PARADIGM pathway analysis of mRNASeq expression data
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C17943DG
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 47 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
HIF-1-alpha transcription factor network 214
TCGA08_retinoblastoma 190
Nephrin/Neph1 signaling in the kidney podocyte 183
TCR signaling in naïve CD8+ T cells 144
TCGA08_p53 142
Aurora B signaling 122
Syndecan-4-mediated signaling events 118
FOXM1 transcription factor network 109
FOXA2 and FOXA3 transcription factor networks 108
IL12-mediated signaling events 106
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 518 . Pathway is significant if Significance.Ratio > 0.05 .

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

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

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

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

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

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

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

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

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

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 518 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
HIF-1-alpha transcription factor network 0.4131 214 16332 76 -1.3 0.026 1000 -1000 -0.16 -1000
TCGA08_retinoblastoma 0.3668 190 1520 8 -0.84 0.22 1000 -1000 -0.049 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.3533 183 6234 34 -0.61 0.016 1000 -1000 -0.098 -1000
TCR signaling in naïve CD8+ T cells 0.2780 144 13415 93 -0.66 0.33 1000 -1000 -0.12 -1000
TCGA08_p53 0.2741 142 999 7 -0.65 0.31 1000 -1000 -0.018 -1000
Aurora B signaling 0.2355 122 8181 67 -0.41 0.016 1000 -1000 -0.1 -1000
Syndecan-4-mediated signaling events 0.2278 118 7941 67 -0.65 0.11 1000 -1000 -0.13 -1000
FOXM1 transcription factor network 0.2104 109 5606 51 -0.82 0.04 1000 -1000 -0.18 -1000
FOXA2 and FOXA3 transcription factor networks 0.2085 108 4983 46 -1.2 0.025 1000 -1000 -0.12 -1000
IL12-mediated signaling events 0.2046 106 9265 87 -0.7 0.16 1000 -1000 -0.16 -1000
PDGFR-alpha signaling pathway 0.1969 102 4510 44 -0.28 0.034 1000 -1000 -0.085 -1000
amb2 Integrin signaling 0.1622 84 6904 82 -0.56 0.016 1000 -1000 -0.11 -1000
Glypican 1 network 0.1525 79 3804 48 -0.56 0.045 1000 -1000 -0.073 -1000
IL4-mediated signaling events 0.1467 76 6974 91 -0.84 0.54 1000 -1000 -0.16 -1000
JNK signaling in the CD4+ TCR pathway 0.1448 75 1284 17 -0.42 0.016 1000 -1000 -0.091 -1000
EGFR-dependent Endothelin signaling events 0.1390 72 1522 21 -0.67 0.016 1000 -1000 -0.1 -1000
Caspase cascade in apoptosis 0.1351 70 5189 74 -0.33 0.16 1000 -1000 -0.068 -1000
Aurora C signaling 0.1332 69 489 7 -0.4 0.012 1000 -1000 -0.051 -1000
Glypican 2 network 0.1313 68 272 4 -0.12 -1000 1000 -1000 -0.06 -1000
Syndecan-1-mediated signaling events 0.1255 65 2239 34 -0.42 0.016 1000 -1000 -0.1 -1000
BMP receptor signaling 0.1197 62 5095 81 -0.7 0.016 1000 -1000 -0.13 -1000
HIF-2-alpha transcription factor network 0.1139 59 2560 43 -0.76 0.34 1000 -1000 -0.12 -1000
IL23-mediated signaling events 0.1139 59 3571 60 -0.4 0.021 1000 -1000 -0.19 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.1139 59 1955 33 -0.83 0.016 1000 -1000 -0.098 -1000
Signaling events mediated by the Hedgehog family 0.0965 50 2644 52 -0.44 0.12 1000 -1000 -0.11 -1000
Fc-epsilon receptor I signaling in mast cells 0.0869 45 4449 97 -0.32 0.04 1000 -1000 -0.13 -1000
IL27-mediated signaling events 0.0830 43 2213 51 -0.61 0.078 1000 -1000 -0.1 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0830 43 2966 68 -0.55 0.064 1000 -1000 -0.16 -1000
Effects of Botulinum toxin 0.0792 41 1072 26 -0.37 0.016 1000 -1000 -0.086 -1000
Ephrin A reverse signaling 0.0753 39 277 7 -0.057 0 1000 -1000 -0.043 -1000
Arf6 signaling events 0.0734 38 2400 62 -0.67 0.016 1000 -1000 -0.092 -1000
Calcium signaling in the CD4+ TCR pathway 0.0714 37 1164 31 -0.46 0.016 1000 -1000 -0.16 -1000
VEGFR1 specific signals 0.0714 37 2087 56 -0.47 0.046 1000 -1000 -0.12 -1000
p75(NTR)-mediated signaling 0.0676 35 4409 125 -0.42 0.016 1000 -1000 -0.14 -1000
S1P1 pathway 0.0656 34 1255 36 -0.38 0.018 1000 -1000 -0.1 -1000
IL2 signaling events mediated by PI3K 0.0656 34 1972 58 -0.44 0.031 1000 -1000 -0.11 -1000
LPA4-mediated signaling events 0.0637 33 402 12 -0.16 0.026 1000 -1000 -0.038 -1000
PLK1 signaling events 0.0637 33 2829 85 -0.38 0.016 1000 -1000 -0.07 -1000
IL2 signaling events mediated by STAT5 0.0637 33 746 22 -0.44 0.038 1000 -1000 -0.061 -1000
BCR signaling pathway 0.0637 33 3323 99 -0.34 0.035 1000 -1000 -0.12 -1000
Coregulation of Androgen receptor activity 0.0579 30 2283 76 -0.92 0.033 1000 -1000 -0.069 -1000
Integrins in angiogenesis 0.0560 29 2496 84 -0.38 0.039 1000 -1000 -0.14 -1000
Regulation of Telomerase 0.0560 29 3011 102 -0.67 0.051 1000 -1000 -0.14 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0521 27 1506 54 -0.66 0.031 1000 -1000 -0.14 -1000
EPO signaling pathway 0.0521 27 1520 55 -0.29 0.018 1000 -1000 -0.14 -1000
IL6-mediated signaling events 0.0521 27 2035 75 -0.28 0.076 1000 -1000 -0.13 -1000
Glucocorticoid receptor regulatory network 0.0502 26 3004 114 -0.41 0.16 1000 -1000 -0.1 -1000
Aurora A signaling 0.0463 24 1461 60 -0.24 0.053 1000 -1000 -0.091 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0444 23 2046 88 -0.32 0.074 1000 -1000 -0.16 -1000
Visual signal transduction: Rods 0.0444 23 1226 52 -0.29 0.016 1000 -1000 -0.14 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0444 23 1846 78 -0.32 0.045 1000 -1000 -0.11 -1000
Reelin signaling pathway 0.0425 22 1282 56 -0.24 0.016 1000 -1000 -0.12 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0425 22 1006 45 -0.58 0.061 1000 -1000 -0.12 -1000
Syndecan-2-mediated signaling events 0.0386 20 1415 69 -0.56 0.054 1000 -1000 -0.092 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0367 19 2307 120 -0.17 0.14 1000 -1000 -0.11 -1000
Regulation of nuclear SMAD2/3 signaling 0.0328 17 2366 136 -0.45 0.1 1000 -1000 -0.12 -1000
Signaling events mediated by PTP1B 0.0328 17 1361 76 -0.67 0.049 1000 -1000 -0.13 -1000
Endothelins 0.0328 17 1676 96 -0.35 0.088 1000 -1000 -0.11 -1000
Wnt signaling 0.0328 17 123 7 -0.07 0.016 1000 -1000 -0.074 -1000
Presenilin action in Notch and Wnt signaling 0.0309 16 1011 61 -0.19 0.093 1000 -1000 -0.093 -1000
S1P3 pathway 0.0309 16 698 42 -0.38 0.062 1000 -1000 -0.084 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0290 15 590 37 -0.3 0.026 1000 -1000 -0.13 -1000
FoxO family signaling 0.0290 15 988 64 -0.57 0.12 1000 -1000 -0.1 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0270 14 402 28 -0.13 0.025 1000 -1000 -0.088 -1000
PLK2 and PLK4 events 0.0270 14 42 3 -0.015 0.011 1000 -1000 -0.021 -1000
Thromboxane A2 receptor signaling 0.0270 14 1518 105 -0.67 0.066 1000 -1000 -0.11 -1000
Ceramide signaling pathway 0.0270 14 1135 76 -0.67 0.23 1000 -1000 -0.091 -1000
LPA receptor mediated events 0.0270 14 1513 102 -0.4 0.061 1000 -1000 -0.14 -1000
FAS signaling pathway (CD95) 0.0251 13 638 47 -0.43 0.028 1000 -1000 -0.07 -1000
Canonical Wnt signaling pathway 0.0251 13 692 51 -0.19 0.096 1000 -1000 -0.086 -1000
Class I PI3K signaling events 0.0251 13 1013 73 -0.46 0.036 1000 -1000 -0.11 -1000
E-cadherin signaling events 0.0251 13 68 5 -0.023 0.016 1000 -1000 -0.068 -1000
IFN-gamma pathway 0.0232 12 869 68 -0.38 0.017 1000 -1000 -0.14 -1000
Nongenotropic Androgen signaling 0.0232 12 642 52 -0.18 0.071 1000 -1000 -0.082 -1000
Regulation of Androgen receptor activity 0.0232 12 898 70 -0.96 0.04 1000 -1000 -0.098 -1000
ErbB4 signaling events 0.0212 11 802 69 -0.18 0.1 1000 -1000 -0.13 -1000
Noncanonical Wnt signaling pathway 0.0212 11 296 26 -0.11 0.016 1000 -1000 -0.12 -1000
S1P5 pathway 0.0212 11 187 17 -0.13 0.045 1000 -1000 -0.08 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0212 11 1458 125 -0.39 0.044 1000 -1000 -0.14 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0212 11 817 74 -0.67 0.099 1000 -1000 -0.14 -1000
S1P4 pathway 0.0193 10 265 25 -0.13 0.035 1000 -1000 -0.076 -1000
Visual signal transduction: Cones 0.0174 9 354 38 -0.041 0.016 1000 -1000 -0.1 -1000
a4b1 and a4b7 Integrin signaling 0.0174 9 45 5 -0.019 0.016 1000 -1000 -0.056 -1000
Signaling events regulated by Ret tyrosine kinase 0.0154 8 664 82 -0.064 0.027 1000 -1000 -0.13 -1000
TCGA08_rtk_signaling 0.0154 8 232 26 -0.28 0.041 1000 -1000 -0.035 -1000
Canonical NF-kappaB pathway 0.0116 6 269 39 -0.19 0.075 1000 -1000 -0.11 -1000
IL1-mediated signaling events 0.0116 6 393 62 -0.091 0.06 1000 -1000 -0.14 -1000
Signaling events mediated by PRL 0.0116 6 231 34 -0.056 0.046 1000 -1000 -0.08 -1000
Class IB PI3K non-lipid kinase events 0.0116 6 18 3 -0.006 0.006 1000 -1000 -0.023 -1000
ErbB2/ErbB3 signaling events 0.0097 5 357 65 -0.13 0.059 1000 -1000 -0.1 -1000
Insulin-mediated glucose transport 0.0097 5 183 32 -0.086 0.067 1000 -1000 -0.095 -1000
Signaling events mediated by HDAC Class III 0.0097 5 236 40 -0.059 0.033 1000 -1000 -0.07 -1000
Ephrin B reverse signaling 0.0097 5 283 48 -0.027 0.032 1000 -1000 -0.1 -1000
Signaling mediated by p38-gamma and p38-delta 0.0097 5 82 15 0 0.037 1000 -1000 -0.056 -1000
Syndecan-3-mediated signaling events 0.0097 5 205 35 -0.04 0.016 1000 -1000 -0.096 -1000
E-cadherin signaling in the nascent adherens junction 0.0097 5 412 76 -0.026 0.068 1000 -1000 -0.12 -1000
Arf6 trafficking events 0.0097 5 395 71 -0.12 0.058 1000 -1000 -0.11 -1000
BARD1 signaling events 0.0077 4 237 57 -0.17 0.043 1000 -1000 -0.1 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0077 4 370 85 -0.037 0.079 1000 -1000 -0.11 -1000
Arf6 downstream pathway 0.0077 4 214 43 -0.033 0.033 1000 -1000 -0.057 -1000
EPHB forward signaling 0.0077 4 345 85 -0.074 0.07 1000 -1000 -0.14 -1000
p38 MAPK signaling pathway 0.0077 4 199 44 -0.1 0.049 1000 -1000 -0.095 -1000
Ras signaling in the CD4+ TCR pathway 0.0077 4 83 17 -0.037 0.055 1000 -1000 -0.071 -1000
Cellular roles of Anthrax toxin 0.0058 3 119 39 -0.022 0.027 1000 -1000 -0.048 -1000
Plasma membrane estrogen receptor signaling 0.0058 3 331 86 -0.17 0.072 1000 -1000 -0.12 -1000
E-cadherin signaling in keratinocytes 0.0058 3 142 43 -0.29 0.054 1000 -1000 -0.12 -1000
Osteopontin-mediated events 0.0039 2 113 38 -0.03 0.099 1000 -1000 -0.15 -1000
Hedgehog signaling events mediated by Gli proteins 0.0039 2 131 65 -0.062 0.093 1000 -1000 -0.089 -1000
ceramide signaling pathway 0.0039 2 131 49 -0.12 0.054 1000 -1000 -0.061 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0039 2 129 52 -0.031 0.093 1000 -1000 -0.096 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0039 2 176 83 -0.086 0.081 1000 -1000 -0.12 -1000
Signaling events mediated by HDAC Class I 0.0039 2 211 104 -0.029 0.064 1000 -1000 -0.098 -1000
Retinoic acid receptors-mediated signaling 0.0039 2 122 58 -0.026 0.063 1000 -1000 -0.11 -1000
Paxillin-dependent events mediated by a4b1 0.0039 2 101 36 -0.026 0.031 1000 -1000 -0.11 -1000
Regulation of p38-alpha and p38-beta 0.0039 2 148 54 -0.041 0.073 1000 -1000 -0.084 -1000
IGF1 pathway 0.0039 2 114 57 -0.065 0.071 1000 -1000 -0.15 -1000
Insulin Pathway 0.0039 2 195 74 -0.034 0.055 1000 -1000 -0.14 -1000
PDGFR-beta signaling pathway 0.0039 2 243 97 -0.057 0.087 1000 -1000 -0.14 -1000
Signaling events mediated by HDAC Class II 0.0019 1 120 75 -0.027 0.051 1000 -1000 -0.097 -1000
Circadian rhythm pathway 0.0019 1 33 22 -0.019 0.064 1000 -1000 -0.094 -1000
mTOR signaling pathway 0.0019 1 65 53 -0.008 0.044 1000 -1000 -0.091 -1000
Class I PI3K signaling events mediated by Akt 0.0019 1 104 68 -0.086 0.06 1000 -1000 -0.094 -1000
Nectin adhesion pathway 0.0019 1 74 63 -0.015 0.08 1000 -1000 -0.12 -1000
Atypical NF-kappaB pathway 0.0019 1 52 31 -0.021 0.037 1000 -1000 -0.095 -1000
Signaling mediated by p38-alpha and p38-beta 0.0019 1 67 44 -0.043 0.051 1000 -1000 -0.075 -1000
Alternative NF-kappaB pathway 0.0019 1 14 13 -0.005 0.016 1000 -1000 -0.091 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 2 23 -0.001 0.062 1000 -1000 -0.11 -1000
TRAIL signaling pathway 0.0000 0 30 48 -0.002 0.071 1000 -1000 -0.087 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 0 27 0 0.039 1000 -1000 -0.082 -1000
Rapid glucocorticoid signaling 0.0000 0 12 20 -0.005 0.016 1000 -1000 -0.059 -1000
Arf1 pathway 0.0000 0 31 54 -0.01 0.043 1000 -1000 -0.075 -1000
Total NA 3930 214381 7203 -40 -990 131000 -131000 -13 -131000
HIF-1-alpha transcription factor network

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
PKM2 -0.98 0.53 -9999 0 -1.3 332 332
HDAC7 0.014 0.005 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.68 0.33 -9999 0 -0.91 303 303
SMAD4 0.017 0 -9999 0 -10000 0 0
ID2 -0.98 0.53 -9999 0 -1.3 332 332
AP1 -0.014 0.088 -9999 0 -0.56 13 13
ABCG2 -0.98 0.53 -9999 0 -1.3 333 333
HIF1A -0.11 0.068 -9999 0 -0.89 2 2
TFF3 -0.99 0.53 -9999 0 -1.3 335 335
GATA2 0 0.12 -9999 0 -0.74 12 12
AKT1 -0.094 0.052 -9999 0 -10000 0 0
response to hypoxia -0.13 0.057 -9999 0 -10000 0 0
MCL1 -0.98 0.53 -9999 0 -1.3 331 331
NDRG1 -0.98 0.53 -9999 0 -1.3 334 334
SERPINE1 -1 0.56 -9999 0 -1.4 333 333
FECH -0.98 0.53 -9999 0 -1.3 332 332
FURIN -0.98 0.53 -9999 0 -1.3 334 334
NCOA2 -0.002 0.099 -9999 0 -0.75 9 9
EP300 -0.1 0.074 -9999 0 -0.36 7 7
HMOX1 -1 0.54 -9999 0 -1.3 335 335
BHLHE40 -0.98 0.53 -9999 0 -1.3 332 332
BHLHE41 -1.1 0.58 -9999 0 -1.4 341 341
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.079 0.056 -9999 0 -0.6 2 2
ENG -0.059 0.062 -9999 0 -10000 0 0
JUN 0.016 0.003 -9999 0 -10000 0 0
RORA -0.98 0.53 -9999 0 -1.3 334 334
ABCB1 -0.3 0.42 -9999 0 -1.3 68 68
TFRC -0.98 0.53 -9999 0 -1.3 332 332
CXCR4 -1.1 0.59 -9999 0 -1.4 341 341
TF -1 0.58 -9999 0 -1.4 339 339
CITED2 -0.98 0.53 -9999 0 -1.3 332 332
HIF1A/ARNT -1.3 0.85 -9999 0 -1.7 350 350
LDHA -0.086 0.063 -9999 0 -0.86 2 2
ETS1 -0.98 0.53 -9999 0 -1.3 332 332
PGK1 -0.98 0.53 -9999 0 -1.3 329 329
NOS2 -0.99 0.53 -9999 0 -1.3 336 336
ITGB2 -1 0.56 -9999 0 -1.4 338 338
ALDOA -0.98 0.53 -9999 0 -1.3 332 332
Cbp/p300/CITED2 -0.98 0.53 -9999 0 -1.4 298 298
FOS -0.003 0.12 -9999 0 -0.75 13 13
HK2 -1.2 0.58 -9999 0 -1.5 393 393
SP1 0.021 0.029 -9999 0 -10000 0 0
GCK -0.18 0.18 -9999 0 -1.2 9 9
HK1 -0.98 0.53 -9999 0 -1.3 332 332
NPM1 -0.98 0.53 -9999 0 -1.3 332 332
EGLN1 -0.98 0.53 -9999 0 -1.3 327 327
CREB1 0.026 0.002 -9999 0 -10000 0 0
PGM1 -0.98 0.53 -9999 0 -1.3 332 332
SMAD3 0.017 0 -9999 0 -10000 0 0
EDN1 -0.091 0.16 -9999 0 -0.8 18 18
IGFBP1 -1 0.57 -9999 0 -1.4 337 337
VEGFA -0.78 0.41 -9999 0 -1.2 235 235
HIF1A/JAB1 -0.055 0.047 -9999 0 -0.7 2 2
CP -1.2 0.58 -9999 0 -1.5 394 394
CXCL12 -0.99 0.53 -9999 0 -1.3 336 336
COPS5 0.011 0.008 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0 -9999 0 -10000 0 0
BNIP3 -0.98 0.53 -9999 0 -1.3 332 332
EGLN3 -1.3 0.51 -9999 0 -1.5 412 412
CA9 -1.3 0.47 -9999 0 -1.5 421 421
TERT -1 0.55 -9999 0 -1.4 342 342
ENO1 -0.98 0.53 -9999 0 -1.3 329 329
PFKL -0.98 0.53 -9999 0 -1.3 332 332
NCOA1 0.015 0.003 -9999 0 -10000 0 0
ADM -1.1 0.56 -9999 0 -1.4 345 345
ARNT -0.1 0.046 -9999 0 -10000 0 0
HNF4A -0.045 0.21 -9999 0 -0.75 44 44
ADFP -0.99 0.52 -9999 0 -1.3 335 335
SLC2A1 -0.63 0.33 -9999 0 -0.97 171 171
LEP -1 0.54 -9999 0 -1.3 337 337
HIF1A/ARNT/Cbp/p300 -0.71 0.34 -9999 0 -0.93 312 312
EPO -0.61 0.39 -9999 0 -1.1 181 181
CREBBP -0.099 0.072 -9999 0 -0.34 6 6
HIF1A/ARNT/Cbp/p300/HDAC7 -0.75 0.38 -9999 0 -1 294 294
PFKFB3 -0.98 0.53 -9999 0 -1.3 332 332
NT5E -0.98 0.53 -9999 0 -1.3 332 332
TCGA08_retinoblastoma

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
CDKN2B -0.01 0.093 -10000 0 -0.87 6 6
CDKN2C 0.079 0.017 -10000 0 -10000 0 0
CDKN2A -0.84 0.16 -10000 0 -0.88 499 499
CCND2 0.18 0.048 0.47 6 -10000 0 6
RB1 -0.2 0.05 -10000 0 -0.48 6 6
CDK4 0.22 0.051 0.22 498 -10000 0 498
CDK6 0.2 0.054 0.51 6 -0.18 1 7
G1/S progression 0.2 0.053 0.21 498 -10000 0 498
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.48 0.26 0.62 402 -10000 0 402
KIRREL -0.055 0.11 -10000 0 -0.82 9 9
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.49 0.26 -10000 0 -0.62 402 402
PLCG1 0.016 0 -10000 0 -10000 0 0
ARRB2 0.014 0.039 -10000 0 -0.86 1 1
WASL 0.016 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.53 0.31 -10000 0 -0.84 224 224
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.41 0.26 -10000 0 -0.66 224 224
FYN -0.5 0.3 -10000 0 -0.8 224 224
mol:Ca2+ -0.52 0.3 -10000 0 -0.83 224 224
mol:DAG -0.53 0.31 -10000 0 -0.83 224 224
NPHS2 -0.41 0.38 -10000 0 -0.81 248 248
mol:IP3 -0.53 0.31 -10000 0 -0.83 224 224
regulation of endocytosis -0.47 0.28 -10000 0 -0.75 224 224
Nephrin/NEPH1/podocin/Cholesterol -0.54 0.31 -10000 0 -0.65 429 429
establishment of cell polarity -0.48 0.26 -10000 0 -0.62 402 402
Nephrin/NEPH1/podocin/NCK1-2 -0.49 0.29 -10000 0 -0.78 224 224
Nephrin/NEPH1/beta Arrestin2 -0.48 0.28 -10000 0 -0.76 224 224
NPHS1 -0.61 0.33 -10000 0 -0.78 400 400
Nephrin/NEPH1/podocin -0.51 0.3 -10000 0 -0.8 224 224
TJP1 0.016 0 -10000 0 -10000 0 0
NCK1 0.014 0.033 -10000 0 -0.75 1 1
NCK2 0.016 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.53 0.31 -10000 0 -0.84 224 224
CD2AP 0.016 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.53 0.31 -10000 0 -0.84 224 224
GRB2 0.016 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.49 0.3 -10000 0 -0.79 224 224
cytoskeleton organization -0.53 0.32 -10000 0 -0.85 224 224
Nephrin/NEPH1 -0.36 0.2 -10000 0 -0.47 402 402
Nephrin/NEPH1/ZO-1 -0.39 0.22 -10000 0 -0.5 402 402
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.34 0.33 -10000 0 -0.69 228 228
FYN -0.41 0.5 -10000 0 -0.93 232 232
LAT/GRAP2/SLP76 -0.36 0.39 -10000 0 -0.76 234 234
IKBKB 0.016 0 -10000 0 -10000 0 0
AKT1 -0.25 0.29 -10000 0 -0.54 236 236
B2M 0.009 0.009 -10000 0 -10000 0 0
IKBKG -0.08 0.072 -10000 0 -0.19 80 80
MAP3K8 0.012 0.055 -10000 0 -0.86 2 2
mol:Ca2+ -0.11 0.045 -10000 0 -0.14 341 341
integrin-mediated signaling pathway -0.018 0.1 -10000 0 -0.58 16 16
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.41 0.45 -10000 0 -0.86 245 245
TRPV6 -0.66 0.26 -10000 0 -0.76 448 448
CD28 -0.058 0.23 -10000 0 -0.87 39 39
SHC1 -0.44 0.49 -10000 0 -0.94 241 241
receptor internalization -0.52 0.56 -10000 0 -1.1 248 248
PRF1 -0.49 0.6 -10000 0 -1.1 216 216
KRAS 0.016 0 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
COT/AKT1 -0.18 0.22 -10000 0 -0.41 222 222
LAT -0.5 0.53 -10000 0 -1 257 257
EntrezGene:6955 -0.003 0.005 -10000 0 -10000 0 0
CD3D -0.38 0.44 -10000 0 -0.87 234 234
CD3E -0.34 0.44 -10000 0 -0.88 208 208
CD3G -0.33 0.43 -10000 0 -0.87 202 202
RASGRP2 -0.023 0.029 -10000 0 -0.14 2 2
RASGRP1 -0.23 0.27 -10000 0 -0.51 228 228
HLA-A 0.005 0.056 -10000 0 -0.88 2 2
RASSF5 -0.011 0.15 -10000 0 -0.86 16 16
RAP1A/GTP/RAPL -0.018 0.1 -10000 0 -0.59 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.036 0.082 -10000 0 -0.14 3 3
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.15 0.13 -10000 0 -0.34 103 103
PRKCA -0.14 0.17 -10000 0 -0.31 197 197
GRAP2 -0.043 0.22 -10000 0 -0.86 35 35
mol:IP3 -0.16 0.34 0.26 168 -0.5 219 387
EntrezGene:6957 -0.003 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.53 0.63 -10000 0 -1.1 248 248
ORAI1 0.33 0.13 0.38 447 -10000 0 447
CSK -0.46 0.51 -10000 0 -0.98 240 240
B7 family/CD28 -0.52 0.52 -10000 0 -1 243 243
CHUK 0.016 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.56 0.62 -10000 0 -1.2 243 243
PTPN6 -0.44 0.52 -10000 0 -1 230 230
VAV1 -0.49 0.53 -10000 0 -1 250 250
Monovalent TCR/CD3 -0.46 0.53 -10000 0 -0.99 237 237
CBL 0.014 0.033 -10000 0 -0.75 1 1
LCK -0.44 0.53 -10000 0 -0.99 234 234
PAG1 -0.46 0.51 -10000 0 -0.98 240 240
RAP1A 0.016 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.53 0.63 -10000 0 -1.2 239 239
CD80 -0.18 0.37 -10000 0 -0.87 115 115
CD86 -0.13 0.32 -10000 0 -0.87 81 81
PDK1/CARD11/BCL10/MALT1 -0.18 0.17 -10000 0 -0.37 179 179
HRAS 0.014 0.039 -10000 0 -0.86 1 1
GO:0035030 -0.36 0.42 -10000 0 -0.78 242 242
CD8A -0.39 0.44 -10000 0 -0.87 234 234
CD8B -0.31 0.43 -10000 0 -0.88 186 186
PTPRC -0.086 0.27 -10000 0 -0.87 56 56
PDK1/PKC theta -0.32 0.36 -10000 0 -0.69 237 237
CSK/PAG1 -0.44 0.49 -10000 0 -0.95 237 237
SOS1 0.016 0 -10000 0 -10000 0 0
peptide-MHC class I -0.003 0.042 -10000 0 -0.68 2 2
GRAP2/SLP76 -0.44 0.44 -10000 0 -0.89 239 239
STIM1 0.17 0.065 -10000 0 -10000 0 0
RAS family/GTP -0.064 0.11 -10000 0 -0.25 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.59 0.65 -10000 0 -1.2 248 248
mol:DAG -0.2 0.26 -10000 0 -0.46 235 235
RAP1A/GDP -0.014 0.036 -10000 0 -10000 0 0
PLCG1 0.016 0 -10000 0 -10000 0 0
CD247 -0.28 0.42 -10000 0 -0.87 171 171
cytotoxic T cell degranulation -0.45 0.55 -10000 0 -1 220 220
RAP1A/GTP -0.008 0.008 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.32 0.35 -10000 0 -0.66 245 245
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.27 0.44 0.3 107 -0.7 234 341
NRAS 0.016 0 -10000 0 -10000 0 0
ZAP70 -0.46 0.44 -10000 0 -0.86 281 281
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.38 0.35 -10000 0 -0.73 242 242
MALT1 0.016 0 -10000 0 -10000 0 0
TRAF6 0.016 0 -10000 0 -10000 0 0
CD8 heterodimer -0.5 0.57 -10000 0 -1.1 240 240
CARD11 -0.17 0.36 -10000 0 -0.86 110 110
PRKCB -0.14 0.17 -10000 0 -0.32 174 174
PRKCE -0.14 0.17 -10000 0 -0.31 197 197
PRKCQ -0.39 0.42 -10000 0 -0.81 244 244
LCP2 -0.04 0.22 -10000 0 -0.86 33 33
BCL10 0.016 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.2 0.24 -10000 0 -0.45 235 235
IKK complex -0.028 0.085 -10000 0 -10000 0 0
RAS family/GDP -0.012 0.012 -10000 0 -0.11 1 1
MAP3K14 -0.13 0.18 -10000 0 -0.32 150 150
PDPK1 -0.23 0.27 -10000 0 -0.51 231 231
TCR/CD3/MHC I/CD8/Fyn -0.56 0.65 -10000 0 -1.2 237 237
TCGA08_p53

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
CDKN2A -0.65 0.13 -10000 0 -0.68 499 499
TP53 -0.17 0.037 -10000 0 -10000 0 0
Senescence -0.17 0.037 -10000 0 -10000 0 0
Apoptosis -0.17 0.037 -10000 0 -10000 0 0
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.31 0.061 0.32 499 -10000 0 499
MDM4 0.014 0.039 -10000 0 -0.86 1 1
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.24 0.32 -9999 0 -0.68 161 161
STMN1 -0.29 0.35 -9999 0 -0.66 243 243
Aurora B/RasGAP/Survivin -0.41 0.48 -9999 0 -0.88 249 249
Chromosomal passenger complex/Cul3 protein complex -0.17 0.23 -9999 0 -0.49 149 149
BIRC5 -0.26 0.41 -9999 0 -0.89 153 153
DES -0.38 0.34 -9999 0 -0.58 329 329
Aurora C/Aurora B/INCENP -0.24 0.28 -9999 0 -0.53 244 244
Aurora B/TACC1 -0.26 0.3 -9999 0 -0.58 243 243
Aurora B/PP2A -0.3 0.34 -9999 0 -0.66 243 243
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.073 0.09 -9999 0 -0.17 125 125
mitotic metaphase/anaphase transition 0.001 0.008 -9999 0 -10000 0 0
NDC80 -0.41 0.5 -9999 0 -0.89 247 247
Cul3 protein complex -0.016 0.085 -9999 0 -0.48 17 17
KIF2C -0.15 0.18 -9999 0 -0.32 233 233
PEBP1 0.007 0.008 -9999 0 -10000 0 0
KIF20A -0.38 0.44 -9999 0 -0.87 234 234
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.3 0.34 -9999 0 -0.66 244 244
SEPT1 -0.096 0.29 -9999 0 -0.86 66 66
SMC2 0.016 0 -9999 0 -10000 0 0
SMC4 0.016 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.18 0.24 -9999 0 -0.44 233 233
PSMA3 0.016 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.003 0.005 -9999 0 -10000 0 0
H3F3B -0.17 0.21 -9999 0 -0.39 243 243
AURKB -0.4 0.44 -9999 0 -0.87 243 243
AURKC 0.012 0.055 -9999 0 -0.86 2 2
CDCA8 -0.025 0.17 -9999 0 -0.9 19 19
cytokinesis -0.35 0.37 -9999 0 -0.75 214 214
Aurora B/Septin1 -0.36 0.42 -9999 0 -0.83 206 206
AURKA 0.002 0.095 -9999 0 -0.87 6 6
INCENP 0.008 0.009 -9999 0 -10000 0 0
KLHL13 -0.009 0.14 -9999 0 -0.75 17 17
BUB1 -0.37 0.44 -9999 0 -0.87 227 227
hSgo1/Aurora B/Survivin -0.4 0.49 -9999 0 -0.86 250 250
EVI5 0.01 0.008 -9999 0 -10000 0 0
RhoA/GTP -0.31 0.34 -9999 0 -0.71 194 194
SGOL1 -0.015 0.16 -9999 0 -0.86 18 18
CENPA -0.29 0.35 -9999 0 -0.62 253 253
NCAPG -0.28 0.42 -9999 0 -0.86 174 174
Aurora B/HC8 Proteasome -0.3 0.34 -9999 0 -0.66 243 243
NCAPD2 0.016 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.3 0.34 -9999 0 -0.66 243 243
RHOA 0.016 0 -9999 0 -10000 0 0
NCAPH -0.13 0.33 -9999 0 -0.86 87 87
NPM1 -0.22 0.24 -9999 0 -0.47 243 243
RASA1 0.014 0.033 -9999 0 -0.75 1 1
KLHL9 0.016 0 -9999 0 -10000 0 0
mitotic prometaphase -0.01 0.011 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.3 0.34 -9999 0 -0.66 243 243
PPP1CC 0.016 0 -9999 0 -10000 0 0
Centraspindlin -0.34 0.38 -9999 0 -0.78 202 202
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.22 0.24 -9999 0 -0.47 243 243
MYLK -0.17 0.21 -9999 0 -0.39 243 243
KIF23 -0.007 0.11 -9999 0 -0.88 8 8
VIM -0.35 0.4 -9999 0 -0.73 257 257
RACGAP1 0.004 0.055 -9999 0 -0.88 2 2
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.22 0.24 -9999 0 -0.47 243 243
Chromosomal passenger complex -0.35 0.41 -9999 0 -0.74 248 248
Chromosomal passenger complex/EVI5 -0.37 0.48 -9999 0 -0.91 196 196
TACC1 0.016 0 -9999 0 -10000 0 0
PPP2R5D 0.016 0 -9999 0 -10000 0 0
CUL3 0.016 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.055 0.14 -9999 0 -0.54 38 38
Syndecan-4/Syndesmos -0.46 0.39 -9999 0 -0.85 233 233
positive regulation of JNK cascade -0.54 0.37 -9999 0 -0.84 281 281
Syndecan-4/ADAM12 -0.57 0.5 -9999 0 -1 257 257
CCL5 -0.36 0.44 -9999 0 -0.86 221 221
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.016 0 -9999 0 -10000 0 0
ITGA5 -0.049 0.23 -9999 0 -0.86 38 38
SDCBP 0.016 0 -9999 0 -10000 0 0
PLG -0.37 0.37 -9999 0 -0.72 269 269
ADAM12 -0.22 0.39 -9999 0 -0.86 140 140
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.1 0.071 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.48 0.4 -9999 0 -0.86 235 235
Syndecan-4/CXCL12/CXCR4 -0.59 0.43 -9999 0 -0.94 281 281
Syndecan-4/Laminin alpha3 -0.47 0.39 -9999 0 -0.85 238 238
MDK -0.05 0.23 -9999 0 -0.86 39 39
Syndecan-4/FZD7 -0.46 0.39 -9999 0 -0.84 234 234
Syndecan-4/Midkine -0.5 0.42 -9999 0 -0.88 246 246
FZD7 0.014 0.033 -9999 0 -0.75 1 1
Syndecan-4/FGFR1/FGF -0.44 0.34 -9999 0 -0.77 236 236
THBS1 0.011 0.058 -9999 0 -0.75 3 3
integrin-mediated signaling pathway -0.45 0.36 -9999 0 -0.79 239 239
positive regulation of MAPKKK cascade -0.54 0.37 -9999 0 -0.84 281 281
Syndecan-4/TACI -0.5 0.42 -9999 0 -0.9 246 246
CXCR4 -0.29 0.42 -9999 0 -0.86 178 178
cell adhesion -0.007 0.12 -9999 0 -0.5 15 15
Syndecan-4/Dynamin -0.46 0.39 -9999 0 -0.85 233 233
Syndecan-4/TSP1 -0.47 0.39 -9999 0 -0.85 235 235
Syndecan-4/GIPC -0.46 0.39 -9999 0 -0.84 234 234
Syndecan-4/RANTES -0.65 0.46 -9999 0 -1 289 289
ITGB1 0.016 0 -9999 0 -10000 0 0
LAMA1 -0.007 0.13 -9999 0 -0.75 15 15
LAMA3 0.004 0.1 -9999 0 -0.86 7 7
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA 0.11 0.066 -9999 0 -10000 0 0
Syndecan-4/alpha-Actinin -0.47 0.39 -9999 0 -0.85 234 234
TFPI 0.001 0.11 -9999 0 -0.81 9 9
F2 -0.32 0.42 -9999 0 -0.87 194 194
alpha5/beta1 Integrin -0.049 0.17 -9999 0 -0.67 38 38
positive regulation of cell adhesion -0.45 0.38 -9999 0 -0.82 240 240
ACTN1 0.013 0.051 -9999 0 -0.8 2 2
TNC -0.003 0.12 -9999 0 -0.75 13 13
Syndecan-4/CXCL12 -0.47 0.39 -9999 0 -0.85 238 238
FGF6 0 0.002 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
CXCL12 0 0.11 -9999 0 -0.75 11 11
TNFRSF13B -0.071 0.26 -9999 0 -0.86 50 50
FGF2 0.008 0.077 -9999 0 -0.77 5 5
FGFR1 0.016 0 -9999 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.47 0.39 -9999 0 -0.86 233 233
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.039 0.22 -9999 0 -0.83 38 38
cell migration -0.03 0.022 -9999 0 -10000 0 0
PRKCD 0.024 0.045 -9999 0 -0.85 1 1
vasculogenesis -0.44 0.36 -9999 0 -0.79 235 235
SDC4 -0.51 0.43 -9999 0 -0.93 233 233
Syndecan-4/Tenascin C -0.47 0.39 -9999 0 -0.84 239 239
Syndecan-4/PI-4-5-P2/PKC alpha -0.08 0.055 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.46 0.39 -9999 0 -0.85 233 233
MMP9 -0.4 0.44 -9999 0 -0.86 247 247
Rac1/GTP -0.008 0.12 -9999 0 -0.52 15 15
cytoskeleton organization -0.44 0.36 -9999 0 -0.8 233 233
GIPC1 0.014 0.033 -9999 0 -0.75 1 1
Syndecan-4/TFPI -0.47 0.39 -9999 0 -0.85 237 237
FOXM1 transcription factor network

