Breast Invasive Carcinoma: PARADIGM pathway analysis of mRNASeq expression and copy number data
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/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 35 significant pathways identified in this analysis.

Table 1.  Get Full Table Top 10 out of 131 pathways in order of significance.

Pathway.Name Avg.Num.Perturbations
Signaling events regulated by Ret tyrosine kinase 125
IL4-mediated signaling events 113
Syndecan-1-mediated signaling events 100
Glucocorticoid receptor regulatory network 93
Plasma membrane estrogen receptor signaling 91
IL23-mediated signaling events 84
TCR signaling in naïve CD8+ T cells 82
Endothelins 77
EGFR-dependent Endothelin signaling events 72
FOXA2 and FOXA3 transcription factor networks 71
Results
Summary Table

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 125 10286 82 -0.12 0.029 1000 -1000 -0.05 -1000
IL4-mediated signaling events 113 10296 91 -0.59 0.51 1000 -1000 -0.11 -1000
Syndecan-1-mediated signaling events 100 3412 34 -0.12 0.029 1000 -1000 -0.027 -1000
Glucocorticoid receptor regulatory network 93 10642 114 -0.44 0.26 1000 -1000 -0.063 -1000
Plasma membrane estrogen receptor signaling 91 7855 86 -0.19 0.18 1000 -1000 -0.052 -1000
IL23-mediated signaling events 84 5045 60 -0.32 0.028 1000 -1000 -0.089 -1000
TCR signaling in naïve CD8+ T cells 82 7718 93 -0.13 0.04 1000 -1000 -0.045 -1000
Endothelins 77 7445 96 -0.19 0.07 1000 -1000 -0.05 -1000
EGFR-dependent Endothelin signaling events 72 1532 21 -0.057 0.04 1000 -1000 -0.039 -1000
FOXA2 and FOXA3 transcription factor networks 71 3293 46 -0.29 0.032 1000 -1000 -0.077 -1000
Noncanonical Wnt signaling pathway 68 1771 26 -0.068 0.029 1000 -1000 -0.033 -1000
Ephrin A reverse signaling 65 458 7 -0.032 0.023 1000 -1000 -0.006 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 64 4413 68 -0.21 0.064 1000 -1000 -0.081 -1000
IL12-mediated signaling events 62 5417 87 -0.2 0.053 1000 -1000 -0.066 -1000
HIF-1-alpha transcription factor network 62 4786 76 -0.2 0.04 1000 -1000 -0.068 -1000
Wnt signaling 61 429 7 -0.064 0.001 1000 -1000 -0.01 -1000
IGF1 pathway 59 3401 57 -0.05 0.045 1000 -1000 -0.046 -1000
BMP receptor signaling 56 4573 81 -0.1 0.052 1000 -1000 -0.033 -1000
LPA receptor mediated events 55 5663 102 -0.096 0.037 1000 -1000 -0.074 -1000
Class IB PI3K non-lipid kinase events 55 165 3 -0.009 -1000 1000 -1000 -0.015 -1000
FOXM1 transcription factor network 55 2848 51 -0.25 0.037 1000 -1000 -0.093 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 55 4336 78 -0.13 0.064 1000 -1000 -0.059 -1000
Nongenotropic Androgen signaling 54 2830 52 -0.076 0.05 1000 -1000 -0.03 -1000
BCR signaling pathway 53 5328 99 -0.11 0.043 1000 -1000 -0.047 -1000
p75(NTR)-mediated signaling 52 6588 125 -0.056 0.067 1000 -1000 -0.059 -1000
Fc-epsilon receptor I signaling in mast cells 52 5046 97 -0.074 0.042 1000 -1000 -0.056 -1000
Signaling mediated by p38-alpha and p38-beta 52 2330 44 -0.073 0.029 1000 -1000 -0.019 -1000
Syndecan-4-mediated signaling events 51 3474 67 -0.066 0.066 1000 -1000 -0.026 -1000
Reelin signaling pathway 50 2831 56 -0.081 0.062 1000 -1000 -0.028 -1000
FAS signaling pathway (CD95) 49 2311 47 -0.13 0.043 1000 -1000 -0.031 -1000
Effects of Botulinum toxin 49 1286 26 -0.075 0.026 1000 -1000 -0.004 -1000
Signaling events mediated by the Hedgehog family 45 2380 52 -0.11 0.04 1000 -1000 -0.038 -1000
Stabilization and expansion of the E-cadherin adherens junction 44 3327 74 -0.095 0.058 1000 -1000 -0.057 -1000
Caspase cascade in apoptosis 43 3236 74 -0.058 0.061 1000 -1000 -0.033 -1000
Osteopontin-mediated events 43 1645 38 -0.044 0.037 1000 -1000 -0.04 -1000
LPA4-mediated signaling events 42 512 12 -0.073 0.004 1000 -1000 -0.024 -1000
IL27-mediated signaling events 41 2128 51 -0.16 0.041 1000 -1000 -0.052 -1000
IL6-mediated signaling events 41 3105 75 -0.18 0.061 1000 -1000 -0.056 -1000
Visual signal transduction: Cones 40 1550 38 -0.045 0.033 1000 -1000 -0.006 -1000
Calcium signaling in the CD4+ TCR pathway 40 1257 31 -0.11 0.028 1000 -1000 -0.034 -1000
Visual signal transduction: Rods 40 2090 52 -0.043 0.029 1000 -1000 -0.021 -1000
amb2 Integrin signaling 39 3274 82 -0.088 0.037 1000 -1000 -0.025 -1000
Coregulation of Androgen receptor activity 38 2921 76 -0.12 0.047 1000 -1000 -0.029 -1000
Arf6 signaling events 38 2413 62 -0.057 0.053 1000 -1000 -0.033 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 38 3314 85 -0.063 0.029 1000 -1000 -0.044 -1000
Neurotrophic factor-mediated Trk receptor signaling 38 4645 120 -0.073 0.075 1000 -1000 -0.049 -1000
Thromboxane A2 receptor signaling 37 3889 105 -0.056 0.046 1000 -1000 -0.048 -1000
Signaling events mediated by PTP1B 37 2819 76 -0.096 0.036 1000 -1000 -0.034 -1000
IL2 signaling events mediated by PI3K 36 2096 58 -0.14 0.045 1000 -1000 -0.038 -1000
ErbB2/ErbB3 signaling events 35 2299 65 -0.051 0.04 1000 -1000 -0.073 -1000
Canonical Wnt signaling pathway 35 1805 51 -0.058 0.089 1000 -1000 -0.044 -1000
Nephrin/Neph1 signaling in the kidney podocyte 34 1182 34 -0.008 0.04 1000 -1000 -0.023 -1000
JNK signaling in the CD4+ TCR pathway 34 590 17 -0.037 0.038 1000 -1000 -0.027 -1000
Ephrin B reverse signaling 34 1663 48 -0.064 0.054 1000 -1000 -0.024 -1000
Signaling mediated by p38-gamma and p38-delta 33 509 15 -0.059 0.028 1000 -1000 -0.028 -1000
S1P4 pathway 33 841 25 -0.023 0.038 1000 -1000 -0.023 -1000
Aurora B signaling 32 2156 67 -0.13 0.041 1000 -1000 -0.03 -1000
E-cadherin signaling in the nascent adherens junction 31 2382 76 -0.041 0.048 1000 -1000 -0.046 -1000
E-cadherin signaling in keratinocytes 31 1345 43 -0.033 0.029 1000 -1000 -0.032 -1000
Syndecan-2-mediated signaling events 30 2072 69 -0.026 0.047 1000 -1000 -0.032 -1000
Glypican 1 network 30 1444 48 -0.072 0.051 1000 -1000 -0.031 -1000
E-cadherin signaling events 29 147 5 -0.004 0.028 1000 -1000 0.01 -1000
Integrins in angiogenesis 28 2384 84 -0.076 0.059 1000 -1000 -0.036 -1000
Ras signaling in the CD4+ TCR pathway 28 483 17 -0.017 0.045 1000 -1000 -0.025 -1000
Cellular roles of Anthrax toxin 26 1050 39 -0.08 0.028 1000 -1000 -0.02 -1000
EPHB forward signaling 26 2262 85 -0.073 0.11 1000 -1000 -0.059 -1000
Glypican 2 network 26 105 4 0.005 0.015 1000 -1000 0.016 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 25 1362 54 -0.05 0.041 1000 -1000 -0.031 -1000
PLK1 signaling events 25 2144 85 -0.012 0.047 1000 -1000 -0.037 -1000
PDGFR-alpha signaling pathway 25 1143 44 -0.069 0.043 1000 -1000 -0.037 -1000
Regulation of nuclear SMAD2/3 signaling 24 3336 136 -0.1 0.073 1000 -1000 -0.034 -1000
ceramide signaling pathway 24 1193 49 -0.018 0.041 1000 -1000 -0.031 -1000
S1P1 pathway 24 878 36 -0.053 0.029 1000 -1000 -0.035 -1000
Presenilin action in Notch and Wnt signaling 23 1407 61 -0.064 0.065 1000 -1000 -0.043 -1000
Nectin adhesion pathway 23 1481 63 -0.018 0.056 1000 -1000 -0.05 -1000
IL1-mediated signaling events 23 1464 62 -0.024 0.072 1000 -1000 -0.036 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 23 1075 45 -0.036 0.062 1000 -1000 -0.033 -1000
Regulation of Telomerase 23 2357 102 -0.11 0.055 1000 -1000 -0.039 -1000
Regulation of Androgen receptor activity 23 1639 70 -0.13 0.039 1000 -1000 -0.065 -1000
Ceramide signaling pathway 22 1680 76 -0.056 0.075 1000 -1000 -0.031 -1000
Regulation of p38-alpha and p38-beta 22 1204 54 -0.056 0.062 1000 -1000 -0.048 -1000
IL2 signaling events mediated by STAT5 22 491 22 -0.055 0.032 1000 -1000 -0.044 -1000
Angiopoietin receptor Tie2-mediated signaling 21 1870 88 -0.081 0.043 1000 -1000 -0.06 -1000
ErbB4 signaling events 20 1443 69 -0.088 0.039 1000 -1000 -0.035 -1000
IFN-gamma pathway 20 1415 68 -0.049 0.048 1000 -1000 -0.05 -1000
Class I PI3K signaling events 20 1468 73 -0.068 0.05 1000 -1000 -0.04 -1000
TCGA08_retinoblastoma 20 162 8 -0.003 0.007 1000 -1000 -0.003 -1000
Insulin Pathway 20 1499 74 -0.081 0.065 1000 -1000 -0.043 -1000
EPO signaling pathway 19 1072 55 -0.036 0.056 1000 -1000 -0.035 -1000
mTOR signaling pathway 19 1055 53 -0.042 0.032 1000 -1000 -0.032 -1000
TCGA08_p53 19 139 7 -0.003 0.024 1000 -1000 -0.004 -1000
Hedgehog signaling events mediated by Gli proteins 18 1207 65 -0.053 0.063 1000 -1000 -0.044 -1000
PDGFR-beta signaling pathway 18 1839 97 -0.098 0.063 1000 -1000 -0.051 -1000
RXR and RAR heterodimerization with other nuclear receptor 17 889 52 -0.019 0.061 1000 -1000 -0.043 -1000
Sphingosine 1-phosphate (S1P) pathway 16 464 28 -0.011 0.054 1000 -1000 -0.017 -1000
a4b1 and a4b7 Integrin signaling 16 84 5 0.012 0.035 1000 -1000 0.013 -1000
S1P5 pathway 16 279 17 -0.008 0.029 1000 -1000 -0.011 -1000
TCGA08_rtk_signaling 16 425 26 -0.022 0.059 1000 -1000 -0.008 -1000
S1P3 pathway 16 674 42 -0.009 0.047 1000 -1000 -0.037 -1000
Aurora A signaling 14 871 60 -0.02 0.048 1000 -1000 -0.018 -1000
TRAIL signaling pathway 14 683 48 0 0.044 1000 -1000 -0.03 -1000
Atypical NF-kappaB pathway 14 443 31 -0.017 0.04 1000 -1000 -0.015 -1000
Syndecan-3-mediated signaling events 13 469 35 -0.024 0.065 1000 -1000 -0.021 -1000
Aurora C signaling 12 89 7 0 0.031 1000 -1000 -0.01 -1000
HIF-2-alpha transcription factor network 12 535 43 -0.096 0.098 1000 -1000 -0.05 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 12 998 83 -0.018 0.057 1000 -1000 -0.031 -1000
p38 MAPK signaling pathway 12 563 44 -0.049 0.053 1000 -1000 -0.018 -1000
BARD1 signaling events 11 642 57 -0.05 0.059 1000 -1000 -0.035 -1000
Paxillin-independent events mediated by a4b1 and a4b7 11 427 37 -0.017 0.062 1000 -1000 -0.028 -1000
Signaling events mediated by HDAC Class III 11 467 40 -0.053 0.054 1000 -1000 -0.027 -1000
Signaling events mediated by HDAC Class II 10 766 75 -0.089 0.075 1000 -1000 -0.03 -1000
Retinoic acid receptors-mediated signaling 10 627 58 -0.011 0.06 1000 -1000 -0.048 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 10 349 33 -0.027 0.062 1000 -1000 -0.038 -1000
Canonical NF-kappaB pathway 9 367 39 0 0.062 1000 -1000 -0.033 -1000
FoxO family signaling 9 635 64 -0.084 0.055 1000 -1000 -0.056 -1000
Signaling events mediated by PRL 9 313 34 -0.044 0.042 1000 -1000 -0.041 -1000
Signaling events mediated by HDAC Class I 8 933 104 -0.049 0.067 1000 -1000 -0.029 -1000
Paxillin-dependent events mediated by a4b1 8 295 36 -0.051 0.056 1000 -1000 -0.037 -1000
Signaling events mediated by VEGFR1 and VEGFR2 8 1026 125 -0.01 0.066 1000 -1000 -0.043 -1000
PLK2 and PLK4 events 6 19 3 0.009 0.026 1000 -1000 -0.006 -1000
Arf6 trafficking events 6 462 71 -0.048 0.049 1000 -1000 -0.029 -1000
VEGFR1 specific signals 6 353 56 -0.024 0.065 1000 -1000 -0.046 -1000
Arf6 downstream pathway 5 250 43 -0.047 0.048 1000 -1000 -0.026 -1000
Insulin-mediated glucose transport 5 176 32 -0.001 0.045 1000 -1000 -0.029 -1000
Class I PI3K signaling events mediated by Akt 5 401 68 -0.042 0.05 1000 -1000 -0.036 -1000
Rapid glucocorticoid signaling 4 92 20 0 0.037 1000 -1000 -0.001 -1000
Circadian rhythm pathway 3 66 22 -0.008 0.053 1000 -1000 -0.037 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 2 54 23 -0.001 0.051 1000 -1000 -0.026 -1000
Sumoylation by RanBP2 regulates transcriptional repression 1 37 27 0 0.067 1000 -1000 -0.029 -1000
Arf1 pathway 1 90 54 -0.001 0.052 1000 -1000 -0.017 -1000
Alternative NF-kappaB pathway 0 12 13 0 0.078 1000 -1000 0 -1000
Total 4285 261476 7203 -9.4 -990 131000 -131000 -4.7 -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 -0.028 0.1 -10000 0 -0.47 31 31
Crk/p130 Cas/Paxillin -0.1 0.15 -10000 0 -0.34 200 200
JUN -0.097 0.16 0.18 1 -0.42 114 115
HRAS 0.026 0.036 -10000 0 -0.48 4 4
RET51/GFRalpha1/GDNF/GRB10 -0.083 0.21 -10000 0 -0.36 286 286
RAP1A 0.029 0.005 -10000 0 -10000 0 0
FRS2 0.028 0.009 -10000 0 -10000 0 0
RAP1A/GDP 0.021 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.084 0.21 -10000 0 -0.36 285 285
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.029 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.009 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.042 0.14 -10000 0 -0.27 229 229
RHOA 0.028 0.006 -10000 0 -10000 0 0
RAP1A/GTP -0.08 0.19 -10000 0 -0.32 287 287
GRB7 0.022 0.036 -10000 0 -0.48 4 4
RET51/GFRalpha1/GDNF -0.083 0.21 -10000 0 -0.36 287 287
MAPKKK cascade -0.095 0.19 -10000 0 -0.34 268 268
BCAR1 0.026 0.01 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.057 0.17 -10000 0 -0.31 241 241
lamellipodium assembly -0.084 0.15 -10000 0 -0.32 200 200
RET51/GFRalpha1/GDNF/SHC -0.075 0.19 -10000 0 -0.34 256 256
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.033 0.13 -10000 0 -0.27 174 174
RET9/GFRalpha1/GDNF/Shank3 -0.043 0.14 -10000 0 -0.27 228 228
MAPK3 -0.11 0.16 0.19 3 -0.32 269 272
DOK1 0.027 0.035 -10000 0 -0.48 4 4
DOK6 0.008 0.097 -10000 0 -0.48 31 31
PXN 0.029 0.002 -10000 0 -10000 0 0
neurite development -0.11 0.16 -10000 0 -0.41 118 118
DOK5 0.008 0.086 -10000 0 -0.48 24 24
GFRA1 -0.12 0.23 -10000 0 -0.48 238 238
MAPK8 -0.099 0.17 -10000 0 -0.31 285 285
HRAS/GTP -0.094 0.22 -10000 0 -0.37 288 288
tube development -0.034 0.14 0.21 17 -0.26 220 237
MAPK1 -0.12 0.16 -10000 0 -0.4 128 128
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.05 0.11 -10000 0 -0.23 218 218
Rac1/GDP 0.021 0.003 -10000 0 -10000 0 0
SRC 0.027 0.026 -10000 0 -0.48 2 2
PDLIM7 0.027 0.025 -10000 0 -0.48 2 2
RET51/GFRalpha1/GDNF/Dok6 -0.083 0.22 -10000 0 -0.35 294 294
SHC1 0.024 0.011 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.089 0.21 -10000 0 -0.35 288 288
RET51/GFRalpha1/GDNF/Dok5 -0.094 0.21 -10000 0 -0.36 289 289
PRKCA 0.017 0.06 -10000 0 -0.48 11 11
HRAS/GDP 0.019 0.026 -10000 0 -0.34 4 4
CREB1 -0.085 0.17 -10000 0 -0.35 203 203
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.036 0.1 -10000 0 -0.24 167 167
RET51/GFRalpha1/GDNF/Grb7 -0.079 0.2 -10000 0 -0.36 253 253
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.08 0.2 -10000 0 -0.48 164 164
DOK4 0.024 0.027 -10000 0 -0.48 2 2
JNK cascade -0.095 0.16 0.19 1 -0.41 114 115
RET9/GFRalpha1/GDNF/FRS2 -0.042 0.14 -10000 0 -0.27 228 228
SHANK3 0.027 0.008 -10000 0 -10000 0 0
RASA1 0.028 0.007 -10000 0 -10000 0 0
NCK1 0.029 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.038 0.1 -10000 0 -0.24 169 169
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.093 0.17 -10000 0 -0.32 274 274
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.098 0.18 -10000 0 -0.32 287 287
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.1 0.2 -10000 0 -0.37 243 243
PI3K -0.12 0.23 0.23 1 -0.48 203 204
SOS1 0.029 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.031 0.14 -10000 0 -0.26 220 220
GRB10 0.028 0.018 -10000 0 -0.48 1 1
activation of MAPKK activity -0.073 0.15 -10000 0 -0.37 106 106
RET51/GFRalpha1/GDNF/FRS2 -0.085 0.21 -10000 0 -0.36 285 285
GAB1 0.028 0.018 -10000 0 -0.48 1 1
IRS1 -0.003 0.12 -10000 0 -0.48 52 52
IRS2 0.018 0.057 -10000 0 -0.48 10 10
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.1 0.2 -10000 0 -0.37 244 244
RET51/GFRalpha1/GDNF/PKC alpha -0.087 0.21 -10000 0 -0.36 275 275
GRB2 0.027 0.008 -10000 0 -10000 0 0
PRKACA 0.029 0.004 -10000 0 -10000 0 0
GDNF 0.02 0.017 -10000 0 -10000 0 0
RAC1 0.029 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.099 0.23 -10000 0 -0.38 298 298
Rac1/GTP -0.096 0.18 -10000 0 -0.38 199 199
RET9/GFRalpha1/GDNF -0.063 0.14 -10000 0 -0.29 229 229
GFRalpha1/GDNF -0.076 0.17 -10000 0 -0.35 229 229
IL4-mediated signaling events

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
BCL2L1 -0.44 0.56 -10000 0 -1.3 191 191
STAT6 (cleaved dimer) -0.46 0.59 -10000 0 -1.3 214 214
IGHG1 -0.13 0.18 -10000 0 -0.41 47 47
IGHG3 -0.43 0.54 -10000 0 -1.2 217 217
AKT1 -0.21 0.33 -10000 0 -0.82 117 117
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.17 0.35 -10000 0 -0.99 84 84
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.23 0.36 -10000 0 -0.83 136 136
THY1 -0.44 0.57 -10000 0 -1.3 186 186
MYB -0.031 0.16 -10000 0 -0.48 95 95
HMGA1 0.028 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.28 0.42 -10000 0 -0.83 203 203
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.22 0.36 -10000 0 -0.91 101 101
SP1 0.027 0.03 -10000 0 -10000 0 0
INPP5D 0.026 0.032 -10000 0 -0.48 3 3
SOCS5 0.033 0.027 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.46 0.6 -10000 0 -1.3 209 209
SOCS1 -0.28 0.35 -10000 0 -0.78 198 198
SOCS3 -0.22 0.33 -10000 0 -0.94 81 81
FCER2 -0.41 0.55 -10000 0 -1.3 164 164
PARP14 0.023 0.045 -10000 0 -0.48 6 6
CCL17 -0.51 0.64 -10000 0 -1.4 223 223
GRB2 0.027 0.008 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.16 0.27 -10000 0 -0.73 77 77
T cell proliferation -0.45 0.6 -10000 0 -1.3 209 209
IL4R/JAK1 -0.44 0.57 -10000 0 -1.3 196 196
EGR2 -0.46 0.58 -10000 0 -1.3 193 193
JAK2 -0.018 0.053 -10000 0 -0.52 1 1
JAK3 0.014 0.077 -10000 0 -0.46 20 20
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
JAK1 0.004 0.028 -10000 0 -10000 0 0
COL1A2 -0.18 0.38 -10000 0 -1.5 56 56
CCL26 -0.48 0.6 -10000 0 -1.3 218 218
IL4R -0.47 0.62 -10000 0 -1.4 194 194
PTPN6 0.036 0.015 -10000 0 -10000 0 0
IL13RA2 -0.48 0.6 -10000 0 -1.3 222 222
IL13RA1 -0.018 0.051 -10000 0 -10000 0 0
IRF4 -0.24 0.53 -10000 0 -1.4 125 125
ARG1 -0.089 0.16 -10000 0 -0.7 6 6
CBL -0.26 0.38 -10000 0 -0.78 195 195
GTF3A 0.023 0.032 -10000 0 -0.12 4 4
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.019 0.071 -10000 0 -0.39 1 1
IRF4/BCL6 -0.21 0.48 -10000 0 -1.3 125 125
CD40LG -0.03 0.15 -10000 0 -0.48 77 77
MAPK14 -0.26 0.38 -10000 0 -0.83 167 167
mitosis -0.2 0.31 -10000 0 -0.75 117 117
STAT6 -0.55 0.77 -10000 0 -1.6 210 210
SPI1 0.027 0.04 -10000 0 -0.48 5 5
RPS6KB1 -0.17 0.3 0.45 1 -0.73 111 112
STAT6 (dimer) -0.54 0.77 -10000 0 -1.6 210 210
STAT6 (dimer)/PARP14 -0.49 0.65 -10000 0 -1.4 211 211
mast cell activation 0.01 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.24 0.39 -10000 0 -0.94 122 122
FRAP1 -0.21 0.33 -10000 0 -0.82 117 117
LTA -0.48 0.62 -10000 0 -1.4 207 207
FES 0.022 0.056 -10000 0 -0.48 10 10
T-helper 1 cell differentiation 0.51 0.68 1.5 212 -10000 0 212
CCL11 -0.46 0.59 -10000 0 -1.3 213 213
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.22 0.38 -10000 0 -0.98 98 98
IL2RG 0.002 0.1 -10000 0 -0.46 37 37
IL10 -0.43 0.59 -10000 0 -1.3 186 186
IRS1 -0.003 0.12 -10000 0 -0.48 52 52
IRS2 0.018 0.057 -10000 0 -0.48 10 10
IL4 -0.092 0.12 -10000 0 -0.24 186 186
IL5 -0.44 0.57 -10000 0 -1.2 216 216
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.33 0.42 -10000 0 -0.92 198 198
COL1A1 -0.24 0.48 -10000 0 -1.4 98 98
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.45 0.6 -10000 0 -1.4 191 191
IL2R gamma/JAK3 0.012 0.11 -10000 0 -0.43 41 41
TFF3 -0.59 0.69 -10000 0 -1.4 293 293
ALOX15 -0.55 0.66 -10000 0 -1.4 260 260
MYBL1 0.007 0.086 -10000 0 -0.48 24 24
T-helper 2 cell differentiation -0.37 0.49 -10000 0 -1.1 218 218
SHC1 0.024 0.011 -10000 0 -10000 0 0
CEBPB 0.027 0.021 -10000 0 -0.48 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.22 0.36 -10000 0 -0.87 111 111
mol:PI-3-4-5-P3 -0.21 0.33 -10000 0 -0.82 117 117
PI3K -0.23 0.37 -10000 0 -0.9 117 117
DOK2 0.012 0.071 -10000 0 -0.48 16 16
ETS1 0.029 0.037 -10000 0 -0.44 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.14 0.26 -10000 0 -0.74 63 63
ITGB3 -0.45 0.58 -10000 0 -1.3 198 198
PIGR -0.54 0.7 -10000 0 -1.4 266 266
IGHE 0.026 0.071 0.19 68 -0.2 3 71
MAPKKK cascade -0.14 0.25 -10000 0 -0.72 63 63
BCL6 0.027 0.032 -10000 0 -0.48 3 3
OPRM1 -0.44 0.57 -10000 0 -1.2 216 216
RETNLB -0.44 0.57 -10000 0 -1.2 216 216
SELP -0.5 0.66 -10000 0 -1.4 226 226
AICDA -0.42 0.54 -10000 0 -1.2 194 194
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.027 0.031 -10000 0 -0.48 3 3
CCL5 -0.002 0.11 -10000 0 -0.48 41 41
SDCBP 0.025 0.011 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.11 0.21 -10000 0 -0.39 229 229
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 -0.1 0.21 -10000 0 -0.51 124 124
Syndecan-1/Syntenin -0.094 0.21 0.33 1 -0.49 124 125
MAPK3 -0.092 0.19 0.31 1 -0.49 113 114
HGF/MET -0.015 0.14 -10000 0 -0.38 107 107
TGFB1/TGF beta receptor Type II 0.027 0.031 -10000 0 -0.48 3 3
BSG 0.028 0.006 -10000 0 -10000 0 0
keratinocyte migration -0.1 0.21 -10000 0 -0.5 124 124
Syndecan-1/RANTES -0.11 0.23 0.33 2 -0.51 147 149
Syndecan-1/CD147 -0.087 0.22 0.33 2 -0.51 120 122
Syndecan-1/Syntenin/PIP2 -0.092 0.2 0.31 1 -0.48 124 125
LAMA5 0.026 0.026 -10000 0 -0.48 2 2
positive regulation of cell-cell adhesion -0.09 0.2 0.3 1 -0.46 124 125
MMP7 -0.032 0.15 -10000 0 -0.48 80 80
HGF -0.002 0.12 -10000 0 -0.48 49 49
Syndecan-1/CASK -0.11 0.2 -10000 0 -0.37 236 236
Syndecan-1/HGF/MET -0.12 0.24 0.33 1 -0.53 155 156
regulation of cell adhesion -0.095 0.18 0.26 1 -0.49 109 110
HPSE 0.008 0.098 -10000 0 -0.48 32 32
positive regulation of cell migration -0.11 0.21 -10000 0 -0.39 229 229
SDC1 -0.11 0.22 -10000 0 -0.39 228 228
Syndecan-1/Collagen -0.11 0.21 -10000 0 -0.39 229 229
PPIB 0.028 0.006 -10000 0 -10000 0 0
MET -0.018 0.14 -10000 0 -0.48 71 71
PRKACA 0.029 0.004 -10000 0 -10000 0 0
MMP9 -0.028 0.15 -10000 0 -0.48 82 82
MAPK1 -0.094 0.2 0.31 1 -0.49 114 115
homophilic cell adhesion -0.1 0.22 0.24 10 -0.39 227 237
MMP1 -0.089 0.2 -10000 0 -0.48 165 165
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.082 0.1 0.35 3 -0.84 1 4
SMARCC2 0.03 0.012 -10000 0 -0.14 4 4
SMARCC1 0.027 0.028 -10000 0 -0.48 2 2
TBX21 -0.14 0.24 0.33 3 -0.6 125 128
SUMO2 0.023 0.018 -10000 0 -10000 0 0
STAT1 (dimer) 0.033 0.016 -10000 0 -0.2 3 3
FKBP4 0.027 0.019 -10000 0 -0.48 1 1
FKBP5 0.012 0.086 -10000 0 -0.48 24 24
GR alpha/HSP90/FKBP51/HSP90 0.12 0.12 0.32 119 -0.26 14 133
PRL -0.061 0.11 -10000 0 -0.52 1 1
cortisol/GR alpha (dimer)/TIF2 0.17 0.26 0.57 184 -0.33 5 189
RELA -0.012 0.089 -10000 0 -0.24 43 43
FGG 0.15 0.25 0.47 214 -0.53 30 244
GR beta/TIF2 0.086 0.14 0.31 146 -0.31 25 171
IFNG -0.33 0.41 -10000 0 -0.86 250 250
apoptosis -0.025 0.21 0.52 18 -0.56 60 78
CREB1 -0.032 0.13 -10000 0 -0.33 121 121
histone acetylation -0.034 0.12 0.28 16 -0.36 44 60
BGLAP -0.079 0.16 -10000 0 -0.58 27 27
GR/PKAc 0.12 0.11 0.29 150 -0.24 4 154
NF kappa B1 p50/RelA -0.022 0.15 -10000 0 -0.33 119 119
SMARCD1 0.03 0.011 -10000 0 -10000 0 0
MDM2 0.088 0.1 0.24 220 -10000 0 220
GATA3 -0.041 0.18 -10000 0 -0.48 114 114
AKT1 0.024 0.008 0.19 1 -10000 0 1
CSF2 -0.065 0.11 -10000 0 -0.48 18 18
GSK3B 0.024 0.018 -10000 0 -10000 0 0
NR1I3 0.001 0.21 0.59 11 -0.66 22 33
CSN2 0.14 0.18 0.37 252 -0.26 13 265
BRG1/BAF155/BAF170/BAF60A 0.073 0.042 -10000 0 -0.36 6 6
NFATC1 0.023 0.05 -10000 0 -0.48 8 8
POU2F1 0.026 0.012 -10000 0 -10000 0 0
CDKN1A -0.004 0.14 -10000 0 -1.5 6 6
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.001 0.007 -10000 0 -10000 0 0
SFN 0.014 0.082 -10000 0 -0.48 22 22
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.12 0.13 0.32 106 -0.26 21 127
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.033 0.22 0.48 15 -0.7 41 56
JUN -0.21 0.23 0.3 1 -0.5 269 270
IL4 -0.11 0.15 -10000 0 -0.32 214 214
CDK5R1 0.026 0.02 -10000 0 -0.48 1 1
PRKACA 0.029 0.004 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.1 0.22 0.22 110 -0.41 224 334
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.12 0.32 107 -0.26 10 117
cortisol/GR alpha (monomer) 0.26 0.32 0.66 251 -0.34 12 263
NCOA2 0.006 0.093 -10000 0 -0.48 29 29
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.065 0.14 -10000 0 -0.47 55 55
AP-1/NFAT1-c-4 -0.33 0.36 -10000 0 -0.72 311 311
AFP -0.27 0.43 0.47 1 -1.4 90 91
SUV420H1 0.027 0.008 -10000 0 -10000 0 0
IRF1 0.14 0.16 0.45 100 -0.74 1 101
TP53 0.033 0.054 -10000 0 -0.47 9 9
PPP5C 0.029 0.004 -10000 0 -10000 0 0
KRT17 -0.43 0.56 -10000 0 -1.2 244 244
KRT14 -0.37 0.56 -10000 0 -1.3 202 202
TBP 0.032 0.018 -10000 0 -0.22 3 3
CREBBP 0.084 0.11 0.28 180 -0.38 2 182
HDAC1 0.028 0.018 -10000 0 -0.48 1 1
HDAC2 0.027 0.008 -10000 0 -10000 0 0
AP-1 -0.33 0.36 -10000 0 -0.73 311 311
MAPK14 0.024 0.016 -10000 0 -10000 0 0
MAPK10 -0.036 0.16 -10000 0 -0.48 92 92
MAPK11 0.019 0.042 -10000 0 -0.47 5 5
KRT5 -0.44 0.57 -10000 0 -1.2 250 250
interleukin-1 receptor activity -0.001 0.001 -10000 0 -10000 0 0
NCOA1 0.03 0.019 -10000 0 -0.47 1 1
STAT1 0.033 0.016 -10000 0 -0.2 3 3
CGA -0.24 0.4 -10000 0 -1 149 149
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.12 0.16 0.38 198 -10000 0 198
MAPK3 0.023 0.017 -10000 0 -10000 0 0
MAPK1 0.023 0.017 -10000 0 -10000 0 0
ICAM1 -0.16 0.25 -10000 0 -0.64 112 112
NFKB1 -0.012 0.089 -10000 0 -0.24 45 45
MAPK8 -0.17 0.19 -10000 0 -0.43 232 232
MAPK9 0.024 0.016 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.028 0.22 0.52 18 -0.6 60 78
BAX 0.004 0.069 -10000 0 -10000 0 0
POMC -0.16 0.33 -10000 0 -1.6 32 32
EP300 0.081 0.1 0.28 166 -0.33 1 167
cortisol/GR alpha (dimer)/p53 0.2 0.25 0.56 209 -10000 0 209
proteasomal ubiquitin-dependent protein catabolic process 0.064 0.11 0.25 133 -10000 0 133
SGK1 0.11 0.17 0.49 2 -1.2 4 6
IL13 -0.25 0.27 -10000 0 -0.76 106 106
IL6 -0.22 0.37 -10000 0 -0.91 153 153
PRKACG 0 0 -10000 0 -10000 0 0
IL5 -0.22 0.22 0.23 1 -0.48 287 288
IL2 -0.27 0.32 -10000 0 -0.72 219 219
CDK5 0.028 0.006 -10000 0 -10000 0 0
PRKACB 0.016 0.059 -10000 0 -0.48 10 10
HSP90AA1 0.028 0.005 -10000 0 -10000 0 0
IL8 -0.2 0.34 -10000 0 -0.86 139 139
CDK5R1/CDK5 0.037 0.021 -10000 0 -0.35 1 1
NF kappa B1 p50/RelA/PKAc 0.008 0.13 -10000 0 -0.32 60 60
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.22 0.25 0.54 236 -10000 0 236
SMARCA4 0.029 0.011 -10000 0 -0.14 1 1
chromatin remodeling 0.14 0.16 0.36 202 -0.29 1 203
NF kappa B1 p50/RelA/Cbp 0.056 0.16 0.33 83 -0.37 27 110
JUN (dimer) -0.21 0.23 0.3 1 -0.49 270 271
YWHAH 0.028 0.007 -10000 0 -10000 0 0
VIPR1 -0.13 0.21 -10000 0 -0.61 102 102
NR3C1 0.16 0.2 0.43 231 -10000 0 231
NR4A1 0.01 0.092 -10000 0 -0.44 31 31
TIF2/SUV420H1 0.02 0.071 -10000 0 -0.34 28 28
MAPKKK cascade -0.025 0.21 0.52 18 -0.56 60 78
cortisol/GR alpha (dimer)/Src-1 0.23 0.26 0.56 246 -10000 0 246
PBX1 0.019 0.059 -10000 0 -0.48 11 11
POU1F1 0.002 0.003 -10000 0 -10000 0 0
SELE -0.18 0.32 -10000 0 -0.9 106 106
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.14 0.16 0.36 202 -0.29 1 203
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.22 0.25 0.54 236 -10000 0 236
mol:cortisol 0.14 0.19 0.39 250 -0.19 13 263
MMP1 -0.36 0.52 -10000 0 -1.2 228 228
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.017 0.14 -10000 0 -0.25 201 201
ER alpha/Gai/GDP/Gbeta gamma -0.12 0.22 -10000 0 -0.42 230 230
AKT1 -0.19 0.36 -10000 0 -0.77 224 224
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.19 0.37 -10000 0 -0.78 224 224
mol:Ca2+ -0.05 0.14 -10000 0 -0.46 61 61
IGF1R -0.018 0.14 -10000 0 -0.48 74 74
E2/ER alpha (dimer)/Striatin -0.044 0.14 -10000 0 -0.29 198 198
SHC1 0.024 0.011 -10000 0 -10000 0 0
apoptosis 0.18 0.34 0.73 224 -10000 0 224
RhoA/GTP -0.033 0.1 -10000 0 -0.24 168 168
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.097 0.22 -10000 0 -0.42 219 219
regulation of stress fiber formation 0.036 0.099 0.29 4 -0.22 17 21
E2/ERA-ERB (dimer) -0.046 0.14 -10000 0 -0.29 203 203
KRAS 0.028 0.006 -10000 0 -10000 0 0
G13/GTP -0.035 0.12 -10000 0 -0.26 181 181
pseudopodium formation -0.036 0.099 0.22 17 -0.29 4 21
E2/ER alpha (dimer)/PELP1 -0.042 0.14 -10000 0 -0.29 190 190
GRB2 0.027 0.008 -10000 0 -10000 0 0
GNG2 0.028 0.019 -10000 0 -0.48 1 1
GNAO1 -0.002 0.1 -10000 0 -0.48 33 33
HRAS 0.026 0.036 -10000 0 -0.48 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.13 0.24 -10000 0 -0.49 230 230
E2/ER beta (dimer) 0.014 0.049 -10000 0 -0.34 15 15
mol:GDP -0.079 0.17 -10000 0 -0.38 175 175
mol:NADP -0.13 0.24 -10000 0 -0.49 230 230
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
mol:IP3 -0.054 0.14 -10000 0 -0.49 60 60
IGF-1R heterotetramer -0.018 0.14 -10000 0 -0.48 74 74
PLCB1 -0.051 0.14 -10000 0 -0.49 61 61
PLCB2 -0.04 0.14 -10000 0 -0.5 55 55
IGF1 -0.018 0.14 -10000 0 -0.48 69 69
mol:L-citrulline -0.13 0.24 -10000 0 -0.49 230 230
RHOA 0.028 0.006 -10000 0 -10000 0 0
Gai/GDP -0.092 0.27 -10000 0 -0.66 140 140
JNK cascade 0.014 0.049 -10000 0 -0.34 15 15
BCAR1 0.026 0.01 -10000 0 -10000 0 0
ESR2 0.018 0.068 -10000 0 -0.48 15 15
GNAQ 0.025 0.043 -10000 0 -0.48 6 6
ESR1 -0.089 0.21 -10000 0 -0.48 190 190
Gq family/GDP/Gbeta gamma -0.028 0.18 -10000 0 -0.7 45 45
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.038 0.14 -10000 0 -0.61 12 12
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.089 0.21 -10000 0 -0.43 184 184
GNAZ 0.018 0.07 -10000 0 -0.48 16 16
E2/ER alpha (dimer) -0.064 0.15 -10000 0 -0.34 190 190
STRN 0.021 0.063 -10000 0 -0.48 13 13
GNAL 0.013 0.081 -10000 0 -0.48 21 21
PELP1 0.027 0.009 -10000 0 -10000 0 0
MAPK11 0.006 0.049 -10000 0 -0.3 19 19
GNAI2 0.028 0.006 -10000 0 -10000 0 0
GNAI3 0.029 0.005 -10000 0 -10000 0 0
GNAI1 0.024 0.044 -10000 0 -0.48 6 6
HBEGF -0.11 0.22 0.32 18 -0.55 94 112
cAMP biosynthetic process -0.042 0.12 -10000 0 -0.24 213 213
SRC -0.11 0.22 0.25 3 -0.41 214 217
PI3K 0.04 0.013 -10000 0 -10000 0 0
GNB1 0.028 0.006 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.048 0.16 -10000 0 -0.34 175 175
SOS1 0.029 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.11 0.19 -10000 0 -0.42 199 199
Gs family/GTP -0.037 0.13 -10000 0 -0.25 213 213
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.048 0.035 -10000 0 -0.27 7 7
vasodilation -0.12 0.23 -10000 0 -0.46 230 230
mol:DAG -0.054 0.14 -10000 0 -0.49 60 60
Gs family/GDP/Gbeta gamma -0.066 0.15 -10000 0 -0.34 172 172
MSN -0.039 0.1 0.22 17 -0.31 4 21
Gq family/GTP -0.036 0.15 -10000 0 -0.52 55 55
mol:PI-3-4-5-P3 -0.18 0.35 -10000 0 -0.75 224 224
NRAS 0.026 0.04 -10000 0 -0.48 5 5
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.12 0.23 0.46 230 -10000 0 230
GRB2/SOS1 0.04 0.012 -10000 0 -10000 0 0
RhoA/GDP -0.058 0.17 -10000 0 -0.36 175 175
NOS3 -0.14 0.26 -10000 0 -0.51 228 228
GNA11 0.026 0.036 -10000 0 -0.48 4 4
MAPKKK cascade -0.14 0.27 -10000 0 -0.56 220 220
E2/ER alpha (dimer)/PELP1/Src -0.1 0.22 0.28 1 -0.44 224 225
ruffle organization -0.036 0.099 0.22 17 -0.29 4 21
ROCK2 -0.038 0.11 0.28 10 -0.28 8 18
GNA14 -0.003 0.12 -10000 0 -0.48 45 45
GNA15 0.021 0.059 -10000 0 -0.48 11 11
GNA13 0.027 0.008 -10000 0 -10000 0 0
MMP9 -0.12 0.22 0.37 15 -0.49 125 140
MMP2 -0.1 0.21 0.26 4 -0.55 83 87
IL23-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
CCL2 -0.24 0.49 -10000 0 -1.2 124 124
IL23A -0.25 0.5 -10000 0 -1.3 119 119
NF kappa B1 p50/RelA/I kappa B alpha -0.23 0.52 -10000 0 -1.2 133 133
positive regulation of T cell mediated cytotoxicity -0.29 0.58 -10000 0 -1.4 137 137
ITGA3 -0.24 0.5 -10000 0 -1.2 132 132
IL17F -0.16 0.31 -10000 0 -0.73 138 138
IL12B -0.037 0.14 -10000 0 -0.5 63 63
STAT1 (dimer) -0.27 0.55 -10000 0 -1.3 137 137
CD4 -0.24 0.48 -10000 0 -1.2 130 130
IL23 -0.25 0.49 -10000 0 -1.2 121 121
IL23R -0.023 0.15 -10000 0 -1.1 12 12
IL1B -0.26 0.52 -10000 0 -1.3 125 125
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.25 0.53 -10000 0 -1.3 140 140
TYK2 0.007 0.039 -10000 0 -10000 0 0
STAT4 -0.004 0.12 -10000 0 -0.48 49 49
STAT3 0.027 0.019 -10000 0 -0.48 1 1
IL18RAP -0.013 0.12 -10000 0 -0.48 51 51
IL12RB1 -0.016 0.11 -10000 0 -0.51 35 35
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.003 0.093 -10000 0 -0.38 35 35
IL23R/JAK2 -0.017 0.16 -10000 0 -0.98 12 12
positive regulation of chronic inflammatory response -0.29 0.58 -10000 0 -1.4 137 137
natural killer cell activation 0.003 0.007 -10000 0 -10000 0 0
JAK2 0.008 0.049 -10000 0 -0.49 1 1
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
NFKB1 0.027 0.019 -10000 0 -0.49 1 1
RELA 0.028 0.005 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.24 0.46 -10000 0 -1.1 121 121
ALOX12B -0.24 0.48 -10000 0 -1.2 117 117
CXCL1 -0.31 0.56 -10000 0 -1.2 191 191
T cell proliferation -0.29 0.58 -10000 0 -1.4 137 137
NFKBIA 0.028 0.007 -10000 0 -10000 0 0
IL17A -0.11 0.25 -10000 0 -0.56 130 130
PI3K -0.25 0.53 -10000 0 -1.3 133 133
IFNG -0.016 0.046 0.085 1 -0.12 94 95
STAT3 (dimer) -0.23 0.5 -10000 0 -1.2 132 132
IL18R1 0.007 0.091 -10000 0 -0.48 27 27
IL23/IL23R/JAK2/TYK2/SOCS3 -0.14 0.32 -10000 0 -0.8 98 98
IL18/IL18R 0.006 0.12 -10000 0 -0.35 71 71
macrophage activation -0.012 0.02 -10000 0 -0.045 110 110
TNF -0.27 0.53 -10000 0 -1.3 136 136
STAT3/STAT4 -0.26 0.54 -10000 0 -1.3 138 138
STAT4 (dimer) -0.28 0.56 -10000 0 -1.4 140 140
IL18 0.016 0.053 -10000 0 -0.47 8 8
IL19 -0.23 0.49 -10000 0 -1.2 124 124
STAT5A (dimer) -0.27 0.55 -10000 0 -1.3 135 135
STAT1 0.028 0.008 -10000 0 -10000 0 0
SOCS3 0.023 0.041 -10000 0 -0.48 5 5
CXCL9 -0.29 0.56 -10000 0 -1.3 158 158
MPO -0.26 0.52 -10000 0 -1.2 144 144
positive regulation of humoral immune response -0.29 0.58 -10000 0 -1.4 137 137
IL23/IL23R/JAK2/TYK2 -0.32 0.67 -10000 0 -1.6 135 135
IL6 -0.31 0.56 -10000 0 -1.3 170 170
STAT5A 0.025 0.04 -10000 0 -0.48 5 5
IL2 0.013 0.028 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.003 0.007 -10000 0 -10000 0 0
CD3E -0.27 0.53 -10000 0 -1.3 136 136
keratinocyte proliferation -0.29 0.58 -10000 0 -1.4 137 137
NOS2 -0.25 0.5 -10000 0 -1.2 142 142
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.033 0.25 0.28 62 -0.57 115 177
FYN -0.076 0.31 0.29 22 -0.75 116 138
LAT/GRAP2/SLP76 -0.056 0.25 0.25 21 -0.61 119 140
IKBKB 0.024 0.011 -10000 0 -10000 0 0
AKT1 -0.045 0.2 0.28 31 -0.46 127 158
B2M 0.026 0.021 -10000 0 -0.49 1 1
IKBKG -0.006 0.066 0.13 37 -0.14 88 125
MAP3K8 0.025 0.04 -10000 0 -0.48 5 5
mol:Ca2+ -0.027 0.028 0.094 2 -0.077 144 146
integrin-mediated signaling pathway 0.028 0.037 -10000 0 -0.29 9 9
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.087 0.3 0.3 11 -0.69 132 143
TRPV6 -0.078 0.24 1.1 14 -0.48 148 162
CD28 0.007 0.098 -10000 0 -0.48 31 31
SHC1 -0.071 0.31 0.29 67 -0.73 123 190
receptor internalization -0.12 0.35 -10000 0 -0.71 170 170
PRF1 -0.11 0.37 0.41 1 -1 94 95
KRAS 0.028 0.006 -10000 0 -10000 0 0
GRB2 0.027 0.008 -10000 0 -10000 0 0
COT/AKT1 -0.023 0.17 0.26 30 -0.36 121 151
LAT -0.09 0.31 0.26 23 -0.77 118 141
EntrezGene:6955 0 0.003 -10000 0 -10000 0 0
CD3D -0.016 0.14 -10000 0 -0.49 61 61
CD3E -0.013 0.13 -10000 0 -0.49 55 55
CD3G -0.03 0.15 -10000 0 -0.48 82 82
RASGRP2 -0.005 0.045 0.069 2 -0.17 46 48
RASGRP1 -0.062 0.21 0.29 12 -0.46 141 153
HLA-A 0.024 0.038 -10000 0 -0.49 4 4
RASSF5 0.018 0.054 -10000 0 -0.48 9 9
RAP1A/GTP/RAPL 0.028 0.037 -10000 0 -0.29 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.011 0.08 0.15 87 -0.13 82 169
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.038 0.088 -10000 0 -0.24 106 106
PRKCA -0.025 0.12 0.17 29 -0.29 103 132
GRAP2 0.004 0.1 -10000 0 -0.48 34 34
mol:IP3 -0.036 0.19 0.23 86 -0.44 117 203
EntrezGene:6957 0 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.096 0.33 -10000 0 -0.82 115 115
ORAI1 0.033 0.16 0.61 3 -0.97 13 16
CSK -0.092 0.31 0.27 3 -0.78 119 122
B7 family/CD28 -0.072 0.32 0.27 2 -0.75 124 126
CHUK 0.029 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.12 0.37 0.24 1 -0.88 130 131
PTPN6 -0.093 0.31 0.26 7 -0.79 115 122
VAV1 -0.099 0.31 0.25 4 -0.75 128 132
Monovalent TCR/CD3 -0.072 0.24 -10000 0 -0.59 116 116
CBL 0.026 0.009 -10000 0 -10000 0 0
LCK -0.091 0.34 0.27 22 -0.82 120 142
PAG1 -0.079 0.32 0.27 25 -0.76 118 143
RAP1A 0.029 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.11 0.37 0.24 1 -0.87 127 128
CD80 0.007 0.1 -10000 0 -0.48 33 33
CD86 0.024 0.05 -10000 0 -0.48 8 8
PDK1/CARD11/BCL10/MALT1 -0.034 0.11 -10000 0 -0.29 108 108
HRAS 0.026 0.036 -10000 0 -0.48 4 4
GO:0035030 -0.078 0.24 0.22 4 -0.6 124 128
CD8A -0.007 0.12 -10000 0 -0.49 50 50
CD8B -0.022 0.15 -10000 0 -0.49 75 75
PTPRC 0.005 0.091 -10000 0 -0.48 27 27
PDK1/PKC theta -0.06 0.25 0.34 38 -0.59 120 158
CSK/PAG1 -0.072 0.3 0.27 28 -0.75 113 141
SOS1 0.029 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.037 0.038 -10000 0 -0.41 4 4
GRAP2/SLP76 -0.075 0.3 0.28 1 -0.72 124 125
STIM1 0.024 0.099 1.2 4 -10000 0 4
RAS family/GTP 0.008 0.099 0.17 62 -0.19 89 151
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.13 0.4 -10000 0 -0.79 170 170
mol:DAG -0.059 0.15 0.12 8 -0.39 120 128
RAP1A/GDP 0.008 0.036 0.074 61 -0.066 41 102
PLCG1 0.028 0.006 -10000 0 -10000 0 0
CD247 -0.006 0.11 -10000 0 -0.48 42 42
cytotoxic T cell degranulation -0.099 0.34 0.4 1 -0.96 95 96
RAP1A/GTP -0.002 0.017 -10000 0 -0.066 45 45
mol:PI-3-4-5-P3 -0.063 0.24 0.28 12 -0.55 131 143
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.048 0.25 0.26 70 -0.59 117 187
NRAS 0.026 0.04 -10000 0 -0.48 5 5
ZAP70 -0.018 0.14 -10000 0 -0.48 65 65
GRB2/SOS1 0.04 0.012 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.064 0.24 0.24 7 -0.59 120 127
MALT1 0.027 0.019 -10000 0 -0.48 1 1
TRAF6 0.029 0.005 -10000 0 -10000 0 0
CD8 heterodimer -0.018 0.16 -10000 0 -0.46 90 90
CARD11 0.009 0.094 -10000 0 -0.48 29 29
PRKCB -0.033 0.13 0.18 19 -0.32 104 123
PRKCE -0.024 0.12 0.17 36 -0.29 108 144
PRKCQ -0.082 0.28 0.33 12 -0.68 127 139
LCP2 0.026 0.031 -10000 0 -0.48 3 3
BCL10 0.028 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression -0.033 0.18 0.27 32 -0.38 127 159
IKK complex 0.012 0.081 0.2 64 -0.12 68 132
RAS family/GDP -0.005 0.015 -10000 0 -0.06 8 8
MAP3K14 -0.017 0.13 0.21 33 -0.28 109 142
PDPK1 -0.037 0.19 0.32 34 -0.43 124 158
TCR/CD3/MHC I/CD8/Fyn -0.13 0.39 -10000 0 -0.96 124 124
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.021 0.17 0.26 134 -0.44 61 195
PTK2B 0.023 0.021 -10000 0 -0.48 1 1
mol:Ca2+ 0.004 0.2 -10000 0 -0.76 32 32
EDN1 0.027 0.15 0.22 132 -0.44 53 185
EDN3 -0.056 0.17 -10000 0 -0.48 110 110
EDN2 -0.033 0.16 -10000 0 -0.48 91 91
HRAS/GDP -0.014 0.2 0.27 11 -0.5 83 94
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.008 0.17 0.21 3 -0.44 77 80
ADCY4 0.005 0.15 0.29 3 -0.46 52 55
ADCY5 -0.044 0.19 0.27 2 -0.45 90 92
ADCY6 0.009 0.15 0.29 3 -0.46 47 50
ADCY7 0.005 0.15 0.29 3 -0.46 47 50
ADCY1 -0.022 0.18 0.27 2 -0.43 77 79
ADCY2 -0.025 0.18 0.3 2 -0.47 76 78
ADCY3 0.007 0.15 0.27 2 -0.46 46 48
ADCY8 0.002 0.13 0.26 1 -0.42 45 46
ADCY9 0.006 0.15 0.27 2 -0.46 48 50
arachidonic acid secretion -0.022 0.2 0.34 3 -0.49 87 90
ETB receptor/Endothelin-1/Gq/GTP -0.008 0.14 -10000 0 -0.34 87 87
GNAO1 -0.002 0.1 -10000 0 -0.48 33 33
HRAS 0.026 0.036 -10000 0 -0.48 4 4
ETA receptor/Endothelin-1/G12/GTP 0.07 0.19 0.37 131 -0.41 61 192
ETA receptor/Endothelin-1/Gs/GTP 0.058 0.19 0.34 129 -0.4 69 198
mol:GTP 0.001 0.003 -10000 0 -10000 0 0
COL3A1 0.005 0.22 0.26 118 -0.68 53 171
EDNRB 0.018 0.058 -10000 0 -0.42 10 10
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 0.008 0.2 0.26 117 -0.58 56 173
CYSLTR1 0.01 0.2 0.26 126 -0.54 65 191
SLC9A1 0.019 0.12 0.19 118 -0.34 42 160
mol:GDP -0.026 0.22 0.26 11 -0.53 85 96
SLC9A3 -0.019 0.24 -10000 0 -0.66 77 77
RAF1 -0.036 0.2 0.26 3 -0.5 92 95
JUN 0.007 0.19 -10000 0 -0.7 30 30
JAK2 0.021 0.17 0.26 134 -0.45 61 195
mol:IP3 -0.017 0.18 0.22 1 -0.49 72 73
ETA receptor/Endothelin-1 0.064 0.23 0.42 134 -0.44 86 220
PLCB1 -0.001 0.11 -10000 0 -0.48 41 41
PLCB2 0.024 0.041 -10000 0 -0.48 5 5
ETA receptor/Endothelin-3 -0.011 0.16 -10000 0 -0.34 136 136
FOS -0.054 0.26 0.36 3 -0.84 65 68
Gai/GDP -0.088 0.3 -10000 0 -0.74 135 135
CRK 0.027 0.009 -10000 0 -10000 0 0
mol:Ca ++ -0.018 0.23 0.26 9 -0.59 77 86
BCAR1 0.026 0.01 -10000 0 -10000 0 0
PRKCB1 -0.018 0.17 0.21 1 -0.47 74 75
GNAQ 0.025 0.044 -10000 0 -0.48 6 6
GNAZ 0.018 0.07 -10000 0 -0.48 16 16
GNAL 0.013 0.081 -10000 0 -0.48 21 21
Gs family/GDP -0.019 0.2 0.26 9 -0.5 82 91
ETA receptor/Endothelin-1/Gq/GTP 0.007 0.17 0.21 11 -0.44 64 75
MAPK14 -0.023 0.14 0.22 2 -0.4 68 70
TRPC6 0.002 0.21 -10000 0 -0.83 30 30
GNAI2 0.028 0.006 -10000 0 -10000 0 0
GNAI3 0.029 0.005 -10000 0 -10000 0 0
GNAI1 0.024 0.044 -10000 0 -0.48 6 6
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.018 0.15 -10000 0 -0.38 81 81
ETB receptor/Endothelin-2 -0.014 0.13 -10000 0 -0.35 99 99
ETB receptor/Endothelin-3 -0.029 0.13 -10000 0 -0.35 115 115
ETB receptor/Endothelin-1 0.03 0.13 -10000 0 -0.34 67 67
MAPK3 -0.05 0.25 0.36 3 -0.73 73 76
MAPK1 -0.056 0.25 0.36 3 -0.72 81 84
Rac1/GDP -0.012 0.2 0.27 9 -0.51 78 87
cAMP biosynthetic process -0.052 0.21 0.29 10 -0.48 105 115
MAPK8 0 0.23 -10000 0 -0.74 45 45
SRC 0.027 0.026 -10000 0 -0.48 2 2
ETB receptor/Endothelin-1/Gi/GTP -0.011 0.12 0.17 1 -0.38 53 54
p130Cas/CRK/Src/PYK2 -0.035 0.22 0.28 5 -0.56 83 88
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.012 0.2 0.27 8 -0.51 77 85
COL1A2 -0.003 0.25 0.29 2 -0.7 72 74
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.006 0.16 -10000 0 -0.35 109 109
mol:DAG -0.017 0.18 0.22 1 -0.49 72 73
MAP2K2 -0.043 0.21 0.32 5 -0.56 92 97
MAP2K1 -0.043 0.21 0.32 3 -0.56 90 93
EDNRA 0.041 0.14 0.22 133 -0.45 33 166
positive regulation of muscle contraction 0.017 0.15 0.22 134 -0.4 55 189
Gq family/GDP -0.002 0.2 0.27 1 -0.5 75 76
HRAS/GTP -0.032 0.2 0.26 4 -0.5 88 92
PRKCH -0.018 0.17 0.23 1 -0.5 64 65
RAC1 0.029 0.005 -10000 0 -10000 0 0
PRKCA -0.009 0.18 0.24 41 -0.51 64 105
PRKCB -0.027 0.19 0.24 20 -0.5 83 103
PRKCE -0.023 0.18 -10000 0 -0.48 75 75
PRKCD -0.017 0.17 -10000 0 -0.49 63 63
PRKCG -0.02 0.18 0.26 9 -0.49 67 76
regulation of vascular smooth muscle contraction -0.07 0.3 0.4 3 -1 64 67
PRKCQ -0.033 0.19 0.22 15 -0.49 90 105
PLA2G4A -0.028 0.22 0.35 3 -0.54 87 90
GNA14 -0.003 0.12 -10000 0 -0.48 45 45
GNA15 0.022 0.059 -10000 0 -0.48 11 11
GNA12 0.028 0.005 -10000 0 -10000 0 0
GNA11 0.026 0.036 -10000 0 -0.48 4 4
Rac1/GTP 0.07 0.19 0.37 131 -0.41 61 192
MMP1 -0.19 0.35 0.27 1 -0.83 184 185
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.026 0.036 -9999 0 -0.48 4 4
EGFR -0.018 0.14 -9999 0 -0.48 67 67
EGF/EGFR -0.034 0.15 -9999 0 -0.28 204 204
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.001 0.13 -9999 0 -0.27 137 137
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.019 0.068 -9999 0 -0.48 15 15
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.056 0.18 -9999 0 -0.48 127 127
EGF/EGFR dimer/SHC -0.026 0.14 -9999 0 -0.31 150 150
mol:GDP -0.004 0.13 -9999 0 -0.26 137 137
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.002 0.11 -9999 0 -0.48 39 39
GRB2/SOS1 0.04 0.012 -9999 0 -10000 0 0
HRAS/GTP -0.016 0.11 -9999 0 -0.25 141 141
SHC1 0.024 0.011 -9999 0 -10000 0 0
HRAS/GDP -0.005 0.12 -9999 0 -0.25 141 141
FRAP1 -0.056 0.091 -9999 0 -0.25 137 137
EGF/EGFR dimer -0.057 0.16 -9999 0 -0.36 183 183
SOS1 0.029 0.003 -9999 0 -10000 0 0
GRB2 0.027 0.008 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.015 0.097 -9999 0 -0.36 50 50
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.13 0.28 -10000 0 -0.84 62 62
PCK1 -0.29 0.51 -10000 0 -1.3 149 149
HNF4A -0.13 0.3 -10000 0 -0.88 62 62
KCNJ11 -0.2 0.42 -10000 0 -1.1 121 121
AKT1 -0.068 0.17 -10000 0 -0.4 55 55
response to starvation 0 0.011 -10000 0 -0.17 2 2
DLK1 -0.2 0.39 -10000 0 -0.98 129 129
NKX2-1 -0.015 0.14 0.31 20 -0.38 25 45
ACADM -0.13 0.29 -10000 0 -0.83 69 69
TAT -0.25 0.45 -10000 0 -1.2 121 121
CEBPB 0.026 0.021 -10000 0 -0.48 1 1
CEBPA 0.025 0.047 -10000 0 -0.48 7 7
TTR -0.18 0.3 -10000 0 -0.88 83 83
PKLR -0.11 0.28 -10000 0 -0.82 59 59
APOA1 -0.16 0.35 -10000 0 -1 67 67
CPT1C -0.14 0.3 -10000 0 -0.86 73 73
ALAS1 -0.054 0.16 -10000 0 -0.86 4 4
TFRC -0.16 0.26 -10000 0 -0.77 57 57
FOXF1 0.017 0.062 -10000 0 -0.48 12 12
NF1 0.032 0.008 -10000 0 -10000 0 0
HNF1A (dimer) 0.028 0.02 -10000 0 -0.48 1 1
CPT1A -0.12 0.29 -10000 0 -0.84 66 66
HMGCS1 -0.13 0.28 -10000 0 -0.86 58 58
NR3C1 0.007 0.068 -10000 0 -0.19 68 68
CPT1B -0.14 0.28 -10000 0 -0.83 67 67
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.029 0.003 -10000 0 -10000 0 0
GCK -0.15 0.32 -10000 0 -0.9 90 90
CREB1 -0.002 0.075 -10000 0 -0.19 102 102
IGFBP1 -0.059 0.14 -10000 0 -0.6 4 4
PDX1 -0.055 0.15 -10000 0 -0.36 61 61
UCP2 -0.13 0.3 -10000 0 -0.85 75 75
ALDOB -0.15 0.33 -10000 0 -0.89 86 86
AFP -0.19 0.32 -10000 0 -0.82 131 131
BDH1 -0.13 0.29 -10000 0 -0.86 68 68
HADH -0.14 0.3 -10000 0 -0.88 61 61
F2 -0.14 0.33 -10000 0 -0.97 61 61
HNF1A 0.028 0.02 -10000 0 -0.48 1 1
G6PC -0.051 0.11 -10000 0 -0.26 109 109
SLC2A2 -0.072 0.18 -10000 0 -0.44 72 72
INS -0.006 0.003 -10000 0 -10000 0 0
FOXA1 -0.097 0.21 -10000 0 -0.4 228 228
FOXA3 -0.12 0.19 -10000 0 -0.35 279 279
FOXA2 -0.16 0.35 -10000 0 -0.84 112 112
ABCC8 -0.24 0.45 -10000 0 -1 173 173
ALB -0.2 0.33 -10000 0 -0.83 142 142
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.007 0.12 -10000 0 -0.48 54 54
GNB1/GNG2 -0.035 0.18 -10000 0 -0.43 93 93
mol:DAG -0.046 0.15 -10000 0 -0.41 85 85
PLCG1 -0.048 0.16 -10000 0 -0.42 85 85
YES1 -0.068 0.16 -10000 0 -0.35 161 161
FZD3 0.014 0.07 -10000 0 -0.48 16 16
FZD6 0.007 0.085 -10000 0 -0.48 24 24
G protein -0.025 0.17 0.27 21 -0.43 83 104
MAP3K7 -0.056 0.14 0.24 1 -0.37 90 91
mol:Ca2+ -0.045 0.15 0.18 2 -0.39 85 87
mol:IP3 -0.046 0.15 -10000 0 -0.41 85 85
NLK -0.009 0.13 -10000 0 -0.83 21 21
GNB1 0.028 0.006 -10000 0 -10000 0 0
CAMK2A -0.056 0.15 0.25 1 -0.4 93 94
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.064 0.17 -10000 0 -0.36 165 165
CSNK1A1 0.029 0.004 -10000 0 -10000 0 0
GNAS -0.064 0.16 -10000 0 -0.4 107 107
GO:0007205 -0.051 0.15 0.18 2 -0.4 85 87
WNT6 -0.021 0.13 -10000 0 -0.48 59 59
WNT4 -0.022 0.15 -10000 0 -0.48 76 76
NFAT1/CK1 alpha -0.051 0.18 0.26 2 -0.44 99 101
GNG2 0.028 0.019 -10000 0 -0.48 1 1
WNT5A 0.001 0.11 -10000 0 -0.48 41 41
WNT11 -0.01 0.12 -10000 0 -0.48 48 48
CDC42 -0.053 0.16 0.19 3 -0.45 83 86
Ephrin A reverse signaling

