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) 89
Endothelins 75
Osteopontin-mediated events 71
IGF1 pathway 70
IL4-mediated signaling events 69
FOXM1 transcription factor network 67
Plasma membrane estrogen receptor signaling 65
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 62
EGFR-dependent Endothelin signaling events 61
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 7913 82 -0.16 0.036 1000 -1000 -0.042 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 89 6957 78 -0.31 0.13 1000 -1000 -0.043 -1000
Endothelins 75 7230 96 -0.18 0.035 1000 -1000 -0.038 -1000
Osteopontin-mediated events 71 2698 38 -0.14 0.038 1000 -1000 -0.016 -1000
IGF1 pathway 70 4008 57 -0.08 0.052 1000 -1000 -0.032 -1000
IL4-mediated signaling events 69 6280 91 -0.53 0.43 1000 -1000 -0.042 -1000
FOXM1 transcription factor network 67 3464 51 -0.43 0.033 1000 -1000 -0.059 -1000
Plasma membrane estrogen receptor signaling 65 5669 86 -0.22 0.21 1000 -1000 -0.038 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 62 4218 68 -0.34 0.15 1000 -1000 -0.046 -1000
EGFR-dependent Endothelin signaling events 61 1295 21 -0.074 0.047 1000 -1000 -0.017 -1000
Glucocorticoid receptor regulatory network 57 6555 114 -0.39 0.19 1000 -1000 -0.044 -1000
Syndecan-1-mediated signaling events 56 1927 34 -0.13 0.041 1000 -1000 -0.018 -1000
HIF-1-alpha transcription factor network 53 4064 76 -0.18 0.049 1000 -1000 -0.004 -1000
Fc-epsilon receptor I signaling in mast cells 50 4852 97 -0.097 0.035 1000 -1000 -0.049 -1000
TCR signaling in naïve CD8+ T cells 49 4600 93 -0.074 0.047 1000 -1000 -0.03 -1000
Signaling events mediated by the Hedgehog family 48 2520 52 -0.098 0.051 1000 -1000 -0.021 -1000
Thromboxane A2 receptor signaling 48 5104 105 -0.11 0.061 1000 -1000 -0.032 -1000
IL12-mediated signaling events 46 4012 87 -0.26 0.042 1000 -1000 -0.029 -1000
IL27-mediated signaling events 46 2353 51 -0.2 0.1 1000 -1000 -0.045 -1000
IL23-mediated signaling events 46 2781 60 -0.21 0.036 1000 -1000 -0.044 -1000
Nongenotropic Androgen signaling 45 2378 52 -0.12 0.063 1000 -1000 -0.018 -1000
IL6-mediated signaling events 44 3369 75 -0.14 0.037 1000 -1000 -0.032 -1000
FAS signaling pathway (CD95) 42 1986 47 -0.1 0.048 1000 -1000 -0.028 -1000
Noncanonical Wnt signaling pathway 41 1090 26 -0.071 0.035 1000 -1000 -0.047 -1000
Stabilization and expansion of the E-cadherin adherens junction 40 3033 74 -0.095 0.058 1000 -1000 -0.049 -1000
Syndecan-4-mediated signaling events 39 2675 67 -0.06 0.09 1000 -1000 -0.028 -1000
Wnt signaling 38 268 7 -0.071 0.03 1000 -1000 -0.015 -1000
LPA receptor mediated events 37 3852 102 -0.078 0.035 1000 -1000 -0.078 -1000
Arf6 signaling events 36 2261 62 -0.069 0.079 1000 -1000 -0.012 -1000
Ephrin B reverse signaling 35 1711 48 -0.12 0.071 1000 -1000 -0.034 -1000
Signaling mediated by p38-gamma and p38-delta 35 530 15 -0.056 0.033 1000 -1000 -0.028 -1000
TCGA08_p53 34 243 7 -0.029 0.026 1000 -1000 -0.003 -1000
E-cadherin signaling events 34 173 5 -0.012 0.028 1000 -1000 0.02 -1000
ErbB4 signaling events 33 2328 69 -0.11 0.06 1000 -1000 -0.016 -1000
Coregulation of Androgen receptor activity 32 2503 76 -0.15 0.054 1000 -1000 -0.029 -1000
PLK2 and PLK4 events 32 97 3 -0.015 0.03 1000 -1000 0 -1000
IL2 signaling events mediated by PI3K 32 1879 58 -0.23 0.035 1000 -1000 -0.032 -1000
Canonical Wnt signaling pathway 32 1653 51 -0.15 0.089 1000 -1000 -0.029 -1000
E-cadherin signaling in keratinocytes 32 1394 43 -0.061 0.036 1000 -1000 -0.022 -1000
Signaling events mediated by PTP1B 31 2369 76 -0.089 0.06 1000 -1000 -0.037 -1000
Integrins in angiogenesis 31 2628 84 -0.12 0.058 1000 -1000 -0.022 -1000
E-cadherin signaling in the nascent adherens junction 31 2367 76 -0.082 0.056 1000 -1000 -0.048 -1000
Syndecan-2-mediated signaling events 30 2127 69 -0.019 0.047 1000 -1000 -0.025 -1000
Cellular roles of Anthrax toxin 29 1139 39 -0.075 0.035 1000 -1000 -0.016 -1000
amb2 Integrin signaling 29 2385 82 -0.05 0.046 1000 -1000 -0.017 -1000
Regulation of nuclear SMAD2/3 signaling 28 3906 136 -0.19 0.066 1000 -1000 -0.034 -1000
TCGA08_retinoblastoma 28 227 8 -0.011 0.023 1000 -1000 -0.004 -1000
Caspase cascade in apoptosis 27 2045 74 -0.067 0.047 1000 -1000 -0.028 -1000
BMP receptor signaling 27 2210 81 -0.12 0.067 1000 -1000 -0.019 -1000
Nectin adhesion pathway 27 1707 63 -0.047 0.053 1000 -1000 -0.027 -1000
Reelin signaling pathway 27 1512 56 -0.071 0.068 1000 -1000 -0.019 -1000
VEGFR1 specific signals 26 1498 56 -0.028 0.036 1000 -1000 -0.024 -1000
Visual signal transduction: Rods 26 1382 52 -0.066 0.066 1000 -1000 -0.018 -1000
Aurora B signaling 26 1756 67 -0.065 0.052 1000 -1000 -0.039 -1000
IL1-mediated signaling events 25 1552 62 -0.029 0.074 1000 -1000 -0.03 -1000
BCR signaling pathway 25 2478 99 -0.1 0.065 1000 -1000 -0.042 -1000
mTOR signaling pathway 24 1286 53 -0.067 0.044 1000 -1000 -0.035 -1000
PDGFR-alpha signaling pathway 23 1045 44 -0.14 0.049 1000 -1000 -0.027 -1000
Arf6 downstream pathway 22 976 43 -0.047 0.048 1000 -1000 -0.028 -1000
FOXA2 and FOXA3 transcription factor networks 22 1036 46 -0.2 0.043 1000 -1000 -0.031 -1000
PLK1 signaling events 22 1931 85 -0.073 0.051 1000 -1000 -0.019 -1000
S1P1 pathway 22 796 36 -0.034 0.036 1000 -1000 -0.025 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 22 990 45 -0.043 0.055 1000 -1000 -0.028 -1000
Visual signal transduction: Cones 21 825 38 -0.022 0.05 1000 -1000 0 -1000
Presenilin action in Notch and Wnt signaling 21 1291 61 -0.2 0.07 1000 -1000 -0.043 -1000
Glypican 1 network 21 1037 48 -0.023 0.049 1000 -1000 -0.021 -1000
IFN-gamma pathway 21 1480 68 -0.059 0.058 1000 -1000 -0.033 -1000
Ceramide signaling pathway 20 1564 76 -0.069 0.068 1000 -1000 -0.02 -1000
TRAIL signaling pathway 20 983 48 -0.023 0.036 1000 -1000 -0.022 -1000
Calcium signaling in the CD4+ TCR pathway 20 645 31 -0.036 0.045 1000 -1000 -0.041 -1000
Insulin Pathway 20 1528 74 -0.063 0.079 1000 -1000 -0.025 -1000
Class I PI3K signaling events 19 1457 73 -0.06 0.044 1000 -1000 -0.02 -1000
PDGFR-beta signaling pathway 19 1925 97 -0.066 0.066 1000 -1000 -0.042 -1000
ErbB2/ErbB3 signaling events 18 1207 65 -0.046 0.047 1000 -1000 -0.054 -1000
ceramide signaling pathway 18 920 49 -0.057 0.048 1000 -1000 -0.029 -1000
RXR and RAR heterodimerization with other nuclear receptor 18 961 52 -0.057 0.061 1000 -1000 -0.026 -1000
Regulation of Telomerase 18 1842 102 -0.15 0.062 1000 -1000 -0.044 -1000
Ras signaling in the CD4+ TCR pathway 18 312 17 -0.002 0.05 1000 -1000 -0.011 -1000
p75(NTR)-mediated signaling 16 2025 125 -0.047 0.086 1000 -1000 -0.039 -1000
EPO signaling pathway 16 890 55 -0.11 0.046 1000 -1000 -0.026 -1000
Syndecan-3-mediated signaling events 16 573 35 -0.031 0.068 1000 -1000 -0.03 -1000
EPHB forward signaling 16 1374 85 -0.046 0.11 1000 -1000 -0.047 -1000
Regulation of Androgen receptor activity 15 1066 70 -0.14 0.047 1000 -1000 -0.038 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 14 793 54 -0.036 0.049 1000 -1000 -0.022 -1000
Hedgehog signaling events mediated by Gli proteins 14 967 65 -0.024 0.076 1000 -1000 -0.027 -1000
HIF-2-alpha transcription factor network 14 610 43 -0.11 0.11 1000 -1000 -0.035 -1000
FoxO family signaling 14 934 64 -0.092 0.048 1000 -1000 -0.024 -1000
Signaling events mediated by VEGFR1 and VEGFR2 14 1823 125 -0.026 0.044 1000 -1000 -0.023 -1000
IL2 signaling events mediated by STAT5 14 311 22 -0.025 0.036 1000 -1000 -0.03 -1000
Neurotrophic factor-mediated Trk receptor signaling 14 1721 120 -0.079 0.088 1000 -1000 -0.033 -1000
LPA4-mediated signaling events 13 156 12 -0.028 0.022 1000 -1000 -0.021 -1000
Sphingosine 1-phosphate (S1P) pathway 13 383 28 -0.01 0.043 1000 -1000 -0.004 -1000
Aurora A signaling 13 807 60 -0.011 0.05 1000 -1000 -0.01 -1000
Signaling mediated by p38-alpha and p38-beta 13 587 44 -0.054 0.056 1000 -1000 -0.011 -1000
Regulation of p38-alpha and p38-beta 13 703 54 -0.018 0.072 1000 -1000 -0.02 -1000
Glypican 2 network 13 54 4 0 0.013 1000 -1000 0 -1000
p38 MAPK signaling pathway 13 581 44 -0.05 0.058 1000 -1000 -0.017 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 12 1092 85 -0.14 0.064 1000 -1000 -0.042 -1000
Retinoic acid receptors-mediated signaling 12 745 58 -0.071 0.067 1000 -1000 -0.025 -1000
Atypical NF-kappaB pathway 12 385 31 -0.018 0.035 1000 -1000 -0.013 -1000
S1P4 pathway 12 301 25 -0.009 0.043 1000 -1000 -0.013 -1000
S1P5 pathway 11 191 17 -0.001 0.035 1000 -1000 -0.005 -1000
Effects of Botulinum toxin 11 300 26 -0.064 0.051 1000 -1000 0 -1000
S1P3 pathway 11 497 42 -0.017 0.043 1000 -1000 -0.032 -1000
Angiopoietin receptor Tie2-mediated signaling 11 1026 88 -0.063 0.064 1000 -1000 -0.056 -1000
Nephrin/Neph1 signaling in the kidney podocyte 10 357 34 -0.039 0.075 1000 -1000 -0.032 -1000
BARD1 signaling events 10 584 57 -0.047 0.069 1000 -1000 -0.043 -1000
Paxillin-independent events mediated by a4b1 and a4b7 10 397 37 -0.024 0.073 1000 -1000 -0.024 -1000
Signaling events mediated by HDAC Class III 10 410 40 -0.063 0.064 1000 -1000 -0.038 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 10 841 83 -0.057 0.069 1000 -1000 -0.017 -1000
Paxillin-dependent events mediated by a4b1 10 370 36 -0.061 0.064 1000 -1000 -0.03 -1000
TCGA08_rtk_signaling 10 277 26 -0.026 0.042 1000 -1000 -0.008 -1000
Signaling events mediated by HDAC Class II 9 683 75 -0.088 0.076 1000 -1000 -0.024 -1000
a4b1 and a4b7 Integrin signaling 9 47 5 0.021 0.041 1000 -1000 0.022 -1000
Class I PI3K signaling events mediated by Akt 9 652 68 -0.053 0.075 1000 -1000 -0.011 -1000
Signaling events mediated by PRL 9 327 34 -0.037 0.05 1000 -1000 -0.033 -1000
Class IB PI3K non-lipid kinase events 9 27 3 -0.025 0.025 1000 -1000 -0.026 -1000
JNK signaling in the CD4+ TCR pathway 8 136 17 -0.01 0.078 1000 -1000 -0.015 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 8 285 33 -0.016 0.071 1000 -1000 -0.024 -1000
Insulin-mediated glucose transport 7 239 32 0 0.043 1000 -1000 -0.008 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 6 142 23 -0.001 0.054 1000 -1000 -0.012 -1000
Ephrin A reverse signaling 6 43 7 0 0.041 1000 -1000 0 -1000
Arf6 trafficking events 5 418 71 -0.04 0.042 1000 -1000 -0.025 -1000
Alternative NF-kappaB pathway 5 74 13 0 0.082 1000 -1000 0 -1000
Canonical NF-kappaB pathway 4 156 39 0 0.074 1000 -1000 -0.021 -1000
Circadian rhythm pathway 4 100 22 -0.01 0.067 1000 -1000 -0.04 -1000
Aurora C signaling 3 24 7 0 0.052 1000 -1000 -0.009 -1000
Signaling events mediated by HDAC Class I 3 354 104 -0.046 0.08 1000 -1000 -0.026 -1000
Arf1 pathway 3 196 54 -0.001 0.06 1000 -1000 -0.013 -1000
Rapid glucocorticoid signaling 2 56 20 -0.002 0.044 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 26 27 0 0.08 1000 -1000 -0.02 -1000
Total 3378 209364 7203 -11 8 131000 -131000 -3.4 -131000
Signaling events regulated by Ret tyrosine kinase

Figure S1.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S1.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.038 0.13 -10000 0 -0.53 29 29
Crk/p130 Cas/Paxillin -0.13 0.16 -10000 0 -0.33 165 165
JUN -0.13 0.18 0.19 2 -0.4 116 118
HRAS 0.032 0.036 -10000 0 -0.42 3 3
RET51/GFRalpha1/GDNF/GRB10 -0.1 0.2 -10000 0 -0.31 228 228
RAP1A 0.03 0.05 -10000 0 -0.42 6 6
FRS2 0.033 0.022 -10000 0 -0.42 1 1
RAP1A/GDP 0.022 0.035 -10000 0 -0.3 6 6
RET51/GFRalpha1/GDNF/DOK1 -0.099 0.21 -10000 0 -0.32 221 221
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.036 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.023 -10000 0 -0.42 1 1
RET9/GFRalpha1/GDNF/Enigma -0.041 0.14 -10000 0 -0.23 170 170
RHOA 0.026 0.061 -10000 0 -0.42 9 9
RAP1A/GTP -0.095 0.18 -10000 0 -0.28 223 223
GRB7 0.024 0.058 -10000 0 -0.42 8 8
RET51/GFRalpha1/GDNF -0.094 0.2 -10000 0 -0.31 218 218
MAPKKK cascade -0.11 0.19 -10000 0 -0.33 203 203
BCAR1 0.029 0.014 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.064 0.17 -10000 0 -0.28 180 180
lamellipodium assembly -0.11 0.16 -10000 0 -0.31 164 164
RET51/GFRalpha1/GDNF/SHC -0.082 0.18 -10000 0 -0.3 195 195
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
RET9/GFRalpha1/GDNF/SHC -0.029 0.12 -10000 0 -0.24 122 122
RET9/GFRalpha1/GDNF/Shank3 -0.043 0.14 -10000 0 -0.24 173 173
MAPK3 -0.12 0.16 0.34 1 -0.38 91 92
DOK1 0.027 0.061 -10000 0 -0.42 9 9
DOK6 0.006 0.11 -10000 0 -0.42 30 30
PXN 0.036 0.004 -10000 0 -10000 0 0
neurite development -0.11 0.16 0.28 2 -0.37 101 103
DOK5 0.014 0.083 -10000 0 -0.42 17 17
GFRA1 -0.13 0.21 -10000 0 -0.42 177 177
MAPK8 -0.12 0.18 -10000 0 -0.3 222 222
HRAS/GTP -0.12 0.22 -10000 0 -0.35 217 217
tube development -0.031 0.14 0.22 24 -0.22 162 186
MAPK1 -0.12 0.16 0.34 1 -0.38 91 92
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.054 0.12 -10000 0 -0.22 156 156
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
SRC 0.032 0.03 -10000 0 -0.42 2 2
PDLIM7 0.035 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.095 0.21 -10000 0 -0.32 219 219
SHC1 0.027 0.025 -10000 0 -0.42 1 1
RET51/GFRalpha1/GDNF/Dok4 -0.1 0.2 -10000 0 -0.31 221 221
RET51/GFRalpha1/GDNF/Dok5 -0.1 0.2 -10000 0 -0.32 212 212
PRKCA 0.031 0.012 -10000 0 -10000 0 0
HRAS/GDP 0.024 0.025 -10000 0 -0.3 3 3
CREB1 -0.087 0.17 -10000 0 -0.33 148 148
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.039 0.11 -10000 0 -0.23 114 114
RET51/GFRalpha1/GDNF/Grb7 -0.097 0.2 -10000 0 -0.32 213 213
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.096 0.2 -10000 0 -0.42 138 138
DOK4 0.028 0.032 -10000 0 -0.42 2 2
JNK cascade -0.13 0.17 0.19 2 -0.39 116 118
RET9/GFRalpha1/GDNF/FRS2 -0.043 0.14 -10000 0 -0.24 168 168
SHANK3 0.034 0.029 -10000 0 -0.42 2 2
RASA1 0.028 0.054 -10000 0 -0.42 7 7
NCK1 0.034 0.022 -10000 0 -0.42 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.037 0.1 -10000 0 -0.22 113 113
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.11 0.18 -10000 0 -0.3 205 205
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.12 0.19 -10000 0 -0.32 220 220
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.11 0.2 -10000 0 -0.34 180 180
PI3K -0.16 0.25 -10000 0 -0.47 167 167
SOS1 0.034 0.021 -10000 0 -0.42 1 1
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.029 0.14 -10000 0 -0.22 162 162
GRB10 0.022 0.075 -10000 0 -0.42 14 14
activation of MAPKK activity -0.082 0.15 -10000 0 -0.33 94 94
RET51/GFRalpha1/GDNF/FRS2 -0.097 0.2 -10000 0 -0.32 217 217
GAB1 0.027 0.061 -10000 0 -0.42 9 9
IRS1 -0.014 0.14 -10000 0 -0.42 54 54
IRS2 0.008 0.099 -10000 0 -0.42 25 25
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.12 0.2 -10000 0 -0.35 186 186
RET51/GFRalpha1/GDNF/PKC alpha -0.091 0.2 -10000 0 -0.32 201 201
GRB2 0.033 0.01 -10000 0 -10000 0 0
PRKACA 0.036 0.004 -10000 0 -10000 0 0
GDNF 0.032 0.036 -10000 0 -0.42 3 3
RAC1 0.035 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.12 0.23 -10000 0 -0.35 226 226
Rac1/GTP -0.12 0.2 -10000 0 -0.37 163 163
RET9/GFRalpha1/GDNF -0.061 0.14 -10000 0 -0.26 171 171
GFRalpha1/GDNF -0.075 0.17 -10000 0 -0.3 171 171
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 -0.41 131 132
CRKL -0.13 0.2 -10000 0 -0.43 135 135
HRAS -0.077 0.17 -10000 0 -0.36 91 91
mol:PIP3 -0.087 0.2 0.28 2 -0.42 100 102
SPRED1 0.02 0.08 -10000 0 -0.42 16 16
SPRED2 0.02 0.083 -10000 0 -0.42 17 17
GAB1 -0.14 0.21 -10000 0 -0.45 136 136
FOXO3 -0.1 0.2 -10000 0 -0.39 131 131
AKT1 -0.11 0.22 -10000 0 -0.42 130 130
BAD -0.1 0.2 -10000 0 -0.39 129 129
megakaryocyte differentiation -0.13 0.21 -10000 0 -0.44 133 133
GSK3B -0.1 0.2 0.34 1 -0.39 128 129
RAF1 -0.054 0.15 0.25 9 -0.31 82 91
SHC1 0.027 0.025 -10000 0 -0.42 1 1
STAT3 -0.12 0.21 -10000 0 -0.43 132 132
STAT1 -0.31 0.48 -10000 0 -0.89 183 183
HRAS/SPRED1 -0.055 0.16 0.26 2 -0.32 86 88
cell proliferation -0.13 0.21 -10000 0 -0.44 134 134
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
TEC 0.031 0.046 -10000 0 -0.42 5 5
RPS6KB1 -0.12 0.22 -10000 0 -0.45 133 133
HRAS/SPRED2 -0.053 0.16 0.26 2 -0.31 88 90
LYN/TEC/p62DOK -0.093 0.22 -10000 0 -0.42 126 126
MAPK3 -0.033 0.12 0.24 13 -0.25 37 50
STAP1 -0.13 0.21 -10000 0 -0.44 133 133
GRAP2 0.032 0.023 -10000 0 -0.42 1 1
JAK2 -0.26 0.41 -10000 0 -0.76 176 176
STAT1 (dimer) -0.3 0.46 -10000 0 -0.86 184 184
mol:Gleevec 0.005 0.008 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.099 0.22 -10000 0 -0.42 123 123
actin filament polymerization -0.13 0.21 -10000 0 -0.44 133 133
LYN 0.03 0.014 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.19 0.3 -10000 0 -0.58 160 160
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
CBL/CRKL/GRB2 -0.1 0.2 -10000 0 -0.4 125 125
PI3K -0.1 0.23 -10000 0 -0.45 123 123
PTEN 0.027 0.061 -10000 0 -0.42 9 9
SCF/KIT/EPO/EPOR -0.3 0.53 -10000 0 -1.2 122 122
MAPK8 -0.13 0.21 -10000 0 -0.44 134 134
STAT3 (dimer) -0.12 0.2 -10000 0 -0.43 132 132
positive regulation of transcription -0.024 0.1 0.22 13 -0.21 30 43
mol:GDP -0.084 0.17 -10000 0 -0.38 90 90
PIK3C2B -0.12 0.2 0.28 1 -0.42 127 128
CBL/CRKL -0.12 0.2 -10000 0 -0.41 133 133
FER -0.13 0.21 -10000 0 -0.45 132 132
SH2B3 -0.13 0.21 -10000 0 -0.44 133 133
PDPK1 -0.069 0.2 0.3 14 -0.38 93 107
SNAI2 -0.14 0.22 -10000 0 -0.46 136 136
positive regulation of cell proliferation -0.22 0.36 -10000 0 -0.7 160 160
KITLG -0.052 0.16 -10000 0 -0.45 72 72
cell motility -0.22 0.36 -10000 0 -0.7 160 160
PTPN6 0.038 0.032 -10000 0 -0.41 2 2
EPOR -0.068 0.18 -10000 0 -1 5 5
STAT5A (dimer) -0.19 0.3 -10000 0 -0.59 156 156
SOCS1 0.031 0.023 -10000 0 -0.42 1 1
cell migration 0.13 0.21 0.44 133 -10000 0 133
SOS1 0.034 0.021 -10000 0 -0.42 1 1
EPO 0.012 0.029 -10000 0 -10000 0 0
VAV1 0.018 0.083 -10000 0 -0.42 17 17
GRB10 -0.14 0.21 -10000 0 -0.45 133 133
PTPN11 0.04 0.009 -10000 0 -10000 0 0
SCF/KIT -0.14 0.22 -10000 0 -0.47 133 133
GO:0007205 0.007 0.011 -10000 0 -10000 0 0
MAP2K1 -0.04 0.13 0.25 12 -0.25 72 84
CBL 0.031 0.012 -10000 0 -10000 0 0
KIT -0.27 0.53 -10000 0 -1.3 101 101
MAP2K2 -0.042 0.13 0.26 11 -0.25 74 85
SHC/Grb2/SOS1 -0.08 0.2 -10000 0 -0.42 94 94
STAT5A -0.2 0.32 -10000 0 -0.61 156 156
GRB2 0.033 0.01 -10000 0 -10000 0 0
response to radiation -0.14 0.22 -10000 0 -0.45 137 137
SHC/GRAP2 0.038 0.032 -10000 0 -0.3 2 2
PTPRO -0.14 0.21 -10000 0 -0.46 132 132
SH2B2 -0.13 0.21 -10000 0 -0.44 133 133
DOK1 0.027 0.061 -10000 0 -0.42 9 9
MATK -0.13 0.21 -10000 0 -0.45 133 133
CREBBP -0.009 0.08 -10000 0 -0.18 16 16
BCL2 -0.3 0.56 -10000 0 -1.3 113 113
Endothelins

Figure S3.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S3.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.013 0.2 0.27 74 -0.32 104 178
PTK2B 0.028 0.015 -10000 0 -10000 0 0
mol:Ca2+ -0.057 0.26 -10000 0 -0.68 49 49
EDN1 -0.01 0.19 0.23 68 -0.43 68 136
EDN3 -0.014 0.12 -10000 0 -0.42 40 40
EDN2 -0.055 0.18 -10000 0 -0.42 94 94
HRAS/GDP -0.065 0.24 0.28 5 -0.48 90 95
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.06 0.2 -10000 0 -0.41 94 94
ADCY4 -0.013 0.17 0.25 9 -0.39 49 58
ADCY5 -0.016 0.16 0.24 2 -0.41 42 44
ADCY6 -0.012 0.16 0.24 7 -0.4 44 51
ADCY7 -0.015 0.16 0.26 3 -0.4 40 43
ADCY1 -0.011 0.16 0.26 6 -0.39 43 49
ADCY2 -0.029 0.18 0.24 5 -0.42 55 60
ADCY3 -0.013 0.16 0.25 9 -0.39 47 56
ADCY8 -0.007 0.14 0.26 4 -0.37 37 41
ADCY9 -0.016 0.16 0.24 7 -0.38 47 54
arachidonic acid secretion -0.089 0.25 0.27 1 -0.51 109 110
ETB receptor/Endothelin-1/Gq/GTP -0.051 0.16 -10000 0 -0.32 104 104
GNAO1 0.03 0.014 -10000 0 -10000 0 0
HRAS 0.031 0.036 -10000 0 -0.42 3 3
ETA receptor/Endothelin-1/G12/GTP 0.03 0.22 0.37 75 -0.3 102 177
ETA receptor/Endothelin-1/Gs/GTP 0.024 0.2 0.35 74 -0.29 96 170
mol:GTP -0.001 0.006 -10000 0 -10000 0 0
COL3A1 -0.019 0.22 0.27 73 -0.54 43 116
EDNRB 0.002 0.099 -10000 0 -0.37 26 26
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.01 0.2 0.27 72 -0.4 65 137
CYSLTR1 -0.029 0.23 0.27 75 -0.44 85 160
SLC9A1 -0.006 0.13 0.19 74 -0.3 41 115
mol:GDP -0.081 0.24 0.27 5 -0.5 95 100
SLC9A3 -0.12 0.35 -10000 0 -0.71 108 108
RAF1 -0.095 0.24 -10000 0 -0.49 109 109
JUN -0.099 0.35 -10000 0 -0.95 62 62
JAK2 -0.011 0.19 0.27 74 -0.33 97 171
mol:IP3 -0.073 0.21 0.23 1 -0.44 94 95
ETA receptor/Endothelin-1 0.014 0.26 0.42 75 -0.38 107 182
PLCB1 -0.021 0.14 -10000 0 -0.42 56 56
PLCB2 0.032 0.023 -10000 0 -0.43 1 1
ETA receptor/Endothelin-3 -0.004 0.15 -10000 0 -0.33 76 76
FOS -0.14 0.36 -10000 0 -0.92 79 79
Gai/GDP -0.11 0.32 -10000 0 -0.75 93 93
CRK 0.031 0.023 -10000 0 -0.42 1 1
mol:Ca ++ -0.089 0.27 0.26 6 -0.52 106 112
BCAR1 0.029 0.014 -10000 0 -10000 0 0
PRKCB1 -0.076 0.22 0.26 14 -0.46 92 106
GNAQ -0.001 0.007 -10000 0 -10000 0 0
GNAZ 0.024 0.067 -10000 0 -0.42 11 11
GNAL 0.031 0.036 -10000 0 -0.42 3 3
Gs family/GDP -0.065 0.22 0.26 4 -0.46 90 94
ETA receptor/Endothelin-1/Gq/GTP -0.043 0.2 0.2 67 -0.39 92 159
MAPK14 -0.068 0.17 0.22 1 -0.39 79 80
TRPC6 -0.062 0.27 -10000 0 -0.73 49 49
GNAI2 0.027 0.057 -10000 0 -0.42 8 8
GNAI3 0.035 0.006 -10000 0 -10000 0 0
GNAI1 0.017 0.085 -10000 0 -0.42 18 18
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.067 0.18 -10000 0 -0.38 94 94
ETB receptor/Endothelin-2 -0.041 0.15 -10000 0 -0.31 113 113
ETB receptor/Endothelin-3 -0.011 0.11 -10000 0 -0.31 56 56
ETB receptor/Endothelin-1 -0.012 0.17 -10000 0 -0.32 96 96
MAPK3 -0.14 0.34 -10000 0 -0.77 94 94
MAPK1 -0.14 0.34 -10000 0 -0.8 91 91
Rac1/GDP -0.063 0.23 0.28 5 -0.49 86 91
cAMP biosynthetic process -0.005 0.17 0.26 22 -0.4 45 67
MAPK8 -0.072 0.3 -10000 0 -0.68 71 71
SRC 0.032 0.03 -10000 0 -0.42 2 2
ETB receptor/Endothelin-1/Gi/GTP -0.043 0.16 -10000 0 -0.35 80 80
p130Cas/CRK/Src/PYK2 -0.1 0.26 0.31 1 -0.55 97 98
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.063 0.23 0.28 5 -0.48 90 95
COL1A2 -0.074 0.3 0.39 1 -0.57 106 107
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.034 0.18 -10000 0 -0.32 128 128
mol:DAG -0.073 0.21 0.23 1 -0.44 94 95
MAP2K2 -0.12 0.28 0.32 1 -0.6 104 105
MAP2K1 -0.11 0.28 0.29 2 -0.6 102 104
EDNRA 0.014 0.17 0.23 74 -0.37 63 137
positive regulation of muscle contraction -0.014 0.17 0.22 74 -0.38 50 124
Gq family/GDP -0.059 0.22 -10000 0 -0.46 83 83
HRAS/GTP -0.081 0.23 -10000 0 -0.48 92 92
PRKCH -0.075 0.21 0.23 4 -0.45 89 93
RAC1 0.035 0.006 -10000 0 -10000 0 0
PRKCA -0.06 0.21 0.23 23 -0.45 81 104
PRKCB -0.074 0.2 0.22 1 -0.42 98 99
PRKCE -0.076 0.2 0.21 1 -0.45 85 86
PRKCD -0.075 0.2 0.22 1 -0.45 85 86
PRKCG -0.079 0.2 0.22 1 -0.45 87 88
regulation of vascular smooth muscle contraction -0.18 0.42 -10000 0 -1.1 79 79
PRKCQ -0.069 0.2 0.23 6 -0.44 86 92
PLA2G4A -0.1 0.28 0.27 1 -0.55 109 110
GNA14 -0.014 0.13 -10000 0 -0.43 44 44
GNA15 0.026 0.048 -10000 0 -0.42 5 5
GNA12 0.035 0.006 -10000 0 -10000 0 0
GNA11 0.029 0.039 -10000 0 -0.42 3 3
Rac1/GTP 0.029 0.22 0.37 74 -0.32 84 158
MMP1 -0.17 0.35 0.25 7 -0.78 120 127
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.038 0.15 0.36 1 -0.27 129 130
NF kappa B1 p50/RelA/I kappa B alpha -0.035 0.17 0.33 1 -0.42 49 50
alphaV/beta3 Integrin/Osteopontin/Src -0.046 0.17 -10000 0 -0.32 127 127
AP1 -0.086 0.23 -10000 0 -0.49 84 84
ILK -0.048 0.14 0.38 1 -0.26 128 129
bone resorption -0.055 0.14 0.32 1 -0.35 45 46
PTK2B 0.028 0.015 -10000 0 -10000 0 0
PYK2/p130Cas -0.029 0.16 -10000 0 -0.26 135 135
ITGAV 0.017 0.084 -10000 0 -0.43 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.038 0.066 -10000 0 -0.3 18 18
alphaV/beta3 Integrin/Osteopontin -0.023 0.16 -10000 0 -0.29 129 129
MAP3K1 -0.06 0.14 0.23 6 -0.27 146 152
JUN -0.002 0.12 -10000 0 -0.42 39 39
MAPK3 -0.061 0.14 0.22 8 -0.27 132 140
MAPK1 -0.065 0.15 0.22 8 -0.28 136 144
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
NFKB1 0.035 0.005 -10000 0 -10000 0 0
MAPK8 -0.065 0.13 0.22 9 -0.26 142 151
ITGB3 0.024 0.051 -10000 0 -0.43 5 5
NFKBIA -0.069 0.16 0.35 2 -0.42 58 60
FOS -0.031 0.15 -10000 0 -0.42 66 66
CD44 0.022 0.075 -10000 0 -0.42 14 14
CHUK 0.025 0.067 -10000 0 -0.42 11 11
PLAU -0.14 0.36 -10000 0 -1.1 56 56
NF kappa B1 p50/RelA -0.022 0.19 -10000 0 -0.45 55 55
BCAR1 0.029 0.014 -10000 0 -10000 0 0
RELA 0.035 0.006 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.03 0.082 -10000 0 -0.32 22 22
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.062 0.15 0.22 8 -0.28 149 157
VAV3 -0.1 0.15 0.22 8 -0.27 205 213
MAP3K14 -0.051 0.15 0.23 7 -0.27 131 138
ROCK2 0.032 0.041 -10000 0 -0.42 4 4
SPP1 -0.078 0.19 -10000 0 -0.43 117 117
RAC1 0.035 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.084 0.15 0.19 5 -0.25 200 205
MMP2 -0.1 0.19 -10000 0 -0.45 85 85
IGF1 pathway

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
NCK2 0.036 0.004 -10000 0 -10000 0 0
PTK2 0.027 0.015 -10000 0 -10000 0 0
CRKL -0.073 0.15 0.17 2 -0.3 137 139
GRB2/SOS1/SHC 0.051 0.036 -10000 0 -0.26 1 1
HRAS 0.032 0.036 -10000 0 -0.42 3 3
IRS1/Crk -0.066 0.16 -10000 0 -0.3 143 143
IGF-1R heterotetramer/IGF1/PTP1B -0.037 0.16 -10000 0 -0.29 131 131
AKT1 -0.08 0.14 0.17 13 -0.38 59 72
BAD -0.078 0.13 0.15 13 -0.37 56 69
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.069 0.15 0.17 2 -0.3 131 133
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.062 0.16 0.22 1 -0.3 143 144
RAF1 -0.041 0.14 0.29 3 -0.49 15 18
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.028 0.17 -10000 0 -0.29 130 130
YWHAZ 0.026 0.016 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.065 0.17 -10000 0 -0.31 153 153
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
RPS6KB1 -0.073 0.13 0.17 12 -0.38 55 67
GNB2L1 0.033 0.035 -10000 0 -0.42 3 3
positive regulation of MAPKKK cascade -0.027 0.14 0.31 8 -0.42 13 21
PXN 0.036 0.004 -10000 0 -10000 0 0
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.047 0.023 -10000 0 -0.3 1 1
HRAS/GTP -0.042 0.13 -10000 0 -0.27 114 114
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.001 0.14 -10000 0 -0.24 104 104
IGF-1R heterotetramer -0.062 0.18 -10000 0 -0.47 84 84
IGF-1R heterotetramer/IGF1/IRS/Nck -0.045 0.17 -10000 0 -0.3 143 143
Crk/p130 Cas/Paxillin -0.041 0.16 -10000 0 -0.28 139 139
IGF1R -0.062 0.18 -10000 0 -0.47 84 84
IGF1 -0.062 0.18 -10000 0 -0.46 80 80
IRS2/Crk -0.072 0.16 0.17 2 -0.3 151 153
PI3K -0.04 0.18 -10000 0 -0.29 147 147
apoptosis 0.052 0.12 0.32 46 -0.29 5 51
HRAS/GDP 0.024 0.025 -10000 0 -0.3 3 3
PRKCD -0.066 0.18 -10000 0 -0.34 130 130
RAF1/14-3-3 E -0.021 0.14 0.29 3 -0.42 15 18
BAD/14-3-3 -0.054 0.12 0.3 5 -0.34 46 51
PRKCZ -0.078 0.14 0.16 13 -0.28 130 143
Crk/p130 Cas/Paxillin/FAK1 -0.032 0.13 -10000 0 -0.35 44 44
PTPN1 0.03 0.031 -10000 0 -0.42 2 2
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.078 0.18 -10000 0 -0.35 132 132
BCAR1 0.029 0.014 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.02 0.15 -10000 0 -0.26 123 123
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.034 0.021 -10000 0 -0.42 1 1
IRS1/NCK2 -0.056 0.16 -10000 0 -0.29 143 143
GRB10 0.022 0.075 -10000 0 -0.42 14 14
PTPN11 -0.074 0.15 0.17 2 -0.3 143 145
IRS1 -0.077 0.16 -10000 0 -0.31 153 153
IRS2 -0.08 0.16 0.17 2 -0.31 143 145
IGF-1R heterotetramer/IGF1 -0.074 0.19 -10000 0 -0.37 141 141
GRB2 0.033 0.01 -10000 0 -10000 0 0
PDPK1 -0.077 0.14 0.18 13 -0.29 127 140
YWHAE 0.032 0.011 -10000 0 -10000 0 0
PRKD1 -0.075 0.2 0.21 5 -0.37 129 134
SHC1 0.027 0.025 -10000 0 -0.42 1 1
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.36 0.64 -10000 0 -1.3 130 130
STAT6 (cleaved dimer) -0.38 0.65 -10000 0 -1.3 140 140
IGHG1 -0.082 0.24 -10000 0 -0.56 27 27
IGHG3 -0.35 0.61 -10000 0 -1.2 143 143
AKT1 -0.12 0.33 -10000 0 -0.77 51 51
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.066 0.26 -10000 0 -0.77 28 28
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.14 0.36 -10000 0 -0.83 60 60
THY1 -0.37 0.66 -10000 0 -1.3 133 133
MYB -0.056 0.18 -10000 0 -0.42 98 98
HMGA1 0.033 0.029 -10000 0 -0.42 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.14 0.34 -10000 0 -0.66 95 95
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.12 0.33 -10000 0 -0.86 39 39
SP1 0.024 0.051 -10000 0 -0.2 6 6
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.019 0.056 -10000 0 -0.42 4 4
STAT6 (dimer)/ETS1 -0.37 0.64 -10000 0 -1.3 138 138
SOCS1 -0.2 0.38 -10000 0 -0.74 133 133
SOCS3 -0.12 0.32 -10000 0 -0.97 23 23
FCER2 -0.23 0.46 -10000 0 -0.93 101 101
PARP14 0.03 0.051 -10000 0 -0.42 6 6
CCL17 -0.42 0.71 -10000 0 -1.4 155 155
GRB2 0.033 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.075 0.26 -10000 0 -0.68 33 33
T cell proliferation -0.37 0.67 -10000 0 -1.3 139 139
IL4R/JAK1 -0.37 0.65 -10000 0 -1.3 135 135
EGR2 -0.41 0.7 -10000 0 -1.4 145 145
JAK2 -0.005 0.069 -10000 0 -0.46 2 2
JAK3 0.038 0.014 -10000 0 -10000 0 0
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
JAK1 0.018 0.049 -10000 0 -0.42 3 3
COL1A2 -0.22 0.53 -10000 0 -1.5 70 70
CCL26 -0.37 0.64 -10000 0 -1.3 139 139
IL4R -0.39 0.71 -10000 0 -1.4 136 136
PTPN6 0.021 0.045 -10000 0 -0.41 2 2
IL13RA2 -0.4 0.67 -10000 0 -1.3 152 152
IL13RA1 -0.009 0.087 -10000 0 -0.46 8 8
IRF4 -0.005 0.16 -10000 0 -1 5 5
ARG1 -0.065 0.26 -10000 0 -1.1 17 17
CBL -0.14 0.32 -10000 0 -0.63 93 93
GTF3A 0.024 0.045 -10000 0 -0.14 6 6
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
IL13RA1/JAK2 -0.002 0.1 -10000 0 -0.37 8 8
IRF4/BCL6 -0.005 0.16 -10000 0 -0.97 5 5
CD40LG 0.038 0.038 -10000 0 -0.42 3 3
MAPK14 -0.14 0.33 -10000 0 -0.67 79 79
mitosis -0.11 0.31 -10000 0 -0.72 51 51
STAT6 -0.47 0.88 -10000 0 -1.7 142 142
SPI1 0.032 0.055 -10000 0 -0.26 14 14
RPS6KB1 -0.092 0.3 -10000 0 -0.72 43 43
STAT6 (dimer) -0.47 0.88 -10000 0 -1.7 142 142
STAT6 (dimer)/PARP14 -0.41 0.73 -10000 0 -1.4 141 141
mast cell activation 0.005 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.14 0.34 -10000 0 -0.75 70 70
FRAP1 -0.12 0.33 -10000 0 -0.77 51 51
LTA -0.36 0.64 -10000 0 -1.3 136 136
FES 0.03 0.041 -10000 0 -0.42 4 4
T-helper 1 cell differentiation 0.43 0.78 1.5 142 -10000 0 142
CCL11 -0.4 0.66 -10000 0 -1.3 148 148
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.1 0.31 0.5 1 -0.83 34 35
IL2RG 0.033 0.043 -10000 0 -0.41 4 4
IL10 -0.33 0.65 -10000 0 -1.3 118 118
IRS1 -0.014 0.14 -10000 0 -0.42 54 54
IRS2 0.008 0.099 -10000 0 -0.42 25 25
IL4 -0.064 0.29 -10000 0 -1.3 19 19
IL5 -0.36 0.64 -10000 0 -1.3 136 136
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.26 0.51 -10000 0 -0.93 144 144
COL1A1 -0.26 0.59 -10000 0 -1.4 91 91
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.39 0.69 -10000 0 -1.4 137 137
IL2R gamma/JAK3 0.053 0.036 -10000 0 -0.29 4 4
TFF3 -0.53 0.76 -10000 0 -1.4 204 204
ALOX15 -0.37 0.65 -10000 0 -1.3 134 134
MYBL1 -0.012 0.13 -10000 0 -0.42 43 43
T-helper 2 cell differentiation -0.28 0.52 -10000 0 -0.98 141 141
SHC1 0.027 0.025 -10000 0 -0.42 1 1
CEBPB 0.028 0.056 -10000 0 -0.32 10 10
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.13 0.33 -10000 0 -0.77 54 54
mol:PI-3-4-5-P3 -0.12 0.33 -10000 0 -0.77 51 51
PI3K -0.13 0.35 -10000 0 -0.84 51 51
DOK2 0.01 0.085 -10000 0 -0.42 18 18
ETS1 0.014 0.044 -10000 0 -0.38 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.061 0.25 -10000 0 -0.62 30 30
ITGB3 -0.37 0.64 -10000 0 -1.3 134 134
PIGR -0.46 0.77 -10000 0 -1.4 174 174
IGHE 0.012 0.089 0.19 48 -0.22 10 58
MAPKKK cascade -0.059 0.24 -10000 0 -0.61 30 30
BCL6 0.017 0.085 -10000 0 -0.42 18 18
OPRM1 -0.36 0.64 -10000 0 -1.3 135 135
RETNLB -0.36 0.64 -10000 0 -1.3 136 136
SELP -0.42 0.75 -10000 0 -1.4 158 158
AICDA -0.36 0.62 -10000 0 -1.2 138 138
FOXM1 transcription factor network

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
NFATC3 -0.24 0.51 -9999 0 -1.2 82 82
PLK1 0.017 0.098 -9999 0 -1.1 3 3
BIRC5 -0.086 0.39 -9999 0 -1.4 41 41
HSPA1B -0.24 0.51 -9999 0 -1.1 96 96
MAP2K1 0.005 0.057 -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 94 94
XRCC1 -0.24 0.51 -9999 0 -1.2 83 83
FOXM1B/p19 -0.29 0.57 -9999 0 -1.3 93 93
Cyclin D1/CDK4 -0.29 0.52 -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 0.51 -9999 0 -1.2 78 78
CCNE1 0.023 0.05 -9999 0 -0.44 5 5
CKS1B -0.21 0.52 -9999 0 -1.2 81 81
RB1 -0.15 0.39 -9999 0 -1 63 63
FOXM1C/SP1 -0.29 0.62 -9999 0 -1.4 97 97
AURKB -0.083 0.32 -9999 0 -1 45 45
CENPF -0.23 0.56 -9999 0 -1.3 77 77
CDK4 0.015 0.038 -9999 0 -10000 0 0
MYC -0.23 0.44 -9999 0 -1 89 89
CHEK2 0.001 0.066 -9999 0 -0.45 3 3
ONECUT1 -0.27 0.52 -9999 0 -1.1 101 101
CDKN2A 0.014 0.075 -9999 0 -0.42 14 14
LAMA4 -0.24 0.52 -9999 0 -1.2 83 83
FOXM1B/HNF6 -0.34 0.65 -9999 0 -1.4 101 101
FOS -0.33 0.6 -9999 0 -1.2 131 131
SP1 0.033 0.024 -9999 0 -0.42 1 1
CDC25B -0.24 0.52 -9999 0 -1.2 83 83
response to radiation -0.004 0.031 -9999 0 -10000 0 0
CENPB -0.24 0.51 -9999 0 -1.2 79 79
CENPA -0.26 0.54 -9999 0 -1.2 86 86
NEK2 -0.26 0.58 -9999 0 -1.2 100 100
HIST1H2BA -0.24 0.52 -9999 0 -1.2 85 85
CCNA2 0.004 0.11 -9999 0 -0.44 28 28
EP300 0.033 0.022 -9999 0 -0.42 1 1
CCNB1/CDK1 -0.31 0.64 -9999 0 -1.5 85 85
CCNB2 -0.25 0.53 -9999 0 -1.2 85 85
CCNB1 -0.27 0.56 -9999 0 -1.3 85 85
ETV5 -0.24 0.52 -9999 0 -1.2 79 79
ESR1 -0.43 0.65 -9999 0 -1.2 203 203
CCND1 -0.32 0.52 -9999 0 -1.1 135 135
GSK3A 0.008 0.052 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.022 0.11 -9999 0 -0.33 29 29
CDK2 0.028 0.035 -9999 0 -0.43 2 2
G2/M transition of mitotic cell cycle -0.006 0.036 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.27 0.57 -9999 0 -1.3 93 93
GAS1 -0.32 0.59 -9999 0 -1.2 119 119
MMP2 -0.27 0.56 -9999 0 -1.3 94 94
RB1/FOXM1C -0.29 0.55 -9999 0 -1.1 110 110
CREBBP 0.032 0.011 -9999 0 -10000 0 0
Plasma membrane estrogen receptor signaling