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
NFATC3 -0.19 0.68 -10000 0 -1.2 122 122
PLK1 -0.1 0.41 -10000 0 -0.8 128 128
BIRC5 -0.14 0.43 -10000 0 -0.79 153 153
HSPA1B -0.19 0.68 -10000 0 -1.2 123 123
MAP2K1 0.04 0.047 -10000 0 -10000 0 0
BRCA2 -0.2 0.68 -10000 0 -1.2 128 128
FOXM1 -0.37 0.99 -10000 0 -1.8 137 137
XRCC1 -0.19 0.68 -10000 0 -1.2 123 123
FOXM1B/p19 -0.5 0.49 0.51 1 -1.2 139 140
Cyclin D1/CDK4 -0.18 0.61 -10000 0 -1.1 117 117
CDC2 -0.22 0.72 -10000 0 -1.3 133 133
TGFA -0.16 0.6 -10000 0 -1 122 122
SKP2 -0.19 0.68 -10000 0 -1.2 130 130
CCNE1 0.003 0.1 -10000 0 -0.88 7 7
CKS1B -0.19 0.68 -10000 0 -1.2 123 123
RB1 -0.19 0.26 -10000 0 -0.69 93 93
FOXM1C/SP1 -0.28 0.78 -10000 0 -1.4 136 136
AURKB -0.25 0.46 -10000 0 -0.74 243 243
CENPF -0.21 0.72 -10000 0 -1.3 128 128
CDK4 0.02 0.022 -10000 0 -10000 0 0
MYC -0.16 0.6 -10000 0 -1 122 122
CHEK2 0.038 0.063 -10000 0 -0.91 1 1
ONECUT1 -0.19 0.65 -10000 0 -1.2 124 124
CDKN2A -0.82 0.17 -10000 0 -0.86 499 499
LAMA4 -0.28 0.69 -10000 0 -1.2 147 147
FOXM1B/HNF6 -0.28 0.79 -10000 0 -1.5 127 127
FOS -0.2 0.69 -10000 0 -1.2 126 126
SP1 0.016 0.005 -10000 0 -10000 0 0
CDC25B -0.19 0.68 -10000 0 -1.2 126 126
response to radiation 0.013 0.05 -10000 0 -10000 0 0
CENPB -0.19 0.68 -10000 0 -1.2 123 123
CENPA -0.28 0.78 -10000 0 -1.3 166 166
NEK2 -0.24 0.75 -10000 0 -1.3 138 138
HIST1H2BA -0.2 0.68 -10000 0 -1.2 127 127
CCNA2 -0.16 0.36 -10000 0 -0.88 101 101
EP300 0.014 0.033 -10000 0 -0.75 1 1
CCNB1/CDK1 -0.28 0.81 -10000 0 -1.5 133 133
CCNB2 -0.24 0.76 -10000 0 -1.4 133 133
CCNB1 -0.21 0.72 -10000 0 -1.3 132 132
ETV5 -0.19 0.68 -10000 0 -1.2 127 127
ESR1 -0.19 0.68 -10000 0 -1.2 123 123
CCND1 -0.18 0.63 -10000 0 -1.1 118 118
GSK3A 0.036 0.041 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.082 0.28 -10000 0 -0.64 102 102
CDK2 0.015 0.015 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.015 0.059 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.42 0.58 -10000 0 -1.3 144 144
GAS1 -0.23 0.7 -10000 0 -1.2 135 135
MMP2 -0.19 0.68 -10000 0 -1.2 123 123
RB1/FOXM1C -0.21 0.67 -10000 0 -1.2 122 122
CREBBP 0.016 0 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.45 0.48 -9999 0 -1.2 97 97
PCK1 -0.94 0.71 -9999 0 -1.6 268 268
HNF4A -0.58 0.58 -9999 0 -1.4 129 129
KCNJ11 -0.45 0.51 -9999 0 -1.3 91 91
AKT1 -0.17 0.18 -9999 0 -0.46 2 2
response to starvation -0.02 0.038 -9999 0 -10000 0 0
DLK1 -0.56 0.58 -9999 0 -1.3 145 145
NKX2-1 -0.057 0.21 -9999 0 -0.84 4 4
ACADM -0.45 0.48 -9999 0 -1.2 100 100
TAT -0.52 0.36 -9999 0 -0.96 147 147
CEBPB -0.024 0.14 -9999 0 -0.92 12 12
CEBPA -0.019 0.13 -9999 0 -0.9 10 10
TTR -0.89 0.48 -9999 0 -1.2 327 327
PKLR -0.5 0.56 -9999 0 -1.4 113 113
APOA1 -0.56 0.56 -9999 0 -1.4 115 115
CPT1C -0.45 0.48 -9999 0 -1.2 95 95
ALAS1 -0.17 0.19 -9999 0 -10000 0 0
TFRC -0.63 0.42 -9999 0 -1 207 207
FOXF1 -0.002 0.12 -9999 0 -0.84 10 10
NF1 0.025 0.001 -9999 0 -10000 0 0
HNF1A (dimer) -0.003 0.087 -9999 0 -0.79 5 5
CPT1A -0.45 0.48 -9999 0 -1.2 95 95
HMGCS1 -0.45 0.48 -9999 0 -1.2 99 99
NR3C1 0.003 0.065 -9999 0 -0.97 1 1
CPT1B -0.46 0.5 -9999 0 -1.3 101 101
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.017 0.005 -9999 0 -10000 0 0
GCK -0.46 0.49 -9999 0 -1.3 94 94
CREB1 -0.028 0.066 -9999 0 -10000 0 0
IGFBP1 -0.32 0.42 -9999 0 -1 119 119
PDX1 -0.19 0.22 -9999 0 -1 6 6
UCP2 -0.45 0.48 -9999 0 -1.2 93 93
ALDOB -0.94 0.62 -9999 0 -1.3 343 343
AFP -0.71 0.5 -9999 0 -0.97 319 319
BDH1 -0.6 0.57 -9999 0 -1.3 174 174
HADH -0.44 0.49 -9999 0 -1.3 91 91
F2 -0.66 0.62 -9999 0 -1.4 169 169
HNF1A -0.002 0.087 -9999 0 -0.79 5 5
G6PC -0.81 0.66 -9999 0 -1.5 248 248
SLC2A2 -0.32 0.48 -9999 0 -1.7 47 47
INS 0.01 0.055 -9999 0 -10000 0 0
FOXA1 -0.37 0.39 -9999 0 -0.96 137 137
FOXA3 -0.61 0.37 -9999 0 -0.86 316 316
FOXA2 -0.52 0.57 -9999 0 -1.4 106 106
ABCC8 -0.44 0.49 -9999 0 -1.2 95 95
ALB -1.2 0.49 -9999 0 -1.4 448 448
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.17 0.26 -10000 0 -0.65 69 69
TBX21 -0.55 0.68 -10000 0 -1.3 209 209
B2M 0.011 0.009 -10000 0 -10000 0 0
TYK2 0.012 0.022 -10000 0 -10000 0 0
IL12RB1 -0.27 0.43 -10000 0 -0.91 159 159
GADD45B -0.3 0.43 -10000 0 -0.81 155 155
IL12RB2 -0.11 0.31 -10000 0 -0.87 74 74
GADD45G -0.31 0.43 -10000 0 -0.84 145 145
natural killer cell activation -0.01 0.03 -10000 0 -10000 0 0
RELB 0.016 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
IL18 0.002 0.1 -10000 0 -0.87 7 7
IL2RA -0.16 0.35 -10000 0 -0.86 104 104
IFNG -0.39 0.44 -10000 0 -0.86 237 237
STAT3 (dimer) -0.37 0.47 -10000 0 -0.88 200 200
HLA-DRB5 -0.038 0.21 -10000 0 -0.86 32 32
FASLG -0.61 0.7 -10000 0 -1.3 234 234
NF kappa B2 p52/RelB -0.52 0.53 -10000 0 -1.1 219 219
CD4 0.001 0.12 -10000 0 -0.86 9 9
SOCS1 0.006 0.094 -10000 0 -0.86 6 6
EntrezGene:6955 -0.002 0.009 -10000 0 -10000 0 0
CD3D -0.38 0.44 -10000 0 -0.87 234 234
CD3E -0.34 0.43 -10000 0 -0.87 208 208
CD3G -0.33 0.43 -10000 0 -0.87 202 202
IL12Rbeta2/JAK2 -0.085 0.25 -10000 0 -0.68 74 74
CCL3 -0.49 0.63 -10000 0 -1.2 196 196
CCL4 -0.5 0.66 -10000 0 -1.2 204 204
HLA-A 0.007 0.055 -10000 0 -0.86 2 2
IL18/IL18R -0.13 0.3 -10000 0 -0.6 145 145
NOS2 -0.36 0.5 -10000 0 -0.92 186 186
IL12/IL12R/TYK2/JAK2/SPHK2 -0.16 0.26 -10000 0 -0.65 67 67
IL1R1 -0.45 0.59 -10000 0 -1.2 177 177
IL4 0.014 0.031 -10000 0 -10000 0 0
JAK2 0.012 0.022 -10000 0 -10000 0 0
EntrezGene:6957 -0.002 0.009 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.7 0.82 -10000 0 -1.5 254 254
RAB7A -0.24 0.37 -10000 0 -0.78 57 57
lysosomal transport -0.22 0.36 -10000 0 -0.73 59 59
FOS -0.38 0.5 -10000 0 -0.95 200 200
STAT4 (dimer) -0.41 0.53 -10000 0 -0.98 200 200
STAT5A (dimer) -0.66 0.61 -10000 0 -1.2 247 247
GZMA -0.57 0.7 -10000 0 -1.3 222 222
GZMB -0.54 0.67 -10000 0 -1.3 205 205
HLX -0.088 0.28 -10000 0 -0.86 61 61
LCK -0.52 0.69 -10000 0 -1.2 215 215
TCR/CD3/MHC II/CD4 -0.38 0.47 -10000 0 -0.86 228 228
IL2/IL2R -0.42 0.42 -10000 0 -0.71 306 306
MAPK14 -0.3 0.44 -10000 0 -0.82 162 162
CCR5 -0.45 0.59 -10000 0 -1.2 188 188
IL1B 0.002 0.096 -10000 0 -0.86 6 6
STAT6 -0.084 0.15 -10000 0 -10000 0 0
STAT4 -0.035 0.2 -10000 0 -0.86 30 30
STAT3 0.016 0 -10000 0 -10000 0 0
STAT1 0.014 0.039 -10000 0 -0.86 1 1
NFKB1 0.014 0.033 -10000 0 -0.75 1 1
NFKB2 0.016 0 -10000 0 -10000 0 0
IL12B -0.092 0.29 -10000 0 -0.89 60 60
CD8A -0.38 0.44 -10000 0 -0.87 234 234
CD8B -0.3 0.42 -10000 0 -0.87 186 186
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.16 0.26 0.64 69 -10000 0 69
IL2RB -0.45 0.44 -10000 0 -0.86 272 272
proteasomal ubiquitin-dependent protein catabolic process -0.36 0.47 -10000 0 -0.87 199 199
IL2RG -0.042 0.22 -10000 0 -0.86 34 34
IL12 -0.07 0.24 -10000 0 -0.71 61 61
STAT5A 0.016 0 -10000 0 -10000 0 0
CD247 -0.28 0.42 -10000 0 -0.87 171 171
IL2 -0.007 0.12 -10000 0 -0.86 10 10
SPHK2 0.013 0.047 -10000 0 -0.75 2 2
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.01 0.046 -10000 0 -0.91 1 1
IL12/IL12R/TYK2/JAK2 -0.58 0.78 -10000 0 -1.4 220 220
MAP2K3 -0.31 0.44 -10000 0 -0.83 164 164
RIPK2 0.014 0.039 -10000 0 -0.86 1 1
MAP2K6 -0.31 0.44 -10000 0 -0.83 165 165
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.01 0.077 -10000 0 -0.86 4 4
IL18RAP -0.21 0.39 -10000 0 -0.87 133 133
IL12Rbeta1/TYK2 -0.21 0.34 -10000 0 -0.72 159 159
EOMES -0.3 0.37 -10000 0 -0.74 213 213
STAT1 (dimer) -0.45 0.51 -10000 0 -0.96 233 233
T cell proliferation -0.26 0.37 -10000 0 -0.68 170 170
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.001 0.1 -10000 0 -0.81 8 8
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.37 0.33 -10000 0 -0.76 178 178
ATF2 -0.27 0.41 -10000 0 -0.8 122 122
PDGFR-alpha 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
PDGFRA -0.28 0.37 -9999 0 -0.74 199 199
PDGF/PDGFRA/CRKL -0.21 0.26 -9999 0 -0.54 199 199
positive regulation of JUN kinase activity -0.16 0.2 -9999 0 -0.45 9 9
CRKL 0.016 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.22 0.27 -9999 0 -0.56 202 202
AP1 -0.16 0.24 -9999 0 -1.2 13 13
mol:IP3 -0.19 0.29 -9999 0 -0.56 199 199
PLCG1 -0.19 0.29 -9999 0 -0.56 199 199
PDGF/PDGFRA/alphaV Integrin -0.21 0.26 -9999 0 -0.54 199 199
RAPGEF1 0.016 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ -0.19 0.29 -9999 0 -0.56 199 199
CAV3 -0.001 0.066 -9999 0 -0.86 3 3
CAV1 -0.047 0.23 -9999 0 -0.86 37 37
SHC/Grb2/SOS1 -0.16 0.2 -9999 0 -0.45 9 9
PDGF/PDGFRA/Shf -0.21 0.26 -9999 0 -0.54 200 200
FOS -0.12 0.27 -9999 0 -1.2 13 13
JUN -0.013 0.017 -9999 0 -10000 0 0
oligodendrocyte development -0.21 0.26 -9999 0 -0.54 199 199
GRB2 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
mol:DAG -0.19 0.29 -9999 0 -0.56 199 199
PDGF/PDGFRA -0.27 0.37 -9999 0 -0.74 199 199
actin cytoskeleton reorganization -0.21 0.26 -9999 0 -0.54 199 199
SRF 0.034 0.009 -9999 0 -10000 0 0
SHC1 0.014 0.039 -9999 0 -0.86 1 1
PI3K -0.18 0.22 -9999 0 -0.46 200 200
PDGF/PDGFRA/Crk/C3G -0.18 0.22 -9999 0 -0.46 199 199
JAK1 -0.19 0.28 -9999 0 -0.54 199 199
ELK1/SRF -0.15 0.19 -9999 0 -10000 0 0
SHB 0.016 0 -9999 0 -10000 0 0
SHF 0.014 0.033 -9999 0 -0.75 1 1
CSNK2A1 0.017 0.022 -9999 0 -10000 0 0
GO:0007205 -0.2 0.3 -9999 0 -0.57 199 199
SOS1 0.016 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.16 0.2 -9999 0 -0.45 9 9
PDGF/PDGFRA/SHB -0.21 0.26 -9999 0 -0.54 199 199
PDGF/PDGFRA/Caveolin-1 -0.26 0.3 -9999 0 -0.58 228 228
ITGAV 0.016 0 -9999 0 -10000 0 0
ELK1 -0.16 0.26 -9999 0 -0.49 199 199
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
PDGF/PDGFRA/Crk -0.21 0.26 -9999 0 -0.54 199 199
JAK-STAT cascade -0.19 0.28 -9999 0 -0.54 199 199
cell proliferation -0.21 0.26 -9999 0 -0.54 200 200
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 -0.14 0.29 -9999 0 -0.68 105 105
alphaM/beta2 Integrin/GPIbA -0.13 0.28 -9999 0 -0.68 101 101
alphaM/beta2 Integrin/proMMP-9 -0.4 0.43 -9999 0 -0.75 275 275
PLAUR -0.028 0.19 -9999 0 -0.86 26 26
HMGB1 0.015 0.013 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.13 0.28 -9999 0 -0.68 100 100
AGER -0.14 0.33 -9999 0 -0.86 90 90
RAP1A 0.016 0 -9999 0 -10000 0 0
SELPLG -0.042 0.22 -9999 0 -0.86 34 34
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.23 0.34 -9999 0 -0.66 167 167
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.4 0.44 -9999 0 -0.86 247 247
CYR61 0.007 0.082 -9999 0 -0.75 6 6
TLN1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP -0.25 0.2 -9999 0 -0.57 113 113
RHOA 0.016 0 -9999 0 -10000 0 0
P-selectin oligomer -0.018 0.16 -9999 0 -0.74 23 23
MYH2 -0.34 0.26 -9999 0 -0.64 186 186
MST1R 0.005 0.092 -9999 0 -0.78 7 7
leukocyte activation during inflammatory response -0.28 0.35 -9999 0 -0.63 220 220
APOB -0.27 0.41 -9999 0 -0.86 169 169
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.006 0.092 -9999 0 -0.84 6 6
JAM3 0.016 0 -9999 0 -10000 0 0
GP1BA 0.014 0.033 -9999 0 -0.75 1 1
alphaM/beta2 Integrin/CTGF -0.14 0.29 -9999 0 -0.68 105 105
alphaM/beta2 Integrin -0.3 0.25 -9999 0 -0.54 222 222
JAM3 homodimer 0.016 0 -9999 0 -10000 0 0
ICAM2 0.016 0 -9999 0 -10000 0 0
ICAM1 -0.003 0.13 -9999 0 -0.86 11 11
phagocytosis triggered by activation of immune response cell surface activating receptor -0.3 0.25 -9999 0 -0.53 222 222
cell adhesion -0.13 0.28 -9999 0 -0.67 101 101
NFKB1 -0.17 0.37 -9999 0 -0.95 62 62
THY1 0.014 0.033 -9999 0 -0.75 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.2 0.28 -9999 0 -0.59 170 170
alphaM/beta2 Integrin/LRP/tPA -0.13 0.27 -9999 0 -0.63 102 102
IL6 -0.2 0.41 -9999 0 -0.91 99 99
ITGB2 -0.15 0.34 -9999 0 -0.86 98 98
elevation of cytosolic calcium ion concentration -0.15 0.3 -9999 0 -0.64 120 120
alphaM/beta2 Integrin/JAM2/JAM3 -0.12 0.26 -9999 0 -0.62 100 100
JAM2 0.016 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/ICAM1 -0.14 0.28 -9999 0 -0.87 39 39
alphaM/beta2 Integrin/uPA/Plg -0.35 0.34 -9999 0 -0.78 132 132
RhoA/GTP -0.37 0.27 -9999 0 -0.68 185 185
positive regulation of phagocytosis -0.25 0.27 -9999 0 -0.7 109 109
Ron/MSP -0.018 0.1 -9999 0 -0.62 15 15
alphaM/beta2 Integrin/uPAR/uPA -0.15 0.3 -9999 0 -0.64 120 120
alphaM/beta2 Integrin/uPAR -0.16 0.32 -9999 0 -0.71 116 116
PLAU 0.003 0.1 -9999 0 -0.75 9 9
PLAT -0.005 0.12 -9999 0 -0.75 14 14
actin filament polymerization -0.33 0.24 -9999 0 -0.61 186 186
MST1 0.002 0.11 -9999 0 -0.85 8 8
alphaM/beta2 Integrin/lipoprotein(a) -0.28 0.36 -9999 0 -0.64 220 220
TNF -0.15 0.34 -9999 0 -0.84 66 66
RAP1B 0.016 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.14 0.28 -9999 0 -0.66 109 109
fibrinolysis -0.35 0.34 -9999 0 -0.77 132 132
HCK -0.032 0.2 -9999 0 -0.86 28 28
dendritic cell antigen processing and presentation -0.3 0.25 -9999 0 -0.53 222 222
VTN -0.1 0.28 -9999 0 -0.76 79 79
alphaM/beta2 Integrin/CYR61 -0.14 0.28 -9999 0 -0.67 106 106
LPA 0.002 0.067 -9999 0 -0.86 3 3
LRP1 0.016 0 -9999 0 -10000 0 0
cell migration -0.37 0.4 -9999 0 -0.7 277 277
FN1 -0.049 0.23 -9999 0 -0.86 38 38
alphaM/beta2 Integrin/Thy1 -0.13 0.28 -9999 0 -0.68 101 101
MPO -0.014 0.16 -9999 0 -0.86 17 17
KNG1 -0.56 0.33 -9999 0 -0.75 386 386
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.33 0.26 -9999 0 -0.64 176 176
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.38 0.38 -9999 0 -0.75 269 269
CTGF 0.005 0.088 -9999 0 -0.75 7 7
alphaM/beta2 Integrin/Hck -0.16 0.35 -9999 0 -0.79 104 104
ITGAM -0.021 0.17 -9999 0 -0.86 21 21
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.17 0.34 -9999 0 -0.75 109 109
HP -0.2 0.38 -9999 0 -0.86 129 129
leukocyte adhesion -0.18 0.27 -9999 0 -0.78 60 60
SELP -0.018 0.16 -9999 0 -0.75 23 23
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.006 0.053 -10000 0 -0.49 6 6
fibroblast growth factor receptor signaling pathway -0.006 0.053 -10000 0 -0.49 6 6
LAMA1 -0.007 0.13 -10000 0 -0.75 15 15
PRNP 0.016 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.12 0.23 -10000 0 -0.56 111 111
SMAD2 0.045 0.021 -10000 0 -10000 0 0
GPC1/PrPc/Cu2+ -0.001 0.021 -10000 0 -0.49 1 1
GPC1/Laminin alpha1 -0.017 0.098 -10000 0 -0.57 16 16
TDGF1 -0.56 0.32 -10000 0 -0.75 390 390
CRIPTO/GPC1 -0.42 0.24 -10000 0 -0.56 390 390
APP/GPC1 -0.002 0.035 -10000 0 -0.56 2 2
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.35 0.22 -10000 0 -0.74 2 2
FLT1 0.007 0.086 -10000 0 -0.86 5 5
GPC1/TGFB/TGFBR1/TGFBR2 -0.001 0.021 -10000 0 -0.48 1 1
SERPINC1 -0.054 0.22 -10000 0 -0.76 45 45
FYN -0.35 0.22 -10000 0 -0.74 2 2
FGR -0.35 0.22 -10000 0 -0.9 5 5
positive regulation of MAPKKK cascade -0.36 0.24 -10000 0 -0.73 52 52
SLIT2 -0.15 0.31 -10000 0 -0.75 110 110
GPC1/NRG -0.018 0.1 -10000 0 -0.56 17 17
NRG1 -0.008 0.13 -10000 0 -0.75 16 16
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.26 0.3 -10000 0 -0.59 234 234
LYN -0.35 0.22 -10000 0 -0.48 390 390
mol:Spermine 0.014 0.026 -10000 0 -0.57 1 1
cell growth -0.006 0.053 -10000 0 -0.49 6 6
BMP signaling pathway -0.014 0.033 0.74 1 -10000 0 1
SRC -0.35 0.22 -10000 0 -0.48 390 390
TGFBR1 0.016 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.062 0.24 -10000 0 -0.86 43 43
GPC1 0.014 0.033 -10000 0 -0.75 1 1
TGFBR1 (dimer) 0.016 0 -10000 0 -10000 0 0
VEGFA -0.38 0.44 -10000 0 -0.86 233 233
BLK -0.39 0.26 -10000 0 -0.52 395 395
HCK -0.38 0.24 -10000 0 -0.5 400 400
FGF2 0.008 0.077 -10000 0 -0.77 5 5
FGFR1 0.016 0 -10000 0 -10000 0 0
VEGFR1 homodimer 0.007 0.086 -10000 0 -0.86 5 5
TGFBR2 0.016 0 -10000 0 -10000 0 0
cell death -0.002 0.035 -10000 0 -0.56 2 2
ATIII/GPC1 -0.051 0.16 -10000 0 -0.58 46 46
PLA2G2A/GPC1 -0.056 0.18 -10000 0 -0.66 44 44
LCK -0.37 0.24 -10000 0 -0.5 398 398
neuron differentiation -0.018 0.099 -10000 0 -0.56 17 17
PrPc/Cu2+ 0 0 -10000 0 -10000 0 0
APP 0.014 0.033 -10000 0 -0.75 1 1
TGFBR2 (dimer) 0.016 0 -10000 0 -10000 0 0
IL4-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
BCL2L1 -0.48 0.48 -10000 0 -1.2 108 108
STAT6 (cleaved dimer) -0.58 0.49 -10000 0 -1.1 188 188
IGHG1 -0.17 0.19 -10000 0 -0.62 15 15
IGHG3 -0.48 0.46 -10000 0 -1.1 143 143
AKT1 -0.28 0.33 -10000 0 -0.84 82 82
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.24 0.32 -10000 0 -0.82 86 86
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.27 0.3 -10000 0 -0.82 59 59
THY1 -0.48 0.48 -10000 0 -1.2 111 111
MYB -0.22 0.39 -10000 0 -0.86 139 139
HMGA1 0.014 0.039 -10000 0 -0.86 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.39 0.42 -10000 0 -0.98 124 124
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.27 0.3 -10000 0 -0.82 58 58
SP1 0.022 0.015 -10000 0 -10000 0 0
INPP5D 0.009 0.077 -10000 0 -0.86 4 4
SOCS5 0.027 0.017 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.56 0.48 -10000 0 -1.2 155 155
SOCS1 -0.33 0.34 -10000 0 -0.82 68 68
SOCS3 -0.3 0.34 -10000 0 -0.9 73 73
FCER2 -0.41 0.44 -10000 0 -1.1 84 84
PARP14 0.016 0.004 -10000 0 -10000 0 0
CCL17 -0.5 0.5 -10000 0 -1.2 114 114
GRB2 0.016 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.22 0.28 -10000 0 -0.79 52 52
T cell proliferation -0.5 0.51 -10000 0 -1.2 128 128
IL4R/JAK1 -0.48 0.47 -10000 0 -1.2 113 113
EGR2 -0.49 0.5 -10000 0 -1.2 121 121
JAK2 0.007 0.023 -10000 0 -10000 0 0
JAK3 -0.16 0.36 -10000 0 -0.87 105 105
PIK3R1 0.014 0.033 -10000 0 -0.75 1 1
JAK1 0.007 0.016 -10000 0 -10000 0 0
COL1A2 -0.21 0.3 -10000 0 -0.89 66 66
CCL26 -0.49 0.49 -10000 0 -1.2 110 110
IL4R -0.51 0.51 -10000 0 -1.2 112 112
PTPN6 0.027 0.012 -10000 0 -10000 0 0
IL13RA2 -0.55 0.56 -10000 0 -1.3 138 138
IL13RA1 0.007 0.023 -10000 0 -10000 0 0
IRF4 -0.27 0.42 -10000 0 -0.97 123 123
ARG1 -0.18 0.26 -10000 0 -0.74 58 58
CBL -0.36 0.4 -10000 0 -0.95 112 112
GTF3A 0.011 0.029 -10000 0 -10000 0 0
PIK3CA 0.014 0.033 -10000 0 -0.75 1 1
IL13RA1/JAK2 -0.006 0.043 -10000 0 -10000 0 0
IRF4/BCL6 -0.27 0.38 -10000 0 -0.92 116 116
CD40LG -0.074 0.28 -10000 0 -0.92 53 53
MAPK14 -0.35 0.39 -10000 0 -0.95 107 107
mitosis -0.26 0.31 -10000 0 -0.79 82 82
STAT6 -0.55 0.56 -10000 0 -1.3 125 125
SPI1 -0.098 0.3 -10000 0 -0.86 70 70
RPS6KB1 -0.24 0.3 -10000 0 -0.78 68 68
STAT6 (dimer) -0.55 0.56 -10000 0 -1.3 125 125
STAT6 (dimer)/PARP14 -0.51 0.51 -10000 0 -1.2 122 122
mast cell activation 0.012 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.3 0.36 -10000 0 -0.91 94 94
FRAP1 -0.28 0.33 -10000 0 -0.84 82 82
LTA -0.6 0.56 -10000 0 -1.3 162 162
FES 0.013 0.047 -10000 0 -0.75 2 2
T-helper 1 cell differentiation 0.54 0.54 1.3 125 -10000 0 125
CCL11 -0.7 0.61 -10000 0 -1.3 227 227
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.29 0.34 -10000 0 -0.87 91 91
IL2RG -0.037 0.22 -10000 0 -0.86 34 34
IL10 -0.5 0.5 -10000 0 -1.2 116 116
IRS1 0.01 0.067 -10000 0 -0.75 4 4
IRS2 0.002 0.11 -10000 0 -0.86 8 8
IL4 -0.11 0.12 -10000 0 -10000 0 0
IL5 -0.49 0.48 -10000 0 -1.2 111 111
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.39 0.37 -10000 0 -0.88 106 106
COL1A1 -0.41 0.43 -10000 0 -0.92 198 198
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.48 0.48 -10000 0 -1.2 92 92
IL2R gamma/JAK3 -0.16 0.37 -10000 0 -0.83 109 109
TFF3 -0.5 0.5 -10000 0 -1.2 122 122
ALOX15 -0.48 0.48 -10000 0 -1.2 112 112
MYBL1 -0.045 0.22 -10000 0 -0.86 36 36
T-helper 2 cell differentiation -0.43 0.41 -10000 0 -0.98 123 123
SHC1 0.014 0.039 -10000 0 -0.86 1 1
CEBPB 0 0.14 -10000 0 -0.87 12 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.26 0.3 -10000 0 -0.78 67 67
mol:PI-3-4-5-P3 -0.28 0.33 -10000 0 -0.84 82 82
PI3K -0.3 0.36 -10000 0 -0.92 82 82
DOK2 -0.037 0.21 -10000 0 -0.86 31 31
ETS1 0.028 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.21 0.27 -10000 0 -0.78 52 52
ITGB3 -0.48 0.49 -10000 0 -1.2 111 111
PIGR -0.84 0.7 -10000 0 -1.4 268 268
IGHE 0.028 0.09 0.29 14 -0.37 4 18
MAPKKK cascade -0.2 0.27 -10000 0 -0.76 52 52
BCL6 0.014 0.005 -10000 0 -10000 0 0
OPRM1 -0.49 0.48 -10000 0 -1.2 113 113
RETNLB -0.49 0.48 -10000 0 -1.2 111 111
SELP -0.51 0.52 -10000 0 -1.3 117 117
AICDA -0.62 0.55 -10000 0 -1.2 183 183
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 -0.42 0.54 -9999 0 -0.9 238 238
MAP4K1 -0.34 0.43 -9999 0 -0.86 211 211
MAP3K8 0.012 0.055 -9999 0 -0.86 2 2
PRKCB 0.008 0.082 -9999 0 -0.82 5 5
DBNL 0.016 0 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
MAP3K1 -0.15 0.3 -9999 0 -0.62 121 121
JUN 0.001 0.08 -9999 0 -0.56 5 5
MAP3K7 -0.15 0.3 -9999 0 -0.62 121 121
GRAP2 -0.043 0.22 -9999 0 -0.86 35 35
CRK 0.016 0 -9999 0 -10000 0 0
MAP2K4 -0.14 0.29 -9999 0 -0.59 121 121
LAT -0.23 0.4 -9999 0 -0.86 145 145
LCP2 -0.04 0.22 -9999 0 -0.86 33 33
MAPK8 -0.01 0.084 -9999 0 -0.6 5 5
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.2 0.29 -9999 0 -0.67 121 121
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.39 0.51 -9999 0 -1.2 121 121
EGFR-dependent Endothelin signaling events

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
HRAS 0.014 0.039 -9999 0 -0.86 1 1
EGFR 0.001 0.11 -9999 0 -0.85 9 9
EGF/EGFR -0.38 0.16 -9999 0 -0.86 26 26
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.36 0.14 -9999 0 -0.9 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.012 0.055 -9999 0 -0.86 2 2
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.67 0.23 -9999 0 -0.75 466 466
EGF/EGFR dimer/SHC -0.44 0.16 -9999 0 -0.49 467 467
mol:GDP -0.36 0.14 -9999 0 -0.88 9 9
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.013 0.16 -9999 0 -0.86 17 17
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.33 0.13 -9999 0 -0.82 10 10
SHC1 0.014 0.039 -9999 0 -0.86 1 1
HRAS/GDP -0.33 0.13 -9999 0 -0.83 10 10
FRAP1 -0.34 0.14 -9999 0 -0.85 9 9
EGF/EGFR dimer -0.51 0.18 -9999 0 -0.57 467 467
SOS1 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.024 0.12 -9999 0 -0.66 19 19
Caspase cascade in apoptosis

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
TOP1 -0.13 0.27 -10000 0 -0.49 167 167
ACTA1 -0.19 0.36 -10000 0 -0.67 168 168
NUMA1 -0.13 0.27 -10000 0 -0.57 108 108
SPTAN1 -0.19 0.36 -10000 0 -0.67 167 167
LIMK1 -0.19 0.36 -10000 0 -0.67 168 168
BIRC3 -0.12 0.32 -10000 0 -0.86 80 80
BIRC2 0.012 0.007 -10000 0 -10000 0 0
BAX 0.016 0 -10000 0 -10000 0 0
CASP10 -0.28 0.46 -10000 0 -0.87 185 185
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.015 0.003 -10000 0 -10000 0 0
PTK2 -0.13 0.27 -10000 0 -0.49 167 167
DIABLO 0.016 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.18 0.35 -10000 0 -0.65 167 167
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
GSN -0.19 0.36 -10000 0 -0.67 167 167
MADD 0.016 0 -10000 0 -10000 0 0
TFAP2A -0.3 0.28 -10000 0 -0.54 283 283
BID -0.091 0.17 -10000 0 -0.37 104 104
MAP3K1 -0.044 0.11 -10000 0 -10000 0 0
TRADD 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.19 0.36 -10000 0 -0.67 167 167
CASP9 0.016 0.001 -10000 0 -10000 0 0
DNA repair 0.013 0.094 -10000 0 -0.21 35 35
neuron apoptosis 0.011 0.045 -10000 0 -0.62 1 1
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.17 0.34 -10000 0 -0.77 104 104
APAF1 0.016 0.001 -10000 0 -10000 0 0
CASP6 -0.05 0.15 -10000 0 -0.39 27 27
TRAF2 0.016 0 -10000 0 -10000 0 0
ICAD/CAD -0.17 0.34 -10000 0 -0.77 104 104
CASP7 0.051 0.13 0.34 80 -10000 0 80
KRT18 -0.002 0.046 -10000 0 -0.3 2 2
apoptosis -0.18 0.32 -10000 0 -0.69 111 111
DFFA -0.19 0.36 -10000 0 -0.67 167 167
DFFB -0.19 0.36 -10000 0 -0.67 167 167
PARP1 -0.013 0.095 0.21 35 -10000 0 35
actin filament polymerization 0.16 0.33 0.72 105 -10000 0 105
TNF 0.003 0.1 -10000 0 -0.8 8 8
CYCS -0.069 0.13 -10000 0 -0.27 123 123
SATB1 -0.037 0.15 -10000 0 -0.48 3 3
SLK -0.19 0.36 -10000 0 -0.67 167 167
p15 BID/BAX -0.074 0.15 -10000 0 -0.32 104 104
CASP2 0.031 0.089 -10000 0 -0.42 1 1
JNK cascade 0.044 0.11 -10000 0 -10000 0 0
CASP3 -0.21 0.37 -10000 0 -0.71 167 167
LMNB2 0.011 0.085 -10000 0 -0.39 4 4
RIPK1 0.016 0 -10000 0 -10000 0 0
CASP4 0.016 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO -0.081 0.19 -10000 0 -0.52 80 80
negative regulation of DNA binding -0.29 0.28 -10000 0 -0.54 283 283
stress fiber formation -0.18 0.35 -10000 0 -0.65 167 167
GZMB -0.33 0.51 -10000 0 -0.97 185 185
CASP1 0.023 0 -10000 0 -10000 0 0
LMNB1 0.008 0.09 -10000 0 -0.37 7 7
APP 0.01 0.045 -10000 0 -0.62 1 1
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.015 0 -10000 0 -10000 0 0
VIM -0.17 0.31 -10000 0 -0.66 112 112
LMNA 0.011 0.085 -10000 0 -0.39 4 4
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.03 0.073 -10000 0 -0.41 7 7
LRDD 0.004 0.1 -10000 0 -0.85 7 7
SREBF1 -0.19 0.36 -10000 0 -0.67 168 168
APAF-1/Caspase 9 -0.009 0.063 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis -0.13 0.26 -10000 0 -0.51 144 144
CFL2 -0.17 0.34 -10000 0 -0.75 105 105
GAS2 -0.2 0.36 -10000 0 -0.67 171 171
positive regulation of apoptosis 0.015 0.085 -10000 0 -0.38 4 4
PRF1 -0.21 0.38 -10000 0 -0.86 131 131
Aurora C 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
INCENP 0.016 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.25 0.27 -9999 0 -0.54 244 244
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.064 0.068 -9999 0 -10000 0 0
AURKB -0.4 0.44 -9999 0 -0.86 243 243
AURKC 0.012 0.055 -9999 0 -0.86 2 2
Glypican 2 network

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
MDK -0.05 0.23 -9999 0 -0.86 39 39
GPC2 -0.085 0.28 -9999 0 -0.86 59 59
GPC2/Midkine -0.12 0.28 -9999 0 -0.74 87 87
neuron projection morphogenesis -0.12 0.28 -9999 0 -0.73 87 87
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.007 0.086 -9999 0 -0.86 5 5
CCL5 -0.36 0.44 -9999 0 -0.86 221 221
SDCBP 0.016 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.22 0.23 -9999 0 -0.59 91 91
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.2 0.22 -9999 0 -0.56 91 91
Syndecan-1/Syntenin -0.2 0.22 -9999 0 -0.56 91 91
MAPK3 -0.16 0.2 -9999 0 -0.7 15 15
HGF/MET -0.033 0.15 -9999 0 -0.66 26 26
TGFB1/TGF beta receptor Type II 0.007 0.086 -9999 0 -0.86 5 5
BSG 0.014 0.039 -9999 0 -0.86 1 1
keratinocyte migration -0.2 0.21 -9999 0 -0.55 91 91
Syndecan-1/RANTES -0.42 0.33 -9999 0 -0.68 275 275
Syndecan-1/CD147 -0.2 0.19 -9999 0 -0.54 86 86
Syndecan-1/Syntenin/PIP2 -0.21 0.19 -9999 0 -0.54 91 91
LAMA5 0.014 0.033 -9999 0 -0.75 1 1
positive regulation of cell-cell adhesion -0.21 0.18 -9999 0 -0.52 91 91
MMP7 -0.12 0.3 -9999 0 -0.76 93 93
HGF -0.021 0.17 -9999 0 -0.8 23 23
Syndecan-1/CASK -0.21 0.22 -9999 0 -0.57 91 91
Syndecan-1/HGF/MET -0.23 0.22 -9999 0 -0.59 101 101
regulation of cell adhesion -0.15 0.2 -9999 0 -0.67 15 15
HPSE 0.013 0.047 -9999 0 -0.75 2 2
positive regulation of cell migration -0.22 0.23 -9999 0 -0.59 91 91
SDC1 -0.22 0.23 -9999 0 -0.6 91 91
Syndecan-1/Collagen -0.22 0.23 -9999 0 -0.59 91 91
PPIB 0.016 0 -9999 0 -10000 0 0
MET 0.007 0.086 -9999 0 -0.86 5 5
PRKACA 0.016 0 -9999 0 -10000 0 0
MMP9 -0.4 0.44 -9999 0 -0.86 247 247
MAPK1 -0.16 0.2 -9999 0 -0.7 15 15
homophilic cell adhesion -0.22 0.22 -9999 0 -0.58 91 91
MMP1 -0.15 0.34 -9999 0 -0.83 102 102
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.6 0.31 -9999 0 -0.85 281 281
SMAD6-7/SMURF1 0 0 -9999 0 -10000 0 0
NOG -0.12 0.31 -9999 0 -0.84 82 82
SMAD9 -0.064 0.083 -9999 0 -0.57 10 10
SMAD4 0.016 0 -9999 0 -10000 0 0
SMAD5 -0.18 0.17 -9999 0 -0.52 18 18
BMP7/USAG1 -0.7 0.34 -9999 0 -0.8 452 452
SMAD5/SKI -0.17 0.16 -9999 0 -0.5 14 14
SMAD1 0.002 0.042 -9999 0 -10000 0 0
BMP2 0.01 0.069 -9999 0 -0.78 4 4
SMAD1/SMAD1/SMAD4 0 0.001 -9999 0 -10000 0 0
BMPR1A 0.016 0 -9999 0 -10000 0 0
BMPR1B -0.51 0.35 -9999 0 -0.75 355 355
BMPR1A-1B/BAMBI -0.33 0.23 -9999 0 -0.48 358 358
AHSG -0.013 0.13 -9999 0 -0.86 12 12
CER1 0.004 0.007 -9999 0 -10000 0 0
BMP2-4/CER1 -0.007 0.058 -9999 0 -0.5 7 7
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.14 0.11 -9999 0 -0.49 18 18
BMP2-4 (homodimer) -0.008 0.067 -9999 0 -0.57 7 7
RGMB 0.012 0.055 -9999 0 -0.86 2 2
BMP6/BMPR2/BMPR1A-1B -0.3 0.2 -9999 0 -0.79 5 5
RGMA 0.008 0.074 -9999 0 -0.75 5 5
SMURF1 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.16 0.13 -9999 0 -0.56 18 18
BMP2-4/USAG1 -0.31 0.24 -9999 0 -0.48 335 335
SMAD6/SMURF1/SMAD5 -0.17 0.16 -9999 0 -0.5 14 14
SOSTDC1 -0.48 0.36 -9999 0 -0.75 334 334
BMP7/BMPR2/BMPR1A-1B -0.58 0.3 -9999 0 -0.86 257 257
SKI 0.016 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.004 0.094 -9999 0 -0.74 8 8
HFE2 -0.018 0.16 -9999 0 -0.86 18 18
ZFYVE16 0.016 0 -9999 0 -10000 0 0
MAP3K7 0.016 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.017 0.099 -9999 0 -0.56 16 16
SMAD5/SMAD5/SMAD4 -0.17 0.16 -9999 0 -0.5 14 14
MAPK1 0.016 0 -9999 0 -10000 0 0
TAK1/TAB family -0.13 0.1 -9999 0 -0.5 14 14
BMP7 (homodimer) -0.5 0.35 -9999 0 -0.74 350 350
NUP214 0.016 0 -9999 0 -10000 0 0
BMP6/FETUA -0.024 0.12 -9999 0 -0.62 20 20
SMAD1/SKI 0.012 0.039 -9999 0 -10000 0 0
SMAD6 0.016 0 -9999 0 -10000 0 0
CTDSP2 0.016 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.02 0.1 -9999 0 -0.55 19 19
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.18 0.33 -9999 0 -0.76 128 128
BMPR2 (homodimer) 0.016 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.38 0.26 -9999 0 -0.56 355 355
CHRDL1 -0.38 0.38 -9999 0 -0.75 271 271
ENDOFIN/SMAD1 0.012 0.039 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0.005 0.004 -9999 0 -10000 0 0
SMAD6/SMURF1 0.016 0 -9999 0 -10000 0 0
BAMBI 0.005 0.088 -9999 0 -0.75 7 7
SMURF2 0.014 0.033 -9999 0 -0.75 1 1
BMP2-4/CHRDL1 -0.26 0.25 -9999 0 -0.48 273 273
BMP2-4/GREM1 -0.13 0.22 -9999 0 -0.49 133 133
SMAD7 0.016 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.037 0.088 -9999 0 -0.61 6 6
SMAD1/SMAD6 0.012 0.039 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.5 0.35 -9999 0 -0.75 350 350
BMP6 0.004 0.094 -9999 0 -0.75 8 8
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.12 0.13 -9999 0 -0.46 18 18
PPM1A 0.016 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.011 0.042 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.016 0 -9999 0 -10000 0 0
PPP1CA 0.016 0 -9999 0 -10000 0 0
XIAP 0.016 0 -9999 0 -10000 0 0
CTDSP1 0.016 0 -9999 0 -10000 0 0
PPP1R15A 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.21 0.18 -9999 0 -0.6 62 62
CHRD -0.001 0.12 -9999 0 -0.78 11 11
BMPR2 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.17 0.13 -9999 0 -0.58 18 18
BMP4 0.011 0.058 -9999 0 -0.75 3 3
FST -0.074 0.25 -9999 0 -0.77 59 59
BMP2-4/NOG -0.095 0.21 -9999 0 -0.56 88 88
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.55 0.29 -9999 0 -0.81 257 257
HIF-2-alpha transcription factor network