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
MAPKKK cascade -0.007 0.1 -10000 0 -0.29 91 91
EFNA5 -0.032 0.16 -10000 0 -0.48 91 91
FYN -0.024 0.089 0.18 5 -0.27 89 94
neuron projection morphogenesis -0.007 0.1 -10000 0 -0.29 91 91
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.007 0.1 -10000 0 -0.29 91 91
EPHA5 0.023 0.016 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.011 0.12 -10000 0 -0.34 76 76
NFATC2 -0.053 0.23 -10000 0 -0.58 94 94
NFATC3 0.007 0.069 -10000 0 -0.25 25 25
CD40LG -0.16 0.36 0.46 1 -0.91 120 121
ITCH 0.011 0.058 -10000 0 -0.23 40 40
CBLB 0.012 0.058 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.21 0.44 -10000 0 -1 154 154
JUNB 0.027 0.026 -10000 0 -0.48 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.022 0.07 -10000 0 -0.28 43 43
T cell anergy -0.013 0.1 0.28 1 -0.42 42 43
TLE4 -0.043 0.19 -10000 0 -0.57 60 60
Jun/NFAT1-c-4/p21SNFT -0.078 0.31 -10000 0 -0.92 72 72
AP-1/NFAT1-c-4 -0.14 0.4 -10000 0 -1 103 103
IKZF1 -0.046 0.2 -10000 0 -0.63 56 56
T-helper 2 cell differentiation -0.13 0.27 -10000 0 -0.59 169 169
AP-1/NFAT1 -0.039 0.19 -10000 0 -0.46 86 86
CALM1 0.026 0.045 -10000 0 -0.17 39 39
EGR2 -0.095 0.31 -10000 0 -1 60 60
EGR3 -0.13 0.39 -10000 0 -1.2 78 78
NFAT1/FOXP3 -0.05 0.23 -10000 0 -0.52 113 113
EGR1 0.008 0.085 -10000 0 -0.48 23 23
JUN 0.012 0.033 -10000 0 -10000 0 0
EGR4 0.014 0.05 -10000 0 -0.48 6 6
mol:Ca2+ -0.002 0.038 -10000 0 -0.16 43 43
GBP3 -0.071 0.24 -10000 0 -0.65 99 99
FOSL1 0.016 0.055 -10000 0 -0.48 8 8
NFAT1-c-4/MAF/IRF4 -0.084 0.33 -10000 0 -0.89 88 88
DGKA -0.038 0.17 -10000 0 -0.55 54 54
CREM 0.028 0.005 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.075 0.31 -10000 0 -0.92 72 72
CTLA4 -0.088 0.25 -10000 0 -0.64 112 112
NFAT1-c-4 (dimer)/EGR1 -0.081 0.32 -10000 0 -0.91 80 80
NFAT1-c-4 (dimer)/EGR4 -0.078 0.31 -10000 0 -0.89 80 80
FOS -0.021 0.12 -10000 0 -0.49 45 45
IFNG -0.18 0.4 -10000 0 -0.99 138 138
T cell activation -0.05 0.18 0.49 1 -0.68 28 29
MAF 0.025 0.02 -10000 0 -0.48 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.064 0.23 0.72 62 -10000 0 62
TNF -0.12 0.3 -10000 0 -0.83 94 94
FASLG -0.2 0.55 -10000 0 -1.5 114 114
TBX21 -0.024 0.14 -10000 0 -0.36 97 97
BATF3 0.018 0.054 -10000 0 -0.48 9 9
PRKCQ -0.021 0.14 -10000 0 -0.49 65 65
PTPN1 -0.039 0.17 -10000 0 -0.5 60 60
NFAT1-c-4/ICER1 -0.073 0.3 -10000 0 -0.9 72 72
GATA3 -0.042 0.17 -10000 0 -0.48 114 114
T-helper 1 cell differentiation -0.17 0.39 -10000 0 -0.96 138 138
IL2RA -0.17 0.4 -10000 0 -0.97 140 140
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.037 0.16 -10000 0 -0.52 54 54
E2F1 0.018 0.082 -10000 0 -0.48 22 22
PPARG 0.022 0.046 -10000 0 -0.48 6 6
SLC3A2 -0.037 0.16 -10000 0 -0.52 55 55
IRF4 -0.026 0.15 -10000 0 -0.48 77 77
PTGS2 -0.14 0.34 0.46 1 -0.9 103 104
CSF2 -0.15 0.33 0.46 1 -0.87 103 104
JunB/Fra1/NFAT1-c-4 -0.064 0.3 -10000 0 -0.89 73 73
IL4 -0.14 0.28 -10000 0 -0.62 169 169
IL5 -0.16 0.31 -10000 0 -0.86 108 108
IL2 -0.051 0.19 0.49 1 -0.69 27 28
IL3 -0.018 0.058 -10000 0 -10000 0 0
RNF128 -0.009 0.13 -10000 0 -0.57 43 43
NFATC1 -0.064 0.23 -10000 0 -0.73 61 61
CDK4 0.052 0.17 0.58 36 -10000 0 36
PTPRK -0.054 0.21 -10000 0 -0.59 80 80
IL8 -0.16 0.34 -10000 0 -0.87 116 116
POU2F1 0.025 0.011 -10000 0 -10000 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.054 0.18 -10000 0 -0.44 111 111
TBX21 -0.17 0.49 -10000 0 -1.3 118 118
B2M 0.024 0.025 -10000 0 -0.48 1 1
TYK2 0.017 0.035 -10000 0 -10000 0 0
IL12RB1 -0.005 0.11 -10000 0 -0.51 35 35
GADD45B -0.12 0.39 -10000 0 -1 96 96
IL12RB2 -0.031 0.14 -10000 0 -0.49 61 61
GADD45G -0.13 0.41 -10000 0 -1.1 107 107
natural killer cell activation 0 0.019 -10000 0 -10000 0 0
RELB 0.027 0.026 -10000 0 -0.48 2 2
RELA 0.029 0.004 -10000 0 -10000 0 0
IL18 0.02 0.054 -10000 0 -0.49 8 8
IL2RA -0.025 0.15 -10000 0 -0.48 79 79
IFNG -0.023 0.13 -10000 0 -0.48 63 63
STAT3 (dimer) -0.12 0.35 -10000 0 -0.84 126 126
HLA-DRB5 -0.003 0.11 -10000 0 -0.48 40 40
FASLG -0.16 0.49 -10000 0 -1.3 113 113
NF kappa B2 p52/RelB -0.14 0.44 -10000 0 -1.1 123 123
CD4 0.023 0.038 -10000 0 -0.48 4 4
SOCS1 0.012 0.081 -10000 0 -0.48 21 21
EntrezGene:6955 -0.002 0.011 -10000 0 -10000 0 0
CD3D -0.021 0.13 -10000 0 -0.48 61 61
CD3E -0.017 0.13 -10000 0 -0.48 55 55
CD3G -0.033 0.15 -10000 0 -0.48 82 82
IL12Rbeta2/JAK2 -0.003 0.11 -10000 0 -0.36 60 60
CCL3 -0.16 0.46 -10000 0 -1.2 120 120
CCL4 -0.15 0.45 -10000 0 -1.1 116 116
HLA-A 0.022 0.04 -10000 0 -0.48 4 4
IL18/IL18R 0.027 0.13 -10000 0 -0.37 71 71
NOS2 -0.14 0.44 -10000 0 -1.1 125 125
IL12/IL12R/TYK2/JAK2/SPHK2 -0.05 0.17 -10000 0 -0.41 110 110
IL1R1 -0.16 0.45 -10000 0 -1.1 119 119
IL4 0 0.019 -10000 0 -10000 0 0
JAK2 0.016 0.039 -10000 0 -0.46 1 1
EntrezGene:6957 -0.002 0.011 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.18 0.49 -10000 0 -1.2 132 132
RAB7A -0.088 0.32 -10000 0 -0.82 95 95
lysosomal transport -0.081 0.3 -10000 0 -0.77 95 95
FOS -0.16 0.44 -10000 0 -1.1 138 138
STAT4 (dimer) -0.11 0.41 -10000 0 -0.98 123 123
STAT5A (dimer) -0.16 0.44 -10000 0 -1 134 134
GZMA -0.18 0.5 -10000 0 -1.3 116 116
GZMB -0.2 0.52 -10000 0 -1.3 137 137
HLX 0.024 0.021 -10000 0 -0.48 1 1
LCK -0.18 0.51 -10000 0 -1.2 133 133
TCR/CD3/MHC II/CD4 -0.078 0.26 -10000 0 -0.61 126 126
IL2/IL2R 0.008 0.15 -10000 0 -0.38 97 97
MAPK14 -0.12 0.41 -10000 0 -1 116 116
CCR5 -0.13 0.42 -10000 0 -1.2 94 94
IL1B -0.004 0.11 -10000 0 -0.5 33 33
STAT6 -0.019 0.14 -10000 0 -0.77 10 10
STAT4 -0.004 0.12 -10000 0 -0.48 49 49
STAT3 0.027 0.019 -10000 0 -0.48 1 1
STAT1 0.028 0.008 -10000 0 -10000 0 0
NFKB1 0.028 0.018 -10000 0 -0.48 1 1
NFKB2 0.029 0.005 -10000 0 -10000 0 0
IL12B -0.025 0.14 -10000 0 -0.48 63 63
CD8A -0.01 0.12 -10000 0 -0.48 50 50
CD8B -0.025 0.15 -10000 0 -0.48 75 75
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.053 0.18 0.44 111 -10000 0 111
IL2RB 0.009 0.086 -10000 0 -0.48 24 24
proteasomal ubiquitin-dependent protein catabolic process -0.092 0.36 -10000 0 -0.86 123 123
IL2RG 0.003 0.11 -10000 0 -0.48 37 37
IL12 -0.027 0.14 -10000 0 -0.37 109 109
STAT5A 0.025 0.04 -10000 0 -0.48 5 5
CD247 -0.009 0.11 -10000 0 -0.48 42 42
IL2 0.022 0.013 -10000 0 -10000 0 0
SPHK2 0.029 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.023 0.13 -10000 0 -0.49 52 52
IL12/IL12R/TYK2/JAK2 -0.2 0.59 -10000 0 -1.4 128 128
MAP2K3 -0.13 0.42 -10000 0 -1 118 118
RIPK2 0.023 0.013 -10000 0 -10000 0 0
MAP2K6 -0.13 0.41 -10000 0 -1 114 114
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.02 0.057 -10000 0 -0.48 10 10
IL18RAP -0.01 0.12 -10000 0 -0.48 51 51
IL12Rbeta1/TYK2 0.011 0.096 -10000 0 -0.39 35 35
EOMES -0.12 0.41 -10000 0 -1.3 86 86
STAT1 (dimer) -0.13 0.36 -10000 0 -0.82 141 141
T cell proliferation -0.058 0.29 0.35 1 -0.66 118 119
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.011 0.093 -10000 0 -0.48 27 27
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.082 0.31 -10000 0 -0.75 116 116
ATF2 -0.11 0.36 -10000 0 -0.89 118 118
HIF-1-alpha transcription factor network

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
PKM2 -0.14 0.34 -10000 0 -0.88 78 78
HDAC7 0.03 0.003 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.11 0.31 -10000 0 -0.76 85 85
SMAD4 0.028 0.019 -10000 0 -0.48 1 1
ID2 -0.14 0.34 -10000 0 -0.88 78 78
AP1 0.011 0.09 -10000 0 -0.35 44 44
ABCG2 -0.14 0.35 -10000 0 -0.9 85 85
HIF1A -0.029 0.1 -10000 0 -0.45 20 20
TFF3 -0.18 0.38 -10000 0 -0.87 124 124
GATA2 -0.031 0.16 -10000 0 -0.48 87 87
AKT1 -0.024 0.088 -10000 0 -0.25 20 20
response to hypoxia -0.038 0.074 -10000 0 -0.2 66 66
MCL1 -0.14 0.32 -10000 0 -0.88 74 74
NDRG1 -0.12 0.32 -10000 0 -0.87 72 72
SERPINE1 -0.14 0.35 -10000 0 -0.89 83 83
FECH -0.13 0.34 -10000 0 -0.88 78 78
FURIN -0.13 0.34 -10000 0 -0.87 79 79
NCOA2 0.006 0.093 -10000 0 -0.48 29 29
EP300 -0.029 0.12 -10000 0 -0.33 65 65
HMOX1 -0.14 0.34 -10000 0 -0.88 80 80
BHLHE40 -0.14 0.34 -10000 0 -0.88 83 83
BHLHE41 -0.14 0.34 -10000 0 -0.9 77 77
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.015 0.12 -10000 0 -0.4 14 14
ENG 0.005 0.11 0.35 6 -0.37 15 21
JUN 0.026 0.015 -10000 0 -10000 0 0
RORA -0.14 0.34 -10000 0 -0.88 79 79
ABCB1 -0.089 0.3 -10000 0 -1.1 63 63
TFRC -0.14 0.34 -10000 0 -0.88 78 78
CXCR4 -0.14 0.34 -10000 0 -0.88 80 80
TF -0.19 0.39 -10000 0 -0.87 131 131
CITED2 -0.14 0.34 -10000 0 -0.88 78 78
HIF1A/ARNT -0.15 0.4 -10000 0 -1 75 75
LDHA -0.007 0.13 -10000 0 -0.72 18 18
ETS1 -0.14 0.34 -10000 0 -0.89 78 78
PGK1 -0.14 0.34 -10000 0 -0.88 79 79
NOS2 -0.14 0.35 -10000 0 -0.91 79 79
ITGB2 -0.14 0.34 -10000 0 -0.88 82 82
ALDOA -0.13 0.34 -10000 0 -0.88 77 77
Cbp/p300/CITED2 -0.14 0.36 -10000 0 -0.89 95 95
FOS -0.008 0.12 -10000 0 -0.48 45 45
HK2 -0.14 0.34 -10000 0 -0.88 79 79
SP1 0.025 0.037 -10000 0 -0.16 4 4
GCK -0.077 0.32 -10000 0 -1.4 39 39
HK1 -0.14 0.34 -10000 0 -0.88 79 79
NPM1 -0.13 0.34 -10000 0 -0.88 78 78
EGLN1 -0.14 0.32 -10000 0 -0.89 73 73
CREB1 0.034 0.005 -10000 0 -10000 0 0
PGM1 -0.14 0.34 -10000 0 -0.87 79 79
SMAD3 0.027 0.031 -10000 0 -0.48 3 3
EDN1 -0.11 0.32 -10000 0 -1 72 72
IGFBP1 -0.14 0.34 -10000 0 -0.89 76 76
VEGFA -0.086 0.27 0.42 1 -0.66 76 77
HIF1A/JAB1 -0.001 0.076 -10000 0 -0.43 11 11
CP -0.19 0.38 -10000 0 -0.9 119 119
CXCL12 -0.14 0.35 -10000 0 -0.91 83 83
COPS5 0.024 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4 0.04 0.029 -10000 0 -0.34 4 4
BNIP3 -0.14 0.34 -10000 0 -0.88 79 79
EGLN3 -0.14 0.35 -10000 0 -0.89 84 84
CA9 -0.2 0.37 -10000 0 -0.89 107 107
TERT -0.15 0.35 -10000 0 -0.87 93 93
ENO1 -0.14 0.34 -10000 0 -0.88 79 79
PFKL -0.13 0.34 -10000 0 -0.88 80 80
NCOA1 0.028 0.018 -10000 0 -0.48 1 1
ADM -0.14 0.35 -10000 0 -0.89 85 85
ARNT -0.013 0.065 -10000 0 -10000 0 0
HNF4A 0.016 0.029 -10000 0 -0.13 5 5
ADFP -0.15 0.33 -10000 0 -0.85 86 86
SLC2A1 -0.087 0.28 0.42 1 -0.66 77 78
LEP -0.19 0.38 -10000 0 -0.86 133 133
HIF1A/ARNT/Cbp/p300 -0.12 0.32 -10000 0 -0.77 87 87
EPO -0.088 0.27 -10000 0 -0.9 40 40
CREBBP -0.025 0.11 -10000 0 -0.33 54 54
HIF1A/ARNT/Cbp/p300/HDAC7 -0.1 0.32 -10000 0 -0.76 80 80
PFKFB3 -0.14 0.34 -10000 0 -0.88 79 79
NT5E -0.14 0.35 -10000 0 -0.9 80 80
Wnt signaling

Figure S16.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S16.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.064 0.17 -9999 0 -0.36 165 165
FZD6 0.007 0.085 -9999 0 -0.48 24 24
WNT6 -0.021 0.13 -9999 0 -0.48 59 59
WNT4 -0.022 0.15 -9999 0 -0.48 76 76
FZD3 0.014 0.07 -9999 0 -0.48 16 16
WNT5A 0.001 0.11 -9999 0 -0.48 41 41
WNT11 -0.01 0.12 -9999 0 -0.48 48 48
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.028 0.018 -10000 0 -0.48 1 1
PTK2 0.023 0.012 -10000 0 -10000 0 0
CRKL -0.043 0.13 0.16 1 -0.31 141 142
GRB2/SOS1/SHC 0.045 0.026 -10000 0 -10000 0 0
HRAS 0.026 0.036 -10000 0 -0.48 4 4
IRS1/Crk -0.036 0.14 -10000 0 -0.32 129 129
IGF-1R heterotetramer/IGF1/PTP1B -0.008 0.14 -10000 0 -0.32 123 123
AKT1 -0.045 0.11 0.25 2 -0.42 37 39
BAD -0.045 0.11 0.24 2 -0.4 36 38
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.043 0.13 0.16 1 -0.32 127 128
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.028 0.14 0.21 1 -0.33 129 130
RAF1 -0.023 0.12 0.28 2 -0.53 17 19
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.001 0.14 -10000 0 -0.31 119 119
YWHAZ 0.022 0.013 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.029 0.15 -10000 0 -0.33 145 145
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
RPS6KB1 -0.042 0.11 0.25 2 -0.43 37 39
GNB2L1 0.029 0.005 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.009 0.11 0.3 12 -0.4 18 30
PXN 0.029 0.002 -10000 0 -10000 0 0
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.04 0.012 -10000 0 -10000 0 0
HRAS/GTP -0.018 0.11 -10000 0 -0.29 105 105
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.022 0.11 -10000 0 -0.26 96 96
IGF-1R heterotetramer -0.029 0.16 -10000 0 -0.52 74 74
IGF-1R heterotetramer/IGF1/IRS/Nck -0.012 0.15 -10000 0 -0.32 128 128
Crk/p130 Cas/Paxillin -0.005 0.14 -10000 0 -0.3 122 122
IGF1R -0.029 0.16 -10000 0 -0.52 74 74
IGF1 -0.029 0.15 -10000 0 -0.51 69 69
IRS2/Crk -0.038 0.13 -10000 0 -0.32 129 129
PI3K 0.001 0.14 -10000 0 -0.31 124 124
apoptosis 0.029 0.093 0.36 25 -0.26 5 30
HRAS/GDP 0.019 0.026 -10000 0 -0.34 4 4
PRKCD -0.043 0.14 -10000 0 -0.35 120 120
RAF1/14-3-3 E -0.001 0.12 0.28 3 -0.45 17 20
BAD/14-3-3 -0.03 0.098 0.27 5 -0.38 25 30
PRKCZ -0.046 0.12 0.25 2 -0.43 39 41
Crk/p130 Cas/Paxillin/FAK1 -0.01 0.098 -10000 0 -0.39 24 24
PTPN1 0.026 0.011 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.042 0.15 -10000 0 -0.37 124 124
BCAR1 0.026 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.011 0.12 -10000 0 -0.28 105 105
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.029 0.003 -10000 0 -10000 0 0
IRS1/NCK2 -0.023 0.14 -10000 0 -0.32 128 128
GRB10 0.028 0.018 -10000 0 -0.48 1 1
PTPN11 -0.044 0.13 0.16 1 -0.32 129 130
IRS1 -0.043 0.14 -10000 0 -0.33 145 145
IRS2 -0.047 0.14 0.16 1 -0.33 129 130
IGF-1R heterotetramer/IGF1 -0.037 0.17 -10000 0 -0.41 129 129
GRB2 0.027 0.008 -10000 0 -10000 0 0
PDPK1 -0.031 0.12 0.28 1 -0.3 110 111
YWHAE 0.027 0.009 -10000 0 -10000 0 0
PRKD1 -0.05 0.15 0.19 1 -0.38 121 122
SHC1 0.024 0.011 -10000 0 -10000 0 0
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.045 0.18 -10000 0 -0.31 238 238
SMAD6-7/SMURF1 0.052 0.032 -10000 0 -0.3 5 5
NOG -0.005 0.11 -10000 0 -0.48 41 41
SMAD9 -0.054 0.2 -10000 0 -0.55 93 93
SMAD4 0.027 0.019 -10000 0 -0.48 1 1
SMAD5 -0.057 0.14 -10000 0 -0.41 59 59
BMP7/USAG1 -0.091 0.19 -10000 0 -0.39 209 209
SMAD5/SKI -0.047 0.15 -10000 0 -0.4 66 66
SMAD1 0.005 0.059 0.25 1 -0.41 5 6
BMP2 0.01 0.086 -10000 0 -0.48 24 24
SMAD1/SMAD1/SMAD4 0.013 0.077 -10000 0 -0.41 9 9
BMPR1A 0.028 0.018 -10000 0 -0.48 1 1
BMPR1B -0.1 0.19 -10000 0 -0.48 169 169
BMPR1A-1B/BAMBI -0.057 0.17 -10000 0 -0.31 237 237
AHSG 0 0 -10000 0 -10000 0 0
CER1 0 0 -10000 0 -10000 0 0
BMP2-4/CER1 -0.002 0.1 -10000 0 -0.32 78 78
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.046 0.14 -10000 0 -0.38 67 67
BMP2-4 (homodimer) -0.005 0.12 -10000 0 -0.37 78 78
RGMB 0.028 0.018 -10000 0 -0.48 1 1
BMP6/BMPR2/BMPR1A-1B -0.007 0.14 -10000 0 -0.27 170 170
RGMA -0.001 0.1 -10000 0 -0.48 36 36
SMURF1 0.029 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.055 0.14 -10000 0 -0.42 65 65
BMP2-4/USAG1 -0.054 0.18 -10000 0 -0.33 220 220
SMAD6/SMURF1/SMAD5 -0.048 0.15 -10000 0 -0.4 67 67
SOSTDC1 -0.09 0.2 -10000 0 -0.48 170 170
BMP7/BMPR2/BMPR1A-1B -0.039 0.16 -10000 0 -0.3 218 218
SKI 0.028 0.006 -10000 0 -10000 0 0
BMP6 (homodimer) 0.02 0.057 -10000 0 -0.48 10 10
HFE2 0.02 0.011 -10000 0 -10000 0 0
ZFYVE16 0.028 0.006 -10000 0 -10000 0 0
MAP3K7 0.028 0.007 -10000 0 -10000 0 0
BMP2-4/CHRD -0.01 0.16 -10000 0 -0.39 114 114
SMAD5/SMAD5/SMAD4 -0.048 0.15 -10000 0 -0.41 65 65
MAPK1 0.028 0.007 -10000 0 -10000 0 0
TAK1/TAB family -0.036 0.14 -10000 0 -0.38 63 63
BMP7 (homodimer) -0.036 0.15 -10000 0 -0.48 88 88
NUP214 0.029 0.005 -10000 0 -10000 0 0
BMP6/FETUA 0.015 0.041 -10000 0 -0.34 10 10
SMAD1/SKI 0.012 0.08 -10000 0 -0.47 9 9
SMAD6 0.026 0.036 -10000 0 -0.48 4 4
CTDSP2 0.029 0.004 -10000 0 -10000 0 0
BMP2-4/FETUA -0.002 0.1 -10000 0 -0.32 78 78
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.01 0.13 -10000 0 -0.48 60 60
BMPR2 (homodimer) 0.028 0.018 -10000 0 -0.48 1 1
GADD34/PP1CA 0.052 0.02 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) -0.063 0.15 -10000 0 -0.34 168 168
CHRDL1 -0.07 0.19 -10000 0 -0.48 145 145
ENDOFIN/SMAD1 0.012 0.081 -10000 0 -0.49 9 9
SMAD6-7/SMURF1/SMAD1 0.028 0.09 -10000 0 -0.46 9 9
SMAD6/SMURF1 0.029 0.005 -10000 0 -10000 0 0
BAMBI -0.03 0.16 -10000 0 -0.48 90 90
SMURF2 0.026 0.02 -10000 0 -0.48 1 1
BMP2-4/CHRDL1 -0.041 0.17 -10000 0 -0.33 199 199
BMP2-4/GREM1 -0.006 0.15 -10000 0 -0.35 117 117
SMAD7 0.027 0.019 -10000 0 -0.48 1 1
SMAD8A/SMAD8A/SMAD4 -0.049 0.2 -10000 0 -0.53 103 103
SMAD1/SMAD6 0.011 0.082 -10000 0 -0.5 9 9
TAK1/SMAD6 0.04 0.012 -10000 0 -10000 0 0
BMP7 -0.037 0.16 -10000 0 -0.48 88 88
BMP6 0.02 0.057 -10000 0 -0.48 10 10
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.048 0.14 -10000 0 -0.38 74 74
PPM1A 0.029 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 0.009 0.078 -10000 0 -0.47 9 9
SMAD7/SMURF1 0.04 0.017 -10000 0 -0.34 1 1
CTDSPL 0.029 0.005 -10000 0 -10000 0 0
PPP1CA 0.027 0.008 -10000 0 -10000 0 0
XIAP 0.029 0.002 -10000 0 -10000 0 0
CTDSP1 0.029 0.004 -10000 0 -10000 0 0
PPP1R15A 0.029 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.078 0.19 -10000 0 -0.52 90 90
CHRD -0.024 0.15 -10000 0 -0.48 77 77
BMPR2 0.028 0.018 -10000 0 -0.48 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.062 0.15 -10000 0 -0.35 105 105
BMP4 -0.013 0.13 -10000 0 -0.48 61 61
FST -0.008 0.12 -10000 0 -0.48 52 52
BMP2-4/NOG -0.002 0.13 -10000 0 -0.33 107 107
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.028 0.16 -10000 0 -0.28 217 217
LPA receptor mediated 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
GNB1/GNG2 0.037 0.083 -10000 0 -0.29 43 43
NF kappa B1 p50/RelA/I kappa B alpha -0.014 0.13 0.25 2 -0.38 30 32
AP1 -0.028 0.14 -10000 0 -0.27 173 173
mol:PIP3 -0.058 0.12 -10000 0 -0.36 57 57
AKT1 0.011 0.074 0.3 4 -0.36 9 13
PTK2B -0.04 0.12 -10000 0 -0.35 67 67
RHOA 0 0.071 0.22 6 -0.32 26 32
PIK3CB 0.029 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.029 0.11 0.19 34 -0.26 104 138
MAGI3 0.028 0.018 -10000 0 -0.48 1 1
RELA 0.029 0.004 -10000 0 -10000 0 0
apoptosis -0.041 0.12 -10000 0 -0.28 148 148
HRAS/GDP 0.019 0.026 -10000 0 -0.34 4 4
positive regulation of microtubule depolymerization -0.082 0.14 0.25 1 -0.37 89 90
NF kappa B1 p50/RelA -0.034 0.13 -10000 0 -0.31 114 114
endothelial cell migration -0.013 0.13 -10000 0 -0.46 52 52
ADCY4 -0.023 0.12 -10000 0 -0.4 53 53
ADCY5 -0.063 0.16 -10000 0 -0.45 83 83
ADCY6 -0.021 0.11 -10000 0 -0.38 54 54
ADCY7 -0.018 0.11 -10000 0 -0.4 47 47
ADCY1 -0.043 0.13 -10000 0 -0.42 63 63
ADCY2 -0.047 0.15 -10000 0 -0.47 62 62
ADCY3 -0.021 0.11 -10000 0 -0.38 54 54
ADCY8 -0.019 0.1 -10000 0 -0.39 42 42
ADCY9 -0.023 0.11 -10000 0 -0.39 54 54
GSK3B -0.039 0.11 0.23 6 -0.34 60 66
arachidonic acid secretion -0.027 0.12 -10000 0 -0.39 56 56
GNG2 0.028 0.019 -10000 0 -0.48 1 1
TRIP6 0.006 0.074 -10000 0 -0.38 29 29
GNAO1 -0.015 0.099 -10000 0 -0.32 70 70
HRAS 0.026 0.036 -10000 0 -0.48 4 4
NFKBIA -0.038 0.13 0.24 3 -0.32 100 103
GAB1 0.028 0.018 -10000 0 -0.48 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.016 0.18 -10000 0 -0.89 32 32
JUN 0.028 0.008 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.031 0.036 -10000 0 -0.29 5 5
TIAM1 -0.005 0.21 -10000 0 -1.1 32 32
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
mol:IP3 -0.029 0.11 0.19 34 -0.26 104 138
PLCB3 0.024 0.054 0.18 61 -0.26 5 66
FOS -0.006 0.12 -10000 0 -0.48 45 45
positive regulation of mitosis -0.027 0.12 -10000 0 -0.39 56 56
LPA/LPA1-2-3 -0.008 0.14 -10000 0 -0.28 149 149
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.026 0.01 -10000 0 -10000 0 0
stress fiber formation -0.028 0.11 -10000 0 -0.4 39 39
GNAZ -0.005 0.088 -10000 0 -0.3 62 62
EGFR/PI3K-beta/Gab1 -0.044 0.14 -10000 0 -0.38 57 57
positive regulation of dendritic cell cytokine production -0.01 0.14 -10000 0 -0.28 149 149
LPA/LPA2/MAGI-3 0.034 0.029 -10000 0 -0.21 2 2
ARHGEF1 0.015 0.08 0.19 55 -0.27 36 91
GNAI2 0 0.078 -10000 0 -0.28 50 50
GNAI3 0.001 0.078 -10000 0 -0.31 41 41
GNAI1 -0.003 0.085 -10000 0 -0.3 54 54
LPA/LPA3 -0.042 0.13 -10000 0 -0.33 126 126
LPA/LPA2 0.018 0.024 -10000 0 -0.11 19 19
LPA/LPA1 0.005 0.092 -10000 0 -0.33 52 52
HB-EGF/EGFR -0.034 0.13 -10000 0 -0.32 130 130
HBEGF -0.027 0.11 -10000 0 -0.35 82 82
mol:DAG -0.029 0.11 0.19 34 -0.26 104 138
cAMP biosynthetic process -0.042 0.13 0.28 3 -0.39 70 73
NFKB1 0.028 0.018 -10000 0 -0.48 1 1
SRC 0.027 0.026 -10000 0 -0.48 2 2
GNB1 0.028 0.006 -10000 0 -10000 0 0
LYN -0.027 0.13 0.26 19 -0.32 83 102
GNAQ -0.033 0.1 -10000 0 -0.27 122 122
LPAR2 0.029 0.005 -10000 0 -10000 0 0
LPAR3 -0.057 0.17 -10000 0 -0.48 116 116
LPAR1 0.009 0.098 -10000 0 -0.37 42 42
IL8 -0.096 0.19 -10000 0 -0.46 135 135
PTK2 -0.028 0.099 -10000 0 -0.28 98 98
Rac1/GDP 0.021 0.003 -10000 0 -10000 0 0
CASP3 -0.041 0.12 -10000 0 -0.28 148 148
EGFR -0.018 0.14 -10000 0 -0.48 67 67
PLCG1 -0.038 0.12 0.16 10 -0.29 122 132
PLD2 -0.041 0.11 -10000 0 -0.27 140 140
G12/G13 0.037 0.077 -10000 0 -0.28 37 37
PI3K-beta 0.005 0.07 -10000 0 -0.39 11 11
cell migration -0.005 0.076 -10000 0 -0.27 32 32
SLC9A3R2 0.024 0.04 -10000 0 -0.48 5 5
PXN -0.029 0.11 -10000 0 -0.41 39 39
HRAS/GTP -0.027 0.12 -10000 0 -0.4 55 55
RAC1 0.029 0.005 -10000 0 -10000 0 0
MMP9 -0.028 0.15 -10000 0 -0.48 82 82
PRKCE 0.024 0.05 -10000 0 -0.48 8 8
PRKCD -0.03 0.11 0.2 4 -0.35 25 29
Gi(beta/gamma) -0.014 0.11 -10000 0 -0.4 43 43
mol:LPA -0.003 0.029 -10000 0 -0.16 20 20
TRIP6/p130 Cas/FAK1/Paxillin -0.025 0.13 -10000 0 -0.44 41 41
MAPKKK cascade -0.027 0.12 -10000 0 -0.39 56 56
contractile ring contraction involved in cytokinesis 0 0.072 0.22 6 -0.31 26 32
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.048 0.12 -10000 0 -0.29 152 152
GNA15 -0.034 0.1 -10000 0 -0.27 126 126
GNA12 0.028 0.005 -10000 0 -10000 0 0
GNA13 0.027 0.008 -10000 0 -10000 0 0
MAPT -0.085 0.14 0.25 1 -0.38 90 91
GNA11 -0.032 0.099 -10000 0 -0.26 121 121
Rac1/GTP 0.016 0.2 -10000 0 -0.95 32 32
MMP2 -0.013 0.13 -10000 0 -0.47 52 52
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process 0.009 0.13 0.48 55 -10000 0 55
PI3K Class IB/PDE3B -0.009 0.13 -10000 0 -0.48 55 55
PDE3B -0.009 0.13 -10000 0 -0.48 55 55
FOXM1 transcription factor network

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
NFATC3 -0.063 0.4 -9999 0 -1.1 60 60
PLK1 -0.036 0.31 -9999 0 -1.4 42 42
BIRC5 -0.042 0.32 -9999 0 -1.3 46 46
HSPA1B -0.065 0.4 -9999 0 -1.1 61 61
MAP2K1 0.02 0.047 -9999 0 -10000 0 0
BRCA2 -0.069 0.41 -9999 0 -1.1 65 65
FOXM1 -0.11 0.54 -9999 0 -1.5 68 68
XRCC1 -0.063 0.4 -9999 0 -1.1 60 60
FOXM1B/p19 -0.08 0.41 -9999 0 -1.1 69 69
Cyclin D1/CDK4 -0.1 0.39 -9999 0 -1 90 90
CDC2 -0.07 0.42 -9999 0 -1.2 67 67
TGFA -0.076 0.4 -9999 0 -1 74 74
SKP2 -0.063 0.4 -9999 0 -1.1 63 63
CCNE1 0.015 0.062 -9999 0 -0.49 10 10
CKS1B -0.036 0.4 -9999 0 -1.1 57 57
RB1 -0.064 0.31 -9999 0 -0.95 67 67
FOXM1C/SP1 -0.081 0.46 -9999 0 -1.3 70 70
AURKB -0.11 0.4 -9999 0 -1 118 118
CENPF -0.042 0.42 -9999 0 -1.2 61 61
CDK4 0.025 0.026 -9999 0 -10000 0 0
MYC -0.075 0.35 -9999 0 -0.94 73 73
CHEK2 0.018 0.049 -9999 0 -0.47 1 1
ONECUT1 -0.071 0.41 -9999 0 -1 81 81
CDKN2A 0.01 0.065 -9999 0 -0.48 12 12
LAMA4 -0.064 0.4 -9999 0 -1.1 61 61
FOXM1B/HNF6 -0.098 0.48 -9999 0 -1.3 81 81
FOS -0.1 0.46 -9999 0 -1.2 93 93
SP1 0.028 0.011 -9999 0 -10000 0 0
CDC25B -0.062 0.4 -9999 0 -1.1 60 60
response to radiation 0.005 0.026 -9999 0 -10000 0 0
CENPB -0.062 0.4 -9999 0 -1.1 64 64
CENPA -0.08 0.43 -9999 0 -1.2 70 70
NEK2 -0.048 0.43 -9999 0 -1.2 67 67
HIST1H2BA -0.064 0.4 -9999 0 -1.1 70 70
CCNA2 0.012 0.087 -9999 0 -0.49 23 23
EP300 0.028 0.007 -9999 0 -10000 0 0
CCNB1/CDK1 -0.088 0.46 -9999 0 -1.3 64 64
CCNB2 -0.071 0.42 -9999 0 -1.2 63 63
CCNB1 -0.07 0.42 -9999 0 -1.2 64 64
ETV5 -0.061 0.4 -9999 0 -1.1 62 62
ESR1 -0.25 0.6 -9999 0 -1.1 245 245
CCND1 -0.11 0.4 -9999 0 -1 93 93
GSK3A 0.02 0.043 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.037 0.092 -9999 0 -0.36 29 29
CDK2 0.027 0.017 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.004 0.03 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.076 0.43 -9999 0 -1.2 68 68
GAS1 -0.093 0.45 -9999 0 -1.2 81 81
MMP2 -0.087 0.45 -9999 0 -1.2 79 79
RB1/FOXM1C -0.083 0.43 -9999 0 -1.1 95 95
CREBBP 0.027 0.019 -9999 0 -0.48 1 1
Signaling events mediated by Stem cell factor receptor (c-Kit)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.051 0.15 0.37 1 -0.43 78 79
CRKL -0.047 0.14 -10000 0 -0.43 77 77
HRAS -0.032 0.15 -10000 0 -0.43 71 71
mol:PIP3 -0.017 0.15 0.27 3 -0.4 59 62
SPRED1 0.026 0.031 -10000 0 -0.48 3 3
SPRED2 0.026 0.039 -10000 0 -0.48 5 5
GAB1 -0.047 0.15 -10000 0 -0.44 80 80
FOXO3 -0.027 0.15 0.3 1 -0.42 59 60
AKT1 -0.03 0.16 0.32 1 -0.45 66 67
BAD -0.029 0.15 0.3 1 -0.42 60 61
megakaryocyte differentiation -0.049 0.15 -10000 0 -0.45 83 83
GSK3B -0.028 0.15 0.3 2 -0.42 61 63
RAF1 -0.013 0.13 0.25 15 -0.35 61 76
SHC1 0.024 0.011 -10000 0 -10000 0 0
STAT3 -0.047 0.15 -10000 0 -0.44 80 80
STAT1 -0.12 0.34 -10000 0 -0.94 98 98
HRAS/SPRED1 -0.007 0.14 0.25 1 -0.35 68 69
cell proliferation -0.047 0.15 -10000 0 -0.43 81 81
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
TEC 0.025 0.043 -10000 0 -0.48 6 6
RPS6KB1 -0.038 0.16 -10000 0 -0.44 86 86
HRAS/SPRED2 -0.007 0.14 0.25 1 -0.37 54 55
LYN/TEC/p62DOK -0.011 0.16 -10000 0 -0.43 69 69
MAPK3 -0.004 0.1 0.22 18 -0.29 33 51
STAP1 -0.069 0.17 -10000 0 -0.48 90 90
GRAP2 0.004 0.1 -10000 0 -0.48 34 34
JAK2 -0.094 0.29 -10000 0 -0.82 91 91
STAT1 (dimer) -0.12 0.33 -10000 0 -0.87 110 110
mol:Gleevec 0.002 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.021 0.17 -10000 0 -0.46 68 68
actin filament polymerization -0.05 0.15 -10000 0 -0.43 81 81
LYN 0.023 0.028 -10000 0 -0.48 2 2
STAP1/STAT5A (dimer) -0.096 0.24 -10000 0 -0.64 103 103
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.019 0.14 -10000 0 -0.4 70 70
PI3K -0.011 0.16 -10000 0 -0.44 74 74
PTEN 0.027 0.031 -10000 0 -0.48 3 3
SCF/KIT/EPO/EPOR -0.1 0.39 -10000 0 -1.2 80 80
MAPK8 -0.048 0.15 -10000 0 -0.44 81 81
STAT3 (dimer) -0.046 0.15 -10000 0 -0.43 80 80
positive regulation of transcription 0 0.089 0.21 19 -0.24 32 51
mol:GDP -0.032 0.15 -10000 0 -0.45 65 65
PIK3C2B -0.045 0.14 -10000 0 -0.45 64 64
CBL/CRKL -0.032 0.14 -10000 0 -0.41 75 75
FER -0.05 0.15 -10000 0 -0.45 82 82
SH2B3 -0.049 0.15 -10000 0 -0.44 81 81
PDPK1 -0.007 0.14 0.33 15 -0.38 50 65
SNAI2 -0.048 0.15 -10000 0 -0.45 76 76
positive regulation of cell proliferation -0.088 0.26 -10000 0 -0.72 97 97
KITLG -0.005 0.11 -10000 0 -0.5 39 39
cell motility -0.088 0.26 -10000 0 -0.72 97 97
PTPN6 0.03 0.011 -10000 0 -10000 0 0
EPOR -0.03 0.19 -10000 0 -1 16 16
STAT5A (dimer) -0.073 0.23 -10000 0 -0.62 95 95
SOCS1 0.012 0.081 -10000 0 -0.48 21 21
cell migration 0.064 0.16 0.46 91 -10000 0 91
SOS1 0.029 0.003 -10000 0 -10000 0 0
EPO 0.001 0.062 -10000 0 -0.48 9 9
VAV1 0.017 0.076 -10000 0 -0.48 19 19
GRB10 -0.048 0.15 -10000 0 -0.44 79 79
PTPN11 0.031 0.007 -10000 0 -10000 0 0
SCF/KIT -0.047 0.16 -10000 0 -0.46 83 83
GO:0007205 0.003 0.008 -10000 0 -10000 0 0
MAP2K1 -0.007 0.11 0.23 18 -0.32 34 52
CBL 0.026 0.009 -10000 0 -10000 0 0
KIT -0.099 0.36 -10000 0 -1.3 65 65
MAP2K2 -0.007 0.11 0.24 17 -0.31 35 52
SHC/Grb2/SOS1 -0.008 0.15 -10000 0 -0.44 56 56
STAT5A -0.075 0.23 -10000 0 -0.65 94 94
GRB2 0.027 0.008 -10000 0 -10000 0 0
response to radiation -0.046 0.15 -10000 0 -0.44 76 76
SHC/GRAP2 0.019 0.069 -10000 0 -0.34 25 25
PTPRO -0.051 0.16 -10000 0 -0.46 83 83
SH2B2 -0.051 0.15 -10000 0 -0.44 82 82
DOK1 0.027 0.035 -10000 0 -0.48 4 4
MATK -0.065 0.17 -10000 0 -0.47 91 91
CREBBP 0.015 0.06 -10000 0 -0.22 7 7
BCL2 -0.13 0.42 -10000 0 -1.3 95 95
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.006 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.011 0.13 -10000 0 -0.27 164 164
regulation of S phase of mitotic cell cycle -0.027 0.11 -10000 0 -0.25 150 150
GNAO1 -0.002 0.1 -10000 0 -0.48 33 33
HRAS 0.026 0.036 -10000 0 -0.48 4 4
SHBG/T-DHT 0.016 0.014 -10000 0 -0.29 1 1
PELP1 0.027 0.009 -10000 0 -10000 0 0
AKT1 0.007 0.001 -10000 0 -10000 0 0
MAP2K1 -0.049 0.1 0.21 7 -0.29 18 25
T-DHT/AR -0.052 0.14 -10000 0 -0.34 165 165
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.006 48 48
GNAI2 0.028 0.006 -10000 0 -10000 0 0
GNAI3 0.029 0.005 -10000 0 -10000 0 0
GNAI1 0.024 0.044 -10000 0 -0.48 6 6
mol:GDP -0.076 0.16 -10000 0 -0.4 166 166
cell proliferation -0.052 0.14 0.28 4 -0.43 55 59
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
FOS -0.057 0.2 -10000 0 -0.8 49 49
mol:Ca2+ -0.009 0.024 -10000 0 -0.067 74 74
MAPK3 -0.046 0.12 0.27 6 -0.33 51 57
MAPK1 -0.033 0.11 0.21 1 -0.4 48 49
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.004 48 48
cAMP biosynthetic process 0.004 0.022 0.12 1 -0.28 1 2
GNG2 0.028 0.019 -10000 0 -0.48 1 1
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 48 48
HRAS/GTP -0.014 0.12 -10000 0 -0.24 166 166
actin cytoskeleton reorganization 0.04 0.016 -10000 0 -10000 0 0
SRC 0.027 0.026 -10000 0 -0.48 2 2
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 48 48
PI3K 0.036 0.012 -10000 0 -10000 0 0
apoptosis 0.038 0.13 0.41 63 -0.24 3 66
T-DHT/AR/PELP1 -0.03 0.13 -10000 0 -0.29 165 165
HRAS/GDP -0.061 0.16 -10000 0 -0.38 169 169
CREB1 -0.041 0.14 0.28 1 -0.44 63 64
RAC1-CDC42/GTP 0.05 0.02 -10000 0 -10000 0 0
AR -0.073 0.2 -10000 0 -0.48 165 165
GNB1 0.028 0.006 -10000 0 -10000 0 0
RAF1 -0.035 0.11 0.35 1 -0.24 138 139
RAC1-CDC42/GDP -0.038 0.17 -10000 0 -0.37 162 162
T-DHT/AR/PELP1/Src -0.014 0.13 -10000 0 -0.26 163 163
MAP2K2 -0.05 0.099 0.21 7 -0.29 18 25
T-DHT/AR/PELP1/Src/PI3K -0.028 0.11 -10000 0 -0.25 150 150
GNAZ 0.018 0.07 -10000 0 -0.48 16 16
SHBG 0.024 0.022 -10000 0 -0.48 1 1
Gi family/GNB1/GNG2/GDP -0.05 0.16 -10000 0 -0.47 72 72
mol:T-DHT 0 0.001 0.002 1 -0.002 33 34
RAC1 0.029 0.005 -10000 0 -10000 0 0
GNRH1 0.004 0.025 -10000 0 -0.34 4 4
Gi family/GTP -0.035 0.095 -10000 0 -0.27 70 70
CDC42 0.028 0.006 -10000 0 -10000 0 0
BCR 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
JUN -0.034 0.16 0.28 13 -0.41 82 95
IKBKB -0.005 0.097 0.31 5 -0.29 23 28
AKT1 -0.017 0.12 0.24 51 -0.24 62 113
IKBKG 0.002 0.087 0.28 6 -0.29 12 18
CALM1 -0.031 0.14 -10000 0 -0.39 70 70
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
MAP3K1 -0.063 0.22 0.33 7 -0.53 111 118
MAP3K7 0.028 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.033 0.14 -10000 0 -0.4 77 77
DOK1 0.027 0.035 -10000 0 -0.48 4 4
AP-1 -0.019 0.095 0.26 5 -0.25 50 55
LYN 0.023 0.028 -10000 0 -0.48 2 2
BLNK 0.019 0.07 -10000 0 -0.48 16 16
SHC1 0.024 0.011 -10000 0 -10000 0 0
BCR complex -0.051 0.17 -10000 0 -0.41 139 139
CD22 -0.069 0.19 -10000 0 -0.45 118 118
CAMK2G -0.029 0.13 0.25 6 -0.41 54 60
CSNK2A1 0.028 0.006 -10000 0 -10000 0 0
INPP5D 0.026 0.032 -10000 0 -0.48 3 3
SHC/GRB2/SOS1 -0.026 0.11 -10000 0 -0.3 103 103
GO:0007205 -0.034 0.15 -10000 0 -0.41 78 78
SYK 0.021 0.063 -10000 0 -0.48 13 13
ELK1 -0.032 0.14 0.29 2 -0.44 56 58
NFATC1 -0.044 0.18 0.27 22 -0.46 90 112
B-cell antigen/BCR complex -0.051 0.17 -10000 0 -0.41 139 139
PAG1/CSK 0.033 0.026 -10000 0 -0.34 2 2
NFKBIB 0.016 0.047 0.16 8 -0.13 31 39
HRAS -0.023 0.14 0.26 11 -0.41 62 73
NFKBIA 0.016 0.046 0.16 8 -0.12 31 39
NF-kappa-B/RelA/I kappa B beta 0.02 0.041 0.16 8 -0.16 1 9
RasGAP/Csk 0 0.14 -10000 0 -0.32 118 118
mol:GDP -0.03 0.14 -10000 0 -0.4 72 72
PTEN 0.027 0.031 -10000 0 -0.48 3 3
CD79B -0.005 0.11 -10000 0 -0.48 42 42
NF-kappa-B/RelA/I kappa B alpha 0.021 0.041 0.16 8 -0.16 1 9
GRB2 0.027 0.008 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.07 0.21 0.3 7 -0.54 103 110
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
mol:IP3 -0.033 0.14 -10000 0 -0.41 78 78
CSK 0.029 0.005 -10000 0 -10000 0 0
FOS -0.044 0.14 0.28 2 -0.43 64 66
CHUK -0.001 0.093 0.28 6 -0.31 20 26
IBTK 0.027 0.019 -10000 0 -0.48 1 1
CARD11/BCL10/MALT1/TAK1 -0.015 0.14 -10000 0 -0.42 59 59
PTPN6 -0.064 0.18 -10000 0 -0.53 76 76
RELA 0.029 0.004 -10000 0 -10000 0 0
BCL2A1 0.014 0.034 0.22 3 -0.12 1 4
VAV2 -0.073 0.21 -10000 0 -0.58 94 94
ubiquitin-dependent protein catabolic process 0.018 0.046 0.16 8 -0.12 31 39
BTK 0.002 0.15 -10000 0 -1.1 17 17
CD19 -0.079 0.2 -10000 0 -0.49 118 118
MAP4K1 0.002 0.11 -10000 0 -0.48 40 40
CD72 0.023 0.048 -10000 0 -0.48 7 7
PAG1 0.022 0.028 -10000 0 -0.48 2 2
MAPK14 -0.051 0.19 0.31 10 -0.48 95 105
SH3BP5 0.028 0.018 -10000 0 -0.48 1 1
PIK3AP1 -0.033 0.16 -10000 0 -0.48 62 62
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.055 0.2 -10000 0 -0.44 136 136
RAF1 -0.023 0.14 0.26 8 -0.41 53 61
RasGAP/p62DOK/SHIP -0.002 0.14 -10000 0 -0.31 124 124
CD79A -0.069 0.19 -10000 0 -0.48 141 141
re-entry into mitotic cell cycle -0.02 0.095 0.26 5 -0.25 51 56
RASA1 0.028 0.007 -10000 0 -10000 0 0
MAPK3 -0.011 0.12 0.27 20 -0.37 39 59
MAPK1 -0.018 0.12 0.25 11 -0.37 44 55
CD72/SHP1 -0.033 0.19 0.27 17 -0.5 76 93
NFKB1 0.028 0.018 -10000 0 -0.48 1 1
MAPK8 -0.052 0.19 0.32 9 -0.48 95 104
actin cytoskeleton organization -0.056 0.19 0.29 14 -0.49 96 110
NF-kappa-B/RelA 0.043 0.078 0.28 8 -0.2 12 20
Calcineurin -0.01 0.13 -10000 0 -0.4 47 47
PI3K -0.074 0.15 -10000 0 -0.44 94 94
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.031 0.16 -10000 0 -0.45 79 79
SOS1 0.029 0.003 -10000 0 -10000 0 0
Bam32/HPK1 -0.086 0.3 -10000 0 -0.8 106 106
DAPP1 -0.11 0.33 -10000 0 -0.92 98 98
cytokine secretion -0.04 0.17 0.26 24 -0.42 90 114
mol:DAG -0.033 0.14 -10000 0 -0.41 78 78
PLCG2 0.023 0.023 -10000 0 -0.48 1 1
MAP2K1 -0.021 0.13 0.26 11 -0.39 51 62
B-cell antigen/BCR complex/FcgammaRIIB -0.027 0.15 -10000 0 -0.36 119 119
mol:PI-3-4-5-P3 -0.051 0.12 0.21 7 -0.32 78 85
ETS1 -0.028 0.12 0.24 7 -0.39 50 57
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.004 0.15 -10000 0 -0.33 129 129
B-cell antigen/BCR complex/LYN -0.054 0.19 -10000 0 -0.47 106 106
MALT1 0.027 0.019 -10000 0 -0.48 1 1
TRAF6 0.029 0.005 -10000 0 -10000 0 0
RAC1 -0.065 0.2 0.29 8 -0.53 96 104
B-cell antigen/BCR complex/LYN/SYK -0.044 0.19 0.38 1 -0.44 111 112
CARD11 -0.04 0.16 0.26 5 -0.46 68 73
FCGR2B 0.016 0.064 -10000 0 -0.48 13 13
PPP3CA 0.026 0.032 -10000 0 -0.48 3 3
BCL10 0.028 0.005 -10000 0 -10000 0 0
IKK complex 0.011 0.049 0.15 27 -0.13 3 30
PTPRC 0.005 0.091 -10000 0 -0.48 27 27
PDPK1 -0.027 0.094 0.21 29 -0.23 61 90
PPP3CB 0.029 0.004 -10000 0 -10000 0 0
PPP3CC 0.021 0.037 -10000 0 -0.48 4 4
POU2F2 0.016 0.033 0.18 6 -10000 0 6
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.04 0.022 -10000 0 -0.34 2 2
Necdin/E2F1 0.023 0.08 -10000 0 -0.34 36 36
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.016 0.13 -10000 0 -0.28 122 122
NGF (dimer)/p75(NTR)/BEX1 -0.037 0.16 -10000 0 -0.34 172 172
NT-4/5 (dimer)/p75(NTR) -0.043 0.16 -10000 0 -0.37 139 139
IKBKB 0.024 0.011 -10000 0 -10000 0 0
AKT1 -0.022 0.11 0.18 87 -0.27 94 181
IKBKG 0.029 0.002 -10000 0 -10000 0 0
BDNF 0.001 0.095 -10000 0 -0.48 29 29
MGDIs/NGR/p75(NTR)/LINGO1 0.004 0.12 -10000 0 -0.31 97 97
FURIN 0.028 0.008 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.003 0.12 -10000 0 -0.32 98 98
LINGO1 0.01 0.079 -10000 0 -0.48 19 19
Sortilin/TRAF6/NRIF 0.028 0.029 -10000 0 -0.3 3 3
proBDNF (dimer) 0.001 0.095 -10000 0 -0.48 29 29
NTRK1 -0.001 0.1 -10000 0 -0.48 34 34
RTN4R 0.023 0.047 -10000 0 -0.48 7 7
neuron apoptosis -0.039 0.16 0.36 8 -0.48 43 51
IRAK1 0.029 0.005 -10000 0 -10000 0 0
SHC1 -0.021 0.094 -10000 0 -0.31 76 76
ARHGDIA 0.027 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.021 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.065 0.042 -10000 0 -0.26 2 2
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.018 0.12 -10000 0 -0.29 101 101
MAGEH1 0.025 0.043 -10000 0 -0.48 6 6
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.014 0.13 -10000 0 -0.3 101 101
Mammalian IAPs/DIABLO 0.061 0.05 -10000 0 -0.27 14 14
proNGF (dimer) 0.01 0.089 -10000 0 -0.48 26 26
MAGED1 0.025 0.043 -10000 0 -0.48 6 6
APP 0.027 0.031 -10000 0 -0.48 3 3
NT-4/5 (dimer) -0.034 0.16 -10000 0 -0.48 93 93
ZNF274 0.028 0.018 -10000 0 -0.48 1 1
RhoA/GDP/RHOGDI -0.006 0.098 -10000 0 -0.27 92 92
NGF 0.01 0.089 -10000 0 -0.48 26 26
cell cycle arrest -0.014 0.12 0.23 66 -0.24 95 161
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.008 0.084 -10000 0 -0.25 75 75
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.018 0.14 -10000 0 -0.32 138 138
NCSTN 0.025 0.011 -10000 0 -10000 0 0
mol:GTP 0.001 0.13 -10000 0 -0.32 102 102
PSENEN 0.029 0.004 -10000 0 -10000 0 0
mol:ceramide -0.017 0.11 0.18 46 -0.28 98 144
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.007 0.074 -10000 0 -0.34 13 13
p75(NTR)/beta APP -0.005 0.11 -10000 0 -0.35 80 80
BEX1 -0.056 0.16 -10000 0 -0.48 102 102
mol:GDP -0.043 0.098 -10000 0 -0.31 96 96
NGF (dimer) 0.005 0.11 -10000 0 -0.28 101 101
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.019 0.12 -10000 0 -0.29 92 92
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
RAC1/GTP 0.006 0.1 -10000 0 -0.26 96 96
MYD88 0.029 0.005 -10000 0 -10000 0 0
CHUK 0.029 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.001 0.13 -10000 0 -0.32 102 102
RHOB 0.013 0.089 -10000 0 -0.48 26 26
RHOA 0.028 0.006 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.03 0.063 -10000 0 -0.34 22 22
NT3 (dimer) -0.009 0.12 -10000 0 -0.48 46 46
TP53 -0.028 0.11 0.44 6 -0.27 98 104
PRDM4 -0.014 0.11 0.18 56 -0.28 97 153
BDNF (dimer) -0.026 0.15 -10000 0 -0.32 159 159
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
SORT1 0.027 0.031 -10000 0 -0.48 3 3
activation of caspase activity 0.011 0.13 -10000 0 -0.28 122 122
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.02 0.12 -10000 0 -0.29 97 97
RHOC 0.029 0.005 -10000 0 -10000 0 0
XIAP 0.029 0.002 -10000 0 -10000 0 0
MAPK10 -0.053 0.14 0.29 7 -0.36 94 101
DIABLO 0.029 0.002 -10000 0 -10000 0 0
SMPD2 -0.017 0.11 0.18 46 -0.28 98 144
APH1B 0.025 0.04 -10000 0 -0.48 5 5
APH1A 0.024 0.011 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.005 0.12 -10000 0 -0.31 98 98
PSEN1 0.028 0.006 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.041 0.017 -10000 0 -0.34 1 1
NT3 (dimer)/p75(NTR) -0.031 0.14 -10000 0 -0.36 116 116
MAPK8 -0.029 0.12 0.29 12 -0.33 79 91
MAPK9 -0.029 0.12 0.28 10 -0.33 79 89
APAF1 0.028 0.018 -10000 0 -0.48 1 1
NTF3 -0.009 0.12 -10000 0 -0.48 46 46
NTF4 -0.034 0.16 -10000 0 -0.48 93 93
NDN 0.019 0.066 -10000 0 -0.48 14 14
RAC1/GDP 0.021 0.003 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.013 0.13 -10000 0 -0.28 116 116
p75 CTF/Sortilin/TRAF6/NRIF 0.067 0.031 -10000 0 -0.27 3 3
RhoA-B-C/GTP 0 0.12 -10000 0 -0.32 102 102
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.027 0.12 -10000 0 -0.28 95 95
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.018 0.12 -10000 0 -0.3 96 96
PRKACB 0.016 0.059 -10000 0 -0.48 10 10
proBDNF (dimer)/p75 ECD 0.019 0.073 -10000 0 -0.34 28 28
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.015 0.067 -10000 0 -0.48 14 14
BIRC2 0.027 0.009 -10000 0 -10000 0 0
neuron projection morphogenesis -0.022 0.12 0.22 22 -0.29 99 121
BAD -0.04 0.14 0.34 15 -0.35 82 97
RIPK2 0.023 0.013 -10000 0 -10000 0 0
NGFR -0.028 0.15 -10000 0 -0.48 80 80
CYCS -0.032 0.11 0.19 58 -0.27 102 160
ADAM17 0.029 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.015 0.1 -10000 0 -0.28 75 75
BCL2L11 -0.04 0.14 0.37 12 -0.35 82 94
BDNF (dimer)/p75(NTR) -0.023 0.13 -10000 0 -0.37 97 97
PI3K 0.017 0.12 -10000 0 -0.28 96 96
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.019 0.12 -10000 0 -0.29 97 97
NDNL2 0.028 0.006 -10000 0 -10000 0 0
YWHAE 0.027 0.009 -10000 0 -10000 0 0
PRKCI 0.028 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.016 0.13 -10000 0 -0.36 96 96
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.018 0.12 -10000 0 -0.29 103 103
TRAF6 0.029 0.005 -10000 0 -10000 0 0
RAC1 0.029 0.005 -10000 0 -10000 0 0
PRKCZ 0.027 0.026 -10000 0 -0.48 2 2
PLG 0 0 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.034 0.12 -10000 0 -0.32 112 112
SQSTM1 0.028 0.006 -10000 0 -10000 0 0
NGFRAP1 0.008 0.1 -10000 0 -0.48 34 34
CASP3 -0.038 0.13 0.35 12 -0.33 87 99
E2F1 0.015 0.082 -10000 0 -0.48 22 22
CASP9 0.028 0.006 -10000 0 -10000 0 0
IKK complex 0.02 0.11 -10000 0 -0.38 19 19
NGF (dimer)/TRKA 0.004 0.1 -10000 0 -0.36 54 54
MMP7 -0.032 0.15 -10000 0 -0.48 80 80
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.028 0.12 -10000 0 -0.27 97 97
MMP3 -0.025 0.15 -10000 0 -0.48 77 77
APAF-1/Caspase 9 -0.051 0.077 -10000 0 -0.38 13 13
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.027 0.019 -10000 0 -0.48 1 1
LAT2 -0.028 0.13 -10000 0 -0.35 84 84
AP1 -0.005 0.17 -10000 0 -0.5 56 56
mol:PIP3 -0.006 0.18 0.32 36 -0.4 82 118
IKBKB 0.019 0.13 0.27 78 -0.26 57 135
AKT1 0.017 0.16 0.32 106 -0.41 18 124
IKBKG 0.001 0.12 0.23 51 -0.27 58 109
MS4A2 -0.043 0.17 -10000 0 -0.46 112 112
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
MAP3K1 -0.006 0.14 0.26 27 -0.42 46 73
mol:Ca2+ 0.002 0.14 0.23 101 -0.33 57 158
LYN 0.023 0.03 -10000 0 -0.49 2 2
CBLB -0.026 0.12 -10000 0 -0.34 82 82
SHC1 0.024 0.011 -10000 0 -10000 0 0
RasGAP/p62DOK 0.042 0.061 -10000 0 -0.27 29 29
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.026 0.032 -10000 0 -0.48 3 3
PLD2 -0.003 0.16 0.33 89 -0.33 61 150
PTPN13 -0.036 0.18 -10000 0 -0.56 54 54
PTPN11 0.027 0.02 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.006 0.13 0.29 36 -0.34 32 68
SYK 0.022 0.066 -10000 0 -0.49 13 13
GRB2 0.027 0.008 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.033 0.15 -10000 0 -0.4 86 86
LAT -0.032 0.13 -10000 0 -0.36 85 85
PAK2 -0.007 0.16 0.27 28 -0.47 46 74
NFATC2 -0.036 0.14 -10000 0 -0.54 48 48
HRAS -0.011 0.17 0.26 16 -0.5 49 65
GAB2 0.025 0.026 -10000 0 -0.48 2 2
PLA2G1B 0.003 0.12 -10000 0 -0.9 12 12
Fc epsilon R1 -0.014 0.14 -10000 0 -0.34 121 121
Antigen/IgE/Fc epsilon R1 -0.011 0.13 -10000 0 -0.3 122 122
mol:GDP -0.031 0.16 -10000 0 -0.53 50 50
JUN 0.028 0.008 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
FOS -0.006 0.12 -10000 0 -0.48 45 45
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.024 0.13 -10000 0 -0.35 88 88
CHUK 0.001 0.12 0.23 50 -0.27 59 109
KLRG1 -0.025 0.11 -10000 0 -0.37 52 52
VAV1 -0.031 0.13 -10000 0 -0.35 87 87
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.025 0.12 -10000 0 -0.34 81 81
negative regulation of mast cell degranulation 0 0.13 0.2 1 -0.4 41 42
BTK -0.03 0.16 -10000 0 -0.56 47 47
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.033 0.15 -10000 0 -0.37 88 88
GAB2/PI3K/SHP2 -0.044 0.086 -10000 0 -0.35 35 35
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.031 0.13 -10000 0 -0.39 63 63
RAF1 0.003 0.12 -10000 0 -0.98 12 12
Fc epsilon R1/FcgammaRIIB/SHIP 0.007 0.15 -10000 0 -0.3 128 128
FCER1G 0.024 0.039 -10000 0 -0.49 4 4
FCER1A -0.023 0.14 -10000 0 -0.49 65 65
Antigen/IgE/Fc epsilon R1/Fyn 0 0.13 -10000 0 -0.29 118 118
MAPK3 0.003 0.12 -10000 0 -0.92 12 12
MAPK1 -0.001 0.12 -10000 0 -0.92 12 12
NFKB1 0.028 0.018 -10000 0 -0.48 1 1
MAPK8 -0.022 0.2 -10000 0 -0.63 54 54
DUSP1 0.011 0.087 -10000 0 -0.48 25 25
NF-kappa-B/RelA 0.009 0.071 0.15 16 -0.17 46 62
actin cytoskeleton reorganization -0.024 0.17 -10000 0 -0.6 41 41
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0 0.15 0.24 1 -0.47 45 46
FER -0.029 0.13 -10000 0 -0.34 87 87
RELA 0.029 0.004 -10000 0 -10000 0 0
ITK -0.038 0.13 -10000 0 -0.4 82 82
SOS1 0.029 0.003 -10000 0 -10000 0 0
PLCG1 -0.014 0.17 0.26 11 -0.51 51 62
cytokine secretion -0.005 0.042 -10000 0 -0.16 6 6
SPHK1 -0.031 0.13 -10000 0 -0.34 91 91
PTK2 -0.026 0.18 -10000 0 -0.64 41 41
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.028 0.15 -10000 0 -0.4 85 85
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.007 0.17 0.3 34 -0.42 64 98
MAP2K2 -0.001 0.12 -10000 0 -0.91 12 12
MAP2K1 -0.001 0.12 -10000 0 -0.92 12 12
MAP2K7 0.029 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 -0.012 0.11 0.2 3 -0.39 40 43
MAP2K4 -0.074 0.31 -10000 0 -0.87 104 104
Fc epsilon R1/FcgammaRIIB -0.002 0.15 -10000 0 -0.32 127 127
mol:Choline -0.003 0.16 0.33 89 -0.33 60 149
SHC/Grb2/SOS1 0.009 0.13 -10000 0 -0.42 37 37
FYN 0.026 0.027 -10000 0 -0.48 2 2
DOK1 0.027 0.035 -10000 0 -0.48 4 4
PXN -0.025 0.17 -10000 0 -0.58 40 40
HCLS1 -0.028 0.13 -10000 0 -0.34 83 83
PRKCB -0.005 0.15 0.26 50 -0.36 68 118
FCGR2B 0.016 0.064 -10000 0 -0.48 13 13
IGHE 0 0.007 -10000 0 -10000 0 0
KLRG1/SHIP 0 0.13 0.2 1 -0.41 41 42
LCP2 0.027 0.031 -10000 0 -0.48 3 3
PLA2G4A -0.03 0.13 -10000 0 -0.36 83 83
RASA1 0.028 0.007 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.003 0.16 0.33 89 -0.33 60 149
IKK complex 0.02 0.11 0.25 74 -0.21 36 110
WIPF1 0.023 0.056 -10000 0 -0.48 10 10
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.039 0.25 -10000 0 -1 45 45
MKNK1 0.029 0.005 -10000 0 -10000 0 0
MAPK14 0.015 0.095 -10000 0 -0.33 56 56
ATF2/c-Jun -0.002 0.088 -10000 0 -0.38 20 20
MAPK11 0.011 0.1 -10000 0 -0.36 56 56
MITF -0.004 0.13 -10000 0 -0.43 61 61
MAPKAPK5 0 0.11 -10000 0 -0.39 60 60
KRT8 -0.004 0.12 -10000 0 -0.39 69 69
MAPKAPK3 0.028 0.006 -10000 0 -10000 0 0
MAPKAPK2 0.022 0.032 -10000 0 -0.48 3 3
p38alpha-beta/CK2 0.011 0.15 -10000 0 -0.5 60 60
CEBPB -0.002 0.11 -10000 0 -0.39 58 58
SLC9A1 -0.001 0.12 -10000 0 -0.41 59 59
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.003 0.12 -10000 0 -0.39 59 59
p38alpha-beta/MNK1 0.028 0.13 -10000 0 -0.41 60 60
JUN -0.003 0.086 -10000 0 -0.38 20 20
PPARGC1A -0.027 0.16 -10000 0 -0.42 101 101
USF1 -0.001 0.1 -10000 0 -0.39 53 53
RAB5/GDP/GDI1 0.006 0.092 -10000 0 -0.29 61 61
NOS2 -0.018 0.2 -10000 0 -0.95 30 30
DDIT3 0 0.11 -10000 0 -0.39 60 60
RAB5A 0.029 0.004 -10000 0 -10000 0 0
HSPB1 -0.015 0.11 0.28 4 -0.33 73 77
p38alpha-beta/HBP1 0.029 0.13 -10000 0 -0.41 59 59
CREB1 -0.003 0.12 -10000 0 -0.42 59 59
RAB5/GDP 0.021 0.003 -10000 0 -10000 0 0
EIF4E -0.007 0.11 0.23 2 -0.38 56 58
RPS6KA4 0 0.11 -10000 0 -0.4 58 58
PLA2G4A -0.017 0.12 0.24 1 -0.38 65 66
GDI1 0 0.11 -10000 0 -0.39 60 60
TP53 -0.019 0.14 -10000 0 -0.51 55 55
RPS6KA5 -0.006 0.12 -10000 0 -0.38 73 73
ESR1 -0.073 0.17 -10000 0 -0.33 234 234
HBP1 0.029 0.004 -10000 0 -10000 0 0
MEF2C -0.001 0.12 -10000 0 -0.4 60 60
MEF2A 0 0.11 -10000 0 -0.4 58 58
EIF4EBP1 -0.008 0.12 -10000 0 -0.44 58 58
KRT19 -0.009 0.12 -10000 0 -0.37 80 80
ELK4 -0.003 0.11 -10000 0 -0.39 55 55
ATF6 -0.001 0.1 -10000 0 -0.39 53 53
ATF1 -0.004 0.12 -10000 0 -0.42 60 60
p38alpha-beta/MAPKAPK2 0.02 0.12 -10000 0 -0.41 56 56
p38alpha-beta/MAPKAPK3 0.028 0.13 -10000 0 -0.41 60 60
Syndecan-4-mediated signaling 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
PTK2 -0.007 0.14 -10000 0 -0.48 52 52
Syndecan-4/Syndesmos -0.017 0.17 -10000 0 -0.47 84 84
positive regulation of JNK cascade -0.012 0.18 -10000 0 -0.45 98 98
Syndecan-4/ADAM12 -0.028 0.19 -10000 0 -0.49 104 104
CCL5 -0.002 0.11 -10000 0 -0.48 41 41
Rac1/GDP 0.021 0.003 -10000 0 -10000 0 0
DNM2 0.029 0.005 -10000 0 -10000 0 0
ITGA5 0.028 0.025 -10000 0 -0.48 2 2
SDCBP 0.025 0.011 -10000 0 -10000 0 0
PLG -0.003 0.015 0.035 6 -0.043 76 82
ADAM12 0.005 0.1 -10000 0 -0.48 37 37
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.027 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.027 0.015 -10000 0 -0.064 9 9
Syndecan-4/Laminin alpha1 -0.037 0.2 -10000 0 -0.5 109 109
Syndecan-4/CXCL12/CXCR4 -0.012 0.19 -10000 0 -0.47 98 98
Syndecan-4/Laminin alpha3 -0.041 0.19 -10000 0 -0.49 91 91
MDK 0.019 0.064 -10000 0 -0.48 13 13
Syndecan-4/FZD7 -0.02 0.18 -10000 0 -0.48 94 94
Syndecan-4/Midkine -0.02 0.18 -10000 0 -0.47 89 89
FZD7 0.02 0.062 -10000 0 -0.48 12 12
Syndecan-4/FGFR1/FGF -0.023 0.17 -10000 0 -0.46 88 88
THBS1 0.019 0.068 -10000 0 -0.48 15 15
integrin-mediated signaling pathway -0.03 0.19 -10000 0 -0.48 103 103
positive regulation of MAPKKK cascade -0.012 0.18 -10000 0 -0.45 98 98
Syndecan-4/TACI -0.038 0.18 -10000 0 -0.48 89 89
CXCR4 0.026 0.027 -10000 0 -0.48 2 2
cell adhesion 0.015 0.088 0.2 69 -0.3 39 108
Syndecan-4/Dynamin -0.016 0.17 -10000 0 -0.47 90 90
Syndecan-4/TSP1 -0.021 0.18 -10000 0 -0.47 93 93
Syndecan-4/GIPC -0.017 0.17 -10000 0 -0.47 90 90
Syndecan-4/RANTES -0.03 0.18 -10000 0 -0.49 94 94
ITGB1 0.029 0.005 -10000 0 -10000 0 0
LAMA1 -0.018 0.14 -10000 0 -0.48 70 70
LAMA3 -0.026 0.15 -10000 0 -0.48 82 82
RAC1 0.029 0.005 -10000 0 -10000 0 0
PRKCA 0.066 0.24 0.77 79 -0.42 11 90
Syndecan-4/alpha-Actinin -0.016 0.17 -10000 0 -0.47 90 90
TFPI 0.025 0.037 -10000 0 -0.48 4 4
F2 0.016 0.026 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.041 0.021 -10000 0 -0.34 2 2
positive regulation of cell adhesion -0.066 0.2 0.27 1 -0.5 113 114
ACTN1 0.028 0.006 -10000 0 -10000 0 0
TNC -0.007 0.12 -10000 0 -0.48 53 53
Syndecan-4/CXCL12 -0.025 0.18 -10000 0 -0.48 98 98
FGF6 0 0 -10000 0 -10000 0 0
RHOA 0.028 0.006 -10000 0 -10000 0 0
CXCL12 0.011 0.092 -10000 0 -0.48 28 28
TNFRSF13B -0.019 0.13 -10000 0 -0.48 58 58
FGF2 0.006 0.092 -10000 0 -0.48 27 27
FGFR1 0.019 0.048 -10000 0 -0.48 7 7
Syndecan-4/PI-4-5-P2 -0.044 0.16 -10000 0 -0.47 90 90
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.003 0.1 -10000 0 -0.45 39 39
cell migration -0.012 0.011 -10000 0 -0.064 1 1
PRKCD 0.02 0.027 -10000 0 -0.15 1 1
vasculogenesis -0.02 0.17 -10000 0 -0.46 94 94
SDC4 -0.041 0.17 -10000 0 -0.5 88 88
Syndecan-4/Tenascin C -0.032 0.19 -10000 0 -0.49 103 103
Syndecan-4/PI-4-5-P2/PKC alpha -0.022 0.012 -10000 0 -0.056 3 3
Syndecan-4/Syntenin -0.02 0.17 -10000 0 -0.47 80 80
MMP9 -0.029 0.15 -10000 0 -0.47 82 82
Rac1/GTP 0.015 0.09 0.2 69 -0.3 39 108
cytoskeleton organization -0.016 0.16 -10000 0 -0.45 84 84
GIPC1 0.028 0.018 -10000 0 -0.48 1 1
Syndecan-4/TFPI -0.018 0.18 -10000 0 -0.47 92 92
Reelin signaling pathway