Figure S8.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S8.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.007 0.13 -10000 0 -0.22 132 132
ER alpha/Gai/GDP/Gbeta gamma -0.12 0.21 -10000 0 -0.37 158 158
AKT1 -0.22 0.37 -10000 0 -0.74 164 164
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.22 0.37 -10000 0 -0.75 164 164
mol:Ca2+ -0.07 0.15 0.17 1 -0.43 58 59
IGF1R -0.043 0.17 -10000 0 -0.42 84 84
E2/ER alpha (dimer)/Striatin -0.037 0.13 -10000 0 -0.25 133 133
SHC1 0.027 0.025 -10000 0 -0.42 1 1
apoptosis 0.21 0.35 0.7 164 -10000 0 164
RhoA/GTP -0.039 0.11 -10000 0 -0.22 129 129
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.1 0.21 -10000 0 -0.38 150 150
regulation of stress fiber formation 0.041 0.1 0.33 7 -0.26 3 10
E2/ERA-ERB (dimer) -0.037 0.13 -10000 0 -0.25 130 130
KRAS 0.027 0.057 -10000 0 -0.42 8 8
G13/GTP -0.033 0.12 -10000 0 -0.23 124 124
pseudopodium formation -0.041 0.1 0.26 3 -0.33 7 10
E2/ER alpha (dimer)/PELP1 -0.038 0.13 -10000 0 -0.25 129 129
GRB2 0.033 0.01 -10000 0 -10000 0 0
GNG2 0.034 0.021 -10000 0 -0.42 1 1
GNAO1 0.03 0.014 -10000 0 -10000 0 0
HRAS 0.032 0.036 -10000 0 -0.42 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.14 0.24 0.24 1 -0.44 165 166
E2/ER beta (dimer) 0.025 0.006 -10000 0 -10000 0 0
mol:GDP -0.075 0.17 -10000 0 -0.34 136 136
mol:NADP -0.14 0.24 0.24 1 -0.44 165 166
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
mol:IP3 -0.073 0.15 -10000 0 -0.44 58 58
IGF-1R heterotetramer -0.043 0.17 -10000 0 -0.42 84 84
PLCB1 -0.071 0.16 -10000 0 -0.45 58 58
PLCB2 -0.052 0.15 -10000 0 -0.45 52 52
IGF1 -0.041 0.17 -10000 0 -0.42 80 80
mol:L-citrulline -0.14 0.24 0.24 1 -0.44 165 166
RHOA 0.026 0.061 -10000 0 -0.42 9 9
Gai/GDP -0.1 0.28 -10000 0 -0.63 100 100
JNK cascade 0.025 0.006 -10000 0 -10000 0 0
BCAR1 0.029 0.014 -10000 0 -10000 0 0
ESR2 0.034 0.008 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -10000 0 0
ESR1 -0.088 0.2 -10000 0 -0.42 130 130
Gq family/GDP/Gbeta gamma -0.019 0.17 -10000 0 -0.67 23 23
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.034 0.13 -10000 0 -0.57 7 7
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.089 0.19 -10000 0 -0.38 122 122
GNAZ 0.024 0.067 -10000 0 -0.42 11 11
E2/ER alpha (dimer) -0.061 0.14 -10000 0 -0.3 130 130
STRN 0.031 0.046 -10000 0 -0.42 5 5
GNAL 0.031 0.036 -10000 0 -0.42 3 3
PELP1 0.032 0.011 -10000 0 -10000 0 0
MAPK11 0.016 0.006 -10000 0 -10000 0 0
GNAI2 0.027 0.057 -10000 0 -0.42 8 8
GNAI3 0.035 0.006 -10000 0 -10000 0 0
GNAI1 0.017 0.085 -10000 0 -0.42 18 18
HBEGF -0.11 0.21 0.32 8 -0.48 64 72
cAMP biosynthetic process -0.028 0.1 -10000 0 -0.21 127 127
SRC -0.11 0.2 0.26 2 -0.35 157 159
PI3K 0.035 0.067 -10000 0 -0.3 18 18
GNB1 0.032 0.045 -10000 0 -0.42 5 5
G13/GDP/Gbeta gamma -0.05 0.17 -10000 0 -0.33 116 116
SOS1 0.034 0.021 -10000 0 -0.42 1 1
IGF-1R heterotetramer/IGF1 -0.13 0.19 -10000 0 -0.4 147 147
Gs family/GTP -0.022 0.11 -10000 0 -0.21 127 127
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.053 0.054 -10000 0 -0.23 15 15
vasodilation -0.13 0.22 0.24 1 -0.42 165 166
mol:DAG -0.073 0.15 -10000 0 -0.44 58 58
Gs family/GDP/Gbeta gamma -0.065 0.15 -10000 0 -0.32 112 112
MSN -0.044 0.11 0.26 3 -0.34 8 11
Gq family/GTP -0.053 0.15 -10000 0 -0.44 59 59
mol:PI-3-4-5-P3 -0.21 0.36 -10000 0 -0.72 164 164
NRAS 0.029 0.05 -10000 0 -0.42 6 6
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.13 0.22 0.42 165 -0.24 1 166
GRB2/SOS1 0.047 0.023 -10000 0 -0.3 1 1
RhoA/GDP -0.061 0.17 -10000 0 -0.32 142 142
NOS3 -0.14 0.25 0.25 1 -0.47 165 166
GNA11 0.032 0.036 -10000 0 -0.42 3 3
MAPKKK cascade -0.14 0.27 -10000 0 -0.52 157 157
E2/ER alpha (dimer)/PELP1/Src -0.11 0.21 0.25 1 -0.39 153 154
ruffle organization -0.041 0.1 0.26 3 -0.33 7 10
ROCK2 -0.041 0.12 0.33 2 -0.36 8 10
GNA14 -0.01 0.13 -10000 0 -0.42 44 44
GNA15 0.029 0.046 -10000 0 -0.42 5 5
GNA13 0.028 0.042 -10000 0 -0.42 4 4
MMP9 -0.12 0.21 0.37 10 -0.48 65 75
MMP2 -0.11 0.2 0.26 3 -0.47 63 66
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 0.034 0.034 -10000 0 -0.26 4 4
NFATC2 -0.051 0.21 -10000 0 -0.52 47 47
NFATC3 -0.018 0.12 -10000 0 -0.26 73 73
CD40LG -0.19 0.38 -10000 0 -0.76 128 128
ITCH 0.012 0.071 -10000 0 -10000 0 0
CBLB 0.013 0.074 -10000 0 -0.22 42 42
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.14 0.33 -10000 0 -0.82 67 67
JUNB 0.032 0.041 -10000 0 -0.42 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.087 -10000 0 -0.26 45 45
T cell anergy -0.016 0.12 0.26 2 -0.36 45 47
TLE4 -0.044 0.17 -10000 0 -0.49 41 41
Jun/NFAT1-c-4/p21SNFT -0.17 0.39 -10000 0 -0.79 119 119
AP-1/NFAT1-c-4 -0.19 0.45 -10000 0 -0.86 127 127
IKZF1 -0.038 0.14 -10000 0 -0.36 47 47
T-helper 2 cell differentiation -0.17 0.3 -10000 0 -0.74 79 79
AP-1/NFAT1 -0.045 0.2 -10000 0 -0.4 81 81
CALM1 0.027 0.058 -10000 0 -0.16 43 43
EGR2 -0.22 0.48 -10000 0 -1.2 79 79
EGR3 -0.29 0.55 -10000 0 -1.1 138 138
NFAT1/FOXP3 -0.017 0.16 -10000 0 -0.4 40 40
EGR1 -0.038 0.16 -10000 0 -0.42 75 75
JUN -0.003 0.12 -10000 0 -0.42 39 39
EGR4 0 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.006 0.046 -10000 0 -0.15 46 46
GBP3 -0.088 0.25 -10000 0 -0.64 74 74
FOSL1 0.035 0.007 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 -0.15 0.39 -10000 0 -0.77 122 122
DGKA -0.04 0.16 -10000 0 -0.44 38 38
CREM 0.034 0.008 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.18 0.4 -10000 0 -0.8 122 122
CTLA4 -0.026 0.14 -10000 0 -0.41 28 28
NFAT1-c-4 (dimer)/EGR1 -0.19 0.42 -10000 0 -0.84 130 130
NFAT1-c-4 (dimer)/EGR4 -0.17 0.39 -10000 0 -0.78 123 123
FOS -0.034 0.15 -10000 0 -0.42 66 66
IFNG -0.2 0.43 -10000 0 -1.1 77 77
T cell activation -0.1 0.26 -10000 0 -0.71 38 38
MAF 0.016 0.075 -10000 0 -0.42 14 14
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.15 0.34 0.69 115 -10000 0 115
TNF -0.19 0.37 -10000 0 -0.76 131 131
FASLG -0.34 0.64 -10000 0 -1.2 155 155
TBX21 -0.046 0.17 -10000 0 -0.4 92 92
BATF3 0 0.001 -10000 0 -10000 0 0
PRKCQ 0.021 0.061 -10000 0 -0.29 13 13
PTPN1 -0.037 0.15 -10000 0 -0.41 38 38
NFAT1-c-4/ICER1 -0.16 0.39 -10000 0 -0.78 121 121
GATA3 -0.047 0.18 -10000 0 -0.42 90 90
T-helper 1 cell differentiation -0.19 0.41 -10000 0 -1 78 78
IL2RA -0.14 0.33 -10000 0 -0.78 74 74
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.035 0.14 -10000 0 -0.44 24 24
E2F1 0.032 0.054 -10000 0 -0.42 7 7
PPARG 0.012 0.091 -10000 0 -0.42 21 21
SLC3A2 -0.035 0.14 -10000 0 -0.41 32 32
IRF4 0.031 0.031 -10000 0 -0.42 2 2
PTGS2 -0.18 0.36 -10000 0 -0.77 107 107
CSF2 -0.19 0.38 -10000 0 -0.76 129 129
JunB/Fra1/NFAT1-c-4 -0.15 0.39 -10000 0 -0.76 120 120
IL4 -0.17 0.32 -10000 0 -0.79 75 75
IL5 -0.19 0.38 -10000 0 -0.76 128 128
IL2 -0.1 0.26 -10000 0 -0.74 35 35
IL3 -0.013 0.14 -10000 0 -0.88 9 9
RNF128 -0.017 0.16 -10000 0 -0.51 45 45
NFATC1 -0.16 0.34 -10000 0 -0.7 115 115
CDK4 0.1 0.21 0.58 30 -10000 0 30
PTPRK -0.067 0.22 -10000 0 -0.6 61 61
IL8 -0.2 0.38 -10000 0 -0.77 128 128
POU2F1 0.034 0.017 -10000 0 -10000 0 0
EGFR-dependent Endothelin 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
HRAS 0.032 0.036 -10000 0 -0.42 3 3
EGFR -0.013 0.13 -10000 0 -0.42 47 47
EGF/EGFR -0.074 0.18 -10000 0 -0.27 200 200
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.002 0.13 -10000 0 -0.23 104 104
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA -0.004 0.13 -10000 0 -0.42 43 43
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.069 0.19 -10000 0 -0.42 110 110
EGF/EGFR dimer/SHC -0.03 0.14 -10000 0 -0.26 120 120
mol:GDP -0.006 0.12 -10000 0 -0.23 104 104
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.038 0.16 -10000 0 -0.42 77 77
GRB2/SOS1 0.047 0.023 -10000 0 -0.3 1 1
HRAS/GTP -0.018 0.11 -10000 0 -0.22 106 106
SHC1 0.027 0.025 -10000 0 -0.42 1 1
HRAS/GDP -0.007 0.12 -10000 0 -0.22 106 106
FRAP1 -0.016 0.14 0.37 13 -0.4 4 17
EGF/EGFR dimer -0.061 0.16 -10000 0 -0.31 151 151
SOS1 0.034 0.021 -10000 0 -0.42 1 1
GRB2 0.033 0.01 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.03 0.16 -10000 0 -0.33 104 104
Glucocorticoid receptor regulatory 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
PCK2 0.054 0.15 0.35 1 -0.82 9 10
SMARCC2 0.036 0.004 -10000 0 -10000 0 0
SMARCC1 0.032 0.03 -10000 0 -0.42 2 2
TBX21 -0.15 0.28 0.36 1 -0.65 107 108
SUMO2 0.028 0.02 -10000 0 -10000 0 0
STAT1 (dimer) 0.019 0.093 -10000 0 -0.38 24 24
FKBP4 0.029 0.046 -10000 0 -0.42 5 5
FKBP5 -0.004 0.13 -10000 0 -0.42 42 42
GR alpha/HSP90/FKBP51/HSP90 0.06 0.14 0.25 112 -0.25 27 139
PRL -0.035 0.13 -10000 0 -0.97 2 2
cortisol/GR alpha (dimer)/TIF2 0.13 0.24 0.52 112 -10000 0 112
RELA -0.022 0.11 -10000 0 -0.22 68 68
FGG 0.14 0.23 0.45 135 -0.38 1 136
GR beta/TIF2 0.069 0.14 0.28 98 -0.29 9 107
IFNG -0.27 0.41 -10000 0 -0.86 126 126
apoptosis -0.004 0.17 0.5 5 -0.5 10 15
CREB1 0.038 0.042 -10000 0 -0.37 5 5
histone acetylation -0.025 0.11 0.31 4 -0.32 36 40
BGLAP -0.048 0.14 -10000 0 -0.53 11 11
GR/PKAc 0.11 0.12 0.32 54 -0.27 13 67
NF kappa B1 p50/RelA -0.043 0.19 -10000 0 -0.33 129 129
SMARCD1 0.036 0.004 -10000 0 -10000 0 0
MDM2 0.072 0.1 0.22 133 -10000 0 133
GATA3 -0.039 0.18 -10000 0 -0.42 90 90
AKT1 0.029 0.042 0.19 9 -0.43 3 12
CSF2 -0.05 0.13 -10000 0 -0.86 5 5
GSK3B 0.029 0.02 -10000 0 -10000 0 0
NR1I3 0.03 0.18 0.52 6 -0.61 8 14
CSN2 0.12 0.19 0.38 128 -0.39 3 131
BRG1/BAF155/BAF170/BAF60A 0.083 0.036 -10000 0 -0.24 3 3
NFATC1 0.022 0.09 -10000 0 -0.4 21 21
POU2F1 0.033 0.021 -10000 0 -0.25 1 1
CDKN1A -0.046 0.26 -10000 0 -1.5 13 13
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.001 0.006 -10000 0 -10000 0 0
SFN 0.011 0.099 -10000 0 -0.42 25 25
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.068 0.14 0.29 59 -0.23 44 103
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.078 0.31 0.46 4 -0.77 78 82
JUN -0.16 0.23 0.36 4 -0.46 144 148
IL4 -0.087 0.19 -10000 0 -0.48 57 57
CDK5R1 0.032 0.01 -10000 0 -10000 0 0
PRKACA 0.036 0.004 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.097 0.21 0.21 72 -0.37 146 218
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.085 0.13 0.29 68 -0.23 32 100
cortisol/GR alpha (monomer) 0.19 0.31 0.6 150 -0.38 2 152
NCOA2 0.025 0.047 -10000 0 -0.42 5 5
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.083 0.16 -10000 0 -0.44 70 70
AP-1/NFAT1-c-4 -0.27 0.37 -10000 0 -0.71 178 178
AFP -0.12 0.2 -10000 0 -0.7 14 14
SUV420H1 0.033 0.022 -10000 0 -0.42 1 1
IRF1 0.093 0.21 0.41 62 -0.69 14 76
TP53 0.015 0.12 -10000 0 -0.46 31 31
PPP5C 0.031 0.041 -10000 0 -0.42 4 4
KRT17 -0.39 0.56 -10000 0 -1.2 149 149
KRT14 -0.26 0.49 -10000 0 -1.2 97 97
TBP 0.04 0.018 -10000 0 -0.28 1 1
CREBBP 0.065 0.096 0.28 78 -10000 0 78
HDAC1 0.03 0.021 -10000 0 -0.43 1 1
HDAC2 0.03 0.023 -10000 0 -0.42 1 1
AP-1 -0.28 0.37 -10000 0 -0.71 179 179
MAPK14 0.031 0.016 -10000 0 -10000 0 0
MAPK10 0.008 0.091 -10000 0 -0.42 21 21
MAPK11 0.027 0.02 -10000 0 -10000 0 0
KRT5 -0.39 0.57 -10000 0 -1.2 150 150
interleukin-1 receptor activity -0.001 0.006 -10000 0 -10000 0 0
NCOA1 0.031 0.048 -10000 0 -0.42 5 5
STAT1 0.019 0.093 -10000 0 -0.38 24 24
CGA -0.072 0.17 -10000 0 -0.57 26 26
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.082 0.16 0.37 87 -0.36 3 90
MAPK3 0.026 0.028 -10000 0 -0.42 1 1
MAPK1 0.029 0.026 -10000 0 -0.42 1 1
ICAM1 -0.16 0.31 -10000 0 -0.68 101 101
NFKB1 -0.024 0.11 -10000 0 -0.21 89 89
MAPK8 -0.11 0.19 0.48 2 -0.38 127 129
MAPK9 0.014 0.087 -10000 0 -0.42 19 19
cortisol/GR alpha (dimer) -0.006 0.18 0.5 5 -0.52 10 15
BAX -0.011 0.1 -10000 0 -10000 0 0
POMC -0.092 0.2 0.5 1 -1.2 5 6
EP300 0.066 0.097 0.28 84 -0.43 1 85
cortisol/GR alpha (dimer)/p53 0.12 0.25 0.52 109 -0.37 1 110
proteasomal ubiquitin-dependent protein catabolic process 0.053 0.11 0.25 80 -10000 0 80
SGK1 0.081 0.14 0.33 94 -0.42 2 96
IL13 -0.22 0.26 -10000 0 -0.66 83 83
IL6 -0.2 0.38 -10000 0 -0.89 96 96
PRKACG 0.034 0.029 -10000 0 -0.42 2 2
IL5 -0.18 0.22 -10000 0 -0.62 48 48
IL2 -0.22 0.33 -10000 0 -0.72 121 121
CDK5 0.034 0.007 -10000 0 -10000 0 0
PRKACB 0.009 0.097 -10000 0 -0.42 24 24
HSP90AA1 0 0 -10000 0 -10000 0 0
IL8 -0.18 0.34 -10000 0 -0.79 98 98
CDK5R1/CDK5 0.046 0.017 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.004 0.18 -10000 0 -0.34 66 66
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.16 0.24 0.49 144 -10000 0 144
SMARCA4 0.034 0.021 -10000 0 -0.42 1 1
chromatin remodeling 0.11 0.16 0.33 134 -10000 0 134
NF kappa B1 p50/RelA/Cbp 0.022 0.18 0.35 39 -0.36 40 79
JUN (dimer) -0.16 0.23 0.36 4 -0.46 143 147
YWHAH 0.031 0.036 -10000 0 -0.42 3 3
VIPR1 -0.1 0.21 -10000 0 -0.58 58 58
NR3C1 0.12 0.21 0.39 142 -0.39 8 150
NR4A1 0.037 0.045 -10000 0 -0.44 4 4
TIF2/SUV420H1 0.036 0.046 -10000 0 -0.35 5 5
MAPKKK cascade -0.004 0.17 0.5 5 -0.5 10 15
cortisol/GR alpha (dimer)/Src-1 0.18 0.26 0.52 150 -0.36 1 151
PBX1 0.019 0.077 -10000 0 -0.41 15 15
POU1F1 0.039 0.025 -10000 0 -0.33 2 2
SELE -0.24 0.42 -10000 0 -0.92 126 126
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.11 0.16 0.33 134 -10000 0 134
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.16 0.24 0.49 144 -10000 0 144
mol:cortisol 0.11 0.18 0.35 151 -10000 0 151
MMP1 -0.37 0.54 -10000 0 -1.1 165 165
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 0.035 0.021 -10000 0 -0.42 1 1
CCL5 -0.013 0.14 -10000 0 -0.42 51 51
SDCBP 0.022 0.061 -10000 0 -0.42 9 9
FGFR/FGF2/Syndecan-1 -0.11 0.23 0.22 6 -0.54 88 94
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.11 0.22 -10000 0 -0.52 88 88
Syndecan-1/Syntenin -0.11 0.22 0.26 1 -0.5 91 92
MAPK3 -0.097 0.2 0.24 1 -0.47 89 90
HGF/MET 0.041 0.057 -10000 0 -0.3 13 13
TGFB1/TGF beta receptor Type II 0.035 0.021 -10000 0 -0.42 1 1
BSG 0.034 0.008 -10000 0 -10000 0 0
keratinocyte migration -0.11 0.22 -10000 0 -0.51 88 88
Syndecan-1/RANTES -0.13 0.24 0.26 1 -0.5 112 113
Syndecan-1/CD147 -0.096 0.23 0.27 1 -0.5 91 92
Syndecan-1/Syntenin/PIP2 -0.1 0.21 0.25 1 -0.48 91 92
LAMA5 0.026 0.051 -10000 0 -0.42 6 6
positive regulation of cell-cell adhesion -0.1 0.21 0.24 1 -0.47 91 92
MMP7 -0.033 0.16 -10000 0 -0.42 69 69
HGF 0.028 0.057 -10000 0 -0.42 8 8
Syndecan-1/CASK -0.12 0.22 -10000 0 -0.51 92 92
Syndecan-1/HGF/MET -0.1 0.23 0.27 1 -0.49 94 95
regulation of cell adhesion -0.1 0.19 0.23 1 -0.46 87 88
HPSE 0.014 0.093 -10000 0 -0.42 22 22
positive regulation of cell migration -0.11 0.23 0.22 6 -0.54 88 94
SDC1 -0.11 0.23 0.28 1 -0.55 88 89
Syndecan-1/Collagen -0.11 0.23 0.22 6 -0.54 88 94
PPIB 0.033 0.03 -10000 0 -0.42 2 2
MET 0.029 0.046 -10000 0 -0.42 5 5
PRKACA 0.036 0.004 -10000 0 -10000 0 0
MMP9 -0.014 0.14 -10000 0 -0.42 52 52
MAPK1 -0.1 0.21 0.24 1 -0.47 91 92
homophilic cell adhesion -0.12 0.22 0.22 6 -0.53 88 94
MMP1 -0.076 0.18 -10000 0 -0.42 109 109
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.058 0.35 -9999 0 -0.74 70 70
HDAC7 0 0.003 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.011 0.34 -9999 0 -0.72 52 52
SMAD4 0.029 0.054 -9999 0 -0.42 7 7
ID2 -0.058 0.35 -9999 0 -0.73 73 73
AP1 -0.035 0.16 -9999 0 -0.35 89 89
ABCG2 -0.061 0.35 -9999 0 -0.76 70 70
HIF1A -0.023 0.16 -9999 0 -0.47 47 47
TFF3 -0.11 0.37 -9999 0 -0.75 85 85
GATA2 0.018 0.054 -9999 0 -0.42 5 5
AKT1 0.009 0.093 -9999 0 -0.25 14 14
response to hypoxia -0.008 0.065 -9999 0 -0.15 32 32
MCL1 -0.06 0.35 -9999 0 -0.73 73 73
NDRG1 -0.069 0.33 -9999 0 -0.76 63 63
SERPINE1 -0.065 0.36 -9999 0 -0.75 73 73
FECH -0.065 0.36 -9999 0 -0.75 73 73
FURIN -0.061 0.35 -9999 0 -0.73 74 74
NCOA2 0.026 0.047 -9999 0 -0.42 5 5
EP300 0.007 0.11 -9999 0 -0.3 27 27
HMOX1 -0.07 0.36 -9999 0 -0.76 74 74
BHLHE40 -0.08 0.34 -9999 0 -0.72 74 74
BHLHE41 -0.08 0.34 -9999 0 -0.72 74 74
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.049 0.17 -9999 0 -0.33 44 44
ENG -0.009 0.13 -9999 0 -0.31 42 42
JUN -0.009 0.12 -9999 0 -0.43 39 39
RORA -0.068 0.36 -9999 0 -0.74 74 74
ABCB1 -0.03 0.25 -9999 0 -0.95 28 28
TFRC -0.075 0.36 -9999 0 -0.76 76 76
CXCR4 -0.071 0.37 -9999 0 -0.75 80 80
TF -0.059 0.35 -9999 0 -0.75 68 68
CITED2 -0.061 0.35 -9999 0 -0.75 69 69
HIF1A/ARNT -0.039 0.42 -9999 0 -0.88 60 60
LDHA 0.009 0.19 -9999 0 -0.86 17 17
ETS1 -0.069 0.34 -9999 0 -0.75 68 68
PGK1 -0.056 0.35 -9999 0 -0.74 71 71
NOS2 -0.08 0.34 -9999 0 -0.72 74 74
ITGB2 -0.067 0.36 -9999 0 -0.75 76 76
ALDOA -0.054 0.35 -9999 0 -0.76 64 64
Cbp/p300/CITED2 -0.058 0.36 -9999 0 -0.82 59 59
FOS -0.039 0.15 -9999 0 -0.43 66 66
HK2 -0.058 0.35 -9999 0 -0.75 68 68
SP1 0.035 0.039 -9999 0 -0.17 11 11
GCK 0.013 0.18 -9999 0 -1.2 4 4
HK1 -0.056 0.35 -9999 0 -0.75 68 68
NPM1 -0.056 0.35 -9999 0 -0.74 70 70
EGLN1 -0.068 0.33 -9999 0 -0.75 63 63
CREB1 0.039 0.027 -9999 0 -0.22 3 3
PGM1 -0.062 0.35 -9999 0 -0.73 74 74
SMAD3 0.027 0.061 -9999 0 -0.42 9 9
EDN1 -0.18 0.47 -9999 0 -1.2 87 87
IGFBP1 -0.057 0.35 -9999 0 -0.74 70 70
VEGFA -0.044 0.27 -9999 0 -0.6 58 58
HIF1A/JAB1 0.002 0.12 -9999 0 -0.34 42 42
CP -0.12 0.38 -9999 0 -0.79 86 86
CXCL12 -0.074 0.37 -9999 0 -0.77 79 79
COPS5 0.027 0.043 -9999 0 -0.42 4 4
SMAD3/SMAD4 0.04 0.063 -9999 0 -0.3 16 16
BNIP3 -0.064 0.36 -9999 0 -0.75 71 71
EGLN3 -0.083 0.37 -9999 0 -0.77 82 82
CA9 -0.063 0.35 -9999 0 -0.74 70 70
TERT -0.058 0.35 -9999 0 -0.76 67 67
ENO1 -0.059 0.35 -9999 0 -0.76 67 67
PFKL -0.059 0.35 -9999 0 -0.75 70 70
NCOA1 0.031 0.046 -9999 0 -0.42 5 5
ADM -0.082 0.38 -9999 0 -0.77 83 83
ARNT 0.014 0.077 -9999 0 -10000 0 0
HNF4A 0.034 0.033 -9999 0 -0.25 5 5
ADFP -0.067 0.36 -9999 0 -0.77 73 73
SLC2A1 -0.032 0.28 -9999 0 -0.61 56 56
LEP -0.077 0.36 -9999 0 -0.75 73 73
HIF1A/ARNT/Cbp/p300 -0.025 0.34 -9999 0 -0.73 55 55
EPO -0.029 0.27 -9999 0 -0.72 37 37
CREBBP 0.015 0.097 -9999 0 -0.29 16 16
HIF1A/ARNT/Cbp/p300/HDAC7 -0.024 0.33 -9999 0 -0.71 53 53
PFKFB3 -0.061 0.35 -9999 0 -0.76 68 68
NT5E -0.06 0.36 -9999 0 -0.75 72 72
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.029 0.05 -10000 0 -0.42 6 6
LAT2 -0.049 0.14 -10000 0 -0.31 85 85
AP1 -0.059 0.21 0.29 1 -0.47 71 72
mol:PIP3 -0.023 0.19 0.31 23 -0.37 78 101
IKBKB 0.013 0.14 0.25 54 -0.24 43 97
AKT1 0.014 0.18 0.33 79 -0.37 24 103
IKBKG -0.007 0.12 0.19 58 -0.24 46 104
MS4A2 -0.076 0.19 -10000 0 -0.41 120 120
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
MAP3K1 -0.039 0.17 0.25 12 -0.39 60 72
mol:Ca2+ -0.011 0.16 0.26 30 -0.32 52 82
LYN 0.031 0.018 -10000 0 -10000 0 0
CBLB -0.048 0.13 -10000 0 -0.31 84 84
SHC1 0.027 0.025 -10000 0 -0.42 1 1
RasGAP/p62DOK 0.034 0.095 -10000 0 -0.25 47 47
positive regulation of cell migration -0.007 0.066 -10000 0 -0.3 25 25
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.003 0.18 0.31 78 -0.26 91 169
PTPN13 -0.068 0.2 -10000 0 -0.54 45 45
PTPN11 0.033 0.024 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.003 0.15 0.32 23 -0.32 31 54
SYK 0.007 0.12 -10000 0 -0.43 33 33
GRB2 0.033 0.011 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.056 0.16 -10000 0 -0.37 85 85
LAT -0.046 0.13 -10000 0 -0.3 83 83
PAK2 -0.033 0.17 0.26 12 -0.42 51 63
NFATC2 -0.012 0.066 -10000 0 -0.59 4 4
HRAS -0.034 0.18 0.27 14 -0.44 51 65
GAB2 0.031 0.013 -10000 0 -10000 0 0
PLA2G1B 0.008 0.12 -10000 0 -0.92 7 7
Fc epsilon R1 -0.03 0.16 -10000 0 -0.31 109 109
Antigen/IgE/Fc epsilon R1 -0.025 0.14 -10000 0 -0.27 109 109
mol:GDP -0.051 0.18 0.25 1 -0.48 51 52
JUN -0.001 0.12 -10000 0 -0.42 39 39
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
FOS -0.031 0.15 -10000 0 -0.42 66 66
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.044 0.14 -10000 0 -0.32 85 85
CHUK -0.01 0.12 0.19 53 -0.25 50 103
KLRG1 -0.039 0.12 -10000 0 -0.37 39 39
VAV1 -0.051 0.14 -10000 0 -0.32 86 86
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.047 0.13 -10000 0 -0.31 82 82
negative regulation of mast cell degranulation -0.041 0.11 -10000 0 -0.35 38 38
BTK -0.057 0.18 -10000 0 -0.52 47 47
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.063 0.18 -10000 0 -0.34 117 117
GAB2/PI3K/SHP2 -0.053 0.1 -10000 0 -0.3 51 51
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.048 0.13 -10000 0 -0.26 108 108
RAF1 0.009 0.13 -10000 0 -1 7 7
Fc epsilon R1/FcgammaRIIB/SHIP -0.025 0.16 -10000 0 -0.29 116 116
FCER1G 0.032 0.019 -10000 0 -10000 0 0
FCER1A -0.023 0.14 -10000 0 -0.43 55 55
Antigen/IgE/Fc epsilon R1/Fyn -0.015 0.14 -10000 0 -0.26 106 106
MAPK3 0.008 0.12 -10000 0 -0.95 7 7
MAPK1 0.003 0.12 -10000 0 -0.92 7 7
NFKB1 0.035 0.005 -10000 0 -10000 0 0
MAPK8 -0.039 0.22 -10000 0 -0.65 43 43
DUSP1 0.001 0.12 -10000 0 -0.42 35 35
NF-kappa-B/RelA 0.011 0.084 0.16 31 -0.16 31 62
actin cytoskeleton reorganization -0.042 0.18 -10000 0 -0.52 34 34
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.027 0.18 -10000 0 -0.43 49 49
FER -0.046 0.13 -10000 0 -0.31 84 84
RELA 0.035 0.006 -10000 0 -10000 0 0
ITK -0.032 0.11 -10000 0 -0.39 39 39
SOS1 0.035 0.021 -10000 0 -0.42 1 1
PLCG1 -0.039 0.19 0.26 6 -0.47 51 57
cytokine secretion -0.003 0.051 -10000 0 -0.13 12 12
SPHK1 -0.054 0.14 -10000 0 -0.32 84 84
PTK2 -0.045 0.19 -10000 0 -0.55 33 33
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.057 0.17 -10000 0 -0.38 86 86
EDG1 -0.007 0.066 -10000 0 -0.3 25 25
mol:DAG -0.028 0.19 0.31 18 -0.43 54 72
MAP2K2 0.003 0.12 -10000 0 -0.94 7 7
MAP2K1 0.005 0.12 -10000 0 -0.94 7 7
MAP2K7 0.034 0.021 -10000 0 -0.42 1 1
KLRG1/SHP2 -0.025 0.12 0.25 1 -0.36 33 34
MAP2K4 -0.097 0.35 -10000 0 -0.93 75 75
Fc epsilon R1/FcgammaRIIB -0.026 0.17 -10000 0 -0.31 116 116
mol:Choline -0.002 0.18 0.31 78 -0.26 91 169
SHC/Grb2/SOS1 -0.011 0.14 -10000 0 -0.38 34 34
FYN 0.027 0.05 -10000 0 -0.42 6 6
DOK1 0.027 0.061 -10000 0 -0.42 9 9
PXN -0.043 0.18 -10000 0 -0.5 34 34
HCLS1 -0.051 0.14 -10000 0 -0.32 87 87
PRKCB -0.015 0.15 0.25 30 -0.32 50 80
FCGR2B 0.002 0.11 -10000 0 -0.42 29 29
IGHE 0.001 0.009 -10000 0 -10000 0 0
KLRG1/SHIP -0.042 0.12 -10000 0 -0.35 38 38
LCP2 0.023 0.07 -10000 0 -0.42 12 12
PLA2G4A -0.052 0.14 -10000 0 -0.32 88 88
RASA1 0.028 0.054 -10000 0 -0.42 7 7
mol:Phosphatidic acid -0.002 0.18 0.31 78 -0.26 91 169
IKK complex 0.012 0.12 0.24 49 -0.2 31 80
WIPF1 0 0 -10000 0 -10000 0 0
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 0.003 0.17 0.24 40 -0.34 70 110
FYN -0.039 0.2 0.28 5 -0.42 80 85
LAT/GRAP2/SLP76 -0.021 0.17 0.24 10 -0.35 82 92
IKBKB 0.029 0.014 -10000 0 -10000 0 0
AKT1 -0.027 0.15 0.25 15 -0.31 83 98
B2M 0.025 0.065 -10000 0 -0.43 10 10
IKBKG 0 0.056 0.13 20 -0.13 27 47
MAP3K8 0.003 0.11 -10000 0 -0.42 32 32
mol:Ca2+ -0.017 0.02 0.089 1 -0.058 70 71
integrin-mediated signaling pathway 0.029 0.048 -10000 0 -0.25 12 12
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.053 0.2 0.26 2 -0.43 89 91
TRPV6 -0.03 0.22 1.2 9 -0.42 59 68
CD28 -0.002 0.12 -10000 0 -0.43 38 38
SHC1 -0.022 0.2 0.24 47 -0.39 84 131
receptor internalization -0.07 0.2 -10000 0 -0.4 125 125
PRF1 -0.052 0.22 -10000 0 -0.88 22 22
KRAS 0.027 0.057 -10000 0 -0.42 8 8
GRB2 0.033 0.01 -10000 0 -10000 0 0
COT/AKT1 -0.016 0.14 0.24 14 -0.28 77 91
LAT -0.043 0.19 0.24 14 -0.38 95 109
EntrezGene:6955 0 0.003 -10000 0 -0.016 8 8
CD3D 0.016 0.074 -10000 0 -0.43 13 13
CD3E 0.031 0.015 -10000 0 -10000 0 0
CD3G -0.022 0.14 -10000 0 -0.43 54 54
RASGRP2 -0.001 0.044 -10000 0 -0.17 28 28
RASGRP1 -0.043 0.17 0.28 4 -0.34 93 97
HLA-A 0.017 0.089 -10000 0 -0.43 19 19
RASSF5 0.019 0.061 -10000 0 -0.42 9 9
RAP1A/GTP/RAPL 0.03 0.049 -10000 0 -0.25 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.067 0.14 37 -0.12 29 66
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.022 0.071 -10000 0 -0.18 58 58
PRKCA -0.01 0.092 0.18 17 -0.22 47 64
GRAP2 0.032 0.023 -10000 0 -0.42 1 1
mol:IP3 -0.021 0.14 0.21 33 -0.31 64 97
EntrezGene:6957 0 0.004 0.011 2 -0.021 8 10
TCR/CD3/MHC I/CD8 -0.032 0.15 -10000 0 -0.36 65 65
ORAI1 0.007 0.16 0.48 2 -1 9 11
CSK -0.047 0.18 0.26 2 -0.39 87 89
B7 family/CD28 -0.03 0.22 0.29 1 -0.47 77 78
CHUK 0.025 0.067 -10000 0 -0.42 11 11
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.061 0.21 0.26 1 -0.42 104 105
PTPN6 -0.055 0.19 0.24 4 -0.39 94 98
VAV1 -0.06 0.2 0.26 2 -0.41 102 104
Monovalent TCR/CD3 -0.018 0.11 -10000 0 -0.3 61 61
CBL 0.031 0.012 -10000 0 -10000 0 0
LCK -0.048 0.21 0.25 5 -0.44 86 91
PAG1 -0.032 0.19 0.23 12 -0.39 87 99
RAP1A 0.03 0.05 -10000 0 -0.42 6 6
TCR/CD3/MHC I/CD8/LCK -0.063 0.21 0.28 1 -0.42 105 106
CD80 0.033 0.022 -10000 0 -0.42 1 1
CD86 0.016 0.092 -10000 0 -0.43 21 21
PDK1/CARD11/BCL10/MALT1 -0.015 0.091 -10000 0 -0.21 61 61
HRAS 0.032 0.036 -10000 0 -0.42 3 3
GO:0035030 -0.054 0.17 0.25 1 -0.4 79 80
CD8A 0 0.003 0.011 2 -0.018 8 10
CD8B 0 0.004 0.011 3 -0.015 17 20
PTPRC 0.005 0.098 -10000 0 -0.43 24 24
PDK1/PKC theta -0.029 0.18 0.31 22 -0.37 81 103
CSK/PAG1 -0.027 0.18 0.23 11 -0.4 73 84
SOS1 0.034 0.021 -10000 0 -0.42 1 1
peptide-MHC class I 0.031 0.091 -10000 0 -0.35 25 25
GRAP2/SLP76 -0.035 0.2 0.29 1 -0.38 98 99
STIM1 0.006 0.092 1.3 2 -10000 0 2
RAS family/GTP 0.012 0.086 0.18 7 -0.18 36 43
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.074 0.21 -10000 0 -0.41 125 125
mol:DAG -0.042 0.11 0.12 1 -0.26 84 85
RAP1A/GDP 0.011 0.035 0.076 18 -0.07 17 35
PLCG1 0.033 0.009 -10000 0 -10000 0 0
CD247 0 0.003 -10000 0 -0.016 8 8
cytotoxic T cell degranulation -0.049 0.21 -10000 0 -0.83 22 22
RAP1A/GTP 0 0.018 -10000 0 -0.065 33 33
mol:PI-3-4-5-P3 -0.042 0.17 0.23 3 -0.36 89 92
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.021 0.17 0.24 24 -0.39 64 88
NRAS 0.029 0.05 -10000 0 -0.42 6 6
ZAP70 0.033 0.022 -10000 0 -0.42 1 1
GRB2/SOS1 0.047 0.023 -10000 0 -0.3 1 1
LAT/GRAP2/SLP76/VAV1 -0.031 0.17 0.22 9 -0.37 76 85
MALT1 0.031 0.041 -10000 0 -0.42 4 4
TRAF6 0.034 0.021 -10000 0 -0.42 1 1
CD8 heterodimer 0.001 0.006 0.02 3 -0.022 12 15
CARD11 0.027 0.054 -10000 0 -0.42 7 7
PRKCB -0.034 0.077 0.11 4 -0.18 85 89
PRKCE -0.011 0.098 0.18 19 -0.22 52 71
PRKCQ -0.046 0.19 0.27 5 -0.4 89 94
LCP2 0.023 0.07 -10000 0 -0.42 12 12
BCL10 0.034 0.008 -10000 0 -10000 0 0
regulation of survival gene product expression -0.02 0.13 0.23 17 -0.27 83 100
IKK complex 0.014 0.063 0.16 36 -0.11 14 50
RAS family/GDP -0.004 0.015 -10000 0 -0.049 19 19
MAP3K14 -0.015 0.11 0.19 17 -0.22 70 87
PDPK1 -0.022 0.15 0.28 20 -0.3 80 100
TCR/CD3/MHC I/CD8/Fyn -0.062 0.21 -10000 0 -0.43 93 93
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.039 0.19 -10000 0 -0.59 52 52
IHH 0.017 0.088 -10000 0 -0.28 24 24
SHH Np/Cholesterol/GAS1 -0.026 0.1 -10000 0 -0.24 98 98
LRPAP1 0.035 0.007 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.026 0.1 0.24 98 -10000 0 98
SMO/beta Arrestin2 -0.02 0.17 -10000 0 -0.41 55 55
SMO -0.036 0.16 -10000 0 -0.42 54 54
AKT1 -0.013 0.16 -10000 0 -0.55 28 28
ARRB2 0.032 0.011 -10000 0 -10000 0 0
BOC 0.015 0.089 -10000 0 -0.42 20 20
ADRBK1 0.033 0.01 -10000 0 -10000 0 0
heart looping -0.035 0.16 -10000 0 -0.42 54 54
STIL -0.005 0.13 0.2 70 -0.26 51 121
DHH N/PTCH2 0.051 0.011 -10000 0 -10000 0 0
DHH N/PTCH1 0 0.12 -10000 0 -0.29 68 68
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
DHH 0.036 0.004 -10000 0 -10000 0 0
PTHLH -0.064 0.25 -10000 0 -0.74 55 55
determination of left/right symmetry -0.035 0.16 -10000 0 -0.42 54 54
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
skeletal system development -0.063 0.25 -10000 0 -0.73 55 55
IHH N/Hhip 0.034 0.065 -10000 0 -0.29 12 12
DHH N/Hhip 0.049 0.029 -10000 0 -0.3 3 3
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.035 0.16 -10000 0 -0.42 54 54
pancreas development 0.032 0.036 -10000 0 -0.42 3 3
HHAT -0.016 0.13 -10000 0 -0.42 49 49
PI3K 0.035 0.067 -10000 0 -0.3 18 18
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.03 0.16 -10000 0 -0.42 71 71
somite specification -0.035 0.16 -10000 0 -0.42 54 54
SHH Np/Cholesterol/PTCH1 -0.03 0.11 -10000 0 -0.24 100 100
SHH Np/Cholesterol/PTCH2 0.003 0.074 -10000 0 -0.23 43 43
SHH Np/Cholesterol/Megalin -0.056 0.14 -10000 0 -0.27 134 134
SHH -0.016 0.09 -10000 0 -0.3 45 45
catabolic process -0.024 0.12 -10000 0 -0.32 69 69
SMO/Vitamin D3 -0.018 0.15 -10000 0 -0.33 60 60
SHH Np/Cholesterol/Hhip 0.002 0.074 -10000 0 -0.23 44 44
LRP2 -0.098 0.21 -10000 0 -0.42 146 146
receptor-mediated endocytosis -0.071 0.17 -10000 0 -0.37 89 89
SHH Np/Cholesterol/BOC -0.007 0.085 -10000 0 -0.23 61 61
SHH Np/Cholesterol/CDO -0.007 0.083 -10000 0 -0.24 56 56
mesenchymal cell differentiation -0.002 0.074 0.23 44 -10000 0 44
mol:Vitamin D3 -0.005 0.13 0.2 61 -0.24 96 157
IHH N/PTCH2 0.036 0.06 -10000 0 -0.27 10 10
CDON 0.019 0.07 -10000 0 -0.42 12 12
IHH N/PTCH1 -0.004 0.13 -10000 0 -0.32 69 69
Megalin/LRPAP1 -0.051 0.16 -10000 0 -0.3 146 146
PTCH2 0.035 0.006 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.007 0.07 -10000 0 -0.23 45 45
PTCH1 -0.024 0.12 -10000 0 -0.32 69 69
HHIP 0.032 0.036 -10000 0 -0.42 3 3
Thromboxane A2 receptor 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
TGM2 0.016 0.085 -10000 0 -0.42 18 18
GNB1/GNG2 -0.051 0.08 -10000 0 -0.18 129 129
AKT1 -0.015 0.12 0.23 5 -0.23 48 53
EGF -0.069 0.19 -10000 0 -0.42 110 110
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.014 0.065 0.25 5 -0.26 3 8
mol:Ca2+ -0.037 0.17 -10000 0 -0.3 128 128
LYN 0.013 0.058 0.26 4 -0.28 2 6
RhoA/GTP -0.016 0.075 -10000 0 -0.13 111 111
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.057 0.19 -10000 0 -0.35 131 131
GNG2 0.034 0.021 -10000 0 -0.42 1 1
ARRB2 0.032 0.011 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.013 0.14 -10000 0 -0.47 31 31
G beta5/gamma2 -0.054 0.11 -10000 0 -0.24 124 124
PRKCH -0.053 0.2 0.3 3 -0.36 132 135
DNM1 0.032 0.041 -10000 0 -0.42 4 4
TXA2/TP beta/beta Arrestin3 0.028 0.027 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR 0.027 0.054 -10000 0 -0.42 7 7
G12 family/GTP -0.051 0.16 -10000 0 -0.3 119 119
ADRBK1 0.033 0.01 -10000 0 -10000 0 0
ADRBK2 0.022 0.07 -10000 0 -0.42 12 12
RhoA/GTP/ROCK1 0.04 0.04 -10000 0 -0.25 8 8
mol:GDP 0.024 0.14 0.43 32 -0.23 2 34
mol:NADP 0.035 0.007 -10000 0 -10000 0 0
RAB11A 0.034 0.021 -10000 0 -0.42 1 1
PRKG1 0.035 0.005 -10000 0 -10000 0 0
mol:IP3 -0.055 0.21 -10000 0 -0.38 130 130
cell morphogenesis 0.04 0.04 -10000 0 -0.25 8 8
PLCB2 -0.089 0.27 -10000 0 -0.52 129 129
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.006 0.06 0.25 4 -0.28 2 6
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.008 0.076 0.25 5 -0.34 7 12
RHOA 0.026 0.061 -10000 0 -0.42 9 9
PTGIR 0.033 0.03 -10000 0 -0.42 2 2
PRKCB1 -0.058 0.21 -10000 0 -0.4 122 122
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.035 0.007 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.09 0.27 -10000 0 -0.52 131 131
LCK -0.006 0.092 0.25 5 -0.32 12 17
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.049 0.047 0.23 1 -0.26 1 2
TXA2-R family/G12 family/GDP/G beta/gamma 0.035 0.094 -10000 0 -0.48 13 13
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.043 0.047 0.23 1 -0.25 1 2
MAPK14 -0.033 0.13 0.22 3 -0.24 127 130
TGM2/GTP -0.066 0.22 -10000 0 -0.42 125 125
MAPK11 -0.034 0.13 0.25 3 -0.23 129 132
ARHGEF1 -0.013 0.11 0.22 5 -0.18 112 117
GNAI2 0.027 0.057 -10000 0 -0.42 8 8
JNK cascade -0.056 0.21 -10000 0 -0.38 131 131
RAB11/GDP 0.034 0.021 -10000 0 -0.42 1 1
ICAM1 -0.039 0.16 -10000 0 -0.3 130 130
cAMP biosynthetic process -0.051 0.19 -10000 0 -0.35 123 123
Gq family/GTP/EBP50 -0.022 0.096 -10000 0 -0.23 80 80
actin cytoskeleton reorganization 0.04 0.04 -10000 0 -0.25 8 8
SRC 0.014 0.065 0.25 5 -0.27 2 7
GNB5 0.024 0.067 -10000 0 -0.42 11 11
GNB1 0.032 0.045 -10000 0 -0.42 5 5
EGF/EGFR -0.033 0.11 0.25 8 -0.3 35 43
VCAM1 -0.042 0.17 -10000 0 -0.31 131 131
TP beta/Gq family/GDP/G beta5/gamma2 -0.013 0.14 -10000 0 -0.47 31 31
platelet activation -0.042 0.17 0.31 1 -0.3 129 130
PGI2/IP 0.024 0.021 -10000 0 -0.3 2 2
PRKACA 0.018 0.035 -10000 0 -0.23 9 9
Gq family/GDP/G beta5/gamma2 -0.008 0.12 -10000 0 -0.41 30 30
TXA2/TP beta/beta Arrestin2 0.008 0.069 -10000 0 -0.44 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.008 0.029 -10000 0 -0.21 8 8
mol:DAG -0.066 0.23 -10000 0 -0.43 131 131
EGFR -0.013 0.13 -10000 0 -0.42 47 47
TXA2/TP alpha -0.077 0.25 -10000 0 -0.48 123 123
Gq family/GTP -0.017 0.078 0.22 2 -0.22 59 61
YES1 0.013 0.07 0.25 5 -0.29 6 11
GNAI2/GTP 0.02 0.055 -10000 0 -0.27 4 4
PGD2/DP 0.02 0.038 -10000 0 -0.3 7 7
SLC9A3R1 -0.009 0.13 -10000 0 -0.42 46 46
FYN 0.01 0.069 0.25 4 -0.3 6 10
mol:NO 0.035 0.007 -10000 0 -10000 0 0
GNA15 0.029 0.046 -10000 0 -0.42 5 5
PGK/cGMP 0.046 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.026 0.06 -10000 0 -0.42 9 9
TP alpha/TGM2/GDP/G beta/gamma 0.053 0.074 0.28 2 -0.32 4 6
NOS3 0.035 0.007 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
PRKCA -0.043 0.19 0.3 4 -0.35 116 120
PRKCB -0.054 0.19 -10000 0 -0.36 132 132
PRKCE -0.054 0.2 0.29 2 -0.36 129 131
PRKCD -0.061 0.2 -10000 0 -0.39 130 130
PRKCG -0.06 0.21 -10000 0 -0.39 133 133
muscle contraction -0.083 0.25 -10000 0 -0.48 132 132
PRKCZ -0.048 0.18 -10000 0 -0.34 131 131
ARR3 0.036 0.002 -10000 0 -10000 0 0
TXA2/TP beta 0.04 0.058 0.27 1 -0.22 9 10
PRKCQ -0.05 0.2 0.3 1 -0.37 124 125
MAPKKK cascade -0.073 0.24 -10000 0 -0.45 131 131
SELE -0.058 0.19 -10000 0 -0.37 130 130
TP beta/GNAI2/GDP/G beta/gamma 0.061 0.068 0.28 2 -0.4 3 5
ROCK1 0.035 0.005 -10000 0 -10000 0 0
GNA14 -0.01 0.13 -10000 0 -0.42 44 44
chemotaxis -0.11 0.31 -10000 0 -0.61 131 131
GNA12 0.035 0.006 -10000 0 -10000 0 0
GNA13 0.028 0.042 -10000 0 -0.42 4 4
GNA11 0.032 0.036 -10000 0 -0.42 3 3
Rac1/GTP 0.026 0.005 -10000 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.006 0.1 -10000 0 -0.33 20 20
TBX21 -0.26 0.57 -10000 0 -1.3 108 108
B2M 0.023 0.066 -10000 0 -0.42 10 10
TYK2 0.013 0.042 -10000 0 -10000 0 0
IL12RB1 0.013 0.043 -10000 0 -10000 0 0
GADD45B -0.18 0.44 -10000 0 -1.1 82 82
IL12RB2 -0.011 0.1 -10000 0 -0.43 26 26
GADD45G -0.17 0.42 -10000 0 -1 84 84
natural killer cell activation -0.005 0.022 -10000 0 -0.04 118 118
RELB 0.029 0.05 -10000 0 -0.42 6 6
RELA 0.035 0.006 -10000 0 -10000 0 0
IL18 -0.001 0.11 -10000 0 -0.43 32 32
IL2RA 0.004 0.11 -10000 0 -0.42 31 31
IFNG -0.008 0.12 -10000 0 -0.42 38 38
STAT3 (dimer) -0.14 0.36 -10000 0 -0.8 99 99
HLA-DRB5 0.014 0.082 -10000 0 -0.42 16 16
FASLG -0.18 0.49 -10000 0 -1.1 88 88
NF kappa B2 p52/RelB -0.16 0.44 -10000 0 -0.95 100 100
CD4 0.028 0.021 -10000 0 -10000 0 0
SOCS1 0.031 0.023 -10000 0 -0.42 1 1
EntrezGene:6955 -0.003 0.012 -10000 0 -0.03 67 67
CD3D 0.009 0.076 -10000 0 -0.43 13 13
CD3E 0.024 0.026 -10000 0 -10000 0 0
CD3G -0.028 0.14 -10000 0 -0.43 54 54
IL12Rbeta2/JAK2 0.003 0.095 -10000 0 -0.33 26 26
CCL3 -0.17 0.43 -10000 0 -1 90 90
CCL4 -0.18 0.45 -10000 0 -1 87 87
HLA-A 0.016 0.088 -10000 0 -0.42 19 19
IL18/IL18R -0.003 0.17 -10000 0 -0.35 84 84
NOS2 -0.18 0.43 -10000 0 -0.88 113 113
IL12/IL12R/TYK2/JAK2/SPHK2 -0.01 0.11 -10000 0 -0.36 19 19
IL1R1 -0.22 0.5 -10000 0 -1.1 103 103
IL4 0.034 0.052 -10000 0 -0.42 5 5
JAK2 0.011 0.051 -10000 0 -0.46 2 2
EntrezGene:6957 -0.003 0.012 -10000 0 -0.029 66 66
TCR/CD3/MHC I/CD8 -0.071 0.27 -10000 0 -0.77 49 49
RAB7A -0.13 0.34 -10000 0 -0.77 95 95
lysosomal transport -0.12 0.32 -10000 0 -0.72 95 95
FOS -0.24 0.5 -10000 0 -1.1 105 105
STAT4 (dimer) -0.15 0.41 -10000 0 -0.9 98 98
STAT5A (dimer) -0.18 0.44 -10000 0 -0.96 100 100
GZMA -0.18 0.42 -10000 0 -0.92 101 101
GZMB -0.26 0.56 -10000 0 -1.3 104 104
HLX 0 0 -10000 0 -10000 0 0
LCK -0.21 0.5 -10000 0 -1.1 105 105
TCR/CD3/MHC II/CD4 -0.058 0.17 -10000 0 -0.37 91 91
IL2/IL2R 0.042 0.11 -10000 0 -0.29 45 45
MAPK14 -0.18 0.44 -10000 0 -1 95 95
CCR5 -0.17 0.4 -10000 0 -0.82 113 113
IL1B -0.022 0.13 -10000 0 -0.45 40 40
STAT6 -0.056 0.2 -10000 0 -0.59 35 35
STAT4 0.01 0.1 -10000 0 -0.42 26 26
STAT3 0.028 0.031 -10000 0 -0.42 2 2
STAT1 0.02 0.075 -10000 0 -0.42 14 14
NFKB1 0.035 0.005 -10000 0 -10000 0 0
NFKB2 0.034 0.021 -10000 0 -0.42 1 1
IL12B 0.008 0.066 -10000 0 -0.42 7 7
CD8A 0 0.008 -10000 0 -0.038 18 18
CD8B 0 0.009 -10000 0 -0.045 19 19
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.006 0.1 0.33 20 -10000 0 20
IL2RB 0.012 0.095 -10000 0 -0.42 23 23
proteasomal ubiquitin-dependent protein catabolic process -0.13 0.37 -10000 0 -0.8 98 98
IL2RG 0.03 0.041 -10000 0 -0.42 4 4
IL12 0.014 0.076 -10000 0 -0.33 10 10
STAT5A 0.028 0.037 -10000 0 -0.42 3 3
CD247 -0.002 0.011 -10000 0 -0.027 65 65
IL2 0.032 0.036 -10000 0 -0.42 3 3
SPHK2 0.034 0.021 -10000 0 -0.42 1 1
FRAP1 0.034 0.008 -10000 0 -10000 0 0
IL12A 0.005 0.059 -10000 0 -0.43 5 5
IL12/IL12R/TYK2/JAK2 -0.22 0.53 -10000 0 -1.1 101 101
MAP2K3 -0.19 0.46 -10000 0 -1 98 98
RIPK2 0.028 0.015 -10000 0 -10000 0 0
MAP2K6 -0.18 0.44 -10000 0 -1 93 93
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.019 0.064 -10000 0 -0.42 9 9
IL18RAP -0.023 0.15 -10000 0 -0.43 60 60
IL12Rbeta1/TYK2 0.026 0.056 -10000 0 -10000 0 0
EOMES -0.046 0.27 -10000 0 -1.2 26 26
STAT1 (dimer) -0.15 0.38 -10000 0 -0.81 103 103
T cell proliferation -0.11 0.3 -10000 0 -0.64 102 102
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.016 0.091 -10000 0 -0.43 20 20
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.11 0.33 -10000 0 -0.67 108 108
ATF2 -0.16 0.4 -10000 0 -0.9 95 95
IL27-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
TGFB1 0.035 0.021 -10000 0 -0.42 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.1 0.25 0.63 69 -0.52 2 71
IL27/IL27R/JAK1 -0.09 0.34 0.88 2 -1 45 47
TBX21 -0.097 0.3 0.59 25 -0.56 106 131
IL12B 0.025 0.055 -10000 0 -0.42 7 7
IL12A 0.003 0.031 -10000 0 -0.3 5 5
IL6ST -0.05 0.16 -10000 0 -0.4 87 87
IL27RA/JAK1 -0.062 0.33 0.41 3 -1.2 35 38
IL27 -0.038 0.16 -10000 0 -0.43 74 74
TYK2 0.028 0.029 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.014 0.086 0.2 12 -0.25 54 66
T-helper 2 cell differentiation 0.1 0.25 0.63 69 -0.52 2 71
T cell proliferation during immune response 0.1 0.25 0.63 69 -0.52 2 71
MAPKKK cascade -0.1 0.25 0.52 2 -0.63 69 71
STAT3 0.028 0.031 -10000 0 -0.42 2 2
STAT2 0.035 0.005 -10000 0 -10000 0 0
STAT1 0.022 0.077 -10000 0 -0.42 14 14
IL12RB1 0.035 0.006 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.081 0.29 0.61 24 -0.59 79 103
IL27/IL27R/JAK2/TYK2 -0.1 0.26 0.52 2 -0.64 68 70
positive regulation of T cell mediated cytotoxicity -0.1 0.25 0.52 2 -0.63 69 71
STAT1 (dimer) -0.1 0.39 0.56 32 -0.87 70 102
JAK2 0.024 0.038 -10000 0 -0.43 2 2
JAK1 0.034 0.036 -10000 0 -0.39 3 3
STAT2 (dimer) -0.088 0.25 0.46 2 -0.6 69 71
T cell proliferation -0.12 0.26 0.47 2 -0.61 78 80
IL12/IL12R/TYK2/JAK2 -0.004 0.21 -10000 0 -0.93 19 19
IL17A -0.014 0.087 0.2 12 -0.25 54 66
mast cell activation 0.1 0.25 0.63 69 -0.52 2 71
IFNG -0.01 0.05 0.13 6 -0.12 55 61
T cell differentiation -0.005 0.011 0.029 13 -0.023 91 104
STAT3 (dimer) -0.079 0.24 0.46 2 -0.61 65 67
STAT5A (dimer) -0.08 0.24 0.46 2 -0.61 65 67
STAT4 (dimer) -0.098 0.26 0.46 2 -0.6 78 80
STAT4 0.01 0.1 -10000 0 -0.42 26 26
T cell activation -0.002 0.032 0.12 31 -10000 0 31
IL27R/JAK2/TYK2 -0.08 0.32 -10000 0 -1.1 38 38
GATA3 -0.2 0.52 0.78 8 -1.3 90 98
IL18 -0.013 0.074 -10000 0 -0.3 32 32
positive regulation of mast cell cytokine production -0.077 0.24 0.46 2 -0.59 65 67
IL27/EBI3 -0.01 0.13 0.23 4 -0.31 77 81
IL27RA -0.091 0.33 0.38 3 -1.3 35 38
IL6 -0.019 0.14 -10000 0 -0.42 53 53
STAT5A 0.028 0.037 -10000 0 -0.42 3 3
monocyte differentiation 0 0.002 -10000 0 -0.015 1 1
IL2 0.022 0.15 0.47 35 -1.2 3 38
IL1B -0.017 0.083 -10000 0 -0.3 40 40
EBI3 0.026 0.053 -10000 0 -0.43 5 5
TNF 0.002 0.041 -10000 0 -0.3 9 9
IL23-mediated signaling events

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
CCL2 -0.16 0.54 -10000 0 -1.3 79 79
IL23A -0.14 0.49 -10000 0 -1.2 65 65
NF kappa B1 p50/RelA/I kappa B alpha -0.1 0.48 -10000 0 -1.1 71 71
positive regulation of T cell mediated cytotoxicity -0.14 0.52 -10000 0 -1.2 70 70
ITGA3 -0.14 0.48 -10000 0 -1.1 73 73
IL17F -0.053 0.33 0.47 4 -0.69 72 76
IL12B 0.018 0.078 -10000 0 -0.44 7 7
STAT1 (dimer) -0.15 0.5 -10000 0 -1.2 71 71
CD4 -0.11 0.45 -10000 0 -1.1 65 65
IL23 -0.13 0.47 -10000 0 -1.2 64 64
IL23R -0.002 0.22 -10000 0 -1.3 11 11
IL1B -0.16 0.53 -10000 0 -1.3 74 74
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.082 0.46 -10000 0 -1.1 60 60
TYK2 0.019 0.046 -10000 0 -10000 0 0
STAT4 0.01 0.1 -10000 0 -0.42 26 26
STAT3 0.029 0.031 -10000 0 -0.42 2 2
IL18RAP -0.024 0.15 -10000 0 -0.43 60 60
IL12RB1 0.019 0.046 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
IL12Rbeta1/TYK2 0.029 0.059 -10000 0 -10000 0 0
IL23R/JAK2 0.01 0.22 -10000 0 -1.2 11 11
positive regulation of chronic inflammatory response -0.14 0.52 -10000 0 -1.2 70 70
natural killer cell activation 0.001 0.012 0.081 7 -10000 0 7
JAK2 0.022 0.063 -10000 0 -0.46 2 2
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
NFKB1 0.036 0.007 -10000 0 -10000 0 0
RELA 0.036 0.007 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.12 0.45 -10000 0 -1.1 66 66
ALOX12B -0.12 0.45 -10000 0 -1.1 66 66
CXCL1 -0.18 0.55 -10000 0 -1.2 103 103
T cell proliferation -0.14 0.52 -10000 0 -1.2 70 70
NFKBIA 0.033 0.03 -10000 0 -0.42 2 2
IL17A -0.03 0.26 -10000 0 -0.53 71 71
PI3K -0.12 0.49 -10000 0 -1.1 73 73
IFNG -0.007 0.049 0.15 5 -0.13 46 51
STAT3 (dimer) -0.12 0.46 -10000 0 -1.1 72 72
IL18R1 0.015 0.09 -10000 0 -0.43 20 20
IL23/IL23R/JAK2/TYK2/SOCS3 -0.039 0.29 0.51 1 -0.67 47 48
IL18/IL18R -0.011 0.16 -10000 0 -0.34 84 84
macrophage activation -0.007 0.021 -10000 0 -0.044 59 59
TNF -0.14 0.48 -10000 0 -1.2 69 69
STAT3/STAT4 -0.14 0.49 -10000 0 -1.2 72 72
STAT4 (dimer) -0.14 0.52 -10000 0 -1.2 73 73
IL18 -0.001 0.11 -10000 0 -0.43 32 32
IL19 -0.082 0.46 -10000 0 -1.1 58 58
STAT5A (dimer) -0.15 0.49 -10000 0 -1.2 69 69
STAT1 0.02 0.075 -10000 0 -0.42 14 14
SOCS3 0.028 0.046 -10000 0 -0.42 5 5
CXCL9 -0.21 0.57 -10000 0 -1.2 109 109
MPO -0.1 0.45 -10000 0 -1.1 65 65
positive regulation of humoral immune response -0.14 0.52 -10000 0 -1.2 70 70
IL23/IL23R/JAK2/TYK2 -0.16 0.56 -10000 0 -1.3 70 70
IL6 -0.18 0.56 -10000 0 -1.3 90 90
STAT5A 0.028 0.037 -10000 0 -0.42 3 3
IL2 0.029 0.039 -10000 0 -0.42 3 3
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.012 0.081 7 -10000 0 7
CD3E -0.11 0.45 -10000 0 -1.1 65 65
keratinocyte proliferation -0.14 0.52 -10000 0 -1.2 70 70
NOS2 -0.12 0.45 -10000 0 -1 70 70
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 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.006 0.12 -10000 0 -0.24 102 102
regulation of S phase of mitotic cell cycle -0.027 0.11 -10000 0 -0.23 101 101
GNAO1 0.029 0.014 -10000 0 -10000 0 0
HRAS 0.031 0.036 -10000 0 -0.42 3 3
SHBG/T-DHT 0.021 0.008 -10000 0 -10000 0 0
PELP1 0.032 0.011 -10000 0 -10000 0 0
AKT1 0.007 0.024 -10000 0 -0.3 3 3
MAP2K1 -0.054 0.098 0.17 18 -0.23 85 103
T-DHT/AR -0.037 0.13 -10000 0 -0.3 99 99
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.006 70 70
GNAI2 0.027 0.058 -10000 0 -0.42 8 8
GNAI3 0.035 0.006 -10000 0 -10000 0 0
GNAI1 0.017 0.085 -10000 0 -0.42 18 18
mol:GDP -0.072 0.15 -10000 0 -0.37 101 101
cell proliferation -0.075 0.17 0.26 1 -0.44 73 74
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
FOS -0.12 0.28 -10000 0 -0.79 73 73
mol:Ca2+ -0.009 0.023 -10000 0 -0.063 56 56
MAPK3 -0.06 0.14 0.26 3 -0.34 69 72
MAPK1 -0.044 0.12 -10000 0 -0.41 29 29
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
mol:IP3 0 0.002 -10000 0 -0.004 71 71
cAMP biosynthetic process 0.003 0.017 -10000 0 -10000 0 0
GNG2 0.034 0.021 -10000 0 -0.42 1 1
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 71 71
HRAS/GTP -0.007 0.12 -10000 0 -0.22 97 97
actin cytoskeleton reorganization 0.038 0.052 -10000 0 -0.21 18 18
SRC 0.032 0.03 -10000 0 -0.42 2 2
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 71 71
PI3K 0.032 0.057 -10000 0 -0.25 18 18
apoptosis 0.063 0.17 0.43 77 -10000 0 77
T-DHT/AR/PELP1 -0.016 0.12 -10000 0 -0.26 99 99
HRAS/GDP -0.051 0.16 -10000 0 -0.36 102 102
CREB1 -0.071 0.18 -10000 0 -0.47 76 76
RAC1-CDC42/GTP 0.049 0.057 -10000 0 -0.21 18 18
AR -0.054 0.18 -10000 0 -0.42 99 99
GNB1 0.032 0.045 -10000 0 -0.42 5 5
RAF1 -0.039 0.1 0.18 19 -0.22 93 112
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 -0.056 0.099 0.17 19 -0.23 86 105
T-DHT/AR/PELP1/Src/PI3K -0.028 0.11 -10000 0 -0.23 101 101
GNAZ 0.024 0.067 -10000 0 -0.42 11 11
SHBG 0.032 0.012 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.038 0.14 -10000 0 -0.42 38 38
mol:T-DHT 0 0.001 0.002 1 -0.004 16 17
RAC1 0.035 0.006 -10000 0 -10000 0 0
GNRH1 0.005 0.02 -10000 0 -0.3 2 2
Gi family/GTP -0.029 0.086 -10000 0 -0.24 45 45
CDC42 0.034 0.008 -10000 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.074 0.28 -10000 0 -0.77 41 41
CRP -0.043 0.3 0.56 3 -0.73 48 51
cell cycle arrest -0.096 0.34 0.49 1 -0.79 68 69
TIMP1 -0.069 0.3 -10000 0 -0.77 54 54
IL6ST -0.049 0.17 -10000 0 -0.42 88 88
Rac1/GDP -0.051 0.19 0.29 2 -0.41 68 70
AP1 0.011 0.18 -10000 0 -0.54 22 22
GAB2 0.032 0.014 -10000 0 -10000 0 0
TNFSF11 -0.14 0.4 0.46 1 -0.94 85 86
HSP90B1 0 0.12 -10000 0 -0.83 8 8
GAB1 0.028 0.061 -10000 0 -0.42 9 9
MAPK14 -0.048 0.17 -10000 0 -0.52 33 33
AKT1 0.029 0.08 -10000 0 -0.48 3 3
FOXO1 0.037 0.081 0.35 1 -0.45 3 4
MAP2K6 -0.054 0.16 0.24 1 -0.42 56 57
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.061 0.21 0.33 2 -0.46 73 75
MITF -0.055 0.17 -10000 0 -0.38 75 75
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 -0.056 0.33 -10000 0 -1.3 33 33
CEBPB 0.027 0.051 -10000 0 -0.42 6 6
GRB2/SOS1/GAB family/SHP2 0.005 0.12 0.3 1 -0.44 18 19
STAT3 -0.11 0.37 0.5 1 -0.87 68 69
STAT1 -0.011 0.17 -10000 0 -0.88 17 17
CEBPD -0.099 0.37 -10000 0 -0.91 69 69
PIK3CA 0.034 0.022 -10000 0 -0.42 1 1
PI3K 0.037 0.067 -10000 0 -0.3 18 18
JUN -0.001 0.12 -10000 0 -0.42 39 39
PIAS3/MITF -0.046 0.17 0.29 1 -0.39 63 64
MAPK11 -0.046 0.16 -10000 0 -0.52 33 33
STAT3 (dimer)/FOXO1 -0.054 0.28 0.56 2 -0.65 55 57
GRB2/SOS1/GAB family -0.017 0.17 0.29 1 -0.44 36 37
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.064 0.17 -10000 0 -0.31 118 118
GRB2 0.034 0.011 -10000 0 -10000 0 0
JAK2 0.031 0.03 -10000 0 -0.42 2 2
LBP -0.032 0.24 0.45 1 -0.58 44 45
PIK3R1 0.019 0.083 -10000 0 -0.42 17 17
JAK1 0.031 0.039 -10000 0 -0.42 3 3
MYC -0.066 0.36 0.59 2 -0.9 61 63
FGG -0.077 0.29 -10000 0 -0.75 48 48
macrophage differentiation -0.096 0.34 0.49 1 -0.79 68 69
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.025 0.16 -10000 0 -0.26 136 136
JUNB -0.076 0.28 -10000 0 -0.72 50 50
FOS -0.031 0.15 -10000 0 -0.42 66 66
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.062 0.17 -10000 0 -0.39 75 75
STAT1/PIAS1 -0.047 0.19 0.3 1 -0.41 69 70
GRB2/SOS1/GAB family/SHP2/PI3K 0.03 0.081 -10000 0 -0.37 8 8
STAT3 (dimer) -0.1 0.37 0.49 1 -0.85 68 69
PRKCD -0.073 0.24 0.36 1 -0.54 75 76
IL6R 0.02 0.06 -10000 0 -0.43 8 8
SOCS3 -0.044 0.19 0.43 2 -0.79 16 18
gp130 (dimer)/JAK1/JAK1/LMO4 -0.028 0.15 -10000 0 -0.26 136 136
Rac1/GTP -0.054 0.2 0.29 2 -0.43 72 74
HCK 0.017 0.087 -10000 0 -0.42 19 19
MAPKKK cascade 0.021 0.14 -10000 0 -0.57 16 16
bone resorption -0.13 0.37 0.46 1 -0.86 86 87
IRF1 -0.092 0.32 -10000 0 -0.83 55 55
mol:GDP -0.058 0.18 -10000 0 -0.4 76 76
SOS1 0.036 0.022 -10000 0 -0.42 1 1
VAV1 -0.059 0.18 -10000 0 -0.4 77 77
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.045 0.19 0.33 1 -0.51 41 42
PTPN11 0.016 0.091 -10000 0 -1.1 3 3
IL6/IL6RA 0.003 0.1 -10000 0 -0.3 48 48
gp130 (dimer)/TYK2/TYK2/LMO4 -0.024 0.14 -10000 0 -0.26 135 135
gp130 (dimer)/JAK2/JAK2/LMO4 -0.026 0.15 -10000 0 -0.26 135 135
IL6 -0.022 0.14 -10000 0 -0.43 53 53
PIAS3 0.035 0.006 -10000 0 -10000 0 0
PTPRE 0.021 0.064 -10000 0 -0.41 10 10
PIAS1 0.035 0.006 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.056 0.13 -10000 0 -0.26 134 134
LMO4 -0.02 0.14 -10000 0 -0.42 54 54
STAT3 (dimer)/PIAS3 -0.091 0.34 -10000 0 -0.8 64 64
MCL1 0.037 0.094 -10000 0 -0.78 2 2
FAS signaling pathway (CD95)

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
SPTAN1 0.024 0.084 0.2 75 -10000 0 75
RFC1 0.02 0.076 0.19 70 -10000 0 70
PRKDC 0.044 0.1 0.22 111 -0.23 1 112
RIPK1 0.035 0.008 -10000 0 -10000 0 0
CASP7 -0.007 0.14 -10000 0 -0.69 18 18
FASLG/FAS/FADD/FAF1 0.004 0.093 0.2 40 -0.26 28 68
MAP2K4 -0.025 0.17 0.44 2 -0.46 42 44
mol:ceramide -0.013 0.11 -10000 0 -0.36 33 33
GSN 0.018 0.088 0.2 73 -0.24 9 82
FASLG/FAS/FADD/FAF1/Caspase 8 0.007 0.11 0.23 4 -0.33 28 32
FAS 0.003 0.1 -10000 0 -0.42 28 28
BID -0.018 0.053 0.26 12 -0.27 7 19
MAP3K1 -0.011 0.14 0.3 4 -0.48 22 26
MAP3K7 0.032 0.01 -10000 0 -10000 0 0
RB1 0.019 0.073 0.19 62 -0.23 1 63
CFLAR 0.032 0.046 -10000 0 -0.42 5 5
HGF/MET 0.015 0.12 -10000 0 -0.27 78 78
ARHGDIB 0.016 0.092 0.2 70 -0.25 13 83
FADD 0.024 0.021 -10000 0 -10000 0 0
actin filament polymerization -0.017 0.089 0.24 11 -0.2 71 82
NFKB1 0.003 0.1 -10000 0 -0.63 8 8
MAPK8 -0.044 0.21 0.51 2 -0.5 67 69
DFFA 0.022 0.08 0.2 71 -10000 0 71
DNA fragmentation during apoptosis 0.022 0.081 0.2 71 -0.2 1 72
FAS/FADD/MET 0.032 0.079 -10000 0 -0.26 28 28
CFLAR/RIP1 0.048 0.038 -10000 0 -0.3 5 5
FAIM3 0.015 0.078 -10000 0 -0.42 15 15
FAF1 0.028 0.03 -10000 0 -0.42 1 1
PARP1 0.028 0.097 0.22 79 -0.24 3 82
DFFB 0.022 0.081 0.2 74 -0.2 1 75
CHUK -0.007 0.1 -10000 0 -0.55 10 10
FASLG -0.009 0.11 -10000 0 -0.43 34 34
FAS/FADD 0.02 0.077 -10000 0 -0.31 23 23
HGF 0.028 0.057 -10000 0 -0.42 8 8
LMNA 0.022 0.096 0.32 25 -0.22 6 31
CASP6 0.019 0.081 0.19 68 -0.22 4 72
CASP10 0.029 0.02 -10000 0 -10000 0 0
CASP3 0.032 0.094 0.24 81 -0.22 6 87
PTPN13 -0.031 0.16 -10000 0 -0.42 72 72
CASP8 -0.013 0.057 0.33 13 -10000 0 13
IL6 -0.1 0.41 -10000 0 -1.2 60 60
MET 0.029 0.046 -10000 0 -0.42 5 5
ICAD/CAD 0.019 0.073 0.38 4 -10000 0 4
FASLG/FAS/FADD/FAF1/Caspase 10 -0.013 0.11 -10000 0 -0.36 33 33
activation of caspase activity by cytochrome c -0.017 0.053 0.26 12 -0.27 7 19
PAK2 0.021 0.078 0.19 71 -0.2 1 72
BCL2 -0.057 0.18 -10000 0 -0.42 99 99
Noncanonical Wnt signaling pathway

