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 96
Signaling events mediated by Stem cell factor receptor (c-Kit) 83
Endothelins 77
IGF1 pathway 75
FOXM1 transcription factor network 68
Plasma membrane estrogen receptor signaling 66
Osteopontin-mediated events 65
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 63
EGFR-dependent Endothelin signaling events 62
IL4-mediated signaling events 60
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 96 7886 82 -0.16 0.035 1000 -1000 -0.041 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 83 6527 78 -0.31 0.13 1000 -1000 -0.044 -1000
Endothelins 77 7469 96 -0.17 0.034 1000 -1000 -0.032 -1000
IGF1 pathway 75 4294 57 -0.085 0.052 1000 -1000 -0.025 -1000
FOXM1 transcription factor network 68 3486 51 -0.43 0.034 1000 -1000 -0.059 -1000
Plasma membrane estrogen receptor signaling 66 5743 86 -0.22 0.21 1000 -1000 -0.038 -1000
Osteopontin-mediated events 65 2492 38 -0.13 0.038 1000 -1000 -0.02 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 63 4305 68 -0.35 0.16 1000 -1000 -0.055 -1000
EGFR-dependent Endothelin signaling events 62 1310 21 -0.077 0.048 1000 -1000 -0.015 -1000
IL4-mediated signaling events 60 5502 91 -0.52 0.41 1000 -1000 -0.079 -1000
HIF-1-alpha transcription factor network 57 4364 76 -0.17 0.043 1000 -1000 -0.016 -1000
Syndecan-1-mediated signaling events 56 1912 34 -0.13 0.04 1000 -1000 -0.022 -1000
Signaling events mediated by the Hedgehog family 54 2839 52 -0.1 0.051 1000 -1000 -0.018 -1000
Glucocorticoid receptor regulatory network 53 6062 114 -0.39 0.2 1000 -1000 -0.043 -1000
TCR signaling in naïve CD8+ T cells 52 4859 93 -0.072 0.048 1000 -1000 -0.028 -1000
Noncanonical Wnt signaling pathway 50 1319 26 -0.073 0.034 1000 -1000 -0.043 -1000
Wnt signaling 50 355 7 -0.073 0.029 1000 -1000 -0.002 -1000
Thromboxane A2 receptor signaling 47 4988 105 -0.1 0.055 1000 -1000 -0.03 -1000
IL12-mediated signaling events 46 4057 87 -0.26 0.038 1000 -1000 -0.039 -1000
FAS signaling pathway (CD95) 46 2204 47 -0.1 0.047 1000 -1000 -0.041 -1000
Nongenotropic Androgen signaling 46 2416 52 -0.11 0.06 1000 -1000 -0.016 -1000
Fc-epsilon receptor I signaling in mast cells 45 4431 97 -0.084 0.035 1000 -1000 -0.046 -1000
IL23-mediated signaling events 45 2704 60 -0.2 0.035 1000 -1000 -0.04 -1000
Stabilization and expansion of the E-cadherin adherens junction 44 3260 74 -0.094 0.057 1000 -1000 -0.051 -1000
IL27-mediated signaling events 43 2242 51 -0.22 0.1 1000 -1000 -0.054 -1000
IL6-mediated signaling events 42 3156 75 -0.15 0.067 1000 -1000 -0.036 -1000
Arf6 signaling events 38 2395 62 -0.07 0.077 1000 -1000 -0.012 -1000
LPA receptor mediated events 38 3881 102 -0.075 0.034 1000 -1000 -0.057 -1000
Ephrin B reverse signaling 36 1759 48 -0.12 0.068 1000 -1000 -0.034 -1000
E-cadherin signaling events 36 182 5 -0.014 0.031 1000 -1000 0.021 -1000
PLK2 and PLK4 events 33 100 3 -0.016 0.029 1000 -1000 0 -1000
TCGA08_p53 33 237 7 -0.03 0.026 1000 -1000 -0.002 -1000
Signaling mediated by p38-gamma and p38-delta 33 503 15 -0.06 0.033 1000 -1000 -0.024 -1000
IL2 signaling events mediated by PI3K 33 1921 58 -0.23 0.035 1000 -1000 -0.021 -1000
Canonical Wnt signaling pathway 33 1723 51 -0.14 0.082 1000 -1000 -0.025 -1000
Coregulation of Androgen receptor activity 32 2435 76 -0.15 0.054 1000 -1000 -0.025 -1000
ErbB4 signaling events 32 2256 69 -0.11 0.059 1000 -1000 -0.035 -1000
E-cadherin signaling in keratinocytes 32 1397 43 -0.052 0.035 1000 -1000 -0.021 -1000
Syndecan-2-mediated signaling events 31 2165 69 -0.023 0.047 1000 -1000 -0.033 -1000
E-cadherin signaling in the nascent adherens junction 31 2419 76 -0.078 0.052 1000 -1000 -0.047 -1000
Signaling events mediated by PTP1B 30 2326 76 -0.094 0.057 1000 -1000 -0.025 -1000
Integrins in angiogenesis 30 2525 84 -0.11 0.059 1000 -1000 -0.03 -1000
Syndecan-4-mediated signaling events 30 2076 67 -0.061 0.082 1000 -1000 -0.033 -1000
amb2 Integrin signaling 29 2431 82 -0.055 0.041 1000 -1000 -0.017 -1000
VEGFR1 specific signals 28 1573 56 -0.03 0.035 1000 -1000 -0.025 -1000
Caspase cascade in apoptosis 27 2058 74 -0.07 0.046 1000 -1000 -0.026 -1000
Regulation of nuclear SMAD2/3 signaling 27 3765 136 -0.18 0.061 1000 -1000 -0.032 -1000
Cellular roles of Anthrax toxin 27 1062 39 -0.078 0.035 1000 -1000 -0.017 -1000
Reelin signaling pathway 27 1552 56 -0.067 0.071 1000 -1000 -0.02 -1000
TCGA08_retinoblastoma 27 218 8 -0.009 0.023 1000 -1000 -0.005 -1000
Visual signal transduction: Rods 27 1408 52 -0.061 0.064 1000 -1000 -0.017 -1000
BMP receptor signaling 26 2182 81 -0.12 0.065 1000 -1000 -0.022 -1000
BCR signaling pathway 26 2647 99 -0.11 0.066 1000 -1000 -0.038 -1000
Nectin adhesion pathway 25 1577 63 -0.05 0.05 1000 -1000 -0.029 -1000
IL1-mediated signaling events 25 1570 62 -0.029 0.075 1000 -1000 -0.029 -1000
Aurora B signaling 25 1738 67 -0.059 0.05 1000 -1000 -0.034 -1000
PDGFR-alpha signaling pathway 24 1085 44 -0.14 0.048 1000 -1000 -0.021 -1000
mTOR signaling pathway 24 1287 53 -0.061 0.043 1000 -1000 -0.027 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 23 1045 45 -0.045 0.052 1000 -1000 -0.04 -1000
TRAIL signaling pathway 22 1065 48 -0.024 0.038 1000 -1000 -0.031 -1000
S1P1 pathway 22 793 36 -0.033 0.035 1000 -1000 -0.017 -1000
Visual signal transduction: Cones 21 801 38 -0.026 0.046 1000 -1000 0 -1000
FOXA2 and FOXA3 transcription factor networks 21 1010 46 -0.2 0.04 1000 -1000 -0.03 -1000
Glypican 1 network 21 1054 48 -0.024 0.046 1000 -1000 -0.023 -1000
PLK1 signaling events 21 1824 85 -0.07 0.05 1000 -1000 -0.023 -1000
Calcium signaling in the CD4+ TCR pathway 21 669 31 -0.045 0.046 1000 -1000 -0.034 -1000
Class I PI3K signaling events 21 1590 73 -0.059 0.043 1000 -1000 -0.024 -1000
Insulin Pathway 21 1610 74 -0.064 0.076 1000 -1000 -0.023 -1000
PDGFR-beta signaling pathway 21 2046 97 -0.067 0.068 1000 -1000 -0.024 -1000
ErbB2/ErbB3 signaling events 20 1315 65 -0.038 0.047 1000 -1000 -0.06 -1000
Presenilin action in Notch and Wnt signaling 20 1264 61 -0.21 0.067 1000 -1000 -0.024 -1000
Arf6 downstream pathway 20 870 43 -0.044 0.046 1000 -1000 -0.03 -1000
RXR and RAR heterodimerization with other nuclear receptor 20 1053 52 -0.062 0.064 1000 -1000 -0.021 -1000
Regulation of Telomerase 20 2132 102 -0.15 0.062 1000 -1000 -0.015 -1000
IFN-gamma pathway 19 1357 68 -0.037 0.053 1000 -1000 -0.035 -1000
Ceramide signaling pathway 19 1484 76 -0.07 0.067 1000 -1000 -0.023 -1000
ceramide signaling pathway 19 950 49 -0.062 0.048 1000 -1000 -0.032 -1000
EPHB forward signaling 19 1618 85 -0.045 0.11 1000 -1000 -0.045 -1000
p75(NTR)-mediated signaling 18 2304 125 -0.048 0.076 1000 -1000 -0.038 -1000
Ras signaling in the CD4+ TCR pathway 18 316 17 -0.001 0.047 1000 -1000 -0.006 -1000
Atypical NF-kappaB pathway 17 547 31 -0.019 0.035 1000 -1000 -0.006 -1000
Hedgehog signaling events mediated by Gli proteins 16 1044 65 -0.026 0.076 1000 -1000 -0.022 -1000
HIF-2-alpha transcription factor network 16 701 43 -0.072 0.079 1000 -1000 -0.044 -1000
Syndecan-3-mediated signaling events 16 583 35 -0.033 0.065 1000 -1000 -0.021 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 15 825 54 -0.039 0.049 1000 -1000 -0.017 -1000
EPO signaling pathway 15 828 55 -0.12 0.046 1000 -1000 -0.022 -1000
S1P5 pathway 15 262 17 -0.005 0.034 1000 -1000 -0.007 -1000
Regulation of Androgen receptor activity 15 1050 70 -0.14 0.05 1000 -1000 -0.03 -1000
Sphingosine 1-phosphate (S1P) pathway 14 397 28 -0.011 0.044 1000 -1000 -0.004 -1000
FoxO family signaling 14 945 64 -0.093 0.047 1000 -1000 -0.027 -1000
Retinoic acid receptors-mediated signaling 14 860 58 -0.07 0.068 1000 -1000 -0.016 -1000
Signaling mediated by p38-alpha and p38-beta 14 624 44 -0.057 0.055 1000 -1000 -0.008 -1000
Glypican 2 network 14 57 4 0 0.012 1000 -1000 0 -1000
IL2 signaling events mediated by STAT5 14 325 22 -0.025 0.036 1000 -1000 -0.02 -1000
S1P4 pathway 14 373 25 -0.009 0.044 1000 -1000 -0.01 -1000
LPA4-mediated signaling events 13 164 12 -0.029 0.016 1000 -1000 -0.019 -1000
Aurora A signaling 13 819 60 -0.008 0.047 1000 -1000 -0.011 -1000
Regulation of p38-alpha and p38-beta 13 721 54 -0.019 0.073 1000 -1000 -0.02 -1000
S1P3 pathway 13 556 42 -0.019 0.044 1000 -1000 -0.019 -1000
Neurotrophic factor-mediated Trk receptor signaling 13 1637 120 -0.091 0.089 1000 -1000 -0.035 -1000
Signaling events mediated by VEGFR1 and VEGFR2 12 1600 125 -0.029 0.044 1000 -1000 -0.025 -1000
Angiopoietin receptor Tie2-mediated signaling 12 1093 88 -0.064 0.061 1000 -1000 -0.052 -1000
p38 MAPK signaling pathway 12 534 44 -0.042 0.059 1000 -1000 -0.022 -1000
Nephrin/Neph1 signaling in the kidney podocyte 11 375 34 -0.036 0.076 1000 -1000 -0.028 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 11 1004 85 -0.14 0.062 1000 -1000 -0.038 -1000
Paxillin-independent events mediated by a4b1 and a4b7 11 431 37 -0.025 0.068 1000 -1000 -0.021 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 11 928 83 -0.062 0.068 1000 -1000 -0.018 -1000
TCGA08_rtk_signaling 11 289 26 -0.022 0.049 1000 -1000 -0.009 -1000
BARD1 signaling events 10 575 57 -0.047 0.069 1000 -1000 -0.041 -1000
Signaling events mediated by HDAC Class III 10 408 40 -0.063 0.064 1000 -1000 -0.031 -1000
Paxillin-dependent events mediated by a4b1 10 377 36 -0.057 0.063 1000 -1000 -0.027 -1000
Effects of Botulinum toxin 10 263 26 -0.064 0.049 1000 -1000 -0.001 -1000
Signaling events mediated by PRL 10 350 34 -0.038 0.05 1000 -1000 -0.024 -1000
Signaling events mediated by HDAC Class II 9 695 75 -0.092 0.074 1000 -1000 -0.025 -1000
a4b1 and a4b7 Integrin signaling 9 49 5 0.02 0.039 1000 -1000 0.021 -1000
JNK signaling in the CD4+ TCR pathway 8 142 17 -0.014 0.075 1000 -1000 -0.014 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 8 292 33 -0.016 0.072 1000 -1000 -0.028 -1000
Class IB PI3K non-lipid kinase events 8 24 3 -0.025 0.025 1000 -1000 -0.021 -1000
Class I PI3K signaling events mediated by Akt 7 476 68 -0.051 0.074 1000 -1000 -0.018 -1000
Ephrin A reverse signaling 6 45 7 0 0.04 1000 -1000 0 -1000
Insulin-mediated glucose transport 6 202 32 0 0.04 1000 -1000 -0.011 -1000
Arf6 trafficking events 6 468 71 -0.039 0.041 1000 -1000 -0.024 -1000
Alternative NF-kappaB pathway 6 82 13 0 0.081 1000 -1000 0 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 5 127 23 0.001 0.053 1000 -1000 -0.008 -1000
Canonical NF-kappaB pathway 4 190 39 0 0.072 1000 -1000 -0.012 -1000
Circadian rhythm pathway 4 100 22 -0.01 0.065 1000 -1000 -0.028 -1000
Signaling events mediated by HDAC Class I 4 436 104 -0.045 0.079 1000 -1000 -0.024 -1000
Aurora C signaling 3 23 7 0 0.05 1000 -1000 -0.007 -1000
Arf1 pathway 3 193 54 -0.001 0.061 1000 -1000 -0.014 -1000
Rapid glucocorticoid signaling 2 53 20 -0.002 0.041 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 1 37 27 0 0.078 1000 -1000 -0.019 -1000
Total 3421 209984 7203 -11 7.8 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 -0.041 0.14 -10000 0 -0.54 30 30
Crk/p130 Cas/Paxillin -0.13 0.16 -10000 0 -0.34 165 165
JUN -0.14 0.18 0.19 2 -0.42 112 114
HRAS 0.031 0.037 -10000 0 -0.43 3 3
RET51/GFRalpha1/GDNF/GRB10 -0.11 0.2 -10000 0 -0.32 227 227
RAP1A 0.03 0.046 -10000 0 -0.43 5 5
FRS2 0.032 0.022 -10000 0 -0.43 1 1
RAP1A/GDP 0.022 0.033 -10000 0 -0.3 5 5
RET51/GFRalpha1/GDNF/DOK1 -0.11 0.21 -10000 0 -0.33 220 220
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.035 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.023 -10000 0 -0.43 1 1
RET9/GFRalpha1/GDNF/Enigma -0.049 0.14 -10000 0 -0.24 175 175
RHOA 0.025 0.062 -10000 0 -0.43 9 9
RAP1A/GTP -0.1 0.18 -10000 0 -0.29 221 221
GRB7 0.022 0.059 -10000 0 -0.43 8 8
RET51/GFRalpha1/GDNF -0.1 0.2 -10000 0 -0.32 219 219
MAPKKK cascade -0.12 0.19 -10000 0 -0.33 205 205
BCAR1 0.03 0.013 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.072 0.18 -10000 0 -0.29 184 184
lamellipodium assembly -0.11 0.16 -10000 0 -0.31 165 165
RET51/GFRalpha1/GDNF/SHC -0.089 0.18 -10000 0 -0.31 192 192
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
RET9/GFRalpha1/GDNF/SHC -0.036 0.12 -10000 0 -0.24 129 129
RET9/GFRalpha1/GDNF/Shank3 -0.052 0.14 -10000 0 -0.24 176 176
MAPK3 -0.12 0.16 0.19 4 -0.3 175 179
DOK1 0.026 0.062 -10000 0 -0.43 9 9
DOK6 0.005 0.11 -10000 0 -0.43 29 29
PXN 0.035 0.004 -10000 0 -10000 0 0
neurite development -0.11 0.16 0.26 2 -0.37 107 109
DOK5 0.012 0.088 -10000 0 -0.43 19 19
GFRA1 -0.14 0.22 -10000 0 -0.43 178 178
MAPK8 -0.12 0.19 -10000 0 -0.43 102 102
HRAS/GTP -0.12 0.22 -10000 0 -0.36 219 219
tube development -0.044 0.13 0.22 12 -0.23 167 179
MAPK1 -0.12 0.16 0.19 5 -0.39 93 98
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.057 0.12 -10000 0 -0.22 163 163
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
SRC 0.031 0.03 -10000 0 -0.43 2 2
PDLIM7 0.034 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.1 0.21 -10000 0 -0.32 223 223
SHC1 0.027 0.025 -10000 0 -0.43 1 1
RET51/GFRalpha1/GDNF/Dok4 -0.11 0.2 -10000 0 -0.32 219 219
RET51/GFRalpha1/GDNF/Dok5 -0.11 0.2 -10000 0 -0.33 217 217
PRKCA 0.031 0.012 -10000 0 -10000 0 0
HRAS/GDP 0.023 0.026 -10000 0 -0.3 3 3
CREB1 -0.1 0.17 -10000 0 -0.38 108 108
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.043 0.11 -10000 0 -0.23 122 122
RET51/GFRalpha1/GDNF/Grb7 -0.097 0.2 -10000 0 -0.33 190 190
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.098 0.2 -10000 0 -0.43 136 136
DOK4 0.029 0.024 -10000 0 -0.43 1 1
JNK cascade -0.13 0.18 0.19 3 -0.41 112 115
RET9/GFRalpha1/GDNF/FRS2 -0.05 0.14 -10000 0 -0.24 172 172
SHANK3 0.032 0.023 -10000 0 -0.43 1 1
RASA1 0.026 0.058 -10000 0 -0.43 8 8
NCK1 0.033 0.022 -10000 0 -0.43 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.041 0.1 -10000 0 -0.22 123 123
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.11 0.18 -10000 0 -0.3 204 204
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.12 0.2 -10000 0 -0.32 221 221
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.12 0.2 -10000 0 -0.35 180 180
PI3K -0.16 0.25 0.24 1 -0.47 169 170
SOS1 0.034 0.021 -10000 0 -0.43 1 1
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.038 0.14 -10000 0 -0.23 167 167
GRB10 0.021 0.077 -10000 0 -0.43 14 14
activation of MAPKK activity -0.087 0.15 -10000 0 -0.34 93 93
RET51/GFRalpha1/GDNF/FRS2 -0.11 0.2 -10000 0 -0.32 216 216
GAB1 0.026 0.062 -10000 0 -0.43 9 9
IRS1 -0.017 0.14 -10000 0 -0.43 55 55
IRS2 0.008 0.099 -10000 0 -0.43 24 24
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.12 0.2 -10000 0 -0.36 182 182
RET51/GFRalpha1/GDNF/PKC alpha -0.099 0.2 -10000 0 -0.32 203 203
GRB2 0.033 0.009 -10000 0 -10000 0 0
PRKACA 0.035 0.004 -10000 0 -10000 0 0
GDNF 0.032 0.036 -10000 0 -0.43 3 3
RAC1 0.034 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.13 0.23 -10000 0 -0.36 228 228
Rac1/GTP -0.13 0.2 0.2 1 -0.38 165 166
RET9/GFRalpha1/GDNF -0.071 0.14 -10000 0 -0.26 176 176
GFRalpha1/GDNF -0.086 0.17 -10000 0 -0.31 176 176
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 0.2 0.38 1 -0.42 129 130
CRKL -0.13 0.2 -10000 0 -0.44 135 135
HRAS -0.082 0.18 0.28 1 -0.38 90 91
mol:PIP3 -0.09 0.2 0.27 2 -0.42 100 102
SPRED1 0.02 0.079 -10000 0 -0.43 15 15
SPRED2 0.018 0.086 -10000 0 -0.43 18 18
GAB1 -0.13 0.22 -10000 0 -0.45 136 136
FOXO3 -0.1 0.2 -10000 0 -0.4 118 118
AKT1 -0.11 0.21 -10000 0 -0.43 118 118
BAD -0.1 0.2 -10000 0 -0.4 114 114
megakaryocyte differentiation -0.13 0.21 -10000 0 -0.45 131 131
GSK3B -0.1 0.2 0.31 1 -0.4 115 116
RAF1 -0.058 0.15 0.26 6 -0.32 79 85
SHC1 0.027 0.025 -10000 0 -0.43 1 1
STAT3 -0.13 0.21 -10000 0 -0.45 131 131
STAT1 -0.31 0.47 -10000 0 -0.99 137 137
HRAS/SPRED1 -0.059 0.16 0.26 1 -0.33 87 88
cell proliferation -0.13 0.21 -10000 0 -0.44 136 136
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
TEC 0.03 0.046 -10000 0 -0.43 5 5
RPS6KB1 -0.12 0.22 -10000 0 -0.45 132 132
HRAS/SPRED2 -0.057 0.16 0.26 2 -0.32 86 88
LYN/TEC/p62DOK -0.095 0.22 -10000 0 -0.44 118 118
MAPK3 -0.037 0.12 0.25 8 -0.26 34 42
STAP1 -0.13 0.21 -10000 0 -0.44 135 135
GRAP2 0.032 0.023 -10000 0 -0.43 1 1
JAK2 -0.26 0.4 -10000 0 -0.84 135 135
STAT1 (dimer) -0.3 0.46 -10000 0 -0.91 159 159
mol:Gleevec 0.005 0.008 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.099 0.22 -10000 0 -0.43 117 117
actin filament polymerization -0.13 0.21 -10000 0 -0.43 135 135
LYN 0.03 0.013 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.18 0.29 -10000 0 -0.61 139 139
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
CBL/CRKL/GRB2 -0.1 0.2 -10000 0 -0.4 121 121
PI3K -0.1 0.23 -10000 0 -0.45 121 121
PTEN 0.024 0.068 -10000 0 -0.43 11 11
SCF/KIT/EPO/EPOR -0.31 0.53 -10000 0 -1.3 100 100
MAPK8 -0.13 0.21 -10000 0 -0.44 135 135
STAT3 (dimer) -0.13 0.21 -10000 0 -0.44 131 131
positive regulation of transcription -0.029 0.1 0.23 9 -0.21 32 41
mol:GDP -0.086 0.18 -10000 0 -0.39 87 87
PIK3C2B -0.12 0.2 0.28 1 -0.45 108 109
CBL/CRKL -0.12 0.2 -10000 0 -0.42 132 132
FER -0.13 0.21 -10000 0 -0.45 132 132
SH2B3 -0.13 0.21 -10000 0 -0.44 135 135
PDPK1 -0.074 0.2 0.32 10 -0.39 92 102
SNAI2 -0.14 0.22 -10000 0 -0.48 125 125
positive regulation of cell proliferation -0.22 0.35 -10000 0 -0.74 137 137
KITLG -0.054 0.17 -10000 0 -0.45 72 72
cell motility -0.22 0.35 -10000 0 -0.74 137 137
PTPN6 0.037 0.032 -10000 0 -0.42 2 2
EPOR -0.073 0.19 -10000 0 -0.96 7 7
STAT5A (dimer) -0.18 0.3 -10000 0 -0.62 138 138
SOCS1 0.031 0.023 -10000 0 -0.43 1 1
cell migration 0.13 0.21 0.44 133 -10000 0 133
SOS1 0.034 0.021 -10000 0 -0.43 1 1
EPO 0.013 0.029 -10000 0 -10000 0 0
VAV1 0.017 0.084 -10000 0 -0.43 17 17
GRB10 -0.14 0.22 -10000 0 -0.45 133 133
PTPN11 0.039 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 -0.045 0.13 0.24 7 -0.28 37 44
CBL 0.031 0.012 -10000 0 -10000 0 0
KIT -0.27 0.53 -10000 0 -1.3 103 103
MAP2K2 -0.045 0.13 0.27 9 -0.27 52 61
SHC/Grb2/SOS1 -0.083 0.21 -10000 0 -0.43 93 93
STAT5A -0.19 0.31 -10000 0 -0.64 138 138
GRB2 0.033 0.009 -10000 0 -10000 0 0
response to radiation -0.14 0.22 -10000 0 -0.47 125 125
SHC/GRAP2 0.037 0.032 -10000 0 -0.31 2 2
PTPRO -0.14 0.22 -10000 0 -0.46 131 131
SH2B2 -0.13 0.21 -10000 0 -0.44 135 135
DOK1 0.026 0.062 -10000 0 -0.43 9 9
MATK -0.13 0.21 -10000 0 -0.45 133 133
CREBBP -0.01 0.083 -10000 0 -0.2 17 17
BCL2 -0.3 0.55 -10000 0 -1.3 115 115
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 -0.015 0.2 0.27 72 -0.35 92 164
PTK2B 0.028 0.014 -10000 0 -10000 0 0
mol:Ca2+ -0.06 0.26 -10000 0 -0.69 49 49
EDN1 -0.015 0.2 0.23 65 -0.45 67 132
EDN3 -0.014 0.12 -10000 0 -0.43 40 40
EDN2 -0.056 0.18 -10000 0 -0.43 92 92
HRAS/GDP -0.065 0.24 0.26 6 -0.45 102 108
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.061 0.21 0.18 45 -0.39 106 151
ADCY4 -0.014 0.17 0.23 3 -0.4 49 52
ADCY5 -0.023 0.16 0.24 2 -0.42 43 45
ADCY6 -0.012 0.17 0.24 2 -0.41 44 46
ADCY7 -0.017 0.16 0.23 2 -0.4 46 48
ADCY1 -0.012 0.17 0.23 1 -0.4 46 47
ADCY2 -0.033 0.18 -10000 0 -0.44 55 55
ADCY3 -0.014 0.17 0.24 2 -0.39 51 53
ADCY8 -0.009 0.15 0.24 1 -0.39 39 40
ADCY9 -0.015 0.17 0.24 2 -0.42 42 44
arachidonic acid secretion -0.089 0.26 0.28 3 -0.5 113 116
ETB receptor/Endothelin-1/Gq/GTP -0.053 0.16 -10000 0 -0.32 105 105
GNAO1 0.03 0.013 -10000 0 -10000 0 0
HRAS 0.03 0.036 -10000 0 -0.43 3 3
ETA receptor/Endothelin-1/G12/GTP 0.023 0.22 0.37 72 -0.34 81 153
ETA receptor/Endothelin-1/Gs/GTP 0.019 0.21 0.35 73 -0.33 78 151
mol:GTP -0.001 0.006 -10000 0 -10000 0 0
COL3A1 -0.021 0.22 0.27 72 -0.48 58 130
EDNRB 0.002 0.098 -10000 0 -0.38 24 24
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.014 0.2 0.27 67 -0.51 43 110
CYSLTR1 -0.034 0.24 0.27 64 -0.57 57 121
SLC9A1 -0.005 0.13 0.19 71 -0.29 44 115
mol:GDP -0.081 0.24 0.26 6 -0.46 113 119
SLC9A3 -0.13 0.36 -10000 0 -0.75 99 99
RAF1 -0.092 0.25 -10000 0 -0.49 109 109
JUN -0.1 0.36 -10000 0 -0.93 65 65
JAK2 -0.015 0.2 0.27 69 -0.34 95 164
mol:IP3 -0.075 0.21 0.23 1 -0.41 113 114
ETA receptor/Endothelin-1 0.006 0.26 0.42 73 -0.39 102 175
PLCB1 -0.023 0.14 -10000 0 -0.43 56 56
PLCB2 0.031 0.024 -10000 0 -0.44 1 1
ETA receptor/Endothelin-3 -0.01 0.15 -10000 0 -0.33 75 75
FOS -0.14 0.36 -10000 0 -0.86 85 85
Gai/GDP -0.11 0.32 -10000 0 -0.73 97 97
CRK 0.031 0.023 -10000 0 -0.43 1 1
mol:Ca ++ -0.09 0.27 0.27 4 -0.5 121 125
BCAR1 0.03 0.013 -10000 0 -10000 0 0
PRKCB1 -0.079 0.22 0.25 8 -0.43 110 118
GNAQ -0.001 0.007 -10000 0 -10000 0 0
GNAZ 0.022 0.071 -10000 0 -0.43 12 12
GNAL 0.031 0.036 -10000 0 -0.43 3 3
Gs family/GDP -0.064 0.23 0.25 6 -0.42 109 115
ETA receptor/Endothelin-1/Gq/GTP -0.044 0.2 0.2 61 -0.39 93 154
MAPK14 -0.07 0.17 -10000 0 -0.35 100 100
TRPC6 -0.065 0.28 -10000 0 -0.75 46 46
GNAI2 0.026 0.058 -10000 0 -0.43 8 8
GNAI3 0.034 0.006 -10000 0 -10000 0 0
GNAI1 0.015 0.091 -10000 0 -0.43 20 20
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.069 0.18 -10000 0 -0.36 104 104
ETB receptor/Endothelin-2 -0.045 0.15 -10000 0 -0.31 110 110
ETB receptor/Endothelin-3 -0.019 0.11 -10000 0 -0.31 57 57
ETB receptor/Endothelin-1 -0.019 0.17 -10000 0 -0.31 107 107
MAPK3 -0.13 0.33 0.32 1 -0.75 96 97
MAPK1 -0.14 0.35 0.32 2 -0.77 97 99
Rac1/GDP -0.063 0.24 0.26 6 -0.45 102 108
cAMP biosynthetic process -0.009 0.18 0.26 8 -0.43 44 52
MAPK8 -0.075 0.3 -10000 0 -0.66 77 77
SRC 0.031 0.03 -10000 0 -0.43 2 2
ETB receptor/Endothelin-1/Gi/GTP -0.044 0.15 0.18 2 -0.33 86 88
p130Cas/CRK/Src/PYK2 -0.096 0.26 0.3 3 -0.54 99 102
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.063 0.23 0.26 6 -0.44 103 109
COL1A2 -0.079 0.31 0.39 1 -0.57 110 111
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.037 0.18 -10000 0 -0.33 121 121
mol:DAG -0.075 0.21 0.23 1 -0.41 113 114
MAP2K2 -0.11 0.28 0.36 2 -0.58 107 109
MAP2K1 -0.11 0.28 0.36 1 -0.59 102 103
EDNRA 0.014 0.17 0.23 71 -0.43 47 118
positive regulation of muscle contraction -0.015 0.17 0.23 72 -0.38 55 127
Gq family/GDP -0.064 0.22 -10000 0 -0.44 95 95
HRAS/GTP -0.08 0.23 0.23 1 -0.44 109 110
PRKCH -0.077 0.21 0.23 3 -0.42 105 108
RAC1 0.034 0.006 -10000 0 -10000 0 0
PRKCA -0.061 0.2 0.25 15 -0.42 94 109
PRKCB -0.074 0.21 0.22 1 -0.39 116 117
PRKCE -0.077 0.21 0.21 1 -0.41 108 109
PRKCD -0.076 0.21 0.22 1 -0.42 105 106
PRKCG -0.073 0.21 0.23 6 -0.41 107 113
regulation of vascular smooth muscle contraction -0.17 0.42 -10000 0 -1 84 84
PRKCQ -0.069 0.21 0.23 7 -0.4 106 113
PLA2G4A -0.1 0.28 0.29 3 -0.55 113 116
GNA14 -0.015 0.13 -10000 0 -0.43 44 44
GNA15 0.025 0.049 -10000 0 -0.43 5 5
GNA12 0.034 0.006 -10000 0 -10000 0 0
GNA11 0.028 0.039 -10000 0 -0.43 3 3
Rac1/GTP 0.022 0.22 0.37 71 -0.35 74 145
MMP1 -0.17 0.36 0.36 2 -0.79 120 122
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 0.035 0.005 -10000 0 -10000 0 0
PTK2 0.027 0.025 -10000 0 -0.43 1 1
CRKL -0.076 0.16 0.17 1 -0.3 139 140
GRB2/SOS1/SHC 0.052 0.035 -10000 0 -0.26 1 1
HRAS 0.031 0.037 -10000 0 -0.43 3 3
IRS1/Crk -0.069 0.16 -10000 0 -0.29 153 153
IGF-1R heterotetramer/IGF1/PTP1B -0.04 0.16 -10000 0 -0.29 130 130
AKT1 -0.077 0.14 0.18 18 -0.28 120 138
BAD -0.076 0.13 0.17 19 -0.28 116 135
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.075 0.15 0.17 1 -0.3 138 139
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.065 0.16 0.22 2 -0.3 141 143
RAF1 -0.039 0.14 0.29 4 -0.36 46 50
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.033 0.17 -10000 0 -0.29 131 131
YWHAZ 0.027 0.015 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.069 0.17 -10000 0 -0.31 153 153
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
RPS6KB1 -0.07 0.14 0.18 15 -0.29 104 119
GNB2L1 0.033 0.03 -10000 0 -0.43 2 2
positive regulation of MAPKKK cascade -0.029 0.13 0.28 8 -0.31 45 53
PXN 0.035 0.004 -10000 0 -10000 0 0
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.048 0.021 -10000 0 -0.31 1 1
HRAS/GTP -0.046 0.13 -10000 0 -0.27 117 117
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.004 0.14 -10000 0 -0.24 109 109
IGF-1R heterotetramer -0.065 0.19 -10000 0 -0.47 85 85
IGF-1R heterotetramer/IGF1/IRS/Nck -0.049 0.17 -10000 0 -0.29 152 152
Crk/p130 Cas/Paxillin -0.044 0.16 -10000 0 -0.28 141 141
IGF1R -0.065 0.19 -10000 0 -0.48 85 85
IGF1 -0.062 0.18 -10000 0 -0.46 78 78
IRS2/Crk -0.075 0.16 0.17 1 -0.3 150 151
PI3K -0.043 0.17 -10000 0 -0.29 145 145
apoptosis 0.047 0.12 0.31 47 -0.27 6 53
HRAS/GDP 0.023 0.026 -10000 0 -0.3 3 3
PRKCD -0.068 0.18 -10000 0 -0.38 98 98
RAF1/14-3-3 E -0.02 0.14 0.29 6 -0.31 47 53
BAD/14-3-3 -0.05 0.13 0.28 6 -0.33 47 53
PRKCZ -0.074 0.14 0.18 19 -0.27 136 155
Crk/p130 Cas/Paxillin/FAK1 -0.037 0.12 -10000 0 -0.35 42 42
PTPN1 0.029 0.031 -10000 0 -0.43 2 2
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.084 0.18 -10000 0 -0.36 134 134
BCAR1 0.03 0.013 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.024 0.14 -10000 0 -0.26 124 124
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.034 0.021 -10000 0 -0.43 1 1
IRS1/NCK2 -0.056 0.16 -10000 0 -0.28 152 152
GRB10 0.021 0.077 -10000 0 -0.43 14 14
PTPN11 -0.076 0.16 0.17 1 -0.3 141 142
IRS1 -0.078 0.17 -10000 0 -0.31 153 153
IRS2 -0.085 0.17 0.17 1 -0.31 147 148
IGF-1R heterotetramer/IGF1 -0.079 0.19 -10000 0 -0.38 140 140
GRB2 0.033 0.009 -10000 0 -10000 0 0
PDPK1 -0.063 0.15 0.21 7 -0.28 138 145
YWHAE 0.032 0.01 -10000 0 -10000 0 0
PRKD1 -0.081 0.2 0.21 2 -0.41 106 108
SHC1 0.027 0.025 -10000 0 -0.43 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 83 83
PLK1 0.018 0.09 -9999 0 -1.1 2 2
BIRC5 -0.087 0.39 -9999 0 -1.4 40 40
HSPA1B -0.24 0.52 -9999 0 -1.1 95 95
MAP2K1 0.006 0.056 -9999 0 -10000 0 0
BRCA2 -0.26 0.54 -9999 0 -1.2 92 92
FOXM1 -0.38 0.86 -9999 0 -1.8 93 93
XRCC1 -0.24 0.52 -9999 0 -1.2 83 83
FOXM1B/p19 -0.29 0.58 -9999 0 -1.3 95 95
Cyclin D1/CDK4 -0.29 0.53 -9999 0 -1 134 134
CDC2 -0.26 0.56 -9999 0 -1.3 84 84
TGFA -0.28 0.5 -9999 0 -1 112 112
SKP2 -0.24 0.52 -9999 0 -1.2 79 79
CCNE1 0.023 0.051 -9999 0 -0.44 5 5
CKS1B -0.21 0.53 -9999 0 -1.2 79 79
RB1 -0.15 0.38 -9999 0 -1.1 55 55
FOXM1C/SP1 -0.29 0.62 -9999 0 -1.3 97 97
AURKB -0.073 0.31 -9999 0 -0.93 52 52
CENPF -0.23 0.56 -9999 0 -1.2 83 83
CDK4 0.015 0.037 -9999 0 -10000 0 0
MYC -0.23 0.45 -9999 0 -0.99 91 91
CHEK2 0.002 0.065 -9999 0 -0.46 3 3
ONECUT1 -0.27 0.53 -9999 0 -1.1 102 102
CDKN2A 0.014 0.074 -9999 0 -0.43 13 13
LAMA4 -0.24 0.53 -9999 0 -1.2 79 79
FOXM1B/HNF6 -0.34 0.65 -9999 0 -1.4 103 103
FOS -0.32 0.6 -9999 0 -1.2 130 130
SP1 0.034 0.012 -9999 0 -10000 0 0
CDC25B -0.24 0.52 -9999 0 -1.2 83 83
response to radiation -0.003 0.032 -9999 0 -10000 0 0
CENPB -0.24 0.52 -9999 0 -1.2 83 83
CENPA -0.26 0.55 -9999 0 -1.2 91 91
NEK2 -0.26 0.58 -9999 0 -1.2 99 99
HIST1H2BA -0.24 0.52 -9999 0 -1.2 82 82
CCNA2 0.004 0.11 -9999 0 -0.44 27 27
EP300 0.031 0.03 -9999 0 -0.43 2 2
CCNB1/CDK1 -0.31 0.64 -9999 0 -1.5 84 84
CCNB2 -0.25 0.53 -9999 0 -1.2 85 85
CCNB1 -0.27 0.57 -9999 0 -1.3 85 85
ETV5 -0.24 0.53 -9999 0 -1.2 83 83
ESR1 -0.43 0.65 -9999 0 -1.2 204 204
CCND1 -0.32 0.52 -9999 0 -1.1 135 135
GSK3A 0.01 0.052 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.021 0.11 -9999 0 -0.34 28 28
CDK2 0.028 0.035 -9999 0 -0.44 2 2
G2/M transition of mitotic cell cycle -0.006 0.037 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.27 0.57 -9999 0 -1.3 92 92
GAS1 -0.31 0.59 -9999 0 -1.2 115 115
MMP2 -0.27 0.57 -9999 0 -1.3 95 95
RB1/FOXM1C -0.29 0.55 -9999 0 -1.1 126 126
CREBBP 0.031 0.023 -9999 0 -0.43 1 1
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 -0.011 0.13 -10000 0 -0.22 130 130
ER alpha/Gai/GDP/Gbeta gamma -0.13 0.23 -10000 0 -0.39 163 163
AKT1 -0.22 0.37 -10000 0 -0.74 162 162
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.22 0.38 -10000 0 -0.76 161 161
mol:Ca2+ -0.069 0.15 0.18 2 -0.43 56 58
IGF1R -0.046 0.17 -10000 0 -0.43 85 85
E2/ER alpha (dimer)/Striatin -0.044 0.13 -10000 0 -0.26 137 137
SHC1 0.027 0.025 -10000 0 -0.43 1 1
apoptosis 0.21 0.35 0.71 162 -10000 0 162
RhoA/GTP -0.041 0.11 -10000 0 -0.22 131 131
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.11 0.22 -10000 0 -0.39 157 157
regulation of stress fiber formation 0.041 0.11 0.32 9 -0.26 4 13
E2/ERA-ERB (dimer) -0.041 0.13 -10000 0 -0.26 132 132
KRAS 0.027 0.055 -10000 0 -0.43 7 7
G13/GTP -0.036 0.12 -10000 0 -0.23 126 126
pseudopodium formation -0.041 0.11 0.26 4 -0.32 9 13
E2/ER alpha (dimer)/PELP1 -0.042 0.13 -10000 0 -0.26 132 132
GRB2 0.033 0.009 -10000 0 -10000 0 0
GNG2 0.033 0.021 -10000 0 -0.43 1 1
GNAO1 0.03 0.013 -10000 0 -10000 0 0
HRAS 0.031 0.037 -10000 0 -0.43 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.14 0.24 -10000 0 -0.46 162 162
E2/ER beta (dimer) 0.025 0.005 -10000 0 -10000 0 0
mol:GDP -0.079 0.17 -10000 0 -0.34 133 133
mol:NADP -0.14 0.24 -10000 0 -0.46 162 162
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
mol:IP3 -0.073 0.16 -10000 0 -0.44 59 59
IGF-1R heterotetramer -0.046 0.17 -10000 0 -0.43 85 85
PLCB1 -0.072 0.16 -10000 0 -0.36 91 91
PLCB2 -0.053 0.15 -10000 0 -0.43 56 56
IGF1 -0.041 0.17 -10000 0 -0.43 78 78
mol:L-citrulline -0.14 0.24 -10000 0 -0.46 162 162
RHOA 0.025 0.062 -10000 0 -0.43 9 9
Gai/GDP -0.099 0.27 -10000 0 -0.63 97 97
JNK cascade 0.025 0.005 -10000 0 -10000 0 0
BCAR1 0.03 0.013 -10000 0 -10000 0 0
ESR2 0.034 0.006 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -10000 0 0
ESR1 -0.092 0.2 -10000 0 -0.43 132 132
Gq family/GDP/Gbeta gamma -0.027 0.19 -10000 0 -0.75 22 22
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.039 0.14 -10000 0 -0.58 9 9
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.097 0.2 -10000 0 -0.39 128 128
GNAZ 0.022 0.071 -10000 0 -0.43 12 12
E2/ER alpha (dimer) -0.065 0.14 -10000 0 -0.3 132 132
STRN 0.03 0.046 -10000 0 -0.43 5 5
GNAL 0.031 0.036 -10000 0 -0.43 3 3
PELP1 0.032 0.01 -10000 0 -10000 0 0
MAPK11 0.016 0.006 -10000 0 -10000 0 0
GNAI2 0.026 0.058 -10000 0 -0.43 8 8
GNAI3 0.034 0.006 -10000 0 -10000 0 0
GNAI1 0.015 0.091 -10000 0 -0.43 20 20
HBEGF -0.12 0.22 0.32 10 -0.51 72 82
cAMP biosynthetic process -0.031 0.11 -10000 0 -0.21 130 130
SRC -0.12 0.22 0.26 4 -0.38 159 163
PI3K 0.033 0.066 -10000 0 -0.31 17 17
GNB1 0.03 0.042 -10000 0 -0.43 4 4
G13/GDP/Gbeta gamma -0.052 0.16 -10000 0 -0.33 112 112
SOS1 0.034 0.021 -10000 0 -0.43 1 1
IGF-1R heterotetramer/IGF1 -0.14 0.2 -10000 0 -0.4 158 158
Gs family/GTP -0.025 0.11 -10000 0 -0.21 130 130
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.051 0.056 -10000 0 -0.23 16 16
vasodilation -0.13 0.23 -10000 0 -0.44 162 162
mol:DAG -0.073 0.16 -10000 0 -0.44 59 59
Gs family/GDP/Gbeta gamma -0.065 0.15 -10000 0 -0.32 110 110
MSN -0.044 0.11 0.3 3 -0.34 9 12
Gq family/GTP -0.054 0.16 -10000 0 -0.45 57 57
mol:PI-3-4-5-P3 -0.21 0.36 -10000 0 -0.72 161 161
NRAS 0.028 0.055 -10000 0 -0.43 7 7
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.13 0.23 0.44 162 -10000 0 162
GRB2/SOS1 0.048 0.021 -10000 0 -0.31 1 1
RhoA/GDP -0.067 0.17 -10000 0 -0.35 117 117
NOS3 -0.15 0.26 -10000 0 -0.48 162 162
GNA11 0.031 0.036 -10000 0 -0.43 3 3
MAPKKK cascade -0.15 0.27 0.32 1 -0.53 156 157
E2/ER alpha (dimer)/PELP1/Src -0.12 0.22 -10000 0 -0.4 162 162
ruffle organization -0.041 0.11 0.26 4 -0.32 9 13
ROCK2 -0.042 0.12 0.32 3 -0.36 10 13
GNA14 -0.011 0.13 -10000 0 -0.43 44 44
GNA15 0.029 0.047 -10000 0 -0.43 5 5
GNA13 0.029 0.037 -10000 0 -0.43 3 3
MMP9 -0.12 0.22 0.36 10 -0.48 76 86
MMP2 -0.12 0.21 0.27 4 -0.49 73 77
Osteopontin-mediated 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
IKK alpha homodimer -0.033 0.15 -10000 0 -0.27 120 120
NF kappa B1 p50/RelA/I kappa B alpha -0.029 0.17 0.31 2 -0.43 46 48
alphaV/beta3 Integrin/Osteopontin/Src -0.049 0.16 -10000 0 -0.33 121 121
AP1 -0.087 0.22 -10000 0 -0.48 89 89
ILK -0.041 0.14 0.38 1 -0.26 119 120
bone resorption -0.051 0.14 -10000 0 -0.33 48 48
PTK2B 0.028 0.014 -10000 0 -10000 0 0
PYK2/p130Cas -0.025 0.15 -10000 0 -0.26 129 129
ITGAV 0.017 0.081 -10000 0 -0.44 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.038 0.065 -10000 0 -0.31 17 17
alphaV/beta3 Integrin/Osteopontin -0.023 0.16 -10000 0 -0.29 120 120
MAP3K1 -0.055 0.14 0.27 3 -0.26 140 143
JUN -0.003 0.12 -10000 0 -0.43 39 39
MAPK3 -0.056 0.14 0.21 1 -0.28 124 125
MAPK1 -0.058 0.15 0.21 1 -0.38 52 53
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
NFKB1 0.034 0.021 -10000 0 -0.43 1 1
MAPK8 -0.06 0.13 0.22 10 -0.25 137 147
ITGB3 0.025 0.048 -10000 0 -0.44 4 4
NFKBIA -0.067 0.16 0.21 1 -0.41 60 61
FOS -0.033 0.16 -10000 0 -0.43 66 66
CD44 0.021 0.077 -10000 0 -0.43 14 14
CHUK 0.024 0.071 -10000 0 -0.43 12 12
PLAU -0.13 0.36 0.46 1 -1.1 53 54
NF kappa B1 p50/RelA -0.018 0.19 -10000 0 -0.45 55 55
BCAR1 0.03 0.013 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.03 0.076 -10000 0 -0.31 19 19
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.056 0.15 0.22 11 -0.28 140 151
VAV3 -0.095 0.16 0.21 11 -0.27 193 204
MAP3K14 -0.046 0.14 0.21 1 -0.27 123 124
ROCK2 0.032 0.036 -10000 0 -0.43 3 3
SPP1 -0.077 0.19 -10000 0 -0.43 112 112
RAC1 0.034 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.079 0.15 0.2 2 -0.26 187 189
MMP2 -0.1 0.2 0.32 3 -0.46 87 90
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.034 0.033 -10000 0 -0.21 5 5
NFATC2 -0.056 0.22 -10000 0 -0.52 51 51
NFATC3 -0.02 0.12 -10000 0 -0.26 79 79
CD40LG -0.19 0.39 -10000 0 -0.75 134 134
ITCH 0.014 0.072 -10000 0 -0.22 43 43
CBLB 0.013 0.077 -10000 0 -0.22 45 45
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.15 0.33 -10000 0 -0.82 68 68
JUNB 0.031 0.042 -10000 0 -0.43 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.02 0.089 -10000 0 -0.26 46 46
T cell anergy -0.018 0.12 -10000 0 -0.38 44 44
TLE4 -0.047 0.18 -10000 0 -0.57 29 29
Jun/NFAT1-c-4/p21SNFT -0.17 0.4 -10000 0 -0.78 127 127
AP-1/NFAT1-c-4 -0.19 0.45 -10000 0 -0.85 131 131
IKZF1 -0.041 0.14 -10000 0 -0.36 51 51
T-helper 2 cell differentiation -0.17 0.31 -10000 0 -0.83 61 61
AP-1/NFAT1 -0.051 0.2 -10000 0 -0.41 81 81
CALM1 0.027 0.059 -10000 0 -0.16 45 45
EGR2 -0.23 0.49 -10000 0 -1.2 82 82
EGR3 -0.3 0.56 -10000 0 -1.1 137 137
NFAT1/FOXP3 -0.022 0.17 -10000 0 -0.4 42 42
EGR1 -0.039 0.16 -10000 0 -0.43 74 74
JUN -0.004 0.12 -10000 0 -0.43 39 39
EGR4 0 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.006 0.046 -10000 0 -0.15 46 46
GBP3 -0.089 0.25 -10000 0 -0.66 68 68
FOSL1 0.034 0.006 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 -0.16 0.4 -10000 0 -0.77 127 127
DGKA -0.042 0.16 -10000 0 -0.52 24 24
CREM 0.033 0.007 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.18 0.41 -10000 0 -0.81 128 128
CTLA4 -0.031 0.14 -10000 0 -0.45 24 24
NFAT1-c-4 (dimer)/EGR1 -0.2 0.43 -10000 0 -0.84 134 134
NFAT1-c-4 (dimer)/EGR4 -0.18 0.4 -10000 0 -0.78 129 129
FOS -0.035 0.15 -10000 0 -0.42 66 66
IFNG -0.19 0.42 -10000 0 -1 79 79
T cell activation -0.1 0.26 -10000 0 -0.7 42 42
MAF 0.015 0.077 -10000 0 -0.43 14 14
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.16 0.35 0.69 122 -10000 0 122
TNF -0.2 0.38 -10000 0 -0.76 136 136
FASLG -0.35 0.65 -10000 0 -1.2 153 153
TBX21 -0.045 0.17 -10000 0 -0.43 82 82
BATF3 0 0.001 -10000 0 -10000 0 0
PRKCQ 0.021 0.062 -10000 0 -0.45 7 7
PTPN1 -0.037 0.15 -10000 0 -0.4 42 42
NFAT1-c-4/ICER1 -0.17 0.4 -10000 0 -0.78 128 128
GATA3 -0.055 0.18 -10000 0 -0.43 97 97
T-helper 1 cell differentiation -0.19 0.41 -10000 0 -1 80 80
IL2RA -0.14 0.33 -10000 0 -0.77 77 77
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.037 0.14 -10000 0 -0.44 23 23
E2F1 0.032 0.055 -10000 0 -0.43 7 7
PPARG 0.01 0.095 -10000 0 -0.43 22 22
SLC3A2 -0.037 0.14 -10000 0 -0.43 27 27
IRF4 0.029 0.032 -10000 0 -0.43 2 2
PTGS2 -0.19 0.37 -10000 0 -0.76 120 120
CSF2 -0.19 0.38 -10000 0 -0.75 134 134
JunB/Fra1/NFAT1-c-4 -0.16 0.4 -10000 0 -0.77 124 124
IL4 -0.18 0.32 -10000 0 -0.87 61 61
IL5 -0.18 0.39 -10000 0 -0.75 133 133
IL2 -0.1 0.27 -10000 0 -0.72 40 40
IL3 -0.014 0.14 -10000 0 -0.91 9 9
RNF128 -0.022 0.16 -10000 0 -0.53 45 45
NFATC1 -0.16 0.35 -10000 0 -0.7 120 120
CDK4 0.1 0.22 0.59 31 -10000 0 31
PTPRK -0.073 0.23 -10000 0 -0.65 54 54
IL8 -0.21 0.38 -10000 0 -0.77 130 130
POU2F1 0.034 0.016 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.031 0.037 -10000 0 -0.43 3 3
EGFR -0.016 0.14 -10000 0 -0.43 48 48
EGF/EGFR -0.077 0.17 -10000 0 -0.27 197 197
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.005 0.13 -10000 0 -0.23 108 108
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA -0.004 0.13 -10000 0 -0.43 41 41
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.07 0.19 -10000 0 -0.43 108 108
EGF/EGFR dimer/SHC -0.031 0.14 -10000 0 -0.27 116 116
mol:GDP -0.009 0.13 -10000 0 -0.23 108 108
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.04 0.17 -10000 0 -0.43 77 77
GRB2/SOS1 0.048 0.021 -10000 0 -0.31 1 1
HRAS/GTP -0.02 0.11 -10000 0 -0.22 109 109
SHC1 0.027 0.025 -10000 0 -0.43 1 1
HRAS/GDP -0.01 0.12 -10000 0 -0.22 108 108
FRAP1 -0.021 0.14 0.24 27 -0.41 5 32
EGF/EGFR dimer -0.067 0.16 -10000 0 -0.31 149 149
SOS1 0.034 0.021 -10000 0 -0.43 1 1
GRB2 0.033 0.009 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.034 0.16 -10000 0 -0.34 103 103
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 -0.34 0.63 -10000 0 -1.3 114 114
STAT6 (cleaved dimer) -0.36 0.64 -10000 0 -1.3 133 133
IGHG1 -0.079 0.24 -10000 0 -0.68 16 16
IGHG3 -0.34 0.6 -10000 0 -1.2 133 133
AKT1 -0.12 0.32 -10000 0 -0.88 32 32
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.065 0.26 -10000 0 -0.94 18 18
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.14 0.36 -10000 0 -0.88 48 48
THY1 -0.36 0.65 -10000 0 -1.4 119 119
MYB -0.06 0.18 -10000 0 -0.43 100 100
HMGA1 0.033 0.03 -10000 0 -0.43 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.13 0.34 -10000 0 -0.73 58 58
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.12 0.33 -10000 0 -0.97 27 27
SP1 0.024 0.047 -10000 0 -0.14 7 7
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.019 0.056 -10000 0 -0.43 4 4
STAT6 (dimer)/ETS1 -0.35 0.63 -10000 0 -1.3 131 131
SOCS1 -0.19 0.38 -10000 0 -0.78 103 103
SOCS3 -0.11 0.32 -10000 0 -0.98 23 23
FCER2 -0.23 0.47 -10000 0 -0.95 94 94
PARP14 0.028 0.055 -10000 0 -0.43 7 7
CCL17 -0.41 0.7 -10000 0 -1.4 150 150
GRB2 0.033 0.009 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.074 0.26 -10000 0 -0.75 25 25
T cell proliferation -0.36 0.66 -10000 0 -1.4 125 125
IL4R/JAK1 -0.35 0.64 -10000 0 -1.3 128 128
EGR2 -0.39 0.69 -10000 0 -1.4 134 134
JAK2 -0.004 0.068 -10000 0 -0.46 2 2
JAK3 0.038 0.014 -10000 0 -10000 0 0
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
JAK1 0.018 0.048 -10000 0 -0.42 3 3
COL1A2 -0.22 0.54 -10000 0 -1.5 70 70
CCL26 -0.35 0.64 -10000 0 -1.3 130 130
IL4R -0.38 0.7 -10000 0 -1.5 120 120
PTPN6 0.021 0.045 -10000 0 -0.42 2 2
IL13RA2 -0.39 0.67 -10000 0 -1.3 137 137
IL13RA1 -0.009 0.086 -10000 0 -0.46 8 8
IRF4 -0.018 0.19 -10000 0 -0.88 12 12
ARG1 -0.058 0.26 -10000 0 -1.1 16 16
CBL -0.13 0.32 -10000 0 -0.69 59 59
GTF3A 0.023 0.045 -10000 0 -0.14 7 7
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
IL13RA1/JAK2 0 0.1 -10000 0 -0.38 7 7
IRF4/BCL6 -0.017 0.19 -10000 0 -0.83 12 12
CD40LG 0.037 0.038 -10000 0 -0.43 3 3
MAPK14 -0.13 0.33 -10000 0 -0.87 30 30
mitosis -0.11 0.31 -10000 0 -0.82 32 32
STAT6 -0.45 0.86 -10000 0 -1.7 132 132
SPI1 0.033 0.048 -10000 0 -0.3 8 8
RPS6KB1 -0.086 0.3 -10000 0 -0.8 29 29
STAT6 (dimer) -0.45 0.86 -10000 0 -1.7 132 132
STAT6 (dimer)/PARP14 -0.4 0.72 -10000 0 -1.4 133 133
mast cell activation 0.004 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.14 0.34 -10000 0 -0.91 40 40
FRAP1 -0.12 0.32 -10000 0 -0.88 32 32
LTA -0.35 0.63 -10000 0 -1.3 118 118
FES 0.029 0.047 -10000 0 -0.43 5 5
T-helper 1 cell differentiation 0.41 0.76 1.5 132 -10000 0 132
CCL11 -0.38 0.65 -10000 0 -1.3 136 136
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.1 0.32 -10000 0 -0.95 25 25
IL2RG 0.032 0.043 -10000 0 -0.42 4 4
IL10 -0.32 0.64 -10000 0 -1.3 116 116
IRS1 -0.017 0.14 -10000 0 -0.43 55 55
IRS2 0.008 0.099 -10000 0 -0.43 24 24
IL4 -0.06 0.29 -10000 0 -1.3 18 18
IL5 -0.35 0.63 -10000 0 -1.3 118 118
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.24 0.51 -10000 0 -0.97 120 120
COL1A1 -0.25 0.58 -10000 0 -1.5 83 83
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.38 0.68 -10000 0 -1.5 109 109
IL2R gamma/JAK3 0.051 0.036 -10000 0 -0.3 4 4
TFF3 -0.52 0.76 -10000 0 -1.4 197 197
ALOX15 -0.36 0.64 -10000 0 -1.3 130 130
MYBL1 -0.012 0.13 -10000 0 -0.43 42 42
T-helper 2 cell differentiation -0.26 0.51 -10000 0 -1 117 117
SHC1 0.027 0.025 -10000 0 -0.43 1 1
CEBPB 0.027 0.057 -10000 0 -0.31 11 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.12 0.33 -10000 0 -0.87 37 37
mol:PI-3-4-5-P3 -0.12 0.32 -10000 0 -0.88 32 32
PI3K -0.12 0.34 -10000 0 -0.97 32 32
DOK2 0.008 0.09 -10000 0 -0.43 20 20
ETS1 0.012 0.047 -10000 0 -0.39 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.061 0.25 -10000 0 -0.71 21 21
ITGB3 -0.35 0.64 -10000 0 -1.3 118 118
PIGR -0.45 0.76 -10000 0 -1.4 168 168
IGHE 0.014 0.088 0.18 58 -0.22 8 66
MAPKKK cascade -0.059 0.24 -10000 0 -0.69 21 21
BCL6 0.017 0.086 -10000 0 -0.43 18 18
OPRM1 -0.35 0.63 -10000 0 -1.3 118 118
RETNLB -0.35 0.63 -10000 0 -1.3 117 117
SELP -0.42 0.74 -10000 0 -1.4 149 149
AICDA -0.34 0.61 -10000 0 -1.3 113 113
HIF-1-alpha transcription factor network