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
CDK5R1/CDK5 0.039 0.019 -10000 0 -0.34 1 1
VLDLR 0.016 0.073 -10000 0 -0.48 17 17
CRKL 0.027 0.019 -10000 0 -0.48 1 1
LRPAP1 0.028 0.006 -10000 0 -10000 0 0
FYN 0.026 0.027 -10000 0 -0.48 2 2
ITGA3 0.015 0.074 -10000 0 -0.48 18 18
RELN/VLDLR/Fyn 0 0.13 -10000 0 -0.3 116 116
MAPK8IP1/MKK7/MAP3K11/JNK1 0.062 0.058 -10000 0 -0.26 16 16
AKT1 -0.027 0.089 -10000 0 -0.24 110 110
MAP2K7 0.029 0.004 -10000 0 -10000 0 0
RAPGEF1 0.029 0.005 -10000 0 -10000 0 0
DAB1 0.017 0.038 -10000 0 -0.48 3 3
RELN/LRP8/DAB1 0.003 0.11 -10000 0 -0.28 112 112
LRPAP1/LRP8 0.035 0.039 -10000 0 -0.34 7 7
RELN/LRP8/DAB1/Fyn 0.014 0.11 -10000 0 -0.26 111 111
DAB1/alpha3/beta1 Integrin 0.002 0.12 -10000 0 -0.26 123 123
long-term memory 0.003 0.14 -10000 0 -0.29 134 134
DAB1/LIS1 0.019 0.12 -10000 0 -0.26 123 123
DAB1/CRLK/C3G 0.01 0.11 -10000 0 -0.25 121 121
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
DAB1/NCK2 0.023 0.12 -10000 0 -0.26 120 120
ARHGEF2 0.024 0.027 -10000 0 -0.48 2 2
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.014 0.13 -10000 0 -0.48 59 59
CDK5R1 0.026 0.02 -10000 0 -0.48 1 1
RELN -0.05 0.17 -10000 0 -0.48 107 107
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
RELN/LRP8/Fyn 0.003 0.12 -10000 0 -0.3 109 109
GRIN2A/RELN/LRP8/DAB1/Fyn 0.005 0.15 -10000 0 -0.3 136 136
MAPK8 0.029 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.001 0.12 -10000 0 -0.28 118 118
ITGB1 0.029 0.005 -10000 0 -10000 0 0
MAP1B -0.04 0.11 -10000 0 -0.28 128 128
RELN/LRP8 0.004 0.12 -10000 0 -0.3 110 110
GRIN2B/RELN/LRP8/DAB1/Fyn 0.023 0.12 -10000 0 -0.27 109 109
PI3K 0.04 0.013 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.029 0.058 -10000 0 -0.34 18 18
RAP1A -0.046 0.095 0.35 5 -0.29 24 29
PAFAH1B1 0.027 0.008 -10000 0 -10000 0 0
MAPK8IP1 0.016 0.075 -10000 0 -0.48 18 18
CRLK/C3G 0.04 0.017 -10000 0 -0.34 1 1
GRIN2B 0.019 0.018 -10000 0 -10000 0 0
NCK2 0.028 0.018 -10000 0 -0.48 1 1
neuron differentiation -0.003 0.094 -10000 0 -0.36 21 21
neuron adhesion -0.035 0.11 0.36 7 -0.41 9 16
LRP8 0.022 0.049 -10000 0 -0.48 7 7
GSK3B -0.028 0.085 -10000 0 -0.25 50 50
RELN/VLDLR/DAB1/Fyn 0.01 0.12 -10000 0 -0.26 117 117
MAP3K11 0.029 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.021 0.098 -10000 0 -0.25 116 116
CDK5 0.028 0.005 -10000 0 -10000 0 0
MAPT -0.081 0.21 0.75 14 -0.44 173 187
neuron migration -0.039 0.12 0.28 2 -0.32 93 95
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.003 0.095 -10000 0 -0.37 21 21
RELN/VLDLR 0.013 0.12 -10000 0 -0.28 120 120
FAS signaling pathway (CD95)

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
SPTAN1 0.011 0.071 0.23 56 -10000 0 56
RFC1 0.011 0.069 0.23 55 -0.19 1 56
PRKDC 0.032 0.1 0.25 119 -0.19 2 121
RIPK1 0.029 0.007 -10000 0 -10000 0 0
CASP7 0.004 0.1 0.25 1 -0.6 17 18
FASLG/FAS/FADD/FAF1 0.002 0.081 0.24 39 -0.28 31 70
MAP2K4 -0.025 0.16 0.39 3 -0.39 95 98
mol:ceramide -0.013 0.11 -10000 0 -0.37 51 51
GSN 0.011 0.073 0.24 56 -0.27 1 57
FASLG/FAS/FADD/FAF1/Caspase 8 0.003 0.096 0.27 6 -0.32 43 49
FAS 0.014 0.068 -10000 0 -0.48 14 14
BID -0.007 0.051 0.26 27 -10000 0 27
MAP3K1 -0.003 0.12 0.28 12 -0.39 31 43
MAP3K7 0.026 0.009 -10000 0 -10000 0 0
RB1 0.009 0.065 0.22 55 -0.27 3 58
CFLAR 0.029 0.019 -10000 0 -0.48 1 1
HGF/MET -0.011 0.15 -10000 0 -0.34 138 138
ARHGDIB 0.011 0.078 0.23 69 -0.21 17 86
FADD 0.02 0.018 -10000 0 -10000 0 0
actin filament polymerization -0.009 0.077 0.27 1 -0.24 56 57
NFKB1 -0.01 0.12 -10000 0 -0.67 16 16
MAPK8 -0.046 0.2 0.5 3 -0.48 120 123
DFFA 0.011 0.068 0.23 53 -0.19 2 55
DNA fragmentation during apoptosis 0.008 0.071 0.23 54 -0.19 2 56
FAS/FADD/MET 0.01 0.11 -10000 0 -0.33 66 66
CFLAR/RIP1 0.043 0.018 -10000 0 -0.35 1 1
FAIM3 0.004 0.096 -10000 0 -0.48 31 31
FAF1 0.022 0.021 -10000 0 -10000 0 0
PARP1 0.015 0.08 0.24 66 -0.19 2 68
DFFB 0.01 0.068 0.23 54 -0.18 12 66
CHUK -0.01 0.1 -10000 0 -0.61 14 14
FASLG -0.015 0.12 -10000 0 -0.48 48 48
FAS/FADD 0.024 0.053 -10000 0 -0.35 12 12
HGF -0.002 0.12 -10000 0 -0.48 49 49
LMNA 0.012 0.077 0.22 70 -0.26 2 72
CASP6 0.012 0.068 0.22 66 -0.18 9 75
CASP10 0.02 0.04 -10000 0 -0.48 4 4
CASP3 0.02 0.08 0.27 70 -10000 0 70
PTPN13 0 0.12 -10000 0 -0.48 46 46
CASP8 -0.004 0.07 0.35 30 -10000 0 30
IL6 -0.13 0.43 -10000 0 -1.2 110 110
MET -0.018 0.14 -10000 0 -0.48 71 71
ICAD/CAD 0.007 0.061 0.3 11 -10000 0 11
FASLG/FAS/FADD/FAF1/Caspase 10 -0.014 0.11 -10000 0 -0.37 51 51
activation of caspase activity by cytochrome c -0.007 0.051 0.26 27 -10000 0 27
PAK2 0.014 0.079 0.24 65 -10000 0 65
BCL2 -0.018 0.14 -10000 0 -0.48 74 74
Effects of Botulinum toxin

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
STX1A 0.006 0.006 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B -0.024 0.13 -10000 0 -0.34 112 112
STXBP1 0.026 0.04 -10000 0 -0.48 5 5
ACh/CHRNA1 -0.026 0.11 -10000 0 -0.27 120 120
RAB3GAP2/RIMS1/UNC13B 0.004 0.11 -10000 0 -0.3 90 90
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 -0.052 0.17 -10000 0 -0.48 110 110
mol:ACh -0.01 0.038 0.078 19 -0.12 59 78
RAB3GAP2 0.024 0.011 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.009 0.1 -10000 0 -0.23 106 106
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.026 0.11 -10000 0 -0.27 120 120
UNC13B 0.026 0.027 -10000 0 -0.48 2 2
CHRNA1 -0.031 0.16 -10000 0 -0.48 92 92
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.053 0.12 -10000 0 -0.3 152 152
SNAP25 -0.013 0.067 -10000 0 -0.28 50 50
VAMP2 0.005 0.002 -10000 0 -10000 0 0
SYT1 -0.075 0.18 -10000 0 -0.48 138 138
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.023 0.027 -10000 0 -0.29 5 5
STX1A/SNAP25 fragment 1/VAMP2 -0.009 0.1 -10000 0 -0.23 106 106
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.042 0.2 -10000 0 -0.65 70 70
IHH 0.006 0.061 -10000 0 -0.19 39 39
SHH Np/Cholesterol/GAS1 0.002 0.069 -10000 0 -0.27 48 48
LRPAP1 0.028 0.006 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.002 0.069 0.27 48 -10000 0 48
SMO/beta Arrestin2 -0.01 0.18 -10000 0 -0.58 58 58
SMO -0.033 0.18 -10000 0 -0.6 60 60
AKT1 0.001 0.12 -10000 0 -0.52 19 19
ARRB2 0.027 0.009 -10000 0 -10000 0 0
BOC 0.019 0.062 -10000 0 -0.48 12 12
ADRBK1 0.027 0.008 -10000 0 -10000 0 0
heart looping -0.03 0.18 -10000 0 -0.59 60 60
STIL -0.004 0.14 0.26 1 -0.45 37 38
DHH N/PTCH2 0.009 0.11 -10000 0 -0.36 59 59
DHH N/PTCH1 -0.023 0.17 -10000 0 -0.39 120 120
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
DHH -0.003 0.12 -10000 0 -0.48 49 49
PTHLH -0.059 0.24 -10000 0 -0.77 76 76
determination of left/right symmetry -0.03 0.18 -10000 0 -0.59 60 60
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
skeletal system development -0.058 0.24 -10000 0 -0.76 76 76
IHH N/Hhip 0.023 0.047 -10000 0 -0.38 2 2
DHH N/Hhip 0.012 0.093 -10000 0 -0.35 50 50
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.03 0.18 -10000 0 -0.59 60 60
pancreas development 0.022 0.031 -10000 0 -0.48 2 2
HHAT 0.016 0.066 -10000 0 -0.48 14 14
PI3K 0.04 0.013 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.004 0.11 -10000 0 -0.48 40 40
somite specification -0.03 0.18 -10000 0 -0.59 60 60
SHH Np/Cholesterol/PTCH1 -0.02 0.12 -10000 0 -0.36 73 73
SHH Np/Cholesterol/PTCH2 0.01 0.05 -10000 0 -0.27 23 23
SHH Np/Cholesterol/Megalin -0.057 0.12 -10000 0 -0.28 178 178
SHH -0.01 0.043 -10000 0 -0.35 12 12
catabolic process -0.025 0.16 -10000 0 -0.45 86 86
SMO/Vitamin D3 -0.009 0.16 -10000 0 -0.52 50 50
SHH Np/Cholesterol/Hhip 0.009 0.042 -10000 0 -0.27 15 15
LRP2 -0.11 0.21 -10000 0 -0.48 208 208
receptor-mediated endocytosis -0.068 0.19 -10000 0 -0.54 69 69
SHH Np/Cholesterol/BOC 0.01 0.05 -10000 0 -0.27 23 23
SHH Np/Cholesterol/CDO 0.008 0.052 -10000 0 -0.28 23 23
mesenchymal cell differentiation -0.009 0.042 0.27 15 -10000 0 15
mol:Vitamin D3 0.004 0.14 0.37 1 -0.44 42 43
IHH N/PTCH2 0.02 0.069 -10000 0 -0.38 15 15
CDON 0.015 0.072 -10000 0 -0.48 17 17
IHH N/PTCH1 -0.015 0.16 -10000 0 -0.45 86 86
Megalin/LRPAP1 -0.069 0.16 -10000 0 -0.34 208 208
PTCH2 0.017 0.069 -10000 0 -0.48 15 15
SHH Np/Cholesterol 0.007 0.036 -10000 0 -0.27 13 13
PTCH1 -0.025 0.16 -10000 0 -0.45 86 86
HHIP 0.022 0.031 -10000 0 -0.48 2 2
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.002 0.07 -10000 0 -0.23 59 59
epithelial cell differentiation 0.033 0.077 -10000 0 -0.25 49 49
CYFIP2 0.007 0.1 -10000 0 -0.48 34 34
ENAH -0.008 0.065 0.26 9 -10000 0 9
EGFR -0.018 0.14 -10000 0 -0.48 67 67
EPHA2 0.024 0.04 -10000 0 -0.48 5 5
MYO6 -0.021 0.064 0.18 16 -0.24 50 66
CTNNB1 0.028 0.019 -10000 0 -0.48 1 1
ABI1/Sra1/Nap1 0.042 0.068 -10000 0 -0.3 30 30
AQP5 -0.095 0.19 -10000 0 -0.47 160 160
CTNND1 0.028 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.021 0.062 0.18 16 -0.24 48 64
regulation of calcium-dependent cell-cell adhesion -0.025 0.068 0.18 16 -0.24 59 75
EGF -0.056 0.18 -10000 0 -0.48 127 127
NCKAP1 0.029 0.004 -10000 0 -10000 0 0
AQP3 -0.057 0.16 -10000 0 -0.45 96 96
cortical microtubule organization 0.033 0.077 -10000 0 -0.25 49 49
GO:0000145 -0.02 0.058 0.16 16 -0.23 48 64
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.037 0.079 -10000 0 -0.25 49 49
MLLT4 0.025 0.032 -10000 0 -0.48 3 3
ARF6/GDP -0.027 0.048 -10000 0 -0.22 42 42
ARF6 0.029 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.053 0.043 -10000 0 -0.27 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.007 0.061 -10000 0 -0.35 1 1
PVRL2 0.029 0.005 -10000 0 -10000 0 0
ZYX -0.021 0.062 0.18 14 -0.24 48 62
ARF6/GTP 0.058 0.046 -10000 0 -0.25 6 6
CDH1 -0.004 0.12 -10000 0 -0.48 48 48
EGFR/EGFR/EGF/EGF -0.039 0.14 -10000 0 -0.25 224 224
RhoA/GDP 0.034 0.075 -10000 0 -0.24 49 49
actin cytoskeleton organization -0.023 0.061 0.16 15 -0.24 50 65
IGF-1R heterotetramer -0.018 0.14 -10000 0 -0.48 74 74
GIT1 0.027 0.008 -10000 0 -10000 0 0
IGF1R -0.018 0.14 -10000 0 -0.48 74 74
IGF1 -0.018 0.14 -10000 0 -0.48 69 69
DIAPH1 0.017 0.16 -10000 0 -0.59 27 27
Wnt receptor signaling pathway -0.033 0.077 0.25 49 -10000 0 49
RHOA 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.027 0.049 -10000 0 -10000 0 0
CTNNA1 0.029 0.005 -10000 0 -10000 0 0
VCL -0.023 0.062 0.17 15 -0.24 50 65
EFNA1 0.024 0.021 -10000 0 -0.48 1 1
LPP -0.023 0.062 0.17 16 -0.24 52 68
Ephrin A1/EPHA2 0.022 0.069 -10000 0 -0.24 44 44
SEC6/SEC8 -0.03 0.053 -10000 0 -0.23 51 51
MGAT3 -0.025 0.069 0.18 15 -0.25 59 74
HGF/MET -0.009 0.12 -10000 0 -0.26 149 149
HGF -0.002 0.12 -10000 0 -0.48 49 49
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.002 0.07 -10000 0 -0.23 59 59
actin cable formation 0.033 0.097 0.27 41 -0.26 2 43
KIAA1543 -0.022 0.061 0.16 15 -0.24 50 65
KIFC3 -0.023 0.063 0.18 14 -0.24 51 65
NCK1 0.029 0.004 -10000 0 -10000 0 0
EXOC3 0.028 0.006 -10000 0 -10000 0 0
ACTN1 -0.021 0.063 0.18 16 -0.24 48 64
NCK1/GIT1 0.039 0.013 -10000 0 -10000 0 0
mol:GDP 0.033 0.077 -10000 0 -0.25 49 49
EXOC4 0.029 0.005 -10000 0 -10000 0 0
STX4 -0.021 0.063 0.18 14 -0.24 50 64
PIP5K1C -0.021 0.063 0.18 16 -0.24 48 64
LIMA1 0.025 0.043 -10000 0 -0.48 6 6
ABI1 0.029 0.005 -10000 0 -10000 0 0
ROCK1 0.01 0.093 0.3 20 -10000 0 20
adherens junction assembly -0.033 0.12 0.27 2 -0.6 17 19
IGF-1R heterotetramer/IGF1 -0.02 0.13 -10000 0 -0.26 171 171
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.027 -10000 0 -0.34 3 3
MET -0.018 0.14 -10000 0 -0.48 71 71
PLEKHA7 -0.022 0.065 0.18 15 -0.25 50 65
mol:GTP 0.051 0.042 -10000 0 -0.26 6 6
establishment of epithelial cell apical/basal polarity -0.017 0.076 0.35 5 -0.27 1 6
cortical actin cytoskeleton stabilization 0.002 0.07 -10000 0 -0.23 59 59
regulation of cell-cell adhesion -0.023 0.061 0.16 15 -0.24 50 65
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.002 0.07 -10000 0 -0.23 59 59
Caspase cascade in apoptosis

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
TOP1 -0.032 0.15 0.2 2 -0.46 64 66
ACTA1 -0.051 0.17 0.22 5 -0.44 99 104
NUMA1 -0.037 0.15 0.21 1 -0.46 69 70
SPTAN1 -0.051 0.16 0.29 3 -0.45 91 94
LIMK1 -0.05 0.16 0.25 3 -0.45 92 95
BIRC3 0.015 0.067 -10000 0 -0.48 14 14
BIRC2 0.027 0.009 -10000 0 -10000 0 0
BAX 0.029 0.004 -10000 0 -10000 0 0
CASP10 -0.058 0.13 -10000 0 -0.38 97 97
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.029 0.002 -10000 0 -10000 0 0
PTK2 -0.039 0.16 0.23 1 -0.49 66 67
DIABLO 0.029 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes -0.05 0.16 0.29 3 -0.44 91 94
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.029 0.004 -10000 0 -10000 0 0
GSN -0.052 0.16 0.25 4 -0.45 95 99
MADD 0.029 0.004 -10000 0 -10000 0 0
TFAP2A -0.024 0.2 -10000 0 -0.66 63 63
BID -0.026 0.085 -10000 0 -0.24 99 99
MAP3K1 -0.024 0.11 -10000 0 -0.44 42 42
TRADD 0.025 0.02 -10000 0 -0.48 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.041 0.017 -10000 0 -0.34 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.049 0.17 0.24 1 -0.45 96 97
CASP9 0.028 0.006 -10000 0 -10000 0 0
DNA repair -0.005 0.053 0.26 9 -0.17 4 13
neuron apoptosis 0 0.13 -10000 0 -0.75 20 20
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.046 0.16 -10000 0 -0.42 104 104
APAF1 0.028 0.018 -10000 0 -0.48 1 1
CASP6 -0.029 0.18 -10000 0 -0.86 27 27
TRAF2 0.029 0.005 -10000 0 -10000 0 0
ICAD/CAD -0.052 0.16 0.22 1 -0.44 90 91
CASP7 0.014 0.07 0.27 19 -0.29 10 29
KRT18 -0.005 0.11 -10000 0 -0.59 23 23
apoptosis -0.038 0.16 0.28 3 -0.52 57 60
DFFA -0.051 0.16 0.24 1 -0.45 91 92
DFFB -0.051 0.16 0.24 1 -0.45 90 91
PARP1 0.005 0.053 0.17 4 -0.26 9 13
actin filament polymerization 0.045 0.15 0.42 88 -0.29 5 93
TNF 0 0.11 -10000 0 -0.48 40 40
CYCS -0.015 0.064 0.2 3 -0.21 46 49
SATB1 -0.033 0.17 -10000 0 -0.76 31 31
SLK -0.051 0.16 0.25 3 -0.44 94 97
p15 BID/BAX -0.013 0.089 -10000 0 -0.22 105 105
CASP2 -0.007 0.082 0.21 6 -0.32 26 32
JNK cascade 0.024 0.11 0.43 42 -10000 0 42
CASP3 -0.052 0.17 0.22 3 -0.46 96 99
LMNB2 -0.016 0.15 0.28 3 -0.55 40 43
RIPK1 0.028 0.006 -10000 0 -10000 0 0
CASP4 0.025 0.026 -10000 0 -0.48 2 2
Mammalian IAPs/DIABLO 0.061 0.05 -10000 0 -0.27 14 14
negative regulation of DNA binding -0.023 0.19 -10000 0 -0.66 63 63
stress fiber formation -0.05 0.16 0.25 3 -0.44 94 97
GZMB -0.048 0.15 -10000 0 -0.43 96 96
CASP1 0.01 0.038 -10000 0 -0.37 7 7
LMNB1 -0.013 0.13 0.28 3 -0.48 37 40
APP -0.001 0.13 -10000 0 -0.76 20 20
TNFRSF1A 0.028 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.007 0.001 -10000 0 -10000 0 0
VIM -0.036 0.16 0.3 2 -0.51 58 60
LMNA -0.007 0.099 0.26 3 -0.37 31 34
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.005 0.087 -10000 0 -0.34 30 30
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.051 0.16 0.28 4 -0.45 94 98
APAF-1/Caspase 9 -0.008 0.13 -10000 0 -0.63 31 31
nuclear fragmentation during apoptosis -0.036 0.15 0.21 1 -0.45 69 70
CFL2 -0.047 0.16 0.29 5 -0.44 88 93
GAS2 -0.056 0.17 0.25 3 -0.44 100 103
positive regulation of apoptosis -0.01 0.13 0.26 4 -0.5 35 39
PRF1 -0.001 0.11 -10000 0 -0.48 41 41
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.007 0.1 -10000 0 -0.28 79 79
NF kappa B1 p50/RelA/I kappa B alpha 0.013 0.12 0.31 6 -0.43 21 27
alphaV/beta3 Integrin/Osteopontin/Src 0.01 0.11 -10000 0 -0.35 72 72
AP1 0.005 0.15 0.34 1 -0.51 38 39
ILK -0.009 0.1 -10000 0 -0.29 82 82
bone resorption -0.009 0.1 -10000 0 -0.4 20 20
PTK2B 0.023 0.021 -10000 0 -0.48 1 1
PYK2/p130Cas 0.025 0.12 -10000 0 -0.28 83 83
ITGAV 0.028 0.027 -10000 0 -0.48 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.037 0.043 -10000 0 -0.34 10 10
alphaV/beta3 Integrin/Osteopontin 0.023 0.12 -10000 0 -0.32 83 83
MAP3K1 -0.01 0.1 -10000 0 -0.29 84 84
JUN 0.028 0.008 -10000 0 -10000 0 0
MAPK3 -0.019 0.099 0.19 11 -0.29 76 87
MAPK1 -0.018 0.098 0.19 11 -0.29 78 89
Rac1/GDP 0.021 0.003 -10000 0 -10000 0 0
NFKB1 0.028 0.018 -10000 0 -0.48 1 1
MAPK8 -0.019 0.098 0.2 18 -0.28 83 101
ITGB3 0.017 0.076 -10000 0 -0.48 18 18
NFKBIA -0.021 0.1 -10000 0 -0.43 25 25
FOS -0.006 0.12 -10000 0 -0.48 45 45
CD44 0.024 0.047 -10000 0 -0.48 7 7
CHUK 0.029 0.004 -10000 0 -10000 0 0
PLAU -0.032 0.21 0.48 1 -1.1 25 26
NF kappa B1 p50/RelA 0.031 0.12 -10000 0 -0.43 24 24
BCAR1 0.026 0.01 -10000 0 -10000 0 0
RELA 0.029 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.034 0.067 -10000 0 -0.39 18 18
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.014 0.11 -10000 0 -0.3 91 91
VAV3 -0.044 0.12 0.2 17 -0.28 156 173
MAP3K14 -0.01 0.1 -10000 0 -0.3 83 83
ROCK2 0.026 0.035 -10000 0 -0.48 4 4
SPP1 -0.018 0.14 -10000 0 -0.48 70 70
RAC1 0.029 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.029 0.12 0.34 1 -0.26 150 151
MMP2 -0.036 0.14 0.31 4 -0.51 46 50
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.013 0.041 -10000 0 -0.29 17 17
ADCY5 -0.073 0.12 -10000 0 -0.3 177 177
ADCY6 -0.01 0.028 -10000 0 -0.29 8 8
ADCY7 -0.007 0.014 -10000 0 -0.29 2 2
ADCY1 -0.045 0.094 -10000 0 -0.3 101 101
ADCY2 -0.053 0.1 -10000 0 -0.3 123 123
ADCY3 -0.01 0.028 -10000 0 -0.29 8 8
ADCY8 -0.01 0.021 -10000 0 -0.29 4 4
PRKCE 0.004 0.034 -10000 0 -0.34 8 8
ADCY9 -0.012 0.042 -10000 0 -0.31 16 16
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.019 0.094 0.21 18 -0.28 30 48
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.027 0.031 -10000 0 -0.48 3 3
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.041 0.17 0.64 33 -0.45 9 42
IL27/IL27R/JAK1 -0.002 0.23 0.88 9 -1 17 26
TBX21 -0.051 0.22 0.72 16 -0.56 68 84
IL12B -0.02 0.13 -10000 0 -0.48 63 63
IL12A -0.021 0.085 -10000 0 -0.34 52 52
IL6ST -0.022 0.14 0.15 1 -0.48 73 74
IL27RA/JAK1 -0.003 0.17 0.44 1 -1.2 14 15
IL27 0.012 0.066 0.15 1 -0.49 12 13
TYK2 0.023 0.021 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.025 0.098 0.21 12 -0.27 99 111
T-helper 2 cell differentiation 0.041 0.17 0.64 33 -0.45 9 42
T cell proliferation during immune response 0.041 0.17 0.64 33 -0.45 9 42
MAPKKK cascade -0.041 0.17 0.45 9 -0.64 33 42
STAT3 0.027 0.019 -10000 0 -0.48 1 1
STAT2 0.029 0.002 -10000 0 -10000 0 0
STAT1 0.029 0.014 -10000 0 -10000 0 0
IL12RB1 0.004 0.1 -10000 0 -0.48 35 35
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.056 0.22 0.74 15 -0.53 83 98
IL27/IL27R/JAK2/TYK2 -0.041 0.18 0.45 9 -0.65 33 42
positive regulation of T cell mediated cytotoxicity -0.041 0.17 0.45 9 -0.64 33 42
STAT1 (dimer) -0.007 0.3 0.62 58 -0.78 41 99
JAK2 0.023 0.026 -10000 0 -0.48 1 1
JAK1 0.029 0.013 -10000 0 -10000 0 0
STAT2 (dimer) -0.028 0.17 0.4 9 -0.61 33 42
T cell proliferation -0.069 0.18 0.41 9 -0.59 51 60
IL12/IL12R/TYK2/JAK2 -0.095 0.3 -10000 0 -0.88 89 89
IL17A -0.025 0.098 0.21 12 -0.28 99 111
mast cell activation 0.041 0.17 0.64 33 -0.45 9 42
IFNG -0.01 0.047 0.14 10 -0.12 84 94
T cell differentiation -0.004 0.008 0.023 4 -0.022 93 97
STAT3 (dimer) -0.028 0.17 0.4 9 -0.62 32 41
STAT5A (dimer) -0.029 0.17 0.4 9 -0.61 34 43
STAT4 (dimer) -0.041 0.19 0.4 9 -0.65 37 46
STAT4 -0.004 0.12 -10000 0 -0.48 49 49
T cell activation -0.004 0.016 0.12 12 -10000 0 12
IL27R/JAK2/TYK2 -0.015 0.18 -10000 0 -1.1 15 15
GATA3 -0.16 0.48 0.7 19 -1.3 114 133
IL18 0.002 0.035 -10000 0 -0.34 8 8
positive regulation of mast cell cytokine production -0.027 0.17 0.4 9 -0.6 32 41
IL27/EBI3 0.014 0.089 0.23 9 -0.34 38 47
IL27RA -0.02 0.17 -10000 0 -1.3 14 14
IL6 -0.04 0.16 -10000 0 -0.48 95 95
STAT5A 0.025 0.04 -10000 0 -0.48 5 5
monocyte differentiation 0 0.002 -10000 0 -10000 0 0
IL2 0.001 0.067 0.47 13 -10000 0 13
IL1B -0.009 0.069 -10000 0 -0.34 33 33
EBI3 0.005 0.098 -10000 0 -0.48 31 31
TNF -0.013 0.075 -10000 0 -0.34 40 40
IL6-mediated signaling events

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
BCL2L1 -0.069 0.22 -10000 0 -0.73 34 34
CRP -0.05 0.24 0.48 5 -0.76 29 34
cell cycle arrest -0.084 0.26 -10000 0 -0.72 67 67
TIMP1 -0.046 0.2 -10000 0 -0.66 31 31
IL6ST -0.022 0.14 -10000 0 -0.48 73 73
Rac1/GDP -0.039 0.16 0.25 2 -0.43 65 67
AP1 0.007 0.14 -10000 0 -0.52 21 21
GAB2 0.025 0.027 -10000 0 -0.48 2 2
TNFSF11 -0.11 0.32 -10000 0 -0.99 70 70
HSP90B1 0.016 0.096 -10000 0 -0.84 7 7
GAB1 0.028 0.018 -10000 0 -0.48 1 1
MAPK14 -0.034 0.14 -10000 0 -0.48 38 38
AKT1 0.03 0.057 0.27 1 -0.51 4 5
FOXO1 0.032 0.057 0.36 3 -0.55 2 5
MAP2K6 -0.051 0.13 -10000 0 -0.41 63 63
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.047 0.17 0.28 2 -0.46 65 67
MITF -0.054 0.14 -10000 0 -0.37 85 85
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.029 0.005 -10000 0 -10000 0 0
A2M -0.003 0.18 -10000 0 -1.2 19 19
CEBPB 0.024 0.026 -10000 0 -0.48 1 1
GRB2/SOS1/GAB family/SHP2 0.002 0.11 -10000 0 -0.48 21 21
STAT3 -0.091 0.28 -10000 0 -0.79 67 67
STAT1 0.01 0.079 -10000 0 -0.8 7 7
CEBPD -0.059 0.25 -10000 0 -0.85 34 34
PIK3CA 0.029 0.007 -10000 0 -10000 0 0
PI3K 0.041 0.014 -10000 0 -10000 0 0
JUN 0.028 0.008 -10000 0 -10000 0 0
PIAS3/MITF -0.034 0.15 0.24 1 -0.41 57 58
MAPK11 -0.034 0.14 -10000 0 -0.5 36 36
STAT3 (dimer)/FOXO1 -0.047 0.21 0.44 3 -0.6 42 45
GRB2/SOS1/GAB family 0 0.14 -10000 0 -0.41 33 33
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.045 0.14 -10000 0 -0.34 96 96
GRB2 0.027 0.008 -10000 0 -10000 0 0
JAK2 0.027 0.019 -10000 0 -0.48 1 1
LBP -0.18 0.41 -10000 0 -0.93 175 175
PIK3R1 0.029 0.007 -10000 0 -10000 0 0
JAK1 0.027 0.014 -10000 0 -10000 0 0
MYC -0.048 0.28 0.5 2 -0.91 47 49
FGG -0.11 0.29 -10000 0 -0.91 68 68
macrophage differentiation -0.084 0.26 -10000 0 -0.72 67 67
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.011 0.15 -10000 0 -0.3 145 145
JUNB -0.072 0.22 -10000 0 -0.72 35 35
FOS -0.006 0.12 -10000 0 -0.48 45 45
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.051 0.14 -10000 0 -0.38 86 86
STAT1/PIAS1 -0.033 0.16 -10000 0 -0.42 56 56
GRB2/SOS1/GAB family/SHP2/PI3K 0.03 0.063 -10000 0 -0.51 6 6
STAT3 (dimer) -0.088 0.28 -10000 0 -0.77 67 67
PRKCD -0.055 0.19 0.35 5 -0.55 55 60
IL6R 0.006 0.089 -10000 0 -0.48 26 26
SOCS3 -0.029 0.16 -10000 0 -0.78 16 16
gp130 (dimer)/JAK1/JAK1/LMO4 0.007 0.12 -10000 0 -0.3 89 89
Rac1/GTP -0.043 0.16 -10000 0 -0.44 66 66
HCK 0.024 0.041 -10000 0 -0.48 5 5
MAPKKK cascade 0.011 0.12 -10000 0 -0.54 24 24
bone resorption -0.1 0.29 -10000 0 -0.91 70 70
IRF1 -0.075 0.23 -10000 0 -0.78 33 33
mol:GDP -0.057 0.15 -10000 0 -0.38 95 95
SOS1 0.029 0.004 -10000 0 -10000 0 0
VAV1 -0.059 0.15 -10000 0 -0.38 95 95
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.029 0.15 0.31 1 -0.53 35 36
PTPN11 0.011 0.081 -10000 0 -0.82 7 7
IL6/IL6RA -0.017 0.13 -10000 0 -0.36 94 94
gp130 (dimer)/TYK2/TYK2/LMO4 0.013 0.11 -10000 0 -0.3 89 89
gp130 (dimer)/JAK2/JAK2/LMO4 0.012 0.11 -10000 0 -0.3 85 85
IL6 -0.044 0.16 -10000 0 -0.48 95 95
PIAS3 0.028 0.007 -10000 0 -10000 0 0
PTPRE 0.026 0.028 -10000 0 -0.48 2 2
PIAS1 0.029 0.005 -10000 0 -10000 0 0
RAC1 0.029 0.005 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.045 0.13 -10000 0 -0.29 142 142
LMO4 0.01 0.078 -10000 0 -0.48 18 18
STAT3 (dimer)/PIAS3 -0.082 0.26 -10000 0 -0.72 65 65
MCL1 0.061 0.095 0.43 2 -0.49 4 6
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.031 0.06 -10000 0 -0.25 32 32
RGS9BP -0.014 0.14 -10000 0 -0.48 66 66
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.019 0.01 -10000 0 -10000 0 0
mol:Na + -0.003 0.081 -10000 0 -0.29 53 53
mol:ADP -0.01 0.013 -10000 0 -10000 0 0
GNAT2 0.027 0.019 -10000 0 -0.48 1 1
RGS9-1/Gbeta5/R9AP -0.003 0.13 -10000 0 -0.31 117 117
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.018 0.012 -10000 0 -0.29 1 1
GRK7 0.024 0.012 -10000 0 -10000 0 0
CNGB3 0.016 0.017 -10000 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.025 0.14 0.18 117 -0.29 127 244
Cone PDE6 0.007 0.12 -10000 0 -0.27 116 116
Cone Metarhodopsin II 0.027 0.012 -10000 0 -10000 0 0
Na + (4 Units) -0.019 0.12 -10000 0 -0.29 128 128
GNAT2/GDP 0.009 0.12 -10000 0 -0.26 118 118
GNB5 0.027 0.031 -10000 0 -0.48 3 3
mol:GMP (4 units) -0.002 0.018 0.18 2 -0.27 1 3
Cone Transducin 0.033 0.064 -10000 0 -0.26 32 32
SLC24A2 -0.045 0.17 -10000 0 -0.48 114 114
GNB3/GNGT2 0.021 0.075 -10000 0 -0.34 31 31
GNB3 0.008 0.094 -10000 0 -0.48 29 29
GNAT2/GTP 0.02 0.014 -10000 0 -0.34 1 1
CNGA3 -0.02 0.13 -10000 0 -0.48 61 61
ARR3 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel -0.003 0.081 -10000 0 -0.3 53 53
mol:Pi -0.003 0.13 -10000 0 -0.31 117 117
Cone CNG Channel 0.018 0.073 -10000 0 -0.25 51 51
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + -0.045 0.17 -10000 0 -0.48 114 114
RGS9 -0.019 0.13 -10000 0 -0.48 60 60
PDE6C 0.022 0.007 -10000 0 -10000 0 0
GNGT2 0.023 0.04 -10000 0 -0.48 5 5
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0 0 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.005 0.045 -10000 0 -0.33 8 8
NFATC2 -0.022 0.083 -10000 0 -0.31 54 54
NFATC3 0 0.029 -10000 0 -10000 0 0
CD40LG -0.11 0.25 0.41 3 -0.61 125 128
PTGS2 -0.089 0.22 0.4 3 -0.58 99 102
JUNB 0.027 0.026 -10000 0 -0.48 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.026 -10000 0 -10000 0 0
CaM/Ca2+ 0.008 0.026 -10000 0 -10000 0 0
CALM1 0.016 0.025 -10000 0 -10000 0 0
JUN 0.016 0.025 -10000 0 -10000 0 0
mol:Ca2+ -0.005 0.01 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.015 0.011 -10000 0 -10000 0 0
FOSL1 0.016 0.055 -10000 0 -0.48 8 8
CREM 0.028 0.005 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.018 0.14 -10000 0 -0.37 66 66
FOS -0.017 0.12 -10000 0 -0.48 45 45
IFNG -0.1 0.24 0.39 4 -0.56 138 142
AP-1/NFAT1-c-4 -0.075 0.26 -10000 0 -0.64 107 107
FASLG -0.091 0.23 0.39 4 -0.59 104 108
NFAT1-c-4/ICER1 -0.023 0.1 -10000 0 -0.29 60 60
IL2RA -0.1 0.25 0.39 4 -0.62 122 126
FKBP12/FK506 0.021 0.004 -10000 0 -10000 0 0
CSF2 -0.089 0.21 0.39 4 -0.54 104 108
JunB/Fra1/NFAT1-c-4 -0.007 0.12 -10000 0 -0.32 52 52
IL4 -0.097 0.2 0.34 2 -0.53 107 109
IL2 -0.009 0.15 -10000 0 -0.91 23 23
IL3 0.001 0.027 -10000 0 -10000 0 0
FKBP1A 0.028 0.005 -10000 0 -10000 0 0
BATF3 0.018 0.054 -10000 0 -0.48 9 9
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.025 0.011 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.029 0.005 -10000 0 -10000 0 0
GNAT1/GTP 0.016 0.009 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.027 0.018 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.025 0.043 -10000 0 -0.29 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.021 0.014 -10000 0 -10000 0 0
GRK1 0.019 0.01 -10000 0 -10000 0 0
CNG Channel -0.024 0.12 -10000 0 -0.26 164 164
mol:Na + -0.011 0.1 -10000 0 -0.25 115 115
mol:ADP 0.019 0.01 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.003 0.13 -10000 0 -0.31 117 117
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.004 0.11 -10000 0 -0.26 115 115
CNGB1 0.015 0.023 -10000 0 -10000 0 0
RDH5 0.016 0.064 -10000 0 -0.48 12 12
SAG 0.019 0.018 -10000 0 -10000 0 0
mol:Ca2+ -0.043 0.098 0.31 13 -0.26 84 97
Na + (4 Units) -0.013 0.099 -10000 0 -0.24 114 114
RGS9 -0.019 0.13 -10000 0 -0.48 60 60
GNB1/GNGT1 0.012 0.09 -10000 0 -0.34 48 48
GNAT1/GDP 0.007 0.12 -10000 0 -0.27 117 117
GUCY2D 0.004 0.095 -10000 0 -0.48 30 30
GNGT1 -0.009 0.12 -10000 0 -0.48 48 48
GUCY2F 0 0 -10000 0 -10000 0 0
GNB5 0.027 0.031 -10000 0 -0.48 3 3
mol:GMP (4 units) -0.015 0.092 -10000 0 -0.26 101 101
mol:11-cis-retinal 0.016 0.064 -10000 0 -0.48 12 12
mol:cGMP 0.015 0.07 -10000 0 -0.25 51 51
GNB1 0.028 0.006 -10000 0 -10000 0 0
Rhodopsin 0.026 0.051 -10000 0 -0.35 12 12
SLC24A1 0.029 0.005 -10000 0 -10000 0 0
CNGA1 -0.029 0.15 -10000 0 -0.48 77 77
Metarhodopsin II 0.026 0.012 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.027 0.078 -10000 0 -0.27 51 51
RGS9BP -0.014 0.14 -10000 0 -0.48 66 66
Metarhodopsin II/Transducin -0.001 0.061 -10000 0 -0.24 47 47
GCAP Family/Ca ++ 0.027 0.049 -10000 0 -0.26 22 22
PDE6A/B -0.008 0.12 -10000 0 -0.35 95 95
mol:Pi -0.003 0.13 -10000 0 -0.31 117 117
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.025 0.074 -10000 0 -0.27 48 48
PDE6B -0.03 0.16 -10000 0 -0.48 94 94
PDE6A 0.024 0.024 -10000 0 -0.48 1 1
PDE6G 0.018 0.062 -10000 0 -0.48 12 12
RHO 0.023 0.013 -10000 0 -10000 0 0
PDE6 -0.016 0.15 -10000 0 -0.28 188 188
GUCA1A 0.023 0.016 -10000 0 -10000 0 0
GC2/GCAP Family 0.027 0.049 -10000 0 -0.26 22 22
GUCA1C 0 0 -10000 0 -10000 0 0
GUCA1B 0.014 0.082 -10000 0 -0.48 22 22
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.015 0.098 -10000 0 -0.34 43 43
alphaM/beta2 Integrin/GPIbA 0.016 0.094 -10000 0 -0.34 39 39
alphaM/beta2 Integrin/proMMP-9 -0.006 0.13 -10000 0 -0.34 90 90
PLAUR 0.026 0.04 -10000 0 -0.48 5 5
HMGB1 0.016 0.031 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.028 0.077 -10000 0 -0.39 16 16
AGER 0.006 0.078 -10000 0 -0.5 16 16
RAP1A 0.029 0.005 -10000 0 -10000 0 0
SELPLG 0.025 0.043 -10000 0 -0.48 6 6
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.016 0.13 -10000 0 -0.26 119 119
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.028 0.15 -10000 0 -0.48 82 82
CYR61 0.015 0.079 -10000 0 -0.48 20 20
TLN1 0.028 0.005 -10000 0 -10000 0 0
Rap1/GTP -0.025 0.13 -10000 0 -0.35 64 64
RHOA 0.028 0.006 -10000 0 -10000 0 0
P-selectin oligomer -0.045 0.17 -10000 0 -0.48 105 105
MYH2 -0.058 0.15 -10000 0 -0.36 99 99
MST1R 0.002 0.11 -10000 0 -0.48 43 43
leukocyte activation during inflammatory response 0.003 0.094 -10000 0 -0.28 66 66
APOB -0.015 0.13 -10000 0 -0.48 55 55
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.009 0.09 -10000 0 -0.48 27 27
JAM3 0.023 0.036 -10000 0 -0.48 4 4
GP1BA 0.007 0.088 -10000 0 -0.48 25 25
alphaM/beta2 Integrin/CTGF 0.019 0.095 -10000 0 -0.35 37 37
alphaM/beta2 Integrin -0.05 0.13 -10000 0 -0.39 67 67
JAM3 homodimer 0.023 0.036 -10000 0 -0.48 4 4
ICAM2 0.024 0.036 -10000 0 -0.48 4 4
ICAM1 0.023 0.048 -10000 0 -0.48 7 7
phagocytosis triggered by activation of immune response cell surface activating receptor -0.049 0.13 -10000 0 -0.37 71 71
cell adhesion 0.016 0.093 -10000 0 -0.34 39 39
NFKB1 -0.036 0.17 0.43 4 -0.4 118 122
THY1 0.023 0.044 -10000 0 -0.48 6 6
RhoA/GDP 0.021 0.004 -10000 0 -10000 0 0
Lipoprotein(a) -0.007 0.077 -10000 0 -0.29 55 55
alphaM/beta2 Integrin/LRP/tPA 0.023 0.098 -10000 0 -0.32 42 42
IL6 -0.088 0.26 0.37 2 -0.64 127 129
ITGB2 0.01 0.06 -10000 0 -0.5 8 8
elevation of cytosolic calcium ion concentration 0.032 0.1 -10000 0 -0.37 31 31
alphaM/beta2 Integrin/JAM2/JAM3 0.031 0.089 -10000 0 -0.34 29 29
JAM2 0.019 0.066 -10000 0 -0.48 14 14
alphaM/beta2 Integrin/ICAM1 0.023 0.12 -10000 0 -0.3 77 77
alphaM/beta2 Integrin/uPA/Plg 0.022 0.089 -10000 0 -0.36 30 30
RhoA/GTP -0.065 0.16 -10000 0 -0.32 163 163
positive regulation of phagocytosis -0.023 0.12 -10000 0 -0.39 45 45
Ron/MSP 0.01 0.1 -10000 0 -0.34 68 68
alphaM/beta2 Integrin/uPAR/uPA 0.034 0.1 -10000 0 -0.38 31 31
alphaM/beta2 Integrin/uPAR 0.027 0.083 -10000 0 -0.4 19 19
PLAU 0.015 0.08 -10000 0 -0.48 21 21
PLAT 0.001 0.091 -10000 0 -0.48 27 27
actin filament polymerization -0.054 0.14 -10000 0 -0.38 82 82
MST1 0.014 0.08 -10000 0 -0.48 21 21
alphaM/beta2 Integrin/lipoprotein(a) 0.006 0.096 -10000 0 -0.29 66 66
TNF -0.06 0.21 0.37 3 -0.52 109 112
RAP1B 0.028 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.022 0.097 -10000 0 -0.39 30 30
fibrinolysis 0.02 0.088 -10000 0 -0.36 30 30
HCK 0.024 0.041 -10000 0 -0.48 5 5
dendritic cell antigen processing and presentation -0.049 0.13 -10000 0 -0.37 71 71
VTN 0.004 0.087 -10000 0 -0.48 24 24
alphaM/beta2 Integrin/CYR61 0.02 0.094 -10000 0 -0.36 34 34
LPA 0 0 -10000 0 -10000 0 0
LRP1 0.022 0.058 -10000 0 -0.48 11 11
cell migration -0.021 0.13 -10000 0 -0.32 108 108
FN1 0.005 0.11 -10000 0 -0.48 38 38
alphaM/beta2 Integrin/Thy1 0.023 0.081 -10000 0 -0.35 23 23
MPO -0.002 0.11 -10000 0 -0.48 41 41
KNG1 0 0 -10000 0 -10000 0 0
RAP1/GDP 0.037 0.01 -10000 0 -10000 0 0
ROCK1 -0.058 0.15 -10000 0 -0.39 83 83
ELA2 0 0 -10000 0 -10000 0 0
PLG 0 0 -10000 0 -10000 0 0
CTGF 0.014 0.08 -10000 0 -0.48 21 21
alphaM/beta2 Integrin/Hck 0.026 0.086 -10000 0 -0.45 17 17
ITGAM 0.008 0.072 -10000 0 -0.5 13 13
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.001 0.13 -10000 0 -0.32 102 102
HP -0.068 0.18 -10000 0 -0.48 131 131
leukocyte adhesion 0 0.12 -10000 0 -0.4 36 36
SELP -0.045 0.17 -10000 0 -0.48 105 105
Coregulation of Androgen receptor activity