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
NFATC2 0.03 0.037 -10000 0 -0.42 3 3
GNB1/GNG2 -0.05 0.17 -10000 0 -0.38 62 62
mol:DAG -0.059 0.15 -10000 0 -0.35 60 60
PLCG1 -0.061 0.15 -10000 0 -0.36 60 60
YES1 -0.067 0.15 -10000 0 -0.4 57 57
FZD3 0.006 0.097 -10000 0 -0.42 24 24
FZD6 -0.03 0.15 -10000 0 -0.42 61 61
G protein -0.036 0.17 0.29 11 -0.37 56 67
MAP3K7 -0.058 0.12 0.24 3 -0.32 54 57
mol:Ca2+ -0.056 0.14 -10000 0 -0.34 60 60
mol:IP3 -0.059 0.15 -10000 0 -0.35 60 60
NLK -0.035 0.25 -10000 0 -0.82 45 45
GNB1 0.032 0.045 -10000 0 -0.42 5 5
CAMK2A -0.058 0.14 0.25 3 -0.33 57 60
MAP3K7IP1 0.034 0.009 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.071 0.15 -10000 0 -0.41 57 57
CSNK1A1 0.035 0.005 -10000 0 -10000 0 0
GNAS -0.065 0.15 -10000 0 -0.39 55 55
GO:0007205 -0.06 0.14 0.26 3 -0.35 58 61
WNT6 0.03 0.031 -10000 0 -0.42 2 2
WNT4 -0.019 0.14 -10000 0 -0.42 58 58
NFAT1/CK1 alpha -0.049 0.16 0.29 2 -0.38 53 55
GNG2 0.034 0.021 -10000 0 -0.42 1 1
WNT5A -0.027 0.15 -10000 0 -0.42 64 64
WNT11 0.027 0.032 -10000 0 -0.42 2 2
CDC42 -0.065 0.15 -10000 0 -0.4 54 54
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.013 0.083 -10000 0 -0.22 66 66
epithelial cell differentiation 0.025 0.093 -10000 0 -0.22 56 56
CYFIP2 -0.006 0.13 -10000 0 -0.42 44 44
ENAH -0.027 0.079 0.33 4 -0.31 8 12
EGFR -0.013 0.13 -10000 0 -0.42 47 47
EPHA2 0.031 0.036 -10000 0 -0.42 3 3
MYO6 -0.037 0.078 0.18 1 -0.22 63 64
CTNNB1 0.024 0.067 -10000 0 -0.42 11 11
ABI1/Sra1/Nap1 0.041 0.089 -10000 0 -0.26 39 39
AQP5 -0.095 0.17 -10000 0 -0.45 83 83
CTNND1 0.034 0.022 -10000 0 -0.42 1 1
mol:PI-4-5-P2 -0.032 0.07 -10000 0 -0.21 53 53
regulation of calcium-dependent cell-cell adhesion -0.032 0.069 -10000 0 -0.21 54 54
EGF -0.069 0.19 -10000 0 -0.42 110 110
NCKAP1 0.034 0.021 -10000 0 -0.42 1 1
AQP3 -0.095 0.17 -10000 0 -0.46 83 83
cortical microtubule organization 0.025 0.093 -10000 0 -0.22 56 56
GO:0000145 -0.034 0.065 -10000 0 -0.2 53 53
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.03 0.096 -10000 0 -0.22 56 56
MLLT4 0.02 0.075 -10000 0 -0.42 14 14
ARF6/GDP -0.042 0.068 -10000 0 -0.28 16 16
ARF6 0.033 0.029 -10000 0 -0.42 2 2
Ephrin A1/EPHA2/NCK1/GIT1 0.052 0.072 -10000 0 -0.24 20 20
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.027 0.093 -10000 0 -0.37 14 14
PVRL2 0.026 0.064 -10000 0 -0.42 10 10
ZYX -0.034 0.074 -10000 0 -0.22 57 57
ARF6/GTP 0.058 0.077 -10000 0 -0.24 20 20
CDH1 -0.012 0.13 -10000 0 -0.42 45 45
EGFR/EGFR/EGF/EGF -0.057 0.14 -10000 0 -0.22 189 189
RhoA/GDP 0.022 0.099 -10000 0 -0.22 63 63
actin cytoskeleton organization -0.041 0.074 -10000 0 -0.22 51 51
IGF-1R heterotetramer -0.043 0.17 -10000 0 -0.42 84 84
GIT1 0.033 0.022 -10000 0 -0.42 1 1
IGF1R -0.043 0.17 -10000 0 -0.42 84 84
IGF1 -0.041 0.17 -10000 0 -0.42 80 80
DIAPH1 0.002 0.2 -10000 0 -0.59 36 36
Wnt receptor signaling pathway -0.025 0.093 0.22 56 -10000 0 56
RHOA 0.026 0.061 -10000 0 -0.42 9 9
RhoA/GTP -0.044 0.069 -10000 0 -0.22 58 58
CTNNA1 0.035 0.006 -10000 0 -10000 0 0
VCL -0.042 0.075 -10000 0 -0.23 51 51
EFNA1 0.014 0.08 -10000 0 -0.42 16 16
LPP -0.039 0.071 -10000 0 -0.3 2 2
Ephrin A1/EPHA2 0.009 0.092 -10000 0 -0.22 57 57
SEC6/SEC8 -0.049 0.068 -10000 0 -0.21 65 65
MGAT3 -0.033 0.069 -10000 0 -0.21 54 54
HGF/MET 0.015 0.093 -10000 0 -0.21 66 66
HGF 0.028 0.057 -10000 0 -0.42 8 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.013 0.083 -10000 0 -0.22 66 66
actin cable formation 0.015 0.11 0.26 14 -0.31 8 22
KIAA1543 -0.037 0.069 -10000 0 -0.22 53 53
KIFC3 -0.032 0.067 -10000 0 -0.21 50 50
NCK1 0.034 0.022 -10000 0 -0.42 1 1
EXOC3 0.036 0.002 -10000 0 -10000 0 0
ACTN1 -0.034 0.074 -10000 0 -0.22 56 56
NCK1/GIT1 0.048 0.025 -10000 0 -0.3 2 2
mol:GDP 0.025 0.093 -10000 0 -0.22 56 56
EXOC4 0.034 0.021 -10000 0 -0.42 1 1
STX4 -0.034 0.062 -10000 0 -0.21 56 56
PIP5K1C -0.032 0.07 -10000 0 -0.22 53 53
LIMA1 0 0 -10000 0 -10000 0 0
ABI1 0.034 0.008 -10000 0 -10000 0 0
ROCK1 -0.008 0.1 0.33 7 -0.33 7 14
adherens junction assembly -0.045 0.12 0.26 1 -0.48 15 16
IGF-1R heterotetramer/IGF1 -0.057 0.15 -10000 0 -0.24 176 176
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.074 -10000 0 -0.3 23 23
MET 0.029 0.046 -10000 0 -0.42 5 5
PLEKHA7 -0.031 0.07 0.18 1 -0.21 55 56
mol:GTP 0.05 0.07 -10000 0 -0.23 20 20
establishment of epithelial cell apical/basal polarity -0.044 0.072 0.15 1 -0.32 3 4
cortical actin cytoskeleton stabilization -0.013 0.083 -10000 0 -0.22 66 66
regulation of cell-cell adhesion -0.041 0.074 -10000 0 -0.22 51 51
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.013 0.083 -10000 0 -0.22 66 66
Syndecan-4-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
PTK2 -0.026 0.18 -10000 0 -0.45 62 62
Syndecan-4/Syndesmos -0.031 0.2 -10000 0 -0.5 61 61
positive regulation of JNK cascade -0.044 0.22 -10000 0 -0.48 78 78
Syndecan-4/ADAM12 -0.049 0.23 -10000 0 -0.51 80 80
CCL5 -0.013 0.14 -10000 0 -0.42 51 51
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
DNM2 0.035 0.005 -10000 0 -10000 0 0
ITGA5 0.033 0.035 -10000 0 -0.42 3 3
SDCBP 0.022 0.061 -10000 0 -0.42 9 9
PLG 0.021 0.04 -10000 0 -0.31 3 3
ADAM12 -0.012 0.14 -10000 0 -0.42 51 51
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.028 0.046 -10000 0 -0.42 5 5
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.032 0.02 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.032 0.21 -10000 0 -0.5 66 66
Syndecan-4/CXCL12/CXCR4 -0.047 0.23 -10000 0 -0.51 78 78
Syndecan-4/Laminin alpha3 -0.054 0.22 -10000 0 -0.51 68 68
MDK 0.017 0.085 -10000 0 -0.42 18 18
Syndecan-4/FZD7 -0.05 0.22 -10000 0 -0.5 76 76
Syndecan-4/Midkine -0.038 0.21 -10000 0 -0.5 67 67
FZD7 -0.007 0.13 -10000 0 -0.42 44 44
Syndecan-4/FGFR1/FGF -0.033 0.2 -10000 0 -0.47 63 63
THBS1 0.001 0.12 -10000 0 -0.42 37 37
integrin-mediated signaling pathway -0.041 0.21 -10000 0 -0.48 76 76
positive regulation of MAPKKK cascade -0.044 0.22 -10000 0 -0.48 78 78
Syndecan-4/TACI -0.033 0.21 -10000 0 -0.5 66 66
CXCR4 0.006 0.11 -10000 0 -0.42 31 31
cell adhesion 0.012 0.099 0.2 46 -0.27 40 86
Syndecan-4/Dynamin -0.029 0.21 -10000 0 -0.49 66 66
Syndecan-4/TSP1 -0.043 0.22 -10000 0 -0.49 75 75
Syndecan-4/GIPC -0.03 0.21 -10000 0 -0.49 66 66
Syndecan-4/RANTES -0.05 0.22 -10000 0 -0.51 70 70
ITGB1 0.033 0.03 -10000 0 -0.42 2 2
LAMA1 0.034 0.009 -10000 0 -10000 0 0
LAMA3 -0.019 0.14 -10000 0 -0.42 57 57
RAC1 0.035 0.006 -10000 0 -10000 0 0
PRKCA 0.09 0.26 0.79 59 -10000 0 59
Syndecan-4/alpha-Actinin -0.033 0.22 -10000 0 -0.51 67 67
TFPI 0.034 0.008 -10000 0 -10000 0 0
F2 0.031 0.025 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.047 0.037 -10000 0 -0.3 5 5
positive regulation of cell adhesion -0.06 0.2 -10000 0 -0.5 68 68
ACTN1 0.026 0.061 -10000 0 -0.42 9 9
TNC 0.004 0.11 -10000 0 -0.42 31 31
Syndecan-4/CXCL12 -0.048 0.22 -10000 0 -0.5 76 76
FGF6 0.026 0.058 -10000 0 -0.42 8 8
RHOA 0.026 0.061 -10000 0 -0.42 9 9
CXCL12 -0.007 0.13 -10000 0 -0.42 46 46
TNFRSF13B 0.032 0.012 -10000 0 -10000 0 0
FGF2 -0.001 0.11 -10000 0 -0.42 34 34
FGFR1 0.021 0.061 -10000 0 -0.42 9 9
Syndecan-4/PI-4-5-P2 -0.059 0.19 -10000 0 -0.49 66 66
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.019 0.13 -10000 0 -0.41 48 48
cell migration -0.015 0.015 -10000 0 -10000 0 0
PRKCD 0.022 0.04 -10000 0 -0.3 3 3
vasculogenesis -0.041 0.21 -10000 0 -0.47 75 75
SDC4 -0.059 0.2 -10000 0 -0.52 66 66
Syndecan-4/Tenascin C -0.044 0.22 -10000 0 -0.5 75 75
Syndecan-4/PI-4-5-P2/PKC alpha -0.026 0.016 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.034 0.2 -10000 0 -0.5 60 60
MMP9 -0.014 0.14 -10000 0 -0.42 52 52
Rac1/GTP 0.012 0.1 0.2 46 -0.27 40 86
cytoskeleton organization -0.029 0.2 -10000 0 -0.48 61 61
GIPC1 0.033 0.035 -10000 0 -0.42 3 3
Syndecan-4/TFPI -0.033 0.21 -10000 0 -0.5 66 66
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.071 0.15 -9999 0 -0.41 57 57
FZD6 -0.03 0.15 -9999 0 -0.42 61 61
WNT6 0.03 0.031 -9999 0 -0.42 2 2
WNT4 -0.019 0.14 -9999 0 -0.42 58 58
FZD3 0.006 0.097 -9999 0 -0.42 24 24
WNT5A -0.027 0.15 -9999 0 -0.42 64 64
WNT11 0.027 0.032 -9999 0 -0.42 2 2
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 0.032 0.071 -10000 0 -0.22 32 32
NF kappa B1 p50/RelA/I kappa B alpha 0.021 0.096 0.27 6 -0.31 9 15
AP1 -0.034 0.12 -10000 0 -0.25 101 101
mol:PIP3 -0.03 0.09 -10000 0 -0.22 85 85
AKT1 -0.006 0.1 0.25 3 -0.31 28 31
PTK2B -0.041 0.1 0.14 1 -0.21 110 111
RHOA -0.015 0.1 -10000 0 -0.34 32 32
PIK3CB 0.031 0.046 -10000 0 -0.42 5 5
mol:Ca2+ -0.009 0.092 0.19 44 -0.2 53 97
MAGI3 0.012 0.099 -10000 0 -0.42 25 25
RELA 0.035 0.006 -10000 0 -10000 0 0
apoptosis 0.004 0.052 -10000 0 -0.18 36 36
HRAS/GDP 0.024 0.025 -10000 0 -0.3 3 3
positive regulation of microtubule depolymerization -0.076 0.12 0.18 3 -0.24 127 130
NF kappa B1 p50/RelA -0.021 0.082 -10000 0 -0.22 57 57
endothelial cell migration -0.008 0.12 -10000 0 -0.52 25 25
ADCY4 -0.014 0.086 -10000 0 -0.28 37 37
ADCY5 -0.014 0.083 -10000 0 -0.28 33 33
ADCY6 -0.012 0.08 -10000 0 -0.26 35 35
ADCY7 -0.013 0.085 -10000 0 -0.29 32 32
ADCY1 -0.012 0.081 -10000 0 -0.27 36 36
ADCY2 -0.024 0.097 -10000 0 -0.3 41 41
ADCY3 -0.013 0.081 -10000 0 -0.27 34 34
ADCY8 -0.012 0.072 -10000 0 -0.27 27 27
ADCY9 -0.015 0.08 -10000 0 -0.24 42 42
GSK3B -0.042 0.097 0.16 1 -0.21 105 106
arachidonic acid secretion -0.017 0.088 -10000 0 -0.27 44 44
GNG2 0.034 0.021 -10000 0 -0.42 1 1
TRIP6 0.008 0.071 -10000 0 -0.36 17 17
GNAO1 0.006 0.053 -10000 0 -0.22 25 25
HRAS 0.032 0.036 -10000 0 -0.42 3 3
NFKBIA -0.008 0.092 0.21 14 -0.26 19 33
GAB1 0.027 0.061 -10000 0 -0.42 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.023 0.2 -10000 0 -0.92 21 21
JUN -0.001 0.12 -10000 0 -0.42 39 39
LPA/LPA2/NHERF2 -0.004 0.077 -10000 0 -0.2 57 57
TIAM1 0.002 0.23 -10000 0 -1.1 21 21
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
mol:IP3 -0.008 0.092 0.18 47 -0.21 50 97
PLCB3 0.01 0.091 0.19 47 -0.23 42 89
FOS -0.031 0.15 -10000 0 -0.42 66 66
positive regulation of mitosis -0.017 0.088 -10000 0 -0.27 44 44
LPA/LPA1-2-3 -0.006 0.049 -10000 0 -0.17 39 39
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.029 0.014 -10000 0 -10000 0 0
stress fiber formation -0.006 0.081 -10000 0 -0.28 21 21
GNAZ 0 0.069 -10000 0 -0.21 46 46
EGFR/PI3K-beta/Gab1 -0.022 0.097 -10000 0 -0.22 85 85
positive regulation of dendritic cell cytokine production -0.006 0.048 -10000 0 -0.17 39 39
LPA/LPA2/MAGI-3 0.005 0.065 -10000 0 -0.17 49 49
ARHGEF1 0.026 0.076 0.19 51 -0.21 22 73
GNAI2 0.002 0.07 -10000 0 -0.22 41 41
GNAI3 0.007 0.056 -10000 0 -0.19 35 35
GNAI1 -0.004 0.08 -10000 0 -0.23 51 51
LPA/LPA3 -0.004 0.025 -10000 0 -0.086 39 39
LPA/LPA2 -0.004 0.024 -10000 0 -0.086 39 39
LPA/LPA1 -0.009 0.065 -10000 0 -0.23 39 39
HB-EGF/EGFR -0.025 0.12 -10000 0 -0.28 89 89
HBEGF -0.021 0.098 -10000 0 -0.3 55 55
mol:DAG -0.008 0.092 0.18 47 -0.21 50 97
cAMP biosynthetic process -0.019 0.088 0.2 3 -0.27 37 40
NFKB1 0.035 0.005 -10000 0 -10000 0 0
SRC 0.032 0.03 -10000 0 -0.42 2 2
GNB1 0.032 0.045 -10000 0 -0.42 5 5
LYN 0.006 0.095 0.2 45 -0.24 19 64
GNAQ -0.003 0.02 -10000 0 -0.07 39 39
LPAR2 0 0.001 -10000 0 -10000 0 0
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 -0.007 0.038 -10000 0 -0.14 39 39
IL8 -0.069 0.18 -10000 0 -0.42 86 86
PTK2 0.011 0.042 -10000 0 -0.16 25 25
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
CASP3 0.004 0.053 -10000 0 -0.18 36 36
EGFR -0.013 0.13 -10000 0 -0.42 47 47
PLCG1 -0.003 0.043 -10000 0 -0.12 48 48
PLD2 0.01 0.052 -10000 0 -0.17 36 36
G12/G13 0.031 0.063 -10000 0 -0.22 22 22
PI3K-beta -0.019 0.1 -10000 0 -0.34 28 28
cell migration 0.009 0.067 -10000 0 -0.26 20 20
SLC9A3R2 -0.004 0.12 -10000 0 -0.42 40 40
PXN -0.006 0.082 -10000 0 -0.28 21 21
HRAS/GTP -0.017 0.09 -10000 0 -0.28 44 44
RAC1 0.035 0.006 -10000 0 -10000 0 0
MMP9 -0.014 0.14 -10000 0 -0.42 52 52
PRKCE 0.031 0.046 -10000 0 -0.42 5 5
PRKCD -0.011 0.089 0.18 43 -0.21 42 85
Gi(beta/gamma) -0.007 0.085 -10000 0 -0.26 38 38
mol:LPA -0.007 0.038 -10000 0 -0.14 39 39
TRIP6/p130 Cas/FAK1/Paxillin 0.009 0.08 -10000 0 -0.26 23 23
MAPKKK cascade -0.017 0.088 -10000 0 -0.27 44 44
contractile ring contraction involved in cytokinesis -0.016 0.1 -10000 0 -0.34 34 34
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.015 0.075 -10000 0 -0.21 55 55
GNA15 0.007 0.035 -10000 0 -0.12 24 24
GNA12 0.035 0.006 -10000 0 -10000 0 0
GNA13 0.028 0.042 -10000 0 -0.42 4 4
MAPT -0.078 0.12 0.18 3 -0.25 127 130
GNA11 0.008 0.03 -10000 0 -0.25 3 3
Rac1/GTP 0.023 0.21 -10000 0 -0.98 21 21
MMP2 -0.008 0.12 -10000 0 -0.52 25 25
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.015 0.032 -10000 0 -0.25 6 6
ARNO/beta Arrestin1-2 0.013 0.069 -10000 0 -0.2 40 40
EGFR -0.013 0.13 -10000 0 -0.42 47 47
EPHA2 0.031 0.036 -10000 0 -0.42 3 3
USP6 0.032 0.012 -10000 0 -10000 0 0
IQSEC1 0.034 0.021 -10000 0 -0.42 1 1
EGFR/EGFR/EGF/EGF -0.061 0.16 -10000 0 -0.31 151 151
ARRB2 0.011 0.043 -10000 0 -0.3 9 9
mol:GTP 0.007 0.019 0.11 5 -0.11 2 7
ARRB1 0.026 0.05 -10000 0 -0.42 6 6
FBXO8 0.035 0.007 -10000 0 -10000 0 0
TSHR 0.029 0.05 -10000 0 -0.42 6 6
EGF -0.069 0.19 -10000 0 -0.42 110 110
somatostatin receptor activity 0 0 0 3 -0.001 75 78
ARAP2 0 0 0 2 0 68 70
mol:GDP -0.029 0.099 -10000 0 -0.25 57 57
mol:PI-3-4-5-P3 0 0 0 2 -0.001 73 75
ITGA2B 0.034 0.009 -10000 0 -10000 0 0
ARF6 0.033 0.029 -10000 0 -0.42 2 2
Ephrin A1/EPHA2/NCK1/GIT1 0.052 0.072 -10000 0 -0.24 20 20
ADAP1 0 0 0 2 0 44 46
KIF13B 0.022 0.051 -10000 0 -0.42 6 6
HGF/MET 0.041 0.057 -10000 0 -0.3 13 13
PXN 0.036 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.035 0.1 0.15 2 -0.24 76 78
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.035 0.15 -10000 0 -0.26 150 150
ADRB2 0.003 0.11 -10000 0 -0.42 33 33
receptor agonist activity 0 0 0 2 0 54 56
actin filament binding 0 0 0 3 0 77 80
SRC 0.032 0.03 -10000 0 -0.42 2 2
ITGB3 0.029 0.046 -10000 0 -0.42 5 5
GNAQ 0 0 0.001 4 -0.001 54 58
EFA6/PI-4-5-P2 0 0 0.001 4 -0.001 51 55
ARF6/GDP 0.004 0.074 0.2 2 -0.27 12 14
ARF6/GDP/GULP/ACAP1 -0.017 0.12 -10000 0 -0.27 71 71
alphaIIb/beta3 Integrin/paxillin/GIT1 0.079 0.042 -10000 0 -0.24 5 5
ACAP1 0 0 0 1 -10000 0 1
ACAP2 0 0 0 1 0 70 71
LHCGR/beta Arrestin2 0.018 0.06 -10000 0 -0.38 9 9
EFNA1 0.014 0.08 -10000 0 -0.42 16 16
HGF 0.028 0.057 -10000 0 -0.42 8 8
CYTH3 0 0 0.001 3 -0.001 61 64
CYTH2 -0.001 0.002 -10000 0 -0.004 80 80
NCK1 0.034 0.022 -10000 0 -0.42 1 1
fibronectin binding 0 0 0 2 0 52 54
endosomal lumen acidification 0 0 0 2 0 62 64
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.001 0.12 -10000 0 -0.42 37 37
GNAQ/ARNO -0.001 0.003 0.006 4 -0.006 52 56
mol:Phosphatidic acid 0 0 0 1 0 70 71
PIP3-E 0.028 0.042 -10000 0 -0.42 4 4
MET 0.028 0.046 -10000 0 -0.42 5 5
GNA14 -0.01 0.13 -10000 0 -0.42 44 44
GNA15 0.029 0.046 -10000 0 -0.42 5 5
GIT1 0.033 0.022 -10000 0 -0.42 1 1
mol:PI-4-5-P2 0 0 0.001 2 -0.001 56 58
GNA11 0.032 0.036 -10000 0 -0.42 3 3
LHCGR 0.027 0.061 -10000 0 -0.42 9 9
AGTR1 -0.045 0.16 -10000 0 -0.42 78 78
desensitization of G-protein coupled receptor protein signaling pathway 0.018 0.06 -10000 0 -0.38 9 9
IPCEF1/ARNO -0.024 0.12 -10000 0 -0.2 149 149
alphaIIb/beta3 Integrin 0.046 0.034 -10000 0 -0.3 4 4
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.019 0.075 -10000 0 -0.42 14 14
EPHB2 0.032 0.03 -10000 0 -0.43 2 2
EFNB1 0.013 0.032 -10000 0 -0.3 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.071 0.067 -10000 0 -0.24 17 17
Ephrin B2/EPHB1-2 0.045 0.064 -10000 0 -0.24 20 20
neuron projection morphogenesis 0.046 0.058 -10000 0 -0.23 17 17
Ephrin B1/EPHB1-2/Tiam1 0.062 0.066 -10000 0 -0.26 17 17
DNM1 0.032 0.041 -10000 0 -0.42 4 4
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.08 0.2 0.23 1 -0.55 78 79
YES1 -0.11 0.3 -10000 0 -0.8 79 79
Ephrin B1/EPHB1-2/NCK2 0.067 0.054 -10000 0 -0.24 12 12
PI3K -0.048 0.23 -10000 0 -0.56 79 79
mol:GDP 0.06 0.065 -10000 0 -0.25 17 17
ITGA2B 0.034 0.009 -10000 0 -10000 0 0
endothelial cell proliferation 0.023 0.076 -10000 0 -0.27 30 30
FYN -0.11 0.3 -10000 0 -0.8 79 79
MAP3K7 -0.08 0.21 0.23 2 -0.59 75 77
FGR -0.1 0.29 -10000 0 -0.78 79 79
TIAM1 0.028 0.057 -10000 0 -0.42 8 8
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
RGS3 0.035 0.005 -10000 0 -10000 0 0
cell adhesion -0.056 0.21 -10000 0 -0.53 77 77
LYN -0.1 0.29 -10000 0 -0.78 79 79
Ephrin B1/EPHB1-2/Src Family Kinases -0.1 0.27 -10000 0 -0.73 79 79
Ephrin B1/EPHB1-2 -0.086 0.23 -10000 0 -0.64 75 75
SRC -0.099 0.29 -10000 0 -0.78 78 78
ITGB3 0.029 0.046 -10000 0 -0.42 5 5
EPHB1 0.026 0.051 -10000 0 -0.42 6 6
EPHB4 0.018 0.085 -10000 0 -0.42 18 18
RAC1 0.035 0.006 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.023 0.076 -10000 0 -0.27 30 30
alphaIIb/beta3 Integrin 0.046 0.034 -10000 0 -0.3 4 4
BLK -0.12 0.29 -10000 0 -0.8 78 78
HCK -0.11 0.29 -10000 0 -0.78 78 78
regulation of stress fiber formation -0.065 0.053 0.24 12 -10000 0 12
MAPK8 -0.079 0.2 -10000 0 -0.53 78 78
Ephrin B1/EPHB1-2/RGS3 0.067 0.054 -10000 0 -0.24 12 12
endothelial cell migration -0.077 0.19 0.2 4 -0.5 75 79
NCK2 0.036 0.004 -10000 0 -10000 0 0
PTPN13 -0.046 0.2 -10000 0 -0.54 72 72
regulation of focal adhesion formation -0.065 0.053 0.24 12 -10000 0 12
chemotaxis -0.065 0.053 0.24 12 -10000 0 12
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
Rac1/GTP 0.06 0.063 -10000 0 -0.24 17 17
angiogenesis -0.088 0.23 -10000 0 -0.63 78 78
LCK -0.12 0.3 -10000 0 -0.8 79 79
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.017 0.036 -10000 0 -0.26 11 11
SNTA1 0.031 0.041 -10000 0 -0.42 4 4
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.022 0.05 -10000 0 -0.26 22 22
MAPK12 0.001 0.084 0.21 40 -0.23 33 73
CCND1 -0.056 0.16 -10000 0 -0.42 81 81
p38 gamma/SNTA1 0.026 0.088 0.34 2 -0.22 35 37
MAP2K3 0.032 0.023 -10000 0 -0.42 1 1
PKN1 0.033 0.035 -10000 0 -0.42 3 3
G2/M transition checkpoint 0.001 0.083 0.21 40 -0.23 33 73
MAP2K6 0.013 0.095 0.24 45 -0.24 33 78
MAPT -0.055 0.13 0.28 5 -0.28 106 111
MAPK13 0.006 0.052 -10000 0 -0.3 14 14
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.005 0.062 -10000 0 -0.29 22 22
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 -0.002 0.05 -10000 0 -0.3 14 14
TP53 -0.026 0.092 0.26 1 -0.26 61 62
Senescence -0.029 0.094 0.26 1 -0.25 69 70
Apoptosis -0.029 0.094 0.26 1 -0.25 69 70
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.004 0.061 0.26 25 -10000 0 25
MDM4 0.026 0.032 -10000 0 -0.42 2 2
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.013 0.1 -9999 0 -0.26 58 58
E-cadherin/beta catenin 0.004 0.11 -9999 0 -0.3 55 55
CTNNB1 0.024 0.067 -9999 0 -0.42 11 11
JUP 0.028 0.042 -9999 0 -0.42 4 4
CDH1 -0.012 0.13 -9999 0 -0.42 45 45
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.06 0.29 -10000 0 -0.93 46 46
epithelial cell differentiation -0.028 0.25 -10000 0 -0.7 50 50
ITCH 0.035 0.038 -10000 0 -10000 0 0
WWP1 -0.087 0.39 -10000 0 -1.4 42 42
FYN 0.027 0.05 -10000 0 -0.42 6 6
EGFR -0.013 0.13 -10000 0 -0.42 47 47
PRL 0.033 0.022 -10000 0 -0.42 1 1
neuron projection morphogenesis -0.019 0.22 0.32 14 -0.65 43 57
PTPRZ1 0.023 0.058 -10000 0 -0.42 8 8
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.03 0.23 -10000 0 -0.72 43 43
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.064 0.26 -10000 0 -0.88 43 43
ADAM17 0.035 0.037 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.08 0.3 -10000 0 -1 45 45
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.062 0.29 -10000 0 -0.91 47 47
NCOR1 0.032 0.011 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.053 0.25 -10000 0 -0.82 43 43
GRIN2B -0.062 0.22 0.25 1 -0.75 43 44
ErbB4/ErbB2/betacellulin -0.07 0.26 -10000 0 -0.73 56 56
STAT1 0.02 0.075 -10000 0 -0.42 14 14
HBEGF 0.03 0.046 -10000 0 -0.42 5 5
PRLR -0.002 0.12 -10000 0 -0.42 40 40
E4ICDs/ETO2 -0.11 0.32 -10000 0 -0.84 62 62
axon guidance -0.069 0.28 -10000 0 -0.9 46 46
NEDD4 0.024 0.079 -10000 0 -0.43 12 12
Prolactin receptor/Prolactin receptor/Prolactin 0.022 0.095 -10000 0 -0.3 39 39
CBFA2T3 -0.047 0.16 -10000 0 -0.42 81 81
ErbB4/ErbB2/HBEGF -0.051 0.26 -10000 0 -0.78 50 50
MAPK3 -0.016 0.22 0.35 9 -0.67 43 52
STAT1 (dimer) -0.064 0.29 -10000 0 -0.91 47 47
MAPK1 -0.016 0.22 0.35 9 -0.67 43 52
JAK2 0.031 0.03 -10000 0 -0.42 2 2
ErbB4/ErbB2/neuregulin 1 beta -0.064 0.25 -10000 0 -0.78 50 50
NRG1 0.012 0.021 -10000 0 -10000 0 0
NRG3 0.028 0.054 -10000 0 -0.42 7 7
NRG2 0.025 0.058 -10000 0 -0.42 8 8
NRG4 0.033 0.022 -10000 0 -0.42 1 1
heart development -0.069 0.28 -10000 0 -0.9 46 46
neural crest cell migration -0.063 0.25 -10000 0 -0.76 50 50
ERBB2 0.006 0.058 -10000 0 -0.3 15 15
WWOX/E4ICDs -0.071 0.29 -10000 0 -0.91 47 47
SHC1 0.027 0.025 -10000 0 -0.42 1 1
ErbB4/EGFR/neuregulin 4 -0.065 0.28 -10000 0 -0.84 48 48
apoptosis 0.06 0.28 0.84 50 -10000 0 50
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.062 0.29 -10000 0 -0.92 47 47
ErbB4/ErbB2/epiregulin -0.054 0.26 -10000 0 -0.77 51 51
ErbB4/ErbB4/betacellulin/betacellulin -0.081 0.3 -10000 0 -0.86 53 53
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.034 0.28 -10000 0 -0.71 59 59
MDM2 -0.069 0.29 0.28 14 -0.93 45 59
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.045 0.23 -10000 0 -0.78 43 43
STAT5A -0.042 0.28 0.32 7 -0.87 45 52
ErbB4/EGFR/neuregulin 1 beta -0.07 0.25 -10000 0 -0.81 45 45
DLG4 0.032 0.012 -10000 0 -10000 0 0
GRB2/SHC 0.038 0.028 -10000 0 -0.3 1 1
E4ICDs/TAB2/NCoR1 -0.048 0.28 -10000 0 -0.87 46 46
STAT5A (dimer) -0.022 0.28 -10000 0 -0.81 48 48
MAP3K7IP2 0.031 0.03 -10000 0 -0.42 2 2
STAT5B (dimer) -0.045 0.28 -10000 0 -0.86 47 47
LRIG1 0.005 0.11 -10000 0 -0.42 32 32
EREG 0.025 0.051 -10000 0 -0.42 6 6
BTC -0.012 0.14 -10000 0 -0.42 50 50
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.071 0.28 -10000 0 -0.91 46 46
ERBB4 -0.081 0.31 -10000 0 -1 45 45
STAT5B 0.03 0.024 -10000 0 -0.42 1 1
YAP1 -0.023 0.15 -10000 0 -0.42 46 46
GRB2 0.033 0.01 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.049 0.26 -10000 0 -0.77 50 50
glial cell differentiation 0.047 0.27 0.85 46 -10000 0 46
WWOX 0.027 0.016 -10000 0 -10000 0 0
cell proliferation -0.08 0.26 0.33 1 -0.8 49 50
Coregulation of Androgen receptor activity

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
NRIP1 -0.01 0.14 -9999 0 -0.42 51 51
SVIL 0.022 0.078 -9999 0 -0.42 15 15
ZNF318 0.032 0.007 -9999 0 -10000 0 0
JMJD2C 0.039 0.01 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 -0.038 0.13 -9999 0 -0.25 111 111
CARM1 0.034 0.021 -9999 0 -0.42 1 1
PRDX1 0.032 0.036 -9999 0 -0.42 3 3
PELP1 0.032 0.011 -9999 0 -10000 0 0
CTNNB1 0.025 0.067 -9999 0 -0.42 11 11
AKT1 0.031 0.036 -9999 0 -0.42 3 3
PTK2B 0.028 0.016 -9999 0 -10000 0 0
MED1 -0.001 0 -9999 0 -10000 0 0
MAK 0.024 0.046 -9999 0 -0.42 5 5
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.036 0.006 -9999 0 -10000 0 0
GSN 0.022 0.08 -9999 0 -0.42 16 16
NCOA2 0.025 0.047 -9999 0 -0.42 5 5
NCOA6 0.036 0.008 -9999 0 -10000 0 0
DNA-PK 0.054 0.035 -9999 0 -0.25 2 2
NCOA4 0.03 0.05 -9999 0 -0.42 6 6
PIAS3 0.036 0.006 -9999 0 -10000 0 0
cell proliferation -0.014 0.096 -9999 0 -0.57 12 12
XRCC5 0.035 0.004 -9999 0 -10000 0 0
UBE3A 0.036 0.029 -9999 0 -0.42 2 2
T-DHT/AR/SNURF -0.052 0.12 -9999 0 -0.17 213 213
FHL2 -0.12 0.32 -9999 0 -0.9 69 69
RANBP9 0.036 0.007 -9999 0 -10000 0 0
JMJD1A 0.009 0.072 -9999 0 -0.15 88 88
CDK6 0.025 0.054 -9999 0 -0.42 7 7
TGFB1I1 0.017 0.085 -9999 0 -0.42 18 18
T-DHT/AR/CyclinD1 -0.074 0.17 -9999 0 -0.34 133 133
XRCC6 0.033 0.009 -9999 0 -10000 0 0
T-DHT/AR -0.065 0.14 -9999 0 -0.22 213 213
CTDSP1 0.034 0.029 -9999 0 -0.42 2 2
CTDSP2 0.032 0.029 -9999 0 -0.42 2 2
BRCA1 0.022 0.07 -9999 0 -0.42 12 12
TCF4 0.015 0.089 -9999 0 -0.42 20 20
CDKN2A 0.014 0.075 -9999 0 -0.42 14 14
SRF 0.016 0.061 -9999 0 -0.15 47 47
NKX3-1 -0.049 0.1 -9999 0 -0.24 92 92
KLK3 0.021 0.053 -9999 0 -10000 0 0
TMF1 0.035 0.007 -9999 0 -10000 0 0
HNRNPA1 -0.001 0 -9999 0 -10000 0 0
AOF2 0.036 0.008 -9999 0 -10000 0 0
APPL1 -0.007 0.023 -9999 0 -0.3 3 3
T-DHT/AR/Caspase 8 -0.04 0.13 -9999 0 -0.25 113 113
AR -0.078 0.18 -9999 0 -0.39 114 114
UBA3 0 0 -9999 0 -10000 0 0
PATZ1 -0.001 0 -9999 0 -10000 0 0
PAWR 0.024 0.073 -9999 0 -0.42 13 13
PRKDC 0.028 0.031 -9999 0 -0.42 2 2
PA2G4 0.034 0.005 -9999 0 -10000 0 0
UBE2I 0.032 0.011 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.032 0.12 -9999 0 -0.23 108 108
RPS6KA3 0.033 0.041 -9999 0 -0.42 4 4
T-DHT/AR/ARA70 -0.043 0.13 -9999 0 -0.26 118 118
LATS2 0.024 0.061 -9999 0 -0.42 9 9
T-DHT/AR/PRX1 -0.037 0.12 -9999 0 -0.23 116 116
Cyclin D3/CDK11 p58 0.026 0.005 -9999 0 -10000 0 0
VAV3 -0.039 0.17 -9999 0 -0.42 81 81
KLK2 -0.014 0.088 -9999 0 -0.39 15 15
CASP8 0.035 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.022 0.12 -9999 0 -0.23 98 98
TMPRSS2 -0.15 0.35 -9999 0 -0.88 91 91
CCND1 -0.042 0.16 -9999 0 -0.42 79 79
PIAS1 0.037 0.007 -9999 0 -10000 0 0
mol:T-DHT -0.014 0.03 -9999 0 -0.065 120 120
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.035 0.036 -9999 0 -0.42 3 3
T-DHT/AR/CDK6 -0.042 0.13 -9999 0 -0.25 117 117
CMTM2 0.028 0.024 -9999 0 -0.42 1 1
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 -0.014 0.03 -9999 0 -0.065 120 120
CCND3 0.035 0.007 -9999 0 -10000 0 0
TGIF1 -0.001 0 -9999 0 -10000 0 0
FKBP4 0.03 0.046 -9999 0 -0.42 5 5
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 -0.007 0.13 -9999 0 -0.42 43 43
PLK4 0.03 0.05 -9999 0 -0.42 6 6
regulation of centriole replication -0.015 0.093 -9999 0 -0.3 48 48
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.013 0.12 -10000 0 -0.57 3 3
UGCG -0.09 0.27 -10000 0 -0.72 73 73
AKT1/mTOR/p70S6K/Hsp90/TERT -0.063 0.19 0.31 1 -0.38 92 93
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.089 0.26 -10000 0 -0.71 74 74
mol:DAG -0.006 0.027 0.17 11 -10000 0 11
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.08 0.23 0.34 1 -0.47 87 88
FRAP1 -0.1 0.26 0.36 1 -0.54 89 90
FOXO3 -0.05 0.2 0.36 1 -0.51 49 50
AKT1 -0.055 0.22 0.38 1 -0.56 49 50
GAB2 0.028 0.015 -10000 0 -10000 0 0
SMPD1 -0.004 0.13 -10000 0 -0.69 15 15
SGMS1 -0.004 0.034 0.058 1 -0.079 45 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 -0.009 0.049 -10000 0 -0.25 18 18
CALM1 0.035 0.007 -10000 0 -10000 0 0
cell proliferation -0.041 0.18 0.28 3 -0.37 95 98
EIF3A 0 0 -10000 0 -10000 0 0
PI3K 0.033 0.068 -10000 0 -0.3 18 18
RPS6KB1 -0.043 0.16 -10000 0 -0.84 13 13
mol:sphingomyelin -0.006 0.027 0.17 11 -10000 0 11
natural killer cell activation -0.002 0.004 -10000 0 -0.011 57 57
JAK3 0.035 0.009 -10000 0 -10000 0 0
PIK3R1 0.017 0.083 -10000 0 -0.42 17 17
JAK1 0.031 0.037 -10000 0 -0.42 3 3
NFKB1 0.035 0.005 -10000 0 -10000 0 0
MYC -0.027 0.29 0.49 2 -0.95 35 37
MYB -0.23 0.5 -10000 0 -1.2 106 106
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.022 0.15 -10000 0 -0.4 37 37
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.025 0.16 -10000 0 -0.74 13 13
mol:PI-3-4-5-P3 -0.02 0.15 -10000 0 -0.39 37 37
Rac1/GDP 0.007 0.052 -10000 0 -0.23 18 18
T cell proliferation -0.018 0.14 0.29 3 -0.37 37 40
SHC1 0.025 0.026 -10000 0 -0.42 1 1
RAC1 0.035 0.006 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.01 0.028 -10000 0 -0.065 103 103
PRKCZ -0.021 0.15 -10000 0 -0.38 37 37
NF kappa B1 p50/RelA -0.07 0.24 0.36 1 -0.47 86 87
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.012 0.13 -10000 0 -0.42 30 30
HSP90AA1 0 0 -10000 0 -10000 0 0
RELA 0.035 0.006 -10000 0 -10000 0 0
IL2RA 0.001 0.11 -10000 0 -0.42 31 31
IL2RB 0.011 0.095 -10000 0 -0.42 23 23
TERT 0.032 0.03 -10000 0 -0.42 2 2
E2F1 -0.073 0.2 -10000 0 -0.43 113 113
SOS1 0.032 0.023 -10000 0 -0.43 1 1
RPS6 0.034 0.022 -10000 0 -0.42 1 1
mol:cAMP 0.004 0.013 0.031 100 -10000 0 100
PTPN11 0.032 0.013 -10000 0 -10000 0 0
IL2RG 0.029 0.042 -10000 0 -0.42 4 4
actin cytoskeleton organization -0.018 0.14 0.29 3 -0.37 37 40
GRB2 0.03 0.013 -10000 0 -10000 0 0
IL2 0.03 0.037 -10000 0 -0.42 3 3
PIK3CA 0.032 0.024 -10000 0 -0.43 1 1
Rac1/GTP 0.032 0.065 -10000 0 -0.22 18 18
LCK -0.019 0.14 -10000 0 -0.42 54 54
BCL2 -0.18 0.38 -10000 0 -0.84 114 114
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.052 0.052 0.23 20 -0.43 1 21
AES 0.051 0.042 0.21 20 -10000 0 20
FBXW11 0.034 0.021 -10000 0 -0.42 1 1
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.04 0.053 -10000 0 -0.3 11 11
SMAD4 0.028 0.054 -10000 0 -0.42 7 7
DKK2 0.006 0.11 -10000 0 -0.42 31 31
TLE1 0.021 0.12 0.22 21 -0.42 33 54
MACF1 0.034 0.021 -10000 0 -0.42 1 1
CTNNB1 -0.001 0.1 0.27 5 -0.37 11 16
WIF1 0.03 0.014 -10000 0 -10000 0 0
beta catenin/RanBP3 0.073 0.2 0.41 113 -0.36 7 120
KREMEN2 -0.091 0.19 -10000 0 -0.42 129 129
DKK1 -0.028 0.15 -10000 0 -0.42 61 61
beta catenin/beta TrCP1 0.012 0.11 0.28 5 -0.37 9 14
FZD1 0.028 0.054 -10000 0 -0.42 7 7
AXIN2 -0.049 0.39 0.6 51 -1.3 32 83
AXIN1 0.036 0.002 -10000 0 -10000 0 0
RAN 0.036 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.044 0.065 -10000 0 -0.59 4 4
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.007 0.17 0.33 5 -0.48 35 40
Axin1/APC/GSK3 0.033 0.049 -10000 0 -0.31 1 1
Axin1/APC/GSK3/beta catenin/Macf1 0.021 0.08 0.31 4 -0.36 5 9
HNF1A 0.017 0.045 0.19 22 -10000 0 22
CTBP1 0.049 0.045 0.23 17 -10000 0 17
MYC 0.032 0.47 0.59 113 -1.3 37 150
RANBP3 0.036 0.007 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.044 0.15 -10000 0 -0.26 153 153
NKD1 0.026 0.037 -10000 0 -0.42 3 3
TCF4 0.033 0.099 0.22 20 -0.4 20 40
TCF3 0.047 0.056 0.22 18 -0.42 3 21
WNT1/LRP6/FZD1/Axin1 0.076 0.057 -10000 0 -0.24 12 12
Ran/GTP 0.028 0.005 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.089 0.26 0.53 100 -0.47 12 112
LEF1 0.037 0.086 0.25 12 -0.41 13 25
DVL1 0.031 0.049 -10000 0 -0.28 3 3
CSNK2A1 0.035 0.008 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.044 0.18 -10000 0 -0.53 37 37
DKK1/LRP6/Kremen 2 -0.062 0.16 -10000 0 -0.28 169 169
LRP6 0.029 0.046 -10000 0 -0.42 5 5
CSNK1A1 0.053 0.047 0.23 20 -10000 0 20
NLK 0.028 0.027 -10000 0 -0.43 1 1
CCND1 -0.15 0.6 0.58 73 -1.4 86 159
WNT1 0.034 0.021 -10000 0 -0.42 1 1
GSK3A 0.035 0.004 -10000 0 -10000 0 0
GSK3B 0.035 0.005 -10000 0 -10000 0 0
FRAT1 0.029 0.054 -10000 0 -0.42 7 7
PPP2R5D 0.029 0.065 0.24 2 -0.31 7 9
APC -0.014 0.058 0.2 18 -0.22 16 34
WNT1/LRP6/FZD1 0.022 0.049 -10000 0 -0.23 8 8
CREBBP 0.048 0.044 0.22 15 -10000 0 15
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.013 0.089 0.22 1 -0.29 17 18
adherens junction organization -0.045 0.13 -10000 0 -0.38 34 34
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.013 0.11 0.27 2 -0.31 16 18
FMN1 -0.034 0.12 -10000 0 -0.26 84 84
mol:IP3 -0.016 0.076 -10000 0 -0.25 17 17
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.033 0.13 -10000 0 -0.27 84 84
CTNNB1 0.026 0.067 -10000 0 -0.42 11 11
AKT1 -0.017 0.094 0.19 1 -0.29 19 20
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.061 0.19 -10000 0 -0.43 74 74
CTNND1 0.034 0.022 -10000 0 -0.43 1 1
mol:PI-4-5-P2 -0.031 0.12 0.22 1 -0.26 75 76
VASP -0.038 0.12 -10000 0 -0.27 78 78
ZYX -0.037 0.12 -10000 0 -0.27 81 81
JUB -0.047 0.13 -10000 0 -0.28 83 83
EGFR(dimer) -0.04 0.14 -10000 0 -0.33 51 51
E-cadherin/beta catenin-gamma catenin 0.015 0.1 -10000 0 -0.24 58 58
mol:PI-3-4-5-P3 0 0.11 -10000 0 -0.3 17 17
PIK3CA 0.034 0.022 -10000 0 -0.42 1 1
PI3K 0 0.11 -10000 0 -0.3 17 17
FYN -0.018 0.091 0.22 1 -0.3 20 21
mol:Ca2+ -0.015 0.074 -10000 0 -0.25 17 17
JUP 0.03 0.042 -10000 0 -0.42 4 4
PIK3R1 0.019 0.083 -10000 0 -0.42 17 17
mol:DAG -0.016 0.076 -10000 0 -0.25 17 17
CDH1 -0.012 0.13 -10000 0 -0.42 45 45
RhoA/GDP -0.016 0.11 0.23 1 -0.28 31 32
establishment of polarity of embryonic epithelium -0.036 0.12 0.22 1 -0.27 78 79
SRC 0.032 0.03 -10000 0 -0.42 2 2
RAC1 0.035 0.006 -10000 0 -10000 0 0
RHOA 0.026 0.061 -10000 0 -0.42 9 9
EGFR -0.013 0.13 -10000 0 -0.42 47 47
CASR -0.014 0.077 0.22 1 -0.27 11 12
RhoA/GTP -0.002 0.089 0.21 1 -0.26 15 16
AKT2 -0.016 0.093 0.19 1 -0.29 17 18
actin cable formation -0.036 0.12 0.2 5 -0.34 32 37
apoptosis 0.009 0.1 0.29 20 -0.26 4 24
CTNNA1 0.036 0.007 -10000 0 -10000 0 0
mol:GDP -0.029 0.099 0.22 1 -0.28 33 34
PIP5K1A -0.033 0.12 -10000 0 -0.26 75 75
PLCG1 -0.016 0.077 -10000 0 -0.26 17 17
Rac1/GTP -0.029 0.14 -10000 0 -0.32 48 48
homophilic cell adhesion 0 0.004 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.028 0.057 -10000 0 -0.42 8 8
Jak2/Leptin Receptor -0.034 0.14 -10000 0 -0.36 45 45
PTP1B/AKT1 -0.043 0.13 0.26 3 -0.3 67 70
FYN 0.027 0.05 -10000 0 -0.42 6 6
p210 bcr-abl/PTP1B -0.06 0.14 0.28 3 -0.33 69 72
EGFR -0.023 0.13 -10000 0 -0.43 47 47
EGF/EGFR -0.089 0.18 0.29 2 -0.31 157 159
CSF1 0.034 0.022 -10000 0 -0.42 1 1
AKT1 0.032 0.036 -10000 0 -0.43 3 3
INSR 0.034 0.03 -10000 0 -0.43 2 2
PTP1B/N-cadherin -0.054 0.15 0.29 2 -0.35 64 66
Insulin Receptor/Insulin -0.008 0.13 0.31 2 -0.34 35 37
HCK 0.017 0.087 -10000 0 -0.42 19 19
CRK 0.031 0.023 -10000 0 -0.42 1 1
TYK2 -0.058 0.13 0.26 6 -0.33 60 66
EGF -0.074 0.19 -10000 0 -0.43 110 110
YES1 0.029 0.05 -10000 0 -0.42 6 6
CAV1 -0.069 0.15 0.27 3 -0.33 81 84
TXN 0.033 0.007 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.054 0.16 0.3 2 -0.33 80 82
cell migration 0.06 0.14 0.33 69 -0.28 3 72
STAT3 0.028 0.031 -10000 0 -0.42 2 2
PRLR 0.001 0.12 -10000 0 -0.41 42 42
ITGA2B 0.033 0.009 -10000 0 -10000 0 0
CSF1R 0.035 0.006 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.027 0.098 -10000 0 -0.3 41 41
FGR 0.034 0.008 -10000 0 -10000 0 0
PTP1B/p130 Cas -0.043 0.14 0.29 1 -0.32 64 65
Crk/p130 Cas -0.036 0.14 0.3 1 -0.32 58 59
DOK1 -0.053 0.14 0.26 3 -0.36 55 58
JAK2 -0.043 0.14 -10000 0 -0.39 42 42
Jak2/Leptin Receptor/Leptin -0.044 0.14 0.25 1 -0.38 38 39
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
PTPN1 -0.06 0.14 0.28 3 -0.33 70 73
LYN 0.03 0.014 -10000 0 -10000 0 0
CDH2 0.011 0.093 -10000 0 -0.42 22 22
SRC -0.004 0.12 -10000 0 -0.61 15 15
ITGB3 0.028 0.046 -10000 0 -0.43 5 5
CAT1/PTP1B -0.082 0.2 0.31 3 -0.47 72 75
CAPN1 0.024 0.065 -10000 0 -0.43 10 10
CSK 0.033 0.022 -10000 0 -0.42 1 1
PI3K -0.003 0.14 0.28 2 -0.34 39 41
mol:H2O2 -0.001 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.034 0.13 -10000 0 -0.37 33 33
negative regulation of transcription -0.042 0.14 -10000 0 -0.38 42 42
FCGR2A 0.017 0.07 -10000 0 -0.42 12 12
FER 0.032 0.022 -10000 0 -0.43 1 1
alphaIIb/beta3 Integrin 0.044 0.035 -10000 0 -0.31 4 4
BLK 0.021 0.038 -10000 0 -0.42 3 3
Insulin Receptor/Insulin/Shc 0.052 0.04 -10000 0 -0.26 3 3
RHOA 0.025 0.062 -10000 0 -0.43 9 9
LEPR 0.027 0.054 -10000 0 -0.42 7 7
BCAR1 0.029 0.014 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.033 0.01 -10000 0 -10000 0 0
mol:NADPH -0.002 0.004 -10000 0 -10000 0 0
TRPV6 -0.068 0.21 0.26 1 -0.49 74 75
PRL 0.035 0.026 -10000 0 -0.26 3 3
SOCS3 0.008 0.18 -10000 0 -1.3 9 9
SPRY2 0.005 0.11 -10000 0 -0.43 28 28
Insulin Receptor/Insulin/IRS1 0.031 0.11 -10000 0 -0.27 55 55
CSF1/CSF1R -0.033 0.14 0.3 2 -0.32 58 60
Ras protein signal transduction 0.055 0.17 0.62 40 -10000 0 40
IRS1 -0.014 0.14 -10000 0 -0.42 54 54
INS 0.034 0.022 -10000 0 -0.43 1 1
LEP -0.002 0.12 -10000 0 -0.42 36 36
STAT5B -0.05 0.13 0.25 2 -0.33 58 60
STAT5A -0.052 0.14 0.23 3 -0.33 62 65
GRB2 0.033 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.049 0.15 0.29 2 -0.34 65 67
CSN2 0.021 0.1 -10000 0 -1.4 2 2
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
LAT -0.009 0.12 -10000 0 -0.54 19 19
YBX1 0.037 0.044 -10000 0 -0.38 5 5
LCK -0.018 0.14 -10000 0 -0.42 54 54
SHC1 0.027 0.025 -10000 0 -0.42 1 1
NOX4 -0.022 0.14 -10000 0 -0.43 57 57
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.024 0.025 -10000 0 -0.3 3 3
alphaV beta3 Integrin 0.029 0.1 -10000 0 -0.27 52 52
PTK2 0.008 0.12 0.36 4 -0.41 19 23
IGF1R -0.043 0.17 -10000 0 -0.42 84 84
PI4KB 0 0 -10000 0 -10000 0 0
MFGE8 0.016 0.085 -10000 0 -0.42 18 18
SRC 0.032 0.03 -10000 0 -0.42 2 2
CDKN1B -0.009 0.12 -10000 0 -0.46 29 29
VEGFA 0 0 -10000 0 -10000 0 0
ILK 0.014 0.06 -10000 0 -0.5 4 4
ROCK1 0.035 0.005 -10000 0 -10000 0 0
AKT1 0.001 0.073 0.21 4 -0.41 8 12
PTK2B 0.005 0.06 0.21 9 -0.24 21 30
alphaV/beta3 Integrin/JAM-A 0.058 0.1 -10000 0 -0.23 43 43
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 0.076 -10000 0 -0.27 25 25
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.04 0.2 -10000 0 -0.32 153 153
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.007 0.068 -10000 0 -0.23 27 27
alphaV/beta3 Integrin/Syndecan-1 0.029 0.11 -10000 0 -0.27 56 56
PI4KA 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.08 0.22 -10000 0 -0.33 188 188
PI4 Kinase 0 0 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
alphaV/beta3 Integrin/Osteopontin -0.022 0.15 -10000 0 -0.28 127 127
RPS6KB1 -0.12 0.17 0.43 2 -0.45 78 80
TLN1 0.034 0.021 -10000 0 -0.42 1 1
MAPK3 -0.047 0.2 -10000 0 -0.54 56 56
GPR124 0.017 0.073 -10000 0 -0.42 13 13
MAPK1 -0.05 0.2 -10000 0 -0.55 59 59
PXN 0.036 0.004 -10000 0 -10000 0 0
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
alphaV/beta3 Integrin/Tumstatin 0.052 0.074 -10000 0 -0.28 22 22
cell adhesion 0.023 0.1 -10000 0 -0.27 49 49
ANGPTL3 0.03 0.046 -10000 0 -0.42 5 5
VEGFR2 homodimer/VEGFA homodimer/Src 0.043 0.03 -10000 0 -0.25 4 4
IGF-1R heterotetramer -0.043 0.17 -10000 0 -0.42 84 84
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
TGFBR2 0.032 0.036 -10000 0 -0.42 3 3
ITGB3 0.029 0.046 -10000 0 -0.42 5 5
IGF1 -0.041 0.17 -10000 0 -0.42 80 80
RAC1 0.035 0.006 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.034 0.087 -10000 0 -0.3 27 27
apoptosis 0.021 0.08 -10000 0 -0.42 16 16
CD47 0.018 0.085 -10000 0 -0.42 18 18
alphaV/beta3 Integrin/CD47 0.041 0.09 -10000 0 -0.26 38 38
VCL 0.035 0.021 -10000 0 -0.42 1 1
alphaV/beta3 Integrin/Del1 -0.01 0.15 -10000 0 -0.29 104 104
CSF1 0.034 0.022 -10000 0 -0.42 1 1
PIK3C2A 0.009 0.085 -10000 0 -0.55 9 9
PI4 Kinase/Pyk2 0.003 0.076 -10000 0 -0.21 51 51
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.05 0.069 -10000 0 -0.26 21 21
FAK1/Vinculin 0.027 0.11 0.31 6 -0.33 19 25
alphaV beta3/Integrin/ppsTEM5 0.034 0.087 -10000 0 -0.3 27 27
RHOA 0.026 0.061 -10000 0 -0.42 9 9
VTN 0.035 0.007 -10000 0 -10000 0 0
BCAR1 0.029 0.014 -10000 0 -10000 0 0
FGF2 -0.001 0.11 -10000 0 -0.42 34 34
F11R -0.005 0.072 -10000 0 -0.3 28 28
alphaV/beta3 Integrin/Lactadherin 0.043 0.093 -10000 0 -0.31 28 28
alphaV/beta3 Integrin/TGFBR2 0.051 0.072 -10000 0 -0.27 22 22
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.058 0.067 -10000 0 -0.24 16 16
HSP90AA1 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.05 0.065 -10000 0 -0.24 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.009 0.13 -10000 0 -0.42 48 48
alphaV/beta3 Integrin/Pyk2 0.034 0.066 0.2 3 -0.24 21 24
SDC1 -0.002 0.12 -10000 0 -0.42 41 41
VAV3 -0.051 0.089 0.18 3 -0.24 88 91
PTPN11 0.036 0.004 -10000 0 -10000 0 0
IRS1 -0.014 0.14 -10000 0 -0.42 54 54
FAK1/Paxillin 0.026 0.12 0.33 5 -0.33 19 24
cell migration 0.02 0.11 0.24 14 -0.3 19 33
ITGAV 0.021 0.08 -10000 0 -0.42 16 16
PI3K 0.058 0.11 -10000 0 -0.23 49 49
SPP1 -0.075 0.19 -10000 0 -0.42 117 117
KDR 0.033 0.035 -10000 0 -0.42 3 3
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.021 0.08 -10000 0 -0.42 16 16
COL4A3 0.032 0.036 -10000 0 -0.42 3 3
angiogenesis -0.037 0.21 -10000 0 -0.57 52 52
Rac1/GTP -0.013 0.098 -10000 0 -0.22 87 87
EDIL3 -0.056 0.18 -10000 0 -0.42 97 97
cell proliferation 0.051 0.072 -10000 0 -0.27 22 22
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.07 0.16 -10000 0 -0.41 64 64
KLHL20 -0.025 0.09 0.25 1 -0.26 17 18
CYFIP2 -0.006 0.13 -10000 0 -0.42 44 44
Rac1/GDP -0.034 0.12 0.26 5 -0.27 60 65
ENAH -0.064 0.16 -10000 0 -0.42 62 62
AP1M1 0.034 0.021 -10000 0 -0.42 1 1
RAP1B 0.032 0.03 -10000 0 -0.42 2 2
RAP1A 0.03 0.05 -10000 0 -0.42 6 6
CTNNB1 0.024 0.067 -10000 0 -0.42 11 11
CDC42/GTP -0.013 0.084 -10000 0 -0.23 13 13
ABI1/Sra1/Nap1 -0.046 0.054 -10000 0 -0.16 36 36
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.03 0.1 -10000 0 -0.24 58 58
RAPGEF1 -0.071 0.16 -10000 0 -0.37 76 76
CTNND1 0.033 0.022 -10000 0 -0.42 1 1
regulation of calcium-dependent cell-cell adhesion -0.073 0.18 -10000 0 -0.42 81 81
CRK -0.068 0.16 -10000 0 -0.39 79 79
E-cadherin/gamma catenin/alpha catenin 0.019 0.098 -10000 0 -0.26 48 48
alphaE/beta7 Integrin 0.044 0.039 -10000 0 -0.3 5 5
IQGAP1 0.034 0.008 -10000 0 -10000 0 0
NCKAP1 0.034 0.021 -10000 0 -0.42 1 1
Rap1/GTP/I-afadin 0.047 0.063 -10000 0 -0.23 21 21
DLG1 -0.082 0.18 -10000 0 -0.4 85 85
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.031 0.057 -10000 0 -0.17 21 21
MLLT4 0.02 0.075 -10000 0 -0.42 14 14
ARF6/GTP/NME1/Tiam1 0.056 0.045 -10000 0 -0.24 9 9
PI3K -0.036 0.074 -10000 0 -0.22 19 19
ARF6 0.033 0.029 -10000 0 -0.42 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.004 0.1 -10000 0 -0.31 48 48
TIAM1 0.028 0.057 -10000 0 -0.42 8 8
E-cadherin(dimer)/Ca2+ 0.03 0.096 -10000 0 -0.22 56 56
AKT1 -0.025 0.054 0.18 4 -0.17 6 10
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
CDH1 -0.012 0.13 -10000 0 -0.42 45 45
RhoA/GDP -0.034 0.12 0.26 5 -0.27 61 66
actin cytoskeleton organization -0.017 0.068 0.17 2 -0.19 16 18
CDC42/GDP -0.032 0.12 0.26 5 -0.26 60 65
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.01 0.077 -10000 0 -0.22 55 55
ITGB7 0.036 0.004 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.032 0.1 -10000 0 -0.24 56 56
E-cadherin/Ca2+/beta catenin/alpha catenin 0.018 0.087 -10000 0 -0.22 55 55
mol:GDP -0.053 0.12 0.26 5 -0.3 62 67
CDC42/GTP/IQGAP1 0.045 0.014 -10000 0 -10000 0 0
JUP 0.028 0.042 -10000 0 -0.42 4 4
p120 catenin/RhoA/GDP -0.03 0.13 0.27 4 -0.28 60 64
RAC1/GTP/IQGAP1 0.045 0.012 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.048 0.033 -10000 0 -0.3 4 4
RHOA 0.026 0.061 -10000 0 -0.42 9 9
CDC42 0.034 0.008 -10000 0 -10000 0 0
CTNNA1 0.035 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.031 0.077 0.14 2 -0.19 80 82
NME1 0.033 0.01 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.079 0.18 -10000 0 -0.41 81 81
regulation of cell-cell adhesion -0.018 0.069 -10000 0 -0.18 54 54
WASF2 -0.016 0.042 0.11 3 -0.11 9 12
Rap1/GTP -0.014 0.093 0.25 2 -0.25 13 15
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.036 0.1 -10000 0 -0.23 52 52
CCND1 -0.038 0.095 0.16 2 -0.23 80 82
VAV2 -0.066 0.19 -10000 0 -0.56 15 15
RAP1/GDP -0.018 0.1 0.27 2 -0.26 17 19
adherens junction assembly -0.077 0.17 -10000 0 -0.4 82 82
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.034 0.008 -10000 0 -10000 0 0
PIP5K1C 0.032 0.036 -10000 0 -0.42 3 3
regulation of heterotypic cell-cell adhesion 0.028 0.1 -10000 0 -0.22 61 61
E-cadherin/beta catenin -0.025 0.1 -10000 0 -0.29 63 63
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.08 0.17 -10000 0 -0.41 84 84
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
Rac1/GTP -0.076 0.13 -10000 0 -0.39 31 31
E-cadherin/beta catenin/alpha catenin 0.02 0.1 -10000 0 -0.26 55 55
ITGAE 0.028 0.046 -10000 0 -0.42 5 5
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.075 0.19 -10000 0 -0.43 81 81
Syndecan-2-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
Syndecan-2/Fibronectin -0.006 0.1 -10000 0 -0.3 50 50
EPHB2 0.032 0.03 -10000 0 -0.42 2 2
Syndecan-2/TACI 0.011 0.064 -10000 0 -0.25 27 27
LAMA1 0.034 0.009 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 0.02 0.13 -10000 0 -0.25 84 84
HRAS 0.032 0.036 -10000 0 -0.42 3 3
Syndecan-2/CASK -0.005 0.057 -10000 0 -0.24 27 27
ITGA5 0.033 0.035 -10000 0 -0.42 3 3
BAX -0.008 0.051 -10000 0 -10000 0 0
EPB41 0.034 0.021 -10000 0 -0.42 1 1
positive regulation of cell-cell adhesion 0.008 0.065 -10000 0 -0.23 33 33
LAMA3 -0.019 0.14 -10000 0 -0.42 57 57
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.014 0.091 -10000 0 -0.42 21 21
Syndecan-2/MMP2 0 0.088 -10000 0 -0.29 38 38
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.016 0.1 -10000 0 -0.3 46 46
dendrite morphogenesis 0.012 0.065 -10000 0 -0.25 28 28
Syndecan-2/GM-CSF 0.011 0.066 -10000 0 -0.25 29 29
determination of left/right symmetry -0.005 0.068 -10000 0 -0.29 27 27
Syndecan-2/PKC delta 0.012 0.066 -10000 0 -0.25 29 29
GNB2L1 0.033 0.035 -10000 0 -0.42 3 3
MAPK3 0.032 0.09 0.2 82 -0.22 27 109
MAPK1 0.036 0.094 0.2 94 -0.22 28 122
Syndecan-2/RACK1 0.025 0.067 -10000 0 -0.22 30 30
NF1 0.032 0.03 -10000 0 -0.42 2 2
FGFR/FGF/Syndecan-2 -0.005 0.068 -10000 0 -0.29 27 27
ITGA2 -0.009 0.13 -10000 0 -0.42 47 47
MAPK8 -0.005 0.058 -10000 0 -0.24 28 28
Syndecan-2/alpha2/beta1 Integrin 0.044 0.11 -10000 0 -0.24 48 48
Syndecan-2/Kininogen 0.012 0.064 -10000 0 -0.25 27 27
ITGB1 0.033 0.03 -10000 0 -0.42 2 2
SRC 0.037 0.093 0.19 98 -0.22 28 126
Syndecan-2/CASK/Protein 4.1 0.012 0.059 -10000 0 -0.22 28 28
extracellular matrix organization 0.013 0.064 -10000 0 -0.25 27 27
actin cytoskeleton reorganization -0.006 0.1 -10000 0 -0.3 50 50
Syndecan-2/Caveolin-2/Ras 0.017 0.09 -10000 0 -0.27 39 39
Syndecan-2/Laminin alpha3 -0.012 0.1 -10000 0 -0.26 67 67
Syndecan-2/RasGAP 0.033 0.075 -10000 0 -0.21 35 35
alpha5/beta1 Integrin 0.047 0.037 -10000 0 -0.3 5 5
PRKCD 0.032 0.03 -10000 0 -0.42 2 2
Syndecan-2 dimer 0.012 0.065 -10000 0 -0.25 28 28
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 0.067 0.19 1 -0.21 33 34
RHOA 0.026 0.061 -10000 0 -0.42 9 9
SDCBP 0.022 0.061 -10000 0 -0.42 9 9
TNFRSF13B 0.032 0.012 -10000 0 -10000 0 0
RASA1 0.028 0.054 -10000 0 -0.42 7 7
alpha2/beta1 Integrin 0.016 0.1 -10000 0 -0.3 46 46
Syndecan-2/Synbindin 0.011 0.063 -10000 0 -0.25 27 27
TGFB1 0.035 0.021 -10000 0 -0.42 1 1
CASP3 0.036 0.094 0.2 93 -0.22 28 121
FN1 -0.009 0.13 -10000 0 -0.42 48 48
Syndecan-2/IL8 -0.007 0.094 -10000 0 -0.27 52 52
SDC2 -0.005 0.068 -10000 0 -0.29 27 27
KNG1 0.034 0.008 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.011 0.066 -10000 0 -0.25 29 29
TRAPPC4 0.031 0.012 -10000 0 -10000 0 0
CSF2 0.03 0.036 -10000 0 -0.42 3 3
Syndecan-2/TGFB1 0.013 0.064 -10000 0 -0.25 27 27
Syndecan-2/Syntenin/PI-4-5-P2 0.008 0.065 -10000 0 -0.23 33 33
Syndecan-2/Ezrin 0.009 0.062 -10000 0 -0.22 32 32
PRKACA 0.036 0.095 0.2 95 -0.23 29 124
angiogenesis -0.007 0.094 -10000 0 -0.27 52 52
MMP2 0.006 0.099 -10000 0 -0.42 25 25
IL8 -0.005 0.12 -10000 0 -0.42 37 37
calcineurin-NFAT signaling pathway 0.011 0.063 -10000 0 -0.25 27 27
Cellular roles of Anthrax toxin

