 21 21
RAN 0.036 0.005 -10000 0 -10000 0 0
HDAC4/MEF2C 0.076 0.073 -10000 0 -0.22 19 19
GNG2 0.034 0.021 -10000 0 -0.42 1 1
NCOR2 0.036 0.005 -10000 0 -10000 0 0
TUBB2A 0.019 0.082 -10000 0 -0.42 17 17
HDAC11 0.013 0.099 -10000 0 -0.42 25 25
HSP90AA1 0 0 -10000 0 -10000 0 0
RANBP2 0.036 0.004 -10000 0 -10000 0 0
ANKRA2 0.023 0.072 -10000 0 -0.42 13 13
RFXANK 0.036 0.005 -10000 0 -10000 0 0
nuclear import -0.037 0.028 0.26 2 -10000 0 2
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.017 0.003 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.042 0.031 -10000 0 -0.23 1 1
CDKN1B 0.01 0.077 0.26 2 -0.32 15 17
CDKN1A 0.012 0.071 0.2 1 -0.3 17 18
FRAP1 0.035 0.007 -10000 0 -10000 0 0
PRKDC 0.029 0.031 -10000 0 -0.42 2 2
FOXO3 0.012 0.056 -10000 0 -0.29 15 15
AKT1 0.012 0.059 -10000 0 -0.3 15 15
BAD 0.034 0.021 -10000 0 -0.42 1 1
AKT3 0.012 0.025 -10000 0 -0.29 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.012 0.056 -10000 0 -0.29 15 15
AKT1/ASK1 0.035 0.085 0.22 2 -0.28 16 18
BAD/YWHAZ 0.051 0.037 -10000 0 -0.26 1 1
RICTOR 0.035 0.007 -10000 0 -10000 0 0
RAF1 0.036 0.006 -10000 0 -10000 0 0
JNK cascade -0.034 0.082 0.27 16 -0.22 2 18
TSC1 0.014 0.061 -10000 0 -0.29 14 14
YWHAZ 0.027 0.016 -10000 0 -10000 0 0
AKT1/RAF1 0.053 0.08 0.25 5 -0.29 15 20
EP300 0.032 0.03 -10000 0 -0.42 2 2
mol:GDP 0.012 0.058 -10000 0 -0.3 15 15
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.008 0.061 0.26 1 -0.3 15 16
YWHAQ 0.034 0.029 -10000 0 -0.42 2 2
TBC1D4 0.005 0.034 0.24 2 -0.24 8 10
MAP3K5 0.012 0.095 -10000 0 -0.42 23 23
MAPKAP1 0.035 0.021 -10000 0 -0.42 1 1
negative regulation of cell cycle -0.034 0.072 0.25 6 -0.2 1 7
YWHAH 0.031 0.036 -10000 0 -0.42 3 3
AKT1S1 0.018 0.074 0.27 1 -0.3 16 17
CASP9 0.016 0.055 -10000 0 -0.29 11 11
YWHAB 0.035 0.008 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.043 0.095 0.28 7 -0.3 15 22
GBL 0.032 0.023 -10000 0 -0.42 1 1
PDK1/Src/Hsp90 0.042 0.025 -10000 0 -0.25 2 2
YWHAE 0.032 0.012 -10000 0 -10000 0 0
SRC 0.033 0.029 -10000 0 -0.42 2 2
AKT2/p21CIP1 0.015 0.066 0.21 6 -0.33 7 13
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.035 0.073 -10000 0 -0.4 6 6
CHUK 0.01 0.069 -10000 0 -0.3 16 16
BAD/BCL-XL 0.056 0.079 0.26 3 -0.28 15 18
mTORC2 0.076 0.041 -10000 0 -0.23 2 2
AKT2 0.016 0.015 -10000 0 -0.28 1 1
FOXO1-3a-4/14-3-3 family 0.044 0.091 0.24 14 -0.3 7 21
PDPK1 0.032 0.023 -10000 0 -0.42 1 1
MDM2 0.017 0.068 0.26 2 -0.29 15 17
MAPKKK cascade -0.053 0.079 0.28 15 -0.25 5 20
MDM2/Cbp/p300 0.055 0.082 0.28 8 -0.33 8 16
TSC1/TSC2 0.017 0.082 0.3 19 -0.3 14 33
proteasomal ubiquitin-dependent protein catabolic process 0.053 0.079 0.27 8 -0.3 10 18
glucose import -0.001 0.03 0.21 2 -0.22 8 10
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.032 0.078 0.26 1 -0.44 6 7
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.001 0.031 0.21 2 -0.22 8 10
GSK3A 0.015 0.064 0.26 1 -0.29 15 16
FOXO1 0.012 0.056 -10000 0 -0.29 15 15
GSK3B 0.014 0.063 -10000 0 -0.29 15 15
SFN 0.012 0.099 -10000 0 -0.42 25 25