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
NRIP1 0.02 0.063 -9999 0 -0.48 13 13
SVIL 0.026 0.04 -9999 0 -0.48 5 5
ZNF318 0.028 0.005 -9999 0 -10000 0 0
JMJD2C 0 0.021 -9999 0 -0.12 22 22
T-DHT/AR/Ubc9 -0.044 0.14 -9999 0 -0.3 170 170
CARM1 0.029 0.005 -9999 0 -10000 0 0
PRDX1 0.029 0.005 -9999 0 -10000 0 0
PELP1 0.027 0.009 -9999 0 -10000 0 0
CTNNB1 0.028 0.019 -9999 0 -0.48 1 1
AKT1 0.028 0.005 -9999 0 -10000 0 0
PTK2B 0.023 0.021 -9999 0 -0.48 1 1
MED1 0.025 0.01 -9999 0 -10000 0 0
MAK -0.002 0.1 -9999 0 -0.48 36 36
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.027 0.031 -9999 0 -0.48 3 3
GSN 0.028 0.025 -9999 0 -0.48 2 2
NCOA2 0.006 0.093 -9999 0 -0.48 29 29
NCOA6 0.029 0.006 -9999 0 -10000 0 0
DNA-PK 0.047 0.024 -9999 0 -10000 0 0
NCOA4 0.029 0.005 -9999 0 -10000 0 0
PIAS3 0.028 0.007 -9999 0 -10000 0 0
cell proliferation -0.039 0.16 -9999 0 -0.66 47 47
XRCC5 0.029 0.004 -9999 0 -10000 0 0
UBE3A 0.028 0.007 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.065 0.17 -9999 0 -0.33 211 211
FHL2 -0.039 0.19 -9999 0 -0.95 30 30
RANBP9 0.029 0.006 -9999 0 -10000 0 0
JMJD1A -0.014 0.05 -9999 0 -0.13 125 125
CDK6 0.017 0.065 -9999 0 -0.48 13 13
TGFB1I1 0.02 0.063 -9999 0 -0.48 13 13
T-DHT/AR/CyclinD1 -0.058 0.16 -9999 0 -0.34 180 180
XRCC6 0.027 0.007 -9999 0 -10000 0 0
T-DHT/AR -0.052 0.17 -9999 0 -0.28 258 258
CTDSP1 0.029 0.004 -9999 0 -10000 0 0
CTDSP2 0.028 0.004 -9999 0 -10000 0 0
BRCA1 0.02 0.066 -9999 0 -0.48 14 14
TCF4 0.022 0.053 -9999 0 -0.48 9 9
CDKN2A 0.011 0.065 -9999 0 -0.48 12 12
SRF 0.028 0.029 -9999 0 -10000 0 0
NKX3-1 -0.1 0.24 -9999 0 -0.72 88 88
KLK3 0.011 0.046 -9999 0 -10000 0 0
TMF1 0.028 0.006 -9999 0 -10000 0 0
HNRNPA1 0.029 0.003 -9999 0 -10000 0 0
AOF2 0 0.001 -9999 0 -10000 0 0
APPL1 0.012 0.013 -9999 0 -0.35 1 1
T-DHT/AR/Caspase 8 -0.045 0.14 -9999 0 -0.3 174 174
AR -0.088 0.21 -9999 0 -0.49 165 165
UBA3 0.028 0.006 -9999 0 -10000 0 0
PATZ1 0.027 0.007 -9999 0 -10000 0 0
PAWR 0.027 0.031 -9999 0 -0.48 3 3
PRKDC 0.025 0.01 -9999 0 -10000 0 0
PA2G4 0.029 0.003 -9999 0 -10000 0 0
UBE2I 0.027 0.008 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.037 0.13 -9999 0 -0.27 167 167
RPS6KA3 0.027 0.036 -9999 0 -0.48 4 4
T-DHT/AR/ARA70 -0.044 0.14 -9999 0 -0.29 181 181
LATS2 0.026 0.019 -9999 0 -0.48 1 1
T-DHT/AR/PRX1 -0.039 0.13 -9999 0 -0.28 175 175
Cyclin D3/CDK11 p58 0.021 0.004 -9999 0 -10000 0 0
VAV3 -0.017 0.14 -9999 0 -0.48 74 74
KLK2 -0.047 0.17 -9999 0 -0.93 25 25
CASP8 0.029 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.032 0.14 -9999 0 -0.31 143 143
TMPRSS2 -0.12 0.32 -9999 0 -0.93 102 102
CCND1 -0.005 0.12 -9999 0 -0.48 48 48
PIAS1 0.029 0.005 -9999 0 -10000 0 0
mol:T-DHT -0.009 0.027 -9999 0 -0.07 125 125
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.029 0.005 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.051 0.15 -9999 0 -0.3 190 190
CMTM2 0.024 0.021 -9999 0 -0.48 1 1
SNURF -0.006 0.13 -9999 0 -0.48 55 55
ZMIZ1 0.013 0.04 -9999 0 -0.14 2 2
CCND3 0.028 0.005 -9999 0 -10000 0 0
TGIF1 0.026 0.026 -9999 0 -0.48 2 2
FKBP4 0.028 0.019 -9999 0 -0.48 1 1
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.012 0.08 -10000 0 -0.3 47 47
ARNO/beta Arrestin1-2 0.026 0.097 -10000 0 -0.82 8 8
EGFR -0.018 0.14 -10000 0 -0.48 67 67
EPHA2 0.024 0.04 -10000 0 -0.48 5 5
USP6 0.026 0.011 -10000 0 -10000 0 0
IQSEC1 0.029 0.005 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.057 0.16 -10000 0 -0.36 183 183
ARRB2 0.01 0.005 -10000 0 -10000 0 0
mol:GTP -0.004 0.068 0.13 31 -0.2 50 81
ARRB1 0.025 0.031 -10000 0 -0.48 3 3
FBXO8 0.028 0.006 -10000 0 -10000 0 0
TSHR 0.005 0.094 -10000 0 -0.48 29 29
EGF -0.056 0.18 -10000 0 -0.48 127 127
somatostatin receptor activity 0 0 0.001 3 -0.001 83 86
ARAP2 0.018 0.07 -10000 0 -0.48 16 16
mol:GDP -0.031 0.12 0.2 1 -0.33 71 72
mol:PI-3-4-5-P3 0 0 0.001 2 -0.001 44 46
ITGA2B -0.002 0.11 -10000 0 -0.48 38 38
ARF6 0.029 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.053 0.043 -10000 0 -0.27 6 6
ADAP1 0.003 0.11 -10000 0 -0.48 40 40
KIF13B 0.018 0.056 -10000 0 -0.48 10 10
HGF/MET -0.016 0.14 -10000 0 -0.38 107 107
PXN 0.029 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.036 0.11 0.21 3 -0.3 80 83
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.028 0.15 -10000 0 -0.31 182 182
ADRB2 0.013 0.084 -10000 0 -0.48 23 23
receptor agonist activity 0 0 0 4 0 68 72
actin filament binding 0 0 0 3 -0.001 89 92
SRC 0.027 0.026 -10000 0 -0.48 2 2
ITGB3 0.015 0.075 -10000 0 -0.48 18 18
GNAQ 0.025 0.043 -10000 0 -0.48 6 6
EFA6/PI-4-5-P2 0 0 0.001 5 -0.001 55 60
ARF6/GDP -0.027 0.16 0.25 4 -0.44 77 81
ARF6/GDP/GULP/ACAP1 -0.022 0.16 -10000 0 -0.37 97 97
alphaIIb/beta3 Integrin/paxillin/GIT1 0.043 0.088 -10000 0 -0.27 56 56
ACAP1 -0.009 0.12 -10000 0 -0.48 50 50
ACAP2 0.028 0.005 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.014 0.023 -10000 0 -10000 0 0
EFNA1 0.024 0.021 -10000 0 -0.48 1 1
HGF -0.002 0.12 -10000 0 -0.48 49 49
CYTH3 0.005 0.024 -10000 0 -0.34 4 4
CYTH2 0.011 0.1 -10000 0 -1 8 8
NCK1 0.029 0.004 -10000 0 -10000 0 0
fibronectin binding 0 0 0 5 0 65 70
endosomal lumen acidification 0 0 0 5 0 83 88
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.006 0.1 -10000 0 -0.48 35 35
GNAQ/ARNO 0.025 0.099 -10000 0 -0.95 8 8
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 0 1 0 24 25
MET -0.018 0.14 -10000 0 -0.48 71 71
GNA14 -0.003 0.12 -10000 0 -0.48 45 45
GNA15 0.021 0.059 -10000 0 -0.48 11 11
GIT1 0.027 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 4 -0.001 65 69
GNA11 0.026 0.036 -10000 0 -0.48 4 4
LHCGR 0.019 0.014 -10000 0 -10000 0 0
AGTR1 -0.031 0.14 -10000 0 -0.48 68 68
desensitization of G-protein coupled receptor protein signaling pathway 0.014 0.023 -10000 0 -10000 0 0
IPCEF1/ARNO -0.021 0.14 -10000 0 -0.89 8 8
alphaIIb/beta3 Integrin 0.008 0.099 -10000 0 -0.35 56 56
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.005 0.11 -10000 0 -0.34 70 70
CRKL -0.02 0.13 -10000 0 -0.43 45 45
mol:PIP3 0.004 0.042 0.46 3 -0.85 1 4
AKT1 0.013 0.066 0.38 5 -0.75 1 6
PTK2B 0.023 0.021 -10000 0 -0.48 1 1
RAPGEF1 -0.02 0.12 -10000 0 -0.45 35 35
RANBP10 0.026 0.01 -10000 0 -10000 0 0
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.006 0.13 -10000 0 -0.32 104 104
MAP3K5 -0.028 0.14 -10000 0 -0.46 54 54
HGF/MET/CIN85/CBL/ENDOPHILINS 0.019 0.13 -10000 0 -0.3 106 106
AP1 -0.004 0.088 -10000 0 -0.32 44 44
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.024 0.011 -10000 0 -10000 0 0
apoptosis -0.063 0.26 -10000 0 -0.8 88 88
STAT3 (dimer) -0.017 0.12 -10000 0 -0.43 42 42
GAB1/CRKL/SHP2/PI3K 0.017 0.13 -10000 0 -0.44 32 32
INPP5D 0.026 0.032 -10000 0 -0.48 3 3
CBL/CRK -0.006 0.13 0.34 1 -0.44 35 36
PTPN11 0.029 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.028 0.006 -10000 0 -10000 0 0
PTEN 0.027 0.031 -10000 0 -0.48 3 3
ELK1 -0.014 0.082 0.29 25 -10000 0 25
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.006 0.075 -10000 0 -0.26 34 34
PAK1 0.025 0.082 0.4 8 -0.71 1 9
HGF/MET/RANBP10 0.005 0.13 -10000 0 -0.32 106 106
HRAS -0.049 0.2 -10000 0 -0.61 84 84
DOCK1 -0.02 0.12 -10000 0 -0.44 36 36
GAB1 -0.021 0.14 -10000 0 -0.45 48 48
CRK -0.021 0.13 0.35 1 -0.47 35 36
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.048 0.2 -10000 0 -0.53 115 115
JUN 0.028 0.008 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.024 0.096 -10000 0 -0.26 109 109
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
cell morphogenesis -0.017 0.14 0.3 9 -0.44 39 48
GRB2/SHC 0.009 0.086 -10000 0 -0.26 53 53
FOS -0.006 0.12 -10000 0 -0.48 45 45
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility -0.014 0.082 0.28 25 -0.2 1 26
HGF/MET/MUC20 -0.011 0.12 -10000 0 -0.32 107 107
cell migration 0.008 0.084 -10000 0 -0.26 53 53
GRB2 0.027 0.008 -10000 0 -10000 0 0
CBL 0.026 0.009 -10000 0 -10000 0 0
MET/RANBP10 0.003 0.11 -10000 0 -0.34 71 71
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.015 0.11 -10000 0 -0.31 81 81
MET/MUC20 -0.012 0.1 -10000 0 -0.34 71 71
RAP1B -0.015 0.12 0.27 2 -0.43 33 35
RAP1A -0.02 0.12 0.29 2 -0.43 33 35
HGF/MET/RANBP9 0.007 0.13 -10000 0 -0.32 105 105
RAF1 -0.045 0.19 -10000 0 -0.57 83 83
STAT3 -0.017 0.12 -10000 0 -0.43 42 42
cell proliferation -0.004 0.16 0.28 29 -0.41 72 101
RPS6KB1 -0.003 0.057 -10000 0 -0.29 16 16
MAPK3 -0.027 0.088 0.72 7 -10000 0 7
MAPK1 0 0.17 0.68 42 -10000 0 42
RANBP9 0.028 0.006 -10000 0 -10000 0 0
MAPK8 -0.01 0.12 -10000 0 -0.4 41 41
SRC -0.024 0.1 -10000 0 -0.37 42 42
PI3K 0.007 0.099 -10000 0 -0.26 75 75
MET/Glomulin -0.009 0.093 -10000 0 -0.3 72 72
SOS1 0.029 0.003 -10000 0 -10000 0 0
MAP2K1 -0.04 0.18 0.46 1 -0.54 82 83
MET -0.018 0.14 -10000 0 -0.48 71 71
MAP4K1 -0.03 0.15 -10000 0 -0.49 54 54
PTK2 0.023 0.012 -10000 0 -10000 0 0
MAP2K2 -0.04 0.18 0.46 1 -0.53 82 83
BAD 0.011 0.063 0.36 4 -0.71 1 5
MAP2K4 -0.025 0.13 -10000 0 -0.41 54 54
SHP2/GRB2/SOS1/GAB1 0.003 0.14 -10000 0 -0.38 72 72
INPPL1 0.027 0.008 -10000 0 -10000 0 0
PXN 0.029 0.002 -10000 0 -10000 0 0
SH3KBP1 0.029 0.004 -10000 0 -10000 0 0
HGS -0.024 0.086 -10000 0 -0.24 101 101
PLCgamma1/PKC 0.021 0.005 -10000 0 -10000 0 0
HGF -0.002 0.12 -10000 0 -0.48 49 49
RASA1 0.028 0.007 -10000 0 -10000 0 0
NCK1 0.029 0.004 -10000 0 -10000 0 0
PTPRJ 0.027 0.031 -10000 0 -0.48 3 3
NCK/PLCgamma1 0.01 0.1 -10000 0 -0.24 101 101
PDPK1 0.016 0.069 0.44 4 -0.79 1 5
HGF/MET/SHIP 0.006 0.13 -10000 0 -0.33 107 107
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.027 0.019 -10000 0 -0.48 1 1
RAS family/GTP/Tiam1 -0.018 0.084 -10000 0 -0.28 35 35
NT3 (dimer)/TRKC -0.048 0.15 -10000 0 -0.37 143 143
NT3 (dimer)/TRKB -0.03 0.16 -10000 0 -0.35 147 147
SHC/Grb2/SOS1/GAB1/PI3K 0.022 0.023 -10000 0 -10000 0 0
RAPGEF1 0.029 0.005 -10000 0 -10000 0 0
BDNF 0.001 0.095 -10000 0 -0.48 29 29
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
DYNLT1 0.028 0.007 -10000 0 -10000 0 0
NTRK1 -0.001 0.1 -10000 0 -0.48 34 34
NTRK2 -0.022 0.14 -10000 0 -0.48 70 70
NTRK3 -0.051 0.17 -10000 0 -0.48 109 109
NT-4/5 (dimer)/TRKB -0.043 0.17 -10000 0 -0.35 177 177
neuron apoptosis 0.046 0.18 0.42 105 -10000 0 105
SHC 2-3/Grb2 -0.051 0.19 -10000 0 -0.46 105 105
SHC1 0.024 0.011 -10000 0 -10000 0 0
SHC2 -0.073 0.21 -10000 0 -0.53 118 118
SHC3 -0.044 0.16 -10000 0 -0.47 78 78
STAT3 (dimer) 0.012 0.085 -10000 0 -0.34 43 43
NT3 (dimer)/TRKA -0.017 0.13 -10000 0 -0.33 113 113
RIN/GDP 0.01 0.093 0.21 24 -0.25 28 52
GIPC1 0.028 0.018 -10000 0 -0.48 1 1
KRAS 0.028 0.006 -10000 0 -10000 0 0
DNAJA3 -0.036 0.11 0.21 3 -0.3 109 112
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 -0.027 0.17 -10000 0 -0.7 49 49
MAGED1 0.025 0.043 -10000 0 -0.48 6 6
PTPN11 0.029 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.034 0.16 -10000 0 -0.48 93 93
SHC/GRB2/SOS1 0.045 0.026 -10000 0 -10000 0 0
GRB2 0.027 0.008 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.001 0.12 -10000 0 -0.32 95 95
TRKA/NEDD4-2 0.013 0.081 -10000 0 -0.34 37 37
ELMO1 0.027 0.026 -10000 0 -0.48 2 2
RhoG/GTP/ELMO1/DOCK1 0.036 0.022 -10000 0 -0.28 3 3
NGF 0.01 0.089 -10000 0 -0.48 26 26
HRAS 0.026 0.036 -10000 0 -0.48 4 4
DOCK1 0.028 0.018 -10000 0 -0.48 1 1
GAB2 0.025 0.026 -10000 0 -0.48 2 2
RIT2 0 0 -10000 0 -10000 0 0
RIT1 0.025 0.011 -10000 0 -10000 0 0
FRS2 0.028 0.009 -10000 0 -10000 0 0
DNM1 0.02 0.066 -10000 0 -0.48 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.009 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.014 0.12 0.22 3 -0.29 114 117
mol:GDP 0.009 0.13 0.28 18 -0.38 31 49
NGF (dimer) 0.01 0.089 -10000 0 -0.48 26 26
RhoG/GDP 0.02 0.019 -10000 0 -0.34 2 2
RIT1/GDP 0.006 0.087 0.24 8 -0.26 24 32
TIAM1 0.022 0.058 -10000 0 -0.48 11 11
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB 0.011 0.12 -10000 0 -0.31 93 93
KIDINS220/CRKL/C3G 0.04 0.017 -10000 0 -0.34 1 1
SHC/RasGAP 0.035 0.018 -10000 0 -10000 0 0
FRS2 family/SHP2 0.055 0.016 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.056 0.033 -10000 0 -10000 0 0
RIT1/GTP 0.018 0.008 -10000 0 -10000 0 0
NT3 (dimer) -0.009 0.12 -10000 0 -0.48 46 46
RAP1/GDP 0.009 0.077 0.14 2 -0.22 23 25
KIDINS220/CRKL 0.027 0.019 -10000 0 -0.48 1 1
BDNF (dimer) 0.001 0.095 -10000 0 -0.48 29 29
ubiquitin-dependent protein catabolic process 0.021 0.092 -10000 0 -0.3 57 57
Schwann cell development -0.021 0.027 -10000 0 -10000 0 0
EHD4 0.028 0.006 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.065 0.026 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.024 0.051 -10000 0 -0.27 8 8
RAP1B 0.028 0.006 -10000 0 -10000 0 0
RAP1A 0.029 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.043 0.16 -10000 0 -0.31 184 184
ABL1 0.029 0.005 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.04 0.012 -10000 0 -10000 0 0
Rap1/GTP 0.007 0.085 -10000 0 -0.39 11 11
STAT3 0.012 0.085 -10000 0 -0.34 43 43
axon guidance -0.049 0.15 -10000 0 -0.3 184 184
MAPK3 -0.009 0.12 0.18 77 -0.29 89 166
MAPK1 -0.009 0.12 0.18 83 -0.29 94 177
CDC42/GDP 0.019 0.098 0.23 22 -0.26 25 47
NTF3 -0.009 0.12 -10000 0 -0.48 46 46
NTF4 -0.034 0.16 -10000 0 -0.48 93 93
NGF (dimer)/TRKA/FAIM 0.023 0.091 -10000 0 -0.3 54 54
PI3K 0.04 0.013 -10000 0 -10000 0 0
FRS3 0.028 0.006 -10000 0 -10000 0 0
FAIM 0.029 0.005 -10000 0 -10000 0 0
GAB1 0.028 0.018 -10000 0 -0.48 1 1
RASGRF1 -0.046 0.13 0.2 3 -0.31 124 127
SOS1 0.029 0.003 -10000 0 -10000 0 0
MCF2L -0.054 0.12 -10000 0 -0.31 145 145
RGS19 0.027 0.008 -10000 0 -10000 0 0
CDC42 0.028 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.035 0.09 0.28 1 -0.44 7 8
Rac1/GDP 0.018 0.098 0.24 15 -0.26 25 40
NGF (dimer)/TRKA/GRIT 0.005 0.085 -10000 0 -0.3 54 54
neuron projection morphogenesis -0.034 0.22 -10000 0 -0.84 35 35
NGF (dimer)/TRKA/NEDD4-2 0.021 0.093 -10000 0 -0.3 57 57
MAP2K1 0.031 0.088 0.19 176 -10000 0 176
NGFR -0.028 0.15 -10000 0 -0.48 80 80
NGF (dimer)/TRKA/GIPC/GAIP 0 0.082 -10000 0 -0.26 62 62
RAS family/GTP/PI3K 0.021 0.027 -10000 0 -0.24 7 7
FRS2 family/SHP2/GRB2/SOS1 0.075 0.031 -10000 0 -10000 0 0
NRAS 0.026 0.04 -10000 0 -0.48 5 5
GRB2/SOS1 0.04 0.012 -10000 0 -10000 0 0
PRKCI 0.028 0.006 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.029 0.005 -10000 0 -10000 0 0
PRKCZ 0.027 0.026 -10000 0 -0.48 2 2
MAPKKK cascade -0.043 0.18 -10000 0 -0.59 75 75
RASA1 0.028 0.007 -10000 0 -10000 0 0
TRKA/c-Abl 0.016 0.078 -10000 0 -0.34 34 34
SQSTM1 0.028 0.006 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.027 0.11 -10000 0 -0.28 93 93
NGF (dimer)/TRKA/p62/Atypical PKCs 0.043 0.09 -10000 0 -0.26 54 54
MATK -0.014 0.13 -10000 0 -0.48 60 60
NEDD4L 0.026 0.036 -10000 0 -0.48 4 4
RAS family/GDP -0.024 0.052 -10000 0 -0.2 26 26
NGF (dimer)/TRKA -0.035 0.12 0.23 3 -0.31 113 116
Rac1/GTP -0.039 0.096 -10000 0 -0.28 78 78
FRS2 family/SHP2/CRK family 0.072 0.034 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.024 0.037 -10000 0 -0.48 4 4
GNB1/GNG2 -0.025 0.06 -10000 0 -0.19 78 78
AKT1 0.007 0.098 0.33 3 -0.31 15 18
EGF -0.056 0.18 -10000 0 -0.48 127 127
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.013 0.061 0.25 2 -0.31 4 6
mol:Ca2+ -0.002 0.12 0.34 3 -0.31 84 87
LYN 0.013 0.055 0.25 2 -0.44 1 3
RhoA/GTP 0.001 0.053 -10000 0 -0.14 24 24
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.01 0.14 0.4 2 -0.36 86 88
GNG2 0.028 0.019 -10000 0 -0.48 1 1
ARRB2 0.027 0.009 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.016 0.14 -10000 0 -0.49 50 50
G beta5/gamma2 -0.023 0.084 -10000 0 -0.26 77 77
PRKCH -0.009 0.14 0.35 3 -0.36 86 89
DNM1 0.02 0.066 -10000 0 -0.48 14 14
TXA2/TP beta/beta Arrestin3 -0.002 0.031 0.09 3 -0.2 14 17
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.014 0.077 -10000 0 -0.48 19 19
G12 family/GTP -0.014 0.11 -10000 0 -0.31 78 78
ADRBK1 0.027 0.008 -10000 0 -10000 0 0
ADRBK2 0.025 0.036 -10000 0 -0.48 4 4
RhoA/GTP/ROCK1 0.037 0.015 -10000 0 -0.29 1 1
mol:GDP 0.004 0.11 0.4 34 -0.32 2 36
mol:NADP 0.028 0.019 -10000 0 -0.48 1 1
RAB11A 0.029 0.005 -10000 0 -10000 0 0
PRKG1 -0.009 0.13 -10000 0 -0.48 61 61
mol:IP3 -0.009 0.15 0.41 2 -0.39 85 87
cell morphogenesis 0.037 0.015 -10000 0 -0.29 1 1
PLCB2 -0.025 0.2 0.44 2 -0.53 86 88
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.011 0.076 0.25 1 -0.26 9 10
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.012 0.059 0.25 2 -0.25 2 4
RHOA 0.028 0.006 -10000 0 -10000 0 0
PTGIR 0.024 0.05 -10000 0 -0.48 8 8
PRKCB1 -0.01 0.15 0.38 2 -0.38 89 91
GNAQ 0.025 0.043 -10000 0 -0.48 6 6
mol:L-citrulline 0.028 0.019 -10000 0 -0.48 1 1
TXA2/TXA2-R family -0.024 0.2 0.46 2 -0.53 89 91
LCK -0.003 0.092 0.25 2 -0.29 38 40
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.014 0.047 -10000 0 -0.21 24 24
TXA2-R family/G12 family/GDP/G beta/gamma 0.012 0.1 -10000 0 -0.41 41 41
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.028 0.05 -10000 0 -0.22 14 14
MAPK14 -0.001 0.097 0.26 7 -0.24 80 87
TGM2/GTP -0.016 0.17 0.45 2 -0.44 73 75
MAPK11 -0.004 0.097 0.25 7 -0.24 79 86
ARHGEF1 -0.002 0.071 0.15 1 -0.19 59 60
GNAI2 0.028 0.006 -10000 0 -10000 0 0
JNK cascade -0.009 0.15 0.43 2 -0.39 89 91
RAB11/GDP 0.028 0.005 -10000 0 -10000 0 0
ICAM1 -0.002 0.12 0.37 2 -0.3 86 88
cAMP biosynthetic process -0.011 0.14 0.41 2 -0.37 71 73
Gq family/GTP/EBP50 -0.003 0.072 0.23 1 -0.27 31 32
actin cytoskeleton reorganization 0.037 0.015 -10000 0 -0.29 1 1
SRC 0.013 0.057 0.25 2 -0.25 2 4
GNB5 0.027 0.031 -10000 0 -0.48 3 3
GNB1 0.028 0.006 -10000 0 -10000 0 0
EGF/EGFR -0.034 0.1 0.21 6 -0.3 55 61
VCAM1 -0.005 0.12 0.33 3 -0.32 87 90
TP beta/Gq family/GDP/G beta5/gamma2 -0.016 0.14 -10000 0 -0.49 50 50
platelet activation -0.002 0.13 0.38 4 -0.31 76 80
PGI2/IP 0.018 0.036 -10000 0 -0.34 8 8
PRKACA 0.01 0.049 -10000 0 -0.25 27 27
Gq family/GDP/G beta5/gamma2 -0.012 0.12 -10000 0 -0.43 48 48
TXA2/TP beta/beta Arrestin2 -0.005 0.085 -10000 0 -0.46 22 22
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.003 0.042 -10000 0 -0.23 25 25
mol:DAG -0.013 0.16 0.41 2 -0.43 88 90
EGFR -0.018 0.14 -10000 0 -0.48 67 67
TXA2/TP alpha -0.02 0.19 0.46 2 -0.51 72 74
Gq family/GTP -0.014 0.081 0.22 1 -0.23 86 87
YES1 0.013 0.062 0.25 2 -0.25 3 5
GNAI2/GTP 0.017 0.048 -10000 0 -0.22 17 17
PGD2/DP 0.011 0.055 -10000 0 -0.34 19 19
SLC9A3R1 0.019 0.063 -10000 0 -0.48 13 13
FYN 0.013 0.059 0.26 1 -0.35 3 4
mol:NO 0.028 0.019 -10000 0 -0.48 1 1
GNA15 0.021 0.059 -10000 0 -0.48 11 11
PGK/cGMP 0.014 0.087 -10000 0 -0.3 59 59
RhoA/GDP 0.028 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.043 0.061 0.27 1 -0.3 7 8
NOS3 0.028 0.019 -10000 0 -0.48 1 1
RAC1 0.029 0.005 -10000 0 -10000 0 0
PRKCA -0.004 0.14 0.34 4 -0.37 71 75
PRKCB -0.013 0.15 0.33 5 -0.4 81 86
PRKCE -0.009 0.14 0.42 2 -0.36 79 81
PRKCD -0.011 0.14 0.37 2 -0.38 86 88
PRKCG -0.011 0.15 0.37 3 -0.39 87 90
muscle contraction -0.022 0.19 0.47 2 -0.49 91 93
PRKCZ -0.009 0.13 0.4 2 -0.35 85 87
ARR3 0 0 -10000 0 -10000 0 0
TXA2/TP beta 0.028 0.056 -10000 0 -0.23 22 22
PRKCQ -0.016 0.15 0.36 4 -0.4 87 91
MAPKKK cascade -0.019 0.18 0.42 2 -0.47 88 90
SELE -0.011 0.14 0.33 3 -0.38 85 88
TP beta/GNAI2/GDP/G beta/gamma 0.046 0.057 0.27 1 -0.33 3 4
ROCK1 0.028 0.018 -10000 0 -0.48 1 1
GNA14 -0.003 0.12 -10000 0 -0.48 45 45
chemotaxis -0.03 0.22 0.57 1 -0.62 87 88
GNA12 0.028 0.005 -10000 0 -10000 0 0
GNA13 0.027 0.008 -10000 0 -10000 0 0
GNA11 0.026 0.036 -10000 0 -0.48 4 4
Rac1/GTP 0.021 0.004 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.021 0.063 -10000 0 -0.48 13 13
Jak2/Leptin Receptor -0.013 0.13 0.25 1 -0.42 43 44
PTP1B/AKT1 -0.015 0.11 0.24 1 -0.34 51 52
FYN 0.026 0.027 -10000 0 -0.48 2 2
p210 bcr-abl/PTP1B -0.029 0.11 0.19 4 -0.34 64 68
EGFR -0.026 0.14 -10000 0 -0.49 67 67
EGF/EGFR -0.056 0.16 -10000 0 -0.32 183 183
CSF1 0.024 0.041 -10000 0 -0.48 5 5
AKT1 0.029 0.006 -10000 0 -10000 0 0
INSR 0.029 0.005 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.029 0.14 0.22 2 -0.34 92 94
Insulin Receptor/Insulin -0.003 0.096 -10000 0 -0.34 30 30
HCK 0.024 0.041 -10000 0 -0.48 5 5
CRK 0.027 0.009 -10000 0 -10000 0 0
TYK2 -0.028 0.11 0.23 7 -0.34 54 61
EGF -0.059 0.18 -10000 0 -0.48 127 127
YES1 0.024 0.043 -10000 0 -0.48 6 6
CAV1 -0.038 0.13 0.22 5 -0.36 65 70
TXN 0.027 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.021 0.13 -10000 0 -0.35 71 71
cell migration 0.029 0.11 0.34 64 -0.19 4 68
STAT3 0.027 0.019 -10000 0 -0.48 1 1
PRLR 0.007 0.1 -10000 0 -0.48 34 34
ITGA2B -0.002 0.11 -10000 0 -0.48 38 38
CSF1R 0.024 0.047 -10000 0 -0.48 7 7
Prolactin Receptor/Prolactin 0.019 0.076 -10000 0 -0.35 32 32
FGR 0.025 0.037 -10000 0 -0.48 4 4
PTP1B/p130 Cas -0.014 0.11 0.22 2 -0.32 60 62
Crk/p130 Cas -0.005 0.11 0.22 2 -0.34 48 50
DOK1 -0.023 0.12 0.24 2 -0.38 50 52
JAK2 -0.023 0.13 -10000 0 -0.42 47 47
Jak2/Leptin Receptor/Leptin -0.055 0.15 -10000 0 -0.35 87 87
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
PTPN1 -0.029 0.11 0.2 4 -0.34 64 68
LYN 0.023 0.028 -10000 0 -0.48 2 2
CDH2 -0.005 0.12 -10000 0 -0.48 46 46
SRC 0.005 0.095 -10000 0 -0.55 19 19
ITGB3 0.015 0.075 -10000 0 -0.48 18 18
CAT1/PTP1B -0.076 0.19 0.26 8 -0.44 123 131
CAPN1 0.028 0.004 -10000 0 -10000 0 0
CSK 0.028 0.005 -10000 0 -10000 0 0
PI3K 0.007 0.096 -10000 0 -0.36 20 20
mol:H2O2 -0.001 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.048 0.14 -10000 0 -0.34 62 62
negative regulation of transcription -0.022 0.12 -10000 0 -0.41 47 47
FCGR2A 0.022 0.037 -10000 0 -0.48 4 4
FER 0.021 0.054 -10000 0 -0.49 9 9
alphaIIb/beta3 Integrin 0.006 0.099 -10000 0 -0.35 56 56
BLK -0.03 0.14 -10000 0 -0.48 67 67
Insulin Receptor/Insulin/Shc 0.032 0.016 -10000 0 -10000 0 0
RHOA 0.028 0.006 -10000 0 -10000 0 0
LEPR 0.023 0.045 -10000 0 -0.48 6 6
BCAR1 0.026 0.01 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.027 0.008 -10000 0 -10000 0 0
mol:NADPH -0.002 0.003 -10000 0 -10000 0 0
TRPV6 -0.089 0.21 0.53 1 -0.5 120 121
PRL 0.012 0.021 -10000 0 -10000 0 0
SOCS3 0.006 0.16 -10000 0 -1.2 14 14
SPRY2 0.024 0.028 -10000 0 -0.48 2 2
Insulin Receptor/Insulin/IRS1 0.017 0.081 -10000 0 -0.3 51 51
CSF1/CSF1R -0.008 0.12 0.22 2 -0.36 55 57
Ras protein signal transduction 0.036 0.14 0.57 51 -10000 0 51
IRS1 -0.003 0.12 -10000 0 -0.48 52 52
INS 0 0.002 -10000 0 -10000 0 0
LEP -0.096 0.2 -10000 0 -0.48 172 172
STAT5B -0.026 0.12 0.2 3 -0.38 60 63
STAT5A -0.027 0.13 0.2 3 -0.37 65 68
GRB2 0.027 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.02 0.12 0.22 2 -0.37 60 62
CSN2 0.003 0.043 0.15 16 -0.15 32 48
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
LAT -0.002 0.12 -10000 0 -0.57 27 27
YBX1 0.033 0.011 -10000 0 -10000 0 0
LCK -0.017 0.14 -10000 0 -0.48 68 68
SHC1 0.024 0.011 -10000 0 -10000 0 0
NOX4 0.009 0.093 -10000 0 -0.48 28 28
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.018 0.15 -10000 0 -0.65 30 30
UGCG -0.015 0.15 -10000 0 -0.72 33 33
AKT1/mTOR/p70S6K/Hsp90/TERT -0.036 0.18 0.27 4 -0.42 94 98
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.013 0.15 -10000 0 -0.7 34 34
mol:DAG 0.006 0.079 -10000 0 -0.79 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.036 0.2 0.29 3 -0.45 127 130
FRAP1 -0.053 0.23 0.32 3 -0.52 128 131
FOXO3 -0.027 0.2 0.29 9 -0.53 74 83
AKT1 -0.032 0.21 0.32 3 -0.56 80 83
GAB2 0.024 0.027 -10000 0 -0.48 2 2
SMPD1 -0.004 0.12 -10000 0 -0.72 22 22
SGMS1 0.009 0.069 -10000 0 -0.64 7 7
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 0.003 0.01 -10000 0 -10000 0 0
CALM1 0.028 0.005 -10000 0 -10000 0 0
cell proliferation 0.014 0.14 0.29 3 -0.46 29 32
EIF3A 0.028 0.005 -10000 0 -10000 0 0
PI3K 0.04 0.016 -10000 0 -10000 0 0
RPS6KB1 -0.015 0.12 -10000 0 -0.9 9 9
mol:sphingomyelin 0.006 0.079 -10000 0 -0.79 7 7
natural killer cell activation -0.001 0.003 -10000 0 -0.012 25 25
JAK3 0.015 0.079 -10000 0 -0.48 20 20
PIK3R1 0.028 0.009 -10000 0 -10000 0 0
JAK1 0.029 0.007 -10000 0 -10000 0 0
NFKB1 0.028 0.018 -10000 0 -0.48 1 1
MYC 0.004 0.25 0.37 13 -0.76 53 66
MYB -0.14 0.4 -10000 0 -1.2 101 101
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.026 0.19 -10000 0 -0.53 71 71
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.013 0.12 -10000 0 -0.81 9 9
mol:PI-3-4-5-P3 -0.023 0.18 -10000 0 -0.51 71 71
Rac1/GDP 0.019 0.017 -10000 0 -10000 0 0
T cell proliferation -0.018 0.17 0.25 5 -0.52 56 61
SHC1 0.024 0.012 -10000 0 -10000 0 0
RAC1 0.029 0.005 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.005 0.022 -10000 0 -0.066 96 96
PRKCZ -0.021 0.18 0.23 1 -0.54 58 59
NF kappa B1 p50/RelA -0.027 0.21 0.31 3 -0.46 116 119
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.018 0.16 -10000 0 -0.59 48 48
HSP90AA1 0.028 0.005 -10000 0 -10000 0 0
RELA 0.029 0.004 -10000 0 -10000 0 0
IL2RA -0.025 0.15 -10000 0 -0.48 79 79
IL2RB 0.009 0.086 -10000 0 -0.48 24 24
TERT -0.005 0.11 -10000 0 -0.48 44 44
E2F1 -0.043 0.17 -10000 0 -0.43 125 125
SOS1 0.028 0.006 -10000 0 -10000 0 0
RPS6 0.028 0.006 -10000 0 -10000 0 0
mol:cAMP 0.002 0.011 0.031 96 -10000 0 96
PTPN11 0.027 0.009 -10000 0 -10000 0 0
IL2RG 0.003 0.11 -10000 0 -0.48 37 37
actin cytoskeleton organization -0.018 0.17 0.25 5 -0.52 56 61
GRB2 0.026 0.009 -10000 0 -10000 0 0
IL2 0.019 0.019 -10000 0 -10000 0 0
PIK3CA 0.028 0.009 -10000 0 -10000 0 0
Rac1/GTP 0.045 0.03 -10000 0 -10000 0 0
LCK -0.017 0.14 -10000 0 -0.48 68 68
BCL2 -0.081 0.3 0.49 1 -0.79 106 107
ErbB2/ErbB3 signaling events

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
USP8 -0.006 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.017 0.11 -10000 0 -0.32 26 26
NFATC4 -0.024 0.082 0.28 5 -0.24 31 36
ERBB2IP 0.028 0.019 -10000 0 -0.47 1 1
HSP90 (dimer) 0.028 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.017 0.087 -10000 0 -0.26 70 70
JUN 0.007 0.077 0.22 8 -0.38 6 14
HRAS 0.026 0.036 -10000 0 -0.48 4 4
DOCK7 -0.028 0.091 0.27 4 -0.26 65 69
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.002 0.09 -10000 0 -0.28 63 63
AKT1 0.004 0.008 -10000 0 -10000 0 0
BAD -0.006 0.006 -10000 0 -10000 0 0
MAPK10 -0.03 0.08 0.21 13 -0.21 70 83
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.009 0.1 -10000 0 -0.28 70 70
RAF1 0.006 0.12 0.28 21 -0.32 27 48
ErbB2/ErbB3/neuregulin 2 -0.009 0.086 -10000 0 -0.29 63 63
STAT3 0.001 0.18 -10000 0 -0.88 31 31
cell migration -0.019 0.077 0.23 16 -0.22 25 41
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.051 0.25 0.52 2 -0.61 110 112
FOS -0.031 0.18 0.34 6 -0.4 139 145
NRAS 0.025 0.04 -10000 0 -0.48 5 5
mol:Ca2+ -0.017 0.087 -10000 0 -0.26 70 70
MAPK3 -0.029 0.2 0.4 5 -0.5 91 96
MAPK1 -0.041 0.22 0.41 5 -0.53 99 104
JAK2 -0.026 0.091 0.28 3 -0.26 66 69
NF2 0.004 0.058 -10000 0 -0.66 6 6
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.003 0.086 0.19 9 -0.27 57 66
NRG1 -0.024 0.14 -10000 0 -0.48 70 70
GRB2/SOS1 0.04 0.012 -10000 0 -10000 0 0
MAPK8 -0.017 0.1 0.23 4 -0.28 62 66
MAPK9 -0.013 0.063 0.2 15 -0.22 3 18
ERBB2 -0.021 0.04 0.65 1 -0.36 7 8
ERBB3 0.023 0.053 -10000 0 -0.48 9 9
SHC1 0.024 0.011 -10000 0 -10000 0 0
RAC1 0.029 0.005 -10000 0 -10000 0 0
apoptosis 0.005 0.008 -10000 0 -10000 0 0
STAT3 (dimer) 0.002 0.17 -10000 0 -0.86 31 31
RNF41 -0.009 0.009 -10000 0 -10000 0 0
FRAP1 -0.003 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.023 0.06 -10000 0 -0.2 61 61
ErbB2/ErbB2/HSP90 (dimer) 0 0.035 -10000 0 -0.3 7 7
CHRNA1 -0.045 0.24 0.38 5 -0.63 100 105
myelination -0.016 0.092 0.3 16 -0.3 5 21
PPP3CB -0.025 0.086 0.27 3 -0.24 63 66
KRAS 0.028 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.025 0.1 0.23 6 -0.25 53 59
NRG2 -0.017 0.12 -10000 0 -0.48 53 53
mol:GDP -0.004 0.085 0.19 9 -0.27 57 66
SOS1 0.029 0.003 -10000 0 -10000 0 0
MAP2K2 -0.005 0.12 0.28 21 -0.34 29 50
SRC 0.027 0.026 -10000 0 -0.48 2 2
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.026 0.093 0.27 4 -0.26 67 71
MAP2K1 -0.034 0.2 0.49 2 -0.56 54 56
heart morphogenesis -0.017 0.087 -10000 0 -0.26 70 70
RAS family/GDP 0.026 0.11 0.24 5 -0.31 26 31
GRB2 0.027 0.008 -10000 0 -10000 0 0
PRKACA 0.005 0.071 -10000 0 -0.67 9 9
CHRNE 0.006 0.024 0.1 2 -0.18 6 8
HSP90AA1 0.028 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.004 0.008 -10000 0 -10000 0 0
nervous system development -0.017 0.087 -10000 0 -0.26 70 70
CDC42 0.028 0.006 -10000 0 -10000 0 0
Canonical Wnt 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
HDAC1 0.034 0.038 0.21 16 -0.48 1 17
AES 0.033 0.026 0.23 2 -10000 0 2
FBXW11 0.029 0.005 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.039 0.03 -10000 0 -0.35 4 4
SMAD4 0.027 0.019 -10000 0 -0.48 1 1
DKK2 0.009 0.095 -10000 0 -0.48 30 30
TLE1 0.02 0.091 0.19 16 -0.48 24 40
MACF1 0.029 0.005 -10000 0 -10000 0 0
CTNNB1 0.031 0.094 0.32 17 -0.39 6 23
WIF1 -0.054 0.16 -10000 0 -0.48 99 99
beta catenin/RanBP3 0.043 0.14 0.42 78 -0.35 5 83
KREMEN2 -0.028 0.14 -10000 0 -0.48 72 72
DKK1 -0.058 0.17 -10000 0 -0.48 114 114
beta catenin/beta TrCP1 0.042 0.093 0.33 15 -0.37 5 20
FZD1 0.027 0.031 -10000 0 -0.48 3 3
AXIN2 -0.014 0.33 0.59 68 -1.4 30 98
AXIN1 0.027 0.008 -10000 0 -10000 0 0
RAN 0.029 0.004 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.033 0.079 -10000 0 -0.53 14 14
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.024 0.15 0.3 3 -0.55 31 34
Axin1/APC/GSK3 0.03 0.055 0.32 4 -0.27 1 5
Axin1/APC/GSK3/beta catenin/Macf1 0.022 0.064 0.34 2 -0.36 5 7
HNF1A 0.034 0.035 0.19 15 -0.48 1 16
CTBP1 0.032 0.027 0.2 11 -10000 0 11
MYC 0.089 0.38 0.57 200 -1.3 31 231
RANBP3 0.029 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.007 0.12 -10000 0 -0.3 98 98
NKD1 0.008 0.092 -10000 0 -0.48 28 28
TCF4 0.028 0.06 0.22 5 -0.47 9 14
TCF3 0.033 0.027 0.2 12 -10000 0 12
WNT1/LRP6/FZD1/Axin1 0.063 0.035 -10000 0 -0.27 4 4
Ran/GTP 0.022 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.029 0.18 0.49 71 -0.49 16 87
LEF1 0.025 0.063 0.24 2 -0.47 10 12
DVL1 0.031 0.048 -10000 0 -0.35 4 4
CSNK2A1 0.028 0.006 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.008 0.17 0.26 1 -0.64 32 33
DKK1/LRP6/Kremen 2 -0.029 0.15 -10000 0 -0.32 162 162
LRP6 0.027 0.019 -10000 0 -0.48 1 1
CSNK1A1 0.035 0.031 0.22 13 -10000 0 13
NLK 0.024 0.015 -10000 0 -10000 0 0
CCND1 0.004 0.43 0.56 136 -1.4 51 187
WNT1 0.025 0.013 -10000 0 -10000 0 0
GSK3A 0.029 0.004 -10000 0 -10000 0 0
GSK3B 0.029 0.004 -10000 0 -10000 0 0
FRAT1 0.025 0.043 -10000 0 -0.48 6 6
PPP2R5D 0.034 0.068 0.27 25 -0.3 9 34
APC 0.007 0.064 0.2 71 -0.26 4 75
WNT1/LRP6/FZD1 0.045 0.069 0.21 93 -0.28 5 98
CREBBP 0.031 0.033 0.2 12 -0.48 1 13
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.008 0.095 0.36 46 -10000 0 46
KIRREL -0.001 0.12 -10000 0 -0.48 44 44
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.009 0.095 -10000 0 -0.36 46 46
PLCG1 0.028 0.006 -10000 0 -10000 0 0
ARRB2 0.027 0.009 -10000 0 -10000 0 0
WASL 0.029 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.027 0.078 -10000 0 -0.27 46 46
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.005 0.065 -10000 0 -0.25 45 45
FYN 0.015 0.084 0.15 77 -0.26 45 122
mol:Ca2+ 0.025 0.076 -10000 0 -0.27 44 44
mol:DAG 0.026 0.076 -10000 0 -0.27 44 44
NPHS2 -0.003 0.013 -10000 0 -10000 0 0
mol:IP3 0.026 0.076 -10000 0 -0.27 44 44
regulation of endocytosis 0.025 0.072 -10000 0 -0.25 45 45
Nephrin/NEPH1/podocin/Cholesterol 0.014 0.072 -10000 0 -0.27 46 46
establishment of cell polarity 0.008 0.095 -10000 0 -0.36 46 46
Nephrin/NEPH1/podocin/NCK1-2 0.04 0.078 -10000 0 -0.25 46 46
Nephrin/NEPH1/beta Arrestin2 0.026 0.073 -10000 0 -0.25 45 45
NPHS1 0.016 0.053 -10000 0 -0.48 6 6
Nephrin/NEPH1/podocin 0.015 0.072 0.17 10 -0.26 45 55
TJP1 0.027 0.019 -10000 0 -0.48 1 1
NCK1 0.029 0.004 -10000 0 -10000 0 0
NCK2 0.028 0.018 -10000 0 -0.48 1 1
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.027 0.077 -10000 0 -0.27 44 44
CD2AP 0.028 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.026 0.075 -10000 0 -0.27 42 42
GRB2 0.027 0.008 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.015 0.088 0.16 103 -0.26 50 153
cytoskeleton organization 0.002 0.081 0.2 37 -0.29 41 78
Nephrin/NEPH1 0.014 0.068 -10000 0 -0.25 46 46
Nephrin/NEPH1/ZO-1 0.027 0.084 -10000 0 -0.29 47 47
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.027 0.12 -10000 0 -0.35 64 64
MAP4K1 0.002 0.11 -10000 0 -0.48 40 40
MAP3K8 0.025 0.04 -10000 0 -0.48 5 5
PRKCB -0.009 0.12 -10000 0 -0.48 52 52
DBNL 0.029 0.005 -10000 0 -10000 0 0
CRKL 0.027 0.019 -10000 0 -0.48 1 1
MAP3K1 -0.009 0.11 -10000 0 -0.48 33 33
JUN -0.035 0.21 -10000 0 -0.66 74 74
MAP3K7 -0.009 0.11 -10000 0 -0.47 34 34
GRAP2 0.004 0.1 -10000 0 -0.48 34 34
CRK 0.027 0.009 -10000 0 -10000 0 0
MAP2K4 -0.012 0.12 0.21 2 -0.48 40 42
LAT 0.014 0.077 -10000 0 -0.48 19 19
LCP2 0.026 0.031 -10000 0 -0.48 3 3
MAPK8 -0.037 0.22 -10000 0 -0.7 74 74
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.003 0.12 -10000 0 -0.4 54 54
LAT/GRAP2/SLP76/HPK1/HIP-55 0.038 0.12 -10000 0 -0.34 61 61
Ephrin B reverse 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
EFNB2 0.023 0.044 -10000 0 -0.48 6 6
EPHB2 0.024 0.041 -10000 0 -0.48 5 5
EFNB1 0.005 0.05 -10000 0 -0.36 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.054 0.072 -10000 0 -0.26 34 34
Ephrin B2/EPHB1-2 0.041 0.053 -10000 0 -0.29 17 17
neuron projection morphogenesis 0.033 0.064 -10000 0 -0.25 34 34
Ephrin B1/EPHB1-2/Tiam1 0.044 0.072 -10000 0 -0.28 34 34
DNM1 0.02 0.066 -10000 0 -0.48 14 14
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.039 0.15 -10000 0 -0.55 64 64
YES1 -0.048 0.22 -10000 0 -0.79 66 66
Ephrin B1/EPHB1-2/NCK2 0.048 0.062 -10000 0 -0.27 26 26
PI3K -0.002 0.16 -10000 0 -0.55 65 65
mol:GDP 0.042 0.071 -10000 0 -0.28 34 34
ITGA2B -0.002 0.11 -10000 0 -0.48 38 38
endothelial cell proliferation 0.031 0.038 -10000 0 -0.29 10 10
FYN -0.048 0.22 -10000 0 -0.79 65 65
MAP3K7 -0.039 0.16 0.23 2 -0.58 63 65
FGR -0.044 0.22 -10000 0 -0.78 66 66
TIAM1 0.022 0.058 -10000 0 -0.48 11 11
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
RGS3 0.029 0.004 -10000 0 -10000 0 0
cell adhesion -0.029 0.16 -10000 0 -0.53 65 65
LYN -0.045 0.22 -10000 0 -0.78 65 65
Ephrin B1/EPHB1-2/Src Family Kinases -0.048 0.2 -10000 0 -0.72 66 66
Ephrin B1/EPHB1-2 -0.043 0.17 -10000 0 -0.63 64 64
SRC -0.043 0.22 -10000 0 -0.77 66 66
ITGB3 0.015 0.075 -10000 0 -0.48 18 18
EPHB1 0.016 0.054 -10000 0 -0.47 8 8
EPHB4 0.026 0.04 -10000 0 -0.48 5 5
RAC1 0.029 0.005 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.031 0.038 -10000 0 -0.29 10 10
alphaIIb/beta3 Integrin 0.008 0.099 -10000 0 -0.35 56 56
BLK -0.064 0.22 -10000 0 -0.8 65 65
HCK -0.045 0.22 -10000 0 -0.77 65 65
regulation of stress fiber formation -0.046 0.061 0.27 26 -10000 0 26
MAPK8 -0.038 0.15 -10000 0 -0.52 66 66
Ephrin B1/EPHB1-2/RGS3 0.048 0.061 -10000 0 -0.27 25 25
endothelial cell migration -0.034 0.14 -10000 0 -0.49 62 62
NCK2 0.028 0.018 -10000 0 -0.48 1 1
PTPN13 -0.005 0.14 -10000 0 -0.59 46 46
regulation of focal adhesion formation -0.046 0.061 0.27 26 -10000 0 26
chemotaxis -0.047 0.06 0.27 25 -10000 0 25
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.043 0.068 -10000 0 -0.26 34 34
angiogenesis -0.043 0.17 -10000 0 -0.62 65 65
LCK -0.057 0.22 -10000 0 -0.79 66 66
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.01 0.02 -10000 0 -0.3 4 4
SNTA1 0.028 0.018 -10000 0 -0.48 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.011 0.023 -10000 0 -0.3 5 5
MAPK12 0.005 0.074 0.21 54 -0.26 30 84
CCND1 -0.013 0.11 -10000 0 -0.42 48 48
p38 gamma/SNTA1 0.023 0.076 0.23 8 -0.25 30 38
MAP2K3 0.027 0.008 -10000 0 -10000 0 0
PKN1 0.028 0.025 -10000 0 -0.48 2 2
G2/M transition checkpoint 0.006 0.075 0.21 58 -0.26 30 88
MAP2K6 -0.004 0.053 -10000 0 -0.28 30 30
MAPT -0.059 0.14 0.26 8 -0.29 190 198
MAPK13 0.011 0.025 -10000 0 -0.35 4 4
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.012 0.03 -10000 0 -0.31 7 7
S1P4 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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.002 0.1 -10000 0 -0.48 33 33
CDC42/GTP -0.012 0.11 -10000 0 -0.29 82 82
PLCG1 -0.023 0.11 -10000 0 -0.3 82 82
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.028 0.006 -10000 0 -10000 0 0
GNAI3 0.029 0.005 -10000 0 -10000 0 0
G12/G13 0.038 0.014 -10000 0 -10000 0 0
cell migration -0.012 0.11 -10000 0 -0.29 82 82
S1PR5 0.013 0.079 -10000 0 -0.48 20 20
S1PR4 -0.004 0.12 -10000 0 -0.48 46 46
MAPK3 -0.02 0.1 -10000 0 -0.3 70 70
MAPK1 -0.019 0.1 -10000 0 -0.3 76 76
S1P/S1P5/Gi -0.008 0.097 -10000 0 -0.29 65 65
GNAI1 0.024 0.044 -10000 0 -0.48 6 6
CDC42/GDP 0.021 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.027 0.053 -10000 0 -0.29 20 20
RHOA 0.01 0.077 0.18 64 -0.25 42 106
S1P/S1P4/Gi -0.016 0.11 -10000 0 -0.3 95 95
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.018 0.07 -10000 0 -0.48 16 16
S1P/S1P4/G12/G13 0.031 0.072 -10000 0 -0.27 42 42
GNA12 0.028 0.005 -10000 0 -10000 0 0
GNA13 0.027 0.008 -10000 0 -10000 0 0
CDC42 0.028 0.006 -10000 0 -10000 0 0
Aurora B signaling