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
ANTXR1 0.005 0.11 -10000 0 -0.42 33 33
ANTXR2 0.022 0.075 -10000 0 -0.42 14 14
negative regulation of myeloid dendritic cell antigen processing and presentation -0.006 0.017 -10000 0 -0.062 41 41
monocyte activation -0.015 0.12 -10000 0 -0.37 53 53
MAP2K2 0.003 0.1 -10000 0 -0.62 13 13
MAP2K1 -0.009 0.015 -10000 0 -0.087 5 5
MAP2K7 -0.009 0.018 -10000 0 -0.11 6 6
MAP2K6 -0.013 0.042 0.13 4 -0.23 15 19
CYAA -0.026 0.065 -10000 0 -0.24 41 41
MAP2K4 -0.008 0.018 -10000 0 -0.12 5 5
IL1B -0.027 0.069 0.14 1 -0.21 53 54
Channel 0.02 0.084 -10000 0 -0.25 41 41
NLRP1 -0.006 0.016 -10000 0 -0.058 41 41
CALM1 0.035 0.007 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.074 -10000 0 -0.43 13 13
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.006 0.017 0.062 41 -10000 0 41
MAPK3 -0.008 0.023 0.14 5 -0.11 6 11
MAPK1 -0.009 0.018 -10000 0 -0.11 6 6
PGR -0.075 0.1 -10000 0 -0.22 170 170
PA/Cellular Receptors 0.02 0.092 -10000 0 -0.28 41 41
apoptosis -0.006 0.017 -10000 0 -0.062 41 41
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.02 0.08 -10000 0 -0.24 41 41
macrophage activation 0.002 0.053 0.17 39 -0.21 2 41
TNF 0.026 0.061 -10000 0 -0.42 9 9
VCAM1 -0.016 0.12 -10000 0 -0.37 53 53
platelet activation -0.001 0.074 -10000 0 -0.43 13 13
MAPKKK cascade 0.002 0.032 0.13 5 -0.088 14 19
IL18 -0.021 0.063 -10000 0 -0.24 34 34
negative regulation of macrophage activation -0.006 0.017 -10000 0 -0.062 41 41
LEF -0.006 0.017 -10000 0 -0.063 41 41
CASP1 -0.008 0.031 -10000 0 -0.083 63 63
mol:cAMP -0.001 0.075 -10000 0 -0.44 13 13
necrosis -0.006 0.017 -10000 0 -0.062 41 41
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.02 0.079 -10000 0 -0.24 41 41
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.018 0.11 -10000 0 -0.31 42 42
alphaM/beta2 Integrin/GPIbA 0.033 0.084 -10000 0 -0.3 22 22
alphaM/beta2 Integrin/proMMP-9 0.007 0.12 -10000 0 -0.29 62 62
PLAUR 0.009 0.11 -10000 0 -0.42 29 29
HMGB1 0.025 0.031 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.036 0.087 -10000 0 -0.3 23 23
AGER 0.025 0.038 -10000 0 -0.42 1 1
RAP1A 0.03 0.05 -10000 0 -0.42 6 6
SELPLG 0.024 0.07 -10000 0 -0.42 12 12
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 -0.014 0.14 -10000 0 -0.42 52 52
CYR61 -0.003 0.12 -10000 0 -0.42 39 39
TLN1 0.034 0.021 -10000 0 -0.42 1 1
Rap1/GTP 0.01 0.13 -10000 0 -0.34 39 39
RHOA 0.026 0.061 -10000 0 -0.42 9 9
P-selectin oligomer -0.04 0.16 -10000 0 -0.42 73 73
MYH2 -0.017 0.14 0.23 1 -0.42 34 35
MST1R -0.005 0.13 -10000 0 -0.42 43 43
leukocyte activation during inflammatory response 0.04 0.079 -10000 0 -0.25 22 22
APOB 0.036 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.006 0.099 -10000 0 -0.42 25 25
JAM3 0.015 0.085 -10000 0 -0.42 18 18
GP1BA 0.03 0.014 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CTGF 0.017 0.12 -10000 0 -0.32 44 44
alphaM/beta2 Integrin -0.009 0.13 -10000 0 -0.38 38 38
JAM3 homodimer 0.015 0.085 -10000 0 -0.42 18 18
ICAM2 0.027 0.047 -10000 0 -0.42 5 5
ICAM1 0.016 0.089 -10000 0 -0.42 20 20
phagocytosis triggered by activation of immune response cell surface activating receptor -0.009 0.13 -10000 0 -0.37 38 38
cell adhesion 0.033 0.084 -10000 0 -0.29 22 22
NFKB1 0 0.15 0.38 1 -0.37 52 53
THY1 0.017 0.08 -10000 0 -0.42 16 16
RhoA/GDP 0.02 0.043 -10000 0 -0.3 9 9
Lipoprotein(a) 0.044 0.014 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.017 0.11 -10000 0 -0.26 59 59
IL6 -0.05 0.23 0.36 2 -0.61 65 67
ITGB2 0.005 0.098 -10000 0 -0.43 22 22
elevation of cytosolic calcium ion concentration 0.014 0.15 -10000 0 -0.36 60 60
alphaM/beta2 Integrin/JAM2/JAM3 0.024 0.13 -10000 0 -0.31 49 49
JAM2 0.011 0.099 -10000 0 -0.42 25 25
alphaM/beta2 Integrin/ICAM1 0.038 0.13 -10000 0 -0.28 64 64
alphaM/beta2 Integrin/uPA/Plg 0.025 0.12 -10000 0 -0.29 57 57
RhoA/GTP -0.029 0.14 -10000 0 -0.44 37 37
positive regulation of phagocytosis 0 0.14 -10000 0 -0.42 35 35
Ron/MSP 0.02 0.099 -10000 0 -0.3 43 43
alphaM/beta2 Integrin/uPAR/uPA 0.016 0.15 -10000 0 -0.36 60 60
alphaM/beta2 Integrin/uPAR 0.023 0.12 -10000 0 -0.33 39 39
PLAU -0.012 0.14 -10000 0 -0.42 50 50
PLAT -0.02 0.13 -10000 0 -0.42 49 49
actin filament polymerization -0.015 0.14 0.24 3 -0.4 33 36
MST1 0.034 0.008 -10000 0 -10000 0 0
alphaM/beta2 Integrin/lipoprotein(a) 0.046 0.082 -10000 0 -0.26 22 22
TNF -0.016 0.16 0.35 2 -0.42 45 47
RAP1B 0.032 0.03 -10000 0 -0.42 2 2
alphaM/beta2 Integrin/uPA 0.012 0.13 -10000 0 -0.32 55 55
fibrinolysis 0.023 0.12 -10000 0 -0.28 57 57
HCK 0.017 0.087 -10000 0 -0.42 19 19
dendritic cell antigen processing and presentation -0.009 0.13 -10000 0 -0.37 38 38
VTN 0.035 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 0.018 0.12 -10000 0 -0.3 48 48
LPA 0.033 0.01 -10000 0 -10000 0 0
LRP1 0.035 0.021 -10000 0 -0.42 1 1
cell migration -0.012 0.13 -10000 0 -0.28 75 75
FN1 -0.009 0.13 -10000 0 -0.42 48 48
alphaM/beta2 Integrin/Thy1 0.024 0.1 -10000 0 -0.29 36 36
MPO 0.031 0.012 -10000 0 -10000 0 0
KNG1 0.034 0.008 -10000 0 -10000 0 0
RAP1/GDP 0.041 0.037 -10000 0 -0.25 7 7
ROCK1 -0.019 0.14 0.21 2 -0.42 36 38
ELA2 0.034 0.008 -10000 0 -10000 0 0
PLG 0.031 0.03 -10000 0 -0.42 2 2
CTGF 0.003 0.11 -10000 0 -0.42 32 32
alphaM/beta2 Integrin/Hck 0.029 0.11 -10000 0 -0.37 27 27
ITGAM 0.021 0.053 -10000 0 -0.43 5 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.002 0.14 -10000 0 -0.29 76 76
HP 0.027 0.037 -10000 0 -0.42 3 3
leukocyte adhesion 0 0.15 -10000 0 -0.39 43 43
SELP -0.04 0.16 -10000 0 -0.42 73 73
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.036 0.029 -10000 0 -0.41 1 1
HSPA8 0.018 0.073 -10000 0 -0.42 13 13
SMAD3/SMAD4/ER alpha -0.033 0.17 0.24 3 -0.29 136 139
AKT1 0.029 0.043 -10000 0 -0.34 4 4
GSC -0.19 0.48 -10000 0 -1.3 74 74
NKX2-5 0.028 0.022 -10000 0 -10000 0 0
muscle cell differentiation 0.011 0.17 0.37 63 -10000 0 63
SMAD2-3/SMAD4/SP1 0.024 0.18 -10000 0 -0.35 60 60
SMAD4 -0.004 0.096 -10000 0 -0.22 53 53
CBFB 0.029 0.014 -10000 0 -10000 0 0
SAP18 0.033 0.01 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.061 0.047 -10000 0 -0.22 3 3
SMAD3/SMAD4/VDR 0.059 0.12 -10000 0 -0.26 30 30
MYC -0.002 0.1 -10000 0 -0.42 29 29
CDKN2B -0.1 0.32 -10000 0 -1.1 36 36
AP1 -0.031 0.18 -10000 0 -0.38 88 88
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.007 0.099 -10000 0 -0.35 19 19
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.007 0.091 -10000 0 -0.27 45 45
SP3 0.028 0.03 -10000 0 -10000 0 0
CREB1 0.034 0.021 -10000 0 -0.42 1 1
FOXH1 0.013 0.059 -10000 0 -0.12 67 67
SMAD3/SMAD4/GR 0.026 0.12 -10000 0 -0.28 43 43
GATA3 -0.043 0.17 -10000 0 -0.42 90 90
SKI/SIN3/HDAC complex/NCoR1 0.014 0.072 -10000 0 -0.32 11 11
MEF2C/TIF2 -0.014 0.13 0.33 1 -0.35 42 43
endothelial cell migration 0.002 0.24 1 21 -10000 0 21
MAX 0.034 0.011 -10000 0 -10000 0 0
RBBP7 0.033 0.029 -10000 0 -0.42 2 2
RBBP4 0.034 0.021 -10000 0 -0.42 1 1
RUNX2 0.031 0.041 -10000 0 -0.42 4 4
RUNX3 -0.01 0.13 -10000 0 -0.42 46 46
RUNX1 0.008 0.11 -10000 0 -0.42 29 29
CTBP1 0.034 0.008 -10000 0 -10000 0 0
NR3C1 0.021 0.078 -10000 0 -0.42 15 15
VDR 0.02 0.083 -10000 0 -0.42 17 17
CDKN1A -0.039 0.23 -10000 0 -1.2 16 16
KAT2B 0.001 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.016 0.14 -10000 0 -0.28 87 87
DCP1A 0.033 0.022 -10000 0 -0.42 1 1
SKI 0.036 0.002 -10000 0 -10000 0 0
SERPINE1 -0.003 0.24 -10000 0 -1.1 21 21
SMAD3/SMAD4/ATF2 0.034 0.11 -10000 0 -0.26 34 34
SMAD3/SMAD4/ATF3 0.015 0.12 -10000 0 -0.3 42 42
SAP30 0.03 0.046 -10000 0 -0.42 5 5
Cbp/p300/PIAS3 0.066 0.049 0.22 3 -10000 0 3
JUN -0.043 0.18 -10000 0 -0.43 68 68
SMAD3/SMAD4/IRF7 0.033 0.12 -10000 0 -0.27 42 42
TFE3 0.033 0.034 -10000 0 -0.15 5 5
COL1A2 -0.072 0.32 -10000 0 -0.87 68 68
mesenchymal cell differentiation -0.03 0.11 0.28 32 -10000 0 32
DLX1 0.032 0.011 -10000 0 -10000 0 0
TCF3 0.031 0.036 -10000 0 -0.42 3 3
FOS -0.039 0.16 -10000 0 -0.45 66 66
SMAD3/SMAD4/Max 0.032 0.11 -10000 0 -0.26 31 31
Cbp/p300/SNIP1 0.059 0.043 -10000 0 -0.26 3 3
ZBTB17 0.034 0.013 -10000 0 -10000 0 0
LAMC1 -0.006 0.1 -10000 0 -0.39 25 25
TGIF2/HDAC complex/SMAD3/SMAD4 0.027 0.11 -10000 0 -0.26 37 37
IRF7 0.029 0.056 -10000 0 -0.3 12 12
ESR1 -0.082 0.19 -10000 0 -0.41 130 130
HNF4A 0.032 0.03 -10000 0 -0.42 2 2
MEF2C -0.029 0.14 0.34 3 -0.34 57 60
SMAD2-3/SMAD4 0.018 0.13 -10000 0 -0.27 47 47
Cbp/p300/Src-1 0.061 0.047 -10000 0 -0.23 4 4
IGHV3OR16-13 -0.004 0.065 -10000 0 -0.44 8 8
TGIF2/HDAC complex 0.027 0.054 -10000 0 -0.42 7 7
CREBBP 0.033 0.019 -10000 0 -10000 0 0
SKIL 0.028 0.05 -10000 0 -0.42 6 6
HDAC1 0.034 0.021 -10000 0 -0.42 1 1
HDAC2 0.031 0.023 -10000 0 -0.42 1 1
SNIP1 0.031 0.036 -10000 0 -0.42 3 3
GCN5L2 0.032 0.029 -10000 0 -0.42 1 1
SMAD3/SMAD4/TFE3 0.039 0.12 -10000 0 -0.31 36 36
MSG1/HSC70 0.031 0.062 -10000 0 -0.3 15 15
SMAD2 0.012 0.058 -10000 0 -0.15 13 13
SMAD3 0.01 0.09 -10000 0 -0.32 20 20
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.001 0.078 -10000 0 -0.24 36 36
SMAD2/SMAD2/SMAD4 -0.001 0.062 0.24 5 -0.21 20 25
NCOR1 0.032 0.011 -10000 0 -10000 0 0
NCOA2 0.025 0.047 -10000 0 -0.42 5 5
NCOA1 0.031 0.045 -10000 0 -0.42 5 5
MYOD/E2A 0.03 0.08 -10000 0 -0.3 27 27
SMAD2-3/SMAD4/SP1/MIZ-1 0.037 0.18 -10000 0 -0.34 56 56
IFNB1 -0.005 0.095 0.36 1 -0.31 25 26
SMAD3/SMAD4/MEF2C -0.003 0.17 -10000 0 -0.4 49 49
CITED1 0.029 0.031 -10000 0 -0.42 2 2
SMAD2-3/SMAD4/ARC105 0.022 0.12 -10000 0 -0.24 47 47
RBL1 0.032 0.022 -10000 0 -0.42 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.003 0.12 -10000 0 -0.4 33 33
RUNX1-3/PEBPB2 0.012 0.12 -10000 0 -0.26 71 71
SMAD7 -0.04 0.2 -10000 0 -0.52 52 52
MYC/MIZ-1 0.015 0.083 0.19 5 -0.3 29 34
SMAD3/SMAD4 0.041 0.13 0.31 42 -0.4 17 59
IL10 -0.034 0.12 -10000 0 -0.32 45 45
PIASy/HDAC complex 0.023 0.043 -10000 0 -0.42 3 3
PIAS3 0.036 0.011 -10000 0 -10000 0 0
CDK2 0.035 0.033 -10000 0 -0.42 2 2
IL5 -0.034 0.13 -10000 0 -0.28 79 79
CDK4 0.037 0.017 -10000 0 -10000 0 0
PIAS4 0.023 0.043 -10000 0 -0.42 3 3
ATF3 0.011 0.085 -10000 0 -0.42 18 18
SMAD3/SMAD4/SP1 0.016 0.16 -10000 0 -0.33 69 69
FOXG1 -0.001 0.003 -10000 0 -10000 0 0
FOXO3 0.005 0.032 -10000 0 -0.25 4 4
FOXO1 0.005 0.032 -10000 0 -0.25 4 4
FOXO4 0.005 0.032 -10000 0 -0.25 4 4
heart looping -0.029 0.14 0.34 3 -0.34 57 60
CEBPB 0.024 0.053 -10000 0 -0.42 6 6
SMAD3/SMAD4/DLX1 0.033 0.1 -10000 0 -0.26 30 30
MYOD1 0.013 0.097 -10000 0 -0.42 24 24
SMAD3/SMAD4/HNF4 0.032 0.11 -10000 0 -0.26 31 31
SMAD3/SMAD4/GATA3 -0.01 0.17 -10000 0 -0.3 103 103
SnoN/SIN3/HDAC complex/NCoR1 0.028 0.05 -10000 0 -0.42 6 6
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.016 0.15 -10000 0 -0.28 79 79
SMAD3/SMAD4/SP1-3 0.031 0.18 -10000 0 -0.36 63 63
MED15 0 0 -10000 0 -10000 0 0
SP1 0.01 0.075 -10000 0 -0.19 38 38
SIN3B 0.035 0.005 -10000 0 -10000 0 0
SIN3A 0.034 0.007 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.034 0.15 -10000 0 -0.26 91 91
ITGB5 -0.045 0.18 -10000 0 -0.49 59 59
TGIF/SIN3/HDAC complex/CtBP 0.017 0.06 -10000 0 -0.29 9 9
SMAD3/SMAD4/AR -0.023 0.17 -10000 0 -0.31 115 115
AR -0.054 0.18 -10000 0 -0.42 99 99
negative regulation of cell growth 0.011 0.099 -10000 0 -0.33 22 22
SMAD3/SMAD4/MYOD 0.018 0.12 -10000 0 -0.26 56 56
E2F5 0.011 0.087 -10000 0 -0.42 19 19
E2F4 0.029 0.014 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.047 0.13 -10000 0 -0.22 69 69
SMAD2-3/SMAD4/FOXO1-3a-4 -0.003 0.099 -10000 0 -0.29 44 44
TFDP1 0.032 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.008 0.2 -10000 0 -0.39 83 83
SMAD3/SMAD4/RUNX2 0.031 0.11 -10000 0 -0.28 32 32
TGIF2 0.027 0.054 -10000 0 -0.42 7 7
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 0.036 0.003 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B 0.021 0.065 -10000 0 -0.39 11 11
CDKN2C 0.023 0.065 -10000 0 -0.39 11 11
CDKN2A 0.018 0.072 -10000 0 -0.39 14 14
CCND2 0.003 0.046 0.18 27 -0.13 2 29
RB1 -0.011 0.061 0.24 2 -0.21 38 40
CDK4 0.007 0.055 0.21 29 -10000 0 29
CDK6 0.004 0.058 0.22 28 -0.17 6 34
G1/S progression 0.018 0.075 0.21 56 -0.26 3 59
Caspase cascade in apoptosis

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
TOP1 -0.005 0.11 0.24 1 -0.49 10 11
ACTA1 -0.016 0.13 0.23 11 -0.33 39 50
NUMA1 -0.014 0.12 -10000 0 -0.43 15 15
SPTAN1 -0.021 0.12 0.24 8 -0.32 47 55
LIMK1 -0.033 0.13 0.23 3 -0.34 50 53
BIRC3 -0.01 0.12 -10000 0 -0.42 42 42
BIRC2 0.031 0.012 -10000 0 -10000 0 0
BAX 0.035 0.007 -10000 0 -10000 0 0
CASP10 -0.049 0.092 -10000 0 -0.27 75 75
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 -0.01 0.12 0.26 1 -0.49 12 13
DIABLO 0.036 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes -0.02 0.12 0.24 8 -0.31 47 55
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.029 0.054 -10000 0 -0.42 7 7
GSN -0.028 0.13 0.27 4 -0.33 51 55
MADD 0.035 0.005 -10000 0 -10000 0 0
TFAP2A 0.001 0.16 -10000 0 -0.57 30 30
BID -0.022 0.07 -10000 0 -0.18 82 82
MAP3K1 -0.033 0.14 -10000 0 -0.42 49 49
TRADD 0.029 0.014 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.047 0.037 -10000 0 -0.3 5 5
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.03 0.13 0.32 5 -0.34 51 56
CASP9 0.034 0.022 -10000 0 -0.42 1 1
DNA repair -0.023 0.069 0.25 12 -0.17 24 36
neuron apoptosis -0.03 0.19 -10000 0 -0.67 41 41
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.018 0.12 -10000 0 -0.42 17 17
APAF1 0.032 0.041 -10000 0 -0.42 4 4
CASP6 -0.013 0.15 -10000 0 -0.78 14 14
TRAF2 0.033 0.029 -10000 0 -0.42 2 2
ICAD/CAD -0.024 0.12 0.26 2 -0.32 40 42
CASP7 0.031 0.1 0.26 45 -0.32 14 59
KRT18 -0.067 0.22 -10000 0 -0.57 74 74
apoptosis -0.016 0.12 0.28 3 -0.39 21 24
DFFA -0.023 0.12 0.23 4 -0.32 46 50
DFFB -0.023 0.12 0.23 3 -0.32 46 49
PARP1 0.023 0.07 0.17 23 -0.25 12 35
actin filament polymerization 0.033 0.13 0.33 46 -0.3 7 53
TNF 0.026 0.061 -10000 0 -0.42 9 9
CYCS -0.008 0.056 0.14 8 -0.2 10 18
SATB1 -0.027 0.15 -10000 0 -0.7 16 16
SLK -0.023 0.12 0.25 4 -0.32 47 51
p15 BID/BAX -0.002 0.077 -10000 0 -0.25 15 15
CASP2 -0.016 0.1 0.22 5 -0.32 30 35
JNK cascade 0.033 0.14 0.41 49 -10000 0 49
CASP3 -0.021 0.13 0.23 5 -0.33 50 55
LMNB2 -0.009 0.12 0.24 1 -0.42 21 22
RIPK1 0.035 0.007 -10000 0 -10000 0 0
CASP4 0.023 0.061 -10000 0 -0.42 9 9
Mammalian IAPs/DIABLO 0.032 0.084 -10000 0 -0.23 41 41
negative regulation of DNA binding 0.001 0.15 -10000 0 -0.57 30 30
stress fiber formation -0.023 0.12 0.24 4 -0.31 47 51
GZMB -0.034 0.12 -10000 0 -0.31 75 75
CASP1 -0.009 0.1 -10000 0 -0.36 33 33
LMNB1 -0.06 0.16 -10000 0 -0.4 44 44
APP -0.031 0.2 -10000 0 -0.68 41 41
TNFRSF1A 0.033 0.022 -10000 0 -0.42 1 1
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.009 0.001 -10000 0 -10000 0 0
VIM -0.012 0.13 0.29 2 -0.4 22 24
LMNA -0.008 0.098 0.24 1 -0.32 18 19
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.017 0.11 -10000 0 -0.34 33 33
LRDD 0.035 0.007 -10000 0 -10000 0 0
SREBF1 -0.036 0.13 0.25 2 -0.33 47 49
APAF-1/Caspase 9 0.016 0.12 -10000 0 -0.64 13 13
nuclear fragmentation during apoptosis -0.013 0.12 -10000 0 -0.43 15 15
CFL2 -0.034 0.13 0.3 7 -0.33 48 55
GAS2 -0.031 0.13 0.24 5 -0.33 51 56
positive regulation of apoptosis -0.028 0.12 0.26 1 -0.39 23 24
PRF1 0.026 0.058 -10000 0 -0.42 8 8
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.046 0.1 -9999 0 -0.24 46 46
SMAD6-7/SMURF1 0.067 0.024 -9999 0 -0.26 1 1
NOG 0.029 0.037 -9999 0 -0.42 3 3
SMAD9 -0.028 0.16 -9999 0 -0.45 53 53
SMAD4 0.028 0.054 -9999 0 -0.42 7 7
SMAD5 -0.028 0.12 -9999 0 -0.34 39 39
BMP7/USAG1 -0.064 0.16 -9999 0 -0.31 140 140
SMAD5/SKI -0.016 0.13 -9999 0 -0.39 29 29
SMAD1 0.011 0.07 -9999 0 -0.32 6 6
BMP2 0.021 0.07 -9999 0 -0.42 12 12
SMAD1/SMAD1/SMAD4 0.033 0.078 -9999 0 -0.29 5 5
BMPR1A 0.031 0.046 -9999 0 -0.42 5 5
BMPR1B -0.004 0.11 -9999 0 -0.42 30 30
BMPR1A-1B/BAMBI -0.021 0.14 -9999 0 -0.26 120 120
AHSG 0.034 0.008 -9999 0 -10000 0 0
CER1 0.034 0.009 -9999 0 -10000 0 0
BMP2-4/CER1 0.014 0.12 -9999 0 -0.26 71 71
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.017 0.13 -9999 0 -0.35 35 35
BMP2-4 (homodimer) -0.007 0.13 -9999 0 -0.31 74 74
RGMB 0.026 0.061 -9999 0 -0.42 9 9
BMP6/BMPR2/BMPR1A-1B 0.05 0.091 -9999 0 -0.24 41 41
RGMA 0.019 0.073 -9999 0 -0.42 13 13
SMURF1 0.035 0.006 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.031 0.12 -9999 0 -0.38 31 31
BMP2-4/USAG1 -0.079 0.17 -9999 0 -0.29 192 192
SMAD6/SMURF1/SMAD5 -0.015 0.13 -9999 0 -0.39 28 28
SOSTDC1 -0.12 0.2 -9999 0 -0.42 155 155
BMP7/BMPR2/BMPR1A-1B 0.04 0.095 -9999 0 -0.24 45 45
SKI 0.036 0.002 -9999 0 -10000 0 0
BMP6 (homodimer) 0.027 0.05 -9999 0 -0.42 6 6
HFE2 0.026 0.064 -9999 0 -0.42 10 10
ZFYVE16 0.033 0.03 -9999 0 -0.42 2 2
MAP3K7 0.033 0.01 -9999 0 -10000 0 0
BMP2-4/CHRD 0.012 0.12 -9999 0 -0.28 70 70
SMAD5/SMAD5/SMAD4 -0.019 0.13 -9999 0 -0.38 32 32
MAPK1 0.033 0.022 -9999 0 -0.42 1 1
TAK1/TAB family 0.013 0.14 -9999 0 -0.37 24 24
BMP7 (homodimer) 0.015 0.073 -9999 0 -0.42 13 13
NUP214 0.035 0.021 -9999 0 -0.42 1 1
BMP6/FETUA 0.044 0.041 -9999 0 -0.3 6 6
SMAD1/SKI 0.026 0.08 -9999 0 -0.31 8 8
SMAD6 0.035 0.007 -9999 0 -10000 0 0
CTDSP2 0.034 0.029 -9999 0 -0.42 2 2
BMP2-4/FETUA 0.015 0.12 -9999 0 -0.26 69 69
MAP3K7IP1 0.034 0.009 -9999 0 -10000 0 0
GREM1 -0.003 0.12 -9999 0 -0.42 40 40
BMPR2 (homodimer) 0.034 0.029 -9999 0 -0.42 2 2
GADD34/PP1CA 0.059 0.041 -9999 0 -0.26 5 5
BMPR1A-1B (homodimer) 0.019 0.087 -9999 0 -0.3 34 34
CHRDL1 0.03 0.037 -9999 0 -0.42 3 3
ENDOFIN/SMAD1 0.025 0.08 -9999 0 -0.32 7 7
SMAD6-7/SMURF1/SMAD1 0.055 0.085 -9999 0 -0.31 5 5
SMAD6/SMURF1 0.035 0.006 -9999 0 -10000 0 0
BAMBI -0.055 0.18 -9999 0 -0.42 93 93
SMURF2 0.028 0.042 -9999 0 -0.42 4 4
BMP2-4/CHRDL1 0.012 0.12 -9999 0 -0.27 75 75
BMP2-4/GREM1 -0.011 0.15 -9999 0 -0.29 102 102
SMAD7 0.034 0.021 -9999 0 -0.42 1 1
SMAD8A/SMAD8A/SMAD4 -0.022 0.17 -9999 0 -0.44 58 58
SMAD1/SMAD6 0.025 0.08 -9999 0 -0.31 8 8
TAK1/SMAD6 0.048 0.016 -9999 0 -10000 0 0
BMP7 0.015 0.073 -9999 0 -0.42 13 13
BMP6 0.027 0.05 -9999 0 -0.42 6 6
MAP3K7IP2 0.031 0.03 -9999 0 -0.42 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.02 0.12 -9999 0 -0.34 35 35
PPM1A 0.034 0.022 -9999 0 -0.42 1 1
SMAD1/SMURF2 0.021 0.076 -9999 0 -0.32 6 6
SMAD7/SMURF1 0.05 0.02 -9999 0 -0.3 1 1
CTDSPL 0.028 0.054 -9999 0 -0.42 7 7
PPP1CA 0.031 0.03 -9999 0 -0.42 2 2
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.034 0.029 -9999 0 -0.42 2 2
PPP1R15A 0.034 0.021 -9999 0 -0.42 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.033 0.13 -9999 0 -0.4 35 35
CHRD 0.029 0.046 -9999 0 -0.42 5 5
BMPR2 0.034 0.029 -9999 0 -0.42 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.03 0.12 -9999 0 -0.39 30 30
BMP4 -0.028 0.15 -9999 0 -0.42 65 65
FST 0.024 0.058 -9999 0 -0.42 8 8
BMP2-4/NOG 0.01 0.12 -9999 0 -0.26 73 73
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.051 0.097 -9999 0 -0.23 45 45
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.028 0.057 -10000 0 -0.42 8 8
alphaV beta3 Integrin 0.035 0.073 -10000 0 -0.32 20 20
PTK2 -0.025 0.14 -10000 0 -0.43 36 36
positive regulation of JNK cascade -0.001 0.12 -10000 0 -0.31 46 46
CDC42/GDP 0.009 0.17 -10000 0 -0.42 48 48
Rac1/GDP 0.01 0.16 -10000 0 -0.41 47 47
RAP1B 0.032 0.03 -10000 0 -0.42 2 2
RAP1A 0.03 0.05 -10000 0 -0.42 6 6
CTNNB1 0.024 0.067 -10000 0 -0.42 11 11
CDC42/GTP 0.001 0.15 -10000 0 -0.39 46 46
nectin-3/I-afadin 0.022 0.097 -10000 0 -0.33 34 34
RAPGEF1 -0.015 0.16 -10000 0 -0.44 48 48
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.02 0.18 -10000 0 -0.5 48 48
PDGFB-D/PDGFRB 0.028 0.057 -10000 0 -0.42 8 8
TLN1 -0.014 0.071 0.19 4 -0.34 14 18
Rap1/GTP -0.006 0.12 -10000 0 -0.33 45 45
IQGAP1 0.034 0.008 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.047 0.063 -10000 0 -0.23 21 21
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.022 0.097 -10000 0 -0.33 34 34
PVR 0.032 0.036 -10000 0 -0.42 3 3
Necl-5(dimer) 0.032 0.036 -10000 0 -0.42 3 3
mol:GDP -0.012 0.19 -10000 0 -0.51 48 48
MLLT4 0.02 0.075 -10000 0 -0.42 14 14
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
PI3K 0.053 0.12 -10000 0 -0.28 48 48
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.033 0.062 -10000 0 -0.3 15 15
positive regulation of lamellipodium assembly 0.005 0.13 -10000 0 -0.32 45 45
PVRL1 0.03 0.024 -10000 0 -0.42 1 1
PVRL3 0.011 0.099 -10000 0 -0.42 25 25
PVRL2 0.026 0.064 -10000 0 -0.42 10 10
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
CDH1 -0.012 0.13 -10000 0 -0.42 45 45
CLDN1 -0.047 0.17 -10000 0 -0.42 85 85
JAM-A/CLDN1 0.002 0.13 -10000 0 -0.27 85 85
SRC -0.033 0.19 -10000 0 -0.51 62 62
ITGB3 0.029 0.046 -10000 0 -0.42 5 5
nectin-1(dimer)/I-afadin/I-afadin 0.033 0.062 -10000 0 -0.3 15 15
FARP2 -0.015 0.2 -10000 0 -0.52 48 48
RAC1 0.035 0.006 -10000 0 -10000 0 0
CTNNA1 0.035 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.038 0.095 -10000 0 -0.29 36 36
nectin-1/I-afadin 0.033 0.062 -10000 0 -0.3 15 15
nectin-2/I-afadin 0.032 0.074 -10000 0 -0.3 23 23
RAC1/GTP/IQGAP1/filamentous actin 0.045 0.012 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.035 0.092 -10000 0 -0.28 35 35
CDC42/GTP/IQGAP1/filamentous actin 0.045 0.014 -10000 0 -10000 0 0
F11R 0.026 0.038 -10000 0 -0.42 3 3
positive regulation of filopodium formation -0.001 0.12 -10000 0 -0.31 46 46
alphaV/beta3 Integrin/Talin 0.008 0.11 0.27 1 -0.33 27 28
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.074 -10000 0 -0.3 23 23
nectin-2(dimer)/I-afadin/I-afadin 0.032 0.074 -10000 0 -0.3 23 23
PIP5K1C -0.01 0.074 -10000 0 -0.23 37 37
VAV2 -0.006 0.19 -10000 0 -0.52 43 43
RAP1/GDP 0.01 0.16 -10000 0 -0.39 46 46
ITGAV 0.021 0.08 -10000 0 -0.42 16 16
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.035 0.1 -10000 0 -0.28 41 41
nectin-3(dimer)/I-afadin/I-afadin 0.022 0.097 -10000 0 -0.33 34 34
Rac1/GTP 0.008 0.15 -10000 0 -0.39 45 45
PTPRM -0.005 0.085 -10000 0 -0.26 38 38
E-cadherin/beta catenin/alpha catenin 0.025 0.12 -10000 0 -0.22 74 74
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.034 0.008 -10000 0 -10000 0 0
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.048 0.016 -10000 0 -10000 0 0
VLDLR -0.007 0.13 -10000 0 -0.42 42 42
CRKL 0.03 0.041 -10000 0 -0.42 4 4
LRPAP1 0.035 0.007 -10000 0 -10000 0 0
FYN 0.027 0.05 -10000 0 -0.42 6 6
ITGA3 0.023 0.07 -10000 0 -0.42 12 12
RELN/VLDLR/Fyn 0.027 0.1 -10000 0 -0.27 50 50
MAPK8IP1/MKK7/MAP3K11/JNK1 0.068 0.071 -10000 0 -0.22 16 16
AKT1 -0.018 0.088 -10000 0 -0.23 58 58
MAP2K7 0.034 0.021 -10000 0 -0.42 1 1
RAPGEF1 0.036 0.004 -10000 0 -10000 0 0
DAB1 0.035 0.006 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.039 0.08 -10000 0 -0.23 39 39
LRPAP1/LRP8 0.023 0.088 -10000 0 -0.3 34 34
RELN/LRP8/DAB1/Fyn 0.045 0.088 -10000 0 -0.22 45 45
DAB1/alpha3/beta1 Integrin 0.016 0.11 -10000 0 -0.22 83 83
long-term memory 0.049 0.1 -10000 0 -0.22 54 54
DAB1/LIS1 0.032 0.12 -10000 0 -0.22 79 79
DAB1/CRLK/C3G 0.021 0.11 -10000 0 -0.22 81 81
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
DAB1/NCK2 0.039 0.12 -10000 0 -0.22 79 79
ARHGEF2 0.021 0.058 -10000 0 -0.42 8 8
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.032 0.011 -10000 0 -10000 0 0
CDK5R1 0.033 0.01 -10000 0 -10000 0 0
RELN 0.03 0.046 -10000 0 -0.42 5 5
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
RELN/LRP8/Fyn 0.032 0.093 -10000 0 -0.26 45 45
GRIN2A/RELN/LRP8/DAB1/Fyn 0.055 0.092 -10000 0 -0.22 39 39
MAPK8 0.033 0.035 -10000 0 -0.42 3 3
RELN/VLDLR/DAB1 0.032 0.088 -10000 0 -0.24 46 46
ITGB1 0.033 0.03 -10000 0 -0.42 2 2
MAP1B -0.027 0.12 0.32 5 -0.24 95 100
RELN/LRP8 0.038 0.088 -10000 0 -0.26 39 39
GRIN2B/RELN/LRP8/DAB1/Fyn 0.046 0.11 -10000 0 -0.23 62 62
PI3K 0.035 0.067 -10000 0 -0.3 18 18
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.04 0.057 -10000 0 -0.32 11 11
RAP1A -0.043 0.097 0.34 7 -0.44 3 10
PAFAH1B1 0.032 0.023 -10000 0 -0.42 1 1
MAPK8IP1 0.033 0.029 -10000 0 -0.42 2 2
CRLK/C3G 0.047 0.034 -10000 0 -0.3 4 4
GRIN2B 0.016 0.087 -10000 0 -0.42 19 19
NCK2 0.036 0.004 -10000 0 -10000 0 0
neuron differentiation 0.018 0.081 -10000 0 -0.34 6 6
neuron adhesion -0.043 0.1 0.35 7 -0.4 5 12
LRP8 0 0.11 -10000 0 -0.42 34 34
GSK3B -0.016 0.092 0.19 5 -0.41 10 15
RELN/VLDLR/DAB1/Fyn 0.039 0.096 -10000 0 -0.23 50 50
MAP3K11 0.033 0.029 -10000 0 -0.42 2 2
RELN/VLDLR/DAB1/P13K -0.007 0.096 -10000 0 -0.24 61 61
CDK5 0.035 0.007 -10000 0 -10000 0 0
MAPT -0.071 0.17 0.79 4 -0.39 96 100
neuron migration -0.025 0.11 0.29 11 -0.32 21 32
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.017 0.081 -10000 0 -0.34 6 6
RELN/VLDLR 0.025 0.12 -10000 0 -0.24 79 79
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.004 0.11 -10000 0 -0.31 50 50
VEGFR1 homodimer/NRP1 -0.016 0.1 -10000 0 -0.3 50 50
mol:DAG -0.009 0.1 -10000 0 -0.28 49 49
VEGFR1 homodimer/NRP1/VEGFR 121 -0.014 0.095 -10000 0 -0.28 50 50
CaM/Ca2+ 0.009 0.1 -10000 0 -0.27 47 47
HIF1A -0.005 0.14 -10000 0 -0.42 51 51
GAB1 0.027 0.061 -10000 0 -0.42 9 9
AKT1 -0.016 0.1 -10000 0 -0.44 15 15
PLCG1 -0.009 0.1 -10000 0 -0.28 49 49
NOS3 0.002 0.11 0.38 2 -0.47 15 17
CBL 0.031 0.012 -10000 0 -10000 0 0
mol:NO 0.005 0.11 0.34 4 -0.46 15 19
FLT1 -0.013 0.12 -10000 0 -0.37 45 45
PGF 0.031 0.041 -10000 0 -0.42 4 4
VEGFR1 homodimer/NRP2/VEGFR121 0.004 0.1 -10000 0 -0.29 50 50
CALM1 0.035 0.007 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
eNOS/Hsp90 -0.002 0.1 0.27 1 -0.44 15 16
endothelial cell proliferation 0 0.11 0.3 9 -0.42 15 24
mol:Ca2+ -0.009 0.1 -10000 0 -0.28 49 49
MAPK3 -0.024 0.08 0.35 1 -0.48 9 10
MAPK1 -0.028 0.083 0.35 1 -0.49 8 9
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
PLGF homodimer 0.031 0.041 -10000 0 -0.42 4 4
PRKACA 0.036 0.004 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.028 0.05 -10000 0 -0.42 6 6
VEGFA homodimer 0 0 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer -0.016 0.1 -10000 0 -0.3 50 50
platelet activating factor biosynthetic process -0.003 0.1 0.33 6 -0.45 9 15
PI3K 0.027 0.13 -10000 0 -0.27 66 66
PRKCA -0.027 0.09 0.2 11 -0.28 37 48
PRKCB -0.028 0.091 0.18 13 -0.27 45 58
VEGFR1 homodimer/PLGF homodimer 0.003 0.12 -10000 0 -0.31 53 53
VEGFA 0 0 -10000 0 -10000 0 0
VEGFB 0.034 0.021 -10000 0 -0.42 1 1
mol:IP3 -0.009 0.1 -10000 0 -0.28 49 49
RASA1 -0.012 0.11 -10000 0 -0.29 55 55
NRP2 0.034 0.021 -10000 0 -0.42 1 1
VEGFR1 homodimer -0.013 0.12 -10000 0 -0.37 45 45
VEGFB homodimer 0.034 0.021 -10000 0 -0.42 1 1
NCK1 0.034 0.022 -10000 0 -0.42 1 1
eNOS/Caveolin-1 0.017 0.12 0.36 3 -0.48 15 18
PTPN11 0.036 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.025 0.13 -10000 0 -0.27 66 66
mol:L-citrulline 0.005 0.11 0.34 4 -0.46 15 19
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.018 0.1 -10000 0 -0.27 49 49
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.003 0.1 -10000 0 -0.28 51 51
CD2AP 0.035 0.007 -10000 0 -10000 0 0
PI3K/GAB1 0.033 0.13 -10000 0 -0.32 31 31
PDPK1 -0.026 0.1 0.34 1 -0.46 11 12
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.005 0.1 -10000 0 -0.28 50 50
mol:NADP 0.005 0.11 0.34 4 -0.46 15 19
HSP90AA1 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.016 0.1 -10000 0 -0.26 49 49
VEGFR1 homodimer/NRP2 0.004 0.11 -10000 0 -0.31 50 50
Visual signal transduction: Rods

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
mol:K + 0.03 0.046 -10000 0 -0.42 5 5
GNAT1/GTP 0.023 0.025 -10000 0 -0.3 3 3
Metarhodopsin II/Arrestin 0.008 0.094 -10000 0 -0.25 57 57
PDE6G/GNAT1/GTP 0.041 0.028 -10000 0 -0.25 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.032 0.036 -10000 0 -0.42 3 3
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel -0.018 0.12 -10000 0 -0.22 125 125
mol:Na + 0.023 0.098 -10000 0 -0.24 47 47
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.007 0.12 -10000 0 -0.27 72 72
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.034 0.11 -10000 0 -0.27 30 30
CNGB1 0.03 0.014 -10000 0 -10000 0 0
RDH5 0.033 0.01 -10000 0 -10000 0 0
SAG -0.024 0.14 -10000 0 -0.42 58 58
mol:Ca2+ -0.034 0.091 0.35 8 -0.4 9 17
Na + (4 Units) 0.014 0.093 -10000 0 -0.37 10 10
RGS9 0.017 0.067 -10000 0 -0.42 11 11
GNB1/GNGT1 0.034 0.064 -10000 0 -0.3 17 17
GNAT1/GDP 0.019 0.11 -10000 0 -0.23 75 75
GUCY2D 0.032 0.012 -10000 0 -10000 0 0
GNGT1 0.016 0.07 -10000 0 -0.42 12 12
GUCY2F 0.027 0.064 -10000 0 -0.42 10 10
GNB5 0.024 0.067 -10000 0 -0.42 11 11
mol:GMP (4 units) -0.022 0.1 -10000 0 -0.22 107 107
mol:11-cis-retinal 0.033 0.01 -10000 0 -10000 0 0
mol:cGMP 0.047 0.084 -10000 0 -0.26 29 29
GNB1 0.032 0.045 -10000 0 -0.42 5 5
Rhodopsin 0.05 0.011 -10000 0 -10000 0 0
SLC24A1 0.03 0.046 -10000 0 -0.42 5 5
CNGA1 0.003 0.11 -10000 0 -0.42 29 29
Metarhodopsin II 0.023 0.004 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.063 0.077 -10000 0 -0.25 23 23
RGS9BP -0.022 0.15 -10000 0 -0.42 60 60
Metarhodopsin II/Transducin 0.014 0.049 -10000 0 -0.22 21 21
GCAP Family/Ca ++ 0.05 0.069 -10000 0 -0.25 23 23
PDE6A/B -0.028 0.15 -10000 0 -0.3 113 113
mol:Pi 0.007 0.12 -10000 0 -0.27 72 72
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.048 0.06 -10000 0 -0.23 20 20
PDE6B -0.066 0.19 -10000 0 -0.42 112 112
PDE6A 0.033 0.029 -10000 0 -0.42 2 2
PDE6G 0.033 0.01 -10000 0 -10000 0 0
RHO 0.035 0.005 -10000 0 -10000 0 0
PDE6 -0.016 0.15 -10000 0 -0.24 141 141
GUCA1A 0.022 0.075 -10000 0 -0.42 14 14
GC2/GCAP Family 0.066 0.09 -10000 0 -0.28 29 29
GUCA1C 0.026 0.064 -10000 0 -0.42 10 10
GUCA1B 0.034 0.022 -10000 0 -0.42 1 1
Aurora B signaling