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
MMP14 -0.027 0.08 -10000 0 -0.73 6 6
oxygen homeostasis -0.001 0.015 -10000 0 -10000 0 0
TCEB2 0.011 0.064 -10000 0 -0.82 3 3
TCEB1 0.016 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.23 0.14 -10000 0 -0.7 3 3
EPO -0.4 0.41 -10000 0 -0.9 147 147
FIH (dimer) 0.014 0.02 -10000 0 -10000 0 0
APEX1 0.013 0.014 -10000 0 -10000 0 0
SERPINE1 -0.34 0.41 -10000 0 -0.93 118 118
FLT1 -0.019 0.078 -10000 0 -0.76 5 5
ADORA2A -0.3 0.34 -10000 0 -0.82 81 81
germ cell development -0.4 0.44 -10000 0 -0.93 170 170
SLC11A2 -0.29 0.34 -10000 0 -0.81 81 81
BHLHE40 -0.29 0.34 -10000 0 -0.81 81 81
HIF1AN 0.014 0.02 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.3 0.22 -10000 0 -0.55 147 147
ETS1 0.037 0.004 -10000 0 -10000 0 0
CITED2 -0.023 0.057 -10000 0 -1.2 1 1
KDR -0.015 0.066 -10000 0 -1.4 1 1
PGK1 -0.29 0.34 -10000 0 -0.81 81 81
SIRT1 0.014 0.005 -10000 0 -10000 0 0
response to hypoxia -0.002 0.005 -10000 0 -10000 0 0
HIF2A/ARNT -0.35 0.42 -10000 0 -1 81 81
EPAS1 -0.27 0.19 -10000 0 -0.47 155 155
SP1 0.026 0.005 -10000 0 -10000 0 0
ABCG2 -0.29 0.35 -10000 0 -0.81 82 82
EFNA1 -0.29 0.35 -10000 0 -0.81 82 82
FXN -0.3 0.34 -10000 0 -0.82 81 81
POU5F1 -0.43 0.48 -10000 0 -1 170 170
neuron apoptosis 0.34 0.4 0.96 81 -10000 0 81
EP300 0.014 0.033 -10000 0 -0.75 1 1
EGLN3 -0.76 0.29 -10000 0 -0.87 456 456
EGLN2 0.011 0.016 -10000 0 -10000 0 0
EGLN1 0.014 0.02 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C -0.004 0.046 -10000 0 -0.53 4 4
VHL 0.014 0.033 -10000 0 -0.75 1 1
ARNT 0.013 0.014 -10000 0 -10000 0 0
SLC2A1 -0.32 0.37 -10000 0 -0.9 84 84
TWIST1 -0.31 0.35 -10000 0 -0.83 84 84
ELK1 0.026 0.001 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.26 0.2 -10000 0 -0.56 82 82
VEGFA -0.47 0.49 -10000 0 -1 191 191
CREBBP 0.016 0 -10000 0 -10000 0 0
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.25 0.48 -10000 0 -1.1 69 69
IL23A -0.24 0.47 -10000 0 -1.1 55 55
NF kappa B1 p50/RelA/I kappa B alpha -0.33 0.39 -10000 0 -1 82 82
positive regulation of T cell mediated cytotoxicity -0.29 0.53 -10000 0 -1.1 89 89
ITGA3 -0.24 0.47 -10000 0 -1.1 58 58
IL17F -0.15 0.34 -10000 0 -0.75 34 34
IL12B -0.085 0.29 -10000 0 -0.89 60 60
STAT1 (dimer) -0.28 0.5 -10000 0 -1.1 86 86
CD4 -0.25 0.48 -10000 0 -1.1 64 64
IL23 -0.28 0.48 -10000 0 -1.1 69 69
IL23R -0.012 0.15 -10000 0 -0.8 10 10
IL1B -0.25 0.48 -10000 0 -1.1 66 66
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.25 0.47 -10000 0 -1.1 67 67
TYK2 0.016 0.025 -10000 0 -10000 0 0
STAT4 -0.035 0.2 -10000 0 -0.86 30 30
STAT3 0.016 0.001 -10000 0 -10000 0 0
IL18RAP -0.22 0.39 -10000 0 -0.88 133 133
IL12RB1 -0.26 0.42 -10000 0 -0.89 159 159
PIK3CA 0.014 0.033 -10000 0 -0.75 1 1
IL12Rbeta1/TYK2 -0.2 0.34 -10000 0 -0.7 159 159
IL23R/JAK2 -0.011 0.16 -10000 0 -0.78 9 9
positive regulation of chronic inflammatory response -0.29 0.53 -10000 0 -1.1 89 89
natural killer cell activation 0.002 0.012 0.063 10 -10000 0 10
JAK2 0.021 0.035 -10000 0 -10000 0 0
PIK3R1 0.014 0.033 -10000 0 -0.75 1 1
NFKB1 0.01 0.034 -10000 0 -0.74 1 1
RELA 0.011 0.009 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.26 0.46 -10000 0 -1.1 69 69
ALOX12B -0.31 0.5 -10000 0 -1.1 85 85
CXCL1 -0.29 0.52 -10000 0 -1.2 79 79
T cell proliferation -0.29 0.53 -10000 0 -1.1 89 89
NFKBIA 0.011 0.009 -10000 0 -10000 0 0
IL17A -0.1 0.29 -10000 0 -0.61 4 4
PI3K -0.33 0.4 -10000 0 -1 89 89
IFNG -0.053 0.07 0.13 4 -0.12 205 209
STAT3 (dimer) -0.32 0.38 -10000 0 -1 77 77
IL18R1 -0.004 0.1 -10000 0 -0.81 8 8
IL23/IL23R/JAK2/TYK2/SOCS3 -0.18 0.38 -10000 0 -0.85 63 63
IL18/IL18R -0.17 0.28 -10000 0 -0.62 145 145
macrophage activation -0.017 0.018 -10000 0 -0.046 5 5
TNF -0.26 0.49 -10000 0 -1.1 68 68
STAT3/STAT4 -0.36 0.43 -10000 0 -1.1 95 95
STAT4 (dimer) -0.3 0.53 -10000 0 -1.2 91 91
IL18 -0.003 0.1 -10000 0 -0.86 7 7
IL19 -0.25 0.46 -10000 0 -1.1 62 62
STAT5A (dimer) -0.28 0.5 -10000 0 -1.1 84 84
STAT1 0.014 0.039 -10000 0 -0.86 1 1
SOCS3 0.012 0.055 -10000 0 -0.86 2 2
CXCL9 -0.4 0.59 -10000 0 -1.1 161 161
MPO -0.26 0.48 -10000 0 -1.1 71 71
positive regulation of humoral immune response -0.29 0.53 -10000 0 -1.1 89 89
IL23/IL23R/JAK2/TYK2 -0.3 0.55 -10000 0 -1.2 89 89
IL6 -0.3 0.53 -10000 0 -1.2 91 91
STAT5A 0.016 0 -10000 0 -10000 0 0
IL2 -0.016 0.12 -10000 0 -0.86 10 10
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.012 0.063 10 -10000 0 10
CD3E -0.39 0.6 -10000 0 -1.1 156 156
keratinocyte proliferation -0.29 0.53 -10000 0 -1.1 89 89
NOS2 -0.25 0.47 -10000 0 -1 72 72
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.006 0.13 -9999 0 -0.78 14 14
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.011 0.064 -9999 0 -0.82 3 3
TCEB1 0.016 0 -9999 0 -10000 0 0
HIF1A/p53 -0.08 0.047 -9999 0 -0.39 1 1
HIF1A -0.099 0.039 -9999 0 -0.42 1 1
COPS5 0.016 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.003 0.039 -9999 0 -10000 0 0
FIH (dimer) 0.016 0 -9999 0 -10000 0 0
CDKN2A -0.83 0.16 -9999 0 -0.86 499 499
ARNT/IPAS -0.016 0.096 -9999 0 -0.59 14 14
HIF1AN 0.016 0 -9999 0 -10000 0 0
GNB2L1 0.014 0.039 -9999 0 -0.86 1 1
HIF1A/ARNT -0.08 0.047 -9999 0 -0.39 1 1
CUL2 0.016 0 -9999 0 -10000 0 0
OS9 0.016 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.004 0.048 -9999 0 -0.55 4 4
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.08 0.047 -9999 0 -0.39 1 1
PHD1-3/OS9 -0.46 0.17 -9999 0 -0.52 455 455
HIF1A/RACK1/Elongin B/Elongin C -0.067 0.05 -9999 0 -0.59 3 3
VHL 0.014 0.033 -9999 0 -0.75 1 1
HSP90AA1 0.016 0 -9999 0 -10000 0 0
HIF1A/JAB1 -0.08 0.047 -9999 0 -0.39 1 1
EGLN3 -0.76 0.29 -9999 0 -0.86 456 456
EGLN2 0.016 0 -9999 0 -10000 0 0
EGLN1 0.016 0 -9999 0 -10000 0 0
TP53 0.016 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.003 0.035 -9999 0 -0.61 1 1
ARNT 0.016 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.016 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.56 0.11 -9999 0 -0.57 499 499
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.25 0.26 -10000 0 -0.74 32 32
IHH -0.099 0.23 -10000 0 -0.82 47 47
SHH Np/Cholesterol/GAS1 -0.037 0.12 -10000 0 -0.45 42 42
LRPAP1 0.016 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.036 0.12 0.45 42 -10000 0 42
SMO/beta Arrestin2 -0.15 0.15 -10000 0 -0.6 34 34
SMO -0.13 0.19 -10000 0 -0.64 33 33
AKT1 -0.042 0.093 -10000 0 -0.46 1 1
ARRB2 0.014 0.039 -10000 0 -0.86 1 1
BOC 0.016 0 -10000 0 -10000 0 0
ADRBK1 0.016 0 -10000 0 -10000 0 0
heart looping -0.13 0.19 -10000 0 -0.62 33 33
STIL -0.095 0.17 -10000 0 -0.67 10 10
DHH N/PTCH2 -0.044 0.16 -10000 0 -0.63 36 36
DHH N/PTCH1 -0.16 0.16 -10000 0 -0.62 36 36
PIK3CA 0.014 0.033 -10000 0 -0.75 1 1
DHH -0.001 0.11 -10000 0 -0.75 11 11
PTHLH -0.44 0.41 -10000 0 -0.74 322 322
determination of left/right symmetry -0.13 0.19 -10000 0 -0.62 33 33
PIK3R1 0.014 0.033 -10000 0 -0.75 1 1
skeletal system development -0.44 0.4 -10000 0 -0.73 322 322
IHH N/Hhip -0.2 0.31 -10000 0 -0.65 160 160
DHH N/Hhip -0.15 0.26 -10000 0 -0.57 138 138
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.13 0.19 -10000 0 -0.62 33 33
pancreas development -0.18 0.33 -10000 0 -0.75 129 129
HHAT 0.016 0 -10000 0 -10000 0 0
PI3K -0.002 0.035 -10000 0 -0.56 2 2
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.032 0.18 -10000 0 -0.75 32 32
somite specification -0.13 0.19 -10000 0 -0.62 33 33
SHH Np/Cholesterol/PTCH1 -0.14 0.14 -10000 0 -0.55 36 36
SHH Np/Cholesterol/PTCH2 -0.035 0.13 -10000 0 -0.51 36 36
SHH Np/Cholesterol/Megalin -0.048 0.15 -10000 0 -0.48 51 51
SHH 0.018 0.087 -10000 0 -0.57 11 11
catabolic process -0.16 0.19 -10000 0 -0.65 32 32
SMO/Vitamin D3 -0.11 0.18 -10000 0 -0.58 36 36
SHH Np/Cholesterol/Hhip -0.12 0.21 -10000 0 -0.46 135 135
LRP2 -0.051 0.22 -10000 0 -0.75 45 45
receptor-mediated endocytosis -0.15 0.18 -10000 0 -0.62 44 44
SHH Np/Cholesterol/BOC -0.009 0.064 -10000 0 -0.45 11 11
SHH Np/Cholesterol/CDO -0.07 0.18 -10000 0 -0.53 69 69
mesenchymal cell differentiation 0.12 0.21 0.46 135 -10000 0 135
mol:Vitamin D3 -0.11 0.17 -10000 0 -0.56 36 36
IHH N/PTCH2 -0.084 0.22 -10000 0 -0.62 70 70
CDON -0.084 0.28 -10000 0 -0.86 59 59
IHH N/PTCH1 -0.16 0.2 -10000 0 -0.66 32 32
Megalin/LRPAP1 -0.049 0.16 -10000 0 -0.56 45 45
PTCH2 -0.027 0.19 -10000 0 -0.86 25 25
SHH Np/Cholesterol -0.01 0.066 -10000 0 -0.46 11 11
PTCH1 -0.16 0.19 -10000 0 -0.66 32 32
HHIP -0.18 0.33 -10000 0 -0.76 129 129
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 0.016 0 -9999 0 -10000 0 0
LAT2 -0.16 0.23 -9999 0 -0.7 61 61
AP1 -0.16 0.21 -9999 0 -0.56 88 88
mol:PIP3 -0.23 0.34 -9999 0 -0.7 143 143
IKBKB -0.088 0.17 -9999 0 -0.34 76 76
AKT1 -0.17 0.21 -9999 0 -0.73 22 22
IKBKG -0.088 0.17 -9999 0 -0.34 76 76
MS4A2 -0.18 0.36 -9999 0 -0.86 114 114
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.034 -9999 0 -0.75 1 1
MAP3K1 -0.12 0.26 -9999 0 -0.55 111 111
mol:Ca2+ -0.16 0.24 -9999 0 -0.48 143 143
LYN 0.011 0.009 -9999 0 -10000 0 0
CBLB -0.12 0.15 -9999 0 -0.54 21 21
SHC1 0.014 0.039 -9999 0 -0.86 1 1
RasGAP/p62DOK -0.002 0.03 -9999 0 -0.48 2 2
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.009 0.077 -9999 0 -0.86 4 4
PLD2 -0.18 0.28 -9999 0 -0.73 35 35
PTPN13 -0.069 0.16 -9999 0 -0.49 20 20
PTPN11 0.014 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.044 0.17 -9999 0 -0.4 11 11
SYK 0.008 0.048 -9999 0 -0.76 2 2
GRB2 0.015 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.3 0.32 -9999 0 -0.76 141 141
LAT -0.25 0.3 -9999 0 -0.65 155 155
PAK2 -0.15 0.29 -9999 0 -0.63 117 117
NFATC2 -0.069 0.095 -9999 0 -0.74 3 3
HRAS -0.18 0.32 -9999 0 -0.7 123 123
GAB2 0.016 0 -9999 0 -10000 0 0
PLA2G1B 0.04 0.027 -9999 0 -10000 0 0
Fc epsilon R1 -0.26 0.32 -9999 0 -0.62 213 213
Antigen/IgE/Fc epsilon R1 -0.24 0.3 -9999 0 -0.58 213 213
mol:GDP -0.21 0.36 -9999 0 -0.76 131 131
JUN 0.016 0 -9999 0 -10000 0 0
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.011 0.034 -9999 0 -0.75 1 1
FOS -0.004 0.12 -9999 0 -0.76 13 13
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.13 0.16 -9999 0 -0.58 21 21
CHUK -0.088 0.17 -9999 0 -0.34 76 76
KLRG1 -0.12 0.15 -9999 0 -0.55 21 21
VAV1 -0.2 0.32 -9999 0 -0.69 135 135
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.12 0.15 -9999 0 -0.55 22 22
negative regulation of mast cell degranulation -0.11 0.15 -9999 0 -0.56 23 23
BTK -0.18 0.24 -9999 0 -0.58 113 113
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.17 0.22 -9999 0 -0.58 85 85
GAB2/PI3K/SHP2 -0.18 0.24 -9999 0 -0.82 22 22
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.12 0.15 -9999 0 -0.55 21 21
RAF1 0.026 0.028 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.31 0.39 -9999 0 -1 85 85
FCER1G -0.16 0.34 -9999 0 -0.87 97 97
FCER1A -0.022 0.16 -9999 0 -0.77 22 22
Antigen/IgE/Fc epsilon R1/Fyn -0.22 0.28 -9999 0 -0.55 199 199
MAPK3 0.04 0.026 -9999 0 -10000 0 0
MAPK1 0.04 0.026 -9999 0 -10000 0 0
NFKB1 0.014 0.033 -9999 0 -0.75 1 1
MAPK8 -0.012 0.076 -9999 0 -0.68 1 1
DUSP1 0.014 0.039 -9999 0 -0.86 1 1
NF-kappa-B/RelA -0.07 0.074 -9999 0 -0.33 1 1
actin cytoskeleton reorganization -0.074 0.16 -9999 0 -0.48 21 21
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.22 0.29 -9999 0 -0.72 115 115
FER -0.12 0.16 -9999 0 -0.55 23 23
RELA 0.016 0 -9999 0 -10000 0 0
ITK -0.15 0.19 -9999 0 -0.42 161 161
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG1 -0.2 0.36 -9999 0 -0.75 131 131
cytokine secretion -0.051 0.053 -9999 0 -10000 0 0
SPHK1 -0.16 0.22 -9999 0 -0.64 58 58
PTK2 -0.077 0.16 -9999 0 -0.5 21 21
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.25 0.31 -9999 0 -0.77 109 109
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.19 0.31 -9999 0 -0.68 109 109
MAP2K2 0.034 0.031 -9999 0 -0.42 1 1
MAP2K1 0.035 0.024 -9999 0 -10000 0 0
MAP2K7 0.016 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.11 0.15 -9999 0 -0.53 21 21
MAP2K4 0.017 0.015 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.32 0.41 -9999 0 -0.73 224 224
mol:Choline -0.17 0.28 -9999 0 -0.62 56 56
SHC/Grb2/SOS1 -0.1 0.14 -9999 0 -0.52 16 16
FYN 0.016 0 -9999 0 -10000 0 0
DOK1 0.016 0 -9999 0 -10000 0 0
PXN -0.062 0.15 -9999 0 -0.46 17 17
HCLS1 -0.13 0.18 -9999 0 -0.67 29 29
PRKCB -0.14 0.23 -9999 0 -0.48 116 116
FCGR2B -0.14 0.34 -9999 0 -0.86 95 95
IGHE -0.005 0.01 -9999 0 -10000 0 0
KLRG1/SHIP -0.11 0.16 -9999 0 -0.58 23 23
LCP2 -0.041 0.22 -9999 0 -0.87 33 33
PLA2G4A -0.12 0.16 -9999 0 -0.56 25 25
RASA1 0.014 0.033 -9999 0 -0.75 1 1
mol:Phosphatidic acid -0.17 0.28 -9999 0 -0.62 56 56
IKK complex -0.048 0.13 -9999 0 -0.28 1 1
WIPF1 0.016 0 -9999 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.009 0.086 -10000 0 -0.86 5 5
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.078 0.2 0.6 33 -0.44 3 36
IL27/IL27R/JAK1 -0.083 0.35 0.58 1 -0.85 58 59
TBX21 -0.21 0.41 0.5 1 -0.75 157 158
IL12B -0.093 0.28 -10000 0 -0.87 60 60
IL12A 0.008 0.032 -10000 0 -0.69 1 1
IL6ST -0.014 0.14 -10000 0 -0.76 17 17
IL27RA/JAK1 0.01 0.062 -10000 0 -0.7 1 1
IL27 -0.045 0.21 -10000 0 -0.88 32 32
TYK2 0.011 0.012 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.025 0.13 -10000 0 -0.74 2 2
T-helper 2 cell differentiation 0.078 0.2 0.6 33 -0.44 3 36
T cell proliferation during immune response 0.078 0.2 0.6 33 -0.44 3 36
MAPKKK cascade -0.078 0.2 0.44 3 -0.6 33 36
STAT3 0.016 0 -10000 0 -10000 0 0
STAT2 0.016 0 -10000 0 -10000 0 0
STAT1 0.015 0.039 -10000 0 -0.86 1 1
IL12RB1 -0.26 0.41 -10000 0 -0.87 159 159
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.16 0.35 0.5 1 -0.71 100 101
IL27/IL27R/JAK2/TYK2 -0.08 0.2 0.44 3 -0.61 33 36
positive regulation of T cell mediated cytotoxicity -0.078 0.2 0.44 3 -0.6 33 36
STAT1 (dimer) -0.07 0.51 0.54 118 -0.98 72 190
JAK2 0.011 0.012 -10000 0 -10000 0 0
JAK1 0.017 0.006 -10000 0 -10000 0 0
STAT2 (dimer) -0.082 0.18 0.39 3 -0.62 23 26
T cell proliferation -0.12 0.25 0.4 1 -0.69 53 54
IL12/IL12R/TYK2/JAK2 -0.18 0.27 -10000 0 -0.75 46 46
IL17A -0.025 0.13 -10000 0 -0.74 2 2
mast cell activation 0.078 0.2 0.6 33 -0.44 3 36
IFNG -0.041 0.066 0.13 3 -0.11 237 240
T cell differentiation -0.011 0.011 0.03 3 -0.026 141 144
STAT3 (dimer) -0.082 0.18 0.39 3 -0.63 22 25
STAT5A (dimer) -0.082 0.18 0.39 3 -0.62 24 27
STAT4 (dimer) -0.11 0.24 0.39 2 -0.77 42 44
STAT4 -0.035 0.2 -10000 0 -0.86 30 30
T cell activation -0.012 0.007 0.1 1 -10000 0 1
IL27R/JAK2/TYK2 -0.043 0.1 -10000 0 -0.62 3 3
GATA3 -0.61 0.68 -10000 0 -1.3 251 251
IL18 0.005 0.08 -10000 0 -0.68 7 7
positive regulation of mast cell cytokine production -0.082 0.18 0.38 3 -0.62 22 25
IL27/EBI3 -0.12 0.33 -10000 0 -0.83 85 85
IL27RA -0.003 0.063 -10000 0 -0.76 1 1
IL6 -0.087 0.28 -10000 0 -0.82 65 65
STAT5A 0.016 0 -10000 0 -10000 0 0
monocyte differentiation -0.002 0.003 -10000 0 -10000 0 0
IL2 0 0.088 -10000 0 -0.6 10 10
IL1B 0.006 0.073 -10000 0 -0.66 6 6
EBI3 -0.12 0.31 -10000 0 -0.88 75 75
TNF 0.004 0.079 -10000 0 -0.63 8 8
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.19 0.36 -10000 0 -1.1 69 69
NFATC2 -0.079 0.23 -10000 0 -0.66 34 34
NFATC3 -0.021 0.064 -10000 0 -10000 0 0
CD40LG -0.24 0.44 -10000 0 -1.1 61 61
ITCH 0.054 0.058 -10000 0 -10000 0 0
CBLB 0.054 0.058 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.55 0.56 -10000 0 -1.1 219 219
JUNB 0.013 0.047 -10000 0 -0.75 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.011 0.058 -10000 0 -10000 0 0
T cell anergy 0.023 0.095 -10000 0 -0.6 1 1
TLE4 -0.03 0.17 -10000 0 -0.7 7 7
Jun/NFAT1-c-4/p21SNFT -0.24 0.28 -10000 0 -0.93 35 35
AP-1/NFAT1-c-4 -0.3 0.37 -10000 0 -1.1 54 54
IKZF1 -0.13 0.36 -10000 0 -0.88 91 91
T-helper 2 cell differentiation -0.35 0.28 -10000 0 -0.76 82 82
AP-1/NFAT1 -0.093 0.16 -10000 0 -0.64 15 15
CALM1 0.028 0.036 -10000 0 -10000 0 0
EGR2 -0.11 0.29 -10000 0 -1.3 10 10
EGR3 -0.11 0.29 -10000 0 -1.4 8 8
NFAT1/FOXP3 -0.28 0.4 -10000 0 -0.94 116 116
EGR1 0.001 0.11 -10000 0 -0.74 11 11
JUN 0.005 0.022 -10000 0 -10000 0 0
EGR4 0.006 0.077 -10000 0 -0.86 4 4
mol:Ca2+ 0.009 0.04 -10000 0 -10000 0 0
GBP3 -0.034 0.18 -10000 0 -0.79 9 9
FOSL1 -0.027 0.19 -10000 0 -0.86 25 25
NFAT1-c-4/MAF/IRF4 -0.27 0.36 -10000 0 -0.9 104 104
DGKA -0.034 0.19 -10000 0 -1 7 7
CREM 0.015 0.002 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.17 0.21 -10000 0 -0.94 12 12
CTLA4 -0.44 0.58 -10000 0 -1 237 237
NFAT1-c-4 (dimer)/EGR1 -0.17 0.24 -10000 0 -0.99 17 17
NFAT1-c-4 (dimer)/EGR4 -0.17 0.23 -10000 0 -0.99 12 12
FOS -0.014 0.12 -10000 0 -0.76 13 13
IFNG -0.5 0.52 -10000 0 -1 238 238
T cell activation -0.049 0.22 -10000 0 -0.82 17 17
MAF 0.016 0 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.064 0.2 0.8 5 -10000 0 5
TNF -0.095 0.28 -10000 0 -1 15 15
FASLG -0.34 0.48 -10000 0 -0.95 82 82
TBX21 -0.31 0.44 -10000 0 -0.93 169 169
BATF3 -0.061 0.25 -10000 0 -0.86 45 45
PRKCQ -0.034 0.13 -10000 0 -0.75 15 15
PTPN1 -0.03 0.17 -10000 0 -0.7 7 7
NFAT1-c-4/ICER1 -0.17 0.21 -10000 0 -0.96 11 11
GATA3 -0.35 0.38 -10000 0 -0.75 251 251
T-helper 1 cell differentiation -0.49 0.5 -10000 0 -0.99 238 238
IL2RA -0.39 0.46 -10000 0 -1.1 129 129
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.03 0.17 -10000 0 -0.7 7 7
E2F1 -0.081 0.28 -10000 0 -0.85 62 62
PPARG 0.016 0.001 -10000 0 -10000 0 0
SLC3A2 -0.03 0.17 -10000 0 -0.7 7 7
IRF4 -0.18 0.37 -10000 0 -0.86 118 118
PTGS2 -0.21 0.4 -10000 0 -1 42 42
CSF2 -0.21 0.4 -10000 0 -1.1 39 39
JunB/Fra1/NFAT1-c-4 -0.18 0.22 -10000 0 -0.94 13 13
IL4 -0.36 0.29 -10000 0 -0.8 78 78
IL5 -0.2 0.37 -10000 0 -1 33 33
IL2 -0.05 0.22 -10000 0 -0.84 17 17
IL3 -0.05 0.049 -10000 0 -10000 0 0
RNF128 0.033 0.16 -10000 0 -0.79 19 19
NFATC1 -0.064 0.2 -10000 0 -0.8 5 5
CDK4 0.035 0.18 -10000 0 -10000 0 0
PTPRK -0.03 0.17 -10000 0 -0.7 7 7
IL8 -0.22 0.42 -10000 0 -1.1 42 42
POU2F1 0.016 0.003 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.007 0.073 -9999 0 -0.66 6 6
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.021 0.12 -9999 0 -0.67 16 16
STXBP1 0.014 0.033 -9999 0 -0.75 1 1
ACh/CHRNA1 -0.27 0.31 -9999 0 -0.63 226 226
RAB3GAP2/RIMS1/UNC13B -0.018 0.1 -9999 0 -0.58 16 16
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.015 0.15 -9999 0 -0.86 16 16
mol:ACh -0.009 0.053 -9999 0 -0.13 80 80
RAB3GAP2 0.016 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.039 0.1 -9999 0 -0.62 4 4
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.27 0.31 -9999 0 -0.63 226 226
UNC13B 0.016 0 -9999 0 -10000 0 0
CHRNA1 -0.37 0.44 -9999 0 -0.86 226 226
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.083 0.2 -9999 0 -0.53 84 84
SNAP25 -0.039 0.12 -9999 0 -0.33 76 76
VAMP2 0.009 0 -9999 0 -10000 0 0
SYT1 -0.11 0.28 -9999 0 -0.75 84 84
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.008 0.065 -9999 0 -0.56 7 7
STX1A/SNAP25 fragment 1/VAMP2 -0.039 0.1 -9999 0 -0.62 4 4
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.056 0.17 -9999 0 -0.53 55 55
EFNA5 -0.057 0.22 -9999 0 -0.75 49 49
FYN -0.026 0.16 -9999 0 -0.48 55 55
neuron projection morphogenesis -0.056 0.17 -9999 0 -0.53 55 55
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.056 0.17 -9999 0 -0.53 55 55
EPHA5 -0.008 0.11 -9999 0 -0.86 8 8
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.004 0.043 -9999 0 -0.49 4 4
ARNO/beta Arrestin1-2 -0.018 0.063 -9999 0 -10000 0 0
EGFR 0 0.11 -9999 0 -0.85 9 9
EPHA2 0.014 0.033 -9999 0 -0.75 1 1
USP6 0.014 0.039 -9999 0 -0.86 1 1
IQSEC1 0.016 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.51 0.18 -9999 0 -0.57 467 467
ARRB2 -0.014 0.11 -9999 0 -0.39 38 38
mol:GTP -0.011 0.048 -9999 0 -0.29 1 1
ARRB1 0.016 0 -9999 0 -10000 0 0
FBXO8 0.016 0 -9999 0 -10000 0 0
TSHR -0.085 0.28 -9999 0 -0.86 59 59
EGF -0.67 0.23 -9999 0 -0.75 466 466
somatostatin receptor activity 0 0 -9999 0 -0.001 20 20
ARAP2 0.013 0.047 -9999 0 -0.75 2 2
mol:GDP -0.057 0.095 -9999 0 -0.33 25 25
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 9 9
ITGA2B -0.015 0.16 -9999 0 -0.86 18 18
ARF6 0.016 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.035 -9999 0 -0.52 1 1
ADAP1 0.01 0.067 -9999 0 -0.75 4 4
KIF13B 0.016 0 -9999 0 -10000 0 0
HGF/MET -0.033 0.15 -9999 0 -0.66 26 26
PXN 0.016 0 -9999 0 -10000 0 0
ARF6/GTP -0.087 0.09 -9999 0 -0.33 23 23
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.44 0.16 -9999 0 -0.48 467 467
ADRB2 0.013 0.047 -9999 0 -0.75 2 2
receptor agonist activity 0 0 -9999 0 0 15 15
actin filament binding 0 0 -9999 0 -0.001 21 21
SRC 0.016 0 -9999 0 -10000 0 0
ITGB3 0.01 0.067 -9999 0 -0.75 4 4
GNAQ 0.015 0.001 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 11 11
ARF6/GDP -0.068 0.14 -9999 0 -0.4 6 6
ARF6/GDP/GULP/ACAP1 -0.23 0.26 -9999 0 -0.54 193 193
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.021 0.1 -9999 0 -0.52 17 17
ACAP1 -0.32 0.43 -9999 0 -0.86 196 196
ACAP2 0.016 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.043 0.15 -9999 0 -0.59 38 38
EFNA1 0.014 0.039 -9999 0 -0.86 1 1
HGF -0.021 0.17 -9999 0 -0.8 23 23
CYTH3 0.015 0 -9999 0 -10000 0 0
CYTH2 0.01 0.001 -9999 0 -10000 0 0
NCK1 0.014 0.033 -9999 0 -0.75 1 1
fibronectin binding 0 0 -9999 0 -0.001 12 12
endosomal lumen acidification 0 0 -9999 0 -0.001 23 23
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.011 0.14 -9999 0 -0.75 18 18
GNAQ/ARNO 0.009 0.01 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 2 2
MET 0.007 0.086 -9999 0 -0.86 5 5
GNA14 0.005 0.088 -9999 0 -0.75 7 7
GNA15 -0.01 0.15 -9999 0 -0.86 15 15
GIT1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 12 12
GNA11 0.011 0.058 -9999 0 -0.75 3 3
LHCGR -0.057 0.22 -9999 0 -0.86 37 37
AGTR1 -0.027 0.18 -9999 0 -0.75 29 29
desensitization of G-protein coupled receptor protein signaling pathway -0.043 0.15 -9999 0 -0.59 38 38
IPCEF1/ARNO -0.34 0.13 -9999 0 -0.82 8 8
alphaIIb/beta3 Integrin -0.027 0.13 -9999 0 -0.64 22 22
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.014 0.047 -9999 0 -10000 0 0
NFATC2 -0.017 0.064 -9999 0 -0.59 3 3
NFATC3 -0.014 0.047 -9999 0 -10000 0 0
CD40LG -0.31 0.42 -9999 0 -0.94 100 100
PTGS2 -0.29 0.39 -9999 0 -0.86 94 94
JUNB 0.013 0.047 -9999 0 -0.75 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.02 0.018 -9999 0 -10000 0 0
CaM/Ca2+ -0.02 0.018 -9999 0 -10000 0 0
CALM1 0.006 0.013 -9999 0 -10000 0 0
JUN 0.006 0.013 -9999 0 -10000 0 0
mol:Ca2+ -0.02 0.019 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 -0.002 0.003 -9999 0 -10000 0 0
FOSL1 -0.027 0.19 -9999 0 -0.86 25 25
CREM 0.016 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.19 0.2 -9999 0 -0.74 35 35
FOS -0.014 0.12 -9999 0 -0.76 13 13
IFNG -0.44 0.52 -9999 0 -0.98 224 224
AP-1/NFAT1-c-4 -0.41 0.41 -9999 0 -1.1 91 91
FASLG -0.46 0.52 -9999 0 -0.98 227 227
NFAT1-c-4/ICER1 -0.081 0.081 -9999 0 -0.58 3 3
IL2RA -0.34 0.44 -9999 0 -1 105 105
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.29 0.38 -9999 0 -0.87 91 91
JunB/Fra1/NFAT1-c-4 -0.094 0.12 -9999 0 -0.63 8 8
IL4 -0.28 0.37 -9999 0 -0.84 88 88
IL2 -0.012 0.11 -9999 0 -0.77 10 10
IL3 -0.028 0.026 -9999 0 -10000 0 0
FKBP1A 0.016 0 -9999 0 -10000 0 0
BATF3 -0.061 0.25 -9999 0 -0.86 45 45
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.016 0.003 -9999 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.008 0.072 -9999 0 -0.68 5 5
VEGFR1 homodimer/NRP1 -0.008 0.073 -9999 0 -0.62 7 7
mol:DAG -0.26 0.29 -9999 0 -0.97 7 7
VEGFR1 homodimer/NRP1/VEGFR 121 -0.24 0.27 -9999 0 -0.54 234 234
CaM/Ca2+ -0.27 0.25 -9999 0 -0.92 7 7
HIF1A 0.02 0.058 -9999 0 -0.72 2 2
GAB1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.23 0.21 -9999 0 -0.95 6 6
PLCG1 -0.27 0.29 -9999 0 -0.98 7 7
NOS3 -0.18 0.24 -9999 0 -0.85 6 6
CBL 0.014 0.033 -9999 0 -0.75 1 1
mol:NO -0.17 0.24 -9999 0 -0.8 6 6
FLT1 0.031 0.087 -9999 0 -0.71 7 7
PGF -0.47 0.44 -9999 0 -0.86 286 286
VEGFR1 homodimer/NRP2/VEGFR121 -0.25 0.27 -9999 0 -1 7 7
CALM1 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
eNOS/Hsp90 -0.16 0.23 -9999 0 -0.76 6 6
endothelial cell proliferation -0.2 0.26 -9999 0 -0.86 8 8
mol:Ca2+ -0.26 0.29 -9999 0 -0.95 7 7
MAPK3 -0.21 0.26 -9999 0 -0.88 6 6
MAPK1 -0.21 0.26 -9999 0 -0.88 6 6
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
PLGF homodimer -0.47 0.44 -9999 0 -0.86 286 286
PRKACA 0.016 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.047 0.23 -9999 0 -0.86 37 37
VEGFA homodimer -0.38 0.44 -9999 0 -0.86 233 233
VEGFR1 homodimer/VEGFA homodimer -0.26 0.29 -9999 0 -0.58 234 234
platelet activating factor biosynthetic process -0.2 0.25 -9999 0 -0.85 6 6
PI3K -0.27 0.25 -9999 0 -0.99 7 7
PRKCA -0.24 0.27 -9999 0 -0.89 7 7
PRKCB -0.24 0.28 -9999 0 -0.91 9 9
VEGFR1 homodimer/PLGF homodimer -0.32 0.3 -9999 0 -0.58 287 287
VEGFA -0.38 0.44 -9999 0 -0.86 233 233
VEGFB 0.016 0 -9999 0 -10000 0 0
mol:IP3 -0.26 0.29 -9999 0 -0.97 7 7
RASA1 0.046 0.079 -9999 0 -0.65 6 6
NRP2 0.004 0.1 -9999 0 -0.86 7 7
VEGFR1 homodimer 0.031 0.087 -9999 0 -0.71 7 7
VEGFB homodimer 0.016 0 -9999 0 -10000 0 0
NCK1 0.014 0.033 -9999 0 -0.75 1 1
eNOS/Caveolin-1 -0.19 0.26 -9999 0 -0.8 31 31
PTPN11 0.016 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.27 0.25 -9999 0 -0.96 7 7
mol:L-citrulline -0.17 0.24 -9999 0 -0.8 6 6
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.22 0.25 -9999 0 -0.94 6 6
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.24 0.27 -9999 0 -0.99 6 6
CD2AP 0.016 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.25 0.23 -9999 0 -0.99 6 6
PDPK1 -0.22 0.27 -9999 0 -1 6 6
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.24 0.27 -9999 0 -1 5 5
mol:NADP -0.17 0.24 -9999 0 -0.8 6 6
HSP90AA1 0.016 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.22 0.25 -9999 0 -0.92 6 6
VEGFR1 homodimer/NRP2 -0.016 0.097 -9999 0 -0.61 12 12
p75(NTR)-mediated signaling