Figure S57.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S57.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.008 0.12 -10000 0 -0.46 37 37
STMN1 -0.004 0.077 -10000 0 -0.37 34 34
Aurora B/RasGAP/Survivin 0.022 0.12 -10000 0 -0.46 45 45
Chromosomal passenger complex/Cul3 protein complex -0.029 0.12 -10000 0 -0.3 98 98
BIRC5 0.003 0.11 -10000 0 -0.5 37 37
DES -0.13 0.33 -10000 0 -0.71 182 182
Aurora C/Aurora B/INCENP 0.031 0.077 -10000 0 -0.28 43 43
Aurora B/TACC1 0.012 0.074 -10000 0 -0.29 42 42
Aurora B/PP2A 0.022 0.079 -10000 0 -0.35 34 34
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.002 0.033 -10000 0 -0.15 34 34
mitotic metaphase/anaphase transition 0 0.004 -10000 0 -10000 0 0
NDC80 -0.012 0.11 -10000 0 -0.51 36 36
Cul3 protein complex 0.022 0.1 -10000 0 -0.29 76 76
KIF2C -0.027 0.2 -10000 0 -0.8 41 41
PEBP1 0.027 0.012 -10000 0 -10000 0 0
KIF20A 0.012 0.093 -10000 0 -0.48 28 28
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.022 0.08 -10000 0 -0.35 34 34
SEPT1 0.021 0.045 -10000 0 -0.48 6 6
SMC2 0.029 0.004 -10000 0 -10000 0 0
SMC4 0.028 0.005 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.062 0.22 -10000 0 -0.59 118 118
PSMA3 0.028 0.005 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.004 -10000 0 -10000 0 0
H3F3B 0 0.066 -10000 0 -0.32 34 34
AURKB 0.004 0.1 -10000 0 -0.5 34 34
AURKC 0.02 0.057 -10000 0 -0.48 10 10
CDCA8 0.022 0.051 -10000 0 -0.51 7 7
cytokinesis -0.027 0.21 0.19 1 -0.69 55 56
Aurora B/Septin1 -0.012 0.2 -10000 0 -0.66 54 54
AURKA 0.018 0.071 -10000 0 -0.48 16 16
INCENP 0.026 0.014 -10000 0 -10000 0 0
KLHL13 -0.023 0.15 -10000 0 -0.48 78 78
BUB1 0.014 0.088 -10000 0 -0.48 25 25
hSgo1/Aurora B/Survivin 0.01 0.15 -10000 0 -0.51 54 54
EVI5 0.028 0.018 -10000 0 -0.48 1 1
RhoA/GTP 0.008 0.19 -10000 0 -0.73 40 40
SGOL1 0.007 0.1 -10000 0 -0.48 35 35
CENPA -0.032 0.22 -10000 0 -0.62 63 63
NCAPG 0.018 0.072 -10000 0 -0.48 17 17
Aurora B/HC8 Proteasome 0.022 0.079 -10000 0 -0.35 34 34
NCAPD2 0.028 0.007 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.022 0.079 -10000 0 -0.35 34 34
RHOA 0.028 0.006 -10000 0 -10000 0 0
NCAPH 0.015 0.083 -10000 0 -0.48 23 23
NPM1 -0.04 0.16 -10000 0 -0.4 114 114
RASA1 0.028 0.007 -10000 0 -10000 0 0
KLHL9 0.028 0.007 -10000 0 -10000 0 0
mitotic prometaphase -0.001 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.079 -10000 0 -0.35 34 34
PPP1CC 0.029 0.003 -10000 0 -10000 0 0
Centraspindlin -0.003 0.21 -10000 0 -0.69 50 50
RhoA/GDP 0.021 0.004 -10000 0 -10000 0 0
NSUN2 -0.033 0.15 -10000 0 -0.37 112 112
MYLK -0.005 0.079 -10000 0 -0.33 46 46
KIF23 0.019 0.07 -10000 0 -0.49 15 15
VIM -0.005 0.075 -10000 0 -0.35 36 36
RACGAP1 0.027 0.021 -10000 0 -0.49 1 1
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.041 0.17 -10000 0 -0.44 97 97
Chromosomal passenger complex -0.03 0.2 -10000 0 -0.62 57 57
Chromosomal passenger complex/EVI5 0.041 0.14 -10000 0 -0.47 45 45
TACC1 0.018 0.053 -10000 0 -0.48 9 9
PPP2R5D 0.028 0.005 -10000 0 -10000 0 0
CUL3 0.029 0.004 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.036 0.14 -10000 0 -0.4 78 78
KLHL20 -0.002 0.083 0.18 8 -0.24 27 35
CYFIP2 0.007 0.1 -10000 0 -0.48 34 34
Rac1/GDP -0.009 0.1 0.26 11 -0.28 53 64
ENAH -0.031 0.13 -10000 0 -0.4 72 72
AP1M1 0.029 0.004 -10000 0 -10000 0 0
RAP1B 0.028 0.006 -10000 0 -10000 0 0
RAP1A 0.029 0.005 -10000 0 -10000 0 0
CTNNB1 0.028 0.019 -10000 0 -0.48 1 1
CDC42/GTP 0.003 0.065 -10000 0 -0.26 4 4
ABI1/Sra1/Nap1 -0.027 0.048 -10000 0 -0.16 35 35
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.031 0.1 -10000 0 -0.27 73 73
RAPGEF1 -0.033 0.13 0.24 7 -0.37 75 82
CTNND1 0.028 0.006 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.035 0.15 -10000 0 -0.36 134 134
CRK -0.03 0.14 -10000 0 -0.4 73 73
E-cadherin/gamma catenin/alpha catenin 0.027 0.086 -10000 0 -0.3 47 47
alphaE/beta7 Integrin 0.027 0.067 -10000 0 -0.34 25 25
IQGAP1 0.028 0.006 -10000 0 -10000 0 0
NCKAP1 0.029 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.048 0.028 -10000 0 -0.27 3 3
DLG1 -0.04 0.15 -10000 0 -0.41 81 81
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.011 0.044 -10000 0 -0.19 4 4
MLLT4 0.025 0.032 -10000 0 -0.48 3 3
ARF6/GTP/NME1/Tiam1 0.045 0.04 -10000 0 -0.26 10 10
PI3K -0.011 0.057 -10000 0 -0.24 4 4
ARF6 0.029 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.014 0.092 -10000 0 -0.35 47 47
TIAM1 0.022 0.058 -10000 0 -0.48 11 11
E-cadherin(dimer)/Ca2+ 0.037 0.079 -10000 0 -0.25 49 49
AKT1 -0.011 0.041 0.15 1 -10000 0 1
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
CDH1 -0.004 0.12 -10000 0 -0.48 48 48
RhoA/GDP -0.007 0.1 0.26 11 -0.28 52 63
actin cytoskeleton organization 0.001 0.064 0.15 17 -0.17 27 44
CDC42/GDP -0.007 0.1 0.26 11 -0.28 53 64
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0 0.065 -10000 0 -0.24 49 49
ITGB7 0.012 0.087 -10000 0 -0.48 25 25
RAC1 0.029 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.041 0.085 -10000 0 -0.27 49 49
E-cadherin/Ca2+/beta catenin/alpha catenin 0.025 0.073 -10000 0 -0.25 49 49
mol:GDP -0.024 0.11 0.26 12 -0.31 58 70
CDC42/GTP/IQGAP1 0.037 0.011 -10000 0 -10000 0 0
JUP 0.027 0.019 -10000 0 -0.48 1 1
p120 catenin/RhoA/GDP -0.001 0.11 0.27 9 -0.28 52 61
RAC1/GTP/IQGAP1 0.037 0.009 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.042 0.009 -10000 0 -10000 0 0
RHOA 0.028 0.006 -10000 0 -10000 0 0
CDC42 0.028 0.006 -10000 0 -10000 0 0
CTNNA1 0.029 0.005 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.005 0.063 0.15 7 -0.2 50 57
NME1 0.026 0.009 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.039 0.15 -10000 0 -0.42 81 81
regulation of cell-cell adhesion -0.003 0.055 -10000 0 -0.23 4 4
WASF2 -0.001 0.037 0.097 3 -0.12 6 9
Rap1/GTP 0.006 0.076 0.24 1 -0.29 4 5
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.039 0.1 -10000 0 -0.26 72 72
CCND1 -0.008 0.076 0.17 7 -0.25 50 57
VAV2 -0.034 0.18 -10000 0 -0.47 76 76
RAP1/GDP 0.003 0.087 0.26 4 -0.29 7 11
adherens junction assembly -0.037 0.14 -10000 0 -0.4 81 81
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.029 0.005 -10000 0 -10000 0 0
PIP5K1C 0.028 0.005 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.027 0.093 -10000 0 -0.25 71 71
E-cadherin/beta catenin -0.013 0.089 -10000 0 -0.31 65 65
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.041 0.15 -10000 0 -0.41 83 83
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
Rac1/GTP -0.039 0.11 -10000 0 -0.39 34 34
E-cadherin/beta catenin/alpha catenin 0.028 0.086 -10000 0 -0.29 49 49
ITGAE 0.027 0.008 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.036 0.16 -10000 0 -0.37 134 134
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.003 0.062 0.22 1 -0.33 5 6
adherens junction organization -0.026 0.11 -10000 0 -0.3 79 79
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.006 0.088 -10000 0 -0.27 21 21
FMN1 -0.031 0.11 -10000 0 -0.27 114 114
mol:IP3 -0.001 0.056 -10000 0 -0.3 4 4
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.014 0.1 -10000 0 -0.29 77 77
CTNNB1 0.029 0.019 -10000 0 -0.48 1 1
AKT1 0.002 0.069 0.18 2 -0.28 9 11
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.025 0.16 -10000 0 -0.45 67 67
CTNND1 0.029 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.014 0.088 -10000 0 -0.27 63 63
VASP -0.017 0.097 -10000 0 -0.27 75 75
ZYX -0.016 0.097 -10000 0 -0.28 75 75
JUB -0.016 0.099 -10000 0 -0.28 77 77
EGFR(dimer) -0.022 0.12 -10000 0 -0.29 94 94
E-cadherin/beta catenin-gamma catenin 0.028 0.082 -10000 0 -0.28 48 48
mol:PI-3-4-5-P3 0.017 0.081 0.21 2 -0.27 14 16
PIK3CA 0.029 0.007 -10000 0 -10000 0 0
PI3K 0.018 0.083 0.22 2 -0.27 14 16
FYN -0.004 0.066 0.22 2 -0.3 9 11
mol:Ca2+ -0.001 0.055 -10000 0 -0.3 4 4
JUP 0.028 0.019 -10000 0 -0.47 1 1
PIK3R1 0.029 0.008 -10000 0 -10000 0 0
mol:DAG -0.001 0.055 -10000 0 -0.3 4 4
CDH1 -0.004 0.12 -10000 0 -0.48 48 48
RhoA/GDP -0.004 0.088 0.23 1 -0.28 20 21
establishment of polarity of embryonic epithelium -0.016 0.095 -10000 0 -0.27 75 75
SRC 0.027 0.026 -10000 0 -0.48 2 2
RAC1 0.029 0.005 -10000 0 -10000 0 0
RHOA 0.028 0.006 -10000 0 -10000 0 0
EGFR -0.018 0.14 -10000 0 -0.48 67 67
CASR -0.005 0.058 0.22 2 -0.29 4 6
RhoA/GTP 0.015 0.061 -10000 0 -0.28 3 3
AKT2 0 0.07 0.18 2 -0.26 13 15
actin cable formation -0.033 0.11 0.2 7 -0.28 80 87
apoptosis -0.005 0.077 0.29 15 -0.22 8 23
CTNNA1 0.029 0.005 -10000 0 -10000 0 0
mol:GDP -0.019 0.084 -10000 0 -0.29 20 20
PIP5K1A -0.014 0.089 -10000 0 -0.28 63 63
PLCG1 -0.001 0.056 -10000 0 -0.31 4 4
Rac1/GTP -0.011 0.12 -10000 0 -0.32 47 47
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

Figure S60.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S60.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.007 0.074 -10000 0 -0.32 37 37
EPHB2 0.024 0.04 -10000 0 -0.48 5 5
Syndecan-2/TACI -0.005 0.078 -10000 0 -0.29 55 55
LAMA1 -0.018 0.14 -10000 0 -0.48 70 70
Syndecan-2/alpha2 ITGB1 0.013 0.1 -10000 0 -0.28 75 75
HRAS 0.026 0.036 -10000 0 -0.48 4 4
Syndecan-2/CASK 0.003 0.032 -10000 0 -0.28 10 10
ITGA5 0.028 0.025 -10000 0 -0.48 2 2
BAX 0.001 0.025 -10000 0 -10000 0 0
EPB41 0.028 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.017 0.033 -10000 0 -0.26 10 10
LAMA3 -0.026 0.15 -10000 0 -0.48 82 82
EZR 0.027 0.019 -10000 0 -0.48 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.026 0.036 -10000 0 -0.48 4 4
Syndecan-2/MMP2 0.009 0.068 -10000 0 -0.34 26 26
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.028 0.069 -10000 0 -0.34 26 26
dendrite morphogenesis 0.016 0.046 -10000 0 -0.3 14 14
Syndecan-2/GM-CSF 0.015 0.036 -10000 0 -0.28 10 10
determination of left/right symmetry 0.005 0.038 -10000 0 -0.34 10 10
Syndecan-2/PKC delta 0.019 0.036 -10000 0 -0.28 10 10
GNB2L1 0.029 0.005 -10000 0 -10000 0 0
MAPK3 0.038 0.077 0.19 146 -0.26 10 156
MAPK1 0.043 0.08 0.19 167 -0.26 10 177
Syndecan-2/RACK1 0.03 0.039 -10000 0 -0.24 12 12
NF1 0.028 0.007 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.005 0.038 -10000 0 -0.34 10 10
ITGA2 0.01 0.093 -10000 0 -0.48 29 29
MAPK8 0.005 0.029 -10000 0 -0.28 8 8
Syndecan-2/alpha2/beta1 Integrin 0.015 0.1 -10000 0 -0.3 64 64
Syndecan-2/Kininogen 0.003 0.032 -10000 0 -0.28 10 10
ITGB1 0.029 0.005 -10000 0 -10000 0 0
SRC 0.042 0.078 0.19 153 -0.24 14 167
Syndecan-2/CASK/Protein 4.1 0.017 0.033 -10000 0 -0.26 10 10
extracellular matrix organization 0.019 0.04 -10000 0 -0.29 12 12
actin cytoskeleton reorganization 0.007 0.074 -10000 0 -0.32 37 37
Syndecan-2/Caveolin-2/Ras 0.03 0.05 -10000 0 -0.3 14 14
Syndecan-2/Laminin alpha3 -0.004 0.088 -10000 0 -0.3 64 64
Syndecan-2/RasGAP 0.039 0.043 -10000 0 -0.23 12 12
alpha5/beta1 Integrin 0.041 0.021 -10000 0 -0.34 2 2
PRKCD 0.028 0.006 -10000 0 -10000 0 0
Syndecan-2 dimer 0.016 0.046 -10000 0 -0.31 14 14
GO:0007205 0.002 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.025 0.039 -10000 0 -0.23 13 13
RHOA 0.028 0.006 -10000 0 -10000 0 0
SDCBP 0.025 0.011 -10000 0 -10000 0 0
TNFRSF13B -0.019 0.13 -10000 0 -0.48 58 58
RASA1 0.028 0.007 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.028 0.069 -10000 0 -0.34 26 26
Syndecan-2/Synbindin 0.018 0.036 -10000 0 -0.28 10 10
TGFB1 0.027 0.031 -10000 0 -0.48 3 3
CASP3 0.045 0.078 0.19 158 -0.26 10 168
FN1 0.005 0.11 -10000 0 -0.48 38 38
Syndecan-2/IL8 -0.007 0.084 -10000 0 -0.29 62 62
SDC2 0.005 0.038 -10000 0 -0.34 10 10
KNG1 0 0 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.018 0.037 -10000 0 -0.28 10 10
TRAPPC4 0.026 0.009 -10000 0 -10000 0 0
CSF2 0.02 0.015 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.019 0.04 -10000 0 -0.29 12 12
Syndecan-2/Syntenin/PI-4-5-P2 0.018 0.033 -10000 0 -0.26 10 10
Syndecan-2/Ezrin 0.03 0.04 -10000 0 -0.26 11 11
PRKACA 0.047 0.08 0.19 171 -0.26 10 181
angiogenesis -0.007 0.084 -10000 0 -0.29 62 62
MMP2 0.009 0.09 -10000 0 -0.48 27 27
IL8 -0.024 0.14 -10000 0 -0.48 67 67
calcineurin-NFAT signaling pathway -0.005 0.077 -10000 0 -0.29 55 55
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.029 0.073 -10000 0 -0.29 35 35
fibroblast growth factor receptor signaling pathway 0.029 0.073 -10000 0 -0.29 35 35
LAMA1 -0.018 0.14 -10000 0 -0.48 70 70
PRNP 0.021 0.058 -10000 0 -0.48 11 11
GPC1/SLIT2 0.013 0.099 -10000 0 -0.34 58 58
SMAD2 0.01 0.039 0.18 4 -0.26 14 18
GPC1/PrPc/Cu2+ 0.03 0.05 -10000 0 -0.31 16 16
GPC1/Laminin alpha1 0.003 0.11 -10000 0 -0.35 75 75
TDGF1 0.015 0.063 -10000 0 -0.48 12 12
CRIPTO/GPC1 0.027 0.059 -10000 0 -0.34 18 18
APP/GPC1 0.037 0.041 -10000 0 -0.34 9 9
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0 0.052 -10000 0 -0.29 23 23
FLT1 0.027 0.008 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.051 0.047 -10000 0 -0.29 14 14
SERPINC1 0.009 0.079 -10000 0 -0.48 20 20
FYN 0.001 0.049 -10000 0 -0.29 20 20
FGR 0 0.052 -10000 0 -0.3 21 21
positive regulation of MAPKKK cascade -0.032 0.12 0.28 1 -0.39 53 54
SLIT2 -0.004 0.12 -10000 0 -0.48 52 52
GPC1/NRG -0.005 0.11 -10000 0 -0.34 76 76
NRG1 -0.024 0.14 -10000 0 -0.48 70 70
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.05 0.033 -10000 0 -0.29 5 5
LYN 0.001 0.045 -10000 0 -0.29 17 17
mol:Spermine 0.004 0.03 -10000 0 -0.34 6 6
cell growth 0.029 0.073 -10000 0 -0.29 35 35
BMP signaling pathway -0.025 0.043 0.48 6 -10000 0 6
SRC 0.002 0.047 -10000 0 -0.29 18 18
TGFBR1 0.027 0.026 -10000 0 -0.48 2 2
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.072 0.18 -10000 0 -0.48 138 138
GPC1 0.025 0.043 -10000 0 -0.48 6 6
TGFBR1 (dimer) 0.027 0.026 -10000 0 -0.48 2 2
VEGFA 0.028 0.009 -10000 0 -10000 0 0
BLK -0.032 0.094 -10000 0 -0.3 84 84
HCK 0 0.051 -10000 0 -0.29 22 22
FGF2 0.006 0.092 -10000 0 -0.48 27 27
FGFR1 0.019 0.048 -10000 0 -0.48 7 7
VEGFR1 homodimer 0.027 0.008 -10000 0 -10000 0 0
TGFBR2 0.025 0.043 -10000 0 -0.48 6 6
cell death 0.037 0.041 -10000 0 -0.34 9 9
ATIII/GPC1 0.021 0.068 -10000 0 -0.34 25 25
PLA2G2A/GPC1 -0.041 0.14 -10000 0 -0.35 143 143
LCK -0.025 0.097 -10000 0 -0.3 83 83
neuron differentiation -0.005 0.11 -10000 0 -0.34 76 76
PrPc/Cu2+ 0.016 0.042 -10000 0 -0.34 11 11
APP 0.027 0.031 -10000 0 -0.48 3 3
TGFBR2 (dimer) 0.025 0.043 -10000 0 -0.48 6 6
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.027 0.086 -9999 0 -0.3 48 48
E-cadherin/beta catenin 0.014 0.092 -9999 0 -0.34 49 49
CTNNB1 0.028 0.019 -9999 0 -0.48 1 1
JUP 0.027 0.019 -9999 0 -0.48 1 1
CDH1 -0.004 0.12 -9999 0 -0.48 48 48
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.039 0.03 -10000 0 -0.34 4 4
alphaV beta3 Integrin 0.035 0.087 -10000 0 -0.33 40 40
PTK2 0.011 0.13 0.33 12 -0.47 27 39
IGF1R -0.018 0.14 -10000 0 -0.48 74 74
PI4KB 0.024 0.011 -10000 0 -10000 0 0
MFGE8 0.018 0.058 -10000 0 -0.48 10 10
SRC 0.027 0.026 -10000 0 -0.48 2 2
CDKN1B -0.008 0.11 -10000 0 -0.49 39 39
VEGFA 0.028 0.009 -10000 0 -10000 0 0
ILK 0 0.092 -10000 0 -0.46 27 27
ROCK1 0.028 0.018 -10000 0 -0.48 1 1
AKT1 -0.006 0.086 -10000 0 -0.44 26 26
PTK2B -0.011 0.064 0.19 29 -0.31 20 49
alphaV/beta3 Integrin/JAM-A 0.026 0.092 -10000 0 -0.3 48 48
CBL 0.026 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.042 0.059 -10000 0 -0.33 18 18
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.005 0.17 -10000 0 -0.35 145 145
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.009 0.067 -10000 0 -0.4 11 11
alphaV/beta3 Integrin/Syndecan-1 0.036 0.083 -10000 0 -0.31 41 41
PI4KA 0.028 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.03 0.19 -10000 0 -0.36 169 169
PI4 Kinase 0.034 0.018 -10000 0 -10000 0 0
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.016 0.12 -10000 0 -0.32 82 82
RPS6KB1 -0.076 0.16 0.45 3 -0.51 63 66
TLN1 0.028 0.005 -10000 0 -10000 0 0
MAPK3 -0.035 0.17 -10000 0 -0.67 43 43
GPR124 0.021 0.037 -10000 0 -0.48 4 4
MAPK1 -0.035 0.17 -10000 0 -0.66 45 45
PXN 0.029 0.002 -10000 0 -10000 0 0
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.019 0.11 -10000 0 -0.31 78 78
cell adhesion 0.032 0.071 -10000 0 -0.32 28 28
ANGPTL3 0.022 0.011 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.051 0.035 -10000 0 -0.3 6 6
IGF-1R heterotetramer -0.018 0.14 -10000 0 -0.48 74 74
Rac1/GDP 0.021 0.003 -10000 0 -10000 0 0
TGFBR2 0.025 0.043 -10000 0 -0.48 6 6
ITGB3 0.015 0.075 -10000 0 -0.48 18 18
IGF1 -0.018 0.14 -10000 0 -0.48 69 69
RAC1 0.029 0.005 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.036 0.061 -10000 0 -0.33 17 17
apoptosis 0.028 0.025 -10000 0 -0.48 2 2
CD47 0.028 0.025 -10000 0 -0.48 2 2
alphaV/beta3 Integrin/CD47 0.045 0.062 -10000 0 -0.32 20 20
VCL 0.029 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.01 0.13 -10000 0 -0.34 89 89
CSF1 0.024 0.041 -10000 0 -0.48 5 5
PIK3C2A 0.001 0.091 -10000 0 -0.46 26 26
PI4 Kinase/Pyk2 0.006 0.082 -10000 0 -0.4 14 14
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.058 0.067 -10000 0 -0.34 19 19
FAK1/Vinculin 0.027 0.12 0.31 17 -0.37 26 43
alphaV beta3/Integrin/ppsTEM5 0.037 0.062 -10000 0 -0.33 17 17
RHOA 0.028 0.006 -10000 0 -10000 0 0
VTN 0.004 0.087 -10000 0 -0.48 24 24
BCAR1 0.026 0.01 -10000 0 -10000 0 0
FGF2 0.006 0.092 -10000 0 -0.48 27 27
F11R -0.001 0.057 -10000 0 -0.34 21 21
alphaV/beta3 Integrin/Lactadherin 0.04 0.072 -10000 0 -0.34 26 26
alphaV/beta3 Integrin/TGFBR2 0.044 0.068 -10000 0 -0.34 22 22
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.059 0.042 -10000 0 -0.26 7 7
HSP90AA1 0.028 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.044 0.054 -10000 0 -0.3 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.005 0.11 -10000 0 -0.48 38 38
alphaV/beta3 Integrin/Pyk2 0.034 0.065 -10000 0 -0.31 20 20
SDC1 0.013 0.087 -10000 0 -0.48 25 25
VAV3 -0.034 0.075 0.18 3 -0.26 76 79
PTPN11 0.029 0.003 -10000 0 -10000 0 0
IRS1 -0.003 0.12 -10000 0 -0.48 52 52
FAK1/Paxillin 0.028 0.12 0.31 20 -0.37 26 46
cell migration 0.022 0.11 0.27 26 -0.34 23 49
ITGAV 0.028 0.025 -10000 0 -0.48 2 2
PI3K 0.051 0.095 -10000 0 -0.28 44 44
SPP1 -0.019 0.14 -10000 0 -0.48 70 70
KDR 0.026 0.036 -10000 0 -0.48 4 4
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.028 0.025 -10000 0 -0.48 2 2
COL4A3 -0.02 0.14 -10000 0 -0.48 64 64
angiogenesis -0.017 0.18 0.28 4 -0.67 43 47
Rac1/GTP 0.002 0.081 -10000 0 -0.24 74 74
EDIL3 -0.027 0.15 -10000 0 -0.48 86 86
cell proliferation 0.043 0.068 -10000 0 -0.34 22 22
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.012 0.17 0.32 1 -0.56 42 43
MAP3K8 0.024 0.041 -10000 0 -0.48 5 5
FOS 0.005 0.16 0.3 2 -0.56 39 41
PRKCA 0.015 0.06 -10000 0 -0.48 11 11
PTPN7 0.012 0.065 -10000 0 -0.48 13 13
HRAS 0.026 0.036 -10000 0 -0.48 4 4
PRKCB -0.011 0.12 -10000 0 -0.48 52 52
NRAS 0.025 0.04 -10000 0 -0.48 5 5
RAS family/GTP 0.045 0.038 -10000 0 -0.27 7 7
MAPK3 0.007 0.13 -10000 0 -0.7 23 23
MAP2K1 -0.005 0.14 -10000 0 -0.44 64 64
ELK1 0.026 0.015 -10000 0 -10000 0 0
BRAF -0.017 0.12 -10000 0 -0.42 62 62
mol:GTP 0 0.001 -10000 0 -0.005 48 48
MAPK1 -0.005 0.15 -10000 0 -0.54 44 44
RAF1 -0.016 0.12 -10000 0 -0.42 61 61
KRAS 0.028 0.006 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.016 0.078 -10000 0 -0.48 20 20
ANTXR2 0.024 0.05 -10000 0 -0.48 8 8
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.012 -10000 0 -0.068 26 26
monocyte activation -0.02 0.13 -10000 0 -0.4 82 82
MAP2K2 0.002 0.094 -10000 0 -0.59 20 20
MAP2K1 -0.005 0.011 -10000 0 -0.097 1 1
MAP2K7 -0.005 0.011 0.13 1 -0.097 2 3
MAP2K6 -0.011 0.042 0.13 3 -0.23 25 28
CYAA -0.014 0.047 -10000 0 -0.26 26 26
MAP2K4 -0.005 0.01 -10000 0 -0.082 3 3
IL1B -0.014 0.056 0.18 3 -0.25 37 40
Channel 0.026 0.058 -10000 0 -0.28 26 26
NLRP1 -0.007 0.024 -10000 0 -0.25 6 6
CALM1 0.028 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.073 -10000 0 -0.41 24 24
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.012 0.068 26 -10000 0 26
MAPK3 -0.005 0.012 0.13 2 -0.097 2 4
MAPK1 -0.005 0.011 0.13 1 -10000 0 1
PGR -0.08 0.11 -10000 0 -0.25 244 244
PA/Cellular Receptors 0.027 0.063 -10000 0 -0.31 26 26
apoptosis -0.003 0.012 -10000 0 -0.068 26 26
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.026 0.055 -10000 0 -0.27 26 26
macrophage activation -0.007 0.011 0.12 2 -10000 0 2
TNF 0 0.11 -10000 0 -0.48 40 40
VCAM1 -0.02 0.13 -10000 0 -0.4 82 82
platelet activation -0.001 0.073 -10000 0 -0.41 24 24
MAPKKK cascade -0.001 0.028 0.1 5 -0.075 64 69
IL18 -0.006 0.031 -10000 0 -0.24 12 12
negative regulation of macrophage activation -0.003 0.012 -10000 0 -0.068 26 26
LEF -0.003 0.012 -10000 0 -0.068 26 26
CASP1 -0.002 0.02 -10000 0 -0.093 27 27
mol:cAMP -0.001 0.073 -10000 0 -0.41 24 24
necrosis -0.003 0.012 -10000 0 -0.068 26 26
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.026 0.054 -10000 0 -0.27 26 26
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.006 0.11 -10000 0 -0.3 94 94
cell-cell adhesion 0.032 0.061 0.27 40 -10000 0 40
Ephrin B/EPHB2/RasGAP 0.053 0.086 -10000 0 -0.29 40 40
ITSN1 0.028 0.025 -10000 0 -0.48 2 2
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
SHC1 0.024 0.011 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.035 0.022 -10000 0 -0.29 2 2
Ephrin B1/EPHB1 0.029 0.04 -10000 0 -0.29 9 9
HRAS/GDP 0.001 0.1 -10000 0 -0.31 42 42
Ephrin B/EPHB1/GRB7 0.044 0.089 -10000 0 -0.29 42 42
Endophilin/SYNJ1 -0.018 0.065 0.19 5 -0.27 38 43
KRAS 0.028 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.049 0.091 -10000 0 -0.29 44 44
endothelial cell migration 0.049 0.041 -10000 0 -0.25 10 10
GRB2 0.027 0.008 -10000 0 -10000 0 0
GRB7 0.022 0.036 -10000 0 -0.48 4 4
PAK1 -0.025 0.084 0.28 4 -0.31 44 48
HRAS 0.026 0.036 -10000 0 -0.48 4 4
RRAS -0.019 0.067 0.18 16 -0.27 41 57
DNM1 0.02 0.066 -10000 0 -0.48 14 14
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.021 0.072 0.2 18 -0.28 40 58
lamellipodium assembly -0.032 0.061 -10000 0 -0.27 40 40
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.007 0.074 -10000 0 -0.42 12 12
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
EPHB2 0.024 0.04 -10000 0 -0.48 5 5
EPHB3 0.025 0.024 -10000 0 -0.48 1 1
EPHB1 0.016 0.055 -10000 0 -0.48 8 8
EPHB4 0.026 0.04 -10000 0 -0.48 5 5
mol:GDP -0.017 0.083 -10000 0 -0.33 39 39
Ephrin B/EPHB2 0.04 0.08 -10000 0 -0.28 40 40
Ephrin B/EPHB3 0.04 0.076 -10000 0 -0.28 38 38
JNK cascade -0.016 0.053 0.3 10 -0.28 14 24
Ephrin B/EPHB1 0.039 0.083 -10000 0 -0.29 42 42
RAP1/GDP -0.004 0.097 -10000 0 -0.36 19 19
EFNB2 0.023 0.044 -10000 0 -0.48 6 6
EFNB3 0.001 0.1 -10000 0 -0.48 35 35
EFNB1 0.028 0.018 -10000 0 -0.48 1 1
Ephrin B2/EPHB1-2 0.042 0.054 -10000 0 -0.29 17 17
RAP1B 0.028 0.006 -10000 0 -10000 0 0
RAP1A 0.029 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.026 0.094 -10000 0 -0.32 39 39
Rap1/GTP 0.004 0.07 -10000 0 -0.36 12 12
axon guidance -0.006 0.11 -10000 0 -0.29 94 94
MAPK3 0.005 0.071 0.19 23 -0.38 10 33
MAPK1 0.001 0.065 0.19 5 -0.41 9 14
Rac1/GDP -0.017 0.095 -10000 0 -0.31 42 42
actin cytoskeleton reorganization -0.019 0.068 -10000 0 -0.34 13 13
CDC42/GDP -0.016 0.095 -10000 0 -0.31 42 42
PI3K 0.054 0.043 -10000 0 -0.25 10 10
EFNA5 -0.032 0.16 -10000 0 -0.48 91 91
Ephrin B2/EPHB4 0.031 0.038 -10000 0 -0.29 10 10
Ephrin B/EPHB2/Intersectin/N-WASP 0.007 0.077 -10000 0 -0.28 41 41
CDC42 0.028 0.006 -10000 0 -10000 0 0
RAS family/GTP 0 0.07 -10000 0 -0.35 13 13
PTK2 0.11 0.22 0.55 171 -10000 0 171
MAP4K4 -0.016 0.053 0.31 10 -0.29 14 24
SRC 0.027 0.026 -10000 0 -0.48 2 2
KALRN 0.018 0.074 -10000 0 -0.48 18 18
Intersectin/N-WASP 0.041 0.021 -10000 0 -0.34 2 2
neuron projection morphogenesis -0.012 0.085 0.28 9 -0.4 15 24
MAP2K1 0 0.069 -10000 0 -0.41 11 11
WASL 0.029 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.064 0.048 -10000 0 -0.27 14 14
cell migration 0.016 0.1 0.28 9 -0.42 13 22
NRAS 0.026 0.04 -10000 0 -0.48 5 5
SYNJ1 -0.019 0.066 0.19 5 -0.28 38 43
PXN 0.029 0.002 -10000 0 -10000 0 0
TF -0.073 0.12 0.19 3 -0.27 165 168
HRAS/GTP 0.029 0.082 -10000 0 -0.27 44 44
Ephrin B1/EPHB1-2 0.046 0.044 -10000 0 -0.27 14 14
cell adhesion mediated by integrin 0.014 0.066 0.27 37 -0.2 15 52
RAC1 0.029 0.005 -10000 0 -10000 0 0
mol:GTP 0.032 0.084 -10000 0 -0.28 45 45
RAC1-CDC42/GTP -0.034 0.059 -10000 0 -0.37 12 12
RASA1 0.028 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.003 0.097 -10000 0 -0.38 17 17
ruffle organization -0.026 0.077 0.35 5 -0.47 8 13
NCK1 0.029 0.004 -10000 0 -10000 0 0
receptor internalization -0.024 0.078 0.19 4 -0.3 43 47
Ephrin B/EPHB2/KALRN 0.047 0.1 -10000 0 -0.31 51 51
ROCK1 0.018 0.034 0.18 24 -0.27 3 27
RAS family/GDP -0.039 0.063 -10000 0 -0.36 13 13
Rac1/GTP -0.004 0.074 -10000 0 -0.29 40 40
Ephrin B/EPHB1/Src/Paxillin 0.004 0.082 -10000 0 -0.29 44 44
Glypican 2 network

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
MDK 0.019 0.064 -9999 0 -0.48 13 13
GPC2 0.005 0.088 -9999 0 -0.48 24 24
GPC2/Midkine 0.015 0.084 -9999 0 -0.36 34 34
neuron projection morphogenesis 0.015 0.084 -9999 0 -0.36 34 34
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.028 0.005 -10000 0 -10000 0 0
VLDLR 0.016 0.073 -10000 0 -0.48 17 17
LRPAP1 0.028 0.006 -10000 0 -10000 0 0
NUDC 0.028 0.006 -10000 0 -10000 0 0
RELN/LRP8 0.004 0.12 -10000 0 -0.3 110 110
CaM/Ca2+ 0.021 0.004 -10000 0 -10000 0 0
KATNA1 0.028 0.007 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.031 0.099 0.18 11 -0.27 109 120
IQGAP1/CaM 0.041 0.011 -10000 0 -10000 0 0
DAB1 0.017 0.038 -10000 0 -0.48 3 3
IQGAP1 0.028 0.006 -10000 0 -10000 0 0
PLA2G7 -0.004 0.12 -10000 0 -0.48 48 48
CALM1 0.028 0.005 -10000 0 -10000 0 0
DYNLT1 0.028 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.035 0.039 -10000 0 -0.34 7 7
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.029 0.002 -10000 0 -10000 0 0
CDK5R1 0.026 0.02 -10000 0 -0.48 1 1
LIS1/Poliovirus Protein 3A 0.009 0.004 -10000 0 -10000 0 0
CDK5R2 0.016 0.024 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.003 0.13 -10000 0 -0.3 118 118
YWHAE 0.027 0.009 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.017 0.091 0.31 3 -0.37 4 7
MAP1B 0.002 0.036 -10000 0 -0.29 12 12
RAC1 0.013 0.006 -10000 0 -10000 0 0
p35/CDK5 -0.024 0.09 -10000 0 -0.25 104 104
RELN -0.05 0.17 -10000 0 -0.48 107 107
PAFAH/LIS1 0.007 0.076 -10000 0 -0.29 48 48
LIS1/CLIP170 0.028 0.011 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.007 0.082 -10000 0 -0.34 3 3
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.023 0.11 -10000 0 -0.26 128 128
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.032 0.087 0.32 2 -0.31 17 19
LIS1/IQGAP1 0.027 0.012 -10000 0 -10000 0 0
RHOA 0.013 0.006 -10000 0 -10000 0 0
PAFAH1B1 0.012 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.029 0.005 -10000 0 -10000 0 0
PAFAH1B2 0.024 0.032 -10000 0 -0.48 3 3
MAP1B/LIS1/Dynein heavy chain 0.019 0.04 -10000 0 -0.2 13 13
NDEL1/Katanin 60/Dynein heavy chain -0.007 0.096 0.31 3 -0.34 6 9
LRP8 0.022 0.049 -10000 0 -0.48 7 7
NDEL1/Katanin 60 -0.02 0.091 0.31 3 -0.31 14 17
P39/CDK5 -0.038 0.088 -10000 0 -0.25 108 108
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0.012 -10000 0 -10000 0 0
CDK5 -0.047 0.086 0.18 8 -0.26 108 116
PPP2R5D 0.028 0.005 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.025 0.009 -10000 0 -10000 0 0
CSNK2A1 0.028 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.004 0.11 -10000 0 -0.26 117 117
RELN/VLDLR 0.013 0.12 -10000 0 -0.28 120 120
CDC42 0.013 0.006 -10000 0 -10000 0 0
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0.005 0.058 0.24 44 -0.11 2 46
BUB1B -0.003 0.079 0.14 4 -0.31 39 43
PLK1 0.007 0.042 0.096 17 -0.16 27 44
PLK1S1 0.007 0.039 0.15 2 -0.2 18 20
KIF2A 0.002 0.041 0.22 3 -0.19 18 21
regulation of mitotic centrosome separation 0.007 0.042 0.096 17 -0.16 27 44
GOLGA2 0.029 0.004 -10000 0 -10000 0 0
Hec1/SPC24 0.014 0.12 -10000 0 -0.37 56 56
WEE1 0.009 0.063 0.18 2 -0.3 24 26
cytokinesis -0.003 0.12 0.26 1 -0.55 30 31
PP2A-alpha B56 0.026 0.16 -10000 0 -0.6 49 49
AURKA 0.006 0.053 0.14 1 -0.32 18 19
PICH/PLK1 0.009 0.064 -10000 0 -0.33 22 22
CENPE -0.005 0.074 0.21 3 -0.34 31 34
RhoA/GTP 0.021 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.003 0.041 0.21 3 -0.19 18 21
PPP2CA 0.029 0.005 -10000 0 -10000 0 0
FZR1 0.028 0.005 -10000 0 -10000 0 0
TPX2 0.003 0.062 0.14 4 -0.32 26 30
PAK1 0.025 0.027 -10000 0 -0.49 2 2
SPC24 -0.003 0.12 -10000 0 -0.48 50 50
FBXW11 0.029 0.005 -10000 0 -10000 0 0
CLSPN -0.008 0.089 -10000 0 -0.31 58 58
GORASP1 0.028 0.005 -10000 0 -10000 0 0
metaphase 0 0.006 0.018 55 -0.019 34 89
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.003 0.021 0.053 19 -0.075 27 46
G2 phase of mitotic cell cycle 0 0.003 0.012 14 -0.011 16 30
STAG2 0.029 0.018 -10000 0 -0.48 1 1
GRASP65/GM130/RAB1/GTP 0.011 0.09 -10000 0 -0.54 21 21
spindle elongation 0.007 0.042 0.096 17 -0.16 27 44
ODF2 0.029 0.005 -10000 0 -10000 0 0
BUB1 -0.006 0.17 -10000 0 -0.64 51 51
TPT1 -0.007 0.061 0.12 1 -0.19 75 76
CDC25C -0.012 0.11 -10000 0 -0.39 60 60
CDC25B 0.027 0.022 -10000 0 -0.49 1 1
SGOL1 -0.005 0.058 0.11 2 -0.24 44 46
RHOA 0.028 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.035 0.047 -10000 0 -0.35 5 5
CDC14B 0.001 0.043 -10000 0 -0.35 12 12
CDC20 0.011 0.089 -10000 0 -0.48 26 26
PLK1/PBIP1 0.004 0.049 0.1 4 -0.21 27 31
mitosis -0.001 0.005 0.03 18 -10000 0 18
FBXO5 0.004 0.038 0.14 10 -0.16 9 19
CDC2 0.001 0.003 -10000 0 -0.015 7 7
NDC80 0.013 0.084 -10000 0 -0.48 23 23
metaphase plate congression 0.002 0.058 -10000 0 -0.23 38 38
ERCC6L 0.011 0.065 -10000 0 -0.34 20 20
NLP/gamma Tubulin 0.004 0.028 0.076 7 -0.089 38 45
microtubule cytoskeleton organization -0.007 0.06 0.12 1 -0.18 75 76
G2/M transition DNA damage checkpoint 0 0.002 0.011 21 -10000 0 21
PPP1R12A 0.029 0.004 -10000 0 -10000 0 0
interphase 0 0.002 0.011 21 -10000 0 21
PLK1/PRC1-2 0.025 0.098 -10000 0 -0.43 30 30
GRASP65/GM130/RAB1/GTP/PLK1 0.047 0.045 -10000 0 -0.17 13 13
RAB1A 0.029 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.007 0.035 0.089 23 -0.16 18 41
mitotic prometaphase 0 0.005 0.018 38 -0.013 21 59
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.043 -10000 0 -0.26 1 1
microtubule-based process 0.014 0.078 0.16 1 -0.34 31 32
Golgi organization 0.007 0.042 0.096 17 -0.16 27 44
Cohesin/SA2 0.021 0.042 0.12 4 -0.16 26 30
PPP1CB/MYPT1 0.043 0.008 -10000 0 -10000 0 0
KIF20A 0.012 0.092 -10000 0 -0.48 28 28
APC/C/CDC20 0.015 0.077 0.13 4 -0.33 31 35
PPP2R1A 0.029 0.005 -10000 0 -10000 0 0
chromosome segregation 0.004 0.048 0.1 4 -0.21 27 31
PRC1 0.021 0.061 -10000 0 -0.48 12 12
ECT2 0.01 0.058 0.23 28 -0.2 18 46
C13orf34 0.007 0.035 0.082 22 -0.13 26 48
NUDC 0.002 0.058 -10000 0 -0.23 38 38
regulation of attachment of spindle microtubules to kinetochore -0.003 0.079 0.14 4 -0.3 39 43
spindle assembly 0.006 0.033 0.083 17 -0.12 28 45
spindle stabilization 0.008 0.038 0.15 2 -0.2 18 20
APC/C/HCDH1 0.021 0.039 -10000 0 -0.29 12 12
MKLP2/PLK1 0.014 0.078 0.16 1 -0.35 31 32
CCNB1 0.027 0.032 -10000 0 -0.49 3 3
PPP1CB 0.029 0.003 -10000 0 -10000 0 0
BTRC 0.028 0.008 -10000 0 -10000 0 0
ROCK2 0.01 0.056 0.19 1 -0.31 14 15
TUBG1 0.004 0.043 0.12 1 -0.19 30 31
G2/M transition of mitotic cell cycle 0.005 0.04 -10000 0 -0.34 5 5
MLF1IP 0.002 0.034 -10000 0 -0.36 7 7
INCENP 0.028 0.006 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.001 0.11 -10000 0 -0.48 40 40
PDGF/PDGFRA/CRKL 0.019 0.083 -10000 0 -0.34 40 40
positive regulation of JUN kinase activity 0.041 0.068 -10000 0 -0.26 32 32
CRKL 0.027 0.019 -10000 0 -0.48 1 1
PDGF/PDGFRA/Caveolin-3 0.013 0.083 -10000 0 -0.34 40 40
AP1 -0.067 0.22 0.31 1 -0.91 48 49
mol:IP3 -0.009 0.077 -10000 0 -0.35 36 36
PLCG1 -0.009 0.077 -10000 0 -0.36 36 36
PDGF/PDGFRA/alphaV Integrin 0.019 0.086 -10000 0 -0.34 42 42
RAPGEF1 0.029 0.005 -10000 0 -10000 0 0
CRK 0.027 0.009 -10000 0 -10000 0 0
mol:Ca2+ -0.009 0.077 -10000 0 -0.35 36 36
CAV3 0.019 0.014 -10000 0 -10000 0 0
CAV1 0.025 0.04 -10000 0 -0.48 5 5
SHC/Grb2/SOS1 0.043 0.07 -10000 0 -0.26 32 32
PDGF/PDGFRA/Shf 0.017 0.087 -10000 0 -0.35 42 42
FOS -0.069 0.22 -10000 0 -0.9 48 48
JUN -0.023 0.023 0.25 1 -10000 0 1
oligodendrocyte development 0.019 0.085 -10000 0 -0.34 42 42
GRB2 0.027 0.008 -10000 0 -10000 0 0
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
mol:DAG -0.009 0.077 -10000 0 -0.35 36 36
PDGF/PDGFRA 0.001 0.11 -10000 0 -0.48 40 40
actin cytoskeleton reorganization 0.02 0.082 -10000 0 -0.34 39 39
SRF 0.013 0.01 -10000 0 -10000 0 0
SHC1 0.024 0.011 -10000 0 -10000 0 0
PI3K 0.037 0.073 -10000 0 -0.28 38 38
PDGF/PDGFRA/Crk/C3G 0.036 0.075 -10000 0 -0.28 40 40
JAK1 -0.007 0.075 -10000 0 -0.34 39 39
ELK1/SRF -0.019 0.069 0.16 39 -0.28 35 74
SHB 0.029 0.005 -10000 0 -10000 0 0
SHF 0.025 0.032 -10000 0 -0.48 3 3
CSNK2A1 0.029 0.018 -10000 0 -10000 0 0
GO:0007205 -0.016 0.081 -10000 0 -0.38 37 37
SOS1 0.029 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.041 0.068 -10000 0 -0.26 32 32
PDGF/PDGFRA/SHB 0.02 0.082 -10000 0 -0.34 39 39
PDGF/PDGFRA/Caveolin-1 0.017 0.09 -10000 0 -0.35 44 44
ITGAV 0.028 0.025 -10000 0 -0.48 2 2
ELK1 -0.025 0.071 -10000 0 -0.33 37 37
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.017 0.083 -10000 0 -0.34 40 40
JAK-STAT cascade -0.007 0.075 -10000 0 -0.34 39 39
cell proliferation 0.017 0.087 -10000 0 -0.34 42 42
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.029 0.016 -10000 0 -10000 0 0
HSPA8 0.024 0.021 -10000 0 -0.48 1 1
SMAD3/SMAD4/ER alpha -0.029 0.16 0.24 1 -0.31 189 190
AKT1 0.029 0.013 -10000 0 -10000 0 0
GSC -0.1 0.39 -10000 0 -1.3 72 72
NKX2-5 0.002 0.073 -10000 0 -0.48 16 16
muscle cell differentiation -0.011 0.086 0.36 19 -10000 0 19
SMAD2-3/SMAD4/SP1 0.061 0.11 -10000 0 -0.3 30 30
SMAD4 0.018 0.058 -10000 0 -0.22 19 19
CBFB 0.026 0.01 -10000 0 -10000 0 0
SAP18 0.027 0.008 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.016 0.11 -10000 0 -0.29 86 86
SMAD3/SMAD4/VDR 0.073 0.073 -10000 0 -0.26 13 13
MYC 0.005 0.086 -10000 0 -0.48 25 25
CDKN2B -0.051 0.21 -10000 0 -0.88 29 29
AP1 0.026 0.079 -10000 0 -0.25 48 48
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.008 0.1 -10000 0 -0.37 35 35
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.012 0.063 0.22 1 -0.33 16 17
SP3 0.029 0.013 -10000 0 -10000 0 0
CREB1 0.029 0.004 -10000 0 -10000 0 0
FOXH1 -0.003 0.1 -10000 0 -0.48 32 32
SMAD3/SMAD4/GR 0.049 0.065 -10000 0 -0.26 12 12
GATA3 -0.045 0.18 -10000 0 -0.47 119 119
SKI/SIN3/HDAC complex/NCoR1 0.008 0.084 -10000 0 -0.34 32 32
MEF2C/TIF2 0 0.11 0.32 2 -0.38 15 17
endothelial cell migration 0.005 0.21 1.2 23 -10000 0 23
MAX 0.028 0.009 -10000 0 -10000 0 0
RBBP7 0.028 0.009 -10000 0 -10000 0 0
RBBP4 0.028 0.005 -10000 0 -10000 0 0
RUNX2 0.014 0.084 -10000 0 -0.48 23 23
RUNX3 0.016 0.069 -10000 0 -0.48 15 15
RUNX1 0.026 0.04 -10000 0 -0.48 5 5
CTBP1 0.028 0.006 -10000 0 -10000 0 0
NR3C1 0.027 0.03 -10000 0 -0.45 3 3
VDR 0.024 0.05 -10000 0 -0.48 8 8
CDKN1A 0.006 0.13 -10000 0 -1.1 9 9
KAT2B 0.027 0.031 -10000 0 -0.47 3 3
SMAD2/SMAD2/SMAD4/FOXH1 0.021 0.11 -10000 0 -0.29 72 72
DCP1A 0.028 0.006 -10000 0 -10000 0 0
SKI 0.028 0.006 -10000 0 -10000 0 0
SERPINE1 -0.006 0.22 -10000 0 -1.2 23 23
SMAD3/SMAD4/ATF2 0.05 0.064 -10000 0 -0.26 11 11
SMAD3/SMAD4/ATF3 0.036 0.077 -10000 0 -0.32 21 21
SAP30 0.023 0.05 -10000 0 -0.48 8 8
Cbp/p300/PIAS3 0.054 0.037 0.23 1 -10000 0 1
JUN 0.01 0.074 0.28 2 -0.24 48 50
SMAD3/SMAD4/IRF7 0.044 0.083 -10000 0 -0.32 22 22
TFE3 0.03 0.022 -10000 0 -0.19 3 3
COL1A2 -0.006 0.23 -10000 0 -0.87 50 50
mesenchymal cell differentiation -0.039 0.091 0.34 30 -10000 0 30
DLX1 -0.031 0.14 -10000 0 -0.48 67 67
TCF3 0.028 0.006 -10000 0 -10000 0 0
FOS -0.004 0.12 -10000 0 -0.48 45 45
SMAD3/SMAD4/Max 0.049 0.062 -10000 0 -0.27 6 6
Cbp/p300/SNIP1 0.052 0.028 -10000 0 -0.27 1 1
ZBTB17 0.026 0.019 -10000 0 -0.48 1 1
LAMC1 0.012 0.065 -10000 0 -0.46 9 9
TGIF2/HDAC complex/SMAD3/SMAD4 0.046 0.066 -10000 0 -0.26 13 13
IRF7 0.019 0.07 -10000 0 -0.48 16 16
ESR1 -0.087 0.21 -10000 0 -0.47 190 190
HNF4A 0.02 0.012 -10000 0 -10000 0 0
MEF2C 0.016 0.12 0.4 9 -0.38 12 21
SMAD2-3/SMAD4 0.043 0.083 -10000 0 -0.25 22 22
Cbp/p300/Src-1 0.053 0.033 -10000 0 -0.26 2 2
IGHV3OR16-13 0.006 0.05 -10000 0 -0.39 11 11
TGIF2/HDAC complex 0.026 0.031 -10000 0 -0.48 3 3
CREBBP 0.027 0.021 -10000 0 -0.45 1 1
SKIL 0.025 0.032 -10000 0 -0.48 3 3
HDAC1 0.028 0.018 -10000 0 -0.48 1 1
HDAC2 0.027 0.008 -10000 0 -10000 0 0
SNIP1 0.028 0.006 -10000 0 -10000 0 0
GCN5L2 0.002 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.056 0.072 -10000 0 -0.32 12 12
MSG1/HSC70 -0.015 0.12 -10000 0 -0.34 90 90
SMAD2 0.019 0.046 -10000 0 -0.17 25 25
SMAD3 0.026 0.049 -10000 0 -0.28 8 8
SMAD3/E2F4-5/DP1/p107/SMAD4 0.018 0.047 -10000 0 -0.27 10 10
SMAD2/SMAD2/SMAD4 0.011 0.059 0.2 10 -0.28 11 21
NCOR1 0.026 0.009 -10000 0 -10000 0 0
NCOA2 0.006 0.093 -10000 0 -0.48 29 29
NCOA1 0.028 0.018 -10000 0 -0.48 1 1
MYOD/E2A 0.021 0.004 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.07 0.11 -10000 0 -0.32 20 20
IFNB1 0.005 0.061 -10000 0 -0.3 17 17
SMAD3/SMAD4/MEF2C 0.043 0.12 0.37 1 -0.36 14 15
CITED1 -0.038 0.16 -10000 0 -0.48 90 90
SMAD2-3/SMAD4/ARC105 0.057 0.08 -10000 0 -0.25 14 14
RBL1 0.027 0.026 -10000 0 -0.48 2 2
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.018 0.083 -10000 0 -0.45 17 17
RUNX1-3/PEBPB2 0.042 0.057 -10000 0 -0.3 19 19
SMAD7 0.021 0.11 -10000 0 -0.47 15 15
MYC/MIZ-1 0.016 0.068 -10000 0 -0.34 26 26
SMAD3/SMAD4 0.029 0.1 0.29 46 -0.46 15 61
IL10 -0.029 0.14 -10000 0 -0.32 120 120
PIASy/HDAC complex 0.024 0.018 -10000 0 -10000 0 0
PIAS3 0.028 0.009 -10000 0 -10000 0 0
CDK2 0.03 0.012 -10000 0 -10000 0 0
IL5 -0.039 0.11 -10000 0 -0.28 137 137
CDK4 0.03 0.013 -10000 0 -10000 0 0
PIAS4 0.025 0.018 -10000 0 -10000 0 0
ATF3 0.013 0.071 -10000 0 -0.48 16 16
SMAD3/SMAD4/SP1 0.051 0.093 -10000 0 -0.3 30 30
FOXG1 -0.002 0.026 -10000 0 -10000 0 0
FOXO3 0.013 0.018 -10000 0 -0.34 1 1
FOXO1 0.013 0.013 -10000 0 -10000 0 0
FOXO4 0.014 0.018 -10000 0 -0.34 1 1
heart looping 0.016 0.12 0.4 9 -0.37 12 21
CEBPB 0.025 0.023 -10000 0 -0.48 1 1
SMAD3/SMAD4/DLX1 0.018 0.12 -10000 0 -0.3 77 77
MYOD1 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.044 0.062 -10000 0 -0.25 10 10
SMAD3/SMAD4/GATA3 -0.001 0.15 -10000 0 -0.33 137 137
SnoN/SIN3/HDAC complex/NCoR1 0.025 0.032 -10000 0 -0.48 3 3
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.062 0.086 -10000 0 -0.3 23 23
SMAD3/SMAD4/SP1-3 0.068 0.095 -10000 0 -0.3 24 24
MED15 0.028 0.007 -10000 0 -10000 0 0
SP1 0.023 0.044 -10000 0 -0.21 7 7
SIN3B 0.029 0.005 -10000 0 -10000 0 0
SIN3A 0.028 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.026 0.11 -10000 0 -0.27 84 84
ITGB5 0.007 0.087 0.29 1 -0.45 16 17
TGIF/SIN3/HDAC complex/CtBP 0.015 0.071 -10000 0 -0.29 28 28
SMAD3/SMAD4/AR -0.02 0.16 -10000 0 -0.32 167 167
AR -0.073 0.2 -10000 0 -0.48 165 165
negative regulation of cell growth 0.019 0.064 -10000 0 -0.39 6 6
SMAD3/SMAD4/MYOD 0.034 0.055 -10000 0 -0.2 18 18
E2F5 0.023 0.021 -10000 0 -0.48 1 1
E2F4 0.026 0.01 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.043 0.097 -10000 0 -0.26 43 43
SMAD2-3/SMAD4/FOXO1-3a-4 0.017 0.066 -10000 0 -0.34 18 18
TFDP1 0.027 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.047 0.089 -10000 0 -0.25 49 49
SMAD3/SMAD4/RUNX2 0.04 0.091 -10000 0 -0.34 30 30
TGIF2 0.026 0.031 -10000 0 -0.48 3 3
TGIF1 0.027 0.026 -10000 0 -0.48 2 2
ATF2 0.028 0.018 -10000 0 -0.48 1 1
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.012 0.12 0.26 2 -0.42 37 39
BAG4 0.023 0.021 -10000 0 -0.48 1 1
BAD 0.002 0.045 0.18 7 -0.17 11 18
NFKBIA 0.028 0.006 -10000 0 -10000 0 0
BIRC3 0.015 0.067 -10000 0 -0.48 14 14
BAX 0.002 0.047 0.17 9 -0.16 16 25
EnzymeConsortium:3.1.4.12 -0.001 0.03 0.077 6 -0.094 36 42
IKBKB 0.006 0.11 0.29 8 -0.4 27 35
MAP2K2 0.004 0.056 0.18 34 -0.21 3 37
MAP2K1 0.004 0.057 0.19 34 -0.21 2 36
SMPD1 0 0.036 0.12 4 -0.14 19 23
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.02 0.13 0.26 20 -0.43 28 48
MAP2K4 0.002 0.04 0.17 3 -0.2 7 10
protein ubiquitination -0.006 0.12 0.32 5 -0.4 33 38
EnzymeConsortium:2.7.1.37 0.003 0.059 0.19 30 -0.21 7 37
response to UV 0 0.001 0.002 34 -0.002 8 42
RAF1 0.005 0.057 0.19 31 -0.2 7 38
CRADD 0.029 0.004 -10000 0 -10000 0 0
mol:ceramide 0.002 0.046 0.13 6 -0.15 31 37
I-kappa-B-alpha/RELA/p50/ubiquitin 0.037 0.01 -10000 0 -10000 0 0
MADD 0.029 0.004 -10000 0 -10000 0 0
MAP3K1 0 0.045 0.15 3 -0.19 13 16
TRADD 0.025 0.02 -10000 0 -0.48 1 1
RELA/p50 0.029 0.004 -10000 0 -10000 0 0
MAPK3 0.007 0.057 0.19 30 -0.22 3 33
MAPK1 0.003 0.063 0.19 30 -0.22 7 37
p50/RELA/I-kappa-B-alpha 0.041 0.01 -10000 0 -10000 0 0
FADD 0.015 0.12 0.24 29 -0.42 28 57
KSR1 0.006 0.055 0.18 32 -0.18 14 46
MAPK8 -0.001 0.043 0.23 5 -0.21 3 8
TRAF2 0.029 0.005 -10000 0 -10000 0 0
response to radiation 0 0 0.002 10 -10000 0 10
CHUK -0.012 0.11 0.24 2 -0.41 34 36
TNF R/SODD 0.032 0.023 -10000 0 -0.35 1 1
TNF 0 0.11 -10000 0 -0.48 40 40
CYCS 0.011 0.056 0.16 32 -0.17 10 42
IKBKG -0.012 0.11 0.33 2 -0.41 34 36
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.009 0.12 -10000 0 -0.44 36 36
RELA 0.029 0.004 -10000 0 -10000 0 0
RIPK1 0.028 0.006 -10000 0 -10000 0 0
AIFM1 0.01 0.056 0.15 39 -0.16 14 53
TNF/TNF R/SODD 0.031 0.069 -10000 0 -0.29 30 30
TNFRSF1A 0.028 0.006 -10000 0 -10000 0 0
response to heat 0 0 0.002 10 -10000 0 10
CASP8 0.012 0.12 -10000 0 -0.65 22 22
NSMAF 0.007 0.12 0.25 8 -0.41 35 43
response to hydrogen peroxide 0 0.001 0.002 34 -0.002 8 42
BCL2 -0.018 0.14 -10000 0 -0.48 74 74
S1P1 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
VEGFR2 homodimer/VEGFA homodimer 0.037 0.032 -10000 0 -0.35 4 4
PDGFRB 0.021 0.064 -10000 0 -0.48 13 13
SPHK1 -0.015 0.15 -10000 0 -0.78 29 29
mol:S1P -0.015 0.14 -10000 0 -0.68 29 29
S1P1/S1P/Gi -0.03 0.16 -10000 0 -0.47 68 68
GNAO1 -0.003 0.1 -10000 0 -0.48 33 33
PDGFB-D/PDGFRB/PLCgamma1 -0.016 0.15 0.35 3 -0.44 62 65
PLCG1 -0.032 0.14 0.21 2 -0.44 66 68
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.021 0.064 -10000 0 -0.48 13 13
GNAI2 0.027 0.012 -10000 0 -10000 0 0
GNAI3 0.027 0.012 -10000 0 -10000 0 0
GNAI1 0.022 0.046 -10000 0 -0.49 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.006 0.022 -10000 0 -0.29 4 4
S1P1/S1P -0.003 0.12 0.2 1 -0.49 30 31
negative regulation of cAMP metabolic process -0.028 0.15 -10000 0 -0.45 68 68
MAPK3 -0.035 0.18 0.29 23 -0.58 63 86
calcium-dependent phospholipase C activity -0.001 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.021 0.003 -10000 0 -10000 0 0
RhoA/GDP 0.021 0.004 -10000 0 -10000 0 0
KDR 0.025 0.036 -10000 0 -0.48 4 4
PLCB2 0.004 0.11 0.29 4 -0.44 30 34
RAC1 0.029 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.004 0.091 -10000 0 -0.42 29 29
receptor internalization -0.008 0.1 -10000 0 -0.45 30 30
PTGS2 -0.053 0.26 -10000 0 -0.94 53 53
Rac1/GTP -0.005 0.091 -10000 0 -0.42 29 29
RHOA 0.028 0.006 -10000 0 -10000 0 0
VEGFA 0.027 0.011 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.028 0.15 -10000 0 -0.45 68 68
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.016 0.071 -10000 0 -0.48 16 16
MAPK1 -0.038 0.18 -10000 0 -0.59 63 63
S1P1/S1P/PDGFB-D/PDGFRB 0.01 0.12 0.26 3 -0.47 30 33
ABCC1 0.026 0.026 -10000 0 -0.48 2 2
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.026 0.094 -10000 0 -0.43 24 24
HDAC1 0.029 0.022 -10000 0 -0.48 1 1
AES 0.029 0.007 -10000 0 -10000 0 0
FBXW11 0.029 0.005 -10000 0 -10000 0 0
DTX1 0.007 0.1 -10000 0 -0.48 36 36
LRP6/FZD1 0.039 0.029 -10000 0 -0.34 4 4
TLE1 0.014 0.085 -10000 0 -0.48 24 24
AP1 -0.008 0.087 -10000 0 -0.28 64 64
NCSTN 0.025 0.011 -10000 0 -10000 0 0
ADAM10 0.027 0.025 -10000 0 -0.48 2 2
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.005 0.14 -10000 0 -0.74 16 16
NICD/RBPSUH 0.041 0.095 -10000 0 -0.42 25 25
WIF1 -0.053 0.16 -10000 0 -0.48 99 99
NOTCH1 0.012 0.08 -10000 0 -0.44 23 23
PSENEN 0.029 0.004 -10000 0 -10000 0 0
KREMEN2 -0.028 0.14 -10000 0 -0.48 72 72
DKK1 -0.058 0.17 -10000 0 -0.48 114 114
beta catenin/beta TrCP1 0.029 0.079 0.27 9 -0.36 7 16
APH1B 0.025 0.04 -10000 0 -0.48 5 5
APH1A 0.024 0.011 -10000 0 -10000 0 0
AXIN1 0.012 0.066 0.26 4 -0.47 7 11
CtBP/CBP/TCF1/TLE1/AES 0.019 0.064 0.29 2 -0.26 24 26
PSEN1 0.028 0.006 -10000 0 -10000 0 0
FOS -0.006 0.12 -10000 0 -0.48 45 45
JUN 0.028 0.008 -10000 0 -10000 0 0
MAP3K7 0.028 0.009 -10000 0 -10000 0 0
CTNNB1 0.015 0.079 0.27 9 -0.38 7 16
MAPK3 0.027 0.007 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.007 0.12 -10000 0 -0.3 98 98
HNF1A 0.028 0.02 -10000 0 -0.48 1 1
CTBP1 0.028 0.007 -10000 0 -10000 0 0
MYC -0.033 0.26 -10000 0 -1.3 30 30
NKD1 0.008 0.092 -10000 0 -0.48 28 28
FZD1 0.027 0.031 -10000 0 -0.48 3 3
NOTCH1 precursor/Deltex homolog 1 0.032 0.11 -10000 0 -0.46 25 25
apoptosis -0.008 0.086 -10000 0 -0.28 64 64
Delta 1/NOTCHprecursor 0.038 0.099 -10000 0 -0.43 24 24
DLL1 0.023 0.044 -10000 0 -0.48 6 6
PPARD 0.011 0.11 -10000 0 -0.93 10 10
Gamma Secretase 0.065 0.042 -10000 0 -0.26 2 2
APC 0.005 0.091 0.27 1 -0.48 19 20
DVL1 0.007 0.05 -10000 0 -0.31 13 13
CSNK2A1 0.028 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0.005 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.029 0.15 -10000 0 -0.32 162 162
LRP6 0.027 0.019 -10000 0 -0.48 1 1
CSNK1A1 0.029 0.004 -10000 0 -10000 0 0
NLK 0.014 0.012 -10000 0 -10000 0 0
CCND1 -0.064 0.33 -10000 0 -1.3 51 51
WNT1 0.025 0.013 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.032 0.11 0.32 13 -0.43 15 28
DKK2 0.009 0.095 -10000 0 -0.48 30 30
NOTCH1 precursor/DVL1 0.009 0.11 -10000 0 -0.58 18 18
GSK3B 0.029 0.004 -10000 0 -10000 0 0
FRAT1 0.025 0.043 -10000 0 -0.48 6 6
NOTCH/Deltex homolog 1 0.02 0.11 -10000 0 -0.46 25 25
PPP2R5D 0.02 0.068 0.26 25 -0.32 15 40
MAPK1 0.028 0.007 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.023 0.11 -10000 0 -0.27 98 98
RBPJ 0.028 0.006 -10000 0 -10000 0 0
CREBBP 0.026 0.021 -10000 0 -0.48 1 1
Nectin adhesion 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
PDGFRB 0.021 0.063 -10000 0 -0.48 13 13
alphaV beta3 Integrin 0.03 0.064 -10000 0 -0.38 18 18
PTK2 -0.01 0.11 -10000 0 -0.43 35 35
positive regulation of JNK cascade 0.003 0.1 -10000 0 -0.33 41 41
CDC42/GDP 0.016 0.14 0.43 1 -0.44 46 47
Rac1/GDP 0.016 0.14 -10000 0 -0.43 49 49
RAP1B 0.028 0.006 -10000 0 -10000 0 0
RAP1A 0.029 0.005 -10000 0 -10000 0 0
CTNNB1 0.028 0.019 -10000 0 -0.48 1 1
CDC42/GTP 0.01 0.13 -10000 0 -0.4 41 41
nectin-3/I-afadin 0.021 0.085 -10000 0 -0.34 41 41
RAPGEF1 -0.004 0.13 0.45 1 -0.45 42 43
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.016 0.14 -10000 0 -0.51 42 42
PDGFB-D/PDGFRB 0.021 0.063 -10000 0 -0.48 13 13
TLN1 -0.006 0.04 -10000 0 -0.32 4 4
Rap1/GTP 0 0.099 -10000 0 -0.33 37 37
IQGAP1 0.028 0.006 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.048 0.028 -10000 0 -0.27 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.021 0.085 -10000 0 -0.34 41 41
PVR 0.028 0.019 -10000 0 -0.48 1 1
Necl-5(dimer) 0.028 0.019 -10000 0 -0.48 1 1
mol:GDP -0.001 0.17 0.45 1 -0.52 54 55
MLLT4 0.025 0.032 -10000 0 -0.48 3 3
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
PI3K 0.056 0.088 -10000 0 -0.29 41 41
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.035 0.031 -10000 0 -0.34 4 4
positive regulation of lamellipodium assembly 0.007 0.11 -10000 0 -0.33 55 55
PVRL1 0.025 0.02 -10000 0 -0.48 1 1
PVRL3 0.005 0.11 -10000 0 -0.48 38 38
PVRL2 0.029 0.005 -10000 0 -10000 0 0
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
CDH1 -0.004 0.12 -10000 0 -0.48 48 48
CLDN1 -0.015 0.13 -10000 0 -0.48 62 62
JAM-A/CLDN1 0.022 0.11 -10000 0 -0.28 80 80
SRC -0.018 0.16 -10000 0 -0.56 44 44
ITGB3 0.015 0.075 -10000 0 -0.48 18 18
nectin-1(dimer)/I-afadin/I-afadin 0.035 0.031 -10000 0 -0.34 4 4
FARP2 -0.001 0.17 0.45 1 -0.55 43 44
RAC1 0.029 0.005 -10000 0 -10000 0 0
CTNNA1 0.029 0.005 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.037 0.078 -10000 0 -0.29 41 41
nectin-1/I-afadin 0.035 0.031 -10000 0 -0.34 4 4
nectin-2/I-afadin 0.038 0.027 -10000 0 -0.34 3 3
RAC1/GTP/IQGAP1/filamentous actin 0.037 0.009 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.033 0.079 -10000 0 -0.3 42 42
CDC42/GTP/IQGAP1/filamentous actin 0.037 0.011 -10000 0 -10000 0 0
F11R 0.024 0.021 -10000 0 -0.48 1 1
positive regulation of filopodium formation 0.003 0.1 -10000 0 -0.33 41 41
alphaV/beta3 Integrin/Talin 0.017 0.077 0.27 2 -0.33 20 22
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.027 -10000 0 -0.34 3 3
nectin-2(dimer)/I-afadin/I-afadin 0.038 0.027 -10000 0 -0.34 3 3
PIP5K1C -0.002 0.044 -10000 0 -0.19 31 31
VAV2 -0.001 0.18 0.43 1 -0.56 48 49
RAP1/GDP 0.018 0.13 -10000 0 -0.4 42 42
ITGAV 0.028 0.025 -10000 0 -0.48 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.037 0.077 -10000 0 -0.29 40 40
nectin-3(dimer)/I-afadin/I-afadin 0.021 0.085 -10000 0 -0.34 41 41
Rac1/GTP 0.009 0.14 -10000 0 -0.41 55 55
PTPRM 0.002 0.054 -10000 0 -0.22 41 41
E-cadherin/beta catenin/alpha catenin 0.044 0.087 -10000 0 -0.25 52 52
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.028 0.006 -10000 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0.035 0.013 -10000 0 -10000 0 0
PRKCZ 0.027 0.026 -10000 0 -0.48 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.028 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.008 0.072 -10000 0 -0.36 18 18
IRAK/TOLLIP 0.028 0.012 -10000 0 -10000 0 0
IKBKB 0.024 0.011 -10000 0 -10000 0 0
IKBKG 0.029 0.002 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.017 0.13 -10000 0 -0.36 103 103
IL1A 0.005 0.1 -10000 0 -0.48 33 33
IL1B -0.004 0.075 -10000 0 -0.37 32 32
IRAK/TRAF6/p62/Atypical PKCs 0.072 0.044 -10000 0 -0.24 2 2
IL1R2 -0.024 0.14 -10000 0 -0.48 74 74
IL1R1 0.017 0.076 -10000 0 -0.48 19 19
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.003 0.08 -10000 0 -0.39 16 16
TOLLIP 0.028 0.006 -10000 0 -10000 0 0
TICAM2 0.026 0.036 -10000 0 -0.48 4 4
MAP3K3 0.026 0.009 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.019 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0.039 0.073 0.3 19 -0.37 1 20
JUN -0.007 0.057 0.16 57 -0.22 19 76
MAP3K7 0.028 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.042 0.091 -10000 0 -0.27 56 56
IL1 alpha/IL1R1/IL1RAP/MYD88 0.046 0.09 -10000 0 -0.28 55 55
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.057 0.09 -10000 0 -0.26 55 55
IL1 beta fragment/IL1R1/IL1RAP 0.018 0.089 -10000 0 -0.29 58 58
NFKB1 0.028 0.018 -10000 0 -0.48 1 1
MAPK8 -0.004 0.062 0.17 62 -0.23 19 81
IRAK1 -0.001 0.016 -10000 0 -10000 0 0
IL1RN/IL1R1 0.014 0.1 -10000 0 -0.36 56 56
IRAK4 0.029 0.004 -10000 0 -10000 0 0
PRKCI 0.028 0.006 -10000 0 -10000 0 0
TRAF6 0.029 0.005 -10000 0 -10000 0 0
PI3K 0.04 0.013 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.008 0.082 -10000 0 -0.38 20 20
CHUK 0.029 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.018 0.089 -10000 0 -0.29 58 58
IL1 beta/IL1R2 -0.017 0.12 -10000 0 -0.31 105 105
IRAK/TRAF6/TAK1/TAB1/TAB2 0.035 0.016 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.029 0.082 -10000 0 -0.35 10 10
IRAK3 0.019 0.051 -10000 0 -0.48 7 7
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.042 0.096 -10000 0 -0.28 57 57
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.01 0.073 -10000 0 -0.24 54 54
IL1 alpha/IL1R1/IL1RAP 0.031 0.093 -10000 0 -0.3 56 56
RELA 0.029 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.028 0.006 -10000 0 -10000 0 0
MYD88 0.029 0.005 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.051 0.037 -10000 0 -10000 0 0
IL1RAP 0.024 0.044 -10000 0 -0.48 6 6
UBE2N 0.029 0.004 -10000 0 -10000 0 0
IRAK/TRAF6 0.01 0.076 -10000 0 -0.4 8 8
CASP1 0.022 0.044 -10000 0 -0.48 6 6
IL1RN/IL1R2 -0.018 0.14 -10000 0 -0.37 105 105
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.032 0.089 -10000 0 -0.27 58 58
TMEM189-UBE2V1 0.021 0.01 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.013 0.092 -10000 0 -0.35 30 30
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
IL1RN 0.003 0.11 -10000 0 -0.48 39 39
TRAF6/TAK1/TAB1/TAB2 0.046 0.021 -10000 0 -10000 0 0
MAP2K6 -0.002 0.068 0.19 64 -0.24 20 84
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.023 0.021 -10000 0 -0.48 1 1
Caspase 8 (4 units) 0.028 0.092 -10000 0 -0.35 20 20
NEF -0.012 0.053 -10000 0 -0.22 40 40
NFKBIA 0.027 0.02 -10000 0 -10000 0 0
BIRC3 0.01 0.079 -10000 0 -0.45 19 19
CYCS 0.014 0.1 0.19 75 -0.29 47 122
RIPK1 0.028 0.006 -10000 0 -10000 0 0
CD247 -0.014 0.13 -10000 0 -0.42 66 66
MAP2K7 0.022 0.15 0.32 1 -0.65 23 24
protein ubiquitination 0.004 0.095 0.26 6 -0.36 18 24
CRADD 0.029 0.004 -10000 0 -10000 0 0
DAXX 0.029 0.004 -10000 0 -10000 0 0
FAS 0.02 0.066 -10000 0 -0.48 14 14
BID 0.013 0.1 0.18 63 -0.3 50 113
NF-kappa-B/RelA/I kappa B alpha 0.054 0.052 -10000 0 -0.27 15 15
TRADD 0.025 0.02 -10000 0 -0.48 1 1
MAP3K5 0.027 0.026 -10000 0 -0.48 2 2
CFLAR 0.028 0.018 -10000 0 -0.48 1 1
FADD 0.024 0.011 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.054 0.052 -10000 0 -0.27 15 15
MAPK8 0.021 0.14 0.46 2 -0.6 22 24
APAF1 0.028 0.018 -10000 0 -0.48 1 1
TRAF1 0.025 0.04 -10000 0 -0.48 5 5
TRAF2 0.029 0.005 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.019 0.1 0.19 66 -0.31 50 116
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.001 0.11 0.24 1 -0.42 28 29
CHUK 0.003 0.1 0.28 5 -0.39 18 23
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.062 0.056 -10000 0 -0.25 14 14
TCRz/NEF -0.017 0.12 -10000 0 -0.41 66 66
TNF 0 0.11 -10000 0 -0.48 40 40
FASLG -0.036 0.17 -10000 0 -0.57 66 66
NFKB1 0.026 0.026 -10000 0 -0.47 1 1
TNFR1A/BAG4/TNF-alpha 0.031 0.069 -10000 0 -0.29 30 30
CASP6 0.042 0.12 -10000 0 -0.51 24 24
CASP7 0.017 0.13 0.34 6 -0.43 39 45
RELA 0.027 0.02 -10000 0 -10000 0 0
CASP2 0.028 0.005 -10000 0 -10000 0 0
CASP3 0.014 0.13 0.32 4 -0.46 33 37
TNFRSF1A 0.028 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4 0.032 0.023 -10000 0 -0.34 1 1
CASP8 0.029 0.004 -10000 0 -10000 0 0
CASP9 0.028 0.006 -10000 0 -10000 0 0
MAP3K14 0.004 0.1 -10000 0 -0.42 21 21
APAF-1/Caspase 9 0.014 0.093 -10000 0 -0.36 24 24
BCL2 0.004 0.14 0.39 6 -0.56 25 31
Regulation of Telomerase

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
Telomerase catalytic core complex -0.1 0.3 -9999 0 -0.91 79 79
RAD9A 0.027 0.008 -9999 0 -10000 0 0
AP1 0.009 0.09 -9999 0 -0.35 44 44
IFNAR2 0.024 0.025 -9999 0 -0.48 1 1
AKT1 -0.032 0.092 -9999 0 -0.24 52 52
ER alpha/Oestrogen -0.065 0.15 -9999 0 -0.34 190 190
NFX1/SIN3/HDAC complex 0.014 0.068 -9999 0 -0.32 19 19
EGF -0.058 0.18 -9999 0 -0.48 127 127
SMG5 0.025 0.011 -9999 0 -10000 0 0
SMG6 0.027 0.008 -9999 0 -10000 0 0
SP3/HDAC2 0.034 0.027 -9999 0 -10000 0 0
TERT/c-Abl -0.087 0.28 -9999 0 -0.84 80 80
SAP18 0.027 0.008 -9999 0 -10000 0 0
MRN complex 0.042 0.027 -9999 0 -10000 0 0
WT1 -0.058 0.17 -9999 0 -0.48 110 110
WRN 0.024 0.011 -9999 0 -10000 0 0
SP1 0.023 0.021 -9999 0 -10000 0 0
SP3 0.026 0.013 -9999 0 -10000 0 0
TERF2IP 0.026 0.01 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.062 0.26 -9999 0 -0.79 72 72
Mad/Max 0.036 0.022 -9999 0 -10000 0 0
TERT -0.11 0.32 -9999 0 -0.99 75 75
CCND1 -0.1 0.36 -9999 0 -1.1 93 93
MAX 0.025 0.013 -9999 0 -10000 0 0
RBBP7 0.028 0.009 -9999 0 -10000 0 0
RBBP4 0.028 0.005 -9999 0 -10000 0 0
TERF2 0.024 0.014 -9999 0 -10000 0 0
PTGES3 0.029 0.002 -9999 0 -10000 0 0
SIN3A 0.028 0.005 -9999 0 -10000 0 0
Telomerase/911 0.021 0.055 -9999 0 -0.36 7 7
CDKN1B -0.021 0.11 -9999 0 -0.35 73 73
RAD1 0.029 0.005 -9999 0 -10000 0 0
XRCC5 0.029 0.004 -9999 0 -10000 0 0
XRCC6 0.028 0.007 -9999 0 -10000 0 0
SAP30 0.023 0.05 -9999 0 -0.48 8 8
TRF2/PARP2 0.037 0.017 -9999 0 -10000 0 0
UBE3A 0.026 0.012 -9999 0 -10000 0 0
JUN 0.025 0.014 -9999 0 -10000 0 0
E6 -0.001 0.004 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.017 0.014 -9999 0 -10000 0 0
FOS -0.008 0.12 -9999 0 -0.48 45 45
IFN-gamma/IRF1 0.004 0.11 -9999 0 -0.34 74 74
PARP2 0.029 0.005 -9999 0 -10000 0 0
BLM 0.021 0.061 -9999 0 -0.48 12 12
Telomerase -0.004 0.11 -9999 0 -0.44 32 32
IRF1 0.026 0.032 -9999 0 -0.2 11 11
ESR1 -0.09 0.21 -9999 0 -0.48 190 190
KU/TER 0.04 0.012 -9999 0 -10000 0 0
ATM/TRF2 0.036 0.017 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.021 0.061 -9999 0 -0.3 11 11
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.021 0.062 -9999 0 -0.31 11 11
HDAC1 0.028 0.018 -9999 0 -0.48 1 1
HDAC2 0.022 0.021 -9999 0 -10000 0 0
ATM 0.014 0.016 -9999 0 -10000 0 0
SMAD3 0.012 0.028 -9999 0 -0.35 5 5
ABL1 0.029 0.005 -9999 0 -10000 0 0
MXD1 0.026 0.013 -9999 0 -10000 0 0
MRE11A 0.027 0.008 -9999 0 -10000 0 0
HUS1 0.029 0.004 -9999 0 -10000 0 0
RPS6KB1 0.026 0.01 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.087 0.28 -9999 0 -0.82 84 84
NR2F2 0.018 0.074 -9999 0 -0.48 18 18
MAPK3 -0.003 0.017 -9999 0 -10000 0 0
MAPK1 -0.003 0.017 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.027 0.031 -9999 0 -0.48 3 3
NFKB1 0.028 0.018 -9999 0 -0.48 1 1
HNRNPC 0.029 0.005 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.014 0.016 -9999 0 -10000 0 0
NBN 0.023 0.012 -9999 0 -10000 0 0
EGFR -0.02 0.14 -9999 0 -0.48 67 67
mol:Oestrogen 0 0.002 -9999 0 -10000 0 0
EGF/EGFR -0.061 0.16 -9999 0 -0.36 183 183
MYC 0.004 0.087 -9999 0 -0.48 25 25
IL2 0.015 0.025 -9999 0 -10000 0 0
KU 0.04 0.012 -9999 0 -10000 0 0
RAD50 0.028 0.005 -9999 0 -10000 0 0
HSP90AA1 0.028 0.005 -9999 0 -10000 0 0
TGFB1 0.027 0.031 -9999 0 -0.48 3 3
TRF2/BLM 0.032 0.047 -9999 0 -0.32 12 12
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.077 0.29 -9999 0 -0.86 76 76
SP1/HDAC2 0.034 0.031 -9999 0 -10000 0 0
PINX1 0.024 0.012 -9999 0 -10000 0 0
Telomerase/EST1A -0.063 0.26 -9999 0 -0.78 74 74
Smad3/Myc 0.012 0.059 -9999 0 -0.29 27 27
911 complex 0.053 0.019 -9999 0 -10000 0 0
IFNG -0.025 0.14 -9999 0 -0.44 73 73
Telomerase/PinX1 -0.069 0.26 -9999 0 -0.78 74 74
Telomerase/AKT1/mTOR/p70S6K -0.02 0.11 -9999 0 -0.49 23 23
SIN3B 0.028 0.005 -9999 0 -10000 0 0
YWHAE 0.027 0.009 -9999 0 -10000 0 0
Telomerase/EST1B -0.063 0.25 -9999 0 -0.8 69 69
response to DNA damage stimulus -0.001 0.027 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0.055 0.04 -9999 0 -10000 0 0
TRF2/WRN 0.032 0.019 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.062 0.26 -9999 0 -0.78 74 74
E2F1 0.01 0.083 -9999 0 -0.48 22 22
ZNFX1 0.027 0.008 -9999 0 -10000 0 0
PIF1 0.009 0.091 -9999 0 -0.48 27 27
NCL 0.029 0.004 -9999 0 -10000 0 0
DKC1 0.029 0.005 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.013 0.013 -10000 0 -0.35 1 1
SMARCC1 0.008 0.063 -10000 0 -0.94 3 3
REL 0.012 0.092 -10000 0 -0.48 28 28
HDAC7 -0.033 0.1 0.31 1 -0.33 46 47
JUN 0.028 0.008 -10000 0 -10000 0 0
EP300 0.028 0.007 -10000 0 -10000 0 0
KAT2B 0.027 0.031 -10000 0 -0.48 3 3
KAT5 0.029 0.004 -10000 0 -10000 0 0
MAPK14 -0.004 0.061 -10000 0 -0.35 22 22
FOXO1 0.026 0.009 -10000 0 -10000 0 0
T-DHT/AR -0.015 0.12 0.33 1 -0.34 48 49
MAP2K6 0.006 0.085 -10000 0 -0.48 23 23
BRM/BAF57 0.039 0.014 -10000 0 -10000 0 0
MAP2K4 0.02 0.02 -10000 0 -10000 0 0
SMARCA2 0.028 0.007 -10000 0 -10000 0 0
PDE9A -0.055 0.23 -10000 0 -1.1 32 32
NCOA2 0.006 0.093 -10000 0 -0.48 29 29
CEBPA 0.024 0.047 -10000 0 -0.48 7 7
EHMT2 0.029 0.004 -10000 0 -10000 0 0
cell proliferation -0.008 0.16 0.33 35 -0.47 36 71
NR0B1 0.014 0.023 -10000 0 -10000 0 0
EGR1 0.01 0.085 -10000 0 -0.48 23 23
RXRs/9cRA 0.036 0.055 -10000 0 -0.27 22 22
AR/RACK1/Src -0.007 0.099 0.28 14 -0.32 23 37
AR/GR -0.031 0.12 0.21 2 -0.25 159 161
GNB2L1 0.028 0.006 -10000 0 -10000 0 0
PKN1 0.028 0.025 -10000 0 -0.48 2 2
RCHY1 0.028 0.006 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -10000 0 -0.014 4 4
MAPK8 0.007 0.019 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.005 0.1 0.28 4 -0.29 38 42
SRC -0.012 0.062 0.19 36 -0.28 18 54
NR3C1 0.027 0.031 -10000 0 -0.48 3 3
KLK3 -0.072 0.15 -10000 0 -0.56 16 16
APPBP2 0.02 0.02 -10000 0 -10000 0 0
TRIM24 0.029 0.006 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.011 0.092 0.28 5 -0.3 27 32
TMPRSS2 -0.13 0.35 -10000 0 -1 100 100
RXRG 0.006 0.083 -10000 0 -0.48 22 22
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.029 0.005 -10000 0 -10000 0 0
RXRB 0.029 0.004 -10000 0 -10000 0 0
CARM1 0.028 0.006 -10000 0 -10000 0 0
NR2C2 0.028 0.005 -10000 0 -10000 0 0
KLK2 -0.019 0.13 0.28 6 -0.58 26 32
AR -0.042 0.12 -10000 0 -0.27 151 151
SENP1 0.029 0.003 -10000 0 -10000 0 0
HSP90AA1 0.028 0.005 -10000 0 -10000 0 0
MDM2 0.028 0.006 -10000 0 -10000 0 0
SRY 0 0.001 -10000 0 -10000 0 0
GATA2 -0.029 0.16 -10000 0 -0.48 87 87
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.088 0.2 -10000 0 -0.48 168 168
T-DHT/AR/RACK1/Src -0.007 0.099 0.29 18 -0.31 23 41
positive regulation of transcription -0.029 0.16 -10000 0 -0.48 87 87
DNAJA1 0.022 0.02 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.01 -10000 0 -0.2 1 1
NCOA1 0.033 0.025 -10000 0 -0.34 2 2
SPDEF -0.04 0.17 -10000 0 -0.48 112 112
T-DHT/AR/TIF2 0.003 0.094 0.22 12 -0.33 24 36
T-DHT/AR/Hsp90 -0.01 0.091 0.28 5 -0.31 25 30
GSK3B 0.028 0.007 -10000 0 -10000 0 0
NR2C1 0.028 0.025 -10000 0 -0.48 2 2
mol:T-DHT -0.02 0.048 0.2 1 -0.29 18 19
SIRT1 0.029 0.004 -10000 0 -10000 0 0
ZMIZ2 0.028 0.005 -10000 0 -10000 0 0
POU2F1 0.014 0.049 -10000 0 -0.18 6 6
T-DHT/AR/DAX-1 -0.018 0.091 0.28 5 -0.31 26 31
CREBBP 0.027 0.019 -10000 0 -0.48 1 1
SMARCE1 0.027 0.008 -10000 0 -10000 0 0
Ceramide 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
SPHK2 0.013 0.013 -10000 0 -0.34 1 1
MAP4K4 -0.008 0.085 0.21 1 -0.4 19 20
BAG4 0.023 0.021 -10000 0 -0.48 1 1
PKC zeta/ceramide 0.006 0.051 -10000 0 -0.24 16 16
NFKBIA 0.028 0.006 -10000 0 -10000 0 0
BIRC3 0.015 0.067 -10000 0 -0.48 14 14
BAX 0.005 0.041 -10000 0 -0.34 9 9
RIPK1 0.028 0.006 -10000 0 -10000 0 0
AKT1 0 0.067 0.67 8 -10000 0 8
BAD -0.01 0.044 0.19 3 -0.23 14 17
SMPD1 0.007 0.069 0.18 14 -0.21 44 58
RB1 -0.013 0.046 0.14 1 -0.23 20 21
FADD/Caspase 8 0.023 0.1 0.22 86 -0.4 16 102
MAP2K4 -0.012 0.041 0.18 2 -0.22 15 17
NSMAF 0.024 0.027 -10000 0 -0.48 2 2
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.005 0.055 0.2 24 -0.25 9 33
EGF -0.056 0.18 -10000 0 -0.48 127 127
mol:ceramide -0.009 0.045 0.14 2 -0.24 15 17
MADD 0.029 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.009 0.019 -10000 0 -0.34 2 2
ASAH1 0.022 0.023 -10000 0 -0.48 1 1
negative regulation of cell cycle -0.014 0.045 0.14 1 -0.22 20 21
cell proliferation 0.003 0.082 0.23 3 -0.24 37 40
BID -0.028 0.18 -10000 0 -0.66 53 53
MAP3K1 -0.012 0.043 0.14 1 -0.23 16 17
EIF2A -0.009 0.048 0.19 21 -0.2 10 31
TRADD 0.025 0.02 -10000 0 -0.48 1 1
CRADD 0.029 0.004 -10000 0 -10000 0 0
MAPK3 -0.002 0.053 0.19 21 -0.31 5 26
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.006 0.058 0.19 21 -0.3 5 26
Cathepsin D/ceramide 0.007 0.047 0.14 2 -0.21 16 18
FADD 0.016 0.097 0.21 83 -0.34 19 102
KSR1 -0.004 0.053 0.19 21 -0.24 12 33
MAPK8 -0.007 0.052 -10000 0 -0.27 10 10
PRKRA -0.01 0.045 0.19 4 -0.23 14 18
PDGFA 0.027 0.019 -10000 0 -0.48 1 1
TRAF2 0.029 0.005 -10000 0 -10000 0 0
IGF1 -0.018 0.14 -10000 0 -0.48 69 69
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.009 0.045 0.14 2 -0.23 15 17
CTSD 0.026 0.021 -10000 0 -0.48 1 1
regulation of nitric oxide biosynthetic process 0.041 0.016 -10000 0 -0.34 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.005 0.088 0.24 3 -0.26 33 36
PRKCD 0.028 0.006 -10000 0 -10000 0 0
PRKCZ 0.027 0.026 -10000 0 -0.48 2 2
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.009 0.019 -10000 0 -0.34 2 2
RelA/NF kappa B1 0.041 0.016 -10000 0 -0.34 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.027 0.031 -10000 0 -0.48 3 3
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.001 0.083 -10000 0 -0.42 19 19
TNFR1A/BAG4/TNF-alpha 0.031 0.069 -10000 0 -0.29 30 30
mol:Sphingosine-1-phosphate 0.013 0.013 -10000 0 -0.34 1 1
MAP2K1 -0.005 0.053 0.18 26 -0.32 4 30
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.029 0.004 -10000 0 -10000 0 0
CYCS 0.013 0.056 0.16 48 -0.2 12 60
TNFRSF1A 0.028 0.006 -10000 0 -10000 0 0
NFKB1 0.028 0.018 -10000 0 -0.48 1 1
TNFR1A/BAG4 0.032 0.023 -10000 0 -0.34 1 1
EIF2AK2 -0.012 0.04 0.19 4 -0.21 14 18
TNF-alpha/TNFR1A/FAN 0.033 0.07 -10000 0 -0.3 31 31
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.012 0.086 -10000 0 -0.39 22 22
MAP2K2 -0.006 0.053 0.18 27 -0.3 5 32
SMPD3 -0.027 0.13 0.19 3 -0.31 111 114
TNF 0 0.11 -10000 0 -0.48 40 40
PKC zeta/PAR4 0.039 0.032 -10000 0 -0.34 5 5
mol:PHOSPHOCHOLINE 0.028 0.084 0.21 128 -0.16 8 136
NF kappa B1/RelA/I kappa B alpha 0.075 0.04 -10000 0 -0.26 6 6
AIFM1 0.012 0.057 0.16 51 -0.19 14 65
BCL2 -0.018 0.14 -10000 0 -0.48 74 74
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.034 0.014 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.028 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.011 0.084 -10000 0 -0.48 23 23
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.026 0.01 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.002 0.065 -10000 0 -0.23 54 54
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.024 0.043 -10000 0 -0.48 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 0.026 0.009 -10000 0 -10000 0 0
FYN 0.026 0.027 -10000 0 -0.48 2 2
MAP3K12 0.023 0.056 -10000 0 -0.48 10 10
FGR 0.025 0.037 -10000 0 -0.48 4 4
p38 alpha/TAB1 -0.056 0.12 -10000 0 -0.35 81 81
PRKG1 -0.009 0.13 -10000 0 -0.48 61 61
DUSP8 0.023 0.053 -10000 0 -0.48 9 9
PGK/cGMP/p38 alpha -0.032 0.15 0.17 7 -0.36 92 99
apoptosis -0.054 0.11 -10000 0 -0.34 81 81
RAL/GTP 0.038 0.008 -10000 0 -10000 0 0
LYN 0.023 0.028 -10000 0 -0.48 2 2
DUSP1 0.011 0.087 -10000 0 -0.48 25 25
PAK1 0.024 0.027 -10000 0 -0.48 2 2
SRC 0.027 0.026 -10000 0 -0.48 2 2
RAC1/OSM/MEKK3/MKK3 0.062 0.029 -10000 0 -10000 0 0
TRAF6 0.029 0.005 -10000 0 -10000 0 0
RAC1 0.029 0.005 -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 0.029 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.037 0.01 -10000 0 -10000 0 0
MAPK11 -0.026 0.15 0.25 14 -0.42 60 74
BLK -0.03 0.14 -10000 0 -0.48 67 67
HCK 0.024 0.041 -10000 0 -0.48 5 5
MAP2K3 0.027 0.008 -10000 0 -10000 0 0
DUSP16 0.028 0.006 -10000 0 -10000 0 0
DUSP10 0.017 0.059 -10000 0 -0.48 11 11
TRAF6/MEKK3 0.033 0.013 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.023 0.15 0.22 14 -0.39 77 91
positive regulation of innate immune response -0.029 0.17 0.28 14 -0.46 70 84
LCK -0.017 0.14 -10000 0 -0.48 68 68
p38alpha-beta/MKP7 -0.017 0.17 0.28 12 -0.46 60 72
p38alpha-beta/MKP5 -0.019 0.16 0.25 10 -0.45 62 72
PGK/cGMP -0.006 0.095 -10000 0 -0.34 61 61
PAK2 0.028 0.005 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.023 0.18 0.29 11 -0.46 67 78
CDC42 0.028 0.006 -10000 0 -10000 0 0
RALB 0.029 0.004 -10000 0 -10000 0 0
RALA 0.029 0.005 -10000 0 -10000 0 0
PAK3 -0.015 0.13 -10000 0 -0.48 60 60
IL2 signaling events mediated by STAT5

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
GAB2 0.025 0.027 -10000 0 -0.48 2 2
ELF1 -0.005 0.11 -10000 0 -0.36 72 72
CCNA2 0.014 0.084 -10000 0 -0.48 23 23
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
JAK3 0.015 0.079 -10000 0 -0.48 20 20
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
JAK1 0.029 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.007 0.18 0.24 4 -0.56 60 64
SHC1 0.025 0.011 -10000 0 -10000 0 0
SP1 0.032 0.032 -10000 0 -0.34 6 6
IL2RA -0.055 0.22 -10000 0 -0.71 79 79
IL2RB 0.009 0.086 -10000 0 -0.48 24 24
SOS1 0.029 0.003 -10000 0 -10000 0 0
IL2RG 0.003 0.11 -10000 0 -0.48 37 37
G1/S transition of mitotic cell cycle -0.007 0.15 -10000 0 -0.52 44 44
PTPN11 0.03 0.003 -10000 0 -10000 0 0
CCND2 0.012 0.067 -10000 0 -0.7 7 7
LCK -0.017 0.14 -10000 0 -0.48 68 68
GRB2 0.028 0.008 -10000 0 -10000 0 0
IL2 0.022 0.013 -10000 0 -10000 0 0
CDK6 0.017 0.065 -10000 0 -0.48 13 13
CCND3 0 0.16 0.41 3 -0.61 29 32
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.011 0.19 -10000 0 -0.9 28 28
NCK1/PAK1/Dok-R -0.025 0.082 -10000 0 -0.42 27 27
NCK1/Dok-R 0.01 0.21 -10000 0 -1 26 26
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
mol:beta2-estradiol -0.002 0.032 0.23 15 -10000 0 15
RELA 0.029 0.004 -10000 0 -10000 0 0
SHC1 0.025 0.011 -10000 0 -10000 0 0
Rac/GDP 0.021 0.003 -10000 0 -10000 0 0
F2 -0.005 0.043 0.26 14 -10000 0 14
TNIP2 0.028 0.006 -10000 0 -10000 0 0
NF kappa B/RelA 0.031 0.2 -10000 0 -0.97 26 26
FN1 0.005 0.11 -10000 0 -0.48 38 38
PLD2 -0.005 0.2 -10000 0 -1.1 26 26
PTPN11 0.029 0.003 -10000 0 -10000 0 0
GRB14 -0.081 0.19 -10000 0 -0.48 150 150
ELK1 0 0.19 -10000 0 -0.95 27 27
GRB7 0.022 0.036 -10000 0 -0.48 4 4
PAK1 0.024 0.027 -10000 0 -0.48 2 2
Tie2/Ang1/alpha5/beta1 Integrin 0.02 0.22 -10000 0 -1.1 26 26
CDKN1A 0.003 0.16 -10000 0 -0.68 30 30
ITGA5 0.028 0.025 -10000 0 -0.48 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.009 0.21 -10000 0 -1 26 26
CRK 0.027 0.009 -10000 0 -10000 0 0
mol:NO 0.017 0.14 0.35 1 -0.65 29 30
PLG -0.004 0.2 -10000 0 -1.1 26 26
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.004 0.18 -10000 0 -0.85 28 28
GRB2 0.027 0.008 -10000 0 -10000 0 0
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
ANGPT2 -0.04 0.18 -10000 0 -0.76 25 25
BMX -0.029 0.22 -10000 0 -1.1 26 26
ANGPT1 -0.015 0.18 -10000 0 -1.3 15 15
tube development -0.002 0.16 -10000 0 -0.71 30 30
ANGPT4 0.021 0.02 -10000 0 -10000 0 0
response to hypoxia -0.001 0.013 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.04 0.24 -10000 0 -1.1 26 26
alpha5/beta1 Integrin 0.041 0.021 -10000 0 -0.34 2 2
FGF2 0.005 0.091 -10000 0 -0.48 27 27
STAT5A (dimer) 0.004 0.19 -10000 0 -0.82 31 31
mol:L-citrulline 0.017 0.14 0.35 1 -0.65 29 30
AGTR1 -0.03 0.14 -10000 0 -0.48 68 68
MAPK14 -0.003 0.23 -10000 0 -1.1 28 28
Tie2/SHP2 -0.001 0.19 -10000 0 -0.96 21 21
TEK -0.001 0.19 -10000 0 -0.98 24 24
RPS6KB1 0.025 0.19 -10000 0 -0.85 28 28
Angiotensin II/AT1 -0.018 0.099 -10000 0 -0.34 68 68
Tie2/Ang1/GRB2 0.006 0.21 -10000 0 -1.1 26 26
MAPK3 0.001 0.19 -10000 0 -0.98 26 26
MAPK1 -0.007 0.19 -10000 0 -0.99 26 26
Tie2/Ang1/GRB7 0.002 0.22 -10000 0 -1.1 26 26
NFKB1 0.028 0.018 -10000 0 -0.48 1 1
MAPK8 -0.007 0.2 -10000 0 -1.1 26 26
PI3K 0.006 0.21 -10000 0 -1 28 28
FES -0.009 0.24 -10000 0 -1.1 31 31
Crk/Dok-R 0.009 0.21 -10000 0 -1 26 26
Tie2/Ang1/ABIN2 0.007 0.22 -10000 0 -1.1 26 26
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.014 0.17 -10000 0 -0.79 29 29
STAT5A 0.025 0.04 -10000 0 -0.48 5 5
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.039 0.19 0.43 1 -0.83 28 29
Tie2/Ang2 -0.013 0.21 -10000 0 -0.99 30 30
Tie2/Ang1 -0.003 0.22 -10000 0 -1.2 26 26
FOXO1 0.017 0.17 0.43 1 -0.78 30 31
ELF1 0.03 0.023 -10000 0 -10000 0 0
ELF2 -0.002 0.2 -10000 0 -1.1 26 26
mol:Choline -0.003 0.19 -10000 0 -1 26 26
cell migration -0.008 0.052 -10000 0 -0.23 30 30
FYN -0.006 0.18 -10000 0 -0.82 30 30
DOK2 0.012 0.071 -10000 0 -0.48 16 16
negative regulation of cell cycle 0.005 0.14 -10000 0 -0.6 31 31
ETS1 0.025 0.049 -10000 0 -0.32 13 13
PXN 0.043 0.17 0.41 1 -0.68 29 30
ITGB1 0.029 0.005 -10000 0 -10000 0 0
NOS3 0.014 0.16 -10000 0 -0.75 28 28
RAC1 0.029 0.005 -10000 0 -10000 0 0
TNF 0.001 0.12 -10000 0 -0.43 53 53
MAPKKK cascade -0.003 0.19 -10000 0 -1 26 26
RASA1 0.028 0.007 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.001 0.21 -10000 0 -1.1 26 26
NCK1 0.029 0.004 -10000 0 -10000 0 0
vasculogenesis 0.018 0.13 0.34 2 -0.58 29 31
mol:Phosphatidic acid -0.003 0.19 -10000 0 -1 26 26
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.017 0.14 0.35 1 -0.65 29 30
Rac1/GTP 0.019 0.17 -10000 0 -0.79 29 29
MMP2 -0.015 0.22 -10000 0 -1.1 27 27
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.005 0.13 -10000 0 -0.91 9 9
epithelial cell differentiation 0.02 0.11 -10000 0 -0.75 8 8
ITCH 0.038 0.021 -10000 0 -10000 0 0
WWP1 0.009 0.16 -10000 0 -1.4 7 7
FYN 0.026 0.027 -10000 0 -0.48 2 2
EGFR -0.018 0.14 -10000 0 -0.48 67 67
PRL 0.021 0.014 -10000 0 -10000 0 0
neuron projection morphogenesis 0.007 0.12 0.32 16 -0.69 7 23
PTPRZ1 -0.088 0.2 -10000 0 -0.48 161 161
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0 0.12 -10000 0 -0.56 14 14
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.028 0.13 -10000 0 -0.57 20 20
ADAM17 0.037 0.021 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.004 0.14 -10000 0 -0.98 9 9
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.013 0.14 -10000 0 -0.64 19 19
NCOR1 0.026 0.009 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.017 0.13 -10000 0 -0.56 19 19
GRIN2B -0.025 0.11 0.25 4 -0.52 18 22
ErbB4/ErbB2/betacellulin -0.006 0.13 -10000 0 -0.6 17 17
STAT1 0.028 0.008 -10000 0 -10000 0 0
HBEGF 0.027 0.026 -10000 0 -0.48 2 2
PRLR 0.008 0.1 -10000 0 -0.48 34 34
E4ICDs/ETO2 -0.025 0.16 -10000 0 -0.5 49 49
axon guidance 0.024 0.12 0.29 10 -0.88 8 18
NEDD4 0.03 0.056 -10000 0 -0.47 9 9
Prolactin receptor/Prolactin receptor/Prolactin 0.02 0.076 -10000 0 -0.35 32 32
CBFA2T3 -0.024 0.15 -10000 0 -0.48 77 77
ErbB4/ErbB2/HBEGF 0.012 0.11 -10000 0 -0.76 10 10
MAPK3 0.005 0.12 0.31 5 -0.53 13 18
STAT1 (dimer) 0.006 0.13 -10000 0 -0.95 8 8
MAPK1 0.008 0.13 0.35 9 -0.54 13 22
JAK2 0.027 0.019 -10000 0 -0.48 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.024 0.12 -10000 0 -0.55 20 20
NRG1 -0.018 0.099 -10000 0 -0.35 67 67
NRG3 -0.008 0.12 -10000 0 -0.48 45 45
NRG2 -0.017 0.12 -10000 0 -0.48 53 53
NRG4 0.023 0.034 -10000 0 -0.48 3 3
heart development 0.024 0.12 0.29 10 -0.88 8 18
neural crest cell migration -0.024 0.12 -10000 0 -0.54 20 20
ERBB2 0.012 0.037 -10000 0 -0.34 8 8
WWOX/E4ICDs 0 0.13 -10000 0 -0.85 10 10
SHC1 0.024 0.011 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.008 0.14 -10000 0 -0.68 14 14
apoptosis 0.023 0.15 0.54 41 -10000 0 41
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.015 0.14 -10000 0 -0.63 19 19
ErbB4/ErbB2/epiregulin -0.01 0.12 -10000 0 -0.6 16 16
ErbB4/ErbB4/betacellulin/betacellulin -0.018 0.15 -10000 0 -0.6 22 22
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.025 0.14 -10000 0 -0.5 29 29
MDM2 -0.002 0.13 0.28 22 -0.91 9 31
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.016 0.12 -10000 0 -0.52 19 19
STAT5A 0.025 0.12 0.39 3 -0.9 7 10
ErbB4/EGFR/neuregulin 1 beta -0.037 0.15 -10000 0 -0.49 46 46
DLG4 0.026 0.02 -10000 0 -0.48 1 1
GRB2/SHC 0.034 0.018 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.001 0.12 -10000 0 -0.86 9 9
STAT5A (dimer) 0.037 0.13 0.38 1 -0.85 8 9
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.039 0.12 -10000 0 -0.9 7 7
LRIG1 0.026 0.031 -10000 0 -0.48 3 3
EREG -0.025 0.13 -10000 0 -0.48 63 63
BTC -0.013 0.14 -10000 0 -0.48 65 65
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.019 0.12 0.29 10 -0.9 8 18
ERBB4 -0.02 0.13 -10000 0 -0.99 9 9
STAT5B 0.026 0.036 -10000 0 -0.48 4 4
YAP1 -0.015 0.12 -10000 0 -0.47 39 39
GRB2 0.027 0.008 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.01 0.11 -10000 0 -0.69 12 12
glial cell differentiation -0.001 0.12 0.85 9 -10000 0 9
WWOX 0.023 0.023 -10000 0 -0.48 1 1
cell proliferation -0.011 0.15 0.32 7 -0.62 19 26
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.04 0.083 -10000 0 -0.24 60 60
positive regulation of NF-kappaB transcription factor activity 0 0.002 -10000 0 -10000 0 0
CRKL 0.027 0.019 -10000 0 -0.48 1 1
STAT1 (dimer)/Cbp/p300 0.031 0.08 0.28 1 -0.37 2 3
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.045 0.038 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.01 0.069 -10000 0 -0.24 18 18
CaM/Ca2+ 0.042 0.081 -10000 0 -0.23 58 58
RAP1A 0.029 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.013 0.077 -10000 0 -0.23 55 55
AKT1 -0.011 0.078 0.29 8 -10000 0 8
MAP2K1 -0.018 0.069 0.27 2 -0.27 2 4
MAP3K11 -0.005 0.073 0.27 2 -0.23 56 58
IFNGR1 0.025 0.019 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.037 0.15 -10000 0 -0.44 52 52
Rap1/GTP -0.003 0.057 -10000 0 -0.23 1 1
CRKL/C3G 0.04 0.017 -10000 0 -0.34 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.048 0.091 -10000 0 -0.25 61 61
CEBPB 0.003 0.12 -10000 0 -0.52 14 14
STAT3 0.027 0.019 -10000 0 -0.48 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.009 0.23 -10000 0 -1 33 33
STAT1 -0.003 0.074 0.27 2 -0.23 49 51
CALM1 0.029 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.022 0.13 -10000 0 -0.48 63 63
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.014 0.077 0.28 2 -0.29 1 3
CEBPB/PTGES2/Cbp/p300 0.015 0.087 -10000 0 -0.43 8 8
mol:Ca2+ 0.037 0.081 -10000 0 -0.23 60 60
MAPK3 -0.001 0.11 -10000 0 -0.64 13 13
STAT1 (dimer) -0.006 0.094 -10000 0 -0.32 17 17
MAPK1 -0.03 0.18 -10000 0 -0.7 47 47
JAK2 0.023 0.026 -10000 0 -0.45 1 1
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
JAK1 0.025 0.019 -10000 0 -10000 0 0
CAMK2D 0.022 0.056 -10000 0 -0.48 10 10
DAPK1 0.007 0.1 0.27 1 -0.5 13 14
SMAD7 0 0.045 0.16 5 -0.22 2 7
CBL/CRKL/C3G 0.026 0.076 0.28 2 -0.22 44 46
PI3K 0.037 0.08 -10000 0 -0.24 2 2
IFNG -0.022 0.14 -10000 0 -0.48 63 63
apoptosis 0.004 0.096 0.25 1 -0.43 20 21
CAMK2G 0.029 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.027 0.019 -10000 0 -0.48 1 1
CAMK2A 0.006 0.1 -10000 0 -0.48 36 36
CAMK2B -0.049 0.17 -10000 0 -0.48 110 110
FRAP1 -0.012 0.072 0.27 8 -10000 0 8
PRKCD -0.011 0.079 0.29 9 -10000 0 9
RAP1B 0.028 0.006 -10000 0 -10000 0 0
negative regulation of cell growth -0.01 0.069 -10000 0 -0.24 18 18
PTPN2 0.028 0.006 -10000 0 -10000 0 0
EP300 0.028 0.007 -10000 0 -10000 0 0
IRF1 -0.009 0.094 0.28 7 -0.36 27 34
STAT1 (dimer)/PIASy 0.014 0.079 0.27 2 -0.29 1 3
SOCS1 -0.025 0.26 -10000 0 -1.3 33 33
mol:GDP 0.023 0.073 0.26 2 -0.21 46 48
CASP1 -0.001 0.051 0.2 7 -0.25 9 16
PTGES2 0.029 0.004 -10000 0 -10000 0 0
IRF9 0.019 0.051 0.2 6 -0.27 4 10
mol:PI-3-4-5-P3 0.024 0.072 -10000 0 -0.22 48 48
RAP1/GDP 0.022 0.065 -10000 0 -0.23 1 1
CBL -0.006 0.072 0.27 2 -0.23 53 55
MAP3K1 -0.005 0.073 0.27 2 -0.23 50 52
PIAS1 0.029 0.005 -10000 0 -10000 0 0
PIAS4 0.029 0.005 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.01 0.069 -10000 0 -0.24 18 18
PTPN11 0 0.078 0.29 2 -0.24 58 60
CREBBP 0.027 0.019 -10000 0 -0.48 1 1
RAPGEF1 0.029 0.005 -10000 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.018 0.048 0.28 4 -0.24 9 13
DAPP1 -0.036 0.15 0.32 2 -0.44 68 70
Src family/SYK family/BLNK-LAT/BTK-ITK -0.068 0.22 -10000 0 -0.6 93 93
mol:DAG -0.02 0.099 0.24 17 -0.26 67 84
HRAS 0.026 0.036 -10000 0 -0.48 4 4
RAP1A 0.029 0.008 -10000 0 -10000 0 0
ARF5/GDP 0.016 0.088 0.27 1 -0.34 24 25
PLCG2 0.023 0.023 -10000 0 -0.48 1 1
PLCG1 0.028 0.006 -10000 0 -10000 0 0
ARF5 0.029 0.006 -10000 0 -10000 0 0
mol:GTP -0.014 0.048 0.31 6 -0.24 8 14
ARF1/GTP -0.003 0.044 0.26 6 -0.23 5 11
RHOA 0.028 0.006 -10000 0 -10000 0 0
YES1 0.024 0.043 -10000 0 -0.48 6 6
RAP1A/GTP -0.015 0.042 0.16 33 -0.24 8 41
ADAP1 -0.026 0.062 0.29 3 -0.26 37 40
ARAP3 -0.014 0.047 0.31 6 -0.24 8 14
INPPL1 0.027 0.008 -10000 0 -10000 0 0
PREX1 -0.003 0.12 -10000 0 -0.48 48 48
ARHGEF6 0.025 0.04 -10000 0 -0.48 5 5
ARHGEF7 0.027 0.008 -10000 0 -10000 0 0
ARF1 0.024 0.011 -10000 0 -10000 0 0
NRAS 0.026 0.039 -10000 0 -0.47 5 5
FYN 0.026 0.027 -10000 0 -0.48 2 2
ARF6 0.029 0.005 -10000 0 -10000 0 0
FGR 0.025 0.037 -10000 0 -0.48 4 4
mol:Ca2+ -0.009 0.055 0.19 13 -0.15 9 22
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.022 0.058 -10000 0 -0.48 11 11
ZAP70 -0.018 0.14 -10000 0 -0.48 65 65
mol:IP3 -0.017 0.073 0.19 19 -0.19 58 77
LYN 0.023 0.028 -10000 0 -0.48 2 2
ARF1/GDP 0.013 0.084 0.3 2 -0.34 23 25
RhoA/GDP 0.028 0.061 0.21 7 -0.25 6 13
PDK1/Src/Hsp90 0.05 0.027 -10000 0 -0.3 2 2
BLNK 0.019 0.07 -10000 0 -0.48 16 16
actin cytoskeleton reorganization 0.003 0.091 0.34 7 -0.4 14 21
SRC 0.027 0.026 -10000 0 -0.48 2 2
PLEKHA2 -0.01 0.023 -10000 0 -0.3 5 5
RAC1 0.029 0.005 -10000 0 -10000 0 0
PTEN 0.026 0.031 -10000 0 -0.45 3 3
HSP90AA1 0.028 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.017 0.046 0.28 5 -10000 0 5
RhoA/GTP -0.014 0.049 0.18 30 -0.23 8 38
Src family/SYK family/BLNK-LAT -0.047 0.19 -10000 0 -0.54 79 79
BLK -0.03 0.14 -10000 0 -0.48 67 67
PDPK1 0.027 0.008 -10000 0 -10000 0 0
CYTH1 -0.014 0.047 0.29 6 -0.24 6 12
HCK 0.024 0.041 -10000 0 -0.48 5 5
CYTH3 -0.017 0.046 0.26 4 -0.24 10 14
CYTH2 -0.016 0.045 0.27 5 -0.24 6 11
KRAS 0.028 0.009 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.015 0.052 0.32 1 -0.41 6 7
SGK1 0.009 0.074 -10000 0 -0.34 26 26
INPP5D 0.026 0.032 -10000 0 -0.48 3 3
mol:GDP 0.001 0.088 0.27 3 -0.35 25 28
SOS1 0.029 0.003 -10000 0 -10000 0 0
SYK 0.021 0.063 -10000 0 -0.48 13 13
ARF6/GDP 0.015 0.063 0.32 8 -0.29 2 10
mol:PI-3-4-5-P3 -0.015 0.041 0.26 4 -0.24 8 12
ARAP3/RAP1A/GTP -0.015 0.043 0.16 33 -0.24 8 41
VAV1 0.017 0.076 -10000 0 -0.48 19 19
mol:PI-3-4-P2 0.011 0.019 -10000 0 -0.34 2 2
RAS family/GTP/PI3K Class I 0.039 0.04 -10000 0 -0.24 8 8
PLEKHA1 -0.011 0.02 -10000 0 -0.3 4 4
Rac1/GDP 0.016 0.087 0.27 1 -0.33 24 25
LAT 0.014 0.077 -10000 0 -0.48 19 19
Rac1/GTP 0.002 0.094 -10000 0 -0.41 27 27
ITK -0.036 0.078 0.32 5 -0.25 71 76
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.034 0.13 0.29 13 -0.37 70 83
LCK -0.017 0.14 -10000 0 -0.48 68 68
BTK -0.019 0.054 0.32 5 -0.25 17 22
TCGA08_retinoblastoma

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
CDKN2B 0.026 0.017 -10000 0 -10000 0 0
CDKN2C 0.026 0.029 -10000 0 -0.45 2 2
CDKN2A 0.012 0.064 -10000 0 -0.46 12 12
CCND2 -0.003 0.023 0.16 13 -0.12 4 17
RB1 -0.002 0.042 0.23 3 -0.22 23 26
CDK4 0 0.034 0.21 18 -0.12 4 22
CDK6 -0.002 0.038 0.21 18 -0.15 14 32
G1/S progression 0.007 0.052 0.19 47 -0.24 4 51
Insulin Pathway

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
CBL/APS/CAP 0.022 0.084 -10000 0 -0.25 67 67
TC10/GTP 0.04 0.048 -10000 0 -0.23 20 20
Insulin Receptor/Insulin/IRS1/Shp2 0.037 0.081 -10000 0 -0.27 51 51
HRAS 0.026 0.036 -10000 0 -0.48 4 4
APS homodimer 0.023 0.048 -10000 0 -0.48 7 7
GRB14 -0.081 0.19 -10000 0 -0.48 150 150
FOXO3 -0.023 0.16 -10000 0 -0.62 56 56
AKT1 -0.045 0.12 0.31 5 -0.4 13 18
INSR 0.032 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.052 0.038 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.028 0.018 -10000 0 -0.48 1 1
SORBS1 0.02 0.064 -10000 0 -0.48 13 13
CRK 0.027 0.009 -10000 0 -10000 0 0
PTPN1 0.009 0.017 -10000 0 -10000 0 0
CAV1 -0.001 0.069 0.18 3 -0.25 56 59
CBL/APS/CAP/Crk-II/C3G 0.065 0.06 -10000 0 -0.25 20 20
Insulin Receptor/Insulin/IRS1/NCK2 0.037 0.08 -10000 0 -0.27 50 50
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.029 0.068 -10000 0 -0.24 47 47
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.012 0.068 -10000 0 -0.32 12 12
RPS6KB1 -0.039 0.1 0.3 5 -0.39 9 14
PARD6A 0.022 0.044 -10000 0 -0.48 6 6
CBL 0.026 0.009 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.013 0.064 -10000 0 -0.66 7 7
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.022 0.1 -10000 0 -0.36 10 10
HRAS/GTP 0.001 0.052 -10000 0 -0.22 34 34
Insulin Receptor 0.032 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.039 0.072 -10000 0 -0.26 35 35
PRKCI 0.01 0.065 -10000 0 -0.46 5 5
Insulin Receptor/Insulin/GRB14/PDK1 -0.042 0.11 -10000 0 -0.25 160 160
SHC1 0.024 0.011 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.047 0.06 -10000 0 -0.57 7 7
PI3K 0.038 0.072 -10000 0 -0.24 47 47
NCK2 0.028 0.018 -10000 0 -0.48 1 1
RHOQ 0.029 0.003 -10000 0 -10000 0 0
mol:H2O2 0 0.002 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.026 -10000 0 -0.34 4 4
AKT2 -0.045 0.12 0.3 4 -0.4 13 17
PRKCZ -0.001 0.096 -10000 0 -0.48 17 17
SH2B2 0.023 0.048 -10000 0 -0.48 7 7
SHC/SHIP 0.015 0.063 -10000 0 -0.24 41 41
F2RL2 -0.026 0.16 -10000 0 -0.48 87 87
TRIP10 0.028 0.025 -10000 0 -0.48 2 2
Insulin Receptor/Insulin/Shc 0.033 0.018 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.038 0.018 -10000 0 -0.29 2 2
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.055 0.033 -10000 0 -10000 0 0
RAPGEF1 0.029 0.005 -10000 0 -10000 0 0
RASA1 0.028 0.007 -10000 0 -10000 0 0
NCK1 0.029 0.004 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.055 0.058 -10000 0 -0.26 20 20
TC10/GDP 0.021 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.048 0.026 -10000 0 -10000 0 0
INPP5D 0 0.069 0.18 3 -0.25 54 57
SOS1 0.029 0.003 -10000 0 -10000 0 0
SGK1 -0.017 0.14 -10000 0 -0.71 32 32
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.029 0.003 -10000 0 -10000 0 0
IRS1 -0.003 0.12 -10000 0 -0.48 52 52
p62DOK/RasGAP 0.047 0.061 -10000 0 -0.58 7 7
INS 0.002 0.006 -10000 0 -10000 0 0
mol:PI-3-4-P2 0 0.068 0.18 3 -0.25 54 57
GRB2 0.027 0.008 -10000 0 -10000 0 0
EIF4EBP1 -0.044 0.099 0.27 3 -0.38 13 16
PTPRA 0.031 0.008 -10000 0 -10000 0 0
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.038 0.018 -10000 0 -0.29 2 2
PDPK1 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.008 0.056 -10000 0 -0.23 34 34
Insulin Receptor/Insulin/IRS1 0.02 0.075 -10000 0 -0.27 51 51
Insulin Receptor/Insulin/IRS3 0.025 0.011 -10000 0 -10000 0 0
Par3/Par6 0.021 0.1 -10000 0 -0.26 93 93
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.018 0.12 -10000 0 -0.42 3 3
CRKL 0.003 0.06 0.29 5 -0.23 10 15
mol:DAG 0.013 0.064 0.24 2 -0.3 12 14
HRAS 0.017 0.09 0.3 22 -10000 0 22
MAPK8 0.023 0.072 0.18 96 -0.24 13 109
RAP1A 0.003 0.06 0.29 5 -0.22 11 16
GAB1 0.003 0.061 0.3 4 -0.24 11 15
MAPK14 0.022 0.071 0.18 92 -0.25 12 104
EPO 0.006 0.062 -10000 0 -0.48 9 9
PLCG1 0.013 0.065 0.24 2 -0.3 12 14
EPOR/TRPC2/IP3 Receptors 0.021 0.046 -10000 0 -0.46 6 6
RAPGEF1 0.029 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.038 0.06 -10000 0 -0.29 19 19
GAB1/SHC/GRB2/SOS1 0.032 0.058 0.28 3 -0.25 1 4
EPO/EPOR (dimer) 0.028 0.058 -10000 0 -0.34 15 15
IRS2 -0.002 0.066 0.29 4 -0.26 20 24
STAT1 0.01 0.085 0.25 2 -0.31 13 15
STAT5B 0.01 0.079 0.25 2 -0.32 15 17
cell proliferation 0.008 0.076 0.18 110 -0.24 10 120
GAB1/SHIP/PIK3R1/SHP2/SHC 0.026 0.054 -10000 0 -0.24 1 1
TEC 0.001 0.062 0.29 4 -0.23 16 20
SOCS3 0.023 0.041 -10000 0 -0.48 5 5
STAT1 (dimer) 0.01 0.084 0.25 2 -0.3 13 15
JAK2 0.024 0.025 -10000 0 -0.48 1 1
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.056 0.074 -10000 0 -0.23 13 13
EPO/EPOR 0.028 0.058 -10000 0 -0.34 15 15
LYN 0.02 0.031 -10000 0 -0.48 2 2
TEC/VAV2 0.019 0.064 0.28 3 -0.22 16 19
elevation of cytosolic calcium ion concentration 0.021 0.046 -10000 0 -0.46 6 6
SHC1 0.024 0.011 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.039 0.058 -10000 0 -0.28 14 14
mol:IP3 0.013 0.064 0.24 2 -0.3 12 14
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.025 0.071 0.3 2 -0.3 9 11
SH2B3 0.026 0.018 -10000 0 -10000 0 0
NFKB1 0.021 0.073 0.19 90 -0.26 14 104
EPO/EPOR (dimer)/JAK2/SOCS3 0.009 0.048 -10000 0 -0.24 21 21
PTPN6 0 0.055 0.3 1 -0.23 13 14
TEC/VAV2/GRB2 0.03 0.066 0.28 4 -0.23 5 9
EPOR 0.021 0.046 -10000 0 -0.47 6 6
INPP5D 0.026 0.032 -10000 0 -0.48 3 3
mol:GDP 0.031 0.058 0.28 3 -0.26 1 4
SOS1 0.029 0.003 -10000 0 -10000 0 0
PLCG2 0.023 0.023 -10000 0 -0.48 1 1
CRKL/CBL/C3G 0.03 0.064 0.28 4 -0.22 9 13
VAV2 0.004 0.06 0.29 5 -0.22 11 16
CBL 0.002 0.059 0.3 4 -0.23 10 14
SHC/Grb2/SOS1 0.025 0.052 -10000 0 -0.22 8 8
STAT5A 0.009 0.08 0.25 2 -0.31 17 19
GRB2 0.027 0.008 -10000 0 -10000 0 0
STAT5 (dimer) 0.015 0.12 -10000 0 -0.33 54 54
LYN/PLCgamma2 0.029 0.031 -10000 0 -0.34 3 3
PTPN11 0.029 0.003 -10000 0 -10000 0 0
BTK -0.001 0.065 0.3 4 -0.24 21 25
BCL2 -0.036 0.27 -10000 0 -0.82 81 81
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.029 0.005 -10000 0 -10000 0 0
mol:PIP3 -0.01 0.073 0.24 1 -0.28 50 51
FRAP1 -0.001 0.081 0.26 1 -0.47 18 19
AKT1 -0.01 0.069 0.18 7 -0.25 36 43
INSR 0.029 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.019 0.003 -10000 0 -10000 0 0
mol:GTP 0.024 0.069 0.23 2 -0.3 2 4
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.004 0.036 -10000 0 -0.2 4 4
TSC2 0.027 0.008 -10000 0 -10000 0 0
RHEB/GDP 0.013 0.052 -10000 0 -0.26 2 2
TSC1 0.029 0.005 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.001 0.091 -10000 0 -0.3 64 64
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.019 0.047 -10000 0 -0.22 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.028 0.005 -10000 0 -10000 0 0
RPS6KB1 0.01 0.073 0.26 5 -0.31 16 21
MAP3K5 0.001 0.045 0.19 8 -0.19 34 42
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
apoptosis 0.001 0.044 0.19 8 -0.19 34 42
mol:LY294002 0 0 -10000 0 -0.001 60 60
EIF4B 0.009 0.067 0.24 5 -0.29 12 17
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.032 0.066 0.23 2 -0.27 12 14
eIF4E/eIF4G1/eIF4A1 0.008 0.052 -10000 0 -0.28 18 18
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.018 0.088 -10000 0 -0.29 55 55
mTOR/RHEB/GTP/Raptor/GBL 0.018 0.052 0.15 52 -0.19 2 54
FKBP1A 0.029 0.006 -10000 0 -10000 0 0
RHEB/GTP 0.03 0.062 0.21 2 -0.26 2 4
mol:Amino Acids 0 0 -10000 0 -0.001 60 60
FKBP12/Rapamycin 0.021 0.005 -10000 0 -10000 0 0
PDPK1 -0.019 0.071 0.17 6 -0.26 46 52
EIF4E 0.029 0.005 -10000 0 -10000 0 0
ASK1/PP5C 0.001 0.14 -10000 0 -0.52 49 49
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.005 0.05 -10000 0 -0.24 5 5
TSC1/TSC2 0.027 0.075 0.25 4 -0.32 2 6
tumor necrosis factor receptor activity 0 0 0.001 60 -10000 0 60
RPS6 0.028 0.006 -10000 0 -10000 0 0
PPP5C 0.029 0.004 -10000 0 -10000 0 0
EIF4G1 0.028 0.005 -10000 0 -10000 0 0
IRS1 -0.018 0.092 -10000 0 -0.32 66 66
INS 0 0 -10000 0 -10000 0 0
PTEN 0.026 0.031 -10000 0 -0.48 3 3
PDK2 -0.016 0.068 0.16 30 -0.26 41 71
EIF4EBP1 -0.042 0.24 -10000 0 -1.1 42 42
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
PPP2R5D 0 0.078 0.29 4 -0.42 18 22
peptide biosynthetic process 0.016 0.011 0.18 3 -10000 0 3
RHEB 0.029 0.005 -10000 0 -10000 0 0
EIF4A1 0.026 0.009 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 48 -0.002 4 52
EEF2 0.016 0.011 0.18 3 -10000 0 3
eIF4E/4E-BP1 -0.026 0.23 -10000 0 -1 42 42
TCGA08_p53

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
CDKN2A -0.003 0.043 -10000 0 -0.34 12 12
TP53 -0.002 0.039 -10000 0 -0.21 24 24
Senescence -0.003 0.042 -10000 0 -0.2 31 31
Apoptosis -0.003 0.042 -10000 0 -0.2 31 31
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.008 0.061 0.27 41 -10000 0 41
MDM4 0.024 0.011 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.028 0.018 -10000 0 -0.48 1 1
HDAC2 0.027 0.008 -10000 0 -10000 0 0
GNB1/GNG2 0.041 0.069 -10000 0 -0.29 32 32
forebrain development -0.035 0.2 0.34 1 -0.55 84 85
GNAO1 -0.002 0.1 -10000 0 -0.48 33 33
SMO/beta Arrestin2 0.024 0.074 -10000 0 -0.34 31 31
SMO 0.008 0.097 -10000 0 -0.48 31 31
ARRB2 0.026 0.01 -10000 0 -10000 0 0
GLI3/SPOP 0.022 0.1 0.27 1 -0.44 17 18
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.029 0.004 -10000 0 -10000 0 0
GNAI2 0.028 0.008 -10000 0 -10000 0 0
SIN3/HDAC complex 0.063 0.041 -10000 0 -0.26 8 8
GNAI1 0.024 0.044 -10000 0 -0.48 6 6
XPO1 0.028 0.011 -10000 0 -10000 0 0
GLI1/Su(fu) -0.031 0.19 -10000 0 -0.64 52 52
SAP30 0.023 0.05 -10000 0 -0.48 8 8
mol:GDP 0.008 0.097 -10000 0 -0.48 31 31
MIM/GLI2A 0.016 0.054 -10000 0 -0.48 9 9
IFT88 0.027 0.008 -10000 0 -10000 0 0
GNAI3 0.029 0.006 -10000 0 -10000 0 0
GLI2 0.01 0.073 -10000 0 -0.3 21 21
GLI3 0.01 0.1 0.26 2 -0.45 19 21
CSNK1D 0.028 0.007 -10000 0 -10000 0 0
CSNK1E 0.028 0.007 -10000 0 -10000 0 0
SAP18 0.027 0.008 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.027 0.008 -10000 0 -10000 0 0
GNG2 0.028 0.019 -10000 0 -0.48 1 1
Gi family/GTP -0.009 0.1 -10000 0 -0.29 75 75
SIN3B 0.029 0.004 -10000 0 -10000 0 0
SIN3A 0.029 0.005 -10000 0 -10000 0 0
GLI3/Su(fu) 0.015 0.1 0.25 1 -0.41 30 31
GLI2/Su(fu) 0.011 0.096 -10000 0 -0.36 31 31
FOXA2 -0.005 0.098 -10000 0 -0.75 12 12
neural tube patterning -0.035 0.2 0.34 1 -0.55 84 85
SPOP 0.026 0.009 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.02 0.06 -10000 0 -0.33 5 5
GNB1 0.028 0.006 -10000 0 -10000 0 0
CSNK1G2 0.028 0.006 -10000 0 -10000 0 0
CSNK1G3 0.028 0.005 -10000 0 -10000 0 0
MTSS1 0.016 0.054 -10000 0 -0.48 9 9
embryonic limb morphogenesis -0.035 0.2 0.34 1 -0.55 84 85
SUFU 0.013 0.049 -10000 0 -0.28 10 10
LGALS3 0.017 0.076 -10000 0 -0.48 19 19
catabolic process 0.025 0.12 0.29 1 -0.5 21 22
GLI3A/CBP 0.003 0.096 -10000 0 -0.34 56 56
KIF3A 0.028 0.005 -10000 0 -10000 0 0
GLI1 -0.037 0.21 0.34 1 -0.56 84 85
RAB23 0.027 0.025 -10000 0 -0.48 2 2
CSNK1A1 0.029 0.004 -10000 0 -10000 0 0
IFT172 0.028 0.018 -10000 0 -0.48 1 1
RBBP7 0.028 0.009 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.015 0.077 -10000 0 -0.3 26 26
GNAZ 0.018 0.07 -10000 0 -0.48 16 16
RBBP4 0.028 0.005 -10000 0 -10000 0 0
CSNK1G1 0.028 0.005 -10000 0 -10000 0 0
PIAS1 0.029 0.005 -10000 0 -10000 0 0
PRKACA 0.029 0.004 -10000 0 -10000 0 0
GLI2/SPOP 0.02 0.077 -10000 0 -0.35 17 17
STK36 0.025 0.041 -10000 0 -0.48 5 5
Gi family/GNB1/GNG2/GDP -0.01 0.1 -10000 0 -0.4 30 30
PTCH1 -0.053 0.26 -10000 0 -1 43 43
MIM/GLI1 -0.027 0.19 0.33 1 -0.57 64 65
CREBBP 0.003 0.096 -10000 0 -0.34 56 56
Su(fu)/SIN3/HDAC complex 0.008 0.098 -10000 0 -0.4 33 33
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.009 0.11 -10000 0 -0.42 31 31
PDGFB-D/PDGFRB/SLAP 0.025 0.055 -10000 0 -0.35 15 15
PDGFB-D/PDGFRB/APS/CBL 0.044 0.057 -10000 0 -0.29 20 20
AKT1 0.017 0.099 0.33 28 -10000 0 28
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.011 0.12 0.31 1 -0.48 28 29
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
FGR -0.005 0.12 0.35 1 -0.47 40 41
mol:Ca2+ 0.007 0.12 0.27 4 -0.5 27 31
MYC 0.034 0.2 0.34 32 -0.74 33 65
SHC1 0.024 0.011 -10000 0 -10000 0 0
HRAS/GDP 0.033 0.057 -10000 0 -0.25 15 15
LRP1/PDGFRB/PDGFB 0.045 0.069 -10000 0 -0.36 21 21
GRB10 0.028 0.018 -10000 0 -0.48 1 1
PTPN11 0.029 0.003 -10000 0 -10000 0 0
GO:0007205 0.006 0.12 0.27 4 -0.5 27 31
PTEN 0.027 0.031 -10000 0 -0.48 3 3
GRB2 0.027 0.008 -10000 0 -10000 0 0
GRB7 0.022 0.036 -10000 0 -0.48 4 4
PDGFB-D/PDGFRB/SHP2 0.037 0.049 -10000 0 -0.35 13 13
PDGFB-D/PDGFRB/GRB10 0.036 0.051 -10000 0 -0.35 14 14
cell cycle arrest 0.025 0.055 -10000 0 -0.35 15 15
HRAS 0.026 0.036 -10000 0 -0.48 4 4
HIF1A 0.011 0.096 0.31 28 -0.36 3 31
GAB1 0.002 0.13 0.27 5 -0.49 30 35
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.004 0.12 0.3 7 -0.45 27 34
PDGFB-D/PDGFRB 0.046 0.05 -10000 0 -0.31 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.036 0.049 -10000 0 -0.35 13 13
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.006 0.1 -10000 0 -0.42 28 28
positive regulation of MAPKKK cascade 0.036 0.049 -10000 0 -0.35 13 13
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
mol:IP3 0.006 0.12 0.27 4 -0.51 27 31
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.028 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.029 0.057 -10000 0 -0.35 17 17
SHB 0.029 0.005 -10000 0 -10000 0 0
BLK -0.098 0.23 -10000 0 -0.48 188 188
PTPN2 0.029 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.036 0.049 -10000 0 -0.34 13 13
BCAR1 0.026 0.01 -10000 0 -10000 0 0
VAV2 0.003 0.14 0.27 7 -0.5 35 42
CBL 0.026 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.035 0.054 -10000 0 -0.35 16 16
LCK -0.042 0.19 0.35 1 -0.55 90 91
PDGFRB 0.021 0.064 -10000 0 -0.48 13 13
ACP1 0.029 0.004 -10000 0 -10000 0 0
HCK 0.012 0.085 -10000 0 -0.46 16 16
ABL1 -0.004 0.12 0.25 6 -0.44 35 41
PDGFB-D/PDGFRB/CBL -0.005 0.14 -10000 0 -0.54 36 36
PTPN1 0.026 0.012 -10000 0 -10000 0 0
SNX15 0.029 0.004 -10000 0 -10000 0 0
STAT3 0.027 0.019 -10000 0 -0.48 1 1
STAT1 0.028 0.008 -10000 0 -10000 0 0
cell proliferation 0.036 0.18 0.32 41 -0.63 35 76
SLA 0.017 0.051 -10000 0 -0.48 8 8
actin cytoskeleton reorganization 0.035 0.06 0.33 2 -0.26 5 7
SRC 0.009 0.076 -10000 0 -0.49 10 10
PI3K -0.007 0.047 -10000 0 -0.25 10 10
PDGFB-D/PDGFRB/GRB7/SHC 0.034 0.054 -10000 0 -0.3 16 16
SH2B2 0.023 0.048 -10000 0 -0.48 7 7
PLCgamma1/SPHK1 0.011 0.12 0.32 1 -0.5 28 29
LYN 0.006 0.089 -10000 0 -0.5 16 16
LRP1 0.022 0.058 -10000 0 -0.48 11 11
SOS1 0.029 0.003 -10000 0 -10000 0 0
STAT5B 0.026 0.036 -10000 0 -0.48 4 4
STAT5A 0.025 0.04 -10000 0 -0.48 5 5
NCK1-2/p130 Cas 0.063 0.057 -10000 0 -0.25 13 13
SPHK1 0.016 0.075 -10000 0 -0.48 18 18
EDG1 0 0.003 -10000 0 -10000 0 0
mol:DAG 0.006 0.12 0.27 4 -0.51 27 31
PLCG1 0.006 0.12 0.27 4 -0.52 27 31
NHERF/PDGFRB 0.037 0.069 -10000 0 -0.3 29 29
YES1 -0.005 0.12 0.35 1 -0.5 39 40
cell migration 0.037 0.069 -10000 0 -0.3 29 29
SHC/Grb2/SOS1 0.055 0.057 -10000 0 -0.26 11 11
SLC9A3R2 0.024 0.04 -10000 0 -0.48 5 5
SLC9A3R1 0.019 0.063 -10000 0 -0.48 13 13
NHERF1-2/PDGFRB/PTEN 0.048 0.072 -10000 0 -0.28 31 31
FYN -0.006 0.12 0.34 1 -0.46 39 40
DOK1 0.02 0.062 0.18 15 -0.29 14 29
HRAS/GTP 0.019 0.026 -10000 0 -0.34 4 4
PDGFB 0.026 0.026 -10000 0 -0.48 2 2
RAC1 -0.001 0.15 0.29 4 -0.52 46 50
PRKCD 0.02 0.06 0.19 5 -0.28 12 17
FER 0.016 0.066 0.19 17 -0.28 20 37
MAPKKK cascade 0.035 0.1 0.35 30 -0.26 6 36
RASA1 0.019 0.06 0.19 6 -0.28 12 18
NCK1 0.029 0.004 -10000 0 -10000 0 0
NCK2 0.028 0.018 -10000 0 -0.48 1 1
p62DOK/Csk 0.036 0.056 -10000 0 -0.27 14 14
PDGFB-D/PDGFRB/SHB 0.036 0.049 -10000 0 -0.34 13 13
chemotaxis -0.004 0.12 0.25 6 -0.43 35 41
STAT1-3-5/STAT1-3-5 0.054 0.059 -10000 0 -0.27 19 19
Bovine Papilomavirus E5/PDGFRB 0.015 0.047 -10000 0 -0.35 13 13
PTPRJ 0.027 0.031 -10000 0 -0.48 3 3
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.028 0.12 0.89 1 -1.2 3 4
VDR 0.024 0.05 -10000 0 -0.48 8 8
FAM120B 0.027 0.007 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.012 0.081 -10000 0 -0.27 39 39
RXRs/LXRs/DNA/Oxysterols 0.019 0.12 -10000 0 -0.41 41 41
MED1 0.025 0.01 -10000 0 -10000 0 0
mol:9cRA 0 0.015 -10000 0 -0.18 1 1
RARs/THRs/DNA/Src-1 0.009 0.077 -10000 0 -0.27 44 44
RXRs/NUR77 0.049 0.074 -10000 0 -0.28 24 24
RXRs/PPAR 0.013 0.057 -10000 0 -0.33 4 4
NCOR2 0.029 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.036 -10000 0 -0.34 8 8
RARs/VDR/DNA/Vit D3 0.053 0.059 -10000 0 -0.28 21 21
RARA 0.021 0.056 -10000 0 -0.48 10 10
NCOA1 0.028 0.018 -10000 0 -0.48 1 1
VDR/VDR/DNA 0.024 0.05 -10000 0 -0.48 8 8
RARs/RARs/DNA/9cRA 0.039 0.048 -10000 0 -0.26 16 16
RARG 0.029 0.003 -10000 0 -10000 0 0
RPS6KB1 0.06 0.16 0.55 82 -0.42 3 85
RARs/THRs/DNA/SMRT 0.01 0.073 -10000 0 -0.26 43 43
THRA 0.025 0.02 -10000 0 -0.48 1 1
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.018 0.036 -10000 0 -0.34 8 8
RXRs/PPAR/9cRA/PGJ2/DNA 0.037 0.072 0.3 3 -0.26 24 27
NR1H4 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.061 0.087 -10000 0 -0.25 21 21
NR1H2 0.027 0.022 -10000 0 -0.14 1 1
NR1H3 0.027 0.023 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.044 0.072 -10000 0 -0.26 28 28
NR4A1 0.022 0.036 -10000 0 -0.48 3 3
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.004 0.047 -10000 0 -0.2 27 27
RXRG 0.005 0.084 -10000 0 -0.48 22 22
RXR alpha/CCPG 0.038 0.022 -10000 0 -10000 0 0
RXRA 0.027 0.022 -10000 0 -0.14 1 1
RXRB 0.027 0.023 -10000 0 -10000 0 0
THRB 0.011 0.092 -10000 0 -0.48 28 28
PPARG 0.022 0.046 -10000 0 -0.48 6 6
PPARD 0.029 0.005 -10000 0 -10000 0 0
TNF -0.019 0.24 -10000 0 -1 42 42
mol:Oxysterols 0.001 0.013 -10000 0 -0.13 1 1
cholesterol transport 0.019 0.12 -10000 0 -0.41 41 41
PPARA 0.026 0.026 -10000 0 -0.48 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.024 0.045 -10000 0 -0.48 6 6
RXRs/NUR77/BCL2 -0.008 0.089 -10000 0 -0.26 78 78
SREBF1 0.011 0.12 -10000 0 -0.92 6 6
RXRs/RXRs/DNA/9cRA 0.037 0.072 0.3 3 -0.26 24 27
ABCA1 0.009 0.15 -10000 0 -0.69 19 19
RARs/THRs 0.057 0.083 -10000 0 -0.27 41 41
RXRs/FXR 0.037 0.063 -10000 0 -0.26 22 22
BCL2 -0.018 0.14 -10000 0 -0.48 74 74
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.029 0.004 -10000 0 -10000 0 0
SPHK1 0.015 0.075 -10000 0 -0.48 18 18
GNAI2 0.028 0.006 -10000 0 -10000 0 0
mol:S1P 0.008 0.043 -10000 0 -0.27 18 18
GNAO1 -0.002 0.1 -10000 0 -0.48 33 33
mol:Sphinganine-1-P 0.004 0.053 -10000 0 -0.34 18 18
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.054 0.053 -10000 0 -0.21 16 16
GNAI3 0.029 0.005 -10000 0 -10000 0 0
G12/G13 0.038 0.014 -10000 0 -10000 0 0
S1PR3 0.023 0.05 -10000 0 -0.48 8 8
S1PR2 0.029 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.002 0.042 -10000 0 -0.24 21 21
S1PR5 0.013 0.079 -10000 0 -0.48 20 20
S1PR4 -0.004 0.12 -10000 0 -0.48 46 46
GNAI1 0.024 0.044 -10000 0 -0.48 6 6
S1P/S1P5/G12 0.038 0.068 -10000 0 -0.24 33 33
S1P/S1P3/Gq 0.006 0.1 -10000 0 -0.31 62 62
S1P/S1P4/Gi -0.011 0.12 0.26 1 -0.32 80 81
GNAQ 0.025 0.043 -10000 0 -0.48 6 6
GNAZ 0.018 0.07 -10000 0 -0.48 16 16
GNA14 -0.003 0.12 -10000 0 -0.48 45 45
GNA15 0.021 0.059 -10000 0 -0.48 11 11
GNA12 0.028 0.005 -10000 0 -10000 0 0
GNA13 0.027 0.008 -10000 0 -10000 0 0
GNA11 0.026 0.036 -10000 0 -0.48 4 4
ABCC1 0.026 0.026 -10000 0 -0.48 2 2
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.029 0.005 -9999 0 -10000 0 0
ITGB7 0.012 0.087 -9999 0 -0.48 25 25
ITGA4 0.02 0.061 -9999 0 -0.48 12 12
alpha4/beta7 Integrin 0.023 0.082 -9999 0 -0.35 36 36
alpha4/beta1 Integrin 0.035 0.046 -9999 0 -0.34 11 11
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.003 0.097 0.36 27 -10000 0 27
GNAI2 0.028 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.027 0.053 -10000 0 -0.29 20 20
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.002 0.1 -10000 0 -0.48 33 33
RhoA/GTP -0.003 0.099 -10000 0 -0.37 27 27
negative regulation of cAMP metabolic process -0.008 0.096 -10000 0 -0.29 65 65
GNAZ 0.018 0.07 -10000 0 -0.48 16 16
GNAI3 0.029 0.005 -10000 0 -10000 0 0
GNA12 0.028 0.005 -10000 0 -10000 0 0
S1PR5 0.013 0.079 -10000 0 -0.48 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.008 0.097 -10000 0 -0.29 65 65
RhoA/GDP 0.021 0.004 -10000 0 -10000 0 0
RHOA 0.028 0.006 -10000 0 -10000 0 0
GNAI1 0.024 0.044 -10000 0 -0.48 6 6
TCGA08_rtk_signaling

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
PDGFRA 0.004 0.11 -10000 0 -0.48 40 40
HRAS 0.026 0.036 -10000 0 -0.48 4 4
EGFR -0.018 0.14 -10000 0 -0.48 67 67
AKT 0.024 0.092 0.29 6 -0.34 21 27
FOXO3 0.026 0.019 -10000 0 -0.48 1 1
AKT1 0.028 0.005 -10000 0 -10000 0 0
FOXO1 0.026 0.009 -10000 0 -10000 0 0
AKT3 0.018 0.051 -10000 0 -0.48 8 8
FOXO4 0.029 0.018 -10000 0 -0.48 1 1
MET -0.018 0.14 -10000 0 -0.48 71 71
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
PIK3CB 0.029 0.005 -10000 0 -10000 0 0
NRAS 0.026 0.04 -10000 0 -0.48 5 5
PIK3CG 0.01 0.094 -10000 0 -0.48 29 29
PIK3R3 0.026 0.036 -10000 0 -0.48 4 4
PIK3R2 0.029 0.004 -10000 0 -10000 0 0
NF1 0.028 0.007 -10000 0 -10000 0 0
RAS -0.005 0.095 0.16 1 -0.32 46 47
ERBB2 0.02 0.05 -10000 0 -0.48 8 8
proliferation/survival/translation -0.022 0.089 0.33 32 -0.26 3 35
PI3K 0.005 0.098 0.24 10 -0.3 48 58
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
KRAS 0.028 0.006 -10000 0 -10000 0 0
FOXO 0.059 0.053 0.21 17 -10000 0 17
AKT2 0.029 0.005 -10000 0 -10000 0 0
PTEN 0.027 0.031 -10000 0 -0.48 3 3
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.021 0.063 -9999 0 -0.48 13 13
mol:S1P 0 0.003 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.006 0.082 -9999 0 -0.25 65 65
GNAO1 -0.002 0.1 -9999 0 -0.48 33 33
S1P/S1P3/G12/G13 0.047 0.035 -9999 0 -0.26 6 6
AKT1 0.002 0.12 -9999 0 -0.57 30 30
AKT3 -0.005 0.16 -9999 0 -1.1 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.021 0.063 -9999 0 -0.48 13 13
GNAI2 0.028 0.01 -9999 0 -10000 0 0
GNAI3 0.029 0.009 -9999 0 -10000 0 0
GNAI1 0.024 0.046 -9999 0 -0.49 6 6
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.023 0.051 -9999 0 -0.48 8 8
S1PR2 0.029 0.004 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.001 0.092 -9999 0 -0.29 56 56
MAPK3 -0.008 0.086 -9999 0 -0.38 22 22
MAPK1 -0.004 0.085 -9999 0 -0.4 20 20
JAK2 -0.007 0.1 -9999 0 -0.4 27 27
CXCR4 -0.009 0.09 -9999 0 -0.37 26 26
FLT1 0.028 0.012 -9999 0 -10000 0 0
RhoA/GDP 0.021 0.004 -9999 0 -10000 0 0
Rac1/GDP 0.021 0.003 -9999 0 -10000 0 0
SRC -0.009 0.09 -9999 0 -0.38 25 25
S1P/S1P3/Gi 0.001 0.093 -9999 0 -0.29 56 56
RAC1 0.029 0.005 -9999 0 -10000 0 0
RhoA/GTP 0.003 0.099 -9999 0 -0.36 27 27
VEGFA 0.028 0.013 -9999 0 -10000 0 0
S1P/S1P2/Gi 0.002 0.084 -9999 0 -0.28 49 49
VEGFR1 homodimer/VEGFA homodimer 0.041 0.021 -9999 0 -10000 0 0
RHOA 0.028 0.006 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.002 0.085 -9999 0 -0.27 68 68
GNAQ 0.025 0.043 -9999 0 -0.48 6 6
GNAZ 0.018 0.071 -9999 0 -0.48 16 16
G12/G13 0.038 0.014 -9999 0 -10000 0 0
GNA14 -0.003 0.12 -9999 0 -0.48 45 45
GNA15 0.021 0.059 -9999 0 -0.48 11 11
GNA12 0.028 0.005 -9999 0 -10000 0 0
GNA13 0.027 0.008 -9999 0 -10000 0 0
GNA11 0.026 0.036 -9999 0 -0.48 4 4
Rac1/GTP 0.002 0.1 -9999 0 -0.36 27 27
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.027 0.043 -10000 0 -0.29 4 4
BIRC5 0.004 0.1 -10000 0 -0.48 37 37
NFKBIA 0.007 0.041 0.25 8 -0.2 15 23
CPEB1 -0.02 0.14 -10000 0 -0.48 73 73
AKT1 0.007 0.039 0.25 6 -0.26 3 9
NDEL1 0.026 0.009 -10000 0 -10000 0 0
Aurora A/BRCA1 0.019 0.05 -10000 0 -0.22 28 28
NDEL1/TACC3 0.04 0.05 -10000 0 -0.28 9 9
GADD45A 0.028 0.019 -10000 0 -0.48 1 1
GSK3B 0.029 0.011 -10000 0 -10000 0 0
PAK1/Aurora A 0.024 0.044 -10000 0 -0.21 17 17
MDM2 0.028 0.006 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.002 0.062 -10000 0 -0.35 25 25
TP53 0.015 0.043 -10000 0 -0.27 11 11
DLG7 0.007 0.033 -10000 0 -0.2 16 16
AURKAIP1 0.026 0.031 -10000 0 -0.48 3 3
ARHGEF7 0.027 0.008 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.043 0.053 -10000 0 -0.29 9 9
G2/M transition of mitotic cell cycle 0.018 0.05 -10000 0 -0.22 28 28
AURKA 0.015 0.041 -10000 0 -0.24 16 16
AURKB -0.008 0.1 -10000 0 -0.36 49 49
CDC25B 0.014 0.035 -10000 0 -0.27 4 4
G2/M transition checkpoint 0.007 0.031 -10000 0 -0.18 16 16
mRNA polyadenylation -0.002 0.085 -10000 0 -0.24 87 87
Aurora A/CPEB -0.001 0.086 -10000 0 -0.24 87 87
Aurora A/TACC1/TRAP/chTOG 0.048 0.057 -10000 0 -0.24 11 11
BRCA1 0.019 0.066 -10000 0 -0.48 14 14
centrosome duplication 0.024 0.043 -10000 0 -0.21 17 17
regulation of centrosome cycle 0.039 0.049 -10000 0 -0.27 9 9
spindle assembly 0.046 0.056 -10000 0 -0.24 11 11
TDRD7 0.029 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.037 0.085 -10000 0 -0.3 34 34
CENPA -0.006 0.1 -10000 0 -0.43 40 40
Aurora A/PP2A 0.027 0.041 -10000 0 -0.26 3 3
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.009 0.038 -10000 0 -0.24 4 4
negative regulation of DNA binding 0.003 0.065 -10000 0 -0.2 65 65
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.037 0.016 -10000 0 -10000 0 0
RASA1 0.028 0.007 -10000 0 -10000 0 0
Ajuba/Aurora A 0.007 0.032 -10000 0 -0.18 16 16
mitotic prometaphase 0.007 0.026 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.041 -10000 0 -0.24 16 16
TACC1 0.018 0.053 -10000 0 -0.48 9 9
TACC3 0.024 0.043 -10000 0 -0.48 6 6
Aurora A/Antizyme1 0.047 0.046 -10000 0 -0.25 6 6
Aurora A/RasGAP 0.027 0.041 -10000 0 -0.25 4 4
OAZ1 0.028 0.006 -10000 0 -10000 0 0
RAN 0.029 0.004 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.029 0.011 -10000 0 -10000 0 0
GIT1 0.027 0.008 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.045 0.031 -10000 0 -0.32 2 2
Importin alpha/Importin beta/TPX2 0.002 0.062 -10000 0 -0.34 25 25
PPP2R5D 0.028 0.005 -10000 0 -10000 0 0
Aurora A/TPX2 0.009 0.066 -10000 0 -0.33 25 25
PAK1 0.024 0.027 -10000 0 -0.48 2 2
CKAP5 0.029 0.004 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.01 0.092 -10000 0 -0.48 28 28
positive regulation of NF-kappaB transcription factor activity 0.014 0.079 -10000 0 -0.34 36 36
MAP2K4 0.011 0.066 -10000 0 -0.38 11 11
IKBKB 0.024 0.011 -10000 0 -10000 0 0
TNFRSF10B 0.024 0.012 -10000 0 -10000 0 0
TNFRSF10A 0.022 0.032 -10000 0 -0.48 3 3
SMPD1 0.004 0.043 -10000 0 -0.21 27 27
IKBKG 0.029 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.015 0.055 -10000 0 -0.48 9 9
TRAIL/TRAILR2 0.021 0.071 -10000 0 -0.34 28 28
TRAIL/TRAILR3 0.013 0.084 -10000 0 -0.36 36 36
TRAIL/TRAILR1 0.02 0.074 -10000 0 -0.35 30 30
TRAIL/TRAILR4 0.014 0.079 -10000 0 -0.34 36 36
TRAIL/TRAILR1/DAP3/GTP 0.027 0.06 -10000 0 -0.27 23 23
IKK complex 0.013 0.046 -10000 0 -0.36 3 3
RIPK1 0.028 0.006 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.018 0.008 -10000 0 -10000 0 0
MAPK3 0.001 0.063 -10000 0 -0.34 26 26
MAP3K1 0.013 0.08 -10000 0 -0.39 18 18
TRAILR4 (trimer) 0.015 0.055 -10000 0 -0.48 9 9
TRADD 0.025 0.02 -10000 0 -0.48 1 1
TRAILR1 (trimer) 0.022 0.032 -10000 0 -0.48 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.008 0.063 -10000 0 -0.3 25 25
CFLAR 0.028 0.018 -10000 0 -0.48 1 1
MAPK1 0.002 0.06 -10000 0 -0.34 24 24
TRAIL/TRAILR1/FADD/TRADD/RIP 0.043 0.067 -10000 0 -0.25 23 23
mol:ceramide 0.004 0.043 -10000 0 -0.21 27 27
FADD 0.024 0.011 -10000 0 -10000 0 0
MAPK8 0.006 0.072 -10000 0 -0.34 15 15
TRAF2 0.029 0.005 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.014 0.058 -10000 0 -0.48 10 10
CHUK 0.029 0.004 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.03 0.062 -10000 0 -0.28 23 23
DAP3 0.025 0.011 -10000 0 -10000 0 0
CASP10 0.02 0.069 0.24 8 -0.32 13 21
JNK cascade 0.014 0.079 -10000 0 -0.34 36 36
TRAIL (trimer) 0.01 0.092 -10000 0 -0.48 28 28
TNFRSF10C 0.014 0.058 -10000 0 -0.48 10 10
TRAIL/TRAILR1/DAP3/GTP/FADD 0.033 0.055 -10000 0 -0.25 16 16
TRAIL/TRAILR2/FADD 0.03 0.06 -10000 0 -0.29 21 21
cell death 0.004 0.043 -10000 0 -0.21 27 27
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.008 0.061 -10000 0 -0.31 23 23
TRAILR2 (trimer) 0.024 0.012 -10000 0 -10000 0 0
CASP8 0.018 0.048 -10000 0 -0.54 4 4
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.044 0.065 -10000 0 -0.25 22 22
Atypical NF-kappaB 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
BCL3/RelA 0.041 0.016 -10000 0 -0.34 1 1
FBXW11 0.029 0.005 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.017 0.053 -10000 0 -0.29 22 22
NF kappa B1 p50/RelA/I kappa B alpha 0.011 0.078 0.19 1 -0.31 16 17
NFKBIA -0.006 0.081 -10000 0 -0.24 76 76
MAPK14 0.029 0.004 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.025 0.017 -10000 0 -0.27 1 1
ARRB2 0.014 0.005 -10000 0 -10000 0 0
REL 0.012 0.092 -10000 0 -0.48 28 28
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.025 0.021 -10000 0 -0.3 2 2
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.025 0.018 -10000 0 -0.3 1 1
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.018 0.018 0.25 1 -0.34 1 2
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
NFKB1 0.011 0.014 -10000 0 -0.35 1 1
RELA 0.029 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.006 0.081 -10000 0 -0.23 68 68
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.011 0.079 -10000 0 -0.34 14 14
SRC 0.027 0.026 -10000 0 -0.48 2 2
PI3K 0.04 0.013 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.006 0.081 -10000 0 -0.23 68 68
IKBKB 0.024 0.011 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.028 0.005 -10000 0 -10000 0 0
SYK 0.021 0.063 -10000 0 -0.48 13 13
I kappa B alpha/PIK3R1 0.009 0.086 0.2 4 -0.35 18 22
cell death 0.011 0.076 -10000 0 -0.33 14 14
NF kappa B1 p105/c-Rel 0.017 0.053 -10000 0 -0.29 22 22
LCK -0.017 0.14 -10000 0 -0.48 68 68
BCL3 0.028 0.018 -10000 0 -0.48 1 1
Syndecan-3-mediated signaling events

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
CTTN 0.025 0.011 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.041 0.09 -10000 0 -0.42 13 13
Syndecan-3/Neurocan 0.021 0.063 -10000 0 -0.38 17 17
POMC 0.006 0.096 -10000 0 -0.48 30 30
EGFR -0.018 0.14 -10000 0 -0.48 67 67
Syndecan-3/EGFR 0.004 0.092 -10000 0 -0.41 18 18
AGRP 0.021 0.013 -10000 0 -10000 0 0
NCSTN 0.025 0.011 -10000 0 -10000 0 0
PSENEN 0.029 0.004 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.025 0.04 -10000 0 -0.48 5 5
APH1A 0.024 0.011 -10000 0 -10000 0 0
NCAN 0.02 0.021 -10000 0 -10000 0 0
long-term memory 0.041 0.067 -10000 0 -0.37 12 12
Syndecan-3/IL8 0.004 0.092 -10000 0 -0.4 18 18
PSEN1 0.028 0.006 -10000 0 -10000 0 0
Src/Cortactin 0.034 0.025 -10000 0 -0.34 2 2
FYN 0.026 0.027 -10000 0 -0.48 2 2
limb bud formation 0.003 0.06 -10000 0 -0.4 17 17
MC4R 0.021 0.015 -10000 0 -10000 0 0
SRC 0.027 0.026 -10000 0 -0.48 2 2
PTN -0.004 0.11 -10000 0 -0.48 39 39
FGFR/FGF/Syndecan-3 0.003 0.06 -10000 0 -0.41 17 17
neuron projection morphogenesis 0.022 0.091 0.32 1 -0.41 12 13
Syndecan-3/AgRP 0.017 0.062 -10000 0 -0.38 17 17
Syndecan-3/AgRP/MC4R 0.039 0.069 -10000 0 -0.37 16 16
Fyn/Cortactin 0.034 0.023 -10000 0 -0.34 1 1
SDC3 0.003 0.061 -10000 0 -0.41 17 17
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.004 0.091 -10000 0 -0.4 18 18
IL8 -0.024 0.14 -10000 0 -0.48 67 67
Syndecan-3/Fyn/Cortactin 0.042 0.068 -10000 0 -0.38 12 12
Syndecan-3/CASK 0.002 0.058 -10000 0 -0.39 17 17
alpha-MSH/MC4R 0.018 0.075 -10000 0 -0.35 30 30
Gamma Secretase 0.065 0.042 -10000 0 -0.26 2 2
Aurora C signaling

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
INCENP 0.028 0.005 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.031 0.075 -9999 0 -0.27 43 43
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.006 0.027 -9999 0 -0.33 2 2
AURKB 0.004 0.1 -9999 0 -0.48 34 34
AURKC 0.02 0.057 -9999 0 -0.48 10 10
HIF-2-alpha transcription factor network

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
MMP14 0.015 0.19 -10000 0 -1 23 23
oxygen homeostasis 0.005 0.01 -10000 0 -10000 0 0
TCEB2 0.027 0.009 -10000 0 -10000 0 0
TCEB1 0.024 0.011 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.067 0.082 0.25 2 -0.29 4 6
EPO 0.059 0.14 -10000 0 -0.56 18 18
FIH (dimer) 0.029 0.021 -10000 0 -10000 0 0
APEX1 0.029 0.024 -10000 0 -10000 0 0
SERPINE1 0.056 0.15 -10000 0 -0.61 20 20
FLT1 -0.013 0.2 -10000 0 -0.83 25 25
ADORA2A 0.085 0.15 0.38 3 -0.64 11 14
germ cell development 0.058 0.14 -10000 0 -0.53 18 18
SLC11A2 0.061 0.13 -10000 0 -0.6 10 10
BHLHE40 0.057 0.14 -10000 0 -0.56 18 18
HIF1AN 0.03 0.021 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.066 0.099 -10000 0 -0.36 11 11
ETS1 0.033 0.034 -10000 0 -0.48 3 3
CITED2 0.024 0.12 -10000 0 -0.75 11 11
KDR -0.005 0.19 -10000 0 -0.85 22 22
PGK1 0.061 0.13 -10000 0 -0.57 12 12
SIRT1 0.029 0.004 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.098 0.16 -10000 0 -0.65 12 12
EPAS1 0.025 0.068 -10000 0 -0.31 13 13
SP1 0.031 0.019 -10000 0 -10000 0 0
ABCG2 0.052 0.15 -10000 0 -0.55 27 27
EFNA1 0.062 0.13 -10000 0 -0.57 13 13
FXN 0.089 0.15 0.34 42 -0.55 12 54
POU5F1 0.058 0.14 -10000 0 -0.55 18 18
neuron apoptosis -0.096 0.16 0.63 12 -10000 0 12
EP300 0.028 0.007 -10000 0 -10000 0 0
EGLN3 0.015 0.08 -10000 0 -0.48 19 19
EGLN2 0.029 0.027 -10000 0 -0.47 1 1
EGLN1 0.024 0.032 -10000 0 -0.48 2 2
VHL/Elongin B/Elongin C 0.046 0.025 -10000 0 -10000 0 0
VHL 0.029 0.005 -10000 0 -10000 0 0
ARNT 0.026 0.022 -10000 0 -10000 0 0
SLC2A1 0.087 0.15 0.34 51 -0.54 14 65
TWIST1 0.079 0.17 0.34 39 -0.6 27 66
ELK1 0.034 0.005 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.071 0.1 -10000 0 -0.36 9 9
VEGFA 0.061 0.13 -10000 0 -0.57 12 12
CREBBP 0.027 0.019 -10000 0 -0.48 1 1
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.029 0.005 -10000 0 -10000 0 0
NFATC1 0.021 0.093 0.3 5 -0.43 11 16
NFATC2 0.009 0.065 0.17 3 -0.26 21 24
NFATC3 0.019 0.022 -10000 0 -0.32 3 3
YWHAE 0.027 0.009 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.009 0.12 0.34 1 -0.4 50 51
Exportin 1/Ran/NUP214 0.057 0.013 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.01 0.13 -10000 0 -0.4 48 48
BCL2/BAX 0.006 0.11 -10000 0 -0.34 74 74
CaM/Ca2+/Calcineurin A alpha-beta B1 0.022 0.005 -10000 0 -10000 0 0
CaM/Ca2+ 0.022 0.005 -10000 0 -10000 0 0
BAX 0.029 0.004 -10000 0 -10000 0 0
MAPK14 0.029 0.004 -10000 0 -10000 0 0
BAD 0.028 0.006 -10000 0 -10000 0 0
CABIN1/MEF2D 0.004 0.11 -10000 0 -0.39 38 38
Calcineurin A alpha-beta B1/BCL2 -0.018 0.14 -10000 0 -0.48 74 74
FKBP8 0.029 0.004 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.004 0.11 0.38 38 -10000 0 38
KPNB1 0.027 0.007 -10000 0 -10000 0 0
KPNA2 0.026 0.009 -10000 0 -10000 0 0
XPO1 0.029 0.004 -10000 0 -10000 0 0
SFN 0.014 0.082 -10000 0 -0.48 22 22
MAP3K8 0.025 0.04 -10000 0 -0.48 5 5
NFAT4/CK1 alpha 0.027 0.028 -10000 0 -0.24 4 4
MEF2D/NFAT1/Cbp/p300 0.043 0.072 -10000 0 -0.3 9 9
CABIN1 -0.008 0.12 0.34 1 -0.4 49 50
CALM1 0.029 0.005 -10000 0 -10000 0 0
RAN 0.029 0.004 -10000 0 -10000 0 0
MAP3K1 0.027 0.026 -10000 0 -0.48 2 2
CAMK4 0.003 0.11 -10000 0 -0.48 39 39
mol:Ca2+ 0 0.001 -10000 0 -10000 0 0
MAPK3 0.027 0.007 -10000 0 -10000 0 0
YWHAH 0.028 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.033 0.048 -10000 0 -0.34 11 11
YWHAB 0.028 0.007 -10000 0 -10000 0 0
MAPK8 0.029 0.004 -10000 0 -10000 0 0
MAPK9 0.029 0.005 -10000 0 -10000 0 0
YWHAG 0.029 0.004 -10000 0 -10000 0 0
FKBP1A 0.028 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.032 0.1 0.29 2 -0.45 12 14
PRKCH 0.028 0.018 -10000 0 -0.48 1 1
CABIN1/Cbp/p300 0.038 0.02 -10000 0 -0.34 1 1
CASP3 0.028 0.007 -10000 0 -10000 0 0
PIM1 0.024 0.044 -10000 0 -0.48 6 6
Calcineurin A alpha-beta B1/FKBP12/FK506 0.019 0.004 -10000 0 -10000 0 0
apoptosis 0.009 0.04 -10000 0 -0.31 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.026 0.049 -10000 0 -0.3 2 2
PRKCB -0.009 0.12 -10000 0 -0.48 52 52
PRKCE 0.024 0.05 -10000 0 -0.48 8 8
JNK2/NFAT4 0.015 0.061 -10000 0 -0.33 2 2
BAD/BCL-XL 0.041 0.011 -10000 0 -10000 0 0
PRKCD 0.028 0.006 -10000 0 -10000 0 0
NUP214 0.029 0.005 -10000 0 -10000 0 0
PRKCZ 0.027 0.026 -10000 0 -0.48 2 2
PRKCA 0.017 0.06 -10000 0 -0.48 11 11
PRKCG 0.021 0.017 -10000 0 -10000 0 0
PRKCQ -0.018 0.14 -10000 0 -0.48 65 65
FKBP38/BCL2 0.006 0.11 -10000 0 -0.34 73 73
EP300 0.028 0.008 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.028 0.006 -10000 0 -10000 0 0
NFATc/JNK1 0.035 0.094 0.28 4 -0.41 10 14
CaM/Ca2+/FKBP38 0.038 0.01 -10000 0 -10000 0 0
FKBP12/FK506 0.021 0.004 -10000 0 -10000 0 0
CSNK1A1 0.015 0.004 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.022 0.071 -10000 0 -0.29 39 39
NFATc/ERK1 0.033 0.093 0.28 4 -0.41 10 14
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.012 0.14 -10000 0 -0.4 56 56
NR4A1 0.04 0.082 0.22 9 -0.38 7 16
GSK3B 0.029 0.004 -10000 0 -10000 0 0
positive T cell selection 0.019 0.022 -10000 0 -0.32 3 3
NFAT1/CK1 alpha 0.013 0.05 0.17 1 -0.26 10 11
RCH1/ KPNB1 0.038 0.015 -10000 0 -10000 0 0
YWHAQ 0.029 0.004 -10000 0 -10000 0 0
PRKACA 0.029 0.004 -10000 0 -10000 0 0
AKAP5 0.017 0.063 -10000 0 -0.48 12 12
MEF2D 0.025 0.011 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.022 0.013 -10000 0 -10000 0 0
NFATc/p38 alpha 0.035 0.092 0.3 2 -0.41 10 12
CREBBP 0.027 0.019 -10000 0 -0.48 1 1
BCL2 -0.018 0.14 -10000 0 -0.48 74 74
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.021 0.016 -10000 0 -0.24 2 2
TRAF2/ASK1 0.036 0.02 -10000 0 -0.29 2 2
ATM 0.026 0.01 -10000 0 -10000 0 0
MAP2K3 -0.02 0.11 0.25 2 -0.35 51 53
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.016 0.1 0.3 1 -0.34 38 39
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.014 0.082 -10000 0 -0.48 22 22
TXN 0.008 0.001 -10000 0 -10000 0 0
CALM1 0.028 0.005 -10000 0 -10000 0 0
GADD45A 0.028 0.019 -10000 0 -0.48 1 1
GADD45B 0.026 0.031 -10000 0 -0.48 3 3
MAP3K1 0.027 0.026 -10000 0 -0.48 2 2
MAP3K6 0.027 0.019 -10000 0 -0.48 1 1
MAP3K7 0.028 0.007 -10000 0 -10000 0 0
MAP3K4 0.028 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.038 0.026 -10000 0 -0.34 3 3
TAK1/TAB family 0 0.022 0.16 4 -0.14 6 10
RAC1/OSM/MEKK3 0.049 0.02 -10000 0 -10000 0 0
TRAF2 0.029 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.001 0.097 -10000 0 -0.31 29 29
TRAF6 0.008 0.001 -10000 0 -10000 0 0
RAC1 0.029 0.005 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.049 0.17 -10000 0 -0.48 110 110
CCM2 0.029 0.004 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.014 0.11 -10000 0 -0.29 110 110
MAPK11 0.024 0.04 -10000 0 -0.48 5 5
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.007 0.11 -10000 0 -0.27 111 111
OSM/MEKK3 0.038 0.015 -10000 0 -10000 0 0
TAOK1 0 0.065 -10000 0 -0.32 33 33
TAOK2 0.013 0.006 -10000 0 -10000 0 0
TAOK3 0.014 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.029 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.027 0.026 -10000 0 -0.48 2 2
MAP3K10 0.028 0.018 -10000 0 -0.48 1 1
MAP3K3 0.026 0.009 -10000 0 -10000 0 0
TRX/ASK1 0.023 0.023 -10000 0 -0.28 2 2
GADD45/MTK1/MTK1 0.053 0.056 -10000 0 -0.25 22 22
BARD1 signaling events

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
BARD1/CSTF1 0.033 0.05 -10000 0 -0.34 13 13
ATM 0.026 0.01 -10000 0 -10000 0 0
UBE2D3 0.029 0.005 -10000 0 -10000 0 0
PRKDC 0.025 0.01 -10000 0 -10000 0 0
ATR 0.029 0.005 -10000 0 -10000 0 0
UBE2L3 0.028 0.007 -10000 0 -10000 0 0
FANCD2 0.02 0.008 -10000 0 -10000 0 0
protein ubiquitination 0.051 0.073 -10000 0 -0.26 35 35
XRCC5 0.029 0.004 -10000 0 -10000 0 0
XRCC6 0.028 0.007 -10000 0 -10000 0 0
M/R/N Complex 0.042 0.027 -10000 0 -10000 0 0
MRE11A 0.027 0.008 -10000 0 -10000 0 0
DNA-PK 0.047 0.024 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.004 0.092 -10000 0 -0.42 21 21
FANCF 0.028 0.005 -10000 0 -10000 0 0
BRCA1 0.019 0.066 -10000 0 -0.48 14 14
CCNE1 0.016 0.059 -10000 0 -0.48 10 10
CDK2/Cyclin E1 0.031 0.047 -10000 0 -0.34 10 10
FANCG 0.028 0.005 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.029 0.069 -10000 0 -0.34 26 26
FANCE 0.028 0.007 -10000 0 -10000 0 0
FANCC 0.029 0.004 -10000 0 -10000 0 0
NBN 0.023 0.012 -10000 0 -10000 0 0
FANCA 0.018 0.059 -10000 0 -0.48 11 11
DNA repair -0.007 0.09 0.25 2 -0.38 13 15
BRCA1/BARD1/ubiquitin 0.029 0.069 -10000 0 -0.34 26 26
BARD1/DNA-PK 0.055 0.049 -10000 0 -0.27 11 11
FANCL 0.029 0.005 -10000 0 -10000 0 0
mRNA polyadenylation -0.033 0.05 0.34 13 -10000 0 13
BRCA1/BARD1/CTIP/M/R/N Complex 0.015 0.074 -10000 0 -0.3 9 9
BRCA1/BACH1/BARD1/TopBP1 0.044 0.062 -10000 0 -0.3 24 24
BRCA1/BARD1/P53 0.052 0.069 -10000 0 -0.27 30 30
BARD1/CSTF1/BRCA1 0.041 0.062 -10000 0 -0.3 24 24
BRCA1/BACH1 0.019 0.065 -10000 0 -0.48 14 14
BARD1 0.02 0.066 -10000 0 -0.48 14 14
PCNA 0.028 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.044 0.063 -10000 0 -0.29 26 26
BRCA1/BARD1/UbcH7 0.043 0.064 -10000 0 -0.3 26 26
BRCA1/BARD1/RAD51/PCNA 0.047 0.082 -10000 0 -0.27 47 47
BARD1/DNA-PK/P53 0.059 0.058 -10000 0 -0.26 14 14
BRCA1/BARD1/Ubiquitin 0.029 0.069 -10000 0 -0.34 26 26
BRCA1/BARD1/CTIP 0.031 0.056 -10000 0 -0.27 25 25
FA complex 0.024 0.037 -10000 0 -0.22 12 12
BARD1/EWS 0.034 0.051 -10000 0 -0.34 14 14
RBBP8 0.011 0.008 -10000 0 -10000 0 0
TP53 0.023 0.04 -10000 0 -0.48 5 5
TOPBP1 0.029 0.004 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.05 0.068 0.27 30 -10000 0 30
BRCA1/BARD1 0.057 0.076 -10000 0 -0.26 35 35
CSTF1 0.027 0.008 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.015 0.047 -10000 0 -0.34 14 14
CDK2 0.029 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.015 0.082 -10000 0 -0.48 22 22
RAD50 0.028 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.029 0.069 -10000 0 -0.34 26 26
EWSR1 0.028 0.007 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.008 0.059 -10000 0 -0.32 24 24
CRKL 0.027 0.019 -10000 0 -0.48 1 1
Rac1/GDP 0.021 0.003 -10000 0 -10000 0 0
DOCK1 0.028 0.018 -10000 0 -0.48 1 1
ITGA4 0.02 0.061 -10000 0 -0.48 12 12
alpha4/beta7 Integrin/MAdCAM1 0.053 0.073 -10000 0 -0.28 36 36
EPO 0.008 0.06 -10000 0 -0.48 9 9
alpha4/beta7 Integrin 0.023 0.082 -10000 0 -0.35 36 36
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.035 0.046 -10000 0 -0.34 11 11
EPO/EPOR (dimer) 0.02 0.058 -10000 0 -0.35 15 15
lamellipodium assembly 0.019 0.069 -10000 0 -0.54 9 9
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
PI3K 0.04 0.013 -10000 0 -10000 0 0
ARF6 0.029 0.005 -10000 0 -10000 0 0
JAK2 0.015 0.055 -10000 0 -0.28 24 24
PXN 0.029 0.002 -10000 0 -10000 0 0
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
MADCAM1 0.021 0.021 -10000 0 -10000 0 0
cell adhesion 0.051 0.073 -10000 0 -0.27 36 36
CRKL/CBL 0.038 0.02 -10000 0 -0.34 1 1
ITGB1 0.029 0.005 -10000 0 -10000 0 0
SRC 0.005 0.065 -10000 0 -0.28 34 34
ITGB7 0.012 0.087 -10000 0 -0.48 25 25
RAC1 0.029 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.041 0.071 -10000 0 -0.3 32 32
p130Cas/Crk/Dock1 0.026 0.066 0.36 1 -0.25 21 22
VCAM1 0.014 0.082 -10000 0 -0.48 22 22
RHOA 0.028 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.062 0.046 -10000 0 -0.27 11 11
BCAR1 -0.017 0.059 0.2 19 -0.26 32 51
EPOR 0.025 0.044 -10000 0 -0.48 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.026 0.009 -10000 0 -10000 0 0
GIT1 0.027 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.018 0.071 -10000 0 -0.56 9 9
Signaling events mediated by HDAC Class III

Figure S110.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S110.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.028 0.007 -10000 0 -10000 0 0
HDAC4 0.028 0.018 -10000 0 -0.48 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.002 0.055 0.34 19 -10000 0 19
CDKN1A -0.011 0.05 -10000 0 -0.63 5 5
KAT2B 0.027 0.031 -10000 0 -0.48 3 3
BAX 0.029 0.004 -10000 0 -10000 0 0
FOXO3 -0.006 0.008 -10000 0 -0.22 1 1
FOXO1 0.026 0.009 -10000 0 -10000 0 0
FOXO4 0.014 0.015 -10000 0 -0.26 2 2
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.028 0.007 -10000 0 -10000 0 0
TAT -0.048 0.15 -10000 0 -0.48 81 81
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.006 0.021 -10000 0 -0.34 3 3
PPARGC1A -0.016 0.13 -10000 0 -0.48 59 59
FHL2 0.012 0.087 -10000 0 -0.48 25 25
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.039 0.014 -10000 0 -10000 0 0
HIST2H4A 0.002 0.055 -10000 0 -0.34 19 19
SIRT1/FOXO3a 0.02 0.029 0.19 2 -0.18 3 5
SIRT1 0.027 0.013 0.21 3 -10000 0 3
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.047 0.026 -10000 0 -0.3 1 1
SIRT1/Histone H1b 0.02 0.06 -10000 0 -0.23 28 28
apoptosis -0.053 0.018 -10000 0 -10000 0 0
SIRT1/PGC1A 0.006 0.086 -10000 0 -0.29 58 58
p53/SIRT1 0.031 0.039 0.4 3 -0.35 5 8
SIRT1/FOXO4 0.027 0.04 -10000 0 -0.22 5 5
FOXO1/FHL2/SIRT1 0.039 0.056 -10000 0 -0.26 24 24
HIST1H1E 0.006 0.048 -10000 0 -0.28 22 22
SIRT1/p300 0.039 0.014 -10000 0 -10000 0 0
muscle cell differentiation -0.038 0.022 0.27 3 -10000 0 3
TP53 0.021 0.041 0.21 3 -0.48 5 8
KU70/SIRT1/BAX 0.054 0.018 -10000 0 -10000 0 0
CREBBP 0.027 0.019 -10000 0 -0.48 1 1
MEF2D 0.025 0.011 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.024 0.11 -10000 0 -0.35 80 80
ACSS2 0.012 0.01 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.038 0.022 -10000 0 -0.27 3 3
Signaling events mediated by HDAC Class II

Figure S111.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S111.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0.063 0.03 -10000 0 -0.27 1 1
HDAC3 0.029 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.01 0.008 -10000 0 -0.22 1 1
GATA1/HDAC4 0.038 0.019 -10000 0 -0.34 1 1
GATA1/HDAC5 0.038 0.014 -10000 0 -10000 0 0
GATA2/HDAC5 -0.003 0.12 -10000 0 -0.34 87 87
HDAC5/BCL6/BCoR 0.05 0.042 -10000 0 -0.29 10 10
HDAC9 0.018 0.058 -10000 0 -0.48 10 10
Glucocorticoid receptor/Hsp90/HDAC6 0.055 0.025 -10000 0 -0.29 3 3
HDAC4/ANKRA2 0.04 0.022 -10000 0 -0.34 2 2
HDAC5/YWHAB 0.039 0.013 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.014 0.006 -10000 0 -10000 0 0
GATA2 -0.029 0.16 -10000 0 -0.48 87 87
HDAC4/RFXANK 0.041 0.016 -10000 0 -0.34 1 1
BCOR 0.025 0.047 -10000 0 -0.48 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.027 0.008 -10000 0 -10000 0 0
HDAC5 0.028 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.04 0.018 -10000 0 -0.34 1 1
Histones 0.016 0.059 -10000 0 -0.32 10 10
ADRBK1 0.027 0.008 -10000 0 -10000 0 0
HDAC4 0.028 0.018 -10000 0 -0.48 1 1
XPO1 0.029 0.004 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.04 0.018 -10000 0 -0.34 1 1
HDAC4/Ubc9 0.039 0.019 -10000 0 -0.34 1 1
HDAC7 0.029 0.003 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.039 0.013 -10000 0 -10000 0 0
TUBA1B 0.029 0.003 -10000 0 -10000 0 0
HDAC6 0.029 0.002 -10000 0 -10000 0 0
HDAC5/RFXANK 0.041 0.011 -10000 0 -10000 0 0
CAMK4 0.003 0.11 -10000 0 -0.48 39 39
Tubulin/HDAC6 0.054 0.033 -10000 0 -0.3 6 6
SUMO1 0.029 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.028 0.007 -10000 0 -10000 0 0
GATA1 0.025 0.012 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.027 0.009 -10000 0 -10000 0 0
NR3C1 0.027 0.031 -10000 0 -0.48 3 3
SUMO1/HDAC4 0.042 0.041 -10000 0 -0.22 4 4
SRF 0.028 0.005 -10000 0 -10000 0 0
HDAC4/YWHAB 0.04 0.018 -10000 0 -0.34 1 1
Tubulin 0.038 0.035 -10000 0 -0.34 6 6
HDAC4/14-3-3 E 0.038 0.019 -10000 0 -0.34 1 1
GNB1 0.028 0.006 -10000 0 -10000 0 0
RANGAP1 0.028 0.007 -10000 0 -10000 0 0
BCL6/BCoR 0.037 0.043 -10000 0 -0.34 10 10
HDAC4/HDAC3/SMRT (N-CoR2) 0.056 0.018 -10000 0 -0.3 1 1
HDAC4/SRF 0.039 0.076 -10000 0 -0.3 37 37
HDAC4/ER alpha -0.05 0.16 -10000 0 -0.34 191 191
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.016 0.059 -10000 0 -0.32 10 10
cell motility 0.053 0.032 -10000 0 -0.29 6 6
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.027 0.008 -10000 0 -10000 0 0
HDAC7/HDAC3 0.043 0.007 -10000 0 -10000 0 0
BCL6 0.026 0.031 -10000 0 -0.48 3 3
HDAC4/CaMK II delta B 0.028 0.018 -10000 0 -0.48 1 1
Hsp90/HDAC6 0.042 0.009 -10000 0 -10000 0 0
ESR1 -0.089 0.21 -10000 0 -0.48 190 190
HDAC6/HDAC11 0.039 0.039 -10000 0 -0.34 8 8
Ran/GTP/Exportin 1 0.042 0.04 -10000 0 -0.23 3 3
NPC 0.017 0.002 -10000 0 -10000 0 0
MEF2C 0.027 0.026 -10000 0 -0.48 2 2
RAN 0.029 0.004 -10000 0 -10000 0 0
HDAC4/MEF2C 0.075 0.036 -10000 0 -0.25 3 3
GNG2 0.028 0.019 -10000 0 -0.48 1 1
NCOR2 0.029 0.004 -10000 0 -10000 0 0
TUBB2A 0.024 0.044 -10000 0 -0.48 6 6
HDAC11 0.024 0.05 -10000 0 -0.48 8 8
HSP90AA1 0.028 0.005 -10000 0 -10000 0 0
RANBP2 0.029 0.003 -10000 0 -10000 0 0
ANKRA2 0.027 0.019 -10000 0 -0.48 1 1
RFXANK 0.029 0.004 -10000 0 -10000 0 0
nuclear import -0.032 0.019 0.29 1 -10000 0 1
Retinoic acid receptors-mediated 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
HDAC1 0.028 0.018 -10000 0 -0.48 1 1
HDAC3 0.029 0.004 -10000 0 -10000 0 0
VDR 0.024 0.05 -10000 0 -0.48 8 8
Cbp/p300/PCAF 0.05 0.031 -10000 0 -0.28 4 4
EP300 0.028 0.007 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.018 0.065 0.18 1 -0.4 11 12
KAT2B 0.027 0.031 -10000 0 -0.48 3 3
MAPK14 0.029 0.004 -10000 0 -10000 0 0
AKT1 0.023 0.069 0.2 42 -0.34 8 50
RAR alpha/9cRA/Cyclin H 0.055 0.074 0.25 2 -0.3 17 19
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.024 0.073 -10000 0 -0.43 13 13
CDC2 0 0.002 -10000 0 -10000 0 0
response to UV 0 0.004 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.03 0.057 -10000 0 -0.31 6 6
NCOR2 0.029 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.036 -10000 0 -0.34 8 8
RXRs/RARs/NRIP1/9cRA 0.027 0.12 -10000 0 -0.55 25 25
NCOA2 0.006 0.093 -10000 0 -0.48 29 29
NCOA3 0.027 0.019 -10000 0 -0.48 1 1
NCOA1 0.028 0.018 -10000 0 -0.48 1 1
VDR/VDR/DNA 0.024 0.05 -10000 0 -0.48 8 8
RARG 0.029 0.007 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.039 0.007 -10000 0 -10000 0 0
MAPK3 0.027 0.011 -10000 0 -10000 0 0
MAPK1 0.028 0.007 -10000 0 -10000 0 0
MAPK8 0.028 0.009 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.031 0.089 -10000 0 -0.4 22 22
RARA 0.008 0.043 -10000 0 -0.23 22 22
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.011 0.077 -10000 0 -0.43 13 13
PRKCA 0.018 0.061 -10000 0 -0.48 11 11
RXRs/RARs/NRIP1/9cRA/HDAC1 0.029 0.13 0.48 1 -0.57 25 26
RXRG 0.003 0.06 -10000 0 -0.31 27 27
RXRA 0.023 0.059 -10000 0 -0.26 17 17
RXRB 0.013 0.043 -10000 0 -0.32 11 11
VDR/Vit D3/DNA 0.018 0.036 -10000 0 -0.34 8 8
RBP1 -0.011 0.12 -10000 0 -0.48 52 52
CRBP1/9-cic-RA -0.007 0.088 -10000 0 -0.34 52 52
RARB 0.024 0.045 -10000 0 -0.48 6 6
PRKCG 0.022 0.021 -10000 0 -10000 0 0
MNAT1 0.029 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs 0.016 0.099 0.27 1 -0.46 19 20
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.032 0.093 -10000 0 -0.44 15 15
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.081 0.23 8 -0.4 13 21
RXRs/RARs/NRIP1/9cRA/HDAC3 0.029 0.13 0.48 1 -0.57 26 27
positive regulation of DNA binding 0.039 0.064 -10000 0 -0.28 17 17
NRIP1 0.018 0.2 0.57 1 -1.2 18 19
RXRs/RARs 0.03 0.12 -10000 0 -0.48 26 26
RXRs/RXRs/DNA/9cRA 0.007 0.076 -10000 0 -0.39 21 21
PRKACA 0.029 0.004 -10000 0 -10000 0 0
CDK7 0.028 0.006 -10000 0 -10000 0 0
TFIIH 0.056 0.014 -10000 0 -10000 0 0
RAR alpha/9cRA 0.06 0.059 -10000 0 -0.28 5 5
CCNH 0.028 0.005 -10000 0 -10000 0 0
CREBBP 0.027 0.019 -10000 0 -0.48 1 1
RAR gamma2/9cRA 0.054 0.017 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.027 0.14 -9999 0 -0.48 72 72
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.027 0.009 -9999 0 -10000 0 0
TCEB1 0.024 0.011 -9999 0 -10000 0 0
HIF1A/p53 0.026 0.063 -9999 0 -0.25 27 27
HIF1A 0.014 0.051 -9999 0 -0.25 20 20
COPS5 0.025 0.011 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.062 0.04 -9999 0 -10000 0 0
FIH (dimer) 0.029 0.004 -9999 0 -10000 0 0
CDKN2A 0.011 0.065 -9999 0 -0.48 12 12
ARNT/IPAS -0.001 0.097 -9999 0 -0.34 54 54
HIF1AN 0.029 0.004 -9999 0 -10000 0 0
GNB2L1 0.029 0.005 -9999 0 -10000 0 0
HIF1A/ARNT 0.019 0.057 -9999 0 -0.26 24 24
CUL2 0.028 0.005 -9999 0 -10000 0 0
OS9 0.029 0.004 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.046 0.025 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.03 0.06 -9999 0 -0.27 17 17
PHD1-3/OS9 0.05 0.057 -9999 0 -0.27 16 16
HIF1A/RACK1/Elongin B/Elongin C 0.041 0.062 -9999 0 -0.26 15 15
VHL 0.029 0.005 -9999 0 -10000 0 0
HSP90AA1 0.028 0.005 -9999 0 -10000 0 0
HIF1A/JAB1 0.025 0.058 -9999 0 -0.26 21 21
EGLN3 0.014 0.077 -9999 0 -0.48 19 19
EGLN2 0.028 0.019 -9999 0 -0.48 1 1
EGLN1 0.023 0.027 -9999 0 -0.48 2 2
TP53 0.023 0.04 -9999 0 -0.48 5 5
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.03 0.073 -9999 0 -0.51 13 13
ARNT 0.024 0.011 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.028 0.007 -9999 0 -10000 0 0
HIF1A/p19ARF 0.023 0.065 -9999 0 -0.24 31 31
Canonical NF-kappaB pathway

Figure S114.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S114.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.03 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.042 0.11 0.27 15 -0.33 20 35
ERC1 0.028 0.007 -10000 0 -10000 0 0
RIP2/NOD2 0.023 0.055 -10000 0 -0.34 15 15
NFKBIA 0.012 0.022 -10000 0 -0.24 1 1
BIRC2 0.027 0.009 -10000 0 -10000 0 0
IKBKB 0.024 0.011 -10000 0 -10000 0 0
RIPK2 0.023 0.013 -10000 0 -10000 0 0
IKBKG 0.025 0.077 -10000 0 -0.41 15 15
IKK complex/A20 0.016 0.14 -10000 0 -0.43 37 37
NEMO/A20/RIP2 0.023 0.013 -10000 0 -10000 0 0
XPO1 0.029 0.004 -10000 0 -10000 0 0
NEMO/ATM 0.016 0.13 -10000 0 -0.41 43 43
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.029 0.004 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.039 0.007 -10000 0 -10000 0 0
IKK complex/ELKS 0.015 0.12 -10000 0 -0.4 31 31
BCL10/MALT1/TRAF6 0.054 0.021 -10000 0 -0.3 1 1
NOD2 0.013 0.078 -10000 0 -0.48 20 20
NFKB1 0.03 0.018 -10000 0 -0.47 1 1
RELA 0.03 0.005 -10000 0 -10000 0 0
MALT1 0.027 0.019 -10000 0 -0.48 1 1
cIAP1/UbcH5C 0.039 0.014 -10000 0 -10000 0 0
ATM 0.026 0.01 -10000 0 -10000 0 0
TNF/TNFR1A 0.018 0.084 -10000 0 -0.34 40 40
TRAF6 0.029 0.005 -10000 0 -10000 0 0
PRKCA 0.017 0.06 -10000 0 -0.48 11 11
CHUK 0.029 0.004 -10000 0 -10000 0 0
UBE2D3 0.029 0.005 -10000 0 -10000 0 0
TNF 0 0.11 -10000 0 -0.48 40 40
NF kappa B1 p50/RelA 0.062 0.02 -10000 0 -0.27 1 1
BCL10 0.028 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.022 -10000 0 -0.24 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.03 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.028 0.006 -10000 0 -10000 0 0
IKK complex 0.019 0.13 -10000 0 -0.41 40 40
CYLD 0.026 0.009 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.021 0.13 -10000 0 -0.42 34 34
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.006 0.05 0.19 2 -0.24 7 9
PLK1 -0.014 0.29 -10000 0 -1.2 38 38
CDKN1B 0.055 0.12 0.36 2 -0.44 20 22
FOXO3 0.017 0.17 -10000 0 -0.75 13 13
KAT2B 0.024 0.041 -10000 0 -0.47 3 3
FOXO1/SIRT1 0.024 0.056 -10000 0 -0.27 5 5
CAT 0.014 0.17 -10000 0 -0.89 9 9
CTNNB1 0.028 0.019 -10000 0 -0.48 1 1
AKT1 0.027 0.027 -10000 0 -10000 0 0
FOXO1 0.007 0.056 0.22 2 -0.26 7 9
MAPK10 -0.009 0.087 0.19 12 -0.24 90 102
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.028 0.074 0.32 6 -0.32 1 7
response to oxidative stress 0.004 0.015 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.036 0.15 -10000 0 -0.72 10 10
XPO1 0.029 0.004 -10000 0 -10000 0 0
EP300 0.028 0.007 -10000 0 -10000 0 0
BCL2L11 0.021 0.096 -10000 0 -0.88 8 8
FOXO1/SKP2 0.021 0.056 0.19 2 -0.25 8 10
mol:GDP 0.004 0.015 -10000 0 -10000 0 0
RAN 0.03 0.004 -10000 0 -10000 0 0
GADD45A 0.049 0.12 -10000 0 -0.64 9 9
YWHAQ 0.029 0.004 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.026 0.12 -10000 0 -0.46 34 34
MST1 0.012 0.083 -10000 0 -0.47 21 21
CSNK1D 0.028 0.007 -10000 0 -10000 0 0
CSNK1E 0.028 0.007 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.009 0.13 -10000 0 -0.45 41 41
YWHAB 0.028 0.007 -10000 0 -10000 0 0
MAPK8 0.022 0.027 0.19 14 -10000 0 14
MAPK9 0.022 0.027 0.19 15 -10000 0 15
YWHAG 0.029 0.004 -10000 0 -10000 0 0
YWHAE 0.027 0.009 -10000 0 -10000 0 0
YWHAZ 0.022 0.013 -10000 0 -10000 0 0
SIRT1 0.031 0.017 -10000 0 -10000 0 0
SOD2 0.04 0.12 0.51 1 -0.51 3 4
RBL2 -0.031 0.26 -10000 0 -0.73 81 81
RAL/GDP 0.041 0.021 -10000 0 -10000 0 0
CHUK 0.026 0.027 -10000 0 -10000 0 0
Ran/GTP 0.024 0.004 -10000 0 -10000 0 0
CSNK1G2 0.028 0.006 -10000 0 -10000 0 0
RAL/GTP 0.045 0.017 -10000 0 -10000 0 0
CSNK1G1 0.028 0.005 -10000 0 -10000 0 0
FASLG -0.084 0.38 -10000 0 -1.4 65 65
SKP2 0.027 0.021 -10000 0 -0.48 1 1
USP7 0.028 0.008 -10000 0 -10000 0 0
IKBKB 0.022 0.027 -10000 0 -10000 0 0
CCNB1 0.011 0.17 -10000 0 -1.1 7 7
FOXO1-3a-4/beta catenin 0.052 0.12 0.42 6 -0.41 6 12
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.056 0.19 2 -0.25 8 10
CSNK1A1 0.029 0.004 -10000 0 -10000 0 0
SGK1 0.024 0.041 -10000 0 -0.48 3 3
CSNK1G3 0.028 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.042 0.008 -10000 0 -10000 0 0
ZFAND5 0.027 0.066 0.41 1 -10000 0 1
SFN 0.014 0.082 -10000 0 -0.48 22 22
CDK2 0.029 0.003 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.015 0.12 0.25 1 -0.45 29 30
CREBBP 0.026 0.019 -10000 0 -0.48 1 1
FBXO32 0.053 0.21 0.56 1 -1.1 10 11
BCL6 0.029 0.15 -10000 0 -0.92 7 7
RALB 0.03 0.004 -10000 0 -10000 0 0
RALA 0.029 0.005 -10000 0 -10000 0 0
YWHAH 0.028 0.007 -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 0.016 0.059 -10000 0 -0.48 10 10
mol:Halofuginone 0.003 0.001 -10000 0 -10000 0 0
ITGA1 0.026 0.036 -10000 0 -0.48 4 4
CDKN1A 0.008 0.065 -10000 0 -0.34 24 24
PRL-3/alpha Tubulin 0.034 0.018 -10000 0 -10000 0 0
mol:Ca2+ -0.044 0.095 -10000 0 -0.36 69 69
AGT -0.039 0.16 -10000 0 -0.48 93 93
CCNA2 -0.019 0.055 -10000 0 -10000 0 0
TUBA1B 0.029 0.003 -10000 0 -10000 0 0
EGR1 0.003 0.058 -10000 0 -0.34 23 23
CDK2/Cyclin E1 0.039 0.08 -10000 0 -0.37 9 9
MAPK3 0.01 0.006 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.042 0.009 -10000 0 -10000 0 0
MAPK1 0.01 0.006 -10000 0 -10000 0 0
PTP4A1 -0.006 0.043 -10000 0 -10000 0 0
PTP4A3 0.023 0.012 -10000 0 -10000 0 0
PTP4A2 0.028 0.005 -10000 0 -10000 0 0
ITGB1 0.011 0.006 -10000 0 -10000 0 0
SRC 0.027 0.026 -10000 0 -0.48 2 2
RAC1 0.011 0.043 -10000 0 -0.31 12 12
Rab GGTase beta/Rab GGTase alpha 0.042 0.009 -10000 0 -10000 0 0
PRL-1/ATF-5 0.021 0.058 -10000 0 -10000 0 0
RABGGTA 0.028 0.005 -10000 0 -10000 0 0
BCAR1 -0.015 0.01 -10000 0 -10000 0 0
RHOC 0.009 0.048 -10000 0 -0.31 16 16
RHOA 0.008 0.053 -10000 0 -0.32 18 18
cell motility 0.023 0.066 0.34 1 -0.3 16 17
PRL-1/alpha Tubulin 0.021 0.06 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.031 0.03 -10000 0 -0.34 3 3
ROCK1 0.024 0.061 -10000 0 -0.3 13 13
RABGGTB 0.029 0.005 -10000 0 -10000 0 0
CDK2 0.029 0.002 -10000 0 -10000 0 0
mitosis -0.006 0.043 -10000 0 -10000 0 0
ATF5 0.028 0.006 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.047 0.091 -10000 0 -0.32 39 39
Ran/GTP/Exportin 1/HDAC1 -0.01 0.008 -10000 0 -0.22 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.024 0.09 -10000 0 -0.31 38 38
SUMO1 0.029 0.004 -10000 0 -10000 0 0
ZFPM1 0.021 0.047 -10000 0 -0.48 7 7
NPC/RanGAP1/SUMO1/Ubc9 0.014 0.006 -10000 0 -10000 0 0
FKBP3 0.029 0.005 -10000 0 -10000 0 0
Histones 0.055 0.06 -10000 0 -0.32 3 3
YY1/LSF 0.026 0.065 -10000 0 -0.28 24 24
SMG5 0.025 0.011 -10000 0 -10000 0 0
RAN 0.029 0.004 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.015 0.055 -10000 0 -0.24 35 35
I kappa B alpha/HDAC1 0.027 0.057 -10000 0 -0.32 5 5
SAP18 0.027 0.008 -10000 0 -10000 0 0
RELA 0.013 0.06 -10000 0 -0.24 35 35
HDAC1/Smad7 0.054 0.024 -10000 0 -0.3 2 2
RANGAP1 0.028 0.007 -10000 0 -10000 0 0
HDAC3/TR2 0.028 0.055 -10000 0 -0.32 4 4
NuRD/MBD3 Complex 0.031 0.052 -10000 0 -0.3 8 8
NF kappa B1 p50/RelA 0.022 0.083 0.38 1 -0.36 11 12
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.029 0.16 -10000 0 -0.48 87 87
GATA1 0.025 0.012 -10000 0 -10000 0 0
Mad/Max 0.042 0.01 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.02 0.084 -10000 0 -0.36 20 20
RBBP7 0.028 0.009 -10000 0 -10000 0 0
NPC 0.017 0.002 -10000 0 -10000 0 0
RBBP4 0.028 0.005 -10000 0 -10000 0 0
MAX 0.028 0.006 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.029 0.005 -10000 0 -10000 0 0
NFKBIA 0.013 0.046 -10000 0 -0.19 36 36
KAT2B 0.027 0.031 -10000 0 -0.48 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.019 0.043 -10000 0 -0.33 5 5
SIN3 complex 0.063 0.041 -10000 0 -0.26 8 8
SMURF1 0.029 0.005 -10000 0 -10000 0 0
CHD3 0.026 0.009 -10000 0 -10000 0 0
SAP30 0.023 0.05 -10000 0 -0.48 8 8
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.026 0.009 -10000 0 -10000 0 0
YY1/HDAC3 0.02 0.064 -10000 0 -0.37 8 8
YY1/HDAC2 0.029 0.053 -10000 0 -0.27 14 14
YY1/HDAC1 0.029 0.056 -10000 0 -0.27 15 15
NuRD/MBD2 Complex (MeCP1) 0.029 0.056 -10000 0 -0.27 11 11
PPARG 0.006 0.091 -10000 0 -0.34 43 43
HDAC8/hEST1B 0.05 0.022 -10000 0 -10000 0 0
UBE2I 0.027 0.008 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.028 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.028 0.006 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.029 0.053 -10000 0 -0.38 2 2
MBD3L2 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.053 0.024 -10000 0 -0.29 2 2
CREBBP 0.027 0.019 -10000 0 -0.48 1 1
NuRD/MBD3/MBD3L2 Complex 0.029 0.062 -10000 0 -0.32 10 10
HDAC1 0.028 0.018 -10000 0 -0.48 1 1
HDAC3 0.014 0.042 -10000 0 -0.18 36 36
HDAC2 0.027 0.008 -10000 0 -10000 0 0
YY1 0.018 0.022 -10000 0 -0.31 3 3
HDAC8 0.029 0.001 -10000 0 -10000 0 0
SMAD7 0.027 0.019 -10000 0 -0.48 1 1
NCOR2 0.029 0.004 -10000 0 -10000 0 0
MXD1 0.029 0.005 -10000 0 -10000 0 0
STAT3 0.019 0.018 -10000 0 -0.3 2 2
NFKB1 0.028 0.018 -10000 0 -0.48 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.029 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.041 0.064 -10000 0 -0.28 18 18
YY1/SAP30/HDAC1 0.041 0.061 -10000 0 -0.27 17 17
EP300 0.028 0.007 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.019 0.018 -10000 0 -0.3 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.046 -10000 0 -0.19 36 36
histone deacetylation 0.029 0.055 -10000 0 -0.27 11 11
STAT3 (dimer non-phopshorylated)/HDAC3 0.016 0.053 -10000 0 -0.32 6 6
nuclear export -0.049 0.022 -10000 0 -10000 0 0
PRKACA 0.029 0.004 -10000 0 -10000 0 0
GATAD2B 0.025 0.011 -10000 0 -10000 0 0
GATAD2A 0.029 0.004 -10000 0 -10000 0 0
GATA2/HDAC3 -0.001 0.1 -10000 0 -0.27 72 72
GATA1/HDAC1 0.038 0.019 -10000 0 -0.35 1 1
GATA1/HDAC3 0.027 0.053 -10000 0 -0.39 2 2
CHD4 0.028 0.006 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.018 0.084 -10000 0 -0.34 40 40
SIN3/HDAC complex/Mad/Max 0.018 0.061 -10000 0 -0.27 21 21
NuRD Complex 0.03 0.069 -10000 0 -0.35 10 10
positive regulation of chromatin silencing 0.052 0.059 -10000 0 -0.31 3 3
SIN3B 0.029 0.004 -10000 0 -10000 0 0
MTA2 0.028 0.005 -10000 0 -10000 0 0
SIN3A 0.029 0.005 -10000 0 -10000 0 0
XPO1 0.029 0.004 -10000 0 -10000 0 0
SUMO1/HDAC1 0.042 0.041 -10000 0 -0.23 4 4
HDAC complex 0.067 0.027 -10000 0 -0.27 1 1
GATA1/Fog1 0.031 0.039 -10000 0 -0.35 7 7
FKBP25/HDAC1/HDAC2 0.053 0.022 -10000 0 -0.3 1 1
TNF 0 0.11 -10000 0 -0.48 40 40
negative regulation of cell growth 0.018 0.061 -10000 0 -0.27 21 21
NuRD/MBD2/PRMT5 Complex 0.029 0.056 -10000 0 -0.27 11 11
Ran/GTP/Exportin 1 0.042 0.04 -10000 0 -0.23 3 3
NF kappa B/RelA/I kappa B alpha 0.009 0.082 -10000 0 -0.32 38 38
SIN3/HDAC complex/NCoR1 0.009 0.072 -10000 0 -0.31 27 27
TFCP2 0.024 0.053 -10000 0 -0.48 9 9
NR2C1 0.028 0.025 -10000 0 -0.48 2 2
MBD3 0.028 0.006 -10000 0 -10000 0 0
MBD2 0.028 0.006 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.027 0.019 -10000 0 -0.48 1 1
Rac1/GDP 0.027 0.012 -10000 0 -10000 0 0
DOCK1 0.028 0.018 -10000 0 -0.48 1 1
ITGA4 0.02 0.061 -10000 0 -0.48 12 12
RAC1 0.029 0.005 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.023 0.082 -10000 0 -0.35 36 36
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.051 0.043 -10000 0 -0.29 11 11
alpha4/beta7 Integrin/Paxillin 0.032 0.067 -10000 0 -0.28 36 36
lamellipodium assembly 0.006 0.082 -10000 0 -0.41 20 20
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
PI3K 0.04 0.013 -10000 0 -10000 0 0
ARF6 0.029 0.005 -10000 0 -10000 0 0
TLN1 0.028 0.005 -10000 0 -10000 0 0
PXN 0.014 0.002 -10000 0 -10000 0 0
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
ARF6/GTP 0.051 0.041 -10000 0 -0.24 11 11
cell adhesion 0.054 0.04 -10000 0 -0.25 11 11
CRKL/CBL 0.038 0.02 -10000 0 -0.34 1 1
alpha4/beta1 Integrin/Paxillin 0.042 0.038 -10000 0 -0.27 11 11
ITGB1 0.029 0.005 -10000 0 -10000 0 0
ITGB7 0.012 0.087 -10000 0 -0.48 25 25
ARF6/GDP 0.027 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.047 0.065 -10000 0 -0.26 32 32
p130Cas/Crk/Dock1 0.048 0.026 -10000 0 -0.27 1 1
VCAM1 0.014 0.082 -10000 0 -0.48 22 22
alpha4/beta1 Integrin/Paxillin/Talin 0.056 0.041 -10000 0 -0.26 11 11
alpha4/beta1 Integrin/Paxillin/GIT1 0.053 0.042 -10000 0 -0.26 11 11
BCAR1 0.026 0.01 -10000 0 -10000 0 0
mol:GDP -0.051 0.042 0.25 11 -10000 0 11
CBL 0.026 0.009 -10000 0 -10000 0 0
PRKACA 0.029 0.004 -10000 0 -10000 0 0
GIT1 0.027 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.056 0.041 -10000 0 -0.26 11 11
Rac1/GTP 0.006 0.09 -10000 0 -0.46 20 20
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.03 0.064 -10000 0 -0.38 18 18
AKT1 0.035 0.089 0.32 5 -0.51 7 12
PTK2B 0.009 0.075 0.34 2 -0.59 7 9
VEGFR2 homodimer/Frs2 0.032 0.046 -10000 0 -0.53 5 5
CAV1 0.025 0.04 -10000 0 -0.48 5 5
CALM1 0.028 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.048 0.047 -10000 0 -0.49 5 5
endothelial cell proliferation 0.041 0.12 0.32 38 -0.49 9 47
mol:Ca2+ 0.015 0.053 -10000 0 -0.52 5 5
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.062 0.053 -10000 0 -0.54 5 5
RP11-342D11.1 0.005 0.052 -10000 0 -0.35 12 12
CDH5 0.025 0.027 -10000 0 -0.48 2 2
VEGFA homodimer 0.054 0.05 -10000 0 -0.27 11 11
SHC1 0.024 0.011 -10000 0 -10000 0 0
SHC2 -0.008 0.13 -10000 0 -0.48 59 59
HRAS/GDP 0.034 0.054 -10000 0 -0.47 4 4
SH2D2A -0.008 0.12 -10000 0 -0.48 49 49
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.052 0.095 -10000 0 -0.5 12 12
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.023 0.09 -10000 0 -0.3 51 51
VEGFR1 homodimer 0.027 0.008 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.058 0.063 -10000 0 -0.51 4 4
GRB10 0.016 0.055 -10000 0 -0.51 6 6
PTPN11 0.029 0.003 -10000 0 -10000 0 0
GRB2 0.027 0.008 -10000 0 -10000 0 0
PAK1 0.024 0.027 -10000 0 -0.48 2 2
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.065 0.064 -10000 0 -0.48 7 7
HRAS 0.026 0.036 -10000 0 -0.48 4 4
VEGF/Rho/ROCK1/Integrin Complex 0.018 0.069 -10000 0 -0.49 8 8
HIF1A 0.021 0.061 -10000 0 -0.48 12 12
FRS2 0.028 0.009 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.059 0.052 -10000 0 -0.53 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.026 0.031 -10000 0 -0.48 3 3
Nck/Pak 0.037 0.024 -10000 0 -0.34 2 2
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.045 0.057 -10000 0 -0.55 6 6
mol:GDP 0.046 0.056 -10000 0 -0.5 4 4
mol:NADP 0.028 0.09 0.36 3 -0.45 13 16
eNOS/Hsp90 0.042 0.087 0.4 2 -0.43 12 14
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
mol:IP3 0.015 0.054 -10000 0 -0.53 5 5
HIF1A/ARNT 0.029 0.047 -10000 0 -0.34 11 11
SHB 0.029 0.005 -10000 0 -10000 0 0
VEGFA 0.029 0.01 -10000 0 -10000 0 0
VEGFC 0.025 0.036 -10000 0 -0.48 4 4
FAK1/Vinculin 0.031 0.096 0.35 1 -0.61 7 8
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.028 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.054 0.08 -10000 0 -0.38 20 20
PTPN6 0.028 0.007 -10000 0 -10000 0 0
EPAS1 0.034 0.029 -10000 0 -0.33 5 5
mol:L-citrulline 0.028 0.09 0.36 3 -0.45 13 16
ITGAV 0.028 0.025 -10000 0 -0.48 2 2
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.058 0.049 -10000 0 -0.48 4 4
VEGFR2 homodimer/VEGFA homodimer 0.048 0.06 -10000 0 -0.39 12 12
VEGFR2/3 heterodimer 0.031 0.061 -10000 0 -0.63 6 6
VEGFB 0.028 0.006 -10000 0 -10000 0 0
MAPK11 0.002 0.066 0.25 6 -0.46 8 14
VEGFR2 homodimer 0.017 0.056 -10000 0 -0.68 5 5
FLT1 0.027 0.008 -10000 0 -10000 0 0
NEDD4 0.024 0.053 -10000 0 -0.48 9 9
MAPK3 0.001 0.073 0.25 13 -0.55 4 17
MAPK1 0.003 0.076 0.25 15 -0.58 4 19
VEGFA145/NRP2 0.039 0.033 -10000 0 -0.35 5 5
VEGFR1/2 heterodimer 0.03 0.053 -10000 0 -0.62 5 5
KDR 0.017 0.056 -10000 0 -0.69 5 5
VEGFA165/NRP1/VEGFR2 homodimer 0.047 0.062 -10000 0 -0.32 17 17
SRC 0.027 0.026 -10000 0 -0.48 2 2
platelet activating factor biosynthetic process 0.01 0.084 0.27 14 -0.49 6 20
PI3K 0.031 0.07 -10000 0 -0.58 5 5
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.049 0.051 -10000 0 -0.56 5 5
FES 0.012 0.06 -10000 0 -0.53 5 5
GAB1 0.038 0.067 -10000 0 -0.61 4 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.046 0.054 -10000 0 -0.48 7 7
CTNNB1 0.028 0.019 -10000 0 -0.48 1 1
SOS1 0.029 0.003 -10000 0 -10000 0 0
ARNT 0.024 0.011 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.039 0.09 0.27 1 -0.44 13 14
VEGFR2 homodimer/VEGFA homodimer/Yes 0.045 0.057 -10000 0 -0.41 10 10
PI3K/GAB1 0.046 0.075 -10000 0 -0.52 5 5
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.066 0.054 -10000 0 -0.42 5 5
PRKACA 0.029 0.004 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.044 0.063 -10000 0 -0.46 10 10
HSP90AA1 0.028 0.005 -10000 0 -10000 0 0
CDC42 0.015 0.055 -10000 0 -0.53 5 5
actin cytoskeleton reorganization 0.023 0.089 -10000 0 -0.29 51 51
PTK2 0.01 0.077 0.26 1 -0.62 8 9
EDG1 0.005 0.052 -10000 0 -0.35 12 12
mol:DAG 0.015 0.054 -10000 0 -0.53 5 5
CaM/Ca2+ 0.032 0.055 -10000 0 -0.49 5 5
MAP2K3 0.003 0.059 -10000 0 -0.5 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.047 0.061 -10000 0 -0.52 6 6
PLCG1 0.015 0.054 -10000 0 -0.53 5 5
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.059 0.056 -10000 0 -0.46 7 7
IQGAP1 0.028 0.006 -10000 0 -10000 0 0
YES1 0.024 0.043 -10000 0 -0.48 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.049 0.051 -10000 0 -0.56 5 5
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.047 0.052 -10000 0 -0.56 5 5
cell migration 0.035 0.088 0.35 3 -0.54 7 10
mol:PI-3-4-5-P3 0.03 0.066 -10000 0 -0.54 5 5
FYN 0.026 0.027 -10000 0 -0.48 2 2
VEGFB/NRP1 0.021 0.052 -10000 0 -0.49 5 5
mol:NO 0.028 0.09 0.36 3 -0.45 13 16
PXN 0.029 0.002 -10000 0 -10000 0 0
HRAS/GTP 0.018 0.047 -10000 0 -0.47 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.038 0.058 -10000 0 -0.52 6 6
VHL 0.029 0.005 -10000 0 -10000 0 0
ITGB3 0.015 0.075 -10000 0 -0.48 18 18
NOS3 0.028 0.099 0.42 2 -0.51 13 15
VEGFR2 homodimer/VEGFA homodimer/Sck 0.027 0.092 -10000 0 -0.29 56 56
RAC1 0.029 0.005 -10000 0 -10000 0 0
PRKCA 0.003 0.062 0.35 1 -0.51 5 6
PRKCB -0.01 0.08 -10000 0 -0.61 4 4
VCL 0.029 0.005 -10000 0 -10000 0 0
VEGFA165/NRP1 0.026 0.054 -10000 0 -0.36 12 12
VEGFR1/2 heterodimer/VEGFA homodimer 0.046 0.053 -10000 0 -0.57 5 5
VEGFA165/NRP2 0.039 0.033 -10000 0 -0.35 5 5
MAPKKK cascade 0.054 0.083 0.34 8 -0.47 4 12
NRP2 0.025 0.04 -10000 0 -0.48 5 5
VEGFC homodimer 0.025 0.036 -10000 0 -0.48 4 4
NCK1 0.029 0.004 -10000 0 -10000 0 0
ROCK1 0.028 0.018 -10000 0 -0.48 1 1
FAK1/Paxillin 0.031 0.098 0.42 2 -0.58 8 10
MAP3K13 0.012 0.061 -10000 0 -0.52 6 6
PDPK1 0.017 0.059 0.25 2 -0.48 4 6
PLK2 and PLK4 events

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
PLK2 0.024 0.044 -9999 0 -0.48 6 6
PLK4 0.026 0.036 -9999 0 -0.48 4 4
regulation of centriole replication 0.009 0.038 -9999 0 -0.34 9 9
Arf6 trafficking events

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
SLC2A4 0.004 0.091 -10000 0 -0.48 27 27
CLTC 0.028 0.065 -10000 0 -0.46 9 9
calcium ion-dependent exocytosis 0.014 0.023 -10000 0 -0.25 1 1
Dynamin 2/GTP 0.025 0.01 -10000 0 -10000 0 0
EXOC4 0.029 0.005 -10000 0 -10000 0 0
CD59 0.018 0.045 -10000 0 -0.34 8 8
CPE 0.007 0.043 -10000 0 -0.29 16 16
CTNNB1 0.028 0.019 -10000 0 -0.48 1 1
membrane fusion 0.013 0.018 -10000 0 -10000 0 0
CTNND1 0.008 0.059 0.19 78 -10000 0 78
DNM2 0.029 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.019 0.046 0.2 3 -0.35 6 9
TSHR 0 0.057 -10000 0 -0.29 29 29
INS 0.008 0.016 -10000 0 -0.12 2 2
BIN1 0.023 0.05 -10000 0 -0.48 8 8
mol:Choline 0.013 0.018 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.005 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.029 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.025 0.01 -10000 0 -10000 0 0
JUP 0.019 0.037 -10000 0 -0.32 5 5
ASAP2/amphiphysin II 0.049 0.037 -10000 0 -0.27 9 9
ARF6/GTP 0.021 0.003 -10000 0 -10000 0 0
CDH1 0.004 0.065 -10000 0 -0.37 8 8
clathrin-independent pinocytosis 0.021 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.025 0.031 -10000 0 -0.48 3 3
positive regulation of endocytosis 0.021 0.003 -10000 0 -10000 0 0
EXOC2 0.027 0.013 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.023 0.038 -10000 0 -0.33 5 5
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.026 0.009 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.039 0.074 0.32 9 -10000 0 9
positive regulation of phagocytosis 0.014 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.035 0.023 -10000 0 -0.29 3 3
ACAP1 0.009 0.043 -10000 0 -0.25 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.016 0.042 -10000 0 -0.33 8 8
clathrin heavy chain/ACAP1 0.027 0.065 0.28 6 -0.36 9 15
JIP4/KLC1 0.049 0.02 -10000 0 -10000 0 0
EXOC1 0.029 0.005 -10000 0 -10000 0 0
exocyst 0.022 0.038 -10000 0 -0.34 5 5
RALA/GTP 0.021 0.003 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.035 0.013 -10000 0 -10000 0 0
receptor recycling 0.021 0.003 -10000 0 -10000 0 0
CTNNA1 0.009 0.06 0.19 81 -10000 0 81
NME1 0.013 0.005 -10000 0 -10000 0 0
clathrin coat assembly 0.032 0.068 0.26 3 -0.45 9 12
IL2RA 0.002 0.076 -10000 0 -0.32 13 13
VAMP3 0.014 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.018 0.069 -10000 0 -0.35 10 10
EXOC6 0.027 0.031 -10000 0 -0.48 3 3
PLD1 0.012 0.025 -10000 0 -0.29 5 5
PLD2 0.014 0.007 -10000 0 -10000 0 0
EXOC5 0.029 0.005 -10000 0 -10000 0 0
PIP5K1C 0.016 0.042 0.18 2 -0.36 6 8
SDC1 0.013 0.052 -10000 0 -0.32 8 8
ARF6/GDP 0.024 0.009 -10000 0 -10000 0 0
EXOC7 0.027 0.008 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.042 0.077 -10000 0 -0.34 8 8
mol:Phosphatidic acid 0.013 0.018 -10000 0 -10000 0 0
endocytosis -0.048 0.036 0.27 9 -10000 0 9
SCAMP2 0.028 0.005 -10000 0 -10000 0 0
ADRB2 0.02 0.079 0.25 3 -0.47 9 12
EXOC3 0.028 0.006 -10000 0 -10000 0 0
ASAP2 0.027 0.031 -10000 0 -0.48 3 3
Dynamin 2/GDP 0.029 0.012 -10000 0 -10000 0 0
KLC1 0.028 0.005 -10000 0 -10000 0 0
AVPR2 0.012 0.095 0.25 5 -0.5 11 16
RALA 0.029 0.005 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.036 0.076 0.32 2 -0.33 6 8
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.027 0.042 -10000 0 -0.3 11 11
VEGFR1 homodimer/NRP1 0.008 0.038 -10000 0 -0.29 13 13
mol:DAG 0.01 0.047 -10000 0 -0.29 12 12
VEGFR1 homodimer/NRP1/VEGFR 121 0.024 0.039 -10000 0 -0.27 13 13
CaM/Ca2+ 0.026 0.047 -10000 0 -0.41 2 2
HIF1A 0.026 0.062 -10000 0 -0.46 13 13
GAB1 0.028 0.018 -10000 0 -0.48 1 1
AKT1 0.013 0.051 -10000 0 -0.41 2 2
PLCG1 0.011 0.047 -10000 0 -0.29 12 12
NOS3 0.018 0.064 0.28 3 -0.44 5 8
CBL 0.026 0.009 -10000 0 -10000 0 0
mol:NO 0.021 0.072 0.29 5 -0.42 8 13
FLT1 0.013 0.043 -10000 0 -0.35 11 11
PGF 0.026 0.031 -10000 0 -0.48 3 3
VEGFR1 homodimer/NRP2/VEGFR121 0.04 0.054 -10000 0 -0.33 13 13
CALM1 0.028 0.005 -10000 0 -10000 0 0
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
eNOS/Hsp90 0.036 0.075 0.29 3 -0.4 9 12
endothelial cell proliferation 0.004 0.097 0.31 13 -0.47 12 25
mol:Ca2+ 0.01 0.047 -10000 0 -0.29 12 12
MAPK3 -0.014 0.05 -10000 0 -0.48 4 4
MAPK1 -0.014 0.051 -10000 0 -0.47 4 4
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
PLGF homodimer 0.026 0.031 -10000 0 -0.48 3 3
PRKACA 0.029 0.004 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.025 0.04 -10000 0 -0.48 5 5
VEGFA homodimer 0.028 0.009 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.027 0.043 -10000 0 -0.29 13 13
platelet activating factor biosynthetic process -0.015 0.048 -10000 0 -0.46 4 4
PI3K 0.052 0.051 -10000 0 -0.41 2 2
PRKCA -0.013 0.054 -10000 0 -0.5 4 4
PRKCB -0.024 0.074 -10000 0 -0.48 8 8
VEGFR1 homodimer/PLGF homodimer 0.026 0.048 -10000 0 -0.31 15 15
VEGFA 0.028 0.009 -10000 0 -10000 0 0
VEGFB 0.028 0.006 -10000 0 -10000 0 0
mol:IP3 0.01 0.047 -10000 0 -0.29 12 12
RASA1 0.012 0.044 -10000 0 -0.34 1 1
NRP2 0.025 0.04 -10000 0 -0.48 5 5
VEGFR1 homodimer 0.013 0.043 -10000 0 -0.35 11 11
VEGFB homodimer 0.028 0.005 -10000 0 -10000 0 0
NCK1 0.029 0.004 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.033 0.084 0.29 4 -0.45 11 15
PTPN11 0.029 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.05 0.05 -10000 0 -0.41 2 2
mol:L-citrulline 0.021 0.072 0.29 5 -0.42 8 13
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.052 0.047 -10000 0 -0.33 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.041 0.043 -10000 0 -0.27 11 11
CD2AP 0.028 0.005 -10000 0 -10000 0 0
PI3K/GAB1 0.065 0.057 -10000 0 -0.4 2 2
PDPK1 0.016 0.052 -10000 0 -0.39 2 2
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.042 0.043 -10000 0 -0.27 11 11
mol:NADP 0.021 0.072 0.29 5 -0.42 8 13
HSP90AA1 0.028 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.05 0.046 -10000 0 -0.33 1 1
VEGFR1 homodimer/NRP2 0.025 0.054 -10000 0 -0.35 15 15
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.019 0.085 -10000 0 -1 5 5
regulation of axonogenesis -0.008 0.025 0.26 4 -10000 0 4
myoblast fusion -0.018 0.046 0.44 5 -10000 0 5
mol:GTP 0.019 0.027 -10000 0 -0.23 5 5
regulation of calcium-dependent cell-cell adhesion -0.047 0.051 0.27 15 -10000 0 15
ARF1/GTP 0.029 0.027 -10000 0 -0.18 3 3
mol:GM1 0.008 0.019 -10000 0 -0.18 4 4
mol:Choline 0.006 0.027 -10000 0 -0.28 5 5
lamellipodium assembly 0.009 0.056 -10000 0 -0.4 10 10
MAPK3 0.021 0.032 -10000 0 -0.34 5 5
ARF6/GTP/NME1/Tiam1 0.048 0.051 -10000 0 -0.27 15 15
ARF1 0.024 0.011 -10000 0 -10000 0 0
ARF6/GDP 0.018 0.046 -10000 0 -0.44 5 5
ARF1/GDP 0.019 0.049 -10000 0 -0.34 7 7
ARF6 0.033 0.018 -10000 0 -10000 0 0
RAB11A 0.029 0.005 -10000 0 -10000 0 0
TIAM1 0.022 0.059 -10000 0 -0.48 11 11
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.022 0.03 -10000 0 -0.35 4 4
actin filament bundle formation -0.033 0.049 0.34 8 -10000 0 8
KALRN 0.005 0.049 -10000 0 -0.27 22 22
RAB11FIP3/RAB11A 0.037 0.03 -10000 0 -0.34 4 4
RhoA/GDP 0.033 0.049 -10000 0 -0.34 8 8
NME1 0.027 0.011 -10000 0 -10000 0 0
Rac1/GDP 0.034 0.049 -10000 0 -0.33 9 9
substrate adhesion-dependent cell spreading 0.018 0.027 -10000 0 -0.23 5 5
cortical actin cytoskeleton organization 0.009 0.056 -10000 0 -0.4 10 10
RAC1 0.029 0.005 -10000 0 -10000 0 0
liver development 0.018 0.027 -10000 0 -0.23 5 5
ARF6/GTP 0.019 0.027 -10000 0 -0.23 5 5
RhoA/GTP 0.034 0.026 -10000 0 -0.18 4 4
mol:GDP 0.009 0.043 -10000 0 -0.38 7 7
ARF6/GTP/RAB11FIP3/RAB11A 0.047 0.036 -10000 0 -0.26 5 5
RHOA 0.028 0.006 -10000 0 -10000 0 0
PLD1 0.014 0.037 -10000 0 -0.27 10 10
RAB11FIP3 0.025 0.036 -10000 0 -0.48 4 4
tube morphogenesis 0.009 0.056 -10000 0 -0.4 10 10
ruffle organization 0.008 0.025 -10000 0 -0.26 4 4
regulation of epithelial cell migration 0.018 0.027 -10000 0 -0.23 5 5
PLD2 0.017 0.02 -10000 0 -0.19 3 3
PIP5K1A 0.008 0.025 -10000 0 -0.26 4 4
mol:Phosphatidic acid 0.006 0.027 -10000 0 -0.28 5 5
Rac1/GTP 0.009 0.056 -10000 0 -0.41 10 10
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.018 0.13 -10000 0 -0.42 32 32
CaM/Ca2+ 0.021 0.004 -10000 0 -10000 0 0
AKT1 0.028 0.005 -10000 0 -10000 0 0
AKT2 0.029 0.005 -10000 0 -10000 0 0
STXBP4 0.026 0.02 -10000 0 -0.48 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.002 0.13 0.36 1 -0.42 41 42
YWHAZ 0.022 0.013 -10000 0 -10000 0 0
CALM1 0.028 0.005 -10000 0 -10000 0 0
YWHAQ 0.029 0.004 -10000 0 -10000 0 0
TBC1D4 0.013 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.028 0.007 -10000 0 -10000 0 0
YWHAB 0.028 0.007 -10000 0 -10000 0 0
SNARE/Synip 0.045 0.032 -10000 0 -0.29 3 3
YWHAG 0.029 0.004 -10000 0 -10000 0 0
ASIP 0.023 0.013 -10000 0 -10000 0 0
PRKCI 0.028 0.006 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.021 0.004 -10000 0 -10000 0 0
RHOQ 0.029 0.003 -10000 0 -10000 0 0
GYS1 0.012 0.015 0.25 3 -10000 0 3
PRKCZ 0.027 0.026 -10000 0 -0.48 2 2
TRIP10 0.028 0.025 -10000 0 -0.48 2 2
TC10/GTP/CIP4/Exocyst 0.038 0.018 -10000 0 -0.29 2 2
AS160/14-3-3 0.022 0.063 -10000 0 -0.28 12 12
VAMP2 0.026 0.009 -10000 0 -10000 0 0
SLC2A4 -0.001 0.14 0.37 1 -0.47 41 42
STX4 0.026 0.026 -10000 0 -0.48 2 2
GSK3B 0.022 0.006 -10000 0 -10000 0 0
SFN 0.014 0.082 -10000 0 -0.48 22 22
LNPEP 0.021 0.058 -10000 0 -0.48 11 11
YWHAE 0.027 0.009 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.013 0.003 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.035 0.022 -10000 0 -10000 0 0
CDKN1B 0.011 0.062 -10000 0 -0.42 6 6
CDKN1A 0.011 0.064 -10000 0 -0.4 9 9
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.025 0.01 -10000 0 -10000 0 0
FOXO3 0.014 0.061 -10000 0 -0.46 6 6
AKT1 0.009 0.056 -10000 0 -0.39 11 11
BAD 0.028 0.006 -10000 0 -10000 0 0
AKT3 0.008 0.032 -10000 0 -0.31 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.01 0.063 -10000 0 -0.44 7 7
AKT1/ASK1 0.037 0.071 -10000 0 -0.34 14 14
BAD/YWHAZ 0.043 0.027 -10000 0 -10000 0 0
RICTOR 0.028 0.018 -10000 0 -0.48 1 1
RAF1 0.029 0.005 -10000 0 -10000 0 0
JNK cascade -0.035 0.068 0.33 14 -10000 0 14
TSC1 0.013 0.053 -10000 0 -0.61 2 2
YWHAZ 0.022 0.013 -10000 0 -10000 0 0
AKT1/RAF1 0.042 0.074 0.27 1 -0.43 7 8
EP300 0.028 0.007 -10000 0 -10000 0 0
mol:GDP 0.014 0.064 -10000 0 -0.36 16 16
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.009 0.056 -10000 0 -0.39 7 7
YWHAQ 0.029 0.004 -10000 0 -10000 0 0
TBC1D4 0.006 0.003 -10000 0 -10000 0 0
MAP3K5 0.027 0.026 -10000 0 -0.48 2 2
MAPKAP1 0.029 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.029 0.077 0.3 19 -0.2 10 29
YWHAH 0.028 0.007 -10000 0 -10000 0 0
AKT1S1 0.014 0.064 -10000 0 -0.42 8 8
CASP9 0.013 0.047 -10000 0 -0.4 3 3
YWHAB 0.028 0.007 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.038 0.078 0.28 5 -0.49 4 9
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.05 0.027 -10000 0 -0.3 2 2
YWHAE 0.027 0.009 -10000 0 -10000 0 0
SRC 0.027 0.026 -10000 0 -0.48 2 2
AKT2/p21CIP1 0.015 0.065 0.25 3 -0.44 6 9
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.011 0.055 -10000 0 -0.32 17 17
CHUK 0.012 0.057 -10000 0 -0.4 6 6
BAD/BCL-XL 0.044 0.072 0.27 2 -0.58 3 5
mTORC2 0.036 0.013 -10000 0 -0.26 1 1
AKT2 0.014 0.005 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.036 0.1 0.31 5 -0.43 17 22
PDPK1 0.027 0.008 -10000 0 -10000 0 0
MDM2 0.013 0.067 -10000 0 -0.44 7 7
MAPKKK cascade -0.042 0.073 0.42 7 -0.26 1 8
MDM2/Cbp/p300 0.05 0.078 0.31 6 -0.56 3 9
TSC1/TSC2 0.016 0.07 0.26 28 -0.59 3 31
proteasomal ubiquitin-dependent protein catabolic process 0.047 0.074 0.28 8 -0.53 3 11
glucose import -0.006 0.046 0.2 6 -0.25 23 29
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.013 0.051 0.18 1 -0.41 4 5
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.006 0.046 0.2 6 -0.26 23 29
GSK3A 0.012 0.062 -10000 0 -0.44 7 7
FOXO1 0.016 0.034 -10000 0 -0.29 3 3
GSK3B 0.012 0.063 -10000 0 -0.44 7 7
SFN 0.014 0.082 -10000 0 -0.48 22 22
G1/S transition of mitotic cell cycle 0.016 0.066 0.28 2 -0.6 3 5
p27Kip1/14-3-3 family 0.021 0.05 -10000 0 -0.41 3 3
PRKACA 0.029 0.004 -10000 0 -10000 0 0
KPNA1 0.029 0.004 -10000 0 -10000 0 0
HSP90AA1 0.028 0.005 -10000 0 -10000 0 0
YWHAG 0.029 0.004 -10000 0 -10000 0 0
RHEB 0.028 0.005 -10000 0 -10000 0 0
CREBBP 0.027 0.019 -10000 0 -0.48 1 1
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.039 0.05 -10000 0 -0.25 22 22
MAPK9 0.008 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion 0 0 -10000 0 -10000 0 0
GNB1/GNG2 0.037 0.016 -10000 0 -0.29 1 1
GNB1 0.028 0.006 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.008 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.01 0.045 -10000 0 -0.26 21 21
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 0.003 0.011 0.071 21 -10000 0 21
GNAL 0.013 0.081 -10000 0 -0.48 21 21
GNG2 0.028 0.019 -10000 0 -0.48 1 1
CRH 0 0 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.008 0.001 -10000 0 -10000 0 0
MAPK11 0.005 0.025 -10000 0 -0.32 5 5
Circadian rhythm pathway

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
chromatin modification 0.044 0.032 -10000 0 -10000 0 0
CLOCK 0.026 0.047 -10000 0 -0.48 7 7
TIMELESS/CRY2 0.035 0.027 -10000 0 -10000 0 0
DEC1/BMAL1 0.022 0.013 -10000 0 -0.34 1 1
ATR 0.029 0.005 -10000 0 -10000 0 0
NR1D1 0.016 0.048 -10000 0 -1.3 1 1
ARNTL 0.03 0.019 -10000 0 -0.48 1 1
TIMELESS 0.019 0.021 -10000 0 -10000 0 0
NPAS2 0.014 0.083 -10000 0 -0.48 22 22
CRY2 0.029 0.004 -10000 0 -10000 0 0
mol:CO -0.008 0.005 0.14 1 -10000 0 1
CHEK1 0.026 0.011 -10000 0 -10000 0 0
mol:HEME 0.008 0.005 -10000 0 -0.14 1 1
PER1 0.025 0.013 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.053 0.068 -10000 0 -0.29 29 29
BMAL1/CLOCK 0.024 0.07 -10000 0 -0.68 2 2
S phase of mitotic cell cycle 0.044 0.032 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.045 0.033 -10000 0 -10000 0 0
mol:NADPH 0.008 0.005 -10000 0 -0.14 1 1
PER1/TIMELESS 0.033 0.025 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0 0 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.027 0.019 -10000 0 -0.48 1 1
SMAD2 -0.001 0.038 0.2 1 -0.23 5 6
SMAD3 0.025 0.032 -10000 0 -0.41 1 1
SMAD3/SMAD4 0.035 0.06 -10000 0 -0.49 7 7
SMAD4/Ubc9/PIASy 0.051 0.024 -10000 0 -0.3 1 1
SMAD2/SMAD2/SMAD4 0.042 0.057 -10000 0 -0.28 2 2
PPM1A 0.029 0.005 -10000 0 -10000 0 0
CALM1 0.028 0.005 -10000 0 -10000 0 0
SMAD2/SMAD4 0.012 0.046 -10000 0 -0.26 7 7
MAP3K1 0.027 0.026 -10000 0 -0.48 2 2
TRAP-1/SMAD4 0.035 0.051 -10000 0 -0.34 14 14
MAPK3 0.027 0.007 -10000 0 -10000 0 0
MAPK1 0.028 0.007 -10000 0 -10000 0 0
NUP214 0.029 0.005 -10000 0 -10000 0 0
CTDSP1 0.029 0.004 -10000 0 -10000 0 0
CTDSP2 0.029 0.004 -10000 0 -10000 0 0
CTDSPL 0.029 0.005 -10000 0 -10000 0 0
KPNB1 0.027 0.007 -10000 0 -10000 0 0
TGFBRAP1 0.021 0.063 -10000 0 -0.48 13 13
UBE2I 0.027 0.008 -10000 0 -10000 0 0
NUP153 0.028 0.005 -10000 0 -10000 0 0
KPNA2 0.026 0.009 -10000 0 -10000 0 0
PIAS4 0.028 0.005 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.028 0.018 -10000 0 -0.48 1 1
Ran/GTP/Exportin 1/HDAC4 0.005 0.012 -10000 0 -0.21 1 1
MDM2/SUMO1 0.04 0.042 -10000 0 -0.23 3 3
HDAC4 0.028 0.018 -10000 0 -0.48 1 1
Ran/GTP/Exportin 1/HDAC1 0.005 0.012 -10000 0 -0.21 1 1
SUMO1 0.029 0.004 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.011 0.019 -10000 0 -0.22 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.009 0.011 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.029 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.029 0.003 -10000 0 -10000 0 0
SUMO1/HDAC4 0.042 0.041 -10000 0 -0.22 4 4
SUMO1/HDAC1 0.042 0.041 -10000 0 -0.23 4 4
RANGAP1 0.028 0.007 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.067 0.026 -10000 0 -0.25 1 1
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.014 0.006 -10000 0 -10000 0 0
Ran/GTP 0.028 0.037 -10000 0 -0.2 7 7
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.028 0.006 -10000 0 -10000 0 0
UBE2I 0.027 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.027 0.039 0.2 6 -0.23 3 9
NPC 0.017 0.002 -10000 0 -10000 0 0
PIAS2 0.028 0.018 -10000 0 -0.48 1 1
PIAS1 0.029 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.012 0.032 0.16 3 -10000 0 3
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.027 0.047 -10000 0 -0.18 3 3
AP2 0.041 0.01 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.037 0.012 -10000 0 -10000 0 0
CLTB 0.028 0.019 -10000 0 -0.48 1 1
coatomer protein complex/ARF1/GTP/ER cargo protein 0.016 0.013 -10000 0 -0.23 1 1
CD4 0.025 0.036 -10000 0 -0.48 4 4
CLTA 0.028 0.005 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.007 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.009 0.016 -10000 0 -10000 0 0
ARF1/GTP 0.029 0.018 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.009 0.008 -10000 0 -10000 0 0
mol:Choline 0.008 0.016 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.026 0.012 -10000 0 -10000 0 0
DDEF1 0.008 0.017 -10000 0 -10000 0 0
ARF1/GDP 0.001 0.021 -10000 0 -0.11 8 8
AP2M1 0.028 0.005 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.012 0.007 -10000 0 -10000 0 0
Rac/GTP 0.024 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.031 0.02 -10000 0 -10000 0 0
ARFIP2 0.018 0.02 -10000 0 -10000 0 0
COPA 0.025 0.011 -10000 0 -10000 0 0
RAC1 0.029 0.005 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.015 0.03 -10000 0 -0.2 2 2
ARF1/GTP/ARHGAP10 0.016 0.01 -10000 0 -10000 0 0
GGA3 0.027 0.008 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.015 0.045 -10000 0 -0.24 18 18
AP2A1 0.029 0.005 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.01 0.026 -10000 0 -0.22 6 6
ARF1/GDP/Membrin 0.015 0.054 -10000 0 -0.26 26 26
Arfaptin 2/Rac/GDP 0.034 0.012 -10000 0 -10000 0 0
CYTH2 0.034 0.01 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.031 0.018 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.021 0.003 -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 0.022 0.028 -10000 0 -0.19 3 3
PLD2 0.008 0.017 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.007 0.002 -10000 0 -10000 0 0
PIP5K1A 0.009 0.016 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.017 0.023 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.008 0.016 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.007 0.002 -10000 0 -10000 0 0
GOSR2 0.011 0.028 -10000 0 -0.31 5 5
USO1 0.011 0.023 -10000 0 -0.32 3 3
GBF1 0.012 0.022 -10000 0 -0.31 3 3
ARF1/GTP/Arfaptin 2 0.033 0.018 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.052 0.03 -10000 0 -0.29 4 4
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.041 0.011 -9999 0 -10000 0 0
FBXW11 0.029 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.028 0.005 -9999 0 -10000 0 0
CHUK 0.029 0.004 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.078 0.031 -9999 0 -0.26 2 2
NFKB1 0.028 0.018 -9999 0 -0.48 1 1
MAP3K14 0.028 0.006 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.04 0.026 -9999 0 -0.34 3 3
RELB 0.027 0.026 -9999 0 -0.48 2 2
NFKB2 0.029 0.005 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.037 0.019 -9999 0 -0.29 2 2
regulation of B cell activation 0.036 0.019 -9999 0 -0.29 2 2
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 824 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.HN.A2NL TCGA.GM.A3NY TCGA.GM.A2DO TCGA.GM.A2DN
109_MAP3K5 0.032 0.032 0.024 0.032
47_PPARGC1A -0.055 0.029 0.029 0.029
105_BMP4 -0.48 0.029 -0.48 0.029
105_BMP6 0.029 0.029 0.029 0.029
105_BMP7 -0.055 0.029 0.029 0.029
105_BMP2 -0.055 0.029 0.029 0.029
131_RELN/VLDLR 0.066 -0.27 0.076 -0.27
30_TGFB1/TGF beta receptor Type II 0.034 0.029 0.029 0.029
84_STAT5B -0.2 0.037 -0.03 0.036
84_STAT5A -0.2 0.037 -0.03 0.036
Methods & Data
Input

  • Expression Data Normalization = Expression data was not used in this analysis.

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BRCA-TP/2282001/0.mRNAseq_preprocessor.Finished/BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Pipeline/BRCA-TP/2281994/1.Gistic2_Analysis.Finished/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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