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
Condensin I complex -0.008 0.035 -10000 0 -0.097 62 62
STMN1 0.005 0.051 -10000 0 -0.34 10 10
Aurora B/RasGAP/Survivin 0.027 0.1 -10000 0 -0.28 44 44
Chromosomal passenger complex/Cul3 protein complex -0.046 0.12 -10000 0 -0.25 101 101
BIRC5 -0.004 0.13 -10000 0 -0.44 38 38
DES -0.065 0.26 -10000 0 -0.67 74 74
Aurora C/Aurora B/INCENP 0.052 0.051 -10000 0 -0.24 11 11
Aurora B/TACC1 0.023 0.063 -10000 0 -0.26 22 22
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 0.015 47 -0.01 3 50
NDC80 0.004 0.026 -10000 0 -0.31 3 3
Cul3 protein complex 0.014 0.12 -10000 0 -0.26 76 76
KIF2C -0.057 0.22 -10000 0 -0.66 50 50
PEBP1 -0.001 0.004 0.012 1 -0.014 38 39
KIF20A 0.004 0.12 -10000 0 -0.43 35 35
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.039 0.053 -10000 0 -0.31 10 10
SEPT1 0.031 0.023 -10000 0 -0.42 1 1
SMC2 0 0 -10000 0 -10000 0 0
SMC4 0 0 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.046 0.18 -10000 0 -0.51 62 62
PSMA3 0.035 0.006 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.004 0.01 54 -0.009 8 62
H3F3B 0.013 0.028 -10000 0 -0.3 4 4
AURKB 0.028 0.04 -10000 0 -0.45 3 3
AURKC 0.034 0.021 -10000 0 -0.42 1 1
CDCA8 0.015 0.09 -10000 0 -0.45 18 18
cytokinesis -0.046 0.23 -10000 0 -0.65 49 49
Aurora B/Septin1 -0.029 0.22 -10000 0 -0.61 46 46
AURKA 0 0.004 0.01 54 -0.009 8 62
INCENP 0.024 0.058 -10000 0 -0.44 7 7
KLHL13 -0.035 0.16 -10000 0 -0.42 73 73
BUB1 -0.011 0.14 -10000 0 -0.43 51 51
hSgo1/Aurora B/Survivin 0.024 0.12 -10000 0 -0.34 39 39
EVI5 0.031 0.041 -10000 0 -0.42 4 4
RhoA/GTP -0.023 0.22 -10000 0 -0.57 53 53
SGOL1 0.02 0.08 -10000 0 -0.42 16 16
CENPA -0.041 0.15 -10000 0 -0.38 60 60
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 0.043 0.043 -10000 0 -0.31 6 6
RHOA 0.026 0.061 -10000 0 -0.42 9 9
NCAPH 0 0 -10000 0 -10000 0 0
NPM1 -0.021 0.12 -10000 0 -0.33 48 48
RASA1 0.028 0.054 -10000 0 -0.42 7 7
KLHL9 0.032 0.03 -10000 0 -0.42 2 2
mitotic prometaphase -0.001 0.004 0.012 1 -0.014 38 39
proteasomal ubiquitin-dependent protein catabolic process 0.044 0.034 -10000 0 -0.32 3 3
PPP1CC 0.033 0.035 -10000 0 -0.42 3 3
Centraspindlin -0.032 0.24 -10000 0 -0.61 54 54
RhoA/GDP 0.02 0.043 -10000 0 -0.3 9 9
NSUN2 -0.018 0.11 -10000 0 -0.32 47 47
MYLK 0.006 0.057 -10000 0 -0.31 16 16
KIF23 0.006 0.11 -10000 0 -0.44 30 30
VIM -0.006 0.072 -10000 0 -0.31 27 27
RACGAP1 0.019 0.085 -10000 0 -0.44 17 17
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.023 0.13 -10000 0 -0.34 58 58
Chromosomal passenger complex -0.05 0.19 -10000 0 -0.47 61 61
Chromosomal passenger complex/EVI5 0.037 0.14 -10000 0 -0.34 48 48
TACC1 0.012 0.087 -10000 0 -0.42 19 19
PPP2R5D 0.035 0.007 -10000 0 -10000 0 0
CUL3 0.032 0.041 -10000 0 -0.42 4 4
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
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 0.004 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0.031 0.03 -10000 0 -0.42 2 2
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.01 0.11 -10000 0 -0.37 29 29
IRAK/TOLLIP 0.04 0.017 0.18 5 -10000 0 5
IKBKB 0.029 0.014 -10000 0 -10000 0 0
IKBKG 0.036 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.024 0.092 -10000 0 -0.3 37 37
IL1A 0.031 0.041 -10000 0 -0.42 4 4
IL1B -0.025 0.11 -10000 0 -0.34 54 54
IRAK/TRAF6/p62/Atypical PKCs 0.059 0.049 -10000 0 -0.21 12 12
IL1R2 0.002 0.11 -10000 0 -0.42 33 33
IL1R1 -0.005 0.13 -10000 0 -0.42 43 43
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.022 0.12 -10000 0 -0.4 29 29
TOLLIP 0.035 0.007 -10000 0 -10000 0 0
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.031 0.012 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.06 0.034 -10000 0 -0.26 2 2
IKK complex/ELKS 0.025 0.077 0.27 1 -0.31 9 10
JUN -0.029 0.072 0.28 4 -0.45 2 6
MAP3K7 0.033 0.01 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.005 0.15 -10000 0 -0.28 95 95
IL1 alpha/IL1R1/IL1RAP/MYD88 0.052 0.098 -10000 0 -0.23 50 50
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.063 0.1 -10000 0 -0.22 53 53
IL1 beta fragment/IL1R1/IL1RAP -0.012 0.14 -10000 0 -0.29 87 87
NFKB1 0.035 0.005 -10000 0 -10000 0 0
MAPK8 -0.014 0.063 0.28 6 -0.38 1 7
IRAK1 0.018 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.003 0.13 -10000 0 -0.32 72 72
IRAK4 0.033 0.035 -10000 0 -0.42 3 3
PRKCI 0.024 0.067 -10000 0 -0.42 11 11
TRAF6 0.034 0.021 -10000 0 -0.42 1 1
PI3K 0.035 0.067 -10000 0 -0.3 18 18
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.019 0.13 -10000 0 -0.38 39 39
CHUK 0.025 0.067 -10000 0 -0.42 11 11
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.012 0.14 -10000 0 -0.29 87 87
IL1 beta/IL1R2 -0.021 0.13 -10000 0 -0.3 86 86
IRAK/TRAF6/TAK1/TAB1/TAB2 0.074 0.045 -10000 0 -0.21 3 3
NF kappa B1 p50/RelA -0.005 0.14 -10000 0 -0.27 92 92
IRAK3 0.026 0.047 -10000 0 -0.42 5 5
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0 0.13 -10000 0 -0.27 88 88
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.006 0.085 -10000 0 -0.23 53 53
IL1 alpha/IL1R1/IL1RAP 0.037 0.095 -10000 0 -0.26 46 46
RELA 0.035 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0.034 0.009 -10000 0 -10000 0 0
SQSTM1 0.034 0.021 -10000 0 -0.42 1 1
MYD88 0.031 0.041 -10000 0 -0.42 4 4
IRAK/TRAF6/MEKK3 0.053 0.029 -10000 0 -0.22 1 1
IL1RAP 0.033 0.022 -10000 0 -0.42 1 1
UBE2N 0.035 0.005 -10000 0 -10000 0 0
IRAK/TRAF6 -0.016 0.11 -10000 0 -0.25 81 81
CASP1 0.001 0.11 -10000 0 -0.42 31 31
IL1RN/IL1R2 0.002 0.13 -10000 0 -0.32 63 63
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.002 0.14 -10000 0 -0.28 88 88
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.003 0.11 -10000 0 -0.32 45 45
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
IL1RN 0 0.12 -10000 0 -0.42 37 37
TRAF6/TAK1/TAB1/TAB2 0.071 0.043 -10000 0 -0.22 3 3
MAP2K6 -0.01 0.062 0.29 5 -0.4 1 6
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.025 0.16 0.25 4 -0.42 48 52
IKBKB 0.017 0.09 0.33 2 -0.3 4 6
AKT1 0.022 0.11 0.24 43 -0.23 18 61
IKBKG 0.026 0.079 0.24 5 -0.28 6 11
CALM1 -0.012 0.13 0.25 5 -0.42 26 31
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
MAP3K1 -0.022 0.18 0.32 2 -0.5 40 42
MAP3K7 0.033 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.012 0.14 0.27 5 -0.42 29 34
DOK1 0.027 0.061 -10000 0 -0.42 9 9
AP-1 -0.021 0.1 0.2 4 -0.25 46 50
LYN 0.03 0.014 -10000 0 -10000 0 0
BLNK 0.012 0.1 -10000 0 -0.42 26 26
SHC1 0.027 0.025 -10000 0 -0.42 1 1
BCR complex 0.024 0.076 -10000 0 -0.3 24 24
CD22 -0.021 0.12 0.26 1 -0.49 25 26
CAMK2G -0.011 0.12 0.24 7 -0.41 24 31
CSNK2A1 0.034 0.008 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.003 0.079 -10000 0 -0.25 35 35
GO:0007205 -0.012 0.14 0.27 5 -0.43 29 34
SYK 0.005 0.11 -10000 0 -0.42 33 33
ELK1 -0.014 0.13 0.25 5 -0.42 27 32
NFATC1 0.019 0.14 0.26 21 -0.38 30 51
B-cell antigen/BCR complex 0.024 0.076 -10000 0 -0.3 24 24
PAG1/CSK 0.034 0.051 -10000 0 -0.3 9 9
NFKBIB 0.027 0.05 0.15 9 -0.12 21 30
HRAS 0.002 0.12 0.24 17 -0.35 26 43
NFKBIA 0.028 0.049 0.15 9 -0.12 19 28
NF-kappa-B/RelA/I kappa B beta 0.032 0.044 0.15 9 -10000 0 9
RasGAP/Csk 0.037 0.1 -10000 0 -0.27 35 35
mol:GDP -0.011 0.13 0.26 5 -0.4 32 37
PTEN 0.027 0.061 -10000 0 -0.42 9 9
CD79B 0.006 0.097 -10000 0 -0.42 24 24
NF-kappa-B/RelA/I kappa B alpha 0.032 0.044 0.15 9 -10000 0 9
GRB2 0.033 0.01 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.011 0.18 0.33 3 -0.5 40 43
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
mol:IP3 -0.013 0.14 0.27 4 -0.44 29 33
CSK 0.033 0.022 -10000 0 -0.42 1 1
FOS -0.038 0.14 0.24 4 -0.39 42 46
CHUK 0.015 0.099 0.24 5 -0.32 21 26
IBTK 0.032 0.03 -10000 0 -0.42 2 2
CARD11/BCL10/MALT1/TAK1 0.009 0.13 0.27 1 -0.4 25 26
PTPN6 -0.012 0.12 0.25 1 -0.48 24 25
RELA 0.035 0.006 -10000 0 -10000 0 0
BCL2A1 0.023 0.035 0.14 2 -10000 0 2
VAV2 -0.002 0.14 0.26 3 -0.51 25 28
ubiquitin-dependent protein catabolic process 0.03 0.049 0.15 9 -0.12 21 30
BTK -0.012 0.19 -10000 0 -1.1 15 15
CD19 -0.019 0.12 0.26 1 -0.47 27 28
MAP4K1 0.035 0.007 -10000 0 -10000 0 0
CD72 0.008 0.1 -10000 0 -0.42 27 27
PAG1 0.02 0.061 -10000 0 -0.42 9 9
MAPK14 -0.017 0.16 0.3 2 -0.43 37 39
SH3BP5 0.021 0.078 -10000 0 -0.42 15 15
PIK3AP1 -0.021 0.15 0.28 4 -0.46 35 39
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.02 0.16 -10000 0 -0.52 33 33
RAF1 0.002 0.11 0.24 13 -0.35 22 35
RasGAP/p62DOK/SHIP 0.026 0.1 -10000 0 -0.27 39 39
CD79A 0.031 0.023 -10000 0 -0.42 1 1
re-entry into mitotic cell cycle -0.02 0.1 0.2 4 -0.25 45 49
RASA1 0.028 0.054 -10000 0 -0.42 7 7
MAPK3 0.012 0.11 0.26 15 -0.31 15 30
MAPK1 0.001 0.1 0.26 8 -0.33 16 24
CD72/SHP1 0.016 0.16 0.29 17 -0.46 31 48
NFKB1 0.035 0.005 -10000 0 -10000 0 0
MAPK8 -0.018 0.16 0.29 6 -0.43 38 44
actin cytoskeleton organization 0.017 0.14 0.3 11 -0.46 24 35
NF-kappa-B/RelA 0.065 0.087 0.27 9 -0.27 3 12
Calcineurin 0.003 0.13 0.25 1 -0.38 27 28
PI3K -0.027 0.11 -10000 0 -0.39 29 29
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.012 0.15 0.3 4 -0.44 36 40
SOS1 0.034 0.021 -10000 0 -0.42 1 1
Bam32/HPK1 -0.068 0.31 -10000 0 -0.74 78 78
DAPP1 -0.1 0.34 -10000 0 -0.84 78 78
cytokine secretion 0.02 0.13 0.25 24 -0.35 30 54
mol:DAG -0.013 0.14 0.27 4 -0.44 29 33
PLCG2 0.02 0.055 -10000 0 -0.42 7 7
MAP2K1 0.001 0.11 0.24 10 -0.35 17 27
B-cell antigen/BCR complex/FcgammaRIIB 0.02 0.093 -10000 0 -0.3 33 33
mol:PI-3-4-5-P3 -0.001 0.11 0.23 24 -0.3 26 50
ETS1 -0.011 0.11 0.23 7 -0.38 24 31
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.032 0.12 -10000 0 -0.26 56 56
B-cell antigen/BCR complex/LYN -0.014 0.12 0.27 1 -0.45 32 33
MALT1 0.031 0.041 -10000 0 -0.42 4 4
TRAF6 0.034 0.021 -10000 0 -0.42 1 1
RAC1 0.007 0.14 0.3 8 -0.48 26 34
B-cell antigen/BCR complex/LYN/SYK -0.004 0.14 -10000 0 -0.49 26 26
CARD11 -0.014 0.14 0.26 7 -0.45 28 35
FCGR2B 0.002 0.11 -10000 0 -0.42 29 29
PPP3CA 0.027 0.061 -10000 0 -0.42 9 9
BCL10 0.034 0.008 -10000 0 -10000 0 0
IKK complex 0.024 0.05 0.16 21 -0.13 2 23
PTPRC 0.005 0.097 -10000 0 -0.42 24 24
PDPK1 0.004 0.085 0.2 33 -0.22 17 50
PPP3CB 0.035 0.021 -10000 0 -0.42 1 1
PPP3CC 0.024 0.043 -10000 0 -0.42 4 4
POU2F2 0.025 0.032 0.13 5 -10000 0 5
mTOR 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
GBL 0.031 0.023 -10000 0 -0.42 1 1
MKNK1 0.035 0.006 -10000 0 -10000 0 0
mol:PIP3 -0.024 0.1 0.26 5 -0.27 63 68
FRAP1 -0.009 0.12 -10000 0 -0.45 24 24
AKT1 -0.024 0.096 0.17 25 -0.25 57 82
INSR 0.033 0.029 -10000 0 -0.42 2 2
Insulin Receptor/Insulin 0.044 0.026 -10000 0 -0.25 3 3
mol:GTP 0.011 0.096 0.33 1 -0.22 42 43
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.006 0.051 -10000 0 -0.2 17 17
TSC2 0.031 0.023 -10000 0 -0.42 1 1
RHEB/GDP 0.004 0.081 -10000 0 -0.27 12 12
TSC1 0.036 0.005 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.009 0.11 -10000 0 -0.3 64 64
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.011 0.068 -10000 0 -0.24 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0 0.093 0.24 4 -0.34 17 21
MAP3K5 -0.013 0.084 0.19 8 -0.25 48 56
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
apoptosis -0.013 0.084 0.19 8 -0.25 48 56
mol:LY294002 0 0 0.001 2 -0.001 58 60
EIF4B -0.001 0.085 0.23 4 -0.3 18 22
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.012 0.083 0.22 4 -0.28 16 20
eIF4E/eIF4G1/eIF4A1 0.001 0.077 -10000 0 -0.32 15 15
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.002 0.12 -10000 0 -0.27 74 74
mTOR/RHEB/GTP/Raptor/GBL 0.01 0.061 0.22 3 -0.23 9 12
FKBP1A 0.035 0.008 -10000 0 -10000 0 0
RHEB/GTP 0.019 0.09 0.31 1 -0.28 11 12
mol:Amino Acids 0 0 0.001 2 -0.001 58 60
FKBP12/Rapamycin 0.026 0.006 -10000 0 -10000 0 0
PDPK1 -0.033 0.094 0.17 22 -0.26 57 79
EIF4E 0.035 0.005 -10000 0 -10000 0 0
ASK1/PP5C -0.032 0.21 -10000 0 -0.58 57 57
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.017 0.052 -10000 0 -0.34 2 2
TSC1/TSC2 0.013 0.1 0.36 1 -0.3 15 16
tumor necrosis factor receptor activity 0 0 0.001 58 -0.001 2 60
RPS6 0.034 0.022 -10000 0 -0.42 1 1
PPP5C 0.031 0.041 -10000 0 -0.42 4 4
EIF4G1 0.031 0.041 -10000 0 -0.42 4 4
IRS1 -0.031 0.11 -10000 0 -0.32 64 64
INS 0.034 0.021 -10000 0 -0.42 1 1
PTEN 0.026 0.06 -10000 0 -0.42 9 9
PDK2 -0.032 0.1 0.17 27 -0.26 61 88
EIF4EBP1 -0.067 0.31 -10000 0 -1.1 38 38
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
PPP2R5D -0.006 0.11 -10000 0 -0.41 23 23
peptide biosynthetic process 0.017 0.03 0.19 5 -0.23 5 10
RHEB 0.035 0.007 -10000 0 -10000 0 0
EIF4A1 0.032 0.012 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 19 -0.003 7 26
EEF2 0.017 0.03 0.19 5 -0.23 5 10
eIF4E/4E-BP1 -0.047 0.3 -10000 0 -1.1 38 38
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.004 0.11 -10000 0 -0.44 29 29
PDGF/PDGFRA/CRKL 0.019 0.088 -10000 0 -0.3 32 32
positive regulation of JUN kinase activity 0.047 0.073 -10000 0 -0.23 22 22
CRKL 0.03 0.041 -10000 0 -0.42 4 4
PDGF/PDGFRA/Caveolin-3 0.021 0.086 -10000 0 -0.3 30 30
AP1 -0.14 0.3 -10000 0 -0.81 76 76
mol:IP3 -0.014 0.079 -10000 0 -0.33 26 26
PLCG1 -0.014 0.079 -10000 0 -0.33 26 26
PDGF/PDGFRA/alphaV Integrin 0.013 0.11 -10000 0 -0.32 43 43
RAPGEF1 0.036 0.004 -10000 0 -10000 0 0
CRK 0.031 0.023 -10000 0 -0.42 1 1
mol:Ca2+ -0.014 0.079 -10000 0 -0.33 26 26
CAV3 0.034 0.022 -10000 0 -0.42 1 1
CAV1 0.028 0.05 -10000 0 -0.42 6 6
SHC/Grb2/SOS1 0.049 0.074 -10000 0 -0.23 22 22
PDGF/PDGFRA/Shf 0.021 0.086 -10000 0 -0.3 30 30
FOS -0.14 0.29 0.31 2 -0.8 76 78
JUN -0.051 0.081 -10000 0 -0.34 34 34
oligodendrocyte development 0.012 0.11 -10000 0 -0.32 43 43
GRB2 0.033 0.01 -10000 0 -10000 0 0
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
mol:DAG -0.014 0.079 -10000 0 -0.33 26 26
PDGF/PDGFRA -0.004 0.11 -10000 0 -0.44 29 29
actin cytoskeleton reorganization 0.019 0.09 -10000 0 -0.3 33 33
SRF 0.017 0.012 -10000 0 -10000 0 0
SHC1 0.027 0.025 -10000 0 -0.42 1 1
PI3K 0.034 0.1 -10000 0 -0.29 41 41
PDGF/PDGFRA/Crk/C3G 0.044 0.079 -10000 0 -0.26 30 30
JAK1 -0.01 0.079 -10000 0 -0.31 30 30
ELK1/SRF -0.026 0.071 0.15 19 -0.26 29 48
SHB 0.03 0.046 -10000 0 -0.42 5 5
SHF 0.033 0.022 -10000 0 -0.42 1 1
CSNK2A1 0.039 0.022 -10000 0 -10000 0 0
GO:0007205 -0.023 0.083 -10000 0 -0.36 27 27
SOS1 0.034 0.021 -10000 0 -0.42 1 1
Ras protein signal transduction 0.047 0.073 -10000 0 -0.23 22 22
PDGF/PDGFRA/SHB 0.019 0.09 -10000 0 -0.3 33 33
PDGF/PDGFRA/Caveolin-1 0.017 0.095 -10000 0 -0.32 33 33
ITGAV 0.021 0.08 -10000 0 -0.42 16 16
ELK1 -0.035 0.079 0.22 3 -0.32 29 32
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
PDGF/PDGFRA/Crk 0.019 0.086 -10000 0 -0.3 30 30
JAK-STAT cascade -0.01 0.079 -10000 0 -0.31 30 30
cell proliferation 0.021 0.086 -10000 0 -0.3 30 30
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.029 0.23 -10000 0 -0.98 28 28
regulation of axonogenesis 0 0.058 0.3 12 -10000 0 12
myoblast fusion -0.006 0.11 0.4 31 -10000 0 31
mol:GTP 0.01 0.066 -10000 0 -0.23 32 32
regulation of calcium-dependent cell-cell adhesion -0.047 0.082 0.24 33 -10000 0 33
ARF1/GTP 0.024 0.056 -10000 0 -0.19 22 22
mol:GM1 0 0.047 -10000 0 -0.18 27 27
mol:Choline -0.002 0.058 -10000 0 -0.27 16 16
lamellipodium assembly -0.006 0.12 -10000 0 -0.45 34 34
MAPK3 0.008 0.085 -10000 0 -0.33 29 29
ARF6/GTP/NME1/Tiam1 0.048 0.082 -10000 0 -0.24 33 33
ARF1 0.027 0.025 -10000 0 -0.42 1 1
ARF6/GDP 0.006 0.11 -10000 0 -0.4 31 31
ARF1/GDP 0.008 0.1 -10000 0 -0.36 29 29
ARF6 0.031 0.056 -10000 0 -0.32 5 5
RAB11A 0.034 0.021 -10000 0 -0.42 1 1
TIAM1 0.025 0.06 -10000 0 -0.43 8 8
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.009 0.086 -10000 0 -0.34 28 28
actin filament bundle formation -0.016 0.11 0.37 34 -10000 0 34
KALRN 0.001 0.082 -10000 0 -0.31 31 31
RAB11FIP3/RAB11A 0.047 0.043 -10000 0 -0.3 7 7
RhoA/GDP 0.016 0.11 -10000 0 -0.38 34 34
NME1 0.03 0.02 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.11 -10000 0 -0.37 33 33
substrate adhesion-dependent cell spreading 0.01 0.066 -10000 0 -0.23 32 32
cortical actin cytoskeleton organization -0.006 0.13 -10000 0 -0.46 34 34
RAC1 0.035 0.006 -10000 0 -10000 0 0
liver development 0.01 0.066 -10000 0 -0.23 32 32
ARF6/GTP 0.01 0.066 -10000 0 -0.23 32 32
RhoA/GTP 0.025 0.071 -10000 0 -0.21 35 35
mol:GDP -0.008 0.1 -10000 0 -0.39 31 31
ARF6/GTP/RAB11FIP3/RAB11A 0.047 0.067 -10000 0 -0.18 31 31
RHOA 0.026 0.061 -10000 0 -0.42 9 9
PLD1 0.007 0.067 -10000 0 -0.23 30 30
RAB11FIP3 0.031 0.05 -10000 0 -0.42 6 6
tube morphogenesis -0.006 0.12 -10000 0 -0.45 34 34
ruffle organization 0 0.058 -10000 0 -0.3 12 12
regulation of epithelial cell migration 0.01 0.066 -10000 0 -0.23 32 32
PLD2 0.01 0.054 -10000 0 -0.2 25 25
PIP5K1A 0 0.058 -10000 0 -0.3 12 12
mol:Phosphatidic acid -0.002 0.058 -10000 0 -0.27 16 16
Rac1/GTP -0.006 0.13 -10000 0 -0.46 34 34
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.03 0.24 -10000 0 -0.75 24 24
PCK1 0.018 0.17 -10000 0 -0.99 5 5
HNF4A -0.006 0.26 0.56 7 -0.77 22 29
KCNJ11 -0.053 0.34 -10000 0 -0.98 45 45
AKT1 -0.002 0.17 -10000 0 -0.42 23 23
response to starvation 0.004 0.002 -10000 0 -10000 0 0
DLK1 -0.021 0.27 0.63 1 -0.8 22 23
NKX2-1 0.039 0.13 0.35 5 -0.35 7 12
ACADM -0.031 0.26 -10000 0 -0.77 28 28
TAT -0.005 0.16 -10000 0 -0.58 7 7
CEBPB 0.03 0.051 -10000 0 -0.42 6 6
CEBPA 0.029 0.07 -10000 0 -0.42 12 12
TTR -0.026 0.28 0.57 1 -0.71 43 44
PKLR 0.014 0.25 0.56 1 -0.72 22 23
APOA1 -0.025 0.28 -10000 0 -0.88 22 22
CPT1C -0.028 0.27 0.56 1 -0.8 31 32
ALAS1 0.011 0.18 -10000 0 -1.1 4 4
TFRC -0.039 0.35 -10000 0 -1.2 36 36
FOXF1 0.026 0.032 -10000 0 -0.42 2 2
NF1 0.036 0.035 -10000 0 -0.36 3 3
HNF1A (dimer) 0.008 0.02 -10000 0 -0.21 4 4
CPT1A -0.022 0.27 0.56 3 -0.84 27 30
HMGCS1 -0.02 0.24 -10000 0 -0.74 24 24
NR3C1 0.032 0.079 -10000 0 -0.4 16 16
CPT1B -0.022 0.24 -10000 0 -0.75 22 22
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.035 0.021 -10000 0 -0.42 1 1
GCK -0.024 0.25 -10000 0 -0.76 24 24
CREB1 0.041 0.029 -10000 0 -0.24 4 4
IGFBP1 0.01 0.14 -10000 0 -1.3 1 1
PDX1 0.007 0.15 -10000 0 -0.37 24 24
UCP2 -0.05 0.31 0.56 2 -0.85 47 49
ALDOB -0.022 0.27 -10000 0 -0.8 23 23
AFP -0.024 0.12 -10000 0 -0.82 3 3
BDH1 -0.033 0.26 -10000 0 -0.77 31 31
HADH -0.022 0.26 -10000 0 -0.62 52 52
F2 -0.008 0.29 -10000 0 -0.86 23 23
HNF1A 0.008 0.02 -10000 0 -0.21 4 4
G6PC 0.04 0.091 -10000 0 -1.3 1 1
SLC2A2 0.004 0.2 -10000 0 -0.95 6 6
INS 0.024 0.024 0.2 1 -0.43 1 2
FOXA1 -0.037 0.18 -10000 0 -0.4 97 97
FOXA3 0.043 0.076 -10000 0 -0.26 9 9
FOXA2 -0.009 0.32 -10000 0 -0.72 49 49
ABCC8 -0.2 0.48 -10000 0 -0.9 150 150
ALB -0.03 0.15 -10000 0 -0.95 7 7
PLK1 signaling events

Figure S61.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S61.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.001 0.047 0.2 23 -0.12 5 28
BUB1B -0.018 0.097 0.12 2 -0.3 43 45
PLK1 0.004 0.034 0.092 12 -0.088 21 33
PLK1S1 0.002 0.019 0.053 14 -0.047 21 35
KIF2A 0.003 0.03 0.081 12 -0.079 21 33
regulation of mitotic centrosome separation 0.004 0.034 0.092 12 -0.087 21 33
GOLGA2 0.035 0.005 -10000 0 -10000 0 0
Hec1/SPC24 -0.008 0.019 -10000 0 -0.069 29 29
WEE1 -0.004 0.093 -10000 0 -0.36 24 24
cytokinesis -0.023 0.14 -10000 0 -0.46 38 38
PP2A-alpha B56 -0.034 0.28 -10000 0 -0.71 70 70
AURKA 0.003 0.02 0.059 15 -0.049 15 30
PICH/PLK1 -0.019 0.095 -10000 0 -0.33 35 35
CENPE -0.013 0.069 0.24 2 -0.25 32 34
RhoA/GTP 0.02 0.043 -10000 0 -0.3 9 9
positive regulation of microtubule depolymerization 0.003 0.03 0.081 12 -0.078 21 33
PPP2CA 0.031 0.046 -10000 0 -0.42 5 5
FZR1 0.035 0.006 -10000 0 -10000 0 0
TPX2 -0.008 0.08 0.12 2 -0.27 40 42
PAK1 0.014 0.087 -10000 0 -0.43 18 18
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.034 0.021 -10000 0 -0.42 1 1
CLSPN 0.003 0.058 -10000 0 -0.28 18 18
GORASP1 0.034 0.022 -10000 0 -0.42 1 1
metaphase 0.002 0.006 0.019 48 -10000 0 48
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.002 0.019 0.053 14 -0.047 21 35
G2 phase of mitotic cell cycle -0.001 0.002 0.011 2 -10000 0 2
STAG2 0.036 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.008 0.11 -10000 0 -0.52 19 19
spindle elongation 0.004 0.034 0.092 12 -0.087 21 33
ODF2 0.036 0.005 -10000 0 -10000 0 0
BUB1 -0.073 0.29 -10000 0 -0.76 72 72
TPT1 -0.008 0.063 -10000 0 -0.19 49 49
CDC25C -0.014 0.11 -10000 0 -0.36 42 42
CDC25B 0.027 0.045 -10000 0 -0.44 4 4
SGOL1 0.001 0.047 0.12 5 -0.2 23 28
RHOA 0.026 0.061 -10000 0 -0.42 9 9
CCNB1/CDK1 0.028 0.13 -10000 0 -0.37 41 41
CDC14B 0.005 0.024 -10000 0 -0.3 3 3
CDC20 0.016 0.087 -10000 0 -0.42 19 19
PLK1/PBIP1 -0.005 0.057 0.095 3 -0.21 28 31
mitosis 0 0.003 0.013 12 -10000 0 12
FBXO5 -0.002 0.05 0.13 9 -0.2 11 20
CDC2 0.013 0.097 -10000 0 -0.44 22 22
NDC80 0 0 -10000 0 -10000 0 0
metaphase plate congression 0.004 0.055 -10000 0 -0.25 21 21
ERCC6L -0.013 0.11 -10000 0 -0.36 41 41
NLP/gamma Tubulin 0.007 0.028 0.075 14 -0.082 8 22
microtubule cytoskeleton organization -0.008 0.063 -10000 0 -0.19 49 49
G2/M transition DNA damage checkpoint 0 0.003 0.011 22 -10000 0 22
PPP1R12A 0.035 0.021 -10000 0 -0.43 1 1
interphase 0 0.003 0.011 22 -10000 0 22
PLK1/PRC1-2 0.013 0.12 -10000 0 -0.33 43 43
GRASP65/GM130/RAB1/GTP/PLK1 0.049 0.049 -10000 0 -0.19 2 2
RAB1A 0.034 0.021 -10000 0 -0.42 1 1
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.003 0.025 0.069 16 -0.069 12 28
mitotic prometaphase 0 0.004 0.018 21 -10000 0 21
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.055 -10000 0 -0.35 4 4
microtubule-based process 0.006 0.078 0.12 2 -0.25 35 37
Golgi organization 0.004 0.034 0.092 12 -0.087 21 33
Cohesin/SA2 0.021 0.035 0.11 2 -0.12 1 3
PPP1CB/MYPT1 0.051 0.018 -10000 0 -0.31 1 1
KIF20A 0.003 0.12 -10000 0 -0.42 35 35
APC/C/CDC20 0.013 0.064 -10000 0 -0.25 20 20
PPP2R1A 0.035 0.007 -10000 0 -10000 0 0
chromosome segregation -0.005 0.056 0.093 3 -0.21 28 31
PRC1 0.008 0.1 -10000 0 -0.42 28 28
ECT2 0.004 0.072 0.22 28 -0.22 17 45
C13orf34 0.003 0.028 0.074 16 -0.072 21 37
NUDC 0.004 0.055 -10000 0 -0.25 21 21
regulation of attachment of spindle microtubules to kinetochore -0.018 0.096 0.12 2 -0.3 43 45
spindle assembly 0.01 0.036 0.09 22 -0.082 12 34
spindle stabilization 0.002 0.019 0.053 14 -0.047 21 35
APC/C/HCDH1 0.03 0.023 -10000 0 -0.25 3 3
MKLP2/PLK1 0.006 0.078 0.12 2 -0.25 35 37
CCNB1 0.011 0.1 -10000 0 -0.44 25 25
PPP1CB 0.036 0.005 -10000 0 -10000 0 0
BTRC 0.034 0.022 -10000 0 -0.42 1 1
ROCK2 0.006 0.064 0.21 1 -0.34 10 11
TUBG1 0.009 0.038 -10000 0 -0.17 14 14
G2/M transition of mitotic cell cycle -0.021 0.11 -10000 0 -0.37 41 41
MLF1IP -0.009 0.07 -10000 0 -0.3 27 27
INCENP 0.027 0.055 -10000 0 -0.43 7 7
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.019 0.073 -10000 0 -0.29 26 26
PDGFRB 0.028 0.058 -10000 0 -0.43 8 8
SPHK1 -0.034 0.2 -10000 0 -0.76 35 35
mol:S1P -0.02 0.19 -10000 0 -0.65 35 35
S1P1/S1P/Gi -0.02 0.16 -10000 0 -0.51 32 32
GNAO1 0.03 0.015 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 0.001 0.15 0.33 2 -0.48 25 27
PLCG1 -0.015 0.15 0.3 2 -0.49 28 30
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.028 0.058 -10000 0 -0.43 8 8
GNAI2 0.028 0.058 -10000 0 -0.42 8 8
GNAI3 0.036 0.008 -10000 0 -10000 0 0
GNAI1 0.018 0.086 -10000 0 -0.43 18 18
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.002 0.12 -10000 0 -0.52 25 25
S1P1/S1P -0.011 0.17 0.25 2 -0.46 53 55
negative regulation of cAMP metabolic process -0.018 0.16 -10000 0 -0.49 32 32
MAPK3 -0.012 0.16 0.32 11 -0.55 26 37
calcium-dependent phospholipase C activity 0 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.043 -10000 0 -0.3 9 9
KDR 0.028 0.059 -10000 0 -0.21 23 23
PLCB2 -0.01 0.15 0.24 2 -0.42 48 50
RAC1 0.035 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.018 0.14 -10000 0 -0.38 55 55
receptor internalization -0.01 0.16 0.24 2 -0.42 55 57
PTGS2 -0.012 0.17 -10000 0 -0.77 14 14
Rac1/GTP -0.015 0.14 -10000 0 -0.39 50 50
RHOA 0.026 0.061 -10000 0 -0.42 9 9
VEGFA -0.004 0.034 -10000 0 -0.15 26 26
negative regulation of T cell proliferation -0.018 0.16 -10000 0 -0.49 32 32
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.024 0.068 -10000 0 -0.42 11 11
MAPK1 -0.02 0.15 -10000 0 -0.54 28 28
S1P1/S1P/PDGFB-D/PDGFRB 0.008 0.18 0.31 2 -0.45 50 52
ABCC1 0.029 0.042 -10000 0 -0.43 4 4
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.027 0.025 -10000 0 -0.42 1 1
Caspase 8 (4 units) 0.03 0.13 -10000 0 -0.39 23 23
NEF -0.012 0.049 -10000 0 -0.17 45 45
NFKBIA 0.021 0.05 -10000 0 -0.46 2 2
BIRC3 -0.015 0.14 -10000 0 -0.46 42 42
CYCS -0.005 0.12 0.19 4 -0.33 38 42
RIPK1 0.035 0.007 -10000 0 -10000 0 0
CD247 -0.012 0.049 -10000 0 -0.17 45 45
MAP2K7 0.005 0.18 -10000 0 -0.74 17 17
protein ubiquitination -0.015 0.12 0.22 1 -0.37 25 26
CRADD 0.029 0.054 -10000 0 -0.42 7 7
DAXX 0.035 0.005 -10000 0 -10000 0 0
FAS 0.008 0.1 -10000 0 -0.42 28 28
BID -0.006 0.12 -10000 0 -0.3 57 57
NF-kappa-B/RelA/I kappa B alpha 0.04 0.1 -10000 0 -0.26 41 41
TRADD 0.029 0.014 -10000 0 -10000 0 0
MAP3K5 0.013 0.093 -10000 0 -0.42 22 22
CFLAR 0.031 0.046 -10000 0 -0.42 5 5
FADD 0.029 0.014 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.04 0.1 -10000 0 -0.26 41 41
MAPK8 0.004 0.16 0.42 1 -0.66 17 18
APAF1 0.032 0.041 -10000 0 -0.42 4 4
TRAF1 0.034 0.021 -10000 0 -0.42 1 1
TRAF2 0.033 0.029 -10000 0 -0.42 2 2
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.003 0.13 -10000 0 -0.31 52 52
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.016 0.14 -10000 0 -0.41 33 33
CHUK -0.019 0.13 -10000 0 -0.4 25 25
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.055 0.094 -10000 0 -0.24 34 34
TCRz/NEF -0.018 0.085 -10000 0 -0.29 45 45
TNF 0.026 0.061 -10000 0 -0.42 9 9
FASLG -0.02 0.13 -10000 0 -0.52 34 34
NFKB1 0.022 0.042 -10000 0 -0.14 3 3
TNFR1A/BAG4/TNF-alpha 0.048 0.049 -10000 0 -0.25 7 7
CASP6 0.024 0.15 -10000 0 -0.55 21 21
CASP7 -0.043 0.2 0.29 1 -0.46 73 74
RELA 0.022 0.042 -10000 0 -0.14 3 3
CASP2 0.035 0.007 -10000 0 -10000 0 0
CASP3 -0.041 0.19 -10000 0 -0.46 68 68
TNFRSF1A 0.033 0.022 -10000 0 -0.42 1 1
TNFR1A/BAG4 0.038 0.028 -10000 0 -0.3 1 1
CASP8 0.036 0.004 -10000 0 -10000 0 0
CASP9 0.034 0.022 -10000 0 -0.42 1 1
MAP3K14 -0.014 0.14 0.24 2 -0.41 29 31
APAF-1/Caspase 9 -0.014 0.14 0.2 1 -0.34 55 56
BCL2 -0.031 0.16 0.58 1 -0.54 22 23
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.046 0.056 -10000 0 -0.23 17 17
RGS9BP -0.022 0.15 -10000 0 -0.42 60 60
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.023 0.062 -10000 0 -0.26 20 20
mol:ADP 0.007 0.019 -10000 0 -0.3 2 2
GNAT2 0.018 0.087 -10000 0 -0.42 19 19
RGS9-1/Gbeta5/R9AP 0.007 0.12 -10000 0 -0.27 72 72
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.025 0.077 -10000 0 -0.27 31 31
GRK7 0.033 0.029 -10000 0 -0.42 2 2
CNGB3 0.022 0.051 -10000 0 -0.42 6 6
Cone Metarhodopsin II/X-Arrestin 0.027 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.039 0.09 0.19 93 -0.24 21 114
Cone PDE6 0.021 0.13 -10000 0 -0.25 83 83
Cone Metarhodopsin II 0.022 0.016 -10000 0 -0.22 2 2
Na + (4 Units) 0.037 0.065 -10000 0 -0.24 21 21
GNAT2/GDP 0.011 0.12 -10000 0 -0.24 85 85
GNB5 0.024 0.067 -10000 0 -0.42 11 11
mol:GMP (4 units) 0.004 0.079 0.19 16 -0.26 35 51
Cone Transducin 0.05 0.06 -10000 0 -0.24 17 17
SLC24A2 0.032 0.036 -10000 0 -0.42 3 3
GNB3/GNGT2 0.047 0.022 -10000 0 -0.3 1 1
GNB3 0.034 0.009 -10000 0 -10000 0 0
GNAT2/GTP 0.014 0.062 -10000 0 -0.3 19 19
CNGA3 0.017 0.08 -10000 0 -0.42 16 16
ARR3 0.036 0.002 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.023 0.062 -10000 0 -0.26 20 20
mol:Pi 0.007 0.12 -10000 0 -0.27 72 72
Cone CNG Channel 0.032 0.1 -10000 0 -0.26 45 45
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.032 0.036 -10000 0 -0.42 3 3
RGS9 0.017 0.067 -10000 0 -0.42 11 11
PDE6C 0.03 0.05 -10000 0 -0.42 6 6
GNGT2 0.033 0.03 -10000 0 -0.42 2 2
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.021 0.075 -10000 0 -0.42 14 14
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.04 0.11 -10000 0 -0.46 19 19
HDAC1 0.04 0.028 -10000 0 -0.43 1 1
AES 0.037 0.008 -10000 0 -10000 0 0
FBXW11 0.034 0.021 -10000 0 -0.42 1 1
DTX1 0.032 0.036 -10000 0 -0.42 3 3
LRP6/FZD1 0.041 0.053 -10000 0 -0.3 11 11
TLE1 0.006 0.11 -10000 0 -0.42 33 33
AP1 -0.026 0.11 -10000 0 -0.26 79 79
NCSTN 0.028 0.025 -10000 0 -0.42 1 1
ADAM10 0.033 0.03 -10000 0 -0.42 2 2
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.037 0.15 -10000 0 -0.68 8 8
NICD/RBPSUH 0.004 0.098 -10000 0 -0.45 19 19
WIF1 0.029 0.014 -10000 0 -10000 0 0
NOTCH1 0.013 0.1 -10000 0 -0.48 19 19
PSENEN 0.035 0.006 -10000 0 -10000 0 0
KREMEN2 -0.091 0.19 -10000 0 -0.42 129 129
DKK1 -0.028 0.15 -10000 0 -0.42 61 61
beta catenin/beta TrCP1 0.013 0.099 0.28 1 -0.37 12 13
APH1B 0.023 0.073 -10000 0 -0.42 13 13
APH1A 0.031 0.036 -10000 0 -0.42 3 3
AXIN1 0.015 0.051 -10000 0 -0.47 1 1
CtBP/CBP/TCF1/TLE1/AES 0.025 0.089 0.29 3 -0.24 26 29
PSEN1 0.032 0.036 -10000 0 -0.42 3 3
FOS -0.031 0.15 -10000 0 -0.42 66 66
JUN -0.001 0.12 -10000 0 -0.42 39 39
MAP3K7 0.035 0.013 -10000 0 -10000 0 0
CTNNB1 -0.003 0.096 0.26 2 -0.39 12 14
MAPK3 0.032 0.023 -10000 0 -0.42 1 1
DKK2/LRP6/Kremen 2 -0.045 0.15 -10000 0 -0.26 153 153
HNF1A 0.002 0.006 -10000 0 -10000 0 0
CTBP1 0.036 0.01 -10000 0 -10000 0 0
MYC -0.083 0.34 -10000 0 -1.3 35 35
NKD1 0.027 0.038 -10000 0 -0.42 3 3
FZD1 0.028 0.054 -10000 0 -0.42 7 7
NOTCH1 precursor/Deltex homolog 1 0.041 0.11 -10000 0 -0.46 19 19
apoptosis -0.026 0.11 -10000 0 -0.26 79 79
Delta 1/NOTCHprecursor 0.039 0.11 -10000 0 -0.45 19 19
DLL1 0.033 0.01 -10000 0 -10000 0 0
PPARD 0.006 0.1 -10000 0 -0.84 6 6
Gamma Secretase 0.067 0.07 -10000 0 -0.23 14 14
APC -0.001 0.1 0.26 1 -0.45 18 19
DVL1 0.024 0.028 -10000 0 -0.26 2 2
CSNK2A1 0.034 0.008 -10000 0 -10000 0 0
MAP3K7IP1 0.036 0.012 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.062 0.16 -10000 0 -0.28 169 169
LRP6 0.029 0.046 -10000 0 -0.42 5 5
CSNK1A1 0.035 0.006 -10000 0 -10000 0 0
NLK 0.029 0.024 -10000 0 -0.24 1 1
CCND1 -0.2 0.5 -10000 0 -1.3 84 84
WNT1 0.034 0.021 -10000 0 -0.42 1 1
Axin1/APC/beta catenin 0.023 0.099 0.34 2 -0.48 7 9
DKK2 0.006 0.11 -10000 0 -0.42 31 31
NOTCH1 precursor/DVL1 0.037 0.1 -10000 0 -0.55 9 9
GSK3B 0.036 0.005 -10000 0 -10000 0 0
FRAT1 0.03 0.054 -10000 0 -0.42 7 7
NOTCH/Deltex homolog 1 0.041 0.11 -10000 0 -0.47 19 19
PPP2R5D 0.011 0.068 0.25 2 -0.32 17 19
MAPK1 0.033 0.022 -10000 0 -0.42 1 1
WNT1/LRP6/FZD1 0.07 0.056 -10000 0 -0.24 12 12
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.026 0.02 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.019 0.1 -10000 0 -0.27 53 53
fibroblast growth factor receptor signaling pathway 0.018 0.1 -10000 0 -0.27 53 53
LAMA1 0.034 0.009 -10000 0 -10000 0 0
PRNP 0.028 0.054 -10000 0 -0.42 7 7
GPC1/SLIT2 0.013 0.11 -10000 0 -0.31 51 51
SMAD2 0.004 0.064 0.19 5 -0.24 29 34
GPC1/PrPc/Cu2+ 0.029 0.068 -10000 0 -0.26 25 25
GPC1/Laminin alpha1 0.035 0.068 -10000 0 -0.3 19 19
TDGF1 0.034 0.008 -10000 0 -10000 0 0
CRIPTO/GPC1 0.036 0.068 -10000 0 -0.3 19 19
APP/GPC1 0.016 0.1 -10000 0 -0.31 46 46
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.005 0.06 -10000 0 -0.26 25 25
FLT1 0.026 0.054 -10000 0 -0.42 7 7
GPC1/TGFB/TGFBR1/TGFBR2 0.049 0.081 -10000 0 -0.26 30 30
SERPINC1 0.027 0.025 -10000 0 -0.42 1 1
FYN 0.005 0.057 -10000 0 -0.26 23 23
FGR 0.008 0.053 -10000 0 -0.26 19 19
positive regulation of MAPKKK cascade -0.023 0.12 0.28 1 -0.35 43 44
SLIT2 0.003 0.11 -10000 0 -0.42 34 34
GPC1/NRG 0.028 0.068 -10000 0 -0.3 19 19
NRG1 0.028 0.015 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.028 0.069 -10000 0 -0.26 25 25
LYN 0.009 0.045 -10000 0 -0.26 14 14
mol:Spermine -0.003 0.058 -10000 0 -0.3 19 19
cell growth 0.018 0.1 -10000 0 -0.27 53 53
BMP signaling pathway -0.017 0.087 0.42 19 -10000 0 19
SRC 0.007 0.056 -10000 0 -0.27 19 19
TGFBR1 0.027 0.061 -10000 0 -0.42 9 9
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.014 0.078 -10000 0 -0.42 15 15
GPC1 0.017 0.087 -10000 0 -0.42 19 19
TGFBR1 (dimer) 0.027 0.061 -10000 0 -0.42 9 9
VEGFA 0 0 -10000 0 -10000 0 0
BLK 0.006 0.046 -10000 0 -0.25 15 15
HCK -0.001 0.07 -10000 0 -0.26 35 35
FGF2 -0.001 0.11 -10000 0 -0.42 34 34
FGFR1 0.021 0.061 -10000 0 -0.42 9 9
VEGFR1 homodimer 0.026 0.054 -10000 0 -0.42 7 7
TGFBR2 0.032 0.036 -10000 0 -0.42 3 3
cell death 0.016 0.1 -10000 0 -0.31 46 46
ATIII/GPC1 0.029 0.066 -10000 0 -0.3 17 17
PLA2G2A/GPC1 0.022 0.089 -10000 0 -0.31 33 33
LCK -0.021 0.097 -10000 0 -0.26 71 71
neuron differentiation 0.028 0.068 -10000 0 -0.3 19 19
PrPc/Cu2+ 0.021 0.038 -10000 0 -0.3 7 7
APP 0.008 0.1 -10000 0 -0.42 28 28
TGFBR2 (dimer) 0.032 0.036 -10000 0 -0.42 3 3
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.044 0.086 -10000 0 -0.22 38 38
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.03 0.041 -10000 0 -0.42 4 4
STAT1 (dimer)/Cbp/p300 0.033 0.099 0.31 1 -0.32 16 17
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.051 0.051 -10000 0 -0.26 4 4
antigen processing and presentation of peptide antigen via MHC class I -0.017 0.094 -10000 0 -0.25 46 46
CaM/Ca2+ 0.047 0.085 -10000 0 -0.21 38 38
RAP1A 0.03 0.05 -10000 0 -0.42 6 6
STAT1 (dimer)/SHP2 0.017 0.094 0.28 3 -0.24 46 49
AKT1 -0.012 0.094 0.28 11 -0.32 8 19
MAP2K1 -0.026 0.079 0.26 2 -0.28 13 15
MAP3K11 0.005 0.078 0.26 5 -0.21 38 43
IFNGR1 0.03 0.021 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.006 0.13 -10000 0 -0.45 18 18
Rap1/GTP 0.001 0.067 -10000 0 -0.21 31 31
CRKL/C3G 0.047 0.034 -10000 0 -0.3 4 4
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.058 0.092 -10000 0 -0.22 38 38
CEBPB -0.016 0.16 0.34 2 -0.51 31 33
STAT3 0.028 0.031 -10000 0 -0.42 2 2
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.053 0.13 -10000 0 -0.84 6 6
STAT1 -0.003 0.089 0.29 3 -0.24 42 45
CALM1 0.035 0.007 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.007 0.12 -10000 0 -0.42 38 38
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
STAT1 (dimer)/PIAS1 0.017 0.092 0.29 3 -0.31 13 16
CEBPB/PTGES2/Cbp/p300 0.004 0.11 -10000 0 -0.33 31 31
mol:Ca2+ 0.041 0.083 -10000 0 -0.22 38 38
MAPK3 -0.016 0.14 0.36 1 -0.63 13 14
STAT1 (dimer) -0.012 0.14 -10000 0 -0.35 46 46
MAPK1 -0.044 0.21 0.4 1 -0.74 32 33
JAK2 0.028 0.036 -10000 0 -0.43 2 2
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
JAK1 0.028 0.04 -10000 0 -0.42 3 3
CAMK2D 0.023 0.073 -10000 0 -0.42 13 13
DAPK1 -0.007 0.13 0.3 2 -0.48 22 24
SMAD7 -0.002 0.059 0.16 8 -0.18 13 21
CBL/CRKL/C3G 0.033 0.083 0.3 2 -0.21 31 33
PI3K 0.035 0.096 -10000 0 -0.23 42 42
IFNG -0.007 0.12 -10000 0 -0.43 38 38
apoptosis -0.059 0.18 0.31 1 -0.42 84 85
CAMK2G 0.036 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.028 0.031 -10000 0 -0.42 2 2
CAMK2A 0.034 0.021 -10000 0 -0.42 1 1
CAMK2B -0.014 0.13 -10000 0 -0.42 49 49
FRAP1 -0.019 0.085 0.28 8 -0.32 6 14
PRKCD -0.013 0.092 0.29 10 -0.34 6 16
RAP1B 0.032 0.03 -10000 0 -0.42 2 2
negative regulation of cell growth -0.017 0.094 -10000 0 -0.25 46 46
PTPN2 0.034 0.008 -10000 0 -10000 0 0
EP300 0.033 0.022 -10000 0 -0.42 1 1
IRF1 -0.006 0.11 0.32 7 -0.41 16 23
STAT1 (dimer)/PIASy 0.012 0.093 0.29 3 -0.27 21 24
SOCS1 0.018 0.12 -10000 0 -1.1 6 6
mol:GDP 0.03 0.079 0.28 2 -0.2 32 34
CASP1 -0.014 0.083 0.16 7 -0.25 41 48
PTGES2 0.035 0.005 -10000 0 -10000 0 0
IRF9 0 0.049 0.12 2 -0.15 18 20
mol:PI-3-4-5-P3 0.02 0.087 -10000 0 -0.22 43 43
RAP1/GDP 0.024 0.08 -10000 0 -0.25 15 15
CBL 0.003 0.073 0.29 2 -0.21 36 38
MAP3K1 -0.006 0.088 0.25 4 -0.22 52 56
PIAS1 0.035 0.006 -10000 0 -10000 0 0
PIAS4 0.032 0.036 -10000 0 -0.42 3 3
antigen processing and presentation of peptide antigen via MHC class II -0.017 0.094 -10000 0 -0.25 46 46
PTPN11 0.007 0.079 0.29 4 -0.22 38 42
CREBBP 0.033 0.011 -10000 0 -10000 0 0
RAPGEF1 0.036 0.004 -10000 0 -10000 0 0
Ceramide signaling pathway

Figure S68.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S68.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.007 0.052 -10000 0 -0.3 14 14
MAP4K4 -0.026 0.11 0.22 1 -0.32 36 37
BAG4 0.027 0.025 -10000 0 -0.42 1 1
PKC zeta/ceramide -0.008 0.048 0.12 2 -0.22 14 16
NFKBIA 0.033 0.03 -10000 0 -0.42 2 2
BIRC3 -0.01 0.12 -10000 0 -0.42 42 42
BAX 0.011 0.034 -10000 0 -0.37 2 2
RIPK1 0.035 0.007 -10000 0 -10000 0 0
AKT1 0.002 0.089 0.66 8 -0.39 3 11
BAD -0.011 0.05 0.19 3 -0.23 12 15
SMPD1 0.006 0.065 0.2 2 -0.23 17 19
RB1 -0.016 0.056 -10000 0 -0.23 21 21
FADD/Caspase 8 0.009 0.12 0.28 6 -0.33 23 29
MAP2K4 -0.023 0.064 0.18 1 -0.22 35 36
NSMAF 0.026 0.047 -10000 0 -0.42 5 5
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.01 0.054 0.19 8 -0.24 10 18
EGF -0.069 0.19 -10000 0 -0.42 110 110
mol:ceramide -0.008 0.052 0.13 9 -0.23 14 23
MADD 0.035 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.005 0.075 -10000 0 -0.31 28 28
ASAH1 0.008 0.089 -10000 0 -0.42 20 20
negative regulation of cell cycle -0.015 0.056 0.16 1 -0.23 21 22
cell proliferation -0.013 0.092 0.24 1 -0.22 31 32
BID -0.015 0.14 -10000 0 -0.65 15 15
MAP3K1 -0.021 0.066 -10000 0 -0.23 36 36
EIF2A -0.014 0.065 0.19 14 -0.22 24 38
TRADD 0.029 0.014 -10000 0 -10000 0 0
CRADD 0.029 0.054 -10000 0 -0.42 7 7
MAPK3 -0.007 0.053 0.2 3 -0.23 10 13
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.012 0.061 0.2 3 -0.26 10 13
Cathepsin D/ceramide 0.006 0.06 0.15 1 -0.22 18 19
FADD 0.004 0.12 0.22 53 -0.33 23 76
KSR1 -0.009 0.051 0.19 3 -0.23 12 15
MAPK8 -0.013 0.059 -10000 0 -0.21 21 21
PRKRA -0.009 0.052 0.19 4 -0.23 12 16
PDGFA 0.022 0.078 -10000 0 -0.42 15 15
TRAF2 0.033 0.029 -10000 0 -0.42 2 2
IGF1 -0.041 0.17 -10000 0 -0.42 80 80
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.008 0.051 0.13 9 -0.23 14 23
CTSD 0.029 0.046 -10000 0 -0.42 5 5
regulation of nitric oxide biosynthetic process 0.051 0.012 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.013 0.098 0.25 1 -0.24 31 32
PRKCD 0.032 0.03 -10000 0 -0.42 2 2
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.005 0.075 -10000 0 -0.31 28 28
RelA/NF kappa B1 0.051 0.012 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.024 0.073 -10000 0 -0.42 13 13
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.015 0.11 -10000 0 -0.36 28 28
TNFR1A/BAG4/TNF-alpha 0.048 0.049 -10000 0 -0.25 7 7
mol:Sphingosine-1-phosphate 0.007 0.052 -10000 0 -0.3 14 14
MAP2K1 -0.011 0.053 0.19 5 -0.23 9 14
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.035 0.006 -10000 0 -10000 0 0
CYCS 0.032 0.069 0.16 64 -0.18 3 67
TNFRSF1A 0.033 0.022 -10000 0 -0.42 1 1
NFKB1 0.035 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.028 -10000 0 -0.3 1 1
EIF2AK2 -0.017 0.062 0.18 6 -0.22 25 31
TNF-alpha/TNFR1A/FAN 0.05 0.052 -10000 0 -0.26 9 9
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.008 0.091 -10000 0 -0.36 16 16
MAP2K2 -0.012 0.054 0.2 3 -0.23 9 12
SMPD3 -0.027 0.13 0.19 1 -0.3 76 77
TNF 0.026 0.061 -10000 0 -0.42 9 9
PKC zeta/PAR4 0.018 0.051 -10000 0 -0.3 13 13
mol:PHOSPHOCHOLINE 0.037 0.094 0.2 103 -0.2 4 107
NF kappa B1/RelA/I kappa B alpha 0.068 0.057 -10000 0 -0.22 15 15
AIFM1 0.027 0.067 0.16 64 -0.16 8 72
BCL2 -0.057 0.18 -10000 0 -0.42 99 99
TRAIL 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
TNFSF10 -0.007 0.13 -10000 0 -0.42 44 44
positive regulation of NF-kappaB transcription factor activity 0.01 0.096 -10000 0 -0.29 44 44
MAP2K4 -0.009 0.1 0.22 1 -0.35 27 28
IKBKB 0.029 0.014 -10000 0 -10000 0 0
TNFRSF10B 0.027 0.016 -10000 0 -10000 0 0
TNFRSF10A 0.023 0.047 -10000 0 -0.42 5 5
SMPD1 -0.006 0.072 -10000 0 -0.21 43 43
IKBKG 0.036 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.027 0.016 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.009 0.099 -10000 0 -0.3 44 44
TRAIL/TRAILR3 0.008 0.097 -10000 0 -0.29 45 45
TRAIL/TRAILR1 0.007 0.1 -10000 0 -0.31 46 46
TRAIL/TRAILR4 0.01 0.096 -10000 0 -0.29 44 44
TRAIL/TRAILR1/DAP3/GTP 0.019 0.081 -10000 0 -0.24 36 36
IKK complex 0.014 0.092 -10000 0 -0.4 15 15
RIPK1 0.035 0.007 -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 -0.01 0.084 -10000 0 -0.3 39 39
MAP3K1 -0.008 0.11 -10000 0 -0.37 30 30
TRAILR4 (trimer) 0.027 0.016 -10000 0 -10000 0 0
TRADD 0.029 0.014 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.023 0.047 -10000 0 -0.42 5 5
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.015 0.089 -10000 0 -0.29 34 34
CFLAR 0.031 0.046 -10000 0 -0.42 5 5
MAPK1 -0.009 0.082 -10000 0 -0.3 37 37
TRAIL/TRAILR1/FADD/TRADD/RIP 0.034 0.089 -10000 0 -0.23 33 33
mol:ceramide -0.006 0.071 -10000 0 -0.21 43 43
FADD 0.029 0.014 -10000 0 -10000 0 0
MAPK8 -0.023 0.11 0.2 1 -0.35 31 32
TRAF2 0.033 0.029 -10000 0 -0.42 2 2
TRAILR3 (trimer) 0.024 0.026 -10000 0 -0.42 1 1
CHUK 0.025 0.067 -10000 0 -0.42 11 11
TRAIL/TRAILR1/FADD 0.022 0.087 -10000 0 -0.27 34 34
DAP3 0.027 0.025 -10000 0 -0.42 1 1
CASP10 0.015 0.084 0.33 4 -0.29 18 22
JNK cascade 0.01 0.096 -10000 0 -0.29 44 44
TRAIL (trimer) -0.007 0.13 -10000 0 -0.42 44 44
TNFRSF10C 0.024 0.026 -10000 0 -0.42 1 1
TRAIL/TRAILR1/DAP3/GTP/FADD 0.025 0.077 -10000 0 -0.23 28 28
TRAIL/TRAILR2/FADD 0.023 0.083 -10000 0 -0.26 33 33
cell death -0.006 0.071 -10000 0 -0.21 43 43
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.014 0.087 -10000 0 -0.29 33 33
TRAILR2 (trimer) 0.027 0.016 -10000 0 -10000 0 0
CASP8 0.024 0.043 -10000 0 -0.66 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.035 0.086 -10000 0 -0.22 32 32
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.007 0.055 -10000 0 -0.25 16 16
NFATC2 0.013 0.035 -10000 0 -0.27 3 3
NFATC3 0.015 0.026 -10000 0 -10000 0 0
CD40LG -0.02 0.18 0.37 3 -0.45 50 53
PTGS2 -0.021 0.17 0.37 3 -0.45 44 47
JUNB 0.032 0.041 -10000 0 -0.42 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.025 -10000 0 -0.11 1 1
CaM/Ca2+ 0.021 0.025 -10000 0 -0.11 1 1
CALM1 0.032 0.019 -10000 0 -10000 0 0
JUN -0.003 0.12 -10000 0 -0.42 39 39
mol:Ca2+ -0.001 0.009 -10000 0 -0.084 1 1
Calcineurin A alpha-beta B1/FKBP12/FK506 0.022 0.01 -10000 0 -10000 0 0
FOSL1 0.035 0.007 -10000 0 -10000 0 0
CREM 0.034 0.008 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.016 0.12 -10000 0 -0.32 28 28
FOS -0.033 0.15 -10000 0 -0.42 66 66
IFNG -0.036 0.21 0.37 3 -0.52 56 59
AP-1/NFAT1-c-4 0.001 0.22 -10000 0 -0.5 53 53
FASLG -0.032 0.2 0.37 3 -0.52 52 55
NFAT1-c-4/ICER1 0.027 0.082 0.28 2 -0.24 14 16
IL2RA -0.03 0.2 0.37 3 -0.49 57 60
FKBP12/FK506 0.025 0.006 -10000 0 -10000 0 0
CSF2 -0.021 0.18 0.37 3 -0.45 51 54
JunB/Fra1/NFAT1-c-4 0.045 0.093 0.26 1 -0.28 9 10
IL4 -0.019 0.18 0.37 3 -0.44 54 57
IL2 0.008 0.14 -10000 0 -0.98 10 10
IL3 0.019 0.12 -10000 0 -0.69 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 0.033 0.017 -10000 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.012 0.11 -10000 0 -0.23 75 75
TC10/GTP 0.03 0.066 -10000 0 -0.21 31 31
Insulin Receptor/Insulin/IRS1/Shp2 0.053 0.11 -10000 0 -0.25 55 55
HRAS 0.032 0.036 -10000 0 -0.42 3 3
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 -0.063 0.18 -10000 0 -0.42 98 98
FOXO3 -0.015 0.022 -10000 0 -0.096 2 2
AKT1 -0.047 0.13 0.3 8 -0.37 17 25
INSR 0.037 0.031 -10000 0 -0.42 2 2
Insulin Receptor/Insulin 0.079 0.061 -10000 0 -0.31 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.022 0.075 -10000 0 -0.42 14 14
SORBS1 0.008 0.1 -10000 0 -0.42 28 28
CRK 0.031 0.023 -10000 0 -0.42 1 1
PTPN1 0.004 0.037 -10000 0 -0.3 5 5
CAV1 -0.008 0.083 0.18 5 -0.23 58 63
CBL/APS/CAP/Crk-II/C3G 0.052 0.074 -10000 0 -0.22 29 29
Insulin Receptor/Insulin/IRS1/NCK2 0.054 0.11 -10000 0 -0.25 54 54
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.027 0.1 -10000 0 -0.22 67 67
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.018 0.081 -10000 0 -0.42 6 6
RPS6KB1 -0.041 0.11 0.28 7 -0.34 16 23
PARD6A 0.023 0.055 -10000 0 -0.42 7 7
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 0.11 -10000 0 -0.67 12 12
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.006 0.13 0.28 3 -0.34 18 21
HRAS/GTP -0.001 0.063 -10000 0 -0.2 40 40
Insulin Receptor 0.037 0.031 -10000 0 -0.42 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.048 0.1 -10000 0 -0.23 42 42
PRKCI 0.003 0.11 -10000 0 -0.47 23 23
Insulin Receptor/Insulin/GRB14/PDK1 -0.037 0.12 -10000 0 -0.23 136 136
SHC1 0.027 0.025 -10000 0 -0.42 1 1
negative regulation of MAPKKK cascade 0.044 0.11 -10000 0 -0.58 13 13
PI3K 0.039 0.11 -10000 0 -0.23 67 67
NCK2 0.036 0.004 -10000 0 -10000 0 0
RHOQ 0.033 0.035 -10000 0 -0.42 3 3
mol:H2O2 0 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.024 0.025 -10000 0 -0.3 3 3
AKT2 -0.048 0.13 0.3 8 -0.36 17 25
PRKCZ -0.008 0.082 -10000 0 -0.41 16 16
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.002 0.07 0.17 3 -0.22 44 47
F2RL2 -0.018 0.14 -10000 0 -0.42 56 56
TRIP10 0.032 0.041 -10000 0 -0.42 4 4
Insulin Receptor/Insulin/Shc 0.053 0.041 -10000 0 -0.22 3 3
TC10/GTP/CIP4/Exocyst 0.043 0.036 -10000 0 -0.25 7 7
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.074 0.06 -10000 0 -0.22 4 4
RAPGEF1 0.036 0.004 -10000 0 -10000 0 0
RASA1 0.028 0.054 -10000 0 -0.42 7 7
NCK1 0.034 0.022 -10000 0 -0.42 1 1
CBL/APS/CAP/Crk-II 0.039 0.071 -10000 0 -0.23 29 29
TC10/GDP 0.024 0.025 -10000 0 -0.3 3 3
Insulin Receptor/Insulin/SHC/GRB10 0.062 0.066 -10000 0 -0.23 13 13
INPP5D -0.03 0.07 -10000 0 -0.23 55 55
SOS1 0.034 0.021 -10000 0 -0.42 1 1
SGK1 -0.008 0.01 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.036 0.004 -10000 0 -10000 0 0
IRS1 -0.014 0.14 -10000 0 -0.42 54 54
p62DOK/RasGAP 0.045 0.11 -10000 0 -0.58 13 13
INS 0.037 0.024 -10000 0 -0.42 1 1
mol:PI-3-4-P2 -0.03 0.07 -10000 0 -0.22 55 55
GRB2 0.033 0.01 -10000 0 -10000 0 0
EIF4EBP1 -0.05 0.11 0.24 4 -0.34 18 22
PTPRA 0.037 0.013 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
TC10/GTP/CIP4 0.043 0.036 -10000 0 -0.25 7 7
PDPK1 0.032 0.023 -10000 0 -0.42 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.005 0.077 -10000 0 -0.36 6 6
Insulin Receptor/Insulin/IRS1 0.034 0.1 -10000 0 -0.24 55 55
Insulin Receptor/Insulin/IRS3 0.054 0.034 -10000 0 -0.3 3 3
Par3/Par6 0.025 0.1 -10000 0 -0.22 66 66
Class I PI3K signaling events