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
PKM2 -0.014 0.36 0.55 2 -0.71 74 76
HDAC7 0 0.003 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.017 0.33 -10000 0 -0.68 58 58
SMAD4 0.028 0.055 -10000 0 -0.43 7 7
ID2 -0.016 0.36 0.55 2 -0.7 78 80
AP1 -0.042 0.16 -10000 0 -0.36 90 90
ABCG2 -0.02 0.36 0.55 2 -0.7 78 80
HIF1A -0.023 0.17 -10000 0 -0.42 61 61
TFF3 -0.073 0.38 0.55 2 -0.72 88 90
GATA2 0.017 0.058 -10000 0 -0.43 6 6
AKT1 0.012 0.098 -10000 0 -0.29 12 12
response to hypoxia -0.006 0.071 -10000 0 -0.15 42 42
MCL1 -0.046 0.33 -10000 0 -0.71 71 71
NDRG1 -0.037 0.34 0.55 2 -0.72 67 69
SERPINE1 -0.032 0.36 0.55 2 -0.7 81 83
FECH -0.023 0.37 0.55 2 -0.71 78 80
FURIN -0.021 0.36 0.57 1 -0.7 79 80
NCOA2 0.026 0.048 -10000 0 -0.43 5 5
EP300 0.011 0.12 0.23 1 -0.29 35 36
HMOX1 -0.03 0.37 0.55 2 -0.73 75 77
BHLHE40 -0.061 0.34 -10000 0 -0.7 77 77
BHLHE41 -0.061 0.34 -10000 0 -0.7 77 77
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.043 0.15 -10000 0 -0.33 31 31
ENG 0.03 0.14 0.35 6 -0.32 30 36
JUN -0.011 0.13 -10000 0 -0.44 39 39
RORA -0.028 0.37 0.55 2 -0.7 81 83
ABCB1 -0.039 0.23 -10000 0 -0.9 27 27
TFRC -0.043 0.37 0.55 2 -0.72 81 83
CXCR4 -0.029 0.38 0.57 1 -0.72 81 82
TF -0.02 0.36 0.57 1 -0.71 74 75
CITED2 -0.022 0.36 0.57 1 -0.71 75 76
HIF1A/ARNT -0.046 0.41 -10000 0 -0.86 60 60
LDHA 0.001 0.18 -10000 0 -0.92 15 15
ETS1 -0.027 0.36 0.55 2 -0.71 75 77
PGK1 -0.012 0.36 0.55 2 -0.7 75 77
NOS2 -0.061 0.34 -10000 0 -0.7 77 77
ITGB2 -0.03 0.37 0.55 2 -0.73 78 80
ALDOA -0.015 0.36 0.52 1 -0.72 69 70
Cbp/p300/CITED2 -0.028 0.37 -10000 0 -0.79 60 60
FOS -0.04 0.16 -10000 0 -0.43 66 66
HK2 -0.013 0.36 0.55 2 -0.7 76 78
SP1 0.035 0.034 -10000 0 -0.14 13 13
GCK 0.026 0.19 -10000 0 -0.96 6 6
HK1 -0.012 0.36 0.55 2 -0.71 74 76
NPM1 -0.012 0.36 0.55 2 -0.71 73 75
EGLN1 -0.038 0.34 0.57 1 -0.73 69 70
CREB1 0.038 0.027 -10000 0 -0.43 1 1
PGM1 -0.019 0.36 0.55 2 -0.71 76 78
SMAD3 0.026 0.062 -10000 0 -0.43 9 9
EDN1 -0.17 0.48 -10000 0 -1.2 87 87
IGFBP1 -0.016 0.36 0.55 2 -0.71 73 75
VEGFA -0.037 0.26 0.47 1 -0.57 64 65
HIF1A/JAB1 0.002 0.13 -10000 0 -0.36 43 43
CP -0.11 0.37 -10000 0 -0.74 94 94
CXCL12 -0.036 0.38 0.55 2 -0.73 82 84
COPS5 0.026 0.043 -10000 0 -0.43 4 4
SMAD3/SMAD4 0.038 0.064 -10000 0 -0.3 16 16
BNIP3 -0.023 0.37 0.55 2 -0.72 75 77
EGLN3 -0.054 0.38 0.55 2 -0.73 85 87
CA9 -0.033 0.35 0.55 2 -0.7 75 77
TERT -0.021 0.36 -10000 0 -0.71 75 75
ENO1 -0.016 0.36 0.55 2 -0.71 73 75
PFKL -0.019 0.36 0.55 2 -0.72 73 75
NCOA1 0.03 0.05 -10000 0 -0.43 6 6
ADM -0.054 0.38 0.55 2 -0.73 88 90
ARNT 0.016 0.071 -10000 0 -10000 0 0
HNF4A 0.034 0.034 -10000 0 -0.22 6 6
ADFP -0.03 0.37 0.57 1 -0.75 74 75
SLC2A1 0.002 0.29 0.53 2 -0.59 58 60
LEP -0.054 0.36 0.52 1 -0.73 76 77
HIF1A/ARNT/Cbp/p300 -0.027 0.33 -10000 0 -0.69 58 58
EPO -0.004 0.28 -10000 0 -0.68 44 44
CREBBP 0.019 0.11 0.23 1 -0.26 26 27
HIF1A/ARNT/Cbp/p300/HDAC7 -0.027 0.31 -10000 0 -0.67 58 58
PFKFB3 -0.021 0.36 0.55 2 -0.72 74 76
NT5E -0.021 0.37 0.55 2 -0.72 74 76
Syndecan-1-mediated signaling events

Figure S12.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S12.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.034 0.005 -10000 0 -10000 0 0
CCL5 -0.015 0.14 -10000 0 -0.43 51 51
SDCBP 0.022 0.059 -10000 0 -0.43 8 8
FGFR/FGF2/Syndecan-1 -0.12 0.23 0.2 1 -0.54 90 91
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 -0.12 0.22 -10000 0 -0.51 93 93
Syndecan-1/Syntenin -0.1 0.22 0.34 1 -0.5 91 92
MAPK3 -0.098 0.21 0.32 1 -0.48 86 87
HGF/MET 0.04 0.054 -10000 0 -0.3 11 11
TGFB1/TGF beta receptor Type II 0.034 0.005 -10000 0 -10000 0 0
BSG 0.034 0.008 -10000 0 -10000 0 0
keratinocyte migration -0.11 0.22 -10000 0 -0.5 93 93
Syndecan-1/RANTES -0.13 0.24 0.34 1 -0.51 111 112
Syndecan-1/CD147 -0.096 0.23 0.34 1 -0.51 90 91
Syndecan-1/Syntenin/PIP2 -0.1 0.22 0.32 1 -0.48 91 92
LAMA5 0.027 0.051 -10000 0 -0.43 6 6
positive regulation of cell-cell adhesion -0.1 0.21 0.31 1 -0.47 91 92
MMP7 -0.036 0.16 -10000 0 -0.43 70 70
HGF 0.027 0.058 -10000 0 -0.43 8 8
Syndecan-1/CASK -0.12 0.22 -10000 0 -0.51 93 93
Syndecan-1/HGF/MET -0.1 0.23 0.34 1 -0.5 95 96
regulation of cell adhesion -0.1 0.2 -10000 0 -0.47 86 86
HPSE 0.015 0.091 -10000 0 -0.43 20 20
positive regulation of cell migration -0.12 0.23 0.2 1 -0.54 90 91
SDC1 -0.12 0.23 -10000 0 -0.54 90 90
Syndecan-1/Collagen -0.12 0.23 0.2 1 -0.54 90 91
PPIB 0.032 0.03 -10000 0 -0.43 2 2
MET 0.03 0.037 -10000 0 -0.43 3 3
PRKACA 0.035 0.004 -10000 0 -10000 0 0
MMP9 -0.015 0.14 -10000 0 -0.43 52 52
MAPK1 -0.11 0.21 -10000 0 -0.48 89 89
homophilic cell adhesion -0.12 0.23 0.3 2 -0.53 91 93
MMP1 -0.078 0.18 -10000 0 -0.43 109 109
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.044 0.2 -10000 0 -0.58 56 56
IHH 0.015 0.089 -10000 0 -0.28 25 25
SHH Np/Cholesterol/GAS1 -0.028 0.11 -10000 0 -0.24 99 99
LRPAP1 0.034 0.007 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.028 0.11 0.24 99 -10000 0 99
SMO/beta Arrestin2 -0.019 0.17 -10000 0 -0.36 78 78
SMO -0.04 0.16 -10000 0 -0.36 87 87
AKT1 -0.011 0.15 -10000 0 -0.59 23 23
ARRB2 0.032 0.01 -10000 0 -10000 0 0
BOC 0.012 0.097 -10000 0 -0.43 23 23
ADRBK1 0.032 0.01 -10000 0 -10000 0 0
heart looping -0.037 0.16 -10000 0 -0.36 87 87
STIL -0.008 0.13 0.2 68 -0.23 104 172
DHH N/PTCH2 0.051 0.009 -10000 0 -10000 0 0
DHH N/PTCH1 -0.001 0.12 -10000 0 -0.29 69 69
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
DHH 0.035 0.004 -10000 0 -10000 0 0
PTHLH -0.067 0.26 -10000 0 -0.68 65 65
determination of left/right symmetry -0.037 0.16 -10000 0 -0.36 87 87
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
skeletal system development -0.066 0.25 -10000 0 -0.67 65 65
IHH N/Hhip 0.032 0.065 -10000 0 -0.29 12 12
DHH N/Hhip 0.048 0.03 -10000 0 -0.31 3 3
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.037 0.16 -10000 0 -0.36 87 87
pancreas development 0.031 0.036 -10000 0 -0.43 3 3
HHAT -0.018 0.14 -10000 0 -0.43 50 50
PI3K 0.033 0.066 -10000 0 -0.31 17 17
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.031 0.16 -10000 0 -0.43 70 70
somite specification -0.037 0.16 -10000 0 -0.36 87 87
SHH Np/Cholesterol/PTCH1 -0.031 0.11 -10000 0 -0.24 102 102
SHH Np/Cholesterol/PTCH2 0.002 0.076 -10000 0 -0.24 45 45
SHH Np/Cholesterol/Megalin -0.06 0.14 -10000 0 -0.28 137 137
SHH -0.017 0.093 -10000 0 -0.31 46 46
catabolic process -0.028 0.12 -10000 0 -0.32 69 69
SMO/Vitamin D3 -0.028 0.15 0.2 24 -0.33 64 88
SHH Np/Cholesterol/Hhip 0.001 0.077 -10000 0 -0.24 46 46
LRP2 -0.1 0.21 -10000 0 -0.43 147 147
receptor-mediated endocytosis -0.076 0.18 -10000 0 -0.36 99 99
SHH Np/Cholesterol/BOC -0.009 0.088 -10000 0 -0.23 64 64
SHH Np/Cholesterol/CDO -0.008 0.086 -10000 0 -0.24 56 56
mesenchymal cell differentiation -0.001 0.077 0.23 46 -10000 0 46
mol:Vitamin D3 -0.01 0.13 0.2 55 -0.24 100 155
IHH N/PTCH2 0.035 0.06 -10000 0 -0.28 10 10
CDON 0.018 0.074 -10000 0 -0.43 13 13
IHH N/PTCH1 -0.008 0.13 -10000 0 -0.33 69 69
Megalin/LRPAP1 -0.056 0.16 -10000 0 -0.31 147 147
PTCH2 0.034 0.005 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.007 0.072 -10000 0 -0.23 46 46
PTCH1 -0.028 0.12 -10000 0 -0.32 69 69
HHIP 0.031 0.036 -10000 0 -0.43 3 3
Glucocorticoid receptor regulatory network

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
PCK2 0.057 0.15 0.35 1 -0.78 8 9
SMARCC2 0.035 0.004 -10000 0 -10000 0 0
SMARCC1 0.031 0.037 -10000 0 -0.43 3 3
TBX21 -0.14 0.29 0.39 5 -0.71 89 94
SUMO2 0.028 0.019 -10000 0 -10000 0 0
STAT1 (dimer) 0.017 0.097 -10000 0 -0.39 24 24
FKBP4 0.029 0.047 -10000 0 -0.43 5 5
FKBP5 -0.005 0.13 -10000 0 -0.43 41 41
GR alpha/HSP90/FKBP51/HSP90 0.061 0.14 0.27 89 -0.25 28 117
PRL -0.038 0.13 -10000 0 -1.4 1 1
cortisol/GR alpha (dimer)/TIF2 0.13 0.24 0.53 105 -0.39 2 107
RELA -0.02 0.11 -10000 0 -0.23 55 55
FGG 0.14 0.22 0.47 120 -0.38 3 123
GR beta/TIF2 0.071 0.14 0.31 73 -0.3 9 82
IFNG -0.27 0.41 -10000 0 -0.85 129 129
apoptosis -0.007 0.18 0.5 5 -0.52 12 17
CREB1 0.037 0.042 -10000 0 -0.37 5 5
histone acetylation -0.029 0.12 0.31 4 -0.34 32 36
BGLAP -0.052 0.14 0.34 1 -0.48 20 21
GR/PKAc 0.11 0.12 0.32 49 -0.27 13 62
NF kappa B1 p50/RelA -0.041 0.19 -10000 0 -0.37 88 88
SMARCD1 0.035 0.004 -10000 0 -10000 0 0
MDM2 0.073 0.1 0.23 114 -10000 0 114
GATA3 -0.047 0.18 -10000 0 -0.42 97 97
AKT1 0.028 0.041 0.18 6 -0.44 3 9
CSF2 -0.052 0.14 -10000 0 -0.63 11 11
GSK3B 0.029 0.019 -10000 0 -10000 0 0
NR1I3 0.025 0.18 0.58 4 -0.74 5 9
CSN2 0.12 0.19 0.39 120 -0.39 4 124
BRG1/BAF155/BAF170/BAF60A 0.08 0.037 -10000 0 -0.24 3 3
NFATC1 0.02 0.093 -10000 0 -0.41 22 22
POU2F1 0.034 0.02 -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 0.01 0.1 -10000 0 -0.43 25 25
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.069 0.14 0.3 60 -0.23 44 104
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.079 0.31 0.48 3 -0.77 77 80
JUN -0.15 0.23 0.38 4 -0.47 138 142
IL4 -0.089 0.19 -10000 0 -0.69 21 21
CDK5R1 0.033 0.009 -10000 0 -10000 0 0
PRKACA 0.035 0.004 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.097 0.21 0.21 68 -0.38 145 213
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.085 0.13 0.29 66 -0.23 31 97
cortisol/GR alpha (monomer) 0.2 0.31 0.62 139 -0.43 3 142
NCOA2 0.024 0.047 -10000 0 -0.43 5 5
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.08 0.17 -10000 0 -0.44 72 72
AP-1/NFAT1-c-4 -0.27 0.37 -10000 0 -0.74 164 164
AFP -0.12 0.2 0.5 1 -0.67 17 18
SUV420H1 0.031 0.023 -10000 0 -0.43 1 1
IRF1 0.091 0.21 0.43 55 -0.74 14 69
TP53 0.009 0.13 -10000 0 -0.46 36 36
PPP5C 0.031 0.042 -10000 0 -0.43 4 4
KRT17 -0.39 0.56 -10000 0 -1.2 146 146
KRT14 -0.26 0.5 -10000 0 -1.3 91 91
TBP 0.039 0.019 -10000 0 -0.28 1 1
CREBBP 0.063 0.096 0.28 79 -0.44 1 80
HDAC1 0.029 0.021 -10000 0 -0.43 1 1
HDAC2 0.03 0.024 -10000 0 -0.43 1 1
AP-1 -0.28 0.37 -10000 0 -0.74 164 164
MAPK14 0.031 0.015 -10000 0 -10000 0 0
MAPK10 0.008 0.091 -10000 0 -0.43 20 20
MAPK11 0.027 0.02 -10000 0 -10000 0 0
KRT5 -0.39 0.57 -10000 0 -1.2 146 146
interleukin-1 receptor activity -0.001 0.006 -10000 0 -10000 0 0
NCOA1 0.03 0.053 -10000 0 -0.38 7 7
STAT1 0.017 0.097 -10000 0 -0.39 24 24
CGA -0.069 0.17 -10000 0 -0.5 38 38
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.084 0.16 0.37 94 -0.32 1 95
MAPK3 0.026 0.028 -10000 0 -0.43 1 1
MAPK1 0.028 0.033 -10000 0 -0.43 2 2
ICAM1 -0.16 0.31 -10000 0 -0.74 80 80
NFKB1 -0.023 0.11 -10000 0 -0.26 44 44
MAPK8 -0.11 0.2 0.56 2 -0.4 117 119
MAPK9 0.013 0.089 -10000 0 -0.43 19 19
cortisol/GR alpha (dimer) -0.008 0.18 0.5 5 -0.52 16 21
BAX -0.015 0.11 -10000 0 -0.57 1 1
POMC -0.092 0.19 -10000 0 -1.4 4 4
EP300 0.062 0.096 0.27 79 -0.44 2 81
cortisol/GR alpha (dimer)/p53 0.12 0.25 0.53 102 -0.42 1 103
proteasomal ubiquitin-dependent protein catabolic process 0.053 0.11 0.26 77 -10000 0 77
SGK1 0.077 0.13 0.33 88 -0.32 4 92
IL13 -0.22 0.27 -10000 0 -0.74 56 56
IL6 -0.2 0.38 -10000 0 -0.92 89 89
PRKACG 0.033 0.03 -10000 0 -0.43 2 2
IL5 -0.19 0.22 -10000 0 -0.65 41 41
IL2 -0.22 0.33 -10000 0 -0.72 121 121
CDK5 0.034 0.007 -10000 0 -10000 0 0
PRKACB 0.007 0.1 -10000 0 -0.43 25 25
HSP90AA1 0 0 -10000 0 -10000 0 0
IL8 -0.18 0.35 -10000 0 -0.81 91 91
CDK5R1/CDK5 0.046 0.017 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.004 0.18 -10000 0 -0.37 49 49
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.15 0.24 0.5 134 -0.35 2 136
SMARCA4 0.034 0.008 -10000 0 -10000 0 0
chromatin remodeling 0.11 0.16 0.35 111 -0.3 2 113
NF kappa B1 p50/RelA/Cbp 0.022 0.18 0.34 39 -0.38 34 73
JUN (dimer) -0.15 0.23 0.38 4 -0.47 138 142
YWHAH 0.03 0.037 -10000 0 -0.43 3 3
VIPR1 -0.098 0.21 -10000 0 -0.56 64 64
NR3C1 0.12 0.21 0.42 123 -0.42 8 131
NR4A1 0.036 0.045 -10000 0 -0.45 4 4
TIF2/SUV420H1 0.036 0.046 -10000 0 -0.36 5 5
MAPKKK cascade -0.007 0.18 0.5 5 -0.52 12 17
cortisol/GR alpha (dimer)/Src-1 0.18 0.26 0.54 137 -0.38 3 140
PBX1 0.021 0.078 -10000 0 -0.41 15 15
POU1F1 0.039 0.025 -10000 0 -0.34 2 2
SELE -0.24 0.42 -10000 0 -0.92 124 124
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.11 0.16 0.35 111 -0.31 2 113
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.15 0.24 0.5 134 -0.35 2 136
mol:cortisol 0.11 0.18 0.35 146 -10000 0 146
MMP1 -0.36 0.54 -10000 0 -1.2 150 150
TCR signaling in naïve CD8+ T 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
GRB2/SOS1/SHC 0.004 0.18 0.25 39 -0.33 80 119
FYN -0.039 0.2 0.27 3 -0.42 82 85
LAT/GRAP2/SLP76 -0.022 0.18 0.24 13 -0.35 89 102
IKBKB 0.029 0.024 -10000 0 -0.43 1 1
AKT1 -0.026 0.16 0.26 18 -0.32 82 100
B2M 0.024 0.066 -10000 0 -0.44 10 10
IKBKG 0.001 0.058 0.14 20 -0.13 30 50
MAP3K8 0.002 0.11 -10000 0 -0.43 32 32
mol:Ca2+ -0.016 0.021 0.091 1 -0.06 66 67
integrin-mediated signaling pathway 0.028 0.051 -10000 0 -0.26 13 13
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.051 0.21 0.23 5 -0.42 95 100
TRPV6 -0.023 0.22 1.3 9 -0.43 56 65
CD28 -0.002 0.12 -10000 0 -0.43 37 37
SHC1 -0.027 0.2 0.23 56 -0.39 90 146
receptor internalization -0.067 0.2 -10000 0 -0.4 120 120
PRF1 -0.05 0.22 -10000 0 -0.86 22 22
KRAS 0.027 0.055 -10000 0 -0.43 7 7
GRB2 0.033 0.009 -10000 0 -10000 0 0
COT/AKT1 -0.017 0.14 0.25 17 -0.27 85 102
LAT -0.045 0.19 0.23 21 -0.39 95 116
EntrezGene:6955 0 0.002 -10000 0 -0.015 7 7
CD3D 0.015 0.078 -10000 0 -0.44 14 14
CD3E 0.031 0.014 -10000 0 -10000 0 0
CD3G -0.023 0.14 -10000 0 -0.43 54 54
RASGRP2 0.001 0.04 0.078 2 -0.17 21 23
RASGRP1 -0.043 0.17 0.29 4 -0.35 92 96
HLA-A 0.016 0.09 -10000 0 -0.44 19 19
RASSF5 0.018 0.065 -10000 0 -0.43 10 10
RAP1A/GTP/RAPL 0.029 0.051 -10000 0 -0.26 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.018 0.069 0.15 32 -0.12 30 62
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.026 0.071 -10000 0 -0.18 61 61
PRKCA -0.011 0.093 0.2 10 -0.21 58 68
GRAP2 0.032 0.023 -10000 0 -0.43 1 1
mol:IP3 -0.026 0.14 0.21 29 -0.29 81 110
EntrezGene:6957 0 0.004 -10000 0 -0.021 7 7
TCR/CD3/MHC I/CD8 -0.038 0.15 -10000 0 -0.3 95 95
ORAI1 0.004 0.17 0.49 2 -1.1 9 11
CSK -0.047 0.19 0.21 9 -0.39 93 102
B7 family/CD28 -0.031 0.22 0.28 1 -0.46 82 83
CHUK 0.024 0.071 -10000 0 -0.43 12 12
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.062 0.21 -10000 0 -0.42 105 105
PTPN6 -0.055 0.19 0.2 6 -0.39 98 104
VAV1 -0.059 0.2 0.22 3 -0.41 101 104
Monovalent TCR/CD3 -0.022 0.12 -10000 0 -0.3 64 64
CBL 0.031 0.012 -10000 0 -10000 0 0
LCK -0.049 0.22 0.26 3 -0.44 89 92
PAG1 -0.036 0.2 0.2 54 -0.4 88 142
RAP1A 0.03 0.046 -10000 0 -0.43 5 5
TCR/CD3/MHC I/CD8/LCK -0.065 0.21 -10000 0 -0.42 106 106
CD80 0.033 0.022 -10000 0 -0.43 1 1
CD86 0.016 0.092 -10000 0 -0.43 20 20
PDK1/CARD11/BCL10/MALT1 -0.017 0.092 -10000 0 -0.22 64 64
HRAS 0.031 0.037 -10000 0 -0.43 3 3
GO:0035030 -0.053 0.18 0.25 1 -0.39 86 87
CD8A 0 0.003 -10000 0 -0.018 7 7
CD8B 0 0.004 0.011 1 -0.013 21 22
PTPRC 0.005 0.099 -10000 0 -0.43 24 24
PDK1/PKC theta -0.029 0.19 0.33 20 -0.38 79 99
CSK/PAG1 -0.03 0.19 0.2 55 -0.39 81 136
SOS1 0.034 0.021 -10000 0 -0.43 1 1
peptide-MHC class I 0.028 0.095 -10000 0 -0.38 23 23
GRAP2/SLP76 -0.035 0.2 0.26 2 -0.39 98 100
STIM1 0.008 0.11 1.3 3 -0.43 1 4
RAS family/GTP 0.012 0.087 0.17 16 -0.18 39 55
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.072 0.21 -10000 0 -0.42 120 120
mol:DAG -0.044 0.11 0.1 1 -0.26 85 86
RAP1A/GDP 0.011 0.035 0.083 18 -0.072 16 34
PLCG1 0.033 0.008 -10000 0 -10000 0 0
CD247 0 0.002 -10000 0 -0.015 7 7
cytotoxic T cell degranulation -0.046 0.21 -10000 0 -0.81 22 22
RAP1A/GTP 0 0.017 -10000 0 -0.065 26 26
mol:PI-3-4-5-P3 -0.039 0.18 0.22 6 -0.36 95 101
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.027 0.18 0.24 22 -0.37 78 100
NRAS 0.028 0.055 -10000 0 -0.43 7 7
ZAP70 0.032 0.022 -10000 0 -0.43 1 1
GRB2/SOS1 0.048 0.021 -10000 0 -0.31 1 1
LAT/GRAP2/SLP76/VAV1 -0.033 0.18 0.22 8 -0.36 86 94
MALT1 0.03 0.042 -10000 0 -0.43 4 4
TRAF6 0.034 0.021 -10000 0 -0.43 1 1
CD8 heterodimer 0.001 0.006 0.016 2 -0.021 12 14
CARD11 0.027 0.051 -10000 0 -0.43 6 6
PRKCB -0.034 0.078 0.13 2 -0.19 85 87
PRKCE -0.012 0.1 0.19 14 -0.21 65 79
PRKCQ -0.045 0.2 0.27 4 -0.41 92 96
LCP2 0.023 0.068 -10000 0 -0.43 11 11
BCL10 0.034 0.007 -10000 0 -10000 0 0
regulation of survival gene product expression -0.019 0.14 0.24 19 -0.28 81 100
IKK complex 0.014 0.065 0.18 33 -0.11 19 52
RAS family/GDP -0.004 0.016 -10000 0 -0.049 21 21
MAP3K14 -0.016 0.11 0.21 18 -0.22 73 91
PDPK1 -0.021 0.15 0.3 19 -0.31 79 98
TCR/CD3/MHC I/CD8/Fyn -0.061 0.2 -10000 0 -0.43 90 90
Noncanonical Wnt signaling pathway

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
NFATC2 0.029 0.037 -10000 0 -0.43 3 3
GNB1/GNG2 -0.049 0.17 -10000 0 -0.38 62 62
mol:DAG -0.057 0.15 0.19 4 -0.36 56 60
PLCG1 -0.059 0.15 -10000 0 -0.37 56 56
YES1 -0.071 0.16 -10000 0 -0.28 141 141
FZD3 0.005 0.1 -10000 0 -0.43 25 25
FZD6 -0.029 0.15 -10000 0 -0.43 60 60
G protein -0.038 0.17 0.28 12 -0.38 55 67
MAP3K7 -0.056 0.13 0.24 2 -0.32 49 51
mol:Ca2+ -0.055 0.14 0.19 4 -0.35 56 60
mol:IP3 -0.057 0.15 0.19 4 -0.36 56 60
NLK -0.024 0.23 -10000 0 -0.82 37 37
GNB1 0.03 0.042 -10000 0 -0.43 4 4
CAMK2A -0.055 0.14 0.25 2 -0.34 51 53
MAP3K7IP1 0.033 0.009 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.073 0.16 -10000 0 -0.29 145 145
CSNK1A1 0.034 0.005 -10000 0 -10000 0 0
GNAS -0.069 0.15 -10000 0 -0.28 139 139
GO:0007205 -0.059 0.14 0.26 2 -0.36 55 57
WNT6 0.029 0.031 -10000 0 -0.43 2 2
WNT4 -0.022 0.15 -10000 0 -0.43 59 59
NFAT1/CK1 alpha -0.051 0.16 0.29 2 -0.38 55 57
GNG2 0.033 0.021 -10000 0 -0.43 1 1
WNT5A -0.027 0.15 -10000 0 -0.43 62 62
WNT11 0.027 0.032 -10000 0 -0.43 2 2
CDC42 -0.068 0.15 0.19 1 -0.4 55 56
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 -0.073 0.16 -9999 0 -0.29 145 145
FZD6 -0.029 0.15 -9999 0 -0.43 60 60
WNT6 0.029 0.031 -9999 0 -0.43 2 2
WNT4 -0.022 0.15 -9999 0 -0.43 59 59
FZD3 0.005 0.1 -9999 0 -0.43 25 25
WNT5A -0.027 0.15 -9999 0 -0.43 62 62
WNT11 0.027 0.032 -9999 0 -0.43 2 2
Thromboxane A2 receptor signaling

Figure S18.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S18.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.016 0.084 -10000 0 -0.43 17 17
GNB1/GNG2 -0.05 0.08 -10000 0 -0.18 123 123
AKT1 -0.011 0.12 0.29 4 -0.26 24 28
EGF -0.07 0.19 -10000 0 -0.43 108 108
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.014 0.063 0.26 2 -0.28 2 4
mol:Ca2+ -0.033 0.17 0.31 4 -0.3 126 130
LYN 0.012 0.058 0.26 2 -0.26 3 5
RhoA/GTP -0.014 0.075 -10000 0 -0.14 91 91
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.053 0.19 0.33 2 -0.35 127 129
GNG2 0.033 0.021 -10000 0 -0.43 1 1
ARRB2 0.032 0.01 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.011 0.14 -10000 0 -0.46 31 31
G beta5/gamma2 -0.053 0.11 -10000 0 -0.24 118 118
PRKCH -0.049 0.19 0.31 3 -0.36 124 127
DNM1 0.032 0.036 -10000 0 -0.43 3 3
TXA2/TP beta/beta Arrestin3 0.027 0.026 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR 0.027 0.055 -10000 0 -0.43 7 7
G12 family/GTP -0.047 0.16 -10000 0 -0.3 119 119
ADRBK1 0.032 0.01 -10000 0 -10000 0 0
ADRBK2 0.023 0.068 -10000 0 -0.43 11 11
RhoA/GTP/ROCK1 0.039 0.04 -10000 0 -0.26 8 8
mol:GDP 0.022 0.14 0.44 31 -0.26 4 35
mol:NADP 0.034 0.007 -10000 0 -10000 0 0
RAB11A 0.034 0.007 -10000 0 -10000 0 0
PRKG1 0.034 0.006 -10000 0 -10000 0 0
mol:IP3 -0.05 0.21 0.34 3 -0.38 126 129
cell morphogenesis 0.039 0.04 -10000 0 -0.26 8 8
PLCB2 -0.083 0.27 0.38 2 -0.52 126 128
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.005 0.06 0.25 1 -0.3 3 4
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.007 0.075 0.26 2 -0.36 6 8
RHOA 0.025 0.062 -10000 0 -0.43 9 9
PTGIR 0.033 0.03 -10000 0 -0.43 2 2
PRKCB1 -0.053 0.21 0.32 4 -0.4 118 122
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.034 0.007 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.084 0.27 0.38 2 -0.53 125 127
LCK -0.007 0.092 0.26 2 -0.31 13 15
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.046 0.044 0.23 1 -0.27 1 2
TXA2-R family/G12 family/GDP/G beta/gamma 0.016 0.12 -10000 0 -0.41 29 29
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.042 0.044 0.23 1 -0.26 1 2
MAPK14 -0.03 0.13 0.24 7 -0.24 126 133
TGM2/GTP -0.062 0.22 0.37 3 -0.42 121 124
MAPK11 -0.031 0.13 0.29 4 -0.24 125 129
ARHGEF1 -0.015 0.1 0.18 4 -0.18 109 113
GNAI2 0.026 0.058 -10000 0 -0.43 8 8
JNK cascade -0.051 0.21 0.36 2 -0.39 125 127
RAB11/GDP 0.034 0.007 -10000 0 -10000 0 0
ICAM1 -0.035 0.16 0.29 3 -0.3 125 128
cAMP biosynthetic process -0.047 0.19 0.32 4 -0.35 121 125
Gq family/GTP/EBP50 -0.023 0.099 -10000 0 -0.23 82 82
actin cytoskeleton reorganization 0.039 0.04 -10000 0 -0.26 8 8
SRC 0.013 0.061 0.26 2 -0.33 1 3
GNB5 0.024 0.068 -10000 0 -0.43 11 11
GNB1 0.03 0.042 -10000 0 -0.43 4 4
EGF/EGFR -0.032 0.11 0.23 6 -0.29 43 49
VCAM1 -0.039 0.17 0.3 2 -0.31 126 128
TP beta/Gq family/GDP/G beta5/gamma2 -0.011 0.14 -10000 0 -0.46 31 31
platelet activation -0.038 0.17 0.34 4 -0.3 125 129
PGI2/IP 0.024 0.021 -10000 0 -0.3 2 2
PRKACA 0.019 0.035 -10000 0 -0.24 9 9
Gq family/GDP/G beta5/gamma2 -0.008 0.12 -10000 0 -0.4 32 32
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 0.009 0.03 -10000 0 -0.21 8 8
mol:DAG -0.061 0.23 0.36 2 -0.43 125 127
EGFR -0.016 0.14 -10000 0 -0.43 48 48
TXA2/TP alpha -0.071 0.25 0.4 2 -0.48 120 122
Gq family/GTP -0.018 0.08 0.22 4 -0.22 59 63
YES1 0.012 0.069 0.26 2 -0.28 6 8
GNAI2/GTP 0.02 0.054 -10000 0 -0.21 15 15
PGD2/DP 0.02 0.039 -10000 0 -0.3 7 7
SLC9A3R1 -0.011 0.14 -10000 0 -0.43 47 47
FYN 0.01 0.067 0.26 1 -0.3 5 6
mol:NO 0.034 0.007 -10000 0 -10000 0 0
GNA15 0.029 0.047 -10000 0 -0.43 5 5
PGK/cGMP 0.044 0.012 -10000 0 -10000 0 0
RhoA/GDP 0.025 0.061 -10000 0 -0.42 9 9
TP alpha/TGM2/GDP/G beta/gamma 0.047 0.073 0.28 1 -0.33 5 6
NOS3 0.034 0.007 -10000 0 -10000 0 0
RAC1 0.034 0.006 -10000 0 -10000 0 0
PRKCA -0.038 0.19 0.37 3 -0.35 112 115
PRKCB -0.049 0.19 0.31 3 -0.36 127 130
PRKCE -0.05 0.2 0.32 2 -0.36 124 126
PRKCD -0.056 0.2 0.31 2 -0.39 125 127
PRKCG -0.053 0.21 0.37 2 -0.39 124 126
muscle contraction -0.078 0.25 0.38 2 -0.49 127 129
PRKCZ -0.044 0.18 0.32 3 -0.34 125 128
ARR3 0.035 0.002 -10000 0 -10000 0 0
TXA2/TP beta 0.037 0.055 -10000 0 -0.21 12 12
PRKCQ -0.047 0.2 0.31 5 -0.37 123 128
MAPKKK cascade -0.068 0.24 0.36 2 -0.45 125 127
SELE -0.053 0.19 0.3 2 -0.37 126 128
TP beta/GNAI2/GDP/G beta/gamma 0.055 0.067 0.28 1 -0.4 3 4
ROCK1 0.034 0.005 -10000 0 -10000 0 0
GNA14 -0.011 0.13 -10000 0 -0.43 44 44
chemotaxis -0.1 0.31 -10000 0 -0.61 126 126
GNA12 0.034 0.006 -10000 0 -10000 0 0
GNA13 0.029 0.037 -10000 0 -0.43 3 3
GNA11 0.031 0.036 -10000 0 -0.43 3 3
Rac1/GTP 0.025 0.005 -10000 0 -10000 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.003 0.1 -10000 0 -0.32 19 19
TBX21 -0.25 0.57 -10000 0 -1.3 101 101
B2M 0.023 0.067 -10000 0 -0.43 10 10
TYK2 0.013 0.042 -10000 0 -10000 0 0
IL12RB1 0.013 0.042 -10000 0 -10000 0 0
GADD45B -0.17 0.44 -10000 0 -1.1 84 84
IL12RB2 -0.011 0.1 -10000 0 -0.44 25 25
GADD45G -0.17 0.43 -10000 0 -1 87 87
natural killer cell activation -0.005 0.022 -10000 0 -0.04 114 114
RELB 0.028 0.051 -10000 0 -0.43 6 6
RELA 0.034 0.005 -10000 0 -10000 0 0
IL18 -0.002 0.12 -10000 0 -0.44 33 33
IL2RA 0.003 0.11 -10000 0 -0.43 31 31
IFNG -0.009 0.12 -10000 0 -0.43 38 38
STAT3 (dimer) -0.13 0.37 -10000 0 -0.79 103 103
HLA-DRB5 0.008 0.069 -10000 0 -0.43 11 11
FASLG -0.18 0.5 -10000 0 -1.2 84 84
NF kappa B2 p52/RelB -0.16 0.44 -10000 0 -0.94 103 103
CD4 0.027 0.021 -10000 0 -10000 0 0
SOCS1 0.031 0.023 -10000 0 -0.43 1 1
EntrezGene:6955 -0.003 0.011 -10000 0 -0.029 68 68
CD3D 0.008 0.08 -10000 0 -0.44 14 14
CD3E 0.023 0.026 -10000 0 -10000 0 0
CD3G -0.029 0.14 -10000 0 -0.44 54 54
IL12Rbeta2/JAK2 0.002 0.092 -10000 0 -0.33 24 24
CCL3 -0.17 0.43 -10000 0 -0.97 95 95
CCL4 -0.18 0.45 -10000 0 -1 90 90
HLA-A 0.014 0.09 -10000 0 -0.43 19 19
IL18/IL18R -0.006 0.17 -10000 0 -0.35 85 85
NOS2 -0.18 0.43 -10000 0 -0.86 117 117
IL12/IL12R/TYK2/JAK2/SPHK2 -0.006 0.1 -10000 0 -0.34 19 19
IL1R1 -0.22 0.5 -10000 0 -1.1 108 108
IL4 0.033 0.053 -10000 0 -0.42 5 5
JAK2 0.01 0.05 -10000 0 -0.46 2 2
EntrezGene:6957 -0.003 0.012 -10000 0 -0.03 63 63
TCR/CD3/MHC I/CD8 -0.073 0.28 -10000 0 -0.82 45 45
RAB7A -0.13 0.34 -10000 0 -0.76 97 97
lysosomal transport -0.12 0.33 -10000 0 -0.72 97 97
FOS -0.23 0.5 -10000 0 -1.1 109 109
STAT4 (dimer) -0.15 0.42 -10000 0 -0.9 101 101
STAT5A (dimer) -0.19 0.44 -10000 0 -0.97 101 101
GZMA -0.17 0.42 -10000 0 -0.91 104 104
GZMB -0.26 0.57 -10000 0 -1.3 102 102
HLX 0 0 -10000 0 -10000 0 0
LCK -0.21 0.5 -10000 0 -1.1 106 106
TCR/CD3/MHC II/CD4 -0.057 0.18 -10000 0 -0.37 89 89
IL2/IL2R 0.038 0.12 -10000 0 -0.3 45 45
MAPK14 -0.17 0.44 -10000 0 -0.99 96 96
CCR5 -0.16 0.4 -10000 0 -0.81 114 114
IL1B -0.023 0.13 -10000 0 -0.45 40 40
STAT6 -0.057 0.2 -10000 0 -0.44 60 60
STAT4 0.006 0.11 -10000 0 -0.43 30 30
STAT3 0.032 0.03 -10000 0 -0.43 2 2
STAT1 0.018 0.079 -10000 0 -0.43 15 15
NFKB1 0.034 0.021 -10000 0 -0.43 1 1
NFKB2 0.034 0.021 -10000 0 -0.43 1 1
IL12B 0.009 0.064 -10000 0 -0.43 6 6
CD8A 0 0.007 -10000 0 -0.037 18 18
CD8B 0 0.009 -10000 0 -0.043 19 19
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 -0.43 23 23
proteasomal ubiquitin-dependent protein catabolic process -0.13 0.37 -10000 0 -0.8 101 101
IL2RG 0.029 0.042 -10000 0 -0.43 4 4
IL12 0.013 0.076 -10000 0 -0.34 10 10
STAT5A 0.031 0.036 -10000 0 -0.43 3 3
CD247 -0.002 0.011 -10000 0 -0.027 62 62
IL2 0.031 0.036 -10000 0 -0.43 3 3
SPHK2 0.035 0.004 -10000 0 -10000 0 0
FRAP1 0.034 0.007 -10000 0 -10000 0 0
IL12A 0.005 0.06 -10000 0 -0.43 5 5
IL12/IL12R/TYK2/JAK2 -0.22 0.53 -10000 0 -1.1 104 104
MAP2K3 -0.18 0.46 -10000 0 -1 97 97
RIPK2 0.028 0.014 -10000 0 -10000 0 0
MAP2K6 -0.18 0.45 -10000 0 -1 93 93
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.019 0.065 -10000 0 -0.43 9 9
IL18RAP -0.023 0.15 -10000 0 -0.44 58 58
IL12Rbeta1/TYK2 0.026 0.055 -10000 0 -10000 0 0
EOMES -0.045 0.27 -10000 0 -1.2 23 23
STAT1 (dimer) -0.16 0.38 -10000 0 -0.8 107 107
T cell proliferation -0.11 0.3 -10000 0 -0.65 101 101
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.015 0.093 -10000 0 -0.44 20 20
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.12 0.33 -10000 0 -0.68 108 108
ATF2 -0.16 0.4 -10000 0 -0.89 96 96
FAS signaling pathway (CD95)

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
SPTAN1 0.023 0.083 0.19 85 -0.2 7 92
RFC1 0.022 0.077 0.19 75 -0.19 5 80
PRKDC 0.042 0.1 0.22 112 -0.22 2 114
RIPK1 0.035 0.007 -10000 0 -10000 0 0
CASP7 -0.007 0.14 -10000 0 -0.67 17 17
FASLG/FAS/FADD/FAF1 0.004 0.094 0.2 39 -0.27 29 68
MAP2K4 -0.026 0.17 0.52 1 -0.45 41 42
mol:ceramide -0.016 0.12 -10000 0 -0.36 39 39
GSN 0.017 0.087 0.19 77 -0.23 10 87
FASLG/FAS/FADD/FAF1/Caspase 8 0.004 0.11 0.23 4 -0.33 27 31
FAS 0.002 0.11 -10000 0 -0.43 29 29
BID -0.015 0.051 0.26 12 -0.27 5 17
MAP3K1 -0.007 0.13 0.28 4 -0.47 20 24
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
RB1 0.022 0.082 0.19 76 -0.25 5 81
CFLAR 0.031 0.047 -10000 0 -0.43 5 5
HGF/MET 0.013 0.12 -10000 0 -0.27 76 76
ARHGDIB 0.014 0.093 0.2 75 -0.24 19 94
FADD 0.025 0.02 -10000 0 -10000 0 0
actin filament polymerization -0.016 0.088 0.24 12 -0.19 77 89
NFKB1 -0.001 0.11 -10000 0 -0.71 8 8
MAPK8 -0.045 0.2 0.68 1 -0.48 69 70
DFFA 0.022 0.08 0.19 79 -0.19 6 85
DNA fragmentation during apoptosis 0.022 0.084 0.19 78 -0.19 7 85
FAS/FADD/MET 0.032 0.078 -10000 0 -0.26 27 27
CFLAR/RIP1 0.047 0.038 -10000 0 -0.31 5 5
FAIM3 0.015 0.079 -10000 0 -0.43 15 15
FAF1 0.027 0.03 -10000 0 -0.43 1 1
PARP1 0.026 0.095 0.21 88 -0.23 9 97
DFFB 0.022 0.084 0.19 82 -0.2 7 89
CHUK -0.01 0.11 -10000 0 -0.62 10 10
FASLG -0.012 0.12 -10000 0 -0.43 37 37
FAS/FADD 0.018 0.079 -10000 0 -0.31 24 24
HGF 0.027 0.058 -10000 0 -0.43 8 8
LMNA 0.02 0.096 0.34 19 -0.25 6 25
CASP6 0.02 0.084 0.19 76 -0.26 4 80
CASP10 0.029 0.02 -10000 0 -10000 0 0
CASP3 0.033 0.094 0.24 83 -0.22 7 90
PTPN13 -0.033 0.16 -10000 0 -0.43 72 72
CASP8 -0.012 0.058 0.34 13 -10000 0 13
IL6 -0.1 0.41 -10000 0 -1.2 61 61
MET 0.03 0.037 -10000 0 -0.43 3 3
ICAD/CAD 0.018 0.074 0.17 72 -10000 0 72
FASLG/FAS/FADD/FAF1/Caspase 10 -0.017 0.12 -10000 0 -0.36 39 39
activation of caspase activity by cytochrome c -0.015 0.051 0.26 12 -0.27 5 17
PAK2 0.028 0.091 0.21 84 -0.2 1 85
BCL2 -0.062 0.18 -10000 0 -0.43 101 101
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.006 0.014 -10000 0 -0.3 1 1
GNB1/GNG2 0.002 0.12 -10000 0 -0.24 99 99
regulation of S phase of mitotic cell cycle -0.027 0.11 -10000 0 -0.23 98 98
GNAO1 0.03 0.013 -10000 0 -10000 0 0
HRAS 0.03 0.037 -10000 0 -0.43 3 3
SHBG/T-DHT 0.021 0.007 -10000 0 -10000 0 0
PELP1 0.032 0.01 -10000 0 -10000 0 0
AKT1 0.007 0.024 -10000 0 -0.3 3 3
MAP2K1 -0.052 0.1 0.18 17 -0.23 84 101
T-DHT/AR -0.04 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 71 71
GNAI2 0.026 0.058 -10000 0 -0.43 8 8
GNAI3 0.034 0.006 -10000 0 -10000 0 0
GNAI1 0.015 0.091 -10000 0 -0.43 20 20
mol:GDP -0.072 0.15 -10000 0 -0.35 107 107
cell proliferation -0.072 0.17 0.28 3 -0.43 72 75
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
FOS -0.11 0.28 -10000 0 -0.78 73 73
mol:Ca2+ -0.01 0.024 -10000 0 -0.062 64 64
MAPK3 -0.058 0.14 0.28 4 -0.34 64 68
MAPK1 -0.043 0.13 -10000 0 -0.37 43 43
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
mol:IP3 0 0.002 -10000 0 -0.004 71 71
cAMP biosynthetic process 0.003 0.018 -10000 0 -10000 0 0
GNG2 0.033 0.021 -10000 0 -0.43 1 1
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 71 71
HRAS/GTP -0.007 0.12 -10000 0 -0.23 97 97
actin cytoskeleton reorganization 0.037 0.051 -10000 0 -0.21 17 17
SRC 0.031 0.03 -10000 0 -0.43 2 2
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 71 71
PI3K 0.031 0.057 -10000 0 -0.26 17 17
apoptosis 0.06 0.17 0.43 75 -0.28 1 76
T-DHT/AR/PELP1 -0.017 0.12 -10000 0 -0.26 99 99
HRAS/GDP -0.051 0.16 -10000 0 -0.35 102 102
CREB1 -0.069 0.18 0.29 1 -0.46 75 76
RAC1-CDC42/GTP 0.048 0.056 -10000 0 -0.22 17 17
AR -0.057 0.18 -10000 0 -0.43 99 99
GNB1 0.03 0.042 -10000 0 -0.43 4 4
RAF1 -0.032 0.11 0.21 8 -0.22 94 102
RAC1-CDC42/GDP -0.03 0.16 -10000 0 -0.35 96 96
T-DHT/AR/PELP1/Src -0.001 0.12 -10000 0 -0.24 96 96
MAP2K2 -0.054 0.1 0.18 18 -0.23 84 102
T-DHT/AR/PELP1/Src/PI3K -0.027 0.11 -10000 0 -0.24 98 98
GNAZ 0.022 0.071 -10000 0 -0.43 12 12
SHBG 0.032 0.011 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.049 0.16 -10000 0 -0.49 43 43
mol:T-DHT 0 0.001 0.002 2 -0.003 41 43
RAC1 0.034 0.006 -10000 0 -10000 0 0
GNRH1 0.005 0.02 -10000 0 -0.3 2 2
Gi family/GTP -0.031 0.087 -10000 0 -0.23 51 51
CDC42 0.034 0.007 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.028 0.051 -10000 0 -0.43 6 6
LAT2 -0.051 0.14 -10000 0 -0.32 85 85
AP1 -0.075 0.21 0.32 1 -0.47 71 72
mol:PIP3 -0.032 0.19 0.28 17 -0.4 69 86
IKBKB 0.007 0.13 0.26 42 -0.25 42 84
AKT1 0.011 0.18 0.33 69 -0.37 27 96
IKBKG -0.012 0.12 0.21 17 -0.25 46 63
MS4A2 -0.078 0.19 -10000 0 -0.42 119 119
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.031 0.023 -10000 0 -0.43 1 1
MAP3K1 -0.038 0.17 0.26 14 -0.38 63 77
mol:Ca2+ -0.018 0.15 0.26 18 -0.33 51 69
LYN 0.03 0.017 -10000 0 -10000 0 0
CBLB -0.051 0.14 -10000 0 -0.33 79 79
SHC1 0.027 0.025 -10000 0 -0.43 1 1
RasGAP/p62DOK 0.032 0.095 -10000 0 -0.25 46 46
positive regulation of cell migration -0.006 0.065 -10000 0 -0.3 23 23
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.01 0.18 0.31 69 -0.33 56 125
PTPN13 -0.072 0.2 -10000 0 -0.57 38 38
PTPN11 0.031 0.024 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.007 0.14 0.31 17 -0.32 27 44
SYK 0.005 0.12 -10000 0 -0.44 33 33
GRB2 0.033 0.009 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.06 0.16 -10000 0 -0.38 79 79
LAT -0.048 0.14 -10000 0 -0.32 76 76
PAK2 -0.032 0.17 0.27 16 -0.41 53 69
NFATC2 -0.013 0.068 -10000 0 -0.6 4 4
HRAS -0.038 0.18 0.26 10 -0.45 53 63
GAB2 0.031 0.012 -10000 0 -10000 0 0
PLA2G1B 0.012 0.11 -10000 0 -0.92 6 6
Fc epsilon R1 -0.036 0.16 -10000 0 -0.32 112 112
Antigen/IgE/Fc epsilon R1 -0.031 0.15 -10000 0 -0.28 112 112
mol:GDP -0.06 0.18 0.26 1 -0.49 53 54
JUN -0.003 0.12 -10000 0 -0.43 39 39
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
FOS -0.033 0.16 -10000 0 -0.43 66 66
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.049 0.15 -10000 0 -0.33 85 85
CHUK -0.014 0.12 0.21 18 -0.25 51 69
KLRG1 -0.04 0.13 -10000 0 -0.38 41 41
VAV1 -0.055 0.15 -10000 0 -0.34 82 82
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.05 0.14 -10000 0 -0.32 84 84
negative regulation of mast cell degranulation -0.043 0.12 -10000 0 -0.36 40 40
BTK -0.059 0.18 -10000 0 -0.51 51 51
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.068 0.18 -10000 0 -0.48 66 66
GAB2/PI3K/SHP2 -0.055 0.11 -10000 0 -0.32 47 47
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.051 0.14 -10000 0 -0.28 104 104
RAF1 0.013 0.12 -10000 0 -1 6 6
Fc epsilon R1/FcgammaRIIB/SHIP -0.032 0.16 -10000 0 -0.29 121 121
FCER1G 0.032 0.019 -10000 0 -10000 0 0
FCER1A -0.027 0.15 -10000 0 -0.44 59 59
Antigen/IgE/Fc epsilon R1/Fyn -0.021 0.14 -10000 0 -0.28 107 107
MAPK3 0.012 0.12 -10000 0 -0.97 6 6
MAPK1 0.008 0.11 -10000 0 -0.91 6 6
NFKB1 0.034 0.021 -10000 0 -0.43 1 1
MAPK8 -0.038 0.22 -10000 0 -0.62 46 46
DUSP1 0.001 0.12 -10000 0 -0.43 34 34
NF-kappa-B/RelA 0.005 0.08 0.15 18 -0.16 34 52
actin cytoskeleton reorganization -0.046 0.18 -10000 0 -0.56 22 22
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.032 0.18 0.27 2 -0.41 55 57
FER -0.05 0.14 -10000 0 -0.32 79 79
RELA 0.034 0.005 -10000 0 -10000 0 0
ITK -0.034 0.11 -10000 0 -0.4 40 40
SOS1 0.034 0.021 -10000 0 -0.43 1 1
PLCG1 -0.044 0.19 0.26 5 -0.48 52 57
cytokine secretion -0.005 0.051 -10000 0 -0.14 6 6
SPHK1 -0.057 0.15 -10000 0 -0.34 78 78
PTK2 -0.048 0.18 -10000 0 -0.6 21 21
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.062 0.18 -10000 0 -0.4 82 82
EDG1 -0.006 0.065 -10000 0 -0.3 23 23
mol:DAG -0.035 0.19 0.29 14 -0.46 49 63
MAP2K2 0.008 0.11 -10000 0 -0.93 6 6
MAP2K1 0.008 0.11 -10000 0 -0.93 6 6
MAP2K7 0.035 0.005 -10000 0 -10000 0 0
KLRG1/SHP2 -0.027 0.12 -10000 0 -0.35 40 40
MAP2K4 -0.084 0.34 -10000 0 -0.93 67 67
Fc epsilon R1/FcgammaRIIB -0.034 0.17 -10000 0 -0.31 121 121
mol:Choline -0.01 0.18 0.3 69 -0.32 56 125
SHC/Grb2/SOS1 -0.013 0.15 -10000 0 -0.41 32 32
FYN 0.026 0.055 -10000 0 -0.43 7 7
DOK1 0.026 0.062 -10000 0 -0.43 9 9
PXN -0.046 0.17 -10000 0 -0.56 19 19
HCLS1 -0.053 0.14 -10000 0 -0.33 84 84
PRKCB -0.021 0.15 0.25 17 -0.33 51 68
FCGR2B 0 0.11 -10000 0 -0.43 30 30
IGHE 0.001 0.008 -10000 0 -10000 0 0
KLRG1/SHIP -0.044 0.12 -10000 0 -0.37 40 40
LCP2 0.023 0.068 -10000 0 -0.43 11 11
PLA2G4A -0.054 0.15 -10000 0 -0.35 80 80
RASA1 0.026 0.058 -10000 0 -0.43 8 8
mol:Phosphatidic acid -0.01 0.18 0.3 69 -0.32 56 125
IKK complex 0.007 0.11 0.24 40 -0.2 33 73
WIPF1 0 0 -10000 0 -10000 0 0
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.16 0.54 -10000 0 -1.3 78 78
IL23A -0.13 0.49 -10000 0 -1.2 63 63
NF kappa B1 p50/RelA/I kappa B alpha -0.096 0.48 -10000 0 -1.1 68 68
positive regulation of T cell mediated cytotoxicity -0.13 0.52 -10000 0 -1.2 68 68
ITGA3 -0.11 0.48 -10000 0 -1.1 67 67
IL17F -0.058 0.32 -10000 0 -0.68 69 69
IL12B 0.019 0.075 -10000 0 -0.45 6 6
STAT1 (dimer) -0.14 0.5 -10000 0 -1.2 70 70
CD4 -0.1 0.45 -10000 0 -1 67 67
IL23 -0.13 0.47 -10000 0 -1.1 63 63
IL23R -0.001 0.22 -10000 0 -1.3 11 11
IL1B -0.15 0.53 -10000 0 -1.3 71 71
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.076 0.45 -10000 0 -1.1 57 57
TYK2 0.02 0.045 -10000 0 -10000 0 0
STAT4 0.006 0.11 -10000 0 -0.43 30 30
STAT3 0.032 0.03 -10000 0 -0.43 2 2
IL18RAP -0.024 0.15 -10000 0 -0.43 58 58
IL12RB1 0.02 0.045 -10000 0 -10000 0 0
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
IL12Rbeta1/TYK2 0.03 0.058 -10000 0 -10000 0 0
IL23R/JAK2 0.009 0.22 -10000 0 -1.2 11 11
positive regulation of chronic inflammatory response -0.13 0.52 -10000 0 -1.2 68 68
natural killer cell activation 0 0.012 0.081 7 -10000 0 7
JAK2 0.022 0.062 -10000 0 -0.47 2 2
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
NFKB1 0.034 0.022 -10000 0 -0.43 1 1
RELA 0.035 0.007 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.12 0.44 -10000 0 -1.1 63 63
ALOX12B -0.11 0.45 -10000 0 -1.1 62 62
CXCL1 -0.17 0.55 -10000 0 -1.2 99 99
T cell proliferation -0.13 0.52 -10000 0 -1.2 68 68
NFKBIA 0.033 0.03 -10000 0 -0.43 2 2
IL17A -0.029 0.26 -10000 0 -0.52 69 69
PI3K -0.12 0.48 -10000 0 -1.1 71 71
IFNG -0.006 0.049 0.16 4 -0.13 45 49
STAT3 (dimer) -0.1 0.46 -10000 0 -1.1 69 69
IL18R1 0.014 0.092 -10000 0 -0.43 20 20
IL23/IL23R/JAK2/TYK2/SOCS3 -0.032 0.29 0.54 1 -0.7 41 42
IL18/IL18R -0.013 0.16 -10000 0 -0.34 85 85
macrophage activation -0.007 0.02 -10000 0 -0.044 57 57
TNF -0.13 0.48 -10000 0 -1.1 71 71
STAT3/STAT4 -0.12 0.5 -10000 0 -1.1 71 71
STAT4 (dimer) -0.14 0.51 -10000 0 -1.2 72 72
IL18 -0.002 0.12 -10000 0 -0.43 33 33
IL19 -0.076 0.46 -10000 0 -1.1 57 57
STAT5A (dimer) -0.12 0.5 -10000 0 -1.2 68 68
STAT1 0.018 0.079 -10000 0 -0.43 15 15
SOCS3 0.028 0.047 -10000 0 -0.43 5 5
CXCL9 -0.2 0.58 -10000 0 -1.2 106 106
MPO -0.091 0.45 -10000 0 -1.1 58 58
positive regulation of humoral immune response -0.13 0.52 -10000 0 -1.2 68 68
IL23/IL23R/JAK2/TYK2 -0.15 0.56 -10000 0 -1.3 68 68
IL6 -0.17 0.56 -10000 0 -1.2 90 90
STAT5A 0.031 0.036 -10000 0 -0.43 3 3
IL2 0.029 0.04 -10000 0 -0.43 3 3
positive regulation of tyrosine phosphorylation of STAT protein 0 0.012 0.081 7 -10000 0 7
CD3E -0.1 0.45 -10000 0 -1.1 62 62
keratinocyte proliferation -0.13 0.52 -10000 0 -1.2 68 68
NOS2 -0.11 0.45 -10000 0 -1 68 68
Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization -0.014 0.085 -10000 0 -0.22 68 68
epithelial cell differentiation 0.024 0.096 -10000 0 -0.22 60 60
CYFIP2 -0.008 0.13 -10000 0 -0.43 45 45
ENAH -0.023 0.084 0.26 5 -0.31 8 13
EGFR -0.016 0.14 -10000 0 -0.43 48 48
EPHA2 0.032 0.03 -10000 0 -0.43 2 2
MYO6 -0.036 0.083 0.2 11 -0.22 69 80
CTNNB1 0.022 0.071 -10000 0 -0.43 12 12
ABI1/Sra1/Nap1 0.038 0.092 -10000 0 -0.26 41 41
AQP5 -0.094 0.18 0.33 1 -0.46 83 84
CTNND1 0.033 0.022 -10000 0 -0.43 1 1
mol:PI-4-5-P2 -0.032 0.076 0.2 10 -0.22 58 68
regulation of calcium-dependent cell-cell adhesion -0.031 0.075 0.27 2 -0.21 49 51
EGF -0.07 0.19 -10000 0 -0.43 108 108
NCKAP1 0.034 0.021 -10000 0 -0.43 1 1
AQP3 -0.092 0.17 -10000 0 -0.45 83 83
cortical microtubule organization 0.024 0.096 -10000 0 -0.22 60 60
GO:0000145 -0.032 0.071 0.18 10 -0.21 58 68
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.029 0.1 -10000 0 -0.22 60 60
MLLT4 0.024 0.059 -10000 0 -0.43 8 8
ARF6/GDP -0.042 0.071 -10000 0 -0.37 7 7
ARF6 0.033 0.03 -10000 0 -0.43 2 2
Ephrin A1/EPHA2/NCK1/GIT1 0.052 0.07 -10000 0 -0.24 18 18
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.027 0.1 0.24 3 -0.37 17 20
PVRL2 0.025 0.065 -10000 0 -0.43 10 10
ZYX -0.034 0.081 0.2 11 -0.22 66 77
ARF6/GTP 0.057 0.076 -10000 0 -0.25 18 18
CDH1 -0.014 0.13 -10000 0 -0.43 47 47
EGFR/EGFR/EGF/EGF -0.058 0.14 -10000 0 -0.23 188 188
RhoA/GDP 0.021 0.1 -10000 0 -0.22 67 67
actin cytoskeleton organization -0.039 0.079 0.19 8 -0.22 72 80
IGF-1R heterotetramer -0.046 0.17 -10000 0 -0.43 85 85
GIT1 0.032 0.023 -10000 0 -0.43 1 1
IGF1R -0.046 0.17 -10000 0 -0.43 85 85
IGF1 -0.041 0.17 -10000 0 -0.43 78 78
DIAPH1 -0.002 0.2 -10000 0 -0.59 37 37
Wnt receptor signaling pathway -0.024 0.096 0.22 60 -10000 0 60
RHOA 0.025 0.062 -10000 0 -0.43 9 9
RhoA/GTP -0.044 0.072 -10000 0 -0.35 8 8
CTNNA1 0.034 0.006 -10000 0 -10000 0 0
VCL -0.04 0.081 0.2 6 -0.22 72 78
EFNA1 0.013 0.082 -10000 0 -0.43 16 16
LPP -0.038 0.078 0.19 11 -0.39 2 13
Ephrin A1/EPHA2 0.008 0.096 -10000 0 -0.23 61 61
SEC6/SEC8 -0.047 0.07 -10000 0 -0.22 61 61
MGAT3 -0.032 0.076 0.36 1 -0.22 49 50
HGF/MET 0.014 0.096 -10000 0 -0.21 68 68
HGF 0.027 0.058 -10000 0 -0.43 8 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.014 0.086 -10000 0 -0.22 68 68
actin cable formation 0.016 0.11 0.23 50 -0.32 8 58
KIAA1543 -0.036 0.075 0.19 9 -0.22 55 64
KIFC3 -0.032 0.074 0.2 9 -0.22 53 62
NCK1 0.033 0.022 -10000 0 -0.43 1 1
EXOC3 0.033 0.008 -10000 0 -10000 0 0
ACTN1 -0.034 0.08 0.2 11 -0.22 61 72
NCK1/GIT1 0.046 0.022 -10000 0 -0.31 1 1
mol:GDP 0.024 0.096 -10000 0 -0.22 60 60
EXOC4 0.034 0.006 -10000 0 -10000 0 0
STX4 -0.035 0.066 -10000 0 -0.21 60 60
PIP5K1C -0.032 0.077 0.2 10 -0.22 58 68
LIMA1 0 0 -10000 0 -10000 0 0
ABI1 0.034 0.007 -10000 0 -10000 0 0
ROCK1 -0.005 0.11 0.3 10 -0.33 7 17
adherens junction assembly -0.049 0.13 0.31 3 -0.51 20 23
IGF-1R heterotetramer/IGF1 -0.059 0.15 -10000 0 -0.25 175 175
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.034 0.066 -10000 0 -0.3 17 17
MET 0.03 0.037 -10000 0 -0.43 3 3
PLEKHA7 -0.032 0.076 0.27 2 -0.22 54 56
mol:GTP 0.05 0.068 -10000 0 -0.24 18 18
establishment of epithelial cell apical/basal polarity -0.038 0.079 0.15 4 -0.34 4 8
cortical actin cytoskeleton stabilization -0.014 0.085 -10000 0 -0.22 68 68
regulation of cell-cell adhesion -0.039 0.079 0.19 8 -0.22 72 80
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.014 0.086 -10000 0 -0.22 68 68
IL27-mediated signaling events

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
TGFB1 0.034 0.005 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.1 0.25 0.63 65 -0.54 2 67
IL27/IL27R/JAK1 -0.093 0.34 0.89 2 -1.1 39 41
TBX21 -0.1 0.3 0.64 17 -0.58 98 115
IL12B 0.025 0.052 -10000 0 -0.43 6 6
IL12A 0.003 0.032 -10000 0 -0.3 5 5
IL6ST -0.055 0.17 -10000 0 -0.42 90 90
IL27RA/JAK1 -0.065 0.33 0.45 2 -1.2 35 37
IL27 -0.04 0.17 -10000 0 -0.43 74 74
TYK2 0.028 0.028 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.014 0.087 0.2 11 -0.25 53 64
T-helper 2 cell differentiation 0.1 0.25 0.63 65 -0.54 2 67
T cell proliferation during immune response 0.1 0.25 0.63 65 -0.54 2 67
MAPKKK cascade -0.1 0.25 0.54 2 -0.63 65 67
STAT3 0.032 0.03 -10000 0 -0.43 2 2
STAT2 0.035 0.004 -10000 0 -10000 0 0
STAT1 0.019 0.081 -10000 0 -0.43 15 15
IL12RB1 0.034 0.005 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.09 0.28 0.66 14 -0.6 76 90
IL27/IL27R/JAK2/TYK2 -0.1 0.25 0.54 2 -0.65 65 67
positive regulation of T cell mediated cytotoxicity -0.1 0.25 0.54 2 -0.63 65 67
STAT1 (dimer) -0.11 0.39 0.56 30 -0.92 64 94
JAK2 0.023 0.038 -10000 0 -0.44 2 2
JAK1 0.034 0.038 -10000 0 -0.43 3 3
STAT2 (dimer) -0.089 0.25 0.48 2 -0.62 64 66
T cell proliferation -0.11 0.25 0.5 2 -0.62 73 75
IL12/IL12R/TYK2/JAK2 -0.007 0.21 -10000 0 -0.9 20 20
IL17A -0.014 0.086 0.2 10 -0.25 53 63
mast cell activation 0.1 0.25 0.63 65 -0.54 2 67
IFNG -0.01 0.05 0.14 5 -0.12 51 56
T cell differentiation -0.005 0.01 0.027 7 -0.024 78 85
STAT3 (dimer) -0.088 0.24 0.48 2 -0.62 63 65
STAT5A (dimer) -0.089 0.25 0.48 2 -0.63 63 65
STAT4 (dimer) -0.1 0.26 0.48 2 -0.61 75 77
STAT4 0.006 0.11 -10000 0 -0.43 30 30
T cell activation -0.002 0.032 0.12 31 -10000 0 31
IL27R/JAK2/TYK2 -0.082 0.31 -10000 0 -1.1 36 36
GATA3 -0.22 0.53 0.78 8 -1.3 97 105
IL18 -0.014 0.077 -10000 0 -0.3 33 33
positive regulation of mast cell cytokine production -0.085 0.24 0.48 2 -0.6 63 65
IL27/EBI3 -0.013 0.13 0.23 4 -0.31 77 81
IL27RA -0.092 0.33 -10000 0 -1.3 35 35
IL6 -0.02 0.14 -10000 0 -0.43 52 52
STAT5A 0.031 0.036 -10000 0 -0.43 3 3
monocyte differentiation 0 0.002 -10000 0 -10000 0 0
IL2 0.023 0.16 0.47 35 -1.2 3 38
IL1B -0.017 0.084 -10000 0 -0.3 40 40
EBI3 0.024 0.053 -10000 0 -0.44 5 5
TNF 0.002 0.042 -10000 0 -0.3 9 9
IL6-mediated signaling events

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
BCL2L1 -0.081 0.28 -10000 0 -0.78 38 38
CRP -0.058 0.29 0.53 1 -0.75 43 44
cell cycle arrest -0.11 0.33 -10000 0 -0.78 70 70
TIMP1 -0.078 0.3 -10000 0 -0.78 53 53
IL6ST -0.053 0.18 -10000 0 -0.43 91 91
Rac1/GDP -0.052 0.19 0.27 1 -0.42 66 67
AP1 0.007 0.17 -10000 0 -0.48 22 22
GAB2 0.032 0.014 -10000 0 -10000 0 0
TNFSF11 -0.15 0.4 -10000 0 -0.99 77 77
HSP90B1 -0.005 0.12 -10000 0 -0.9 7 7
GAB1 0.027 0.062 -10000 0 -0.43 9 9
MAPK14 -0.054 0.17 -10000 0 -0.5 37 37
AKT1 0.031 0.075 -10000 0 -0.52 2 2
FOXO1 0.036 0.074 -10000 0 -0.5 2 2
MAP2K6 -0.057 0.17 0.24 1 -0.4 62 63
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.06 0.2 -10000 0 -0.46 71 71
MITF -0.059 0.17 -10000 0 -0.39 73 73
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.035 0.005 -10000 0 -10000 0 0
A2M -0.054 0.32 -10000 0 -1.3 31 31
CEBPB 0.026 0.051 -10000 0 -0.43 6 6
GRB2/SOS1/GAB family/SHP2 0.005 0.11 0.3 1 -0.43 14 15
STAT3 -0.12 0.37 -10000 0 -0.86 70 70
STAT1 -0.012 0.17 -10000 0 -0.87 17 17
CEBPD -0.11 0.37 -10000 0 -0.94 62 62
PIK3CA 0.033 0.023 -10000 0 -0.43 1 1
PI3K 0.035 0.067 -10000 0 -0.31 17 17
JUN -0.003 0.12 -10000 0 -0.43 39 39
PIAS3/MITF -0.046 0.16 -10000 0 -0.4 57 57
MAPK11 -0.053 0.16 -10000 0 -0.51 36 36
STAT3 (dimer)/FOXO1 -0.066 0.27 -10000 0 -0.66 50 50
GRB2/SOS1/GAB family -0.02 0.17 0.29 1 -0.44 36 37
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.065 0.17 -10000 0 -0.38 78 78
GRB2 0.034 0.01 -10000 0 -10000 0 0
JAK2 0.03 0.031 -10000 0 -0.43 2 2
LBP -0.039 0.23 -10000 0 -0.62 34 34
PIK3R1 0.018 0.084 -10000 0 -0.43 17 17
JAK1 0.031 0.039 -10000 0 -0.43 3 3
MYC -0.078 0.36 0.53 1 -0.92 57 58
FGG -0.087 0.28 -10000 0 -0.77 43 43
macrophage differentiation -0.11 0.33 -10000 0 -0.78 70 70
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.029 0.15 -10000 0 -0.26 133 133
JUNB -0.086 0.28 -10000 0 -0.75 43 43
FOS -0.033 0.16 -10000 0 -0.43 66 66
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.064 0.17 0.25 1 -0.4 74 75
STAT1/PIAS1 -0.047 0.19 -10000 0 -0.42 67 67
GRB2/SOS1/GAB family/SHP2/PI3K 0.032 0.074 -10000 0 -0.39 4 4
STAT3 (dimer) -0.12 0.36 -10000 0 -0.84 70 70
PRKCD -0.067 0.24 0.5 1 -0.55 66 67
IL6R 0.021 0.057 -10000 0 -0.43 7 7
SOCS3 -0.051 0.2 -10000 0 -0.71 22 22
gp130 (dimer)/JAK1/JAK1/LMO4 -0.031 0.15 -10000 0 -0.26 140 140
Rac1/GTP -0.055 0.2 -10000 0 -0.44 70 70
HCK 0.017 0.086 -10000 0 -0.43 18 18
MAPKKK cascade 0.021 0.13 -10000 0 -0.54 13 13
bone resorption -0.14 0.37 -10000 0 -0.9 79 79
IRF1 -0.1 0.31 -10000 0 -0.87 47 47
mol:GDP -0.061 0.18 0.23 1 -0.4 75 76
SOS1 0.035 0.022 -10000 0 -0.43 1 1
VAV1 -0.062 0.18 0.23 1 -0.4 75 76
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.049 0.19 -10000 0 -0.51 43 43
PTPN11 0.016 0.089 -10000 0 -1 3 3
IL6/IL6RA 0 0.1 -10000 0 -0.31 46 46
gp130 (dimer)/TYK2/TYK2/LMO4 -0.027 0.14 -10000 0 -0.26 136 136
gp130 (dimer)/JAK2/JAK2/LMO4 -0.029 0.14 -10000 0 -0.26 133 133
IL6 -0.023 0.14 -10000 0 -0.43 52 52
PIAS3 0.03 0.012 -10000 0 -10000 0 0
PTPRE 0.019 0.071 -10000 0 -0.42 12 12
PIAS1 0.034 0.007 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.057 0.13 0.23 1 -0.31 70 71
LMO4 -0.019 0.14 -10000 0 -0.43 52 52
STAT3 (dimer)/PIAS3 -0.1 0.32 -10000 0 -0.8 62 62
MCL1 0.067 0.11 0.43 1 -0.79 2 3
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.015 0.03 -10000 0 -0.25 5 5
ARNO/beta Arrestin1-2 0.011 0.071 -10000 0 -0.2 42 42
EGFR -0.016 0.14 -10000 0 -0.43 48 48
EPHA2 0.032 0.03 -10000 0 -0.43 2 2
USP6 0.031 0.011 -10000 0 -10000 0 0
IQSEC1 0.033 0.022 -10000 0 -0.43 1 1
EGFR/EGFR/EGF/EGF -0.067 0.16 -10000 0 -0.31 149 149
ARRB2 0.011 0.041 -10000 0 -0.29 9 9
mol:GTP 0.011 0.027 0.11 23 -0.15 1 24
ARRB1 0.026 0.051 -10000 0 -0.43 6 6
FBXO8 0.034 0.007 -10000 0 -10000 0 0
TSHR 0.028 0.051 -10000 0 -0.43 6 6
EGF -0.07 0.19 -10000 0 -0.43 108 108
somatostatin receptor activity 0 0 0 3 -0.001 75 78
ARAP2 0 0 0 4 0 75 79
mol:GDP -0.031 0.1 0.15 2 -0.24 69 71
mol:PI-3-4-5-P3 0 0 0 4 -0.001 76 80
ITGA2B 0.034 0.008 -10000 0 -10000 0 0
ARF6 0.032 0.03 -10000 0 -0.43 2 2
Ephrin A1/EPHA2/NCK1/GIT1 0.052 0.07 -10000 0 -0.24 18 18
ADAP1 0 0 0 4 0 51 55
KIF13B 0.023 0.048 -10000 0 -0.43 5 5
HGF/MET 0.04 0.054 -10000 0 -0.3 11 11
PXN 0.035 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.034 0.1 0.17 3 -0.24 75 78
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.04 0.15 -10000 0 -0.26 149 149
ADRB2 0.001 0.12 -10000 0 -0.43 33 33
receptor agonist activity 0 0 0 4 0 68 72
actin filament binding 0 0 0 3 0 77 80
SRC 0.031 0.03 -10000 0 -0.43 2 2
ITGB3 0.029 0.042 -10000 0 -0.43 4 4
GNAQ 0 0 0.001 7 -0.001 56 63
EFA6/PI-4-5-P2 0 0 0.001 6 -0.001 54 60
ARF6/GDP 0.007 0.075 0.18 3 -0.3 10 13
ARF6/GDP/GULP/ACAP1 -0.02 0.12 -10000 0 -0.27 74 74
alphaIIb/beta3 Integrin/paxillin/GIT1 0.077 0.041 -10000 0 -0.24 4 4
ACAP1 0 0 0 1 0 5 6
ACAP2 0 0 0 4 0 79 83
LHCGR/beta Arrestin2 0.018 0.06 -10000 0 -0.39 9 9
EFNA1 0.013 0.082 -10000 0 -0.43 16 16
HGF 0.027 0.058 -10000 0 -0.43 8 8
CYTH3 0 0 0.001 4 -0.001 74 78
CYTH2 -0.001 0.002 -10000 0 -0.004 79 79
NCK1 0.033 0.022 -10000 0 -0.43 1 1
fibronectin binding 0 0 0 5 0 54 59
endosomal lumen acidification 0 0 0 4 0 61 65
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.001 0.12 -10000 0 -0.43 38 38
GNAQ/ARNO -0.001 0.003 0.007 7 -0.006 55 62
mol:Phosphatidic acid 0 0 0 4 0 79 83
PIP3-E 0.027 0.042 -10000 0 -0.43 4 4
MET 0.03 0.037 -10000 0 -0.43 3 3
GNA14 -0.012 0.13 -10000 0 -0.43 44 44
GNA15 0.029 0.047 -10000 0 -0.43 5 5
GIT1 0.032 0.023 -10000 0 -0.43 1 1
mol:PI-4-5-P2 0 0 0.001 3 -0.001 62 65
GNA11 0.031 0.036 -10000 0 -0.43 3 3
LHCGR 0.026 0.062 -10000 0 -0.43 9 9
AGTR1 -0.05 0.17 -10000 0 -0.43 82 82
desensitization of G-protein coupled receptor protein signaling pathway 0.018 0.06 -10000 0 -0.39 9 9
IPCEF1/ARNO -0.029 0.12 -10000 0 -0.2 148 148
alphaIIb/beta3 Integrin 0.044 0.035 -10000 0 -0.31 4 4
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.028 0.07 -10000 0 -0.21 33 33
NF kappa B1 p50/RelA/I kappa B alpha 0.017 0.096 0.26 6 -0.27 17 23
AP1 -0.04 0.12 -10000 0 -0.26 101 101
mol:PIP3 -0.033 0.092 -10000 0 -0.22 88 88
AKT1 -0.004 0.1 0.27 4 -0.3 25 29
PTK2B -0.039 0.1 0.13 1 -0.22 102 103
RHOA -0.017 0.1 -10000 0 -0.33 33 33
PIK3CB 0.03 0.046 -10000 0 -0.43 5 5
mol:Ca2+ -0.014 0.091 0.19 35 -0.21 55 90
MAGI3 0.011 0.1 -10000 0 -0.43 25 25
RELA 0.034 0.005 -10000 0 -10000 0 0
apoptosis 0.003 0.054 -10000 0 -0.18 38 38
HRAS/GDP 0.023 0.026 -10000 0 -0.3 3 3
positive regulation of microtubule depolymerization -0.073 0.12 0.18 5 -0.24 124 129
NF kappa B1 p50/RelA -0.023 0.087 -10000 0 -0.28 25 25
endothelial cell migration -0.011 0.12 -10000 0 -0.52 28 28
ADCY4 -0.019 0.094 -10000 0 -0.29 44 44
ADCY5 -0.019 0.092 -10000 0 -0.29 40 40
ADCY6 -0.016 0.087 -10000 0 -0.27 41 41
ADCY7 -0.017 0.094 -10000 0 -0.29 40 40
ADCY1 -0.016 0.089 -10000 0 -0.28 42 42
ADCY2 -0.029 0.11 -10000 0 -0.32 46 46
ADCY3 -0.018 0.089 -10000 0 -0.26 46 46
ADCY8 -0.015 0.08 -10000 0 -0.27 36 36
ADCY9 -0.018 0.086 -10000 0 -0.25 48 48
GSK3B -0.039 0.095 0.17 2 -0.22 87 89
arachidonic acid secretion -0.018 0.094 -10000 0 -0.28 47 47
GNG2 0.034 0.021 -10000 0 -0.43 1 1
TRIP6 0.008 0.071 -10000 0 -0.36 17 17
GNAO1 0.005 0.057 -10000 0 -0.23 28 28
HRAS 0.031 0.037 -10000 0 -0.43 3 3
NFKBIA -0.012 0.091 0.19 21 -0.25 25 46
GAB1 0.026 0.062 -10000 0 -0.43 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.021 0.2 -10000 0 -0.91 21 21
JUN -0.003 0.12 -10000 0 -0.43 39 39
LPA/LPA2/NHERF2 -0.006 0.08 -10000 0 -0.21 58 58
TIAM1 -0.002 0.23 -10000 0 -1.1 21 21
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
mol:IP3 -0.011 0.091 0.19 35 -0.21 52 87
PLCB3 0.005 0.091 0.19 37 -0.24 44 81
FOS -0.033 0.16 -10000 0 -0.43 66 66
positive regulation of mitosis -0.018 0.094 -10000 0 -0.28 47 47
LPA/LPA1-2-3 -0.007 0.051 -10000 0 -0.17 41 41
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.03 0.013 -10000 0 -10000 0 0
stress fiber formation -0.005 0.077 -10000 0 -0.26 19 19
GNAZ -0.002 0.074 -10000 0 -0.22 48 48
EGFR/PI3K-beta/Gab1 -0.025 0.099 -10000 0 -0.23 89 89
positive regulation of dendritic cell cytokine production -0.007 0.05 -10000 0 -0.17 41 41
LPA/LPA2/MAGI-3 0.004 0.066 -10000 0 -0.17 51 51
ARHGEF1 0.023 0.071 0.19 39 -0.21 21 60
GNAI2 0 0.072 -10000 0 -0.22 45 45
GNAI3 0.005 0.059 -10000 0 -0.2 38 38
GNAI1 -0.007 0.084 -10000 0 -0.24 54 54
LPA/LPA3 -0.005 0.025 -10000 0 -0.088 41 41
LPA/LPA2 -0.004 0.025 -10000 0 -0.087 41 41
LPA/LPA1 -0.01 0.067 -10000 0 -0.23 41 41
HB-EGF/EGFR -0.028 0.12 -10000 0 -0.29 89 89
HBEGF -0.021 0.1 -10000 0 -0.31 55 55
mol:DAG -0.011 0.091 0.19 35 -0.21 52 87
cAMP biosynthetic process -0.024 0.093 0.22 1 -0.27 46 47
NFKB1 0.034 0.021 -10000 0 -0.43 1 1
SRC 0.031 0.03 -10000 0 -0.43 2 2
GNB1 0.03 0.042 -10000 0 -0.43 4 4
LYN 0.002 0.095 0.24 23 -0.24 20 43
GNAQ -0.004 0.02 -10000 0 -0.071 41 41
LPAR2 0 0.001 -10000 0 -10000 0 0
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 -0.008 0.04 -10000 0 -0.14 41 41
IL8 -0.073 0.18 0.27 1 -0.43 82 83
PTK2 0.01 0.046 -10000 0 -0.17 28 28
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
CASP3 0.003 0.054 -10000 0 -0.18 38 38
EGFR -0.016 0.14 -10000 0 -0.43 48 48
PLCG1 -0.003 0.043 -10000 0 -0.12 48 48
PLD2 0.009 0.054 -10000 0 -0.17 39 39
G12/G13 0.031 0.062 -10000 0 -0.22 22 22
PI3K-beta -0.019 0.098 -10000 0 -0.33 26 26
cell migration 0.01 0.068 -10000 0 -0.26 21 21
SLC9A3R2 -0.006 0.13 -10000 0 -0.43 41 41
PXN -0.005 0.078 -10000 0 -0.27 18 18
HRAS/GTP -0.019 0.096 -10000 0 -0.28 47 47
RAC1 0.034 0.006 -10000 0 -10000 0 0
MMP9 -0.015 0.14 -10000 0 -0.43 52 52
PRKCE 0.029 0.051 -10000 0 -0.43 6 6
PRKCD -0.014 0.089 0.18 35 -0.22 42 77
Gi(beta/gamma) -0.012 0.094 -10000 0 -0.28 42 42
mol:LPA -0.008 0.04 -10000 0 -0.14 41 41
TRIP6/p130 Cas/FAK1/Paxillin 0.011 0.081 -10000 0 -0.27 20 20
MAPKKK cascade -0.018 0.094 -10000 0 -0.28 47 47
contractile ring contraction involved in cytokinesis -0.017 0.1 -10000 0 -0.33 34 34
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.015 0.076 -10000 0 -0.21 58 58
GNA15 0.006 0.036 -10000 0 -0.28 5 5
GNA12 0.034 0.006 -10000 0 -10000 0 0
GNA13 0.029 0.037 -10000 0 -0.43 3 3
MAPT -0.075 0.12 0.18 5 -0.25 124 129
GNA11 0.008 0.03 -10000 0 -0.099 27 27
Rac1/GTP 0.021 0.21 -10000 0 -0.98 21 21
MMP2 -0.011 0.12 -10000 0 -0.52 28 28
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.017 0.082 -10000 0 -0.43 16 16
EPHB2 0.032 0.031 -10000 0 -0.43 2 2
EFNB1 0.015 0.029 -10000 0 -0.3 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.068 0.065 -10000 0 -0.23 17 17
Ephrin B2/EPHB1-2 0.041 0.068 -10000 0 -0.24 23 23
neuron projection morphogenesis 0.045 0.056 -10000 0 -0.22 17 17
Ephrin B1/EPHB1-2/Tiam1 0.06 0.064 -10000 0 -0.25 17 17
DNM1 0.033 0.036 -10000 0 -0.43 3 3
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.084 0.21 -10000 0 -0.56 80 80
YES1 -0.11 0.3 -10000 0 -0.8 81 81
Ephrin B1/EPHB1-2/NCK2 0.065 0.051 -10000 0 -0.22 12 12
PI3K -0.053 0.23 -10000 0 -0.56 80 80
mol:GDP 0.057 0.063 -10000 0 -0.24 17 17
ITGA2B 0.034 0.008 -10000 0 -10000 0 0
endothelial cell proliferation 0.019 0.081 -10000 0 -0.27 34 34
FYN -0.11 0.3 -10000 0 -0.8 81 81
MAP3K7 -0.087 0.22 -10000 0 -0.59 80 80
FGR -0.1 0.3 -10000 0 -0.78 81 81
TIAM1 0.027 0.058 -10000 0 -0.43 8 8
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
RGS3 0.035 0.004 -10000 0 -10000 0 0
cell adhesion -0.059 0.21 -10000 0 -0.53 79 79
LYN -0.11 0.3 -10000 0 -0.78 81 81
Ephrin B1/EPHB1-2/Src Family Kinases -0.11 0.28 -10000 0 -0.74 81 81
Ephrin B1/EPHB1-2 -0.09 0.24 -10000 0 -0.64 78 78
SRC -0.1 0.3 -10000 0 -0.78 81 81
ITGB3 0.029 0.042 -10000 0 -0.43 4 4
EPHB1 0.026 0.051 -10000 0 -0.43 6 6
EPHB4 0.015 0.091 -10000 0 -0.43 20 20
RAC1 0.034 0.006 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.02 0.082 -10000 0 -0.27 34 34
alphaIIb/beta3 Integrin 0.044 0.035 -10000 0 -0.31 4 4
BLK -0.12 0.3 -10000 0 -0.8 81 81
HCK -0.11 0.3 -10000 0 -0.79 81 81
regulation of stress fiber formation -0.062 0.05 0.22 12 -10000 0 12
MAPK8 -0.083 0.2 -10000 0 -0.54 80 80
Ephrin B1/EPHB1-2/RGS3 0.065 0.051 -10000 0 -0.22 12 12
endothelial cell migration -0.085 0.2 -10000 0 -0.51 79 79
NCK2 0.035 0.005 -10000 0 -10000 0 0
PTPN13 -0.049 0.2 -10000 0 -0.54 72 72
regulation of focal adhesion formation -0.062 0.05 0.22 12 -10000 0 12
chemotaxis -0.062 0.05 0.22 12 -10000 0 12
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
Rac1/GTP 0.058 0.061 -10000 0 -0.23 17 17
angiogenesis -0.092 0.24 -10000 0 -0.63 81 81
LCK -0.12 0.3 -10000 0 -0.8 81 81
E-cadherin 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
E-cadherin/beta catenin-gamma catenin 0.014 0.11 -9999 0 -0.26 61 61
E-cadherin/beta catenin 0 0.11 -9999 0 -0.31 59 59
CTNNB1 0.022 0.071 -9999 0 -0.43 12 12
JUP 0.031 0.036 -9999 0 -0.43 3 3
CDH1 -0.014 0.13 -9999 0 -0.43 47 47
PLK2 and PLK4 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
PLK2 -0.009 0.13 -9999 0 -0.43 44 44
PLK4 0.029 0.051 -9999 0 -0.43 6 6
regulation of centriole replication -0.016 0.096 -9999 0 -0.31 50 50
TCGA08_p53

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
CDKN2A -0.001 0.049 -10000 0 -0.3 13 13
TP53 -0.024 0.093 0.26 2 -0.26 56 58
Senescence -0.03 0.099 0.26 2 -0.26 69 71
Apoptosis -0.03 0.099 0.26 2 -0.26 69 71
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.003 0.058 0.26 22 -10000 0 22
MDM4 0.026 0.032 -10000 0 -0.43 2 2
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.016 0.037 -10000 0 -0.26 11 11
SNTA1 0.03 0.042 -10000 0 -0.43 4 4
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.021 0.051 -10000 0 -0.26 22 22
MAPK12 0 0.078 0.21 29 -0.22 34 63
CCND1 -0.06 0.16 -10000 0 -0.42 84 84
p38 gamma/SNTA1 0.021 0.083 0.29 2 -0.22 35 37
MAP2K3 0.031 0.023 -10000 0 -0.43 1 1
PKN1 0.033 0.03 -10000 0 -0.43 2 2
G2/M transition checkpoint 0.001 0.079 0.21 32 -0.22 34 66
MAP2K6 0.008 0.091 0.24 35 -0.24 35 70
MAPT -0.057 0.13 0.29 3 -0.29 105 108
MAPK13 0.006 0.053 -10000 0 -0.31 14 14
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.005 0.062 -10000 0 -0.29 21 21
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.011 0.12 -10000 0 -0.55 5 5
UGCG -0.091 0.27 -10000 0 -0.73 71 71
AKT1/mTOR/p70S6K/Hsp90/TERT -0.064 0.19 -10000 0 -0.37 101 101
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.09 0.26 -10000 0 -0.72 72 72
mol:DAG -0.006 0.028 0.17 12 -10000 0 12
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.082 0.23 -10000 0 -0.44 111 111
FRAP1 -0.1 0.26 -10000 0 -0.52 111 111
FOXO3 -0.052 0.2 -10000 0 -0.52 48 48
AKT1 -0.058 0.22 -10000 0 -0.56 48 48
GAB2 0.028 0.014 -10000 0 -10000 0 0
SMPD1 -0.005 0.13 -10000 0 -0.71 15 15
SGMS1 -0.005 0.035 -10000 0 -0.079 46 46
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 0.049 -10000 0 -0.26 17 17
CALM1 0.035 0.005 -10000 0 -10000 0 0
cell proliferation -0.044 0.18 0.23 5 -0.36 96 101
EIF3A 0 0 -10000 0 -10000 0 0
PI3K 0.032 0.067 -10000 0 -0.31 17 17
RPS6KB1 -0.033 0.12 -10000 0 -0.67 6 6
mol:sphingomyelin -0.006 0.028 0.17 12 -10000 0 12
natural killer cell activation -0.002 0.004 -10000 0 -0.013 28 28
JAK3 0.034 0.008 -10000 0 -10000 0 0
PIK3R1 0.016 0.084 -10000 0 -0.43 17 17
JAK1 0.031 0.037 -10000 0 -0.43 3 3
NFKB1 0.034 0.021 -10000 0 -0.43 1 1
MYC -0.031 0.29 0.41 1 -0.93 35 36
MYB -0.23 0.5 -10000 0 -1.2 105 105
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.024 0.15 -10000 0 -0.39 41 41
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.018 0.12 -10000 0 -0.55 8 8
mol:PI-3-4-5-P3 -0.023 0.15 -10000 0 -0.38 41 41
Rac1/GDP 0.008 0.052 -10000 0 -0.24 17 17
T cell proliferation -0.021 0.14 0.25 2 -0.36 39 41
SHC1 0.025 0.026 -10000 0 -0.43 1 1
RAC1 0.034 0.006 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.01 0.028 -10000 0 -0.066 103 103
PRKCZ -0.023 0.14 0.25 1 -0.37 39 40
NF kappa B1 p50/RelA -0.073 0.24 -10000 0 -0.46 99 99
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.014 0.13 -10000 0 -0.42 33 33
HSP90AA1 0 0 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
IL2RA 0.001 0.11 -10000 0 -0.43 31 31
IL2RB 0.01 0.097 -10000 0 -0.43 23 23
TERT 0.031 0.03 -10000 0 -0.43 2 2
E2F1 -0.072 0.2 -10000 0 -0.43 112 112
SOS1 0.031 0.023 -10000 0 -0.44 1 1
RPS6 0.032 0.03 -10000 0 -0.43 2 2
mol:cAMP 0.005 0.014 0.031 103 -10000 0 103
PTPN11 0.031 0.012 -10000 0 -10000 0 0
IL2RG 0.028 0.043 -10000 0 -0.43 4 4
actin cytoskeleton organization -0.021 0.14 0.25 2 -0.36 39 41
GRB2 0.03 0.012 -10000 0 -10000 0 0
IL2 0.029 0.038 -10000 0 -0.43 3 3
PIK3CA 0.03 0.025 -10000 0 -0.43 1 1
Rac1/GTP 0.032 0.064 -10000 0 -0.22 17 17
LCK -0.021 0.14 -10000 0 -0.43 54 54
BCL2 -0.18 0.38 0.4 1 -0.82 119 120
Canonical Wnt signaling pathway

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
HDAC1 0.052 0.052 0.23 21 -0.43 1 22
AES 0.05 0.041 0.21 18 -10000 0 18
FBXW11 0.032 0.03 -10000 0 -0.43 2 2
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.039 0.056 -10000 0 -0.31 12 12
SMAD4 0.027 0.055 -10000 0 -0.43 7 7
DKK2 0.005 0.11 -10000 0 -0.43 31 31
TLE1 0.019 0.12 0.2 19 -0.43 32 51
MACF1 0.034 0.022 -10000 0 -0.43 1 1
CTNNB1 0 0.11 0.28 6 -0.37 14 20
WIF1 0.029 0.014 -10000 0 -10000 0 0
beta catenin/RanBP3 0.071 0.2 0.4 115 -0.38 7 122
KREMEN2 -0.095 0.2 -10000 0 -0.43 131 131
DKK1 -0.029 0.15 -10000 0 -0.43 59 59
beta catenin/beta TrCP1 0.012 0.11 0.29 5 -0.37 13 18
FZD1 0.027 0.058 -10000 0 -0.43 8 8
AXIN2 -0.061 0.38 0.61 39 -1.2 34 73
AXIN1 0.032 0.01 -10000 0 -10000 0 0
RAN 0.035 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.035 0.094 -10000 0 -0.62 8 8
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.003 0.18 0.32 7 -0.55 31 38
Axin1/APC/GSK3 0.027 0.056 -10000 0 -0.31 4 4
Axin1/APC/GSK3/beta catenin/Macf1 0.014 0.081 -10000 0 -0.39 7 7
HNF1A 0.017 0.042 0.17 21 -10000 0 21
CTBP1 0.049 0.044 0.22 18 -10000 0 18
MYC 0.025 0.45 0.59 104 -1.3 35 139
RANBP3 0.035 0.007 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.051 0.15 -10000 0 -0.27 156 156
NKD1 0.027 0.038 -10000 0 -0.43 3 3
TCF4 0.028 0.1 0.21 19 -0.41 23 42
TCF3 0.047 0.052 0.22 15 -0.43 2 17
WNT1/LRP6/FZD1/Axin1 0.068 0.06 -10000 0 -0.24 12 12
Ran/GTP 0.027 0.005 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.082 0.27 0.51 106 -0.49 16 122
LEF1 0.034 0.085 0.21 18 -0.41 13 31
DVL1 0.028 0.053 -10000 0 -0.33 3 3
CSNK2A1 0.034 0.008 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.045 0.2 0.3 1 -0.55 43 44
DKK1/LRP6/Kremen 2 -0.069 0.16 -10000 0 -0.28 171 171
LRP6 0.029 0.047 -10000 0 -0.43 5 5
CSNK1A1 0.052 0.047 0.23 19 -10000 0 19
NLK 0.027 0.027 -10000 0 -0.44 1 1
CCND1 -0.14 0.62 0.58 86 -1.4 87 173
WNT1 0.034 0.021 -10000 0 -0.43 1 1
GSK3A 0.034 0.005 -10000 0 -10000 0 0
GSK3B 0.035 0.005 -10000 0 -10000 0 0
FRAT1 0.028 0.055 -10000 0 -0.43 7 7
PPP2R5D 0.03 0.056 0.25 2 -0.32 7 9
APC 0.002 0.076 0.19 49 -0.23 17 66
WNT1/LRP6/FZD1 0.023 0.05 -10000 0 -0.22 13 13
CREBBP 0.046 0.048 0.21 17 -0.43 1 18
Coregulation of Androgen receptor activity

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
NRIP1 -0.009 0.13 -9999 0 -0.43 46 46
SVIL 0.022 0.074 -9999 0 -0.43 13 13
ZNF318 0.032 0.005 -9999 0 -10000 0 0
JMJD2C 0.039 0.011 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 -0.04 0.13 -9999 0 -0.25 111 111
CARM1 0.034 0.021 -9999 0 -0.43 1 1
PRDX1 0.031 0.036 -9999 0 -0.43 3 3
PELP1 0.032 0.01 -9999 0 -10000 0 0
CTNNB1 0.023 0.071 -9999 0 -0.43 12 12
AKT1 0.031 0.036 -9999 0 -0.43 3 3
PTK2B 0.029 0.015 -9999 0 -10000 0 0
MED1 -0.001 0 -9999 0 -10000 0 0
MAK 0.024 0.047 -9999 0 -0.43 5 5
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.036 0.005 -9999 0 -10000 0 0
GSN 0.022 0.079 -9999 0 -0.43 15 15
NCOA2 0.025 0.047 -9999 0 -0.43 5 5
NCOA6 0.035 0.008 -9999 0 -10000 0 0
DNA-PK 0.054 0.034 -9999 0 -0.26 2 2
NCOA4 0.029 0.051 -9999 0 -0.43 6 6
PIAS3 0.031 0.012 -9999 0 -10000 0 0
cell proliferation -0.013 0.091 -9999 0 -0.58 10 10
XRCC5 0.034 0.004 -9999 0 -10000 0 0
UBE3A 0.034 0.022 -9999 0 -0.43 1 1
T-DHT/AR/SNURF -0.052 0.12 -9999 0 -0.17 206 206
FHL2 -0.11 0.31 -9999 0 -0.9 65 65
RANBP9 0.035 0.007 -9999 0 -10000 0 0
JMJD1A 0.01 0.071 -9999 0 -0.15 81 81
CDK6 0.024 0.059 -9999 0 -0.43 8 8
TGFB1I1 0.018 0.084 -9999 0 -0.43 17 17
T-DHT/AR/CyclinD1 -0.078 0.18 -9999 0 -0.34 135 135
XRCC6 0.032 0.009 -9999 0 -10000 0 0
T-DHT/AR -0.064 0.14 -9999 0 -0.22 209 209
CTDSP1 0.033 0.03 -9999 0 -0.43 2 2
CTDSP2 0.031 0.03 -9999 0 -0.43 2 2
BRCA1 0.024 0.071 -9999 0 -0.43 12 12
TCF4 0.012 0.097 -9999 0 -0.43 23 23
CDKN2A 0.015 0.074 -9999 0 -0.43 13 13
SRF 0.017 0.06 -9999 0 -0.15 36 36
NKX3-1 -0.047 0.1 -9999 0 -0.24 88 88
KLK3 0.019 0.054 -9999 0 -10000 0 0
TMF1 0.034 0.007 -9999 0 -10000 0 0
HNRNPA1 -0.001 0 -9999 0 -10000 0 0
AOF2 0.035 0.007 -9999 0 -10000 0 0
APPL1 0.005 0.024 -9999 0 -0.3 3 3
T-DHT/AR/Caspase 8 -0.04 0.13 -9999 0 -0.26 110 110
AR -0.079 0.18 -9999 0 -0.4 111 111
UBA3 0 0 -9999 0 -10000 0 0
PATZ1 -0.001 0 -9999 0 -10000 0 0
PAWR 0.023 0.074 -9999 0 -0.43 13 13
PRKDC 0.028 0.031 -9999 0 -0.43 2 2
PA2G4 0.034 0.004 -9999 0 -10000 0 0
UBE2I 0.032 0.01 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.033 0.12 -9999 0 -0.23 107 107
RPS6KA3 0.032 0.042 -9999 0 -0.43 4 4
T-DHT/AR/ARA70 -0.043 0.13 -9999 0 -0.26 116 116
LATS2 0.024 0.058 -9999 0 -0.43 8 8
T-DHT/AR/PRX1 -0.037 0.12 -9999 0 -0.23 112 112
Cyclin D3/CDK11 p58 0.025 0.004 -9999 0 -10000 0 0
VAV3 -0.042 0.17 -9999 0 -0.43 82 82
KLK2 -0.013 0.083 -9999 0 -0.38 13 13
CASP8 0.034 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.024 0.12 -9999 0 -0.23 99 99
TMPRSS2 -0.15 0.35 -9999 0 -0.9 88 88
CCND1 -0.046 0.17 -9999 0 -0.43 80 80
PIAS1 0.036 0.007 -9999 0 -10000 0 0
mol:T-DHT -0.013 0.03 -9999 0 -0.064 115 115
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.034 0.036 -9999 0 -0.43 3 3
T-DHT/AR/CDK6 -0.043 0.13 -9999 0 -0.25 118 118
CMTM2 0.029 0.024 -9999 0 -0.43 1 1
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 -0.013 0.03 -9999 0 -0.065 115 115
CCND3 0.034 0.006 -9999 0 -10000 0 0
TGIF1 -0.001 0 -9999 0 -10000 0 0
FKBP4 0.03 0.047 -9999 0 -0.43 5 5
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.058 0.29 -10000 0 -0.91 46 46
epithelial cell differentiation -0.04 0.24 -10000 0 -0.73 47 47
ITCH 0.033 0.038 -10000 0 -10000 0 0
WWP1 -0.095 0.39 -10000 0 -1.3 43 43
FYN 0.026 0.055 -10000 0 -0.43 7 7
EGFR -0.016 0.14 -10000 0 -0.43 48 48
PRL 0.033 0.022 -10000 0 -0.43 1 1
neuron projection morphogenesis -0.018 0.21 0.36 5 -0.63 43 48
PTPRZ1 0.022 0.062 -10000 0 -0.43 9 9
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.024 0.22 -10000 0 -0.7 43 43
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.061 0.25 -10000 0 -0.86 43 43
ADAM17 0.034 0.037 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.081 0.3 -10000 0 -0.97 46 46
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.059 0.29 -10000 0 -0.88 48 48
NCOR1 0.032 0.011 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.05 0.24 -10000 0 -0.81 43 43
GRIN2B -0.059 0.23 0.26 2 -0.75 43 45
ErbB4/ErbB2/betacellulin -0.066 0.26 -10000 0 -0.73 53 53
STAT1 0.018 0.079 -10000 0 -0.43 15 15
HBEGF 0.029 0.047 -10000 0 -0.43 5 5
PRLR -0.004 0.13 -10000 0 -0.43 41 41
E4ICDs/ETO2 -0.11 0.32 -10000 0 -0.85 61 61
axon guidance -0.067 0.28 -10000 0 -0.92 44 44
NEDD4 0.022 0.08 -10000 0 -0.41 13 13
Prolactin receptor/Prolactin receptor/Prolactin 0.02 0.097 -10000 0 -0.31 40 40
CBFA2T3 -0.053 0.17 -10000 0 -0.43 86 86
ErbB4/ErbB2/HBEGF -0.05 0.26 -10000 0 -0.77 49 49
MAPK3 -0.016 0.22 0.38 4 -0.65 43 47
STAT1 (dimer) -0.061 0.29 -10000 0 -0.89 47 47
MAPK1 -0.012 0.22 0.38 5 -0.66 43 48
JAK2 0.03 0.031 -10000 0 -0.43 2 2
ErbB4/ErbB2/neuregulin 1 beta -0.06 0.25 -10000 0 -0.76 49 49
NRG1 0.012 0.022 -10000 0 -10000 0 0
NRG3 0.027 0.055 -10000 0 -0.43 7 7
NRG2 0.023 0.062 -10000 0 -0.43 9 9
NRG4 0.033 0.022 -10000 0 -0.43 1 1
heart development -0.067 0.28 -10000 0 -0.92 44 44
neural crest cell migration -0.059 0.24 -10000 0 -0.74 49 49
ERBB2 0.003 0.057 -10000 0 -0.31 14 14
WWOX/E4ICDs -0.064 0.27 -10000 0 -0.87 46 46
SHC1 0.027 0.025 -10000 0 -0.43 1 1
ErbB4/EGFR/neuregulin 4 -0.064 0.28 -10000 0 -0.86 45 45
apoptosis 0.059 0.27 0.84 48 -10000 0 48
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.06 0.29 -10000 0 -0.88 48 48
ErbB4/ErbB2/epiregulin -0.054 0.25 -10000 0 -0.76 49 49
ErbB4/ErbB4/betacellulin/betacellulin -0.077 0.29 -10000 0 -0.85 52 52
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.032 0.28 -10000 0 -0.75 54 54
MDM2 -0.072 0.28 0.37 2 -0.9 46 48
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.043 0.23 -10000 0 -0.76 43 43
STAT5A -0.062 0.27 0.33 2 -0.89 44 46
ErbB4/EGFR/neuregulin 1 beta -0.067 0.25 -10000 0 -0.79 44 44
DLG4 0.032 0.011 -10000 0 -10000 0 0
GRB2/SHC 0.038 0.028 -10000 0 -0.31 1 1
E4ICDs/TAB2/NCoR1 -0.045 0.28 -10000 0 -0.84 47 47
STAT5A (dimer) -0.037 0.28 -10000 0 -0.86 44 44
MAP3K7IP2 0.031 0.03 -10000 0 -0.43 2 2
STAT5B (dimer) -0.041 0.28 -10000 0 -0.89 44 44
LRIG1 0.004 0.11 -10000 0 -0.43 32 32
EREG 0.024 0.051 -10000 0 -0.43 6 6
BTC -0.011 0.14 -10000 0 -0.43 47 47
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.071 0.28 -10000 0 -0.94 44 44
ERBB4 -0.082 0.3 -10000 0 -0.98 46 46
STAT5B 0.033 0.022 -10000 0 -0.43 1 1
YAP1 -0.034 0.15 -10000 0 -0.52 31 31
GRB2 0.033 0.009 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.048 0.26 -10000 0 -0.76 49 49
glial cell differentiation 0.044 0.27 0.83 47 -10000 0 47
WWOX 0.022 0.017 -10000 0 -10000 0 0
cell proliferation -0.059 0.27 0.42 2 -0.78 48 50
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.011 0.087 -10000 0 -0.28 21 21
adherens junction organization -0.042 0.12 -10000 0 -0.37 30 30
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.014 0.11 0.26 3 -0.28 25 28
FMN1 -0.031 0.12 -10000 0 -0.26 76 76
mol:IP3 -0.014 0.075 -10000 0 -0.24 23 23
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.03 0.12 -10000 0 -0.27 76 76
CTNNB1 0.024 0.071 -10000 0 -0.43 12 12
AKT1 -0.016 0.091 0.19 1 -0.29 19 20
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.052 0.18 -10000 0 -0.41 72 72
CTNND1 0.034 0.022 -10000 0 -0.43 1 1
mol:PI-4-5-P2 -0.024 0.1 -10000 0 -0.25 60 60
VASP -0.035 0.12 -10000 0 -0.26 75 75
ZYX -0.036 0.12 -10000 0 -0.26 77 77
JUB -0.046 0.13 -10000 0 -0.28 80 80
EGFR(dimer) -0.041 0.14 -10000 0 -0.35 39 39
E-cadherin/beta catenin-gamma catenin 0.016 0.1 -10000 0 -0.25 61 61
mol:PI-3-4-5-P3 0 0.1 0.22 1 -0.29 18 19
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
PI3K 0 0.1 0.23 1 -0.3 18 19
FYN -0.016 0.093 0.21 1 -0.31 22 23
mol:Ca2+ -0.013 0.074 -10000 0 -0.23 23 23
JUP 0.033 0.037 -10000 0 -0.43 3 3
PIK3R1 0.019 0.084 -10000 0 -0.43 17 17
mol:DAG -0.014 0.075 -10000 0 -0.24 23 23
CDH1 -0.014 0.13 -10000 0 -0.43 47 47
RhoA/GDP -0.016 0.11 0.26 3 -0.29 27 30
establishment of polarity of embryonic epithelium -0.034 0.11 -10000 0 -0.26 75 75
SRC 0.031 0.03 -10000 0 -0.43 2 2
RAC1 0.034 0.006 -10000 0 -10000 0 0
RHOA 0.025 0.062 -10000 0 -0.43 9 9
EGFR -0.016 0.14 -10000 0 -0.43 48 48
CASR -0.012 0.078 0.21 1 -0.26 14 15
RhoA/GTP 0 0.087 -10000 0 -0.25 17 17
AKT2 -0.015 0.089 0.19 1 -0.29 16 17
actin cable formation -0.035 0.11 0.26 1 -0.26 74 75
apoptosis 0.008 0.098 0.27 27 -0.23 6 33
CTNNA1 0.035 0.007 -10000 0 -10000 0 0
mol:GDP -0.03 0.097 -10000 0 -0.29 29 29
PIP5K1A -0.025 0.1 -10000 0 -0.26 60 60
PLCG1 -0.014 0.077 -10000 0 -0.24 23 23
Rac1/GTP -0.029 0.13 -10000 0 -0.33 38 38
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.008 0.11 -10000 0 -0.31 52 52
EPHB2 0.031 0.03 -10000 0 -0.43 2 2
Syndecan-2/TACI 0.01 0.067 -10000 0 -0.25 29 29
LAMA1 0.033 0.009 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 -0.007 0.13 -10000 0 -0.25 90 90
HRAS 0.031 0.037 -10000 0 -0.43 3 3
Syndecan-2/CASK -0.006 0.06 -10000 0 -0.25 29 29
ITGA5 0.034 0.021 -10000 0 -0.43 1 1
BAX -0.007 0.053 -10000 0 -10000 0 0
EPB41 0.034 0.021 -10000 0 -0.43 1 1
positive regulation of cell-cell adhesion 0.007 0.067 -10000 0 -0.23 34 34
LAMA3 -0.023 0.15 -10000 0 -0.43 59 59
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 -0.43 22 22
Syndecan-2/MMP2 -0.003 0.095 -10000 0 -0.3 42 42
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.013 0.1 -10000 0 -0.31 48 48
dendrite morphogenesis 0.01 0.068 -10000 0 -0.25 30 30
Syndecan-2/GM-CSF 0.009 0.069 -10000 0 -0.25 31 31
determination of left/right symmetry -0.006 0.072 -10000 0 -0.3 29 29
Syndecan-2/PKC delta 0.011 0.069 -10000 0 -0.25 31 31
GNB2L1 0.033 0.03 -10000 0 -0.43 2 2
MAPK3 0.029 0.091 0.2 75 -0.23 29 104
MAPK1 0.034 0.099 0.2 91 -0.23 32 123
Syndecan-2/RACK1 0.024 0.068 -10000 0 -0.22 31 31
NF1 0.032 0.022 -10000 0 -0.43 1 1
FGFR/FGF/Syndecan-2 -0.006 0.072 -10000 0 -0.3 29 29
ITGA2 -0.012 0.14 -10000 0 -0.43 48 48
MAPK8 -0.005 0.061 -10000 0 -0.25 30 30
Syndecan-2/alpha2/beta1 Integrin 0.019 0.1 -10000 0 -0.25 53 53
Syndecan-2/Kininogen 0.012 0.067 -10000 0 -0.25 29 29
ITGB1 0.031 0.036 -10000 0 -0.43 3 3
SRC 0.033 0.088 0.19 74 -0.22 26 100
Syndecan-2/CASK/Protein 4.1 0.011 0.062 -10000 0 -0.23 30 30
extracellular matrix organization 0.012 0.067 -10000 0 -0.25 29 29
actin cytoskeleton reorganization -0.008 0.11 -10000 0 -0.31 52 52
Syndecan-2/Caveolin-2/Ras 0.015 0.094 -10000 0 -0.28 41 41
Syndecan-2/Laminin alpha3 -0.016 0.1 -10000 0 -0.27 70 70
Syndecan-2/RasGAP 0.032 0.077 -10000 0 -0.21 37 37
alpha5/beta1 Integrin 0.047 0.034 -10000 0 -0.31 4 4
PRKCD 0.032 0.03 -10000 0 -0.43 2 2
Syndecan-2 dimer 0.01 0.068 -10000 0 -0.25 30 30
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 0.018 0.066 -10000 0 -0.22 32 32
RHOA 0.025 0.062 -10000 0 -0.43 9 9
SDCBP 0.022 0.059 -10000 0 -0.43 8 8
TNFRSF13B 0.031 0.011 -10000 0 -10000 0 0
RASA1 0.026 0.058 -10000 0 -0.43 8 8
alpha2/beta1 Integrin 0.013 0.1 -10000 0 -0.31 48 48
Syndecan-2/Synbindin 0.01 0.066 -10000 0 -0.25 29 29
TGFB1 0.034 0.005 -10000 0 -10000 0 0
CASP3 0.033 0.095 0.2 86 -0.23 30 116
FN1 -0.011 0.14 -10000 0 -0.43 48 48
Syndecan-2/IL8 -0.009 0.097 -10000 0 -0.28 54 54
SDC2 -0.006 0.072 -10000 0 -0.3 29 29
KNG1 0.034 0.007 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.011 0.068 -10000 0 -0.25 30 30
TRAPPC4 0.031 0.011 -10000 0 -10000 0 0
CSF2 0.03 0.037 -10000 0 -0.43 3 3
Syndecan-2/TGFB1 0.012 0.067 -10000 0 -0.25 29 29
Syndecan-2/Syntenin/PI-4-5-P2 0.008 0.067 -10000 0 -0.23 34 34
Syndecan-2/Ezrin 0.008 0.066 -10000 0 -0.23 35 35
PRKACA 0.036 0.097 0.2 94 -0.23 30 124
angiogenesis -0.009 0.096 -10000 0 -0.27 54 54
MMP2 0.003 0.11 -10000 0 -0.43 28 28
IL8 -0.006 0.12 -10000 0 -0.43 37 37
calcineurin-NFAT signaling pathway 0.01 0.066 -10000 0 -0.25 29 29
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.071 0.17 -10000 0 -0.42 71 71
KLHL20 -0.018 0.1 0.22 8 -0.26 24 32
CYFIP2 -0.008 0.13 -10000 0 -0.43 45 45
Rac1/GDP -0.029 0.12 0.26 7 -0.27 63 70
ENAH -0.065 0.17 -10000 0 -0.42 67 67
AP1M1 0.034 0.021 -10000 0 -0.43 1 1
RAP1B 0.032 0.03 -10000 0 -0.43 2 2
RAP1A 0.03 0.046 -10000 0 -0.43 5 5
CTNNB1 0.022 0.071 -10000 0 -0.43 12 12
CDC42/GTP -0.011 0.087 -10000 0 -0.26 8 8
ABI1/Sra1/Nap1 -0.046 0.057 -10000 0 -0.17 40 40
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.029 0.11 -10000 0 -0.24 63 63
RAPGEF1 -0.065 0.16 -10000 0 -0.37 78 78
CTNND1 0.033 0.022 -10000 0 -0.43 1 1
regulation of calcium-dependent cell-cell adhesion -0.071 0.19 -10000 0 -0.42 85 85
CRK -0.064 0.17 -10000 0 -0.4 80 80
E-cadherin/gamma catenin/alpha catenin 0.022 0.1 -10000 0 -0.26 49 49
alphaE/beta7 Integrin 0.045 0.035 -10000 0 -0.31 4 4
IQGAP1 0.034 0.008 -10000 0 -10000 0 0
NCKAP1 0.034 0.021 -10000 0 -0.43 1 1
Rap1/GTP/I-afadin 0.047 0.057 -10000 0 -0.23 15 15
DLG1 -0.075 0.18 -10000 0 -0.42 81 81
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.029 0.057 -10000 0 -0.18 15 15
MLLT4 0.024 0.059 -10000 0 -0.43 8 8
ARF6/GTP/NME1/Tiam1 0.052 0.048 -10000 0 -0.24 10 10
PI3K -0.034 0.074 -10000 0 -0.24 14 14
ARF6 0.032 0.03 -10000 0 -0.43 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.006 0.11 -10000 0 -0.31 49 49
TIAM1 0.027 0.058 -10000 0 -0.43 8 8
E-cadherin(dimer)/Ca2+ 0.028 0.099 -10000 0 -0.22 60 60
AKT1 -0.02 0.055 0.16 5 -0.17 5 10
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
CDH1 -0.014 0.13 -10000 0 -0.43 47 47
RhoA/GDP -0.031 0.13 0.27 6 -0.28 65 71
actin cytoskeleton organization -0.011 0.08 0.17 16 -0.19 23 39
CDC42/GDP -0.028 0.12 0.27 6 -0.27 63 69
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.007 0.078 -10000 0 -0.22 52 52
ITGB7 0.035 0.004 -10000 0 -10000 0 0
RAC1 0.034 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.031 0.11 -10000 0 -0.24 60 60
E-cadherin/Ca2+/beta catenin/alpha catenin 0.016 0.09 -10000 0 -0.22 59 59
mol:GDP -0.048 0.13 0.27 6 -0.31 64 70
CDC42/GTP/IQGAP1 0.044 0.013 -10000 0 -10000 0 0
JUP 0.031 0.036 -10000 0 -0.43 3 3
p120 catenin/RhoA/GDP -0.025 0.13 0.28 6 -0.28 64 70
RAC1/GTP/IQGAP1 0.044 0.012 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.047 0.034 -10000 0 -0.31 4 4
RHOA 0.025 0.062 -10000 0 -0.43 9 9
CDC42 0.034 0.007 -10000 0 -10000 0 0
CTNNA1 0.034 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.029 0.081 0.14 3 -0.19 80 83
NME1 0.031 0.011 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.077 0.18 -10000 0 -0.41 85 85
regulation of cell-cell adhesion -0.018 0.071 -10000 0 -0.21 13 13
WASF2 -0.012 0.046 0.1 8 -0.11 14 22
Rap1/GTP -0.013 0.096 0.24 1 -0.28 9 10
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.043 0.11 -10000 0 -0.23 53 53
CCND1 -0.036 0.099 0.16 3 -0.24 80 83
VAV2 -0.062 0.2 -10000 0 -0.6 17 17
RAP1/GDP -0.016 0.11 0.26 2 -0.29 13 15
adherens junction assembly -0.073 0.17 -10000 0 -0.4 85 85
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.034 0.007 -10000 0 -10000 0 0
PIP5K1C 0.031 0.036 -10000 0 -0.43 3 3
regulation of heterotypic cell-cell adhesion 0.023 0.1 -10000 0 -0.22 65 65
E-cadherin/beta catenin -0.026 0.1 -10000 0 -0.29 63 63
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.077 0.18 -10000 0 -0.41 85 85
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
Rac1/GTP -0.078 0.14 -10000 0 -0.42 32 32
E-cadherin/beta catenin/alpha catenin 0.017 0.11 -10000 0 -0.26 59 59
ITGAE 0.028 0.042 -10000 0 -0.43 4 4
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.073 0.19 -10000 0 -0.43 85 85
Signaling events mediated by PTP1B

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
PDGFRB 0.027 0.058 -10000 0 -0.43 8 8
Jak2/Leptin Receptor -0.032 0.14 -10000 0 -0.38 38 38
PTP1B/AKT1 -0.042 0.13 0.28 3 -0.3 64 67
FYN 0.026 0.055 -10000 0 -0.43 7 7
p210 bcr-abl/PTP1B -0.057 0.13 0.29 3 -0.31 68 71
EGFR -0.025 0.14 -10000 0 -0.44 48 48
EGF/EGFR -0.094 0.17 0.3 1 -0.31 155 156
CSF1 0.033 0.022 -10000 0 -0.43 1 1
AKT1 0.031 0.037 -10000 0 -0.44 3 3
INSR 0.033 0.03 -10000 0 -0.43 2 2
PTP1B/N-cadherin -0.051 0.14 0.3 2 -0.33 69 71
Insulin Receptor/Insulin -0.007 0.12 0.31 2 -0.32 34 36
HCK 0.017 0.086 -10000 0 -0.43 18 18
CRK 0.031 0.023 -10000 0 -0.43 1 1
TYK2 -0.055 0.13 0.27 6 -0.32 59 65
EGF -0.075 0.19 -10000 0 -0.44 108 108
YES1 0.028 0.051 -10000 0 -0.43 6 6
CAV1 -0.067 0.14 0.29 3 -0.34 73 76
TXN 0.032 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.054 0.15 0.3 2 -0.32 81 83
cell migration 0.057 0.13 0.31 68 -0.29 3 71
STAT3 0.032 0.03 -10000 0 -0.43 2 2
PRLR -0.001 0.13 -10000 0 -0.42 43 43
ITGA2B 0.033 0.008 -10000 0 -10000 0 0
CSF1R 0.034 0.006 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.026 0.1 -10000 0 -0.3 42 42
FGR 0.034 0.007 -10000 0 -10000 0 0
PTP1B/p130 Cas -0.041 0.13 0.26 2 -0.31 64 66
Crk/p130 Cas -0.034 0.13 0.27 2 -0.31 58 60
DOK1 -0.051 0.14 0.28 3 -0.37 49 52
JAK2 -0.039 0.13 -10000 0 -0.4 36 36
Jak2/Leptin Receptor/Leptin -0.041 0.14 0.25 1 -0.36 47 48
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
PTPN1 -0.058 0.13 0.29 3 -0.32 69 72
LYN 0.03 0.013 -10000 0 -10000 0 0
CDH2 0.012 0.091 -10000 0 -0.43 20 20
SRC -0.002 0.11 -10000 0 -0.6 13 13
ITGB3 0.028 0.042 -10000 0 -0.43 4 4
CAT1/PTP1B -0.078 0.2 0.32 2 -0.46 73 75
CAPN1 0.023 0.066 -10000 0 -0.44 10 10
CSK 0.033 0.022 -10000 0 -0.43 1 1
PI3K -0.003 0.13 0.28 2 -0.33 38 40
mol:H2O2 -0.001 0.006 -10000 0 -10000 0 0
STAT3 (dimer) -0.032 0.14 0.23 1 -0.35 41 42
negative regulation of transcription -0.039 0.13 -10000 0 -0.4 36 36
FCGR2A 0.017 0.071 -10000 0 -0.43 12 12
FER 0.031 0.022 -10000 0 -0.44 1 1
alphaIIb/beta3 Integrin 0.042 0.035 -10000 0 -0.31 4 4
BLK 0.02 0.044 -10000 0 -0.43 4 4
Insulin Receptor/Insulin/Shc 0.052 0.04 -10000 0 -0.27 3 3
RHOA 0.024 0.063 -10000 0 -0.44 9 9
LEPR 0.025 0.059 -10000 0 -0.43 8 8
BCAR1 0.03 0.013 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.033 0.009 -10000 0 -10000 0 0
mol:NADPH -0.002 0.004 -10000 0 -10000 0 0
TRPV6 -0.064 0.21 0.3 1 -0.49 71 72
PRL 0.035 0.026 -10000 0 -0.26 3 3
SOCS3 0.01 0.18 -10000 0 -1.4 8 8
SPRY2 0.002 0.11 -10000 0 -0.44 30 30
Insulin Receptor/Insulin/IRS1 0.028 0.11 -10000 0 -0.27 56 56
CSF1/CSF1R -0.032 0.14 0.28 3 -0.31 57 60
Ras protein signal transduction 0.043 0.15 0.62 29 -10000 0 29
IRS1 -0.017 0.14 -10000 0 -0.43 55 55
INS 0.033 0.022 -10000 0 -0.44 1 1
LEP 0 0.11 -10000 0 -0.43 32 32
STAT5B -0.045 0.12 0.24 3 -0.32 54 57
STAT5A -0.046 0.13 0.24 3 -0.32 56 59
GRB2 0.033 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.047 0.14 0.28 3 -0.33 67 70
CSN2 0.018 0.1 -10000 0 -1.4 2 2
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
LAT -0.011 0.12 -10000 0 -0.53 20 20
YBX1 0.035 0.044 -10000 0 -0.38 5 5
LCK -0.019 0.14 -10000 0 -0.43 54 54
SHC1 0.027 0.025 -10000 0 -0.43 1 1
NOX4 -0.021 0.15 -10000 0 -0.44 55 55
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.024 0.026 -10000 0 -0.3 3 3
alphaV beta3 Integrin 0.027 0.099 -10000 0 -0.27 48 48
PTK2 0.018 0.12 0.31 10 -0.42 15 25
IGF1R -0.046 0.17 -10000 0 -0.43 85 85
PI4KB 0 0 -10000 0 -10000 0 0
MFGE8 0.016 0.084 -10000 0 -0.43 17 17
SRC 0.031 0.03 -10000 0 -0.43 2 2
CDKN1B -0.007 0.12 -10000 0 -0.46 27 27
VEGFA 0 0 -10000 0 -10000 0 0
ILK 0.014 0.065 -10000 0 -0.46 6 6
ROCK1 0.034 0.005 -10000 0 -10000 0 0
AKT1 0.004 0.067 -10000 0 -0.39 8 8
PTK2B 0.009 0.06 0.22 12 -0.24 19 31
alphaV/beta3 Integrin/JAM-A 0.052 0.098 -10000 0 -0.23 39 39
CBL 0.031 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.049 0.069 -10000 0 -0.26 21 21
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.045 0.2 -10000 0 -0.32 152 152
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.007 0.068 -10000 0 -0.24 27 27
alphaV/beta3 Integrin/Syndecan-1 0.027 0.11 -10000 0 -0.27 55 55
PI4KA 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.084 0.21 -10000 0 -0.32 192 192
PI4 Kinase 0 0 -10000 0 -10000 0 0
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
alphaV/beta3 Integrin/Osteopontin -0.021 0.14 -10000 0 -0.28 118 118
RPS6KB1 -0.11 0.18 0.53 2 -0.45 77 79
TLN1 0.034 0.021 -10000 0 -0.43 1 1
MAPK3 -0.043 0.19 -10000 0 -0.56 45 45
GPR124 0.016 0.074 -10000 0 -0.43 13 13
MAPK1 -0.046 0.19 -10000 0 -0.55 52 52
PXN 0.035 0.004 -10000 0 -10000 0 0
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
alphaV/beta3 Integrin/Tumstatin 0.052 0.068 -10000 0 -0.27 19 19
cell adhesion 0.025 0.097 -10000 0 -0.27 44 44
ANGPTL3 0.03 0.042 -10000 0 -0.43 4 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.042 0.03 -10000 0 -0.26 4 4
IGF-1R heterotetramer -0.046 0.17 -10000 0 -0.43 85 85
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
TGFBR2 0.031 0.042 -10000 0 -0.43 4 4
ITGB3 0.029 0.042 -10000 0 -0.43 4 4
IGF1 -0.041 0.17 -10000 0 -0.43 78 78
RAC1 0.034 0.006 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.035 0.084 -10000 0 -0.3 25 25
apoptosis 0.022 0.076 -10000 0 -0.43 14 14
CD47 0.018 0.084 -10000 0 -0.43 17 17
alphaV/beta3 Integrin/CD47 0.043 0.083 -10000 0 -0.26 32 32
VCL 0.034 0.021 -10000 0 -0.43 1 1
alphaV/beta3 Integrin/Del1 -0.01 0.14 -10000 0 -0.28 101 101
CSF1 0.033 0.022 -10000 0 -0.43 1 1
PIK3C2A 0.012 0.076 -10000 0 -0.59 6 6
PI4 Kinase/Pyk2 0.003 0.073 -10000 0 -0.21 48 48
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.05 0.063 -10000 0 -0.25 19 19
FAK1/Vinculin 0.034 0.11 0.28 13 -0.34 15 28
alphaV beta3/Integrin/ppsTEM5 0.036 0.084 -10000 0 -0.3 25 25
RHOA 0.025 0.062 -10000 0 -0.43 9 9
VTN 0.033 0.009 -10000 0 -10000 0 0
BCAR1 0.03 0.013 -10000 0 -10000 0 0
FGF2 -0.003 0.12 -10000 0 -0.43 34 34
F11R -0.006 0.075 -10000 0 -0.31 29 29
alphaV/beta3 Integrin/Lactadherin 0.042 0.085 -10000 0 -0.3 26 26
alphaV/beta3 Integrin/TGFBR2 0.051 0.069 -10000 0 -0.26 21 21
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.059 0.065 -10000 0 -0.24 15 15
HSP90AA1 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.051 0.058 -10000 0 -0.24 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.011 0.14 -10000 0 -0.43 48 48
alphaV/beta3 Integrin/Pyk2 0.035 0.061 -10000 0 -0.24 19 19
SDC1 -0.005 0.13 -10000 0 -0.43 42 42
VAV3 -0.05 0.092 0.18 4 -0.24 86 90
PTPN11 0.035 0.004 -10000 0 -10000 0 0
IRS1 -0.017 0.14 -10000 0 -0.43 55 55
FAK1/Paxillin 0.034 0.11 0.27 13 -0.35 14 27
cell migration 0.027 0.1 0.24 22 -0.32 14 36
ITGAV 0.022 0.077 -10000 0 -0.43 14 14
PI3K 0.052 0.1 -10000 0 -0.24 36 36
SPP1 -0.073 0.19 -10000 0 -0.43 112 112
KDR 0.032 0.036 -10000 0 -0.43 3 3
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.022 0.076 -10000 0 -0.43 14 14
COL4A3 0.032 0.036 -10000 0 -0.43 3 3
angiogenesis -0.031 0.2 0.28 3 -0.57 45 48
Rac1/GTP -0.013 0.1 -10000 0 -0.22 86 86
EDIL3 -0.059 0.18 -10000 0 -0.43 97 97
cell proliferation 0.05 0.069 -10000 0 -0.26 21 21
Syndecan-4-mediated signaling events

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
PTK2 -0.029 0.18 -10000 0 -0.45 63 63
Syndecan-4/Syndesmos -0.03 0.2 -10000 0 -0.49 61 61
positive regulation of JNK cascade -0.046 0.21 -10000 0 -0.49 66 66
Syndecan-4/ADAM12 -0.049 0.23 -10000 0 -0.63 39 39
CCL5 -0.015 0.14 -10000 0 -0.43 51 51
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
DNM2 0.035 0.005 -10000 0 -10000 0 0
ITGA5 0.034 0.021 -10000 0 -0.43 1 1
SDCBP 0.022 0.059 -10000 0 -0.43 8 8
PLG 0.022 0.04 -10000 0 -0.41 2 2
ADAM12 -0.016 0.14 -10000 0 -0.43 53 53
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.028 0.042 -10000 0 -0.43 4 4
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.031 0.019 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.031 0.2 -10000 0 -0.62 27 27
Syndecan-4/CXCL12/CXCR4 -0.049 0.23 -10000 0 -0.68 32 32
Syndecan-4/Laminin alpha3 -0.055 0.21 -10000 0 -0.64 32 32
MDK 0.016 0.089 -10000 0 -0.43 19 19
Syndecan-4/FZD7 -0.048 0.22 -10000 0 -0.63 32 32
Syndecan-4/Midkine -0.038 0.21 -10000 0 -0.63 28 28
FZD7 -0.008 0.13 -10000 0 -0.43 43 43
Syndecan-4/FGFR1/FGF -0.034 0.2 -10000 0 -0.56 29 29
THBS1 0 0.12 -10000 0 -0.43 37 37
integrin-mediated signaling pathway -0.041 0.21 -10000 0 -0.5 64 64
positive regulation of MAPKKK cascade -0.046 0.21 -10000 0 -0.49 66 66
Syndecan-4/TACI -0.031 0.2 -10000 0 -0.48 65 65
CXCR4 0.007 0.11 -10000 0 -0.43 28 28
cell adhesion 0.01 0.1 0.2 41 -0.27 41 82
Syndecan-4/Dynamin -0.029 0.2 -10000 0 -0.62 27 27
Syndecan-4/TSP1 -0.044 0.21 -10000 0 -0.5 66 66
Syndecan-4/GIPC -0.029 0.2 -10000 0 -0.48 66 66
Syndecan-4/RANTES -0.051 0.22 -10000 0 -0.52 64 64
ITGB1 0.031 0.036 -10000 0 -0.43 3 3
LAMA1 0.033 0.009 -10000 0 -10000 0 0
LAMA3 -0.023 0.15 -10000 0 -0.43 59 59
RAC1 0.034 0.006 -10000 0 -10000 0 0
PRKCA 0.082 0.25 0.8 52 -10000 0 52
Syndecan-4/alpha-Actinin -0.032 0.21 -10000 0 -0.65 27 27
TFPI 0.033 0.008 -10000 0 -10000 0 0
F2 0.031 0.024 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.047 0.034 -10000 0 -0.31 4 4
positive regulation of cell adhesion -0.061 0.2 -10000 0 -0.62 32 32
ACTN1 0.027 0.058 -10000 0 -0.43 8 8
TNC 0.003 0.11 -10000 0 -0.43 31 31
Syndecan-4/CXCL12 -0.048 0.22 -10000 0 -0.51 67 67
FGF6 0.026 0.058 -10000 0 -0.43 8 8
RHOA 0.025 0.062 -10000 0 -0.43 9 9
CXCL12 -0.009 0.13 -10000 0 -0.43 46 46
TNFRSF13B 0.031 0.011 -10000 0 -10000 0 0
FGF2 -0.003 0.12 -10000 0 -0.43 34 34
FGFR1 0.019 0.065 -10000 0 -0.43 10 10
Syndecan-4/PI-4-5-P2 -0.056 0.19 -10000 0 -0.48 66 66
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.019 0.13 -10000 0 -0.42 48 48
cell migration -0.014 0.014 -10000 0 -10000 0 0
PRKCD 0.023 0.039 -10000 0 -0.4 2 2
vasculogenesis -0.041 0.21 -10000 0 -0.48 66 66
SDC4 -0.055 0.2 -10000 0 -0.51 66 66
Syndecan-4/Tenascin C -0.044 0.22 -10000 0 -0.64 32 32
Syndecan-4/PI-4-5-P2/PKC alpha -0.025 0.015 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.033 0.2 -10000 0 -0.61 27 27
MMP9 -0.015 0.14 -10000 0 -0.42 52 52
Rac1/GTP 0.01 0.1 0.2 41 -0.28 41 82
cytoskeleton organization -0.028 0.19 -10000 0 -0.47 62 62
GIPC1 0.033 0.03 -10000 0 -0.43 2 2
Syndecan-4/TFPI -0.032 0.2 -10000 0 -0.62 26 26
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 0.015 0.12 -10000 0 -0.31 46 46
alphaM/beta2 Integrin/GPIbA 0.031 0.085 -10000 0 -0.3 22 22
alphaM/beta2 Integrin/proMMP-9 0.005 0.12 -10000 0 -0.3 63 63
PLAUR 0.009 0.1 -10000 0 -0.43 27 27
HMGB1 0.024 0.031 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.035 0.087 -10000 0 -0.3 23 23
AGER 0.024 0.038 -10000 0 -0.43 1 1
RAP1A 0.03 0.046 -10000 0 -0.43 5 5
SELPLG 0.022 0.074 -10000 0 -0.43 13 13
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.041 0.12 -10000 0 -0.24 63 63
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.015 0.14 -10000 0 -0.43 52 52
CYR61 -0.004 0.12 -10000 0 -0.43 39 39
TLN1 0.034 0.021 -10000 0 -0.43 1 1
Rap1/GTP 0.013 0.13 -10000 0 -0.35 34 34
RHOA 0.025 0.062 -10000 0 -0.43 9 9
P-selectin oligomer -0.046 0.17 -10000 0 -0.43 79 79
MYH2 -0.012 0.14 -10000 0 -0.42 33 33
MST1R -0.008 0.13 -10000 0 -0.43 45 45
leukocyte activation during inflammatory response 0.036 0.077 -10000 0 -0.26 21 21
APOB 0.035 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 0.003 0.11 -10000 0 -0.43 28 28
JAM3 0.014 0.086 -10000 0 -0.43 18 18
GP1BA 0.029 0.013 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CTGF 0.014 0.12 -10000 0 -0.32 47 47
alphaM/beta2 Integrin -0.005 0.12 -10000 0 -0.37 34 34
JAM3 homodimer 0.014 0.086 -10000 0 -0.43 18 18
ICAM2 0.025 0.055 -10000 0 -0.43 7 7
ICAM1 0.017 0.084 -10000 0 -0.43 17 17
phagocytosis triggered by activation of immune response cell surface activating receptor -0.006 0.12 -10000 0 -0.37 35 35
cell adhesion 0.031 0.084 -10000 0 -0.3 22 22
NFKB1 -0.005 0.14 0.39 1 -0.37 54 55
THY1 0.016 0.082 -10000 0 -0.43 16 16
RhoA/GDP 0.019 0.044 -10000 0 -0.3 9 9
Lipoprotein(a) 0.039 0.022 -10000 0 -0.26 1 1
alphaM/beta2 Integrin/LRP/tPA 0.015 0.11 -10000 0 -0.26 61 61
IL6 -0.055 0.23 0.38 1 -0.62 62 63
ITGB2 0.005 0.099 -10000 0 -0.45 21 21
elevation of cytosolic calcium ion concentration 0.01 0.16 -10000 0 -0.35 64 64
alphaM/beta2 Integrin/JAM2/JAM3 0.021 0.13 -10000 0 -0.31 51 51
JAM2 0.009 0.1 -10000 0 -0.43 26 26
alphaM/beta2 Integrin/ICAM1 0.036 0.13 -10000 0 -0.28 65 65
alphaM/beta2 Integrin/uPA/Plg 0.02 0.13 -10000 0 -0.29 62 62
RhoA/GTP -0.024 0.14 -10000 0 -0.44 33 33
positive regulation of phagocytosis 0.002 0.14 -10000 0 -0.4 37 37
Ron/MSP 0.017 0.1 -10000 0 -0.31 45 45
alphaM/beta2 Integrin/uPAR/uPA 0.011 0.16 -10000 0 -0.36 64 64
alphaM/beta2 Integrin/uPAR 0.022 0.12 -10000 0 -0.34 39 39
PLAU -0.014 0.14 -10000 0 -0.43 51 51
PLAT -0.021 0.14 -10000 0 -0.43 50 50
actin filament polymerization -0.01 0.13 0.24 1 -0.4 32 33
MST1 0.033 0.008 -10000 0 -10000 0 0
alphaM/beta2 Integrin/lipoprotein(a) 0.041 0.081 -10000 0 -0.26 21 21
TNF -0.02 0.16 0.38 1 -0.41 51 52
RAP1B 0.032 0.03 -10000 0 -0.43 2 2
alphaM/beta2 Integrin/uPA 0.007 0.13 -10000 0 -0.32 60 60
fibrinolysis 0.019 0.13 -10000 0 -0.28 62 62
HCK 0.017 0.086 -10000 0 -0.43 18 18
dendritic cell antigen processing and presentation -0.006 0.12 -10000 0 -0.37 35 35
VTN 0.033 0.009 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 0.015 0.12 -10000 0 -0.3 49 49
LPA 0.029 0.024 -10000 0 -0.43 1 1
LRP1 0.034 0.021 -10000 0 -0.43 1 1
cell migration -0.016 0.13 -10000 0 -0.29 80 80
FN1 -0.011 0.14 -10000 0 -0.43 48 48
alphaM/beta2 Integrin/Thy1 0.023 0.1 -10000 0 -0.3 36 36
MPO 0.031 0.012 -10000 0 -10000 0 0
KNG1 0.034 0.007 -10000 0 -10000 0 0
RAP1/GDP 0.04 0.037 -10000 0 -0.26 7 7
ROCK1 -0.012 0.14 -10000 0 -0.42 32 32
ELA2 0.034 0.007 -10000 0 -10000 0 0
PLG 0.031 0.031 -10000 0 -0.43 2 2
CTGF 0 0.12 -10000 0 -0.43 34 34
alphaM/beta2 Integrin/Hck 0.027 0.11 -10000 0 -0.38 27 27
ITGAM 0.021 0.054 -10000 0 -0.44 5 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.003 0.14 -10000 0 -0.29 84 84
HP 0.027 0.038 -10000 0 -0.43 3 3
leukocyte adhesion -0.002 0.15 -10000 0 -0.39 45 45
SELP -0.046 0.17 -10000 0 -0.43 79 79
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.002 0.12 -10000 0 -0.32 53 53
VEGFR1 homodimer/NRP1 -0.018 0.11 -10000 0 -0.31 53 53
mol:DAG -0.011 0.11 -10000 0 -0.29 52 52
VEGFR1 homodimer/NRP1/VEGFR 121 -0.016 0.1 -10000 0 -0.28 53 53
CaM/Ca2+ 0.006 0.11 -10000 0 -0.28 50 50
HIF1A -0.007 0.14 -10000 0 -0.42 53 53
GAB1 0.026 0.062 -10000 0 -0.43 9 9
AKT1 -0.013 0.11 -10000 0 -0.46 16 16
PLCG1 -0.011 0.11 -10000 0 -0.29 52 52
NOS3 -0.001 0.12 0.29 1 -0.46 18 19
CBL 0.031 0.012 -10000 0 -10000 0 0
mol:NO 0.003 0.12 0.29 2 -0.44 18 20
FLT1 -0.016 0.13 -10000 0 -0.38 48 48
PGF 0.031 0.042 -10000 0 -0.43 4 4
VEGFR1 homodimer/NRP2/VEGFR121 0.001 0.11 -10000 0 -0.29 53 53
CALM1 0.035 0.005 -10000 0 -10000 0 0
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
eNOS/Hsp90 -0.003 0.11 0.27 1 -0.43 18 19
endothelial cell proliferation -0.004 0.12 0.32 6 -0.44 16 22
mol:Ca2+ -0.011 0.11 -10000 0 -0.29 52 52
MAPK3 -0.025 0.083 0.18 1 -0.47 11 12
MAPK1 -0.03 0.09 0.18 1 -0.49 10 11
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
PLGF homodimer 0.03 0.042 -10000 0 -0.43 4 4
PRKACA 0.035 0.004 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.026 0.055 -10000 0 -0.43 7 7
VEGFA homodimer 0 0 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer -0.018 0.11 -10000 0 -0.31 53 53
platelet activating factor biosynthetic process -0.008 0.1 0.34 3 -0.46 11 14
PI3K 0.024 0.13 -10000 0 -0.28 67 67
PRKCA -0.029 0.093 0.19 9 -0.52 10 19
PRKCB -0.029 0.096 0.18 12 -0.28 45 57
VEGFR1 homodimer/PLGF homodimer 0 0.12 -10000 0 -0.32 56 56
VEGFA 0 0 -10000 0 -10000 0 0
VEGFB 0.034 0.006 -10000 0 -10000 0 0
mol:IP3 -0.011 0.11 -10000 0 -0.29 52 52
RASA1 -0.015 0.11 -10000 0 -0.3 52 52
NRP2 0.033 0.022 -10000 0 -0.43 1 1
VEGFR1 homodimer -0.016 0.13 -10000 0 -0.38 48 48
VEGFB homodimer 0.034 0.006 -10000 0 -10000 0 0
NCK1 0.033 0.022 -10000 0 -0.43 1 1
eNOS/Caveolin-1 0.014 0.12 0.32 2 -0.45 20 22
PTPN11 0.035 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.022 0.13 -10000 0 -0.27 67 67
mol:L-citrulline 0.003 0.12 0.29 2 -0.44 18 20
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.016 0.11 -10000 0 -0.27 52 52
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.001 0.11 -10000 0 -0.29 54 54
CD2AP 0.034 0.006 -10000 0 -10000 0 0
PI3K/GAB1 0.029 0.14 -10000 0 -0.27 67 67
PDPK1 -0.005 0.11 -10000 0 -0.45 13 13
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.002 0.11 -10000 0 -0.29 53 53
mol:NADP 0.003 0.12 0.29 2 -0.44 18 20
HSP90AA1 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.015 0.11 -10000 0 -0.27 52 52
VEGFR1 homodimer/NRP2 0.001 0.12 -10000 0 -0.32 53 53
Caspase cascade in apoptosis

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
TOP1 -0.007 0.11 0.24 1 -0.44 11 12
ACTA1 -0.02 0.12 0.23 6 -0.31 38 44
NUMA1 -0.017 0.12 0.27 1 -0.42 19 20
SPTAN1 -0.024 0.11 0.29 3 -0.3 48 51
LIMK1 -0.037 0.12 0.28 1 -0.31 52 53
BIRC3 -0.013 0.13 -10000 0 -0.43 44 44
BIRC2 0.031 0.011 -10000 0 -10000 0 0
BAX 0.035 0.005 -10000 0 -10000 0 0
CASP10 -0.051 0.096 -10000 0 -0.27 80 80
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 -0.013 0.12 0.27 1 -0.45 13 14
DIABLO 0.035 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes -0.024 0.11 0.29 3 -0.29 48 51
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.029 0.051 -10000 0 -0.43 6 6
GSN -0.031 0.12 0.25 2 -0.31 52 54
MADD 0.035 0.004 -10000 0 -10000 0 0
TFAP2A 0 0.16 -10000 0 -0.58 29 29
BID -0.026 0.08 -10000 0 -0.19 87 87
MAP3K1 -0.034 0.14 -10000 0 -0.43 46 46
TRADD 0.029 0.024 -10000 0 -0.43 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.046 0.037 -10000 0 -0.31 5 5
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.034 0.12 0.31 4 -0.32 54 58
CASP9 0.033 0.022 -10000 0 -0.43 1 1
DNA repair -0.02 0.068 0.28 10 -0.17 22 32
neuron apoptosis -0.035 0.21 -10000 0 -0.7 42 42
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.022 0.12 0.28 1 -0.4 17 18
APAF1 0.031 0.041 -10000 0 -0.43 4 4
CASP6 -0.017 0.16 -10000 0 -0.87 14 14
TRAF2 0.033 0.03 -10000 0 -0.43 2 2
ICAD/CAD -0.026 0.11 0.26 1 -0.3 40 41
CASP7 0.031 0.1 0.26 50 -0.34 13 63
KRT18 -0.07 0.23 -10000 0 -0.58 73 73
apoptosis -0.019 0.12 0.28 3 -0.38 22 25
DFFA -0.026 0.11 0.28 1 -0.3 49 50
DFFB -0.025 0.11 0.28 1 -0.3 48 49
PARP1 0.02 0.069 0.17 22 -0.28 10 32
actin filament polymerization 0.038 0.12 0.31 48 -0.29 2 50
TNF 0.025 0.062 -10000 0 -0.43 9 9
CYCS -0.012 0.061 0.17 4 -0.21 14 18
SATB1 -0.031 0.16 -10000 0 -0.8 15 15
SLK -0.025 0.11 0.29 3 -0.3 49 52
p15 BID/BAX -0.009 0.088 -10000 0 -0.29 18 18
CASP2 -0.016 0.11 0.22 4 -0.35 28 32
JNK cascade 0.034 0.14 0.43 46 -10000 0 46
CASP3 -0.023 0.12 0.3 1 -0.31 49 50
LMNB2 -0.012 0.14 0.24 1 -0.51 24 25
RIPK1 0.034 0.006 -10000 0 -10000 0 0
CASP4 0.023 0.062 -10000 0 -0.43 9 9
Mammalian IAPs/DIABLO 0.028 0.086 -10000 0 -0.24 43 43
negative regulation of DNA binding 0 0.15 -10000 0 -0.58 29 29
stress fiber formation -0.024 0.11 0.28 3 -0.29 49 52
GZMB -0.037 0.12 -10000 0 -0.31 80 80
CASP1 -0.011 0.1 -10000 0 -0.36 36 36
LMNB1 -0.06 0.16 0.24 1 -0.42 41 42
APP -0.035 0.21 -10000 0 -0.71 42 42
TNFRSF1A 0.032 0.022 -10000 0 -0.43 1 1
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.009 0.001 -10000 0 -10000 0 0
VIM -0.016 0.12 0.3 2 -0.39 22 24
LMNA -0.01 0.1 0.24 1 -0.34 23 24
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.014 0.11 -10000 0 -0.34 34 34
LRDD 0.034 0.007 -10000 0 -10000 0 0
SREBF1 -0.04 0.12 0.28 1 -0.31 47 48
APAF-1/Caspase 9 0.012 0.12 -10000 0 -0.63 15 15
nuclear fragmentation during apoptosis -0.017 0.12 0.27 1 -0.41 19 20
CFL2 -0.039 0.12 0.29 2 -0.31 48 50
GAS2 -0.035 0.12 0.25 2 -0.31 53 55
positive regulation of apoptosis -0.03 0.14 0.26 1 -0.42 30 31
PRF1 0.026 0.055 -10000 0 -0.43 7 7
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.034 0.037 -10000 0 -0.43 2 2
HSPA8 0.016 0.074 -10000 0 -0.43 13 13
SMAD3/SMAD4/ER alpha -0.041 0.18 -10000 0 -0.31 134 134
AKT1 0.028 0.044 -10000 0 -0.43 3 3
GSC -0.18 0.49 -10000 0 -1.3 74 74
NKX2-5 0.028 0.021 -10000 0 -10000 0 0
muscle cell differentiation 0.012 0.16 0.46 34 -10000 0 34
SMAD2-3/SMAD4/SP1 0.015 0.18 -10000 0 -0.36 64 64
SMAD4 -0.009 0.1 -10000 0 -0.26 42 42
CBFB 0.029 0.024 -10000 0 -0.43 1 1
SAP18 0.032 0.009 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.058 0.051 -10000 0 -0.25 5 5
SMAD3/SMAD4/VDR 0.057 0.12 -10000 0 -0.27 35 35
MYC -0.001 0.1 -10000 0 -0.42 28 28
CDKN2B -0.099 0.32 -10000 0 -1.3 27 27
AP1 -0.037 0.19 -10000 0 -0.44 70 70
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.006 0.1 -10000 0 -0.36 24 24
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.011 0.098 -10000 0 -0.3 39 39
SP3 0.027 0.029 -10000 0 -10000 0 0
CREB1 0.034 0.021 -10000 0 -0.43 1 1
FOXH1 0.013 0.048 -10000 0 -0.12 45 45
SMAD3/SMAD4/GR 0.022 0.12 -10000 0 -0.29 42 42
GATA3 -0.052 0.18 -10000 0 -0.42 97 97
SKI/SIN3/HDAC complex/NCoR1 0.014 0.077 -10000 0 -0.36 12 12
MEF2C/TIF2 0.001 0.14 0.33 2 -0.36 41 43
endothelial cell migration 0 0.24 1.1 21 -10000 0 21
MAX 0.034 0.01 -10000 0 -10000 0 0
RBBP7 0.032 0.03 -10000 0 -0.43 2 2
RBBP4 0.033 0.022 -10000 0 -0.43 1 1
RUNX2 0.03 0.042 -10000 0 -0.43 4 4
RUNX3 -0.012 0.13 -10000 0 -0.43 47 47
RUNX1 0.006 0.11 -10000 0 -0.43 29 29
CTBP1 0.034 0.007 -10000 0 -10000 0 0
NR3C1 0.022 0.074 -10000 0 -0.42 13 13
VDR 0.019 0.084 -10000 0 -0.43 17 17
CDKN1A -0.04 0.25 -10000 0 -1.3 16 16
KAT2B 0.001 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.014 0.13 -10000 0 -0.28 64 64
DCP1A 0.033 0.022 -10000 0 -0.43 1 1
SKI 0.033 0.008 -10000 0 -10000 0 0
SERPINE1 -0.001 0.24 -10000 0 -1.1 21 21
SMAD3/SMAD4/ATF2 0.029 0.11 -10000 0 -0.28 30 30
SMAD3/SMAD4/ATF3 0.011 0.12 -10000 0 -0.32 42 42
SAP30 0.029 0.047 -10000 0 -0.43 5 5
Cbp/p300/PIAS3 0.057 0.055 0.22 3 -0.26 3 6
JUN -0.045 0.18 0.29 1 -0.44 69 70
SMAD3/SMAD4/IRF7 0.029 0.12 -10000 0 -0.3 37 37
TFE3 0.031 0.035 -10000 0 -0.15 5 5
COL1A2 -0.077 0.33 -10000 0 -0.88 68 68
mesenchymal cell differentiation -0.026 0.12 0.3 31 -10000 0 31
DLX1 0.032 0.011 -10000 0 -10000 0 0
TCF3 0.032 0.03 -10000 0 -0.43 2 2
FOS -0.042 0.16 -10000 0 -0.46 66 66
SMAD3/SMAD4/Max 0.029 0.11 -10000 0 -0.28 30 30
Cbp/p300/SNIP1 0.058 0.048 -10000 0 -0.26 6 6
ZBTB17 0.034 0.013 -10000 0 -10000 0 0
LAMC1 -0.009 0.11 -10000 0 -0.39 29 29
TGIF2/HDAC complex/SMAD3/SMAD4 0.023 0.11 -10000 0 -0.28 34 34
IRF7 0.027 0.061 -10000 0 -0.32 13 13
ESR1 -0.088 0.2 -10000 0 -0.42 132 132
HNF4A 0.032 0.03 -10000 0 -0.43 2 2
MEF2C 0.009 0.16 0.33 11 -0.36 46 57
SMAD2-3/SMAD4 0.012 0.14 -10000 0 -0.29 48 48
Cbp/p300/Src-1 0.061 0.053 -10000 0 -0.25 7 7
IGHV3OR16-13 -0.003 0.063 -10000 0 -0.48 6 6
TGIF2/HDAC complex 0.027 0.051 -10000 0 -0.43 6 6
CREBBP 0.033 0.028 -10000 0 -0.43 1 1
SKIL 0.027 0.051 -10000 0 -0.43 6 6
HDAC1 0.033 0.021 -10000 0 -0.43 1 1
HDAC2 0.031 0.023 -10000 0 -0.43 1 1
SNIP1 0.03 0.036 -10000 0 -0.43 3 3
GCN5L2 0.034 0.034 -10000 0 -0.43 2 2
SMAD3/SMAD4/TFE3 0.034 0.13 -10000 0 -0.32 38 38
MSG1/HSC70 0.027 0.063 -10000 0 -0.31 15 15
SMAD2 0.008 0.064 -10000 0 -0.15 37 37
SMAD3 0.009 0.092 -10000 0 -0.36 17 17
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.005 0.083 -10000 0 -0.25 31 31
SMAD2/SMAD2/SMAD4 0.005 0.066 0.2 11 -0.24 14 25
NCOR1 0.031 0.011 -10000 0 -10000 0 0
NCOA2 0.024 0.047 -10000 0 -0.43 5 5
NCOA1 0.03 0.051 -10000 0 -0.43 6 6
MYOD/E2A 0.03 0.078 -10000 0 -0.31 25 25
SMAD2-3/SMAD4/SP1/MIZ-1 0.029 0.18 -10000 0 -0.36 54 54
IFNB1 -0.006 0.099 0.36 1 -0.33 23 24
SMAD3/SMAD4/MEF2C 0.026 0.17 0.28 1 -0.43 40 41
CITED1 0.028 0.032 -10000 0 -0.43 2 2
SMAD2-3/SMAD4/ARC105 0.016 0.12 -10000 0 -0.26 48 48
RBL1 0.032 0.023 -10000 0 -0.43 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.008 0.13 -10000 0 -0.45 31 31
RUNX1-3/PEBPB2 0.008 0.12 -10000 0 -0.27 73 73
SMAD7 -0.045 0.21 -10000 0 -0.54 53 53
MYC/MIZ-1 0.016 0.083 0.19 6 -0.3 27 33
SMAD3/SMAD4 0.043 0.14 0.31 50 -0.38 18 68
IL10 -0.042 0.14 -10000 0 -0.33 59 59
PIASy/HDAC complex 0.022 0.044 -10000 0 -0.43 3 3
PIAS3 0.031 0.015 -10000 0 -10000 0 0
CDK2 0.035 0.034 -10000 0 -0.43 2 2
IL5 -0.041 0.14 0.36 1 -0.32 64 65
CDK4 0.037 0.018 -10000 0 -10000 0 0
PIAS4 0.022 0.044 -10000 0 -0.43 3 3
ATF3 0.01 0.088 -10000 0 -0.43 19 19
SMAD3/SMAD4/SP1 0.01 0.17 -10000 0 -0.35 63 63
FOXG1 -0.001 0.003 -10000 0 -10000 0 0
FOXO3 0.005 0.033 -10000 0 -0.23 5 5
FOXO1 0.005 0.033 -10000 0 -0.26 4 4
FOXO4 0.005 0.033 -10000 0 -0.26 4 4
heart looping 0.009 0.16 0.32 12 -0.36 46 58
CEBPB 0.023 0.053 -10000 0 -0.43 6 6
SMAD3/SMAD4/DLX1 0.028 0.11 -10000 0 -0.28 29 29
MYOD1 0.013 0.097 -10000 0 -0.43 23 23
SMAD3/SMAD4/HNF4 0.029 0.11 -10000 0 -0.28 30 30
SMAD3/SMAD4/GATA3 -0.019 0.18 -10000 0 -0.32 109 109
SnoN/SIN3/HDAC complex/NCoR1 0.027 0.051 -10000 0 -0.43 6 6
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.011 0.16 -10000 0 -0.28 84 84
SMAD3/SMAD4/SP1-3 0.024 0.18 -10000 0 -0.36 66 66
MED15 0 0 -10000 0 -10000 0 0
SP1 0.01 0.07 -10000 0 -0.17 47 47
SIN3B 0.034 0.005 -10000 0 -10000 0 0
SIN3A 0.034 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.026 0.13 -10000 0 -0.27 68 68
ITGB5 -0.047 0.19 0.29 1 -0.51 59 60
TGIF/SIN3/HDAC complex/CtBP 0.02 0.057 -10000 0 -0.31 6 6
SMAD3/SMAD4/AR -0.028 0.18 -10000 0 -0.32 114 114
AR -0.056 0.18 -10000 0 -0.43 99 99
negative regulation of cell growth 0.003 0.11 -10000 0 -0.34 27 27
SMAD3/SMAD4/MYOD 0.013 0.12 -10000 0 -0.28 50 50
E2F5 0.011 0.088 -10000 0 -0.43 19 19
E2F4 0.03 0.013 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.038 0.12 -10000 0 -0.24 46 46
SMAD2-3/SMAD4/FOXO1-3a-4 -0.007 0.11 -10000 0 -0.32 40 40
TFDP1 0.031 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.016 0.2 -10000 0 -0.45 70 70
SMAD3/SMAD4/RUNX2 0.027 0.12 -10000 0 -0.3 31 31
TGIF2 0.027 0.051 -10000 0 -0.43 6 6
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 0.035 0.003 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.006 0.11 -10000 0 -0.43 31 31
ANTXR2 0.02 0.079 -10000 0 -0.43 15 15
negative regulation of myeloid dendritic cell antigen processing and presentation -0.006 0.017 -10000 0 -0.064 39 39
monocyte activation -0.016 0.12 -10000 0 -0.38 52 52
MAP2K2 0.002 0.1 -10000 0 -0.63 13 13
MAP2K1 -0.008 0.016 -10000 0 -0.09 6 6
MAP2K7 -0.008 0.016 -10000 0 -0.09 6 6
MAP2K6 -0.014 0.043 0.12 2 -0.23 16 18
CYAA -0.025 0.068 -10000 0 -0.25 39 39
MAP2K4 -0.007 0.015 -10000 0 -0.1 4 4
IL1B -0.027 0.072 0.16 2 -0.22 53 55
Channel 0.019 0.086 -10000 0 -0.26 39 39
NLRP1 -0.005 0.016 -10000 0 -0.059 39 39
CALM1 0.035 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.003 0.063 -10000 0 -0.43 9 9
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.006 0.017 0.064 39 -10000 0 39
MAPK3 -0.007 0.022 0.13 5 -0.11 6 11
MAPK1 -0.009 0.02 -10000 0 -0.22 2 2
PGR -0.078 0.1 -10000 0 -0.22 175 175
PA/Cellular Receptors 0.019 0.094 -10000 0 -0.29 39 39
apoptosis -0.006 0.017 -10000 0 -0.064 39 39
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.019 0.081 -10000 0 -0.25 39 39
macrophage activation -0.01 0.023 0.12 3 -0.21 3 6
TNF 0.025 0.062 -10000 0 -0.43 9 9
VCAM1 -0.017 0.12 -10000 0 -0.38 52 52
platelet activation 0.003 0.063 -10000 0 -0.43 9 9
MAPKKK cascade 0.003 0.032 0.12 7 -0.12 5 12
IL18 -0.021 0.066 0.14 1 -0.25 35 36
negative regulation of macrophage activation -0.006 0.017 -10000 0 -0.064 39 39
LEF -0.006 0.017 -10000 0 -0.064 39 39
CASP1 -0.008 0.031 -10000 0 -0.084 64 64
mol:cAMP 0.003 0.064 -10000 0 -0.44 9 9
necrosis -0.006 0.017 -10000 0 -0.064 39 39
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.019 0.081 -10000 0 -0.25 39 39
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -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 0.047 0.016 -10000 0 -10000 0 0
VLDLR -0.009 0.13 -10000 0 -0.43 43 43
CRKL 0.03 0.042 -10000 0 -0.43 4 4
LRPAP1 0.034 0.007 -10000 0 -10000 0 0
FYN 0.026 0.055 -10000 0 -0.43 7 7
ITGA3 0.021 0.068 -10000 0 -0.43 11 11
RELN/VLDLR/Fyn 0.023 0.1 -10000 0 -0.27 52 52
MAPK8IP1/MKK7/MAP3K11/JNK1 0.071 0.068 -10000 0 -0.23 14 14
AKT1 -0.017 0.09 -10000 0 -0.24 57 57
MAP2K7 0.035 0.005 -10000 0 -10000 0 0
RAPGEF1 0.034 0.005 -10000 0 -10000 0 0
DAB1 0.034 0.006 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.036 0.081 -10000 0 -0.24 39 39
LRPAP1/LRP8 0.018 0.091 -10000 0 -0.31 35 35
RELN/LRP8/DAB1/Fyn 0.042 0.09 -10000 0 -0.23 45 45
DAB1/alpha3/beta1 Integrin 0.011 0.11 -10000 0 -0.22 83 83
long-term memory 0.044 0.1 -10000 0 -0.22 56 56
DAB1/LIS1 0.029 0.12 -10000 0 -0.22 80 80
DAB1/CRLK/C3G 0.017 0.11 -10000 0 -0.22 83 83
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
DAB1/NCK2 0.034 0.12 -10000 0 -0.22 80 80
ARHGEF2 0.02 0.062 -10000 0 -0.43 9 9
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.032 0.01 -10000 0 -10000 0 0
CDK5R1 0.033 0.009 -10000 0 -10000 0 0
RELN 0.029 0.046 -10000 0 -0.43 5 5
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
RELN/LRP8/Fyn 0.028 0.097 -10000 0 -0.26 46 46
GRIN2A/RELN/LRP8/DAB1/Fyn 0.052 0.094 -10000 0 -0.23 42 42
MAPK8 0.032 0.036 -10000 0 -0.43 3 3
RELN/VLDLR/DAB1 0.029 0.089 -10000 0 -0.24 46 46
ITGB1 0.031 0.036 -10000 0 -0.43 3 3
MAP1B -0.03 0.12 -10000 0 -0.25 95 95
RELN/LRP8 0.035 0.09 -10000 0 -0.26 40 40
GRIN2B/RELN/LRP8/DAB1/Fyn 0.045 0.11 -10000 0 -0.23 60 60
PI3K 0.033 0.066 -10000 0 -0.31 17 17
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.036 0.061 -10000 0 -0.33 12 12
RAP1A -0.038 0.099 0.35 5 -0.39 4 9
PAFAH1B1 0.032 0.023 -10000 0 -0.43 1 1
MAPK8IP1 0.033 0.03 -10000 0 -0.43 2 2
CRLK/C3G 0.046 0.034 -10000 0 -0.31 4 4
GRIN2B 0.017 0.084 -10000 0 -0.43 17 17
NCK2 0.035 0.005 -10000 0 -10000 0 0
neuron differentiation 0.015 0.082 -10000 0 -0.33 8 8
neuron adhesion -0.028 0.11 0.33 4 -0.41 5 9
LRP8 -0.003 0.12 -10000 0 -0.43 35 35
GSK3B -0.015 0.091 0.19 2 -0.23 53 55
RELN/VLDLR/DAB1/Fyn 0.036 0.097 -10000 0 -0.23 51 51
MAP3K11 0.033 0.03 -10000 0 -0.43 2 2
RELN/VLDLR/DAB1/P13K -0.007 0.096 -10000 0 -0.25 58 58
CDK5 0.034 0.007 -10000 0 -10000 0 0
MAPT -0.067 0.19 0.77 8 -0.39 97 105
neuron migration -0.024 0.11 0.29 6 -0.35 16 22
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.015 0.083 -10000 0 -0.34 8 8
RELN/VLDLR 0.019 0.12 -10000 0 -0.24 81 81
TCGA08_retinoblastoma

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
CDKN2B 0.019 0.072 -10000 0 -0.4 13 13
CDKN2C 0.023 0.063 -10000 0 -0.4 10 10
CDKN2A 0.018 0.07 -10000 0 -0.4 13 13
CCND2 0.003 0.048 0.19 26 -0.13 2 28
RB1 -0.009 0.064 0.24 2 -0.22 35 37
CDK4 0.007 0.058 0.23 28 -10000 0 28
CDK6 0.005 0.059 0.22 27 -0.17 6 33
G1/S progression 0.016 0.077 0.22 53 -0.25 3 56
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 + 0.029 0.046 -10000 0 -0.43 5 5
GNAT1/GTP 0.024 0.021 -10000 0 -0.3 2 2
Metarhodopsin II/Arrestin 0.002 0.095 -10000 0 -0.26 57 57
PDE6G/GNAT1/GTP 0.041 0.024 -10000 0 -0.26 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.032 0.03 -10000 0 -0.43 2 2
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel -0.015 0.12 -10000 0 -0.22 116 116
mol:Na + 0.022 0.1 -10000 0 -0.25 50 50
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.003 0.12 -10000 0 -0.28 76 76
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.033 0.11 -10000 0 -0.25 50 50
CNGB1 0.029 0.013 -10000 0 -10000 0 0
RDH5 0.032 0.01 -10000 0 -10000 0 0
SAG -0.027 0.15 -10000 0 -0.43 59 59
mol:Ca2+ -0.029 0.09 0.34 5 -0.4 10 15
Na + (4 Units) 0.014 0.095 -10000 0 -0.24 45 45
RGS9 0.016 0.074 -10000 0 -0.43 13 13
GNB1/GNGT1 0.026 0.063 -10000 0 -0.31 15 15
GNAT1/GDP 0.015 0.11 -10000 0 -0.23 78 78
GUCY2D 0.032 0.011 -10000 0 -10000 0 0
GNGT1 0.016 0.068 -10000 0 -0.43 11 11
GUCY2F 0.026 0.065 -10000 0 -0.43 10 10
GNB5 0.024 0.068 -10000 0 -0.43 11 11
mol:GMP (4 units) -0.018 0.1 -10000 0 -0.22 96 96
mol:11-cis-retinal 0.032 0.01 -10000 0 -10000 0 0
mol:cGMP 0.047 0.085 -10000 0 -0.27 29 29
GNB1 0.03 0.042 -10000 0 -0.43 4 4
Rhodopsin 0.047 0.016 -10000 0 -10000 0 0
SLC24A1 0.029 0.046 -10000 0 -0.43 5 5
CNGA1 0.002 0.11 -10000 0 -0.43 29 29
Metarhodopsin II 0.022 0.003 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.062 0.077 -10000 0 -0.26 23 23
RGS9BP -0.026 0.15 -10000 0 -0.43 62 62
Metarhodopsin II/Transducin 0.013 0.049 -10000 0 -0.2 23 23
GCAP Family/Ca ++ 0.05 0.069 -10000 0 -0.25 23 23
PDE6A/B -0.026 0.14 -10000 0 -0.31 103 103
mol:Pi 0.002 0.12 -10000 0 -0.27 76 76
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.043 0.057 -10000 0 -0.24 17 17
PDE6B -0.061 0.19 -10000 0 -0.43 102 102
PDE6A 0.032 0.03 -10000 0 -0.43 2 2
PDE6G 0.033 0.009 -10000 0 -10000 0 0
RHO 0.035 0.004 -10000 0 -10000 0 0
PDE6 -0.019 0.15 -10000 0 -0.24 143 143
GUCA1A 0.021 0.077 -10000 0 -0.43 14 14
GC2/GCAP Family 0.064 0.09 -10000 0 -0.28 29 29
GUCA1C 0.025 0.065 -10000 0 -0.43 10 10
GUCA1B 0.033 0.022 -10000 0 -0.43 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 0.036 0.1 -9999 0 -0.24 52 52
SMAD6-7/SMURF1 0.065 0.025 -9999 0 -0.26 1 1
NOG 0.028 0.037 -9999 0 -0.43 3 3
SMAD9 -0.022 0.16 -9999 0 -0.47 47 47
SMAD4 0.027 0.055 -9999 0 -0.43 7 7
SMAD5 -0.021 0.12 -9999 0 -0.35 39 39
BMP7/USAG1 -0.072 0.16 -9999 0 -0.32 137 137
SMAD5/SKI -0.009 0.13 -9999 0 -0.39 28 28
SMAD1 0.013 0.08 -9999 0 -0.4 7 7
BMP2 0.019 0.074 -9999 0 -0.43 13 13
SMAD1/SMAD1/SMAD4 0.032 0.083 -9999 0 -0.38 4 4
BMPR1A 0.029 0.051 -9999 0 -0.43 6 6
BMPR1B -0.004 0.11 -9999 0 -0.43 29 29
BMPR1A-1B/BAMBI -0.027 0.14 -9999 0 -0.26 120 120
AHSG 0.034 0.007 -9999 0 -10000 0 0
CER1 0.033 0.008 -9999 0 -10000 0 0
BMP2-4/CER1 0.011 0.12 -9999 0 -0.27 71 71
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.016 0.12 -9999 0 -0.35 29 29
BMP2-4 (homodimer) -0.013 0.13 -9999 0 -0.31 74 74
RGMB 0.026 0.062 -9999 0 -0.43 9 9
BMP6/BMPR2/BMPR1A-1B 0.043 0.09 -9999 0 -0.24 42 42
RGMA 0.018 0.074 -9999 0 -0.43 13 13
SMURF1 0.035 0.005 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.027 0.11 -9999 0 -0.38 28 28
BMP2-4/USAG1 -0.085 0.17 -9999 0 -0.29 191 191
SMAD6/SMURF1/SMAD5 -0.009 0.13 -9999 0 -0.39 29 29
SOSTDC1 -0.12 0.21 -9999 0 -0.43 151 151
BMP7/BMPR2/BMPR1A-1B 0.033 0.093 -9999 0 -0.24 45 45
SKI 0.033 0.008 -9999 0 -10000 0 0
BMP6 (homodimer) 0.027 0.051 -9999 0 -0.43 6 6
HFE2 0.021 0.065 -9999 0 -0.43 10 10
ZFYVE16 0.032 0.03 -9999 0 -0.43 2 2
MAP3K7 0.033 0.009 -9999 0 -10000 0 0
BMP2-4/CHRD 0.007 0.12 -9999 0 -0.28 72 72
SMAD5/SMAD5/SMAD4 -0.013 0.14 -9999 0 -0.4 30 30
MAPK1 0.032 0.03 -9999 0 -0.43 2 2
TAK1/TAB family 0.018 0.13 -9999 0 -0.36 22 22
BMP7 (homodimer) 0.015 0.074 -9999 0 -0.43 13 13
NUP214 0.034 0.006 -9999 0 -10000 0 0
BMP6/FETUA 0.042 0.042 -9999 0 -0.31 6 6
SMAD1/SKI 0.029 0.087 -9999 0 -0.38 7 7
SMAD6 0.034 0.007 -9999 0 -10000 0 0
CTDSP2 0.033 0.03 -9999 0 -0.43 2 2
BMP2-4/FETUA 0.01 0.12 -9999 0 -0.27 72 72
MAP3K7IP1 0.033 0.009 -9999 0 -10000 0 0
GREM1 -0.004 0.12 -9999 0 -0.43 39 39
BMPR2 (homodimer) 0.033 0.03 -9999 0 -0.43 2 2
GADD34/PP1CA 0.059 0.04 -9999 0 -0.26 5 5
BMPR1A-1B (homodimer) 0.008 0.089 -9999 0 -0.31 35 35
CHRDL1 0.029 0.037 -9999 0 -0.43 3 3
ENDOFIN/SMAD1 0.027 0.089 -9999 0 -0.38 8 8
SMAD6-7/SMURF1/SMAD1 0.055 0.094 -9999 0 -0.4 5 5
SMAD6/SMURF1 0.035 0.005 -9999 0 -10000 0 0
BAMBI -0.056 0.18 -9999 0 -0.43 92 92
SMURF2 0.027 0.042 -9999 0 -0.43 4 4
BMP2-4/CHRDL1 0.007 0.12 -9999 0 -0.27 75 75
BMP2-4/GREM1 -0.015 0.15 -9999 0 -0.3 100 100
SMAD7 0.033 0.022 -9999 0 -0.43 1 1
SMAD8A/SMAD8A/SMAD4 -0.014 0.17 -9999 0 -0.46 48 48
SMAD1/SMAD6 0.029 0.089 -9999 0 -0.37 8 8
TAK1/SMAD6 0.048 0.014 -9999 0 -10000 0 0
BMP7 0.015 0.074 -9999 0 -0.43 13 13
BMP6 0.027 0.051 -9999 0 -0.43 6 6
MAP3K7IP2 0.031 0.03 -9999 0 -0.43 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.017 0.11 -9999 0 -0.32 34 34
PPM1A 0.033 0.021 -9999 0 -0.43 1 1
SMAD1/SMURF2 0.024 0.084 -9999 0 -0.41 5 5
SMAD7/SMURF1 0.049 0.02 -9999 0 -0.31 1 1
CTDSPL 0.026 0.055 -9999 0 -0.43 7 7
PPP1CA 0.03 0.031 -9999 0 -0.43 2 2
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.033 0.03 -9999 0 -0.43 2 2
PPP1R15A 0.034 0.021 -9999 0 -0.43 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.028 0.14 -9999 0 -0.41 34 34
CHRD 0.029 0.047 -9999 0 -0.43 5 5
BMPR2 0.033 0.03 -9999 0 -0.43 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.025 0.12 -9999 0 -0.38 29 29
BMP4 -0.03 0.15 -9999 0 -0.43 65 65
FST 0.02 0.071 -9999 0 -0.43 12 12
BMP2-4/NOG 0.005 0.12 -9999 0 -0.27 73 73
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.045 0.094 -9999 0 -0.23 44 44
BCR signaling 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
JUN -0.027 0.16 0.27 4 -0.41 48 52
IKBKB 0.019 0.087 0.24 5 -0.28 8 13
AKT1 0.022 0.11 0.25 43 -0.23 22 65
IKBKG 0.024 0.077 0.25 1 -0.29 5 6
CALM1 -0.012 0.12 0.25 4 -0.38 30 34
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
MAP3K1 -0.024 0.18 0.28 2 -0.47 49 51
MAP3K7 0.033 0.009 -10000 0 -10000 0 0
mol:Ca2+ -0.012 0.13 0.26 4 -0.36 39 43
DOK1 0.026 0.062 -10000 0 -0.43 9 9
AP-1 -0.021 0.1 0.24 2 -0.25 43 45
LYN 0.03 0.013 -10000 0 -10000 0 0
BLNK 0.012 0.1 -10000 0 -0.43 25 25
SHC1 0.027 0.025 -10000 0 -0.43 1 1
BCR complex 0.021 0.08 -10000 0 -0.31 26 26
CD22 -0.022 0.13 0.26 1 -0.48 30 31
CAMK2G -0.012 0.12 0.24 6 -0.38 27 33
CSNK2A1 0.034 0.008 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0 0.084 -10000 0 -0.25 42 42
GO:0007205 -0.012 0.13 0.26 4 -0.37 39 43
SYK 0.004 0.12 -10000 0 -0.43 33 33
ELK1 -0.014 0.13 0.25 4 -0.39 30 34
NFATC1 0.014 0.14 0.28 20 -0.38 34 54
B-cell antigen/BCR complex 0.021 0.08 -10000 0 -0.31 26 26
PAG1/CSK 0.032 0.055 -10000 0 -0.31 11 11
NFKBIB 0.028 0.047 0.14 9 -0.13 17 26
HRAS -0.001 0.12 0.23 11 -0.35 29 40
NFKBIA 0.028 0.046 0.14 9 -0.12 16 25
NF-kappa-B/RelA/I kappa B beta 0.032 0.042 0.14 9 -0.14 1 10
RasGAP/Csk 0.031 0.11 -10000 0 -0.27 42 42
mol:GDP -0.011 0.13 0.26 4 -0.39 32 36
PTEN 0.024 0.068 -10000 0 -0.43 11 11
CD79B 0.004 0.1 -10000 0 -0.43 26 26
NF-kappa-B/RelA/I kappa B alpha 0.032 0.042 0.14 9 -0.15 1 10
GRB2 0.033 0.009 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.013 0.18 0.3 2 -0.49 39 41
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
mol:IP3 -0.014 0.13 0.27 3 -0.37 39 42
CSK 0.033 0.022 -10000 0 -0.43 1 1
FOS -0.037 0.14 0.24 3 -0.38 42 45
CHUK 0.013 0.099 0.25 1 -0.33 20 21
IBTK 0.033 0.022 -10000 0 -0.43 1 1
CARD11/BCL10/MALT1/TAK1 0.009 0.13 0.26 3 -0.38 27 30
PTPN6 -0.014 0.13 0.25 1 -0.48 27 28
RELA 0.035 0.005 -10000 0 -10000 0 0
BCL2A1 0.023 0.033 0.14 1 -0.11 1 2
VAV2 -0.01 0.15 0.26 1 -0.5 31 32
ubiquitin-dependent protein catabolic process 0.031 0.046 0.14 9 -0.12 16 25
BTK -0.013 0.19 -10000 0 -1.1 15 15
CD19 -0.023 0.13 0.26 1 -0.46 33 34
MAP4K1 0.034 0.008 -10000 0 -10000 0 0
CD72 0.007 0.1 -10000 0 -0.43 27 27
PAG1 0.018 0.065 -10000 0 -0.43 10 10
MAPK14 -0.019 0.16 0.26 2 -0.41 46 48
SH3BP5 0.021 0.077 -10000 0 -0.43 14 14
PIK3AP1 -0.021 0.14 0.28 3 -0.41 41 44
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.024 0.16 -10000 0 -0.46 46 46
RAF1 -0.001 0.11 0.24 8 -0.34 26 34
RasGAP/p62DOK/SHIP 0.02 0.1 -10000 0 -0.28 44 44
CD79A 0.03 0.024 -10000 0 -0.43 1 1
re-entry into mitotic cell cycle -0.021 0.1 0.24 2 -0.25 41 43
RASA1 0.026 0.058 -10000 0 -0.43 8 8
MAPK3 0.009 0.1 0.26 17 -0.31 17 34
MAPK1 -0.001 0.1 0.28 6 -0.32 19 25
CD72/SHP1 0.013 0.16 0.28 17 -0.45 36 53
NFKB1 0.034 0.021 -10000 0 -0.43 1 1
MAPK8 -0.019 0.16 0.28 3 -0.4 48 51
actin cytoskeleton organization 0.009 0.14 0.27 13 -0.44 30 43
NF-kappa-B/RelA 0.066 0.082 0.26 8 -0.26 3 11
Calcineurin 0.002 0.12 -10000 0 -0.36 29 29
PI3K -0.026 0.11 -10000 0 -0.38 32 32
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.013 0.14 0.26 5 -0.41 38 43
SOS1 0.034 0.021 -10000 0 -0.43 1 1
Bam32/HPK1 -0.074 0.31 -10000 0 -0.72 84 84
DAPP1 -0.11 0.34 -10000 0 -0.83 83 83
cytokine secretion 0.015 0.14 0.27 21 -0.35 34 55
mol:DAG -0.014 0.13 0.27 3 -0.37 39 42
PLCG2 0.019 0.059 -10000 0 -0.43 8 8
MAP2K1 0 0.11 0.24 10 -0.34 21 31
B-cell antigen/BCR complex/FcgammaRIIB 0.014 0.1 -10000 0 -0.3 38 38
mol:PI-3-4-5-P3 -0.001 0.11 0.24 21 -0.3 26 47
ETS1 -0.011 0.11 0.24 6 -0.37 26 32
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.028 0.12 -10000 0 -0.27 55 55
B-cell antigen/BCR complex/LYN -0.018 0.13 0.27 1 -0.47 33 34
MALT1 0.03 0.042 -10000 0 -0.43 4 4
TRAF6 0.034 0.021 -10000 0 -0.43 1 1
RAC1 -0.001 0.15 0.27 7 -0.47 30 37
B-cell antigen/BCR complex/LYN/SYK -0.006 0.15 -10000 0 -0.48 31 31
CARD11 -0.013 0.13 0.26 5 -0.4 32 37
FCGR2B 0 0.11 -10000 0 -0.43 30 30
PPP3CA 0.026 0.062 -10000 0 -0.43 9 9
BCL10 0.034 0.007 -10000 0 -10000 0 0
IKK complex 0.025 0.051 0.15 23 -0.13 2 25
PTPRC 0.005 0.098 -10000 0 -0.43 24 24
PDPK1 0.007 0.088 0.21 31 -0.22 18 49
PPP3CB 0.034 0.021 -10000 0 -0.43 1 1
PPP3CC 0.024 0.043 -10000 0 -0.43 4 4
POU2F2 0.025 0.032 0.15 5 -0.11 1 6
Nectin adhesion pathway

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
PDGFRB 0.027 0.058 -10000 0 -0.43 8 8
alphaV beta3 Integrin 0.035 0.066 -10000 0 -0.31 17 17
PTK2 -0.021 0.14 -10000 0 -0.44 31 31
positive regulation of JNK cascade -0.004 0.13 -10000 0 -0.32 42 42
CDC42/GDP 0.006 0.17 -10000 0 -0.42 46 46
Rac1/GDP 0.005 0.17 -10000 0 -0.42 46 46
RAP1B 0.032 0.03 -10000 0 -0.43 2 2
RAP1A 0.03 0.046 -10000 0 -0.43 5 5
CTNNB1 0.022 0.071 -10000 0 -0.43 12 12
CDC42/GTP -0.001 0.16 -10000 0 -0.4 42 42
nectin-3/I-afadin 0.022 0.09 -10000 0 -0.32 31 31
RAPGEF1 -0.019 0.16 -10000 0 -0.45 41 41
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.024 0.18 -10000 0 -0.5 43 43
PDGFB-D/PDGFRB 0.027 0.058 -10000 0 -0.43 8 8
TLN1 -0.016 0.077 0.19 5 -0.34 18 23
Rap1/GTP -0.01 0.12 -10000 0 -0.33 40 40
IQGAP1 0.034 0.008 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.047 0.057 -10000 0 -0.23 15 15
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.022 0.09 -10000 0 -0.32 31 31
PVR 0.03 0.042 -10000 0 -0.43 4 4
Necl-5(dimer) 0.03 0.042 -10000 0 -0.43 4 4
mol:GDP -0.016 0.2 -10000 0 -0.52 47 47
MLLT4 0.024 0.059 -10000 0 -0.43 8 8
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
PI3K 0.05 0.11 -10000 0 -0.28 43 43
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.035 0.051 -10000 0 -0.3 9 9
positive regulation of lamellipodium assembly 0 0.13 -10000 0 -0.32 46 46
PVRL1 0.03 0.024 -10000 0 -0.43 1 1
PVRL3 0.011 0.099 -10000 0 -0.43 24 24
PVRL2 0.025 0.065 -10000 0 -0.43 10 10
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
CDH1 -0.014 0.13 -10000 0 -0.43 47 47
CLDN1 -0.05 0.17 -10000 0 -0.43 86 86
JAM-A/CLDN1 0.001 0.13 -10000 0 -0.27 83 83
SRC -0.037 0.19 -10000 0 -0.51 58 58
ITGB3 0.029 0.042 -10000 0 -0.43 4 4
nectin-1(dimer)/I-afadin/I-afadin 0.035 0.051 -10000 0 -0.3 9 9
FARP2 -0.019 0.2 -10000 0 -0.56 40 40
RAC1 0.034 0.006 -10000 0 -10000 0 0
CTNNA1 0.034 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.037 0.09 -10000 0 -0.28 34 34
nectin-1/I-afadin 0.035 0.051 -10000 0 -0.3 9 9
nectin-2/I-afadin 0.034 0.066 -10000 0 -0.3 17 17
RAC1/GTP/IQGAP1/filamentous actin 0.044 0.012 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.035 0.085 -10000 0 -0.27 32 32
CDC42/GTP/IQGAP1/filamentous actin 0.044 0.013 -10000 0 -10000 0 0
F11R 0.025 0.038 -10000 0 -0.43 3 3
positive regulation of filopodium formation -0.004 0.13 -10000 0 -0.32 42 42
alphaV/beta3 Integrin/Talin 0.008 0.1 0.27 1 -0.33 25 26
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.034 0.066 -10000 0 -0.3 17 17
nectin-2(dimer)/I-afadin/I-afadin 0.034 0.066 -10000 0 -0.3 17 17
PIP5K1C -0.01 0.075 -10000 0 -0.25 35 35
VAV2 -0.013 0.2 -10000 0 -0.53 42 42
RAP1/GDP 0.006 0.16 -10000 0 -0.39 45 45
ITGAV 0.022 0.077 -10000 0 -0.43 14 14
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.034 0.094 -10000 0 -0.27 39 39
nectin-3(dimer)/I-afadin/I-afadin 0.022 0.09 -10000 0 -0.32 31 31
Rac1/GTP 0.002 0.16 -10000 0 -0.4 45 45
PTPRM -0.005 0.087 -10000 0 -0.28 36 36
E-cadherin/beta catenin/alpha catenin 0.024 0.12 -10000 0 -0.23 69 69
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.034 0.007 -10000 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0.026 0.003 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0.031 0.03 -10000 0 -0.43 2 2
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.012 0.11 -10000 0 -0.38 28 28
IRAK/TOLLIP 0.039 0.014 0.18 3 -10000 0 3
IKBKB 0.029 0.024 -10000 0 -0.43 1 1
IKBKG 0.035 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.021 0.091 -10000 0 -0.31 35 35
IL1A 0.031 0.042 -10000 0 -0.43 4 4
IL1B -0.025 0.12 -10000 0 -0.35 54 54
IRAK/TRAF6/p62/Atypical PKCs 0.058 0.049 -10000 0 -0.21 12 12
IL1R2 0.003 0.11 -10000 0 -0.43 31 31
IL1R1 -0.006 0.13 -10000 0 -0.43 42 42
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.027 0.12 -10000 0 -0.39 34 34
TOLLIP 0.034 0.007 -10000 0 -10000 0 0
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.032 0.011 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.06 0.033 -10000 0 -0.26 2 2
IKK complex/ELKS 0.024 0.075 -10000 0 -0.32 10 10
JUN -0.029 0.071 0.25 2 -0.46 2 4
MAP3K7 0.033 0.009 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.002 0.15 -10000 0 -0.28 100 100
IL1 alpha/IL1R1/IL1RAP/MYD88 0.049 0.099 -10000 0 -0.24 51 51
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.06 0.1 -10000 0 -0.23 53 53
IL1 beta fragment/IL1R1/IL1RAP -0.016 0.14 -10000 0 -0.29 93 93
NFKB1 0.034 0.021 -10000 0 -0.43 1 1
MAPK8 -0.016 0.058 0.26 2 -0.38 1 3
IRAK1 0.018 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.008 0.14 -10000 0 -0.33 72 72
IRAK4 0.032 0.036 -10000 0 -0.43 3 3
PRKCI 0.024 0.065 -10000 0 -0.43 10 10
TRAF6 0.034 0.021 -10000 0 -0.43 1 1
PI3K 0.033 0.066 -10000 0 -0.31 17 17
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.023 0.13 -10000 0 -0.38 43 43
CHUK 0.024 0.071 -10000 0 -0.43 12 12
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.016 0.14 -10000 0 -0.29 93 93
IL1 beta/IL1R2 -0.025 0.14 -10000 0 -0.3 89 89
IRAK/TRAF6/TAK1/TAB1/TAB2 0.075 0.042 -10000 0 -0.21 3 3
NF kappa B1 p50/RelA -0.008 0.14 -10000 0 -0.28 85 85
IRAK3 0.026 0.047 -10000 0 -0.43 5 5
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.003 0.14 -10000 0 -0.27 94 94
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.008 0.084 -10000 0 -0.23 53 53
IL1 alpha/IL1R1/IL1RAP 0.035 0.096 -10000 0 -0.26 47 47
RELA 0.034 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0.033 0.009 -10000 0 -10000 0 0
SQSTM1 0.033 0.022 -10000 0 -0.43 1 1
MYD88 0.03 0.042 -10000 0 -0.43 4 4
IRAK/TRAF6/MEKK3 0.055 0.028 -10000 0 -0.22 1 1
IL1RAP 0.033 0.022 -10000 0 -0.43 1 1
UBE2N 0.035 0.004 -10000 0 -10000 0 0
IRAK/TRAF6 -0.018 0.12 -10000 0 -0.26 75 75
CASP1 -0.002 0.12 -10000 0 -0.43 34 34
IL1RN/IL1R2 -0.003 0.13 -10000 0 -0.33 62 62
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.001 0.14 -10000 0 -0.28 94 94
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.002 0.12 -10000 0 -0.32 49 49
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
IL1RN -0.001 0.12 -10000 0 -0.43 37 37
TRAF6/TAK1/TAB1/TAB2 0.071 0.041 -10000 0 -0.22 3 3
MAP2K6 -0.013 0.055 -10000 0 -0.4 1 1
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.007 0.033 -10000 0 -0.099 54 54
STMN1 0.006 0.052 -10000 0 -0.34 10 10
Aurora B/RasGAP/Survivin 0.026 0.1 -10000 0 -0.29 45 45
Chromosomal passenger complex/Cul3 protein complex -0.044 0.12 -10000 0 -0.29 61 61
BIRC5 -0.005 0.13 -10000 0 -0.45 38 38
DES -0.058 0.25 -10000 0 -0.68 67 67
Aurora C/Aurora B/INCENP 0.05 0.051 -10000 0 -0.25 11 11
Aurora B/TACC1 0.02 0.068 -10000 0 -0.26 25 25
Aurora B/PP2A 0.044 0.034 -10000 0 -0.32 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.008 0.025 -10000 0 -0.19 7 7
mitotic metaphase/anaphase transition 0.001 0.005 0.014 47 -0.01 2 49
NDC80 0.005 0.026 -10000 0 -0.32 3 3
Cul3 protein complex 0.011 0.12 -10000 0 -0.26 75 75
KIF2C -0.059 0.22 -10000 0 -0.63 54 54
PEBP1 -0.001 0.004 -10000 0 -0.014 40 40
KIF20A 0.002 0.12 -10000 0 -0.43 35 35
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.037 0.056 -10000 0 -0.31 11 11
SEPT1 0.03 0.023 -10000 0 -0.43 1 1
SMC2 0 0 -10000 0 -10000 0 0
SMC4 0 0 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.039 0.18 -10000 0 -0.52 54 54
PSMA3 0.034 0.006 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.004 0.01 48 -0.008 10 58
H3F3B 0.014 0.029 -10000 0 -0.3 4 4
AURKB 0.028 0.041 -10000 0 -0.46 3 3
AURKC 0.032 0.022 -10000 0 -0.43 1 1
CDCA8 0.016 0.086 -10000 0 -0.46 16 16
cytokinesis -0.047 0.23 -10000 0 -0.62 54 54
Aurora B/Septin1 -0.03 0.22 -10000 0 -0.57 53 53
AURKA 0 0.004 0.01 48 -0.008 10 58
INCENP 0.024 0.058 -10000 0 -0.44 7 7
KLHL13 -0.036 0.16 -10000 0 -0.43 72 72
BUB1 -0.014 0.14 -10000 0 -0.43 52 52
hSgo1/Aurora B/Survivin 0.022 0.12 -10000 0 -0.35 39 39
EVI5 0.03 0.042 -10000 0 -0.43 4 4
RhoA/GTP -0.023 0.22 -10000 0 -0.55 56 56
SGOL1 0.019 0.082 -10000 0 -0.43 16 16
CENPA -0.038 0.15 -10000 0 -0.33 76 76
NCAPG 0 0 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.044 0.034 -10000 0 -0.32 3 3
NCAPD2 0 0 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.042 0.043 -10000 0 -0.32 6 6
RHOA 0.025 0.062 -10000 0 -0.43 9 9
NCAPH 0 0 -10000 0 -10000 0 0
NPM1 -0.019 0.12 -10000 0 -0.34 54 54
RASA1 0.026 0.058 -10000 0 -0.43 8 8
KLHL9 0.031 0.03 -10000 0 -0.43 2 2
mitotic prometaphase -0.001 0.004 -10000 0 -0.014 40 40
proteasomal ubiquitin-dependent protein catabolic process 0.043 0.034 -10000 0 -0.32 3 3
PPP1CC 0.032 0.036 -10000 0 -0.43 3 3
Centraspindlin -0.031 0.24 -10000 0 -0.59 57 57
RhoA/GDP 0.019 0.044 -10000 0 -0.3 9 9
NSUN2 -0.015 0.12 -10000 0 -0.33 45 45
MYLK 0.006 0.058 -10000 0 -0.31 16 16
KIF23 0.005 0.11 -10000 0 -0.44 30 30
VIM -0.004 0.073 -10000 0 -0.31 26 26
RACGAP1 0.018 0.087 -10000 0 -0.44 17 17
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.018 0.12 -10000 0 -0.34 52 52
Chromosomal passenger complex -0.05 0.18 -10000 0 -0.42 70 70
Chromosomal passenger complex/EVI5 0.037 0.14 -10000 0 -0.33 50 50
TACC1 0.008 0.095 -10000 0 -0.43 22 22
PPP2R5D 0.035 0.005 -10000 0 -10000 0 0
CUL3 0.031 0.042 -10000 0 -0.43 4 4
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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
PDGFRA -0.007 0.12 -10000 0 -0.44 31 31
PDGF/PDGFRA/CRKL 0.016 0.092 -10000 0 -0.31 35 35
positive regulation of JUN kinase activity 0.046 0.074 -10000 0 -0.24 23 23
CRKL 0.03 0.042 -10000 0 -0.43 4 4
PDGF/PDGFRA/Caveolin-3 0.018 0.088 -10000 0 -0.31 31 31
AP1 -0.13 0.3 -10000 0 -0.81 75 75
mol:IP3 -0.013 0.081 -10000 0 -0.33 27 27
PLCG1 -0.013 0.081 -10000 0 -0.33 27 27
PDGF/PDGFRA/alphaV Integrin 0.01 0.11 -10000 0 -0.32 43 43
RAPGEF1 0.034 0.005 -10000 0 -10000 0 0
CRK 0.031 0.023 -10000 0 -0.43 1 1
mol:Ca2+ -0.013 0.081 -10000 0 -0.33 27 27
CAV3 0.033 0.022 -10000 0 -0.43 1 1
CAV1 0.026 0.055 -10000 0 -0.43 7 7
SHC/Grb2/SOS1 0.048 0.075 -10000 0 -0.24 23 23
PDGF/PDGFRA/Shf 0.018 0.089 -10000 0 -0.31 32 32
FOS -0.14 0.29 -10000 0 -0.8 75 75
JUN -0.048 0.083 -10000 0 -0.35 33 33
oligodendrocyte development 0.01 0.11 -10000 0 -0.32 43 43
GRB2 0.033 0.009 -10000 0 -10000 0 0
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
mol:DAG -0.013 0.081 -10000 0 -0.33 27 27
PDGF/PDGFRA -0.007 0.12 -10000 0 -0.44 31 31
actin cytoskeleton reorganization 0.016 0.093 -10000 0 -0.31 35 35
SRF 0.017 0.013 -10000 0 -10000 0 0
SHC1 0.027 0.025 -10000 0 -0.43 1 1
PI3K 0.03 0.1 -10000 0 -0.29 41 41
PDGF/PDGFRA/Crk/C3G 0.04 0.081 -10000 0 -0.26 32 32
JAK1 -0.012 0.082 -10000 0 -0.32 32 32
ELK1/SRF -0.018 0.077 0.15 32 -0.26 30 62
SHB 0.029 0.046 -10000 0 -0.43 5 5
SHF 0.032 0.022 -10000 0 -0.43 1 1
CSNK2A1 0.037 0.022 -10000 0 -10000 0 0
GO:0007205 -0.022 0.086 -10000 0 -0.36 28 28
SOS1 0.034 0.021 -10000 0 -0.43 1 1
Ras protein signal transduction 0.046 0.074 -10000 0 -0.24 23 23
PDGF/PDGFRA/SHB 0.016 0.093 -10000 0 -0.31 35 35
PDGF/PDGFRA/Caveolin-1 0.013 0.1 -10000 0 -0.34 34 34
ITGAV 0.022 0.077 -10000 0 -0.43 14 14
ELK1 -0.034 0.08 0.17 1 -0.32 30 31
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
PDGF/PDGFRA/Crk 0.016 0.089 -10000 0 -0.31 32 32
JAK-STAT cascade -0.012 0.082 -10000 0 -0.32 32 32
cell proliferation 0.018 0.089 -10000 0 -0.3 32 32
mTOR 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
GBL 0.031 0.023 -10000 0 -0.43 1 1
MKNK1 0.034 0.006 -10000 0 -10000 0 0
mol:PIP3 -0.023 0.1 0.3 4 -0.27 61 65
FRAP1 -0.004 0.12 -10000 0 -0.45 24 24
AKT1 -0.019 0.094 0.18 27 -0.25 51 78
INSR 0.033 0.03 -10000 0 -0.43 2 2
Insulin Receptor/Insulin 0.043 0.026 -10000 0 -0.26 3 3
mol:GTP 0.018 0.099 0.27 7 -0.22 39 46
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.004 0.047 -10000 0 -0.2 12 12
TSC2 0.031 0.023 -10000 0 -0.43 1 1
RHEB/GDP 0.008 0.078 -10000 0 -0.23 19 19
TSC1 0.035 0.005 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.01 0.11 -10000 0 -0.31 63 63
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.016 0.064 -10000 0 -0.23 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.009 0.089 0.24 9 -0.33 13 22
MAP3K5 -0.014 0.084 0.2 5 -0.26 45 50
PIK3R1 0.018 0.084 -10000 0 -0.43 17 17
apoptosis -0.014 0.084 0.2 5 -0.26 45 50
mol:LY294002 0 0 0.001 2 -0.001 57 59
EIF4B 0.007 0.082 0.23 7 -0.29 14 21
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.019 0.08 0.22 8 -0.27 14 22
eIF4E/eIF4G1/eIF4A1 0.003 0.076 -10000 0 -0.31 15 15
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.002 0.12 -10000 0 -0.27 71 71
mTOR/RHEB/GTP/Raptor/GBL 0.016 0.064 0.22 6 -0.22 7 13
FKBP1A 0.034 0.008 -10000 0 -10000 0 0
RHEB/GTP 0.025 0.09 0.25 4 -0.27 11 15
mol:Amino Acids 0 0 0.001 2 -0.001 57 59
FKBP12/Rapamycin 0.025 0.006 -10000 0 -10000 0 0
PDPK1 -0.028 0.096 0.18 25 -0.26 58 83
EIF4E 0.034 0.006 -10000 0 -10000 0 0
ASK1/PP5C -0.025 0.21 -10000 0 -0.58 53 53
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.017 0.056 -10000 0 -0.38 1 1
TSC1/TSC2 0.021 0.11 0.28 8 -0.24 39 47
tumor necrosis factor receptor activity 0 0 0.001 57 -0.001 2 59
RPS6 0.032 0.03 -10000 0 -0.43 2 2
PPP5C 0.031 0.042 -10000 0 -0.43 4 4
EIF4G1 0.03 0.042 -10000 0 -0.43 4 4
IRS1 -0.031 0.11 -10000 0 -0.32 63 63
INS 0.033 0.022 -10000 0 -0.43 1 1
PTEN 0.024 0.068 -10000 0 -0.43 11 11
PDK2 -0.027 0.096 0.18 26 -0.25 55 81
EIF4EBP1 -0.061 0.3 -10000 0 -1.1 33 33
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
PPP2R5D -0.002 0.11 -10000 0 -0.4 24 24
peptide biosynthetic process 0.017 0.032 0.19 6 -0.24 5 11
RHEB 0.034 0.006 -10000 0 -10000 0 0
EIF4A1 0.032 0.011 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 21 -0.003 5 26
EEF2 0.017 0.032 0.19 6 -0.24 5 11
eIF4E/4E-BP1 -0.041 0.28 -10000 0 -1.1 33 33
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.027 0.025 -10000 0 -0.43 1 1
Caspase 8 (4 units) 0.025 0.13 -10000 0 -0.4 23 23
NEF -0.012 0.049 -10000 0 -0.17 45 45
NFKBIA 0.02 0.053 -10000 0 -0.12 41 41
BIRC3 -0.02 0.15 0.38 1 -0.47 45 46
CYCS -0.01 0.12 0.19 2 -0.32 43 45
RIPK1 0.034 0.006 -10000 0 -10000 0 0
CD247 -0.012 0.049 -10000 0 -0.17 45 45
MAP2K7 0.001 0.18 -10000 0 -0.68 20 20
protein ubiquitination -0.015 0.12 0.27 3 -0.38 25 28
CRADD 0.029 0.051 -10000 0 -0.43 6 6
DAXX 0.035 0.004 -10000 0 -10000 0 0
FAS 0.006 0.11 -10000 0 -0.43 29 29
BID -0.01 0.13 -10000 0 -0.33 47 47
NF-kappa-B/RelA/I kappa B alpha 0.037 0.1 -10000 0 -0.27 43 43
TRADD 0.029 0.024 -10000 0 -0.43 1 1
MAP3K5 0.011 0.097 -10000 0 -0.43 23 23
CFLAR 0.03 0.046 -10000 0 -0.43 5 5
FADD 0.029 0.013 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.037 0.1 -10000 0 -0.27 43 43
MAPK8 0.001 0.16 0.42 1 -0.62 19 20
APAF1 0.031 0.041 -10000 0 -0.43 4 4
TRAF1 0.033 0.022 -10000 0 -0.43 1 1
TRAF2 0.033 0.03 -10000 0 -0.43 2 2
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.004 0.13 -10000 0 -0.34 45 45
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.014 0.15 0.24 1 -0.45 31 32
CHUK -0.018 0.13 0.38 1 -0.42 25 26
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.052 0.098 -10000 0 -0.25 37 37
TCRz/NEF -0.018 0.084 -10000 0 -0.28 45 45
TNF 0.025 0.062 -10000 0 -0.43 9 9
FASLG -0.024 0.14 -10000 0 -0.53 37 37
NFKB1 0.021 0.047 -10000 0 -0.43 1 1
TNFR1A/BAG4/TNF-alpha 0.047 0.047 -10000 0 -0.26 6 6
CASP6 0.018 0.16 -10000 0 -0.55 21 21
CASP7 -0.045 0.2 0.39 2 -0.47 74 76
RELA 0.022 0.042 -10000 0 -0.15 2 2
CASP2 0.034 0.007 -10000 0 -10000 0 0
CASP3 -0.043 0.2 0.35 1 -0.46 73 74
TNFRSF1A 0.032 0.022 -10000 0 -0.43 1 1
TNFR1A/BAG4 0.038 0.028 -10000 0 -0.31 1 1
CASP8 0.035 0.004 -10000 0 -10000 0 0
CASP9 0.033 0.022 -10000 0 -0.43 1 1
MAP3K14 -0.015 0.14 0.23 2 -0.44 28 30
APAF-1/Caspase 9 -0.02 0.14 -10000 0 -0.35 57 57
BCL2 -0.032 0.16 0.58 1 -0.53 25 26
TRAIL signaling 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
TNFSF10 -0.01 0.13 -10000 0 -0.43 46 46
positive regulation of NF-kappaB transcription factor activity 0.008 0.1 -10000 0 -0.3 46 46
MAP2K4 -0.012 0.11 -10000 0 -0.35 30 30
IKBKB 0.029 0.024 -10000 0 -0.43 1 1
TNFRSF10B 0.027 0.015 -10000 0 -10000 0 0
TNFRSF10A 0.022 0.052 -10000 0 -0.43 6 6
SMPD1 -0.007 0.073 -10000 0 -0.21 45 45
IKBKG 0.035 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.028 0.015 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.007 0.1 -10000 0 -0.31 46 46
TRAIL/TRAILR3 0.004 0.1 -10000 0 -0.3 47 47
TRAIL/TRAILR1 0.004 0.11 -10000 0 -0.32 50 50
TRAIL/TRAILR4 0.008 0.1 -10000 0 -0.3 46 46
TRAIL/TRAILR1/DAP3/GTP 0.016 0.087 -10000 0 -0.24 42 42
IKK complex 0.011 0.096 -10000 0 -0.42 16 16
RIPK1 0.034 0.006 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.02 0.018 -10000 0 -0.3 1 1
MAPK3 -0.012 0.088 -10000 0 -0.31 41 41
MAP3K1 -0.012 0.12 -10000 0 -0.37 34 34
TRAILR4 (trimer) 0.027 0.015 -10000 0 -10000 0 0
TRADD 0.029 0.024 -10000 0 -0.43 1 1
TRAILR1 (trimer) 0.022 0.052 -10000 0 -0.43 6 6
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.005 0.095 -10000 0 -0.3 39 39
CFLAR 0.03 0.046 -10000 0 -0.43 5 5
MAPK1 -0.013 0.091 -10000 0 -0.31 44 44
TRAIL/TRAILR1/FADD/TRADD/RIP 0.035 0.096 -10000 0 -0.24 38 38
mol:ceramide -0.007 0.073 -10000 0 -0.21 45 45
FADD 0.029 0.013 -10000 0 -10000 0 0
MAPK8 -0.024 0.12 0.21 1 -0.36 33 34
TRAF2 0.033 0.03 -10000 0 -0.43 2 2
TRAILR3 (trimer) 0.024 0.026 -10000 0 -0.43 1 1
CHUK 0.024 0.071 -10000 0 -0.43 12 12
TRAIL/TRAILR1/FADD 0.02 0.092 -10000 0 -0.27 38 38
DAP3 0.028 0.025 -10000 0 -0.43 1 1
CASP10 0.009 0.084 0.33 3 -0.29 21 24
JNK cascade 0.008 0.1 -10000 0 -0.3 46 46
TRAIL (trimer) -0.01 0.13 -10000 0 -0.43 46 46
TNFRSF10C 0.024 0.026 -10000 0 -0.43 1 1
TRAIL/TRAILR1/DAP3/GTP/FADD 0.024 0.082 -10000 0 -0.23 33 33
TRAIL/TRAILR2/FADD 0.023 0.086 -10000 0 -0.26 35 35
cell death -0.007 0.073 -10000 0 -0.21 45 45
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.003 0.092 -10000 0 -0.3 36 36
TRAILR2 (trimer) 0.027 0.015 -10000 0 -10000 0 0
CASP8 0.024 0.047 -10000 0 -0.66 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.038 0.091 -10000 0 -0.23 35 35
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.018 0.074 -10000 0 -0.3 24 24
PDGFRB 0.027 0.059 -10000 0 -0.44 8 8
SPHK1 -0.033 0.2 -10000 0 -0.76 34 34
mol:S1P -0.021 0.18 -10000 0 -0.66 34 34
S1P1/S1P/Gi -0.021 0.16 -10000 0 -0.48 35 35
GNAO1 0.03 0.014 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.001 0.15 0.29 3 -0.46 28 31
PLCG1 -0.017 0.14 0.26 2 -0.47 30 32
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.027 0.059 -10000 0 -0.44 8 8
GNAI2 0.027 0.059 -10000 0 -0.43 8 8
GNAI3 0.035 0.007 -10000 0 -10000 0 0
GNAI1 0.015 0.092 -10000 0 -0.43 20 20
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.001 0.12 -10000 0 -0.54 23 23
S1P1/S1P -0.014 0.17 0.25 1 -0.47 50 51
negative regulation of cAMP metabolic process -0.02 0.16 -10000 0 -0.47 35 35
MAPK3 -0.018 0.16 0.32 10 -0.54 26 36
calcium-dependent phospholipase C activity 0 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.044 -10000 0 -0.3 9 9
KDR 0.028 0.06 -10000 0 -0.23 20 20
PLCB2 -0.011 0.15 0.24 1 -0.41 51 52
RAC1 0.034 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.02 0.14 -10000 0 -0.4 50 50
receptor internalization -0.012 0.16 0.24 1 -0.42 54 55
PTGS2 -0.013 0.17 -10000 0 -0.68 18 18
Rac1/GTP -0.016 0.14 -10000 0 -0.39 49 49
RHOA 0.025 0.062 -10000 0 -0.43 9 9
VEGFA -0.003 0.032 -10000 0 -0.14 24 24
negative regulation of T cell proliferation -0.02 0.16 -10000 0 -0.47 35 35
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.023 0.072 -10000 0 -0.43 12 12
MAPK1 -0.021 0.16 0.27 1 -0.54 28 29
S1P1/S1P/PDGFB-D/PDGFRB 0.005 0.18 0.31 1 -0.46 47 48
ABCC1 0.029 0.043 -10000 0 -0.43 4 4
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 0.043 0.053 -10000 0 -0.24 13 13
RGS9BP -0.026 0.15 -10000 0 -0.43 62 62
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.021 0.062 -10000 0 -0.27 19 19
mol:ADP 0.008 0.02 -10000 0 -0.3 2 2
GNAT2 0.018 0.084 -10000 0 -0.43 17 17
RGS9-1/Gbeta5/R9AP 0.003 0.12 -10000 0 -0.28 76 76
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.025 0.076 -10000 0 -0.27 29 29
GRK7 0.033 0.03 -10000 0 -0.43 2 2
CNGB3 0.022 0.048 -10000 0 -0.43 5 5
Cone Metarhodopsin II/X-Arrestin 0.026 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.04 0.086 0.19 88 -0.24 18 106
Cone PDE6 0.018 0.13 -10000 0 -0.25 86 86
Cone Metarhodopsin II 0.021 0.016 -10000 0 -0.23 2 2
Na + (4 Units) 0.037 0.062 -10000 0 -0.24 18 18
GNAT2/GDP 0.009 0.12 -10000 0 -0.24 86 86
GNB5 0.024 0.068 -10000 0 -0.43 11 11
mol:GMP (4 units) 0.003 0.077 0.19 12 -0.26 33 45
Cone Transducin 0.046 0.057 -10000 0 -0.25 13 13
SLC24A2 0.032 0.03 -10000 0 -0.43 2 2
GNB3/GNGT2 0.043 0.025 -10000 0 -0.31 1 1
GNB3 0.033 0.009 -10000 0 -10000 0 0
GNAT2/GTP 0.014 0.06 -10000 0 -0.3 17 17
CNGA3 0.017 0.079 -10000 0 -0.43 15 15
ARR3 0.035 0.002 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.021 0.062 -10000 0 -0.27 19 19
mol:Pi 0.002 0.12 -10000 0 -0.27 76 76
Cone CNG Channel 0.032 0.098 -10000 0 -0.26 42 42
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.032 0.03 -10000 0 -0.43 2 2
RGS9 0.016 0.074 -10000 0 -0.43 13 13
PDE6C 0.029 0.051 -10000 0 -0.43 6 6
GNGT2 0.03 0.031 -10000 0 -0.43 2 2
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.02 0.077 -10000 0 -0.43 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 -0.023 0.24 -10000 0 -0.74 24 24
PCK1 0.02 0.18 -10000 0 -0.99 5 5
HNF4A -0.008 0.25 0.57 2 -0.75 23 25
KCNJ11 -0.051 0.35 -10000 0 -1 44 44
AKT1 -0.001 0.17 -10000 0 -0.42 23 23
response to starvation 0.004 0.002 -10000 0 -10000 0 0
DLK1 -0.019 0.26 0.63 1 -0.79 23 24
NKX2-1 0.04 0.13 0.36 4 -0.35 7 11
ACADM -0.026 0.26 -10000 0 -0.77 27 27
TAT 0 0.15 -10000 0 -0.56 2 2
CEBPB 0.029 0.052 -10000 0 -0.43 6 6
CEBPA 0.029 0.069 -10000 0 -0.43 11 11
TTR -0.025 0.28 0.55 1 -0.7 45 46
PKLR 0.015 0.25 0.56 2 -0.71 22 24
APOA1 -0.02 0.28 -10000 0 -0.86 22 22
CPT1C -0.029 0.27 -10000 0 -0.81 30 30
ALAS1 0.009 0.18 -10000 0 -1.1 4 4
TFRC -0.043 0.36 -10000 0 -1.2 37 37
FOXF1 0.027 0.025 -10000 0 -0.43 1 1
NF1 0.037 0.028 -10000 0 -0.34 2 2
HNF1A (dimer) 0.008 0.02 -10000 0 -0.21 4 4
CPT1A -0.011 0.28 0.56 1 -0.85 25 26
HMGCS1 -0.018 0.24 -10000 0 -0.73 24 24
NR3C1 0.033 0.075 -10000 0 -0.4 14 14
CPT1B -0.019 0.23 -10000 0 -0.72 23 23
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.035 0.004 -10000 0 -10000 0 0
GCK -0.022 0.25 -10000 0 -0.74 26 26
CREB1 0.04 0.029 -10000 0 -0.28 3 3
IGFBP1 0.011 0.14 -10000 0 -1.3 1 1
PDX1 0.009 0.15 -10000 0 -0.36 24 24
UCP2 -0.049 0.31 -10000 0 -0.86 45 45
ALDOB -0.018 0.26 -10000 0 -0.79 23 23
AFP -0.023 0.12 -10000 0 -0.7 4 4
BDH1 -0.023 0.26 -10000 0 -0.75 32 32
HADH -0.02 0.26 -10000 0 -0.62 50 50
F2 -0.004 0.28 -10000 0 -0.85 22 22
HNF1A 0.008 0.02 -10000 0 -0.21 4 4
G6PC 0.039 0.089 -10000 0 -1.3 1 1
SLC2A2 0.004 0.2 -10000 0 -1.2 4 4
INS 0.023 0.024 0.2 1 -0.44 1 2
FOXA1 -0.04 0.18 -10000 0 -0.41 98 98
FOXA3 0.04 0.075 -10000 0 -0.26 8 8
FOXA2 -0.007 0.32 -10000 0 -0.72 47 47
ABCC8 -0.2 0.48 -10000 0 -0.9 150 150
ALB -0.029 0.15 -10000 0 -0.96 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 0.014 0.11 -10000 0 -0.28 52 52
fibroblast growth factor receptor signaling pathway 0.014 0.11 -10000 0 -0.28 52 52
LAMA1 0.033 0.009 -10000 0 -10000 0 0
PRNP 0.026 0.058 -10000 0 -0.43 8 8
GPC1/SLIT2 0.01 0.12 -10000 0 -0.32 52 52
SMAD2 0.003 0.065 0.19 3 -0.24 30 33
GPC1/PrPc/Cu2+ 0.028 0.071 -10000 0 -0.27 26 26
GPC1/Laminin alpha1 0.034 0.069 -10000 0 -0.31 19 19
TDGF1 0.034 0.008 -10000 0 -10000 0 0
CRIPTO/GPC1 0.035 0.069 -10000 0 -0.31 19 19
APP/GPC1 0.013 0.11 -10000 0 -0.31 47 47
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.005 0.06 -10000 0 -0.26 24 24
FLT1 0.025 0.059 -10000 0 -0.43 8 8
GPC1/TGFB/TGFBR1/TGFBR2 0.046 0.082 -10000 0 -0.27 30 30
SERPINC1 0.028 0.025 -10000 0 -0.43 1 1
FYN 0.005 0.06 -10000 0 -0.26 24 24
FGR 0.008 0.054 -10000 0 -0.26 19 19
positive regulation of MAPKKK cascade -0.024 0.12 -10000 0 -0.36 43 43
SLIT2 0 0.12 -10000 0 -0.43 36 36
GPC1/NRG 0.027 0.069 -10000 0 -0.3 19 19
NRG1 0.028 0.014 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.026 0.071 -10000 0 -0.27 26 26
LYN 0.009 0.046 -10000 0 -0.26 14 14
mol:Spermine -0.003 0.059 -10000 0 -0.3 19 19
cell growth 0.014 0.11 -10000 0 -0.28 52 52
BMP signaling pathway -0.016 0.088 0.43 19 -10000 0 19
SRC 0.007 0.058 -10000 0 -0.27 20 20
TGFBR1 0.027 0.058 -10000 0 -0.43 8 8
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.012 0.081 -10000 0 -0.43 16 16
GPC1 0.016 0.089 -10000 0 -0.43 19 19
TGFBR1 (dimer) 0.027 0.058 -10000 0 -0.43 8 8
VEGFA 0 0 -10000 0 -10000 0 0
BLK 0.002 0.055 -10000 0 -0.26 21 21
HCK -0.001 0.073 -10000 0 -0.27 34 34
FGF2 -0.003 0.12 -10000 0 -0.43 34 34
FGFR1 0.019 0.065 -10000 0 -0.43 10 10
VEGFR1 homodimer 0.025 0.059 -10000 0 -0.43 8 8
TGFBR2 0.031 0.042 -10000 0 -0.43 4 4
cell death 0.013 0.11 -10000 0 -0.31 47 47
ATIII/GPC1 0.028 0.07 -10000 0 -0.31 19 19
PLA2G2A/GPC1 0.015 0.091 -10000 0 -0.31 34 34
LCK -0.023 0.099 -10000 0 -0.27 70 70
neuron differentiation 0.027 0.069 -10000 0 -0.3 19 19
PrPc/Cu2+ 0.02 0.041 -10000 0 -0.3 8 8
APP 0.006 0.11 -10000 0 -0.43 29 29
TGFBR2 (dimer) 0.031 0.042 -10000 0 -0.43 4 4
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0 0.047 0.2 23 -0.096 4 27
BUB1B -0.017 0.099 0.11 2 -0.31 42 44
PLK1 0.003 0.033 0.081 8 -0.086 25 33
PLK1S1 0.002 0.019 0.045 12 -0.047 22 34
KIF2A 0.003 0.03 0.073 7 -0.077 25 32
regulation of mitotic centrosome separation 0.003 0.033 0.083 7 -0.085 25 32
GOLGA2 0.035 0.004 -10000 0 -10000 0 0
Hec1/SPC24 -0.008 0.02 -10000 0 -0.069 30 30
WEE1 -0.003 0.092 -10000 0 -0.38 22 22
cytokinesis -0.025 0.14 -10000 0 -0.46 40 40
PP2A-alpha B56 -0.032 0.28 -10000 0 -0.72 67 67
AURKA 0.002 0.02 0.052 11 -0.049 15 26
PICH/PLK1 -0.018 0.097 -10000 0 -0.34 34 34
CENPE -0.013 0.069 0.17 2 -0.25 32 34
RhoA/GTP 0.019 0.044 -10000 0 -0.3 9 9
positive regulation of microtubule depolymerization 0.003 0.03 0.073 7 -0.077 25 32
PPP2CA 0.03 0.046 -10000 0 -0.43 5 5
FZR1 0.034 0.006 -10000 0 -10000 0 0
TPX2 -0.008 0.078 0.1 1 -0.28 37 38
PAK1 0.013 0.088 -10000 0 -0.44 18 18
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.032 0.03 -10000 0 -0.43 2 2
CLSPN 0.003 0.056 -10000 0 -0.28 17 17
GORASP1 0.033 0.022 -10000 0 -0.43 1 1
metaphase 0.002 0.005 0.019 38 -10000 0 38
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.002 0.019 0.045 12 -0.047 22 34
G2 phase of mitotic cell cycle -0.001 0.002 0.012 4 -10000 0 4
STAG2 0.035 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.009 0.11 -10000 0 -0.53 18 18
spindle elongation 0.003 0.033 0.083 7 -0.085 25 32
ODF2 0.035 0.004 -10000 0 -10000 0 0
BUB1 -0.07 0.29 -10000 0 -0.77 68 68
TPT1 -0.006 0.059 -10000 0 -0.19 44 44
CDC25C -0.016 0.11 -10000 0 -0.36 43 43
CDC25B 0.026 0.046 -10000 0 -0.44 4 4
SGOL1 0 0.047 0.096 4 -0.2 23 27
RHOA 0.025 0.062 -10000 0 -0.43 9 9
CCNB1/CDK1 0.026 0.14 -10000 0 -0.38 40 40
CDC14B 0.006 0.024 -10000 0 -0.31 3 3
CDC20 0.015 0.089 -10000 0 -0.43 19 19
PLK1/PBIP1 -0.006 0.058 0.082 2 -0.22 29 31
mitosis 0 0.003 0.012 7 -10000 0 7
FBXO5 -0.002 0.05 0.13 8 -0.15 22 30
CDC2 0.012 0.099 -10000 0 -0.44 22 22
NDC80 0 0 -10000 0 -10000 0 0
metaphase plate congression 0.005 0.052 -10000 0 -0.25 18 18
ERCC6L -0.014 0.11 -10000 0 -0.36 40 40
NLP/gamma Tubulin 0.004 0.024 0.072 3 -0.079 5 8
microtubule cytoskeleton organization -0.006 0.059 -10000 0 -0.19 44 44
G2/M transition DNA damage checkpoint 0 0.003 0.011 17 -10000 0 17
PPP1R12A 0.034 0.021 -10000 0 -0.43 1 1
interphase 0 0.003 0.011 17 -10000 0 17
PLK1/PRC1-2 0.01 0.12 -10000 0 -0.33 43 43
GRASP65/GM130/RAB1/GTP/PLK1 0.05 0.048 -10000 0 -0.19 2 2
RAB1A 0.034 0.021 -10000 0 -0.43 1 1
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.002 0.025 0.063 13 -0.068 14 27
mitotic prometaphase -0.001 0.004 0.018 18 -10000 0 18
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.055 -10000 0 -0.37 4 4
microtubule-based process 0.005 0.079 -10000 0 -0.25 36 36
Golgi organization 0.003 0.033 0.083 7 -0.085 25 32
Cohesin/SA2 0.02 0.034 -10000 0 -0.11 1 1
PPP1CB/MYPT1 0.05 0.018 -10000 0 -0.31 1 1
KIF20A 0.002 0.12 -10000 0 -0.43 35 35
APC/C/CDC20 0.013 0.065 -10000 0 -0.26 20 20
PPP2R1A 0.034 0.006 -10000 0 -10000 0 0
chromosome segregation -0.006 0.057 0.081 2 -0.21 29 31
PRC1 0.008 0.1 -10000 0 -0.43 27 27
ECT2 0.001 0.067 0.22 19 -0.23 17 36
C13orf34 0.003 0.028 0.067 13 -0.073 22 35
NUDC 0.005 0.052 -10000 0 -0.25 18 18
regulation of attachment of spindle microtubules to kinetochore -0.017 0.098 0.11 2 -0.31 42 44
spindle assembly 0.003 0.03 0.079 8 -0.081 13 21
spindle stabilization 0.002 0.019 0.045 12 -0.047 22 34
APC/C/HCDH1 0.029 0.023 -10000 0 -0.26 3 3
MKLP2/PLK1 0.005 0.08 -10000 0 -0.26 36 36
CCNB1 0.01 0.1 -10000 0 -0.44 25 25
PPP1CB 0.035 0.004 -10000 0 -10000 0 0
BTRC 0.033 0.022 -10000 0 -0.43 1 1
ROCK2 0.006 0.06 -10000 0 -0.3 11 11
TUBG1 0.007 0.033 -10000 0 -0.17 12 12
G2/M transition of mitotic cell cycle -0.021 0.12 -10000 0 -0.37 40 40
MLF1IP -0.009 0.073 -10000 0 -0.31 28 28
INCENP 0.026 0.055 -10000 0 -0.44 7 7
Calcium signaling in the CD4+ TCR 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
NFATC1 0.008 0.057 -10000 0 -0.25 17 17
NFATC2 0.014 0.037 -10000 0 -0.24 4 4
NFATC3 0.018 0.027 -10000 0 -10000 0 0
CD40LG -0.015 0.19 0.36 6 -0.45 52 58
PTGS2 -0.02 0.18 0.38 5 -0.45 47 52
JUNB 0.031 0.042 -10000 0 -0.43 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.025 -10000 0 -0.082 2 2
CaM/Ca2+ 0.021 0.025 -10000 0 -0.082 2 2
CALM1 0.032 0.019 -10000 0 -10000 0 0
JUN -0.004 0.12 -10000 0 -0.43 39 39
mol:Ca2+ -0.001 0.008 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.022 0.01 -10000 0 -10000 0 0
FOSL1 0.034 0.006 -10000 0 -10000 0 0
CREM 0.033 0.007 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.012 0.12 -10000 0 -0.31 29 29
FOS -0.035 0.15 -10000 0 -0.43 66 66
IFNG -0.045 0.2 0.38 3 -0.52 58 61
AP-1/NFAT1-c-4 -0.003 0.22 -10000 0 -0.51 51 51
FASLG -0.035 0.2 0.38 3 -0.54 51 54
NFAT1-c-4/ICER1 0.024 0.08 0.22 1 -0.23 20 21
IL2RA -0.027 0.21 0.38 5 -0.49 58 63
FKBP12/FK506 0.025 0.006 -10000 0 -10000 0 0
CSF2 -0.018 0.18 0.36 4 -0.44 53 57
JunB/Fra1/NFAT1-c-4 0.046 0.096 -10000 0 -0.28 10 10
IL4 -0.013 0.19 0.4 4 -0.45 52 56
IL2 0.003 0.15 -10000 0 -0.98 11 11
IL3 0.017 0.12 -10000 0 -0.7 12 12
FKBP1A 0.034 0.008 -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 0.016 -10000 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.017 0.063 0.2 13 -0.21 22 35
DAPP1 -0.038 0.16 0.24 2 -0.4 61 63
Src family/SYK family/BLNK-LAT/BTK-ITK -0.059 0.23 -10000 0 -0.56 65 65
mol:DAG -0.014 0.096 0.22 10 -0.23 46 56
HRAS 0.03 0.039 -10000 0 -0.43 3 3
RAP1A 0.029 0.048 -10000 0 -0.43 5 5
ARF5/GDP -0.005 0.11 -10000 0 -0.31 33 33
PLCG2 0.019 0.059 -10000 0 -0.43 8 8
PLCG1 0.033 0.008 -10000 0 -10000 0 0
ARF5 0.034 0.021 -10000 0 -0.43 1 1
mol:GTP -0.017 0.062 0.19 14 -0.22 21 35
ARF1/GTP -0.008 0.055 0.2 9 -0.2 18 27
RHOA 0.025 0.062 -10000 0 -0.43 9 9
YES1 0.028 0.051 -10000 0 -0.43 6 6
RAP1A/GTP -0.015 0.065 0.18 32 -0.21 21 53
ADAP1 -0.017 0.059 0.19 13 -0.2 21 34
ARAP3 -0.017 0.062 0.19 14 -0.21 21 35
INPPL1 0.03 0.037 -10000 0 -0.43 3 3
PREX1 -0.037 0.16 -10000 0 -0.43 73 73
ARHGEF6 0.015 0.093 -10000 0 -0.43 21 21
ARHGEF7 0.032 0.01 -10000 0 -10000 0 0
ARF1 0.028 0.025 -10000 0 -0.43 1 1
NRAS 0.027 0.056 -10000 0 -0.43 7 7
FYN 0.026 0.055 -10000 0 -0.43 7 7
ARF6 0.033 0.03 -10000 0 -0.43 2 2
FGR 0.034 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.007 0.053 0.16 13 -0.13 22 35
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.027 0.058 -10000 0 -0.43 8 8
ZAP70 0.032 0.022 -10000 0 -0.43 1 1
mol:IP3 -0.013 0.071 0.19 12 -0.18 31 43
LYN 0.03 0.013 -10000 0 -10000 0 0
ARF1/GDP -0.003 0.1 -10000 0 -0.32 27 27
RhoA/GDP 0.011 0.094 0.23 7 -0.3 15 22
PDK1/Src/Hsp90 0.04 0.025 -10000 0 -0.26 2 2
BLNK 0.012 0.1 -10000 0 -0.43 25 25
actin cytoskeleton reorganization -0.021 0.11 0.23 4 -0.36 24 28
SRC 0.031 0.03 -10000 0 -0.43 2 2
PLEKHA2 -0.008 0.023 -10000 0 -0.26 4 4
RAC1 0.034 0.006 -10000 0 -10000 0 0
PTEN 0.024 0.066 -10000 0 -0.4 11 11
HSP90AA1 0 0 -10000 0 -10000 0 0
ARF6/GTP -0.017 0.062 0.2 13 -0.21 21 34
RhoA/GTP -0.02 0.072 0.2 13 -0.24 25 38
Src family/SYK family/BLNK-LAT -0.028 0.16 -10000 0 -0.43 54 54
BLK 0.02 0.044 -10000 0 -0.43 4 4
PDPK1 0.031 0.023 -10000 0 -0.43 1 1
CYTH1 -0.017 0.059 0.19 13 -0.2 21 34
HCK 0.017 0.086 -10000 0 -0.43 18 18
CYTH3 -0.017 0.059 0.19 13 -0.2 21 34
CYTH2 -0.017 0.059 0.19 13 -0.2 21 34
KRAS 0.026 0.056 -10000 0 -0.43 7 7
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.006 0.041 0.23 2 -0.2 2 4
SGK1 0.008 0.043 0.21 3 -0.21 2 5
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.021 0.11 -10000 0 -0.32 34 34
SOS1 0.034 0.021 -10000 0 -0.43 1 1
SYK 0.004 0.12 -10000 0 -0.43 33 33
ARF6/GDP -0.002 0.078 0.2 7 -0.26 14 21
mol:PI-3-4-5-P3 -0.017 0.064 0.22 13 -0.22 21 34
ARAP3/RAP1A/GTP -0.015 0.066 0.18 32 -0.22 21 53
VAV1 0.017 0.084 -10000 0 -0.43 17 17
mol:PI-3-4-P2 0.006 0.024 -10000 0 -0.3 3 3
RAS family/GTP/PI3K Class I 0.043 0.066 0.21 19 -0.22 21 40
PLEKHA1 -0.011 0.027 -10000 0 -0.26 6 6
Rac1/GDP -0.004 0.11 -10000 0 -0.31 32 32
LAT 0.029 0.031 -10000 0 -0.43 2 2
Rac1/GTP -0.019 0.12 -10000 0 -0.35 36 36
ITK -0.031 0.077 0.19 13 -0.22 49 62
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.026 0.13 0.25 8 -0.32 52 60
LCK -0.019 0.14 -10000 0 -0.43 54 54
BTK -0.024 0.071 0.19 13 -0.23 32 45
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 0.008 0.11 -10000 0 -0.23 78 78
TC10/GTP 0.027 0.069 -10000 0 -0.21 34 34
Insulin Receptor/Insulin/IRS1/Shp2 0.05 0.11 -10000 0 -0.25 56 56
HRAS 0.031 0.037 -10000 0 -0.43 3 3
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 -0.064 0.18 -10000 0 -0.43 97 97
FOXO3 -0.014 0.022 -10000 0 -0.11 1 1
AKT1 -0.04 0.13 0.29 7 -0.35 20 27
INSR 0.036 0.032 -10000 0 -0.43 2 2
Insulin Receptor/Insulin 0.076 0.06 -10000 0 -0.31 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.021 0.077 -10000 0 -0.43 14 14
SORBS1 0.006 0.11 -10000 0 -0.43 29 29
CRK 0.031 0.023 -10000 0 -0.43 1 1
PTPN1 0.006 0.039 -10000 0 -0.31 5 5
CAV1 -0.009 0.088 0.18 4 -0.23 61 65
CBL/APS/CAP/Crk-II/C3G 0.05 0.075 -10000 0 -0.22 30 30
Insulin Receptor/Insulin/IRS1/NCK2 0.051 0.11 -10000 0 -0.25 54 54
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.025 0.1 -10000 0 -0.23 64 64
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.017 0.084 -10000 0 -0.41 7 7
RPS6KB1 -0.038 0.12 0.28 7 -0.35 17 24
PARD6A 0.021 0.062 -10000 0 -0.43 9 9
CBL 0.031 0.012 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.007 0.1 -10000 0 -0.65 12 12
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.01 0.12 0.21 1 -0.28 31 32
HRAS/GTP -0.002 0.066 -10000 0 -0.21 43 43
Insulin Receptor 0.036 0.032 -10000 0 -0.43 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.047 0.1 -10000 0 -0.23 42 42
PRKCI 0 0.11 -10000 0 -0.46 23 23
Insulin Receptor/Insulin/GRB14/PDK1 -0.039 0.12 -10000 0 -0.23 134 134
SHC1 0.027 0.025 -10000 0 -0.43 1 1
negative regulation of MAPKKK cascade 0.043 0.11 -10000 0 -0.59 12 12
PI3K 0.037 0.11 -10000 0 -0.23 64 64
NCK2 0.035 0.005 -10000 0 -10000 0 0
RHOQ 0.03 0.046 -10000 0 -0.43 5 5
mol:H2O2 0 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.023 0.026 -10000 0 -0.3 3 3
AKT2 -0.038 0.13 0.31 6 -0.37 16 22
PRKCZ -0.009 0.083 -10000 0 -0.4 18 18
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.002 0.071 0.17 2 -0.22 45 47
F2RL2 -0.025 0.15 -10000 0 -0.43 61 61
TRIP10 0.031 0.042 -10000 0 -0.43 4 4
Insulin Receptor/Insulin/Shc 0.053 0.04 -10000 0 -0.23 3 3
TC10/GTP/CIP4/Exocyst 0.04 0.041 -10000 0 -0.26 9 9
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.074 0.059 -10000 0 -0.22 4 4
RAPGEF1 0.034 0.005 -10000 0 -10000 0 0
RASA1 0.026 0.058 -10000 0 -0.43 8 8
NCK1 0.033 0.022 -10000 0 -0.43 1 1
CBL/APS/CAP/Crk-II 0.037 0.073 -10000 0 -0.23 30 30
TC10/GDP 0.022 0.033 -10000 0 -0.3 5 5
Insulin Receptor/Insulin/SHC/GRB10 0.061 0.067 -10000 0 -0.23 14 14
INPP5D -0.03 0.072 -10000 0 -0.23 56 56
SOS1 0.034 0.021 -10000 0 -0.43 1 1
SGK1 -0.008 0.01 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.035 0.004 -10000 0 -10000 0 0
IRS1 -0.017 0.14 -10000 0 -0.43 55 55
p62DOK/RasGAP 0.043 0.11 -10000 0 -0.59 12 12
INS 0.037 0.025 -10000 0 -0.43 1 1
mol:PI-3-4-P2 -0.03 0.072 -10000 0 -0.23 56 56
GRB2 0.033 0.009 -10000 0 -10000 0 0
EIF4EBP1 -0.049 0.11 0.28 4 -0.33 20 24
PTPRA 0.037 0.013 -10000 0 -10000 0 0
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
TC10/GTP/CIP4 0.04 0.041 -10000 0 -0.26 9 9
PDPK1 0.031 0.023 -10000 0 -0.43 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.003 0.08 -10000 0 -0.22 42 42
Insulin Receptor/Insulin/IRS1 0.032 0.1 -10000 0 -0.25 56 56
Insulin Receptor/Insulin/IRS3 0.053 0.035 -10000 0 -0.31 3 3
Par3/Par6 0.02 0.11 -10000 0 -0.24 72 72
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.01 0.14 0.28 1 -0.43 30 31
PDGFB-D/PDGFRB/SLAP 0.03 0.058 -10000 0 -0.31 12 12
PDGFB-D/PDGFRB/APS/CBL 0.036 0.041 -10000 0 -0.26 8 8
AKT1 -0.014 0.14 0.32 23 -0.38 14 37
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.006 0.14 0.26 1 -0.46 25 26
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
FGR 0.005 0.12 0.3 4 -0.44 22 26
mol:Ca2+ 0.007 0.13 0.25 2 -0.47 23 25
MYC 0.013 0.24 0.37 11 -0.71 40 51
SHC1 0.027 0.025 -10000 0 -0.43 1 1
HRAS/GDP 0.035 0.065 -10000 0 -0.22 17 17
LRP1/PDGFRB/PDGFB 0.056 0.061 -10000 0 -0.3 12 12
GRB10 0.021 0.077 -10000 0 -0.43 14 14
PTPN11 0.035 0.004 -10000 0 -10000 0 0
GO:0007205 0.007 0.13 0.25 2 -0.48 23 25
PTEN 0.024 0.068 -10000 0 -0.43 11 11
GRB2 0.033 0.009 -10000 0 -10000 0 0
GRB7 0.022 0.059 -10000 0 -0.43 8 8
PDGFB-D/PDGFRB/SHP2 0.045 0.047 -10000 0 -0.31 8 8
PDGFB-D/PDGFRB/GRB10 0.034 0.075 -10000 0 -0.31 22 22
cell cycle arrest 0.03 0.058 -10000 0 -0.31 12 12
HRAS 0.031 0.037 -10000 0 -0.43 3 3
HIF1A -0.03 0.13 0.31 20 -0.34 20 40
GAB1 -0.001 0.14 0.28 2 -0.45 29 31
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.002 0.13 0.31 3 -0.43 26 29
PDGFB-D/PDGFRB 0.051 0.055 -10000 0 -0.27 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.044 0.049 -10000 0 -0.31 9 9
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.009 0.14 -10000 0 -0.44 27 27
positive regulation of MAPKKK cascade 0.045 0.046 -10000 0 -0.31 8 8
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
mol:IP3 0.007 0.13 0.25 2 -0.48 23 25
E5 -0.001 0.002 -10000 0 -10000 0 0
CSK 0.033 0.022 -10000 0 -0.42 1 1
PDGFB-D/PDGFRB/GRB7 0.032 0.065 -10000 0 -0.31 16 16
SHB 0.029 0.046 -10000 0 -0.43 5 5
BLK -0.067 0.2 0.29 2 -0.42 98 100
PTPN2 0.034 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.044 0.047 -10000 0 -0.31 8 8
BCAR1 0.03 0.013 -10000 0 -10000 0 0
VAV2 -0.003 0.15 0.28 2 -0.47 32 34
CBL 0.031 0.012 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.041 0.058 -10000 0 -0.31 13 13
LCK -0.053 0.21 0.29 3 -0.54 69 72
PDGFRB 0.026 0.06 -10000 0 -0.44 8 8
ACP1 0.034 0.021 -10000 0 -0.43 1 1
HCK -0.006 0.14 0.31 3 -0.52 28 31
ABL1 -0.004 0.13 0.23 6 -0.42 29 35
PDGFB-D/PDGFRB/CBL -0.008 0.16 0.27 1 -0.55 28 29
PTPN1 0.029 0.032 -10000 0 -0.43 2 2
SNX15 0.035 0.005 -10000 0 -10000 0 0
STAT3 0.032 0.03 -10000 0 -0.43 2 2
STAT1 0.018 0.079 -10000 0 -0.43 15 15
cell proliferation 0.018 0.22 0.35 13 -0.63 40 53
SLA 0.021 0.052 -10000 0 -0.43 6 6
actin cytoskeleton reorganization 0.035 0.069 0.52 1 -0.22 12 13
SRC 0.011 0.089 0.29 4 -0.45 9 13
PI3K -0.039 0.1 -10000 0 -0.24 85 85
PDGFB-D/PDGFRB/GRB7/SHC 0.036 0.064 -10000 0 -0.26 16 16
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.005 0.14 0.26 1 -0.48 25 26
LYN 0.013 0.073 0.28 3 -0.36 9 12
LRP1 0.034 0.021 -10000 0 -0.43 1 1
SOS1 0.034 0.021 -10000 0 -0.43 1 1
STAT5B 0.033 0.022 -10000 0 -0.43 1 1
STAT5A 0.031 0.036 -10000 0 -0.43 3 3
NCK1-2/p130 Cas 0.068 0.066 -10000 0 -0.22 9 9
SPHK1 0.005 0.11 -10000 0 -0.43 29 29
EDG1 0.012 0.098 -10000 0 -0.43 23 23
mol:DAG 0.007 0.13 0.25 2 -0.48 23 25
PLCG1 0.006 0.14 0.26 2 -0.5 23 25
NHERF/PDGFRB -0.002 0.14 -10000 0 -0.29 83 83
YES1 -0.004 0.13 0.29 3 -0.47 29 32
cell migration -0.002 0.14 -10000 0 -0.29 83 83
SHC/Grb2/SOS1 0.061 0.066 -10000 0 -0.23 9 9
SLC9A3R2 -0.006 0.13 -10000 0 -0.43 41 41
SLC9A3R1 -0.011 0.14 -10000 0 -0.43 47 47
NHERF1-2/PDGFRB/PTEN 0.007 0.14 -10000 0 -0.28 89 89
FYN -0.012 0.16 0.29 3 -0.53 32 35
DOK1 0.02 0.067 0.18 33 -0.24 15 48
HRAS/GTP 0.023 0.026 -10000 0 -0.3 3 3
PDGFB 0.028 0.047 -10000 0 -0.43 5 5
RAC1 -0.017 0.2 0.31 2 -0.55 44 46
PRKCD 0.023 0.066 0.18 34 -0.27 10 44
FER 0.023 0.064 0.18 33 -0.25 10 43
MAPKKK cascade 0.039 0.1 0.33 20 -0.22 9 29
RASA1 0.019 0.068 0.18 31 -0.25 15 46
NCK1 0.033 0.022 -10000 0 -0.43 1 1
NCK2 0.035 0.005 -10000 0 -10000 0 0
p62DOK/Csk 0.042 0.064 0.34 1 -0.22 16 17
PDGFB-D/PDGFRB/SHB 0.04 0.059 -10000 0 -0.31 13 13
chemotaxis -0.004 0.13 0.23 6 -0.41 29 35
STAT1-3-5/STAT1-3-5 0.055 0.075 -10000 0 -0.22 26 26
Bovine Papilomavirus E5/PDGFRB 0.018 0.043 -10000 0 -0.31 8 8
PTPRJ 0.03 0.046 -10000 0 -0.43 5 5
ErbB2/ErbB3 signaling events

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
USP8 -0.007 0.022 -10000 0 -0.26 3 3
RAS family/GTP 0.033 0.11 -10000 0 -0.28 19 19
NFATC4 -0.012 0.086 0.25 7 -0.23 30 37
ERBB2IP 0.033 0.022 -10000 0 -0.42 1 1
HSP90 (dimer) 0 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.004 0.09 -10000 0 -0.26 39 39
JUN 0.013 0.078 -10000 0 -10000 0 0
HRAS 0.031 0.037 -10000 0 -0.43 3 3
DOCK7 -0.023 0.091 0.26 1 -0.26 32 33
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.016 0.092 -10000 0 -0.28 34 34
AKT1 0.004 0.025 -10000 0 -0.31 3 3
BAD -0.008 0.023 -10000 0 -0.26 4 4
MAPK10 -0.011 0.07 0.19 11 -0.21 13 24
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.004 0.097 -10000 0 -0.28 39 39
RAF1 0.017 0.11 0.27 11 -0.29 21 32
ErbB2/ErbB3/neuregulin 2 0.004 0.093 -10000 0 -0.28 45 45
STAT3 0.01 0.17 -10000 0 -0.88 17 17
cell migration -0.007 0.073 0.21 12 -0.21 11 23
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.038 0.25 -10000 0 -0.61 62 62
FOS -0.038 0.22 0.31 1 -0.44 102 103
NRAS 0.028 0.055 -10000 0 -0.43 7 7
mol:Ca2+ -0.004 0.09 -10000 0 -0.26 39 39
MAPK3 -0.014 0.2 0.35 1 -0.52 47 48
MAPK1 -0.025 0.22 0.35 2 -0.54 51 53
JAK2 -0.02 0.09 0.26 1 -0.26 32 33
NF2 0.006 0.053 -10000 0 -0.67 3 3
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.007 0.077 0.18 7 -0.26 29 36
NRG1 0.028 0.015 -10000 0 -10000 0 0
GRB2/SOS1 0.047 0.021 -10000 0 -0.31 1 1
MAPK8 -0.01 0.1 0.21 2 -0.28 32 34
MAPK9 -0.01 0.071 0.19 13 -0.22 10 23
ERBB2 -0.029 0.058 0.58 1 -0.32 14 15
ERBB3 0.005 0.11 -10000 0 -0.43 32 32
SHC1 0.027 0.025 -10000 0 -0.43 1 1
RAC1 0.034 0.006 -10000 0 -10000 0 0
apoptosis 0.006 0.027 0.33 3 -10000 0 3
STAT3 (dimer) 0.011 0.17 -10000 0 -0.86 17 17
RNF41 -0.011 0.021 -10000 0 -0.24 3 3
FRAP1 -0.007 0.017 -10000 0 -0.26 2 2
RAC1-CDC42/GTP -0.015 0.061 -10000 0 -0.2 32 32
ErbB2/ErbB2/HSP90 (dimer) -0.024 0.043 -10000 0 -0.27 14 14
CHRNA1 0 0.17 0.32 2 -0.4 49 51
myelination -0.009 0.091 0.26 12 -0.33 7 19
PPP3CB -0.02 0.087 0.25 1 -0.25 32 33
KRAS 0.027 0.055 -10000 0 -0.43 7 7
RAC1-CDC42/GDP 0.042 0.098 0.24 2 -0.24 27 29
NRG2 0.023 0.062 -10000 0 -0.43 9 9
mol:GDP 0.007 0.077 0.18 7 -0.26 29 36
SOS1 0.034 0.021 -10000 0 -0.43 1 1
MAP2K2 0.004 0.12 0.25 11 -0.31 26 37
SRC 0.031 0.03 -10000 0 -0.43 2 2
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.021 0.092 0.26 1 -0.26 32 33
MAP2K1 -0.024 0.21 -10000 0 -0.57 40 40
heart morphogenesis -0.004 0.09 -10000 0 -0.26 39 39
RAS family/GDP 0.043 0.11 -10000 0 -0.29 16 16
GRB2 0.033 0.009 -10000 0 -10000 0 0
PRKACA 0.01 0.063 -10000 0 -0.68 4 4
CHRNE 0.01 0.019 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
activation of caspase activity -0.004 0.025 0.31 3 -10000 0 3
nervous system development -0.004 0.09 -10000 0 -0.26 39 39
CDC42 0.034 0.007 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.032 0.1 -10000 0 -0.49 14 14
HDAC1 0.039 0.028 -10000 0 -0.43 1 1
AES 0.036 0.009 -10000 0 -10000 0 0
FBXW11 0.032 0.03 -10000 0 -0.43 2 2
DTX1 0.032 0.036 -10000 0 -0.43 3 3
LRP6/FZD1 0.039 0.056 -10000 0 -0.31 12 12
TLE1 0.005 0.12 -10000 0 -0.43 33 33
AP1 -0.03 0.12 -10000 0 -0.3 66 66
NCSTN 0.028 0.025 -10000 0 -0.43 1 1
ADAM10 0.031 0.036 -10000 0 -0.43 3 3
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.039 0.16 -10000 0 -0.62 14 14
NICD/RBPSUH 0.006 0.093 -10000 0 -0.49 14 14
WIF1 0.029 0.014 -10000 0 -10000 0 0
NOTCH1 0.012 0.093 -10000 0 -0.51 14 14
PSENEN 0.034 0.006 -10000 0 -10000 0 0
KREMEN2 -0.095 0.2 -10000 0 -0.43 131 131
DKK1 -0.029 0.15 -10000 0 -0.43 59 59
beta catenin/beta TrCP1 0.018 0.099 0.28 2 -0.33 17 19
APH1B 0.024 0.068 -10000 0 -0.43 11 11
APH1A 0.024 0.038 -10000 0 -0.43 3 3
AXIN1 0.012 0.092 0.26 3 -0.57 8 11
CtBP/CBP/TCF1/TLE1/AES 0.026 0.091 0.29 3 -0.25 28 31
PSEN1 0.032 0.036 -10000 0 -0.43 3 3
FOS -0.033 0.16 -10000 0 -0.43 66 66
JUN -0.003 0.12 -10000 0 -0.43 39 39
MAP3K7 0.036 0.012 -10000 0 -10000 0 0
CTNNB1 0.003 0.095 0.28 2 -0.34 16 18
MAPK3 0.032 0.023 -10000 0 -0.43 1 1
DKK2/LRP6/Kremen 2 -0.051 0.15 -10000 0 -0.27 156 156
HNF1A 0.002 0.006 -10000 0 -10000 0 0
CTBP1 0.035 0.009 -10000 0 -10000 0 0
MYC -0.083 0.34 -10000 0 -1.3 34 34
NKD1 0.028 0.038 -10000 0 -0.43 3 3
FZD1 0.027 0.058 -10000 0 -0.43 8 8
NOTCH1 precursor/Deltex homolog 1 0.049 0.11 -10000 0 -0.5 14 14
apoptosis -0.03 0.12 -10000 0 -0.3 66 66
Delta 1/NOTCHprecursor 0.046 0.1 -10000 0 -0.49 14 14
DLL1 0.032 0.01 -10000 0 -10000 0 0
PPARD 0.011 0.073 -10000 0 -0.76 3 3
Gamma Secretase 0.065 0.07 -10000 0 -0.23 15 15
APC 0.007 0.093 -10000 0 -0.47 12 12
DVL1 0.022 0.035 -10000 0 -0.38 2 2
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
MAP3K7IP1 0.036 0.012 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.069 0.16 -10000 0 -0.28 171 171
LRP6 0.029 0.047 -10000 0 -0.43 5 5
CSNK1A1 0.034 0.006 -10000 0 -10000 0 0
NLK 0.029 0.024 -10000 0 -0.24 1 1
CCND1 -0.21 0.51 -10000 0 -1.3 85 85
WNT1 0.034 0.021 -10000 0 -0.43 1 1
Axin1/APC/beta catenin 0.029 0.12 0.36 3 -0.46 10 13
DKK2 0.005 0.11 -10000 0 -0.43 31 31
NOTCH1 precursor/DVL1 0.021 0.12 -10000 0 -0.57 14 14
GSK3B 0.035 0.005 -10000 0 -10000 0 0
FRAT1 0.029 0.055 -10000 0 -0.43 7 7
NOTCH/Deltex homolog 1 0.033 0.1 -10000 0 -0.5 14 14
PPP2R5D 0.017 0.053 0.24 3 -0.33 9 12
MAPK1 0.032 0.03 -10000 0 -0.43 2 2
WNT1/LRP6/FZD1 0.067 0.055 -10000 0 -0.24 11 11
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.025 0.028 -10000 0 -0.43 1 1
Arf6 downstream pathway

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
PLAUR -0.027 0.23 -10000 0 -0.99 27 27
regulation of axonogenesis -0.002 0.051 0.32 7 -10000 0 7
myoblast fusion -0.004 0.1 0.4 30 -10000 0 30
mol:GTP 0.011 0.064 -10000 0 -0.24 28 28
regulation of calcium-dependent cell-cell adhesion -0.044 0.081 0.24 32 -10000 0 32
ARF1/GTP 0.026 0.054 -10000 0 -0.19 23 23
mol:GM1 0.001 0.046 -10000 0 -0.18 26 26
mol:Choline -0.001 0.058 -10000 0 -0.29 14 14
lamellipodium assembly -0.007 0.12 -10000 0 -0.44 31 31
MAPK3 0.009 0.085 -10000 0 -0.33 29 29
ARF6/GTP/NME1/Tiam1 0.045 0.082 -10000 0 -0.24 32 32
ARF1 0.028 0.025 -10000 0 -0.43 1 1
ARF6/GDP 0.004 0.1 -10000 0 -0.4 30 30
ARF1/GDP 0.008 0.095 -10000 0 -0.37 25 25
ARF6 0.03 0.055 -10000 0 -0.36 4 4
RAB11A 0.034 0.007 -10000 0 -10000 0 0
TIAM1 0.024 0.061 -10000 0 -0.43 8 8
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.01 0.085 -10000 0 -0.32 29 29
actin filament bundle formation -0.017 0.11 0.37 31 -10000 0 31
KALRN -0.001 0.08 -10000 0 -0.3 31 31
RAB11FIP3/RAB11A 0.044 0.032 -10000 0 -0.31 3 3
RhoA/GDP 0.018 0.11 -10000 0 -0.38 31 31
NME1 0.029 0.02 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.1 -10000 0 -0.37 29 29
substrate adhesion-dependent cell spreading 0.011 0.063 -10000 0 -0.24 28 28
cortical actin cytoskeleton organization -0.007 0.12 -10000 0 -0.44 31 31
RAC1 0.034 0.006 -10000 0 -10000 0 0
liver development 0.011 0.063 -10000 0 -0.24 28 28
ARF6/GTP 0.011 0.064 -10000 0 -0.24 28 28
RhoA/GTP 0.026 0.07 -10000 0 -0.21 34 34
mol:GDP -0.007 0.096 -10000 0 -0.39 28 28
ARF6/GTP/RAB11FIP3/RAB11A 0.046 0.06 -10000 0 -0.21 9 9
RHOA 0.025 0.062 -10000 0 -0.43 9 9
PLD1 0.006 0.068 -10000 0 -0.24 31 31
RAB11FIP3 0.029 0.037 -10000 0 -0.43 3 3
tube morphogenesis -0.007 0.12 -10000 0 -0.44 31 31
ruffle organization 0.002 0.051 -10000 0 -0.32 7 7
regulation of epithelial cell migration 0.011 0.063 -10000 0 -0.24 28 28
PLD2 0.012 0.052 -10000 0 -0.2 22 22
PIP5K1A 0.002 0.051 -10000 0 -0.32 7 7
mol:Phosphatidic acid -0.001 0.058 -10000 0 -0.29 14 14
Rac1/GTP -0.007 0.12 -10000 0 -0.44 31 31
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.04 0.11 0.91 1 -10000 0 1
VDR 0.019 0.084 -10000 0 -0.43 17 17
FAM120B 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.007 0.1 -10000 0 -0.28 48 48
RXRs/LXRs/DNA/Oxysterols 0.007 0.16 -10000 0 -0.4 58 58
MED1 0 0 -10000 0 -10000 0 0
mol:9cRA -0.001 0.018 -10000 0 -0.087 1 1
RARs/THRs/DNA/Src-1 0.001 0.092 -10000 0 -0.24 48 48
RXRs/NUR77 0.058 0.079 -10000 0 -0.26 11 11
RXRs/PPAR 0.01 0.078 -10000 0 -0.25 32 32
NCOR2 0.034 0.007 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.015 0.06 -10000 0 -0.3 17 17
RARs/VDR/DNA/Vit D3 0.049 0.084 -10000 0 -0.23 35 35
RARA 0.027 0.047 -10000 0 -0.43 5 5
NCOA1 0.03 0.051 -10000 0 -0.43 6 6
VDR/VDR/DNA 0.019 0.084 -10000 0 -0.43 17 17
RARs/RARs/DNA/9cRA 0.038 0.063 -10000 0 -0.22 23 23
RARG 0.035 0.004 -10000 0 -10000 0 0
RPS6KB1 0.062 0.16 0.54 49 -10000 0 49
RARs/THRs/DNA/SMRT 0.004 0.084 -10000 0 -0.24 41 41
THRA 0.018 0.077 -10000 0 -0.43 14 14
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.015 0.06 -10000 0 -0.3 17 17
RXRs/PPAR/9cRA/PGJ2/DNA 0.042 0.082 -10000 0 -0.17 51 51
NR1H4 0.034 0.021 -10000 0 -0.43 1 1
RXRs/LXRs/DNA 0.064 0.11 -10000 0 -0.26 14 14
NR1H2 0.028 0.031 -10000 0 -10000 0 0
NR1H3 0.025 0.052 -10000 0 -0.44 4 4
RXRs/VDR/DNA/Vit D3 0.048 0.085 -10000 0 -0.23 22 22
NR4A1 0.033 0.022 -10000 0 -0.43 1 1
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.023 0.061 -10000 0 -0.22 14 14
RXRG 0.018 0.061 -10000 0 -0.44 7 7
RXR alpha/CCPG 0.021 0.025 -10000 0 -0.33 1 1
RXRA 0.028 0.037 -10000 0 -0.46 1 1
RXRB 0.026 0.048 -10000 0 -0.42 3 3
THRB 0.022 0.074 -10000 0 -0.43 13 13
PPARG 0.01 0.095 -10000 0 -0.43 22 22
PPARD 0.035 0.005 -10000 0 -10000 0 0
TNF -0.006 0.19 -10000 0 -0.78 18 18
mol:Oxysterols -0.001 0.016 -10000 0 -10000 0 0
cholesterol transport 0.008 0.16 -10000 0 -0.4 58 58
PPARA 0.03 0.031 -10000 0 -0.43 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.013 0.091 -10000 0 -0.43 20 20
RXRs/NUR77/BCL2 -0.023 0.1 -10000 0 -0.23 89 89
SREBF1 -0.05 0.3 -10000 0 -0.94 46 46
RXRs/RXRs/DNA/9cRA 0.042 0.082 -10000 0 -0.17 51 51
ABCA1 -0.011 0.21 -10000 0 -0.89 19 19
RARs/THRs 0.054 0.1 -10000 0 -0.24 44 44
RXRs/FXR 0.059 0.08 -10000 0 -0.26 11 11
BCL2 -0.062 0.18 -10000 0 -0.43 101 101
Regulation of Telomerase

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
Telomerase catalytic core complex -0.073 0.23 -10000 0 -0.57 53 53
RAD9A 0.032 0.01 -10000 0 -10000 0 0
AP1 -0.033 0.16 -10000 0 -0.35 88 88
IFNAR2 0.027 0.03 -10000 0 -0.44 1 1
AKT1 -0.036 0.11 -10000 0 -0.2 134 134
ER alpha/Oestrogen -0.066 0.14 -10000 0 -0.31 132 132
NFX1/SIN3/HDAC complex 0.014 0.071 -10000 0 -0.34 12 12
EGF -0.071 0.19 -10000 0 -0.43 108 108
SMG5 0 0 -10000 0 -10000 0 0
SMG6 0 0 -10000 0 -10000 0 0
SP3/HDAC2 0.038 0.036 -10000 0 -0.3 1 1
TERT/c-Abl -0.06 0.22 -10000 0 -0.54 54 54
SAP18 0.033 0.009 -10000 0 -10000 0 0
MRN complex 0.048 0.044 -10000 0 -0.26 4 4
WT1 -0.028 0.14 -10000 0 -0.43 55 55
WRN 0.028 0.025 -10000 0 -0.43 1 1
SP1 0.026 0.026 -10000 0 -10000 0 0
SP3 0.034 0.007 -10000 0 -10000 0 0
TERF2IP 0.03 0.013 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.048 0.21 -10000 0 -0.5 52 52
Mad/Max 0.047 0.018 -10000 0 -10000 0 0
TERT -0.075 0.23 -10000 0 -0.61 47 47
CCND1 -0.15 0.45 -10000 0 -1.1 86 86
MAX 0.033 0.008 -10000 0 -10000 0 0
RBBP7 0.033 0.03 -10000 0 -0.43 2 2
RBBP4 0.033 0.021 -10000 0 -0.43 1 1
TERF2 0.026 0.03 -10000 0 -0.37 2 2
PTGES3 0.034 0.021 -10000 0 -0.43 1 1
SIN3A 0.034 0.006 -10000 0 -10000 0 0
Telomerase/911 0.019 0.069 -10000 0 -0.41 7 7
CDKN1B -0.03 0.15 -10000 0 -0.37 68 68
RAD1 0.033 0.03 -10000 0 -0.43 2 2
XRCC5 0.035 0.004 -10000 0 -10000 0 0
XRCC6 0.033 0.009 -10000 0 -10000 0 0
SAP30 0.029 0.047 -10000 0 -0.43 5 5
TRF2/PARP2 0.042 0.03 -10000 0 -0.29 2 2
UBE3A 0.032 0.023 -10000 0 -0.44 1 1
JUN -0.004 0.12 -10000 0 -0.43 39 39
E6 -0.001 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.019 0.023 -10000 0 -0.32 1 1
FOS -0.034 0.16 -10000 0 -0.43 66 66
IFN-gamma/IRF1 -0.005 0.13 -10000 0 -0.31 70 70
PARP2 0.035 0.004 -10000 0 -10000 0 0
BLM 0.01 0.099 -10000 0 -0.43 24 24
Telomerase 0.012 0.042 -10000 0 -10000 0 0
IRF1 0.015 0.084 -10000 0 -0.27 34 34
ESR1 -0.093 0.2 -10000 0 -0.43 132 132
KU/TER 0.049 0.014 -10000 0 -10000 0 0
ATM/TRF2 0.038 0.032 -10000 0 -0.19 2 2
ubiquitin-dependent protein catabolic process 0.02 0.063 -10000 0 -0.29 10 10
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.02 0.064 -10000 0 -0.29 10 10
HDAC1 0.033 0.021 -10000 0 -0.43 1 1
HDAC2 0.024 0.032 -10000 0 -0.43 1 1
ATM 0.019 0.023 0.19 2 -10000 0 2
SMAD3 0.011 0.04 -10000 0 -0.3 8 8
ABL1 0.035 0.004 -10000 0 -10000 0 0
MXD1 0.034 0.008 -10000 0 -10000 0 0
MRE11A 0.031 0.011 -10000 0 -10000 0 0
HUS1 0.035 0.005 -10000 0 -10000 0 0
RPS6KB1 0.031 0.012 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.058 0.23 -10000 0 -0.55 64 64
NR2F2 -0.011 0.14 -10000 0 -0.43 48 48
MAPK3 0.008 0.032 -10000 0 -0.31 4 4
MAPK1 0.007 0.035 -10000 0 -0.31 5 5
TGFB1/TGF beta receptor Type II 0.035 0.006 -10000 0 -10000 0 0
NFKB1 0.034 0.021 -10000 0 -0.43 1 1
HNRNPC 0 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.019 0.023 0.19 2 -10000 0 2
NBN 0.027 0.025 -10000 0 -0.43 1 1
EGFR -0.016 0.14 -10000 0 -0.43 48 48
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.068 0.16 -10000 0 -0.31 149 149
MYC -0.002 0.1 -10000 0 -0.43 28 28
IL2 0.023 0.044 -10000 0 -0.43 3 3
KU 0.049 0.014 -10000 0 -10000 0 0
RAD50 0.031 0.042 -10000 0 -0.43 4 4
HSP90AA1 0 0 -10000 0 -10000 0 0
TGFB1 0.035 0.006 -10000 0 -10000 0 0
TRF2/BLM 0.025 0.074 -10000 0 -0.28 25 25
FRAP1 0.034 0.007 -10000 0 -10000 0 0
KU/TERT -0.048 0.23 -10000 0 -0.54 52 52
SP1/HDAC2 0.038 0.04 -10000 0 -0.3 1 1
PINX1 0.028 0.015 -10000 0 -10000 0 0
Telomerase/EST1A -0.06 0.2 -10000 0 -0.48 59 59
Smad3/Myc 0.006 0.074 -10000 0 -0.26 34 34
911 complex 0.062 0.031 -10000 0 -0.26 2 2
IFNG -0.015 0.13 -10000 0 -0.35 55 55
Telomerase/PinX1 -0.057 0.2 -10000 0 -0.5 52 52
Telomerase/AKT1/mTOR/p70S6K -0.009 0.1 -10000 0 -0.43 17 17
SIN3B 0.034 0.005 -10000 0 -10000 0 0
YWHAE 0.032 0.01 -10000 0 -10000 0 0
Telomerase/EST1B -0.06 0.2 -10000 0 -0.48 59 59
response to DNA damage stimulus 0 0.03 0.13 1 -0.1 25 26
MRN complex/TRF2/Rap1 0.059 0.06 -10000 0 -0.27 5 5
TRF2/WRN 0.035 0.035 -10000 0 -0.29 3 3
Telomerase/hnRNP C1/C2 -0.06 0.2 -10000 0 -0.48 59 59
E2F1 0.021 0.058 -10000 0 -0.43 7 7
ZNFX1 0 0.001 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL 0.035 0.005 -10000 0 -10000 0 0
DKC1 0.035 0.003 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.04 0.087 -10000 0 -0.22 39 39
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.03 0.042 -10000 0 -0.43 4 4
STAT1 (dimer)/Cbp/p300 0.034 0.11 0.31 1 -0.36 17 18
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.05 0.053 -10000 0 -0.28 5 5
antigen processing and presentation of peptide antigen via MHC class I -0.018 0.095 -10000 0 -0.26 44 44
CaM/Ca2+ 0.044 0.085 -10000 0 -0.21 39 39
RAP1A 0.03 0.046 -10000 0 -0.43 5 5
STAT1 (dimer)/SHP2 0.016 0.099 -10000 0 -0.25 48 48
AKT1 -0.001 0.1 0.31 10 -0.28 12 22
MAP2K1 -0.016 0.087 0.29 1 -0.27 18 19
MAP3K11 0.01 0.081 0.26 2 -0.22 39 41
IFNGR1 0.03 0.021 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.007 0.13 -10000 0 -0.44 22 22
Rap1/GTP 0 0.068 -10000 0 -0.27 11 11
CRKL/C3G 0.046 0.034 -10000 0 -0.31 4 4
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.053 0.093 -10000 0 -0.23 39 39
CEBPB -0.007 0.16 -10000 0 -0.48 32 32
STAT3 0.032 0.03 -10000 0 -0.43 2 2
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.046 0.13 -10000 0 -0.87 6 6
STAT1 0 0.098 0.3 2 -0.25 46 48
CALM1 0.035 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.008 0.12 -10000 0 -0.43 38 38
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
STAT1 (dimer)/PIAS1 0.019 0.1 0.3 2 -0.3 21 23
CEBPB/PTGES2/Cbp/p300 0.005 0.11 -10000 0 -0.33 29 29
mol:Ca2+ 0.037 0.084 -10000 0 -0.22 39 39
MAPK3 -0.01 0.14 -10000 0 -0.64 12 12
STAT1 (dimer) -0.012 0.14 -10000 0 -0.37 42 42
MAPK1 -0.037 0.2 -10000 0 -0.75 29 29
JAK2 0.027 0.037 -10000 0 -0.45 2 2
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
JAK1 0.029 0.041 -10000 0 -0.43 3 3
CAMK2D 0.02 0.079 -10000 0 -0.43 15 15
DAPK1 0.001 0.14 -10000 0 -0.5 19 19
SMAD7 0.003 0.062 0.19 7 -0.18 16 23
CBL/CRKL/C3G 0.038 0.088 0.31 2 -0.25 9 11
PI3K 0.03 0.095 -10000 0 -0.23 43 43
IFNG -0.008 0.12 -10000 0 -0.43 38 38
apoptosis -0.001 0.13 -10000 0 -0.44 25 25
CAMK2G 0.035 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.032 0.03 -10000 0 -0.43 2 2
CAMK2A 0.034 0.021 -10000 0 -0.43 1 1
CAMK2B -0.014 0.13 -10000 0 -0.43 47 47
FRAP1 -0.007 0.093 0.31 8 -0.28 9 17
PRKCD -0.003 0.1 0.33 9 -0.3 9 18
RAP1B 0.032 0.03 -10000 0 -0.43 2 2
negative regulation of cell growth -0.018 0.095 -10000 0 -0.26 44 44
PTPN2 0.034 0.007 -10000 0 -10000 0 0
EP300 0.031 0.03 -10000 0 -0.43 2 2
IRF1 -0.001 0.11 0.28 3 -0.42 18 21
STAT1 (dimer)/PIASy 0.015 0.1 0.3 2 -0.3 21 23
SOCS1 0.017 0.13 -10000 0 -1.1 6 6
mol:GDP 0.034 0.083 0.29 2 -0.24 11 13
CASP1 -0.011 0.088 0.19 7 -0.25 44 51
PTGES2 0.035 0.004 -10000 0 -10000 0 0
IRF9 0.004 0.051 0.13 1 -0.16 12 13
mol:PI-3-4-5-P3 0.017 0.086 -10000 0 -0.22 47 47
RAP1/GDP 0.026 0.082 -10000 0 -0.29 9 9
CBL 0.009 0.079 0.3 2 -0.21 37 39
MAP3K1 -0.001 0.095 0.26 2 -0.23 53 55
PIAS1 0.034 0.007 -10000 0 -10000 0 0
PIAS4 0.031 0.036 -10000 0 -0.43 3 3
antigen processing and presentation of peptide antigen via MHC class II -0.018 0.095 -10000 0 -0.26 44 44
PTPN11 0.013 0.085 0.29 3 -0.22 39 42
CREBBP 0.032 0.023 -10000 0 -0.43 1 1
RAPGEF1 0.034 0.005 -10000 0 -10000 0 0
Ceramide 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
SPHK2 0.006 0.055 -10000 0 -0.31 15 15
MAP4K4 -0.022 0.11 0.22 2 -0.34 35 37
BAG4 0.027 0.025 -10000 0 -0.43 1 1
PKC zeta/ceramide -0.008 0.043 0.12 4 -0.19 11 15
NFKBIA 0.032 0.03 -10000 0 -0.43 2 2
BIRC3 -0.013 0.13 -10000 0 -0.43 44 44
BAX 0.01 0.036 -10000 0 -0.36 3 3
RIPK1 0.034 0.006 -10000 0 -10000 0 0
AKT1 0 0.076 0.69 5 -0.4 3 8
BAD -0.011 0.044 0.19 1 -0.2 10 11
SMPD1 0.007 0.066 0.21 1 -0.24 16 17
RB1 -0.012 0.06 0.19 7 -0.23 17 24
FADD/Caspase 8 0.011 0.12 0.28 4 -0.37 19 23
MAP2K4 -0.022 0.066 0.18 1 -0.23 30 31
NSMAF 0.026 0.043 -10000 0 -0.43 4 4
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.003 0.057 0.2 15 -0.21 6 21
EGF -0.07 0.19 -10000 0 -0.43 108 108
mol:ceramide -0.008 0.047 0.13 10 -0.2 11 21
MADD 0.035 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.004 0.071 -10000 0 -0.31 26 26
ASAH1 0.007 0.092 -10000 0 -0.43 21 21
negative regulation of cell cycle -0.012 0.059 0.19 7 -0.23 17 24
cell proliferation -0.009 0.095 0.27 3 -0.24 22 25
BID -0.042 0.21 -10000 0 -0.73 37 37
MAP3K1 -0.02 0.068 -10000 0 -0.24 32 32
EIF2A -0.016 0.059 0.21 4 -0.25 6 10
TRADD 0.029 0.024 -10000 0 -0.43 1 1
CRADD 0.029 0.051 -10000 0 -0.43 6 6
MAPK3 0 0.057 0.25 4 -0.22 3 7
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.004 0.063 0.21 8 -0.22 3 11
Cathepsin D/ceramide 0.005 0.055 -10000 0 -0.2 15 15
FADD 0.006 0.12 0.22 47 -0.34 26 73
KSR1 -0.003 0.053 0.19 11 -0.2 8 19
MAPK8 -0.013 0.061 -10000 0 -0.23 15 15
PRKRA -0.009 0.046 0.19 3 -0.2 10 13
PDGFA 0.02 0.079 -10000 0 -0.43 15 15
TRAF2 0.033 0.03 -10000 0 -0.43 2 2
IGF1 -0.041 0.17 -10000 0 -0.43 78 78
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.008 0.046 0.13 10 -0.2 11 21
CTSD 0.028 0.047 -10000 0 -0.43 5 5
regulation of nitric oxide biosynthetic process 0.049 0.019 -10000 0 -0.31 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.008 0.1 0.29 3 -0.25 22 25
PRKCD 0.032 0.03 -10000 0 -0.43 2 2
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.004 0.071 -10000 0 -0.31 26 26
RelA/NF kappa B1 0.049 0.019 -10000 0 -0.31 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.022 0.074 -10000 0 -0.43 13 13
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.013 0.11 -10000 0 -0.36 31 31
TNFR1A/BAG4/TNF-alpha 0.047 0.047 -10000 0 -0.26 6 6
mol:Sphingosine-1-phosphate 0.006 0.055 -10000 0 -0.31 15 15
MAP2K1 -0.004 0.057 0.22 6 -0.23 3 9
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
CYCS 0.03 0.067 0.16 66 -0.19 5 71
TNFRSF1A 0.032 0.022 -10000 0 -0.43 1 1
NFKB1 0.034 0.021 -10000 0 -0.43 1 1
TNFR1A/BAG4 0.038 0.028 -10000 0 -0.31 1 1
EIF2AK2 -0.017 0.056 0.19 2 -0.22 20 22
TNF-alpha/TNFR1A/FAN 0.049 0.05 -10000 0 -0.26 8 8
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.014 0.082 -10000 0 -0.37 9 9
MAP2K2 -0.004 0.059 0.22 6 -0.21 5 11
SMPD3 -0.023 0.13 0.19 1 -0.31 70 71
TNF 0.025 0.062 -10000 0 -0.43 9 9
PKC zeta/PAR4 0.017 0.052 -10000 0 -0.3 13 13
mol:PHOSPHOCHOLINE 0.039 0.096 0.21 106 -0.2 3 109
NF kappa B1/RelA/I kappa B alpha 0.067 0.058 -10000 0 -0.22 16 16
AIFM1 0.026 0.066 0.16 67 -0.2 4 71
BCL2 -0.062 0.18 -10000 0 -0.43 101 101
ceramide signaling pathway

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
MAP4K4 -0.033 0.15 -10000 0 -0.45 34 34
BAG4 0.027 0.025 -10000 0 -0.43 1 1
BAD -0.005 0.05 0.19 1 -0.17 13 14
NFKBIA 0.032 0.03 -10000 0 -0.43 2 2
BIRC3 -0.013 0.13 -10000 0 -0.43 44 44
BAX -0.004 0.051 0.2 2 -0.16 15 17
EnzymeConsortium:3.1.4.12 -0.005 0.035 0.073 2 -0.095 32 34
IKBKB -0.012 0.14 0.28 8 -0.43 27 35
MAP2K2 0 0.063 0.19 22 -0.22 4 26
MAP2K1 0.001 0.061 0.2 20 -0.21 3 23
SMPD1 -0.004 0.042 -10000 0 -0.16 13 13
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.005 0.15 0.31 5 -0.45 25 30
MAP2K4 -0.013 0.06 0.22 1 -0.19 25 26
protein ubiquitination -0.028 0.14 0.28 1 -0.44 30 31
EnzymeConsortium:2.7.1.37 -0.003 0.065 0.22 11 -0.21 5 16
response to UV 0 0.001 0.003 10 -0.002 5 15
RAF1 0.001 0.061 0.2 18 -0.2 4 22
CRADD 0.029 0.051 -10000 0 -0.43 6 6
mol:ceramide -0.003 0.052 0.12 2 -0.15 27 29
I-kappa-B-alpha/RELA/p50/ubiquitin 0.044 0.022 -10000 0 -0.26 2 2
MADD 0.035 0.004 -10000 0 -10000 0 0
MAP3K1 -0.014 0.063 0.13 1 -0.18 37 38
TRADD 0.029 0.024 -10000 0 -0.43 1 1
RELA/p50 0.034 0.005 -10000 0 -10000 0 0
MAPK3 0.003 0.063 0.21 13 -0.2 4 17
MAPK1 0 0.069 0.2 18 -0.2 12 30
p50/RELA/I-kappa-B-alpha 0.048 0.026 -10000 0 -0.31 2 2
FADD -0.002 0.15 0.27 7 -0.44 29 36
KSR1 0 0.058 0.19 14 -0.17 11 25
MAPK8 -0.017 0.062 0.22 3 -0.21 13 16
TRAF2 0.033 0.03 -10000 0 -0.43 2 2
response to radiation 0 0 0.002 4 -10000 0 4
CHUK -0.039 0.14 0.27 1 -0.44 33 34
TNF R/SODD 0.038 0.028 -10000 0 -0.31 1 1
TNF 0.025 0.062 -10000 0 -0.43 9 9
CYCS 0.014 0.068 0.15 29 -0.16 12 41
IKBKG -0.035 0.14 0.27 1 -0.44 30 31
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.027 0.15 -10000 0 -0.46 34 34
RELA 0.034 0.005 -10000 0 -10000 0 0
RIPK1 0.034 0.006 -10000 0 -10000 0 0
AIFM1 0.012 0.067 0.14 30 -0.16 13 43
TNF/TNF R/SODD 0.047 0.047 -10000 0 -0.26 6 6
TNFRSF1A 0.032 0.022 -10000 0 -0.43 1 1
response to heat 0 0 0.002 4 -10000 0 4
CASP8 0.02 0.098 -10000 0 -0.63 9 9
NSMAF -0.008 0.14 0.25 3 -0.44 27 30
response to hydrogen peroxide 0 0.001 0.003 10 -0.002 5 15
BCL2 -0.062 0.18 -10000 0 -0.43 101 101
EPHB forward signaling

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
Ephrin A5/EPHB2 0.038 0.038 -10000 0 -0.26 7 7
cell-cell adhesion 0.033 0.063 0.22 41 -10000 0 41
Ephrin B/EPHB2/RasGAP 0.067 0.082 -10000 0 -0.24 24 24
ITSN1 0.033 0.03 -10000 0 -0.43 2 2
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
SHC1 0.027 0.025 -10000 0 -0.43 1 1
Ephrin B1/EPHB3 0.034 0.057 -10000 0 -0.26 18 18
Ephrin B1/EPHB1 0.037 0.038 -10000 0 -0.26 7 7
HRAS/GDP -0.001 0.11 -10000 0 -0.29 35 35
Ephrin B/EPHB1/GRB7 0.055 0.083 -10000 0 -0.23 28 28
Endophilin/SYNJ1 -0.013 0.051 0.19 10 -0.21 20 30
KRAS 0.027 0.055 -10000 0 -0.43 7 7
Ephrin B/EPHB1/Src 0.066 0.078 -10000 0 -0.24 21 21
endothelial cell migration 0.03 0.095 -10000 0 -0.24 48 48
GRB2 0.033 0.009 -10000 0 -10000 0 0
GRB7 0.022 0.059 -10000 0 -0.43 8 8
PAK1 -0.021 0.065 0.2 6 -0.22 36 42
HRAS 0.031 0.037 -10000 0 -0.43 3 3
RRAS -0.016 0.053 0.18 7 -0.22 23 30
DNM1 0.032 0.036 -10000 0 -0.43 3 3
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.013 0.056 0.19 11 -0.22 20 31
lamellipodium assembly -0.033 0.063 -10000 0 -0.22 41 41
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.016 0.07 -10000 0 -0.29 14 14
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
EPHB2 0.031 0.03 -10000 0 -0.43 2 2
EPHB3 0.018 0.084 -10000 0 -0.43 17 17
EPHB1 0.025 0.051 -10000 0 -0.43 6 6
EPHB4 0.015 0.091 -10000 0 -0.43 20 20
mol:GDP -0.017 0.088 -10000 0 -0.34 23 23
Ephrin B/EPHB2 0.057 0.064 -10000 0 -0.22 19 19
Ephrin B/EPHB3 0.048 0.081 -10000 0 -0.23 32 32
JNK cascade -0.015 0.052 0.25 3 -0.24 18 21
Ephrin B/EPHB1 0.053 0.069 -10000 0 -0.23 22 22
RAP1/GDP -0.003 0.11 -10000 0 -0.29 35 35
EFNB2 0.017 0.082 -10000 0 -0.43 16 16
EFNB3 0.032 0.011 -10000 0 -10000 0 0
EFNB1 0.034 0.021 -10000 0 -0.43 1 1
Ephrin B2/EPHB1-2 0.041 0.068 -10000 0 -0.24 23 23
RAP1B 0.032 0.03 -10000 0 -0.43 2 2
RAP1A 0.03 0.046 -10000 0 -0.43 5 5
CDC42/GTP 0.035 0.091 -10000 0 -0.27 23 23
Rap1/GTP 0.014 0.071 -10000 0 -0.26 22 22
axon guidance 0.038 0.038 -10000 0 -0.26 7 7
MAPK3 0.025 0.073 0.2 17 -0.4 6 23
MAPK1 0.019 0.067 0.2 3 -0.41 5 8
Rac1/GDP -0.014 0.1 -10000 0 -0.3 33 33
actin cytoskeleton reorganization -0.022 0.076 -10000 0 -0.24 30 30
CDC42/GDP -0.013 0.1 -10000 0 -0.3 32 32
PI3K 0.035 0.098 -10000 0 -0.24 48 48
EFNA5 0.029 0.047 -10000 0 -0.43 5 5
Ephrin B2/EPHB4 0.019 0.081 -10000 0 -0.27 34 34
Ephrin B/EPHB2/Intersectin/N-WASP 0.012 0.072 -10000 0 -0.23 30 30
CDC42 0.034 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.006 0.07 -10000 0 -0.22 31 31
PTK2 0.11 0.23 0.55 106 -0.42 1 107
MAP4K4 -0.015 0.052 0.25 3 -0.24 18 21
SRC 0.031 0.03 -10000 0 -0.43 2 2
KALRN 0.033 0.022 -10000 0 -0.43 1 1
Intersectin/N-WASP 0.044 0.049 -10000 0 -0.31 9 9
neuron projection morphogenesis -0.012 0.086 0.27 4 -0.31 13 17
MAP2K1 0.011 0.062 -10000 0 -0.48 4 4
WASL 0.028 0.055 -10000 0 -0.43 7 7
Ephrin B1/EPHB1-2/NCK1 0.074 0.051 -10000 0 -0.24 10 10
cell migration 0.029 0.091 0.26 2 -0.41 7 9
NRAS 0.028 0.055 -10000 0 -0.43 7 7
SYNJ1 -0.013 0.051 0.19 10 -0.22 20 30
PXN 0.035 0.004 -10000 0 -10000 0 0
TF -0.017 0.049 0.18 10 -0.21 20 30
HRAS/GTP 0.04 0.076 -10000 0 -0.22 27 27
Ephrin B1/EPHB1-2 0.054 0.044 -10000 0 -0.23 9 9
cell adhesion mediated by integrin 0.013 0.054 0.22 17 -0.19 7 24
RAC1 0.034 0.006 -10000 0 -10000 0 0
mol:GTP 0.046 0.076 -10000 0 -0.23 29 29
RAC1-CDC42/GTP -0.002 0.071 -10000 0 -0.24 27 27
RASA1 0.026 0.058 -10000 0 -0.43 8 8
RAC1-CDC42/GDP 0 0.11 -10000 0 -0.3 30 30
ruffle organization -0.027 0.077 0.33 1 -0.41 5 6
NCK1 0.033 0.022 -10000 0 -0.43 1 1
receptor internalization -0.019 0.05 0.18 5 -0.21 22 27
Ephrin B/EPHB2/KALRN 0.071 0.074 -10000 0 -0.24 19 19
ROCK1 0.016 0.057 0.19 17 -0.23 18 35
RAS family/GDP -0.045 0.071 -10000 0 -0.26 30 30
Rac1/GTP -0.001 0.077 -10000 0 -0.23 41 41
Ephrin B/EPHB1/Src/Paxillin 0.015 0.071 -10000 0 -0.26 22 22
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.045 0.043 -10000 0 -0.31 7 7
Necdin/E2F1 0.011 0.11 -10000 0 -0.32 49 49
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.028 0.1 -10000 0 -0.24 59 59
NGF (dimer)/p75(NTR)/BEX1 0.029 0.039 -10000 0 -0.26 6 6
NT-4/5 (dimer)/p75(NTR) 0.02 0.027 -10000 0 -0.3 3 3
IKBKB 0.029 0.024 -10000 0 -0.43 1 1
AKT1 0.034 0.085 0.19 79 -0.22 20 99
IKBKG 0.035 0 -10000 0 -10000 0 0
BDNF 0.03 0.024 -10000 0 -0.43 1 1
MGDIs/NGR/p75(NTR)/LINGO1 0.03 0.049 -10000 0 -0.26 12 12
FURIN 0.026 0.059 -10000 0 -0.43 8 8
proBDNF (dimer)/p75(NTR)/Sortilin 0.05 0.049 -10000 0 -0.26 9 9
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.024 0.056 -10000 0 -0.22 18 18
proBDNF (dimer) 0.03 0.024 -10000 0 -0.43 1 1
NTRK1 0.027 0.032 -10000 0 -0.43 2 2
RTN4R 0.023 0.068 -10000 0 -0.43 11 11
neuron apoptosis 0.001 0.12 0.3 3 -0.46 14 17
IRAK1 0.035 0.004 -10000 0 -10000 0 0
SHC1 0.011 0.023 -10000 0 -0.26 3 3
ARHGDIA 0.032 0.022 -10000 0 -0.43 1 1
RhoA/GTP 0.019 0.044 -10000 0 -0.3 9 9
Gamma Secretase 0.065 0.07 -10000 0 -0.23 15 15
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.033 0.085 -10000 0 -0.25 38 38
MAGEH1 0.004 0.12 -10000 0 -0.43 34 34
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.024 0.093 -10000 0 -0.25 47 47
Mammalian IAPs/DIABLO 0.028 0.086 -10000 0 -0.24 43 43
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.014 0.097 -10000 0 -0.43 23 23
APP 0.006 0.11 -10000 0 -0.43 29 29
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.032 0.03 -10000 0 -0.43 2 2
RhoA/GDP/RHOGDI 0.046 0.056 0.18 35 -0.22 12 47
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest 0.007 0.076 0.21 52 -0.22 9 61
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.019 0.031 -10000 0 -0.21 6 6
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.037 0.032 -10000 0 -0.26 4 4
NCSTN 0.028 0.025 -10000 0 -0.43 1 1
mol:GTP 0.018 0.07 -10000 0 -0.26 28 28
PSENEN 0.034 0.006 -10000 0 -10000 0 0
mol:ceramide 0.025 0.059 0.19 39 -0.23 10 49
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.012 0.041 -10000 0 -0.19 16 16
p75(NTR)/beta APP 0.022 0.08 -10000 0 -0.31 26 26
BEX1 0.026 0.038 -10000 0 -0.43 3 3
mol:GDP -0.005 0.019 -10000 0 -0.25 3 3
NGF (dimer) 0.004 0.11 -10000 0 -0.24 77 77
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.046 0.053 -10000 0 -0.24 13 13
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
RAC1/GTP 0.033 0.025 -10000 0 -0.22 3 3
MYD88 0.03 0.042 -10000 0 -0.43 4 4
CHUK 0.024 0.071 -10000 0 -0.43 12 12
NGF (dimer)/p75(NTR)/PKA 0.018 0.07 -10000 0 -0.26 28 28
RHOB -0.012 0.14 -10000 0 -0.43 51 51
RHOA 0.025 0.062 -10000 0 -0.43 9 9
MAGE-G1/E2F1 0.042 0.044 -10000 0 -0.31 7 7
NT3 (dimer) 0.022 0.059 -10000 0 -0.43 8 8
TP53 -0.004 0.091 0.26 12 -0.24 26 38
PRDM4 0.031 0.063 0.19 50 -0.23 9 59
BDNF (dimer) -0.026 0.17 -10000 0 -0.32 112 112
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
SORT1 0.029 0.051 -10000 0 -0.43 6 6
activation of caspase activity 0.023 0.1 -10000 0 -0.24 59 59
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.05 0.048 -10000 0 -0.24 10 10
RHOC 0.032 0.036 -10000 0 -0.43 3 3
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.006 0.081 0.26 3 -0.29 11 14
DIABLO 0.035 0.004 -10000 0 -10000 0 0
SMPD2 0.026 0.059 0.19 39 -0.23 10 49
APH1B 0.024 0.068 -10000 0 -0.43 11 11
APH1A 0.025 0.038 -10000 0 -0.43 3 3
proNGF (dimer)/p75(NTR)/Sortilin 0.034 0.043 -10000 0 -0.26 9 9
PSEN1 0.032 0.036 -10000 0 -0.43 3 3
APAF-1/Pro-Caspase 9 0.046 0.037 -10000 0 -0.31 5 5
NT3 (dimer)/p75(NTR) 0.03 0.054 -10000 0 -0.3 11 11
MAPK8 0.001 0.073 0.26 4 -0.28 7 11
MAPK9 -0.005 0.084 0.27 3 -0.32 10 13
APAF1 0.031 0.041 -10000 0 -0.43 4 4
NTF3 0.022 0.059 -10000 0 -0.43 8 8
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.012 0.14 -10000 0 -0.43 48 48
RAC1/GDP 0.025 0.004 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.01 0.11 -10000 0 -0.22 85 85
p75 CTF/Sortilin/TRAF6/NRIF 0.076 0.05 -10000 0 -0.24 9 9
RhoA-B-C/GTP 0.018 0.069 -10000 0 -0.26 28 28
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.074 0.062 -10000 0 -0.22 12 12
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.066 0.054 -10000 0 -0.24 10 10
PRKACB 0.007 0.1 -10000 0 -0.43 25 25
proBDNF (dimer)/p75 ECD 0.044 0.024 -10000 0 -0.31 1 1
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.013 0.13 -10000 0 -0.43 44 44
BIRC2 0.031 0.011 -10000 0 -10000 0 0
neuron projection morphogenesis -0.036 0.083 0.15 3 -0.21 72 75
BAD -0.008 0.085 0.24 5 -0.29 9 14
RIPK2 0.028 0.014 -10000 0 -10000 0 0
NGFR 0.027 0.038 -10000 0 -0.43 3 3
CYCS 0.017 0.077 0.19 42 -0.22 28 70
ADAM17 0.034 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.044 0.04 -10000 0 -0.24 4 4
BCL2L11 -0.007 0.086 0.24 5 -0.29 9 14
BDNF (dimer)/p75(NTR) 0.037 0.035 -10000 0 -0.3 3 3
PI3K 0.04 0.061 -10000 0 -0.24 18 18
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.049 0.047 -10000 0 -0.24 9 9
NDNL2 0.033 0.008 -10000 0 -10000 0 0
YWHAE 0.032 0.01 -10000 0 -10000 0 0
PRKCI 0.024 0.065 -10000 0 -0.43 10 10
NGF (dimer)/p75(NTR) 0.02 0.027 -10000 0 -0.3 3 3
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.039 0.071 -10000 0 -0.24 28 28
TRAF6 0.034 0.021 -10000 0 -0.43 1 1
RAC1 0.034 0.006 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.031 0.031 -10000 0 -0.43 2 2
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.017 0.045 0.16 1 -0.25 13 14
SQSTM1 0.033 0.022 -10000 0 -0.43 1 1
NGFRAP1 -0.027 0.16 -10000 0 -0.43 67 67
CASP3 -0.007 0.082 0.23 4 -0.28 10 14
E2F1 0.027 0.055 -10000 0 -0.43 7 7
CASP9 0.033 0.022 -10000 0 -0.43 1 1
IKK complex 0.045 0.071 -10000 0 -0.31 3 3
NGF (dimer)/TRKA 0.02 0.023 -10000 0 -0.3 2 2
MMP7 -0.036 0.16 -10000 0 -0.43 70 70
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.061 0.055 -10000 0 -0.22 12 12
MMP3 -0.048 0.17 -10000 0 -0.43 82 82
APAF-1/Caspase 9 -0.038 0.064 -10000 0 -0.2 66 66
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.013 0.14 -9999 0 -0.32 54 54
MAP3K8 0.001 0.11 -9999 0 -0.43 32 32
FOS 0.017 0.099 -9999 0 -0.4 9 9
PRKCA 0.025 0.021 -9999 0 -10000 0 0
PTPN7 0.021 0.032 -9999 0 -0.44 1 1
HRAS 0.03 0.037 -9999 0 -0.43 3 3
PRKCB -0.001 0.006 -9999 0 -0.017 71 71
NRAS 0.028 0.055 -9999 0 -0.43 7 7
RAS family/GTP 0.047 0.057 -9999 0 -0.24 16 16
MAPK3 0.024 0.067 -9999 0 -0.44 6 6
MAP2K1 0.006 0.065 -9999 0 -0.28 7 7
ELK1 0.024 0.038 -9999 0 -0.43 2 2
BRAF 0.006 0.047 -9999 0 -0.35 7 7
mol:GTP -0.001 0.002 -9999 0 -0.005 71 71
MAPK1 0.01 0.1 -9999 0 -0.4 22 22
RAF1 0.011 0.023 -9999 0 -0.24 1 1
KRAS 0.027 0.055 -9999 0 -0.43 7 7
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.044 0.046 -10000 0 -0.31 8 8
FBXW11 0.032 0.03 -10000 0 -0.43 2 2
NF kappa B1 p50/c-Rel 0.025 0.042 -10000 0 -0.26 9 9
NF kappa B1 p50/RelA/I kappa B alpha 0.005 0.1 0.2 1 -0.34 21 22
NFKBIA -0.016 0.11 -10000 0 -0.24 74 74
MAPK14 0.035 0.004 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.029 0.03 -10000 0 -0.25 4 4
ARRB2 0.017 0.006 -10000 0 -10000 0 0
REL 0.023 0.071 -10000 0 -0.43 12 12
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.026 0.039 -10000 0 -0.26 8 8
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.03 0.024 -10000 0 -0.26 2 2
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
NF kappa B1 p50 dimer 0.022 0.028 0.26 2 -0.31 2 4
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
NFKB1 0.013 0.021 -10000 0 -0.31 2 2
RELA 0.034 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis -0.003 0.1 -10000 0 -0.23 67 67
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.004 0.1 -10000 0 -0.35 20 20
SRC 0.031 0.03 -10000 0 -0.43 2 2
PI3K 0.033 0.066 -10000 0 -0.31 17 17
NF kappa B1 p50/RelA -0.003 0.1 -10000 0 -0.23 67 67
IKBKB 0.029 0.024 -10000 0 -0.43 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.03 -10000 0 -0.43 2 2
SYK 0.004 0.12 -10000 0 -0.43 33 33
I kappa B alpha/PIK3R1 -0.008 0.12 -10000 0 -0.24 82 82
cell death 0.004 0.099 -10000 0 -0.33 20 20
NF kappa B1 p105/c-Rel 0.025 0.042 -10000 0 -0.26 9 9
LCK -0.019 0.14 -10000 0 -0.43 54 54
BCL3 0.027 0.058 -10000 0 -0.43 8 8
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.034 0.021 -9999 0 -0.43 1 1
HDAC2 0.031 0.023 -9999 0 -0.43 1 1
GNB1/GNG2 0.03 0.099 -9999 0 -0.26 50 50
forebrain development -0.009 0.15 -9999 0 -0.49 29 29
GNAO1 0.03 0.013 -9999 0 -10000 0 0
SMO/beta Arrestin2 0.012 0.1 -9999 0 -0.31 46 46
SMO -0.01 0.13 -9999 0 -0.43 46 46
ARRB2 0.032 0.01 -9999 0 -10000 0 0
GLI3/SPOP 0.002 0.15 -9999 0 -0.44 27 27
mol:GTP 0 0 -9999 0 -10000 0 0
GSK3B 0.035 0.005 -9999 0 -10000 0 0
GNAI2 0.026 0.058 -9999 0 -0.43 8 8
SIN3/HDAC complex 0.076 0.044 -9999 0 -0.24 5 5
GNAI1 0.015 0.091 -9999 0 -0.43 20 20
XPO1 0.036 0.005 -9999 0 -10000 0 0
GLI1/Su(fu) -0.022 0.18 -9999 0 -0.53 35 35
SAP30 0.029 0.047 -9999 0 -0.43 5 5
mol:GDP -0.01 0.13 -9999 0 -0.43 46 46
MIM/GLI2A 0.001 0.11 -9999 0 -0.43 31 31
IFT88 0.019 0.079 -9999 0 -0.43 15 15
GNAI3 0.035 0.006 -9999 0 -10000 0 0
GLI2 0.014 0.08 -9999 0 -0.37 11 11
GLI3 -0.011 0.15 -9999 0 -0.43 31 31
CSNK1D 0.033 0.008 -9999 0 -10000 0 0
CSNK1E 0.033 0.009 -9999 0 -10000 0 0
SAP18 0.033 0.009 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.019 0.079 -9999 0 -0.43 15 15
GNG2 0.033 0.021 -9999 0 -0.43 1 1
Gi family/GTP -0.02 0.12 -9999 0 -0.3 58 58
SIN3B 0.035 0.005 -9999 0 -10000 0 0
SIN3A 0.034 0.006 -9999 0 -10000 0 0
GLI3/Su(fu) -0.009 0.15 -9999 0 -0.42 38 38
GLI2/Su(fu) 0.004 0.11 -9999 0 -0.4 18 18
FOXA2 -0.026 0.21 -9999 0 -0.71 39 39
neural tube patterning -0.009 0.15 -9999 0 -0.49 29 29
SPOP 0.03 0.023 -9999 0 -0.43 1 1
Su(fu)/PIAS1 0.008 0.09 -9999 0 -0.31 17 17
GNB1 0.03 0.042 -9999 0 -0.43 4 4
CSNK1G2 0.032 0.03 -9999 0 -0.43 2 2
CSNK1G3 0.033 0.022 -9999 0 -0.43 1 1
MTSS1 0.001 0.11 -9999 0 -0.43 31 31
embryonic limb morphogenesis -0.009 0.15 -9999 0 -0.49 29 29
SUFU -0.001 0.085 -9999 0 -0.35 16 16
LGALS3 -0.01 0.14 -9999 0 -0.43 47 47
catabolic process 0.011 0.15 -9999 0 -0.48 23 23
GLI3A/CBP 0.032 0.05 -9999 0 -0.34 8 8
KIF3A 0.028 0.055 -9999 0 -0.43 7 7
GLI1 -0.009 0.15 -9999 0 -0.5 29 29
RAB23 0.029 0.046 -9999 0 -0.43 5 5
CSNK1A1 0.034 0.005 -9999 0 -10000 0 0
IFT172 0.032 0.036 -9999 0 -0.43 3 3
RBBP7 0.033 0.03 -9999 0 -0.43 2 2
Su(fu)/Galectin3 -0.014 0.12 -9999 0 -0.29 60 60
GNAZ 0.022 0.071 -9999 0 -0.43 12 12
RBBP4 0.033 0.021 -9999 0 -0.43 1 1
CSNK1G1 0.034 0.007 -9999 0 -10000 0 0
PIAS1 0.034 0.007 -9999 0 -10000 0 0
PRKACA 0.035 0.004 -9999 0 -10000 0 0
GLI2/SPOP 0.025 0.083 -9999 0 -0.41 9 9
STK36 0.02 0.084 -9999 0 -0.43 17 17
Gi family/GNB1/GNG2/GDP -0.021 0.12 -9999 0 -0.38 37 37
PTCH1 -0.007 0.14 -9999 0 -0.44 29 29
MIM/GLI1 -0.005 0.15 -9999 0 -0.51 23 23
CREBBP 0.032 0.05 -9999 0 -0.34 8 8
Su(fu)/SIN3/HDAC complex 0.011 0.095 -9999 0 -0.39 18 18
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.016 0.27 -10000 0 -1.1 29 29
oxygen homeostasis 0.005 0.011 -10000 0 -10000 0 0
TCEB2 0.032 0.01 -10000 0 -10000 0 0
TCEB1 0.028 0.025 -10000 0 -0.43 1 1
VHL/Elongin B/Elongin C/HIF2A 0.051 0.12 -10000 0 -0.32 15 15
EPO 0.047 0.16 -10000 0 -0.5 17 17
FIH (dimer) 0.035 0.03 -10000 0 -0.43 1 1
APEX1 0.034 0.028 -10000 0 -10000 0 0
SERPINE1 0.065 0.2 -10000 0 -0.53 28 28
FLT1 -0.042 0.27 -10000 0 -0.85 38 38
ADORA2A 0.063 0.19 0.36 10 -0.54 23 33
germ cell development 0.079 0.19 -10000 0 -0.51 20 20
SLC11A2 0.073 0.19 -10000 0 -0.54 21 21
BHLHE40 0.032 0.16 -10000 0 -0.49 26 26
HIF1AN 0.035 0.03 -10000 0 -0.43 1 1
HIF2A/ARNT/SIRT1 0.048 0.14 -10000 0 -0.38 20 20
ETS1 0.035 0.038 -10000 0 -0.43 2 2
CITED2 0.011 0.17 -10000 0 -0.9 14 14
KDR -0.023 0.22 -10000 0 -0.8 24 24
PGK1 0.075 0.19 -10000 0 -0.53 20 20
SIRT1 0.035 0.006 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.073 0.21 -10000 0 -0.57 24 24
EPAS1 0.024 0.12 0.22 2 -0.34 25 27
SP1 0.034 0.033 -10000 0 -0.11 8 8
ABCG2 0.069 0.2 -10000 0 -0.55 24 24
EFNA1 0.036 0.19 -10000 0 -0.54 28 28
FXN 0.075 0.19 0.36 18 -0.52 20 38
POU5F1 0.074 0.19 -10000 0 -0.53 20 20
neuron apoptosis -0.072 0.21 0.56 24 -10000 0 24
EP300 0.031 0.03 -10000 0 -0.43 2 2
EGLN3 -0.014 0.14 -10000 0 -0.43 51 51
EGLN2 0.034 0.041 -10000 0 -0.42 3 3
EGLN1 0.024 0.058 -10000 0 -0.42 7 7
VHL/Elongin B/Elongin C 0.053 0.034 -10000 0 -0.26 1 1
VHL 0.034 0.007 -10000 0 -10000 0 0
ARNT 0.028 0.027 -10000 0 -10000 0 0
SLC2A1 0.069 0.19 0.36 15 -0.51 24 39
TWIST1 0.057 0.22 0.36 13 -0.57 34 47
ELK1 0.038 0.033 -10000 0 -0.43 2 2
HIF2A/ARNT/Cbp/p300 0.047 0.14 -10000 0 -0.38 19 19
VEGFA 0.032 0.16 -10000 0 -0.49 26 26
CREBBP 0.031 0.023 -10000 0 -0.43 1 1
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.027 0.032 -9999 0 -0.43 2 2
Syndecan-3/Src/Cortactin 0.01 0.14 -9999 0 -0.48 26 26
Syndecan-3/Neurocan -0.017 0.12 -9999 0 -0.49 27 27
POMC 0.031 0.037 -9999 0 -0.43 3 3
EGFR -0.016 0.14 -9999 0 -0.43 48 48
Syndecan-3/EGFR -0.005 0.15 -9999 0 -0.52 29 29
AGRP 0.029 0.024 -9999 0 -0.43 1 1
NCSTN 0.028 0.025 -9999 0 -0.43 1 1
PSENEN 0.034 0.006 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.024 0.068 -9999 0 -0.43 11 11
APH1A 0.025 0.038 -9999 0 -0.43 3 3
NCAN 0 0 -9999 0 -10000 0 0
long-term memory 0.026 0.12 -9999 0 -0.47 24 24
Syndecan-3/IL8 -0.002 0.15 -9999 0 -0.5 30 30
PSEN1 0.032 0.036 -9999 0 -0.43 3 3
Src/Cortactin 0.039 0.038 -9999 0 -0.31 4 4
FYN 0.026 0.055 -9999 0 -0.43 7 7
limb bud formation -0.015 0.12 -9999 0 -0.52 25 25
MC4R 0.033 0.022 -9999 0 -0.43 1 1
SRC 0.031 0.03 -9999 0 -0.43 2 2
PTN -0.033 0.16 -9999 0 -0.43 66 66
FGFR/FGF/Syndecan-3 -0.015 0.12 -9999 0 -0.53 25 25
neuron projection morphogenesis -0.031 0.12 -9999 0 -0.48 24 24
Syndecan-3/AgRP 0.016 0.13 -9999 0 -0.49 27 27
Syndecan-3/AgRP/MC4R 0.03 0.13 -9999 0 -0.48 26 26
Fyn/Cortactin 0.036 0.043 -9999 0 -0.3 6 6
SDC3 -0.016 0.12 -9999 0 -0.54 25 25
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.002 0.14 -9999 0 -0.5 30 30
IL8 -0.006 0.12 -9999 0 -0.43 37 37
Syndecan-3/Fyn/Cortactin 0.026 0.13 -9999 0 -0.48 24 24
Syndecan-3/CASK -0.017 0.12 -9999 0 -0.49 27 27
alpha-MSH/MC4R 0.045 0.035 -9999 0 -0.31 4 4
Gamma Secretase 0.065 0.07 -9999 0 -0.23 15 15
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.034 0.006 -10000 0 -10000 0 0
VLDLR -0.009 0.13 -10000 0 -0.43 43 43
LRPAP1 0.034 0.007 -10000 0 -10000 0 0
NUDC 0.034 0.007 -10000 0 -10000 0 0
RELN/LRP8 0.035 0.09 -10000 0 -0.26 40 40
CaM/Ca2+ 0.026 0.004 -10000 0 -10000 0 0
KATNA1 0.033 0.009 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.001 0.074 0.19 8 -0.24 40 48
IQGAP1/CaM 0.049 0.014 -10000 0 -10000 0 0
DAB1 0.034 0.006 -10000 0 -10000 0 0
IQGAP1 0.034 0.008 -10000 0 -10000 0 0
PLA2G7 -0.039 0.16 -10000 0 -0.43 75 75
CALM1 0.035 0.005 -10000 0 -10000 0 0
DYNLT1 0.033 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.018 0.091 -10000 0 -0.31 35 35
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0 0 -10000 0 -10000 0 0
CDK5R1 0.033 0.009 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.01 0.013 -10000 0 -0.26 1 1
CDK5R2 0.035 0.005 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.029 0.098 -10000 0 -0.27 46 46
YWHAE 0.032 0.01 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.015 0.072 -10000 0 -0.25 5 5
MAP1B -0.008 0.062 -10000 0 -0.26 27 27
RAC1 0.016 0.007 -10000 0 -10000 0 0
p35/CDK5 0.008 0.07 0.19 8 -0.22 40 48
RELN 0.029 0.046 -10000 0 -0.43 5 5
PAFAH/LIS1 -0.014 0.1 -10000 0 -0.26 75 75
LIS1/CLIP170 0.01 0.013 -10000 0 -0.26 1 1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.017 0.071 -10000 0 -0.23 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.005 0.099 -10000 0 -0.26 57 57
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.001 0.066 0.2 2 -0.27 5 7
LIS1/IQGAP1 0.033 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 -0.31 1 1
PAFAH1B3 0.028 0.055 -10000 0 -0.43 7 7
PAFAH1B2 0.031 0.012 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.016 0.057 -10000 0 -0.18 25 25
NDEL1/Katanin 60/Dynein heavy chain 0.021 0.079 -10000 0 -0.25 5 5
LRP8 -0.003 0.12 -10000 0 -0.43 35 35
NDEL1/Katanin 60 0.009 0.073 -10000 0 -0.26 5 5
P39/CDK5 0.009 0.07 0.2 7 -0.22 40 47
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.033 0.019 -10000 0 -0.26 1 1
CDK5 -0.025 0.065 0.19 8 -0.22 40 48
PPP2R5D 0.035 0.005 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.009 0.011 -10000 0 -0.22 1 1
CSNK2A1 0.034 0.008 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.035 0.094 -10000 0 -0.24 46 46
RELN/VLDLR 0.019 0.12 -10000 0 -0.24 81 81
CDC42 0.016 0.007 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.006 0.15 -10000 0 -0.46 2 2
CRKL 0.007 0.072 0.21 12 -0.23 6 18
mol:DAG 0.014 0.066 0.25 2 -10000 0 2
HRAS 0.025 0.095 0.27 20 -0.36 1 21
MAPK8 0.034 0.068 0.2 57 -0.26 2 59
RAP1A 0.006 0.073 0.24 7 -0.23 8 15
GAB1 0.006 0.073 0.2 9 -0.24 10 19
MAPK14 0.036 0.067 0.2 58 -10000 0 58
EPO 0.024 0.025 -10000 0 -10000 0 0
PLCG1 0.014 0.067 0.25 2 -10000 0 2
EPOR/TRPC2/IP3 Receptors 0.026 0.027 -10000 0 -10000 0 0
RAPGEF1 0.034 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.046 0.05 -10000 0 -0.26 4 4
GAB1/SHC/GRB2/SOS1 0.033 0.072 0.29 1 -0.36 1 2
EPO/EPOR (dimer) 0.035 0.038 -10000 0 -10000 0 0
IRS2 -0.004 0.083 0.22 8 -0.26 22 30
STAT1 0.004 0.12 0.26 2 -0.3 14 16
STAT5B 0.007 0.087 0.26 1 -0.25 3 4
cell proliferation 0.015 0.077 0.19 71 -0.24 2 73
GAB1/SHIP/PIK3R1/SHP2/SHC 0.012 0.069 -10000 0 -0.21 13 13
TEC 0.006 0.071 0.2 10 -0.22 9 19
SOCS3 0.028 0.047 -10000 0 -0.43 5 5
STAT1 (dimer) 0.004 0.12 0.26 2 -0.29 14 16
JAK2 0.029 0.034 -10000 0 -0.44 2 2
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
EPO/EPOR (dimer)/JAK2 0.035 0.079 -10000 0 -0.19 12 12
EPO/EPOR 0.035 0.038 -10000 0 -10000 0 0
LYN 0.02 0.026 -10000 0 -10000 0 0
TEC/VAV2 0.016 0.073 0.29 1 -0.22 8 9
elevation of cytosolic calcium ion concentration 0.026 0.027 -10000 0 -10000 0 0
SHC1 0.027 0.025 -10000 0 -0.43 1 1
EPO/EPOR (dimer)/LYN 0.043 0.05 -10000 0 -10000 0 0
mol:IP3 0.014 0.066 0.25 2 -10000 0 2
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.001 0.091 0.25 2 -0.23 38 40
SH2B3 -0.003 0.008 -10000 0 -10000 0 0
NFKB1 0.035 0.068 0.2 58 -0.28 1 59
EPO/EPOR (dimer)/JAK2/SOCS3 0.02 0.034 -10000 0 -0.21 7 7
PTPN6 0.004 0.064 0.17 15 -0.21 7 22
TEC/VAV2/GRB2 0.029 0.077 0.24 1 -0.22 7 8
EPOR 0.026 0.027 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.032 0.072 0.29 1 -0.37 1 2
SOS1 0.034 0.021 -10000 0 -0.43 1 1
PLCG2 0.019 0.059 -10000 0 -0.43 8 8
CRKL/CBL/C3G 0.026 0.078 0.3 1 -0.23 6 7
VAV2 0.008 0.069 0.21 13 -0.24 4 17
CBL 0.006 0.066 0.2 10 -0.26 3 13
SHC/Grb2/SOS1 0.017 0.057 -10000 0 -0.2 3 3
STAT5A 0.006 0.088 0.26 1 -0.26 5 6
GRB2 0.033 0.009 -10000 0 -10000 0 0
STAT5 (dimer) -0.001 0.14 0.28 1 -0.3 71 72
LYN/PLCgamma2 0.027 0.047 -10000 0 -0.31 7 7
PTPN11 0.035 0.004 -10000 0 -10000 0 0
BTK 0.002 0.078 0.21 12 -0.24 16 28
BCL2 -0.12 0.35 -10000 0 -0.78 107 107
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.004 0.091 0.22 53 -10000 0 53
GNAI2 0.026 0.058 -10000 0 -0.43 8 8
S1P/S1P5/G12 0.023 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.013 -10000 0 -10000 0 0
RhoA/GTP -0.003 0.093 -10000 0 -0.22 53 53
negative regulation of cAMP metabolic process -0.005 0.082 -10000 0 -0.22 56 56
GNAZ 0.022 0.071 -10000 0 -0.43 12 12
GNAI3 0.034 0.006 -10000 0 -10000 0 0
GNA12 0.034 0.006 -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 -0.001 0.078 -10000 0 -0.24 42 42
RhoA/GDP 0.019 0.044 -10000 0 -0.3 9 9
RHOA 0.025 0.062 -10000 0 -0.43 9 9
GNAI1 0.015 0.091 -10000 0 -0.43 20 20
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.016 0.015 -10000 0 -0.31 1 1
SMARCC1 0.002 0.12 -10000 0 -1.2 5 5
REL 0.023 0.071 -10000 0 -0.43 12 12
HDAC7 -0.038 0.1 0.27 2 -0.32 33 35
JUN -0.003 0.12 -10000 0 -0.43 39 39
EP300 0.031 0.03 -10000 0 -0.43 2 2
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.001 0.061 -10000 0 -0.31 16 16
FOXO1 0 0 -10000 0 -10000 0 0
T-DHT/AR -0.011 0.13 0.36 1 -0.33 33 34
MAP2K6 0.01 0.084 -10000 0 -0.43 16 16
BRM/BAF57 0.046 0.024 -10000 0 -0.31 1 1
MAP2K4 0.023 0.031 -10000 0 -0.43 1 1
SMARCA2 0.033 0.022 -10000 0 -0.43 1 1
PDE9A -0.002 0.12 -10000 0 -0.95 5 5
NCOA2 0.025 0.048 -10000 0 -0.43 5 5
CEBPA 0.024 0.068 -10000 0 -0.43 11 11
EHMT2 0.035 0.004 -10000 0 -10000 0 0
cell proliferation 0.022 0.13 0.33 15 -0.35 12 27
NR0B1 0.029 0.037 -10000 0 -0.43 3 3
EGR1 -0.038 0.16 -10000 0 -0.43 74 74
RXRs/9cRA 0.05 0.049 -10000 0 -0.24 10 10
AR/RACK1/Src 0.002 0.098 0.32 6 -0.31 10 16
AR/GR -0.031 0.12 0.22 2 -0.24 99 101
GNB2L1 0.033 0.03 -10000 0 -0.43 2 2
PKN1 0.033 0.03 -10000 0 -0.43 2 2
RCHY1 0.021 0.077 -10000 0 -0.43 14 14
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 0.007 0.033 -10000 0 -0.32 3 3
T-DHT/AR/TIF2/CARM1 0.006 0.093 0.3 2 -0.31 11 13
SRC -0.01 0.069 0.19 29 -0.25 14 43
NR3C1 0.022 0.074 -10000 0 -0.43 13 13
KLK3 -0.016 0.097 -10000 0 -10000 0 0
APPBP2 0.024 0.023 -10000 0 -10000 0 0
TRIM24 0.035 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.033 0.071 0.16 1 -0.28 21 22
TMPRSS2 -0.14 0.38 -10000 0 -0.96 87 87
RXRG 0.023 0.055 -10000 0 -0.43 7 7
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.034 0.021 -10000 0 -0.43 1 1
RXRB 0.032 0.036 -10000 0 -0.43 3 3
CARM1 0.034 0.021 -10000 0 -0.43 1 1
NR2C2 0.034 0.007 -10000 0 -10000 0 0
KLK2 0.009 0.073 0.3 4 -0.32 1 5
AR -0.035 0.11 0.19 1 -0.24 95 96
SENP1 0.035 0.004 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
MDM2 0.032 0.008 -10000 0 -10000 0 0
SRY 0.022 0.071 -10000 0 -0.43 12 12
GATA2 0.027 0.051 -10000 0 -0.43 6 6
MYST2 0.029 0.031 -10000 0 -0.43 2 2
HOXB13 0.023 0.018 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.001 0.1 0.33 6 -0.31 11 17
positive regulation of transcription 0.027 0.051 -10000 0 -0.43 6 6
DNAJA1 0.023 0.042 -10000 0 -0.43 3 3
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.052 -10000 0 -0.29 14 14
NCOA1 0.034 0.059 -10000 0 -0.34 10 10
SPDEF -0.047 0.18 -10000 0 -0.43 90 90
T-DHT/AR/TIF2 0.01 0.078 0.22 7 -0.29 6 13
T-DHT/AR/Hsp90 -0.033 0.071 0.16 1 -0.28 21 22
GSK3B 0.035 0.006 -10000 0 -10000 0 0
NR2C1 0.028 0.055 -10000 0 -0.43 7 7
mol:T-DHT -0.016 0.064 0.22 12 -0.26 17 29
SIRT1 0.034 0.006 -10000 0 -10000 0 0
ZMIZ2 -0.001 0 -10000 0 -10000 0 0
POU2F1 0.017 0.054 -10000 0 -0.11 69 69
T-DHT/AR/DAX-1 -0.012 0.096 0.29 2 -0.3 20 22
CREBBP 0.031 0.023 -10000 0 -0.43 1 1
SMARCE1 0.033 0.01 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.035 0.004 -9999 0 -10000 0 0
SPHK1 0.005 0.11 -9999 0 -0.43 29 29
GNAI2 0.026 0.058 -9999 0 -0.43 8 8
mol:S1P 0.001 0.068 -9999 0 -0.27 27 27
GNAO1 0.03 0.013 -9999 0 -10000 0 0
mol:Sphinganine-1-P -0.003 0.075 -9999 0 -0.31 29 29
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.038 0.072 -9999 0 -0.22 28 28
GNAI3 0.034 0.006 -9999 0 -10000 0 0
G12/G13 0.044 0.032 -9999 0 -0.31 3 3
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0.012 0.097 -9999 0 -0.43 23 23
S1P1/S1P 0.019 0.089 -9999 0 -0.25 41 41
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
GNAI1 0.015 0.091 -9999 0 -0.43 20 20
S1P/S1P5/G12 0.026 0.067 -9999 0 -0.22 28 28
S1P/S1P3/Gq -0.004 0.094 -9999 0 -0.25 51 51
S1P/S1P4/Gi 0.001 0.095 -9999 0 -0.27 39 39
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.022 0.071 -9999 0 -0.43 12 12
GNA14 -0.011 0.13 -9999 0 -0.43 44 44
GNA15 0.029 0.047 -9999 0 -0.43 5 5
GNA12 0.034 0.006 -9999 0 -10000 0 0
GNA13 0.029 0.037 -9999 0 -0.43 3 3
GNA11 0.031 0.036 -9999 0 -0.43 3 3
ABCC1 0.029 0.042 -9999 0 -0.43 4 4
FoxO family signaling

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
G6PC 0.023 0.076 -10000 0 -1.3 1 1
PLK1 0.011 0.2 -10000 0 -0.74 13 13
CDKN1B 0.043 0.17 -10000 0 -0.46 31 31
FOXO3 -0.004 0.22 -10000 0 -0.6 30 30
KAT2B 0.001 0.019 -10000 0 -0.042 62 62
FOXO1/SIRT1 0.042 0.052 -10000 0 -0.24 5 5
CAT -0.005 0.22 -10000 0 -0.88 16 16
CTNNB1 0.022 0.071 -10000 0 -0.43 12 12
AKT1 0.027 0.05 -10000 0 -0.42 3 3
FOXO1 0.025 0.053 0.24 2 -0.26 5 7
MAPK10 0.007 0.059 0.2 7 -0.22 24 31
mol:GTP 0 0.002 -10000 0 -10000 0 0
FOXO4 0.015 0.099 0.31 2 -0.32 19 21
response to oxidative stress 0.004 0.02 -10000 0 -0.041 65 65
FOXO3A/SIRT1 0.022 0.19 -10000 0 -0.44 51 51
XPO1 0.035 0.005 -10000 0 -10000 0 0
EP300 0.033 0.031 -10000 0 -0.43 2 2
BCL2L11 0.028 0.087 -10000 0 -1.2 2 2
FOXO1/SKP2 0.04 0.051 0.21 2 -0.26 4 6
mol:GDP 0.004 0.02 -10000 0 -0.041 65 65
RAN 0.035 0.005 -10000 0 -10000 0 0
GADD45A 0.012 0.22 -10000 0 -0.8 27 27
YWHAQ 0.033 0.03 -10000 0 -0.43 2 2
FOXO1/14-3-3 family 0.036 0.12 -10000 0 -0.45 16 16
MST1 0.027 0.035 -10000 0 -10000 0 0
CSNK1D 0.033 0.008 -10000 0 -10000 0 0
CSNK1E 0.033 0.009 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.01 0.13 -10000 0 -0.44 24 24
YWHAB 0.033 0.008 -10000 0 -10000 0 0
MAPK8 0.017 0.042 0.2 7 -0.22 7 14
MAPK9 0.009 0.059 0.2 7 -0.22 23 30
YWHAG 0.035 0.004 -10000 0 -10000 0 0
YWHAE 0.032 0.01 -10000 0 -10000 0 0
YWHAZ 0.027 0.015 -10000 0 -10000 0 0
SIRT1 0.035 0.02 -10000 0 -10000 0 0
SOD2 0.03 0.16 0.43 1 -0.61 14 15
RBL2 -0.061 0.3 -10000 0 -0.7 74 74
RAL/GDP 0.045 0.038 -10000 0 -0.25 4 4
CHUK 0.017 0.078 -10000 0 -0.43 12 12
Ran/GTP 0.026 0.01 -10000 0 -10000 0 0
CSNK1G2 0.032 0.03 -10000 0 -0.43 2 2
RAL/GTP 0.045 0.038 -10000 0 -0.22 4 4
CSNK1G1 0.034 0.007 -10000 0 -10000 0 0
FASLG -0.093 0.4 -10000 0 -1.4 45 45
SKP2 0.033 0.008 -10000 0 -10000 0 0
USP7 0.032 0.011 -10000 0 -10000 0 0
IKBKB 0.023 0.04 -10000 0 -0.42 1 1
CCNB1 -0.048 0.33 -10000 0 -1.1 38 38
FOXO1-3a-4/beta catenin 0.036 0.16 -10000 0 -0.4 30 30
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.051 0.21 2 -0.25 4 6
CSNK1A1 0.034 0.005 -10000 0 -10000 0 0
SGK1 0.001 0.019 -10000 0 -0.042 62 62
CSNK1G3 0.033 0.022 -10000 0 -0.43 1 1
Ran/GTP/Exportin 1 0.047 0.013 -10000 0 -10000 0 0
ZFAND5 0.016 0.086 0.29 2 -0.27 16 18
SFN 0.01 0.1 -10000 0 -0.43 25 25
CDK2 0.035 0.03 -10000 0 -0.42 2 2
FOXO3A/14-3-3 0.016 0.13 -10000 0 -0.46 18 18
CREBBP 0.033 0.024 -10000 0 -0.43 1 1
FBXO32 0.022 0.31 -10000 0 -1.2 22 22
BCL6 -0.006 0.27 -10000 0 -1.1 22 22
RALB 0.032 0.041 -10000 0 -0.43 4 4
RALA 0.035 0.006 -10000 0 -10000 0 0
YWHAH 0.03 0.037 -10000 0 -0.43 3 3
Retinoic acid receptors-mediated 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
HDAC1 0.034 0.021 -10000 0 -0.43 1 1
HDAC3 0.035 0.005 -10000 0 -10000 0 0
VDR 0.019 0.084 -10000 0 -0.43 17 17
Cbp/p300/PCAF 0.039 0.029 -10000 0 -0.26 3 3
EP300 0.031 0.03 -10000 0 -0.43 2 2
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.014 0.062 0.19 1 -0.27 9 10
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.035 0.004 -10000 0 -10000 0 0
AKT1 0.028 0.092 0.21 55 -0.26 14 69
RAR alpha/9cRA/Cyclin H 0.045 0.1 0.24 3 -0.29 10 13
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.019 0.068 -10000 0 -0.34 7 7
CDC2 0.009 0.095 -10000 0 -0.43 22 22
response to UV -0.002 0.009 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.032 0.062 -10000 0 -0.25 11 11
NCOR2 0.034 0.007 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.015 0.06 -10000 0 -0.3 17 17
RXRs/RARs/NRIP1/9cRA -0.006 0.19 -10000 0 -0.54 51 51
NCOA2 0.024 0.047 -10000 0 -0.43 5 5
NCOA3 0.031 0.031 -10000 0 -0.43 2 2
NCOA1 0.03 0.051 -10000 0 -0.43 6 6
VDR/VDR/DNA 0.019 0.084 -10000 0 -0.43 17 17
RARG 0.031 0.017 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.046 0.01 -10000 0 -10000 0 0
MAPK3 0.026 0.029 -10000 0 -0.43 1 1
MAPK1 0.032 0.03 -10000 0 -0.43 2 2
MAPK8 0.026 0.041 -10000 0 -0.43 3 3
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.021 0.13 -10000 0 -0.34 42 42
RARA 0.01 0.042 -10000 0 -0.23 9 9
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.015 0.059 -10000 0 -0.33 5 5
PRKCA 0.024 0.031 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.011 0.21 -10000 0 -0.58 51 51
RXRG 0.011 0.049 -10000 0 -0.32 7 7
RXRA 0.016 0.084 -10000 0 -0.19 34 34
RXRB 0.016 0.038 -10000 0 -0.28 3 3
VDR/Vit D3/DNA 0.015 0.06 -10000 0 -0.3 17 17
RBP1 -0.029 0.16 -10000 0 -0.43 66 66
CRBP1/9-cic-RA -0.02 0.11 -10000 0 -0.3 66 66
RARB 0.01 0.092 -10000 0 -0.43 20 20
PRKCG 0.027 0.031 -10000 0 -0.099 2 2
MNAT1 0.034 0.006 -10000 0 -10000 0 0
RAR alpha/RXRs 0.003 0.15 0.35 3 -0.39 37 40
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.026 0.12 0.31 1 -0.36 15 16
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.075 0.22 5 -0.26 9 14
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.011 0.21 -10000 0 -0.59 51 51
positive regulation of DNA binding 0.032 0.094 -10000 0 -0.28 10 10
NRIP1 -0.07 0.38 -10000 0 -1.2 51 51
RXRs/RARs 0.006 0.17 -10000 0 -0.43 51 51
RXRs/RXRs/DNA/9cRA -0.01 0.11 -10000 0 -0.33 40 40
PRKACA 0.035 0.004 -10000 0 -10000 0 0
CDK7 0.034 0.007 -10000 0 -10000 0 0
TFIIH 0.067 0.023 -10000 0 -0.25 1 1
RAR alpha/9cRA 0.068 0.066 -10000 0 -0.24 2 2
CCNH 0.033 0.022 -10000 0 -0.43 1 1
CREBBP 0.031 0.023 -10000 0 -0.43 1 1
RAR gamma2/9cRA 0.065 0.025 -10000 0 -0.2 1 1
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 0.013 0.1 -10000 0 -0.96 5 5
MKNK1 0.034 0.006 -10000 0 -10000 0 0
MAPK14 0.03 0.048 -10000 0 -0.26 5 5
ATF2/c-Jun -0.023 0.16 -10000 0 -0.52 45 45
MAPK11 0.029 0.045 -10000 0 -0.29 3 3
MITF 0.02 0.055 -10000 0 -0.32 9 9
MAPKAPK5 0.023 0.045 -10000 0 -0.32 5 5
KRT8 0.01 0.076 -10000 0 -0.28 26 26
MAPKAPK3 0.034 0.008 -10000 0 -10000 0 0
MAPKAPK2 0.025 0.043 -10000 0 -0.43 4 4
p38alpha-beta/CK2 0.04 0.063 -10000 0 -0.36 5 5
CEBPB 0.017 0.058 -10000 0 -0.34 10 10
SLC9A1 0.023 0.043 -10000 0 -0.33 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.016 0.072 -10000 0 -0.3 10 10
p38alpha-beta/MNK1 0.055 0.058 -10000 0 -0.32 3 3
JUN -0.025 0.16 -10000 0 -0.53 42 42
PPARGC1A 0.016 0.068 -10000 0 -0.34 14 14
USF1 0.012 0.064 -10000 0 -0.32 14 14
RAB5/GDP/GDI1 0.024 0.052 -10000 0 -0.24 5 5
NOS2 0.016 0.044 -10000 0 -0.33 5 5
DDIT3 0.023 0.045 -10000 0 -0.32 5 5
RAB5A 0.034 0.006 -10000 0 -10000 0 0
HSPB1 -0.012 0.089 0.28 3 -0.26 50 53
p38alpha-beta/HBP1 0.053 0.066 -10000 0 -0.3 7 7
CREB1 0.015 0.062 -10000 0 -0.3 10 10
RAB5/GDP 0.025 0.004 -10000 0 -10000 0 0
EIF4E 0.016 0.044 0.23 3 -0.28 3 6
RPS6KA4 0.022 0.047 -10000 0 -0.31 6 6
PLA2G4A 0 0.066 -10000 0 -0.28 21 21
GDI1 0.023 0.047 -10000 0 -0.31 6 6
TP53 -0.001 0.064 -10000 0 -0.32 10 10
RPS6KA5 0.008 0.078 -10000 0 -0.28 29 29
ESR1 -0.057 0.14 -10000 0 -0.28 133 133
HBP1 0.032 0.036 -10000 0 -0.43 3 3
MEF2C 0.008 0.089 -10000 0 -0.35 25 25
MEF2A 0.022 0.045 -10000 0 -0.32 5 5
EIF4EBP1 0.01 0.066 -10000 0 -0.31 12 12
KRT19 -0.001 0.092 -10000 0 -0.28 44 44
ELK4 0.017 0.049 -10000 0 -0.33 6 6
ATF6 0.018 0.044 -10000 0 -0.32 5 5
ATF1 0.015 0.064 -10000 0 -0.28 14 14
p38alpha-beta/MAPKAPK2 0.042 0.067 -10000 0 -0.34 6 6
p38alpha-beta/MAPKAPK3 0.054 0.061 -10000 0 -0.31 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 0.016 0.089 -9999 0 -0.43 19 19
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine 0.012 0.063 -9999 0 -0.3 19 19
neuron projection morphogenesis 0.012 0.063 -9999 0 -0.3 19 19
IL2 signaling events mediated by STAT5

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
GAB2 0.031 0.012 -10000 0 -10000 0 0
ELF1 0.013 0.097 -10000 0 -0.35 33 33
CCNA2 0.008 0.1 -10000 0 -0.43 27 27
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
JAK3 0.035 0.005 -10000 0 -10000 0 0
PIK3R1 0.018 0.084 -10000 0 -0.43 17 17
JAK1 0.032 0.036 -10000 0 -0.43 3 3
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.019 0.14 0.25 1 -0.4 25 26
SHC1 0.028 0.025 -10000 0 -0.43 1 1
SP1 0.031 0.068 -10000 0 -0.34 16 16
IL2RA -0.025 0.17 -10000 0 -0.6 37 37
IL2RB 0.011 0.097 -10000 0 -0.43 23 23
SOS1 0.035 0.021 -10000 0 -0.43 1 1
IL2RG 0.03 0.042 -10000 0 -0.43 4 4
G1/S transition of mitotic cell cycle -0.022 0.2 -10000 0 -0.54 47 47
PTPN11 0.036 0.004 -10000 0 -10000 0 0
CCND2 0.003 0.12 -10000 0 -0.67 15 15
LCK -0.019 0.14 -10000 0 -0.43 54 54
GRB2 0.033 0.009 -10000 0 -10000 0 0
IL2 0.032 0.036 -10000 0 -0.43 3 3
CDK6 0.024 0.059 -10000 0 -0.43 8 8
CCND3 0.023 0.13 0.36 1 -0.43 8 9
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.013 -10000 0 -10000 0 0
CDC42/GTP 0.001 0.088 -10000 0 -0.22 44 44
PLCG1 -0.009 0.074 -10000 0 -0.23 38 38
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.026 0.058 -10000 0 -0.43 8 8
GNAI3 0.034 0.006 -10000 0 -10000 0 0
G12/G13 0.044 0.032 -10000 0 -0.31 3 3
cell migration 0 0.086 -10000 0 -0.21 44 44
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.008 0.072 -10000 0 -0.22 38 38
MAPK1 -0.005 0.072 -10000 0 -0.28 18 18
S1P/S1P5/Gi -0.001 0.078 -10000 0 -0.24 42 42
GNAI1 0.015 0.091 -10000 0 -0.43 20 20
CDC42/GDP 0.025 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.023 0.004 -10000 0 -10000 0 0
RHOA 0.028 0.064 0.19 48 -0.24 10 58
S1P/S1P4/Gi -0.001 0.078 -10000 0 -0.24 42 42
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.022 0.071 -10000 0 -0.43 12 12
S1P/S1P4/G12/G13 0.038 0.026 -10000 0 -0.23 3 3
GNA12 0.034 0.006 -10000 0 -10000 0 0
GNA13 0.029 0.037 -10000 0 -0.43 3 3
CDC42 0.034 0.007 -10000 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.014 0.04 -10000 0 -0.26 13 13
ADCY5 -0.012 0.041 -10000 0 -0.26 13 13
ADCY6 -0.011 0.027 -10000 0 -0.26 6 6
ADCY7 -0.009 0.022 -10000 0 -0.25 4 4
ADCY1 -0.01 0.025 -10000 0 -0.26 5 5
ADCY2 -0.029 0.075 -10000 0 -0.26 46 46
ADCY3 -0.014 0.038 -10000 0 -0.26 12 12
ADCY8 -0.008 0.023 -10000 0 -0.26 4 4
PRKCE 0.005 0.034 -10000 0 -0.3 6 6
ADCY9 -0.016 0.048 -10000 0 -0.27 16 16
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.016 0.08 0.19 30 -0.26 9 39
Aurora A signaling

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
Aurora A/GADD45A 0.03 0.057 -10000 0 -0.25 15 15
BIRC5 -0.003 0.12 -10000 0 -0.43 38 38
NFKBIA 0.015 0.045 0.25 10 -0.25 2 12
CPEB1 0.028 0.047 -10000 0 -0.43 5 5
AKT1 0.012 0.042 0.27 5 -0.25 3 8
NDEL1 0.032 0.011 -10000 0 -10000 0 0
Aurora A/BRCA1 0.029 0.046 -10000 0 -0.22 11 11
NDEL1/TACC3 0.042 0.049 -10000 0 -0.2 6 6
GADD45A 0.018 0.082 -10000 0 -0.43 16 16
GSK3B 0.037 0.016 -10000 0 -10000 0 0
PAK1/Aurora A 0.026 0.061 -10000 0 -0.25 18 18
MDM2 0.033 0.008 -10000 0 -10000 0 0
JUB 0.001 0.12 -10000 0 -0.43 36 36
TPX2 -0.008 0.085 -10000 0 -0.31 37 37
TP53 -0.006 0.096 -10000 0 -0.24 66 66
DLG7 -0.008 0.058 0.25 2 -0.19 39 41
AURKAIP1 0 0 -10000 0 -10000 0 0
ARHGEF7 0.032 0.01 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.044 0.052 -10000 0 -0.21 6 6
G2/M transition of mitotic cell cycle 0.029 0.046 -10000 0 -0.22 11 11
AURKA 0.023 0.034 -10000 0 -10000 0 0
AURKB 0.001 0.06 -10000 0 -0.18 41 41
CDC25B 0.013 0.049 -10000 0 -0.28 6 6
G2/M transition checkpoint 0.016 0.071 -10000 0 -0.22 36 36
mRNA polyadenylation 0.031 0.035 -10000 0 -0.21 5 5
Aurora A/CPEB 0.031 0.036 -10000 0 -0.21 5 5
Aurora A/TACC1/TRAP/chTOG 0.047 0.079 -10000 0 -0.24 24 24
BRCA1 0.023 0.071 -10000 0 -0.43 12 12
centrosome duplication 0.026 0.061 -10000 0 -0.25 18 18
regulation of centrosome cycle 0.04 0.048 -10000 0 -0.2 6 6
spindle assembly 0.045 0.078 -10000 0 -0.24 24 24
TDRD7 0.026 0.062 -10000 0 -0.43 9 9
Aurora A/RasGAP/Survivin 0.035 0.081 -10000 0 -0.21 26 26
CENPA -0.005 0.082 -10000 0 -0.28 41 41
Aurora A/PP2A 0.041 0.03 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.001 0.045 0.18 2 -10000 0 2
negative regulation of DNA binding -0.006 0.096 -10000 0 -0.24 66 66
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.044 0.025 -10000 0 -0.31 1 1
RASA1 0.026 0.058 -10000 0 -0.43 8 8
Ajuba/Aurora A 0.016 0.072 -10000 0 -0.22 36 36
mitotic prometaphase 0.003 0.023 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.034 -10000 0 -10000 0 0
TACC1 0.008 0.095 -10000 0 -0.43 22 22
TACC3 0.017 0.086 -10000 0 -0.43 18 18
Aurora A/Antizyme1 0.035 0.025 -10000 0 -10000 0 0
Aurora A/RasGAP 0.035 0.046 -10000 0 -0.25 8 8
OAZ1 0.034 0.006 -10000 0 -10000 0 0
RAN 0.035 0.005 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.038 0.016 -10000 0 -10000 0 0
GIT1 0.032 0.023 -10000 0 -0.43 1 1
GIT1/beta-PIX/PAK1 0.042 0.065 -10000 0 -0.28 15 15
Importin alpha/Importin beta/TPX2 -0.008 0.084 -10000 0 -0.31 37 37
PPP2R5D 0.035 0.005 -10000 0 -10000 0 0
Aurora A/TPX2 0.007 0.053 -10000 0 -0.21 8 8
PAK1 0.014 0.086 -10000 0 -0.43 18 18
CKAP5 0.035 0.004 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.041 0.016 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.034 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.016 0.082 -10000 0 -0.43 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.029 0.024 -10000 0 -0.43 1 1
RAC1-CDC42/GTP/PAK family 0.002 0.064 -10000 0 -0.21 37 37
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.028 0.051 -10000 0 -0.43 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 0.032 0.011 -10000 0 -10000 0 0
FYN 0.026 0.055 -10000 0 -0.43 7 7
MAP3K12 0.035 0.004 -10000 0 -10000 0 0
FGR 0.034 0.007 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.005 0.14 0.22 2 -0.36 47 49
PRKG1 0.034 0.006 -10000 0 -10000 0 0
DUSP8 0.019 0.082 -10000 0 -0.43 16 16
PGK/cGMP/p38 alpha -0.009 0.14 0.2 2 -0.34 51 53
apoptosis -0.005 0.14 0.21 2 -0.34 47 49
RAL/GTP 0.044 0.028 -10000 0 -0.26 4 4
LYN 0.03 0.013 -10000 0 -10000 0 0
DUSP1 0.001 0.12 -10000 0 -0.43 34 34
PAK1 0.014 0.086 -10000 0 -0.43 18 18
SRC 0.031 0.03 -10000 0 -0.43 2 2
RAC1/OSM/MEKK3/MKK3 0.073 0.038 -10000 0 -0.24 1 1
TRAF6 0.034 0.021 -10000 0 -0.43 1 1
RAC1 0.034 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 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.045 0.012 -10000 0 -10000 0 0
MAPK11 -0.015 0.15 0.24 5 -0.4 39 44
BLK 0.02 0.044 -10000 0 -0.43 4 4
HCK 0.017 0.086 -10000 0 -0.43 18 18
MAP2K3 0.031 0.023 -10000 0 -0.43 1 1
DUSP16 0.028 0.051 -10000 0 -0.43 6 6
DUSP10 0.011 0.086 -10000 0 -0.43 18 18
TRAF6/MEKK3 0.039 0.019 -10000 0 -0.23 1 1
MAP3K7IP1 0.033 0.009 -10000 0 -10000 0 0
MAPK14 -0.018 0.15 0.21 6 -0.37 53 59
positive regulation of innate immune response -0.019 0.17 0.26 5 -0.45 45 50
LCK -0.019 0.14 -10000 0 -0.43 54 54
p38alpha-beta/MKP7 -0.009 0.17 0.27 5 -0.43 46 51
p38alpha-beta/MKP5 -0.015 0.16 0.28 3 -0.43 45 48
PGK/cGMP 0.025 0.005 -10000 0 -10000 0 0
PAK2 0.034 0.007 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.019 0.18 0.28 3 -0.44 48 51
CDC42 0.034 0.007 -10000 0 -10000 0 0
RALB 0.031 0.041 -10000 0 -0.43 4 4
RALA 0.034 0.006 -10000 0 -10000 0 0
PAK3 0.014 0.086 -10000 0 -0.43 18 18
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.027 0.058 -9999 0 -0.43 8 8
mol:S1P 0.001 0.002 -9999 0 -0.025 3 3
S1P1/S1P/Gi -0.019 0.11 -9999 0 -0.3 45 45
GNAO1 0.031 0.014 -9999 0 -10000 0 0
S1P/S1P3/G12/G13 0.039 0.027 -9999 0 -0.23 3 3
AKT1 0.002 0.13 -9999 0 -0.48 28 28
AKT3 -0.005 0.13 -9999 0 -0.84 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.027 0.058 -9999 0 -0.43 8 8
GNAI2 0.027 0.059 -9999 0 -0.43 8 8
GNAI3 0.035 0.008 -9999 0 -10000 0 0
GNAI1 0.015 0.091 -9999 0 -0.43 20 20
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.001 0.002 -9999 0 -0.03 3 3
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0.012 0.097 -9999 0 -0.43 23 23
mol:Ca2+ 0.005 0.083 -9999 0 -0.31 21 21
MAPK3 -0.003 0.077 -9999 0 -0.3 17 17
MAPK1 -0.001 0.077 -9999 0 -0.35 13 13
JAK2 -0.014 0.1 -9999 0 -0.34 30 30
CXCR4 -0.016 0.1 -9999 0 -0.32 37 37
FLT1 0.026 0.059 -9999 0 -0.43 8 8
RhoA/GDP 0.019 0.044 -9999 0 -0.3 9 9
Rac1/GDP 0.025 0.004 -9999 0 -10000 0 0
SRC -0.004 0.081 -9999 0 -0.33 17 17
S1P/S1P3/Gi 0.005 0.084 -9999 0 -0.31 21 21
RAC1 0.034 0.006 -9999 0 -10000 0 0
RhoA/GTP 0.003 0.098 -9999 0 -0.29 24 24
VEGFA 0.002 0.003 -9999 0 -0.04 3 3
S1P/S1P2/Gi 0.003 0.08 -9999 0 -0.24 42 42
VEGFR1 homodimer/VEGFA homodimer 0.024 0.043 -9999 0 -0.28 9 9
RHOA 0.025 0.062 -9999 0 -0.43 9 9
S1P/S1P3/Gq -0.007 0.08 -9999 0 -0.24 51 51
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.023 0.071 -9999 0 -0.43 12 12
G12/G13 0.044 0.032 -9999 0 -0.31 3 3
GNA14 -0.011 0.13 -9999 0 -0.43 44 44
GNA15 0.029 0.047 -9999 0 -0.43 5 5
GNA12 0.034 0.006 -9999 0 -10000 0 0
GNA13 0.029 0.037 -9999 0 -0.43 3 3
GNA11 0.031 0.036 -9999 0 -0.43 3 3
Rac1/GTP 0.006 0.093 -9999 0 -0.29 20 20
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.03 0.042 -10000 0 -0.43 4 4
RAS family/GTP/Tiam1 0.01 0.07 -10000 0 -0.27 21 21
NT3 (dimer)/TRKC 0.033 0.049 -10000 0 -0.3 8 8
NT3 (dimer)/TRKB 0.039 0.069 -10000 0 -0.26 20 20
SHC/Grb2/SOS1/GAB1/PI3K 0.017 0.048 -10000 0 -0.21 15 15
RAPGEF1 0.034 0.005 -10000 0 -10000 0 0
BDNF 0.03 0.024 -10000 0 -0.43 1 1
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
DYNLT1 0.033 0.009 -10000 0 -10000 0 0
NTRK1 0.027 0.032 -10000 0 -0.43 2 2
NTRK2 0.019 0.079 -10000 0 -0.43 15 15
NTRK3 0.03 0.012 -10000 0 -10000 0 0
NT-4/5 (dimer)/TRKB 0.028 0.054 -10000 0 -0.26 15 15
neuron apoptosis 0.001 0.14 0.32 54 -0.26 1 55
SHC 2-3/Grb2 -0.003 0.15 -10000 0 -0.34 54 54
SHC1 0.027 0.025 -10000 0 -0.43 1 1
SHC2 -0.043 0.18 0.25 3 -0.44 79 82
SHC3 0.016 0.1 0.24 4 -0.45 16 20
STAT3 (dimer) -0.019 0.14 -10000 0 -0.34 77 77
NT3 (dimer)/TRKA 0.037 0.055 -10000 0 -0.26 11 11
RIN/GDP 0.066 0.082 0.24 18 -0.25 6 24
GIPC1 0.033 0.03 -10000 0 -0.43 2 2
KRAS 0.027 0.055 -10000 0 -0.43 7 7
DNAJA3 0.01 0.056 0.22 19 -0.23 5 24
RIN/GTP 0.024 0.021 -10000 0 -0.3 2 2
CCND1 -0.091 0.26 -10000 0 -0.67 79 79
MAGED1 0.014 0.097 -10000 0 -0.43 23 23
PTPN11 0.035 0.004 -10000 0 -10000 0 0
RICS 0.022 0.062 -10000 0 -0.43 9 9
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.052 0.035 -10000 0 -0.26 1 1
GRB2 0.033 0.009 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.032 0.034 -10000 0 -0.26 4 4
TRKA/NEDD4-2 0.021 0.081 -10000 0 -0.31 27 27
ELMO1 0.034 0.006 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.04 0.04 -10000 0 -0.26 8 8
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.031 0.037 -10000 0 -0.43 3 3
DOCK1 0.027 0.058 -10000 0 -0.43 8 8
GAB2 0.031 0.012 -10000 0 -10000 0 0
RIT2 0.032 0.03 -10000 0 -0.43 2 2
RIT1 0.027 0.032 -10000 0 -0.43 2 2
FRS2 0.032 0.022 -10000 0 -0.43 1 1
DNM1 0.032 0.036 -10000 0 -0.43 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.023 -10000 0 -0.43 1 1
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.037 0.062 0.23 17 -0.23 5 22
mol:GDP 0.068 0.11 0.28 19 -0.37 8 27
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.025 0.004 -10000 0 -10000 0 0
RIT1/GDP 0.042 0.072 0.25 7 -0.26 5 12
TIAM1 0.027 0.058 -10000 0 -0.43 8 8
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
BDNF (dimer)/TRKB 0.048 0.066 -10000 0 -0.26 20 20
KIDINS220/CRKL/C3G 0.046 0.034 -10000 0 -0.31 4 4
SHC/RasGAP 0.035 0.046 -10000 0 -0.31 7 7
FRS2 family/SHP2 0.065 0.025 -10000 0 -0.26 1 1
SHC/GRB2/SOS1/GAB1 0.061 0.052 -10000 0 -0.24 5 5
RIT1/GTP 0.02 0.023 -10000 0 -0.3 2 2
NT3 (dimer) 0.022 0.059 -10000 0 -0.43 8 8
RAP1/GDP 0.047 0.067 0.18 13 -0.24 6 19
KIDINS220/CRKL 0.03 0.042 -10000 0 -0.43 4 4
BDNF (dimer) 0.03 0.024 -10000 0 -0.43 1 1
ubiquitin-dependent protein catabolic process 0.019 0.069 -10000 0 -0.26 27 27
Schwann cell development -0.006 0.013 -10000 0 -10000 0 0
EHD4 0.03 0.042 -10000 0 -0.43 4 4
FRS2 family/GRB2/SOS1 0.077 0.039 -10000 0 -0.45 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.026 0.061 -10000 0 -0.37 1 1
RAP1B 0.032 0.03 -10000 0 -0.43 2 2
RAP1A 0.03 0.046 -10000 0 -0.43 5 5
CDC42/GTP 0.041 0.069 -10000 0 -0.22 25 25
ABL1 0.035 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.048 0.021 -10000 0 -0.31 1 1
Rap1/GTP 0.023 0.091 -10000 0 -0.39 11 11
STAT3 -0.019 0.14 -10000 0 -0.34 77 77
axon guidance 0.025 0.061 -10000 0 -0.21 25 25
MAPK3 0.042 0.068 0.19 77 -0.23 5 82
MAPK1 0.043 0.069 0.19 80 -0.24 5 85
CDC42/GDP 0.066 0.083 0.24 20 -0.25 7 27
NTF3 0.022 0.059 -10000 0 -0.43 8 8
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.036 0.03 -10000 0 -0.26 3 3
PI3K 0.033 0.066 -10000 0 -0.31 17 17
FRS3 0.034 0.006 -10000 0 -10000 0 0
FAIM 0.034 0.021 -10000 0 -0.43 1 1
GAB1 0.026 0.062 -10000 0 -0.43 9 9
RASGRF1 0.011 0.059 0.23 19 -0.22 7 26
SOS1 0.034 0.021 -10000 0 -0.43 1 1
MCF2L 0.013 0.039 -10000 0 -0.26 10 10
RGS19 0.031 0.031 -10000 0 -0.43 2 2
CDC42 0.034 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.068 0.096 0.3 3 -0.36 8 11
Rac1/GDP 0.066 0.083 0.24 20 -0.26 6 26
NGF (dimer)/TRKA/GRIT 0.028 0.045 -10000 0 -0.26 9 9
neuron projection morphogenesis 0.004 0.2 0.44 2 -0.86 16 18
NGF (dimer)/TRKA/NEDD4-2 0.02 0.07 -10000 0 -0.26 27 27
MAP2K1 0.031 0.096 0.2 116 -0.23 5 121
NGFR 0.027 0.038 -10000 0 -0.43 3 3
NGF (dimer)/TRKA/GIPC/GAIP 0.021 0.036 -10000 0 -0.27 6 6
RAS family/GTP/PI3K 0.01 0.068 -10000 0 -0.24 29 29
FRS2 family/SHP2/GRB2/SOS1 0.089 0.044 -10000 0 -0.43 1 1
NRAS 0.028 0.055 -10000 0 -0.43 7 7
GRB2/SOS1 0.048 0.021 -10000 0 -0.31 1 1
PRKCI 0.024 0.065 -10000 0 -0.43 10 10
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.034 0.006 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.007 0.061 -10000 0 -0.41 6 6
RASA1 0.026 0.058 -10000 0 -0.43 8 8
TRKA/c-Abl 0.041 0.03 -10000 0 -0.31 2 2
SQSTM1 0.033 0.022 -10000 0 -0.43 1 1
BDNF (dimer)/TRKB/GIPC 0.064 0.065 -10000 0 -0.24 18 18
NGF (dimer)/TRKA/p62/Atypical PKCs 0.041 0.049 -10000 0 -0.22 12 12
MATK 0.03 0.031 -10000 0 -0.43 2 2
NEDD4L 0.005 0.11 -10000 0 -0.43 31 31
RAS family/GDP -0.012 0.037 -10000 0 -0.18 11 11
NGF (dimer)/TRKA 0.011 0.053 0.23 14 -0.24 5 19
Rac1/GTP -0.001 0.051 -10000 0 -0.22 13 13
FRS2 family/SHP2/CRK family 0.082 0.054 -10000 0 -0.23 6 6
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.035 0.066 -10000 0 -0.31 17 17
AKT1 0.012 0.13 0.32 3 -0.42 21 24
PTK2B 0.002 0.091 0.37 2 -0.46 9 11
VEGFR2 homodimer/Frs2 0.028 0.075 -10000 0 -0.35 14 14
CAV1 0.026 0.055 -10000 0 -0.43 7 7
CALM1 0.035 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.026 0.081 -10000 0 -0.4 10 10
endothelial cell proliferation 0.034 0.12 0.32 19 -0.43 11 30
mol:Ca2+ 0.003 0.1 -10000 0 -0.47 12 12
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.044 0.083 -10000 0 -0.43 8 8
RP11-342D11.1 -0.011 0.1 -10000 0 -0.46 13 13
CDH5 0.027 0.038 -10000 0 -0.43 3 3
VEGFA homodimer 0.029 0.079 -10000 0 -0.24 34 34
SHC1 0.027 0.025 -10000 0 -0.43 1 1
SHC2 -0.029 0.16 -10000 0 -0.43 68 68
HRAS/GDP 0.017 0.095 -10000 0 -0.41 11 11
SH2D2A -0.002 0.11 -10000 0 -0.43 31 31
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.035 0.12 -10000 0 -0.44 13 13
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.003 0.1 -10000 0 -0.29 38 38
VEGFR1 homodimer 0.025 0.059 -10000 0 -0.43 8 8
SHC/GRB2/SOS1 0.039 0.11 -10000 0 -0.44 11 11
GRB10 -0.005 0.13 -10000 0 -0.52 21 21
PTPN11 0.035 0.004 -10000 0 -10000 0 0
GRB2 0.033 0.009 -10000 0 -10000 0 0
PAK1 0.014 0.086 -10000 0 -0.43 18 18
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.04 0.1 -10000 0 -0.43 11 11
HRAS 0.031 0.037 -10000 0 -0.43 3 3
VEGF/Rho/ROCK1/Integrin Complex 0.004 0.098 -10000 0 -0.34 24 24
HIF1A -0.009 0.13 -10000 0 -0.43 46 46
FRS2 0.032 0.022 -10000 0 -0.43 1 1
oxygen and reactive oxygen species metabolic process 0.042 0.082 -10000 0 -0.42 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.034 0.006 -10000 0 -10000 0 0
Nck/Pak 0.03 0.07 -10000 0 -0.31 19 19
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.021 0.097 -10000 0 -0.51 10 10
mol:GDP 0.027 0.1 -10000 0 -0.43 11 11
mol:NADP 0.02 0.11 -10000 0 -0.42 11 11
eNOS/Hsp90 0.018 0.1 -10000 0 -0.39 11 11
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
mol:IP3 0.003 0.1 -10000 0 -0.47 12 12
HIF1A/ARNT 0.015 0.09 -10000 0 -0.31 34 34
SHB 0.029 0.046 -10000 0 -0.43 5 5
VEGFA -0.001 0.015 -10000 0 -10000 0 0
VEGFC 0.021 0.074 -10000 0 -0.43 13 13
FAK1/Vinculin 0.02 0.11 0.31 5 -0.49 11 16
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.025 0.062 -10000 0 -0.43 9 9
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.033 0.1 -10000 0 -0.49 9 9
PTPN6 0.031 0.03 -10000 0 -0.43 2 2
EPAS1 0.027 0.078 -10000 0 -0.42 13 13
mol:L-citrulline 0.02 0.11 -10000 0 -0.42 11 11
ITGAV 0.022 0.077 -10000 0 -0.43 14 14
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.041 0.082 -10000 0 -0.43 8 8
VEGFR2 homodimer/VEGFA homodimer 0.021 0.12 -10000 0 -0.35 34 34
VEGFR2/3 heterodimer 0.029 0.078 -10000 0 -0.37 14 14
VEGFB 0.034 0.006 -10000 0 -10000 0 0
MAPK11 -0.016 0.11 0.24 1 -0.47 17 18
VEGFR2 homodimer 0.012 0.084 -10000 0 -0.43 14 14
FLT1 0.025 0.059 -10000 0 -0.43 8 8
NEDD4 0.02 0.075 -10000 0 -0.43 12 12
MAPK3 0 0.098 0.27 7 -0.41 12 19
MAPK1 -0.005 0.1 0.27 8 -0.43 12 20
VEGFA145/NRP2 0.022 0.023 -10000 0 -0.33 1 1
VEGFR1/2 heterodimer 0.023 0.089 -10000 0 -0.36 19 19
KDR 0.012 0.084 -10000 0 -0.43 14 14
VEGFA165/NRP1/VEGFR2 homodimer 0.022 0.11 -10000 0 -0.47 13 13
SRC 0.031 0.03 -10000 0 -0.43 2 2
platelet activating factor biosynthetic process 0.001 0.1 0.27 6 -0.43 12 18
PI3K 0.003 0.13 -10000 0 -0.48 16 16
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.026 0.085 -10000 0 -0.36 15 15
FES -0.001 0.11 0.24 1 -0.5 11 12
GAB1 0.015 0.12 -10000 0 -0.42 25 25
VEGFR2 homodimer/VEGFA homodimer/Src 0.025 0.082 -10000 0 -0.34 16 16
CTNNB1 0.022 0.071 -10000 0 -0.43 12 12
SOS1 0.034 0.021 -10000 0 -0.43 1 1
ARNT 0.028 0.014 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.029 0.11 -10000 0 -0.42 14 14
VEGFR2 homodimer/VEGFA homodimer/Yes 0.023 0.089 -10000 0 -0.34 19 19
PI3K/GAB1 0.016 0.13 -10000 0 -0.43 20 20
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.041 0.095 -10000 0 -0.38 9 9
PRKACA 0.035 0.004 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.039 0.097 -10000 0 -0.41 14 14
HSP90AA1 0 0 -10000 0 -10000 0 0
CDC42 0.001 0.11 0.24 1 -0.49 12 13
actin cytoskeleton reorganization 0.003 0.1 -10000 0 -0.29 38 38
PTK2 -0.002 0.1 0.32 1 -0.54 11 12
EDG1 -0.01 0.14 -10000 0 -0.53 28 28
mol:DAG 0.003 0.1 -10000 0 -0.47 12 12
CaM/Ca2+ 0.019 0.1 -10000 0 -0.44 12 12
MAP2K3 -0.011 0.1 0.24 1 -0.45 14 15
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.015 0.14 -10000 0 -0.53 21 21
PLCG1 0.003 0.1 -10000 0 -0.48 12 12
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.038 0.089 -10000 0 -0.4 10 10
IQGAP1 0.034 0.008 -10000 0 -10000 0 0
YES1 0.028 0.051 -10000 0 -0.43 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.027 0.085 -10000 0 -0.42 11 11
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.026 0.084 -10000 0 -0.38 14 14
cell migration 0.021 0.1 0.34 4 -0.48 9 13
mol:PI-3-4-5-P3 0.004 0.12 -10000 0 -0.44 16 16
FYN 0.026 0.055 -10000 0 -0.43 7 7
VEGFB/NRP1 0.008 0.1 -10000 0 -0.46 12 12
mol:NO 0.02 0.11 -10000 0 -0.42 11 11
PXN 0.035 0.004 -10000 0 -10000 0 0
HRAS/GTP 0.001 0.087 -10000 0 -0.41 11 11
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.003 0.13 -10000 0 -0.53 21 21
VHL 0.034 0.007 -10000 0 -10000 0 0
ITGB3 0.029 0.042 -10000 0 -0.43 4 4
NOS3 0.018 0.12 -10000 0 -0.47 11 11
VEGFR2 homodimer/VEGFA homodimer/Sck -0.009 0.12 -10000 0 -0.37 25 25
RAC1 0.034 0.006 -10000 0 -10000 0 0
PRKCA -0.006 0.091 0.23 1 -0.45 10 11
PRKCB -0.009 0.094 0.23 1 -0.45 12 13
VCL 0.034 0.021 -10000 0 -0.43 1 1
VEGFA165/NRP1 -0.008 0.1 -10000 0 -0.32 34 34
VEGFR1/2 heterodimer/VEGFA homodimer 0.021 0.094 -10000 0 -0.36 19 19
VEGFA165/NRP2 0.022 0.023 -10000 0 -0.33 1 1
MAPKKK cascade 0.028 0.13 0.34 2 -0.45 19 21
NRP2 0.033 0.022 -10000 0 -0.43 1 1
VEGFC homodimer 0.021 0.074 -10000 0 -0.43 13 13
NCK1 0.033 0.022 -10000 0 -0.43 1 1
ROCK1 0.034 0.005 -10000 0 -10000 0 0
FAK1/Paxillin 0.02 0.12 0.3 4 -0.5 11 15
MAP3K13 0 0.11 0.24 1 -0.47 14 15
PDPK1 -0.004 0.1 0.26 3 -0.39 16 19
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.023 0.17 -10000 0 -0.8 14 14
NCK1/PAK1/Dok-R -0.029 0.076 -10000 0 -0.42 11 11
NCK1/Dok-R 0.03 0.16 -10000 0 -0.89 10 10
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
mol:beta2-estradiol -0.007 0.013 0.26 1 -10000 0 1
RELA 0.034 0.005 -10000 0 -10000 0 0
SHC1 0.028 0.025 -10000 0 -0.43 1 1
Rac/GDP 0.025 0.004 -10000 0 -10000 0 0
F2 0.013 0.024 -10000 0 -10000 0 0
TNIP2 0.032 0.03 -10000 0 -0.43 2 2
NF kappa B/RelA 0.061 0.15 -10000 0 -0.8 11 11
FN1 -0.011 0.14 -10000 0 -0.43 48 48
PLD2 0.019 0.14 -10000 0 -0.89 10 10
PTPN11 0.035 0.004 -10000 0 -10000 0 0
GRB14 -0.064 0.18 -10000 0 -0.43 97 97
ELK1 0.023 0.14 -10000 0 -0.84 10 10
GRB7 0.022 0.059 -10000 0 -0.43 8 8
PAK1 0.014 0.086 -10000 0 -0.43 18 18
Tie2/Ang1/alpha5/beta1 Integrin 0.038 0.17 -10000 0 -0.82 12 12
CDKN1A -0.003 0.19 -10000 0 -0.75 25 25
ITGA5 0.034 0.021 -10000 0 -0.43 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.026 0.16 -10000 0 -0.86 11 11
CRK 0.031 0.023 -10000 0 -0.43 1 1
mol:NO 0.026 0.14 0.43 1 -0.59 14 15
PLG 0.018 0.14 -10000 0 -0.89 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.017 0.15 -10000 0 -0.79 12 12
GRB2 0.033 0.009 -10000 0 -10000 0 0
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
ANGPT2 -0.054 0.21 -10000 0 -0.76 22 22
BMX 0.01 0.16 -10000 0 -1 10 10
ANGPT1 0.014 0.061 -10000 0 -0.7 2 2
tube development -0.001 0.17 -10000 0 -0.72 16 16
ANGPT4 0.033 0.022 -10000 0 -0.43 1 1
response to hypoxia 0 0.01 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.024 0.17 -10000 0 -0.92 10 10
alpha5/beta1 Integrin 0.047 0.034 -10000 0 -0.31 4 4
FGF2 -0.003 0.12 -10000 0 -0.43 34 34
STAT5A (dimer) 0.005 0.21 -10000 0 -0.78 24 24
mol:L-citrulline 0.026 0.14 0.43 1 -0.59 14 15
AGTR1 -0.049 0.17 -10000 0 -0.43 82 82
MAPK14 0.022 0.18 -10000 0 -1.1 10 10
Tie2/SHP2 0.011 0.18 -10000 0 -0.94 11 11
TEK 0.005 0.18 -10000 0 -1 11 11
RPS6KB1 0.038 0.17 -10000 0 -0.82 12 12
Angiotensin II/AT1 -0.033 0.12 -10000 0 -0.3 82 82
Tie2/Ang1/GRB2 0.035 0.15 -10000 0 -0.89 10 10
MAPK3 0.023 0.14 -10000 0 -0.82 10 10
MAPK1 0.013 0.13 -10000 0 -0.84 10 10
Tie2/Ang1/GRB7 0.025 0.15 -10000 0 -0.89 10 10
NFKB1 0.034 0.021 -10000 0 -0.43 1 1
MAPK8 0.019 0.14 -10000 0 -0.89 10 10
PI3K 0.019 0.18 -10000 0 -0.98 12 12
FES 0.013 0.2 -10000 0 -1.1 13 13
Crk/Dok-R 0.029 0.16 -10000 0 -0.89 10 10
Tie2/Ang1/ABIN2 0.034 0.15 -10000 0 -0.9 10 10
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.025 0.16 -10000 0 -0.72 14 14
STAT5A 0.031 0.036 -10000 0 -0.43 3 3
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.052 0.17 -10000 0 -0.81 11 11
Tie2/Ang2 -0.011 0.22 -10000 0 -1.1 14 14
Tie2/Ang1 0.022 0.15 -10000 0 -0.94 10 10
FOXO1 0.026 0.16 -10000 0 -0.73 15 15
ELF1 0.032 0.059 -10000 0 -0.43 7 7
ELF2 0.024 0.14 -10000 0 -0.89 10 10
mol:Choline 0.018 0.14 -10000 0 -0.86 10 10
cell migration -0.014 0.053 -10000 0 -0.21 17 17
FYN -0.006 0.19 -10000 0 -0.83 16 16
DOK2 0.008 0.09 -10000 0 -0.43 20 20
negative regulation of cell cycle 0.001 0.17 -10000 0 -0.67 25 25
ETS1 0.033 0.035 -10000 0 -0.44 2 2
PXN 0.054 0.15 0.39 1 -0.67 11 12
ITGB1 0.031 0.036 -10000 0 -0.43 3 3
NOS3 0.024 0.15 0.44 1 -0.67 14 15
RAC1 0.034 0.006 -10000 0 -10000 0 0
TNF 0.032 0.066 -10000 0 -0.42 10 10
MAPKKK cascade 0.018 0.14 -10000 0 -0.86 10 10
RASA1 0.026 0.058 -10000 0 -0.43 8 8
Tie2/Ang1/Shc 0.026 0.15 -10000 0 -0.89 10 10
NCK1 0.033 0.022 -10000 0 -0.43 1 1
vasculogenesis 0.028 0.12 0.42 1 -0.53 14 15
mol:Phosphatidic acid 0.018 0.14 -10000 0 -0.86 10 10
mol:Angiotensin II 0.001 0.002 -10000 0 -10000 0 0
mol:NADP 0.026 0.14 0.43 1 -0.59 14 15
Rac1/GTP 0.033 0.16 -10000 0 -0.77 12 12
MMP2 0.006 0.16 -10000 0 -0.98 10 10
p38 MAPK signaling 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
TRAF6/ASK1 0.014 0.058 -10000 0 -0.21 27 27
TRAF2/ASK1 0.027 0.067 -10000 0 -0.26 25 25
ATM 0.031 0.012 -10000 0 -10000 0 0
MAP2K3 -0.042 0.16 0.31 1 -0.41 50 51
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.035 0.14 0.29 1 -0.38 40 41
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.025 0.065 -10000 0 -0.43 10 10
TXN 0.009 0.001 -10000 0 -10000 0 0
CALM1 0.035 0.005 -10000 0 -10000 0 0
GADD45A 0.018 0.082 -10000 0 -0.43 16 16
GADD45B 0.023 0.068 -10000 0 -0.43 11 11
MAP3K1 0.008 0.1 -10000 0 -0.43 26 26
MAP3K6 0.033 0.022 -10000 0 -0.43 1 1
MAP3K7 0.033 0.009 -10000 0 -10000 0 0
MAP3K4 0.033 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.03 0.077 -10000 0 -0.3 24 24
TAK1/TAB family 0.015 0.037 -10000 0 -0.27 5 5
RAC1/OSM/MEKK3 0.059 0.023 -10000 0 -10000 0 0
TRAF2 0.033 0.03 -10000 0 -0.43 2 2
RAC1/OSM/MEKK3/MKK3 -0.01 0.13 0.26 1 -0.37 28 29
TRAF6 0.016 0.024 -10000 0 -0.29 3 3
RAC1 0.034 0.006 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.014 0.13 -10000 0 -0.43 47 47
CCM2 0.035 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.01 0.088 -10000 0 -0.26 47 47
MAPK11 0.032 0.01 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.015 0.1 -10000 0 -0.24 68 68
OSM/MEKK3 0.046 0.017 -10000 0 -10000 0 0
TAOK1 0.012 0.034 -10000 0 -0.29 6 6
TAOK2 0.015 0.007 -10000 0 -10000 0 0
TAOK3 0.016 0.015 -10000 0 -0.29 1 1
MAP3K7IP1 0.033 0.009 -10000 0 -10000 0 0
MAPK14 0.035 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0.031 0.03 -10000 0 -0.43 2 2
MAP3K5 0.011 0.097 -10000 0 -0.43 23 23
MAP3K10 0.022 0.074 -10000 0 -0.43 13 13
MAP3K3 0.032 0.011 -10000 0 -10000 0 0
TRX/ASK1 0.016 0.06 -10000 0 -0.25 23 23
GADD45/MTK1/MTK1 0.051 0.084 -10000 0 -0.24 33 33
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.036 0.054 0.32 8 -10000 0 8
KIRREL 0.025 0.059 -10000 0 -0.44 7 7
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.037 0.054 -10000 0 -0.32 8 8
PLCG1 0.033 0.008 -10000 0 -10000 0 0
ARRB2 0.032 0.01 -10000 0 -10000 0 0
WASL 0.028 0.055 -10000 0 -0.43 7 7
Nephrin/NEPH1/podocin/CD2AP 0.065 0.059 -10000 0 -0.24 9 9
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.021 0.048 -10000 0 -0.21 16 16
FYN 0.051 0.099 0.28 58 -0.21 15 73
mol:Ca2+ 0.059 0.058 -10000 0 -0.24 9 9
mol:DAG 0.06 0.059 -10000 0 -0.24 9 9
NPHS2 0.03 0.03 -10000 0 -0.44 1 1
mol:IP3 0.06 0.059 -10000 0 -0.24 9 9
regulation of endocytosis 0.045 0.057 -10000 0 -0.2 14 14
Nephrin/NEPH1/podocin/Cholesterol 0.047 0.052 -10000 0 -0.24 9 9
establishment of cell polarity 0.036 0.054 -10000 0 -0.32 8 8
Nephrin/NEPH1/podocin/NCK1-2 0.076 0.065 -10000 0 -0.22 10 10
Nephrin/NEPH1/beta Arrestin2 0.047 0.058 -10000 0 -0.21 14 14
NPHS1 0.038 0.031 -10000 0 -0.44 1 1
Nephrin/NEPH1/podocin 0.047 0.059 -10000 0 -0.21 15 15
TJP1 0.03 0.042 -10000 0 -0.43 4 4
NCK1 0.033 0.022 -10000 0 -0.43 1 1
NCK2 0.035 0.005 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.062 0.06 -10000 0 -0.24 9 9
CD2AP 0.034 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.061 0.059 -10000 0 -0.24 9 9
GRB2 0.033 0.009 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.051 0.1 0.29 58 -0.22 15 73
cytoskeleton organization 0.019 0.065 0.23 23 -0.26 9 32
Nephrin/NEPH1 0.032 0.04 -10000 0 -0.22 8 8
Nephrin/NEPH1/ZO-1 0.048 0.059 -10000 0 -0.26 12 12
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.044 0.032 -10000 0 -0.31 3 3
CRKL 0.006 0.1 -10000 0 -0.46 15 15
mol:PIP3 0.007 0.089 0.4 11 -0.84 3 14
AKT1 0.015 0.091 0.38 5 -0.63 3 8
PTK2B 0.028 0.014 -10000 0 -10000 0 0
RAPGEF1 0.005 0.097 -10000 0 -0.44 15 15
RANBP10 0.03 0.013 -10000 0 -10000 0 0
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
HGF/MET/SHIP2 0.053 0.056 -10000 0 -0.26 13 13
MAP3K5 0.001 0.11 0.32 1 -0.42 17 18
HGF/MET/CIN85/CBL/ENDOPHILINS 0.062 0.072 -10000 0 -0.26 19 19
AP1 -0.028 0.14 -10000 0 -0.31 88 88
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.027 0.025 -10000 0 -0.43 1 1
apoptosis -0.14 0.33 -10000 0 -0.77 106 106
STAT3 (dimer) 0.012 0.069 -10000 0 -0.31 5 5
GAB1/CRKL/SHP2/PI3K 0.041 0.11 -10000 0 -0.42 16 16
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.025 0.099 -10000 0 -0.43 15 15
PTPN11 0.035 0.004 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.033 0.008 -10000 0 -10000 0 0
PTEN 0.024 0.068 -10000 0 -0.43 11 11
ELK1 0 0.071 0.28 14 -10000 0 14
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.015 0.045 -10000 0 -0.2 7 7
PAK1 0.023 0.11 0.38 12 -0.6 3 15
HGF/MET/RANBP10 0.05 0.053 -10000 0 -0.26 11 11
HRAS 0.014 0.095 -10000 0 -0.47 11 11
DOCK1 0.003 0.1 0.32 1 -0.45 14 15
GAB1 0.01 0.1 -10000 0 -0.48 15 15
CRK 0.007 0.099 -10000 0 -0.46 15 15
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.097 -10000 0 -0.46 13 13
JUN -0.003 0.12 -10000 0 -0.43 39 39
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.007 0.042 -10000 0 -0.21 16 16
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
cell morphogenesis 0.013 0.1 0.36 5 -0.41 5 10
GRB2/SHC 0.035 0.05 -10000 0 -0.22 7 7
FOS -0.033 0.16 -10000 0 -0.43 66 66
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility 0 0.071 0.28 14 -10000 0 14
HGF/MET/MUC20 0.037 0.046 -10000 0 -0.26 11 11
cell migration 0.034 0.05 -10000 0 -0.21 7 7
GRB2 0.033 0.009 -10000 0 -10000 0 0
CBL 0.031 0.012 -10000 0 -10000 0 0
MET/RANBP10 0.039 0.034 -10000 0 -0.3 3 3
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.015 0.056 -10000 0 -0.29 6 6
MET/MUC20 0.022 0.026 -10000 0 -0.3 3 3
RAP1B 0.01 0.1 0.28 5 -0.42 14 19
RAP1A 0.001 0.096 -10000 0 -0.43 16 16
HGF/MET/RANBP9 0.057 0.052 -10000 0 -0.26 11 11
RAF1 0.017 0.091 -10000 0 -0.48 8 8
STAT3 0.012 0.069 -10000 0 -0.32 5 5
cell proliferation 0.048 0.1 0.28 24 -0.34 6 30
RPS6KB1 0.012 0.034 -10000 0 -0.28 4 4
MAPK3 -0.014 0.089 0.68 6 -10000 0 6
MAPK1 0.009 0.16 0.66 25 -10000 0 25
RANBP9 0.034 0.007 -10000 0 -10000 0 0
MAPK8 0.009 0.11 0.3 1 -0.39 19 20
SRC 0.01 0.062 -10000 0 -0.27 5 5
PI3K 0.032 0.074 -10000 0 -0.24 24 24
MET/Glomulin 0.021 0.034 -10000 0 -0.26 3 3
SOS1 0.034 0.021 -10000 0 -0.43 1 1
MAP2K1 0.014 0.089 -10000 0 -0.48 6 6
MET 0.03 0.037 -10000 0 -0.43 3 3
MAP4K1 0.01 0.1 -10000 0 -0.45 15 15
PTK2 0.027 0.025 -10000 0 -0.43 1 1
MAP2K2 0.015 0.091 -10000 0 -0.46 7 7
BAD 0.011 0.086 0.37 4 -0.6 3 7
MAP2K4 0 0.1 0.31 1 -0.39 16 17
SHP2/GRB2/SOS1/GAB1 0.044 0.095 -10000 0 -0.4 14 14
INPPL1 0.03 0.037 -10000 0 -0.43 3 3
PXN 0.035 0.004 -10000 0 -10000 0 0
SH3KBP1 0.025 0.065 -10000 0 -0.43 10 10
HGS 0 0.04 -10000 0 -0.19 19 19
PLCgamma1/PKC 0.025 0.006 -10000 0 -10000 0 0
HGF 0.027 0.058 -10000 0 -0.43 8 8
RASA1 0.026 0.058 -10000 0 -0.43 8 8
NCK1 0.033 0.022 -10000 0 -0.43 1 1
PTPRJ 0.03 0.046 -10000 0 -0.43 5 5
NCK/PLCgamma1 0.047 0.053 -10000 0 -0.19 14 14
PDPK1 0.02 0.093 0.31 12 -0.67 3 15
HGF/MET/SHIP 0.037 0.046 -10000 0 -0.26 11 11
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.012 0.064 -10000 0 -0.33 16 16
CRKL 0.03 0.042 -10000 0 -0.43 4 4
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
DOCK1 0.027 0.058 -10000 0 -0.43 8 8
ITGA4 0.02 0.079 -10000 0 -0.43 15 15
alpha4/beta7 Integrin/MAdCAM1 0.067 0.075 -10000 0 -0.26 22 22
EPO 0.029 0.013 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.039 0.062 -10000 0 -0.31 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.023 -10000 0 -0.43 1 1
alpha4/beta1 Integrin 0.036 0.071 -10000 0 -0.34 16 16
EPO/EPOR (dimer) 0.043 0.02 -10000 0 -10000 0 0
lamellipodium assembly 0.016 0.081 -10000 0 -0.39 7 7
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
PI3K 0.033 0.066 -10000 0 -0.31 17 17
ARF6 0.033 0.03 -10000 0 -0.43 2 2
JAK2 0.022 0.051 -10000 0 -0.25 15 15
PXN 0.035 0.004 -10000 0 -10000 0 0
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
MADCAM1 0.033 0.008 -10000 0 -10000 0 0
cell adhesion 0.065 0.074 -10000 0 -0.25 22 22
CRKL/CBL 0.042 0.036 -10000 0 -0.31 4 4
ITGB1 0.031 0.036 -10000 0 -0.43 3 3
SRC 0 0.088 0.19 13 -0.28 39 52
ITGB7 0.035 0.004 -10000 0 -10000 0 0
RAC1 0.034 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.036 0.1 -10000 0 -0.31 38 38
p130Cas/Crk/Dock1 0.02 0.092 -10000 0 -0.24 44 44
VCAM1 0.007 0.11 -10000 0 -0.43 28 28
RHOA 0.025 0.062 -10000 0 -0.43 9 9
alpha4/beta1 Integrin/Paxillin/GIT1 0.068 0.07 -10000 0 -0.26 17 17
BCAR1 -0.025 0.077 0.18 13 -0.26 37 50
EPOR 0.035 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.031 0.012 -10000 0 -10000 0 0
GIT1 0.032 0.023 -10000 0 -0.43 1 1
Rac1/GTP 0.016 0.083 -10000 0 -0.4 7 7
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.034 0.007 -10000 0 -10000 0 0
NFATC1 0.02 0.093 0.3 2 -0.38 8 10
NFATC2 0.016 0.049 0.16 1 -0.19 7 8
NFATC3 0.014 0.006 -10000 0 -10000 0 0
YWHAE 0.032 0.01 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.015 0.094 0.21 2 -0.35 13 15
Exportin 1/Ran/NUP214 0.068 0.017 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.042 0.092 -10000 0 -0.4 6 6
BCL2/BAX -0.026 0.14 -10000 0 -0.31 101 101
CaM/Ca2+/Calcineurin A alpha-beta B1 0.026 0.005 -10000 0 -10000 0 0
CaM/Ca2+ 0.026 0.005 -10000 0 -10000 0 0
BAX 0.035 0.005 -10000 0 -10000 0 0
MAPK14 0.035 0.004 -10000 0 -10000 0 0
BAD 0.033 0.022 -10000 0 -0.43 1 1
CABIN1/MEF2D 0.027 0.088 -10000 0 -0.36 9 9
Calcineurin A alpha-beta B1/BCL2 -0.062 0.18 -10000 0 -0.43 101 101
FKBP8 0.034 0.006 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.027 0.087 0.35 9 -10000 0 9
KPNB1 0.029 0.047 -10000 0 -0.43 5 5
KPNA2 0.024 0.059 -10000 0 -0.43 8 8
XPO1 0.035 0.004 -10000 0 -10000 0 0
SFN 0.01 0.1 -10000 0 -0.43 25 25
MAP3K8 0.002 0.11 -10000 0 -0.43 32 32
NFAT4/CK1 alpha 0.017 0.059 -10000 0 -0.21 25 25
MEF2D/NFAT1/Cbp/p300 0.055 0.068 -10000 0 -0.22 3 3
CABIN1 0.014 0.094 0.21 2 -0.36 13 15
CALM1 0.035 0.005 -10000 0 -10000 0 0
RAN 0.035 0.005 -10000 0 -10000 0 0
MAP3K1 0.008 0.1 -10000 0 -0.43 26 26
CAMK4 0.031 0.036 -10000 0 -0.43 3 3
mol:Ca2+ 0.001 0.001 -10000 0 -10000 0 0
MAPK3 0.032 0.023 -10000 0 -0.43 1 1
YWHAH 0.03 0.037 -10000 0 -0.43 3 3
Calcineurin A alpha-beta B1/AKAP79/PKA 0.023 0.093 -10000 0 -0.31 36 36
YWHAB 0.033 0.008 -10000 0 -10000 0 0
MAPK8 0.032 0.036 -10000 0 -0.43 3 3
MAPK9 0.017 0.089 -10000 0 -0.43 19 19
YWHAG 0.035 0.004 -10000 0 -10000 0 0
FKBP1A 0.034 0.008 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.033 0.094 0.32 1 -0.35 9 10
PRKCH 0.03 0.046 -10000 0 -0.43 5 5
CABIN1/Cbp/p300 0.044 0.033 -10000 0 -0.31 3 3
CASP3 0.034 0.008 -10000 0 -10000 0 0
PIM1 0.034 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.023 0.005 -10000 0 -10000 0 0
apoptosis 0.001 0.049 -10000 0 -0.29 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.029 0.055 -10000 0 -0.25 2 2
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.029 0.051 -10000 0 -0.43 6 6
JNK2/NFAT4 0 0.078 -10000 0 -0.16 93 93
BAD/BCL-XL 0.048 0.021 -10000 0 -0.31 1 1
PRKCD 0.032 0.03 -10000 0 -0.43 2 2
NUP214 0.034 0.006 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PRKCA 0.031 0.012 -10000 0 -10000 0 0
PRKCG 0.034 0.006 -10000 0 -10000 0 0
PRKCQ 0.024 0.055 -10000 0 -0.43 7 7
FKBP38/BCL2 -0.025 0.14 -10000 0 -0.31 99 99
EP300 0.031 0.031 -10000 0 -0.43 2 2
PRKCB1 0 0.11 -10000 0 -0.43 32 32
CSNK2A1 0.034 0.008 -10000 0 -10000 0 0
NFATc/JNK1 0.035 0.096 0.3 2 -0.36 8 10
CaM/Ca2+/FKBP38 0.046 0.01 -10000 0 -10000 0 0
FKBP12/FK506 0.025 0.006 -10000 0 -10000 0 0
CSNK1A1 0.018 0.004 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.044 0.026 -10000 0 -0.26 3 3
NFATc/ERK1 0.034 0.095 0.3 2 -0.38 8 10
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.048 0.1 -10000 0 -0.37 10 10
NR4A1 0.054 0.078 0.23 5 -0.43 1 6
GSK3B 0.035 0.005 -10000 0 -10000 0 0
positive T cell selection 0.014 0.006 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.02 0.037 -10000 0 -0.22 1 1
RCH1/ KPNB1 0.037 0.055 -10000 0 -0.31 11 11
YWHAQ 0.033 0.03 -10000 0 -0.43 2 2
PRKACA 0.035 0.004 -10000 0 -10000 0 0
AKAP5 -0.001 0.12 -10000 0 -0.43 37 37
MEF2D 0.029 0.014 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.027 0.015 -10000 0 -10000 0 0
NFATc/p38 alpha 0.037 0.094 0.33 1 -0.36 8 9
CREBBP 0.032 0.023 -10000 0 -0.43 1 1
BCL2 -0.062 0.18 -10000 0 -0.43 101 101
TCGA08_rtk_signaling

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
PDGFRA 0.005 0.11 -10000 0 -0.43 31 31
HRAS 0.031 0.037 -10000 0 -0.43 3 3
EGFR -0.016 0.14 -10000 0 -0.43 48 48
AKT 0.035 0.088 0.23 7 -0.3 9 16
FOXO3 0 0 -10000 0 -10000 0 0
AKT1 0.031 0.036 -10000 0 -0.43 3 3
FOXO1 0 0 -10000 0 -10000 0 0
AKT3 0.025 0.032 -10000 0 -0.43 2 2
FOXO4 0 0 -10000 0 -10000 0 0
MET 0.03 0.037 -10000 0 -0.43 3 3
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
PIK3CB 0.03 0.046 -10000 0 -0.43 5 5
NRAS 0.028 0.055 -10000 0 -0.43 7 7
PIK3CG 0.02 0.079 -10000 0 -0.43 15 15
PIK3R3 0.024 0.068 -10000 0 -0.43 11 11
PIK3R2 0.035 0.004 -10000 0 -10000 0 0
NF1 0.032 0.022 -10000 0 -0.43 1 1
RAS 0.004 0.078 0.17 5 -0.29 20 25
ERBB2 0.016 0.077 -10000 0 -0.43 14 14
proliferation/survival/translation -0.022 0.052 0.21 8 -0.18 4 12
PI3K 0.012 0.085 0.2 11 -0.24 30 41
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
KRAS 0.027 0.055 -10000 0 -0.43 7 7
FOXO 0.049 0.045 0.18 16 -10000 0 16
AKT2 0.034 0.006 -10000 0 -10000 0 0
PTEN 0.024 0.068 -10000 0 -0.43 11 11
BARD1 signaling events

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
BARD1/CSTF1 0.045 0.035 -10000 0 -0.31 4 4
ATM 0.031 0.012 -10000 0 -10000 0 0
UBE2D3 0.035 0.005 -10000 0 -10000 0 0
PRKDC 0.029 0.031 -10000 0 -0.43 2 2
ATR 0.035 0.005 -10000 0 -10000 0 0
UBE2L3 0.034 0.008 -10000 0 -10000 0 0
FANCD2 0.024 0.01 -10000 0 -10000 0 0
protein ubiquitination 0.061 0.073 -10000 0 -0.23 21 21
XRCC5 0.035 0.004 -10000 0 -10000 0 0
XRCC6 0.033 0.009 -10000 0 -10000 0 0
M/R/N Complex 0.048 0.044 -10000 0 -0.26 4 4
MRE11A 0.031 0.011 -10000 0 -10000 0 0
DNA-PK 0.056 0.035 -10000 0 -0.26 2 2
FA complex/FANCD2/Ubiquitin 0.002 0.093 -10000 0 -0.41 12 12
FANCF 0.031 0.042 -10000 0 -0.43 4 4
BRCA1 0.023 0.071 -10000 0 -0.43 12 12
CCNE1 0.026 0.047 -10000 0 -0.43 5 5
CDK2/Cyclin E1 0.04 0.048 -10000 0 -0.35 6 6
FANCG 0.034 0.005 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.039 0.062 -10000 0 -0.31 15 15
FANCE 0.031 0.036 -10000 0 -0.43 3 3
FANCC 0.034 0.021 -10000 0 -0.43 1 1
NBN 0.027 0.025 -10000 0 -0.43 1 1
FANCA 0.015 0.068 -10000 0 -0.43 11 11
DNA repair -0.022 0.11 0.27 3 -0.34 19 22
BRCA1/BARD1/ubiquitin 0.039 0.062 -10000 0 -0.31 15 15
BARD1/DNA-PK 0.069 0.048 -10000 0 -0.24 5 5
FANCL 0.035 0.005 -10000 0 -10000 0 0
mRNA polyadenylation -0.044 0.035 0.31 4 -10000 0 4
BRCA1/BARD1/CTIP/M/R/N Complex 0.012 0.079 -10000 0 -0.29 6 6
BRCA1/BACH1/BARD1/TopBP1 0.058 0.057 -10000 0 -0.26 14 14
BRCA1/BARD1/P53 0.049 0.096 -10000 0 -0.25 41 41
BARD1/CSTF1/BRCA1 0.052 0.061 -10000 0 -0.26 15 15
BRCA1/BACH1 0.023 0.071 -10000 0 -0.43 12 12
BARD1 0.032 0.036 -10000 0 -0.43 3 3
PCNA 0.029 0.047 -10000 0 -0.43 5 5
BRCA1/BARD1/UbcH5C 0.058 0.057 -10000 0 -0.26 14 14
BRCA1/BARD1/UbcH7 0.055 0.06 -10000 0 -0.26 15 15
BRCA1/BARD1/RAD51/PCNA 0.039 0.11 -10000 0 -0.25 60 60
BARD1/DNA-PK/P53 0.058 0.086 -10000 0 -0.23 30 30
BRCA1/BARD1/Ubiquitin 0.039 0.062 -10000 0 -0.31 15 15
BRCA1/BARD1/CTIP 0.035 0.063 -10000 0 -0.24 22 22
FA complex 0.018 0.059 -10000 0 -0.36 3 3
BARD1/EWS 0.047 0.031 -10000 0 -0.31 3 3
RBBP8 0.009 0.041 -10000 0 -0.31 8 8
TP53 0.005 0.11 -10000 0 -0.43 28 28
TOPBP1 0.035 0.005 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.047 0.095 0.25 41 -10000 0 41
BRCA1/BARD1 0.068 0.076 -10000 0 -0.23 21 21
CSTF1 0.032 0.023 -10000 0 -0.43 1 1
BARD1/EWS-Fli1 0.024 0.025 -10000 0 -0.3 3 3
CDK2 0.033 0.03 -10000 0 -0.43 2 2
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.009 0.13 -10000 0 -0.43 45 45
RAD50 0.031 0.042 -10000 0 -0.43 4 4
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.039 0.062 -10000 0 -0.31 15 15
EWSR1 0.033 0.009 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.031 0.03 -10000 0 -0.43 2 2
HDAC4 0.033 0.022 -10000 0 -0.43 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.004 0.018 -10000 0 -0.13 6 6
CDKN1A -0.018 0.1 0.4 1 -0.59 14 15
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.035 0.005 -10000 0 -10000 0 0
FOXO3 -0.006 0.024 0.36 2 -10000 0 2
FOXO1 0 0 -10000 0 -10000 0 0
FOXO4 0.01 0.021 -10000 0 -0.25 3 3
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.033 0.009 -10000 0 -10000 0 0
TAT 0.027 0.015 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.006 0.065 -10000 0 -0.3 23 23
PPARGC1A 0.022 0.065 -10000 0 -0.43 10 10
FHL2 -0.025 0.15 -10000 0 -0.43 61 61
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.047 0.02 -10000 0 -10000 0 0
HIST2H4A -0.004 0.018 0.13 6 -10000 0 6
SIRT1/FOXO3a 0.027 0.04 0.26 4 -0.19 4 8
SIRT1 0.034 0.022 0.21 6 -10000 0 6
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.055 0.036 -10000 0 -0.26 1 1
SIRT1/Histone H1b 0.019 0.076 -10000 0 -0.22 35 35
apoptosis -0.063 0.024 -10000 0 -10000 0 0
SIRT1/PGC1A 0.036 0.046 -10000 0 -0.26 10 10
p53/SIRT1 0.024 0.085 0.4 6 -0.31 23 29
SIRT1/FOXO4 0.031 0.045 -10000 0 -0.22 5 5
FOXO1/FHL2/SIRT1 0.007 0.089 0.15 4 -0.23 59 63
HIST1H1E 0 0.065 -10000 0 -0.25 32 32
SIRT1/p300 0.046 0.03 -10000 0 -0.31 2 2
muscle cell differentiation -0.008 0.061 0.26 23 -0.19 1 24
TP53 0.006 0.1 0.21 6 -0.42 27 33
KU70/SIRT1/BAX 0.064 0.025 -10000 0 -10000 0 0
CREBBP 0.031 0.023 -10000 0 -0.43 1 1
MEF2D 0.029 0.013 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.039 0.026 -10000 0 -10000 0 0
ACSS2 0.015 0.016 0.14 6 -10000 0 6
SIRT1/PCAF/MYOD 0.008 0.061 0.2 1 -0.26 23 24
Paxillin-dependent events mediated by a4b1

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
CRKL 0.03 0.042 -10000 0 -0.43 4 4
Rac1/GDP 0.032 0.015 -10000 0 -10000 0 0
DOCK1 0.027 0.058 -10000 0 -0.43 8 8
ITGA4 0.02 0.079 -10000 0 -0.43 15 15
RAC1 0.034 0.006 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.039 0.062 -10000 0 -0.31 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.023 -10000 0 -0.43 1 1
alpha4/beta1 Integrin 0.056 0.066 -10000 0 -0.29 16 16
alpha4/beta7 Integrin/Paxillin 0.047 0.052 -10000 0 -0.24 15 15
lamellipodium assembly -0.01 0.12 -10000 0 -0.42 30 30
PIK3CA 0.032 0.023 -10000 0 -0.43 1 1
PI3K 0.033 0.066 -10000 0 -0.31 17 17
ARF6 0.033 0.03 -10000 0 -0.43 2 2
TLN1 0.034 0.021 -10000 0 -0.43 1 1
PXN 0.016 0.003 -10000 0 -10000 0 0
PIK3R1 0.017 0.084 -10000 0 -0.43 17 17
ARF6/GTP 0.056 0.065 -10000 0 -0.23 19 19
cell adhesion 0.061 0.063 -10000 0 -0.25 17 17
CRKL/CBL 0.042 0.036 -10000 0 -0.31 4 4
alpha4/beta1 Integrin/Paxillin 0.044 0.059 -10000 0 -0.26 16 16
ITGB1 0.031 0.036 -10000 0 -0.43 3 3
ITGB7 0.035 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.03 0.033 -10000 0 -0.42 2 2
alpha4/beta1 Integrin/Paxillin/VCAM1 0.046 0.097 -10000 0 -0.27 38 38
p130Cas/Crk/Dock1 0.05 0.051 -10000 0 -0.26 9 9
VCAM1 0.007 0.11 -10000 0 -0.43 28 28
alpha4/beta1 Integrin/Paxillin/Talin 0.063 0.064 -10000 0 -0.25 17 17
alpha4/beta1 Integrin/Paxillin/GIT1 0.06 0.065 -10000 0 -0.25 17 17
BCAR1 0.03 0.013 -10000 0 -10000 0 0
mol:GDP -0.057 0.064 0.25 17 -10000 0 17
CBL 0.031 0.012 -10000 0 -10000 0 0
PRKACA 0.035 0.004 -10000 0 -10000 0 0
GIT1 0.032 0.023 -10000 0 -0.43 1 1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.063 0.064 -10000 0 -0.25 17 17
Rac1/GTP -0.013 0.14 -10000 0 -0.47 30 30
Effects of Botulinum toxin

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
STX1A 0.009 0.002 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.042 0.029 -10000 0 -0.3 2 2
STXBP1 0.035 0.005 -10000 0 -10000 0 0
ACh/CHRNA1 0.016 0.045 -10000 0 -0.25 7 7
RAB3GAP2/RIMS1/UNC13B 0.049 0.039 -10000 0 -0.26 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 0.03 0.013 -10000 0 -10000 0 0
mol:ACh -0.004 0.03 0.088 4 -0.11 19 23
RAB3GAP2 0.028 0.024 -10000 0 -0.43 1 1
STX1A/SNAP25/VAMP2 0.032 0.056 -10000 0 -0.18 3 3
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.016 0.045 -10000 0 -0.25 7 7
UNC13B 0.032 0.03 -10000 0 -0.43 2 2
CHRNA1 0.03 0.051 -10000 0 -0.43 6 6
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.043 0.12 -10000 0 -0.28 95 95
SNAP25 -0.002 0.045 -10000 0 -0.26 15 15
VAMP2 0.005 0.011 -10000 0 -0.23 1 1
SYT1 -0.064 0.18 -10000 0 -0.43 95 95
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.032 0.006 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.032 0.056 -10000 0 -0.18 3 3
Signaling events mediated by PRL

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
CCNE1 0.026 0.047 -10000 0 -0.43 5 5
mol:Halofuginone 0.004 0.01 -10000 0 -0.22 1 1
ITGA1 0.022 0.074 -10000 0 -0.43 13 13
CDKN1A -0.003 0.11 -10000 0 -0.44 25 25
PRL-3/alpha Tubulin 0.02 0.018 -10000 0 -0.3 1 1
mol:Ca2+ -0.038 0.087 0.34 1 -0.32 42 43
AGT -0.025 0.14 -10000 0 -0.43 54 54
CCNA2 -0.038 0.092 -10000 0 -0.6 3 3
TUBA1B 0 0 -10000 0 -10000 0 0
EGR1 -0.031 0.11 -10000 0 -0.3 75 75
CDK2/Cyclin E1 0.022 0.12 -10000 0 -0.38 28 28
MAPK3 0.012 0.016 -10000 0 -0.31 1 1
PRL-2 /Rab GGTase beta 0.046 0.04 -10000 0 -0.31 6 6
MAPK1 0.011 0.021 -10000 0 -0.31 2 2
PTP4A1 -0.024 0.087 -10000 0 -0.56 3 3
PTP4A3 0.027 0.025 -10000 0 -0.43 1 1
PTP4A2 0.029 0.051 -10000 0 -0.43 6 6
ITGB1 0.011 0.026 -10000 0 -0.31 3 3
SRC 0.031 0.03 -10000 0 -0.43 2 2
RAC1 0.014 0.059 -10000 0 -0.43 4 4
Rab GGTase beta/Rab GGTase alpha 0.05 0.011 -10000 0 -10000 0 0
PRL-1/ATF-5 0.003 0.099 0.37 1 -0.53 3 4
RABGGTA 0.035 0.005 -10000 0 -10000 0 0
BCAR1 -0.017 0.02 0.34 1 -10000 0 1
RHOC 0.012 0.067 -10000 0 -0.41 8 8
RHOA 0.002 0.088 -10000 0 -0.36 22 22
cell motility 0.013 0.083 0.35 1 -0.35 9 10
PRL-1/alpha Tubulin -0.024 0.081 -10000 0 -0.53 3 3
PRL-3/alpha1 Integrin 0.031 0.059 -10000 0 -0.33 11 11
ROCK1 0.014 0.082 0.35 1 -0.36 8 9
RABGGTB 0.034 0.006 -10000 0 -10000 0 0
CDK2 0.033 0.03 -10000 0 -0.43 2 2
mitosis -0.024 0.086 -10000 0 -0.55 3 3
ATF5 0.033 0.022 -10000 0 -0.43 1 1
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.071 0.049 -10000 0 -0.24 6 6
HDAC3 0.035 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.011 0.009 -10000 0 -0.2 1 1
GATA1/HDAC4 0.05 0.018 -10000 0 -0.31 1 1
GATA1/HDAC5 0.05 0.019 -10000 0 -0.31 1 1
GATA2/HDAC5 0.042 0.044 -10000 0 -0.3 7 7
HDAC5/BCL6/BCoR 0.048 0.076 -10000 0 -0.26 27 27
HDAC9 0.033 0.022 -10000 0 -0.43 1 1
Glucocorticoid receptor/Hsp90/HDAC6 0.038 0.049 -10000 0 -0.26 13 13
HDAC4/ANKRA2 0.04 0.058 -10000 0 -0.31 13 13
HDAC5/YWHAB 0.047 0.022 -10000 0 -0.31 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.015 0.018 -10000 0 -0.17 4 4
GATA2 0.027 0.051 -10000 0 -0.43 6 6
HDAC4/RFXANK 0.049 0.02 -10000 0 -0.31 1 1
BCOR 0.027 0.062 -10000 0 -0.43 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.03 0.031 -10000 0 -0.43 2 2
HDAC5 0.033 0.022 -10000 0 -0.43 1 1
GNB1/GNG2 0.045 0.038 -10000 0 -0.31 5 5
Histones 0.008 0.072 -10000 0 -0.23 31 31
ADRBK1 0.032 0.01 -10000 0 -10000 0 0
HDAC4 0.033 0.022 -10000 0 -0.43 1 1
XPO1 0.035 0.004 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.04 0.058 -10000 0 -0.31 13 13
HDAC4/Ubc9 0.045 0.023 -10000 0 -0.31 1 1
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.046 0.023 -10000 0 -0.31 1 1
TUBA1B 0 0 -10000 0 -10000 0 0
HDAC6 0.035 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0.049 0.02 -10000 0 -0.31 1 1
CAMK4 0.031 0.036 -10000 0 -0.43 3 3
Tubulin/HDAC6 0.035 0.056 -10000 0 -0.26 17 17
SUMO1 0.035 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.033 0.008 -10000 0 -10000 0 0
GATA1 0.035 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.032 0.01 -10000 0 -10000 0 0
NR3C1 0.022 0.074 -10000 0 -0.43 13 13
SUMO1/HDAC4 0.051 0.043 -10000 0 -0.18 3 3
SRF 0.034 0.006 -10000 0 -10000 0 0
HDAC4/YWHAB 0.048 0.015 -10000 0 -10000 0 0
Tubulin 0.014 0.06 -10000 0 -0.3 17 17
HDAC4/14-3-3 E 0.046 0.022 -10000 0 -0.28 1 1
GNB1 0.03 0.042 -10000 0 -0.43 4 4
RANGAP1 0.032 0.022 -10000 0 -0.43 1 1
BCL6/BCoR 0.031 0.081 -10000 0 -0.31 27 27
HDAC4/HDAC3/SMRT (N-CoR2) 0.065 0.024 -10000 0 -0.26 1 1
HDAC4/SRF 0.063 0.035 -10000 0 -0.26 4 4
HDAC4/ER alpha -0.051 0.15 -10000 0 -0.31 133 133
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.008 0.071 -10000 0 -0.23 31 31
cell motility 0.035 0.055 -10000 0 -0.26 17 17
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.032 0.01 -10000 0 -10000 0 0
HDAC7/HDAC3 0.026 0.004 -10000 0 -10000 0 0
BCL6 0.017 0.086 -10000 0 -0.43 18 18
HDAC4/CaMK II delta B 0.033 0.022 -10000 0 -0.43 1 1
Hsp90/HDAC6 0.026 0 -10000 0 -10000 0 0
ESR1 -0.092 0.2 -10000 0 -0.43 132 132
HDAC6/HDAC11 0.033 0.078 -10000 0 -0.31 25 25
Ran/GTP/Exportin 1 0.052 0.043 -10000 0 -0.17 2 2
NPC 0.021 0.002 -10000 0 -10000 0 0
MEF2C 0.014 0.093 -10000 0 -0.43 21 21
RAN 0.035 0.005 -10000 0 -10000 0 0
HDAC4/MEF2C 0.074 0.074 -10000 0 -0.22 21 21
GNG2 0.033 0.021 -10000 0 -0.43 1 1
NCOR2 0.034 0.007 -10000 0 -10000 0 0
TUBB2A 0.018 0.084 -10000 0 -0.43 17 17
HDAC11 0.011 0.1 -10000 0 -0.43 25 25
HSP90AA1 0 0 -10000 0 -10000 0 0
RANBP2 0.035 0.004 -10000 0 -10000 0 0
ANKRA2 0.023 0.071 -10000 0 -0.43 12 12
RFXANK 0.035 0.005 -10000 0 -10000 0 0
nuclear import -0.038 0.025 0.26 1 -10000 0 1
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.031 0.036 -9999 0 -0.43 3 3
ITGB7 0.035 0.004 -9999 0 -10000 0 0
ITGA4 0.02 0.079 -9999 0 -0.43 15 15
alpha4/beta7 Integrin 0.039 0.062 -9999 0 -0.31 15 15
alpha4/beta1 Integrin 0.036 0.071 -9999 0 -0.34 16 16
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.064 0.059 -9999 0 -0.26 9 9
MAP4K1 0.034 0.008 -9999 0 -10000 0 0
MAP3K8 0.002 0.11 -9999 0 -0.43 32 32
PRKCB 0 0 -9999 0 -10000 0 0
DBNL 0.032 0.03 -9999 0 -0.43 2 2
CRKL 0.03 0.042 -9999 0 -0.43 4 4
MAP3K1 0.005 0.073 -9999 0 -0.3 7 7
JUN -0.014 0.11 -9999 0 -0.49 14 14
MAP3K7 0.013 0.062 -9999 0 -0.3 7 7
GRAP2 0.032 0.023 -9999 0 -0.43 1 1
CRK 0.031 0.023 -9999 0 -0.43 1 1
MAP2K4 -0.005 0.086 -9999 0 -0.34 15 15
LAT 0.029 0.031 -9999 0 -0.43 2 2
LCP2 0.023 0.068 -9999 0 -0.43 11 11
MAPK8 0.004 0.092 -9999 0 -0.55 12 12
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.021 0.068 -9999 0 -0.24 16 16
LAT/GRAP2/SLP76/HPK1/HIP-55 0.075 0.063 -9999 0 -0.25 9 9
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.034 0.006 -9999 0 -10000 0 0
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.032 0.01 -9999 0 -10000 0 0
TCEB1 0.028 0.025 -9999 0 -0.43 1 1
HIF1A/p53 0.004 0.099 -9999 0 -0.28 23 23
HIF1A -0.002 0.082 -9999 0 -0.27 21 21
COPS5 0.025 0.043 -9999 0 -0.43 4 4
VHL/Elongin B/Elongin C/RBX1/CUL2 0.072 0.051 -9999 0 -0.23 1 1
FIH (dimer) 0.034 0.021 -9999 0 -0.43 1 1
CDKN2A 0.015 0.074 -9999 0 -0.43 13 13
ARNT/IPAS 0.04 0.022 -9999 0 -10000 0 0
HIF1AN 0.034 0.021 -9999 0 -0.43 1 1
GNB2L1 0.033 0.03 -9999 0 -0.43 2 2
HIF1A/ARNT 0.008 0.08 -9999 0 -0.28 16 16
CUL2 0.034 0.007 -9999 0 -10000 0 0
OS9 0.033 0.03 -9999 0 -0.43 2 2
RACK1/Elongin B/Elongin C 0.054 0.034 -9999 0 -0.26 1 1
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.004 0.078 -9999 0 -0.28 16 16
PHD1-3/OS9 0.032 0.099 -9999 0 -0.25 46 46
HIF1A/RACK1/Elongin B/Elongin C 0.035 0.085 -9999 0 -0.26 15 15
VHL 0.034 0.007 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.012 0.081 -9999 0 -0.27 15 15
EGLN3 -0.016 0.14 -9999 0 -0.43 51 51
EGLN2 0.031 0.036 -9999 0 -0.43 3 3
EGLN1 0.022 0.055 -9999 0 -0.43 7 7
TP53 0.005 0.11 -9999 0 -0.43 28 28
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.036 0.063 -9999 0 -0.47 5 5
ARNT 0.028 0.014 -9999 0 -10000 0 0
ARD1A 0.035 0.003 -9999 0 -10000 0 0
RBX1 0.033 0.009 -9999 0 -10000 0 0
HIF1A/p19ARF 0.003 0.094 -9999 0 -0.3 20 20
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.025 0.058 0.43 8 -10000 0 8
PI3K Class IB/PDE3B 0.025 0.059 -10000 0 -0.43 8 8
PDE3B 0.025 0.059 -10000 0 -0.43 8 8
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.016 0.004 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.041 0.03 -10000 0 -0.24 1 1
CDKN1B 0.011 0.077 0.27 1 -0.34 12 13
CDKN1A 0.013 0.071 -10000 0 -0.34 12 12
FRAP1 0.034 0.007 -10000 0 -10000 0 0
PRKDC 0.029 0.031 -10000 0 -0.43 2 2
FOXO3 0.013 0.058 -10000 0 -0.32 12 12
AKT1 0.015 0.061 -10000 0 -0.34 12 12
BAD 0.033 0.022 -10000 0 -0.43 1 1
AKT3 0.012 0.025 -10000 0 -0.29 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.013 0.058 -10000 0 -0.32 12 12
AKT1/ASK1 0.035 0.084 -10000 0 -0.31 13 13
BAD/YWHAZ 0.052 0.035 -10000 0 -0.26 1 1
RICTOR 0.034 0.006 -10000 0 -10000 0 0
RAF1 0.034 0.006 -10000 0 -10000 0 0
JNK cascade -0.034 0.082 0.31 13 -10000 0 13
TSC1 0.015 0.062 -10000 0 -0.32 12 12
YWHAZ 0.027 0.015 -10000 0 -10000 0 0
AKT1/RAF1 0.052 0.076 0.3 1 -0.32 12 13
EP300 0.031 0.03 -10000 0 -0.43 2 2
mol:GDP 0.015 0.06 -10000 0 -0.33 12 12
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.011 0.061 -10000 0 -0.34 12 12
YWHAQ 0.033 0.03 -10000 0 -0.43 2 2
TBC1D4 0.005 0.033 0.24 2 -0.24 7 9
MAP3K5 0.011 0.097 -10000 0 -0.43 23 23
MAPKAP1 0.034 0.021 -10000 0 -0.43 1 1
negative regulation of cell cycle -0.034 0.073 0.26 7 -0.2 2 9
YWHAH 0.03 0.037 -10000 0 -0.43 3 3
AKT1S1 0.018 0.072 -10000 0 -0.33 13 13
CASP9 0.018 0.053 -10000 0 -0.3 9 9
YWHAB 0.033 0.008 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.042 0.093 0.29 5 -0.37 8 13
GBL 0.031 0.023 -10000 0 -0.43 1 1
PDK1/Src/Hsp90 0.04 0.025 -10000 0 -0.26 2 2
YWHAE 0.032 0.01 -10000 0 -10000 0 0
SRC 0.031 0.03 -10000 0 -0.43 2 2
AKT2/p21CIP1 0.016 0.066 -10000 0 -0.36 7 7
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.034 0.076 -10000 0 -0.37 13 13
CHUK 0.011 0.07 -10000 0 -0.34 12 12
BAD/BCL-XL 0.053 0.075 0.26 1 -0.38 6 7
mTORC2 0.074 0.039 -10000 0 -0.24 2 2
AKT2 0.016 0.015 -10000 0 -0.29 1 1
FOXO1-3a-4/14-3-3 family 0.044 0.092 0.24 15 -0.32 8 23
PDPK1 0.031 0.023 -10000 0 -0.43 1 1
MDM2 0.018 0.067 0.27 1 -0.32 12 13
MAPKKK cascade -0.051 0.075 0.32 12 -0.29 1 13
MDM2/Cbp/p300 0.056 0.081 0.28 9 -0.38 7 16
TSC1/TSC2 0.009 0.061 0.24 1 -0.38 8 9
proteasomal ubiquitin-dependent protein catabolic process 0.053 0.078 0.27 9 -0.35 8 17
glucose import 0.001 0.03 0.21 2 -0.22 7 9
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.03 0.081 -10000 0 -0.47 6 6
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.001 0.03 0.21 2 -0.22 7 9
GSK3A 0.017 0.064 0.2 5 -0.32 12 17
FOXO1 0.013 0.058 -10000 0 -0.32 12 12
GSK3B 0.015 0.062 -10000 0 -0.32 12 12
SFN 0.01 0.1 -10000 0 -0.43 25 25
G1/S transition of mitotic cell cycle 0.021 0.071 0.29 3 -0.32 12 15
p27Kip1/14-3-3 family 0.021 0.056 -10000 0 -0.35 3 3
PRKACA 0.035 0.004 -10000 0 -10000 0 0
KPNA1 0.035 0.004 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
YWHAG 0.035 0.004 -10000 0 -10000 0 0
RHEB 0.034 0.006 -10000 0 -10000 0 0
CREBBP 0.031 0.023 -10000 0 -0.43 1 1
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 0.039 0.037 -10000 0 -0.26 7 7
EFNA5 0.029 0.047 -10000 0 -0.43 5 5
FYN 0.011 0.044 0.19 3 -0.24 14 17
neuron projection morphogenesis 0.039 0.037 -10000 0 -0.26 7 7
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.04 0.038 -10000 0 -0.26 7 7
EPHA5 0.033 0.03 -10000 0 -0.43 2 2
Insulin-mediated glucose transport

Figure S121.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S121.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles 0.029 0.1 0.24 1 -0.28 25 26
CaM/Ca2+ 0.026 0.004 -10000 0 -10000 0 0
AKT1 0.031 0.036 -10000 0 -0.43 3 3
AKT2 0.034 0.006 -10000 0 -10000 0 0
STXBP4 0.028 0.042 -10000 0 -0.43 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.009 0.097 0.21 2 -0.26 33 35
YWHAZ 0.027 0.015 -10000 0 -10000 0 0
CALM1 0.035 0.005 -10000 0 -10000 0 0
YWHAQ 0.033 0.03 -10000 0 -0.43 2 2
TBC1D4 0.008 0.047 -10000 0 -0.31 11 11
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.03 0.037 -10000 0 -0.43 3 3
YWHAB 0.033 0.008 -10000 0 -10000 0 0
SNARE/Synip 0.036 0.035 -10000 0 -0.26 5 5
YWHAG 0.035 0.004 -10000 0 -10000 0 0
ASIP 0 0 -10000 0 -10000 0 0
PRKCI 0.024 0.065 -10000 0 -0.43 10 10
AS160/CaM/Ca2+ 0.026 0.004 -10000 0 -10000 0 0
RHOQ 0.03 0.046 -10000 0 -0.43 5 5
GYS1 0.013 0.025 0.25 2 -0.24 3 5
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.031 0.042 -10000 0 -0.43 4 4
TC10/GTP/CIP4/Exocyst 0.04 0.041 -10000 0 -0.26 9 9
AS160/14-3-3 0.014 0.078 -10000 0 -0.29 12 12
VAMP2 0.031 0.023 -10000 0 -0.43 1 1
SLC2A4 0.008 0.1 0.22 2 -0.29 34 36
STX4 0 0 -10000 0 -10000 0 0
GSK3B 0.025 0.025 -10000 0 -0.28 3 3
SFN 0.01 0.1 -10000 0 -0.43 25 25
LNPEP 0.031 0.036 -10000 0 -0.43 3 3
YWHAE 0.032 0.01 -10000 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 0.029 0.024 -10000 0 -0.43 1 1
CLTC 0.027 0.063 -10000 0 -0.5 4 4
calcium ion-dependent exocytosis 0.013 0.041 -10000 0 -0.25 7 7
Dynamin 2/GTP 0.029 0.021 -10000 0 -0.24 2 2
EXOC4 0.034 0.006 -10000 0 -10000 0 0
CD59 0.019 0.049 -10000 0 -0.45 3 3
CPE -0.008 0.08 -10000 0 -0.27 42 42
CTNNB1 0.022 0.071 -10000 0 -0.43 12 12
membrane fusion 0.014 0.034 -10000 0 -0.23 4 4
CTNND1 0.029 0.058 0.19 51 -0.22 3 54
DNM2 0.035 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.022 0.049 -10000 0 -0.38 3 3
TSHR 0.013 0.035 -10000 0 -0.26 8 8
INS 0.005 0.11 -10000 0 -0.49 21 21
BIN1 0.033 0.03 -10000 0 -0.43 2 2
mol:Choline 0.014 0.034 -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 -0.26 2 2
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.033 0.03 -10000 0 -0.43 2 2
mol:Ca2+ 0.029 0.021 -10000 0 -0.23 2 2
JUP 0.02 0.046 -10000 0 -0.43 3 3
ASAP2/amphiphysin II 0.041 0.026 -10000 0 -0.23 4 4
ARF6/GTP 0.024 0.021 -10000 0 -0.3 2 2
CDH1 0 0.072 -10000 0 -0.47 4 4
clathrin-independent pinocytosis 0.024 0.021 -10000 0 -0.3 2 2
MAPK8IP3 0.024 0.062 -10000 0 -0.43 9 9
positive regulation of endocytosis 0.024 0.021 -10000 0 -0.3 2 2
EXOC2 0.03 0.037 -10000 0 -0.43 3 3
substrate adhesion-dependent cell spreading 0.019 0.072 -10000 0 -0.24 25 25
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.03 0.023 -10000 0 -0.43 1 1
regulation of calcium-dependent cell-cell adhesion -0.034 0.093 0.46 4 -10000 0 4
positive regulation of phagocytosis 0.015 0.022 -10000 0 -0.26 3 3
ARF6/GTP/JIP3 0.036 0.045 -10000 0 -0.26 10 10
ACAP1 0.014 0.032 -10000 0 -0.19 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.021 0.043 -10000 0 -0.38 3 3
clathrin heavy chain/ACAP1 0.028 0.072 0.26 4 -0.38 6 10
JIP4/KLC1 0.038 0.026 -10000 0 -0.23 3 3
EXOC1 0.035 0.004 -10000 0 -10000 0 0
exocyst 0.019 0.073 -10000 0 -0.24 25 25
RALA/GTP 0.025 0.004 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.04 0.028 -10000 0 -0.26 3 3
receptor recycling 0.024 0.021 -10000 0 -0.3 2 2
CTNNA1 0.031 0.058 0.19 53 -0.22 2 55
NME1 0.015 0.018 -10000 0 -0.26 2 2
clathrin coat assembly 0.032 0.07 0.26 2 -0.49 4 6
IL2RA 0.012 0.068 -10000 0 -0.44 4 4
VAMP3 0.015 0.022 -10000 0 -0.26 3 3
GLUT4/clathrin heavy chain/ACAP1 0.03 0.062 -10000 0 -0.38 5 5
EXOC6 0.01 0.1 -10000 0 -0.43 27 27
PLD1 0.01 0.046 -10000 0 -0.26 12 12
PLD2 0.015 0.024 -10000 0 -0.25 3 3
EXOC5 0.034 0.021 -10000 0 -0.43 1 1
PIP5K1C 0.018 0.046 0.18 1 -0.39 3 4
SDC1 0.006 0.068 -10000 0 -0.44 4 4
ARF6/GDP 0.027 0.021 -10000 0 -0.26 2 2
EXOC7 0.033 0.009 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.037 0.096 -10000 0 -0.48 4 4
mol:Phosphatidic acid 0.014 0.034 -10000 0 -0.23 4 4
endocytosis -0.039 0.026 0.23 4 -10000 0 4
SCAMP2 0.033 0.022 -10000 0 -0.43 1 1
ADRB2 0.017 0.09 0.25 1 -0.53 5 6
EXOC3 0.033 0.008 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.037 0.03 0.18 10 -0.23 2 12
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 0.028 0.071 0.24 2 -0.45 5 7
RALA 0.034 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.029 0.093 0.34 1 -0.45 4 5
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.04 0.06 -9999 0 -0.31 14 14
FBXW11 0.032 0.03 -9999 0 -0.43 2 2
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.03 -9999 0 -0.43 2 2
CHUK 0.024 0.071 -9999 0 -0.43 12 12
NF kappa B2 p100/RelB 0.081 0.075 -9999 0 -0.24 21 21
NFKB1 0.034 0.021 -9999 0 -0.43 1 1
MAP3K14 0.032 0.03 -9999 0 -0.43 2 2
NF kappa B1 p50/RelB 0.044 0.044 -9999 0 -0.31 7 7
RELB 0.028 0.051 -9999 0 -0.43 6 6
NFKB2 0.034 0.021 -9999 0 -0.43 1 1
NF kappa B2 p52/RelB 0.041 0.037 -9999 0 -0.26 7 7
regulation of B cell activation 0.04 0.037 -9999 0 -0.26 7 7
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.027 0.055 -10000 0 -0.43 7 7
SMAD2 0.001 0.056 0.21 1 -0.21 10 11
SMAD3 0.022 0.061 0.28 3 -0.45 1 4
SMAD3/SMAD4 0.03 0.082 -10000 0 -0.38 13 13
SMAD4/Ubc9/PIASy 0.053 0.053 -10000 0 -0.26 10 10
SMAD2/SMAD2/SMAD4 0.05 0.077 -10000 0 -0.26 3 3
PPM1A 0.033 0.021 -10000 0 -0.43 1 1
CALM1 0.035 0.005 -10000 0 -10000 0 0
SMAD2/SMAD4 0.016 0.062 -10000 0 -0.21 15 15
MAP3K1 0.008 0.1 -10000 0 -0.43 26 26
TRAP-1/SMAD4 0.044 0.044 -10000 0 -0.31 7 7
MAPK3 0.032 0.023 -10000 0 -0.43 1 1
MAPK1 0.032 0.03 -10000 0 -0.43 2 2
NUP214 0.034 0.006 -10000 0 -10000 0 0
CTDSP1 0.033 0.03 -10000 0 -0.43 2 2
CTDSP2 0.033 0.03 -10000 0 -0.43 2 2
CTDSPL 0.026 0.055 -10000 0 -0.43 7 7
KPNB1 0.029 0.047 -10000 0 -0.43 5 5
TGFBRAP1 0.035 0.004 -10000 0 -10000 0 0
UBE2I 0.032 0.01 -10000 0 -10000 0 0
NUP153 0.034 0.007 -10000 0 -10000 0 0
KPNA2 0.024 0.059 -10000 0 -0.43 8 8
PIAS4 0.031 0.036 -10000 0 -0.43 3 3
Canonical 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
FBXW11 0.034 0.031 -10000 0 -0.43 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.046 0.1 0.24 4 -0.3 9 13
ERC1 0 0 -10000 0 -10000 0 0
RIP2/NOD2 0.021 0.011 -10000 0 -10000 0 0
NFKBIA 0.011 0.04 0.22 5 -0.31 5 10
BIRC2 0.031 0.011 -10000 0 -10000 0 0
IKBKB 0.029 0.024 -10000 0 -0.43 1 1
RIPK2 0.028 0.014 -10000 0 -10000 0 0
IKBKG 0.015 0.091 -10000 0 -0.34 16 16
IKK complex/A20 0.034 0.11 -10000 0 -0.34 18 18
NEMO/A20/RIP2 0.028 0.014 -10000 0 -10000 0 0
XPO1 0.035 0.004 -10000 0 -10000 0 0
NEMO/ATM 0.025 0.11 -10000 0 -0.32 19 19
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.035 0.005 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.046 0.009 -10000 0 -10000 0 0
IKK complex/ELKS 0.011 0.1 -10000 0 -0.33 18 18
BCL10/MALT1/TRAF6 0.062 0.041 -10000 0 -0.32 4 4
NOD2 0 0 -10000 0 -10000 0 0
NFKB1 0.035 0.023 -10000 0 -0.43 1 1
RELA 0.036 0.011 -10000 0 -10000 0 0
MALT1 0.03 0.042 -10000 0 -0.43 4 4
cIAP1/UbcH5C 0.046 0.018 -10000 0 -10000 0 0
ATM 0.031 0.012 -10000 0 -10000 0 0
TNF/TNFR1A 0.041 0.049 -10000 0 -0.3 9 9
TRAF6 0.034 0.021 -10000 0 -0.43 1 1
PRKCA 0.031 0.012 -10000 0 -10000 0 0
CHUK 0.024 0.071 -10000 0 -0.43 12 12
UBE2D3 0.035 0.005 -10000 0 -10000 0 0
TNF 0.025 0.062 -10000 0 -0.43 9 9
NF kappa B1 p50/RelA 0.072 0.039 -10000 0 -0.24 5 5
BCL10 0.034 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.04 0.22 5 -0.31 5 10
beta TrCP1/SCF ubiquitin ligase complex 0.034 0.031 -10000 0 -0.43 2 2
TNFRSF1A 0.032 0.022 -10000 0 -0.43 1 1
IKK complex 0.024 0.11 -10000 0 -0.35 18 18
CYLD 0.029 0.024 -10000 0 -0.43 1 1
IKK complex/PKC alpha 0.029 0.11 -10000 0 -0.34 16 16
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 0.032 0.088 -10000 0 -1.3 1 1
CLOCK 0.036 0.022 -10000 0 -0.43 1 1
TIMELESS/CRY2 0.042 0.06 -10000 0 -1.2 1 1
DEC1/BMAL1 0.041 0.062 -10000 0 -0.32 13 13
ATR 0.035 0.005 -10000 0 -10000 0 0
NR1D1 0.021 0.024 -10000 0 -10000 0 0
ARNTL 0.028 0.062 -10000 0 -0.43 9 9
TIMELESS 0.023 0.059 -10000 0 -1.3 1 1
NPAS2 0.026 0.065 -10000 0 -0.43 10 10
CRY2 0.035 0.004 -10000 0 -10000 0 0
mol:CO -0.01 0.007 0.14 1 -10000 0 1
CHEK1 -0.001 0.11 -10000 0 -0.43 31 31
mol:HEME 0.01 0.007 -10000 0 -0.14 1 1
PER1 0.031 0.011 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.065 0.07 -10000 0 -0.26 19 19
BMAL1/CLOCK 0.032 0.079 -10000 0 -0.5 3 3
S phase of mitotic cell cycle 0.032 0.088 -10000 0 -1.3 1 1
TIMELESS/CHEK1/ATR 0.032 0.091 -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 0.03 0.046 -10000 0 -0.43 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 0.068 0.073 -10000 0 -0.28 11 11
Ran/GTP/Exportin 1/HDAC1 -0.011 0.009 -10000 0 -0.2 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.041 0.079 -10000 0 -0.3 13 13
SUMO1 0.035 0.005 -10000 0 -10000 0 0
ZFPM1 0.022 0.055 -10000 0 -0.43 7 7
NPC/RanGAP1/SUMO1/Ubc9 0.015 0.018 -10000 0 -0.17 4 4
FKBP3 0.032 0.036 -10000 0 -0.43 3 3
Histones 0.07 0.063 -10000 0 -0.33 3 3
YY1/LSF 0.027 0.063 -10000 0 -0.23 19 19
SMG5 0 0 -10000 0 -10000 0 0
RAN 0.035 0.005 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.026 0.044 -10000 0 -0.25 11 11
I kappa B alpha/HDAC1 0.038 0.056 -10000 0 -0.31 7 7
SAP18 0.033 0.009 -10000 0 -10000 0 0
RELA 0.025 0.045 -10000 0 -0.32 2 2
HDAC1/Smad7 0.066 0.027 -10000 0 -0.26 2 2
RANGAP1 0.032 0.022 -10000 0 -0.43 1 1
HDAC3/TR2 0.038 0.056 -10000 0 -0.25 9 9
NuRD/MBD3 Complex 0.032 0.065 -10000 0 -0.31 9 9
NF kappa B1 p50/RelA 0.035 0.073 -10000 0 -0.31 6 6
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.027 0.051 -10000 0 -0.43 6 6
GATA1 0.035 0 -10000 0 -10000 0 0
Mad/Max 0.05 0.011 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.02 0.093 -10000 0 -0.38 13 13
RBBP7 0.033 0.03 -10000 0 -0.43 2 2
NPC 0.021 0.002 -10000 0 -10000 0 0
RBBP4 0.034 0.021 -10000 0 -0.43 1 1
MAX 0.034 0.006 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.032 0.03 -10000 0 -0.43 2 2
NFKBIA 0.021 0.049 -10000 0 -0.35 6 6
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.022 0.057 -10000 0 -0.33 5 5
SIN3 complex 0.076 0.044 -10000 0 -0.24 5 5
SMURF1 0.035 0.005 -10000 0 -10000 0 0
CHD3 0.031 0.023 -10000 0 -0.43 1 1
SAP30 0.029 0.047 -10000 0 -0.43 5 5
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.032 0.011 -10000 0 -10000 0 0
YY1/HDAC3 0.027 0.055 -10000 0 -0.33 3 3
YY1/HDAC2 0.032 0.049 -10000 0 -0.22 9 9
YY1/HDAC1 0.033 0.052 -10000 0 -0.22 10 10
NuRD/MBD2 Complex (MeCP1) 0.033 0.061 -10000 0 -0.33 5 5
PPARG 0.008 0.093 -10000 0 -0.35 24 24
HDAC8/hEST1B 0.046 0.02 -10000 0 -0.26 2 2
UBE2I 0.032 0.01 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.03 -10000 0 -0.43 2 2
TNFRSF1A 0.032 0.022 -10000 0 -0.43 1 1
HDAC3/SMRT (N-CoR2) 0.039 0.05 -10000 0 -0.35 3 3
MBD3L2 0.027 0.058 -10000 0 -0.43 8 8
ubiquitin-dependent protein catabolic process 0.065 0.027 -10000 0 -0.26 2 2
CREBBP 0.031 0.023 -10000 0 -0.43 1 1
NuRD/MBD3/MBD3L2 Complex 0.034 0.081 -10000 0 -0.3 14 14
HDAC1 0.034 0.021 -10000 0 -0.43 1 1
HDAC3 0.024 0.035 -10000 0 -0.38 2 2
HDAC2 0.031 0.023 -10000 0 -0.43 1 1
YY1 0.014 0.027 -10000 0 -0.25 5 5
HDAC8 0.033 0.029 -10000 0 -0.43 2 2
SMAD7 0.033 0.022 -10000 0 -0.43 1 1
NCOR2 0.034 0.007 -10000 0 -10000 0 0
MXD1 0.035 0.005 -10000 0 -10000 0 0
STAT3 0.021 0.029 -10000 0 -0.28 4 4
NFKB1 0.034 0.021 -10000 0 -0.43 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.035 0.004 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.044 0.066 -10000 0 -0.21 20 20
YY1/SAP30/HDAC1 0.046 0.062 -10000 0 -0.23 14 14
EP300 0.031 0.03 -10000 0 -0.43 2 2
STAT3 (dimer non-phopshorylated) 0.021 0.029 -10000 0 -0.28 4 4
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.049 -10000 0 -0.35 6 6
histone deacetylation 0.034 0.061 -10000 0 -0.33 5 5
STAT3 (dimer non-phopshorylated)/HDAC3 0.028 0.056 -10000 0 -0.42 3 3
nuclear export -0.045 0.02 0.26 2 -10000 0 2
PRKACA 0.035 0.004 -10000 0 -10000 0 0
GATAD2B 0.028 0.025 -10000 0 -0.43 1 1
GATAD2A 0.035 0.005 -10000 0 -10000 0 0
GATA2/HDAC3 0.036 0.057 -10000 0 -0.32 6 6
GATA1/HDAC1 0.051 0.018 -10000 0 -0.31 1 1
GATA1/HDAC3 0.041 0.05 -10000 0 -0.36 3 3
CHD4 0.032 0.022 -10000 0 -0.43 1 1
TNF-alpha/TNFR1A 0.041 0.049 -10000 0 -0.3 9 9
SIN3/HDAC complex/Mad/Max 0.026 0.057 -10000 0 -0.3 7 7
NuRD Complex 0.037 0.076 -10000 0 -0.33 9 9
positive regulation of chromatin silencing 0.066 0.061 -10000 0 -0.32 3 3
SIN3B 0.035 0.005 -10000 0 -10000 0 0
MTA2 0.034 0.021 -10000 0 -0.43 1 1
SIN3A 0.034 0.006 -10000 0 -10000 0 0
XPO1 0.035 0.004 -10000 0 -10000 0 0
SUMO1/HDAC1 0.051 0.043 -10000 0 -0.18 5 5
HDAC complex 0.079 0.041 -10000 0 -0.24 5 5
GATA1/Fog1 0.037 0.046 -10000 0 -0.31 7 7
FKBP25/HDAC1/HDAC2 0.061 0.039 -10000 0 -0.26 5 5
TNF 0.025 0.062 -10000 0 -0.43 9 9
negative regulation of cell growth 0.026 0.057 -10000 0 -0.3 7 7
NuRD/MBD2/PRMT5 Complex 0.033 0.061 -10000 0 -0.33 5 5
Ran/GTP/Exportin 1 0.052 0.043 -10000 0 -0.17 2 2
NF kappa B/RelA/I kappa B alpha 0.021 0.07 -10000 0 -0.3 13 13
SIN3/HDAC complex/NCoR1 0.017 0.062 -10000 0 -0.3 9 9
TFCP2 0.026 0.065 -10000 0 -0.43 10 10
NR2C1 0.029 0.055 -10000 0 -0.43 7 7
MBD3 0.034 0.007 -10000 0 -10000 0 0
MBD2 0.034 0.007 -10000 0 -10000 0 0
Aurora C signaling

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
INCENP 0.027 0.055 -9999 0 -0.43 7 7
Aurora C/Aurora B/INCENP 0.05 0.049 -9999 0 -0.24 11 11
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.013 0.027 -9999 0 -0.5 1 1
AURKB 0.028 0.037 -9999 0 -0.43 3 3
AURKC 0.032 0.022 -9999 0 -0.43 1 1
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.014 0.037 0.16 4 -0.18 1 5
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.03 0.051 0.14 61 -0.18 4 65
AP2 0.047 0.031 -10000 0 -0.31 3 3
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.039 0.035 -10000 0 -0.23 7 7
CLTB 0.032 0.03 -10000 0 -0.43 2 2
coatomer protein complex/ARF1/GTP/ER cargo protein 0.018 0.022 -10000 0 -0.22 3 3
CD4 0.033 0.009 -10000 0 -10000 0 0
CLTA 0.035 0.005 -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 0.008 0.021 0.16 3 -0.13 2 5
ARF1/GTP 0.015 0.017 -10000 0 -0.17 2 2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.009 0.015 -10000 0 -0.19 1 1
mol:Choline 0.008 0.021 0.16 3 -0.14 2 5
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.029 0.026 -10000 0 -0.44 1 1
DDEF1 0.005 0.017 0.14 2 -0.17 1 3
ARF1/GDP 0.002 0.021 -10000 0 -0.11 5 5
AP2M1 0.031 0.036 -10000 0 -0.43 3 3
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.012 0.014 -10000 0 -0.23 1 1
Rac/GTP 0.029 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.034 0.027 -10000 0 -0.22 1 1
ARFIP2 0.015 0.054 -10000 0 -0.4 7 7
COPA 0.029 0.014 -10000 0 -10000 0 0
RAC1 0.034 0.006 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.017 0.031 -10000 0 -0.2 1 1
ARF1/GTP/ARHGAP10 0.018 0.016 -10000 0 -0.26 1 1
GGA3 0.032 0.023 -10000 0 -0.43 1 1
ARF1/GTP/Membrin 0.018 0.038 -10000 0 -0.2 11 11
AP2A1 0.034 0.007 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.011 0.03 -10000 0 -0.22 4 4
ARF1/GDP/Membrin 0.021 0.046 -10000 0 -0.24 12 12
Arfaptin 2/Rac/GDP 0.037 0.037 -10000 0 -0.25 7 7
CYTH2 -0.001 0.003 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.035 0.025 -10000 0 -0.26 1 1
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.025 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 0.023 0.04 -10000 0 -0.33 3 3
PLD2 0.008 0.021 0.16 3 -0.14 2 5
ARF-GAP1/v-SNARE 0.008 0.003 -10000 0 -10000 0 0
PIP5K1A 0.008 0.021 0.16 3 -0.14 2 5
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 0.008 0.021 0.16 3 -0.14 2 5
KDEL Receptor/Ligand/ARF-GAP1 0.008 0.003 -10000 0 -10000 0 0
GOSR2 0.013 0.02 -10000 0 -0.32 1 1
USO1 0.004 0.011 0.082 3 -0.064 2 5
GBF1 0.01 0.037 -10000 0 -0.33 5 5
ARF1/GTP/Arfaptin 2 0.035 0.031 -10000 0 -0.26 3 3
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.061 0.034 -10000 0 -0.26 3 3
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 0.052 0.04 -10000 0 -0.25 6 6
MAPK9 -0.002 0.058 -10000 0 -0.3 19 19
adrenocorticotropin secretion 0.005 0.024 -10000 0 -0.3 3 3
GNB1/GNG2 0.041 0.033 -10000 0 -0.26 5 5
GNB1 0.03 0.042 -10000 0 -0.43 4 4
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 -0.23 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 0.001 0.005 0.063 3 -10000 0 3
GNAL 0.031 0.036 -10000 0 -0.43 3 3
GNG2 0.033 0.021 -10000 0 -0.43 1 1
CRH 0.026 0.038 -10000 0 -0.43 3 3
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.007 0.023 -10000 0 -0.3 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 0.034 0.021 -10000 0 -0.43 1 1
Ran/GTP/Exportin 1/HDAC4 0.006 0.015 -10000 0 -0.18 1 1
MDM2/SUMO1 0.048 0.044 -10000 0 -0.18 4 4
HDAC4 0.033 0.022 -10000 0 -0.43 1 1
Ran/GTP/Exportin 1/HDAC1 0.006 0.015 -10000 0 -0.19 1 1
SUMO1 0.035 0.005 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.014 0.015 -10000 0 -0.22 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.006 0.025 -10000 0 -0.16 4 4
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.035 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.035 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.051 0.043 -10000 0 -0.18 3 3
SUMO1/HDAC1 0.051 0.043 -10000 0 -0.18 5 5
RANGAP1 0.032 0.022 -10000 0 -0.43 1 1
MDM2/SUMO1/SUMO1 0.078 0.036 -10000 0 -0.24 2 2
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.015 0.018 -10000 0 -0.17 4 4
Ran/GTP 0.035 0.038 -10000 0 -0.18 2 2
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.033 0.008 -10000 0 -10000 0 0
UBE2I 0.032 0.01 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.034 0.041 0.2 5 -10000 0 5
NPC 0.021 0.002 -10000 0 -10000 0 0
PIAS2 0.032 0.03 -10000 0 -0.43 2 2
PIAS1 0.034 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/1216828/2.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/1228785/1.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

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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)
Meta

  • Maintainer = TCGA GDAC Team

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