G1/S transition of mitotic cell cycle 0.019 0.071 0.26 3 -0.32 8 11
p27Kip1/14-3-3 family 0.021 0.054 -10000 0 -0.34 3 3
PRKACA 0.036 0.005 -10000 0 -10000 0 0
KPNA1 0.036 0.005 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
YWHAG 0.036 0.005 -10000 0 -10000 0 0
RHEB 0.035 0.007 -10000 0 -10000 0 0
CREBBP 0.033 0.011 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.035 0.007 -9999 0 -10000 0 0
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.033 0.011 -9999 0 -10000 0 0
TCEB1 0.028 0.025 -9999 0 -0.42 1 1
HIF1A/p53 0.007 0.098 -9999 0 -0.27 25 25
HIF1A 0 0.082 -9999 0 -0.28 17 17
COPS5 0.026 0.042 -9999 0 -0.42 4 4
VHL/Elongin B/Elongin C/RBX1/CUL2 0.072 0.053 -9999 0 -0.22 1 1
FIH (dimer) 0.036 0.005 -9999 0 -10000 0 0
CDKN2A 0.015 0.075 -9999 0 -0.42 14 14
ARNT/IPAS 0.051 0.013 -9999 0 -10000 0 0
HIF1AN 0.036 0.005 -9999 0 -10000 0 0
GNB2L1 0.034 0.035 -9999 0 -0.42 3 3
HIF1A/ARNT 0.019 0.088 -9999 0 -0.27 17 17
CUL2 0.035 0.007 -9999 0 -10000 0 0
OS9 0.034 0.029 -9999 0 -0.42 2 2
RACK1/Elongin B/Elongin C 0.054 0.038 -9999 0 -0.26 2 2
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.004 0.077 -9999 0 -0.27 17 17
PHD1-3/OS9 0.033 0.1 -9999 0 -0.24 49 49
HIF1A/RACK1/Elongin B/Elongin C 0.036 0.084 -9999 0 -0.26 12 12
VHL 0.035 0.007 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.014 0.081 -9999 0 -0.27 14 14
EGLN3 -0.015 0.14 -9999 0 -0.42 52 52
EGLN2 0.032 0.041 -9999 0 -0.42 4 4
EGLN1 0.021 0.055 -9999 0 -0.42 7 7
TP53 0.008 0.1 -9999 0 -0.42 26 26
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.038 0.062 -9999 0 -0.44 5 5
ARNT 0.035 0.006 -9999 0 -10000 0 0
ARD1A 0.036 0.003 -9999 0 -10000 0 0
RBX1 0.034 0.009 -9999 0 -10000 0 0
HIF1A/p19ARF 0.004 0.093 -9999 0 -0.29 21 21
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.029 0.054 -10000 0 -0.42 7 7
SMAD2 0 0.058 0.21 2 -0.22 12 14
SMAD3 0.019 0.058 0.28 1 -0.45 1 2
SMAD3/SMAD4 0.03 0.09 -10000 0 -0.38 17 17
SMAD4/Ubc9/PIASy 0.055 0.052 -10000 0 -0.26 10 10
SMAD2/SMAD2/SMAD4 0.051 0.079 -10000 0 -0.25 5 5
PPM1A 0.034 0.021 -10000 0 -0.42 1 1
CALM1 0.035 0.007 -10000 0 -10000 0 0
SMAD2/SMAD4 0.013 0.066 -10000 0 -0.22 20 20
MAP3K1 0.01 0.099 -10000 0 -0.42 25 25
TRAP-1/SMAD4 0.046 0.043 -10000 0 -0.3 7 7
MAPK3 0.032 0.023 -10000 0 -0.42 1 1
MAPK1 0.033 0.022 -10000 0 -0.42 1 1
NUP214 0.035 0.021 -10000 0 -0.42 1 1
CTDSP1 0.034 0.029 -10000 0 -0.42 2 2
CTDSP2 0.034 0.029 -10000 0 -0.42 2 2
CTDSPL 0.029 0.054 -10000 0 -0.42 7 7
KPNB1 0.03 0.046 -10000 0 -0.42 5 5
TGFBRAP1 0.036 0.004 -10000 0 -10000 0 0
UBE2I 0.032 0.011 -10000 0 -10000 0 0
NUP153 0.035 0.008 -10000 0 -10000 0 0
KPNA2 0.025 0.058 -10000 0 -0.42 8 8
PIAS4 0.033 0.036 -10000 0 -0.42 3 3
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.041 0.037 -10000 0 -0.25 7 7
EFNA5 0.03 0.046 -10000 0 -0.42 5 5
FYN 0.011 0.043 0.19 2 -0.23 14 16
neuron projection morphogenesis 0.041 0.037 -10000 0 -0.25 7 7
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.042 0.037 -10000 0 -0.25 7 7
EPHA5 0.034 0.029 -10000 0 -0.42 2 2
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.068 0.058 -10000 0 -0.26 9 9
MAP4K1 0.035 0.007 -10000 0 -10000 0 0
MAP3K8 0.004 0.11 -10000 0 -0.42 32 32
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0.034 0.029 -10000 0 -0.42 2 2
CRKL 0.031 0.041 -10000 0 -0.42 4 4
MAP3K1 0.004 0.07 -10000 0 -0.32 4 4
JUN -0.01 0.1 -10000 0 -0.5 11 11
MAP3K7 0.013 0.059 0.21 3 -0.33 4 7
GRAP2 0.032 0.023 -10000 0 -0.42 1 1
CRK 0.032 0.023 -10000 0 -0.42 1 1
MAP2K4 -0.003 0.081 -10000 0 -0.36 11 11
LAT 0.03 0.031 -10000 0 -0.42 2 2
LCP2 0.024 0.067 -10000 0 -0.42 11 11
MAPK8 0.008 0.084 -10000 0 -0.58 9 9
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.02 0.067 -10000 0 -0.33 5 5
LAT/GRAP2/SLP76/HPK1/HIP-55 0.08 0.062 -10000 0 -0.24 9 9
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.028 0.1 0.25 1 -0.25 33 34
CaM/Ca2+ 0.026 0.005 -10000 0 -10000 0 0
AKT1 0.033 0.03 -10000 0 -0.42 2 2
AKT2 0.036 0.005 -10000 0 -10000 0 0
STXBP4 0.03 0.037 -10000 0 -0.42 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.008 0.099 0.22 2 -0.25 38 40
YWHAZ 0.027 0.016 -10000 0 -10000 0 0
CALM1 0.035 0.007 -10000 0 -10000 0 0
YWHAQ 0.034 0.029 -10000 0 -0.42 2 2
TBC1D4 0.009 0.042 -10000 0 -0.3 9 9
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.031 0.036 -10000 0 -0.42 3 3
YWHAB 0.035 0.008 -10000 0 -10000 0 0
SNARE/Synip 0.038 0.032 -10000 0 -0.25 4 4
YWHAG 0.036 0.005 -10000 0 -10000 0 0
ASIP 0 0 -10000 0 -10000 0 0
PRKCI 0.025 0.064 -10000 0 -0.42 10 10
AS160/CaM/Ca2+ 0.026 0.005 -10000 0 -10000 0 0
RHOQ 0.031 0.045 -10000 0 -0.42 5 5
GYS1 0.018 0.04 0.25 12 -0.24 2 14
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.032 0.041 -10000 0 -0.42 4 4
TC10/GTP/CIP4/Exocyst 0.042 0.041 -10000 0 -0.25 9 9
AS160/14-3-3 0.018 0.076 -10000 0 -0.28 12 12
VAMP2 0.031 0.023 -10000 0 -0.42 1 1
SLC2A4 0.006 0.11 0.23 2 -0.28 38 40
STX4 0 0 -10000 0 -10000 0 0
GSK3B 0.026 0.021 -10000 0 -0.28 2 2
SFN 0.012 0.099 -10000 0 -0.42 25 25
LNPEP 0.033 0.03 -10000 0 -0.42 2 2
YWHAE 0.032 0.012 -10000 0 -10000 0 0
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.03 0.024 -10000 0 -0.42 1 1
CLTC 0.025 0.063 0.26 2 -0.42 6 8
calcium ion-dependent exocytosis 0.017 0.038 -10000 0 -0.22 5 5
Dynamin 2/GTP 0.031 0.02 -10000 0 -0.23 2 2
EXOC4 0.034 0.021 -10000 0 -0.42 1 1
CD59 0.017 0.05 -10000 0 -0.36 5 5
CPE -0.007 0.079 -10000 0 -0.26 43 43
CTNNB1 0.025 0.067 -10000 0 -0.42 11 11
membrane fusion 0.013 0.033 -10000 0 -0.23 4 4
CTNND1 0 0.056 0.2 33 -0.22 3 36
DNM2 0.036 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.02 0.047 0.19 2 -0.26 5 7
TSHR 0.013 0.034 -10000 0 -0.25 8 8
INS 0.008 0.096 -10000 0 -0.46 19 19
BIN1 0.035 0.021 -10000 0 -0.42 1 1
mol:Choline 0.013 0.033 -10000 0 -0.23 4 4
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.015 0.018 -10000 0 -0.25 2 2
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.034 0.029 -10000 0 -0.42 2 2
mol:Ca2+ 0.031 0.02 -10000 0 -0.23 2 2
JUP 0.02 0.053 -10000 0 -0.37 5 5
ASAP2/amphiphysin II 0.043 0.023 -10000 0 -0.23 3 3
ARF6/GTP 0.025 0.021 -10000 0 -0.3 2 2
CDH1 -0.002 0.069 -10000 0 -0.38 6 6
clathrin-independent pinocytosis 0.025 0.021 -10000 0 -0.3 2 2
MAPK8IP3 0.024 0.061 -10000 0 -0.42 9 9
positive regulation of endocytosis 0.025 0.021 -10000 0 -0.3 2 2
EXOC2 0.029 0.05 -10000 0 -0.42 6 6
substrate adhesion-dependent cell spreading 0.018 0.075 -10000 0 -0.23 31 31
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.033 0.023 -10000 0 -0.42 1 1
regulation of calcium-dependent cell-cell adhesion -0.031 0.086 0.35 7 -10000 0 7
positive regulation of phagocytosis 0.016 0.021 -10000 0 -0.25 3 3
ARF6/GTP/JIP3 0.036 0.046 -10000 0 -0.25 11 11
ACAP1 0.013 0.031 -10000 0 -0.18 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.017 0.045 -10000 0 -0.35 5 5
clathrin heavy chain/ACAP1 0.024 0.063 0.27 4 -0.31 7 11
JIP4/KLC1 0.04 0.025 -10000 0 -0.23 3 3
EXOC1 0.036 0.005 -10000 0 -10000 0 0
exocyst 0.018 0.075 -10000 0 -0.23 31 31
RALA/GTP 0.026 0.005 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.042 0.027 -10000 0 -0.25 3 3
receptor recycling 0.025 0.021 -10000 0 -0.3 2 2
CTNNA1 0 0.057 0.2 34 -0.22 3 37
NME1 0.015 0.018 -10000 0 -0.25 2 2
clathrin coat assembly 0.028 0.069 0.26 3 -0.39 7 10
IL2RA 0.009 0.067 -10000 0 -0.3 9 9
VAMP3 0.016 0.021 -10000 0 -0.25 3 3
GLUT4/clathrin heavy chain/ACAP1 0.031 0.06 -10000 0 -0.31 6 6
EXOC6 0.011 0.1 -10000 0 -0.42 27 27
PLD1 0.011 0.041 -10000 0 -0.24 11 11
PLD2 0.015 0.021 -10000 0 -0.19 4 4
EXOC5 0.035 0.021 -10000 0 -0.42 1 1
PIP5K1C 0.016 0.042 0.19 2 -0.27 5 7
SDC1 0.004 0.068 -10000 0 -0.42 5 5
ARF6/GDP 0.029 0.02 -10000 0 -0.25 2 2
EXOC7 0.033 0.01 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.033 0.089 -10000 0 -0.36 7 7
mol:Phosphatidic acid 0.013 0.033 -10000 0 -0.23 4 4
endocytosis -0.041 0.023 0.22 3 -10000 0 3
SCAMP2 0.033 0.029 -10000 0 -0.42 2 2
ADRB2 0.012 0.087 0.25 3 -0.41 9 12
EXOC3 0.036 0.002 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.039 0.029 0.18 9 -0.23 2 11
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 0.023 0.068 0.25 3 -0.38 7 10
RALA 0.035 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.026 0.086 -10000 0 -0.39 5 5
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.035 0.03 -10000 0 -0.42 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.045 0.1 0.26 12 -0.28 8 20
ERC1 0 0 -10000 0 -10000 0 0
RIP2/NOD2 0.021 0.011 -10000 0 -10000 0 0
NFKBIA 0.011 0.036 0.21 4 -0.37 3 7
BIRC2 0.032 0.012 -10000 0 -10000 0 0
IKBKB 0.03 0.014 -10000 0 -10000 0 0
RIPK2 0.028 0.015 -10000 0 -10000 0 0
IKBKG 0.011 0.099 -10000 0 -0.34 20 20
IKK complex/A20 0.033 0.12 -10000 0 -0.33 18 18
NEMO/A20/RIP2 0.028 0.015 -10000 0 -10000 0 0
XPO1 0.036 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.022 0.11 -10000 0 -0.32 22 22
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.036 0.005 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.047 0.009 -10000 0 -10000 0 0
IKK complex/ELKS 0.011 0.1 -10000 0 -0.32 19 19
BCL10/MALT1/TRAF6 0.063 0.041 -10000 0 -0.31 4 4
NOD2 0 0 -10000 0 -10000 0 0
NFKB1 0.037 0.011 -10000 0 -10000 0 0
RELA 0.037 0.011 -10000 0 -10000 0 0
MALT1 0.031 0.041 -10000 0 -0.42 4 4
cIAP1/UbcH5C 0.046 0.019 -10000 0 -10000 0 0
ATM 0.031 0.013 -10000 0 -10000 0 0
TNF/TNFR1A 0.043 0.048 -10000 0 -0.3 9 9
TRAF6 0.035 0.021 -10000 0 -0.42 1 1
PRKCA 0.032 0.012 -10000 0 -10000 0 0
CHUK 0.026 0.067 -10000 0 -0.42 11 11
UBE2D3 0.036 0.006 -10000 0 -10000 0 0
TNF 0.026 0.061 -10000 0 -0.42 9 9
NF kappa B1 p50/RelA 0.074 0.037 -10000 0 -0.24 4 4
BCL10 0.035 0.008 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.036 0.21 4 -0.37 3 7
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.03 -10000 0 -0.42 2 2
TNFRSF1A 0.033 0.022 -10000 0 -0.42 1 1
IKK complex 0.023 0.12 -10000 0 -0.34 19 19
CYLD 0.029 0.024 -10000 0 -0.42 1 1
IKK complex/PKC alpha 0.029 0.11 -10000 0 -0.32 17 17
Alternative NF-kappaB pathway

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
IKK alpha homodimer 0.041 0.057 -9999 0 -0.3 13 13
FBXW11 0.033 0.029 -9999 0 -0.42 2 2
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.029 -9999 0 -0.42 2 2
CHUK 0.026 0.067 -9999 0 -0.42 11 11
NF kappa B2 p100/RelB 0.082 0.075 -9999 0 -0.24 20 20
NFKB1 0.036 0.005 -9999 0 -10000 0 0
MAP3K14 0.032 0.03 -9999 0 -0.42 2 2
NF kappa B1 p50/RelB 0.047 0.04 -9999 0 -0.3 6 6
RELB 0.029 0.05 -9999 0 -0.42 6 6
NFKB2 0.035 0.021 -9999 0 -0.42 1 1
NF kappa B2 p52/RelB 0.042 0.036 -9999 0 -0.25 7 7
regulation of B cell activation 0.042 0.036 -9999 0 -0.25 7 7
Circadian rhythm 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
chromatin modification 0.034 0.088 -10000 0 -1.2 1 1
CLOCK 0.037 0.021 -10000 0 -0.42 1 1
TIMELESS/CRY2 0.042 0.061 -10000 0 -1.2 1 1
DEC1/BMAL1 0.043 0.061 -10000 0 -0.32 13 13
ATR 0.036 0.006 -10000 0 -10000 0 0
NR1D1 0.022 0.024 -10000 0 -10000 0 0
ARNTL 0.029 0.061 -10000 0 -0.42 9 9
TIMELESS 0.022 0.059 -10000 0 -1.3 1 1
NPAS2 0.027 0.064 -10000 0 -0.42 10 10
CRY2 0.036 0.005 -10000 0 -10000 0 0
mol:CO -0.01 0.007 0.14 1 -10000 0 1
CHEK1 -0.001 0.11 -10000 0 -0.42 32 32
mol:HEME 0.01 0.007 -10000 0 -0.14 1 1
PER1 0.032 0.012 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.067 0.07 -10000 0 -0.26 19 19
BMAL1/CLOCK 0.027 0.076 -10000 0 -0.49 3 3
S phase of mitotic cell cycle 0.034 0.088 -10000 0 -1.2 1 1
TIMELESS/CHEK1/ATR 0.035 0.09 -10000 0 -1.3 1 1
mol:NADPH 0.01 0.007 -10000 0 -0.14 1 1
PER1/TIMELESS 0.039 0.06 -10000 0 -1.2 1 1
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.031 0.045 -10000 0 -0.42 5 5
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.071 0.071 -10000 0 -0.27 11 11
Ran/GTP/Exportin 1/HDAC1 -0.012 0.009 -10000 0 -0.19 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.042 0.077 0.24 1 -0.29 12 13
SUMO1 0.036 0.005 -10000 0 -10000 0 0
ZFPM1 0.023 0.055 -10000 0 -0.42 7 7
NPC/RanGAP1/SUMO1/Ubc9 0.016 0.011 -10000 0 -0.17 1 1
FKBP3 0.033 0.035 -10000 0 -0.42 3 3
Histones 0.071 0.063 -10000 0 -0.23 7 7
YY1/LSF 0.029 0.061 -10000 0 -0.22 15 15
SMG5 0 0 -10000 0 -10000 0 0
RAN 0.036 0.005 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.027 0.039 -10000 0 -0.24 9 9
I kappa B alpha/HDAC1 0.04 0.056 -10000 0 -0.28 7 7
SAP18 0.034 0.01 -10000 0 -10000 0 0
RELA 0.022 0.052 0.28 1 -0.27 3 4
HDAC1/Smad7 0.067 0.028 -10000 0 -0.25 2 2
RANGAP1 0.033 0.022 -10000 0 -0.42 1 1
HDAC3/TR2 0.039 0.056 -10000 0 -0.22 13 13
NuRD/MBD3 Complex 0.032 0.067 -10000 0 -0.34 7 7
NF kappa B1 p50/RelA 0.037 0.073 0.23 2 -0.25 12 14
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.029 0.046 -10000 0 -0.42 5 5
GATA1 0.036 0 -10000 0 -10000 0 0
Mad/Max 0.052 0.011 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.018 0.092 -10000 0 -0.4 11 11
RBBP7 0.034 0.029 -10000 0 -0.42 2 2
NPC 0.021 0.003 -10000 0 -10000 0 0
RBBP4 0.035 0.021 -10000 0 -0.42 1 1
MAX 0.035 0.007 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.033 0.029 -10000 0 -0.42 2 2
NFKBIA 0.022 0.042 -10000 0 -0.24 10 10
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.021 0.057 -10000 0 -0.34 4 4
SIN3 complex 0.077 0.045 -10000 0 -0.23 5 5
SMURF1 0.036 0.006 -10000 0 -10000 0 0
CHD3 0.031 0.023 -10000 0 -0.42 1 1
SAP30 0.03 0.046 -10000 0 -0.42 5 5
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.032 0.012 -10000 0 -10000 0 0
YY1/HDAC3 0.028 0.049 -10000 0 -0.26 4 4
YY1/HDAC2 0.033 0.046 -10000 0 -0.22 6 6
YY1/HDAC1 0.035 0.047 -10000 0 -0.23 5 5
NuRD/MBD2 Complex (MeCP1) 0.032 0.066 -10000 0 -0.34 6 6
PPARG 0.01 0.093 0.3 1 -0.35 24 25
HDAC8/hEST1B 0.047 0.02 -10000 0 -0.25 2 2
UBE2I 0.032 0.011 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.029 -10000 0 -0.42 2 2
TNFRSF1A 0.033 0.022 -10000 0 -0.42 1 1
HDAC3/SMRT (N-CoR2) 0.042 0.05 -10000 0 -0.22 8 8
MBD3L2 0.028 0.057 -10000 0 -0.42 8 8
ubiquitin-dependent protein catabolic process 0.067 0.027 -10000 0 -0.25 2 2
CREBBP 0.033 0.011 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.035 0.079 -10000 0 -0.38 6 6
HDAC1 0.035 0.021 -10000 0 -0.42 1 1
HDAC3 0.025 0.029 -10000 0 -0.18 8 8
HDAC2 0.032 0.023 -10000 0 -0.42 1 1
YY1 0.016 0.018 -10000 0 -0.24 2 2
HDAC8 0.035 0.029 -10000 0 -0.42 2 2
SMAD7 0.034 0.021 -10000 0 -0.42 1 1
NCOR2 0.036 0.005 -10000 0 -10000 0 0
MXD1 0.036 0.005 -10000 0 -10000 0 0
STAT3 0.019 0.023 -10000 0 -0.28 2 2
NFKB1 0.036 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.036 0.004 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.047 0.063 -10000 0 -0.21 15 15
YY1/SAP30/HDAC1 0.048 0.058 -10000 0 -0.23 10 10
EP300 0.032 0.03 -10000 0 -0.42 2 2
STAT3 (dimer non-phopshorylated) 0.019 0.023 -10000 0 -0.28 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.042 -10000 0 -0.24 10 10
histone deacetylation 0.032 0.065 -10000 0 -0.33 6 6
STAT3 (dimer non-phopshorylated)/HDAC3 0.023 0.056 -10000 0 -0.28 7 7
nuclear export -0.047 0.02 0.25 2 -10000 0 2
PRKACA 0.036 0.005 -10000 0 -10000 0 0
GATAD2B 0.028 0.025 -10000 0 -0.42 1 1
GATAD2A 0.036 0.006 -10000 0 -10000 0 0
GATA2/HDAC3 0.04 0.05 -10000 0 -0.22 9 9
GATA1/HDAC1 0.052 0.018 -10000 0 -0.3 1 1
GATA1/HDAC3 0.043 0.05 -10000 0 -0.27 4 4
CHD4 0.033 0.022 -10000 0 -0.42 1 1
TNF-alpha/TNFR1A 0.043 0.048 -10000 0 -0.3 9 9
SIN3/HDAC complex/Mad/Max 0.025 0.058 -10000 0 -0.3 6 6
NuRD Complex 0.037 0.076 -10000 0 -0.36 6 6
positive regulation of chromatin silencing 0.067 0.062 -10000 0 -0.22 7 7
SIN3B 0.036 0.005 -10000 0 -10000 0 0
MTA2 0.033 0.029 -10000 0 -0.42 2 2
SIN3A 0.035 0.007 -10000 0 -10000 0 0
XPO1 0.036 0.005 -10000 0 -10000 0 0
SUMO1/HDAC1 0.053 0.043 -10000 0 -0.22 2 2
HDAC complex 0.081 0.042 -10000 0 -0.23 5 5
GATA1/Fog1 0.038 0.046 -10000 0 -0.3 7 7
FKBP25/HDAC1/HDAC2 0.061 0.04 -10000 0 -0.26 5 5
TNF 0.026 0.061 -10000 0 -0.42 9 9
negative regulation of cell growth 0.025 0.058 -10000 0 -0.3 6 6
NuRD/MBD2/PRMT5 Complex 0.032 0.066 -10000 0 -0.34 6 6
Ran/GTP/Exportin 1 0.054 0.041 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.021 0.066 -10000 0 -0.27 17 17
SIN3/HDAC complex/NCoR1 0.017 0.06 -10000 0 -0.29 8 8
TFCP2 0.027 0.064 -10000 0 -0.42 10 10
NR2C1 0.03 0.05 -10000 0 -0.42 6 6
MBD3 0.035 0.008 -10000 0 -10000 0 0
MBD2 0.035 0.007 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.015 0.039 0.15 33 -0.18 1 34
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.021 0.043 0.15 9 -0.17 5 14
AP2 0.047 0.031 -10000 0 -0.3 3 3
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.042 0.035 -10000 0 -0.24 7 7
CLTB 0.034 0.021 -10000 0 -0.42 1 1
coatomer protein complex/ARF1/GTP/ER cargo protein 0.017 0.02 -10000 0 -0.22 2 2
CD4 0.034 0.009 -10000 0 -10000 0 0
CLTA 0.036 0.006 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
ARFGAP1 0.008 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.019 0.033 0.17 5 -0.16 1 6
ARF1/GTP 0.016 0.017 -10000 0 -0.17 2 2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.02 0.044 0.17 36 -0.19 1 37
mol:Choline 0.019 0.033 0.18 5 -0.16 1 6
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.028 0.026 -10000 0 -0.43 1 1
DDEF1 0.014 0.029 0.16 3 -0.17 1 4
ARF1/GDP 0.001 0.021 -10000 0 -0.088 22 22
AP2M1 0.032 0.036 -10000 0 -0.42 3 3
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.011 0.013 -10000 0 -0.23 1 1
Rac/GTP 0.028 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.032 0.028 -10000 0 -0.21 1 1
ARFIP2 0.021 0.053 -10000 0 -0.39 7 7
COPA 0.029 0.015 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.016 0.028 -10000 0 -0.19 2 2
ARF1/GTP/ARHGAP10 0.018 0.016 -10000 0 -0.25 1 1
GGA3 0.032 0.023 -10000 0 -0.42 1 1
ARF1/GTP/Membrin 0.016 0.048 -10000 0 -0.24 15 15
AP2A1 0.035 0.007 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.01 0.03 -10000 0 -0.22 4 4
ARF1/GDP/Membrin 0.015 0.055 -10000 0 -0.26 16 16
Arfaptin 2/Rac/GDP 0.04 0.037 -10000 0 -0.24 7 7
CYTH2 -0.001 0.003 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.034 0.026 -10000 0 -0.26 1 1
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.026 0.004 -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 0.025 0.039 -10000 0 -0.4 2 2
PLD2 0.019 0.033 0.18 5 -0.17 1 6
ARF-GAP1/v-SNARE 0.008 0.003 -10000 0 -10000 0 0
PIP5K1A 0.019 0.033 0.17 5 -0.16 1 6
ARF1/GTP/Membrin/GBF1/p115 0.014 0.025 -10000 0 -0.22 1 1
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.019 0.033 0.18 5 -0.16 1 6
KDEL Receptor/Ligand/ARF-GAP1 0.008 0.003 -10000 0 -10000 0 0
GOSR2 0.018 0.038 -10000 0 -0.32 5 5
USO1 0.009 0.017 0.091 5 -0.077 1 6
GBF1 0.019 0.036 -10000 0 -0.32 4 4
ARF1/GTP/Arfaptin 2 0.035 0.032 -10000 0 -0.25 3 3
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.062 0.036 -10000 0 -0.26 3 3
Aurora C signaling

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
INCENP 0.029 0.05 -9999 0 -0.42 6 6
Aurora C/Aurora B/INCENP 0.054 0.047 -9999 0 -0.23 10 10
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.013 0.03 -9999 0 -0.4 2 2
AURKB 0.029 0.037 -9999 0 -0.42 3 3
AURKC 0.034 0.021 -9999 0 -0.42 1 1
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.056 0.04 -10000 0 -0.24 7 7
MAPK9 -0.001 0.056 -10000 0 -0.29 18 18
adrenocorticotropin secretion 0.005 0.024 -10000 0 -0.3 3 3
GNB1/GNG2 0.044 0.034 -10000 0 -0.25 6 6
GNB1 0.032 0.045 -10000 0 -0.42 5 5
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.02 0.02 -10000 0 -0.22 3 3
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 0.002 0.005 0.062 3 -10000 0 3
GNAL 0.031 0.036 -10000 0 -0.42 3 3
GNG2 0.034 0.021 -10000 0 -0.42 1 1
CRH 0.026 0.038 -10000 0 -0.42 3 3
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.008 0.023 -10000 0 -0.29 3 3
MAPK11 0.009 0.003 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.035 0.021 -10000 0 -0.42 1 1
Ran/GTP/Exportin 1/HDAC4 0.006 0.014 -10000 0 -0.18 1 1
MDM2/SUMO1 0.05 0.042 -10000 0 -10000 0 0
HDAC4 0.034 0.021 -10000 0 -0.42 1 1
Ran/GTP/Exportin 1/HDAC1 0.006 0.015 -10000 0 -0.21 1 1
SUMO1 0.036 0.005 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.014 0.018 -10000 0 -0.2 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.007 0.021 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.036 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.036 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.052 0.042 -10000 0 -0.19 1 1
SUMO1/HDAC1 0.053 0.043 -10000 0 -0.22 2 2
RANGAP1 0.033 0.022 -10000 0 -0.42 1 1
MDM2/SUMO1/SUMO1 0.081 0.036 -10000 0 -0.23 2 2
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.016 0.011 -10000 0 -0.17 1 1
Ran/GTP 0.036 0.038 -10000 0 -0.16 2 2
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.034 0.009 -10000 0 -10000 0 0
UBE2I 0.032 0.011 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.034 0.038 0.2 4 -10000 0 4
NPC 0.021 0.003 -10000 0 -10000 0 0
PIAS2 0.033 0.03 -10000 0 -0.42 2 2
PIAS1 0.035 0.007 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Methods & Data
Input

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

  • Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BRCA/1551046/2.GDAC_MergeDataFiles.Finished/BRCA.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/writeReducedSegments/BRCA/1589503/1.GetReducedSegments.Finished/BRCA.RS.tsv

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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