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
ARF5/GTP -0.019 0.059 0.21 8 -0.21 14 22
DAPP1 -0.039 0.16 0.24 1 -0.42 50 51
Src family/SYK family/BLNK-LAT/BTK-ITK -0.06 0.22 -10000 0 -0.57 60 60
mol:DAG -0.016 0.092 0.22 6 -0.23 43 49
HRAS 0.031 0.038 -10000 0 -0.43 3 3
RAP1A 0.029 0.051 -10000 0 -0.42 6 6
ARF5/GDP -0.004 0.11 -10000 0 -0.32 29 29
PLCG2 0.02 0.055 -10000 0 -0.42 7 7
PLCG1 0.033 0.009 -10000 0 -10000 0 0
ARF5 0.034 0.021 -10000 0 -0.42 1 1
mol:GTP -0.019 0.061 0.21 10 -0.21 20 30
ARF1/GTP -0.009 0.053 0.22 8 -0.2 16 24
RHOA 0.026 0.061 -10000 0 -0.42 9 9
YES1 0.029 0.05 -10000 0 -0.42 6 6
RAP1A/GTP -0.018 0.062 0.18 28 -0.21 20 48
ADAP1 -0.018 0.056 0.2 9 -0.2 20 29
ARAP3 -0.018 0.06 0.21 10 -0.21 20 30
INPPL1 0.03 0.036 -10000 0 -0.42 3 3
PREX1 -0.036 0.16 -10000 0 -0.42 74 74
ARHGEF6 0.015 0.093 -10000 0 -0.42 22 22
ARHGEF7 0.032 0.011 -10000 0 -10000 0 0
ARF1 0.027 0.025 -10000 0 -0.42 1 1
NRAS 0.028 0.051 -10000 0 -0.42 6 6
FYN 0.027 0.05 -10000 0 -0.42 6 6
ARF6 0.033 0.029 -10000 0 -0.42 2 2
FGR 0.034 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.009 0.05 0.14 10 -0.12 27 37
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.028 0.057 -10000 0 -0.42 8 8
ZAP70 0.033 0.022 -10000 0 -0.42 1 1
mol:IP3 -0.016 0.067 0.17 10 -0.17 33 43
LYN 0.03 0.014 -10000 0 -10000 0 0
ARF1/GDP -0.003 0.1 -10000 0 -0.32 25 25
RhoA/GDP 0.012 0.092 0.23 5 -0.26 23 28
PDK1/Src/Hsp90 0.041 0.025 -10000 0 -0.25 2 2
BLNK 0.012 0.1 -10000 0 -0.42 26 26
actin cytoskeleton reorganization -0.021 0.11 0.23 4 -0.37 20 24
SRC 0.032 0.03 -10000 0 -0.42 2 2
PLEKHA2 -0.009 0.022 -10000 0 -0.25 4 4
RAC1 0.035 0.006 -10000 0 -10000 0 0
PTEN 0.026 0.059 -10000 0 -0.4 9 9
HSP90AA1 0 0 -10000 0 -10000 0 0
ARF6/GTP -0.02 0.06 0.22 9 -0.2 20 29
RhoA/GTP -0.023 0.068 0.22 8 -0.25 23 31
Src family/SYK family/BLNK-LAT -0.028 0.16 -10000 0 -0.45 46 46
BLK 0.021 0.038 -10000 0 -0.42 3 3
PDPK1 0.032 0.023 -10000 0 -0.42 1 1
CYTH1 -0.018 0.056 0.2 9 -0.2 20 29
HCK 0.017 0.087 -10000 0 -0.42 19 19
CYTH3 -0.018 0.056 0.2 9 -0.2 20 29
CYTH2 -0.018 0.056 0.2 9 -0.2 20 29
KRAS 0.026 0.059 -10000 0 -0.43 8 8
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.005 0.038 0.23 2 -0.2 2 4
SGK1 0.008 0.041 0.24 2 -0.2 3 5
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.02 0.11 -10000 0 -0.32 34 34
SOS1 0.034 0.021 -10000 0 -0.42 1 1
SYK 0.005 0.11 -10000 0 -0.42 33 33
ARF6/GDP -0.004 0.075 0.27 2 -0.26 12 14
mol:PI-3-4-5-P3 -0.019 0.061 0.23 9 -0.21 20 29
ARAP3/RAP1A/GTP -0.018 0.062 0.18 28 -0.21 20 48
VAV1 0.018 0.083 -10000 0 -0.42 17 17
mol:PI-3-4-P2 0.006 0.024 -10000 0 -0.3 3 3
RAS family/GTP/PI3K Class I 0.044 0.065 0.22 18 -0.22 20 38
PLEKHA1 -0.012 0.029 -10000 0 -0.25 7 7
Rac1/GDP -0.004 0.11 -10000 0 -0.32 30 30
LAT 0.029 0.031 -10000 0 -0.42 2 2
Rac1/GTP -0.018 0.12 -10000 0 -0.35 38 38
ITK -0.033 0.072 0.2 9 -0.22 48 57
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.028 0.12 0.25 6 -0.31 47 53
LCK -0.018 0.14 -10000 0 -0.42 54 54
BTK -0.026 0.069 0.21 9 -0.23 30 39
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.015 0.15 0.36 1 -0.46 23 24
PDGFB-D/PDGFRB/SLAP 0.031 0.056 -10000 0 -0.31 11 11
PDGFB-D/PDGFRB/APS/CBL 0.037 0.041 -10000 0 -0.25 8 8
AKT1 -0.01 0.14 0.34 22 -0.39 12 34
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.006 0.14 0.35 1 -0.49 20 21
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
FGR 0.002 0.12 0.3 3 -0.44 21 24
mol:Ca2+ 0.008 0.13 0.29 2 -0.51 18 20
MYC 0.012 0.24 0.38 11 -0.72 40 51
SHC1 0.027 0.025 -10000 0 -0.42 1 1
HRAS/GDP 0.034 0.066 0.19 1 -0.22 17 18
LRP1/PDGFRB/PDGFB 0.058 0.06 -10000 0 -0.29 12 12
GRB10 0.022 0.075 -10000 0 -0.42 14 14
PTPN11 0.036 0.004 -10000 0 -10000 0 0
GO:0007205 0.007 0.13 0.29 2 -0.52 18 20
PTEN 0.027 0.061 -10000 0 -0.42 9 9
GRB2 0.033 0.01 -10000 0 -10000 0 0
GRB7 0.024 0.058 -10000 0 -0.42 8 8
PDGFB-D/PDGFRB/SHP2 0.046 0.046 -10000 0 -0.31 8 8
PDGFB-D/PDGFRB/GRB10 0.035 0.073 -10000 0 -0.3 22 22
cell cycle arrest 0.03 0.056 -10000 0 -0.31 11 11
HRAS 0.032 0.036 -10000 0 -0.42 3 3
HIF1A -0.025 0.13 0.33 19 -0.35 18 37
GAB1 -0.002 0.14 0.31 2 -0.5 23 25
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.003 0.14 0.32 4 -0.46 21 25
PDGFB-D/PDGFRB 0.051 0.056 -10000 0 -0.27 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.044 0.053 -10000 0 -0.31 11 11
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.009 0.14 0.3 1 -0.46 23 24
positive regulation of MAPKKK cascade 0.046 0.046 -10000 0 -0.31 8 8
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
mol:IP3 0.007 0.13 0.3 2 -0.53 18 20
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 0.036 0.064 -10000 0 -0.3 16 16
SHB 0.03 0.046 -10000 0 -0.42 5 5
BLK -0.066 0.19 0.28 1 -0.43 93 94
PTPN2 0.034 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.045 0.046 -10000 0 -0.3 8 8
BCAR1 0.029 0.014 -10000 0 -10000 0 0
VAV2 -0.005 0.16 0.31 3 -0.5 27 30
CBL 0.031 0.012 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.042 0.058 -10000 0 -0.31 13 13
LCK -0.052 0.21 -10000 0 -0.56 64 64
PDGFRB 0.027 0.059 -10000 0 -0.43 8 8
ACP1 0.033 0.035 -10000 0 -0.42 3 3
HCK -0.006 0.14 0.32 2 -0.52 28 30
ABL1 -0.005 0.14 0.28 2 -0.44 27 29
PDGFB-D/PDGFRB/CBL -0.009 0.16 -10000 0 -0.56 26 26
PTPN1 0.029 0.031 -10000 0 -0.42 2 2
SNX15 0.035 0.007 -10000 0 -10000 0 0
STAT3 0.028 0.031 -10000 0 -0.42 2 2
STAT1 0.02 0.075 -10000 0 -0.42 14 14
cell proliferation 0.018 0.22 0.36 13 -0.64 40 53
SLA 0.021 0.047 -10000 0 -0.42 5 5
actin cytoskeleton reorganization 0.037 0.071 0.43 2 -0.22 10 12
SRC 0.011 0.095 0.3 3 -0.54 7 10
PI3K -0.052 0.09 -10000 0 -0.25 71 71
PDGFB-D/PDGFRB/GRB7/SHC 0.041 0.062 -10000 0 -0.26 15 15
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.005 0.14 0.35 1 -0.51 20 21
LYN 0.013 0.077 0.29 3 -0.37 8 11
LRP1 0.035 0.021 -10000 0 -0.42 1 1
SOS1 0.034 0.021 -10000 0 -0.42 1 1
STAT5B 0.03 0.024 -10000 0 -0.42 1 1
STAT5A 0.028 0.037 -10000 0 -0.42 3 3
NCK1-2/p130 Cas 0.066 0.068 -10000 0 -0.22 9 9
SPHK1 0.005 0.11 -10000 0 -0.43 30 30
EDG1 0.011 0.1 -10000 0 -0.42 25 25
mol:DAG 0.007 0.13 0.3 2 -0.53 18 20
PLCG1 0.007 0.14 0.33 1 -0.54 18 19
NHERF/PDGFRB 0.001 0.13 -10000 0 -0.29 80 80
YES1 -0.006 0.14 0.28 2 -0.51 28 30
cell migration 0.001 0.13 -10000 0 -0.28 80 80
SHC/Grb2/SOS1 0.058 0.068 -10000 0 -0.23 9 9
SLC9A3R2 -0.004 0.12 -10000 0 -0.42 40 40
SLC9A3R1 -0.009 0.13 -10000 0 -0.42 46 46
NHERF1-2/PDGFRB/PTEN 0.011 0.14 -10000 0 -0.27 84 84
FYN -0.013 0.16 0.28 2 -0.53 32 34
DOK1 0.021 0.072 0.19 32 -0.24 15 47
HRAS/GTP 0.024 0.025 -10000 0 -0.3 3 3
PDGFB 0.029 0.046 -10000 0 -0.42 5 5
RAC1 -0.02 0.2 0.35 1 -0.57 40 41
PRKCD 0.021 0.071 0.19 38 -0.27 10 48
FER 0.022 0.069 0.2 37 -0.25 10 47
MAPKKK cascade 0.045 0.11 0.34 26 -0.23 4 30
RASA1 0.019 0.073 0.19 40 -0.24 15 55
NCK1 0.034 0.022 -10000 0 -0.42 1 1
NCK2 0.036 0.004 -10000 0 -10000 0 0
p62DOK/Csk 0.042 0.065 0.34 1 -0.22 16 17
PDGFB-D/PDGFRB/SHB 0.041 0.058 -10000 0 -0.31 13 13
chemotaxis -0.005 0.13 0.26 3 -0.43 27 30
STAT1-3-5/STAT1-3-5 0.048 0.075 -10000 0 -0.22 24 24
Bovine Papilomavirus E5/PDGFRB 0.019 0.043 -10000 0 -0.31 8 8
PTPRJ 0.03 0.046 -10000 0 -0.42 5 5
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.011 0.02 -10000 0 -0.26 3 3
RAS family/GTP 0.029 0.11 0.25 2 -0.3 17 19
NFATC4 -0.031 0.069 0.24 2 -0.29 10 12
ERBB2IP 0.034 0.022 -10000 0 -0.42 1 1
HSP90 (dimer) 0 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.004 0.088 -10000 0 -0.26 36 36
JUN 0.007 0.074 0.21 3 -10000 0 3
HRAS 0.032 0.036 -10000 0 -0.42 3 3
DOCK7 -0.035 0.078 0.27 2 -0.27 28 30
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.019 0.088 -10000 0 -0.27 34 34
AKT1 0.002 0.025 -10000 0 -0.3 3 3
BAD -0.011 0.022 -10000 0 -0.26 4 4
MAPK10 -0.025 0.062 0.2 7 -0.2 16 23
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.004 0.094 -10000 0 -0.29 30 30
RAF1 0.01 0.11 0.27 12 -0.32 17 29
ErbB2/ErbB3/neuregulin 2 0.011 0.093 -10000 0 -0.28 44 44
STAT3 0.006 0.17 -10000 0 -0.88 18 18
cell migration -0.019 0.065 0.22 9 -0.21 11 20
mol:PI-3-4-5-P3 -0.001 0.001 -10000 0 -10000 0 0
cell proliferation -0.046 0.25 0.41 1 -0.63 59 60
FOS -0.046 0.21 0.36 1 -0.44 105 106
NRAS 0.029 0.05 -10000 0 -0.42 6 6
mol:Ca2+ -0.004 0.088 -10000 0 -0.26 36 36
MAPK3 -0.02 0.2 0.37 2 -0.51 48 50
MAPK1 -0.032 0.21 0.41 1 -0.55 50 51
JAK2 -0.034 0.079 0.27 2 -0.27 26 28
NF2 0.01 0.047 -10000 0 -0.68 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.001 0.071 0.19 2 -0.27 25 27
NRG1 0.028 0.015 -10000 0 -10000 0 0
GRB2/SOS1 0.047 0.023 -10000 0 -0.3 1 1
MAPK8 -0.021 0.098 0.22 4 -0.28 30 34
MAPK9 -0.024 0.06 0.2 7 -0.21 11 18
ERBB2 -0.031 0.055 0.6 1 -0.32 13 14
ERBB3 0.006 0.11 -10000 0 -0.42 32 32
SHC1 0.027 0.025 -10000 0 -0.42 1 1
RAC1 0.035 0.006 -10000 0 -10000 0 0
apoptosis 0.006 0.033 0.32 3 -0.21 4 7
STAT3 (dimer) 0.006 0.17 -10000 0 -0.86 18 18
RNF41 -0.014 0.019 -10000 0 -0.24 3 3
FRAP1 -0.01 0.016 -10000 0 -0.26 2 2
RAC1-CDC42/GTP -0.035 0.052 -10000 0 -0.2 29 29
ErbB2/ErbB2/HSP90 (dimer) -0.025 0.04 -10000 0 -0.27 13 13
CHRNA1 -0.007 0.17 0.35 2 -0.41 47 49
myelination -0.025 0.083 0.27 12 -0.32 7 19
PPP3CB -0.035 0.073 0.26 2 -0.25 29 31
KRAS 0.027 0.058 -10000 0 -0.42 8 8
RAC1-CDC42/GDP 0.038 0.095 0.25 3 -0.28 13 16
NRG2 0.025 0.058 -10000 0 -0.42 8 8
mol:GDP 0.001 0.07 0.19 2 -0.26 25 27
SOS1 0.034 0.021 -10000 0 -0.42 1 1
MAP2K2 -0.002 0.11 0.26 10 -0.32 23 33
SRC 0.032 0.03 -10000 0 -0.42 2 2
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.036 0.077 0.27 2 -0.27 28 30
MAP2K1 -0.029 0.2 0.38 1 -0.58 36 37
heart morphogenesis -0.004 0.088 -10000 0 -0.26 36 36
RAS family/GDP 0.04 0.11 0.26 2 -0.29 16 18
GRB2 0.033 0.01 -10000 0 -10000 0 0
PRKACA 0.014 0.054 -10000 0 -0.68 3 3
CHRNE 0.008 0.018 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
activation of caspase activity -0.002 0.025 0.3 3 -10000 0 3
nervous system development -0.004 0.088 -10000 0 -0.26 36 36
CDC42 0.034 0.008 -10000 0 -10000 0 0
ceramide signaling 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
MAP4K4 -0.036 0.15 -10000 0 -0.42 39 39
BAG4 0.027 0.025 -10000 0 -0.42 1 1
BAD -0.007 0.05 0.19 2 -0.17 13 15
NFKBIA 0.033 0.03 -10000 0 -0.42 2 2
BIRC3 -0.01 0.12 -10000 0 -0.42 42 42
BAX -0.004 0.056 0.2 9 -0.17 15 24
EnzymeConsortium:3.1.4.12 -0.007 0.035 0.075 4 -0.093 36 40
IKBKB -0.017 0.14 0.3 2 -0.41 29 31
MAP2K2 -0.009 0.056 0.19 11 -0.2 7 18
MAP2K1 -0.008 0.052 0.19 10 -0.2 4 14
SMPD1 -0.007 0.041 -10000 0 -0.16 14 14
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.003 0.15 0.3 6 -0.41 29 35
MAP2K4 -0.016 0.057 0.18 1 -0.19 23 24
protein ubiquitination -0.033 0.14 0.25 1 -0.42 33 34
EnzymeConsortium:2.7.1.37 -0.012 0.057 0.22 5 -0.2 7 12
response to UV 0 0.001 0.002 9 -0.002 5 14
RAF1 -0.008 0.053 0.2 8 -0.19 6 14
CRADD 0.029 0.054 -10000 0 -0.42 7 7
mol:ceramide -0.006 0.051 0.11 2 -0.15 29 31
I-kappa-B-alpha/RELA/p50/ubiquitin 0.044 0.023 -10000 0 -0.25 2 2
MADD 0.035 0.005 -10000 0 -10000 0 0
MAP3K1 -0.017 0.061 -10000 0 -0.18 40 40
TRADD 0.029 0.014 -10000 0 -10000 0 0
RELA/p50 0.035 0.006 -10000 0 -10000 0 0
MAPK3 -0.005 0.056 0.2 8 -0.19 4 12
MAPK1 -0.008 0.063 0.2 7 -0.21 10 17
p50/RELA/I-kappa-B-alpha 0.048 0.026 -10000 0 -0.3 2 2
FADD -0.003 0.15 0.28 5 -0.42 29 34
KSR1 -0.008 0.051 0.19 3 -0.17 13 16
MAPK8 -0.021 0.059 0.21 3 -0.21 11 14
TRAF2 0.034 0.029 -10000 0 -0.42 2 2
response to radiation 0 0 0.002 2 -10000 0 2
CHUK -0.044 0.14 -10000 0 -0.4 41 41
TNF R/SODD 0.039 0.028 -10000 0 -0.3 1 1
TNF 0.026 0.061 -10000 0 -0.42 9 9
CYCS 0.014 0.069 0.17 27 -0.17 9 36
IKBKG -0.04 0.14 -10000 0 -0.41 37 37
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.032 0.15 -10000 0 -0.44 38 38
RELA 0.035 0.006 -10000 0 -10000 0 0
RIPK1 0.035 0.007 -10000 0 -10000 0 0
AIFM1 0.012 0.068 0.16 25 -0.17 12 37
TNF/TNF R/SODD 0.048 0.049 -10000 0 -0.25 7 7
TNFRSF1A 0.033 0.022 -10000 0 -0.42 1 1
response to heat 0 0 0.002 2 -10000 0 2
CASP8 0.011 0.12 -10000 0 -0.63 16 16
NSMAF -0.012 0.14 0.27 1 -0.42 29 30
response to hydrogen peroxide 0 0.001 0.002 9 -0.002 5 14
BCL2 -0.057 0.18 -10000 0 -0.42 99 99
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.025 0.1 0.9 1 -0.78 1 2
VDR 0.02 0.083 -10000 0 -0.42 17 17
FAM120B 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.004 0.1 -10000 0 -0.27 48 48
RXRs/LXRs/DNA/Oxysterols 0.013 0.16 -10000 0 -0.42 48 48
MED1 0 0 -10000 0 -10000 0 0
mol:9cRA -0.001 0.019 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.002 0.093 -10000 0 -0.24 49 49
RXRs/NUR77 0.054 0.081 -10000 0 -0.25 12 12
RXRs/PPAR 0.009 0.073 -10000 0 -0.25 28 28
NCOR2 0.036 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.015 0.058 -10000 0 -0.3 17 17
RARs/VDR/DNA/Vit D3 0.051 0.085 -10000 0 -0.23 37 37
RARA 0.027 0.054 -10000 0 -0.42 7 7
NCOA1 0.031 0.045 -10000 0 -0.42 5 5
VDR/VDR/DNA 0.02 0.082 -10000 0 -0.42 17 17
RARs/RARs/DNA/9cRA 0.039 0.065 -10000 0 -0.22 25 25
RARG 0.036 0.004 -10000 0 -10000 0 0
RPS6KB1 0.052 0.14 0.54 40 -10000 0 40
RARs/THRs/DNA/SMRT 0.003 0.092 -10000 0 -0.24 49 49
THRA 0.02 0.075 -10000 0 -0.42 14 14
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.015 0.058 -10000 0 -0.3 17 17
RXRs/PPAR/9cRA/PGJ2/DNA 0.039 0.083 -10000 0 -0.24 17 17
NR1H4 0.035 0.021 -10000 0 -0.42 1 1
RXRs/LXRs/DNA 0.058 0.11 -10000 0 -0.25 14 14
NR1H2 0.028 0.031 -10000 0 -10000 0 0
NR1H3 0.025 0.053 -10000 0 -0.43 4 4
RXRs/VDR/DNA/Vit D3 0.043 0.084 -10000 0 -0.24 20 20
NR4A1 0.034 0.021 -10000 0 -0.42 1 1
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.026 0.063 -10000 0 -0.22 15 15
RXRG 0.016 0.063 -10000 0 -0.43 8 8
RXR alpha/CCPG 0.021 0.029 -10000 0 -0.31 2 2
RXRA 0.027 0.042 -10000 0 -0.44 2 2
RXRB 0.027 0.044 -10000 0 -0.42 2 2
THRB 0.024 0.07 -10000 0 -0.42 12 12
PPARG 0.012 0.091 -10000 0 -0.42 21 21
PPARD 0.035 0.006 -10000 0 -10000 0 0
TNF -0.001 0.19 -10000 0 -0.8 17 17
mol:Oxysterols -0.001 0.017 -10000 0 -10000 0 0
cholesterol transport 0.013 0.16 -10000 0 -0.42 48 48
PPARA 0.032 0.023 -10000 0 -0.42 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.014 0.089 -10000 0 -0.42 20 20
RXRs/NUR77/BCL2 -0.02 0.097 -10000 0 -0.22 84 84
SREBF1 -0.047 0.29 -10000 0 -0.93 46 46
RXRs/RXRs/DNA/9cRA 0.039 0.083 -10000 0 -0.24 17 17
ABCA1 -0.006 0.21 -10000 0 -0.89 18 18
RARs/THRs 0.061 0.1 -10000 0 -0.24 47 47
RXRs/FXR 0.054 0.082 -10000 0 -0.25 13 13
BCL2 -0.057 0.18 -10000 0 -0.42 99 99
Regulation of Telomerase

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
Telomerase catalytic core complex -0.072 0.23 -10000 0 -0.78 22 22
RAD9A 0.033 0.01 -10000 0 -10000 0 0
AP1 -0.026 0.15 -10000 0 -0.34 89 89
IFNAR2 0.027 0.03 -10000 0 -0.43 1 1
AKT1 -0.034 0.11 -10000 0 -0.2 131 131
ER alpha/Oestrogen -0.063 0.14 -10000 0 -0.3 130 130
NFX1/SIN3/HDAC complex 0.012 0.072 -10000 0 -0.34 13 13
EGF -0.07 0.19 -10000 0 -0.42 110 110
SMG5 0 0 -10000 0 -10000 0 0
SMG6 0 0 -10000 0 -10000 0 0
SP3/HDAC2 0.038 0.036 -10000 0 -0.3 1 1
TERT/c-Abl -0.06 0.22 -10000 0 -0.7 24 24
SAP18 0.033 0.01 -10000 0 -10000 0 0
MRN complex 0.047 0.044 -10000 0 -0.26 4 4
WT1 -0.024 0.14 -10000 0 -0.42 52 52
WRN 0.027 0.025 -10000 0 -0.42 1 1
SP1 0.026 0.033 -10000 0 -0.43 1 1
SP3 0.035 0.007 -10000 0 -10000 0 0
TERF2IP 0.029 0.014 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.046 0.21 -10000 0 -0.63 25 25
Mad/Max 0.047 0.019 -10000 0 -10000 0 0
TERT -0.075 0.24 -10000 0 -0.84 20 20
CCND1 -0.15 0.44 -10000 0 -1.1 85 85
MAX 0.034 0.009 -10000 0 -10000 0 0
RBBP7 0.033 0.029 -10000 0 -0.42 2 2
RBBP4 0.034 0.021 -10000 0 -0.42 1 1
TERF2 0.027 0.031 -10000 0 -0.37 2 2
PTGES3 0.035 0.021 -10000 0 -0.42 1 1
SIN3A 0.034 0.007 -10000 0 -10000 0 0
Telomerase/911 0.021 0.069 -10000 0 -0.46 5 5
CDKN1B -0.029 0.14 -10000 0 -0.37 66 66
RAD1 0.033 0.03 -10000 0 -0.42 2 2
XRCC5 0.036 0.004 -10000 0 -10000 0 0
XRCC6 0.033 0.009 -10000 0 -10000 0 0
SAP30 0.03 0.046 -10000 0 -0.42 5 5
TRF2/PARP2 0.043 0.032 -10000 0 -0.29 2 2
UBE3A 0.033 0.029 -10000 0 -0.43 2 2
JUN -0.002 0.12 -10000 0 -0.42 39 39
E6 -0.001 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.02 0.027 -10000 0 -0.3 2 2
FOS -0.032 0.15 -10000 0 -0.42 66 66
IFN-gamma/IRF1 0 0.12 -10000 0 -0.3 70 70
PARP2 0.036 0.002 -10000 0 -10000 0 0
BLM 0.011 0.097 -10000 0 -0.42 24 24
Telomerase 0.013 0.044 0.18 1 -10000 0 1
IRF1 0.015 0.085 -10000 0 -0.27 35 35
ESR1 -0.088 0.2 -10000 0 -0.42 130 130
KU/TER 0.049 0.015 -10000 0 -10000 0 0
ATM/TRF2 0.035 0.035 -10000 0 -0.19 2 2
ubiquitin-dependent protein catabolic process 0.022 0.06 -10000 0 -0.26 12 12
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.023 0.059 -10000 0 -0.27 11 11
HDAC1 0.034 0.021 -10000 0 -0.42 1 1
HDAC2 0.024 0.032 -10000 0 -0.42 1 1
ATM 0.02 0.025 0.19 2 -10000 0 2
SMAD3 0.01 0.044 -10000 0 -0.3 10 10
ABL1 0.035 0.005 -10000 0 -10000 0 0
MXD1 0.034 0.008 -10000 0 -10000 0 0
MRE11A 0.031 0.012 -10000 0 -10000 0 0
HUS1 0.035 0.006 -10000 0 -10000 0 0
RPS6KB1 0.031 0.013 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.056 0.23 -10000 0 -0.68 29 29
NR2F2 -0.011 0.14 -10000 0 -0.42 49 49
MAPK3 0.007 0.032 -10000 0 -0.3 4 4
MAPK1 0.007 0.032 -10000 0 -0.3 4 4
TGFB1/TGF beta receptor Type II 0.035 0.021 -10000 0 -0.42 1 1
NFKB1 0.035 0.005 -10000 0 -10000 0 0
HNRNPC 0 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.02 0.025 0.19 2 -10000 0 2
NBN 0.027 0.025 -10000 0 -0.42 1 1
EGFR -0.013 0.13 -10000 0 -0.42 47 47
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.063 0.16 -10000 0 -0.31 151 151
MYC -0.002 0.1 -10000 0 -0.42 29 29
IL2 0.024 0.043 -10000 0 -0.42 3 3
KU 0.049 0.015 -10000 0 -10000 0 0
RAD50 0.03 0.046 -10000 0 -0.42 5 5
HSP90AA1 0 0 -10000 0 -10000 0 0
TGFB1 0.035 0.021 -10000 0 -0.42 1 1
TRF2/BLM 0.026 0.073 -10000 0 -0.28 25 25
FRAP1 0.034 0.008 -10000 0 -10000 0 0
KU/TERT -0.047 0.23 -10000 0 -0.7 24 24
SP1/HDAC2 0.038 0.043 -10000 0 -0.3 2 2
PINX1 0.028 0.015 -10000 0 -10000 0 0
Telomerase/EST1A -0.059 0.2 -10000 0 -0.63 25 25
Smad3/Myc 0.006 0.074 -10000 0 -0.26 35 35
911 complex 0.062 0.032 -10000 0 -0.26 2 2
IFNG -0.014 0.12 -10000 0 -0.34 56 56
Telomerase/PinX1 -0.057 0.2 -10000 0 -0.63 25 25
Telomerase/AKT1/mTOR/p70S6K -0.007 0.1 -10000 0 -0.41 17 17
SIN3B 0.035 0.005 -10000 0 -10000 0 0
YWHAE 0.032 0.011 -10000 0 -10000 0 0
Telomerase/EST1B -0.059 0.2 -10000 0 -0.63 25 25
response to DNA damage stimulus -0.001 0.034 0.13 1 -0.1 36 37
MRN complex/TRF2/Rap1 0.058 0.061 -10000 0 -0.25 5 5
TRF2/WRN 0.033 0.036 -10000 0 -0.29 3 3
Telomerase/hnRNP C1/C2 -0.059 0.2 -10000 0 -0.63 25 25
E2F1 0.02 0.057 -10000 0 -0.42 7 7
ZNFX1 0 0.001 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL 0.035 0.006 -10000 0 -10000 0 0
DKC1 0.036 0.003 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.016 0.15 -9999 0 -0.34 47 47
MAP3K8 0.002 0.11 -9999 0 -0.42 32 32
FOS 0.019 0.099 -9999 0 -0.4 9 9
PRKCA 0.025 0.022 -9999 0 -10000 0 0
PTPN7 0.02 0.032 -9999 0 -0.44 1 1
HRAS 0.031 0.036 -9999 0 -0.42 3 3
PRKCB -0.002 0.006 -9999 0 -0.016 73 73
NRAS 0.029 0.05 -9999 0 -0.42 6 6
RAS family/GTP 0.05 0.055 -9999 0 -0.23 15 15
MAPK3 0.027 0.07 -9999 0 -0.45 6 6
MAP2K1 0.008 0.066 -9999 0 -0.25 9 9
ELK1 0.025 0.038 -9999 0 -0.42 2 2
BRAF 0.004 0.05 -9999 0 -0.35 8 8
mol:GTP -0.001 0.002 -9999 0 -0.005 73 73
MAPK1 0.012 0.1 -9999 0 -0.4 19 19
RAF1 0.01 0.023 -9999 0 -0.24 1 1
KRAS 0.027 0.057 -9999 0 -0.42 8 8
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 0.047 0.04 -10000 0 -0.3 6 6
Necdin/E2F1 0.013 0.11 -10000 0 -0.31 52 52
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.03 0.11 -10000 0 -0.23 71 71
NGF (dimer)/p75(NTR)/BEX1 0.037 0.035 -10000 0 -0.25 6 6
NT-4/5 (dimer)/p75(NTR) 0.022 0.026 -10000 0 -0.3 3 3
IKBKB 0.029 0.014 -10000 0 -10000 0 0
AKT1 0.019 0.069 0.19 41 -0.22 22 63
IKBKG 0.036 0 -10000 0 -10000 0 0
BDNF 0.03 0.024 -10000 0 -0.42 1 1
MGDIs/NGR/p75(NTR)/LINGO1 0.033 0.051 -10000 0 -0.25 14 14
FURIN 0.026 0.058 -10000 0 -0.42 8 8
proBDNF (dimer)/p75(NTR)/Sortilin 0.058 0.047 -10000 0 -0.25 9 9
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.025 0.055 -10000 0 -0.22 16 16
proBDNF (dimer) 0.03 0.024 -10000 0 -0.42 1 1
NTRK1 0.025 0.032 -10000 0 -0.42 2 2
RTN4R 0.023 0.067 -10000 0 -0.42 11 11
neuron apoptosis -0.009 0.1 0.28 1 -0.46 9 10
IRAK1 0.036 0.004 -10000 0 -10000 0 0
SHC1 0.012 0.022 -10000 0 -0.25 3 3
ARHGDIA 0.032 0.022 -10000 0 -0.42 1 1
RhoA/GTP 0.02 0.043 -10000 0 -0.3 9 9
Gamma Secretase 0.068 0.07 -10000 0 -0.22 14 14
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.04 0.083 -10000 0 -0.24 38 38
MAGEH1 0.006 0.11 -10000 0 -0.42 33 33
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.03 0.097 -10000 0 -0.24 54 54
Mammalian IAPs/DIABLO 0.032 0.083 -10000 0 -0.23 41 41
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.015 0.095 -10000 0 -0.42 23 23
APP 0.008 0.1 -10000 0 -0.42 28 28
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.034 0.029 -10000 0 -0.42 2 2
RhoA/GDP/RHOGDI 0.037 0.044 0.18 3 -0.22 12 15
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.011 0.048 0.2 16 -0.22 9 25
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.02 0.031 -10000 0 -0.21 6 6
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.042 0.03 -10000 0 -0.25 4 4
NCSTN 0.028 0.025 -10000 0 -0.42 1 1
mol:GTP 0.025 0.067 -10000 0 -0.25 27 27
PSENEN 0.035 0.006 -10000 0 -10000 0 0
mol:ceramide 0.015 0.043 0.19 11 -0.23 10 21
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.013 0.037 -10000 0 -10000 0 0
p75(NTR)/beta APP 0.026 0.082 -10000 0 -0.3 29 29
BEX1 0.026 0.037 -10000 0 -0.42 3 3
mol:GDP -0.006 0.019 -10000 0 -0.25 3 3
NGF (dimer) 0.007 0.11 -10000 0 -0.24 76 76
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.049 0.055 -10000 0 -0.23 15 15
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
RAC1/GTP 0.037 0.023 -10000 0 -0.21 3 3
MYD88 0.031 0.041 -10000 0 -0.42 4 4
CHUK 0.025 0.067 -10000 0 -0.42 11 11
NGF (dimer)/p75(NTR)/PKA 0.026 0.068 -10000 0 -0.25 27 27
RHOB -0.011 0.14 -10000 0 -0.42 51 51
RHOA 0.026 0.061 -10000 0 -0.42 9 9
MAGE-G1/E2F1 0.043 0.044 -10000 0 -0.3 7 7
NT3 (dimer) 0.024 0.054 -10000 0 -0.42 7 7
TP53 -0.02 0.066 0.35 1 -0.23 17 18
PRDM4 0.019 0.045 0.19 16 -0.23 9 25
BDNF (dimer) -0.02 0.17 -10000 0 -0.31 114 114
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
SORT1 0.03 0.05 -10000 0 -0.42 6 6
activation of caspase activity 0.024 0.11 -10000 0 -0.23 71 71
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.057 0.044 -10000 0 -0.23 9 9
RHOC 0.032 0.036 -10000 0 -0.42 3 3
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.018 0.079 0.22 1 -0.29 13 14
DIABLO 0.036 0.004 -10000 0 -10000 0 0
SMPD2 0.015 0.043 0.19 11 -0.23 10 21
APH1B 0.023 0.073 -10000 0 -0.42 13 13
APH1A 0.031 0.036 -10000 0 -0.42 3 3
proNGF (dimer)/p75(NTR)/Sortilin 0.039 0.041 -10000 0 -0.25 9 9
PSEN1 0.032 0.036 -10000 0 -0.42 3 3
APAF-1/Pro-Caspase 9 0.047 0.037 -10000 0 -0.3 5 5
NT3 (dimer)/p75(NTR) 0.038 0.051 -10000 0 -0.3 10 10
MAPK8 -0.011 0.065 -10000 0 -0.28 7 7
MAPK9 -0.017 0.078 -10000 0 -0.32 11 11
APAF1 0.032 0.041 -10000 0 -0.42 4 4
NTF3 0.024 0.054 -10000 0 -0.42 7 7
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.011 0.14 -10000 0 -0.42 52 52
RAC1/GDP 0.026 0.004 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.019 0.11 -10000 0 -0.22 84 84
p75 CTF/Sortilin/TRAF6/NRIF 0.081 0.047 -10000 0 -0.24 8 8
RhoA-B-C/GTP 0.025 0.067 -10000 0 -0.25 27 27
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.086 0.058 -10000 0 -0.22 12 12
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.074 0.052 -10000 0 -0.23 10 10
PRKACB 0.009 0.097 -10000 0 -0.42 24 24
proBDNF (dimer)/p75 ECD 0.048 0.02 -10000 0 -0.3 1 1
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.12 -10000 0 -0.42 42 42
BIRC2 0.031 0.012 -10000 0 -10000 0 0
neuron projection morphogenesis -0.038 0.078 0.13 2 -0.26 39 41
BAD -0.02 0.08 -10000 0 -0.3 10 10
RIPK2 0.028 0.015 -10000 0 -10000 0 0
NGFR 0.03 0.036 -10000 0 -0.42 3 3
CYCS 0.004 0.064 0.19 12 -0.22 32 44
ADAM17 0.035 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.047 0.04 -10000 0 -0.23 4 4
BCL2L11 -0.02 0.079 -10000 0 -0.3 10 10
BDNF (dimer)/p75(NTR) 0.043 0.034 -10000 0 -0.3 4 4
PI3K 0.046 0.062 -10000 0 -0.23 20 20
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.055 0.044 -10000 0 -0.23 9 9
NDNL2 0.034 0.008 -10000 0 -10000 0 0
YWHAE 0.032 0.011 -10000 0 -10000 0 0
PRKCI 0.024 0.067 -10000 0 -0.42 11 11
NGF (dimer)/p75(NTR) 0.022 0.026 -10000 0 -0.3 3 3
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.044 0.074 -10000 0 -0.23 32 32
TRAF6 0.034 0.021 -10000 0 -0.42 1 1
RAC1 0.035 0.006 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.031 0.03 -10000 0 -0.42 2 2
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.018 0.046 0.16 2 -0.24 14 16
SQSTM1 0.034 0.021 -10000 0 -0.42 1 1
NGFRAP1 -0.026 0.16 -10000 0 -0.42 68 68
CASP3 -0.018 0.077 -10000 0 -0.28 10 10
E2F1 0.028 0.054 -10000 0 -0.42 7 7
CASP9 0.034 0.022 -10000 0 -0.42 1 1
IKK complex 0.041 0.064 -10000 0 -0.32 1 1
NGF (dimer)/TRKA 0.019 0.023 -10000 0 -0.3 2 2
MMP7 -0.033 0.16 -10000 0 -0.42 69 69
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.07 0.05 -10000 0 -0.22 11 11
MMP3 -0.047 0.17 -10000 0 -0.42 83 83
APAF-1/Caspase 9 -0.046 0.064 -10000 0 -0.2 68 68
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.004 0.14 -10000 0 -0.48 1 1
CRKL -0.001 0.076 0.2 13 -0.24 11 24
mol:DAG 0.019 0.079 0.25 2 -10000 0 2
HRAS 0.022 0.1 0.27 22 -10000 0 22
MAPK8 0.035 0.073 0.2 56 -0.25 2 58
RAP1A 0 0.078 0.2 12 -0.25 12 24
GAB1 -0.001 0.076 0.2 11 -0.25 11 22
MAPK14 0.036 0.071 0.2 54 -10000 0 54
EPO 0.023 0.027 -10000 0 -10000 0 0
PLCG1 0.019 0.08 0.25 2 -10000 0 2
EPOR/TRPC2/IP3 Receptors 0.026 0.028 -10000 0 -10000 0 0
RAPGEF1 0.036 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.046 0.052 -10000 0 -0.27 4 4
GAB1/SHC/GRB2/SOS1 0.028 0.075 0.29 1 -0.21 1 2
EPO/EPOR (dimer) 0.036 0.039 -10000 0 -10000 0 0
IRS2 -0.01 0.087 0.25 4 -0.26 29 33
STAT1 -0.003 0.13 0.26 2 -0.33 35 37
STAT5B 0.02 0.082 0.26 1 -0.26 2 3
cell proliferation 0.013 0.079 0.19 75 -0.24 2 77
GAB1/SHIP/PIK3R1/SHP2/SHC 0.008 0.074 -10000 0 -0.29 4 4
TEC 0.001 0.075 0.2 12 -0.23 11 23
SOCS3 0.028 0.046 -10000 0 -0.42 5 5
STAT1 (dimer) -0.003 0.13 0.26 2 -0.32 35 37
JAK2 0.028 0.036 -10000 0 -0.44 2 2
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
EPO/EPOR (dimer)/JAK2 0.036 0.088 0.22 6 -0.17 34 40
EPO/EPOR 0.036 0.039 -10000 0 -10000 0 0
LYN 0.02 0.026 -10000 0 -10000 0 0
TEC/VAV2 0.014 0.08 0.29 2 -0.22 11 13
elevation of cytosolic calcium ion concentration 0.026 0.028 -10000 0 -10000 0 0
SHC1 0.027 0.025 -10000 0 -0.42 1 1
EPO/EPOR (dimer)/LYN 0.043 0.053 -10000 0 -10000 0 0
mol:IP3 0.019 0.079 0.25 2 -10000 0 2
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.006 0.095 0.29 1 -0.24 43 44
SH2B3 -0.003 0.009 -10000 0 -10000 0 0
NFKB1 0.037 0.071 0.2 56 -10000 0 56
EPO/EPOR (dimer)/JAK2/SOCS3 0.023 0.034 -10000 0 -0.21 6 6
PTPN6 -0.002 0.067 0.17 1 -0.19 20 21
TEC/VAV2/GRB2 0.026 0.083 0.3 2 -0.21 9 11
EPOR 0.026 0.028 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.027 0.075 0.29 1 -0.22 1 2
SOS1 0.034 0.021 -10000 0 -0.42 1 1
PLCG2 0.02 0.055 -10000 0 -0.42 7 7
CRKL/CBL/C3G 0.02 0.085 0.3 1 -0.23 10 11
VAV2 0.002 0.074 0.21 9 -0.25 6 15
CBL 0 0.07 0.19 12 -0.25 6 18
SHC/Grb2/SOS1 0.015 0.062 -10000 0 -0.21 4 4
STAT5A 0.019 0.083 0.26 1 -0.26 3 4
GRB2 0.033 0.01 -10000 0 -10000 0 0
STAT5 (dimer) 0.017 0.12 0.28 1 -0.31 45 46
LYN/PLCgamma2 0.029 0.043 -10000 0 -0.3 6 6
PTPN11 0.036 0.004 -10000 0 -10000 0 0
BTK -0.004 0.083 0.24 5 -0.25 19 24
BCL2 -0.11 0.33 -10000 0 -0.74 105 105
Syndecan-3-mediated signaling events

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
CTTN 0.027 0.032 -9999 0 -0.42 2 2
Syndecan-3/Src/Cortactin 0.006 0.14 -9999 0 -0.51 24 24
Syndecan-3/Neurocan -0.018 0.12 -9999 0 -0.5 27 27
POMC 0.031 0.036 -9999 0 -0.42 3 3
EGFR -0.013 0.13 -9999 0 -0.42 47 47
Syndecan-3/EGFR -0.011 0.15 -9999 0 -0.53 29 29
AGRP 0.028 0.025 -9999 0 -0.42 1 1
NCSTN 0.028 0.025 -9999 0 -0.42 1 1
PSENEN 0.035 0.006 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.023 0.073 -9999 0 -0.42 13 13
APH1A 0.031 0.036 -9999 0 -0.42 3 3
NCAN 0 0 -9999 0 -10000 0 0
long-term memory 0.018 0.12 -9999 0 -0.49 23 23
Syndecan-3/IL8 -0.007 0.14 -9999 0 -0.53 28 28
PSEN1 0.032 0.036 -9999 0 -0.42 3 3
Src/Cortactin 0.038 0.038 -9999 0 -0.3 4 4
FYN 0.027 0.05 -9999 0 -0.42 6 6
limb bud formation -0.015 0.12 -9999 0 -0.52 26 26
MC4R 0.033 0.022 -9999 0 -0.42 1 1
SRC 0.032 0.03 -9999 0 -0.42 2 2
PTN -0.028 0.15 -9999 0 -0.42 63 63
FGFR/FGF/Syndecan-3 -0.016 0.12 -9999 0 -0.53 26 26
neuron projection morphogenesis -0.031 0.12 -9999 0 -0.49 24 24
Syndecan-3/AgRP 0.008 0.13 -9999 0 -0.5 27 27
Syndecan-3/AgRP/MC4R 0.023 0.13 -9999 0 -0.49 25 25
Fyn/Cortactin 0.035 0.044 -9999 0 -0.3 6 6
SDC3 -0.016 0.12 -9999 0 -0.54 26 26
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.007 0.14 -9999 0 -0.52 28 28
IL8 -0.005 0.12 -9999 0 -0.42 37 37
Syndecan-3/Fyn/Cortactin 0.018 0.13 -9999 0 -0.5 23 23
Syndecan-3/CASK -0.018 0.12 -9999 0 -0.5 27 27
alpha-MSH/MC4R 0.047 0.034 -9999 0 -0.3 4 4
Gamma Secretase 0.068 0.07 -9999 0 -0.22 14 14
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.039 0.038 -10000 0 -0.25 7 7
cell-cell adhesion 0.035 0.058 0.23 29 -10000 0 29
Ephrin B/EPHB2/RasGAP 0.069 0.079 -10000 0 -0.24 21 21
ITSN1 0.034 0.029 -10000 0 -0.42 2 2
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
SHC1 0.027 0.025 -10000 0 -0.42 1 1
Ephrin B1/EPHB3 0.034 0.058 -10000 0 -0.25 19 19
Ephrin B1/EPHB1 0.041 0.036 -10000 0 -0.25 7 7
HRAS/GDP 0.002 0.11 -10000 0 -0.28 35 35
Ephrin B/EPHB1/GRB7 0.064 0.082 -10000 0 -0.23 27 27
Endophilin/SYNJ1 -0.012 0.051 0.19 6 -0.21 14 20
KRAS 0.027 0.057 -10000 0 -0.42 8 8
Ephrin B/EPHB1/Src 0.069 0.076 -10000 0 -0.24 19 19
endothelial cell migration 0.035 0.091 -10000 0 -0.24 45 45
GRB2 0.033 0.01 -10000 0 -10000 0 0
GRB7 0.024 0.058 -10000 0 -0.42 8 8
PAK1 -0.021 0.065 0.28 2 -0.24 1 3
HRAS 0.032 0.036 -10000 0 -0.42 3 3
RRAS -0.014 0.055 0.19 5 -0.23 15 20
DNM1 0.032 0.041 -10000 0 -0.42 4 4
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.012 0.057 0.18 17 -0.22 17 34
lamellipodium assembly -0.035 0.058 -10000 0 -0.23 29 29
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.016 0.068 -10000 0 -0.45 5 5
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
EPHB2 0.032 0.03 -10000 0 -0.42 2 2
EPHB3 0.018 0.085 -10000 0 -0.42 18 18
EPHB1 0.026 0.051 -10000 0 -0.42 6 6
EPHB4 0.018 0.085 -10000 0 -0.42 18 18
mol:GDP -0.017 0.085 -10000 0 -0.33 22 22
Ephrin B/EPHB2 0.058 0.062 -10000 0 -0.22 17 17
Ephrin B/EPHB3 0.048 0.079 -10000 0 -0.23 30 30
JNK cascade -0.013 0.062 0.29 10 -0.23 16 26
Ephrin B/EPHB1 0.056 0.066 -10000 0 -0.23 19 19
RAP1/GDP -0.003 0.11 -10000 0 -0.28 36 36
EFNB2 0.019 0.075 -10000 0 -0.42 14 14
EFNB3 0.031 0.012 -10000 0 -10000 0 0
EFNB1 0.034 0.021 -10000 0 -0.42 1 1
Ephrin B2/EPHB1-2 0.045 0.064 -10000 0 -0.24 20 20
RAP1B 0.032 0.03 -10000 0 -0.42 2 2
RAP1A 0.03 0.05 -10000 0 -0.42 6 6
CDC42/GTP 0.036 0.09 -10000 0 -0.28 18 18
Rap1/GTP 0.015 0.069 -10000 0 -0.26 19 19
axon guidance 0.039 0.038 -10000 0 -0.25 7 7
MAPK3 0.025 0.072 0.27 1 -0.42 5 6
MAPK1 0.016 0.065 0.22 3 -0.41 5 8
Rac1/GDP -0.014 0.1 -10000 0 -0.29 30 30
actin cytoskeleton reorganization -0.043 0.064 -10000 0 -0.24 26 26
CDC42/GDP -0.013 0.1 -10000 0 -0.29 33 33
PI3K 0.04 0.094 -10000 0 -0.24 45 45
EFNA5 0.029 0.046 -10000 0 -0.42 5 5
Ephrin B2/EPHB4 0.023 0.076 -10000 0 -0.27 30 30
Ephrin B/EPHB2/Intersectin/N-WASP 0.005 0.077 -10000 0 -0.32 8 8
CDC42 0.034 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.008 0.065 -10000 0 -0.22 27 27
PTK2 0.11 0.23 0.55 112 -10000 0 112
MAP4K4 -0.013 0.063 0.29 10 -0.24 16 26
SRC 0.032 0.03 -10000 0 -0.42 2 2
KALRN 0.033 0.022 -10000 0 -0.42 1 1
Intersectin/N-WASP 0.044 0.048 -10000 0 -0.3 9 9
neuron projection morphogenesis -0.028 0.078 0.26 2 -0.33 10 12
MAP2K1 0.01 0.062 0.21 1 -0.43 5 6
WASL 0.029 0.054 -10000 0 -0.42 7 7
Ephrin B1/EPHB1-2/NCK1 0.077 0.05 -10000 0 -0.23 10 10
cell migration 0.03 0.093 0.26 6 -0.44 6 12
NRAS 0.029 0.05 -10000 0 -0.42 6 6
SYNJ1 -0.012 0.052 0.19 6 -0.21 14 20
PXN 0.036 0.004 -10000 0 -10000 0 0
TF -0.017 0.049 0.18 6 -10000 0 6
HRAS/GTP 0.042 0.074 -10000 0 -0.22 27 27
Ephrin B1/EPHB1-2 0.057 0.043 -10000 0 -0.23 9 9
cell adhesion mediated by integrin 0.011 0.057 0.23 14 -0.21 12 26
RAC1 0.035 0.006 -10000 0 -10000 0 0
mol:GTP 0.048 0.073 -10000 0 -0.23 25 25
RAC1-CDC42/GTP -0.033 0.061 -10000 0 -0.39 5 5
RASA1 0.028 0.054 -10000 0 -0.42 7 7
RAC1-CDC42/GDP -0.001 0.1 -10000 0 -0.3 23 23
ruffle organization -0.03 0.074 -10000 0 -0.4 5 5
NCK1 0.034 0.022 -10000 0 -0.42 1 1
receptor internalization -0.02 0.051 0.17 13 -0.21 17 30
Ephrin B/EPHB2/KALRN 0.073 0.072 -10000 0 -0.23 17 17
ROCK1 0.017 0.06 0.19 23 -0.23 19 42
RAS family/GDP -0.046 0.067 -10000 0 -0.26 26 26
Rac1/GTP 0.002 0.073 -10000 0 -0.24 32 32
Ephrin B/EPHB1/Src/Paxillin 0.009 0.075 -10000 0 -0.38 7 7
Regulation of Androgen receptor activity

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
HDAC1 0.015 0.015 -10000 0 -0.3 1 1
SMARCC1 0.003 0.12 -10000 0 -1.1 5 5
REL 0.023 0.07 -10000 0 -0.42 12 12
HDAC7 -0.038 0.1 0.22 1 -0.32 33 34
JUN -0.001 0.12 -10000 0 -0.42 39 39
EP300 0.033 0.022 -10000 0 -0.42 1 1
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.001 0.058 -10000 0 -0.31 15 15
FOXO1 0 0 -10000 0 -10000 0 0
T-DHT/AR -0.009 0.13 -10000 0 -0.34 33 33
MAP2K6 0.011 0.08 -10000 0 -0.43 15 15
BRM/BAF57 0.047 0.024 -10000 0 -0.3 1 1
MAP2K4 0.022 0.031 -10000 0 -0.42 1 1
SMARCA2 0.034 0.022 -10000 0 -0.42 1 1
PDE9A -0.001 0.11 -10000 0 -0.98 4 4
NCOA2 0.025 0.047 -10000 0 -0.42 5 5
CEBPA 0.024 0.07 -10000 0 -0.42 12 12
EHMT2 0.036 0.005 -10000 0 -10000 0 0
cell proliferation 0.028 0.13 0.31 20 -0.35 12 32
NR0B1 0.03 0.036 -10000 0 -0.42 3 3
EGR1 -0.037 0.16 -10000 0 -0.42 75 75
RXRs/9cRA 0.047 0.053 -10000 0 -0.23 12 12
AR/RACK1/Src 0.004 0.099 0.28 5 -0.3 13 18
AR/GR -0.028 0.12 0.23 2 -0.24 95 97
GNB2L1 0.034 0.035 -10000 0 -0.42 3 3
PKN1 0.033 0.035 -10000 0 -0.42 3 3
RCHY1 0.022 0.075 -10000 0 -0.42 14 14
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 0.006 0.033 -10000 0 -0.31 3 3
T-DHT/AR/TIF2/CARM1 0.009 0.092 0.36 1 -0.33 9 10
SRC -0.01 0.073 0.19 37 -0.25 16 53
NR3C1 0.022 0.078 -10000 0 -0.42 15 15
KLK3 -0.015 0.094 -10000 0 -10000 0 0
APPBP2 0.024 0.024 -10000 0 -10000 0 0
TRIM24 0.035 0.008 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.033 0.07 0.14 1 -0.29 20 21
TMPRSS2 -0.14 0.38 -10000 0 -0.95 88 88
RXRG 0.021 0.058 -10000 0 -0.42 8 8
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.034 0.029 -10000 0 -0.42 2 2
RXRB 0.034 0.029 -10000 0 -0.42 2 2
CARM1 0.035 0.021 -10000 0 -0.42 1 1
NR2C2 0.035 0.008 -10000 0 -10000 0 0
KLK2 0.011 0.073 0.3 3 -0.29 2 5
AR -0.033 0.11 0.18 1 -0.24 92 93
SENP1 0.035 0.006 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
MDM2 0.033 0.008 -10000 0 -10000 0 0
SRY 0.023 0.07 -10000 0 -0.42 12 12
GATA2 0.029 0.046 -10000 0 -0.42 5 5
MYST2 0.032 0.03 -10000 0 -0.42 2 2
HOXB13 0.023 0.018 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src 0 0.1 0.29 5 -0.31 13 18
positive regulation of transcription 0.029 0.046 -10000 0 -0.42 5 5
DNAJA1 0.023 0.043 -10000 0 -0.42 3 3
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.052 -10000 0 -0.29 14 14
NCOA1 0.035 0.054 -10000 0 -0.33 9 9
SPDEF -0.045 0.18 -10000 0 -0.42 90 90
T-DHT/AR/TIF2 0.014 0.078 0.24 8 -0.3 6 14
T-DHT/AR/Hsp90 -0.032 0.07 0.14 1 -0.29 20 21
GSK3B 0.035 0.006 -10000 0 -10000 0 0
NR2C1 0.029 0.054 -10000 0 -0.42 7 7
mol:T-DHT -0.009 0.072 0.21 29 -0.26 14 43
SIRT1 0.035 0.005 -10000 0 -10000 0 0
ZMIZ2 -0.001 0 -10000 0 -10000 0 0
POU2F1 0.016 0.055 -10000 0 -0.11 63 63
T-DHT/AR/DAX-1 -0.009 0.097 0.3 2 -0.3 21 23
CREBBP 0.033 0.011 -10000 0 -10000 0 0
SMARCE1 0.034 0.01 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0.035 0.006 -10000 0 -10000 0 0
VLDLR -0.007 0.13 -10000 0 -0.42 42 42
LRPAP1 0.035 0.007 -10000 0 -10000 0 0
NUDC 0.035 0.007 -10000 0 -10000 0 0
RELN/LRP8 0.038 0.088 -10000 0 -0.26 39 39
CaM/Ca2+ 0.026 0.005 -10000 0 -10000 0 0
KATNA1 0.033 0.01 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.001 0.072 0.19 9 -0.23 39 48
IQGAP1/CaM 0.049 0.015 -10000 0 -10000 0 0
DAB1 0.035 0.006 -10000 0 -10000 0 0
IQGAP1 0.034 0.008 -10000 0 -10000 0 0
PLA2G7 -0.036 0.16 -10000 0 -0.42 74 74
CALM1 0.035 0.007 -10000 0 -10000 0 0
DYNLT1 0.033 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.023 0.088 -10000 0 -0.3 34 34
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0 0 -10000 0 -10000 0 0
CDK5R1 0.033 0.01 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.01 0.012 -10000 0 -0.25 1 1
CDK5R2 0.035 0.005 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.032 0.097 -10000 0 -0.26 46 46
YWHAE 0.032 0.011 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.015 0.069 0.33 1 -0.25 5 6
MAP1B -0.007 0.06 -10000 0 -0.26 26 26
RAC1 0.015 0.007 -10000 0 -10000 0 0
p35/CDK5 0.007 0.067 0.19 7 -0.21 38 45
RELN 0.03 0.046 -10000 0 -0.42 5 5
PAFAH/LIS1 -0.011 0.1 -10000 0 -0.26 73 73
LIS1/CLIP170 0.01 0.012 -10000 0 -0.25 1 1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.017 0.069 -10000 0 -0.23 2 2
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.007 0.1 -10000 0 -0.26 59 59
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.004 0.062 0.33 1 -0.26 5 6
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 -0.3 1 1
PAFAH1B3 0.029 0.054 -10000 0 -0.42 7 7
PAFAH1B2 0.031 0.012 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.016 0.058 -10000 0 -0.24 3 3
NDEL1/Katanin 60/Dynein heavy chain 0.021 0.078 0.33 1 -0.25 5 6
LRP8 0 0.11 -10000 0 -0.42 34 34
NDEL1/Katanin 60 0.008 0.072 0.33 1 -0.25 5 6
P39/CDK5 0.008 0.067 0.19 7 -0.21 39 46
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.033 0.019 -10000 0 -0.26 1 1
CDK5 -0.029 0.061 0.18 8 -0.22 39 47
PPP2R5D 0.035 0.007 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.009 0.011 -10000 0 -0.21 1 1
CSNK2A1 0.034 0.008 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.036 0.092 -10000 0 -0.23 46 46
RELN/VLDLR 0.025 0.12 -10000 0 -0.24 79 79
CDC42 0.015 0.007 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.034 0.021 -10000 0 -0.42 1 1
HDAC2 0.032 0.023 -10000 0 -0.42 1 1
GNB1/GNG2 0.034 0.099 -10000 0 -0.26 51 51
forebrain development -0.004 0.14 -10000 0 -0.56 17 17
GNAO1 0.03 0.014 -10000 0 -10000 0 0
SMO/beta Arrestin2 0.015 0.1 -10000 0 -0.3 46 46
SMO -0.008 0.13 -10000 0 -0.42 46 46
ARRB2 0.033 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.003 0.15 -10000 0 -0.42 30 30
mol:GTP 0 0 -10000 0 -10000 0 0
GSK3B 0.035 0.005 -10000 0 -10000 0 0
GNAI2 0.027 0.057 -10000 0 -0.42 8 8
SIN3/HDAC complex 0.076 0.045 -10000 0 -0.23 5 5
GNAI1 0.018 0.085 -10000 0 -0.42 18 18
XPO1 0.036 0.005 -10000 0 -10000 0 0
GLI1/Su(fu) -0.019 0.17 -10000 0 -0.55 26 26
SAP30 0.03 0.046 -10000 0 -0.42 5 5
mol:GDP -0.008 0.13 -10000 0 -0.42 46 46
MIM/GLI2A 0.001 0.11 -10000 0 -0.42 31 31
IFT88 0.02 0.075 -10000 0 -0.42 14 14
GNAI3 0.035 0.006 -10000 0 -10000 0 0
GLI2 0.013 0.081 0.21 1 -0.35 14 15
GLI3 -0.011 0.15 0.24 3 -0.43 30 33
CSNK1D 0.033 0.009 -10000 0 -10000 0 0
CSNK1E 0.034 0.009 -10000 0 -10000 0 0
SAP18 0.033 0.01 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.02 0.075 -10000 0 -0.42 14 14
GNG2 0.034 0.021 -10000 0 -0.42 1 1
Gi family/GTP -0.017 0.11 -10000 0 -0.3 54 54
SIN3B 0.035 0.005 -10000 0 -10000 0 0
SIN3A 0.035 0.007 -10000 0 -10000 0 0
GLI3/Su(fu) -0.008 0.14 -10000 0 -0.42 38 38
GLI2/Su(fu) 0.003 0.11 -10000 0 -0.4 18 18
FOXA2 -0.024 0.2 -10000 0 -0.69 39 39
neural tube patterning -0.004 0.14 -10000 0 -0.56 17 17
SPOP 0.033 0.022 -10000 0 -0.42 1 1
Su(fu)/PIAS1 0.008 0.09 -10000 0 -0.33 16 16
GNB1 0.032 0.045 -10000 0 -0.42 5 5
CSNK1G2 0.033 0.03 -10000 0 -0.42 2 2
CSNK1G3 0.035 0.007 -10000 0 -10000 0 0
MTSS1 0.001 0.11 -10000 0 -0.42 31 31
embryonic limb morphogenesis -0.004 0.14 -10000 0 -0.56 17 17
SUFU -0.001 0.084 -10000 0 -0.35 16 16
LGALS3 -0.01 0.14 -10000 0 -0.42 49 49
catabolic process 0.013 0.15 -10000 0 -0.5 20 20
GLI3A/CBP 0.034 0.042 -10000 0 -0.33 6 6
KIF3A 0.027 0.061 -10000 0 -0.42 9 9
GLI1 -0.005 0.14 -10000 0 -0.57 17 17
RAB23 0.031 0.041 -10000 0 -0.42 4 4
CSNK1A1 0.035 0.005 -10000 0 -10000 0 0
IFT172 0.033 0.035 -10000 0 -0.42 3 3
RBBP7 0.033 0.029 -10000 0 -0.42 2 2
Su(fu)/Galectin3 -0.015 0.12 -10000 0 -0.29 61 61
GNAZ 0.024 0.067 -10000 0 -0.42 11 11
RBBP4 0.034 0.021 -10000 0 -0.42 1 1
CSNK1G1 0.035 0.007 -10000 0 -10000 0 0
PIAS1 0.035 0.006 -10000 0 -10000 0 0
PRKACA 0.036 0.004 -10000 0 -10000 0 0
GLI2/SPOP 0.027 0.084 -10000 0 -0.33 14 14
STK36 0.021 0.083 -10000 0 -0.42 17 17
Gi family/GNB1/GNG2/GDP -0.021 0.12 -10000 0 -0.38 35 35
PTCH1 -0.002 0.13 -10000 0 -0.5 17 17
MIM/GLI1 0 0.13 -10000 0 -0.51 17 17
CREBBP 0.034 0.042 -10000 0 -0.33 6 6
Su(fu)/SIN3/HDAC complex 0.008 0.097 -10000 0 -0.42 16 16
HIF-2-alpha transcription factor network