Figure S34.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S34.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 -0.001 0.025 -9999 0 -0.56 1 1
Necdin/E2F1 -0.083 0.22 -9999 0 -0.68 63 63
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.081 0.2 -9999 0 -0.98 8 8
NGF (dimer)/p75(NTR)/BEX1 -0.27 0.31 -9999 0 -0.56 249 249
NT-4/5 (dimer)/p75(NTR) -0.054 0.18 -9999 0 -0.67 42 42
IKBKB 0.016 0 -9999 0 -10000 0 0
AKT1 -0.034 0.22 -9999 0 -0.95 9 9
IKBKG 0.016 0 -9999 0 -10000 0 0
BDNF -0.1 0.3 -9999 0 -0.86 69 69
MGDIs/NGR/p75(NTR)/LINGO1 -0.072 0.2 -9999 0 -0.61 61 61
FURIN 0.016 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.12 0.25 -9999 0 -0.61 99 99
LINGO1 -0.022 0.18 -9999 0 -0.86 22 22
Sortilin/TRAF6/NRIF -0.001 0.014 -9999 0 -10000 0 0
proBDNF (dimer) -0.1 0.3 -9999 0 -0.86 69 69
NTRK1 -0.045 0.21 -9999 0 -0.76 40 40
RTN4R 0.004 0.1 -9999 0 -0.85 7 7
neuron apoptosis -0.067 0.23 -9999 0 -0.67 30 30
IRAK1 0.016 0 -9999 0 -10000 0 0
SHC1 -0.062 0.24 -9999 0 -0.63 78 78
ARHGDIA 0.014 0.033 -9999 0 -0.75 1 1
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.086 0.21 -9999 0 -0.58 76 76
MAGEH1 0.016 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.089 0.22 -9999 0 -0.58 77 77
Mammalian IAPs/DIABLO -0.081 0.19 -9999 0 -0.52 80 80
proNGF (dimer) -0.067 0.26 -9999 0 -0.86 49 49
MAGED1 0.014 0.039 -9999 0 -0.86 1 1
APP 0.014 0.033 -9999 0 -0.75 1 1
NT-4/5 (dimer) -0.004 0.093 -9999 0 -0.86 6 6
ZNF274 0.016 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.081 0.2 -9999 0 -0.54 76 76
NGF -0.067 0.26 -9999 0 -0.86 49 49
cell cycle arrest -0.014 0.25 -9999 0 -0.56 76 76
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.046 0.11 -9999 0 -0.57 8 8
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.047 0.16 -9999 0 -0.58 42 42
NCSTN 0.016 0 -9999 0 -10000 0 0
mol:GTP -0.093 0.23 -9999 0 -0.62 77 77
PSENEN 0.016 0 -9999 0 -10000 0 0
mol:ceramide -0.046 0.22 -9999 0 -0.57 76 76
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.035 0.087 -9999 0 -0.44 8 8
p75(NTR)/beta APP -0.047 0.17 -9999 0 -0.66 37 37
BEX1 -0.27 0.37 -9999 0 -0.75 191 191
mol:GDP -0.074 0.24 -9999 0 -0.64 77 77
NGF (dimer) -0.35 0.3 -9999 0 -0.84 88 88
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.066 0.19 -9999 0 -0.56 61 61
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
RAC1/GTP -0.082 0.21 -9999 0 -0.56 77 77
MYD88 0.016 0 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.093 0.23 -9999 0 -0.63 77 77
RHOB 0.016 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.08 0.22 -9999 0 -0.67 62 62
NT3 (dimer) 0.005 0.092 -9999 0 -0.78 7 7
TP53 -0.042 0.22 -9999 0 -0.91 7 7
PRDM4 -0.047 0.23 -9999 0 -0.57 76 76
BDNF (dimer) -0.42 0.36 -9999 0 -0.88 139 139
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
SORT1 0.014 0.033 -9999 0 -0.75 1 1
activation of caspase activity -0.079 0.2 -9999 0 -0.96 8 8
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.086 0.21 -9999 0 -0.58 76 76
RHOC 0.016 0 -9999 0 -10000 0 0
XIAP 0.016 0 -9999 0 -10000 0 0
MAPK10 -0.025 0.21 -9999 0 -0.64 21 21
DIABLO 0.016 0 -9999 0 -10000 0 0
SMPD2 -0.047 0.23 -9999 0 -0.57 76 76
APH1B 0.016 0 -9999 0 -10000 0 0
APH1A 0.016 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.094 0.23 -9999 0 -0.63 78 78
PSEN1 0.016 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.054 0.18 -9999 0 -0.67 42 42
MAPK8 -0.023 0.2 -9999 0 -0.64 20 20
MAPK9 -0.022 0.2 -9999 0 -0.64 20 20
APAF1 0.016 0 -9999 0 -10000 0 0
NTF3 0.005 0.092 -9999 0 -0.78 7 7
NTF4 -0.004 0.093 -9999 0 -0.86 6 6
NDN 0.011 0.058 -9999 0 -0.75 3 3
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.073 0.18 -9999 0 -0.91 8 8
p75 CTF/Sortilin/TRAF6/NRIF -0.001 0.019 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.092 0.23 -9999 0 -0.62 77 77
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.099 0.21 -9999 0 -0.97 7 7
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.11 0.23 -9999 0 -0.56 97 97
PRKACB 0.016 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.088 0.22 -9999 0 -0.66 69 69
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.12 0.32 -9999 0 -0.86 80 80
BIRC2 0.016 0 -9999 0 -10000 0 0
neuron projection morphogenesis 0.006 0.24 -9999 0 -0.53 60 60
BAD -0.011 0.2 -9999 0 -0.6 21 21
RIPK2 0.014 0.039 -9999 0 -0.86 1 1
NGFR -0.045 0.22 -9999 0 -0.86 36 36
CYCS -0.036 0.22 -9999 0 -0.97 9 9
ADAM17 0.016 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.086 0.21 -9999 0 -0.58 77 77
BCL2L11 -0.011 0.2 -9999 0 -0.6 21 21
BDNF (dimer)/p75(NTR) -0.13 0.28 -9999 0 -0.7 99 99
PI3K -0.087 0.22 -9999 0 -0.58 76 76
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.086 0.21 -9999 0 -0.58 76 76
NDNL2 0.016 0 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
PRKCI 0.016 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.11 0.26 -9999 0 -0.72 77 77
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.087 0.21 -9999 0 -0.58 77 77
TRAF6 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCZ 0.011 0.058 -9999 0 -0.75 3 3
PLG -0.38 0.38 -9999 0 -0.75 269 269
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.13 0.23 -9999 0 -0.89 20 20
SQSTM1 0.016 0 -9999 0 -10000 0 0
NGFRAP1 0.016 0 -9999 0 -10000 0 0
CASP3 -0.005 0.18 -9999 0 -0.53 21 21
E2F1 -0.09 0.29 -9999 0 -0.86 62 62
CASP9 0.016 0 -9999 0 -10000 0 0
IKK complex -0.071 0.15 -9999 0 -0.6 11 11
NGF (dimer)/TRKA -0.11 0.24 -9999 0 -0.63 87 87
MMP7 -0.12 0.3 -9999 0 -0.76 93 93
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.081 0.2 -9999 0 -0.98 8 8
MMP3 -0.071 0.25 -9999 0 -0.86 47 47
APAF-1/Caspase 9 -0.11 0.18 -9999 0 -0.69 11 11
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.3 0.33 -9999 0 -0.67 233 233
PDGFRB 0.016 0.004 -9999 0 -10000 0 0
SPHK1 -0.03 0.1 -9999 0 -0.36 43 43
mol:S1P -0.024 0.095 -9999 0 -0.42 5 5
S1P1/S1P/Gi -0.047 0.14 -9999 0 -0.51 13 13
GNAO1 0.01 0.084 -9999 0 -0.84 5 5
PDGFB-D/PDGFRB/PLCgamma1 -0.054 0.087 -9999 0 -0.63 2 2
PLCG1 -0.028 0.13 -9999 0 -0.51 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.016 0.004 -9999 0 -10000 0 0
GNAI2 0.018 0.005 -9999 0 -10000 0 0
GNAI3 0.015 0.006 -9999 0 -10000 0 0
GNAI1 0.011 0.058 -9999 0 -0.75 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.25 0.3 -9999 0 -0.58 233 233
S1P1/S1P -0.21 0.21 -9999 0 -0.63 23 23
negative regulation of cAMP metabolic process -0.046 0.14 -9999 0 -0.5 13 13
MAPK3 -0.038 0.16 -9999 0 -0.57 25 25
calcium-dependent phospholipase C activity 0 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR 0.014 0.034 -9999 0 -0.75 1 1
PLCB2 -0.2 0.26 -9999 0 -0.67 59 59
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.17 0.17 -9999 0 -0.52 22 22
receptor internalization -0.2 0.2 -9999 0 -0.4 234 234
PTGS2 -0.048 0.24 -9999 0 -0.99 26 26
Rac1/GTP -0.17 0.17 -9999 0 -0.51 23 23
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFA -0.38 0.44 -9999 0 -0.86 233 233
negative regulation of T cell proliferation -0.046 0.14 -9999 0 -0.5 13 13
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.011 0.058 -9999 0 -0.75 3 3
MAPK1 -0.038 0.16 -9999 0 -0.66 12 12
S1P1/S1P/PDGFB-D/PDGFRB -0.17 0.24 -9999 0 -0.64 23 23
ABCC1 0.016 0.002 -9999 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.12 0.24 -10000 0 -0.78 35 35
UGCG -0.023 0.047 -10000 0 -0.84 1 1
AKT1/mTOR/p70S6K/Hsp90/TERT -0.081 0.19 -10000 0 -0.48 54 54
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.009 0.057 -10000 0 -0.83 1 1
mol:DAG -0.004 0.006 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.11 0.16 -10000 0 -0.56 37 37
FRAP1 -0.085 0.23 -10000 0 -0.61 50 50
FOXO3 -0.075 0.22 -10000 0 -0.63 38 38
AKT1 -0.093 0.24 -10000 0 -0.64 52 52
GAB2 0.016 0.003 -10000 0 -10000 0 0
SMPD1 -0.021 0.03 -10000 0 -10000 0 0
SGMS1 -0.021 0.03 -10000 0 -10000 0 0
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 0.027 0.032 -10000 0 -0.48 2 2
CALM1 0.016 0 -10000 0 -10000 0 0
cell proliferation -0.022 0.099 -10000 0 -0.58 1 1
EIF3A 0.016 0 -10000 0 -10000 0 0
PI3K -0.002 0.034 -10000 0 -0.56 2 2
RPS6KB1 -0.028 0.087 -10000 0 -10000 0 0
mol:sphingomyelin -0.004 0.006 -10000 0 -10000 0 0
natural killer cell activation 0 0.002 -10000 0 -10000 0 0
JAK3 -0.16 0.35 -10000 0 -0.86 105 105
PIK3R1 0.017 0.034 -10000 0 -0.74 1 1
JAK1 0.019 0.004 -10000 0 -10000 0 0
NFKB1 0.014 0.033 -10000 0 -0.75 1 1
MYC -0.076 0.22 -10000 0 -0.63 43 43
MYB -0.19 0.34 -10000 0 -0.74 139 139
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.12 0.26 -10000 0 -0.68 62 62
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.035 0.067 -10000 0 -0.47 2 2
mol:PI-3-4-5-P3 -0.12 0.25 -10000 0 -0.66 62 62
Rac1/GDP 0.012 0.033 -10000 0 -0.43 2 2
T cell proliferation -0.097 0.24 -10000 0 -0.64 50 50
SHC1 0.014 0.039 -10000 0 -0.86 1 1
RAC1 0.015 0.003 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.008 0.026 -10000 0 -0.05 139 139
PRKCZ -0.1 0.25 -10000 0 -0.68 49 49
NF kappa B1 p50/RelA -0.1 0.16 -10000 0 -0.57 33 33
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.15 0.26 -10000 0 -0.58 102 102
HSP90AA1 0.016 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
IL2RA -0.16 0.35 -10000 0 -0.86 104 104
IL2RB -0.44 0.44 -10000 0 -0.86 272 272
TERT -0.11 0.3 -10000 0 -0.86 73 73
E2F1 -0.1 0.2 -10000 0 -0.37 175 175
SOS1 0.016 0.003 -10000 0 -10000 0 0
RPS6 0.012 0.055 -10000 0 -0.86 2 2
mol:cAMP 0.004 0.013 0.025 139 -10000 0 139
PTPN11 0.016 0.003 -10000 0 -10000 0 0
IL2RG -0.039 0.22 -10000 0 -0.86 34 34
actin cytoskeleton organization -0.097 0.24 -10000 0 -0.64 50 50
GRB2 0.016 0.003 -10000 0 -10000 0 0
IL2 -0.005 0.12 -10000 0 -0.86 10 10
PIK3CA 0.017 0.034 -10000 0 -0.74 1 1
Rac1/GTP 0.031 0.035 -10000 0 -0.41 2 2
LCK -0.018 0.18 -10000 0 -0.85 22 22
BCL2 -0.052 0.18 -10000 0 -0.53 24 24
LPA4-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
ADCY4 0.026 0.023 -9999 0 -0.49 1 1
ADCY5 0.006 0.1 -9999 0 -0.49 22 22
ADCY6 0.026 0.042 -9999 0 -0.93 1 1
ADCY7 0.009 0.11 -9999 0 -0.58 16 16
ADCY1 0.014 0.083 -9999 0 -0.5 13 13
ADCY2 -0.13 0.27 -9999 0 -0.58 135 135
ADCY3 0.026 0.023 -9999 0 -0.49 1 1
ADCY8 -0.16 0.28 -9999 0 -0.59 160 160
PRKCE 0.014 0.026 -9999 0 -0.57 1 1
ADCY9 0.026 0.023 -9999 0 -0.49 1 1
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.091 0.17 -9999 0 -0.51 51 51
PLK1 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
regulation of centriole-centriole cohesion 0 0.057 0.29 18 -10000 0 18
BUB1B -0.023 0.12 -10000 0 -0.51 26 26
PLK1 -0.012 0.059 -10000 0 -0.2 10 10
PLK1S1 0.001 0.031 -10000 0 -10000 0 0
KIF2A -0.003 0.073 -10000 0 -0.56 4 4
regulation of mitotic centrosome separation -0.012 0.059 -10000 0 -0.2 10 10
GOLGA2 0.016 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.18 0.33 -10000 0 -0.72 126 126
WEE1 -0.001 0.056 -10000 0 -0.28 7 7
cytokinesis -0.2 0.27 -10000 0 -0.5 234 234
PP2A-alpha B56 -0.14 0.16 -10000 0 -10000 0 0
AURKA -0.002 0.045 -10000 0 -0.3 6 6
PICH/PLK1 -0.045 0.16 -10000 0 -0.84 18 18
CENPE -0.063 0.21 -10000 0 -0.63 60 60
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.003 0.072 -10000 0 -0.55 4 4
PPP2CA 0.016 0 -10000 0 -10000 0 0
FZR1 0.014 0.033 -10000 0 -0.75 1 1
TPX2 -0.05 0.12 -10000 0 -0.25 125 125
PAK1 0.016 0.002 -10000 0 -10000 0 0
SPC24 -0.076 0.27 -10000 0 -0.86 54 54
FBXW11 0.016 0 -10000 0 -10000 0 0
CLSPN -0.025 0.096 -10000 0 -0.28 59 59
GORASP1 0.016 0 -10000 0 -10000 0 0
metaphase -0.004 0.009 -10000 0 -0.02 128 128
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.006 0.031 -10000 0 -0.098 10 10
G2 phase of mitotic cell cycle 0 0.002 -10000 0 -0.014 6 6
STAG2 0.016 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.009 0.013 -10000 0 -10000 0 0
spindle elongation -0.012 0.059 -10000 0 -0.2 10 10
ODF2 0.016 0.002 -10000 0 -10000 0 0
BUB1 -0.16 0.19 -10000 0 -0.38 227 227
TPT1 0.001 0.031 -10000 0 -10000 0 0
CDC25C -0.13 0.17 -10000 0 -0.31 238 238
CDC25B 0.007 0.088 -10000 0 -0.88 5 5
SGOL1 0 0.057 -10000 0 -0.29 18 18
RHOA 0.016 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.024 0.1 -10000 0 -0.74 9 9
CDC14B 0.016 0.002 -10000 0 -10000 0 0
CDC20 -0.056 0.24 -10000 0 -0.86 42 42
PLK1/PBIP1 -0.041 0.11 -10000 0 -0.59 18 18
mitosis -0.001 0.004 0.03 6 -10000 0 6
FBXO5 0.003 0.045 -10000 0 -0.21 2 2
CDC2 -0.001 0.004 -10000 0 -0.023 9 9
NDC80 -0.17 0.36 -10000 0 -0.86 109 109
metaphase plate congression -0.005 0.041 -10000 0 -10000 0 0
ERCC6L -0.037 0.16 -10000 0 -0.82 18 18
NLP/gamma Tubulin -0.003 0.035 -10000 0 -0.12 5 5
microtubule cytoskeleton organization 0.001 0.031 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0.001 0.001 -10000 0 -10000 0 0
PPP1R12A 0.016 0.002 -10000 0 -10000 0 0
interphase 0.001 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.26 0.29 -10000 0 -0.57 234 234
GRASP65/GM130/RAB1/GTP/PLK1 -0.013 0.027 -10000 0 -10000 0 0
RAB1A 0.016 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.007 0.038 -10000 0 -10000 0 0
mitotic prometaphase -0.003 0.005 -10000 0 -0.012 120 120
proteasomal ubiquitin-dependent protein catabolic process -0.012 0.043 -10000 0 -10000 0 0
microtubule-based process -0.25 0.31 -10000 0 -0.58 234 234
Golgi organization -0.012 0.059 -10000 0 -0.2 10 10
Cohesin/SA2 -0.024 0.045 -10000 0 -0.23 2 2
PPP1CB/MYPT1 0 0 -10000 0 -10000 0 0
KIF20A -0.38 0.44 -10000 0 -0.86 234 234
APC/C/CDC20 -0.045 0.18 -10000 0 -0.64 42 42
PPP2R1A 0.016 0 -10000 0 -10000 0 0
chromosome segregation -0.04 0.11 -10000 0 -0.58 18 18
PRC1 0.006 0.094 -10000 0 -0.86 6 6
ECT2 0.001 0.053 -10000 0 -10000 0 0
C13orf34 0.003 0.043 -10000 0 -10000 0 0
NUDC -0.005 0.041 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.023 0.12 -10000 0 -0.5 26 26
spindle assembly -0.006 0.048 -10000 0 -0.16 8 8
spindle stabilization 0.001 0.031 -10000 0 -10000 0 0
APC/C/HCDH1 -0.001 0.022 -10000 0 -0.49 1 1
MKLP2/PLK1 -0.25 0.31 -10000 0 -0.59 234 234
CCNB1 0.002 0.11 -10000 0 -0.88 8 8
PPP1CB 0.016 0.002 -10000 0 -10000 0 0
BTRC 0.016 0 -10000 0 -10000 0 0
ROCK2 0.005 0.053 -10000 0 -0.46 3 3
TUBG1 0.001 0.031 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.026 0.098 -10000 0 -0.71 9 9
MLF1IP -0.012 0.13 -10000 0 -0.69 18 18
INCENP 0.009 0.008 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.017 0 -9999 0 -10000 0 0
ELF1 -0.046 0.14 -9999 0 -0.72 1 1
CCNA2 -0.16 0.35 -9999 0 -0.86 101 101
PIK3CA 0.015 0.033 -9999 0 -0.75 1 1
JAK3 -0.16 0.35 -9999 0 -0.86 105 105
PIK3R1 0.015 0.033 -9999 0 -0.74 1 1
JAK1 0.017 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.11 0.25 -9999 0 -0.66 59 59
SHC1 0.015 0.039 -9999 0 -0.86 1 1
SP1 0.025 0.022 -9999 0 -10000 0 0
IL2RA -0.12 0.33 -9999 0 -0.77 105 105
IL2RB -0.44 0.44 -9999 0 -0.86 272 272
SOS1 0.017 0 -9999 0 -10000 0 0
IL2RG -0.041 0.22 -9999 0 -0.86 34 34
G1/S transition of mitotic cell cycle -0.046 0.2 -9999 0 -0.81 3 3
PTPN11 0.017 0 -9999 0 -10000 0 0
CCND2 0.038 0.051 -9999 0 -0.78 2 2
LCK -0.02 0.18 -9999 0 -0.85 22 22
GRB2 0.017 0 -9999 0 -10000 0 0
IL2 -0.006 0.12 -9999 0 -0.86 10 10
CDK6 0.014 0.033 -9999 0 -0.75 1 1
CCND3 -0.078 0.21 -9999 0 -0.66 28 28
BCR signaling 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
JUN -0.054 0.17 -10000 0 -0.41 42 42
IKBKB -0.023 0.1 -10000 0 -0.28 2 2
AKT1 -0.023 0.13 -10000 0 -0.31 9 9
IKBKG -0.023 0.11 -10000 0 -0.3 3 3
CALM1 -0.042 0.1 -10000 0 -0.5 3 3
PIK3CA 0.014 0.033 -10000 0 -0.75 1 1
MAP3K1 -0.11 0.25 -10000 0 -0.63 71 71
MAP3K7 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ -0.055 0.11 -10000 0 -0.5 4 4
DOK1 0.016 0 -10000 0 -10000 0 0
AP-1 -0.011 0.09 -10000 0 -0.26 3 3
LYN 0.016 0 -10000 0 -10000 0 0
BLNK 0.014 0.033 -10000 0 -0.75 1 1
SHC1 0.014 0.039 -10000 0 -0.86 1 1
BCR complex -0.17 0.3 -10000 0 -0.68 127 127
CD22 -0.15 0.23 -10000 0 -0.68 51 51
CAMK2G -0.029 0.098 -10000 0 -0.5 2 2
CSNK2A1 0.016 0 -10000 0 -10000 0 0
INPP5D 0.009 0.077 -10000 0 -0.86 4 4
SHC/GRB2/SOS1 -0.1 0.19 -10000 0 -0.85 4 4
GO:0007205 -0.055 0.11 -10000 0 -0.51 4 4
SYK 0.013 0.047 -10000 0 -0.75 2 2
ELK1 -0.043 0.1 -10000 0 -0.51 3 3
NFATC1 -0.071 0.2 -10000 0 -0.5 70 70
B-cell antigen/BCR complex -0.17 0.3 -10000 0 -0.68 127 127
PAG1/CSK -0.003 0.041 -10000 0 -0.67 2 2
NFKBIB 0.005 0.039 -10000 0 -0.13 1 1
HRAS -0.038 0.12 -10000 0 -0.49 4 4
NFKBIA 0.005 0.038 -10000 0 -0.14 1 1
NF-kappa-B/RelA/I kappa B beta 0.013 0.032 -10000 0 -0.18 1 1
RasGAP/Csk -0.21 0.32 -10000 0 -1 47 47
mol:GDP -0.051 0.1 0.29 1 -0.47 4 5
PTEN 0.016 0 -10000 0 -10000 0 0
CD79B 0.011 0.067 -10000 0 -0.86 3 3
NF-kappa-B/RelA/I kappa B alpha 0.013 0.032 -10000 0 -0.19 1 1
GRB2 0.016 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.079 0.22 -10000 0 -0.57 64 64
PIK3R1 0.014 0.033 -10000 0 -0.75 1 1
mol:IP3 -0.066 0.1 -10000 0 -0.51 4 4
CSK 0.016 0 -10000 0 -10000 0 0
FOS -0.04 0.11 -10000 0 -0.48 6 6
CHUK -0.023 0.11 -10000 0 -0.3 2 2
IBTK 0.016 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.13 0.2 -10000 0 -0.54 84 84
PTPN6 -0.14 0.21 -10000 0 -0.68 39 39
RELA 0.016 0 -10000 0 -10000 0 0
BCL2A1 -0.011 0.068 -10000 0 -0.14 105 105
VAV2 -0.17 0.28 -10000 0 -0.8 74 74
ubiquitin-dependent protein catabolic process 0.011 0.037 -10000 0 -0.12 1 1
BTK -0.088 0.17 0.46 1 -0.42 106 107
CD19 -0.19 0.33 -10000 0 -0.82 91 91
MAP4K1 -0.34 0.43 -10000 0 -0.86 211 211
CD72 -0.19 0.37 -10000 0 -0.86 122 122
PAG1 0.012 0.055 -10000 0 -0.86 2 2
MAPK14 -0.084 0.21 -10000 0 -0.52 68 68
SH3BP5 0.014 0.033 -10000 0 -0.75 1 1
PIK3AP1 -0.037 0.11 -10000 0 -0.55 6 6
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.11 0.23 -10000 0 -0.58 77 77
RAF1 -0.025 0.11 -10000 0 -0.54 2 2
RasGAP/p62DOK/SHIP -0.2 0.32 -10000 0 -0.97 48 48
CD79A -0.2 0.38 -10000 0 -0.86 127 127
re-entry into mitotic cell cycle -0.012 0.09 -10000 0 -0.26 2 2
RASA1 0.014 0.033 -10000 0 -0.75 1 1
MAPK3 -0.001 0.1 -10000 0 -10000 0 0
MAPK1 -0.001 0.1 -10000 0 -10000 0 0
CD72/SHP1 -0.23 0.33 -10000 0 -0.83 99 99
NFKB1 0.014 0.033 -10000 0 -0.75 1 1
MAPK8 -0.085 0.22 -10000 0 -0.52 67 67
actin cytoskeleton organization -0.096 0.26 -10000 0 -0.64 74 74
NF-kappa-B/RelA 0.035 0.059 -10000 0 -10000 0 0
Calcineurin -0.042 0.07 -10000 0 -10000 0 0
PI3K -0.14 0.22 -10000 0 -0.6 69 69
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.062 0.1 -10000 0 -0.55 4 4
SOS1 0.016 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.27 0.32 -10000 0 -0.74 133 133
DAPP1 -0.11 0.18 -10000 0 -0.61 36 36
cytokine secretion -0.064 0.19 -10000 0 -0.46 70 70
mol:DAG -0.066 0.1 -10000 0 -0.51 4 4
PLCG2 0.003 0.1 -10000 0 -0.82 8 8
MAP2K1 -0.013 0.11 -10000 0 -0.48 2 2
B-cell antigen/BCR complex/FcgammaRIIB -0.24 0.37 -10000 0 -0.72 175 175
mol:PI-3-4-5-P3 -0.097 0.15 -10000 0 -0.4 65 65
ETS1 -0.017 0.092 -10000 0 -0.44 2 2
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.12 0.22 -10000 0 -0.5 126 126
B-cell antigen/BCR complex/LYN -0.14 0.22 -10000 0 -0.57 71 71
MALT1 0.016 0 -10000 0 -10000 0 0
TRAF6 0.016 0 -10000 0 -10000 0 0
RAC1 -0.11 0.28 -10000 0 -0.71 73 73
B-cell antigen/BCR complex/LYN/SYK -0.16 0.25 -10000 0 -0.67 64 64
CARD11 -0.15 0.26 -10000 0 -0.62 110 110
FCGR2B -0.14 0.34 -10000 0 -0.86 95 95
PPP3CA 0.016 0 -10000 0 -10000 0 0
BCL10 0.016 0 -10000 0 -10000 0 0
IKK complex 0.005 0.048 -10000 0 -10000 0 0
PTPRC -0.079 0.27 -10000 0 -0.86 56 56
PDPK1 -0.061 0.1 -10000 0 -0.31 9 9
PPP3CB 0.016 0 -10000 0 -10000 0 0
PPP3CC 0.016 0 -10000 0 -10000 0 0
POU2F2 0 0.058 -10000 0 -0.14 66 66
Coregulation of Androgen receptor activity

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
NRIP1 0.013 0.036 -9999 0 -0.78 1 1
SVIL 0.015 0.007 -9999 0 -10000 0 0
ZNF318 0.016 0.023 -9999 0 -10000 0 0
JMJD2C -0.001 0.021 -9999 0 -0.11 18 18
T-DHT/AR/Ubc9 -0.077 0.11 -9999 0 -0.55 24 24
CARM1 0.015 0.003 -9999 0 -10000 0 0
PRDX1 0.016 0.001 -9999 0 -10000 0 0
PELP1 0.016 0.003 -9999 0 -10000 0 0
CTNNB1 0.015 0.003 -9999 0 -10000 0 0
AKT1 0.017 0.006 -9999 0 -10000 0 0
PTK2B 0.015 0.003 -9999 0 -10000 0 0
MED1 0.014 0.009 -9999 0 -10000 0 0
MAK 0.015 0.045 -9999 0 -0.86 1 1
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.009 0.069 -9999 0 -0.77 4 4
GSN 0.015 0.008 -9999 0 -10000 0 0
NCOA2 0.002 0.1 -9999 0 -0.75 9 9
NCOA6 0.016 0.003 -9999 0 -10000 0 0
DNA-PK 0.005 0.027 -9999 0 -10000 0 0
NCOA4 0.015 0.002 -9999 0 -10000 0 0
PIAS3 0.015 0.003 -9999 0 -10000 0 0
cell proliferation -0.028 0.036 -9999 0 -0.61 1 1
XRCC5 0.016 0.005 -9999 0 -10000 0 0
UBE3A 0.014 0.013 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.092 0.14 -9999 0 -0.58 37 37
FHL2 -0.04 0.11 -9999 0 -1.1 5 5
RANBP9 0.016 0.003 -9999 0 -10000 0 0
JMJD1A -0.12 0.055 -9999 0 -0.14 449 449
CDK6 0.014 0.033 -9999 0 -0.74 1 1
TGFB1I1 0.013 0.039 -9999 0 -0.86 1 1
T-DHT/AR/CyclinD1 -0.1 0.15 -9999 0 -0.6 44 44
XRCC6 0.016 0.005 -9999 0 -10000 0 0
T-DHT/AR -0.15 0.12 -9999 0 -0.59 24 24
CTDSP1 0.015 0.003 -9999 0 -10000 0 0
CTDSP2 0.015 0.018 -9999 0 -10000 0 0
BRCA1 0.015 0.007 -9999 0 -10000 0 0
TCF4 0.014 0.013 -9999 0 -10000 0 0
CDKN2A -0.83 0.17 -9999 0 -0.86 499 499
SRF 0.026 0.012 -9999 0 -10000 0 0
NKX3-1 -0.19 0.069 -9999 0 -10000 0 0
KLK3 0.023 0.15 -9999 0 -0.71 21 21
TMF1 0.015 0.003 -9999 0 -10000 0 0
HNRNPA1 0.014 0.013 -9999 0 -10000 0 0
AOF2 -0.002 0.01 -9999 0 -10000 0 0
APPL1 0.033 0.013 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.076 0.11 -9999 0 -0.54 24 24
AR -0.068 0.16 -9999 0 -0.79 24 24
UBA3 0.015 0.003 -9999 0 -10000 0 0
PATZ1 0.014 0.013 -9999 0 -10000 0 0
PAWR 0.014 0.034 -9999 0 -0.75 1 1
PRKDC 0.016 0.005 -9999 0 -10000 0 0
PA2G4 0.014 0.012 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.068 0.099 -9999 0 -0.5 24 24
RPS6KA3 0.013 0.036 -9999 0 -0.79 1 1
T-DHT/AR/ARA70 -0.078 0.11 -9999 0 -0.55 24 24
LATS2 0.014 0.011 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.068 0.099 -9999 0 -0.5 24 24
Cyclin D3/CDK11 p58 0 0 -9999 0 -10000 0 0
VAV3 -0.005 0.12 -9999 0 -0.75 14 14
KLK2 -0.084 0.14 -9999 0 -0.8 18 18
CASP8 0.016 0.003 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.067 0.12 -9999 0 -0.54 30 30
TMPRSS2 -0.92 0.35 -9999 0 -1.1 449 449
CCND1 -0.019 0.17 -9999 0 -0.86 20 20
PIAS1 0.014 0.013 -9999 0 -10000 0 0
mol:T-DHT -0.062 0.027 -9999 0 -0.072 439 439
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.013 0.019 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.078 0.11 -9999 0 -0.56 24 24
CMTM2 -0.005 0.13 -9999 0 -0.86 12 12
SNURF -0.008 0.13 -9999 0 -0.75 16 16
ZMIZ1 -0.032 0.022 -9999 0 -10000 0 0
CCND3 0.016 0.001 -9999 0 -10000 0 0
TGIF1 0.014 0.013 -9999 0 -10000 0 0
FKBP4 0.016 0.003 -9999 0 -10000 0 0
Integrins in angiogenesis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.3 0.33 -9999 0 -0.67 233 233
alphaV beta3 Integrin -0.008 0.069 -9999 0 -0.54 8 8
PTK2 -0.15 0.23 -9999 0 -0.55 46 46
IGF1R 0.016 0 -9999 0 -10000 0 0
PI4KB 0.016 0 -9999 0 -10000 0 0
MFGE8 0.014 0.039 -9999 0 -0.86 1 1
SRC 0.016 0 -9999 0 -10000 0 0
CDKN1B -0.083 0.19 -9999 0 -0.53 79 79
VEGFA -0.38 0.44 -9999 0 -0.86 233 233
ILK -0.083 0.19 -9999 0 -0.53 79 79
ROCK1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.076 0.17 -9999 0 -0.49 71 71
PTK2B -0.19 0.27 -9999 0 -0.48 233 233
alphaV/beta3 Integrin/JAM-A -0.069 0.15 -9999 0 -0.81 1 1
CBL 0.014 0.033 -9999 0 -0.75 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.22 0.24 -9999 0 -0.48 243 243
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.009 0.067 -9999 0 -0.52 6 6
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.13 0.14 -9999 0 -0.47 44 44
alphaV/beta3 Integrin/Syndecan-1 -0.009 0.065 -9999 0 -0.48 10 10
PI4KA 0.016 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.046 0.14 -9999 0 -0.8 4 4
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
alphaV/beta3 Integrin/Osteopontin -0.007 0.059 -9999 0 -0.48 8 8
RPS6KB1 -0.043 0.13 -9999 0 -0.73 4 4
TLN1 0.016 0 -9999 0 -10000 0 0
MAPK3 -0.042 0.097 -9999 0 -0.82 3 3
GPR124 0.012 0.055 -9999 0 -0.86 2 2
MAPK1 -0.042 0.097 -9999 0 -0.82 3 3
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
alphaV/beta3 Integrin/Tumstatin -0.057 0.16 -9999 0 -0.48 61 61
cell adhesion -0.17 0.18 -9999 0 -0.83 1 1
ANGPTL3 -0.34 0.38 -9999 0 -0.75 239 239
VEGFR2 homodimer/VEGFA homodimer/Src -0.26 0.29 -9999 0 -0.58 233 233
IGF-1R heterotetramer 0.016 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.016 0 -9999 0 -10000 0 0
ITGB3 0.01 0.067 -9999 0 -0.75 4 4
IGF1 0.006 0.094 -9999 0 -0.86 6 6
RAC1 0.016 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.006 0.054 -9999 0 -0.51 6 6
apoptosis 0.016 0 -9999 0 -10000 0 0
CD47 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.004 0.042 -9999 0 -0.48 4 4
VCL 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.017 0.095 -9999 0 -0.54 16 16
CSF1 0.014 0.033 -9999 0 -0.75 1 1
PIK3C2A -0.085 0.2 -9999 0 -0.54 80 80
PI4 Kinase/Pyk2 -0.23 0.24 -9999 0 -0.76 45 45
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.24 0.26 -9999 0 -0.52 233 233
FAK1/Vinculin -0.11 0.18 -9999 0 -0.56 3 3
alphaV beta3/Integrin/ppsTEM5 -0.006 0.055 -9999 0 -0.51 6 6
RHOA 0.016 0 -9999 0 -10000 0 0
VTN -0.1 0.28 -9999 0 -0.76 79 79
BCAR1 0.014 0.033 -9999 0 -0.75 1 1
FGF2 0.008 0.077 -9999 0 -0.77 5 5
F11R 0.025 0.06 -9999 0 -0.58 5 5
alphaV/beta3 Integrin/Lactadherin -0.005 0.049 -9999 0 -0.5 5 5
alphaV/beta3 Integrin/TGFBR2 -0.004 0.042 -9999 0 -0.48 4 4
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.002 0.042 -9999 0 -0.85 1 1
HSP90AA1 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.003 0.038 -9999 0 -0.44 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.049 0.23 -9999 0 -0.86 38 38
alphaV/beta3 Integrin/Pyk2 -0.22 0.24 -9999 0 -0.88 1 1
SDC1 0.007 0.082 -9999 0 -0.75 6 6
VAV3 0.039 0.084 -9999 0 -0.8 1 1
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 0.01 0.067 -9999 0 -0.75 4 4
FAK1/Paxillin -0.11 0.18 -9999 0 -0.56 3 3
cell migration -0.09 0.17 -9999 0 -0.52 2 2
ITGAV 0.016 0 -9999 0 -10000 0 0
PI3K -0.061 0.14 -9999 0 -1.1 1 1
SPP1 0.01 0.067 -9999 0 -0.75 4 4
KDR 0.014 0.033 -9999 0 -0.75 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.016 0 -9999 0 -10000 0 0
COL4A3 -0.07 0.24 -9999 0 -0.75 58 58
angiogenesis 0.004 0.15 -9999 0 -0.8 3 3
Rac1/GTP -0.012 0.067 -9999 0 -0.73 1 1
EDIL3 -0.005 0.13 -9999 0 -0.79 13 13
cell proliferation -0.004 0.041 -9999 0 -0.47 4 4
Regulation of Telomerase

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
Telomerase catalytic core complex -0.24 0.28 -9999 0 -0.85 75 75
RAD9A 0.016 0 -9999 0 -10000 0 0
AP1 -0.014 0.089 -9999 0 -0.57 13 13
IFNAR2 0.015 0.007 -9999 0 -10000 0 0
AKT1 0.014 0.069 -9999 0 -0.43 10 10
ER alpha/Oestrogen -0.005 0.053 -9999 0 -0.6 4 4
NFX1/SIN3/HDAC complex 0.045 0.054 -9999 0 -10000 0 0
EGF -0.67 0.23 -9999 0 -0.75 466 466
SMG5 0.016 0 -9999 0 -10000 0 0
SMG6 0.016 0 -9999 0 -10000 0 0
SP3/HDAC2 0 0 -9999 0 -10000 0 0
TERT/c-Abl -0.22 0.26 -9999 0 -0.79 75 75
SAP18 0.013 0.006 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.34 0.38 -9999 0 -0.75 242 242
WRN 0.016 0 -9999 0 -10000 0 0
SP1 0.015 0.007 -9999 0 -10000 0 0
SP3 0.014 0.006 -9999 0 -10000 0 0
TERF2IP 0.016 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.18 0.23 -9999 0 -0.72 63 63
Mad/Max 0 0 -9999 0 -10000 0 0
TERT -0.24 0.29 -9999 0 -0.88 75 75
CCND1 -0.22 0.27 -9999 0 -0.8 77 77
MAX 0.014 0.006 -9999 0 -10000 0 0
RBBP7 0.013 0.006 -9999 0 -10000 0 0
RBBP4 0.012 0.034 -9999 0 -0.75 1 1
TERF2 0 0.004 -9999 0 -10000 0 0
PTGES3 0.016 0 -9999 0 -10000 0 0
SIN3A 0.013 0.006 -9999 0 -10000 0 0
Telomerase/911 0.003 0.027 -9999 0 -10000 0 0
CDKN1B -0.23 0.3 -9999 0 -0.55 237 237
RAD1 0.016 0 -9999 0 -10000 0 0
XRCC5 0.016 0 -9999 0 -10000 0 0
XRCC6 0.016 0 -9999 0 -10000 0 0
SAP30 -0.017 0.16 -9999 0 -0.86 18 18
TRF2/PARP2 0 0.004 -9999 0 -10000 0 0
UBE3A 0.014 0.006 -9999 0 -10000 0 0
JUN 0.014 0.006 -9999 0 -10000 0 0
E6 -0.001 0.003 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0 0 -9999 0 -10000 0 0
FOS -0.005 0.12 -9999 0 -0.76 13 13
IFN-gamma/IRF1 -0.3 0.32 -9999 0 -0.65 237 237
PARP2 0.016 0 -9999 0 -10000 0 0
BLM -0.003 0.13 -9999 0 -0.86 11 11
Telomerase -0.019 0.16 -9999 0 -0.4 35 35
IRF1 0.016 0.039 -9999 0 -0.86 1 1
ESR1 0.007 0.07 -9999 0 -0.78 4 4
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 -0.001 0.022 -9999 0 -0.49 1 1
ubiquitin-dependent protein catabolic process 0.051 0.051 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.006 0.033 -9999 0 -10000 0 0
HDAC1 0.013 0.006 -9999 0 -10000 0 0
HDAC2 0.015 0.007 -9999 0 -10000 0 0
ATM -0.001 0.023 -9999 0 -0.52 1 1
SMAD3 0.025 0.068 -9999 0 -0.66 5 5
ABL1 0.016 0 -9999 0 -10000 0 0
MXD1 0.014 0.006 -9999 0 -10000 0 0
MRE11A 0.016 0 -9999 0 -10000 0 0
HUS1 0.016 0 -9999 0 -10000 0 0
RPS6KB1 0.016 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.17 0.25 -9999 0 -0.76 63 63
NR2F2 0.01 0.012 -9999 0 -10000 0 0
MAPK3 0.009 0.096 -9999 0 -0.67 10 10
MAPK1 0.009 0.096 -9999 0 -0.67 10 10
TGFB1/TGF beta receptor Type II 0.008 0.086 -9999 0 -0.86 5 5
NFKB1 0.014 0.033 -9999 0 -0.75 1 1
HNRNPC 0.016 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.001 0.023 -9999 0 -0.52 1 1
NBN 0.016 0 -9999 0 -10000 0 0
EGFR 0 0.11 -9999 0 -0.85 9 9
mol:Oestrogen -0.001 0.002 -9999 0 -10000 0 0
EGF/EGFR -0.51 0.18 -9999 0 -0.57 467 467
MYC -0.018 0.16 -9999 0 -0.86 19 19
IL2 -0.008 0.12 -9999 0 -0.87 10 10
KU 0 0 -9999 0 -10000 0 0
RAD50 0.016 0 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
TGFB1 0.008 0.086 -9999 0 -0.86 5 5
TRF2/BLM -0.013 0.09 -9999 0 -0.63 11 11
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.21 0.26 -9999 0 -0.79 73 73
SP1/HDAC2 0.007 0.014 -9999 0 -10000 0 0
PINX1 0.016 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.18 0.23 -9999 0 -0.72 63 63
Smad3/Myc -0.02 0.13 -9999 0 -0.6 23 23
911 complex 0 0 -9999 0 -10000 0 0
IFNG -0.38 0.43 -9999 0 -0.85 237 237
Telomerase/PinX1 -0.18 0.23 -9999 0 -0.72 63 63
Telomerase/AKT1/mTOR/p70S6K -0.013 0.079 -9999 0 -0.53 2 2
SIN3B 0.013 0.006 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.18 0.23 -9999 0 -0.72 62 62
response to DNA damage stimulus 0.004 0.006 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0.004 -9999 0 -10000 0 0
TRF2/WRN 0 0.004 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.18 0.23 -9999 0 -0.72 62 62
E2F1 -0.091 0.29 -9999 0 -0.87 62 62
ZNFX1 0.013 0.006 -9999 0 -10000 0 0
PIF1 -0.14 0.33 -9999 0 -0.86 89 89
NCL 0.016 0 -9999 0 -10000 0 0
DKC1 0.016 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.016 0 -9999 0 -10000 0 0
VLDLR 0.016 0 -9999 0 -10000 0 0
LRPAP1 0.016 0 -9999 0 -10000 0 0
NUDC 0.016 0 -9999 0 -10000 0 0
RELN/LRP8 -0.16 0.23 -9999 0 -0.48 173 173
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.016 0.001 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.11 0.22 -9999 0 -0.52 6 6
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.01 0.13 -9999 0 -0.86 12 12
IQGAP1 0.016 0 -9999 0 -10000 0 0
PLA2G7 -0.66 0.37 -9999 0 -0.86 397 397
CALM1 0.016 0 -9999 0 -10000 0 0
DYNLT1 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.001 0.029 -9999 0 -0.67 1 1
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.016 0 -9999 0 -10000 0 0
CDK5R1 0.016 0.001 -9999 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.1 0.29 -9999 0 -0.86 66 66
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.17 0.24 -9999 0 -0.49 183 183
YWHAE 0.016 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.13 0.16 -9999 0 -0.59 16 16
MAP1B -0.001 0.02 -9999 0 -0.33 2 2
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.12 0.17 -9999 0 -10000 0 0
RELN -0.24 0.36 -9999 0 -0.75 172 172
PAFAH/LIS1 -0.44 0.24 -9999 0 -0.58 397 397
LIS1/CLIP170 0 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.098 0.12 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.1 0.14 -9999 0 -0.7 1 1
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.13 0.19 -9999 0 -0.64 16 16
LIS1/IQGAP1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.031 0 -9999 0 -10000 0 0
PAFAH1B3 0.014 0.033 -9999 0 -0.75 1 1
PAFAH1B2 0.014 0.033 -9999 0 -0.75 1 1
MAP1B/LIS1/Dynein heavy chain -0.001 0.013 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.13 0.15 -9999 0 -0.56 16 16
LRP8 0.014 0.039 -9999 0 -0.86 1 1
NDEL1/Katanin 60 -0.13 0.16 -9999 0 -0.59 16 16
P39/CDK5 -0.18 0.23 -9999 0 -0.86 16 16
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -9999 0 -10000 0 0
CDK5 -0.094 0.21 -9999 0 -0.48 6 6
PPP2R5D 0.016 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.016 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.14 0.2 -9999 0 -0.9 1 1
RELN/VLDLR -0.14 0.2 -9999 0 -0.52 6 6
CDC42 0 0 -9999 0 -10000 0 0
EPO signaling pathway

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
BCL2L1 -0.02 0.18 -9999 0 -10000 0 0
CRKL -0.094 0.22 -9999 0 -10000 0 0
mol:DAG -0.12 0.17 -9999 0 -10000 0 0
HRAS -0.11 0.15 -9999 0 -0.7 1 1
MAPK8 -0.14 0.25 -9999 0 -0.48 182 182
RAP1A -0.094 0.22 -9999 0 -10000 0 0
GAB1 -0.094 0.22 -9999 0 -10000 0 0
MAPK14 -0.13 0.25 -9999 0 -0.48 182 182
EPO -0.29 0.42 -9999 0 -0.85 182 182
PLCG1 -0.13 0.17 -9999 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.007 0.019 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.19 0.26 -9999 0 -0.55 183 183
GAB1/SHC/GRB2/SOS1 -0.12 0.16 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.23 0.31 -9999 0 -0.65 182 182
IRS2 -0.1 0.23 -9999 0 -0.88 2 2
STAT1 -0.065 0.21 -9999 0 -10000 0 0
STAT5B -0.07 0.21 -9999 0 -10000 0 0
cell proliferation -0.12 0.24 -9999 0 -10000 0 0
GAB1/SHIP/PIK3R1/SHP2/SHC -0.11 0.15 -9999 0 -0.71 1 1
TEC -0.094 0.22 -9999 0 -10000 0 0
SOCS3 0.012 0.055 -9999 0 -0.86 2 2
STAT1 (dimer) -0.063 0.21 -9999 0 -10000 0 0
JAK2 0.006 0.018 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
EPO/EPOR (dimer)/JAK2 -0.1 0.24 -9999 0 -10000 0 0
EPO/EPOR -0.23 0.31 -9999 0 -0.65 182 182
LYN 0.018 0.001 -9999 0 -10000 0 0
TEC/VAV2 -0.081 0.22 -9999 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.007 0.019 -9999 0 -10000 0 0
SHC1 0.014 0.039 -9999 0 -0.86 1 1
EPO/EPOR (dimer)/LYN -0.16 0.28 -9999 0 -0.54 182 182
mol:IP3 -0.12 0.17 -9999 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.13 0.18 -9999 0 -0.79 3 3
SH2B3 0.006 0.018 -9999 0 -10000 0 0
NFKB1 -0.14 0.26 -9999 0 -0.48 182 182
EPO/EPOR (dimer)/JAK2/SOCS3 -0.11 0.15 -9999 0 -0.53 1 1
PTPN6 -0.11 0.23 -9999 0 -10000 0 0
TEC/VAV2/GRB2 -0.12 0.17 -9999 0 -10000 0 0
EPOR 0.007 0.019 -9999 0 -10000 0 0
INPP5D 0.009 0.077 -9999 0 -0.86 4 4
mol:GDP -0.12 0.16 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG2 0.003 0.1 -9999 0 -0.82 8 8
CRKL/CBL/C3G -0.13 0.17 -9999 0 -0.73 1 1
VAV2 -0.094 0.22 -9999 0 -10000 0 0
CBL -0.095 0.22 -9999 0 -0.8 1 1
SHC/Grb2/SOS1 -0.13 0.17 -9999 0 -10000 0 0
STAT5A -0.07 0.21 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
STAT5 (dimer) -0.045 0.21 -9999 0 -10000 0 0
LYN/PLCgamma2 -0.01 0.077 -9999 0 -0.62 8 8
PTPN11 0.016 0 -9999 0 -10000 0 0
BTK -0.2 0.29 -9999 0 -0.88 29 29
BCL2 -0.02 0.18 -9999 0 -10000 0 0
IL6-mediated signaling events

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
BCL2L1 -0.14 0.3 -9999 0 -0.76 37 37
CRP -0.2 0.39 -9999 0 -0.91 87 87
cell cycle arrest -0.18 0.35 -9999 0 -0.79 78 78
TIMP1 -0.15 0.33 -9999 0 -0.77 69 69
IL6ST -0.013 0.14 -9999 0 -0.74 17 17
Rac1/GDP -0.14 0.26 -9999 0 -0.59 91 91
AP1 0.021 0.11 -9999 0 -0.5 5 5
GAB2 0.011 0.008 -9999 0 -10000 0 0
TNFSF11 -0.19 0.37 -9999 0 -0.88 68 68
HSP90B1 0.004 0.088 -9999 0 -10000 0 0
GAB1 0.014 0.006 -9999 0 -10000 0 0
MAPK14 0.017 0.13 -9999 0 -0.69 3 3
AKT1 0.06 0.035 -9999 0 -10000 0 0
FOXO1 0.076 0.024 -9999 0 -10000 0 0
MAP2K6 -0.017 0.14 -9999 0 -0.68 4 4
mol:GTP -0.001 0.003 -9999 0 -10000 0 0
MAP2K4 -0.14 0.28 -9999 0 -0.64 71 71
MITF -0.024 0.14 -9999 0 -0.8 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.016 0 -9999 0 -10000 0 0
A2M 0.028 0.005 -9999 0 -10000 0 0
CEBPB 0.002 0.13 -9999 0 -0.86 12 12
GRB2/SOS1/GAB family/SHP2 0.001 0.069 -9999 0 -10000 0 0
STAT3 -0.18 0.36 -9999 0 -0.83 78 78
STAT1 -0.005 0.025 -9999 0 -0.49 1 1
CEBPD -0.14 0.31 -9999 0 -0.76 37 37
PIK3CA 0.017 0.034 -9999 0 -0.74 1 1
PI3K -0.002 0.035 -9999 0 -0.56 2 2
JUN 0.01 0.008 -9999 0 -10000 0 0
PIAS3/MITF -0.018 0.13 -9999 0 -0.75 2 2
MAPK11 0.016 0.13 -9999 0 -0.7 4 4
STAT3 (dimer)/FOXO1 -0.071 0.27 -9999 0 -0.65 15 15
GRB2/SOS1/GAB family -0.046 0.11 -9999 0 -0.55 6 6
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.038 0.15 -9999 0 -0.63 12 12
GRB2 0.014 0.006 -9999 0 -10000 0 0
JAK2 0.016 0 -9999 0 -10000 0 0
LBP -0.28 0.44 -9999 0 -0.88 159 159
PIK3R1 0.016 0.033 -9999 0 -0.74 1 1
JAK1 0.015 0.006 -9999 0 -10000 0 0
MYC -0.15 0.32 -9999 0 -0.79 48 48
FGG -0.28 0.43 -9999 0 -0.87 130 130
macrophage differentiation -0.18 0.35 -9999 0 -0.79 78 78
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.069 0.17 -9999 0 -0.57 19 19
JUNB -0.14 0.3 -9999 0 -0.75 39 39
FOS -0.009 0.12 -9999 0 -0.76 13 13
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.035 0.15 -9999 0 -0.45 21 21
STAT1/PIAS1 -0.047 0.16 -9999 0 -0.5 18 18
GRB2/SOS1/GAB family/SHP2/PI3K 0.022 0.038 -9999 0 -10000 0 0
STAT3 (dimer) -0.18 0.36 -9999 0 -0.83 78 78
PRKCD -0.15 0.3 -9999 0 -0.7 60 60
IL6R 0.015 0.006 -9999 0 -10000 0 0
SOCS3 0.032 0.12 -9999 0 -0.63 5 5
gp130 (dimer)/JAK1/JAK1/LMO4 -0.003 0.09 -9999 0 -0.47 17 17
Rac1/GTP -0.18 0.23 -9999 0 -0.6 99 99
HCK -0.032 0.2 -9999 0 -0.86 28 28
MAPKKK cascade 0.026 0.06 -9999 0 -10000 0 0
bone resorption -0.18 0.35 -9999 0 -0.82 68 68
IRF1 -0.14 0.31 -9999 0 -0.78 32 32
mol:GDP -0.15 0.27 -9999 0 -0.6 100 100
SOS1 0.01 0.008 -9999 0 -10000 0 0
VAV1 -0.15 0.27 -9999 0 -0.61 100 100
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.003 0.12 -9999 0 -0.64 3 3
PTPN11 -0.004 0.012 -9999 0 -10000 0 0
IL6/IL6RA -0.078 0.21 -9999 0 -0.63 65 65
gp130 (dimer)/TYK2/TYK2/LMO4 -0.013 0.085 -9999 0 -0.48 9 9
gp130 (dimer)/JAK2/JAK2/LMO4 -0.013 0.085 -9999 0 -0.48 8 8
IL6 -0.092 0.28 -9999 0 -0.82 65 65
PIAS3 0.016 0 -9999 0 -10000 0 0
PTPRE 0.017 0.017 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
RAC1 0.015 0.002 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.035 0.13 -9999 0 -0.52 6 6
LMO4 0.012 0.014 -9999 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.22 0.29 -9999 0 -0.79 64 64
MCL1 0.075 0.023 -9999 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 0.019 0.11 -10000 0 -1.4 1 1
SMARCC2 0.018 0 -10000 0 -10000 0 0
SMARCC1 0.018 0 -10000 0 -10000 0 0
TBX21 -0.25 0.41 -10000 0 -0.83 170 170
SUMO2 0.011 0.007 -10000 0 -10000 0 0
STAT1 (dimer) 0.025 0.054 -10000 0 -1.2 1 1
FKBP4 0.016 0 -10000 0 -10000 0 0
FKBP5 0.004 0.1 -10000 0 -0.85 7 7
GR alpha/HSP90/FKBP51/HSP90 0.055 0.13 0.39 5 -0.57 8 13
PRL -0.014 0.11 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.13 0.29 0.59 69 -0.62 2 71
RELA 0.004 0.076 -10000 0 -10000 0 0
FGG -0.15 0.43 0.59 11 -0.71 164 175
GR beta/TIF2 0.052 0.14 0.43 5 -0.54 8 13
IFNG -0.41 0.44 -10000 0 -0.85 226 226
apoptosis -0.093 0.21 -10000 0 -0.8 2 2
CREB1 -0.015 0.1 -10000 0 -0.42 1 1
histone acetylation 0.018 0.13 0.39 10 -0.5 4 14
BGLAP -0.008 0.13 -10000 0 -0.74 3 3
GR/PKAc 0.065 0.1 0.4 2 -0.6 1 3
NF kappa B1 p50/RelA 0.01 0.15 -10000 0 -0.58 7 7
SMARCD1 0.018 0 -10000 0 -10000 0 0
MDM2 0.047 0.093 0.33 8 -10000 0 8
GATA3 -0.35 0.38 -10000 0 -0.74 251 251
AKT1 0 0.005 -10000 0 -10000 0 0
CSF2 -0.027 0.16 -10000 0 -0.7 15 15
GSK3B 0.011 0.007 -10000 0 -10000 0 0
NR1I3 -0.057 0.22 -10000 0 -0.83 12 12
CSN2 0.044 0.19 0.5 4 -0.66 1 5
BRG1/BAF155/BAF170/BAF60A 0.003 0.013 -10000 0 -10000 0 0
NFATC1 0.018 0.005 -10000 0 -10000 0 0
POU2F1 0.02 0.005 -10000 0 -10000 0 0
CDKN1A 0.05 0.053 -10000 0 -0.72 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.006 -10000 0 -10000 0 0
SFN -0.086 0.28 -10000 0 -0.83 62 62
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.005 0.21 0.39 1 -0.57 27 28
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.058 0.22 -10000 0 -0.86 11 11
JUN -0.22 0.25 -10000 0 -0.68 55 55
IL4 -0.023 0.12 -10000 0 -0.63 1 1
CDK5R1 0.012 0.007 -10000 0 -10000 0 0
PRKACA 0.016 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.25 0.26 -10000 0 -0.7 76 76
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.061 0.12 0.38 5 -0.6 4 9
cortisol/GR alpha (monomer) 0.15 0.34 0.68 82 -0.81 1 83
NCOA2 0.003 0.1 -10000 0 -0.75 9 9
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.055 0.14 -10000 0 -0.83 13 13
AP-1/NFAT1-c-4 -0.32 0.34 -10000 0 -0.85 89 89
AFP -0.35 0.56 -10000 0 -1.4 109 109
SUV420H1 0.016 0 -10000 0 -10000 0 0
IRF1 0.084 0.15 0.56 4 -0.62 1 5
TP53 0.044 0.021 -10000 0 -10000 0 0
PPP5C 0.016 0 -10000 0 -10000 0 0
KRT17 -0.25 0.41 -10000 0 -1.1 71 71
KRT14 -0.15 0.3 -10000 0 -0.84 73 73
TBP 0.028 0.01 -10000 0 -10000 0 0
CREBBP 0.047 0.081 -10000 0 -10000 0 0
HDAC1 0.01 0.008 -10000 0 -10000 0 0
HDAC2 0.011 0.014 -10000 0 -10000 0 0
AP-1 -0.33 0.34 -10000 0 -0.86 90 90
MAPK14 0.012 0.007 -10000 0 -10000 0 0
MAPK10 0.004 0.075 -10000 0 -0.75 5 5
MAPK11 0.009 0.04 -10000 0 -0.88 1 1
KRT5 -0.26 0.39 -10000 0 -0.95 98 98
interleukin-1 receptor activity 0 0.011 -10000 0 -10000 0 0
NCOA1 0.019 0.002 -10000 0 -10000 0 0
STAT1 0.025 0.054 -10000 0 -1.2 1 1
CGA -0.13 0.37 -10000 0 -1.2 51 51
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.089 0.15 0.46 33 -10000 0 33
MAPK3 0.011 0.007 -10000 0 -10000 0 0
MAPK1 0.012 0.007 -10000 0 -10000 0 0
ICAM1 -0.049 0.23 -10000 0 -0.81 24 24
NFKB1 0.003 0.086 -10000 0 -0.9 1 1
MAPK8 -0.14 0.2 -10000 0 -0.57 29 29
MAPK9 0.012 0.007 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.098 0.22 -10000 0 -0.78 3 3
BAX 0.052 0.028 -10000 0 -10000 0 0
POMC -0.037 0.17 -10000 0 -0.86 6 6
EP300 0.045 0.085 -10000 0 -0.6 1 1
cortisol/GR alpha (dimer)/p53 0.16 0.29 0.61 71 -0.7 1 72
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.071 0.29 1 -10000 0 1
SGK1 0.1 0.096 -10000 0 -10000 0 0
IL13 -0.36 0.28 -10000 0 -0.76 110 110
IL6 -0.12 0.38 -10000 0 -0.98 73 73
PRKACG 0.003 0.007 -10000 0 -10000 0 0
IL5 -0.29 0.21 -10000 0 -0.7 43 43
IL2 -0.17 0.25 -10000 0 -0.86 26 26
CDK5 0.012 0.007 -10000 0 -10000 0 0
PRKACB 0.016 0 -10000 0 -10000 0 0
HSP90AA1 0.016 0 -10000 0 -10000 0 0
IL8 -0.078 0.3 -10000 0 -0.93 43 43
CDK5R1/CDK5 0 0.003 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.027 0.11 -10000 0 -0.63 1 1
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.15 0.26 0.58 57 -0.65 1 58
SMARCA4 0.018 0 -10000 0 -10000 0 0
chromatin remodeling 0.1 0.15 0.42 31 -10000 0 31
NF kappa B1 p50/RelA/Cbp 0.063 0.14 -10000 0 -0.94 1 1
JUN (dimer) -0.21 0.25 -10000 0 -0.68 56 56
YWHAH 0.016 0 -10000 0 -10000 0 0
VIPR1 -0.058 0.22 -10000 0 -0.86 22 22
NR3C1 0.08 0.19 0.52 26 -0.95 1 27
NR4A1 0.002 0.13 -10000 0 -0.73 16 16
TIF2/SUV420H1 -0.01 0.073 -10000 0 -0.56 9 9
MAPKKK cascade -0.093 0.21 -10000 0 -0.8 2 2
cortisol/GR alpha (dimer)/Src-1 0.15 0.28 0.61 65 -0.8 1 66
PBX1 -0.003 0.13 -10000 0 -0.74 15 15
POU1F1 0.009 0.009 -10000 0 -10000 0 0
SELE -0.097 0.37 -10000 0 -1.3 39 39
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.1 0.15 0.42 28 -10000 0 28
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.15 0.26 0.58 57 -0.65 1 58
mol:cortisol 0.063 0.2 0.41 66 -0.27 2 68
MMP1 -0.23 0.39 -10000 0 -0.97 102 102
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.019 0.045 -9999 0 -10000 0 0
BIRC5 -0.24 0.4 -9999 0 -0.86 153 153
NFKBIA 0.047 0.04 -9999 0 -10000 0 0
CPEB1 -0.14 0.31 -9999 0 -0.76 104 104
AKT1 0.047 0.04 -9999 0 -10000 0 0
NDEL1 0.016 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.017 0.041 -9999 0 -10000 0 0
NDEL1/TACC3 0.016 0.076 -9999 0 -0.74 4 4
GADD45A 0.016 0 -9999 0 -10000 0 0
GSK3B 0.014 0.019 -9999 0 -10000 0 0
PAK1/Aurora A 0.019 0.045 -9999 0 -10000 0 0
MDM2 0.016 0 -9999 0 -10000 0 0
JUB 0.011 0.058 -9999 0 -0.75 3 3
TPX2 -0.14 0.3 -9999 0 -0.67 125 125
TP53 0.025 0.037 -9999 0 -10000 0 0
DLG7 0.02 0.043 -9999 0 -0.29 6 6
AURKAIP1 0.011 0.061 -9999 0 -0.78 3 3
ARHGEF7 0.016 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.017 0.079 -9999 0 -0.77 4 4
G2/M transition of mitotic cell cycle 0.017 0.04 -9999 0 -10000 0 0
AURKA 0.027 0.055 -9999 0 -0.34 6 6
AURKB -0.14 0.15 -9999 0 -0.29 243 243
CDC25B 0.018 0.062 -9999 0 -0.42 5 5
G2/M transition checkpoint 0.015 0.053 -9999 0 -0.44 3 3
mRNA polyadenylation -0.074 0.19 -9999 0 -0.44 104 104
Aurora A/CPEB -0.074 0.19 -9999 0 -0.45 104 104
Aurora A/TACC1/TRAP/chTOG 0.021 0.044 -9999 0 -10000 0 0
BRCA1 0.016 0 -9999 0 -10000 0 0
centrosome duplication 0.019 0.045 -9999 0 -10000 0 0
regulation of centrosome cycle -0.006 0.065 -9999 0 -0.73 4 4
spindle assembly -0.002 0.023 -9999 0 -10000 0 0
TDRD7 0.016 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.14 0.22 -9999 0 -0.47 153 153
CENPA -0.12 0.14 -9999 0 -0.3 168 168
Aurora A/PP2A 0.019 0.045 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.053 0.035 -9999 0 -10000 0 0
negative regulation of DNA binding 0.025 0.037 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.014 0.033 -9999 0 -0.75 1 1
Ajuba/Aurora A 0.015 0.053 -9999 0 -0.44 3 3
mitotic prometaphase 0.037 0.04 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.042 0.049 -9999 0 -0.34 6 6
TACC1 0.016 0 -9999 0 -10000 0 0
TACC3 0.009 0.077 -9999 0 -0.86 4 4
Aurora A/Antizyme1 0.017 0.061 -9999 0 -0.49 3 3
Aurora A/RasGAP 0.018 0.05 -9999 0 -0.47 1 1
OAZ1 0.014 0.039 -9999 0 -0.86 1 1
RAN 0.016 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.014 0.019 -9999 0 -10000 0 0
GIT1 0.016 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.14 0.3 -9999 0 -0.67 125 125
PPP2R5D 0.016 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.088 0.24 -9999 0 -0.52 125 125
PAK1 0.016 0 -9999 0 -10000 0 0
CKAP5 0.016 0 -9999 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.085 0.31 -10000 0 -0.91 29 29
NCK1/PAK1/Dok-R -0.083 0.11 -10000 0 -0.42 27 27
NCK1/Dok-R -0.084 0.27 -10000 0 -1.1 31 31
PIK3CA 0.005 0.034 -10000 0 -0.74 1 1
mol:beta2-estradiol -0.006 0.039 0.29 8 -10000 0 8
RELA 0.016 0 -10000 0 -10000 0 0
SHC1 0.006 0.039 -10000 0 -0.87 1 1
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 -0.32 0.42 -10000 0 -0.85 194 194
TNIP2 0.016 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.058 0.23 -10000 0 -0.96 30 30
FN1 -0.049 0.23 -10000 0 -0.86 38 38
PLD2 0.032 0.3 -10000 0 -1.1 30 30
PTPN11 0.016 0 -10000 0 -10000 0 0
GRB14 -0.025 0.17 -10000 0 -0.75 28 28
ELK1 0.061 0.27 -10000 0 -0.97 30 30
GRB7 0.005 0.088 -10000 0 -0.75 7 7
PAK1 0.016 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.11 0.3 -10000 0 -1 42 42
CDKN1A -0.11 0.31 -10000 0 -0.66 24 24
ITGA5 -0.049 0.23 -10000 0 -0.86 38 38
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.084 0.27 -10000 0 -1.1 31 31
CRK 0.016 0 -10000 0 -10000 0 0
mol:NO -0.05 0.26 -10000 0 -0.65 29 29
PLG -0.19 0.35 -10000 0 -1.3 30 30
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.12 0.21 -10000 0 -0.85 29 29
GRB2 0.016 0 -10000 0 -10000 0 0
PIK3R1 0.007 0.034 -10000 0 -0.75 1 1
ANGPT2 -0.21 0.38 -10000 0 -0.65 164 164
BMX -0.037 0.34 -10000 0 -1.1 30 30
ANGPT1 0.074 0.2 -10000 0 -1.2 8 8
tube development -0.13 0.34 -10000 0 -0.74 24 24
ANGPT4 -0.019 0.15 -10000 0 -0.87 16 16
response to hypoxia -0.003 0.017 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.025 0.32 -10000 0 -1.2 30 30
alpha5/beta1 Integrin -0.049 0.17 -10000 0 -0.67 38 38
FGF2 0.01 0.079 -10000 0 -0.77 5 5
STAT5A (dimer) -0.15 0.36 -10000 0 -0.85 25 25
mol:L-citrulline -0.05 0.26 -10000 0 -0.65 29 29
AGTR1 -0.038 0.18 -10000 0 -0.75 29 29
MAPK14 -0.004 0.31 -10000 0 -1.2 29 29
Tie2/SHP2 -0.061 0.25 -10000 0 -1.1 28 28
TEK -0.046 0.29 -10000 0 -1.2 28 28
RPS6KB1 -0.048 0.28 -10000 0 -0.86 29 29
Angiotensin II/AT1 -0.045 0.13 -10000 0 -0.58 29 29
Tie2/Ang1/GRB2 -0.005 0.3 -10000 0 -1.1 30 30
MAPK3 0.045 0.28 -10000 0 -0.99 30 30
MAPK1 0.045 0.28 -10000 0 -0.99 30 30
Tie2/Ang1/GRB7 -0.009 0.31 -10000 0 -1.2 30 30
NFKB1 0.014 0.033 -10000 0 -0.75 1 1
MAPK8 0.032 0.3 -10000 0 -1.1 30 30
PI3K -0.071 0.32 -10000 0 -1.1 29 29
FES -0.009 0.31 -10000 0 -1.1 30 30
Crk/Dok-R -0.083 0.26 -10000 0 -1.1 30 30
Tie2/Ang1/ABIN2 -0.005 0.3 -10000 0 -1.1 30 30
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.074 0.29 -10000 0 -0.8 29 29
STAT5A 0.016 0.001 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.048 0.28 -10000 0 -0.86 29 29
Tie2/Ang2 -0.19 0.4 -10000 0 -1 25 25
Tie2/Ang1 0.024 0.33 -10000 0 -1.2 30 30
FOXO1 -0.11 0.31 -10000 0 -0.81 29 29
ELF1 0.023 0.036 -10000 0 -0.73 1 1
ELF2 0.028 0.31 -10000 0 -1.1 30 30
mol:Choline 0.035 0.28 -10000 0 -1 30 30
cell migration -0.055 0.071 -10000 0 -10000 0 0
FYN -0.15 0.36 -10000 0 -0.86 24 24
DOK2 -0.037 0.21 -10000 0 -0.86 31 31
negative regulation of cell cycle -0.097 0.3 -10000 0 -0.6 24 24
ETS1 0.028 0.037 -10000 0 -10000 0 0
PXN -0.026 0.25 -10000 0 -0.7 29 29
ITGB1 0.016 0 -10000 0 -10000 0 0
NOS3 -0.061 0.28 -10000 0 -0.75 29 29
RAC1 0.016 0 -10000 0 -10000 0 0
TNF 0.009 0.11 -10000 0 -0.8 8 8
MAPKKK cascade 0.035 0.28 -10000 0 -1 30 30
RASA1 0.014 0.033 -10000 0 -0.75 1 1
Tie2/Ang1/Shc -0.004 0.3 -10000 0 -1.1 30 30
NCK1 0.014 0.033 -10000 0 -0.75 1 1
vasculogenesis -0.041 0.24 -10000 0 -0.58 29 29
mol:Phosphatidic acid 0.035 0.28 -10000 0 -1 30 30
mol:Angiotensin II -0.017 0.022 -10000 0 -10000 0 0
mol:NADP -0.05 0.26 -10000 0 -0.65 29 29
Rac1/GTP -0.13 0.19 -10000 0 -0.8 29 29
MMP2 0.027 0.31 -10000 0 -1.1 30 30
Visual signal transduction: Rods

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
mol:K + 0.016 0 -9999 0 -10000 0 0
GNAT1/GTP -0.009 0.078 -9999 0 -0.68 7 7
Metarhodopsin II/Arrestin -0.018 0.1 -9999 0 -0.59 16 16
PDE6G/GNAT1/GTP -0.013 0.084 -9999 0 -0.56 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.005 0.1 -9999 0 -0.86 7 7
GRK1 0.003 0.006 -9999 0 -10000 0 0
CNG Channel -0.11 0.21 -9999 0 -0.95 12 12
mol:Na + -0.11 0.21 -9999 0 -0.81 21 21
mol:ADP 0.003 0.006 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.037 0.13 -9999 0 -0.5 38 38
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.12 0.22 -9999 0 -0.85 21 21
CNGB1 -0.009 0.13 -9999 0 -0.86 11 11
RDH5 -0.004 0.13 -9999 0 -0.84 12 12
SAG 0.001 0.038 -9999 0 -0.86 1 1
mol:Ca2+ -0.068 0.22 -9999 0 -0.78 21 21
Na + (4 Units) -0.1 0.2 -9999 0 -0.75 21 21
RGS9 -0.008 0.14 -9999 0 -0.82 15 15
GNB1/GNGT1 -0.23 0.32 -9999 0 -0.67 179 179
GNAT1/GDP -0.038 0.13 -9999 0 -0.53 15 15
GUCY2D -0.03 0.19 -9999 0 -0.86 25 25
GNGT1 -0.29 0.42 -9999 0 -0.86 179 179
GUCY2F 0.002 0.005 -9999 0 -10000 0 0
GNB5 0.016 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.038 0.15 -9999 0 -0.6 28 28
mol:11-cis-retinal -0.004 0.13 -9999 0 -0.83 12 12
mol:cGMP -0.041 0.14 -9999 0 -0.59 13 13
GNB1 0.016 0 -9999 0 -10000 0 0
Rhodopsin -0.034 0.15 -9999 0 -0.66 27 27
SLC24A1 0.016 0 -9999 0 -10000 0 0
CNGA1 -0.12 0.3 -9999 0 -0.75 95 95
Metarhodopsin II -0.016 0.093 -9999 0 -0.55 15 15
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.043 0.15 -9999 0 -0.56 38 38
RGS9BP -0.019 0.16 -9999 0 -0.75 23 23
Metarhodopsin II/Transducin -0.12 0.16 -9999 0 -0.62 11 11
GCAP Family/Ca ++ -0.017 0.1 -9999 0 -0.56 16 16
PDE6A/B -0.036 0.15 -9999 0 -0.66 28 28
mol:Pi -0.036 0.13 -9999 0 -0.5 38 38
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.19 0.27 -9999 0 -0.55 181 181
PDE6B 0.007 0.082 -9999 0 -0.75 6 6
PDE6A -0.025 0.18 -9999 0 -0.86 23 23
PDE6G 0.008 0.077 -9999 0 -0.77 5 5
RHO -0.015 0.15 -9999 0 -0.86 15 15
PDE6 -0.057 0.16 -9999 0 -0.83 8 8
GUCA1A -0.01 0.12 -9999 0 -0.86 10 10
GC2/GCAP Family -0.017 0.099 -9999 0 -0.57 14 14
GUCA1C 0.001 0.047 -9999 0 -0.75 2 2
GUCA1B 0.007 0.086 -9999 0 -0.86 5 5
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.17 0.27 -10000 0 -0.54 92 92
CRKL 0.017 0.12 -10000 0 -0.57 8 8
HRAS -0.044 0.18 -10000 0 -0.55 19 19
mol:PIP3 -0.004 0.11 -10000 0 -0.45 21 21
SPRED1 0.016 0 -10000 0 -10000 0 0
SPRED2 0.014 0.033 -10000 0 -0.75 1 1
GAB1 0.006 0.12 -10000 0 -0.5 21 21
FOXO3 0.024 0.11 -10000 0 -0.59 5 5
AKT1 0.014 0.11 -10000 0 -0.46 21 21
BAD 0.022 0.11 -10000 0 -0.59 6 6
megakaryocyte differentiation -0.071 0.21 -10000 0 -0.45 111 111
GSK3B 0.024 0.11 -10000 0 -0.59 5 5
RAF1 -0.012 0.15 -10000 0 -0.54 3 3
SHC1 0.014 0.039 -10000 0 -0.86 1 1
STAT3 0.007 0.12 -10000 0 -0.5 21 21
STAT1 -0.016 0.24 -10000 0 -1 21 21
HRAS/SPRED1 -0.068 0.12 -10000 0 -0.43 19 19
cell proliferation 0.006 0.12 -10000 0 -0.5 21 21
PIK3CA 0.014 0.034 -10000 0 -0.75 1 1
TEC 0.016 0 -10000 0 -10000 0 0
RPS6KB1 0.008 0.12 -10000 0 -0.48 23 23
HRAS/SPRED2 -0.068 0.12 -10000 0 -0.43 20 20
LYN/TEC/p62DOK -0.018 0.1 -10000 0 -0.66 5 5
MAPK3 0.011 0.12 -10000 0 -0.37 2 2
STAP1 -0.32 0.22 -10000 0 -0.49 169 169
GRAP2 -0.043 0.22 -10000 0 -0.86 35 35
JAK2 -0.067 0.19 -10000 0 -0.91 21 21
STAT1 (dimer) -0.014 0.23 -10000 0 -1 21 21
mol:Gleevec -0.002 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.13 0.22 -10000 0 -0.56 48 48
actin filament polymerization 0.001 0.13 -10000 0 -0.48 27 27
LYN 0.016 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.29 0.23 -10000 0 -0.87 30 30
PIK3R1 0.014 0.033 -10000 0 -0.75 1 1
CBL/CRKL/GRB2 -0.014 0.093 -10000 0 -0.59 5 5
PI3K -0.02 0.11 -10000 0 -0.64 6 6
PTEN 0.016 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.13 0.34 -10000 0 -1.3 23 23
MAPK8 0.006 0.13 -10000 0 -0.52 21 21
STAT3 (dimer) 0.007 0.12 -10000 0 -0.49 21 21
positive regulation of transcription 0.014 0.099 -10000 0 -0.31 1 1
mol:GDP -0.11 0.19 -10000 0 -0.62 44 44
PIK3C2B 0.007 0.12 -10000 0 -0.5 21 21
CBL/CRKL 0.026 0.11 -10000 0 -0.62 5 5
FER 0.005 0.13 -10000 0 -0.5 23 23
SH2B3 0.007 0.12 -10000 0 -0.5 21 21
PDPK1 0.006 0.1 -10000 0 -0.56 6 6
SNAI2 0.006 0.13 -10000 0 -0.52 21 21
positive regulation of cell proliferation 0 0.19 -10000 0 -0.79 21 21
KITLG 0 0.11 -10000 0 -0.77 10 10
cell motility 0 0.19 -10000 0 -0.79 21 21
PTPN6 0.008 0.011 -10000 0 -10000 0 0
EPOR 0.04 0.071 -10000 0 -10000 0 0
STAT5A (dimer) 0.003 0.16 -10000 0 -0.65 22 22
SOCS1 0.006 0.094 -10000 0 -0.86 6 6
cell migration 0.044 0.2 0.51 68 -10000 0 68
SOS1 0.016 0 -10000 0 -10000 0 0
EPO -0.29 0.42 -10000 0 -0.86 182 182
VAV1 -0.2 0.38 -10000 0 -0.86 124 124
GRB10 0.006 0.12 -10000 0 -0.5 21 21
PTPN11 0.008 0.01 -10000 0 -10000 0 0
SCF/KIT -0.035 0.12 -10000 0 -0.48 30 30
GO:0007205 -0.001 0.006 -10000 0 -10000 0 0
MAP2K1 0.005 0.13 -10000 0 -0.42 2 2
CBL 0.014 0.033 -10000 0 -0.75 1 1
KIT -0.01 0.28 -10000 0 -1.2 28 28
MAP2K2 0.004 0.13 -10000 0 -0.42 2 2
SHC/Grb2/SOS1 -0.019 0.1 -10000 0 -0.62 6 6
STAT5A 0.002 0.17 -10000 0 -0.68 22 22
GRB2 0.016 0 -10000 0 -10000 0 0
response to radiation 0.006 0.12 -10000 0 -0.5 21 21
SHC/GRAP2 -0.046 0.17 -10000 0 -0.66 36 36
PTPRO -0.073 0.22 -10000 0 -0.46 111 111
SH2B2 0.001 0.13 -10000 0 -0.49 27 27
DOK1 0.016 0 -10000 0 -10000 0 0
MATK -0.045 0.2 -10000 0 -0.52 68 68
CREBBP 0.045 0.012 -10000 0 -10000 0 0
BCL2 0.042 0.069 -10000 0 -10000 0 0
Reelin signaling pathway