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
MMP14 -0.003 0.27 -10000 0 -1 31 31
oxygen homeostasis 0.005 0.009 -10000 0 -10000 0 0
TCEB2 0.032 0.011 -10000 0 -10000 0 0
TCEB1 0.028 0.025 -10000 0 -0.42 1 1
VHL/Elongin B/Elongin C/HIF2A 0.053 0.11 -10000 0 -0.36 8 8
EPO 0.073 0.17 -10000 0 -0.53 14 14
FIH (dimer) 0.037 0.02 -10000 0 -10000 0 0
APEX1 0.035 0.028 -10000 0 -10000 0 0
SERPINE1 0.058 0.2 -10000 0 -0.55 25 25
FLT1 -0.037 0.27 -10000 0 -0.79 45 45
ADORA2A 0.045 0.18 -10000 0 -0.55 21 21
germ cell development 0.066 0.18 -10000 0 -0.53 18 18
SLC11A2 0.067 0.19 -10000 0 -0.55 19 19
BHLHE40 0.055 0.18 -10000 0 -0.49 24 24
HIF1AN 0.037 0.02 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.075 0.15 0.33 1 -0.38 19 20
ETS1 0.037 0.032 -10000 0 -0.42 1 1
CITED2 0.017 0.18 -10000 0 -0.84 16 16
KDR -0.013 0.23 -10000 0 -0.79 27 27
PGK1 0.068 0.18 -10000 0 -0.55 18 18
SIRT1 0.036 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.11 0.22 -10000 0 -0.61 19 19
EPAS1 0.027 0.12 -10000 0 -0.33 23 23
SP1 0.034 0.038 -10000 0 -0.27 2 2
ABCG2 0.062 0.19 -10000 0 -0.58 20 20
EFNA1 0.033 0.18 -10000 0 -0.52 30 30
FXN 0.054 0.17 -10000 0 -0.53 18 18
POU5F1 0.066 0.18 -10000 0 -0.55 18 18
neuron apoptosis -0.11 0.22 0.6 19 -10000 0 19
EP300 0.033 0.022 -10000 0 -0.42 1 1
EGLN3 -0.013 0.14 -10000 0 -0.42 52 52
EGLN2 0.033 0.045 -10000 0 -0.42 4 4
EGLN1 0.023 0.057 -10000 0 -0.42 7 7
VHL/Elongin B/Elongin C 0.053 0.035 -10000 0 -0.26 1 1
VHL 0.035 0.007 -10000 0 -10000 0 0
ARNT 0.035 0.027 -10000 0 -10000 0 0
SLC2A1 0.048 0.18 0.34 2 -0.52 22 24
TWIST1 0.041 0.2 0.34 5 -0.57 33 38
ELK1 0.039 0.032 -10000 0 -0.27 4 4
HIF2A/ARNT/Cbp/p300 0.072 0.15 0.34 1 -0.39 17 18
VEGFA 0.055 0.18 -10000 0 -0.49 24 24
CREBBP 0.032 0.011 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC 0.041 0.097 -10000 0 -1.3 1 1
PLK1 0.01 0.2 -10000 0 -0.77 13 13
CDKN1B 0.044 0.16 -10000 0 -0.46 30 30
FOXO3 -0.006 0.22 -10000 0 -0.48 65 65
KAT2B 0.001 0.019 -10000 0 -0.043 65 65
FOXO1/SIRT1 0.045 0.053 -10000 0 -0.28 3 3
CAT -0.008 0.23 -10000 0 -0.84 19 19
CTNNB1 0.024 0.067 -10000 0 -0.42 11 11
AKT1 0.027 0.05 -10000 0 -0.41 3 3
FOXO1 0.027 0.053 0.24 1 -0.28 4 5
MAPK10 0.007 0.061 0.2 9 -0.21 25 34
mol:GTP 0 0.002 -10000 0 -10000 0 0
FOXO4 0.016 0.098 0.28 1 -0.34 15 16
response to oxidative stress 0.004 0.02 -10000 0 -0.046 40 40
FOXO3A/SIRT1 0.019 0.2 -10000 0 -0.44 55 55
XPO1 0.035 0.005 -10000 0 -10000 0 0
EP300 0.035 0.023 -10000 0 -0.42 1 1
BCL2L11 0.029 0.086 -10000 0 -1.2 2 2
FOXO1/SKP2 0.042 0.049 -10000 0 -0.3 2 2
mol:GDP 0.004 0.02 -10000 0 -0.046 40 40
RAN 0.036 0.005 -10000 0 -10000 0 0
GADD45A 0.013 0.22 -10000 0 -0.77 28 28
YWHAQ 0.033 0.029 -10000 0 -0.42 2 2
FOXO1/14-3-3 family 0.039 0.12 -10000 0 -0.42 14 14
MST1 0.028 0.036 -10000 0 -10000 0 0
CSNK1D 0.033 0.009 -10000 0 -10000 0 0
CSNK1E 0.034 0.009 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.008 0.13 -10000 0 -0.4 26 26
YWHAB 0.034 0.009 -10000 0 -10000 0 0
MAPK8 0.017 0.044 0.2 10 -0.21 7 17
MAPK9 0.008 0.059 0.2 8 -0.22 23 31
YWHAG 0.035 0.005 -10000 0 -10000 0 0
YWHAE 0.032 0.011 -10000 0 -10000 0 0
YWHAZ 0.026 0.016 -10000 0 -10000 0 0
SIRT1 0.036 0.02 -10000 0 -10000 0 0
SOD2 0.031 0.16 -10000 0 -0.62 12 12
RBL2 -0.079 0.32 -10000 0 -0.74 75 75
RAL/GDP 0.045 0.038 -10000 0 -0.25 4 4
CHUK 0.018 0.075 -10000 0 -0.42 11 11
Ran/GTP 0.026 0.01 -10000 0 -10000 0 0
CSNK1G2 0.033 0.03 -10000 0 -0.42 2 2
RAL/GTP 0.046 0.038 -10000 0 -0.22 4 4
CSNK1G1 0.035 0.007 -10000 0 -10000 0 0
FASLG -0.092 0.4 -10000 0 -1.4 45 45
SKP2 0.034 0.009 -10000 0 -10000 0 0
USP7 0.032 0.012 -10000 0 -10000 0 0
IKBKB 0.023 0.035 -10000 0 -10000 0 0
CCNB1 -0.051 0.33 -10000 0 -1 42 42
FOXO1-3a-4/beta catenin 0.038 0.16 0.42 1 -0.41 27 28
proteasomal ubiquitin-dependent protein catabolic process 0.042 0.049 -10000 0 -0.3 2 2
CSNK1A1 0.035 0.005 -10000 0 -10000 0 0
SGK1 0.001 0.019 -10000 0 -0.043 65 65
CSNK1G3 0.035 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.048 0.013 -10000 0 -10000 0 0
ZFAND5 0.017 0.085 0.26 1 -0.28 15 16
SFN 0.011 0.099 -10000 0 -0.42 25 25
CDK2 0.036 0.03 -10000 0 -0.42 2 2
FOXO3A/14-3-3 0.015 0.12 -10000 0 -0.38 24 24
CREBBP 0.035 0.013 -10000 0 -10000 0 0
FBXO32 0.02 0.31 0.44 2 -1.1 23 25
BCL6 -0.008 0.27 -10000 0 -1.1 22 22
RALB 0.032 0.041 -10000 0 -0.42 4 4
RALA 0.035 0.007 -10000 0 -10000 0 0
YWHAH 0.031 0.036 -10000 0 -0.42 3 3
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.035 0.073 -10000 0 -0.32 20 20
AKT1 0.011 0.12 0.32 1 -0.41 18 19
PTK2B -0.001 0.091 0.36 1 -0.51 8 9
VEGFR2 homodimer/Frs2 0.029 0.076 -10000 0 -0.39 11 11
CAV1 0.028 0.05 -10000 0 -0.42 6 6
CALM1 0.035 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.026 0.081 -10000 0 -0.38 11 11
endothelial cell proliferation 0.036 0.12 0.3 16 -0.45 8 24
mol:Ca2+ 0.005 0.096 -10000 0 -0.32 29 29
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.044 0.084 -10000 0 -0.48 7 7
RP11-342D11.1 -0.011 0.097 -10000 0 -0.3 35 35
CDH5 0.027 0.037 -10000 0 -0.42 3 3
VEGFA homodimer 0.037 0.086 -10000 0 -0.24 43 43
SHC1 0.027 0.025 -10000 0 -0.42 1 1
SHC2 -0.026 0.16 -10000 0 -0.42 67 67
HRAS/GDP 0.019 0.091 -10000 0 -0.42 8 8
SH2D2A -0.001 0.1 -10000 0 -0.42 29 29
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.037 0.11 -10000 0 -0.46 12 12
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.005 0.097 -10000 0 -0.28 38 38
VEGFR1 homodimer 0.026 0.054 -10000 0 -0.42 7 7
SHC/GRB2/SOS1 0.041 0.11 -10000 0 -0.46 8 8
GRB10 -0.004 0.12 -10000 0 -0.51 20 20
PTPN11 0.036 0.004 -10000 0 -10000 0 0
GRB2 0.033 0.01 -10000 0 -10000 0 0
PAK1 0.014 0.085 -10000 0 -0.42 18 18
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.042 0.1 -10000 0 -0.46 10 10
HRAS 0.032 0.036 -10000 0 -0.42 3 3
VEGF/Rho/ROCK1/Integrin Complex 0.004 0.1 -10000 0 -0.36 25 25
HIF1A -0.007 0.13 -10000 0 -0.42 45 45
FRS2 0.033 0.022 -10000 0 -0.42 1 1
oxygen and reactive oxygen species metabolic process 0.042 0.083 -10000 0 -0.47 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.035 0.006 -10000 0 -10000 0 0
Nck/Pak 0.031 0.069 -10000 0 -0.3 19 19
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.022 0.092 -10000 0 -0.38 15 15
mol:GDP 0.029 0.097 -10000 0 -0.42 9 9
mol:NADP 0.021 0.1 -10000 0 -0.43 10 10
eNOS/Hsp90 0.019 0.096 -10000 0 -0.41 10 10
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
mol:IP3 0.005 0.097 -10000 0 -0.32 29 29
HIF1A/ARNT 0.02 0.099 -10000 0 -0.3 43 43
SHB 0.03 0.046 -10000 0 -0.42 5 5
VEGFA -0.002 0.016 -10000 0 -10000 0 0
VEGFC 0.022 0.073 -10000 0 -0.42 13 13
FAK1/Vinculin 0.015 0.12 0.36 1 -0.5 11 12
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.026 0.061 -10000 0 -0.42 9 9
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.033 0.1 -10000 0 -0.31 27 27
PTPN6 0.032 0.03 -10000 0 -0.42 2 2
EPAS1 0.029 0.071 -10000 0 -0.39 12 12
mol:L-citrulline 0.021 0.1 -10000 0 -0.43 10 10
ITGAV 0.021 0.08 -10000 0 -0.42 16 16
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.041 0.08 -10000 0 -0.47 6 6
VEGFR2 homodimer/VEGFA homodimer 0.022 0.12 -10000 0 -0.33 36 36
VEGFR2/3 heterodimer 0.03 0.076 -10000 0 -0.4 11 11
VEGFB 0.034 0.021 -10000 0 -0.42 1 1
MAPK11 -0.015 0.11 0.26 2 -0.44 16 18
VEGFR2 homodimer 0.012 0.081 -10000 0 -0.46 11 11
FLT1 0.026 0.054 -10000 0 -0.42 7 7
NEDD4 0.02 0.074 -10000 0 -0.42 12 12
MAPK3 0.005 0.095 0.26 10 -0.39 10 20
MAPK1 -0.001 0.095 0.25 6 -0.41 10 16
VEGFA145/NRP2 0.023 0.024 -10000 0 -0.33 1 1
VEGFR1/2 heterodimer 0.024 0.085 -10000 0 -0.37 16 16
KDR 0.012 0.082 -10000 0 -0.46 11 11
VEGFA165/NRP1/VEGFR2 homodimer 0.023 0.11 -10000 0 -0.31 34 34
SRC 0.032 0.03 -10000 0 -0.42 2 2
platelet activating factor biosynthetic process 0.004 0.099 0.26 9 -0.42 10 19
PI3K 0.006 0.12 -10000 0 -0.5 14 14
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.026 0.082 -10000 0 -0.38 12 12
FES 0 0.11 -10000 0 -0.32 33 33
GAB1 0.015 0.12 -10000 0 -0.41 24 24
VEGFR2 homodimer/VEGFA homodimer/Src 0.026 0.079 -10000 0 -0.36 13 13
CTNNB1 0.024 0.067 -10000 0 -0.42 11 11
SOS1 0.034 0.021 -10000 0 -0.42 1 1
ARNT 0.035 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.032 0.11 -10000 0 -0.42 12 12
VEGFR2 homodimer/VEGFA homodimer/Yes 0.023 0.087 -10000 0 -0.34 17 17
PI3K/GAB1 0.021 0.13 0.28 1 -0.43 20 21
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.042 0.096 -10000 0 -0.43 7 7
PRKACA 0.036 0.004 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.041 0.095 -10000 0 -0.35 20 20
HSP90AA1 0 0 -10000 0 -10000 0 0
CDC42 0.002 0.1 -10000 0 -0.32 32 32
actin cytoskeleton reorganization 0.005 0.097 -10000 0 -0.28 38 38
PTK2 -0.006 0.1 -10000 0 -0.52 12 12
EDG1 -0.009 0.14 -10000 0 -0.53 27 27
mol:DAG 0.005 0.097 -10000 0 -0.32 29 29
CaM/Ca2+ 0.02 0.095 -10000 0 -0.3 26 26
MAP2K3 -0.012 0.099 0.21 1 -0.47 11 12
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.015 0.13 -10000 0 -0.5 21 21
PLCG1 0.005 0.098 -10000 0 -0.32 29 29
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.04 0.086 -10000 0 -0.3 18 18
IQGAP1 0.034 0.008 -10000 0 -10000 0 0
YES1 0.029 0.05 -10000 0 -0.42 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.028 0.082 -10000 0 -0.4 11 11
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.026 0.081 -10000 0 -0.4 11 11
cell migration 0.017 0.1 0.31 2 -0.49 9 11
mol:PI-3-4-5-P3 0.007 0.12 -10000 0 -0.46 14 14
FYN 0.027 0.05 -10000 0 -0.42 6 6
VEGFB/NRP1 0.008 0.1 -10000 0 -0.3 34 34
mol:NO 0.021 0.1 -10000 0 -0.43 10 10
PXN 0.036 0.004 -10000 0 -10000 0 0
HRAS/GTP 0.003 0.083 -10000 0 -0.4 9 9
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.004 0.13 -10000 0 -0.5 21 21
VHL 0.035 0.007 -10000 0 -10000 0 0
ITGB3 0.029 0.046 -10000 0 -0.42 5 5
NOS3 0.02 0.11 -10000 0 -0.49 10 10
VEGFR2 homodimer/VEGFA homodimer/Sck -0.006 0.12 -10000 0 -0.26 73 73
RAC1 0.035 0.006 -10000 0 -10000 0 0
PRKCA -0.005 0.083 0.21 1 -0.41 9 10
PRKCB -0.008 0.088 -10000 0 -0.44 10 10
VCL 0.035 0.021 -10000 0 -0.42 1 1
VEGFA165/NRP1 -0.007 0.096 -10000 0 -0.3 35 35
VEGFR1/2 heterodimer/VEGFA homodimer 0.021 0.09 -10000 0 -0.36 16 16
VEGFA165/NRP2 0.023 0.024 -10000 0 -0.33 1 1
MAPKKK cascade 0.033 0.13 0.36 7 -0.43 17 24
NRP2 0.034 0.021 -10000 0 -0.42 1 1
VEGFC homodimer 0.022 0.073 -10000 0 -0.42 13 13
NCK1 0.034 0.022 -10000 0 -0.42 1 1
ROCK1 0.035 0.005 -10000 0 -10000 0 0
FAK1/Paxillin 0.016 0.12 0.36 1 -0.5 12 13
MAP3K13 0 0.11 -10000 0 -0.32 35 35
PDPK1 -0.003 0.099 0.25 2 -0.4 15 17
IL2 signaling events mediated by STAT5

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
GAB2 0.031 0.013 -10000 0 -10000 0 0
ELF1 0.013 0.099 -10000 0 -0.35 34 34
CCNA2 0.009 0.1 -10000 0 -0.42 28 28
PIK3CA 0.034 0.022 -10000 0 -0.42 1 1
JAK3 0.036 0.005 -10000 0 -10000 0 0
PIK3R1 0.019 0.083 -10000 0 -0.42 17 17
JAK1 0.032 0.036 -10000 0 -0.42 3 3
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.021 0.14 -10000 0 -0.41 24 24
SHC1 0.028 0.025 -10000 0 -0.42 1 1
SP1 0.033 0.069 -10000 0 -0.36 14 14
IL2RA -0.025 0.17 -10000 0 -0.6 37 37
IL2RB 0.012 0.095 -10000 0 -0.42 23 23
SOS1 0.035 0.021 -10000 0 -0.42 1 1
IL2RG 0.031 0.041 -10000 0 -0.42 4 4
G1/S transition of mitotic cell cycle -0.018 0.19 -10000 0 -0.53 43 43
PTPN11 0.036 0.004 -10000 0 -10000 0 0
CCND2 0.005 0.11 -10000 0 -0.68 13 13
LCK -0.017 0.14 -10000 0 -0.42 54 54
GRB2 0.033 0.011 -10000 0 -10000 0 0
IL2 0.033 0.036 -10000 0 -0.42 3 3
CDK6 0.025 0.054 -10000 0 -0.42 7 7
CCND3 0.025 0.13 0.4 1 -0.51 3 4
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.03 0.041 -10000 0 -0.42 4 4
RAS family/GTP/Tiam1 0.011 0.067 -10000 0 -0.27 19 19
NT3 (dimer)/TRKC 0.039 0.044 -10000 0 -0.3 7 7
NT3 (dimer)/TRKB 0.046 0.07 -10000 0 -0.26 21 21
SHC/Grb2/SOS1/GAB1/PI3K 0.014 0.052 -10000 0 -0.24 1 1
RAPGEF1 0.036 0.004 -10000 0 -10000 0 0
BDNF 0.03 0.024 -10000 0 -0.42 1 1
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
DYNLT1 0.033 0.01 -10000 0 -10000 0 0
NTRK1 0.025 0.032 -10000 0 -0.42 2 2
NTRK2 0.019 0.078 -10000 0 -0.42 15 15
NTRK3 0.031 0.012 -10000 0 -10000 0 0
NT-4/5 (dimer)/TRKB 0.033 0.055 -10000 0 -0.25 17 17
neuron apoptosis 0.003 0.14 0.31 56 -0.25 2 58
SHC 2-3/Grb2 -0.004 0.15 0.26 2 -0.33 56 58
SHC1 0.027 0.025 -10000 0 -0.42 1 1
SHC2 -0.036 0.18 0.24 2 -0.43 79 81
SHC3 0.019 0.11 0.24 3 -0.41 20 23
STAT3 (dimer) -0.017 0.13 -10000 0 -0.34 70 70
NT3 (dimer)/TRKA 0.042 0.054 -10000 0 -0.26 10 10
RIN/GDP 0.068 0.085 0.25 26 -0.26 6 32
GIPC1 0.033 0.035 -10000 0 -0.42 3 3
KRAS 0.027 0.057 -10000 0 -0.42 8 8
DNAJA3 0.007 0.055 0.21 18 -0.24 5 23
RIN/GTP 0.024 0.021 -10000 0 -0.3 2 2
CCND1 -0.079 0.24 -10000 0 -0.69 68 68
MAGED1 0.015 0.095 -10000 0 -0.42 23 23
PTPN11 0.036 0.004 -10000 0 -10000 0 0
RICS 0.023 0.061 -10000 0 -0.42 9 9
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.051 0.036 -10000 0 -0.26 1 1
GRB2 0.033 0.01 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.032 0.033 -10000 0 -0.25 4 4
TRKA/NEDD4-2 0.021 0.079 -10000 0 -0.3 26 26
ELMO1 0.035 0.006 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.041 0.039 -10000 0 -0.25 8 8
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.032 0.036 -10000 0 -0.42 3 3
DOCK1 0.027 0.057 -10000 0 -0.42 8 8
GAB2 0.031 0.013 -10000 0 -10000 0 0
RIT2 0.033 0.03 -10000 0 -0.42 2 2
RIT1 0.026 0.032 -10000 0 -0.42 2 2
FRS2 0.033 0.022 -10000 0 -0.42 1 1
DNM1 0.032 0.041 -10000 0 -0.42 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.023 -10000 0 -0.42 1 1
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.043 0.067 0.23 20 -0.23 5 25
mol:GDP 0.071 0.11 0.29 28 -0.39 6 34
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.026 0.005 -10000 0 -10000 0 0
RIT1/GDP 0.039 0.07 0.24 7 -0.25 5 12
TIAM1 0.028 0.057 -10000 0 -0.42 8 8
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
BDNF (dimer)/TRKB 0.052 0.064 -10000 0 -0.26 19 19
KIDINS220/CRKL/C3G 0.047 0.034 -10000 0 -0.3 4 4
SHC/RasGAP 0.035 0.046 -10000 0 -0.3 7 7
FRS2 family/SHP2 0.066 0.025 -10000 0 -0.26 1 1
SHC/GRB2/SOS1/GAB1 0.06 0.054 -10000 0 -0.24 6 6
RIT1/GTP 0.02 0.023 -10000 0 -0.3 2 2
NT3 (dimer) 0.024 0.054 -10000 0 -0.42 7 7
RAP1/GDP 0.048 0.067 0.18 18 -0.23 6 24
KIDINS220/CRKL 0.03 0.041 -10000 0 -0.42 4 4
BDNF (dimer) 0.03 0.024 -10000 0 -0.42 1 1
ubiquitin-dependent protein catabolic process 0.019 0.067 -10000 0 -0.25 26 26
Schwann cell development -0.007 0.013 -10000 0 -10000 0 0
EHD4 0.031 0.041 -10000 0 -0.42 4 4
FRS2 family/GRB2/SOS1 0.076 0.041 -10000 0 -0.44 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.024 0.06 -10000 0 -0.25 5 5
RAP1B 0.032 0.03 -10000 0 -0.42 2 2
RAP1A 0.03 0.05 -10000 0 -0.42 6 6
CDC42/GTP 0.043 0.069 -10000 0 -0.22 25 25
ABL1 0.035 0.005 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.047 0.023 -10000 0 -0.3 1 1
Rap1/GTP 0.022 0.091 -10000 0 -0.4 10 10
STAT3 -0.017 0.13 -10000 0 -0.34 70 70
axon guidance 0.026 0.06 -10000 0 -0.21 26 26
MAPK3 0.051 0.078 0.19 106 -0.23 5 111
MAPK1 0.052 0.078 0.19 108 -0.23 5 113
CDC42/GDP 0.069 0.086 0.24 31 -0.27 5 36
NTF3 0.024 0.054 -10000 0 -0.42 7 7
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.034 0.031 -10000 0 -0.25 3 3
PI3K 0.035 0.067 -10000 0 -0.3 18 18
FRS3 0.035 0.007 -10000 0 -10000 0 0
FAIM 0.034 0.021 -10000 0 -0.42 1 1
GAB1 0.027 0.061 -10000 0 -0.42 9 9
RASGRF1 0.007 0.06 0.22 18 -0.22 8 26
SOS1 0.034 0.021 -10000 0 -0.42 1 1
MCF2L 0.013 0.035 -10000 0 -0.26 8 8
RGS19 0.03 0.031 -10000 0 -0.42 2 2
CDC42 0.034 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.067 0.1 0.32 4 -0.39 6 10
Rac1/GDP 0.068 0.086 0.24 30 -0.27 5 35
NGF (dimer)/TRKA/GRIT 0.026 0.047 -10000 0 -0.25 11 11
neuron projection morphogenesis -0.001 0.19 0.44 2 -0.84 16 18
NGF (dimer)/TRKA/NEDD4-2 0.02 0.067 -10000 0 -0.25 26 26
MAP2K1 0.037 0.1 0.2 129 -0.22 6 135
NGFR 0.03 0.036 -10000 0 -0.42 3 3
NGF (dimer)/TRKA/GIPC/GAIP 0.017 0.044 -10000 0 -0.3 7 7
RAS family/GTP/PI3K 0.011 0.067 -10000 0 -0.24 29 29
FRS2 family/SHP2/GRB2/SOS1 0.088 0.047 -10000 0 -0.42 1 1
NRAS 0.029 0.05 -10000 0 -0.42 6 6
GRB2/SOS1 0.047 0.023 -10000 0 -0.3 1 1
PRKCI 0.024 0.067 -10000 0 -0.42 11 11
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.005 0.061 -10000 0 -0.42 6 6
RASA1 0.028 0.054 -10000 0 -0.42 7 7
TRKA/c-Abl 0.038 0.032 -10000 0 -0.3 2 2
SQSTM1 0.034 0.021 -10000 0 -0.42 1 1
BDNF (dimer)/TRKB/GIPC 0.067 0.065 -10000 0 -0.23 18 18
NGF (dimer)/TRKA/p62/Atypical PKCs 0.039 0.048 -10000 0 -0.22 11 11
MATK 0.031 0.031 -10000 0 -0.42 2 2
NEDD4L 0.006 0.11 -10000 0 -0.42 31 31
RAS family/GDP -0.012 0.036 -10000 0 -0.18 10 10
NGF (dimer)/TRKA 0.01 0.056 0.22 16 -0.25 5 21
Rac1/GTP -0.001 0.052 -10000 0 -0.22 14 14
FRS2 family/SHP2/CRK family 0.081 0.055 -10000 0 -0.22 6 6
LPA4-mediated signaling events

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
ADCY4 -0.015 0.037 -10000 0 -0.25 12 12
ADCY5 -0.013 0.038 -10000 0 -0.25 12 12
ADCY6 -0.011 0.024 -10000 0 -0.25 5 5
ADCY7 -0.01 0.025 -10000 0 -0.25 5 5
ADCY1 -0.011 0.022 -10000 0 -0.25 4 4
ADCY2 -0.028 0.069 -10000 0 -0.25 43 43
ADCY3 -0.014 0.036 -10000 0 -0.25 11 11
ADCY8 -0.008 0.019 -10000 0 -0.25 3 3
PRKCE 0.006 0.03 -10000 0 -0.3 5 5
ADCY9 -0.016 0.046 -10000 0 -0.27 16 16
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.022 0.084 0.21 35 -0.28 5 40
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.034 0.021 -10000 0 -0.42 1 1
SPHK1 0.005 0.11 -10000 0 -0.42 30 30
GNAI2 0.027 0.057 -10000 0 -0.42 8 8
mol:S1P 0.001 0.066 -10000 0 -0.27 26 26
GNAO1 0.03 0.014 -10000 0 -10000 0 0
mol:Sphinganine-1-P -0.004 0.075 -10000 0 -0.3 30 30
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.04 0.07 -10000 0 -0.22 24 24
GNAI3 0.035 0.006 -10000 0 -10000 0 0
G12/G13 0.043 0.036 -10000 0 -0.3 4 4
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0.011 0.099 -10000 0 -0.42 25 25
S1P1/S1P 0.022 0.091 0.18 3 -0.25 40 43
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 0.017 0.085 -10000 0 -0.42 18 18
S1P/S1P5/G12 0.029 0.067 -10000 0 -0.22 26 26
S1P/S1P3/Gq -0.003 0.095 -10000 0 -0.25 53 53
S1P/S1P4/Gi 0.002 0.095 -10000 0 -0.33 24 24
GNAQ 0 0 -10000 0 -10000 0 0
GNAZ 0.024 0.067 -10000 0 -0.42 11 11
GNA14 -0.01 0.13 -10000 0 -0.42 44 44
GNA15 0.029 0.046 -10000 0 -0.42 5 5
GNA12 0.035 0.006 -10000 0 -10000 0 0
GNA13 0.028 0.042 -10000 0 -0.42 4 4
GNA11 0.032 0.036 -10000 0 -0.42 3 3
ABCC1 0.029 0.042 -10000 0 -0.42 4 4
Aurora A signaling

Figure S93.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S93.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.032 0.056 -10000 0 -0.24 15 15
BIRC5 -0.003 0.12 -10000 0 -0.42 38 38
NFKBIA 0.013 0.052 0.25 15 -0.25 2 17
CPEB1 0.03 0.041 -10000 0 -0.42 4 4
AKT1 0.009 0.044 0.25 7 -0.25 3 10
NDEL1 0.032 0.011 -10000 0 -10000 0 0
Aurora A/BRCA1 0.028 0.047 -10000 0 -0.23 12 12
NDEL1/TACC3 0.041 0.049 -10000 0 -0.19 6 6
GADD45A 0.019 0.08 -10000 0 -0.42 16 16
GSK3B 0.038 0.016 -10000 0 -10000 0 0
PAK1/Aurora A 0.027 0.06 -10000 0 -0.24 18 18
MDM2 0.034 0.009 -10000 0 -10000 0 0
JUB 0.002 0.12 -10000 0 -0.42 36 36
TPX2 -0.008 0.084 -10000 0 -0.3 38 38
TP53 -0.005 0.093 -10000 0 -0.23 67 67
DLG7 -0.011 0.06 0.25 5 -0.23 11 16
AURKAIP1 0 0 -10000 0 -10000 0 0
ARHGEF7 0.032 0.011 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.044 0.052 -10000 0 -0.21 6 6
G2/M transition of mitotic cell cycle 0.027 0.047 -10000 0 -0.23 12 12
AURKA 0.023 0.035 -10000 0 -10000 0 0
AURKB 0 0.062 -10000 0 -0.18 43 43
CDC25B 0.013 0.048 -10000 0 -0.29 5 5
G2/M transition checkpoint 0.017 0.07 -10000 0 -0.22 36 36
mRNA polyadenylation 0.033 0.033 -10000 0 -0.2 4 4
Aurora A/CPEB 0.033 0.033 -10000 0 -0.2 4 4
Aurora A/TACC1/TRAP/chTOG 0.05 0.076 -10000 0 -0.24 22 22
BRCA1 0.021 0.07 -10000 0 -0.42 12 12
centrosome duplication 0.027 0.06 -10000 0 -0.24 18 18
regulation of centrosome cycle 0.04 0.048 -10000 0 -0.19 6 6
spindle assembly 0.048 0.075 -10000 0 -0.23 22 22
TDRD7 0.026 0.064 -10000 0 -0.42 10 10
Aurora A/RasGAP/Survivin 0.033 0.081 -10000 0 -0.21 28 28
CENPA -0.006 0.084 -10000 0 -0.28 43 43
Aurora A/PP2A 0.041 0.029 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.001 0.048 0.19 1 -0.32 2 3
negative regulation of DNA binding -0.006 0.097 -10000 0 -0.24 68 68
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.045 0.024 -10000 0 -0.3 1 1
RASA1 0.028 0.054 -10000 0 -0.42 7 7
Ajuba/Aurora A 0.018 0.07 -10000 0 -0.22 36 36
mitotic prometaphase 0.004 0.024 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.035 -10000 0 -10000 0 0
TACC1 0.012 0.087 -10000 0 -0.42 19 19
TACC3 0.017 0.087 -10000 0 -0.42 19 19
Aurora A/Antizyme1 0.036 0.025 -10000 0 -10000 0 0
Aurora A/RasGAP 0.037 0.044 -10000 0 -0.25 7 7
OAZ1 0.035 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 0.033 0.022 -10000 0 -0.42 1 1
GIT1/beta-PIX/PAK1 0.043 0.068 -10000 0 -0.27 18 18
Importin alpha/Importin beta/TPX2 -0.008 0.084 -10000 0 -0.3 38 38
PPP2R5D 0.035 0.007 -10000 0 -10000 0 0
Aurora A/TPX2 0.007 0.052 -10000 0 -0.2 8 8
PAK1 0.014 0.085 -10000 0 -0.42 18 18
CKAP5 0.035 0.006 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.014 0.096 -10000 0 -1 4 4
MKNK1 0.035 0.006 -10000 0 -10000 0 0
MAPK14 0.031 0.049 -10000 0 -0.3 4 4
ATF2/c-Jun -0.022 0.16 -10000 0 -0.55 40 40
MAPK11 0.03 0.047 -10000 0 -0.3 4 4
MITF 0.021 0.051 -10000 0 -0.36 6 6
MAPKAPK5 0.023 0.043 -10000 0 -0.33 4 4
KRT8 0.01 0.075 -10000 0 -0.29 25 25
MAPKAPK3 0.034 0.008 -10000 0 -10000 0 0
MAPKAPK2 0.025 0.043 -10000 0 -0.42 4 4
p38alpha-beta/CK2 0.041 0.064 -10000 0 -0.43 4 4
CEBPB 0.018 0.053 -10000 0 -0.32 9 9
SLC9A1 0.023 0.042 -10000 0 -0.33 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.016 0.072 0.23 1 -0.3 11 12
p38alpha-beta/MNK1 0.056 0.06 -10000 0 -0.36 3 3
JUN -0.025 0.16 -10000 0 -0.55 40 40
PPARGC1A 0.016 0.068 -10000 0 -0.34 13 13
USF1 0.012 0.057 -10000 0 -0.29 13 13
RAB5/GDP/GDI1 0.024 0.053 -10000 0 -0.23 5 5
NOS2 0.016 0.042 -10000 0 -0.34 4 4
DDIT3 0.023 0.045 -10000 0 -0.32 5 5
RAB5A 0.035 0.006 -10000 0 -10000 0 0
HSPB1 -0.012 0.086 0.28 3 -0.26 48 51
p38alpha-beta/HBP1 0.053 0.067 -10000 0 -0.32 7 7
CREB1 0.014 0.062 -10000 0 -0.3 10 10
RAB5/GDP 0.026 0.004 -10000 0 -10000 0 0
EIF4E 0.015 0.044 0.24 2 -0.32 3 5
RPS6KA4 0.022 0.048 -10000 0 -0.36 5 5
PLA2G4A 0 0.066 -10000 0 -0.28 21 21
GDI1 0.023 0.045 -10000 0 -0.32 5 5
TP53 -0.001 0.062 -10000 0 -0.33 9 9
RPS6KA5 0.009 0.075 -10000 0 -0.28 26 26
ESR1 -0.054 0.14 -10000 0 -0.28 130 130
HBP1 0.032 0.036 -10000 0 -0.42 3 3
MEF2C 0.01 0.081 -10000 0 -0.33 23 23
MEF2A 0.022 0.044 -10000 0 -0.32 5 5
EIF4EBP1 0.009 0.066 -10000 0 -0.31 12 12
KRT19 -0.003 0.092 -10000 0 -0.28 43 43
ELK4 0.018 0.041 -10000 0 -0.31 4 4
ATF6 0.017 0.043 -10000 0 -0.32 5 5
ATF1 0.015 0.063 -10000 0 -0.3 10 10
p38alpha-beta/MAPKAPK2 0.042 0.069 -10000 0 -0.36 6 6
p38alpha-beta/MAPKAPK3 0.054 0.062 -10000 0 -0.35 4 4
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.041 0.018 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.035 0.007 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.017 0.078 -10000 0 -0.42 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.029 0.024 -10000 0 -0.42 1 1
RAC1-CDC42/GTP/PAK family 0.002 0.064 -10000 0 -0.21 38 38
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.029 0.05 -10000 0 -0.42 6 6
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.031 0.012 -10000 0 -10000 0 0
FYN 0.027 0.05 -10000 0 -0.42 6 6
MAP3K12 0.036 0.004 -10000 0 -10000 0 0
FGR 0.034 0.008 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.004 0.14 0.2 1 -0.34 49 50
PRKG1 0.035 0.005 -10000 0 -10000 0 0
DUSP8 0.02 0.08 -10000 0 -0.42 16 16
PGK/cGMP/p38 alpha -0.008 0.14 -10000 0 -0.35 44 44
apoptosis -0.005 0.13 0.2 1 -0.33 49 50
RAL/GTP 0.044 0.028 -10000 0 -0.25 4 4
LYN 0.03 0.014 -10000 0 -10000 0 0
DUSP1 0.001 0.12 -10000 0 -0.42 35 35
PAK1 0.014 0.085 -10000 0 -0.42 18 18
SRC 0.032 0.03 -10000 0 -0.42 2 2
RAC1/OSM/MEKK3/MKK3 0.072 0.04 -10000 0 -0.24 1 1
TRAF6 0.034 0.021 -10000 0 -0.42 1 1
RAC1 0.035 0.006 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.035 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.045 0.013 -10000 0 -10000 0 0
MAPK11 -0.014 0.14 0.23 2 -0.39 37 39
BLK 0.021 0.038 -10000 0 -0.42 3 3
HCK 0.017 0.087 -10000 0 -0.42 19 19
MAP2K3 0.032 0.023 -10000 0 -0.42 1 1
DUSP16 0.029 0.046 -10000 0 -0.42 5 5
DUSP10 0.012 0.082 -10000 0 -0.42 17 17
TRAF6/MEKK3 0.039 0.02 -10000 0 -0.23 1 1
MAP3K7IP1 0.034 0.009 -10000 0 -10000 0 0
MAPK14 -0.017 0.14 0.2 5 -0.36 53 58
positive regulation of innate immune response -0.018 0.17 0.26 2 -0.42 48 50
LCK -0.018 0.14 -10000 0 -0.42 54 54
p38alpha-beta/MKP7 -0.006 0.16 0.27 2 -0.4 47 49
p38alpha-beta/MKP5 -0.012 0.16 0.27 1 -0.41 45 46
PGK/cGMP 0.026 0.004 -10000 0 -10000 0 0
PAK2 0.036 0 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.018 0.17 0.27 2 -0.42 51 53
CDC42 0.034 0.008 -10000 0 -10000 0 0
RALB 0.032 0.041 -10000 0 -0.42 4 4
RALA 0.035 0.007 -10000 0 -10000 0 0
PAK3 0.016 0.083 -10000 0 -0.42 17 17
Glypican 2 network

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
MDK 0.017 0.085 -9999 0 -0.42 18 18
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine 0.013 0.06 -9999 0 -0.3 18 18
neuron projection morphogenesis 0.013 0.06 -9999 0 -0.3 18 18
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.014 0.057 -10000 0 -0.2 26 26
TRAF2/ASK1 0.029 0.065 -10000 0 -0.25 24 24
ATM 0.031 0.013 -10000 0 -10000 0 0
MAP2K3 -0.05 0.16 0.28 2 -0.4 59 61
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.04 0.14 0.29 1 -0.35 53 54
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.026 0.064 -10000 0 -0.42 10 10
TXN 0.009 0.002 -10000 0 -10000 0 0
CALM1 0.035 0.007 -10000 0 -10000 0 0
GADD45A 0.019 0.08 -10000 0 -0.42 16 16
GADD45B 0.024 0.067 -10000 0 -0.42 11 11
MAP3K1 0.01 0.099 -10000 0 -0.42 25 25
MAP3K6 0.034 0.022 -10000 0 -0.42 1 1
MAP3K7 0.033 0.01 -10000 0 -10000 0 0
MAP3K4 0.033 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.032 0.074 -10000 0 -0.3 23 23
TAK1/TAB family 0.014 0.037 -10000 0 -0.25 6 6
RAC1/OSM/MEKK3 0.058 0.026 -10000 0 -10000 0 0
TRAF2 0.033 0.029 -10000 0 -0.42 2 2
RAC1/OSM/MEKK3/MKK3 -0.017 0.13 -10000 0 -0.32 46 46
TRAF6 0.015 0.024 -10000 0 -0.29 3 3
RAC1 0.035 0.006 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.014 0.13 -10000 0 -0.42 49 49
CCM2 0.035 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.013 0.088 -10000 0 -0.25 49 49
MAPK11 0.033 0.01 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.017 0.1 -10000 0 -0.23 69 69
OSM/MEKK3 0.045 0.019 -10000 0 -10000 0 0
TAOK1 0.012 0.031 -10000 0 -0.29 5 5
TAOK2 0.015 0.008 -10000 0 -10000 0 0
TAOK3 0.015 0.015 -10000 0 -0.29 1 1
MAP3K7IP1 0.034 0.009 -10000 0 -10000 0 0
MAPK14 0.035 0.005 -10000 0 -10000 0 0
MAP3K7IP2 0.031 0.03 -10000 0 -0.42 2 2
MAP3K5 0.013 0.093 -10000 0 -0.42 22 22
MAP3K10 0.022 0.075 -10000 0 -0.42 14 14
MAP3K3 0.031 0.012 -10000 0 -10000 0 0
TRX/ASK1 0.017 0.059 -10000 0 -0.21 29 29
GADD45/MTK1/MTK1 0.054 0.082 -10000 0 -0.23 33 33
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.045 0.038 -10000 0 -0.3 5 5
CRKL 0.007 0.1 0.32 1 -0.46 14 15
mol:PIP3 0.01 0.066 0.39 9 -0.84 1 10
AKT1 0.021 0.084 0.3 7 -0.74 1 8
PTK2B 0.028 0.015 -10000 0 -10000 0 0
RAPGEF1 0.004 0.096 0.3 1 -0.45 13 14
RANBP10 0.029 0.014 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
HGF/MET/SHIP2 0.054 0.059 -10000 0 -0.26 15 15
MAP3K5 0.001 0.11 0.26 1 -0.43 15 16
HGF/MET/CIN85/CBL/ENDOPHILINS 0.064 0.073 -10000 0 -0.25 20 20
AP1 -0.024 0.13 -10000 0 -0.3 89 89
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.027 0.025 -10000 0 -0.42 1 1
apoptosis -0.14 0.34 -10000 0 -0.77 111 111
STAT3 (dimer) 0.01 0.069 -10000 0 -0.31 6 6
GAB1/CRKL/SHP2/PI3K 0.042 0.12 0.32 1 -0.42 14 15
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.024 0.095 -10000 0 -0.43 13 13
PTPN11 0.036 0.004 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.033 0.009 -10000 0 -10000 0 0
PTEN 0.027 0.061 -10000 0 -0.42 9 9
ELK1 -0.002 0.071 0.24 27 -10000 0 27
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.013 0.046 -10000 0 -0.21 5 5
PAK1 0.027 0.1 0.37 12 -0.71 1 13
HGF/MET/RANBP10 0.049 0.057 -10000 0 -0.25 13 13
HRAS 0.012 0.1 -10000 0 -0.47 16 16
DOCK1 0.003 0.097 0.3 2 -0.44 13 15
GAB1 0.008 0.1 -10000 0 -0.48 14 14
CRK 0.005 0.095 -10000 0 -0.44 14 14
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.017 0.1 -10000 0 -0.46 16 16
JUN -0.001 0.12 -10000 0 -0.42 39 39
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.006 0.045 -10000 0 -0.21 18 18
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
cell morphogenesis 0.007 0.1 0.34 4 -0.37 6 10
GRB2/SHC 0.032 0.054 -10000 0 -0.21 9 9
FOS -0.031 0.15 -10000 0 -0.42 66 66
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility -0.002 0.071 0.24 27 -10000 0 27
HGF/MET/MUC20 0.038 0.048 -10000 0 -0.25 13 13
cell migration 0.031 0.053 -10000 0 -0.21 9 9
GRB2 0.033 0.01 -10000 0 -10000 0 0
CBL 0.031 0.012 -10000 0 -10000 0 0
MET/RANBP10 0.038 0.04 -10000 0 -0.3 5 5
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.006 0.061 -10000 0 -0.23 16 16
MET/MUC20 0.021 0.033 -10000 0 -0.3 5 5
RAP1B 0.008 0.097 0.28 5 -0.42 12 17
RAP1A 0 0.096 0.28 1 -0.43 15 16
HGF/MET/RANBP9 0.058 0.055 -10000 0 -0.26 13 13
RAF1 0.016 0.1 -10000 0 -0.46 15 15
STAT3 0.009 0.068 -10000 0 -0.31 6 6
cell proliferation 0.042 0.1 0.28 21 -0.32 9 30
RPS6KB1 0.007 0.05 -10000 0 -0.28 11 11
MAPK3 -0.018 0.082 0.58 7 -10000 0 7
MAPK1 0.007 0.15 0.65 26 -10000 0 26
RANBP9 0.035 0.007 -10000 0 -10000 0 0
MAPK8 0.011 0.1 -10000 0 -0.4 15 15
SRC 0.008 0.062 -10000 0 -0.26 5 5
PI3K 0.031 0.077 -10000 0 -0.23 26 26
MET/Glomulin 0.019 0.041 -10000 0 -0.25 6 6
SOS1 0.034 0.021 -10000 0 -0.42 1 1
MAP2K1 0.014 0.098 -10000 0 -0.43 15 15
MET 0.029 0.046 -10000 0 -0.42 5 5
MAP4K1 0.008 0.1 0.28 1 -0.46 14 15
PTK2 0.027 0.015 -10000 0 -10000 0 0
MAP2K2 0.013 0.099 -10000 0 -0.42 16 16
BAD 0.016 0.081 0.33 4 -0.71 1 5
MAP2K4 -0.001 0.099 0.25 1 -0.4 15 16
SHP2/GRB2/SOS1/GAB1 0.044 0.095 -10000 0 -0.4 13 13
INPPL1 0.03 0.036 -10000 0 -0.42 3 3
PXN 0.036 0.004 -10000 0 -10000 0 0
SH3KBP1 0.027 0.061 -10000 0 -0.42 9 9
HGS -0.001 0.041 -10000 0 -0.19 20 20
PLCgamma1/PKC 0.025 0.007 -10000 0 -10000 0 0
HGF 0.028 0.057 -10000 0 -0.42 8 8
RASA1 0.028 0.054 -10000 0 -0.42 7 7
NCK1 0.034 0.022 -10000 0 -0.42 1 1
PTPRJ 0.03 0.046 -10000 0 -0.42 5 5
NCK/PLCgamma1 0.046 0.055 -10000 0 -0.19 20 20
PDPK1 0.025 0.087 0.31 11 -0.78 1 12
HGF/MET/SHIP 0.038 0.048 -10000 0 -0.25 13 13
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.034 0.021 -10000 0 -0.42 1 1
HDAC3 0.035 0.005 -10000 0 -10000 0 0
VDR 0.02 0.083 -10000 0 -0.42 17 17
Cbp/p300/PCAF 0.04 0.023 -10000 0 -0.24 1 1
EP300 0.033 0.022 -10000 0 -0.42 1 1
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.014 0.056 0.19 1 -0.31 4 5
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.035 0.005 -10000 0 -10000 0 0
AKT1 0.027 0.093 0.21 56 -0.23 18 74
RAR alpha/9cRA/Cyclin H 0.045 0.1 0.26 1 -0.35 7 8
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.019 0.064 -10000 0 -0.22 17 17
CDC2 0.01 0.094 -10000 0 -0.42 22 22
response to UV -0.002 0.008 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.03 0.062 -10000 0 -0.29 8 8
NCOR2 0.036 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.015 0.058 -10000 0 -0.3 17 17
RXRs/RARs/NRIP1/9cRA -0.004 0.19 -10000 0 -0.53 52 52
NCOA2 0.025 0.047 -10000 0 -0.42 5 5
NCOA3 0.03 0.036 -10000 0 -0.42 3 3
NCOA1 0.031 0.045 -10000 0 -0.42 5 5
VDR/VDR/DNA 0.02 0.082 -10000 0 -0.42 17 17
RARG 0.031 0.018 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.046 0.01 -10000 0 -10000 0 0
MAPK3 0.026 0.029 -10000 0 -0.42 1 1
MAPK1 0.033 0.022 -10000 0 -0.42 1 1
MAPK8 0.027 0.041 -10000 0 -0.42 3 3
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.027 0.13 -10000 0 -0.43 11 11
RARA 0.009 0.047 -10000 0 -0.23 12 12
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.015 0.054 -10000 0 -0.2 13 13
PRKCA 0.024 0.032 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.008 0.2 -10000 0 -0.57 52 52
RXRG 0.01 0.047 -10000 0 -0.3 7 7
RXRA 0.016 0.09 -10000 0 -0.34 7 7
RXRB 0.017 0.037 -10000 0 -0.28 2 2
VDR/Vit D3/DNA 0.015 0.058 -10000 0 -0.3 17 17
RBP1 -0.028 0.15 -10000 0 -0.42 67 67
CRBP1/9-cic-RA -0.019 0.11 -10000 0 -0.3 67 67
RARB 0.011 0.09 -10000 0 -0.42 20 20
PRKCG 0.028 0.032 -10000 0 -10000 0 0
MNAT1 0.035 0.007 -10000 0 -10000 0 0
RAR alpha/RXRs 0.004 0.14 0.41 1 -0.42 17 18
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.029 0.11 0.27 1 -0.37 11 12
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.075 0.23 1 -0.31 7 8
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.008 0.2 -10000 0 -0.58 52 52
positive regulation of DNA binding 0.033 0.095 -10000 0 -0.33 7 7
NRIP1 -0.071 0.38 -10000 0 -1.2 51 51
RXRs/RARs 0.011 0.16 0.33 1 -0.42 46 47
RXRs/RXRs/DNA/9cRA -0.008 0.11 -10000 0 -0.38 10 10
PRKACA 0.036 0.004 -10000 0 -10000 0 0
CDK7 0.034 0.008 -10000 0 -10000 0 0
TFIIH 0.067 0.025 -10000 0 -0.24 1 1
RAR alpha/9cRA 0.065 0.067 -10000 0 -0.22 4 4
CCNH 0.034 0.022 -10000 0 -0.42 1 1
CREBBP 0.032 0.011 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.064 0.028 -10000 0 -0.2 1 1
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.045 0.046 -10000 0 -0.3 8 8
FBXW11 0.034 0.021 -10000 0 -0.42 1 1
NF kappa B1 p50/c-Rel 0.026 0.039 -10000 0 -0.25 8 8
NF kappa B1 p50/RelA/I kappa B alpha 0.004 0.099 -10000 0 -0.34 18 18
NFKBIA -0.014 0.1 -10000 0 -0.24 73 73
MAPK14 0.035 0.005 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.03 0.021 -10000 0 -0.26 1 1
ARRB2 0.017 0.006 -10000 0 -10000 0 0
REL 0.024 0.07 -10000 0 -0.42 12 12
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.026 0.037 -10000 0 -0.25 7 7
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.03 0.017 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
NF kappa B1 p50 dimer 0.023 0.021 0.26 3 -10000 0 3
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
NFKB1 0.013 0.007 -10000 0 -10000 0 0
RELA 0.035 0.006 -10000 0 -10000 0 0
positive regulation of anti-apoptosis -0.004 0.099 -10000 0 -0.3 26 26
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.004 0.1 -10000 0 -0.35 18 18
SRC 0.032 0.03 -10000 0 -0.42 2 2
PI3K 0.035 0.067 -10000 0 -0.3 18 18
NF kappa B1 p50/RelA -0.003 0.098 -10000 0 -0.3 25 25
IKBKB 0.029 0.014 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.034 0.021 -10000 0 -0.42 1 1
SYK 0.005 0.11 -10000 0 -0.42 33 33
I kappa B alpha/PIK3R1 -0.008 0.12 -10000 0 -0.37 25 25
cell death 0.003 0.097 -10000 0 -0.33 18 18
NF kappa B1 p105/c-Rel 0.026 0.039 -10000 0 -0.25 8 8
LCK -0.018 0.14 -10000 0 -0.42 54 54
BCL3 0.028 0.057 -10000 0 -0.42 8 8
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.014 -10000 0 -10000 0 0
CDC42/GTP 0.002 0.087 -10000 0 -0.26 22 22
PLCG1 -0.009 0.073 -10000 0 -0.28 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.027 0.057 -10000 0 -0.42 8 8
GNAI3 0.035 0.006 -10000 0 -10000 0 0
G12/G13 0.043 0.036 -10000 0 -0.3 4 4
cell migration 0.002 0.085 -10000 0 -0.26 22 22
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.007 0.07 -10000 0 -0.28 18 18
MAPK1 -0.005 0.071 -10000 0 -0.28 19 19
S1P/S1P5/Gi 0 0.077 -10000 0 -0.24 40 40
GNAI1 0.017 0.085 -10000 0 -0.42 18 18
CDC42/GDP 0.025 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.024 0.004 -10000 0 -10000 0 0
RHOA 0.031 0.07 0.19 60 -0.24 12 72
S1P/S1P4/Gi 0 0.077 -10000 0 -0.24 40 40
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.024 0.067 -10000 0 -0.42 11 11
S1P/S1P4/G12/G13 0.037 0.029 -10000 0 -0.23 4 4
GNA12 0.035 0.006 -10000 0 -10000 0 0
GNA13 0.028 0.042 -10000 0 -0.42 4 4
CDC42 0.034 0.008 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.002 0.09 0.26 28 -10000 0 28
GNAI2 0.027 0.057 -10000 0 -0.42 8 8
S1P/S1P5/G12 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.014 -10000 0 -10000 0 0
RhoA/GTP -0.001 0.092 -10000 0 -0.26 28 28
negative regulation of cAMP metabolic process 0 0.077 -10000 0 -0.24 40 40
GNAZ 0.024 0.067 -10000 0 -0.42 11 11
GNAI3 0.035 0.006 -10000 0 -10000 0 0
GNA12 0.035 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 0.077 -10000 0 -0.24 40 40
RhoA/GDP 0.02 0.043 -10000 0 -0.3 9 9
RHOA 0.026 0.061 -10000 0 -0.42 9 9
GNAI1 0.017 0.085 -10000 0 -0.42 18 18
Effects of Botulinum toxin

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
STX1A 0.008 0.002 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.046 0.027 -10000 0 -0.3 2 2
STXBP1 0.035 0.005 -10000 0 -10000 0 0
ACh/CHRNA1 0.015 0.046 -10000 0 -0.14 23 23
RAB3GAP2/RIMS1/UNC13B 0.051 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 0.031 0.012 -10000 0 -10000 0 0
mol:ACh -0.005 0.03 0.087 4 -0.11 18 22
RAB3GAP2 0.028 0.025 -10000 0 -0.42 1 1
STX1A/SNAP25/VAMP2 0.033 0.057 -10000 0 -0.18 3 3
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.015 0.046 -10000 0 -0.14 23 23
UNC13B 0.032 0.03 -10000 0 -0.42 2 2
CHRNA1 0.029 0.054 -10000 0 -0.42 7 7
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.044 0.11 -10000 0 -0.27 98 98
SNAP25 -0.001 0.043 -10000 0 -0.26 14 14
VAMP2 0.005 0.011 -10000 0 -0.23 1 1
SYT1 -0.064 0.18 -10000 0 -0.42 98 98
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.032 0.007 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.033 0.057 -10000 0 -0.18 3 3
S1P3 pathway

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
PDGFRB 0.028 0.057 -9999 0 -0.42 8 8
mol:S1P 0.001 0.002 -9999 0 -0.026 2 2
S1P1/S1P/Gi -0.017 0.11 -9999 0 -0.3 43 43
GNAO1 0.03 0.015 -9999 0 -10000 0 0
S1P/S1P3/G12/G13 0.039 0.03 -9999 0 -0.23 4 4
AKT1 0.004 0.12 -9999 0 -0.47 27 27
AKT3 -0.001 0.11 -9999 0 -0.78 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.028 0.057 -9999 0 -0.42 8 8
GNAI2 0.028 0.058 -9999 0 -0.42 8 8
GNAI3 0.036 0.008 -9999 0 -10000 0 0
GNAI1 0.018 0.085 -9999 0 -0.42 18 18
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.001 0.002 -9999 0 -0.03 2 2
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0.011 0.099 -9999 0 -0.42 25 25
mol:Ca2+ 0.006 0.08 -9999 0 -0.3 20 20
MAPK3 -0.002 0.073 -9999 0 -0.33 12 12
MAPK1 0 0.074 -9999 0 -0.32 14 14
JAK2 -0.013 0.1 -9999 0 -0.34 26 26
CXCR4 -0.016 0.1 -9999 0 -0.35 26 26
FLT1 0.028 0.055 -9999 0 -0.42 7 7
RhoA/GDP 0.02 0.043 -9999 0 -0.3 9 9
Rac1/GDP 0.026 0.004 -9999 0 -10000 0 0
SRC -0.004 0.079 -9999 0 -0.34 15 15
S1P/S1P3/Gi 0.006 0.081 -9999 0 -0.31 20 20
RAC1 0.035 0.006 -9999 0 -10000 0 0
RhoA/GTP 0.005 0.094 -9999 0 -0.3 19 19
VEGFA 0.002 0.003 -9999 0 -0.04 2 2
S1P/S1P2/Gi 0.004 0.079 -9999 0 -0.29 22 22
VEGFR1 homodimer/VEGFA homodimer 0.025 0.04 -9999 0 -0.27 8 8
RHOA 0.026 0.061 -9999 0 -0.42 9 9
S1P/S1P3/Gq -0.007 0.08 -9999 0 -0.23 51 51
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.024 0.067 -9999 0 -0.42 11 11
G12/G13 0.043 0.036 -9999 0 -0.3 4 4
GNA14 -0.01 0.13 -9999 0 -0.42 44 44
GNA15 0.029 0.046 -9999 0 -0.42 5 5
GNA12 0.035 0.006 -9999 0 -10000 0 0
GNA13 0.028 0.042 -9999 0 -0.42 4 4
GNA11 0.032 0.036 -9999 0 -0.42 3 3
Rac1/GTP 0.008 0.09 -9999 0 -0.31 16 16
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.025 0.16 -10000 0 -0.81 12 12
NCK1/PAK1/Dok-R -0.027 0.074 -10000 0 -0.4 12 12
NCK1/Dok-R 0.033 0.14 -10000 0 -0.89 8 8
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
mol:beta2-estradiol -0.007 0.015 0.31 1 -10000 0 1
RELA 0.035 0.006 -10000 0 -10000 0 0
SHC1 0.028 0.025 -10000 0 -0.42 1 1
Rac/GDP 0.026 0.004 -10000 0 -10000 0 0
F2 0.011 0.025 -10000 0 -10000 0 0
TNIP2 0.032 0.03 -10000 0 -0.42 2 2
NF kappa B/RelA 0.064 0.14 -10000 0 -0.79 9 9
FN1 -0.009 0.13 -10000 0 -0.42 48 48
PLD2 0.02 0.13 -10000 0 -0.85 9 9
PTPN11 0.036 0.004 -10000 0 -10000 0 0
GRB14 -0.063 0.18 -10000 0 -0.42 98 98
ELK1 0.024 0.13 -10000 0 -0.78 10 10
GRB7 0.024 0.058 -10000 0 -0.42 8 8
PAK1 0.014 0.085 -10000 0 -0.42 18 18
Tie2/Ang1/alpha5/beta1 Integrin 0.042 0.16 -10000 0 -0.88 9 9
CDKN1A 0.002 0.19 -10000 0 -0.74 24 24
ITGA5 0.033 0.035 -10000 0 -0.42 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.029 0.15 -10000 0 -0.86 9 9
CRK 0.031 0.023 -10000 0 -0.42 1 1
mol:NO 0.028 0.13 -10000 0 -0.58 12 12
PLG 0.02 0.13 -10000 0 -0.85 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.018 0.15 -10000 0 -0.81 10 10
GRB2 0.033 0.01 -10000 0 -10000 0 0
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
ANGPT2 -0.055 0.21 -10000 0 -0.77 21 21
BMX 0.009 0.15 -10000 0 -0.94 10 10
ANGPT1 0.015 0.034 -10000 0 -10000 0 0
tube development -0.001 0.16 -10000 0 -0.67 17 17
ANGPT4 0.033 0.03 -10000 0 -0.42 2 2
response to hypoxia 0 0.01 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.008 0.16 -10000 0 -0.88 9 9
alpha5/beta1 Integrin 0.047 0.037 -10000 0 -0.3 5 5
FGF2 -0.002 0.11 -10000 0 -0.42 34 34
STAT5A (dimer) 0 0.2 -10000 0 -0.77 22 22
mol:L-citrulline 0.028 0.13 -10000 0 -0.58 12 12
AGTR1 -0.044 0.16 -10000 0 -0.42 78 78
MAPK14 0.021 0.18 -10000 0 -1.1 11 11
Tie2/SHP2 0.013 0.17 -10000 0 -0.88 11 11
TEK 0.007 0.17 -10000 0 -0.96 11 11
RPS6KB1 0.038 0.16 -10000 0 -0.81 11 11
Angiotensin II/AT1 -0.029 0.12 -10000 0 -0.3 78 78
Tie2/Ang1/GRB2 0.035 0.14 -10000 0 -0.85 9 9
MAPK3 0.026 0.13 -10000 0 -0.78 9 9
MAPK1 0.016 0.12 -10000 0 -0.8 9 9
Tie2/Ang1/GRB7 0.03 0.14 -10000 0 -0.86 9 9
NFKB1 0.035 0.005 -10000 0 -10000 0 0
MAPK8 0.021 0.13 -10000 0 -0.85 9 9
PI3K 0.022 0.18 -10000 0 -0.94 12 12
FES 0.016 0.19 -10000 0 -1 13 13
Crk/Dok-R 0.031 0.15 -10000 0 -0.86 9 9
Tie2/Ang1/ABIN2 0.036 0.14 -10000 0 -0.86 9 9
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.028 0.15 -10000 0 -0.71 13 13
STAT5A 0.028 0.037 -10000 0 -0.42 3 3
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.057 0.17 -10000 0 -0.79 10 10
Tie2/Ang2 -0.009 0.21 -10000 0 -1 13 13
Tie2/Ang1 0.027 0.14 -10000 0 -0.9 9 9
FOXO1 0.028 0.15 -10000 0 -0.72 13 13
ELF1 0.034 0.054 -10000 0 -0.32 9 9
ELF2 0.027 0.13 -10000 0 -0.85 9 9
mol:Choline 0.02 0.12 -10000 0 -0.82 9 9
cell migration -0.013 0.051 -10000 0 -0.22 15 15
FYN -0.005 0.18 -10000 0 -0.81 15 15
DOK2 0.01 0.085 -10000 0 -0.42 18 18
negative regulation of cell cycle 0.006 0.17 -10000 0 -0.66 24 24
ETS1 0.035 0.028 -10000 0 -0.43 1 1
PXN 0.057 0.15 0.39 1 -0.64 11 12
ITGB1 0.033 0.03 -10000 0 -0.42 2 2
NOS3 0.026 0.14 -10000 0 -0.66 12 12
RAC1 0.035 0.006 -10000 0 -10000 0 0
TNF 0.033 0.065 -10000 0 -0.42 10 10
MAPKKK cascade 0.02 0.12 -10000 0 -0.82 9 9
RASA1 0.028 0.054 -10000 0 -0.42 7 7
Tie2/Ang1/Shc 0.029 0.14 -10000 0 -0.9 8 8
NCK1 0.034 0.022 -10000 0 -0.42 1 1
vasculogenesis 0.029 0.12 -10000 0 -0.52 12 12
mol:Phosphatidic acid 0.02 0.12 -10000 0 -0.82 9 9
mol:Angiotensin II 0.001 0.002 -10000 0 -10000 0 0
mol:NADP 0.028 0.13 -10000 0 -0.58 12 12
Rac1/GTP 0.036 0.15 -10000 0 -0.74 12 12
MMP2 0.013 0.14 -10000 0 -0.97 8 8
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.039 0.048 0.31 6 -10000 0 6
KIRREL 0.025 0.053 -10000 0 -0.43 6 6
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.039 0.048 -10000 0 -0.31 6 6
PLCG1 0.033 0.009 -10000 0 -10000 0 0
ARRB2 0.032 0.011 -10000 0 -10000 0 0
WASL 0.029 0.054 -10000 0 -0.42 7 7
Nephrin/NEPH1/podocin/CD2AP 0.064 0.057 -10000 0 -0.24 6 6
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.021 0.044 -10000 0 -0.21 12 12
FYN 0.059 0.1 0.28 70 -0.21 11 81
mol:Ca2+ 0.057 0.056 -10000 0 -0.24 6 6
mol:DAG 0.058 0.057 -10000 0 -0.24 6 6
NPHS2 0.03 0.029 -10000 0 -0.43 1 1
mol:IP3 0.058 0.057 -10000 0 -0.24 6 6
regulation of endocytosis 0.046 0.055 -10000 0 -0.2 11 11
Nephrin/NEPH1/podocin/Cholesterol 0.048 0.049 -10000 0 -0.24 6 6
establishment of cell polarity 0.039 0.048 -10000 0 -0.31 6 6
Nephrin/NEPH1/podocin/NCK1-2 0.075 0.064 -10000 0 -0.22 7 7
Nephrin/NEPH1/beta Arrestin2 0.051 0.058 -10000 0 -0.2 11 11
NPHS1 0.041 0.03 -10000 0 -0.39 1 1
Nephrin/NEPH1/podocin 0.048 0.055 0.2 12 -0.21 11 23
TJP1 0.031 0.036 -10000 0 -0.42 3 3
NCK1 0.034 0.022 -10000 0 -0.42 1 1
NCK2 0.036 0.004 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.06 0.058 -10000 0 -0.24 6 6
CD2AP 0.035 0.007 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.06 0.057 -10000 0 -0.24 6 6
GRB2 0.033 0.01 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.058 0.11 0.29 70 -0.23 11 81
cytoskeleton organization 0.023 0.068 0.24 31 -0.25 6 37
Nephrin/NEPH1 0.033 0.036 -10000 0 -0.21 6 6
Nephrin/NEPH1/ZO-1 0.05 0.054 -10000 0 -0.25 9 9
BARD1 signaling events