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
CDK5R1/CDK5 0 0 -9999 0 -10000 0 0
VLDLR 0.016 0 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
LRPAP1 0.016 0 -9999 0 -10000 0 0
FYN 0.016 0 -9999 0 -10000 0 0
ITGA3 0.012 0.055 -9999 0 -0.86 2 2
RELN/VLDLR/Fyn -0.16 0.23 -9999 0 -0.48 172 172
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.003 0.043 -9999 0 -0.81 1 1
AKT1 -0.067 0.16 -9999 0 -0.57 2 2
MAP2K7 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
DAB1 -0.01 0.13 -9999 0 -0.86 12 12
RELN/LRP8/DAB1 -0.16 0.22 -9999 0 -0.45 184 184
LRPAP1/LRP8 -0.001 0.029 -9999 0 -0.67 1 1
RELN/LRP8/DAB1/Fyn -0.15 0.2 -9999 0 -0.52 18 18
DAB1/alpha3/beta1 Integrin -0.13 0.18 -9999 0 -0.82 1 1
long-term memory -0.21 0.25 -9999 0 -0.88 24 24
DAB1/LIS1 -0.14 0.18 -9999 0 -0.86 1 1
DAB1/CRLK/C3G -0.13 0.18 -9999 0 -0.82 1 1
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
DAB1/NCK2 -0.14 0.18 -9999 0 -0.86 1 1
ARHGEF2 0.016 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.11 0.3 -9999 0 -0.84 76 76
CDK5R1 0.016 0.001 -9999 0 -10000 0 0
RELN -0.24 0.36 -9999 0 -0.75 172 172
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
RELN/LRP8/Fyn -0.16 0.23 -9999 0 -0.48 173 173
GRIN2A/RELN/LRP8/DAB1/Fyn -0.22 0.26 -9999 0 -0.9 24 24
MAPK8 0.014 0.033 -9999 0 -0.75 1 1
RELN/VLDLR/DAB1 -0.16 0.22 -9999 0 -0.45 183 183
ITGB1 0.016 0 -9999 0 -10000 0 0
MAP1B -0.15 0.2 -9999 0 -0.67 4 4
RELN/LRP8 -0.16 0.23 -9999 0 -0.48 173 173
GRIN2B/RELN/LRP8/DAB1/Fyn -0.15 0.2 -9999 0 -0.9 2 2
PI3K -0.002 0.035 -9999 0 -0.56 2 2
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.003 0.041 -9999 0 -0.67 2 2
RAP1A -0.11 0.17 -9999 0 -0.76 1 1
PAFAH1B1 0.016 0 -9999 0 -10000 0 0
MAPK8IP1 0.013 0.047 -9999 0 -0.75 2 2
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B 0.008 0.055 -9999 0 -0.86 2 2
NCK2 0.016 0 -9999 0 -10000 0 0
neuron differentiation -0.029 0.12 -9999 0 -0.53 3 3
neuron adhesion -0.05 0.19 -9999 0 -0.71 1 1
LRP8 0.014 0.039 -9999 0 -0.86 1 1
GSK3B -0.053 0.15 -9999 0 -0.54 2 2
RELN/VLDLR/DAB1/Fyn -0.15 0.2 -9999 0 -0.52 17 17
MAP3K11 0.014 0.033 -9999 0 -0.75 1 1
RELN/VLDLR/DAB1/P13K -0.11 0.15 -9999 0 -0.61 2 2
CDK5 0.016 0 -9999 0 -10000 0 0
MAPT 0.015 0.083 -9999 0 -0.69 6 6
neuron migration -0.059 0.21 -9999 0 -0.61 1 1
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.057 0.1 -9999 0 -0.54 3 3
RELN/VLDLR -0.14 0.2 -9999 0 -0.52 6 6
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.014 0.033 -9999 0 -0.75 1 1
Caspase 8 (4 units) -0.098 0.092 -9999 0 -10000 0 0
NEF -0.058 0.084 -9999 0 -10000 0 0
NFKBIA 0.001 0.045 -9999 0 -10000 0 0
BIRC3 -0.072 0.31 -9999 0 -0.79 80 80
CYCS -0.079 0.14 -9999 0 -0.43 1 1
RIPK1 0.016 0 -9999 0 -10000 0 0
CD247 -0.37 0.48 -9999 0 -1 171 171
MAP2K7 -0.041 0.11 -9999 0 -10000 0 0
protein ubiquitination 0.06 0.071 -9999 0 -0.42 3 3
CRADD 0.016 0 -9999 0 -10000 0 0
DAXX 0.016 0 -9999 0 -10000 0 0
FAS 0.016 0 -9999 0 -10000 0 0
BID -0.093 0.15 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha -0.051 0.12 -9999 0 -0.46 1 1
TRADD 0.016 0 -9999 0 -10000 0 0
MAP3K5 0.016 0 -9999 0 -10000 0 0
CFLAR 0.016 0 -9999 0 -10000 0 0
FADD 0.016 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.051 0.12 -9999 0 -0.46 1 1
MAPK8 -0.03 0.1 -9999 0 -0.51 1 1
APAF1 0.016 0 -9999 0 -10000 0 0
TRAF1 0.014 0.039 -9999 0 -0.86 1 1
TRAF2 0.016 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.14 0.13 -9999 0 -10000 0 0
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.048 0.067 -9999 0 -10000 0 0
CHUK 0.061 0.075 -9999 0 -0.47 3 3
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0 0 -9999 0 -10000 0 0
TCRz/NEF -0.4 0.44 -9999 0 -0.75 279 279
TNF 0.003 0.1 -9999 0 -0.8 8 8
FASLG -0.58 0.61 -9999 0 -1.1 279 279
NFKB1 0 0.055 -9999 0 -0.74 1 1
TNFR1A/BAG4/TNF-alpha -0.009 0.068 -9999 0 -0.52 9 9
CASP6 -0.048 0.052 -9999 0 -10000 0 0
CASP7 -0.062 0.21 -9999 0 -0.55 54 54
RELA 0.001 0.045 -9999 0 -10000 0 0
CASP2 0.016 0 -9999 0 -10000 0 0
CASP3 -0.062 0.21 -9999 0 -0.55 54 54
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.025 -9999 0 -0.56 1 1
CASP8 0.016 0 -9999 0 -10000 0 0
CASP9 0.016 0 -9999 0 -10000 0 0
MAP3K14 0.053 0.08 -9999 0 -0.53 3 3
APAF-1/Caspase 9 -0.12 0.18 -9999 0 -0.56 54 54
BCL2 -0.017 0.098 -9999 0 -0.46 1 1
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.042 0.15 -9999 0 -0.58 38 38
EPHB2 0.001 0.11 -9999 0 -0.77 10 10
Syndecan-2/TACI -0.056 0.17 -9999 0 -0.58 50 50
LAMA1 -0.007 0.13 -9999 0 -0.75 15 15
Syndecan-2/alpha2 ITGB1 -0.01 0.068 -9999 0 -0.49 7 7
HRAS 0.014 0.039 -9999 0 -0.86 1 1
Syndecan-2/CASK 0 0 -9999 0 -10000 0 0
ITGA5 -0.049 0.23 -9999 0 -0.86 38 38
BAX 0.054 0.02 -9999 0 -10000 0 0
EPB41 0.016 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0 0 -9999 0 -10000 0 0
LAMA3 0.004 0.1 -9999 0 -0.86 7 7
EZR 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.002 0.11 -9999 0 -0.86 8 8
Syndecan-2/MMP2 -0.007 0.06 -9999 0 -0.56 6 6
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.005 0.055 -9999 0 -0.56 5 5
dendrite morphogenesis -0.01 0.068 -9999 0 -0.5 10 10
Syndecan-2/GM-CSF -0.017 0.097 -9999 0 -0.58 15 15
determination of left/right symmetry 0.027 0 -9999 0 -10000 0 0
Syndecan-2/PKC delta -0.001 0.025 -9999 0 -0.58 1 1
GNB2L1 0.014 0.039 -9999 0 -0.86 1 1
MAPK3 0.022 0.094 -9999 0 -0.52 15 15
MAPK1 0.022 0.094 -9999 0 -0.52 15 15
Syndecan-2/RACK1 -0.002 0.031 -9999 0 -0.5 2 2
NF1 0.016 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.027 0 -9999 0 -10000 0 0
ITGA2 0.008 0.074 -9999 0 -0.75 5 5
MAPK8 0.046 0.023 -9999 0 -0.47 1 1
Syndecan-2/alpha2/beta1 Integrin -0.016 0.082 -9999 0 -0.65 2 2
Syndecan-2/Kininogen -0.36 0.21 -9999 0 -0.48 386 386
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC 0.048 0.032 -9999 0 -0.46 2 2
Syndecan-2/CASK/Protein 4.1 0 0 -9999 0 -10000 0 0
extracellular matrix organization -0.006 0.056 -9999 0 -0.57 5 5
actin cytoskeleton reorganization -0.042 0.15 -9999 0 -0.57 38 38
Syndecan-2/Caveolin-2/Ras -0.009 0.069 -9999 0 -0.52 9 9
Syndecan-2/Laminin alpha3 -0.008 0.067 -9999 0 -0.58 7 7
Syndecan-2/RasGAP -0.003 0.043 -9999 0 -0.67 2 2
alpha5/beta1 Integrin -0.049 0.17 -9999 0 -0.67 38 38
PRKCD 0.014 0.039 -9999 0 -0.86 1 1
Syndecan-2 dimer -0.01 0.069 -9999 0 -0.5 10 10
GO:0007205 0.005 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.002 0.041 -9999 0 -0.83 1 1
RHOA 0.016 0 -9999 0 -10000 0 0
SDCBP 0.016 0 -9999 0 -10000 0 0
TNFRSF13B -0.071 0.26 -9999 0 -0.86 50 50
RASA1 0.014 0.033 -9999 0 -0.75 1 1
alpha2/beta1 Integrin -0.005 0.055 -9999 0 -0.56 5 5
Syndecan-2/Synbindin 0 0 -9999 0 -10000 0 0
TGFB1 0.007 0.086 -9999 0 -0.86 5 5
CASP3 0.043 0.025 -9999 0 -0.52 1 1
FN1 -0.049 0.23 -9999 0 -0.86 38 38
Syndecan-2/IL8 -0.037 0.14 -9999 0 -0.56 34 34
SDC2 0.027 0 -9999 0 -10000 0 0
KNG1 -0.56 0.33 -9999 0 -0.75 386 386
Syndecan-2/Neurofibromin 0 0 -9999 0 -10000 0 0
TRAPPC4 0.016 0 -9999 0 -10000 0 0
CSF2 -0.018 0.15 -9999 0 -0.86 15 15
Syndecan-2/TGFB1 -0.006 0.057 -9999 0 -0.58 5 5
Syndecan-2/Syntenin/PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-2/Ezrin 0 0 -9999 0 -10000 0 0
PRKACA 0.044 0 -9999 0 -10000 0 0
angiogenesis -0.036 0.14 -9999 0 -0.56 34 34
MMP2 0.006 0.092 -9999 0 -0.84 6 6
IL8 -0.04 0.21 -9999 0 -0.84 34 34
calcineurin-NFAT signaling pathway -0.056 0.17 -9999 0 -0.57 50 50
Neurotrophic factor-mediated Trk receptor signaling

Figure S55.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S55.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.016 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.015 0.059 -10000 0 -0.62 1 1
NT3 (dimer)/TRKC -0.041 0.16 -10000 0 -0.61 35 35
NT3 (dimer)/TRKB -0.14 0.25 -10000 0 -0.54 131 131
SHC/Grb2/SOS1/GAB1/PI3K -0.002 0.022 -10000 0 -10000 0 0
RAPGEF1 0.016 0 -10000 0 -10000 0 0
BDNF -0.1 0.3 -10000 0 -0.86 69 69
PIK3CA 0.014 0.033 -10000 0 -0.75 1 1
DYNLT1 0.016 0 -10000 0 -10000 0 0
NTRK1 -0.045 0.21 -10000 0 -0.76 40 40
NTRK2 -0.13 0.3 -10000 0 -0.75 99 99
NTRK3 -0.03 0.18 -10000 0 -0.75 31 31
NT-4/5 (dimer)/TRKB -0.14 0.25 -10000 0 -0.56 129 129
neuron apoptosis 0.14 0.18 0.62 36 -10000 0 36
SHC 2-3/Grb2 -0.16 0.2 -10000 0 -0.7 36 36
SHC1 0.014 0.039 -10000 0 -0.86 1 1
SHC2 -0.098 0.14 -10000 0 -0.53 31 31
SHC3 -0.16 0.24 -10000 0 -0.64 87 87
STAT3 (dimer) 0.012 0.068 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.084 0.2 -10000 0 -0.56 78 78
RIN/GDP 0.048 0.064 -10000 0 -0.32 1 1
GIPC1 0.014 0.033 -10000 0 -0.75 1 1
KRAS 0.016 0 -10000 0 -10000 0 0
DNAJA3 -0.07 0.14 -10000 0 -0.63 13 13
RIN/GTP -0.001 0.03 -10000 0 -0.68 1 1
CCND1 0.009 0.16 -10000 0 -0.78 20 20
MAGED1 0.014 0.039 -10000 0 -0.86 1 1
PTPN11 0.016 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.004 0.093 -10000 0 -0.86 6 6
SHC/GRB2/SOS1 -0.001 0.025 -10000 0 -0.58 1 1
GRB2 0.016 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.15 0.27 -10000 0 -0.6 129 129
TRKA/NEDD4-2 -0.045 0.16 -10000 0 -0.58 40 40
ELMO1 0.012 0.055 -10000 0 -0.86 2 2
RhoG/GTP/ELMO1/DOCK1 -0.003 0.042 -10000 0 -0.55 3 3
NGF -0.067 0.26 -10000 0 -0.86 49 49
HRAS 0.014 0.039 -10000 0 -0.86 1 1
DOCK1 0.014 0.033 -10000 0 -0.75 1 1
GAB2 0.016 0 -10000 0 -10000 0 0
RIT2 0.002 0.039 -10000 0 -0.86 1 1
RIT1 0.016 0 -10000 0 -10000 0 0
FRS2 0.016 0 -10000 0 -10000 0 0
DNM1 -0.001 0.12 -10000 0 -0.86 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.016 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.07 0.14 -10000 0 -0.6 15 15
mol:GDP 0.062 0.087 -10000 0 -0.48 2 2
NGF (dimer) -0.067 0.26 -10000 0 -0.86 49 49
RhoG/GDP -0.003 0.042 -10000 0 -0.68 2 2
RIT1/GDP 0.055 0.063 -10000 0 -0.31 1 1
TIAM1 0.014 0.033 -10000 0 -0.75 1 1
PIK3R1 0.014 0.033 -10000 0 -0.75 1 1
BDNF (dimer)/TRKB -0.17 0.26 -10000 0 -0.55 156 156
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP -0.002 0.038 -10000 0 -0.61 2 2
FRS2 family/SHP2 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 -0.001 0.023 -10000 0 -0.52 1 1
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) 0.005 0.092 -10000 0 -0.78 7 7
RAP1/GDP -0.008 0.031 -10000 0 -10000 0 0
KIDINS220/CRKL 0.016 0 -10000 0 -10000 0 0
BDNF (dimer) -0.1 0.3 -10000 0 -0.86 69 69
ubiquitin-dependent protein catabolic process -0.092 0.21 -10000 0 -0.55 87 87
Schwann cell development -0.026 0.032 -10000 0 -10000 0 0
EHD4 0.016 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0 0 -10000 0 -10000 0 0
RAP1B 0.016 0 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.15 0.24 -10000 0 -0.82 31 31
ABL1 0.016 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.05 0.078 -10000 0 -10000 0 0
STAT3 0.012 0.068 -10000 0 -10000 0 0
axon guidance -0.14 0.22 -10000 0 -0.76 31 31
MAPK3 -0.1 0.26 -10000 0 -0.58 95 95
MAPK1 -0.1 0.26 -10000 0 -0.58 95 95
CDC42/GDP 0.055 0.063 -10000 0 -0.31 1 1
NTF3 0.005 0.092 -10000 0 -0.78 7 7
NTF4 -0.004 0.093 -10000 0 -0.86 6 6
NGF (dimer)/TRKA/FAIM -0.091 0.21 -10000 0 -0.59 52 52
PI3K -0.002 0.035 -10000 0 -0.56 2 2
FRS3 0.016 0 -10000 0 -10000 0 0
FAIM 0.016 0 -10000 0 -10000 0 0
GAB1 0.016 0 -10000 0 -10000 0 0
RASGRF1 -0.08 0.16 -10000 0 -0.62 22 22
SOS1 0.016 0 -10000 0 -10000 0 0
MCF2L 0 0.14 -10000 0 -0.52 35 35
RGS19 0.016 0 -10000 0 -10000 0 0
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP 0.049 0.066 -10000 0 -10000 0 0
Rac1/GDP 0.055 0.063 -10000 0 -0.31 1 1
NGF (dimer)/TRKA/GRIT -0.093 0.21 -10000 0 -0.56 87 87
neuron projection morphogenesis -0.022 0.14 -10000 0 -0.59 4 4
NGF (dimer)/TRKA/NEDD4-2 -0.092 0.21 -10000 0 -0.55 87 87
MAP2K1 0.053 0.024 -10000 0 -0.48 1 1
NGFR -0.045 0.22 -10000 0 -0.86 36 36
NGF (dimer)/TRKA/GIPC/GAIP -0.054 0.12 -10000 0 -0.59 3 3
RAS family/GTP/PI3K -0.002 0.029 -10000 0 -0.6 1 1
FRS2 family/SHP2/GRB2/SOS1 0 0 -10000 0 -10000 0 0
NRAS 0.016 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.016 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCZ 0.011 0.058 -10000 0 -0.75 3 3
MAPKKK cascade -0.096 0.18 -10000 0 -0.61 44 44
RASA1 0.014 0.033 -10000 0 -0.75 1 1
TRKA/c-Abl -0.044 0.15 -10000 0 -0.57 40 40
SQSTM1 0.016 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.15 0.24 -10000 0 -0.6 68 68
NGF (dimer)/TRKA/p62/Atypical PKCs -0.079 0.18 -10000 0 -0.87 3 3
MATK -0.073 0.26 -10000 0 -0.86 52 52
NEDD4L 0.014 0.033 -10000 0 -0.75 1 1
RAS family/GDP -0.008 0.032 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.076 0.16 -10000 0 -0.68 13 13
Rac1/GTP -0.045 0.085 -10000 0 -0.42 7 7
FRS2 family/SHP2/CRK family 0 0 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.014 0.034 -10000 0 -0.73 1 1
HSPA8 0.016 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.021 0.087 -10000 0 -0.54 3 3
AKT1 0.02 0.006 -10000 0 -10000 0 0
GSC -0.027 0.22 -10000 0 -0.76 43 43
NKX2-5 -0.048 0.22 -10000 0 -0.86 34 34
muscle cell differentiation 0.035 0.11 0.58 9 -10000 0 9
SMAD2-3/SMAD4/SP1 0.04 0.08 -10000 0 -10000 0 0
SMAD4 0.032 0.029 -10000 0 -10000 0 0
CBFB 0.016 0 -10000 0 -10000 0 0
SAP18 0.015 0.004 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.003 0.046 -10000 0 -0.53 3 3
SMAD3/SMAD4/VDR 0.011 0.05 -10000 0 -10000 0 0
MYC -0.031 0.16 -10000 0 -0.86 19 19
CDKN2B 0.056 0.091 -10000 0 -0.68 6 6
AP1 0.06 0.075 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.013 0.05 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.044 0.069 -10000 0 -0.46 3 3
SP3 0.02 0 -10000 0 -10000 0 0
CREB1 0.016 0 -10000 0 -10000 0 0
FOXH1 -0.06 0.25 -10000 0 -0.88 44 44
SMAD3/SMAD4/GR 0.009 0.044 -10000 0 -0.6 1 1
GATA3 -0.35 0.38 -10000 0 -0.74 251 251
SKI/SIN3/HDAC complex/NCoR1 0.055 0.044 -10000 0 -10000 0 0
MEF2C/TIF2 -0.075 0.19 -10000 0 -0.85 17 17
endothelial cell migration 0.097 0.26 0.74 74 -10000 0 74
MAX 0.019 0.016 -10000 0 -10000 0 0
RBBP7 0.015 0.005 -10000 0 -10000 0 0
RBBP4 0.014 0.034 -10000 0 -0.75 1 1
RUNX2 -0.008 0.14 -10000 0 -0.86 14 14
RUNX3 -0.37 0.44 -10000 0 -0.86 225 225
RUNX1 -0.047 0.23 -10000 0 -0.86 37 37
CTBP1 0.016 0 -10000 0 -10000 0 0
NR3C1 0.017 0.042 -10000 0 -0.87 1 1
VDR 0.011 0.058 -10000 0 -0.75 3 3
CDKN1A 0.083 0.075 -10000 0 -0.64 2 2
KAT2B 0.013 0.034 -10000 0 -0.74 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.054 0.18 -10000 0 -0.61 44 44
DCP1A 0.016 0 -10000 0 -10000 0 0
SKI 0.015 0.004 -10000 0 -10000 0 0
SERPINE1 -0.099 0.26 -10000 0 -0.74 74 74
SMAD3/SMAD4/ATF2 0.008 0.037 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.005 0.054 -10000 0 -0.49 4 4
SAP30 -0.016 0.16 -10000 0 -0.86 18 18
Cbp/p300/PIAS3 0.007 0.035 -10000 0 -10000 0 0
JUN 0.075 0.072 -10000 0 -10000 0 0
SMAD3/SMAD4/IRF7 -0.012 0.11 -10000 0 -0.56 18 18
TFE3 0.022 0.012 -10000 0 -10000 0 0
COL1A2 -0.094 0.25 -10000 0 -0.75 66 66
mesenchymal cell differentiation 0.007 0.1 0.59 14 -10000 0 14
DLX1 -0.45 0.44 -10000 0 -0.86 275 275
TCF3 0.016 0 -10000 0 -10000 0 0
FOS 0.006 0.12 -10000 0 -0.74 13 13
SMAD3/SMAD4/Max 0.011 0.035 -10000 0 -10000 0 0
Cbp/p300/SNIP1 -0.001 0.02 -10000 0 -0.46 1 1
ZBTB17 -0.001 0.045 -10000 0 -0.72 2 2
LAMC1 0.071 0.041 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.009 0.031 -10000 0 -10000 0 0
IRF7 -0.014 0.16 -10000 0 -0.85 19 19
ESR1 0.002 0.071 -10000 0 -0.76 4 4
HNF4A -0.049 0.21 -10000 0 -0.75 44 44
MEF2C -0.007 0.22 -10000 0 -0.8 20 20
SMAD2-3/SMAD4 0.005 0.032 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.005 0.029 -10000 0 -0.46 1 1
IGHV3OR16-13 -0.051 0.054 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.016 0 -10000 0 -10000 0 0
CREBBP 0.015 0.008 -10000 0 -10000 0 0
SKIL 0.016 0 -10000 0 -10000 0 0
HDAC1 0.015 0.005 -10000 0 -10000 0 0
HDAC2 0.015 0.004 -10000 0 -10000 0 0
SNIP1 0.015 0.005 -10000 0 -10000 0 0
GCN5L2 -0.002 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.01 0.036 -10000 0 -10000 0 0
MSG1/HSC70 0.002 0.044 -10000 0 -0.67 2 2
SMAD2 0.022 0.019 -10000 0 -10000 0 0
SMAD3 0.033 0.026 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.062 0.034 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.024 0.032 -10000 0 -0.52 1 1
NCOR1 0.015 0.005 -10000 0 -10000 0 0
NCOA2 0.003 0.1 -10000 0 -0.75 9 9
NCOA1 0.016 0 -10000 0 -10000 0 0
MYOD/E2A -0.037 0.15 -10000 0 -0.67 29 29
SMAD2-3/SMAD4/SP1/MIZ-1 0.077 0.085 -10000 0 -10000 0 0
IFNB1 0.045 0.11 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.012 0.21 -10000 0 -0.84 14 14
CITED1 0.011 0.055 -10000 0 -0.86 2 2
SMAD2-3/SMAD4/ARC105 0.007 0.031 -10000 0 -10000 0 0
RBL1 0.016 0.001 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.077 0.065 -10000 0 -0.58 1 1
RUNX1-3/PEBPB2 -0.29 0.32 -10000 0 -0.61 247 247
SMAD7 0.1 0.08 -10000 0 -10000 0 0
MYC/MIZ-1 -0.026 0.13 -10000 0 -0.65 21 21
SMAD3/SMAD4 -0.021 0.12 -10000 0 -10000 0 0
IL10 -0.19 0.31 -10000 0 -0.99 31 31
PIASy/HDAC complex 0.018 0.01 -10000 0 -10000 0 0
PIAS3 0.014 0.006 -10000 0 -10000 0 0
CDK2 0.015 0.008 -10000 0 -10000 0 0
IL5 -0.17 0.25 -10000 0 -0.75 15 15
CDK4 0.015 0.009 -10000 0 -10000 0 0
PIAS4 0.018 0.01 -10000 0 -10000 0 0
ATF3 0.01 0.067 -10000 0 -0.75 4 4
SMAD3/SMAD4/SP1 -0.012 0.053 -10000 0 -10000 0 0
FOXG1 -0.026 0.17 -10000 0 -0.87 20 20
FOXO3 0.037 0.009 -10000 0 -10000 0 0
FOXO1 0.037 0.008 -10000 0 -10000 0 0
FOXO4 0.037 0.008 -10000 0 -10000 0 0
heart looping -0.007 0.22 -10000 0 -0.79 20 20
CEBPB -0.003 0.13 -10000 0 -0.87 12 12
SMAD3/SMAD4/DLX1 -0.31 0.3 -10000 0 -0.58 275 275
MYOD1 -0.043 0.2 -10000 0 -0.86 29 29
SMAD3/SMAD4/HNF4 -0.034 0.14 -10000 0 -0.53 19 19
SMAD3/SMAD4/GATA3 -0.23 0.25 -10000 0 -0.7 26 26
SnoN/SIN3/HDAC complex/NCoR1 0.016 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.24 0.28 -10000 0 -0.7 43 43
SMAD3/SMAD4/SP1-3 -0.005 0.043 -10000 0 -10000 0 0
MED15 0.016 0 -10000 0 -10000 0 0
SP1 0.013 0.05 -10000 0 -10000 0 0
SIN3B 0.015 0.005 -10000 0 -10000 0 0
SIN3A 0.015 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.078 0.22 -10000 0 -0.77 30 30
ITGB5 0.085 0.064 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.053 0.043 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.014 0.11 -10000 0 -0.49 24 24
AR -0.02 0.16 -10000 0 -0.75 24 24
negative regulation of cell growth 0.066 0.066 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.025 0.14 -10000 0 -0.6 29 29
E2F5 0.014 0.033 -10000 0 -0.75 1 1
E2F4 0.016 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.042 0.15 -10000 0 -0.65 14 14
SMAD2-3/SMAD4/FOXO1-3a-4 0.077 0.043 -10000 0 -10000 0 0
TFDP1 0.016 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.007 0.068 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 -0.007 0.1 -10000 0 -0.59 14 14
TGIF2 0.016 0 -10000 0 -10000 0 0
TGIF1 0.016 0 -10000 0 -10000 0 0
ATF2 0.014 0.033 -10000 0 -0.75 1 1
Signaling events mediated by PTP1B

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
PDGFRB 0.016 0 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.048 0.1 -10000 0 -0.55 5 5
PTP1B/AKT1 -0.031 0.047 -10000 0 -0.39 3 3
FYN 0.016 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.049 0.053 -10000 0 -0.41 4 4
EGFR -0.013 0.11 -10000 0 -0.87 9 9
EGF/EGFR -0.37 0.14 -10000 0 -0.46 120 120
CSF1 0.014 0.033 -10000 0 -0.75 1 1
AKT1 0.016 0.001 -10000 0 -10000 0 0
INSR 0.016 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.049 0.087 -10000 0 -0.45 18 18
Insulin Receptor/Insulin -0.008 0.034 -10000 0 -10000 0 0
HCK -0.032 0.2 -10000 0 -0.86 28 28
CRK 0.016 0 -10000 0 -10000 0 0
TYK2 -0.035 0.05 -10000 0 -0.44 2 2
EGF -0.67 0.23 -10000 0 -0.75 466 466
YES1 0.016 0 -10000 0 -10000 0 0
CAV1 -0.15 0.1 -10000 0 -0.42 38 38
TXN 0.002 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.033 0.055 -10000 0 -0.45 6 6
cell migration 0.049 0.053 0.41 4 -10000 0 4
STAT3 0.015 0.001 -10000 0 -10000 0 0
PRLR -0.09 0.26 -10000 0 -0.75 68 68
ITGA2B -0.022 0.16 -10000 0 -0.86 18 18
CSF1R 0.004 0.1 -10000 0 -0.86 7 7
Prolactin Receptor/Prolactin -0.074 0.19 -10000 0 -0.57 68 68
FGR 0.011 0.067 -10000 0 -0.86 3 3
PTP1B/p130 Cas -0.036 0.052 -10000 0 -0.42 3 3
Crk/p130 Cas -0.03 0.042 -10000 0 -0.42 2 2
DOK1 -0.018 0.046 -10000 0 -0.38 2 2
JAK2 -0.054 0.11 -10000 0 -0.49 10 10
Jak2/Leptin Receptor/Leptin -0.052 0.13 -10000 0 -0.56 5 5
PIK3R1 0.014 0.033 -10000 0 -0.75 1 1
PTPN1 -0.049 0.053 -10000 0 -0.41 4 4
LYN 0.016 0 -10000 0 -10000 0 0
CDH2 -0.008 0.13 -10000 0 -0.75 16 16
SRC 0 0.021 -10000 0 -10000 0 0
ITGB3 0.002 0.067 -10000 0 -0.75 4 4
CAT1/PTP1B -0.23 0.13 -10000 0 -0.59 33 33
CAPN1 0.002 0.005 -10000 0 -10000 0 0
CSK 0.016 0 -10000 0 -10000 0 0
PI3K 0.009 0.043 -10000 0 -0.63 1 1
mol:H2O2 -0.007 0.002 -10000 0 -10000 0 0
STAT3 (dimer) -0.034 0.12 -10000 0 -0.61 3 3
negative regulation of transcription -0.053 0.11 -10000 0 -0.48 10 10
FCGR2A -0.023 0.18 -10000 0 -0.86 23 23
FER -0.001 0.047 -10000 0 -0.76 2 2
alphaIIb/beta3 Integrin -0.027 0.13 -10000 0 -0.64 22 22
BLK -0.041 0.22 -10000 0 -0.86 33 33
Insulin Receptor/Insulin/Shc -0.001 0.026 -10000 0 -0.59 1 1
RHOA 0.002 0.005 -10000 0 -10000 0 0
LEPR 0.014 0.004 -10000 0 -10000 0 0
BCAR1 0.014 0.033 -10000 0 -0.75 1 1
p210 bcr-abl/Grb2 0.016 0 -10000 0 -10000 0 0
mol:NADPH -0.007 0.003 -10000 0 -10000 0 0
TRPV6 -0.22 0.15 -10000 0 -0.55 60 60
PRL 0.003 0.007 -10000 0 -10000 0 0
SOCS3 0.028 0.049 -10000 0 -0.73 2 2
SPRY2 0.001 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.004 0.043 -10000 0 -0.49 4 4
CSF1/CSF1R -0.037 0.075 -10000 0 -0.53 10 10
Ras protein signal transduction 0.039 0.016 -10000 0 -10000 0 0
IRS1 0.01 0.067 -10000 0 -0.75 4 4
INS 0.001 0.001 -10000 0 -10000 0 0
LEP -0.073 0.26 -10000 0 -0.86 50 50
STAT5B -0.045 0.068 -10000 0 -0.46 5 5
STAT5A -0.045 0.068 -10000 0 -0.46 5 5
GRB2 0.016 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.035 0.05 -10000 0 -0.44 2 2
CSN2 -0.008 0.069 -10000 0 -10000 0 0
PIK3CA 0.014 0.033 -10000 0 -0.75 1 1
LAT -0.1 0.17 -10000 0 -0.35 146 146
YBX1 0.003 0.008 -10000 0 -10000 0 0
LCK -0.021 0.18 -10000 0 -0.85 22 22
SHC1 0.014 0.039 -10000 0 -0.86 1 1
NOX4 -0.006 0.074 -10000 0 -0.76 5 5
Endothelins

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
AKT1 0.009 0.22 -10000 0 -0.56 18 18
PTK2B 0.016 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.086 0.12 -10000 0 -0.76 2 2
EDN1 -0.015 0.19 -10000 0 -0.79 17 17
EDN3 -0.019 0.16 -10000 0 -0.86 17 17
EDN2 -0.091 0.28 -10000 0 -0.82 66 66
HRAS/GDP 0.052 0.17 -10000 0 -0.7 9 9
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.022 0.15 -10000 0 -0.53 13 13
ADCY4 0.01 0.17 -10000 0 -0.74 3 3
ADCY5 -0.007 0.2 -10000 0 -0.71 13 13
ADCY6 0.009 0.17 -10000 0 -0.74 3 3
ADCY7 -0.005 0.19 -10000 0 -0.73 7 7
ADCY1 0 0.18 -10000 0 -0.74 4 4
ADCY2 -0.12 0.27 -10000 0 -0.71 29 29
ADCY3 0.01 0.17 -10000 0 -0.74 3 3
ADCY8 -0.16 0.27 -10000 0 -0.74 33 33
ADCY9 0.01 0.17 -10000 0 -0.74 3 3
arachidonic acid secretion 0.078 0.15 -10000 0 -0.57 7 7
ETB receptor/Endothelin-1/Gq/GTP 0.035 0.11 -10000 0 -0.52 7 7
GNAO1 0.007 0.084 -10000 0 -0.84 5 5
HRAS 0.014 0.039 -10000 0 -0.86 1 1
ETA receptor/Endothelin-1/G12/GTP -0.013 0.22 0.38 72 -0.83 3 75
ETA receptor/Endothelin-1/Gs/GTP -0.013 0.21 0.36 72 -0.79 3 75
mol:GTP 0.004 0.002 -10000 0 -10000 0 0
COL3A1 -0.042 0.34 -10000 0 -0.95 52 52
EDNRB 0.007 0.069 -10000 0 -0.78 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.041 0.3 -10000 0 -0.75 48 48
CYSLTR1 0.008 0.22 -10000 0 -0.84 4 4
SLC9A1 -0.013 0.11 -10000 0 -0.39 2 2
mol:GDP 0.045 0.18 -10000 0 -0.7 11 11
SLC9A3 -0.35 0.3 -10000 0 -0.7 119 119
RAF1 0.048 0.17 -10000 0 -0.71 9 9
JUN 0.088 0.12 -10000 0 -10000 0 0
JAK2 0.009 0.22 -10000 0 -0.88 3 3
mol:IP3 0.018 0.17 -10000 0 -0.6 15 15
ETA receptor/Endothelin-1 -0.026 0.27 0.45 72 -0.57 53 125
PLCB1 0.003 0.1 -10000 0 -0.75 9 9
PLCB2 -0.081 0.28 -10000 0 -0.86 58 58
ETA receptor/Endothelin-3 -0.022 0.15 -10000 0 -0.68 19 19
FOS 0.06 0.2 -10000 0 -0.86 15 15
Gai/GDP 0.039 0.07 -10000 0 -0.63 1 1
CRK 0.016 0.001 -10000 0 -10000 0 0
mol:Ca ++ 0.003 0.24 -10000 0 -0.77 16 16
BCAR1 0.014 0.033 -10000 0 -0.74 1 1
PRKCB1 0.02 0.16 -10000 0 -0.57 15 15
GNAQ 0.02 0.004 -10000 0 -10000 0 0
GNAZ 0.011 0.058 -10000 0 -0.75 3 3
GNAL 0.016 0 -10000 0 -10000 0 0
Gs family/GDP -0.044 0.11 -10000 0 -0.65 9 9
ETA receptor/Endothelin-1/Gq/GTP 0.045 0.14 -10000 0 -0.5 9 9
MAPK14 0.024 0.13 -10000 0 -0.58 9 9
TRPC6 0.086 0.13 -10000 0 -0.81 2 2
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.011 0.058 -10000 0 -0.75 3 3
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.015 0.14 -10000 0 -0.55 13 13
ETB receptor/Endothelin-2 -0.086 0.21 -10000 0 -0.62 69 69
ETB receptor/Endothelin-3 -0.029 0.13 -10000 0 -0.66 20 20
ETB receptor/Endothelin-1 -0.032 0.16 -10000 0 -0.63 19 19
MAPK3 0.06 0.19 -10000 0 -0.72 17 17
MAPK1 0.06 0.19 -10000 0 -0.72 17 17
Rac1/GDP 0.052 0.17 -10000 0 -0.71 8 8
cAMP biosynthetic process -0.06 0.19 -10000 0 -0.6 14 14
MAPK8 0.08 0.13 -10000 0 -0.64 2 2
SRC 0.016 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.03 0.091 -10000 0 -0.57 3 3
p130Cas/CRK/Src/PYK2 0.073 0.17 -10000 0 -0.73 7 7
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP 0.052 0.17 -10000 0 -0.71 8 8
COL1A2 -0.1 0.34 -10000 0 -0.89 67 67
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.081 0.23 -10000 0 -0.63 68 68
mol:DAG 0.018 0.17 -10000 0 -0.6 15 15
MAP2K2 0.057 0.18 -10000 0 -0.7 10 10
MAP2K1 0.058 0.17 -10000 0 -0.7 9 9
EDNRA -0.008 0.14 -10000 0 -0.98 2 2
positive regulation of muscle contraction 0.02 0.19 -10000 0 -0.78 3 3
Gq family/GDP -0.035 0.14 -10000 0 -0.7 15 15
HRAS/GTP 0.036 0.17 -10000 0 -0.67 12 12
PRKCH 0.03 0.16 -10000 0 -0.66 9 9
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA 0.03 0.16 -10000 0 -0.64 10 10
PRKCB 0.025 0.18 -10000 0 -0.71 13 13
PRKCE 0.028 0.16 -10000 0 -0.64 10 10
PRKCD 0.029 0.16 -10000 0 -0.66 9 9
PRKCG 0.003 0.2 -10000 0 -0.73 20 20
regulation of vascular smooth muscle contraction 0.059 0.23 -10000 0 -1 15 15
PRKCQ 0.017 0.18 -10000 0 -0.71 13 13
PLA2G4A 0.077 0.16 -10000 0 -0.63 7 7
GNA14 0.009 0.088 -10000 0 -0.75 7 7
GNA15 -0.007 0.15 -10000 0 -0.86 15 15
GNA12 0.016 0 -10000 0 -10000 0 0
GNA11 0.014 0.058 -10000 0 -0.74 3 3
Rac1/GTP -0.013 0.22 0.38 72 -0.83 3 75
MMP1 -0.13 0.37 -10000 0 -0.85 102 102
Wnt signaling

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
Noncanonical Wnts/FZD -0.064 0.13 -9999 0 -0.6 8 8
FZD6 0.016 0 -9999 0 -10000 0 0
WNT6 -0.013 0.16 -9999 0 -0.86 17 17
WNT4 -0.07 0.24 -9999 0 -0.75 58 58
FZD3 0.016 0 -9999 0 -10000 0 0
WNT5A 0.011 0.058 -9999 0 -0.75 3 3
WNT11 -0.04 0.2 -9999 0 -0.76 37 37
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.001 0.029 -10000 0 -0.66 1 1
HDAC1 0.003 0.011 -10000 0 -10000 0 0
AES 0.005 0.008 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
DTX1 -0.055 0.22 -10000 0 -0.75 48 48
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 0.015 0.002 -10000 0 -10000 0 0
AP1 -0.097 0.16 -10000 0 -0.34 147 147
NCSTN 0.016 0 -10000 0 -10000 0 0
ADAM10 0.014 0.033 -10000 0 -0.74 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.012 0.067 -10000 0 -0.45 1 1
NICD/RBPSUH -0.001 0.028 -10000 0 -0.64 1 1
WIF1 0.001 0.077 -10000 0 -0.77 5 5
NOTCH1 -0.001 0.03 -10000 0 -0.68 1 1
PSENEN 0.016 0 -10000 0 -10000 0 0
KREMEN2 -0.09 0.28 -10000 0 -0.86 62 62
DKK1 -0.019 0.17 -10000 0 -0.83 21 21
beta catenin/beta TrCP1 0.084 0.084 -10000 0 -10000 0 0
APH1B 0.016 0 -10000 0 -10000 0 0
APH1A 0.016 0 -10000 0 -10000 0 0
AXIN1 -0.011 0.035 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.008 0.048 -10000 0 -10000 0 0
PSEN1 0.016 0 -10000 0 -10000 0 0
FOS -0.004 0.12 -10000 0 -0.76 13 13
JUN 0.016 0 -10000 0 -10000 0 0
MAP3K7 0.002 0.008 -10000 0 -10000 0 0
CTNNB1 0.08 0.091 -10000 0 -10000 0 0
MAPK3 0.016 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.095 0.22 -10000 0 -0.57 86 86
HNF1A -0.002 0.074 -10000 0 -0.75 5 5
CTBP1 0.005 0.008 -10000 0 -10000 0 0
MYC 0.004 0.14 -10000 0 -0.73 19 19
NKD1 -0.19 0.34 -10000 0 -0.75 138 138
FZD1 0.016 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.037 0.12 -10000 0 -0.64 1 1
apoptosis -0.097 0.16 -10000 0 -0.34 147 147
Delta 1/NOTCHprecursor -0.001 0.028 -10000 0 -0.64 1 1
DLL1 0.016 0 -10000 0 -10000 0 0
PPARD 0.029 0.023 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC -0.011 0.035 -10000 0 -10000 0 0
DVL1 -0.005 0.032 -10000 0 -0.47 2 2
CSNK2A1 0.015 0.004 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.004 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.091 0.22 -10000 0 -0.62 76 76
LRP6 0.016 0 -10000 0 -10000 0 0
CSNK1A1 0.015 0.004 -10000 0 -10000 0 0
NLK 0.015 0.013 -10000 0 -10000 0 0
CCND1 0.003 0.15 -10000 0 -0.73 20 20
WNT1 -0.028 0.19 -10000 0 -0.86 25 25
Axin1/APC/beta catenin 0.081 0.052 -10000 0 -10000 0 0
DKK2 -0.025 0.18 -10000 0 -0.83 25 25
NOTCH1 precursor/DVL1 -0.003 0.034 -10000 0 -0.58 1 1
GSK3B 0.012 0.007 -10000 0 -10000 0 0
FRAT1 0.012 0.007 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.037 0.12 -10000 0 -0.66 1 1
PPP2R5D 0.093 0.16 0.36 137 -10000 0 137
MAPK1 0.016 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.03 0.12 -10000 0 -0.52 26 26
RBPJ 0.016 0 -10000 0 -10000 0 0
CREBBP 0.02 0.005 -10000 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.016 0 -9999 0 -10000 0 0
mol:S1P 0.002 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.04 0.044 -9999 0 -10000 0 0
GNAO1 0.01 0.084 -9999 0 -0.84 5 5
S1P/S1P3/G12/G13 -0.001 0.019 -9999 0 -0.44 1 1
AKT1 -0.002 0.013 -9999 0 -10000 0 0
AKT3 -0.025 0.1 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.016 0 -9999 0 -10000 0 0
GNAI2 0.018 0 -9999 0 -10000 0 0
GNAI3 0.018 0 -9999 0 -10000 0 0
GNAI1 0.013 0.058 -9999 0 -0.74 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.017 0.033 -9999 0 -0.74 1 1
S1PR2 0.016 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.054 0.049 -9999 0 -0.54 1 1
MAPK3 0.062 0.047 -9999 0 -0.5 1 1
MAPK1 0.062 0.047 -9999 0 -0.5 1 1
JAK2 -0.023 0.13 -9999 0 -0.48 2 2
CXCR4 -0.12 0.26 -9999 0 -0.47 179 179
FLT1 0.01 0.086 -9999 0 -0.86 5 5
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.062 0.047 -9999 0 -0.5 1 1
S1P/S1P3/Gi 0.054 0.049 -9999 0 -0.54 1 1
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.005 0.036 -9999 0 -0.49 1 1
VEGFA -0.38 0.44 -9999 0 -0.86 233 233
S1P/S1P2/Gi 0.049 0.044 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer -0.28 0.35 -9999 0 -0.67 234 234
RHOA 0.016 0 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.027 0.072 -9999 0 -10000 0 0
GNAQ 0.016 0 -9999 0 -10000 0 0
GNAZ 0.013 0.058 -9999 0 -0.74 3 3
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 0.005 0.088 -9999 0 -0.75 7 7
GNA15 -0.01 0.15 -9999 0 -0.86 15 15
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
GNA11 0.011 0.058 -9999 0 -0.75 3 3
Rac1/GTP -0.005 0.036 -9999 0 -0.49 1 1
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.015 0.087 -9999 0 -0.52 15 15
CRKL 0.016 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.014 0.033 -9999 0 -0.75 1 1
ITGA4 -0.01 0.15 -9999 0 -0.86 15 15
alpha4/beta7 Integrin/MAdCAM1 -0.027 0.12 -9999 0 -0.52 27 27
EPO -0.3 0.42 -9999 0 -0.86 182 182
alpha4/beta7 Integrin -0.019 0.11 -9999 0 -0.67 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.019 0.11 -9999 0 -0.67 15 15
EPO/EPOR (dimer) -0.23 0.32 -9999 0 -0.67 182 182
lamellipodium assembly 0 0.036 -9999 0 -0.53 2 2
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
PI3K -0.002 0.035 -9999 0 -0.56 2 2
ARF6 0.016 0 -9999 0 -10000 0 0
JAK2 -0.12 0.17 -9999 0 -0.66 5 5
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
MADCAM1 -0.007 0.13 -9999 0 -0.86 12 12
cell adhesion -0.027 0.12 -9999 0 -0.52 27 27
CRKL/CBL -0.001 0.025 -9999 0 -0.56 1 1
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC 0.015 0.13 -9999 0 -0.52 24 24
ITGB7 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.031 0.13 -9999 0 -0.56 29 29
p130Cas/Crk/Dock1 -0.024 0.1 -9999 0 -0.8 1 1
VCAM1 -0.007 0.14 -9999 0 -0.82 14 14
RHOA 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.015 0.088 -9999 0 -0.52 15 15
BCAR1 0.026 0.12 -9999 0 -0.89 1 1
EPOR 0.016 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.014 0.033 -9999 0 -0.75 1 1
GIT1 0.016 0 -9999 0 -10000 0 0
Rac1/GTP 0 0.037 -9999 0 -0.55 2 2
FoxO family signaling

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
G6PC -0.57 0.68 -9999 0 -1.3 242 242
PLK1 -0.12 0.37 -9999 0 -0.79 94 94
CDKN1B 0.062 0.16 -9999 0 -10000 0 0
FOXO3 -0.038 0.23 -9999 0 -0.66 14 14
KAT2B 0.012 0.04 -9999 0 -0.78 1 1
FOXO1/SIRT1 -0.14 0.21 -9999 0 -10000 0 0
CAT -0.026 0.23 -9999 0 -0.89 7 7
CTNNB1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.007 0.038 -9999 0 -10000 0 0
FOXO1 -0.16 0.23 -9999 0 -0.41 242 242
MAPK10 0.033 0.049 -9999 0 -0.43 5 5
mol:GTP 0.003 0.001 -9999 0 -10000 0 0
FOXO4 0.11 0.047 -9999 0 -10000 0 0
response to oxidative stress -0.029 0.045 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.028 0.2 -9999 0 -0.58 13 13
XPO1 0.017 0.001 -9999 0 -10000 0 0
EP300 -0.006 0.042 -9999 0 -0.75 1 1
BCL2L11 0.012 0.044 -9999 0 -10000 0 0
FOXO1/SKP2 -0.14 0.21 -9999 0 -0.4 4 4
mol:GDP -0.029 0.045 -9999 0 -10000 0 0
RAN 0.018 0.001 -9999 0 -10000 0 0
GADD45A 0.12 0.098 -9999 0 -10000 0 0
YWHAQ 0.016 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.031 0.086 -9999 0 -10000 0 0
MST1 0 0.11 -9999 0 -0.86 8 8
CSNK1D 0.016 0 -9999 0 -10000 0 0
CSNK1E 0.016 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.043 0.097 -9999 0 -10000 0 0
YWHAB 0.016 0 -9999 0 -10000 0 0
MAPK8 0.037 0.028 -9999 0 -0.43 1 1
MAPK9 0.037 0.019 -9999 0 -10000 0 0
YWHAG 0.016 0 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
YWHAZ 0.016 0 -9999 0 -10000 0 0
SIRT1 0.036 0.028 -9999 0 -10000 0 0
SOD2 0.014 0.2 -9999 0 -0.68 7 7
RBL2 0.023 0.17 -9999 0 -1.3 1 1
RAL/GDP 0.009 0.024 -9999 0 -10000 0 0
CHUK 0.013 0.02 -9999 0 -10000 0 0
Ran/GTP 0.017 0.004 -9999 0 -10000 0 0
CSNK1G2 0.014 0.033 -9999 0 -0.75 1 1
RAL/GTP 0.024 0.026 -9999 0 -10000 0 0
CSNK1G1 0.016 0 -9999 0 -10000 0 0
FASLG -0.34 0.39 -9999 0 -0.73 262 262
SKP2 0.016 0 -9999 0 -10000 0 0
USP7 0.018 0.002 -9999 0 -10000 0 0
IKBKB 0.013 0.02 -9999 0 -10000 0 0
CCNB1 -0.029 0.23 -9999 0 -0.92 10 10
FOXO1-3a-4/beta catenin -0.07 0.1 -9999 0 -0.43 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.14 0.21 -9999 0 -0.39 4 4
CSNK1A1 0.016 0 -9999 0 -10000 0 0
SGK1 0.013 0.02 -9999 0 -10000 0 0
CSNK1G3 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.024 0.014 -9999 0 -10000 0 0
ZFAND5 0.11 0.043 -9999 0 -10000 0 0
SFN -0.086 0.28 -9999 0 -0.83 62 62
CDK2 -0.018 0.041 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.012 0.099 -9999 0 -10000 0 0
CREBBP -0.018 0.041 -9999 0 -10000 0 0
FBXO32 -0.026 0.22 -9999 0 -0.79 8 8
BCL6 0.025 0.16 -9999 0 -10000 0 0
RALB 0.018 0 -9999 0 -10000 0 0
RALA 0.018 0 -9999 0 -10000 0 0
YWHAH 0.016 0 -9999 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.013 0.047 -9999 0 -0.75 2 2
SPHK1 -0.057 0.24 -9999 0 -0.86 43 43
GNAI2 0.016 0 -9999 0 -10000 0 0
mol:S1P 0.001 0.095 -9999 0 -0.31 45 45
GNAO1 0.007 0.084 -9999 0 -0.84 5 5
mol:Sphinganine-1-P -0.029 0.2 -9999 0 -0.66 45 45
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.017 0.055 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0.014 0.033 -9999 0 -0.75 1 1
S1PR2 0.016 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.023 0.074 -9999 0 -10000 0 0
S1PR5 -0.13 0.33 -9999 0 -0.86 88 88
S1PR4 -0.028 0.19 -9999 0 -0.86 26 26
GNAI1 0.011 0.058 -9999 0 -0.75 3 3
S1P/S1P5/G12 -0.11 0.21 -9999 0 -0.54 88 88
S1P/S1P3/Gq 0.023 0.097 -9999 0 -0.42 16 16
S1P/S1P4/Gi 0.025 0.096 -9999 0 -0.38 12 12
GNAQ 0.016 0 -9999 0 -10000 0 0
GNAZ 0.011 0.058 -9999 0 -0.75 3 3
GNA14 0.005 0.088 -9999 0 -0.75 7 7
GNA15 -0.01 0.15 -9999 0 -0.86 15 15
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
GNA11 0.011 0.058 -9999 0 -0.75 3 3
ABCC1 0.016 0 -9999 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 -0.015 0.16 -9999 0 -0.86 18 18
PLK4 0.011 0.067 -9999 0 -0.86 3 3
regulation of centriole replication 0.003 0.14 -9999 0 -0.67 21 21
Thromboxane A2 receptor 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
TGM2 -0.005 0.13 -10000 0 -0.86 11 11
GNB1/GNG2 -0.035 0.063 -10000 0 -0.22 14 14
AKT1 0.054 0.1 -10000 0 -0.25 1 1
EGF -0.67 0.23 -10000 0 -0.75 466 466
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.033 0.081 -10000 0 -0.61 2 2
mol:Ca2+ 0.04 0.14 -10000 0 -0.34 23 23
LYN -0.03 0.071 -10000 0 -10000 0 0
RhoA/GTP -0.017 0.038 -10000 0 -0.19 1 1
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.049 0.16 -10000 0 -0.38 18 18
GNG2 0.016 0 -10000 0 -10000 0 0
ARRB2 0.014 0.039 -10000 0 -0.86 1 1
TP alpha/Gq family/GDP/G beta5/gamma2 0.028 0.079 -10000 0 -0.42 7 7
G beta5/gamma2 -0.046 0.084 -10000 0 -0.3 15 15
PRKCH 0.042 0.16 -10000 0 -0.41 13 13
DNM1 -0.001 0.12 -10000 0 -0.86 10 10
TXA2/TP beta/beta Arrestin3 -0.013 0.041 -10000 0 -0.27 10 10
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.12 0.31 -10000 0 -0.86 77 77
G12 family/GTP -0.043 0.092 -10000 0 -0.33 14 14
ADRBK1 0.016 0 -10000 0 -10000 0 0
ADRBK2 0.016 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP -0.03 0.11 0.33 8 -10000 0 8
mol:NADP 0.016 0 -10000 0 -10000 0 0
RAB11A 0.016 0 -10000 0 -10000 0 0
PRKG1 -0.003 0.12 -10000 0 -0.75 13 13
mol:IP3 0.037 0.17 -10000 0 -0.43 24 24
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 0.027 0.22 -10000 0 -0.59 26 26
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.055 0.13 -10000 0 -0.61 15 15
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.051 0.12 -10000 0 -0.6 9 9
RHOA 0.016 0 -10000 0 -10000 0 0
PTGIR 0.013 0.051 -10000 0 -0.8 2 2
PRKCB1 0.036 0.16 -10000 0 -0.42 24 24
GNAQ 0.016 0 -10000 0 -10000 0 0
mol:L-citrulline 0.016 0 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.034 0.21 -10000 0 -0.57 27 27
LCK -0.047 0.12 -10000 0 -0.6 13 13
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.041 0.097 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.028 0.036 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.041 0.096 -10000 0 -10000 0 0
MAPK14 0.054 0.11 -10000 0 -0.31 1 1
TGM2/GTP 0.035 0.19 -10000 0 -0.5 22 22
MAPK11 0.053 0.11 -10000 0 -0.38 2 2
ARHGEF1 0.041 0.089 -10000 0 -0.33 1 1
GNAI2 0.016 0 -10000 0 -10000 0 0
JNK cascade 0.043 0.17 -10000 0 -0.41 26 26
RAB11/GDP 0.015 0.002 -10000 0 -10000 0 0
ICAM1 0.044 0.14 -10000 0 -0.39 11 11
cAMP biosynthetic process 0.034 0.16 -10000 0 -0.4 21 21
Gq family/GTP/EBP50 0.025 0.06 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC -0.03 0.071 -10000 0 -10000 0 0
GNB5 0.016 0 -10000 0 -10000 0 0
GNB1 0.016 0 -10000 0 -10000 0 0
EGF/EGFR -0.086 0.1 -10000 0 -0.41 15 15
VCAM1 0.043 0.14 -10000 0 -0.38 15 15
TP beta/Gq family/GDP/G beta5/gamma2 0.028 0.079 -10000 0 -0.42 7 7
platelet activation 0.066 0.15 -10000 0 -0.34 14 14
PGI2/IP -0.002 0.039 -10000 0 -0.62 2 2
PRKACA -0.052 0.12 -10000 0 -0.34 79 79
Gq family/GDP/G beta5/gamma2 0.024 0.079 -10000 0 -0.41 7 7
TXA2/TP beta/beta Arrestin2 -0.013 0.059 -10000 0 -0.41 10 10
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.015 0.13 -10000 0 -10000 0 0
mol:DAG 0.036 0.18 -10000 0 -0.48 24 24
EGFR 0.001 0.11 -10000 0 -0.85 9 9
TXA2/TP alpha 0.032 0.21 -10000 0 -0.56 24 24
Gq family/GTP -0.005 0.053 -10000 0 -0.26 7 7
YES1 -0.03 0.071 -10000 0 -10000 0 0
GNAI2/GTP -0.035 0.083 -10000 0 -10000 0 0
PGD2/DP -0.1 0.24 -10000 0 -0.68 77 77
SLC9A3R1 0.016 0 -10000 0 -10000 0 0
FYN -0.03 0.071 -10000 0 -10000 0 0
mol:NO 0.016 0 -10000 0 -10000 0 0
GNA15 -0.01 0.15 -10000 0 -0.86 15 15
PGK/cGMP -0.012 0.076 -10000 0 -0.49 13 13
RhoA/GDP 0.015 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.048 0.11 -10000 0 -0.71 1 1
NOS3 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA 0.042 0.16 -10000 0 -0.4 17 17
PRKCB 0.04 0.16 -10000 0 -0.45 17 17
PRKCE 0.043 0.16 -10000 0 -0.43 13 13
PRKCD 0.04 0.16 -10000 0 -0.42 21 21
PRKCG 0.028 0.19 -10000 0 -0.5 30 30
muscle contraction 0.042 0.2 -10000 0 -0.53 27 27
PRKCZ 0.049 0.16 -10000 0 -0.38 15 15
ARR3 0.004 0.007 -10000 0 -10000 0 0
TXA2/TP beta -0.04 0.095 -10000 0 -10000 0 0
PRKCQ 0.034 0.17 -10000 0 -0.43 21 21
MAPKKK cascade 0.034 0.19 -10000 0 -0.51 23 23
SELE 0.036 0.16 -10000 0 -0.42 36 36
TP beta/GNAI2/GDP/G beta/gamma -0.038 0.091 -10000 0 -10000 0 0
ROCK1 0.016 0 -10000 0 -10000 0 0
GNA14 0.005 0.088 -10000 0 -0.75 7 7
chemotaxis 0.034 0.23 -10000 0 -0.62 41 41
GNA12 0.016 0 -10000 0 -10000 0 0
GNA13 0.016 0 -10000 0 -10000 0 0
GNA11 0.011 0.058 -10000 0 -0.75 3 3
Rac1/GTP 0 0 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.027 0.045 -10000 0 -0.56 3 3
MAP4K4 0.025 0.094 -10000 0 -0.48 1 1
BAG4 0.014 0.033 -10000 0 -0.75 1 1
PKC zeta/ceramide -0.099 0.047 -10000 0 -0.48 3 3
NFKBIA 0.016 0 -10000 0 -10000 0 0
BIRC3 -0.12 0.32 -10000 0 -0.86 80 80
BAX -0.042 0.018 -10000 0 -10000 0 0
RIPK1 0.016 0 -10000 0 -10000 0 0
AKT1 0.046 0.008 -10000 0 -10000 0 0
BAD -0.098 0.043 -10000 0 -0.45 2 2
SMPD1 0.026 0.042 -10000 0 -0.28 1 1
RB1 -0.096 0.038 -10000 0 -10000 0 0
FADD/Caspase 8 0.04 0.088 -10000 0 -0.43 1 1
MAP2K4 -0.081 0.036 -10000 0 -10000 0 0
NSMAF 0.016 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.085 0.057 -10000 0 -0.59 4 4
EGF -0.67 0.23 -10000 0 -0.75 466 466
mol:ceramide -0.12 0.04 0.2 2 -10000 0 2
MADD 0.016 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.03 0.026 -10000 0 -0.56 1 1
ASAH1 0.016 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.095 0.037 -10000 0 -10000 0 0
cell proliferation -0.052 0.06 -10000 0 -0.46 10 10
BID -0.012 0.066 -10000 0 -10000 0 0
MAP3K1 -0.096 0.038 -10000 0 -10000 0 0
EIF2A -0.067 0.034 -10000 0 -10000 0 0
TRADD 0.016 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
MAPK3 -0.065 0.052 -10000 0 -0.54 4 4
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.065 0.052 -10000 0 -0.54 4 4
Cathepsin D/ceramide -0.097 0.036 -10000 0 -0.26 1 1
FADD 0.025 0.094 -10000 0 -0.48 1 1
KSR1 -0.1 0.06 -10000 0 -0.63 4 4
MAPK8 -0.076 0.04 -10000 0 -0.35 3 3
PRKRA -0.096 0.038 -10000 0 -10000 0 0
PDGFA 0.014 0.033 -10000 0 -0.75 1 1
TRAF2 0.016 0 -10000 0 -10000 0 0
IGF1 0.006 0.094 -10000 0 -0.86 6 6
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.11 0.04 0.2 2 -10000 0 2
CTSD 0.014 0.033 -10000 0 -0.75 1 1
regulation of nitric oxide biosynthetic process -0.001 0.024 -10000 0 -0.56 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.055 0.066 -10000 0 -0.5 10 10
PRKCD 0.014 0.039 -10000 0 -0.86 1 1
PRKCZ 0.011 0.058 -10000 0 -0.75 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.03 0.026 -10000 0 -0.56 1 1
RelA/NF kappa B1 -0.001 0.025 -10000 0 -0.56 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.014 0.033 -10000 0 -0.75 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.034 0.078 -10000 0 -0.51 1 1
TNFR1A/BAG4/TNF-alpha -0.009 0.068 -10000 0 -0.52 9 9
mol:Sphingosine-1-phosphate 0.027 0.045 -10000 0 -0.56 3 3
MAP2K1 -0.071 0.054 -10000 0 -0.55 4 4
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
CYCS -0.063 0.023 -10000 0 -0.23 1 1
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
NFKB1 0.014 0.033 -10000 0 -0.75 1 1
TNFR1A/BAG4 -0.001 0.025 -10000 0 -0.56 1 1
EIF2AK2 -0.081 0.036 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.008 0.065 -10000 0 -0.53 8 8
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.016 0.037 -10000 0 -10000 0 0
MAP2K2 -0.071 0.054 -10000 0 -0.55 4 4
SMPD3 0.026 0.052 -10000 0 -0.33 2 2
TNF 0.003 0.1 -10000 0 -0.8 8 8
PKC zeta/PAR4 -0.004 0.049 -10000 0 -0.56 4 4
mol:PHOSPHOCHOLINE 0.23 0.083 0.26 468 -10000 0 468
NF kappa B1/RelA/I kappa B alpha -0.004 0.038 -10000 0 -10000 0 0
AIFM1 -0.063 0.025 -10000 0 -0.23 1 1
BCL2 0.016 0 -10000 0 -10000 0 0
LPA receptor mediated events

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
GNB1/GNG2 -0.021 0.088 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.008 0.038 -9999 0 -10000 0 0
AP1 -0.03 0.1 -9999 0 -0.6 1 1
mol:PIP3 -0.026 0.091 -9999 0 -0.55 1 1
AKT1 -0.014 0.057 -9999 0 -10000 0 0
PTK2B 0.033 0.059 -9999 0 -10000 0 0
RHOA 0.037 0.035 -9999 0 -10000 0 0
PIK3CB 0.015 0 -9999 0 -10000 0 0
mol:Ca2+ 0.051 0.052 -9999 0 -0.48 1 1
MAGI3 0.013 0.047 -9999 0 -0.75 2 2
RELA 0.016 0 -9999 0 -10000 0 0
apoptosis -0.021 0.085 -9999 0 -0.38 17 17
HRAS/GDP -0.001 0.03 -9999 0 -0.68 1 1
positive regulation of microtubule depolymerization 0.046 0.069 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.018 0.073 -9999 0 -10000 0 0
endothelial cell migration 0.007 0.13 -9999 0 -0.54 28 28
ADCY4 0.032 0.12 -9999 0 -0.47 24 24
ADCY5 0.023 0.13 -9999 0 -0.49 27 27
ADCY6 0.032 0.12 -9999 0 -0.47 24 24
ADCY7 0.027 0.12 -9999 0 -0.49 22 22
ADCY1 0.027 0.12 -9999 0 -0.48 25 25
ADCY2 -0.017 0.14 -9999 0 -0.52 25 25
ADCY3 0.032 0.12 -9999 0 -0.47 24 24
ADCY8 -0.027 0.14 -9999 0 -0.48 24 24
ADCY9 0.032 0.12 -9999 0 -0.47 24 24
GSK3B 0.042 0.056 -9999 0 -10000 0 0
arachidonic acid secretion 0.039 0.11 -9999 0 -0.44 22 22
GNG2 0.015 0 -9999 0 -10000 0 0
TRIP6 0.001 0.008 -9999 0 -10000 0 0
GNAO1 0.007 0.12 -9999 0 -0.48 27 27
HRAS 0.014 0.039 -9999 0 -0.86 1 1
NFKBIA 0.061 0.062 -9999 0 -10000 0 0
GAB1 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.002 0.054 -9999 0 -0.86 2 2
JUN 0.016 0 -9999 0 -10000 0 0
LPA/LPA2/NHERF2 -0.002 0.023 -9999 0 -0.48 1 1
TIAM1 -0.003 0.063 -9999 0 -1 2 2
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
mol:IP3 0.051 0.053 -9999 0 -0.48 1 1
PLCB3 0.037 0.023 -9999 0 -0.43 1 1
FOS -0.004 0.12 -9999 0 -0.76 13 13
positive regulation of mitosis 0.039 0.11 -9999 0 -0.44 22 22
LPA/LPA1-2-3 -0.025 0.1 -9999 0 -0.52 4 4
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.014 0.033 -9999 0 -0.75 1 1
stress fiber formation 0.04 0.076 -9999 0 -10000 0 0
GNAZ 0.01 0.12 -9999 0 -0.48 25 25
EGFR/PI3K-beta/Gab1 -0.027 0.095 -9999 0 -0.57 1 1
positive regulation of dendritic cell cytokine production -0.025 0.099 -9999 0 -0.52 4 4
LPA/LPA2/MAGI-3 -0.003 0.031 -9999 0 -0.48 2 2
ARHGEF1 0.031 0.095 -9999 0 -10000 0 0
GNAI2 0.013 0.11 -9999 0 -0.47 22 22
GNAI3 0.013 0.11 -9999 0 -0.47 22 22
GNAI1 0.01 0.12 -9999 0 -0.48 25 25
LPA/LPA3 -0.007 0.06 -9999 0 -0.67 4 4
LPA/LPA2 -0.001 0.013 -9999 0 -10000 0 0
LPA/LPA1 -0.027 0.12 -9999 0 -0.51 27 27
HB-EGF/EGFR -0.28 0.29 -9999 0 -0.58 253 253
HBEGF -0.3 0.35 -9999 0 -0.67 247 247
mol:DAG 0.051 0.053 -9999 0 -0.48 1 1
cAMP biosynthetic process 0.02 0.12 -9999 0 -0.46 24 24
NFKB1 0.014 0.033 -9999 0 -0.75 1 1
SRC 0.016 0 -9999 0 -10000 0 0
GNB1 0.015 0 -9999 0 -10000 0 0
LYN 0.061 0.062 -9999 0 -10000 0 0
GNAQ -0.004 0.036 -9999 0 -0.4 4 4
LPAR2 0.016 0 -9999 0 -10000 0 0
LPAR3 0.003 0.077 -9999 0 -0.86 4 4
LPAR1 -0.012 0.15 -9999 0 -0.73 22 22
IL8 -0.08 0.2 -9999 0 -0.5 35 35
PTK2 0.024 0.1 -9999 0 -0.48 4 4
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.022 0.085 -9999 0 -0.38 17 17
EGFR 0 0.11 -9999 0 -0.85 9 9
PLCG1 0.019 0.054 -9999 0 -0.41 4 4
PLD2 0.024 0.1 -9999 0 -0.48 4 4
G12/G13 -0.021 0.088 -9999 0 -10000 0 0
PI3K-beta -0.016 0.067 -9999 0 -0.52 1 1
cell migration -0.009 0.034 -9999 0 -10000 0 0
SLC9A3R2 0.014 0.033 -9999 0 -0.75 1 1
PXN 0.04 0.077 -9999 0 -10000 0 0
HRAS/GTP -0.026 0.098 -9999 0 -0.45 22 22
RAC1 0.016 0 -9999 0 -10000 0 0
MMP9 -0.4 0.44 -9999 0 -0.86 247 247
PRKCE 0.013 0.034 -9999 0 -0.75 1 1
PRKCD 0.059 0.055 -9999 0 -10000 0 0
Gi(beta/gamma) -0.025 0.097 -9999 0 -0.44 24 24
mol:LPA 0.004 0.023 -9999 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.017 0.081 -9999 0 -10000 0 0
MAPKKK cascade 0.039 0.11 -9999 0 -0.44 22 22
contractile ring contraction involved in cytokinesis 0.037 0.035 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.009 0.059 -9999 0 -0.4 11 11
GNA15 -0.016 0.079 -9999 0 -0.42 18 18
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
MAPT 0.046 0.07 -9999 0 -10000 0 0
GNA11 -0.006 0.046 -9999 0 -0.39 7 7
Rac1/GTP -0.002 0.057 -9999 0 -0.91 2 2
MMP2 0.007 0.13 -9999 0 -0.54 28 28
FAS signaling pathway (CD95)

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
SPTAN1 0.012 0.043 -10000 0 -10000 0 0
RFC1 0.012 0.043 -10000 0 -10000 0 0
PRKDC 0.012 0.043 -10000 0 -10000 0 0
RIPK1 0.014 0.005 -10000 0 -10000 0 0
CASP7 -0.024 0.066 0.25 6 -10000 0 6
FASLG/FAS/FADD/FAF1 -0.14 0.16 -10000 0 -0.35 22 22
MAP2K4 -0.086 0.16 -10000 0 -0.43 23 23
mol:ceramide -0.15 0.2 -10000 0 -0.48 32 32
GSN 0.012 0.043 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 8 -0.17 0.18 -10000 0 -0.44 22 22
FAS 0.015 0.006 -10000 0 -10000 0 0
BID 0.018 0.066 -10000 0 -10000 0 0
MAP3K1 -0.036 0.1 -10000 0 -10000 0 0
MAP3K7 0.014 0.005 -10000 0 -10000 0 0
RB1 0.012 0.043 -10000 0 -10000 0 0
CFLAR 0.014 0.005 -10000 0 -10000 0 0
HGF/MET -0.037 0.15 -10000 0 -0.58 33 33
ARHGDIB 0.012 0.043 -10000 0 -10000 0 0
FADD 0.015 0.006 -10000 0 -10000 0 0
actin filament polymerization -0.012 0.043 -10000 0 -10000 0 0
NFKB1 -0.066 0.077 -10000 0 -0.71 1 1
MAPK8 -0.085 0.18 -10000 0 -0.52 24 24
DFFA 0.012 0.043 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.012 0.043 -10000 0 -10000 0 0
FAS/FADD/MET -0.006 0.056 -10000 0 -0.57 5 5
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.045 0.22 -10000 0 -0.86 36 36
FAF1 0.015 0.006 -10000 0 -10000 0 0
PARP1 0.012 0.043 -10000 0 -10000 0 0
DFFB 0.012 0.043 -10000 0 -10000 0 0
CHUK -0.053 0.067 -10000 0 -0.65 1 1
FASLG -0.43 0.44 -10000 0 -0.87 262 262
FAS/FADD 0 0 -10000 0 -10000 0 0
HGF -0.021 0.17 -10000 0 -0.8 23 23
LMNA 0.01 0.047 -10000 0 -0.52 1 1
CASP6 0.012 0.043 -10000 0 -10000 0 0
CASP10 0.015 0.006 -10000 0 -10000 0 0
CASP3 0.014 0.05 -10000 0 -10000 0 0
PTPN13 0.003 0.1 -10000 0 -0.75 9 9
CASP8 0.028 0.1 0.4 36 -10000 0 36
IL6 -0.13 0.34 -10000 0 -0.96 65 65
MET 0.007 0.086 -10000 0 -0.86 5 5
ICAD/CAD 0.012 0.043 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.15 0.2 -10000 0 -0.49 32 32
activation of caspase activity by cytochrome c 0.018 0.066 -10000 0 -10000 0 0
PAK2 0.012 0.043 -10000 0 -10000 0 0
BCL2 0.016 0.001 -10000 0 -10000 0 0
Canonical Wnt 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
HDAC1 0.005 0.019 -10000 0 -10000 0 0
AES 0.005 0.016 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0 0 -10000 0 -10000 0 0
SMAD4 0.016 0 -10000 0 -10000 0 0
DKK2 -0.025 0.18 -10000 0 -0.83 25 25
TLE1 0.005 0.016 -10000 0 -10000 0 0
MACF1 0.016 0.001 -10000 0 -10000 0 0
CTNNB1 0.048 0.1 -10000 0 -0.45 1 1
WIF1 -0.001 0.076 -10000 0 -0.77 5 5
beta catenin/RanBP3 0.004 0.1 0.36 19 -10000 0 19
KREMEN2 -0.09 0.28 -10000 0 -0.86 62 62
DKK1 -0.019 0.17 -10000 0 -0.83 21 21
beta catenin/beta TrCP1 0.056 0.094 -10000 0 -10000 0 0
FZD1 0.016 0.003 -10000 0 -10000 0 0
AXIN2 0.009 0.1 -10000 0 -1.4 2 2
AXIN1 0.016 0.004 -10000 0 -10000 0 0
RAN 0.016 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.002 0.018 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.073 0.064 -10000 0 -10000 0 0
Axin1/APC/GSK3 0.04 0.083 0.25 2 -10000 0 2
Axin1/APC/GSK3/beta catenin/Macf1 0.059 0.1 -10000 0 -10000 0 0
HNF1A -0.003 0.075 -10000 0 -0.74 5 5
CTBP1 0.005 0.017 -10000 0 -10000 0 0
MYC -0.008 0.15 -10000 0 -0.75 19 19
RANBP3 0.016 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.095 0.22 -10000 0 -0.57 86 86
NKD1 -0.19 0.34 -10000 0 -0.75 138 138
TCF4 0.005 0.017 -10000 0 -10000 0 0
TCF3 0.005 0.017 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.025 0.11 -10000 0 -0.52 25 25
Ran/GTP 0 0.001 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.019 0.11 0.48 4 -10000 0 4
LEF1 -0.02 0.15 -10000 0 -0.87 15 15
DVL1 0.003 0.034 -10000 0 -10000 0 0
CSNK2A1 0.016 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.082 0.07 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.091 0.22 -10000 0 -0.62 76 76
LRP6 0.016 0.002 -10000 0 -10000 0 0
CSNK1A1 0.005 0.019 -10000 0 -10000 0 0
NLK 0.016 0.005 -10000 0 -10000 0 0
CCND1 -0.009 0.15 -10000 0 -0.75 20 20
WNT1 -0.028 0.19 -10000 0 -0.86 25 25
GSK3A 0.016 0.004 -10000 0 -10000 0 0
GSK3B 0.016 0.002 -10000 0 -10000 0 0
FRAT1 0.014 0.004 -10000 0 -10000 0 0
PPP2R5D 0.096 0.16 0.35 137 -10000 0 137
APC -0.017 0.11 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.012 0.064 0.27 5 -10000 0 5
CREBBP 0.005 0.017 -10000 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP -0.001 0.017 -9999 0 -10000 0 0
DAPP1 0.03 0.11 -9999 0 -0.54 9 9
Src family/SYK family/BLNK-LAT/BTK-ITK -0.14 0.26 -9999 0 -0.74 53 53
mol:DAG -0.07 0.15 -9999 0 -0.31 76 76
HRAS 0.015 0.038 -9999 0 -0.86 1 1
RAP1A 0.017 0.001 -9999 0 -10000 0 0
ARF5/GDP 0.018 0.074 -9999 0 -10000 0 0
PLCG2 0.003 0.1 -9999 0 -0.82 8 8
PLCG1 0.016 0 -9999 0 -10000 0 0
ARF5 0.016 0 -9999 0 -10000 0 0
mol:GTP -0.001 0.019 -9999 0 -10000 0 0
ARF1/GTP -0.001 0.017 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
RAP1A/GTP -0.001 0.019 -9999 0 -10000 0 0
ADAP1 -0.004 0.037 -9999 0 -10000 0 0
ARAP3 -0.001 0.019 -9999 0 -10000 0 0
INPPL1 0.016 0 -9999 0 -10000 0 0
PREX1 0.016 0 -9999 0 -10000 0 0
ARHGEF6 0.016 0 -9999 0 -10000 0 0
ARHGEF7 0.016 0 -9999 0 -10000 0 0
ARF1 0.016 0 -9999 0 -10000 0 0
NRAS 0.017 0.001 -9999 0 -10000 0 0
FYN 0.016 0 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
FGR 0.011 0.067 -9999 0 -0.86 3 3
mol:Ca2+ -0.022 0.078 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0.014 0.033 -9999 0 -0.75 1 1
ZAP70 -0.46 0.44 -9999 0 -0.86 281 281
mol:IP3 -0.036 0.11 -9999 0 -10000 0 0
LYN 0.016 0 -9999 0 -10000 0 0
ARF1/GDP 0.018 0.074 -9999 0 -10000 0 0
RhoA/GDP -0.004 0.017 -9999 0 -10000 0 0
PDK1/Src/Hsp90 -0.001 0.021 -9999 0 -0.48 1 1
BLNK 0.014 0.033 -9999 0 -0.75 1 1
actin cytoskeleton reorganization 0.045 0.082 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
PLEKHA2 0.036 0.054 -9999 0 -0.57 4 4
RAC1 0.016 0 -9999 0 -10000 0 0
PTEN 0 0.002 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
ARF6/GTP -0.001 0.017 -9999 0 -10000 0 0
RhoA/GTP -0.001 0.018 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.2 0.24 -9999 0 -0.56 129 129
BLK -0.041 0.22 -9999 0 -0.86 33 33
PDPK1 0.014 0.033 -9999 0 -0.75 1 1
CYTH1 -0.001 0.018 -9999 0 -10000 0 0
HCK -0.032 0.2 -9999 0 -0.86 28 28
CYTH3 -0.001 0.018 -9999 0 -10000 0 0
CYTH2 -0.001 0.018 -9999 0 -10000 0 0
KRAS 0.017 0.001 -9999 0 -10000 0 0
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 -0.001 0.024 -9999 0 -0.55 1 1
SGK1 -0.001 0.026 -9999 0 -0.6 1 1
INPP5D 0.009 0.077 -9999 0 -0.86 4 4
mol:GDP 0.01 0.078 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
SYK 0.013 0.047 -9999 0 -0.75 2 2
ARF6/GDP -0.004 0.017 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.019 -9999 0 -10000 0 0
ARAP3/RAP1A/GTP -0.001 0.019 -9999 0 -10000 0 0
VAV1 -0.2 0.38 -9999 0 -0.86 124 124
mol:PI-3-4-P2 0.025 0.061 -9999 0 -0.67 4 4
RAS family/GTP/PI3K Class I -0.001 0.019 -9999 0 -10000 0 0
PLEKHA1 0.036 0.054 -9999 0 -0.57 4 4
Rac1/GDP 0.018 0.074 -9999 0 -10000 0 0
LAT -0.23 0.4 -9999 0 -0.86 145 145
Rac1/GTP -0.001 0.1 -9999 0 -10000 0 0
ITK -0.14 0.21 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.11 0.21 -9999 0 -0.46 77 77
LCK -0.021 0.18 -9999 0 -0.85 22 22
BTK -0.097 0.19 -9999 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin -0.022 0.1 -9999 0 -0.5 23 23
E-cadherin/beta catenin -0.023 0.11 -9999 0 -0.56 21 21
CTNNB1 0.016 0 -9999 0 -10000 0 0
JUP 0.011 0.058 -9999 0 -0.75 3 3
CDH1 -0.015 0.15 -9999 0 -0.75 21 21
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.2 0.22 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.16 0.17 -9999 0 -1.2 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.026 0.029 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.11 0.09 -9999 0 -0.37 1 1
CaM/Ca2+ -0.18 0.2 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.18 0.2 -9999 0 -1 1 1
AKT1 -0.16 0.17 -9999 0 -10000 0 0
MAP2K1 -0.13 0.22 -9999 0 -10000 0 0
MAP3K11 -0.15 0.23 -9999 0 -0.81 1 1
IFNGR1 0.001 0.019 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.28 0.29 -9999 0 -0.74 113 113
Rap1/GTP -0.13 0.14 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.21 0.23 -9999 0 -10000 0 0
CEBPB -0.07 0.2 -9999 0 -10000 0 0
STAT3 0.016 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.2 0.22 -9999 0 -1 2 2
STAT1 -0.15 0.24 -9999 0 -1 1 1
CALM1 0.016 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.38 0.43 -9999 0 -0.85 237 237
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
STAT1 (dimer)/PIAS1 -0.17 0.19 -9999 0 -0.95 1 1
CEBPB/PTGES2/Cbp/p300 -0.076 0.084 -9999 0 -0.47 1 1
mol:Ca2+ -0.2 0.21 -9999 0 -10000 0 0
MAPK3 -0.091 0.2 -9999 0 -10000 0 0
STAT1 (dimer) -0.14 0.12 -9999 0 -0.54 1 1
MAPK1 -0.091 0.2 -9999 0 -10000 0 0
JAK2 0.001 0.019 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
JAK1 0.001 0.019 -9999 0 -10000 0 0
CAMK2D 0.016 0 -9999 0 -10000 0 0
DAPK1 -0.026 0.15 -9999 0 -0.63 3 3
SMAD7 -0.021 0.082 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.16 0.18 -9999 0 -10000 0 0
PI3K -0.18 0.19 -9999 0 -10000 0 0
IFNG -0.38 0.43 -9999 0 -0.86 237 237
apoptosis -0.038 0.12 -9999 0 -0.44 3 3
CAMK2G 0.016 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.016 0 -9999 0 -10000 0 0
CAMK2A -0.24 0.36 -9999 0 -0.75 173 173
CAMK2B -0.1 0.28 -9999 0 -0.76 78 78
FRAP1 -0.11 0.2 -9999 0 -10000 0 0
PRKCD -0.12 0.22 -9999 0 -10000 0 0
RAP1B 0.016 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.11 0.09 -9999 0 -0.37 1 1
PTPN2 0.016 0 -9999 0 -10000 0 0
EP300 0.015 0.033 -9999 0 -0.74 1 1
IRF1 -0.061 0.19 -9999 0 -0.93 1 1
STAT1 (dimer)/PIASy -0.17 0.19 -9999 0 -0.95 1 1
SOCS1 0.011 0.083 -9999 0 -0.73 6 6
mol:GDP -0.16 0.17 -9999 0 -10000 0 0
CASP1 -0.021 0.082 -9999 0 -10000 0 0
PTGES2 0.013 0.047 -9999 0 -0.75 2 2
IRF9 0.017 0.076 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.17 0.18 -9999 0 -10000 0 0
RAP1/GDP -0.13 0.14 -9999 0 -10000 0 0
CBL -0.15 0.23 -9999 0 -10000 0 0
MAP3K1 -0.15 0.23 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
PIAS4 0.015 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.11 0.09 -9999 0 -0.37 1 1
PTPN11 -0.17 0.24 -9999 0 -10000 0 0
CREBBP 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
Nongenotropic Androgen 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
PTK2 0.015 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.02 0.092 -10000 0 -0.44 24 24
regulation of S phase of mitotic cell cycle -0.014 0.068 -10000 0 -0.62 1 1
GNAO1 0.008 0.084 -10000 0 -0.84 5 5
HRAS 0.014 0.039 -10000 0 -0.86 1 1
SHBG/T-DHT -0.051 0.15 -10000 0 -0.5 53 53
PELP1 0.016 0.001 -10000 0 -10000 0 0
AKT1 0.015 0 -10000 0 -10000 0 0
MAP2K1 0.047 0.091 -10000 0 -10000 0 0
T-DHT/AR -0.027 0.12 -10000 0 -0.57 24 24
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.007 13 13
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.011 0.058 -10000 0 -0.75 3 3
mol:GDP -0.026 0.12 -10000 0 -0.56 24 24
cell proliferation 0.071 0.11 -10000 0 -0.64 4 4
PIK3CA 0.014 0.033 -10000 0 -0.75 1 1
FOS 0.056 0.15 -10000 0 -0.81 13 13
mol:Ca2+ -0.003 0.014 -10000 0 -0.11 4 4
MAPK3 0.063 0.1 -10000 0 -0.57 4 4
MAPK1 0.045 0.054 -10000 0 -0.29 4 4
PIK3R1 0.014 0.033 -10000 0 -0.75 1 1
mol:IP3 0 0.001 -10000 0 -0.004 13 13
cAMP biosynthetic process -0.046 0.15 -10000 0 -0.48 53 53
GNG2 0.016 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 13 13
HRAS/GTP -0.019 0.085 -10000 0 -0.45 5 5
actin cytoskeleton reorganization -0.001 0.024 -10000 0 -10000 0 0
SRC 0.016 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 13 13
PI3K -0.002 0.03 -10000 0 -0.49 2 2
apoptosis -0.061 0.095 0.43 12 -10000 0 12
T-DHT/AR/PELP1 -0.023 0.1 -10000 0 -0.49 24 24
HRAS/GDP -0.025 0.12 -10000 0 -0.53 25 25
CREB1 0.061 0.1 -10000 0 -0.47 12 12
RAC1-CDC42/GTP -0.001 0.024 -10000 0 -10000 0 0
AR -0.019 0.16 -10000 0 -0.75 24 24
GNB1 0.016 0 -10000 0 -10000 0 0
RAF1 0.036 0.093 -10000 0 -0.45 5 5
RAC1-CDC42/GDP -0.023 0.1 -10000 0 -0.49 24 24
T-DHT/AR/PELP1/Src -0.02 0.092 -10000 0 -0.44 24 24
MAP2K2 0.047 0.093 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src/PI3K -0.015 0.068 -10000 0 -0.63 1 1
GNAZ 0.011 0.058 -10000 0 -0.75 3 3
SHBG -0.063 0.23 -10000 0 -0.75 53 53
Gi family/GNB1/GNG2/GDP -0.008 0.045 -10000 0 -0.45 2 2
mol:T-DHT 0 0 -10000 0 -0.003 9 9
RAC1 0.016 0 -10000 0 -10000 0 0
GNRH1 -0.18 0.31 -10000 0 -0.68 142 142
Gi family/GTP -0.013 0.058 -10000 0 -0.48 4 4
CDC42 0.016 0 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.031 0.002 -9999 0 -10000 0 0
SMARCC1 0.026 0.01 -9999 0 -10000 0 0
REL 0.009 0.058 -9999 0 -0.74 3 3
HDAC7 -0.097 0.087 -9999 0 -0.67 3 3
JUN 0.015 0.003 -9999 0 -10000 0 0
EP300 0.014 0.034 -9999 0 -0.75 1 1
KAT2B 0.014 0.034 -9999 0 -0.75 1 1
KAT5 0.016 0 -9999 0 -10000 0 0
MAPK14 0 0.047 -9999 0 -0.59 3 3
FOXO1 0.016 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.11 0.089 -9999 0 -0.68 4 4
MAP2K6 -0.002 0.059 -9999 0 -0.77 3 3
BRM/BAF57 0 0 -9999 0 -10000 0 0
MAP2K4 0.002 0.006 -9999 0 -10000 0 0
SMARCA2 0.015 0.003 -9999 0 -10000 0 0
PDE9A -0.12 0.13 -9999 0 -1.3 4 4
NCOA2 0.002 0.1 -9999 0 -0.75 9 9
CEBPA -0.001 0.12 -9999 0 -0.86 10 10
EHMT2 0.015 0.003 -9999 0 -10000 0 0
cell proliferation -0.092 0.095 -9999 0 -0.54 3 3
NR0B1 -0.053 0.22 -9999 0 -0.86 34 34
EGR1 -0.001 0.11 -9999 0 -0.75 11 11
RXRs/9cRA -0.004 0.047 -9999 0 -0.54 4 4
AR/RACK1/Src -0.015 0.061 -9999 0 -0.58 2 2
AR/GR 0.002 0.084 -9999 0 -0.72 3 3
GNB2L1 0.014 0.039 -9999 0 -0.86 1 1
PKN1 0.015 0.003 -9999 0 -10000 0 0
RCHY1 0.016 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.003 0.029 -9999 0 -0.59 1 1
T-DHT/AR/TIF2/CARM1 -0.019 0.089 -9999 0 -0.81 3 3
SRC 0.003 0.047 -9999 0 -10000 0 0
NR3C1 0.014 0.039 -9999 0 -0.86 1 1
KLK3 -0.053 0.19 -9999 0 -0.72 27 27
APPBP2 0.002 0.006 -9999 0 -10000 0 0
TRIM24 0.015 0.003 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.025 0.054 -9999 0 -0.59 3 3
TMPRSS2 -0.96 0.38 -9999 0 -1.1 449 449
RXRG 0.006 0.077 -9999 0 -0.87 4 4
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.016 0.001 -9999 0 -10000 0 0
RXRB 0.016 0.001 -9999 0 -10000 0 0
CARM1 0.015 0.003 -9999 0 -10000 0 0
NR2C2 0.014 0.034 -9999 0 -0.75 1 1
KLK2 -0.023 0.13 -9999 0 -0.63 19 19
AR -0.009 0.084 -9999 0 -0.42 12 12
SENP1 0.016 0.001 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
MDM2 0.013 0.009 -9999 0 -10000 0 0
SRY 0.002 0.007 -9999 0 -10000 0 0
GATA2 -0.002 0.12 -9999 0 -0.75 12 12
MYST2 0.016 0.001 -9999 0 -10000 0 0
HOXB13 -0.17 0.35 -9999 0 -0.86 104 104
T-DHT/AR/RACK1/Src -0.015 0.059 -9999 0 -0.6 2 2
positive regulation of transcription -0.002 0.11 -9999 0 -0.74 12 12
DNAJA1 0.002 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.002 -9999 0 -10000 0 0
NCOA1 0.024 0.005 -9999 0 -10000 0 0
SPDEF -0.18 0.36 -9999 0 -0.86 112 112
T-DHT/AR/TIF2 0.02 0.07 -9999 0 -0.67 3 3
T-DHT/AR/Hsp90 -0.026 0.053 -9999 0 -0.59 3 3
GSK3B 0.002 0.005 -9999 0 -10000 0 0
NR2C1 0.016 0.001 -9999 0 -10000 0 0
mol:T-DHT -0.011 0.05 -9999 0 -0.5 4 4
SIRT1 0.015 0.003 -9999 0 -10000 0 0
ZMIZ2 0.014 0.008 -9999 0 -10000 0 0
POU2F1 0.005 0.014 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.067 0.14 -9999 0 -0.61 27 27
CREBBP 0.015 0.003 -9999 0 -10000 0 0
SMARCE1 0.015 0.003 -9999 0 -10000 0 0
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF -0.11 0.071 -10000 0 -10000 0 0
epithelial cell differentiation -0.051 0.11 -10000 0 -0.57 1 1
ITCH 0.055 0.018 -10000 0 -10000 0 0
WWP1 -0.096 0.067 -10000 0 -10000 0 0
FYN 0.016 0 -10000 0 -10000 0 0
EGFR 0.001 0.11 -10000 0 -0.85 9 9
PRL 0.006 0.008 -10000 0 -10000 0 0
neuron projection morphogenesis -0.018 0.08 -10000 0 -0.57 1 1
PTPRZ1 -0.082 0.25 -10000 0 -0.76 63 63
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.053 0.073 -10000 0 -0.6 2 2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.083 0.094 -10000 0 -0.57 9 9
ADAM17 0.055 0.018 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.14 0.086 -10000 0 -0.46 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.12 0.1 -10000 0 -0.63 11 11
NCOR1 0.016 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.076 0.077 -10000 0 -0.54 9 9
GRIN2B -0.057 0.091 -10000 0 -0.61 3 3
ErbB4/ErbB2/betacellulin -0.13 0.16 -10000 0 -0.52 70 70
STAT1 0.014 0.039 -10000 0 -0.86 1 1
HBEGF 0.016 0 -10000 0 -10000 0 0
PRLR -0.084 0.26 -10000 0 -0.75 68 68
E4ICDs/ETO2 -0.11 0.08 -10000 0 -0.7 2 2
axon guidance -0.017 0.072 -10000 0 -10000 0 0
NEDD4 0.052 0.052 -10000 0 -0.73 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.074 0.19 -10000 0 -0.57 68 68
CBFA2T3 0.012 0.055 -10000 0 -0.86 2 2
ErbB4/ErbB2/HBEGF -0.064 0.038 -10000 0 -0.52 1 1
MAPK3 -0.029 0.082 -10000 0 -0.6 1 1
STAT1 (dimer) -0.11 0.073 -10000 0 -0.54 1 1
MAPK1 -0.029 0.082 -10000 0 -0.6 1 1
JAK2 0.016 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.077 0.081 -10000 0 -0.53 10 10
NRG1 0.036 0.11 -10000 0 -0.56 16 16
NRG3 -0.003 0.13 -10000 0 -0.86 11 11
NRG2 -0.001 0.12 -10000 0 -0.85 10 10
NRG4 -0.057 0.22 -10000 0 -0.77 47 47
heart development -0.017 0.072 -10000 0 -10000 0 0
neural crest cell migration -0.077 0.08 -10000 0 -0.53 10 10
ERBB2 0.052 0.04 -10000 0 -0.56 2 2
WWOX/E4ICDs -0.11 0.075 -10000 0 -0.7 1 1
SHC1 0.014 0.039 -10000 0 -0.86 1 1
ErbB4/EGFR/neuregulin 4 -0.15 0.15 -10000 0 -0.57 51 51
apoptosis 0.1 0.063 0.44 1 -10000 0 1
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.12 0.089 -10000 0 -0.54 9 9
ErbB4/ErbB2/epiregulin -0.098 0.13 -10000 0 -0.57 34 34
ErbB4/ErbB4/betacellulin/betacellulin -0.18 0.18 -10000 0 -0.59 77 77
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.13 0.14 -10000 0 -0.73 1 1
MDM2 -0.1 0.074 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.054 0.077 -10000 0 -0.52 9 9
STAT5A -0.005 0.067 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.084 0.1 -10000 0 -0.56 17 17
DLG4 0.016 0 -10000 0 -10000 0 0
GRB2/SHC -0.001 0.029 -10000 0 -0.67 1 1
E4ICDs/TAB2/NCoR1 -0.1 0.048 -10000 0 -10000 0 0
STAT5A (dimer) -0.054 0.12 -10000 0 -0.62 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.007 0.064 -10000 0 -10000 0 0
LRIG1 0.016 0 -10000 0 -10000 0 0
EREG -0.041 0.21 -10000 0 -0.86 33 33
BTC -0.098 0.27 -10000 0 -0.75 77 77
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.017 0.072 -10000 0 -10000 0 0
ERBB4 -0.14 0.086 -10000 0 -0.47 1 1
STAT5B 0.016 0 -10000 0 -10000 0 0
YAP1 -0.034 0.016 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.11 0.13 -10000 0 -0.51 44 44
glial cell differentiation 0.1 0.048 -10000 0 -10000 0 0
WWOX 0.014 0.039 -10000 0 -0.86 1 1
cell proliferation -0.075 0.16 -10000 0 -0.62 11 11
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.011 0.061 -9999 0 -0.78 3 3
GNB1/GNG2 -0.054 0.11 -9999 0 -0.53 8 8
mol:DAG 0.01 0.13 -9999 0 -0.48 7 7
PLCG1 0.009 0.13 -9999 0 -0.5 7 7
YES1 -0.011 0.14 -9999 0 -0.56 8 8
FZD3 0.016 0 -9999 0 -10000 0 0
FZD6 0.016 0 -9999 0 -10000 0 0
G protein -0.05 0.1 -9999 0 -0.5 7 7
MAP3K7 -0.095 0.22 -9999 0 -0.55 48 48
mol:Ca2+ 0.01 0.13 -9999 0 -0.47 7 7
mol:IP3 0.01 0.13 -9999 0 -0.48 7 7
NLK -0.007 0.009 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
CAMK2A -0.11 0.24 -9999 0 -0.61 48 48
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.064 0.13 -9999 0 -0.6 8 8
CSNK1A1 0.016 0 -9999 0 -10000 0 0
GNAS -0.011 0.14 -9999 0 -0.56 8 8
GO:0007205 0.011 0.13 -9999 0 -0.47 7 7
WNT6 -0.013 0.16 -9999 0 -0.86 17 17
WNT4 -0.07 0.24 -9999 0 -0.75 58 58
NFAT1/CK1 alpha -0.049 0.1 -9999 0 -10000 0 0
GNG2 0.016 0 -9999 0 -10000 0 0
WNT5A 0.011 0.058 -9999 0 -0.75 3 3
WNT11 -0.04 0.2 -9999 0 -0.76 37 37
CDC42 0 0.14 -9999 0 -0.52 8 8
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.045 0.092 -9999 0 -10000 0 0
GNAI2 0.016 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.1 0.22 -9999 0 -0.59 88 88
mol:GDP 0 0 -9999 0 -10000 0 0
GNAO1 0.007 0.084 -9999 0 -0.84 5 5
RhoA/GTP -0.046 0.094 -9999 0 -10000 0 0
negative regulation of cAMP metabolic process -0.014 0.12 -9999 0 -10000 0 0
GNAZ 0.011 0.058 -9999 0 -0.75 3 3
GNAI3 0.016 0 -9999 0 -10000 0 0
GNA12 0.016 0 -9999 0 -10000 0 0
S1PR5 -0.13 0.33 -9999 0 -0.86 88 88
mol:GTP 0 0 -9999 0 -10000 0 0
S1P/S1P5/Gi -0.052 0.11 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
GNAI1 0.011 0.058 -9999 0 -0.75 3 3
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.004 0.049 -9999 0 -0.56 4 4
AKT1 -0.055 0.2 -9999 0 -0.71 3 3
PTK2B -0.16 0.26 -9999 0 -1.1 1 1
VEGFR2 homodimer/Frs2 -0.002 0.041 -9999 0 -0.83 1 1
CAV1 -0.047 0.23 -9999 0 -0.86 37 37
CALM1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.23 0.25 -9999 0 -1.2 1 1
endothelial cell proliferation -0.041 0.2 -9999 0 -0.69 1 1
mol:Ca2+ -0.16 0.26 -9999 0 -1.1 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.21 0.24 -9999 0 -1.2 1 1
RP11-342D11.1 -0.17 0.26 -9999 0 -1.1 1 1
CDH5 0.014 0.039 -9999 0 -0.86 1 1
VEGFA homodimer -0.24 0.26 -9999 0 -0.52 233 233
SHC1 0.014 0.039 -9999 0 -0.86 1 1
SHC2 0.008 0.082 -9999 0 -0.82 5 5
HRAS/GDP -0.17 0.19 -9999 0 -0.83 2 2
SH2D2A -0.27 0.41 -9999 0 -0.86 168 168
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.14 0.15 -9999 0 -0.78 1 1
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.39 0.34 -9999 0 -1 67 67
VEGFR1 homodimer 0.007 0.086 -9999 0 -0.86 5 5
SHC/GRB2/SOS1 -0.19 0.21 -9999 0 -1.1 1 1
GRB10 -0.16 0.26 -9999 0 -1.1 1 1
PTPN11 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
PAK1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.2 0.22 -9999 0 -1 2 2
HRAS 0.014 0.039 -9999 0 -0.86 1 1
VEGF/Rho/ROCK1/Integrin Complex -0.085 0.094 -9999 0 -0.58 1 1
HIF1A 0.013 0.047 -9999 0 -0.75 2 2
FRS2 0.016 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.21 0.23 -9999 0 -1.2 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.016 0 -9999 0 -10000 0 0
Nck/Pak -0.001 0.025 -9999 0 -0.56 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.23 0.25 -9999 0 -1.2 1 1
mol:GDP -0.18 0.2 -9999 0 -1 1 1
mol:NADP -0.063 0.19 -9999 0 -0.62 1 1
eNOS/Hsp90 -0.053 0.18 -9999 0 -0.57 1 1
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
mol:IP3 -0.16 0.27 -9999 0 -1.1 1 1
HIF1A/ARNT -0.002 0.035 -9999 0 -0.56 2 2
SHB 0.016 0 -9999 0 -10000 0 0
VEGFA -0.38 0.44 -9999 0 -0.86 233 233
VEGFC 0.014 0.039 -9999 0 -0.86 1 1
FAK1/Vinculin -0.1 0.22 -9999 0 -1 1 1
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.22 0.24 -9999 0 -1.2 1 1
PTPN6 0.016 0 -9999 0 -10000 0 0
EPAS1 0.026 0.037 -9999 0 -0.72 1 1
mol:L-citrulline -0.063 0.19 -9999 0 -0.62 1 1
ITGAV 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.21 0.24 -9999 0 -1.2 1 1
VEGFR2 homodimer/VEGFA homodimer -0.23 0.25 -9999 0 -1.2 1 1
VEGFR2/3 heterodimer -0.002 0.041 -9999 0 -0.83 1 1
VEGFB 0.016 0 -9999 0 -10000 0 0
MAPK11 -0.15 0.26 -9999 0 -0.84 2 2
VEGFR2 homodimer 0.044 0.05 -9999 0 -0.73 2 2
FLT1 0.007 0.086 -9999 0 -0.86 5 5
NEDD4 0.015 0.047 -9999 0 -0.74 2 2
MAPK3 -0.14 0.25 -9999 0 -0.76 2 2
MAPK1 -0.14 0.25 -9999 0 -0.76 2 2
VEGFA145/NRP2 -0.3 0.33 -9999 0 -0.66 238 238
VEGFR1/2 heterodimer -0.008 0.069 -9999 0 -0.61 6 6
KDR 0.044 0.05 -9999 0 -0.73 2 2
VEGFA165/NRP1/VEGFR2 homodimer -0.21 0.23 -9999 0 -1.2 2 2
SRC 0.016 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.14 0.25 -9999 0 -0.78 2 2
PI3K -0.16 0.18 -9999 0 -0.78 6 6
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.23 0.25 -9999 0 -1.2 1 1
FES -0.17 0.27 -9999 0 -1 2 2
GAB1 -0.17 0.19 -9999 0 -0.81 5 5
VEGFR2 homodimer/VEGFA homodimer/Src -0.23 0.25 -9999 0 -1.2 1 1
CTNNB1 0.016 0 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
ARNT 0.016 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.083 0.2 -9999 0 -0.61 12 12
VEGFR2 homodimer/VEGFA homodimer/Yes -0.23 0.25 -9999 0 -1.2 1 1
PI3K/GAB1 -0.055 0.2 -9999 0 -0.64 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.2 0.22 -9999 0 -1.1 1 1
PRKACA 0.016 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.003 0.044 -9999 0 -0.64 2 2
HSP90AA1 0.016 0 -9999 0 -10000 0 0
CDC42 -0.16 0.27 -9999 0 -1.2 1 1
actin cytoskeleton reorganization -0.39 0.33 -9999 0 -1 67 67
PTK2 -0.12 0.24 -9999 0 -1.1 1 1
EDG1 -0.17 0.26 -9999 0 -1.1 1 1
mol:DAG -0.16 0.27 -9999 0 -1.1 1 1
CaM/Ca2+ -0.19 0.2 -9999 0 -1 1 1
MAP2K3 -0.15 0.26 -9999 0 -1.1 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.21 0.23 -9999 0 -1.2 1 1
PLCG1 -0.16 0.27 -9999 0 -1.2 1 1
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.21 0.24 -9999 0 -1.2 1 1
IQGAP1 0.016 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.23 0.25 -9999 0 -1.2 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.23 0.25 -9999 0 -1.2 1 1
cell migration -0.052 0.2 -9999 0 -0.77 1 1
mol:PI-3-4-5-P3 -0.15 0.17 -9999 0 -0.7 6 6
FYN 0.016 0 -9999 0 -10000 0 0
VEGFB/NRP1 -0.19 0.21 -9999 0 -1 1 1
mol:NO -0.063 0.19 -9999 0 -0.62 1 1
PXN 0.016 0 -9999 0 -10000 0 0
HRAS/GTP -0.17 0.19 -9999 0 -0.82 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.21 0.23 -9999 0 -1.2 1 1
VHL 0.014 0.033 -9999 0 -0.75 1 1
ITGB3 0.01 0.067 -9999 0 -0.75 4 4
NOS3 -0.074 0.2 -9999 0 -0.73 1 1
VEGFR2 homodimer/VEGFA homodimer/Sck -0.23 0.26 -9999 0 -1.1 3 3
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA -0.14 0.25 -9999 0 -1 1 1
PRKCB -0.15 0.25 -9999 0 -0.96 2 2
VCL 0.016 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.22 0.24 -9999 0 -1.2 1 1
VEGFR1/2 heterodimer/VEGFA homodimer -0.23 0.26 -9999 0 -1.1 5 5
VEGFA165/NRP2 -0.3 0.33 -9999 0 -0.66 238 238
MAPKKK cascade -0.16 0.18 -9999 0 -0.8 2 2
NRP2 0.004 0.1 -9999 0 -0.86 7 7
VEGFC homodimer 0.014 0.039 -9999 0 -0.86 1 1
NCK1 0.014 0.033 -9999 0 -0.75 1 1
ROCK1 0.016 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.1 0.22 -9999 0 -1 1 1
MAP3K13 -0.16 0.27 -9999 0 -1.2 1 1
PDPK1 -0.073 0.2 -9999 0 -0.65 6 6
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.012 0.058 -9999 0 -10000 0 0
epithelial cell differentiation -0.016 0.079 -9999 0 -10000 0 0
CYFIP2 0.004 0.094 -9999 0 -0.75 8 8
ENAH 0.079 0.065 -9999 0 -10000 0 0
EGFR 0.001 0.11 -9999 0 -0.85 9 9
EPHA2 0.014 0.033 -9999 0 -0.75 1 1
MYO6 0.032 0.097 -9999 0 -0.78 2 2
CTNNB1 0.016 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.007 0.059 -9999 0 -0.48 8 8
AQP5 -0.17 0.24 -9999 0 -0.52 159 159
CTNND1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.035 0.083 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.018 0.12 -9999 0 -0.84 1 1
EGF -0.67 0.23 -9999 0 -0.75 466 466
NCKAP1 0.016 0 -9999 0 -10000 0 0
AQP3 -0.051 0.16 -9999 0 -0.57 38 38
cortical microtubule organization -0.016 0.079 -9999 0 -10000 0 0
GO:0000145 0.035 0.079 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.016 0.08 -9999 0 -10000 0 0
MLLT4 0.016 0 -9999 0 -10000 0 0
ARF6/GDP -0.014 0.063 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.035 -9999 0 -0.52 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.051 0.084 -9999 0 -0.58 1 1
PVRL2 0.016 0 -9999 0 -10000 0 0
ZYX 0.035 0.084 -9999 0 -10000 0 0
ARF6/GTP -0.002 0.032 -9999 0 -10000 0 0
CDH1 -0.015 0.15 -9999 0 -0.75 21 21
EGFR/EGFR/EGF/EGF -0.35 0.14 -9999 0 -0.77 27 27
RhoA/GDP -0.015 0.073 -9999 0 -10000 0 0
actin cytoskeleton organization 0.042 0.092 -9999 0 -0.72 2 2
IGF-1R heterotetramer 0.016 0 -9999 0 -10000 0 0
GIT1 0.016 0 -9999 0 -10000 0 0
IGF1R 0.016 0 -9999 0 -10000 0 0
IGF1 0.006 0.094 -9999 0 -0.86 6 6
DIAPH1 -0.01 0.086 -9999 0 -0.7 8 8
Wnt receptor signaling pathway 0.016 0.079 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.014 0.063 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
VCL 0.042 0.094 -9999 0 -0.74 2 2
EFNA1 0.014 0.039 -9999 0 -0.86 1 1
LPP 0.044 0.089 -9999 0 -0.8 1 1
Ephrin A1/EPHA2 -0.016 0.074 -9999 0 -10000 0 0
SEC6/SEC8 -0.013 0.062 -9999 0 -10000 0 0
MGAT3 0.018 0.12 -9999 0 -0.87 1 1
HGF/MET -0.037 0.13 -9999 0 -0.96 4 4
HGF -0.021 0.17 -9999 0 -0.8 23 23
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.012 0.059 -9999 0 -10000 0 0
actin cable formation 0.099 0.07 -9999 0 -10000 0 0
KIAA1543 0.037 0.12 -9999 0 -0.86 6 6
KIFC3 0.034 0.086 -9999 0 -10000 0 0
NCK1 0.014 0.033 -9999 0 -0.75 1 1
EXOC3 0.016 0 -9999 0 -10000 0 0
ACTN1 0.033 0.093 -9999 0 -0.87 1 1
NCK1/GIT1 -0.001 0.025 -9999 0 -0.56 1 1
mol:GDP -0.016 0.079 -9999 0 -10000 0 0
EXOC4 0.016 0 -9999 0 -10000 0 0
STX4 0.035 0.084 -9999 0 -10000 0 0
PIP5K1C 0.035 0.084 -9999 0 -10000 0 0
LIMA1 0.016 0 -9999 0 -10000 0 0
ABI1 0.016 0 -9999 0 -10000 0 0
ROCK1 -0.012 0.055 -9999 0 -10000 0 0
adherens junction assembly 0.059 0.12 -9999 0 -0.79 7 7
IGF-1R heterotetramer/IGF1 -0.02 0.084 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
MET 0.007 0.086 -9999 0 -0.86 5 5
PLEKHA7 0.032 0.1 -9999 0 -0.78 3 3
mol:GTP -0.003 0.035 -9999 0 -0.52 1 1
establishment of epithelial cell apical/basal polarity 0.071 0.076 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.012 0.058 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0.042 0.092 -9999 0 -0.72 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.012 0.059 -9999 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.007 0.084 -9999 0 -0.84 5 5
CDC42/GTP -0.017 0.061 -9999 0 -10000 0 0
PLCG1 0.035 0.077 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.016 0 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.017 0.06 -9999 0 -10000 0 0
S1PR5 -0.13 0.33 -9999 0 -0.86 88 88
S1PR4 -0.028 0.19 -9999 0 -0.86 26 26
MAPK3 0.035 0.077 -9999 0 -10000 0 0
MAPK1 0.035 0.077 -9999 0 -10000 0 0
S1P/S1P5/Gi -0.052 0.11 -9999 0 -10000 0 0
GNAI1 0.011 0.058 -9999 0 -0.75 3 3
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.1 0.22 -9999 0 -0.59 88 88
RHOA 0.016 0.12 -9999 0 -0.49 26 26
S1P/S1P4/Gi -0.019 0.07 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.011 0.058 -9999 0 -0.75 3 3
S1P/S1P4/G12/G13 -0.027 0.12 -9999 0 -0.53 26 26
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.031 0.12 -9999 0 -0.51 32 32
RGS9BP -0.019 0.16 -9999 0 -0.75 23 23
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.003 0.006 -9999 0 -10000 0 0
mol:Na + -0.013 0.085 -9999 0 -0.59 11 11
mol:ADP 0.012 0.044 -9999 0 -0.68 2 2
GNAT2 0.014 0.005 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.037 0.13 -9999 0 -0.5 38 38
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.026 -9999 0 -0.59 1 1
GRK7 0.008 0.055 -9999 0 -0.86 2 2
CNGB3 -0.007 0.11 -9999 0 -0.86 8 8
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.009 0.12 -9999 0 -0.64 15 15
Cone PDE6 -0.034 0.12 -9999 0 -0.9 1 1
Cone Metarhodopsin II -0.002 0.034 -9999 0 -0.55 2 2
Na + (4 Units) -0.019 0.11 -9999 0 -0.64 15 15
GNAT2/GDP -0.031 0.11 -9999 0 -0.5 9 9
GNB5 0.016 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.015 0.043 -9999 0 -0.54 3 3
Cone Transducin -0.033 0.13 -9999 0 -0.54 32 32
SLC24A2 -0.009 0.1 -9999 0 -0.86 7 7
GNB3/GNGT2 -0.041 0.16 -9999 0 -0.67 32 32
GNB3 -0.038 0.21 -9999 0 -0.86 31 31
GNAT2/GTP 0 0 -9999 0 -10000 0 0
CNGA3 0 0.066 -9999 0 -0.86 3 3
ARR3 0.004 0.007 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.013 0.086 -9999 0 -0.6 11 11
mol:Pi -0.036 0.13 -9999 0 -0.5 38 38
Cone CNG Channel -0.013 0.085 -9999 0 -0.53 12 12
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.009 0.1 -9999 0 -0.86 7 7
RGS9 -0.008 0.14 -9999 0 -0.82 15 15
PDE6C 0.004 0.055 -9999 0 -0.86 2 2
GNGT2 0.014 0.039 -9999 0 -0.86 1 1
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.003 0.039 -9999 0 -0.86 1 1
a4b1 and a4b7 Integrin 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
ITGB1 0.016 0 -9999 0 -10000 0 0
ITGB7 0.016 0 -9999 0 -10000 0 0
ITGA4 -0.01 0.15 -9999 0 -0.86 15 15
alpha4/beta7 Integrin -0.019 0.11 -9999 0 -0.67 15 15
alpha4/beta1 Integrin -0.019 0.11 -9999 0 -0.67 15 15
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.012 0.036 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.035 0.096 -9999 0 -0.48 7 7
JUN 0.027 0.11 -9999 0 -0.55 7 7
HRAS 0.014 0.039 -9999 0 -0.86 1 1
RET51/GFRalpha1/GDNF/GRB10 -0.051 0.16 -9999 0 -0.7 11 11
RAP1A 0.016 0 -9999 0 -10000 0 0
FRS2 0.016 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.051 0.16 -9999 0 -0.7 11 11
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.04 0.13 -9999 0 -0.47 44 44
RHOA 0.016 0 -9999 0 -10000 0 0
RAP1A/GTP -0.045 0.14 -9999 0 -0.83 5 5
GRB7 0.005 0.088 -9999 0 -0.75 7 7
RET51/GFRalpha1/GDNF -0.051 0.16 -9999 0 -0.7 11 11
MAPKKK cascade -0.041 0.12 -9999 0 -0.71 6 6
BCAR1 0.014 0.033 -9999 0 -0.75 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.039 0.13 -9999 0 -0.47 43 43
lamellipodium assembly -0.033 0.091 -9999 0 -0.44 7 7
RET51/GFRalpha1/GDNF/SHC -0.052 0.16 -9999 0 -0.69 12 12
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
RET9/GFRalpha1/GDNF/SHC -0.037 0.12 -9999 0 -0.46 41 41
RET9/GFRalpha1/GDNF/Shank3 -0.036 0.12 -9999 0 -0.46 40 40
MAPK3 0.007 0.15 -9999 0 -0.77 5 5
DOK1 0.016 0 -9999 0 -10000 0 0
DOK6 -0.002 0.12 -9999 0 -0.75 12 12
PXN 0.016 0 -9999 0 -10000 0 0
neurite development -0.042 0.13 -9999 0 -0.73 5 5
DOK5 -0.007 0.13 -9999 0 -0.76 15 15
GFRA1 -0.039 0.2 -9999 0 -0.76 37 37
MAPK8 0.016 0.12 -9999 0 -0.58 7 7
HRAS/GTP -0.047 0.14 -9999 0 -0.84 6 6
tube development -0.033 0.11 -9999 0 -0.5 6 6
MAPK1 0.007 0.15 -9999 0 -0.77 5 5
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.023 0.08 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
PDLIM7 0.009 0.077 -9999 0 -0.86 4 4
RET51/GFRalpha1/GDNF/Dok6 -0.057 0.17 -9999 0 -0.87 12 12
SHC1 0.014 0.039 -9999 0 -0.86 1 1
RET51/GFRalpha1/GDNF/Dok4 -0.051 0.16 -9999 0 -0.7 11 11
RET51/GFRalpha1/GDNF/Dok5 -0.064 0.19 -9999 0 -0.8 19 19
PRKCA 0.016 0 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.03 -9999 0 -0.68 1 1
CREB1 -0.031 0.097 -9999 0 -0.54 5 5
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.024 0.081 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Grb7 -0.057 0.18 -9999 0 -0.8 14 14
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.013 0.15 -9999 0 -0.76 19 19
DOK4 0.016 0 -9999 0 -10000 0 0
JNK cascade 0.027 0.11 -9999 0 -0.53 7 7
RET9/GFRalpha1/GDNF/FRS2 -0.036 0.12 -9999 0 -0.46 40 40
SHANK3 0.016 0 -9999 0 -10000 0 0
RASA1 0.014 0.033 -9999 0 -0.75 1 1
NCK1 0.014 0.033 -9999 0 -0.75 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.024 0.082 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.034 0.1 -9999 0 -0.6 5 5
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.035 0.11 -9999 0 -0.61 6 6
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.036 0.11 -9999 0 -0.77 5 5
PI3K -0.05 0.14 -9999 0 -0.74 7 7
SOS1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.033 0.11 -9999 0 -0.5 6 6
GRB10 0.016 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.03 0.092 -9999 0 -0.53 5 5
RET51/GFRalpha1/GDNF/FRS2 -0.051 0.16 -9999 0 -0.7 11 11
GAB1 0.016 0 -9999 0 -10000 0 0
IRS1 0.01 0.067 -9999 0 -0.75 4 4
IRS2 0.002 0.11 -9999 0 -0.86 8 8
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.036 0.11 -9999 0 -0.77 5 5
RET51/GFRalpha1/GDNF/PKC alpha -0.051 0.16 -9999 0 -0.7 11 11
GRB2 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GDNF 0.001 0.066 -9999 0 -0.86 3 3
RAC1 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.054 0.16 -9999 0 -0.72 12 12
Rac1/GTP -0.039 0.11 -9999 0 -0.54 7 7
RET9/GFRalpha1/GDNF -0.039 0.14 -9999 0 -0.51 40 40
GFRalpha1/GDNF -0.045 0.16 -9999 0 -0.58 40 40
TCGA08_rtk_signaling

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
PDGFRA -0.28 0.37 -9999 0 -0.75 199 199
HRAS 0.014 0.039 -9999 0 -0.86 1 1
EGFR 0.001 0.11 -9999 0 -0.85 9 9
AKT 0.035 0.03 -9999 0 -10000 0 0
FOXO3 0.016 0 -9999 0 -10000 0 0
AKT1 0.016 0 -9999 0 -10000 0 0
FOXO1 0.016 0 -9999 0 -10000 0 0
AKT3 0.016 0 -9999 0 -10000 0 0
FOXO4 0.016 0 -9999 0 -10000 0 0
MET 0.007 0.086 -9999 0 -0.86 5 5
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
PIK3CB 0.016 0 -9999 0 -10000 0 0
NRAS 0.016 0 -9999 0 -10000 0 0
PIK3CG 0.011 0.067 -9999 0 -0.86 3 3
PIK3R3 0.016 0 -9999 0 -10000 0 0
PIK3R2 0.016 0 -9999 0 -10000 0 0
NF1 0.016 0 -9999 0 -10000 0 0
RAS -0.041 0.097 -9999 0 -0.38 5 5
ERBB2 0.013 0.047 -9999 0 -0.75 2 2
proliferation/survival/translation -0.041 0.013 -9999 0 -10000 0 0
PI3K -0.022 0.092 -9999 0 -0.29 6 6
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
KRAS 0.016 0 -9999 0 -10000 0 0
FOXO 0.041 0.034 -9999 0 -10000 0 0
AKT2 0.016 0 -9999 0 -10000 0 0
PTEN 0.016 0 -9999 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.02 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.075 0.075 -9999 0 -10000 0 0
ERC1 0.016 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.16 0.29 -9999 0 -0.67 123 123
NFKBIA 0.063 0.02 -9999 0 -10000 0 0
BIRC2 0.016 0 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
RIPK2 0.014 0.039 -9999 0 -0.86 1 1
IKBKG -0.047 0.085 -9999 0 -10000 0 0
IKK complex/A20 -0.041 0.08 -9999 0 -0.59 2 2
NEMO/A20/RIP2 0.014 0.039 -9999 0 -0.86 1 1
XPO1 0.016 0 -9999 0 -10000 0 0
NEMO/ATM -0.043 0.078 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.035 0.062 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 -0.19 0.37 -9999 0 -0.86 123 123
NFKB1 0.019 0.033 -9999 0 -0.74 1 1
RELA 0.02 0 -9999 0 -10000 0 0
MALT1 0.016 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.014 0.033 -9999 0 -0.75 1 1
TNF/TNFR1A -0.009 0.076 -9999 0 -0.61 8 8
TRAF6 0.016 0 -9999 0 -10000 0 0
PRKCA 0.016 0 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
UBE2D3 0.016 0 -9999 0 -10000 0 0
TNF 0.003 0.1 -9999 0 -0.8 8 8
NF kappa B1 p50/RelA -0.001 0.02 -9999 0 -0.46 1 1
BCL10 0.016 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.063 0.02 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0 -9999 0 -10000 0 0
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
IKK complex -0.039 0.07 -9999 0 -10000 0 0
CYLD 0.016 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.036 0.064 -9999 0 -10000 0 0
IL1-mediated signaling events

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