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
BARD1/CSTF1 0.044 0.036 -10000 0 -0.3 4 4
ATM 0.031 0.013 -10000 0 -10000 0 0
UBE2D3 0.035 0.005 -10000 0 -10000 0 0
PRKDC 0.029 0.031 -10000 0 -0.42 2 2
ATR 0.035 0.006 -10000 0 -10000 0 0
UBE2L3 0.034 0.009 -10000 0 -10000 0 0
FANCD2 0.023 0.011 -10000 0 -10000 0 0
protein ubiquitination 0.059 0.072 -10000 0 -0.23 20 20
XRCC5 0.036 0.004 -10000 0 -10000 0 0
XRCC6 0.033 0.009 -10000 0 -10000 0 0
M/R/N Complex 0.047 0.044 -10000 0 -0.26 4 4
MRE11A 0.031 0.012 -10000 0 -10000 0 0
DNA-PK 0.056 0.036 -10000 0 -0.25 2 2
FA complex/FANCD2/Ubiquitin 0.001 0.097 -10000 0 -0.42 12 12
FANCF 0.031 0.041 -10000 0 -0.42 4 4
BRCA1 0.021 0.07 -10000 0 -0.42 12 12
CCNE1 0.027 0.046 -10000 0 -0.42 5 5
CDK2/Cyclin E1 0.044 0.045 -10000 0 -0.34 6 6
FANCG 0.035 0.006 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.037 0.062 -10000 0 -0.3 15 15
FANCE 0.032 0.036 -10000 0 -0.42 3 3
FANCC 0.034 0.021 -10000 0 -0.42 1 1
NBN 0.027 0.025 -10000 0 -0.42 1 1
FANCA 0.015 0.067 -10000 0 -0.42 11 11
DNA repair -0.016 0.12 0.28 3 -0.35 16 19
BRCA1/BARD1/ubiquitin 0.037 0.062 -10000 0 -0.3 15 15
BARD1/DNA-PK 0.069 0.049 -10000 0 -0.23 5 5
FANCL 0.035 0.006 -10000 0 -10000 0 0
mRNA polyadenylation -0.044 0.035 0.3 4 -10000 0 4
BRCA1/BARD1/CTIP/M/R/N Complex 0.017 0.08 -10000 0 -0.22 38 38
BRCA1/BACH1/BARD1/TopBP1 0.054 0.06 -10000 0 -0.26 15 15
BRCA1/BARD1/P53 0.049 0.091 -10000 0 -0.25 35 35
BARD1/CSTF1/BRCA1 0.049 0.06 -10000 0 -0.26 14 14
BRCA1/BACH1 0.021 0.07 -10000 0 -0.42 12 12
BARD1 0.033 0.035 -10000 0 -0.42 3 3
PCNA 0.03 0.041 -10000 0 -0.42 4 4
BRCA1/BARD1/UbcH5C 0.054 0.06 -10000 0 -0.26 15 15
BRCA1/BARD1/UbcH7 0.052 0.059 -10000 0 -0.26 14 14
BRCA1/BARD1/RAD51/PCNA 0.037 0.11 -10000 0 -0.24 58 58
BARD1/DNA-PK/P53 0.057 0.085 -10000 0 -0.22 29 29
BRCA1/BARD1/Ubiquitin 0.037 0.062 -10000 0 -0.3 15 15
BRCA1/BARD1/CTIP 0.033 0.063 -10000 0 -0.23 22 22
FA complex 0.019 0.057 -10000 0 -0.4 2 2
BARD1/EWS 0.047 0.031 -10000 0 -0.3 3 3
RBBP8 0.007 0.044 -10000 0 -0.3 10 10
TP53 0.008 0.1 -10000 0 -0.42 26 26
TOPBP1 0.035 0.006 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.047 0.09 0.25 35 -10000 0 35
BRCA1/BARD1 0.066 0.076 -10000 0 -0.23 20 20
CSTF1 0.031 0.023 -10000 0 -0.42 1 1
BARD1/EWS-Fli1 0.024 0.025 -10000 0 -0.3 3 3
CDK2 0.033 0.029 -10000 0 -0.42 2 2
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.005 0.13 -10000 0 -0.42 43 43
RAD50 0.03 0.046 -10000 0 -0.42 5 5
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.037 0.062 -10000 0 -0.3 15 15
EWSR1 0.034 0.009 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.012 0.06 -10000 0 -0.34 13 13
CRKL 0.03 0.041 -10000 0 -0.42 4 4
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
DOCK1 0.027 0.057 -10000 0 -0.42 8 8
ITGA4 0.021 0.078 -10000 0 -0.42 15 15
alpha4/beta7 Integrin/MAdCAM1 0.068 0.075 -10000 0 -0.25 22 22
EPO 0.03 0.014 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.041 0.061 -10000 0 -0.3 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.023 -10000 0 -0.42 1 1
alpha4/beta1 Integrin 0.039 0.068 -10000 0 -0.34 15 15
EPO/EPOR (dimer) 0.047 0.014 -10000 0 -10000 0 0
lamellipodium assembly 0.012 0.084 -10000 0 -0.49 5 5
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
PI3K 0.035 0.067 -10000 0 -0.3 18 18
ARF6 0.033 0.029 -10000 0 -0.42 2 2
JAK2 0.024 0.048 -10000 0 -0.26 13 13
PXN 0.036 0.004 -10000 0 -10000 0 0
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
MADCAM1 0.034 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 -0.3 4 4
ITGB1 0.033 0.03 -10000 0 -0.42 2 2
SRC 0.001 0.084 0.19 15 -0.27 37 52
ITGB7 0.036 0.004 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.04 0.099 -10000 0 -0.3 36 36
p130Cas/Crk/Dock1 0.02 0.087 -10000 0 -0.25 25 25
VCAM1 0.009 0.1 -10000 0 -0.42 27 27
RHOA 0.026 0.061 -10000 0 -0.42 9 9
alpha4/beta1 Integrin/Paxillin/GIT1 0.073 0.067 -10000 0 -0.26 16 16
BCAR1 -0.024 0.072 0.18 15 -0.25 34 49
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 0.033 0.022 -10000 0 -0.42 1 1
Rac1/GTP 0.012 0.086 -10000 0 -0.51 5 5
Signaling events mediated by HDAC Class III

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
EP300 0.033 0.022 -10000 0 -0.42 1 1
HDAC4 0.034 0.021 -10000 0 -0.42 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.005 0.016 -10000 0 -0.11 8 8
CDKN1A -0.018 0.095 0.4 1 -0.57 13 14
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.035 0.007 -10000 0 -10000 0 0
FOXO3 -0.007 0.016 0.34 1 -10000 0 1
FOXO1 0 0 -10000 0 -10000 0 0
FOXO4 0.011 0.02 -10000 0 -0.42 1 1
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.033 0.009 -10000 0 -10000 0 0
TAT 0.027 0.016 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.006 0.065 -10000 0 -0.3 24 24
PPARGC1A 0.023 0.064 -10000 0 -0.42 10 10
FHL2 -0.026 0.15 -10000 0 -0.42 65 65
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.048 0.019 -10000 0 -10000 0 0
HIST2H4A -0.005 0.016 0.11 8 -10000 0 8
SIRT1/FOXO3a 0.028 0.038 0.2 7 -0.2 3 10
SIRT1 0.035 0.019 0.21 4 -10000 0 4
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.053 0.036 -10000 0 -0.26 1 1
SIRT1/Histone H1b 0.021 0.077 -10000 0 -0.22 31 31
apoptosis -0.063 0.024 -10000 0 -10000 0 0
SIRT1/PGC1A 0.038 0.044 -10000 0 -0.25 10 10
p53/SIRT1 0.025 0.079 0.4 4 -0.31 22 26
SIRT1/FOXO4 0.032 0.044 -10000 0 -0.18 5 5
FOXO1/FHL2/SIRT1 0.008 0.09 0.15 4 -0.23 63 67
HIST1H1E 0 0.065 -10000 0 -0.26 30 30
SIRT1/p300 0.048 0.022 0.18 3 -0.23 1 4
muscle cell differentiation -0.008 0.061 0.26 24 -0.15 5 29
TP53 0.009 0.095 0.21 4 -0.43 22 26
KU70/SIRT1/BAX 0.064 0.024 -10000 0 -10000 0 0
CREBBP 0.032 0.011 -10000 0 -10000 0 0
MEF2D 0.028 0.015 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.04 0.024 -10000 0 -10000 0 0
ACSS2 -0.006 0.025 0.19 4 -10000 0 4
SIRT1/PCAF/MYOD 0.008 0.061 0.16 6 -0.26 24 30
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.035 0.006 -10000 0 -10000 0 0
NFATC1 0.019 0.092 0.3 2 -0.38 9 11
NFATC2 0.018 0.049 0.16 1 -0.2 6 7
NFATC3 0.013 0.007 -10000 0 -10000 0 0
YWHAE 0.032 0.011 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.019 0.091 0.21 4 -0.36 11 15
Exportin 1/Ran/NUP214 0.069 0.022 -10000 0 -0.26 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.042 0.086 -10000 0 -0.44 4 4
BCL2/BAX -0.018 0.14 -10000 0 -0.3 95 95
CaM/Ca2+/Calcineurin A alpha-beta B1 0.027 0.006 -10000 0 -10000 0 0
CaM/Ca2+ 0.027 0.006 -10000 0 -10000 0 0
BAX 0.035 0.007 -10000 0 -10000 0 0
MAPK14 0.036 0.005 -10000 0 -10000 0 0
BAD 0.034 0.021 -10000 0 -0.42 1 1
CABIN1/MEF2D 0.029 0.083 -10000 0 -0.37 7 7
Calcineurin A alpha-beta B1/BCL2 -0.057 0.18 -10000 0 -0.42 99 99
FKBP8 0.035 0.005 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.029 0.082 0.37 7 -10000 0 7
KPNB1 0.031 0.041 -10000 0 -0.42 4 4
KPNA2 0.023 0.061 -10000 0 -0.42 9 9
XPO1 0.035 0.005 -10000 0 -10000 0 0
SFN 0.011 0.099 -10000 0 -0.42 25 25
MAP3K8 0.003 0.11 -10000 0 -0.42 32 32
NFAT4/CK1 alpha 0.016 0.057 -10000 0 -0.21 23 23
MEF2D/NFAT1/Cbp/p300 0.055 0.064 -10000 0 -0.23 2 2
CABIN1 0.019 0.09 0.21 4 -0.37 10 14
CALM1 0.035 0.007 -10000 0 -10000 0 0
RAN 0.035 0.005 -10000 0 -10000 0 0
MAP3K1 0.01 0.099 -10000 0 -0.42 25 25
CAMK4 0.032 0.03 -10000 0 -0.42 2 2
mol:Ca2+ 0.001 0.001 -10000 0 -10000 0 0
MAPK3 0.032 0.023 -10000 0 -0.42 1 1
YWHAH 0.031 0.036 -10000 0 -0.42 3 3
Calcineurin A alpha-beta B1/AKAP79/PKA 0.023 0.092 -10000 0 -0.3 37 37
YWHAB 0.034 0.009 -10000 0 -10000 0 0
MAPK8 0.033 0.035 -10000 0 -0.42 3 3
MAPK9 0.018 0.087 -10000 0 -0.42 19 19
YWHAG 0.035 0.005 -10000 0 -10000 0 0
FKBP1A 0.034 0.008 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.031 0.093 0.32 1 -0.36 8 9
PRKCH 0.03 0.046 -10000 0 -0.42 5 5
CABIN1/Cbp/p300 0.045 0.025 -10000 0 -0.28 1 1
CASP3 0.035 0.008 -10000 0 -10000 0 0
PIM1 0.035 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.024 0.005 -10000 0 -10000 0 0
apoptosis 0.002 0.048 -10000 0 -0.29 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.028 0.059 -10000 0 -0.23 3 3
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.031 0.046 -10000 0 -0.42 5 5
JNK2/NFAT4 -0.002 0.08 -10000 0 -0.21 25 25
BAD/BCL-XL 0.049 0.02 -10000 0 -0.3 1 1
PRKCD 0.032 0.03 -10000 0 -0.42 2 2
NUP214 0.035 0.021 -10000 0 -0.42 1 1
PRKCZ 0 0 -10000 0 -10000 0 0
PRKCA 0.031 0.012 -10000 0 -10000 0 0
PRKCG 0.036 0 -10000 0 -10000 0 0
PRKCQ 0.025 0.054 -10000 0 -0.42 7 7
FKBP38/BCL2 -0.019 0.14 -10000 0 -0.3 97 97
EP300 0.033 0.022 -10000 0 -0.42 1 1
PRKCB1 0.003 0.11 -10000 0 -0.42 29 29
CSNK2A1 0.034 0.008 -10000 0 -10000 0 0
NFATc/JNK1 0.036 0.096 0.31 2 -0.36 9 11
CaM/Ca2+/FKBP38 0.047 0.011 -10000 0 -10000 0 0
FKBP12/FK506 0.025 0.006 -10000 0 -10000 0 0
CSNK1A1 0.018 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.045 0.023 -10000 0 -0.25 2 2
NFATc/ERK1 0.033 0.092 0.31 2 -0.35 8 10
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.05 0.096 -10000 0 -0.38 7 7
NR4A1 0.064 0.079 0.23 15 -0.43 1 16
GSK3B 0.036 0.005 -10000 0 -10000 0 0
positive T cell selection 0.013 0.007 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.021 0.036 -10000 0 -0.21 1 1
RCH1/ KPNB1 0.037 0.056 -10000 0 -0.3 12 12
YWHAQ 0.033 0.029 -10000 0 -0.42 2 2
PRKACA 0.036 0.005 -10000 0 -10000 0 0
AKAP5 -0.001 0.12 -10000 0 -0.42 38 38
MEF2D 0.028 0.015 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.026 0.016 -10000 0 -10000 0 0
NFATc/p38 alpha 0.037 0.094 0.33 1 -0.36 9 10
CREBBP 0.033 0.011 -10000 0 -10000 0 0
BCL2 -0.057 0.18 -10000 0 -0.42 99 99
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 0.041 -10000 0 -0.42 4 4
Rac1/GDP 0.035 0.013 -10000 0 -10000 0 0
DOCK1 0.027 0.057 -10000 0 -0.42 8 8
ITGA4 0.021 0.078 -10000 0 -0.42 15 15
RAC1 0.035 0.006 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.041 0.061 -10000 0 -0.3 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.023 -10000 0 -0.42 1 1
alpha4/beta1 Integrin 0.058 0.064 -10000 0 -0.29 15 15
alpha4/beta7 Integrin/Paxillin 0.048 0.051 -10000 0 -0.24 15 15
lamellipodium assembly -0.014 0.13 -10000 0 -0.43 32 32
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
PI3K 0.035 0.067 -10000 0 -0.3 18 18
ARF6 0.033 0.029 -10000 0 -0.42 2 2
TLN1 0.034 0.021 -10000 0 -0.42 1 1
PXN 0.016 0.003 -10000 0 -10000 0 0
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
ARF6/GTP 0.059 0.062 -10000 0 -0.23 18 18
cell adhesion 0.061 0.062 -10000 0 -0.25 16 16
CRKL/CBL 0.042 0.036 -10000 0 -0.3 4 4
alpha4/beta1 Integrin/Paxillin 0.046 0.057 -10000 0 -0.26 15 15
ITGB1 0.033 0.03 -10000 0 -0.42 2 2
ITGB7 0.036 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.033 0.031 -10000 0 -0.42 2 2
alpha4/beta1 Integrin/Paxillin/VCAM1 0.049 0.092 -10000 0 -0.26 36 36
p130Cas/Crk/Dock1 0.049 0.052 -10000 0 -0.25 9 9
VCAM1 0.009 0.1 -10000 0 -0.42 27 27
alpha4/beta1 Integrin/Paxillin/Talin 0.064 0.063 -10000 0 -0.25 16 16
alpha4/beta1 Integrin/Paxillin/GIT1 0.063 0.063 -10000 0 -0.25 16 16
BCAR1 0.029 0.014 -10000 0 -10000 0 0
mol:GDP -0.061 0.062 0.24 16 -10000 0 16
CBL 0.031 0.012 -10000 0 -10000 0 0
PRKACA 0.036 0.004 -10000 0 -10000 0 0
GIT1 0.033 0.022 -10000 0 -0.42 1 1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.064 0.063 -10000 0 -0.25 16 16
Rac1/GTP -0.018 0.14 -10000 0 -0.48 32 32
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.009 0.11 -10000 0 -0.42 29 29
HRAS 0.032 0.036 -10000 0 -0.42 3 3
EGFR -0.013 0.13 -10000 0 -0.42 47 47
AKT 0.025 0.085 0.26 3 -0.28 11 14
FOXO3 0 0 -10000 0 -10000 0 0
AKT1 0.032 0.036 -10000 0 -0.42 3 3
FOXO1 0 0 -10000 0 -10000 0 0
AKT3 0.024 0.032 -10000 0 -0.42 2 2
FOXO4 0 0 -10000 0 -10000 0 0
MET 0.029 0.046 -10000 0 -0.42 5 5
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
PIK3CB 0.03 0.046 -10000 0 -0.42 5 5
NRAS 0.029 0.05 -10000 0 -0.42 6 6
PIK3CG 0.022 0.073 -10000 0 -0.42 13 13
PIK3R3 0.025 0.067 -10000 0 -0.42 11 11
PIK3R2 0.036 0.004 -10000 0 -10000 0 0
NF1 0.032 0.03 -10000 0 -0.42 2 2
RAS -0.003 0.077 0.17 3 -0.29 21 24
ERBB2 0.017 0.078 -10000 0 -0.42 15 15
proliferation/survival/translation -0.026 0.057 0.24 8 -0.18 4 12
PI3K 0.003 0.085 0.2 7 -0.23 37 44
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
KRAS 0.027 0.057 -10000 0 -0.42 8 8
FOXO 0.042 0.039 0.19 7 -10000 0 7
AKT2 0.035 0.005 -10000 0 -10000 0 0
PTEN 0.027 0.061 -10000 0 -0.42 9 9
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.075 0.048 -10000 0 -0.23 6 6
HDAC3 0.035 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.013 0.009 -10000 0 -0.2 1 1
GATA1/HDAC4 0.051 0.019 -10000 0 -0.3 1 1
GATA1/HDAC5 0.049 0.021 -10000 0 -0.3 1 1
GATA2/HDAC5 0.044 0.041 -10000 0 -0.3 6 6
HDAC5/BCL6/BCoR 0.048 0.075 -10000 0 -0.26 26 26
HDAC9 0.033 0.022 -10000 0 -0.42 1 1
Glucocorticoid receptor/Hsp90/HDAC6 0.038 0.052 -10000 0 -0.25 15 15
HDAC4/ANKRA2 0.04 0.059 -10000 0 -0.3 14 14
HDAC5/YWHAB 0.046 0.024 -10000 0 -0.3 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.016 0.011 -10000 0 -0.17 1 1
GATA2 0.029 0.046 -10000 0 -0.42 5 5
HDAC4/RFXANK 0.05 0.02 -10000 0 -0.3 1 1
BCOR 0.028 0.061 -10000 0 -0.42 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.031 0.03 -10000 0 -0.42 2 2
HDAC5 0.033 0.022 -10000 0 -0.42 1 1
GNB1/GNG2 0.048 0.039 -10000 0 -0.3 6 6
Histones 0.008 0.068 -10000 0 -0.23 28 28
ADRBK1 0.033 0.01 -10000 0 -10000 0 0
HDAC4 0.034 0.021 -10000 0 -0.42 1 1
XPO1 0.035 0.005 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.038 0.06 -10000 0 -0.3 14 14
HDAC4/Ubc9 0.045 0.024 -10000 0 -0.3 1 1
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.046 0.024 -10000 0 -0.3 1 1
TUBA1B 0 0 -10000 0 -10000 0 0
HDAC6 0.036 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0.048 0.022 -10000 0 -0.3 1 1
CAMK4 0.032 0.03 -10000 0 -0.42 2 2
Tubulin/HDAC6 0.036 0.055 -10000 0 -0.25 17 17
SUMO1 0.036 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.034 0.009 -10000 0 -10000 0 0
GATA1 0.036 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.032 0.011 -10000 0 -10000 0 0
NR3C1 0.022 0.078 -10000 0 -0.42 15 15
SUMO1/HDAC4 0.051 0.044 -10000 0 -0.21 2 2
SRF 0.035 0.007 -10000 0 -10000 0 0
HDAC4/YWHAB 0.048 0.022 -10000 0 -0.3 1 1
Tubulin 0.014 0.058 -10000 0 -0.3 17 17
HDAC4/14-3-3 E 0.046 0.023 -10000 0 -0.29 1 1
GNB1 0.032 0.045 -10000 0 -0.42 5 5
RANGAP1 0.032 0.022 -10000 0 -0.42 1 1
BCL6/BCoR 0.032 0.08 -10000 0 -0.3 27 27
HDAC4/HDAC3/SMRT (N-CoR2) 0.068 0.023 -10000 0 -0.26 1 1
HDAC4/SRF 0.064 0.033 -10000 0 -0.26 3 3
HDAC4/ER alpha -0.045 0.15 -10000 0 -0.3 131 131
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.008 0.068 -10000 0 -0.22 28 28
cell motility 0.036 0.055 -10000 0 -0.25 17 17
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.032 0.011 -10000 0 -10000 0 0
HDAC7/HDAC3 0.026 0.004 -10000 0 -10000 0 0
BCL6 0.018 0.085 -10000 0 -0.42 18 18
HDAC4/CaMK II delta B 0.034 0.021 -10000 0 -0.42 1 1
Hsp90/HDAC6 0.027 0 -10000 0 -10000 0 0
ESR1 -0.088 0.2 -10000 0 -0.42 130 130
HDAC6/HDAC11 0.034 0.077 -10000 0 -0.3 25 25
Ran/GTP/Exportin 1 0.053 0.042 -10000 0 -0.24 1 1
NPC 0.021 0.002 -10000 0 -10000 0 0
MEF2C 0.016 0.089 -10000 0 -0.42 20 20
RAN 0.035 0.005 -10000 0 -10000 0 0
HDAC4/MEF2C 0.076 0.072 -10000 0 -0.22 19 19
GNG2 0.034 0.021 -10000 0 -0.42 1 1
NCOR2 0.036 0.004 -10000 0 -10000 0 0
TUBB2A 0.019 0.083 -10000 0 -0.42 17 17
HDAC11 0.012 0.099 -10000 0 -0.42 25 25
HSP90AA1 0 0 -10000 0 -10000 0 0
RANBP2 0.036 0.004 -10000 0 -10000 0 0
ANKRA2 0.022 0.073 -10000 0 -0.42 13 13
RFXANK 0.035 0.005 -10000 0 -10000 0 0
nuclear import -0.036 0.028 0.26 2 -10000 0 2
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.033 0.03 -9999 0 -0.42 2 2
ITGB7 0.036 0.004 -9999 0 -10000 0 0
ITGA4 0.021 0.078 -9999 0 -0.42 15 15
alpha4/beta7 Integrin 0.041 0.061 -9999 0 -0.3 15 15
alpha4/beta1 Integrin 0.039 0.068 -9999 0 -0.34 15 15
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.016 0.003 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.041 0.031 -10000 0 -0.24 1 1
CDKN1B 0.01 0.082 0.22 8 -0.34 15 23
CDKN1A 0.011 0.073 0.2 4 -0.33 15 19
FRAP1 0.034 0.008 -10000 0 -10000 0 0
PRKDC 0.029 0.031 -10000 0 -0.42 2 2
FOXO3 0.011 0.061 -10000 0 -0.31 15 15
AKT1 0.011 0.064 -10000 0 -0.33 15 15
BAD 0.034 0.021 -10000 0 -0.42 1 1
AKT3 0.011 0.025 -10000 0 -0.29 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.011 0.061 -10000 0 -0.31 15 15
AKT1/ASK1 0.037 0.087 0.24 4 -0.3 16 20
BAD/YWHAZ 0.05 0.036 -10000 0 -0.26 1 1
RICTOR 0.035 0.007 -10000 0 -10000 0 0
RAF1 0.035 0.006 -10000 0 -10000 0 0
JNK cascade -0.035 0.084 0.3 16 -0.22 3 19
TSC1 0.014 0.065 -10000 0 -0.32 14 14
YWHAZ 0.026 0.016 -10000 0 -10000 0 0
AKT1/RAF1 0.054 0.083 0.27 5 -0.32 15 20
EP300 0.033 0.022 -10000 0 -0.42 1 1
mol:GDP 0.011 0.064 -10000 0 -0.32 15 15
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.008 0.065 0.25 1 -0.33 15 16
YWHAQ 0.033 0.029 -10000 0 -0.42 2 2
TBC1D4 0.004 0.034 0.24 2 -0.24 8 10
MAP3K5 0.013 0.093 -10000 0 -0.42 22 22
MAPKAP1 0.035 0.021 -10000 0 -0.42 1 1
negative regulation of cell cycle -0.035 0.075 0.23 9 -0.2 7 16
YWHAH 0.031 0.036 -10000 0 -0.42 3 3
AKT1S1 0.017 0.077 0.21 14 -0.32 16 30
CASP9 0.016 0.055 -10000 0 -0.29 11 11
YWHAB 0.034 0.009 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.044 0.099 0.27 10 -0.33 15 25
GBL 0.031 0.023 -10000 0 -0.42 1 1
PDK1/Src/Hsp90 0.041 0.025 -10000 0 -0.25 2 2
YWHAE 0.032 0.011 -10000 0 -10000 0 0
SRC 0.032 0.03 -10000 0 -0.42 2 2
AKT2/p21CIP1 0.014 0.068 0.21 5 -0.35 8 13
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.036 0.076 -10000 0 -0.37 12 12
CHUK 0.01 0.074 0.2 1 -0.33 15 16
BAD/BCL-XL 0.055 0.081 0.26 3 -0.3 15 18
mTORC2 0.075 0.04 -10000 0 -0.23 2 2
AKT2 0.016 0.015 -10000 0 -0.29 1 1
FOXO1-3a-4/14-3-3 family 0.046 0.095 0.24 18 -0.32 9 27
PDPK1 0.032 0.023 -10000 0 -0.42 1 1
MDM2 0.016 0.071 0.22 4 -0.32 15 19
MAPKKK cascade -0.053 0.082 0.31 15 -0.26 6 21
MDM2/Cbp/p300 0.054 0.081 0.29 6 -0.3 15 21
TSC1/TSC2 0.016 0.084 0.3 19 -0.32 15 34
proteasomal ubiquitin-dependent protein catabolic process 0.051 0.078 0.28 6 -0.29 15 21
glucose import -0.003 0.03 0.21 2 -0.22 8 10
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.032 0.084 0.26 1 -0.44 8 9
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.003 0.031 0.21 2 -0.22 8 10
GSK3A 0.014 0.067 0.2 2 -0.32 15 17
FOXO1 0.011 0.061 -10000 0 -0.31 15 15
GSK3B 0.014 0.067 -10000 0 -0.32 15 15
SFN 0.011 0.099 -10000 0 -0.42 25 25
G1/S transition of mitotic cell cycle 0.02 0.075 0.26 3 -0.31 15 18
p27Kip1/14-3-3 family 0.021 0.054 -10000 0 -0.34 2 2
PRKACA 0.036 0.004 -10000 0 -10000 0 0
KPNA1 0.035 0.005 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
YWHAG 0.035 0.005 -10000 0 -10000 0 0
RHEB 0.035 0.007 -10000 0 -10000 0 0
CREBBP 0.032 0.011 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.027 0.046 -10000 0 -0.42 5 5
mol:Halofuginone 0.004 0.009 -10000 0 -0.19 1 1
ITGA1 0.023 0.073 -10000 0 -0.42 13 13
CDKN1A -0.005 0.12 -10000 0 -0.44 28 28
PRL-3/alpha Tubulin 0.02 0.018 -10000 0 -0.3 1 1
mol:Ca2+ -0.037 0.083 0.34 1 -0.32 39 40
AGT -0.024 0.14 -10000 0 -0.42 54 54
CCNA2 -0.037 0.096 -10000 0 -0.52 3 3
TUBA1B 0 0 -10000 0 -10000 0 0
EGR1 -0.028 0.11 -10000 0 -0.29 76 76
CDK2/Cyclin E1 0.021 0.12 -10000 0 -0.44 22 22
MAPK3 0.011 0.016 -10000 0 -0.3 1 1
PRL-2 /Rab GGTase beta 0.046 0.043 -10000 0 -0.3 7 7
MAPK1 0.011 0.016 -10000 0 -0.3 1 1
PTP4A1 -0.027 0.083 -10000 0 -0.48 3 3
PTP4A3 0.027 0.025 -10000 0 -0.42 1 1
PTP4A2 0.028 0.054 -10000 0 -0.42 7 7
ITGB1 0.011 0.021 -10000 0 -0.3 2 2
SRC 0.032 0.03 -10000 0 -0.42 2 2
RAC1 0.013 0.059 -10000 0 -0.63 2 2
Rab GGTase beta/Rab GGTase alpha 0.05 0.013 -10000 0 -10000 0 0
PRL-1/ATF-5 0.001 0.096 0.37 1 -0.46 3 4
RABGGTA 0.035 0.007 -10000 0 -10000 0 0
BCAR1 -0.017 0.021 0.34 1 -10000 0 1
RHOC 0.01 0.071 -10000 0 -0.51 5 5
RHOA 0.002 0.091 -10000 0 -0.45 12 12
cell motility 0.015 0.085 0.35 1 -0.41 7 8
PRL-1/alpha Tubulin -0.027 0.078 -10000 0 -0.46 3 3
PRL-3/alpha1 Integrin 0.032 0.059 -10000 0 -0.32 11 11
ROCK1 0.019 0.081 0.35 1 -0.41 7 8
RABGGTB 0.035 0.007 -10000 0 -10000 0 0
CDK2 0.033 0.029 -10000 0 -0.42 2 2
mitosis -0.027 0.082 -10000 0 -0.48 3 3
ATF5 0.033 0.022 -10000 0 -0.42 1 1
Class IB PI3K non-lipid kinase events

Figure S117.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S117.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.025 0.061 0.42 9 -10000 0 9
PI3K Class IB/PDE3B 0.025 0.061 -10000 0 -0.42 9 9
PDE3B 0.025 0.061 -10000 0 -0.42 9 9
JNK signaling in the CD4+ TCR pathway

Figure S118.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S118.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.067 0.058 -10000 0 -0.26 9 9
MAP4K1 0.035 0.007 -10000 0 -10000 0 0
MAP3K8 0.003 0.11 -10000 0 -0.42 32 32
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0.033 0.029 -10000 0 -0.42 2 2
CRKL 0.03 0.041 -10000 0 -0.42 4 4
MAP3K1 0.004 0.07 -10000 0 -0.31 5 5
JUN -0.01 0.098 -10000 0 -0.51 10 10
MAP3K7 0.013 0.062 0.21 4 -0.31 6 10
GRAP2 0.032 0.023 -10000 0 -0.42 1 1
CRK 0.031 0.023 -10000 0 -0.42 1 1
MAP2K4 -0.005 0.084 0.21 1 -0.34 15 16
LAT 0.029 0.031 -10000 0 -0.42 2 2
LCP2 0.023 0.07 -10000 0 -0.42 12 12
MAPK8 0.008 0.081 -10000 0 -0.59 8 8
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.02 0.067 -10000 0 -0.25 15 15
LAT/GRAP2/SLP76/HPK1/HIP-55 0.078 0.062 -10000 0 -0.25 9 9
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.035 0.007 -9999 0 -10000 0 0
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.032 0.011 -9999 0 -10000 0 0
TCEB1 0.028 0.025 -9999 0 -0.42 1 1
HIF1A/p53 0.006 0.097 -9999 0 -0.27 24 24
HIF1A -0.001 0.081 -9999 0 -0.28 16 16
COPS5 0.026 0.042 -9999 0 -0.42 4 4
VHL/Elongin B/Elongin C/RBX1/CUL2 0.071 0.052 -9999 0 -0.22 1 1
FIH (dimer) 0.035 0.005 -9999 0 -10000 0 0
CDKN2A 0.015 0.075 -9999 0 -0.42 14 14
ARNT/IPAS 0.05 0.013 -9999 0 -10000 0 0
HIF1AN 0.035 0.005 -9999 0 -10000 0 0
GNB2L1 0.033 0.035 -9999 0 -0.42 3 3
HIF1A/ARNT 0.018 0.087 -9999 0 -0.27 16 16
CUL2 0.035 0.007 -9999 0 -10000 0 0
OS9 0.034 0.029 -9999 0 -0.42 2 2
RACK1/Elongin B/Elongin C 0.053 0.038 -9999 0 -0.26 2 2
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.004 0.076 -9999 0 -0.27 16 16
PHD1-3/OS9 0.032 0.1 -9999 0 -0.24 49 49
HIF1A/RACK1/Elongin B/Elongin C 0.035 0.083 -9999 0 -0.26 11 11
VHL 0.035 0.007 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.013 0.08 -9999 0 -0.27 13 13
EGLN3 -0.016 0.14 -9999 0 -0.42 52 52
EGLN2 0.031 0.041 -9999 0 -0.42 4 4
EGLN1 0.021 0.055 -9999 0 -0.42 7 7
TP53 0.008 0.1 -9999 0 -0.42 26 26
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.037 0.06 -9999 0 -0.44 4 4
ARNT 0.035 0.006 -9999 0 -10000 0 0
ARD1A 0.036 0.003 -9999 0 -10000 0 0
RBX1 0.034 0.009 -9999 0 -10000 0 0
HIF1A/p19ARF 0.004 0.092 -9999 0 -0.29 20 20
Insulin-mediated glucose transport

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles 0.026 0.1 0.21 2 -0.24 40 42
CaM/Ca2+ 0.026 0.005 -10000 0 -10000 0 0
AKT1 0.032 0.036 -10000 0 -0.42 3 3
AKT2 0.035 0.005 -10000 0 -10000 0 0
STXBP4 0.03 0.037 -10000 0 -0.42 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.007 0.1 0.2 3 -0.25 42 45
YWHAZ 0.026 0.016 -10000 0 -10000 0 0
CALM1 0.035 0.007 -10000 0 -10000 0 0
YWHAQ 0.033 0.029 -10000 0 -0.42 2 2
TBC1D4 0.008 0.044 -10000 0 -0.3 10 10
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.031 0.036 -10000 0 -0.42 3 3
YWHAB 0.034 0.009 -10000 0 -10000 0 0
SNARE/Synip 0.037 0.032 -10000 0 -0.25 4 4
YWHAG 0.035 0.005 -10000 0 -10000 0 0
ASIP 0 0 -10000 0 -10000 0 0
PRKCI 0.024 0.067 -10000 0 -0.42 11 11
AS160/CaM/Ca2+ 0.026 0.005 -10000 0 -10000 0 0
RHOQ 0.033 0.035 -10000 0 -0.42 3 3
GYS1 0.017 0.042 0.25 12 -0.24 3 15
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.032 0.041 -10000 0 -0.42 4 4
TC10/GTP/CIP4/Exocyst 0.043 0.036 -10000 0 -0.25 7 7
AS160/14-3-3 0.018 0.074 -10000 0 -0.27 11 11
VAMP2 0.031 0.023 -10000 0 -0.42 1 1
SLC2A4 0.005 0.11 0.2 3 -0.28 42 45
STX4 0 0 -10000 0 -10000 0 0
GSK3B 0.024 0.025 -10000 0 -0.28 3 3
SFN 0.011 0.099 -10000 0 -0.42 25 25
LNPEP 0.032 0.03 -10000 0 -0.42 2 2
YWHAE 0.032 0.011 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.028 0.054 -10000 0 -0.42 7 7
SMAD2 -0.001 0.059 0.21 2 -0.22 12 14
SMAD3 0.019 0.059 0.28 1 -0.25 5 6
SMAD3/SMAD4 0.03 0.089 -10000 0 -0.38 17 17
SMAD4/Ubc9/PIASy 0.054 0.052 -10000 0 -0.26 10 10
SMAD2/SMAD2/SMAD4 0.05 0.08 -10000 0 -0.26 4 4
PPM1A 0.034 0.022 -10000 0 -0.42 1 1
CALM1 0.035 0.007 -10000 0 -10000 0 0
SMAD2/SMAD4 0.013 0.067 -10000 0 -0.21 21 21
MAP3K1 0.01 0.099 -10000 0 -0.42 25 25
TRAP-1/SMAD4 0.046 0.043 -10000 0 -0.3 7 7
MAPK3 0.032 0.023 -10000 0 -0.42 1 1
MAPK1 0.033 0.022 -10000 0 -0.42 1 1
NUP214 0.035 0.021 -10000 0 -0.42 1 1
CTDSP1 0.034 0.029 -10000 0 -0.42 2 2
CTDSP2 0.034 0.029 -10000 0 -0.42 2 2
CTDSPL 0.028 0.054 -10000 0 -0.42 7 7
KPNB1 0.031 0.041 -10000 0 -0.42 4 4
TGFBRAP1 0.036 0.004 -10000 0 -10000 0 0
UBE2I 0.032 0.011 -10000 0 -10000 0 0
NUP153 0.035 0.007 -10000 0 -10000 0 0
KPNA2 0.023 0.061 -10000 0 -0.42 9 9
PIAS4 0.032 0.036 -10000 0 -0.42 3 3
Ephrin A reverse signaling

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
MAPKKK cascade 0.041 0.037 -10000 0 -0.25 7 7
EFNA5 0.029 0.046 -10000 0 -0.42 5 5
FYN 0.011 0.041 0.19 2 -0.23 13 15
neuron projection morphogenesis 0.041 0.037 -10000 0 -0.25 7 7
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.041 0.037 -10000 0 -0.25 7 7
EPHA5 0.034 0.029 -10000 0 -0.42 2 2
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.029 0.024 -10000 0 -0.42 1 1
CLTC 0.025 0.062 0.26 2 -0.42 6 8
calcium ion-dependent exocytosis 0.017 0.038 -10000 0 -0.22 5 5
Dynamin 2/GTP 0.031 0.02 -10000 0 -0.23 2 2
EXOC4 0.034 0.021 -10000 0 -0.42 1 1
CD59 0.016 0.049 -10000 0 -0.36 5 5
CPE -0.008 0.079 -10000 0 -0.26 43 43
CTNNB1 0.024 0.067 -10000 0 -0.42 11 11
membrane fusion 0.013 0.033 -10000 0 -0.23 4 4
CTNND1 -0.002 0.055 0.2 31 -0.22 3 34
DNM2 0.035 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.018 0.046 0.19 2 -0.27 5 7
TSHR 0.013 0.034 -10000 0 -0.25 8 8
INS 0.008 0.093 -10000 0 -0.46 18 18
BIN1 0.034 0.029 -10000 0 -0.42 2 2
mol:Choline 0.013 0.033 -10000 0 -0.23 4 4
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.015 0.018 -10000 0 -0.25 2 2
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.033 0.029 -10000 0 -0.42 2 2
mol:Ca2+ 0.03 0.02 -10000 0 -0.23 2 2
JUP 0.019 0.053 -10000 0 -0.37 5 5
ASAP2/amphiphysin II 0.042 0.026 -10000 0 -0.23 4 4
ARF6/GTP 0.025 0.021 -10000 0 -0.3 2 2
CDH1 -0.003 0.069 -10000 0 -0.42 5 5
clathrin-independent pinocytosis 0.024 0.021 -10000 0 -0.3 2 2
MAPK8IP3 0.023 0.064 -10000 0 -0.42 10 10
positive regulation of endocytosis 0.024 0.021 -10000 0 -0.3 2 2
EXOC2 0.029 0.05 -10000 0 -0.42 6 6
substrate adhesion-dependent cell spreading 0.017 0.075 -10000 0 -0.33 4 4
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.032 0.022 -10000 0 -0.42 1 1
regulation of calcium-dependent cell-cell adhesion -0.029 0.085 0.4 5 -10000 0 5
positive regulation of phagocytosis 0.015 0.021 -10000 0 -0.25 3 3
ARF6/GTP/JIP3 0.035 0.048 -10000 0 -0.25 12 12
ACAP1 0.013 0.032 -10000 0 -0.19 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.016 0.045 -10000 0 -0.35 5 5
clathrin heavy chain/ACAP1 0.023 0.062 0.28 3 -0.31 7 10
JIP4/KLC1 0.04 0.025 -10000 0 -0.23 3 3
EXOC1 0.035 0.005 -10000 0 -10000 0 0
exocyst 0.017 0.075 -10000 0 -0.33 4 4
RALA/GTP 0.026 0.005 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.042 0.027 -10000 0 -0.25 3 3
receptor recycling 0.024 0.021 -10000 0 -0.3 2 2
CTNNA1 -0.001 0.054 0.2 31 -0.22 2 33
NME1 0.015 0.018 -10000 0 -0.25 2 2
clathrin coat assembly 0.027 0.068 0.26 3 -0.4 7 10
IL2RA 0.009 0.067 -10000 0 -0.37 5 5
VAMP3 0.015 0.021 -10000 0 -0.25 3 3
GLUT4/clathrin heavy chain/ACAP1 0.03 0.06 -10000 0 -0.32 5 5
EXOC6 0.01 0.1 -10000 0 -0.42 28 28
PLD1 0.011 0.039 -10000 0 -0.28 8 8
PLD2 0.014 0.024 -10000 0 -0.2 5 5
EXOC5 0.034 0.021 -10000 0 -0.42 1 1
PIP5K1C 0.015 0.042 0.19 2 -0.27 5 7
SDC1 0.003 0.068 -10000 0 -0.43 5 5
ARF6/GDP 0.029 0.02 -10000 0 -0.25 2 2
EXOC7 0.033 0.01 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.032 0.088 -10000 0 -0.41 5 5
mol:Phosphatidic acid 0.013 0.033 -10000 0 -0.23 4 4
endocytosis -0.04 0.026 0.23 4 -10000 0 4
SCAMP2 0.033 0.03 -10000 0 -0.42 2 2
ADRB2 0.01 0.087 0.26 1 -0.42 9 10
EXOC3 0.036 0.002 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.038 0.028 0.18 9 -0.23 2 11
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 0.021 0.067 0.25 3 -0.38 7 10
RALA 0.035 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.023 0.085 -10000 0 -0.39 5 5
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.041 0.057 -9999 0 -0.3 13 13
FBXW11 0.034 0.021 -9999 0 -0.42 1 1
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.034 0.021 -9999 0 -0.42 1 1
CHUK 0.025 0.067 -9999 0 -0.42 11 11
NF kappa B2 p100/RelB 0.082 0.074 -9999 0 -0.24 19 19
NFKB1 0.035 0.005 -9999 0 -10000 0 0
MAP3K14 0.032 0.03 -9999 0 -0.42 2 2
NF kappa B1 p50/RelB 0.046 0.04 -9999 0 -0.3 6 6
RELB 0.029 0.05 -9999 0 -0.42 6 6
NFKB2 0.034 0.021 -9999 0 -0.42 1 1
NF kappa B2 p52/RelB 0.042 0.036 -9999 0 -0.25 7 7
regulation of B cell activation 0.041 0.036 -9999 0 -0.25 7 7
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 0.036 0.023 -10000 0 -0.42 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.046 0.1 0.26 12 -0.28 6 18
ERC1 0 0 -10000 0 -10000 0 0
RIP2/NOD2 0.02 0.011 -10000 0 -10000 0 0
NFKBIA 0.011 0.036 -10000 0 -0.37 3 3
BIRC2 0.031 0.012 -10000 0 -10000 0 0
IKBKB 0.029 0.014 -10000 0 -10000 0 0
RIPK2 0.028 0.015 -10000 0 -10000 0 0
IKBKG 0.01 0.098 -10000 0 -0.34 19 19
IKK complex/A20 0.033 0.12 -10000 0 -0.4 5 5
NEMO/A20/RIP2 0.028 0.015 -10000 0 -10000 0 0
XPO1 0.035 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.022 0.11 -10000 0 -0.32 20 20
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 0.047 0.01 -10000 0 -10000 0 0
IKK complex/ELKS 0.011 0.1 -10000 0 -0.32 18 18
BCL10/MALT1/TRAF6 0.063 0.041 -10000 0 -0.31 4 4
NOD2 0 0 -10000 0 -10000 0 0
NFKB1 0.037 0.011 -10000 0 -10000 0 0
RELA 0.036 0.011 -10000 0 -10000 0 0
MALT1 0.031 0.041 -10000 0 -0.42 4 4
cIAP1/UbcH5C 0.046 0.019 -10000 0 -10000 0 0
ATM 0.031 0.013 -10000 0 -10000 0 0
TNF/TNFR1A 0.043 0.048 -10000 0 -0.3 9 9
TRAF6 0.034 0.021 -10000 0 -0.42 1 1
PRKCA 0.031 0.012 -10000 0 -10000 0 0
CHUK 0.025 0.067 -10000 0 -0.42 11 11
UBE2D3 0.035 0.005 -10000 0 -10000 0 0
TNF 0.026 0.061 -10000 0 -0.42 9 9
NF kappa B1 p50/RelA 0.074 0.034 -10000 0 -0.24 3 3
BCL10 0.034 0.008 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.036 0.21 4 -0.37 3 7
beta TrCP1/SCF ubiquitin ligase complex 0.036 0.023 -10000 0 -0.42 1 1
TNFRSF1A 0.033 0.022 -10000 0 -0.42 1 1
IKK complex 0.023 0.12 -10000 0 -0.34 18 18
CYLD 0.029 0.024 -10000 0 -0.42 1 1
IKK complex/PKC alpha 0.028 0.11 -10000 0 -0.41 3 3
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 0.035 0.087 -10000 0 -1.2 1 1
CLOCK 0.037 0.022 -10000 0 -0.42 1 1
TIMELESS/CRY2 0.042 0.061 -10000 0 -1.2 1 1
DEC1/BMAL1 0.043 0.061 -10000 0 -0.32 13 13
ATR 0.035 0.006 -10000 0 -10000 0 0
NR1D1 0.022 0.024 -10000 0 -10000 0 0
ARNTL 0.029 0.061 -10000 0 -0.42 9 9
TIMELESS 0.022 0.059 -10000 0 -1.3 1 1
NPAS2 0.027 0.064 -10000 0 -0.42 10 10
CRY2 0.035 0.005 -10000 0 -10000 0 0
mol:CO -0.01 0.006 0.14 1 -10000 0 1
CHEK1 0 0.11 -10000 0 -0.42 31 31
mol:HEME 0.01 0.006 -10000 0 -0.14 1 1
PER1 0.031 0.012 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.067 0.069 -10000 0 -0.26 19 19
BMAL1/CLOCK 0.026 0.077 -10000 0 -0.49 3 3
S phase of mitotic cell cycle 0.035 0.087 -10000 0 -1.2 1 1
TIMELESS/CHEK1/ATR 0.035 0.089 -10000 0 -1.3 1 1
mol:NADPH 0.01 0.006 -10000 0 -0.14 1 1
PER1/TIMELESS 0.038 0.06 -10000 0 -1.2 1 1
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.031 0.046 -10000 0 -0.42 5 5
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.028 0.054 -9999 0 -0.42 7 7
Aurora C/Aurora B/INCENP 0.052 0.049 -9999 0 -0.23 11 11
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.012 0.03 -9999 0 -0.4 2 2
AURKB 0.029 0.037 -9999 0 -0.42 3 3
AURKC 0.034 0.021 -9999 0 -0.42 1 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.072 0.069 -10000 0 -0.29 9 9
Ran/GTP/Exportin 1/HDAC1 -0.013 0.009 -10000 0 -0.2 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.043 0.075 -10000 0 -0.3 10 10
SUMO1 0.036 0.004 -10000 0 -10000 0 0
ZFPM1 0.022 0.055 -10000 0 -0.42 7 7
NPC/RanGAP1/SUMO1/Ubc9 0.016 0.011 -10000 0 -0.17 1 1
FKBP3 0.032 0.036 -10000 0 -0.42 3 3
Histones 0.071 0.062 -10000 0 -0.31 2 2
YY1/LSF 0.03 0.059 -10000 0 -0.23 13 13
SMG5 0 0 -10000 0 -10000 0 0
RAN 0.035 0.005 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.027 0.039 -10000 0 -0.24 9 9
I kappa B alpha/HDAC1 0.041 0.054 -10000 0 -0.31 5 5
SAP18 0.033 0.01 -10000 0 -10000 0 0
RELA 0.019 0.057 0.28 1 -0.25 7 8
HDAC1/Smad7 0.067 0.028 -10000 0 -0.25 2 2
RANGAP1 0.032 0.022 -10000 0 -0.42 1 1
HDAC3/TR2 0.039 0.056 -10000 0 -0.25 9 9
NuRD/MBD3 Complex 0.031 0.066 -10000 0 -0.34 7 7
NF kappa B1 p50/RelA 0.037 0.072 0.25 1 -0.36 3 4
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.029 0.046 -10000 0 -0.42 5 5
GATA1 0.036 0 -10000 0 -10000 0 0
Mad/Max 0.051 0.012 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.017 0.092 -10000 0 -0.4 11 11
RBBP7 0.034 0.029 -10000 0 -0.42 2 2
NPC 0.021 0.002 -10000 0 -10000 0 0
RBBP4 0.034 0.021 -10000 0 -0.42 1 1
MAX 0.035 0.007 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.034 0.021 -10000 0 -0.42 1 1
NFKBIA 0.022 0.042 -10000 0 -0.37 4 4
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.021 0.057 -10000 0 -0.33 5 5
SIN3 complex 0.076 0.045 -10000 0 -0.23 5 5
SMURF1 0.035 0.006 -10000 0 -10000 0 0
CHD3 0.031 0.023 -10000 0 -0.42 1 1
SAP30 0.03 0.046 -10000 0 -0.42 5 5
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.032 0.011 -10000 0 -10000 0 0
YY1/HDAC3 0.029 0.05 -10000 0 -0.35 2 2
YY1/HDAC2 0.034 0.045 -10000 0 -0.22 4 4
YY1/HDAC1 0.036 0.046 -10000 0 -0.25 3 3
NuRD/MBD2 Complex (MeCP1) 0.031 0.066 -10000 0 -0.34 6 6
PPARG 0.011 0.092 0.3 1 -0.36 23 24
HDAC8/hEST1B 0.047 0.02 -10000 0 -0.25 2 2
UBE2I 0.032 0.011 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.034 0.021 -10000 0 -0.42 1 1
TNFRSF1A 0.033 0.022 -10000 0 -0.42 1 1
HDAC3/SMRT (N-CoR2) 0.042 0.048 -10000 0 -0.33 2 2
MBD3L2 0.028 0.057 -10000 0 -0.42 8 8
ubiquitin-dependent protein catabolic process 0.066 0.027 -10000 0 -0.25 2 2
CREBBP 0.032 0.011 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.034 0.08 -10000 0 -0.38 6 6
HDAC1 0.034 0.021 -10000 0 -0.42 1 1
HDAC3 0.025 0.029 -10000 0 -0.33 1 1
HDAC2 0.032 0.023 -10000 0 -0.42 1 1
YY1 0.016 0.014 -10000 0 -0.24 1 1
HDAC8 0.034 0.029 -10000 0 -0.42 2 2
SMAD7 0.034 0.021 -10000 0 -0.42 1 1
NCOR2 0.036 0.004 -10000 0 -10000 0 0
MXD1 0.035 0.005 -10000 0 -10000 0 0
STAT3 0.019 0.027 -10000 0 -0.36 2 2
NFKB1 0.035 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.036 0.004 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.048 0.061 -10000 0 -0.22 13 13
YY1/SAP30/HDAC1 0.049 0.058 -10000 0 -0.26 8 8
EP300 0.033 0.022 -10000 0 -0.42 1 1
STAT3 (dimer non-phopshorylated) 0.019 0.027 -10000 0 -0.36 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.042 -10000 0 -0.37 4 4
histone deacetylation 0.031 0.065 -10000 0 -0.34 6 6
STAT3 (dimer non-phopshorylated)/HDAC3 0.023 0.056 -10000 0 -0.38 4 4
nuclear export -0.046 0.02 0.25 2 -10000 0 2
PRKACA 0.036 0.004 -10000 0 -10000 0 0
GATAD2B 0.027 0.025 -10000 0 -0.42 1 1
GATAD2A 0.035 0.006 -10000 0 -10000 0 0
GATA2/HDAC3 0.04 0.049 -10000 0 -0.26 5 5
GATA1/HDAC1 0.051 0.018 -10000 0 -0.3 1 1
GATA1/HDAC3 0.043 0.048 -10000 0 -0.34 2 2
CHD4 0.033 0.022 -10000 0 -0.42 1 1
TNF-alpha/TNFR1A 0.043 0.048 -10000 0 -0.3 9 9
SIN3/HDAC complex/Mad/Max 0.024 0.06 -10000 0 -0.32 6 6
NuRD Complex 0.036 0.076 -10000 0 -0.37 6 6
positive regulation of chromatin silencing 0.067 0.06 -10000 0 -0.3 2 2
SIN3B 0.035 0.005 -10000 0 -10000 0 0
MTA2 0.033 0.03 -10000 0 -0.42 2 2
SIN3A 0.035 0.007 -10000 0 -10000 0 0
XPO1 0.035 0.005 -10000 0 -10000 0 0
SUMO1/HDAC1 0.052 0.044 -10000 0 -0.26 2 2
HDAC complex 0.08 0.042 -10000 0 -0.24 5 5
GATA1/Fog1 0.037 0.046 -10000 0 -0.3 7 7
FKBP25/HDAC1/HDAC2 0.061 0.04 -10000 0 -0.26 5 5
TNF 0.026 0.061 -10000 0 -0.42 9 9
negative regulation of cell growth 0.024 0.059 -10000 0 -0.32 6 6
NuRD/MBD2/PRMT5 Complex 0.031 0.066 -10000 0 -0.34 6 6
Ran/GTP/Exportin 1 0.053 0.042 -10000 0 -0.24 1 1
NF kappa B/RelA/I kappa B alpha 0.021 0.065 -10000 0 -0.31 11 11
SIN3/HDAC complex/NCoR1 0.016 0.06 -10000 0 -0.28 9 9
TFCP2 0.027 0.064 -10000 0 -0.42 10 10
NR2C1 0.029 0.054 -10000 0 -0.42 7 7
MBD3 0.034 0.008 -10000 0 -10000 0 0
MBD2 0.035 0.007 -10000 0 -10000 0 0
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 0.015 0.039 0.16 5 -0.18 1 6
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.021 0.042 0.17 5 -0.21 2 7
AP2 0.046 0.034 -10000 0 -0.3 4 4
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.042 0.035 -10000 0 -0.24 7 7
CLTB 0.033 0.029 -10000 0 -0.42 2 2
coatomer protein complex/ARF1/GTP/ER cargo protein 0.016 0.022 -10000 0 -0.22 3 3
CD4 0.034 0.009 -10000 0 -10000 0 0
CLTA 0.035 0.006 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
ARFGAP1 0.008 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.019 0.033 0.17 5 -0.13 2 7
ARF1/GTP 0.016 0.017 -10000 0 -0.25 1 1
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.021 0.045 0.17 37 -0.19 1 38
mol:Choline 0.019 0.033 0.18 5 -0.14 2 7
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.028 0.026 -10000 0 -0.43 1 1
DDEF1 0.014 0.029 0.16 3 -0.17 1 4
ARF1/GDP 0.001 0.021 -10000 0 -0.11 6 6
AP2M1 0.031 0.041 -10000 0 -0.42 4 4
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.011 0.013 -10000 0 -0.23 1 1
Rac/GTP 0.028 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.032 0.027 -10000 0 -0.22 1 1
ARFIP2 0.02 0.053 -10000 0 -0.39 7 7
COPA 0.029 0.015 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.015 0.028 -10000 0 -0.19 2 2
ARF1/GTP/ARHGAP10 0.018 0.016 -10000 0 -0.25 1 1
GGA3 0.032 0.023 -10000 0 -0.42 1 1
ARF1/GTP/Membrin 0.016 0.046 -10000 0 -0.24 13 13
AP2A1 0.035 0.007 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.01 0.029 -10000 0 -0.22 4 4
ARF1/GDP/Membrin 0.015 0.052 -10000 0 -0.27 14 14
Arfaptin 2/Rac/GDP 0.039 0.037 -10000 0 -0.25 7 7
CYTH2 -0.001 0.003 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.033 0.026 -10000 0 -0.26 1 1
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.026 0.004 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.023 0.04 -10000 0 -0.4 2 2
PLD2 0.019 0.033 0.18 5 -0.14 2 7
ARF-GAP1/v-SNARE 0.008 0.003 -10000 0 -10000 0 0
PIP5K1A 0.019 0.033 0.17 5 -0.13 2 7
ARF1/GTP/Membrin/GBF1/p115 0.013 0.025 -10000 0 -0.22 1 1
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.019 0.033 0.18 5 -0.14 2 7
KDEL Receptor/Ligand/ARF-GAP1 0.008 0.003 -10000 0 -10000 0 0
GOSR2 0.018 0.038 -10000 0 -0.32 5 5
USO1 0.009 0.017 0.091 5 -0.063 2 7
GBF1 0.019 0.036 -10000 0 -0.32 4 4
ARF1/GTP/Arfaptin 2 0.034 0.032 -10000 0 -0.25 3 3
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.06 0.038 -10000 0 -0.26 4 4
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 0.055 0.04 -10000 0 -0.24 7 7
MAPK9 -0.002 0.057 -10000 0 -0.29 19 19
adrenocorticotropin secretion 0.005 0.024 -10000 0 -0.3 3 3
GNB1/GNG2 0.044 0.034 -10000 0 -0.25 6 6
GNB1 0.032 0.045 -10000 0 -0.42 5 5
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.02 0.02 -10000 0 -0.22 3 3
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.002 0.005 0.062 3 -10000 0 3
GNAL 0.031 0.036 -10000 0 -0.42 3 3
GNG2 0.034 0.021 -10000 0 -0.42 1 1
CRH 0.026 0.038 -10000 0 -0.42 3 3
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.008 0.023 -10000 0 -0.29 3 3
MAPK11 0.009 0.003 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

Figure S131.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S131.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.034 0.021 -10000 0 -0.42 1 1
Ran/GTP/Exportin 1/HDAC4 0.006 0.014 -10000 0 -0.18 1 1
MDM2/SUMO1 0.05 0.042 -10000 0 -10000 0 0
HDAC4 0.034 0.021 -10000 0 -0.42 1 1
Ran/GTP/Exportin 1/HDAC1 0.006 0.015 -10000 0 -0.21 1 1
SUMO1 0.036 0.004 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.013 0.02 -10000 0 -0.25 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.006 0.024 -10000 0 -0.26 1 1
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 0.036 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.051 0.044 -10000 0 -0.21 2 2
SUMO1/HDAC1 0.052 0.044 -10000 0 -0.26 2 2
RANGAP1 0.032 0.022 -10000 0 -0.42 1 1
MDM2/SUMO1/SUMO1 0.08 0.036 -10000 0 -0.24 2 2
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.016 0.011 -10000 0 -0.17 1 1
Ran/GTP 0.036 0.039 -10000 0 -0.2 2 2
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.034 0.009 -10000 0 -10000 0 0
UBE2I 0.032 0.011 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0.041 0.21 6 -0.24 1 7
NPC 0.021 0.002 -10000 0 -10000 0 0
PIAS2 0.033 0.03 -10000 0 -0.42 2 2
PIAS1 0.035 0.006 -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/1970996/2.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/2008269/1.GetReducedSegments.Finished/BRCA.RS.tsv

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

References
[2] Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, and Joshua M. Stuart, Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, Bioinformatics 12(26):237-245 (2010)
Copyright © 2012 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle