Uterine Corpus Endometrioid Carcinoma: PARADIGM pathway analysis of mRNASeq expression data
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

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

Summary

There were 51 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
Signaling events mediated by the Hedgehog family 69
IL23-mediated signaling events 54
TCGA08_retinoblastoma 53
Ephrin A reverse signaling 51
FOXA2 and FOXA3 transcription factor networks 51
Signaling mediated by p38-alpha and p38-beta 50
Wnt signaling 47
IL4-mediated signaling events 46
Syndecan-1-mediated signaling events 44
Glypican 1 network 41
Results
Summary Table

The following list describes the columns found in Table 2.

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

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

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

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

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

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

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

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

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

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

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

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Signaling events mediated by the Hedgehog family 69 3603 52 -0.26 0.11 1000 -1000 -0.048 -1000
IL23-mediated signaling events 54 3253 60 -0.51 0.012 1000 -1000 -0.16 -1000
TCGA08_retinoblastoma 53 430 8 -0.1 0.051 1000 -1000 -0.012 -1000
Ephrin A reverse signaling 51 360 7 -0.077 0 1000 -1000 -0.018 -1000
FOXA2 and FOXA3 transcription factor networks 51 2377 46 -0.43 0.014 1000 -1000 -0.092 -1000
Signaling mediated by p38-alpha and p38-beta 50 2216 44 -0.19 0.012 1000 -1000 -0.036 -1000
Wnt signaling 47 333 7 -0.13 -0.014 1000 -1000 -0.028 -1000
IL4-mediated signaling events 46 4254 91 -0.7 0.55 1000 -1000 -0.16 -1000
Syndecan-1-mediated signaling events 44 1528 34 -0.17 0.012 1000 -1000 -0.044 -1000
Glypican 1 network 41 1991 48 -0.14 0.023 1000 -1000 -0.036 -1000
BMP receptor signaling 40 3319 81 -0.21 0.04 1000 -1000 -0.079 -1000
p75(NTR)-mediated signaling 39 4968 125 -0.25 0.032 1000 -1000 -0.079 -1000
TCR signaling in naïve CD8+ T cells 38 3609 93 -0.13 0.077 1000 -1000 -0.07 -1000
EPHB forward signaling 37 3162 85 -0.13 0.1 1000 -1000 -0.071 -1000
Class IB PI3K non-lipid kinase events 37 111 3 -0.038 -1000 1000 -1000 -0.009 -1000
HIF-1-alpha transcription factor network 35 2689 76 -0.32 0.019 1000 -1000 -0.15 -1000
Glypican 2 network 35 140 4 -0.039 -0.03 1000 -1000 -0.011 -1000
Noncanonical Wnt signaling pathway 32 855 26 -0.13 0.012 1000 -1000 -0.04 -1000
Signaling events regulated by Ret tyrosine kinase 32 2672 82 -0.16 0.012 1000 -1000 -0.077 -1000
Ephrin B reverse signaling 32 1547 48 -0.1 0.061 1000 -1000 -0.052 -1000
TCGA08_p53 32 227 7 -0.077 0.046 1000 -1000 -0.013 -1000
IL12-mediated signaling events 30 2692 87 -0.23 0.04 1000 -1000 -0.14 -1000
Syndecan-4-mediated signaling events 30 2076 67 -0.16 0.016 1000 -1000 -0.06 -1000
Endothelins 29 2803 96 -0.24 0.028 1000 -1000 -0.076 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 29 1991 68 -0.25 0.087 1000 -1000 -0.11 -1000
amb2 Integrin signaling 28 2367 82 -0.25 0.017 1000 -1000 -0.064 -1000
Glucocorticoid receptor regulatory network 28 3288 114 -0.47 0.25 1000 -1000 -0.063 -1000
Reelin signaling pathway 27 1545 56 -0.14 0.03 1000 -1000 -0.071 -1000
BCR signaling pathway 27 2723 99 -0.15 0.018 1000 -1000 -0.075 -1000
IGF1 pathway 27 1561 57 -0.075 0.025 1000 -1000 -0.081 -1000
Neurotrophic factor-mediated Trk receptor signaling 27 3296 120 -0.15 0.12 1000 -1000 -0.062 -1000
LPA receptor mediated events 26 2657 102 -0.12 0.014 1000 -1000 -0.077 -1000
Canonical Wnt signaling pathway 25 1303 51 -0.25 0.1 1000 -1000 -0.057 -1000
Visual signal transduction: Rods 25 1301 52 -0.14 0.012 1000 -1000 -0.068 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 25 2024 78 -0.12 0.06 1000 -1000 -0.072 -1000
Plasma membrane estrogen receptor signaling 24 2085 86 -0.092 0.077 1000 -1000 -0.073 -1000
Caspase cascade in apoptosis 23 1721 74 -0.1 0.029 1000 -1000 -0.041 -1000
Nephrin/Neph1 signaling in the kidney podocyte 23 787 34 -0.047 0.012 1000 -1000 -0.035 -1000
Syndecan-2-mediated signaling events 23 1632 69 -0.14 0.023 1000 -1000 -0.028 -1000
PDGFR-alpha signaling pathway 23 1041 44 -0.056 0.019 1000 -1000 -0.052 -1000
Nectin adhesion pathway 23 1454 63 -0.068 0.027 1000 -1000 -0.063 -1000
Effects of Botulinum toxin 23 605 26 -0.11 0.012 1000 -1000 -0.054 -1000
Angiopoietin receptor Tie2-mediated signaling 23 2105 88 -0.12 0.016 1000 -1000 -0.092 -1000
Thromboxane A2 receptor signaling 22 2363 105 -0.11 0.032 1000 -1000 -0.055 -1000
Integrins in angiogenesis 22 1924 84 -0.13 0.021 1000 -1000 -0.084 -1000
LPA4-mediated signaling events 21 259 12 -0.042 0.015 1000 -1000 -0.02 -1000
Presenilin action in Notch and Wnt signaling 21 1281 61 -0.25 0.038 1000 -1000 -0.062 -1000
RXR and RAR heterodimerization with other nuclear receptor 19 989 52 -0.12 0.023 1000 -1000 -0.038 -1000
Retinoic acid receptors-mediated signaling 19 1155 58 -0.14 0.024 1000 -1000 -0.063 -1000
Calcium signaling in the CD4+ TCR pathway 19 617 31 -0.16 0.012 1000 -1000 -0.055 -1000
EGFR-dependent Endothelin signaling events 19 404 21 -0.065 0.018 1000 -1000 -0.056 -1000
Signaling events mediated by PTP1B 18 1374 76 -0.14 0.018 1000 -1000 -0.071 -1000
FAS signaling pathway (CD95) 18 866 47 -0.071 0.024 1000 -1000 -0.043 -1000
Coregulation of Androgen receptor activity 17 1318 76 -0.11 0.029 1000 -1000 -0.03 -1000
Osteopontin-mediated events 17 655 38 -0.065 0.012 1000 -1000 -0.085 -1000
Arf6 signaling events 17 1065 62 -0.075 0.016 1000 -1000 -0.044 -1000
Nongenotropic Androgen signaling 17 919 52 -0.068 0.012 1000 -1000 -0.047 -1000
Visual signal transduction: Cones 16 641 38 -0.054 0.007 1000 -1000 -0.032 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 16 1405 85 -0.051 0.012 1000 -1000 -0.064 -1000
IL6-mediated signaling events 16 1208 75 -0.17 0.036 1000 -1000 -0.068 -1000
IL1-mediated signaling events 15 978 62 -0.076 0.031 1000 -1000 -0.082 -1000
FOXM1 transcription factor network 15 807 51 -0.16 0.029 1000 -1000 -0.2 -1000
Cellular roles of Anthrax toxin 14 580 39 -0.074 0.012 1000 -1000 -0.02 -1000
Regulation of nuclear SMAD2/3 signaling 13 1820 136 -0.26 0.053 1000 -1000 -0.056 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 13 737 54 -0.14 0.024 1000 -1000 -0.079 -1000
a4b1 and a4b7 Integrin signaling 13 69 5 -0.013 0.001 1000 -1000 -0.019 -1000
Fc-epsilon receptor I signaling in mast cells 13 1353 97 -0.068 0.025 1000 -1000 -0.075 -1000
Paxillin-independent events mediated by a4b1 and a4b7 13 484 37 -0.049 0.018 1000 -1000 -0.037 -1000
S1P1 pathway 13 490 36 -0.15 0.012 1000 -1000 -0.05 -1000
IL27-mediated signaling events 13 683 51 -0.086 0.025 1000 -1000 -0.081 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 13 441 33 -0.16 0.036 1000 -1000 -0.032 -1000
Regulation of Androgen receptor activity 13 968 70 -0.15 0.024 1000 -1000 -0.058 -1000
ErbB4 signaling events 12 853 69 -0.11 0.033 1000 -1000 -0.08 -1000
Ceramide signaling pathway 12 983 76 -0.069 0.035 1000 -1000 -0.038 -1000
Signaling events mediated by HDAC Class III 12 483 40 -0.13 0.024 1000 -1000 -0.025 -1000
TRAIL signaling pathway 12 619 48 -0.041 0.025 1000 -1000 -0.062 -1000
Syndecan-3-mediated signaling events 12 428 35 -0.094 0.032 1000 -1000 -0.037 -1000
IL2 signaling events mediated by PI3K 12 738 58 -0.083 0.019 1000 -1000 -0.075 -1000
Ras signaling in the CD4+ TCR pathway 12 211 17 -0.026 0.019 1000 -1000 -0.038 -1000
PLK2 and PLK4 events 11 34 3 -0.003 0.003 1000 -1000 -0.014 -1000
JNK signaling in the CD4+ TCR pathway 11 195 17 -0.028 0.012 1000 -1000 -0.034 -1000
EPO signaling pathway 11 613 55 -0.038 0.025 1000 -1000 -0.08 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 11 496 45 -0.069 0.025 1000 -1000 -0.077 -1000
IL2 signaling events mediated by STAT5 11 260 22 -0.022 0.013 1000 -1000 -0.045 -1000
Regulation of Telomerase 11 1158 102 -0.18 0.035 1000 -1000 -0.1 -1000
Signaling mediated by p38-gamma and p38-delta 10 159 15 -0.012 0.014 1000 -1000 -0.026 -1000
Signaling events mediated by PRL 10 370 34 -0.12 0.02 1000 -1000 -0.03 -1000
Hedgehog signaling events mediated by Gli proteins 9 646 65 -0.24 0.041 1000 -1000 -0.054 -1000
S1P5 pathway 9 162 17 -0.029 0.012 1000 -1000 -0.027 -1000
TCGA08_rtk_signaling 9 252 26 -0.041 0.033 1000 -1000 -0.019 -1000
Stabilization and expansion of the E-cadherin adherens junction 9 723 74 -0.079 0.05 1000 -1000 -0.065 -1000
ErbB2/ErbB3 signaling events 8 567 65 -0.048 0.02 1000 -1000 -0.059 -1000
BARD1 signaling events 8 484 57 -0.014 0.039 1000 -1000 -0.049 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 8 701 83 -0.14 0.058 1000 -1000 -0.065 -1000
Class I PI3K signaling events 8 632 73 -0.071 0.03 1000 -1000 -0.052 -1000
S1P4 pathway 8 212 25 -0.029 0.018 1000 -1000 -0.031 -1000
p38 MAPK signaling pathway 8 363 44 -0.11 0.024 1000 -1000 -0.059 -1000
Aurora B signaling 8 551 67 -0.16 0.016 1000 -1000 -0.052 -1000
Sphingosine 1-phosphate (S1P) pathway 7 213 28 -0.029 0.03 1000 -1000 -0.029 -1000
ceramide signaling pathway 7 387 49 -0.069 0.018 1000 -1000 -0.041 -1000
IFN-gamma pathway 6 426 68 -0.11 0.035 1000 -1000 -0.086 -1000
HIF-2-alpha transcription factor network 6 297 43 -0.046 0.046 1000 -1000 -0.076 -1000
Paxillin-dependent events mediated by a4b1 6 243 36 -0.044 0.024 1000 -1000 -0.063 -1000
Regulation of p38-alpha and p38-beta 6 335 54 -0.071 0.032 1000 -1000 -0.055 -1000
Insulin Pathway 6 476 74 -0.11 0.032 1000 -1000 -0.077 -1000
Rapid glucocorticoid signaling 6 121 20 -0.01 0.012 1000 -1000 -0.012 -1000
Signaling events mediated by HDAC Class II 5 434 75 -0.059 0.033 1000 -1000 -0.034 -1000
mTOR signaling pathway 5 312 53 -0.022 0.016 1000 -1000 -0.055 -1000
S1P3 pathway 5 241 42 -0.013 0.021 1000 -1000 -0.025 -1000
PDGFR-beta signaling pathway 5 572 97 -0.056 0.034 1000 -1000 -0.075 -1000
E-cadherin signaling in keratinocytes 5 221 43 -0.018 0.024 1000 -1000 -0.039 -1000
E-cadherin signaling events 5 26 5 0.002 0.016 1000 -1000 -0.012 -1000
Canonical NF-kappaB pathway 4 185 39 -0.069 0.059 1000 -1000 -0.078 -1000
Aurora C signaling 4 32 7 -0.004 0.011 1000 -1000 -0.022 -1000
Signaling events mediated by HDAC Class I 4 485 104 -0.069 0.046 1000 -1000 -0.055 -1000
Atypical NF-kappaB pathway 4 141 31 -0.018 0.029 1000 -1000 -0.037 -1000
E-cadherin signaling in the nascent adherens junction 4 315 76 -0.023 0.041 1000 -1000 -0.073 -1000
Aurora A signaling 3 207 60 -0.03 0.031 1000 -1000 -0.033 -1000
Insulin-mediated glucose transport 3 105 32 -0.056 0.025 1000 -1000 -0.044 -1000
Class I PI3K signaling events mediated by Akt 3 265 68 -0.056 0.039 1000 -1000 -0.038 -1000
FoxO family signaling 3 197 64 -0.076 0.097 1000 -1000 -0.075 -1000
Signaling events mediated by VEGFR1 and VEGFR2 3 491 125 -0.068 0.047 1000 -1000 -0.085 -1000
VEGFR1 specific signals 3 191 56 -0.018 0.037 1000 -1000 -0.049 -1000
Circadian rhythm pathway 2 44 22 -0.012 0.039 1000 -1000 -0.041 -1000
Arf6 downstream pathway 2 100 43 -0.022 0.023 1000 -1000 -0.037 -1000
PLK1 signaling events 2 250 85 -0.017 0.03 1000 -1000 -0.037 -1000
Arf6 trafficking events 2 148 71 -0.035 0.035 1000 -1000 -0.056 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0 21 23 0.003 0.04 1000 -1000 -0.047 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 17 27 -0.001 0.029 1000 -1000 -0.041 -1000
Arf1 pathway 0 35 54 -0.004 0.024 1000 -1000 -0.026 -1000
Alternative NF-kappaB pathway 0 0 13 0 0.037 1000 -1000 -0.024 -1000
Total 2326 134980 7203 -14 -1000 131000 -131000 -7.4 -131000
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.18 0.26 -10000 0 -0.71 54 54
IHH -0.26 0.27 -10000 0 -0.52 184 184
SHH Np/Cholesterol/GAS1 -0.1 0.18 -10000 0 -0.31 138 138
LRPAP1 0.012 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.1 0.17 0.31 138 -10000 0 138
SMO/beta Arrestin2 -0.16 0.22 -10000 0 -0.52 58 58
SMO -0.17 0.23 -10000 0 -0.55 60 60
AKT1 -0.083 0.15 -10000 0 -0.58 18 18
ARRB2 0.012 0 -10000 0 -10000 0 0
BOC -0.019 0.12 -10000 0 -0.47 24 24
ADRBK1 0.011 0.024 -10000 0 -0.45 1 1
heart looping -0.17 0.23 -10000 0 -0.54 60 60
STIL -0.16 0.2 -10000 0 -0.51 65 65
DHH N/PTCH2 -0.026 0.13 -10000 0 -0.41 38 38
DHH N/PTCH1 -0.15 0.19 -10000 0 -0.51 45 45
PIK3CA 0.01 0.034 -10000 0 -0.45 2 2
DHH -0.024 0.13 -10000 0 -0.51 25 25
PTHLH -0.2 0.31 -10000 0 -0.84 49 49
determination of left/right symmetry -0.17 0.23 -10000 0 -0.54 60 60
PIK3R1 -0.018 0.12 -10000 0 -0.52 21 21
skeletal system development -0.2 0.31 -10000 0 -0.83 49 49
IHH N/Hhip -0.22 0.24 -10000 0 -0.39 215 215
DHH N/Hhip -0.088 0.18 -10000 0 -0.38 97 97
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.17 0.23 -10000 0 -0.54 60 60
pancreas development -0.099 0.21 -10000 0 -0.51 78 78
HHAT -0.004 0.093 -10000 0 -0.54 11 11
PI3K -0.006 0.093 -10000 0 -0.37 23 23
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.09 0.2 -10000 0 -0.49 75 75
somite specification -0.17 0.23 -10000 0 -0.54 60 60
SHH Np/Cholesterol/PTCH1 -0.17 0.21 -10000 0 -0.53 69 69
SHH Np/Cholesterol/PTCH2 -0.063 0.15 -10000 0 -0.3 97 97
SHH Np/Cholesterol/Megalin -0.16 0.19 -10000 0 -0.32 197 197
SHH -0.072 0.17 -10000 0 -0.37 85 85
catabolic process -0.15 0.2 -10000 0 -0.55 35 35
SMO/Vitamin D3 -0.18 0.23 -10000 0 -0.57 66 66
SHH Np/Cholesterol/Hhip -0.11 0.18 -10000 0 -0.31 147 147
LRP2 -0.19 0.25 -10000 0 -0.49 149 149
receptor-mediated endocytosis -0.24 0.24 -10000 0 -0.56 99 99
SHH Np/Cholesterol/BOC -0.065 0.15 -10000 0 -0.3 100 100
SHH Np/Cholesterol/CDO -0.058 0.15 -10000 0 -0.31 89 89
mesenchymal cell differentiation 0.11 0.17 0.31 147 -10000 0 147
mol:Vitamin D3 -0.17 0.22 -10000 0 -0.53 69 69
IHH N/PTCH2 -0.16 0.18 -10000 0 -0.37 132 132
CDON -0.005 0.092 -10000 0 -0.48 13 13
IHH N/PTCH1 -0.16 0.2 -10000 0 -0.56 35 35
Megalin/LRPAP1 -0.13 0.18 -10000 0 -0.34 149 149
PTCH2 -0.014 0.11 -10000 0 -0.5 19 19
SHH Np/Cholesterol -0.056 0.13 -10000 0 -0.29 85 85
PTCH1 -0.15 0.2 -10000 0 -0.55 35 35
HHIP -0.099 0.21 -10000 0 -0.51 78 78
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.41 0.47 -10000 0 -1.1 86 86
IL23A -0.43 0.49 -10000 0 -1.2 81 81
NF kappa B1 p50/RelA/I kappa B alpha -0.43 0.45 -10000 0 -1.1 88 88
positive regulation of T cell mediated cytotoxicity -0.46 0.54 -10000 0 -1.3 88 88
ITGA3 -0.41 0.46 -10000 0 -1.1 85 85
IL17F -0.28 0.3 -10000 0 -0.72 75 75
IL12B -0.017 0.063 -10000 0 -0.49 5 5
STAT1 (dimer) -0.44 0.51 -10000 0 -1.2 87 87
CD4 -0.4 0.46 -10000 0 -1.1 86 86
IL23 -0.42 0.47 -10000 0 -1.1 81 81
IL23R -0.06 0.082 -10000 0 -0.47 2 2
IL1B -0.43 0.5 -10000 0 -1.2 86 86
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.41 0.45 -10000 0 -1.1 81 81
TYK2 -0.003 0.019 -10000 0 -10000 0 0
STAT4 -0.006 0.096 -10000 0 -0.5 13 13
STAT3 0.012 0 -10000 0 -10000 0 0
IL18RAP -0.036 0.15 -10000 0 -0.51 34 34
IL12RB1 -0.039 0.14 -10000 0 -0.53 26 26
PIK3CA 0.01 0.034 -10000 0 -0.45 2 2
IL12Rbeta1/TYK2 -0.029 0.1 -10000 0 -0.39 26 26
IL23R/JAK2 -0.078 0.11 -10000 0 -0.46 7 7
positive regulation of chronic inflammatory response -0.46 0.54 -10000 0 -1.3 88 88
natural killer cell activation 0.006 0.007 0.042 3 -10000 0 3
JAK2 -0.016 0.09 -10000 0 -0.56 9 9
PIK3R1 -0.018 0.12 -10000 0 -0.52 21 21
NFKB1 0.01 0.003 -10000 0 -10000 0 0
RELA 0.01 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.4 0.44 -10000 0 -1.1 81 81
ALOX12B -0.42 0.48 -10000 0 -1.1 90 90
CXCL1 -0.51 0.54 -10000 0 -1.2 107 107
T cell proliferation -0.46 0.54 -10000 0 -1.3 88 88
NFKBIA 0.01 0.003 -10000 0 -10000 0 0
IL17A -0.21 0.24 -10000 0 -0.57 63 63
PI3K -0.45 0.46 -10000 0 -1.2 88 88
IFNG -0.023 0.038 -10000 0 -0.11 30 30
STAT3 (dimer) -0.42 0.43 -10000 0 -1.1 88 88
IL18R1 -0.019 0.12 -10000 0 -0.51 22 22
IL23/IL23R/JAK2/TYK2/SOCS3 -0.24 0.28 -10000 0 -0.68 56 56
IL18/IL18R -0.037 0.15 -10000 0 -0.36 61 61
macrophage activation -0.023 0.017 -10000 0 -0.044 67 67
TNF -0.45 0.52 -10000 0 -1.2 95 95
STAT3/STAT4 -0.44 0.46 -10000 0 -1.1 90 90
STAT4 (dimer) -0.44 0.52 -10000 0 -1.2 87 87
IL18 -0.014 0.12 -10000 0 -0.52 18 18
IL19 -0.49 0.53 -10000 0 -1.2 107 107
STAT5A (dimer) -0.43 0.51 -10000 0 -1.2 86 86
STAT1 0.01 0.034 -10000 0 -0.45 2 2
SOCS3 -0.009 0.1 -10000 0 -0.52 15 15
CXCL9 -0.49 0.54 -10000 0 -1.2 108 108
MPO -0.43 0.49 -10000 0 -1.2 90 90
positive regulation of humoral immune response -0.46 0.54 -10000 0 -1.3 88 88
IL23/IL23R/JAK2/TYK2 -0.48 0.6 -10000 0 -1.4 86 86
IL6 -0.43 0.48 -10000 0 -1.2 85 85
STAT5A 0.011 0.024 -10000 0 -0.45 1 1
IL2 -0.01 0.091 -10000 0 -0.45 15 15
positive regulation of tyrosine phosphorylation of STAT protein 0.006 0.007 0.042 3 -10000 0 3
CD3E -0.43 0.5 -10000 0 -1.2 91 91
keratinocyte proliferation -0.46 0.54 -10000 0 -1.3 88 88
NOS2 -0.44 0.49 -10000 0 -1.1 97 97
TCGA08_retinoblastoma

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
CDKN2B -0.01 0.11 -10000 0 -0.49 17 17
CDKN2C -0.012 0.12 -10000 0 -0.45 25 25
CDKN2A -0.1 0.21 -10000 0 -0.46 91 91
CCND2 0.038 0.082 0.2 57 -0.14 2 59
RB1 -0.037 0.097 -10000 0 -0.23 58 58
CDK4 0.051 0.095 0.24 57 -10000 0 57
CDK6 0.042 0.094 0.22 57 -0.16 8 65
G1/S progression 0.037 0.097 0.23 58 -10000 0 58
Ephrin A reverse signaling

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
MAPKKK cascade -0.051 0.13 -9999 0 -0.31 72 72
EFNA5 -0.077 0.2 -9999 0 -0.53 61 61
FYN -0.04 0.12 -9999 0 -0.28 72 72
neuron projection morphogenesis -0.051 0.13 -9999 0 -0.31 72 72
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.051 0.13 -9999 0 -0.31 72 72
EPHA5 -0.008 0.078 -9999 0 -0.45 11 11
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.26 0.37 -9999 0 -0.9 63 63
PCK1 -0.4 0.48 -9999 0 -1 112 112
HNF4A -0.43 0.52 -9999 0 -1.1 119 119
KCNJ11 -0.27 0.4 -9999 0 -0.97 62 62
AKT1 -0.09 0.14 -9999 0 -0.44 16 16
response to starvation -0.01 0.026 -9999 0 -10000 0 0
DLK1 -0.28 0.4 -9999 0 -0.98 64 64
NKX2-1 -0.055 0.24 -9999 0 -0.66 15 15
ACADM -0.26 0.38 -9999 0 -0.92 67 67
TAT -0.2 0.23 -9999 0 -0.74 18 18
CEBPB 0.012 0.007 -9999 0 -10000 0 0
CEBPA -0.025 0.14 -9999 0 -0.52 26 26
TTR -0.36 0.33 -9999 0 -0.86 88 88
PKLR -0.27 0.38 -9999 0 -0.91 67 67
APOA1 -0.43 0.54 -9999 0 -1.2 87 87
CPT1C -0.28 0.4 -9999 0 -0.97 68 68
ALAS1 -0.1 0.17 -9999 0 -0.58 3 3
TFRC -0.26 0.29 -9999 0 -0.8 40 40
FOXF1 -0.003 0.098 -9999 0 -0.47 15 15
NF1 0.014 0.05 -9999 0 -0.54 3 3
HNF1A (dimer) -0.11 0.22 -9999 0 -0.54 74 74
CPT1A -0.26 0.37 -9999 0 -0.88 67 67
HMGCS1 -0.25 0.36 -9999 0 -0.9 60 60
NR3C1 -0.005 0.095 -9999 0 -0.52 11 11
CPT1B -0.27 0.39 -9999 0 -0.94 67 67
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 -0.003 0.048 -9999 0 -10000 0 0
GCK -0.29 0.41 -9999 0 -0.97 74 74
CREB1 -0.021 0.062 -9999 0 -10000 0 0
IGFBP1 -0.14 0.2 -9999 0 -0.64 22 22
PDX1 -0.29 0.42 -9999 0 -1.1 61 61
UCP2 -0.26 0.38 -9999 0 -0.96 57 57
ALDOB -0.27 0.38 -9999 0 -0.95 59 59
AFP -0.2 0.21 -9999 0 -0.59 46 46
BDH1 -0.26 0.37 -9999 0 -0.9 65 65
HADH -0.25 0.38 -9999 0 -0.93 59 59
F2 -0.37 0.46 -9999 0 -1.1 76 76
HNF1A -0.11 0.22 -9999 0 -0.54 74 74
G6PC -0.16 0.21 -9999 0 -0.66 32 32
SLC2A2 -0.25 0.33 -9999 0 -0.78 72 72
INS -0.002 0.036 -9999 0 -0.46 1 1
FOXA1 -0.21 0.26 -9999 0 -0.52 148 148
FOXA3 -0.18 0.25 -9999 0 -0.54 109 109
FOXA2 -0.3 0.43 -9999 0 -1 66 66
ABCC8 -0.28 0.4 -9999 0 -0.94 70 70
ALB -0.25 0.3 -9999 0 -0.74 74 74
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.19 0.38 -9999 0 -0.99 56 56
MKNK1 0.012 0 -9999 0 -10000 0 0
MAPK14 -0.061 0.13 -9999 0 -0.29 70 70
ATF2/c-Jun -0.034 0.12 -9999 0 -0.49 6 6
MAPK11 -0.065 0.14 -9999 0 -0.46 11 11
MITF -0.07 0.16 -9999 0 -0.37 66 66
MAPKAPK5 -0.065 0.16 -9999 0 -0.35 72 72
KRT8 -0.067 0.16 -9999 0 -0.36 72 72
MAPKAPK3 0.012 0 -9999 0 -10000 0 0
MAPKAPK2 0.012 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.092 0.2 -9999 0 -0.44 72 72
CEBPB -0.065 0.16 -9999 0 -0.36 63 63
SLC9A1 -0.065 0.16 -9999 0 -0.35 72 72
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.06 0.16 -9999 0 -0.34 72 72
p38alpha-beta/MNK1 -0.062 0.16 -9999 0 -0.35 71 71
JUN -0.033 0.12 -9999 0 -0.49 6 6
PPARGC1A -0.15 0.24 -9999 0 -0.47 98 98
USF1 -0.065 0.16 -9999 0 -0.35 72 72
RAB5/GDP/GDI1 -0.043 0.11 -9999 0 -0.39 9 9
NOS2 -0.12 0.29 -9999 0 -0.88 33 33
DDIT3 -0.065 0.16 -9999 0 -0.35 72 72
RAB5A 0.012 0 -9999 0 -10000 0 0
HSPB1 -0.053 0.14 -9999 0 -0.42 15 15
p38alpha-beta/HBP1 -0.062 0.16 -9999 0 -0.35 71 71
CREB1 -0.068 0.17 -9999 0 -0.38 63 63
RAB5/GDP 0.009 0 -9999 0 -10000 0 0
EIF4E -0.052 0.14 -9999 0 -0.51 10 10
RPS6KA4 -0.065 0.16 -9999 0 -0.35 72 72
PLA2G4A -0.1 0.2 -9999 0 -0.49 50 50
GDI1 -0.065 0.16 -9999 0 -0.36 62 62
TP53 -0.094 0.2 -9999 0 -0.45 74 74
RPS6KA5 -0.073 0.17 -9999 0 -0.36 76 76
ESR1 -0.12 0.23 -9999 0 -0.47 83 83
HBP1 0.012 0 -9999 0 -10000 0 0
MEF2C -0.067 0.16 -9999 0 -0.35 75 75
MEF2A -0.065 0.16 -9999 0 -0.35 72 72
EIF4EBP1 -0.069 0.17 -9999 0 -0.38 63 63
KRT19 -0.085 0.18 -9999 0 -0.36 88 88
ELK4 -0.065 0.16 -9999 0 -0.35 72 72
ATF6 -0.065 0.16 -9999 0 -0.35 72 72
ATF1 -0.068 0.17 -9999 0 -0.38 63 63
p38alpha-beta/MAPKAPK2 -0.062 0.16 -9999 0 -0.35 71 71
p38alpha-beta/MAPKAPK3 -0.062 0.16 -9999 0 -0.35 71 71
Wnt signaling

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
Noncanonical Wnts/FZD -0.12 0.2 -9999 0 -0.45 62 62
FZD6 0.008 0.049 -9999 0 -0.54 3 3
WNT6 -0.12 0.22 -9999 0 -0.48 98 98
WNT4 -0.054 0.17 -9999 0 -0.5 48 48
FZD3 0.012 0 -9999 0 -10000 0 0
WNT5A -0.014 0.12 -9999 0 -0.52 18 18
WNT11 -0.13 0.23 -9999 0 -0.5 104 104
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.49 0.48 -10000 0 -1.2 79 79
STAT6 (cleaved dimer) -0.53 0.48 -10000 0 -1.2 109 109
IGHG1 -0.17 0.15 -10000 0 -0.42 2 2
IGHG3 -0.47 0.46 -10000 0 -1.1 101 101
AKT1 -0.26 0.29 -10000 0 -0.81 45 45
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.21 0.29 -10000 0 -0.88 35 35
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.27 0.3 -10000 0 -0.83 46 46
THY1 -0.49 0.48 -10000 0 -1.2 81 81
MYB -0.012 0.11 -10000 0 -0.54 16 16
HMGA1 0.008 0.044 -10000 0 -0.48 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.33 0.36 -10000 0 -0.87 68 68
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.27 0.31 -10000 0 -0.88 41 41
SP1 0.017 0.014 -10000 0 -10000 0 0
INPP5D -0.002 0.088 -10000 0 -0.53 10 10
SOCS5 0.027 0.015 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.5 0.51 -10000 0 -1.2 94 94
SOCS1 -0.32 0.32 -10000 0 -0.77 73 73
SOCS3 -0.29 0.33 -10000 0 -0.92 49 49
FCER2 -0.41 0.4 -10000 0 -1 73 73
PARP14 0.006 0.057 -10000 0 -0.54 4 4
CCL17 -0.54 0.53 -10000 0 -1.3 93 93
GRB2 0.012 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.21 0.24 -10000 0 -0.77 31 31
T cell proliferation -0.5 0.51 -10000 0 -1.2 87 87
IL4R/JAK1 -0.49 0.49 -10000 0 -1.2 82 82
EGR2 -0.5 0.5 -10000 0 -1.3 80 80
JAK2 -0.028 0.09 -10000 0 -0.57 9 9
JAK3 0.003 0.075 -10000 0 -0.49 8 8
PIK3R1 -0.018 0.12 -10000 0 -0.52 21 21
JAK1 -0.003 0.063 -10000 0 -0.54 5 5
COL1A2 -0.18 0.25 -10000 0 -1.1 15 15
CCL26 -0.49 0.48 -10000 0 -1.2 77 77
IL4R -0.52 0.52 -10000 0 -1.3 80 80
PTPN6 0.02 0.05 -10000 0 -0.52 3 3
IL13RA2 -0.55 0.54 -10000 0 -1.3 90 90
IL13RA1 -0.015 0.027 -10000 0 -10000 0 0
IRF4 -0.26 0.44 -10000 0 -1 72 72
ARG1 -0.13 0.15 -10000 0 -0.74 8 8
CBL -0.31 0.33 -10000 0 -0.83 63 63
GTF3A 0.018 0.005 -10000 0 -10000 0 0
PIK3CA 0.01 0.034 -10000 0 -0.45 2 2
IL13RA1/JAK2 -0.029 0.073 -10000 0 -0.42 9 9
IRF4/BCL6 -0.24 0.41 -10000 0 -1 67 67
CD40LG -0.038 0.16 -10000 0 -0.52 35 35
MAPK14 -0.31 0.34 -10000 0 -0.88 59 59
mitosis -0.25 0.27 -10000 0 -0.76 45 45
STAT6 -0.57 0.63 -10000 0 -1.4 94 94
SPI1 0.001 0.085 -10000 0 -0.51 10 10
RPS6KB1 -0.24 0.26 -10000 0 -0.74 41 41
STAT6 (dimer) -0.57 0.63 -10000 0 -1.4 94 94
STAT6 (dimer)/PARP14 -0.52 0.53 -10000 0 -1.3 95 95
mast cell activation 0.012 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.26 0.32 -10000 0 -0.91 40 40
FRAP1 -0.26 0.29 -10000 0 -0.81 45 45
LTA -0.52 0.52 -10000 0 -1.3 83 83
FES 0.008 0.049 -10000 0 -0.54 3 3
T-helper 1 cell differentiation 0.55 0.56 1.3 96 -10000 0 96
CCL11 -0.52 0.51 -10000 0 -1.2 97 97
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.26 0.31 -10000 0 -0.88 40 40
IL2RG -0.02 0.13 -10000 0 -0.5 25 25
IL10 -0.53 0.52 -10000 0 -1.3 89 89
IRS1 -0.011 0.11 -10000 0 -0.53 16 16
IRS2 -0.035 0.14 -10000 0 -0.47 36 36
IL4 -0.12 0.11 -10000 0 -0.53 1 1
IL5 -0.49 0.48 -10000 0 -1.2 77 77
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.4 0.39 -10000 0 -0.94 81 81
COL1A1 -0.18 0.24 -10000 0 -1.2 11 11
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.5 0.5 -10000 0 -1.3 78 78
IL2R gamma/JAK3 -0.015 0.12 -10000 0 -0.39 30 30
TFF3 -0.7 0.65 -10000 0 -1.4 138 138
ALOX15 -0.58 0.56 -10000 0 -1.3 102 102
MYBL1 0.007 0.055 -10000 0 -0.52 4 4
T-helper 2 cell differentiation -0.42 0.4 -10000 0 -0.98 90 90
SHC1 0.012 0 -10000 0 -10000 0 0
CEBPB 0.015 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.26 0.3 -10000 0 -0.79 48 48
mol:PI-3-4-5-P3 -0.26 0.29 -10000 0 -0.81 45 45
PI3K -0.28 0.32 -10000 0 -0.89 45 45
DOK2 0 0.078 -10000 0 -0.49 9 9
ETS1 0.024 0.03 -10000 0 -0.5 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.2 0.23 -10000 0 -0.72 30 30
ITGB3 -0.54 0.53 -10000 0 -1.3 97 97
PIGR -0.7 0.66 -10000 0 -1.5 136 136
IGHE 0.041 0.041 0.27 3 -10000 0 3
MAPKKK cascade -0.19 0.22 -10000 0 -0.71 30 30
BCL6 0.011 0.029 -10000 0 -0.54 1 1
OPRM1 -0.5 0.48 -10000 0 -1.2 79 79
RETNLB -0.49 0.48 -10000 0 -1.2 79 79
SELP -0.54 0.56 -10000 0 -1.4 86 86
AICDA -0.48 0.47 -10000 0 -1.2 79 79
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.01 0.034 -9999 0 -0.45 2 2
CCL5 -0.034 0.15 -9999 0 -0.49 34 34
SDCBP 0.012 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.14 0.18 -9999 0 -0.43 67 67
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 -0.13 0.18 -9999 0 -0.43 63 63
Syndecan-1/Syntenin -0.12 0.17 -9999 0 -0.42 61 61
MAPK3 -0.1 0.16 -9999 0 -0.44 37 37
HGF/MET -0.056 0.16 -9999 0 -0.38 69 69
TGFB1/TGF beta receptor Type II 0.01 0.034 -9999 0 -0.45 2 2
BSG 0.012 0 -9999 0 -10000 0 0
keratinocyte migration -0.13 0.18 -9999 0 -0.42 63 63
Syndecan-1/RANTES -0.15 0.19 -9999 0 -0.44 79 79
Syndecan-1/CD147 -0.11 0.17 -9999 0 -0.4 61 61
Syndecan-1/Syntenin/PIP2 -0.12 0.17 -9999 0 -0.41 61 61
LAMA5 0.008 0.047 -9999 0 -0.51 3 3
positive regulation of cell-cell adhesion -0.12 0.16 -9999 0 -0.4 61 61
MMP7 -0.17 0.25 -9999 0 -0.52 127 127
HGF -0.043 0.16 -9999 0 -0.5 40 40
Syndecan-1/CASK -0.13 0.17 -9999 0 -0.41 67 67
Syndecan-1/HGF/MET -0.16 0.21 -9999 0 -0.46 91 91
regulation of cell adhesion -0.096 0.16 -9999 0 -0.43 35 35
HPSE -0.014 0.11 -9999 0 -0.49 19 19
positive regulation of cell migration -0.14 0.18 -9999 0 -0.43 67 67
SDC1 -0.14 0.18 -9999 0 -0.43 67 67
Syndecan-1/Collagen -0.14 0.18 -9999 0 -0.43 67 67
PPIB 0.012 0 -9999 0 -10000 0 0
MET -0.035 0.15 -9999 0 -0.52 33 33
PRKACA 0.012 0 -9999 0 -10000 0 0
MMP9 -0.076 0.2 -9999 0 -0.5 64 64
MAPK1 -0.1 0.16 -9999 0 -0.44 36 36
homophilic cell adhesion -0.14 0.18 -9999 0 -0.42 67 67
MMP1 -0.1 0.21 -9999 0 -0.5 85 85
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.009 0.1 -10000 0 -0.31 38 38
fibroblast growth factor receptor signaling pathway -0.01 0.1 -10000 0 -0.31 38 38
LAMA1 -0.14 0.24 -10000 0 -0.52 102 102
PRNP -0.007 0.099 -10000 0 -0.52 13 13
GPC1/SLIT2 -0.057 0.15 -10000 0 -0.36 74 74
SMAD2 0.023 0.04 -10000 0 -0.28 5 5
GPC1/PrPc/Cu2+ 0.001 0.073 -10000 0 -0.33 17 17
GPC1/Laminin alpha1 -0.094 0.18 -10000 0 -0.38 105 105
TDGF1 -0.12 0.23 -10000 0 -0.5 98 98
CRIPTO/GPC1 -0.085 0.17 -10000 0 -0.36 100 100
APP/GPC1 0.013 0.043 -10000 0 -0.36 5 5
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.065 0.15 -10000 0 -0.3 101 101
FLT1 0.008 0.044 -10000 0 -0.48 3 3
GPC1/TGFB/TGFBR1/TGFBR2 0.019 0.045 -10000 0 -0.3 7 7
SERPINC1 0.001 0.063 -10000 0 -0.45 7 7
FYN -0.065 0.15 -10000 0 -0.3 101 101
FGR -0.074 0.16 -10000 0 -0.31 108 108
positive regulation of MAPKKK cascade -0.09 0.19 -10000 0 -0.44 68 68
SLIT2 -0.085 0.2 -10000 0 -0.5 70 70
GPC1/NRG -0.027 0.12 -10000 0 -0.36 44 44
NRG1 -0.044 0.16 -10000 0 -0.49 41 41
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.016 0.052 -10000 0 -0.28 11 11
LYN -0.067 0.15 -10000 0 -0.31 101 101
mol:Spermine 0.005 0.043 -10000 0 -0.36 5 5
cell growth -0.01 0.1 -10000 0 -0.31 38 38
BMP signaling pathway -0.005 0.06 0.5 5 -10000 0 5
SRC -0.066 0.15 -10000 0 -0.3 102 102
TGFBR1 0.012 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.051 0.16 -10000 0 -0.47 47 47
GPC1 0.005 0.06 -10000 0 -0.5 5 5
TGFBR1 (dimer) 0.012 0 -10000 0 -10000 0 0
VEGFA 0.009 0.042 -10000 0 -0.45 3 3
BLK -0.11 0.18 -10000 0 -0.33 142 142
HCK -0.079 0.16 -10000 0 -0.31 112 112
FGF2 -0.027 0.14 -10000 0 -0.5 28 28
FGFR1 0.002 0.073 -10000 0 -0.53 7 7
VEGFR1 homodimer 0.008 0.044 -10000 0 -0.48 3 3
TGFBR2 0.009 0.04 -10000 0 -0.54 2 2
cell death 0.013 0.043 -10000 0 -0.36 5 5
ATIII/GPC1 0.005 0.066 -10000 0 -0.36 11 11
PLA2G2A/GPC1 -0.033 0.12 -10000 0 -0.33 52 52
LCK -0.081 0.17 -10000 0 -0.34 108 108
neuron differentiation -0.027 0.12 -10000 0 -0.36 44 44
PrPc/Cu2+ -0.005 0.072 -10000 0 -0.38 13 13
APP 0.012 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.009 0.04 -10000 0 -0.54 2 2
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.15 0.2 -9999 0 -0.52 56 56
SMAD6-7/SMURF1 0.023 0.027 -9999 0 -0.28 3 3
NOG -0.084 0.2 -9999 0 -0.51 68 68
SMAD9 -0.056 0.17 -9999 0 -0.6 25 25
SMAD4 0.011 0.029 -9999 0 -0.54 1 1
SMAD5 -0.047 0.14 -9999 0 -0.42 29 29
BMP7/USAG1 -0.21 0.23 -9999 0 -0.41 199 199
SMAD5/SKI -0.039 0.13 -9999 0 -0.42 23 23
SMAD1 0.027 0.031 -9999 0 -10000 0 0
BMP2 -0.071 0.19 -9999 0 -0.48 62 62
SMAD1/SMAD1/SMAD4 -0.003 0.025 -9999 0 -10000 0 0
BMPR1A 0.011 0.029 -9999 0 -0.54 1 1
BMPR1B -0.055 0.18 -9999 0 -0.53 46 46
BMPR1A-1B/BAMBI -0.073 0.17 -9999 0 -0.34 101 101
AHSG -0.007 0.082 -9999 0 -0.45 12 12
CER1 -0.004 0.062 -9999 0 -0.45 7 7
BMP2-4/CER1 -0.089 0.17 -9999 0 -0.31 122 122
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.059 0.15 -9999 0 -0.41 36 36
BMP2-4 (homodimer) -0.1 0.19 -9999 0 -0.37 117 117
RGMB 0.012 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.028 0.13 -9999 0 -0.32 52 52
RGMA -0.048 0.17 -9999 0 -0.52 42 42
SMURF1 0.011 0.024 -9999 0 -0.45 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.066 0.15 -9999 0 -0.42 38 38
BMP2-4/USAG1 -0.17 0.21 -9999 0 -0.35 194 194
SMAD6/SMURF1/SMAD5 -0.039 0.13 -9999 0 -0.43 23 23
SOSTDC1 -0.14 0.24 -9999 0 -0.5 110 110
BMP7/BMPR2/BMPR1A-1B -0.1 0.18 -9999 0 -0.35 93 93
SKI 0.012 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.024 0.13 -9999 0 -0.48 27 27
HFE2 -0.003 0.058 -9999 0 -0.45 6 6
ZFYVE16 0.012 0 -9999 0 -10000 0 0
MAP3K7 0.012 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.11 0.19 -9999 0 -0.33 140 140
SMAD5/SMAD5/SMAD4 -0.039 0.13 -9999 0 -0.44 23 23
MAPK1 0.011 0.024 -9999 0 -0.45 1 1
TAK1/TAB family -0.069 0.12 -9999 0 -0.43 24 24
BMP7 (homodimer) -0.16 0.24 -9999 0 -0.49 130 130
NUP214 0.012 0 -9999 0 -10000 0 0
BMP6/FETUA -0.021 0.11 -9999 0 -0.34 38 38
SMAD1/SKI 0.033 0.031 -9999 0 -10000 0 0
SMAD6 0.01 0.037 -9999 0 -0.5 2 2
CTDSP2 0.012 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.091 0.17 -9999 0 -0.31 126 126
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.075 0.19 -9999 0 -0.5 63 63
BMPR2 (homodimer) 0.012 0 -9999 0 -10000 0 0
GADD34/PP1CA 0.024 0.021 -9999 0 -0.26 2 2
BMPR1A-1B (homodimer) -0.032 0.13 -9999 0 -0.38 47 47
CHRDL1 -0.13 0.23 -9999 0 -0.49 102 102
ENDOFIN/SMAD1 0.033 0.031 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0.04 0.037 -9999 0 -10000 0 0
SMAD6/SMURF1 0.011 0.024 -9999 0 -0.45 1 1
BAMBI -0.079 0.2 -9999 0 -0.5 66 66
SMURF2 0.012 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.16 0.21 -9999 0 -0.34 189 189
BMP2-4/GREM1 -0.13 0.2 -9999 0 -0.33 161 161
SMAD7 0.012 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.047 0.16 -9999 0 -0.56 26 26
SMAD1/SMAD6 0.032 0.033 -9999 0 -10000 0 0
TAK1/SMAD6 0.017 0.017 -9999 0 -0.31 1 1
BMP7 -0.16 0.24 -9999 0 -0.49 130 130
BMP6 -0.024 0.13 -9999 0 -0.48 27 27
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.056 0.14 -9999 0 -0.37 38 38
PPM1A 0.012 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.033 0.031 -9999 0 -10000 0 0
SMAD7/SMURF1 0.017 0.017 -9999 0 -0.31 1 1
CTDSPL 0.011 0.029 -9999 0 -0.54 1 1
PPP1CA 0.012 0 -9999 0 -10000 0 0
XIAP 0.012 0 -9999 0 -10000 0 0
CTDSP1 0.012 0 -9999 0 -10000 0 0
PPP1R15A 0.01 0.034 -9999 0 -0.45 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.12 0.2 -9999 0 -0.47 63 63
CHRD -0.039 0.16 -9999 0 -0.5 37 37
BMPR2 0.012 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.075 0.16 -9999 0 -0.44 38 38
BMP4 -0.077 0.19 -9999 0 -0.47 69 69
FST -0.11 0.21 -9999 0 -0.48 88 88
BMP2-4/NOG -0.14 0.2 -9999 0 -0.34 164 164
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.093 0.17 -9999 0 -0.5 25 25
p75(NTR)-mediated 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
Sortilin/TRAF6 0.018 0 -10000 0 -10000 0 0
Necdin/E2F1 -0.009 0.097 -10000 0 -0.35 27 27
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.047 0.14 -10000 0 -0.31 61 61
NGF (dimer)/p75(NTR)/BEX1 -0.15 0.21 -10000 0 -0.36 168 168
NT-4/5 (dimer)/p75(NTR) -0.1 0.18 -10000 0 -0.37 116 116
IKBKB 0.012 0 -10000 0 -10000 0 0
AKT1 -0.063 0.15 -10000 0 -0.38 32 32
IKBKG 0.012 0 -10000 0 -10000 0 0
BDNF -0.087 0.2 -10000 0 -0.48 74 74
MGDIs/NGR/p75(NTR)/LINGO1 -0.072 0.17 -10000 0 -0.34 99 99
FURIN 0.011 0.029 -10000 0 -0.54 1 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.092 0.17 -10000 0 -0.32 125 125
LINGO1 -0.035 0.14 -10000 0 -0.47 36 36
Sortilin/TRAF6/NRIF -0.004 0.028 -10000 0 -10000 0 0
proBDNF (dimer) -0.087 0.2 -10000 0 -0.48 74 74
NTRK1 -0.043 0.16 -10000 0 -0.5 40 40
RTN4R -0.008 0.1 -10000 0 -0.49 15 15
neuron apoptosis -0.074 0.16 -10000 0 -0.43 29 29
IRAK1 0.012 0 -10000 0 -10000 0 0
SHC1 -0.068 0.16 -10000 0 -0.32 99 99
ARHGDIA 0.012 0 -10000 0 -10000 0 0
RhoA/GTP 0.009 0 -10000 0 -10000 0 0
Gamma Secretase 0.032 0.037 -10000 0 -0.26 5 5
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.063 0.16 -10000 0 -0.34 61 61
MAGEH1 -0.007 0.096 -10000 0 -0.49 14 14
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.068 0.16 -10000 0 -0.35 67 67
Mammalian IAPs/DIABLO -0.003 0.099 -10000 0 -0.3 28 28
proNGF (dimer) -0.045 0.16 -10000 0 -0.5 41 41
MAGED1 0.002 0.075 -10000 0 -0.54 7 7
APP 0.012 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.068 0.18 -10000 0 -0.49 57 57
ZNF274 0.011 0.024 -10000 0 -0.45 1 1
RhoA/GDP/RHOGDI -0.05 0.14 -10000 0 -0.31 56 56
NGF -0.045 0.16 -10000 0 -0.5 41 41
cell cycle arrest -0.043 0.15 -10000 0 -0.27 83 83
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.03 0.11 -10000 0 -0.33 13 13
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.081 0.16 -10000 0 -0.31 116 116
NCSTN 0.012 0 -10000 0 -10000 0 0
mol:GTP -0.072 0.16 -10000 0 -0.33 102 102
PSENEN 0.011 0.029 -10000 0 -0.54 1 1
mol:ceramide -0.055 0.14 -10000 0 -0.33 57 57
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.018 0.097 -10000 0 -0.38 6 6
p75(NTR)/beta APP -0.049 0.14 -10000 0 -0.34 69 69
BEX1 -0.13 0.23 -10000 0 -0.49 103 103
mol:GDP -0.076 0.16 -10000 0 -0.32 99 99
NGF (dimer) -0.15 0.19 -10000 0 -0.36 127 127
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.057 0.16 -10000 0 -0.37 51 51
PIK3R1 -0.018 0.12 -10000 0 -0.52 21 21
RAC1/GTP -0.057 0.14 -10000 0 -0.27 99 99
MYD88 0.012 0 -10000 0 -10000 0 0
CHUK 0.012 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.072 0.16 -10000 0 -0.33 102 102
RHOB 0.011 0.029 -10000 0 -0.54 1 1
RHOA 0.012 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.011 0.051 -10000 0 -0.33 8 8
NT3 (dimer) -0.067 0.18 -10000 0 -0.48 59 59
TP53 -0.07 0.15 -10000 0 -0.45 19 19
PRDM4 -0.055 0.14 -10000 0 -0.33 56 56
BDNF (dimer) -0.25 0.24 -10000 0 -0.47 162 162
PIK3CA 0.01 0.034 -10000 0 -0.45 2 2
SORT1 0.012 0 -10000 0 -10000 0 0
activation of caspase activity -0.049 0.14 -10000 0 -0.3 61 61
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.053 0.15 -10000 0 -0.33 56 56
RHOC 0.012 0 -10000 0 -10000 0 0
XIAP 0.012 0 -10000 0 -10000 0 0
MAPK10 -0.075 0.17 -10000 0 -0.43 38 38
DIABLO 0.012 0 -10000 0 -10000 0 0
SMPD2 -0.056 0.14 -10000 0 -0.33 57 57
APH1B 0.006 0.057 -10000 0 -0.54 4 4
APH1A 0.011 0.024 -10000 0 -0.45 1 1
proNGF (dimer)/p75(NTR)/Sortilin -0.067 0.16 -10000 0 -0.32 99 99
PSEN1 0.012 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.017 0.017 -10000 0 -0.31 1 1
NT3 (dimer)/p75(NTR) -0.1 0.19 -10000 0 -0.38 112 112
MAPK8 -0.056 0.14 -10000 0 -0.42 20 20
MAPK9 -0.054 0.14 -10000 0 -0.42 19 19
APAF1 0.012 0 -10000 0 -10000 0 0
NTF3 -0.067 0.18 -10000 0 -0.48 59 59
NTF4 -0.068 0.18 -10000 0 -0.49 57 57
NDN -0.016 0.12 -10000 0 -0.51 20 20
RAC1/GDP 0.009 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.068 0.12 -10000 0 -0.44 14 14
p75 CTF/Sortilin/TRAF6/NRIF 0.029 0.027 -10000 0 -0.28 2 2
RhoA-B-C/GTP -0.072 0.16 -10000 0 -0.32 102 102
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.065 0.15 -10000 0 -0.44 21 21
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.075 0.16 -10000 0 -0.35 58 58
PRKACB 0.003 0.07 -10000 0 -0.54 6 6
proBDNF (dimer)/p75 ECD -0.055 0.15 -10000 0 -0.34 75 75
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.047 0.16 -10000 0 -0.51 42 42
BIRC2 0.009 0.04 -10000 0 -0.54 2 2
neuron projection morphogenesis -0.049 0.16 0.18 33 -0.35 52 85
BAD -0.057 0.15 -10000 0 -0.41 25 25
RIPK2 0.01 0.037 -10000 0 -0.5 2 2
NGFR -0.081 0.2 -10000 0 -0.49 69 69
CYCS -0.052 0.14 -10000 0 -0.3 63 63
ADAM17 0.009 0.04 -10000 0 -0.54 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.054 0.15 -10000 0 -0.33 57 57
BCL2L11 -0.057 0.15 -10000 0 -0.41 25 25
BDNF (dimer)/p75(NTR) -0.12 0.2 -10000 0 -0.38 125 125
PI3K -0.071 0.16 -10000 0 -0.34 72 72
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.053 0.15 -10000 0 -0.33 57 57
NDNL2 0.011 0.024 -10000 0 -0.45 1 1
YWHAE 0.012 0 -10000 0 -10000 0 0
PRKCI 0.008 0.044 -10000 0 -0.48 3 3
NGF (dimer)/p75(NTR) -0.089 0.18 -10000 0 -0.38 99 99
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.058 0.15 -10000 0 -0.33 63 63
TRAF6 0.012 0 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCZ 0.009 0.04 -10000 0 -0.54 2 2
PLG -0.079 0.19 -10000 0 -0.47 69 69
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.093 0.17 -10000 0 -0.42 50 50
SQSTM1 0.011 0.024 -10000 0 -0.45 1 1
NGFRAP1 0.005 0.064 -10000 0 -0.54 5 5
CASP3 -0.052 0.14 -10000 0 -0.38 25 25
E2F1 0.003 0.067 -10000 0 -0.48 7 7
CASP9 0.011 0.024 -10000 0 -0.45 1 1
IKK complex -0.067 0.12 -10000 0 -0.42 21 21
NGF (dimer)/TRKA -0.062 0.16 -10000 0 -0.38 74 74
MMP7 -0.17 0.25 -10000 0 -0.52 127 127
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.044 0.14 -10000 0 -0.3 56 56
MMP3 -0.12 0.22 -10000 0 -0.49 100 100
APAF-1/Caspase 9 -0.075 0.12 -10000 0 -0.4 26 26
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.11 0.2 -10000 0 -0.54 56 56
FYN -0.1 0.3 -10000 0 -0.7 59 59
LAT/GRAP2/SLP76 -0.11 0.23 -10000 0 -0.59 61 61
IKBKB 0.012 0 -10000 0 -10000 0 0
AKT1 -0.056 0.19 -10000 0 -0.45 59 59
B2M 0.003 0.067 -10000 0 -0.52 6 6
IKBKG -0.029 0.051 -10000 0 -0.15 33 33
MAP3K8 0.006 0.057 -10000 0 -0.54 4 4
mol:Ca2+ -0.024 0.037 -10000 0 -0.099 49 49
integrin-mediated signaling pathway 0.014 0.029 -10000 0 -0.3 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.097 0.28 -10000 0 -0.66 62 62
TRPV6 -0.13 0.23 -10000 0 -0.53 94 94
CD28 -0.029 0.14 -10000 0 -0.53 28 28
SHC1 -0.1 0.29 -10000 0 -0.68 60 60
receptor internalization -0.11 0.3 -10000 0 -0.73 58 58
PRF1 -0.12 0.34 -10000 0 -0.95 44 44
KRAS 0.012 0 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
COT/AKT1 -0.038 0.15 -10000 0 -0.36 57 57
LAT -0.1 0.3 -10000 0 -0.69 61 61
EntrezGene:6955 -0.001 0.004 -10000 0 -10000 0 0
CD3D -0.053 0.18 -10000 0 -0.52 46 46
CD3E -0.053 0.17 -10000 0 -0.51 46 46
CD3G -0.036 0.15 -10000 0 -0.5 34 34
RASGRP2 -0.003 0.035 -10000 0 -0.16 11 11
RASGRP1 -0.058 0.19 -10000 0 -0.44 60 60
HLA-A -0.005 0.092 -10000 0 -0.53 11 11
RASSF5 0.008 0.047 -10000 0 -0.51 3 3
RAP1A/GTP/RAPL 0.014 0.029 -10000 0 -0.31 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.002 0.058 -10000 0 -0.12 45 45
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.053 0.09 -10000 0 -0.25 54 54
PRKCA -0.054 0.11 -10000 0 -0.28 57 57
GRAP2 -0.028 0.14 -10000 0 -0.5 29 29
mol:IP3 -0.051 0.2 0.21 59 -0.44 55 114
EntrezGene:6957 -0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.11 0.31 -10000 0 -0.71 57 57
ORAI1 0.077 0.13 0.29 94 -10000 0 94
CSK -0.11 0.3 -10000 0 -0.72 58 58
B7 family/CD28 -0.11 0.31 -10000 0 -0.72 62 62
CHUK 0.012 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.13 0.35 -10000 0 -0.82 60 60
PTPN6 -0.11 0.3 -10000 0 -0.72 58 58
VAV1 -0.11 0.3 -10000 0 -0.68 64 64
Monovalent TCR/CD3 -0.077 0.24 -10000 0 -0.52 65 65
CBL 0.012 0 -10000 0 -10000 0 0
LCK -0.11 0.32 -10000 0 -0.74 61 61
PAG1 -0.11 0.3 -10000 0 -0.73 58 58
RAP1A 0.012 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.13 0.34 -10000 0 -0.82 58 58
CD80 -0.015 0.12 -10000 0 -0.52 18 18
CD86 -0.011 0.11 -10000 0 -0.52 16 16
PDK1/CARD11/BCL10/MALT1 -0.065 0.11 -10000 0 -0.3 55 55
HRAS 0.011 0.024 -10000 0 -0.45 1 1
GO:0035030 -0.088 0.25 -10000 0 -0.58 62 62
CD8A -0.057 0.18 -10000 0 -0.51 50 50
CD8B -0.076 0.19 -10000 0 -0.49 65 65
PTPRC -0.032 0.15 -10000 0 -0.52 31 31
PDK1/PKC theta -0.083 0.24 -10000 0 -0.56 62 62
CSK/PAG1 -0.1 0.29 -10000 0 -0.72 56 56
SOS1 0.012 0 -10000 0 -10000 0 0
peptide-MHC class I -0.001 0.086 -10000 0 -0.4 16 16
GRAP2/SLP76 -0.13 0.28 -10000 0 -0.68 63 63
STIM1 0.039 0.062 -10000 0 -10000 0 0
RAS family/GTP -0.003 0.081 -10000 0 -0.18 42 42
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.12 0.34 -10000 0 -0.81 57 57
mol:DAG -0.067 0.16 -10000 0 -0.39 57 57
RAP1A/GDP 0.002 0.026 -10000 0 -0.063 7 7
PLCG1 0.012 0 -10000 0 -10000 0 0
CD247 -0.026 0.14 -10000 0 -0.51 27 27
cytotoxic T cell degranulation -0.11 0.32 -10000 0 -0.89 44 44
RAP1A/GTP -0.004 0.011 -10000 0 -0.068 7 7
mol:PI-3-4-5-P3 -0.073 0.23 -10000 0 -0.54 61 61
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.076 0.25 0.23 51 -0.58 57 108
NRAS 0.005 0.064 -10000 0 -0.54 5 5
ZAP70 -0.046 0.16 -10000 0 -0.5 42 42
GRB2/SOS1 0.018 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.11 0.23 -10000 0 -0.57 62 62
MALT1 0.006 0.054 -10000 0 -0.45 5 5
TRAF6 0.012 0 -10000 0 -10000 0 0
CD8 heterodimer -0.091 0.21 -10000 0 -0.43 91 91
CARD11 -0.049 0.16 -10000 0 -0.49 45 45
PRKCB -0.057 0.12 -10000 0 -0.31 58 58
PRKCE -0.048 0.1 -10000 0 -0.27 53 53
PRKCQ -0.1 0.27 -10000 0 -0.64 64 64
LCP2 0 0.079 -10000 0 -0.5 9 9
BCL10 0.012 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.044 0.16 -10000 0 -0.38 59 59
IKK complex 0.005 0.058 -10000 0 -0.11 38 38
RAS family/GDP -0.006 0.012 -10000 0 -0.076 3 3
MAP3K14 -0.021 0.12 -10000 0 -0.28 47 47
PDPK1 -0.05 0.18 -10000 0 -0.43 57 57
TCR/CD3/MHC I/CD8/Fyn -0.13 0.36 -10000 0 -0.81 64 64
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.077 0.16 -10000 0 -0.32 102 102
cell-cell adhesion 0.1 0.15 0.44 46 -10000 0 46
Ephrin B/EPHB2/RasGAP -0.062 0.17 -10000 0 -0.34 81 81
ITSN1 0.011 0.024 -10000 0 -0.45 1 1
PIK3CA 0.01 0.034 -10000 0 -0.45 2 2
SHC1 0.012 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.037 0.12 -10000 0 -0.31 61 61
Ephrin B1/EPHB1 -0.044 0.12 -10000 0 -0.29 73 73
HRAS/GDP -0.09 0.14 -10000 0 -0.4 40 40
Ephrin B/EPHB1/GRB7 -0.09 0.19 -10000 0 -0.36 95 95
Endophilin/SYNJ1 -0.061 0.16 -10000 0 -0.53 21 21
KRAS 0.012 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.079 0.18 -10000 0 -0.35 87 87
endothelial cell migration -0.005 0.091 -10000 0 -0.28 30 30
GRB2 0.012 0 -10000 0 -10000 0 0
GRB7 -0.014 0.11 -10000 0 -0.47 20 20
PAK1 -0.061 0.17 -10000 0 -0.54 25 25
HRAS 0.011 0.024 -10000 0 -0.45 1 1
RRAS -0.062 0.16 -10000 0 -0.54 21 21
DNM1 -0.012 0.11 -10000 0 -0.48 18 18
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.076 0.16 -10000 0 -0.32 87 87
lamellipodium assembly -0.1 0.15 -10000 0 -0.44 46 46
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.051 0.14 -10000 0 -0.41 24 24
PIK3R1 -0.018 0.12 -10000 0 -0.52 21 21
EPHB2 -0.051 0.17 -10000 0 -0.51 45 45
EPHB3 -0.069 0.19 -10000 0 -0.5 59 59
EPHB1 -0.08 0.19 -10000 0 -0.48 69 69
EPHB4 0.009 0.04 -10000 0 -0.54 2 2
mol:GDP -0.059 0.17 -10000 0 -0.41 40 40
Ephrin B/EPHB2 -0.069 0.17 -10000 0 -0.35 81 81
Ephrin B/EPHB3 -0.078 0.18 -10000 0 -0.36 82 82
JNK cascade -0.051 0.14 -10000 0 -0.31 61 61
Ephrin B/EPHB1 -0.084 0.17 -10000 0 -0.34 87 87
RAP1/GDP -0.041 0.15 -10000 0 -0.38 30 30
EFNB2 -0.011 0.11 -10000 0 -0.5 17 17
EFNB3 -0.082 0.2 -10000 0 -0.52 66 66
EFNB1 0.007 0.055 -10000 0 -0.52 4 4
Ephrin B2/EPHB1-2 -0.076 0.17 -10000 0 -0.32 106 106
RAP1B 0.012 0 -10000 0 -10000 0 0
RAP1A 0.012 0 -10000 0 -10000 0 0
CDC42/GTP -0.12 0.17 -10000 0 -0.49 45 45
Rap1/GTP -0.1 0.16 -10000 0 -0.45 45 45
axon guidance -0.077 0.16 -10000 0 -0.32 102 102
MAPK3 -0.035 0.12 -10000 0 -0.39 20 20
MAPK1 -0.035 0.12 -10000 0 -0.39 20 20
Rac1/GDP -0.048 0.16 -10000 0 -0.38 36 36
actin cytoskeleton reorganization -0.085 0.12 -10000 0 -0.36 46 46
CDC42/GDP -0.048 0.16 -10000 0 -0.38 36 36
PI3K -0.002 0.092 -10000 0 -0.28 30 30
EFNA5 -0.077 0.2 -10000 0 -0.53 61 61
Ephrin B2/EPHB4 0 0.071 -10000 0 -0.3 19 19
Ephrin B/EPHB2/Intersectin/N-WASP -0.052 0.16 -10000 0 -0.52 21 21
CDC42 0.012 0 -10000 0 -10000 0 0
RAS family/GTP -0.1 0.15 -10000 0 -0.44 45 45
PTK2 0.02 0.033 -10000 0 -10000 0 0
MAP4K4 -0.051 0.14 -10000 0 -0.32 61 61
SRC 0.009 0.04 -10000 0 -0.54 2 2
KALRN 0.002 0.075 -10000 0 -0.54 7 7
Intersectin/N-WASP 0.017 0.017 -10000 0 -0.31 1 1
neuron projection morphogenesis -0.054 0.16 -10000 0 -0.41 34 34
MAP2K1 -0.042 0.13 -10000 0 -0.41 20 20
WASL 0.012 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.059 0.16 -10000 0 -0.3 102 102
cell migration -0.044 0.15 -10000 0 -0.45 20 20
NRAS 0.005 0.064 -10000 0 -0.54 5 5
SYNJ1 -0.062 0.16 -10000 0 -0.54 21 21
PXN 0.012 0 -10000 0 -10000 0 0
TF -0.084 0.18 -10000 0 -0.52 33 33
HRAS/GTP -0.11 0.17 -10000 0 -0.47 45 45
Ephrin B1/EPHB1-2 -0.066 0.16 -10000 0 -0.3 102 102
cell adhesion mediated by integrin 0.069 0.14 0.32 70 -10000 0 70
RAC1 0.012 0 -10000 0 -10000 0 0
mol:GTP -0.097 0.19 -10000 0 -0.51 45 45
RAC1-CDC42/GTP -0.13 0.18 -10000 0 -0.46 62 62
RASA1 0.012 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.041 0.15 -10000 0 -0.4 25 25
ruffle organization -0.075 0.18 -10000 0 -0.45 46 46
NCK1 0.012 0 -10000 0 -10000 0 0
receptor internalization -0.065 0.17 -10000 0 -0.5 30 30
Ephrin B/EPHB2/KALRN -0.068 0.18 -10000 0 -0.35 84 84
ROCK1 -0.027 0.11 -10000 0 -0.27 61 61
RAS family/GDP -0.083 0.12 -10000 0 -0.39 33 33
Rac1/GTP -0.11 0.16 -10000 0 -0.47 46 46
Ephrin B/EPHB1/Src/Paxillin -0.061 0.15 -10000 0 -0.41 30 30
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.037 0.15 0.48 37 -10000 0 37
PI3K Class IB/PDE3B -0.038 0.15 -10000 0 -0.49 37 37
PDE3B -0.038 0.15 -10000 0 -0.49 37 37
HIF-1-alpha transcription factor network

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
PKM2 -0.2 0.45 -9999 0 -1.1 46 46
HDAC7 0.012 0.024 -9999 0 -0.45 1 1
HIF1A/ARNT/Cbp/p300/Src-1 -0.2 0.31 -9999 0 -0.84 35 35
SMAD4 0.012 0.029 -9999 0 -0.54 1 1
ID2 -0.21 0.45 -9999 0 -1.1 48 48
AP1 -0.005 0.092 -9999 0 -0.34 25 25
ABCG2 -0.22 0.47 -9999 0 -1.1 50 50
HIF1A -0.018 0.072 -9999 0 -10000 0 0
TFF3 -0.32 0.51 -9999 0 -1.1 77 77
GATA2 -0.059 0.18 -9999 0 -0.53 49 49
AKT1 -0.026 0.09 -9999 0 -0.63 1 1
response to hypoxia -0.04 0.087 -9999 0 -0.25 3 3
MCL1 -0.2 0.45 -9999 0 -1.1 47 47
NDRG1 -0.22 0.46 -9999 0 -1.1 47 47
SERPINE1 -0.22 0.46 -9999 0 -1 52 52
FECH -0.2 0.45 -9999 0 -1 48 48
FURIN -0.21 0.45 -9999 0 -1.1 47 47
NCOA2 -0.007 0.1 -9999 0 -0.52 14 14
EP300 -0.021 0.12 -9999 0 -0.31 15 15
HMOX1 -0.21 0.46 -9999 0 -1.1 47 47
BHLHE40 -0.21 0.45 -9999 0 -1.1 47 47
BHLHE41 -0.23 0.48 -9999 0 -1.1 56 56
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.018 0.07 -9999 0 -0.38 2 2
ENG 0.017 0.095 -9999 0 -0.56 1 1
JUN 0.01 0.037 -9999 0 -0.49 2 2
RORA -0.21 0.45 -9999 0 -1.1 50 50
ABCB1 -0.13 0.3 -9999 0 -1.2 24 24
TFRC -0.21 0.45 -9999 0 -1.1 48 48
CXCR4 -0.21 0.45 -9999 0 -1 50 50
TF -0.23 0.47 -9999 0 -1.1 55 55
CITED2 -0.21 0.45 -9999 0 -1.1 47 47
HIF1A/ARNT -0.29 0.48 -9999 0 -1.2 55 55
LDHA -0.029 0.048 -9999 0 -10000 0 0
ETS1 -0.21 0.45 -9999 0 -1.1 46 46
PGK1 -0.21 0.45 -9999 0 -1 48 48
NOS2 -0.24 0.47 -9999 0 -1.1 55 55
ITGB2 -0.21 0.46 -9999 0 -1.1 47 47
ALDOA -0.21 0.45 -9999 0 -1 48 48
Cbp/p300/CITED2 -0.22 0.46 -9999 0 -1.1 45 45
FOS -0.019 0.12 -9999 0 -0.47 24 24
HK2 -0.21 0.45 -9999 0 -1.1 47 47
SP1 0.016 0.017 -9999 0 -10000 0 0
GCK -0.12 0.3 -9999 0 -0.82 35 35
HK1 -0.2 0.45 -9999 0 -1.1 47 47
NPM1 -0.2 0.45 -9999 0 -1.1 47 47
EGLN1 -0.2 0.45 -9999 0 -1.1 47 47
CREB1 0.019 0 -9999 0 -10000 0 0
PGM1 -0.2 0.45 -9999 0 -1 48 48
SMAD3 0.013 0.001 -9999 0 -10000 0 0
EDN1 -0.086 0.29 -9999 0 -1.2 16 16
IGFBP1 -0.23 0.46 -9999 0 -1.1 51 51
VEGFA -0.11 0.33 -9999 0 -0.78 25 25
HIF1A/JAB1 -0.013 0.034 -9999 0 -10000 0 0
CP -0.26 0.49 -9999 0 -1.1 68 68
CXCL12 -0.23 0.47 -9999 0 -1.1 48 48
COPS5 0.012 0.004 -9999 0 -10000 0 0
SMAD3/SMAD4 0.019 0.021 -9999 0 -0.38 1 1
BNIP3 -0.21 0.45 -9999 0 -1.1 48 48
EGLN3 -0.22 0.46 -9999 0 -1.1 49 49
CA9 -0.27 0.5 -9999 0 -1.1 66 66
TERT -0.25 0.48 -9999 0 -1.1 57 57
ENO1 -0.2 0.45 -9999 0 -1.1 47 47
PFKL -0.2 0.45 -9999 0 -1.1 46 46
NCOA1 0.012 0.002 -9999 0 -10000 0 0
ADM -0.22 0.46 -9999 0 -1.1 48 48
ARNT -0.018 0.072 -9999 0 -10000 0 0
HNF4A -0.16 0.24 -9999 0 -0.5 117 117
ADFP -0.23 0.44 -9999 0 -1 53 53
SLC2A1 -0.11 0.33 -9999 0 -0.8 24 24
LEP -0.22 0.45 -9999 0 -1.1 49 49
HIF1A/ARNT/Cbp/p300 -0.16 0.36 -9999 0 -0.87 35 35
EPO -0.1 0.28 -9999 0 -0.87 8 8
CREBBP -0.021 0.12 -9999 0 -0.31 13 13
HIF1A/ARNT/Cbp/p300/HDAC7 -0.19 0.31 -9999 0 -0.85 35 35
PFKFB3 -0.22 0.46 -9999 0 -1.1 51 51
NT5E -0.25 0.49 -9999 0 -1.1 60 60
Glypican 2 network

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
MDK -0.004 0.092 -9999 0 -0.53 11 11
GPC2 -0.039 0.15 -9999 0 -0.5 37 37
GPC2/Midkine -0.03 0.13 -9999 0 -0.37 46 46
neuron projection morphogenesis -0.03 0.13 -9999 0 -0.37 46 46
Noncanonical Wnt signaling pathway

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
NFATC2 -0.02 0.13 -9999 0 -0.53 22 22
GNB1/GNG2 -0.1 0.19 -9999 0 -0.53 39 39
mol:DAG -0.092 0.17 -9999 0 -0.47 39 39
PLCG1 -0.095 0.18 -9999 0 -0.49 39 39
YES1 -0.11 0.19 -9999 0 -0.55 36 36
FZD3 0.012 0 -9999 0 -10000 0 0
FZD6 0.008 0.049 -9999 0 -0.54 3 3
G protein -0.096 0.18 -9999 0 -0.52 35 35
MAP3K7 -0.075 0.15 -9999 0 -0.42 33 33
mol:Ca2+ -0.089 0.17 -9999 0 -0.46 39 39
mol:IP3 -0.092 0.17 -9999 0 -0.47 39 39
NLK -0.004 0.009 -9999 0 -10000 0 0
GNB1 0.012 0 -9999 0 -10000 0 0
CAMK2A -0.087 0.16 -9999 0 -0.43 41 41
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.12 0.2 -9999 0 -0.45 62 62
CSNK1A1 0.012 0 -9999 0 -10000 0 0
GNAS -0.11 0.19 -9999 0 -0.56 35 35
GO:0007205 -0.09 0.17 -9999 0 -0.47 39 39
WNT6 -0.12 0.22 -9999 0 -0.48 98 98
WNT4 -0.054 0.17 -9999 0 -0.5 48 48
NFAT1/CK1 alpha -0.097 0.19 -9999 0 -0.51 39 39
GNG2 -0.002 0.084 -9999 0 -0.48 11 11
WNT5A -0.014 0.12 -9999 0 -0.52 18 18
WNT11 -0.13 0.23 -9999 0 -0.5 104 104
CDC42 -0.098 0.18 -9999 0 -0.52 36 36
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.025 0.048 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.095 0.12 -9999 0 -0.37 39 39
JUN -0.051 0.12 -9999 0 -0.39 14 14
HRAS 0.011 0.024 -9999 0 -0.45 1 1
RET51/GFRalpha1/GDNF/GRB10 -0.12 0.18 -9999 0 -0.39 80 80
RAP1A 0.012 0 -9999 0 -10000 0 0
FRS2 0.012 0 -9999 0 -10000 0 0
RAP1A/GDP 0.009 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.11 0.18 -9999 0 -0.37 78 78
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.046 0.13 -9999 0 -0.28 80 80
RHOA 0.012 0 -9999 0 -10000 0 0
RAP1A/GTP -0.11 0.14 -9999 0 -0.36 53 53
GRB7 -0.014 0.11 -9999 0 -0.47 20 20
RET51/GFRalpha1/GDNF -0.11 0.18 -9999 0 -0.37 78 78
MAPKKK cascade -0.093 0.13 -9999 0 -0.4 27 27
BCAR1 0.011 0.029 -9999 0 -0.54 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.058 0.14 -9999 0 -0.29 91 91
lamellipodium assembly -0.089 0.12 -9999 0 -0.34 43 43
RET51/GFRalpha1/GDNF/SHC -0.11 0.18 -9999 0 -0.37 78 78
PIK3CA 0.01 0.034 -9999 0 -0.45 2 2
RET9/GFRalpha1/GDNF/SHC -0.044 0.13 -9999 0 -0.28 79 79
RET9/GFRalpha1/GDNF/Shank3 -0.044 0.13 -9999 0 -0.28 79 79
MAPK3 -0.084 0.15 -9999 0 -0.43 27 27
DOK1 0.012 0 -9999 0 -10000 0 0
DOK6 -0.054 0.17 -9999 0 -0.49 49 49
PXN 0.012 0 -9999 0 -10000 0 0
neurite development -0.083 0.15 -9999 0 -0.4 40 40
DOK5 -0.076 0.19 -9999 0 -0.48 66 66
GFRA1 -0.087 0.2 -9999 0 -0.5 72 72
MAPK8 -0.058 0.12 -9999 0 -0.41 13 13
HRAS/GTP -0.11 0.14 -9999 0 -0.45 27 27
tube development -0.036 0.12 -9999 0 -0.3 39 39
MAPK1 -0.084 0.15 -9999 0 -0.43 28 28
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.022 0.094 -9999 0 -0.26 39 39
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
SRC 0.009 0.04 -9999 0 -0.54 2 2
PDLIM7 0.01 0.034 -9999 0 -0.45 2 2
RET51/GFRalpha1/GDNF/Dok6 -0.13 0.2 -9999 0 -0.52 51 51
SHC1 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.11 0.18 -9999 0 -0.37 78 78
RET51/GFRalpha1/GDNF/Dok5 -0.16 0.21 -9999 0 -0.44 96 96
PRKCA -0.013 0.11 -9999 0 -0.53 17 17
HRAS/GDP 0.008 0.017 -9999 0 -0.32 1 1
CREB1 -0.045 0.12 -9999 0 -0.32 38 38
PIK3R1 -0.018 0.12 -9999 0 -0.52 21 21
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.023 0.099 -9999 0 -0.27 39 39
RET51/GFRalpha1/GDNF/Grb7 -0.12 0.19 -9999 0 -0.38 86 86
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.12 0.22 -9999 0 -0.48 99 99
DOK4 0.012 0 -9999 0 -10000 0 0
JNK cascade -0.05 0.12 -9999 0 -0.38 14 14
RET9/GFRalpha1/GDNF/FRS2 -0.044 0.13 -9999 0 -0.28 79 79
SHANK3 0.012 0 -9999 0 -10000 0 0
RASA1 0.012 0 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.022 0.095 -9999 0 -0.26 39 39
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.067 0.13 -9999 0 -0.31 41 41
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.067 0.13 -9999 0 -0.35 27 27
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.068 0.14 -9999 0 -0.38 27 27
PI3K -0.1 0.2 -9999 0 -0.47 61 61
SOS1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.035 0.12 -9999 0 -0.3 39 39
GRB10 0 0.08 -9999 0 -0.54 8 8
activation of MAPKK activity -0.054 0.11 -9999 0 -0.38 15 15
RET51/GFRalpha1/GDNF/FRS2 -0.11 0.18 -9999 0 -0.37 78 78
GAB1 0.011 0.029 -9999 0 -0.54 1 1
IRS1 -0.011 0.11 -9999 0 -0.53 16 16
IRS2 -0.035 0.14 -9999 0 -0.47 36 36
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.069 0.14 -9999 0 -0.38 28 28
RET51/GFRalpha1/GDNF/PKC alpha -0.12 0.19 -9999 0 -0.39 87 87
GRB2 0.012 0 -9999 0 -10000 0 0
PRKACA 0.012 0 -9999 0 -10000 0 0
GDNF -0.011 0.084 -9999 0 -0.45 13 13
RAC1 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.12 0.19 -9999 0 -0.38 89 89
Rac1/GTP -0.1 0.14 -9999 0 -0.4 43 43
RET9/GFRalpha1/GDNF -0.058 0.14 -9999 0 -0.32 79 79
GFRalpha1/GDNF -0.069 0.16 -9999 0 -0.37 79 79
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 -0.011 0.11 -10000 0 -0.5 17 17
EPHB2 -0.051 0.17 -10000 0 -0.51 45 45
EFNB1 -0.002 0.091 -10000 0 -0.37 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.058 0.16 -10000 0 -0.47 27 27
Ephrin B2/EPHB1-2 -0.075 0.17 -10000 0 -0.32 106 106
neuron projection morphogenesis -0.081 0.14 -10000 0 -0.45 27 27
Ephrin B1/EPHB1-2/Tiam1 -0.067 0.17 -10000 0 -0.39 52 52
DNM1 -0.012 0.11 -10000 0 -0.48 18 18
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.043 0.18 -10000 0 -0.63 32 32
YES1 -0.073 0.24 -10000 0 -0.86 31 31
Ephrin B1/EPHB1-2/NCK2 -0.061 0.16 -10000 0 -0.35 61 61
PI3K -0.056 0.19 -10000 0 -0.57 40 40
mol:GDP -0.067 0.17 -10000 0 -0.38 52 52
ITGA2B -0.038 0.15 -10000 0 -0.51 36 36
endothelial cell proliferation 0 0.071 -10000 0 -0.3 19 19
FYN -0.073 0.24 -10000 0 -0.86 31 31
MAP3K7 -0.05 0.19 -10000 0 -0.68 31 31
FGR -0.076 0.24 -10000 0 -0.87 31 31
TIAM1 0 0.08 -10000 0 -0.54 8 8
PIK3R1 -0.018 0.12 -10000 0 -0.52 21 21
RGS3 0.012 0 -10000 0 -10000 0 0
cell adhesion -0.1 0.22 -10000 0 -0.6 46 46
LYN -0.074 0.24 -10000 0 -0.86 31 31
Ephrin B1/EPHB1-2/Src Family Kinases -0.071 0.22 -10000 0 -0.81 31 31
Ephrin B1/EPHB1-2 -0.067 0.2 -10000 0 -0.73 31 31
SRC -0.074 0.24 -10000 0 -0.86 31 31
ITGB3 -0.068 0.18 -10000 0 -0.48 60 60
EPHB1 -0.081 0.19 -10000 0 -0.48 69 69
EPHB4 0.009 0.04 -10000 0 -0.54 2 2
RAC1 0.012 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0.071 -10000 0 -0.3 19 19
alphaIIb/beta3 Integrin -0.075 0.17 -10000 0 -0.36 92 92
BLK -0.089 0.25 -10000 0 -0.88 31 31
HCK -0.078 0.24 -10000 0 -0.86 31 31
regulation of stress fiber formation 0.061 0.16 0.35 61 -10000 0 61
MAPK8 -0.036 0.18 -10000 0 -0.61 31 31
Ephrin B1/EPHB1-2/RGS3 -0.061 0.16 -10000 0 -0.5 22 22
endothelial cell migration -0.05 0.18 -10000 0 -0.52 41 41
NCK2 0.011 0.029 -10000 0 -0.54 1 1
PTPN13 -0.05 0.19 -10000 0 -0.62 37 37
regulation of focal adhesion formation 0.061 0.16 0.35 61 -10000 0 61
chemotaxis 0.061 0.16 0.49 22 -10000 0 22
PIK3CA 0.01 0.034 -10000 0 -0.45 2 2
Rac1/GTP -0.078 0.14 -10000 0 -0.46 27 27
angiogenesis -0.067 0.2 -10000 0 -0.73 31 31
LCK -0.08 0.24 -10000 0 -0.84 32 32
TCGA08_p53

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
CDKN2A -0.077 0.15 -10000 0 -0.34 91 91
TP53 -0.038 0.085 -10000 0 -0.37 15 15
Senescence -0.038 0.084 -10000 0 -0.37 15 15
Apoptosis -0.038 0.084 -10000 0 -0.37 15 15
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.046 0.089 0.2 89 -0.3 2 91
MDM4 0.012 0 -10000 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.04 0.15 -10000 0 -0.41 31 31
TBX21 -0.17 0.46 -10000 0 -1.1 56 56
B2M 0.003 0.067 -10000 0 -0.51 6 6
TYK2 0.011 0.022 -10000 0 -10000 0 0
IL12RB1 -0.025 0.14 -10000 0 -0.52 26 26
GADD45B -0.12 0.36 -10000 0 -0.94 41 41
IL12RB2 -0.031 0.14 -10000 0 -0.49 32 32
GADD45G -0.12 0.37 -10000 0 -0.96 40 40
natural killer cell activation -0.001 0.023 -10000 0 -10000 0 0
RELB 0.012 0 -10000 0 -10000 0 0
RELA 0.012 0 -10000 0 -10000 0 0
IL18 -0.013 0.12 -10000 0 -0.53 18 18
IL2RA -0.022 0.13 -10000 0 -0.51 24 24
IFNG -0.038 0.15 -10000 0 -0.48 36 36
STAT3 (dimer) -0.11 0.34 -10000 0 -0.77 60 60
HLA-DRB5 -0.063 0.18 -10000 0 -0.51 54 54
FASLG -0.19 0.49 -10000 0 -1.1 62 62
NF kappa B2 p52/RelB -0.21 0.37 -10000 0 -0.94 62 62
CD4 -0.004 0.092 -10000 0 -0.53 11 11
SOCS1 0.004 0.066 -10000 0 -0.51 6 6
EntrezGene:6955 -0.001 0.01 -10000 0 -10000 0 0
CD3D -0.053 0.17 -10000 0 -0.51 46 46
CD3E -0.053 0.17 -10000 0 -0.51 46 46
CD3G -0.036 0.15 -10000 0 -0.5 34 34
IL12Rbeta2/JAK2 -0.022 0.12 -10000 0 -0.36 41 41
CCL3 -0.16 0.45 -10000 0 -1.1 56 56
CCL4 -0.16 0.45 -10000 0 -1.1 55 55
HLA-A -0.004 0.091 -10000 0 -0.52 11 11
IL18/IL18R -0.023 0.17 -10000 0 -0.39 54 54
NOS2 -0.18 0.46 -10000 0 -1.1 64 64
IL12/IL12R/TYK2/JAK2/SPHK2 -0.036 0.14 -10000 0 -0.39 27 27
IL1R1 -0.16 0.43 -10000 0 -1 57 57
IL4 0.005 0.034 -10000 0 -0.47 1 1
JAK2 -0.003 0.089 -10000 0 -0.55 9 9
EntrezGene:6957 -0.001 0.01 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.13 0.36 -10000 0 -0.87 57 57
RAB7A -0.083 0.3 -10000 0 -0.8 31 31
lysosomal transport -0.076 0.29 -10000 0 -0.76 31 31
FOS -0.12 0.33 -10000 0 -0.87 44 44
STAT4 (dimer) -0.12 0.38 -10000 0 -0.9 54 54
STAT5A (dimer) -0.23 0.39 -10000 0 -0.94 69 69
GZMA -0.19 0.5 -10000 0 -1.2 60 60
GZMB -0.21 0.51 -10000 0 -1.2 68 68
HLX 0.011 0.024 -10000 0 -0.45 1 1
LCK -0.18 0.48 -10000 0 -1.1 63 63
TCR/CD3/MHC II/CD4 -0.1 0.3 -10000 0 -0.64 62 62
IL2/IL2R -0.04 0.17 -10000 0 -0.44 45 45
MAPK14 -0.12 0.38 -10000 0 -0.91 47 47
CCR5 -0.14 0.41 -10000 0 -1.1 40 40
IL1B -0.022 0.13 -10000 0 -0.53 23 23
STAT6 -0.023 0.13 0.21 1 -0.29 22 23
STAT4 -0.006 0.096 -10000 0 -0.5 13 13
STAT3 0.012 0 -10000 0 -10000 0 0
STAT1 0.01 0.034 -10000 0 -0.45 2 2
NFKB1 0.012 0 -10000 0 -10000 0 0
NFKB2 0.012 0 -10000 0 -10000 0 0
IL12B 0.001 0.059 -10000 0 -0.46 5 5
CD8A -0.058 0.18 -10000 0 -0.5 50 50
CD8B -0.076 0.19 -10000 0 -0.48 65 65
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.04 0.15 0.4 31 -10000 0 31
IL2RB -0.023 0.13 -10000 0 -0.51 25 25
proteasomal ubiquitin-dependent protein catabolic process -0.1 0.35 -10000 0 -0.8 54 54
IL2RG -0.022 0.13 -10000 0 -0.5 25 25
IL12 -0.035 0.13 -10000 0 -0.34 52 52
STAT5A 0.011 0.024 -10000 0 -0.45 1 1
CD247 -0.026 0.14 -10000 0 -0.51 27 27
IL2 -0.014 0.09 -10000 0 -0.45 15 15
SPHK2 0.012 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.054 0.17 -10000 0 -0.49 47 47
IL12/IL12R/TYK2/JAK2 -0.19 0.53 -10000 0 -1.2 63 63
MAP2K3 -0.12 0.38 -10000 0 -0.9 48 48
RIPK2 0.01 0.037 -10000 0 -0.5 2 2
MAP2K6 -0.13 0.39 -10000 0 -0.92 50 50
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.025 0.14 -10000 0 -0.52 26 26
IL18RAP -0.035 0.15 -10000 0 -0.51 34 34
IL12Rbeta1/TYK2 -0.009 0.11 -10000 0 -0.39 26 26
EOMES -0.06 0.26 -10000 0 -1.3 14 14
STAT1 (dimer) -0.13 0.35 -10000 0 -0.77 63 63
T cell proliferation -0.081 0.28 -10000 0 -0.65 50 50
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.018 0.13 -10000 0 -0.52 22 22
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.16 0.26 -10000 0 -0.71 53 53
ATF2 -0.1 0.34 -10000 0 -0.83 45 45
Syndecan-4-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
PTK2 -0.01 0.085 -9999 0 -0.51 6 6
Syndecan-4/Syndesmos -0.088 0.19 -9999 0 -0.5 49 49
positive regulation of JNK cascade -0.098 0.18 -9999 0 -0.47 52 52
Syndecan-4/ADAM12 -0.099 0.2 -9999 0 -0.5 52 52
CCL5 -0.034 0.15 -9999 0 -0.49 34 34
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
DNM2 0.012 0 -9999 0 -10000 0 0
ITGA5 0.01 0.037 -9999 0 -0.5 2 2
SDCBP 0.012 0 -9999 0 -10000 0 0
PLG -0.076 0.19 -9999 0 -0.47 69 69
ADAM12 -0.012 0.11 -9999 0 -0.48 18 18
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.029 0.039 -9999 0 -0.18 2 2
Syndecan-4/Laminin alpha1 -0.16 0.22 -9999 0 -0.52 74 74
Syndecan-4/CXCL12/CXCR4 -0.1 0.2 -9999 0 -0.5 52 52
Syndecan-4/Laminin alpha3 -0.11 0.21 -9999 0 -0.52 55 55
MDK -0.004 0.092 -9999 0 -0.53 11 11
Syndecan-4/FZD7 -0.12 0.21 -9999 0 -0.49 67 67
Syndecan-4/Midkine -0.096 0.2 -9999 0 -0.5 53 53
FZD7 -0.061 0.18 -9999 0 -0.5 53 53
Syndecan-4/FGFR1/FGF -0.12 0.17 -9999 0 -0.48 46 46
THBS1 -0.011 0.11 -9999 0 -0.49 17 17
integrin-mediated signaling pathway -0.1 0.2 -9999 0 -0.5 54 54
positive regulation of MAPKKK cascade -0.098 0.18 -9999 0 -0.47 52 52
Syndecan-4/TACI -0.11 0.2 -9999 0 -0.49 59 59
CXCR4 0.008 0.049 -9999 0 -0.54 3 3
cell adhesion 0.002 0.074 -9999 0 -0.3 9 9
Syndecan-4/Dynamin -0.088 0.19 -9999 0 -0.5 49 49
Syndecan-4/TSP1 -0.099 0.2 -9999 0 -0.51 51 51
Syndecan-4/GIPC -0.088 0.19 -9999 0 -0.5 49 49
Syndecan-4/RANTES -0.11 0.21 -9999 0 -0.52 54 54
ITGB1 0.012 0 -9999 0 -10000 0 0
LAMA1 -0.14 0.24 -9999 0 -0.52 102 102
LAMA3 -0.027 0.14 -9999 0 -0.53 27 27
RAC1 0.012 0 -9999 0 -10000 0 0
PRKCA 0.008 0.11 -9999 0 -0.48 17 17
Syndecan-4/alpha-Actinin -0.088 0.19 -9999 0 -0.5 49 49
TFPI -0.033 0.14 -9999 0 -0.48 34 34
F2 -0.034 0.13 -9999 0 -0.45 33 33
alpha5/beta1 Integrin 0.016 0.027 -9999 0 -0.35 2 2
positive regulation of cell adhesion -0.16 0.23 -9999 0 -0.52 77 77
ACTN1 0.012 0 -9999 0 -10000 0 0
TNC -0.033 0.15 -9999 0 -0.51 32 32
Syndecan-4/CXCL12 -0.11 0.2 -9999 0 -0.51 53 53
FGF6 -0.001 0.033 -9999 0 -0.45 2 2
RHOA 0.012 0 -9999 0 -10000 0 0
CXCL12 -0.034 0.15 -9999 0 -0.51 33 33
TNFRSF13B -0.034 0.14 -9999 0 -0.46 34 34
FGF2 -0.027 0.14 -9999 0 -0.5 28 28
FGFR1 0.002 0.073 -9999 0 -0.53 7 7
Syndecan-4/PI-4-5-P2 -0.095 0.19 -9999 0 -0.5 49 49
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.018 0.12 -9999 0 -0.46 25 25
cell migration -0.008 0.016 -9999 0 -10000 0 0
PRKCD 0.011 0.039 -9999 0 -0.5 2 2
vasculogenesis -0.095 0.19 -9999 0 -0.49 51 51
SDC4 -0.1 0.2 -9999 0 -0.53 49 49
Syndecan-4/Tenascin C -0.11 0.21 -9999 0 -0.53 54 54
Syndecan-4/PI-4-5-P2/PKC alpha -0.023 0.031 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.088 0.19 -9999 0 -0.5 49 49
MMP9 -0.075 0.2 -9999 0 -0.5 64 64
Rac1/GTP 0.002 0.076 -9999 0 -0.31 9 9
cytoskeleton organization -0.085 0.18 -9999 0 -0.48 49 49
GIPC1 0.012 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.11 0.21 -9999 0 -0.51 53 53
Endothelins

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
AKT1 0.007 0.17 0.27 31 -0.54 16 47
PTK2B 0.009 0.04 -10000 0 -0.54 2 2
mol:Ca2+ -0.02 0.23 -10000 0 -0.79 20 20
EDN1 -0.001 0.14 -10000 0 -0.47 20 20
EDN3 -0.24 0.26 -10000 0 -0.5 178 178
EDN2 -0.06 0.18 -10000 0 -0.49 53 53
HRAS/GDP -0.033 0.17 -10000 0 -0.5 23 23
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0 0.15 -10000 0 -0.45 21 21
ADCY4 -0.01 0.15 -10000 0 -0.47 21 21
ADCY5 -0.047 0.18 -10000 0 -0.47 33 33
ADCY6 -0.006 0.15 -10000 0 -0.48 20 20
ADCY7 -0.007 0.15 -10000 0 -0.49 19 19
ADCY1 -0.052 0.18 -10000 0 -0.46 34 34
ADCY2 -0.044 0.2 -10000 0 -0.5 39 39
ADCY3 -0.005 0.15 -10000 0 -0.47 20 20
ADCY8 -0.022 0.16 -10000 0 -0.48 24 24
ADCY9 -0.018 0.17 -10000 0 -0.48 30 30
arachidonic acid secretion -0.043 0.18 -10000 0 -0.48 30 30
ETB receptor/Endothelin-1/Gq/GTP -0.009 0.13 -10000 0 -0.37 23 23
GNAO1 -0.014 0.11 -10000 0 -0.47 20 20
HRAS 0.011 0.024 -10000 0 -0.45 1 1
ETA receptor/Endothelin-1/G12/GTP 0.028 0.18 0.3 58 -0.51 15 73
ETA receptor/Endothelin-1/Gs/GTP 0.006 0.19 0.28 53 -0.5 20 73
mol:GTP 0 0.004 -10000 0 -10000 0 0
COL3A1 -0.014 0.23 -10000 0 -0.71 26 26
EDNRB -0.024 0.13 -10000 0 -0.49 27 27
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.005 0.19 -10000 0 -0.51 26 26
CYSLTR1 -0.013 0.22 -10000 0 -0.62 28 28
SLC9A1 -0.005 0.098 0.19 31 -0.3 12 43
mol:GDP -0.042 0.18 -10000 0 -0.49 29 29
SLC9A3 -0.045 0.22 -10000 0 -0.6 38 38
RAF1 -0.035 0.16 -10000 0 -0.48 21 21
JUN 0.003 0.18 -10000 0 -0.7 11 11
JAK2 -0.001 0.18 0.27 31 -0.54 20 51
mol:IP3 -0.008 0.15 -10000 0 -0.48 19 19
ETA receptor/Endothelin-1 -0.004 0.22 0.35 64 -0.58 19 83
PLCB1 -0.011 0.11 -10000 0 -0.53 16 16
PLCB2 -0.001 0.083 -10000 0 -0.5 10 10
ETA receptor/Endothelin-3 -0.17 0.21 -10000 0 -0.37 173 173
FOS -0.027 0.18 -10000 0 -0.69 11 11
Gai/GDP -0.004 0.12 -10000 0 -0.64 8 8
CRK 0.012 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.016 0.21 -10000 0 -0.57 27 27
BCAR1 0.011 0.029 -10000 0 -0.54 1 1
PRKCB1 -0.008 0.14 -10000 0 -0.46 19 19
GNAQ 0.011 0.029 -10000 0 -0.54 1 1
GNAZ -0.005 0.094 -10000 0 -0.52 12 12
GNAL -0.01 0.1 -10000 0 -0.48 17 17
Gs family/GDP -0.08 0.15 -10000 0 -0.45 37 37
ETA receptor/Endothelin-1/Gq/GTP 0.006 0.16 0.21 19 -0.52 17 36
MAPK14 -0.006 0.12 -10000 0 -0.45 13 13
TRPC6 -0.023 0.24 -10000 0 -0.85 20 20
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 -0.005 0.095 -10000 0 -0.52 12 12
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.012 0.13 -10000 0 -0.41 19 19
ETB receptor/Endothelin-2 -0.06 0.16 -10000 0 -0.36 77 77
ETB receptor/Endothelin-3 -0.18 0.2 -10000 0 -0.37 192 192
ETB receptor/Endothelin-1 -0.016 0.15 -10000 0 -0.37 39 39
MAPK3 -0.029 0.17 -10000 0 -0.59 16 16
MAPK1 -0.029 0.18 -10000 0 -0.61 15 15
Rac1/GDP -0.033 0.17 -10000 0 -0.49 23 23
cAMP biosynthetic process -0.054 0.18 -10000 0 -0.47 38 38
MAPK8 -0.007 0.2 -10000 0 -0.63 20 20
SRC 0.009 0.04 -10000 0 -0.54 2 2
ETB receptor/Endothelin-1/Gi/GTP -0.006 0.1 -10000 0 -0.36 13 13
p130Cas/CRK/Src/PYK2 -0.049 0.19 -10000 0 -0.54 25 25
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.033 0.17 -10000 0 -0.49 23 23
COL1A2 -0.018 0.23 -10000 0 -0.73 23 23
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.038 0.16 -10000 0 -0.37 62 62
mol:DAG -0.008 0.15 -10000 0 -0.48 19 19
MAP2K2 -0.029 0.16 -10000 0 -0.5 20 20
MAP2K1 -0.029 0.16 -10000 0 -0.52 18 18
EDNRA 0.007 0.14 -10000 0 -0.55 12 12
positive regulation of muscle contraction 0.013 0.15 0.24 27 -0.48 15 42
Gq family/GDP -0.078 0.15 -10000 0 -0.53 25 25
HRAS/GTP -0.042 0.16 -10000 0 -0.46 26 26
PRKCH -0.004 0.15 -10000 0 -0.51 17 17
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCA -0.015 0.16 -10000 0 -0.46 25 25
PRKCB -0.02 0.17 -10000 0 -0.46 32 32
PRKCE -0.002 0.14 -10000 0 -0.47 17 17
PRKCD -0.004 0.14 -10000 0 -0.48 17 17
PRKCG -0.077 0.19 -10000 0 -0.45 39 39
regulation of vascular smooth muscle contraction -0.032 0.2 -10000 0 -0.81 11 11
PRKCQ -0.05 0.18 -10000 0 -0.46 36 36
PLA2G4A -0.048 0.19 -10000 0 -0.52 30 30
GNA14 -0.002 0.09 -10000 0 -0.54 10 10
GNA15 -0.004 0.093 -10000 0 -0.51 12 12
GNA12 0.012 0 -10000 0 -10000 0 0
GNA11 0 0.082 -10000 0 -0.52 9 9
Rac1/GTP 0.028 0.18 0.3 58 -0.51 15 73
MMP1 -0.12 0.31 0.31 2 -0.64 85 87
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.023 0.1 -10000 0 -0.47 10 10
NFATC2 -0.061 0.22 -10000 0 -0.6 32 32
NFATC3 -0.019 0.071 -10000 0 -0.3 1 1
CD40LG -0.21 0.38 -10000 0 -0.94 56 56
ITCH -0.01 0.095 -10000 0 -0.61 1 1
CBLB -0.008 0.09 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.23 0.42 -10000 0 -1 65 65
JUNB 0.006 0.057 -10000 0 -0.54 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.024 0.11 -10000 0 -0.28 19 19
T cell anergy -0.043 0.13 -10000 0 -0.37 25 25
TLE4 -0.035 0.18 -10000 0 -0.56 23 23
Jun/NFAT1-c-4/p21SNFT -0.14 0.34 -10000 0 -0.92 39 39
AP-1/NFAT1-c-4 -0.22 0.42 -10000 0 -1.1 50 50
IKZF1 -0.044 0.21 -10000 0 -0.68 25 25
T-helper 2 cell differentiation -0.077 0.23 -10000 0 -0.74 26 26
AP-1/NFAT1 -0.061 0.17 -10000 0 -0.49 24 24
CALM1 -0.009 0.062 -10000 0 -10000 0 0
EGR2 -0.1 0.33 -10000 0 -0.95 31 31
EGR3 -0.13 0.38 -10000 0 -1.1 37 37
NFAT1/FOXP3 -0.066 0.21 -10000 0 -0.57 31 31
EGR1 -0.017 0.11 -10000 0 -0.49 19 19
JUN -0.004 0.045 -10000 0 -0.52 2 2
EGR4 -0.017 0.1 -10000 0 -0.46 18 18
mol:Ca2+ -0.022 0.065 -10000 0 -10000 0 0
GBP3 -0.061 0.24 -10000 0 -0.72 34 34
FOSL1 -0.024 0.13 -10000 0 -0.49 27 27
NFAT1-c-4/MAF/IRF4 -0.15 0.34 -10000 0 -0.9 47 47
DGKA -0.027 0.16 -10000 0 -0.56 14 14
CREM 0.012 0.003 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.18 0.35 -10000 0 -0.92 46 46
CTLA4 -0.11 0.28 -10000 0 -0.63 69 69
NFAT1-c-4 (dimer)/EGR1 -0.14 0.34 -10000 0 -0.92 42 42
NFAT1-c-4 (dimer)/EGR4 -0.14 0.34 -10000 0 -0.91 42 42
FOS -0.032 0.12 -10000 0 -0.48 24 24
IFNG -0.14 0.31 -10000 0 -0.87 42 42
T cell activation -0.084 0.2 -10000 0 -0.69 9 9
MAF 0 0.076 -10000 0 -0.48 9 9
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.087 0.28 0.83 30 -10000 0 30
TNF -0.18 0.36 -10000 0 -0.85 61 61
FASLG -0.22 0.51 -10000 0 -1.4 48 48
TBX21 -0.038 0.15 -10000 0 -0.51 34 34
BATF3 -0.005 0.092 -10000 0 -0.48 13 13
PRKCQ -0.086 0.21 -10000 0 -0.53 66 66
PTPN1 -0.026 0.16 -10000 0 -0.55 13 13
NFAT1-c-4/ICER1 -0.12 0.32 -10000 0 -0.91 37 37
GATA3 -0.029 0.14 -10000 0 -0.48 32 32
T-helper 1 cell differentiation -0.13 0.31 -10000 0 -0.83 44 44
IL2RA -0.19 0.31 -10000 0 -0.86 52 52
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.026 0.16 -10000 0 -0.54 14 14
E2F1 0.009 0.067 -10000 0 -0.47 7 7
PPARG -0.096 0.21 -10000 0 -0.51 76 76
SLC3A2 -0.026 0.16 -10000 0 -0.55 13 13
IRF4 -0.08 0.2 -10000 0 -0.49 68 68
PTGS2 -0.25 0.4 -10000 0 -0.94 65 65
CSF2 -0.2 0.36 -10000 0 -0.91 51 51
JunB/Fra1/NFAT1-c-4 -0.12 0.32 -10000 0 -0.89 40 40
IL4 -0.08 0.24 -10000 0 -0.77 26 26
IL5 -0.2 0.35 -10000 0 -0.91 49 49
IL2 -0.085 0.2 -10000 0 -0.7 9 9
IL3 -0.047 0.056 -10000 0 -10000 0 0
RNF128 -0.071 0.21 -10000 0 -0.45 82 82
NFATC1 -0.088 0.28 -10000 0 -0.84 30 30
CDK4 0.06 0.16 0.64 7 -10000 0 7
PTPRK -0.027 0.16 -10000 0 -0.58 13 13
IL8 -0.22 0.39 -10000 0 -0.96 59 59
POU2F1 0.001 0.071 -10000 0 -0.45 9 9
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.043 0.14 -9999 0 -0.36 53 53
alphaM/beta2 Integrin/GPIbA -0.021 0.12 -9999 0 -0.39 26 26
alphaM/beta2 Integrin/proMMP-9 -0.064 0.17 -9999 0 -0.36 77 77
PLAUR 0.007 0.053 -9999 0 -0.5 4 4
HMGB1 0.001 0.044 -9999 0 -0.54 2 2
alphaM/beta2 Integrin/Talin -0.011 0.1 -9999 0 -0.39 19 19
AGER -0.008 0.081 -9999 0 -0.51 9 9
RAP1A 0.012 0 -9999 0 -10000 0 0
SELPLG 0.004 0.064 -9999 0 -0.5 6 6
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.034 0.14 -9999 0 -0.5 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.076 0.2 -9999 0 -0.5 64 64
CYR61 0.001 0.075 -9999 0 -0.47 9 9
TLN1 0.012 0 -9999 0 -10000 0 0
Rap1/GTP -0.091 0.12 -9999 0 -0.4 27 27
RHOA 0.012 0 -9999 0 -10000 0 0
P-selectin oligomer -0.055 0.18 -9999 0 -0.52 47 47
MYH2 -0.12 0.16 -9999 0 -0.4 48 48
MST1R -0.041 0.16 -9999 0 -0.53 36 36
leukocyte activation during inflammatory response -0.069 0.14 -9999 0 -0.34 50 50
APOB -0.009 0.085 -9999 0 -0.45 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.04 0.16 -9999 0 -0.5 38 38
JAM3 0.007 0.05 -9999 0 -0.47 4 4
GP1BA -0.004 0.086 -9999 0 -0.49 11 11
alphaM/beta2 Integrin/CTGF -0.018 0.11 -9999 0 -0.35 33 33
alphaM/beta2 Integrin -0.1 0.15 -9999 0 -0.38 50 50
JAM3 homodimer 0.007 0.05 -9999 0 -0.47 4 4
ICAM2 0.007 0.055 -9999 0 -0.52 4 4
ICAM1 0.004 0.062 -9999 0 -0.48 6 6
phagocytosis triggered by activation of immune response cell surface activating receptor -0.1 0.15 -9999 0 -0.38 50 50
cell adhesion -0.021 0.12 -9999 0 -0.39 25 25
NFKB1 -0.054 0.18 -9999 0 -0.52 22 22
THY1 0.006 0.056 -9999 0 -0.47 5 5
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.055 0.13 -9999 0 -0.3 79 79
alphaM/beta2 Integrin/LRP/tPA -0.022 0.12 -9999 0 -0.38 28 28
IL6 -0.073 0.23 -9999 0 -0.68 29 29
ITGB2 -0.012 0.091 -9999 0 -0.5 12 12
elevation of cytosolic calcium ion concentration -0.015 0.12 -9999 0 -0.38 25 25
alphaM/beta2 Integrin/JAM2/JAM3 -0.022 0.12 -9999 0 -0.37 33 33
JAM2 -0.021 0.12 -9999 0 -0.5 24 24
alphaM/beta2 Integrin/ICAM1 -0.036 0.15 -9999 0 -0.44 24 24
alphaM/beta2 Integrin/uPA/Plg -0.061 0.15 -9999 0 -0.35 47 47
RhoA/GTP -0.12 0.16 -9999 0 -0.42 45 45
positive regulation of phagocytosis -0.09 0.14 -9999 0 -0.46 32 32
Ron/MSP -0.036 0.14 -9999 0 -0.37 51 51
alphaM/beta2 Integrin/uPAR/uPA -0.014 0.12 -9999 0 -0.38 25 25
alphaM/beta2 Integrin/uPAR -0.014 0.11 -9999 0 -0.41 21 21
PLAU -0.005 0.093 -9999 0 -0.49 13 13
PLAT -0.017 0.12 -9999 0 -0.49 22 22
actin filament polymerization -0.11 0.15 -9999 0 -0.39 48 48
MST1 -0.009 0.1 -9999 0 -0.48 16 16
alphaM/beta2 Integrin/lipoprotein(a) -0.062 0.14 -9999 0 -0.34 50 50
TNF -0.091 0.26 -9999 0 -0.7 42 42
RAP1B 0.012 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.022 0.12 -9999 0 -0.37 31 31
fibrinolysis -0.062 0.15 -9999 0 -0.35 47 47
HCK -0.012 0.11 -9999 0 -0.51 17 17
dendritic cell antigen processing and presentation -0.1 0.15 -9999 0 -0.38 50 50
VTN -0.009 0.095 -9999 0 -0.46 16 16
alphaM/beta2 Integrin/CYR61 -0.018 0.11 -9999 0 -0.39 22 22
LPA -0.083 0.19 -9999 0 -0.47 71 71
LRP1 0.005 0.06 -9999 0 -0.47 6 6
cell migration -0.08 0.18 -9999 0 -0.39 76 76
FN1 -0.02 0.12 -9999 0 -0.47 25 25
alphaM/beta2 Integrin/Thy1 -0.015 0.11 -9999 0 -0.34 30 30
MPO -0.044 0.16 -9999 0 -0.49 41 41
KNG1 -0.017 0.1 -9999 0 -0.45 19 19
RAP1/GDP 0.017 0 -9999 0 -10000 0 0
ROCK1 -0.11 0.15 -9999 0 -0.4 43 43
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.079 0.19 -9999 0 -0.47 69 69
CTGF 0 0.078 -9999 0 -0.49 9 9
alphaM/beta2 Integrin/Hck -0.025 0.13 -9999 0 -0.4 35 35
ITGAM -0.021 0.11 -9999 0 -0.49 19 19
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.043 0.15 -9999 0 -0.36 52 52
HP -0.25 0.26 -9999 0 -0.5 191 191
leukocyte adhesion -0.067 0.12 -9999 0 -0.42 28 28
SELP -0.055 0.18 -9999 0 -0.52 47 47
Glucocorticoid receptor regulatory network

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
PCK2 0.029 0.079 0.33 2 -10000 0 2
SMARCC2 0.013 0.008 -10000 0 -10000 0 0
SMARCC1 0.013 0.008 -10000 0 -10000 0 0
TBX21 -0.11 0.23 -10000 0 -0.66 44 44
SUMO2 0.014 0.012 -10000 0 -10000 0 0
STAT1 (dimer) 0.016 0.037 -10000 0 -0.44 2 2
FKBP4 0.012 0 -10000 0 -10000 0 0
FKBP5 -0.016 0.12 -10000 0 -0.49 21 21
GR alpha/HSP90/FKBP51/HSP90 0.076 0.13 0.3 33 -0.32 10 43
PRL -0.079 0.15 -10000 0 -0.53 9 9
cortisol/GR alpha (dimer)/TIF2 0.2 0.24 0.54 81 -0.38 5 86
RELA -0.019 0.071 -10000 0 -10000 0 0
FGG 0.16 0.19 0.5 44 -0.42 4 48
GR beta/TIF2 0.083 0.14 0.32 35 -0.37 14 49
IFNG -0.28 0.32 -10000 0 -0.78 77 77
apoptosis 0.036 0.21 0.53 28 -0.64 6 34
CREB1 0.005 0.04 -10000 0 -10000 0 0
histone acetylation -0.015 0.14 0.3 9 -0.36 20 29
BGLAP -0.061 0.14 -10000 0 -0.54 11 11
GR/PKAc 0.086 0.11 0.29 29 -0.33 4 33
NF kappa B1 p50/RelA -0.03 0.13 -10000 0 -0.4 11 11
SMARCD1 0.013 0.008 -10000 0 -10000 0 0
MDM2 0.084 0.089 0.26 43 -0.27 2 45
GATA3 -0.028 0.14 -10000 0 -0.48 32 32
AKT1 0.004 0.024 -10000 0 -0.46 1 1
CSF2 -0.05 0.12 -10000 0 -0.5 8 8
GSK3B 0.014 0.012 -10000 0 -10000 0 0
NR1I3 0.026 0.27 0.53 24 -0.87 19 43
CSN2 0.14 0.16 0.4 44 -0.35 4 48
BRG1/BAF155/BAF170/BAF60A 0.033 0.035 -10000 0 -0.28 2 2
NFATC1 0.003 0.081 -10000 0 -0.54 8 8
POU2F1 -0.002 0.078 -10000 0 -0.46 9 9
CDKN1A -0.046 0.3 -10000 0 -1.5 15 15
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.002 0.012 -10000 0 -10000 0 0
SFN -0.056 0.18 -10000 0 -0.51 49 49
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.039 0.15 0.31 18 -0.36 13 31
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.04 0.22 0.51 24 -0.73 11 35
JUN -0.18 0.19 -10000 0 -0.49 60 60
IL4 -0.078 0.14 -10000 0 -0.5 15 15
CDK5R1 0.002 0.074 -10000 0 -0.49 8 8
PRKACA 0.012 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.15 0.21 0.22 17 -0.49 73 90
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.083 0.12 0.29 32 -0.32 6 38
cortisol/GR alpha (monomer) 0.25 0.28 0.65 84 -0.45 2 86
NCOA2 -0.008 0.1 -10000 0 -0.52 14 14
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.081 0.13 -10000 0 -0.52 24 24
AP-1/NFAT1-c-4 -0.31 0.32 -10000 0 -0.73 104 104
AFP -0.12 0.15 -10000 0 -0.74 3 3
SUV420H1 0.012 0 -10000 0 -10000 0 0
IRF1 0.14 0.14 0.46 19 -10000 0 19
TP53 -0.009 0.15 -10000 0 -0.53 26 26
PPP5C 0.012 0 -10000 0 -10000 0 0
KRT17 -0.38 0.46 -10000 0 -1 107 107
KRT14 -0.3 0.45 -10000 0 -1 79 79
TBP 0.019 0.018 -10000 0 -0.3 1 1
CREBBP 0.068 0.1 0.28 40 -10000 0 40
HDAC1 0.012 0.002 -10000 0 -10000 0 0
HDAC2 0.012 0.006 -10000 0 -10000 0 0
AP-1 -0.31 0.32 -10000 0 -0.73 104 104
MAPK14 0.014 0.01 -10000 0 -10000 0 0
MAPK10 -0.04 0.16 -10000 0 -0.52 38 38
MAPK11 0.01 0.046 -10000 0 -0.48 3 3
KRT5 -0.47 0.51 -10000 0 -1.1 130 130
interleukin-1 receptor activity 0 0.006 -10000 0 -10000 0 0
NCOA1 0.015 0.001 -10000 0 -10000 0 0
STAT1 0.016 0.037 -10000 0 -0.44 2 2
CGA -0.089 0.16 -10000 0 -0.53 20 20
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.13 0.14 0.37 61 -10000 0 61
MAPK3 0.013 0.027 -10000 0 -0.45 1 1
MAPK1 0.013 0.027 -10000 0 -0.46 1 1
ICAM1 -0.12 0.21 -10000 0 -0.65 29 29
NFKB1 -0.019 0.071 -10000 0 -10000 0 0
MAPK8 -0.14 0.17 -10000 0 -0.44 58 58
MAPK9 0.014 0.01 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.027 0.21 0.54 28 -0.67 6 34
BAX -0.002 0.1 -10000 0 -0.46 4 4
POMC -0.21 0.36 -10000 0 -1.2 34 34
EP300 0.068 0.1 0.28 44 -0.23 2 46
cortisol/GR alpha (dimer)/p53 0.2 0.25 0.55 79 -0.48 4 83
proteasomal ubiquitin-dependent protein catabolic process 0.058 0.07 0.22 16 -0.24 2 18
SGK1 0.098 0.2 -10000 0 -1.3 4 4
IL13 -0.2 0.22 -10000 0 -0.74 27 27
IL6 -0.16 0.29 -10000 0 -0.83 40 40
PRKACG 0.001 0.034 -10000 0 -0.45 2 2
IL5 -0.18 0.18 -10000 0 -0.68 15 15
IL2 -0.25 0.26 -10000 0 -0.7 57 57
CDK5 0.013 0.005 -10000 0 -10000 0 0
PRKACB 0.003 0.07 -10000 0 -0.54 6 6
HSP90AA1 0.012 0 -10000 0 -10000 0 0
IL8 -0.18 0.33 -10000 0 -0.94 48 48
CDK5R1/CDK5 0.012 0.055 -10000 0 -0.34 8 8
NF kappa B1 p50/RelA/PKAc -0.007 0.1 -10000 0 -0.42 2 2
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.21 0.21 0.52 83 -10000 0 83
SMARCA4 0.01 0.041 -10000 0 -0.54 2 2
chromatin remodeling 0.14 0.14 0.37 59 -0.32 1 60
NF kappa B1 p50/RelA/Cbp 0.044 0.15 0.33 20 -0.48 2 22
JUN (dimer) -0.18 0.19 -10000 0 -0.49 59 59
YWHAH 0.012 0 -10000 0 -10000 0 0
VIPR1 -0.12 0.25 -10000 0 -0.74 41 41
NR3C1 0.14 0.18 0.45 55 -0.46 5 60
NR4A1 -0.051 0.16 -10000 0 -0.48 41 41
TIF2/SUV420H1 0.004 0.074 -10000 0 -0.37 14 14
MAPKKK cascade 0.036 0.21 0.53 28 -0.64 6 34
cortisol/GR alpha (dimer)/Src-1 0.22 0.23 0.55 84 -0.38 1 85
PBX1 0.001 0.074 -10000 0 -0.54 6 6
POU1F1 -0.003 0.044 -10000 0 -0.45 2 2
SELE -0.18 0.32 -10000 0 -0.82 57 57
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.14 0.14 0.37 59 -0.32 1 60
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.21 0.21 0.52 83 -10000 0 83
mol:cortisol 0.14 0.16 0.38 86 -10000 0 86
MMP1 -0.24 0.41 -10000 0 -0.92 79 79
Reelin signaling pathway

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
CDK5R1/CDK5 0.01 0.054 -9999 0 -0.35 8 8
VLDLR -0.004 0.093 -9999 0 -0.54 11 11
CRKL 0.012 0 -9999 0 -10000 0 0
LRPAP1 0.012 0 -9999 0 -10000 0 0
FYN 0.011 0.024 -9999 0 -0.45 1 1
ITGA3 0 0.081 -9999 0 -0.51 9 9
RELN/VLDLR/Fyn -0.082 0.15 -9999 0 -0.29 124 124
MAPK8IP1/MKK7/MAP3K11/JNK1 0.03 0.045 -9999 0 -10000 0 0
AKT1 -0.065 0.13 -9999 0 -0.44 11 11
MAP2K7 0.012 0 -9999 0 -10000 0 0
RAPGEF1 0.012 0 -9999 0 -10000 0 0
DAB1 -0.03 0.13 -9999 0 -0.45 31 31
RELN/LRP8/DAB1 -0.091 0.15 -9999 0 -0.28 135 135
LRPAP1/LRP8 0.013 0.045 -9999 0 -0.34 6 6
RELN/LRP8/DAB1/Fyn -0.08 0.15 -9999 0 -0.31 69 69
DAB1/alpha3/beta1 Integrin -0.095 0.13 -9999 0 -0.42 20 20
long-term memory -0.12 0.19 -9999 0 -0.5 45 45
DAB1/LIS1 -0.094 0.13 -9999 0 -0.42 18 18
DAB1/CRLK/C3G -0.09 0.12 -9999 0 -0.4 18 18
PIK3CA 0.01 0.034 -9999 0 -0.45 2 2
DAB1/NCK2 -0.075 0.14 -9999 0 -0.43 19 19
ARHGEF2 0.012 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.075 0.19 -9999 0 -0.48 64 64
CDK5R1 0.001 0.074 -9999 0 -0.5 8 8
RELN -0.14 0.23 -9999 0 -0.49 114 114
PIK3R1 -0.018 0.12 -9999 0 -0.52 21 21
RELN/LRP8/Fyn -0.077 0.15 -9999 0 -0.3 116 116
GRIN2A/RELN/LRP8/DAB1/Fyn -0.12 0.18 -9999 0 -0.49 39 39
MAPK8 0.009 0.04 -9999 0 -0.54 2 2
RELN/VLDLR/DAB1 -0.096 0.15 -9999 0 -0.28 142 142
ITGB1 0.012 0 -9999 0 -10000 0 0
MAP1B -0.1 0.17 -9999 0 -0.41 48 48
RELN/LRP8 -0.076 0.15 -9999 0 -0.3 116 116
GRIN2B/RELN/LRP8/DAB1/Fyn -0.087 0.16 -9999 0 -0.41 37 37
PI3K -0.006 0.093 -9999 0 -0.37 23 23
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.009 0.059 -9999 0 -0.36 9 9
RAP1A -0.057 0.13 -9999 0 -0.38 18 18
PAFAH1B1 0.012 0 -9999 0 -10000 0 0
MAPK8IP1 0.002 0.073 -9999 0 -0.53 7 7
CRLK/C3G 0.018 0 -9999 0 -10000 0 0
GRIN2B -0.016 0.099 -9999 0 -0.45 18 18
NCK2 0.011 0.029 -9999 0 -0.54 1 1
neuron differentiation -0.026 0.089 -9999 0 -0.3 6 6
neuron adhesion -0.05 0.13 -9999 0 -0.43 7 7
LRP8 0.004 0.062 -9999 0 -0.48 6 6
GSK3B -0.056 0.12 -9999 0 -0.41 11 11
RELN/VLDLR/DAB1/Fyn -0.085 0.15 -9999 0 -0.3 76 76
MAP3K11 0.012 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.075 0.13 -9999 0 -0.35 26 26
CDK5 0.012 0 -9999 0 -10000 0 0
MAPT -0.002 0.096 -9999 0 -0.44 16 16
neuron migration -0.056 0.14 -9999 0 -0.39 13 13
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.026 0.09 -9999 0 -0.31 6 6
RELN/VLDLR -0.07 0.14 -9999 0 -0.3 68 68
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.047 0.13 -10000 0 -0.35 32 32
IKBKB -0.021 0.072 -10000 0 -0.25 5 5
AKT1 -0.057 0.1 0.2 1 -0.23 53 54
IKBKG -0.021 0.076 -10000 0 -0.26 7 7
CALM1 -0.041 0.12 0.24 1 -0.4 21 22
PIK3CA 0.01 0.034 -10000 0 -0.45 2 2
MAP3K1 -0.082 0.19 -10000 0 -0.48 47 47
MAP3K7 0.012 0 -10000 0 -10000 0 0
mol:Ca2+ -0.049 0.13 0.21 5 -0.41 23 28
DOK1 0.012 0 -10000 0 -10000 0 0
AP-1 -0.02 0.08 0.16 1 -0.24 16 17
LYN 0.008 0.049 -10000 0 -0.54 3 3
BLNK -0.006 0.097 -10000 0 -0.54 12 12
SHC1 0.012 0 -10000 0 -10000 0 0
BCR complex -0.11 0.2 -10000 0 -0.4 109 109
CD22 -0.15 0.22 -10000 0 -0.53 66 66
CAMK2G -0.033 0.11 0.24 1 -0.4 17 18
CSNK2A1 0.012 0 -10000 0 -10000 0 0
INPP5D -0.002 0.088 -10000 0 -0.53 10 10
SHC/GRB2/SOS1 -0.083 0.14 -10000 0 -0.42 31 31
GO:0007205 -0.05 0.13 0.21 5 -0.42 23 28
SYK 0.001 0.079 -10000 0 -0.53 8 8
ELK1 -0.042 0.12 0.24 1 -0.41 21 22
NFATC1 -0.076 0.18 -10000 0 -0.42 54 54
B-cell antigen/BCR complex -0.11 0.2 -10000 0 -0.4 109 109
PAG1/CSK 0.008 0.061 -10000 0 -0.36 10 10
NFKBIB 0.001 0.027 -10000 0 -10000 0 0
HRAS -0.042 0.12 0.22 1 -0.38 24 25
NFKBIA 0.001 0.026 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.007 0.022 -10000 0 -10000 0 0
RasGAP/Csk -0.07 0.17 -10000 0 -0.48 29 29
mol:GDP -0.047 0.12 0.23 2 -0.4 23 25
PTEN 0.002 0.075 -10000 0 -0.54 7 7
CD79B -0.043 0.16 -10000 0 -0.48 41 41
NF-kappa-B/RelA/I kappa B alpha 0.007 0.022 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.11 0.2 -10000 0 -0.47 70 70
PIK3R1 -0.018 0.12 -10000 0 -0.52 21 21
mol:IP3 -0.051 0.13 0.21 5 -0.43 23 28
CSK 0.012 0 -10000 0 -10000 0 0
FOS -0.047 0.13 0.24 1 -0.46 18 19
CHUK -0.021 0.076 -10000 0 -0.26 7 7
IBTK 0.009 0.04 -10000 0 -0.54 2 2
CARD11/BCL10/MALT1/TAK1 -0.07 0.12 -10000 0 -0.39 32 32
PTPN6 -0.13 0.22 -10000 0 -0.5 67 67
RELA 0.012 0 -10000 0 -10000 0 0
BCL2A1 0.004 0.028 -10000 0 -0.097 12 12
VAV2 -0.12 0.23 -10000 0 -0.51 70 70
ubiquitin-dependent protein catabolic process 0.005 0.026 -10000 0 -10000 0 0
BTK -0.029 0.18 0.34 6 -1 11 17
CD19 -0.14 0.22 -10000 0 -0.53 70 70
MAP4K1 -0.006 0.095 -10000 0 -0.48 14 14
CD72 0 0.076 -10000 0 -0.48 9 9
PAG1 -0.002 0.084 -10000 0 -0.5 10 10
MAPK14 -0.064 0.16 -10000 0 -0.41 45 45
SH3BP5 -0.006 0.098 -10000 0 -0.54 12 12
PIK3AP1 -0.052 0.15 0.22 4 -0.43 30 34
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.066 0.17 -10000 0 -0.42 53 53
RAF1 -0.034 0.12 0.22 1 -0.4 16 17
RasGAP/p62DOK/SHIP -0.072 0.17 -10000 0 -0.49 32 32
CD79A -0.11 0.22 -10000 0 -0.48 91 91
re-entry into mitotic cell cycle -0.02 0.08 0.16 1 -0.24 16 17
RASA1 0.012 0 -10000 0 -10000 0 0
MAPK3 -0.018 0.1 0.21 1 -0.37 11 12
MAPK1 -0.018 0.1 0.21 1 -0.38 11 12
CD72/SHP1 -0.12 0.22 -10000 0 -0.53 58 58
NFKB1 0.012 0 -10000 0 -10000 0 0
MAPK8 -0.065 0.16 -10000 0 -0.42 45 45
actin cytoskeleton organization -0.095 0.2 -10000 0 -0.47 56 56
NF-kappa-B/RelA 0.018 0.042 -10000 0 -10000 0 0
Calcineurin -0.032 0.11 -10000 0 -0.4 16 16
PI3K -0.15 0.18 -10000 0 -0.46 78 78
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.053 0.14 0.23 4 -0.44 27 31
SOS1 0.012 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.11 0.26 -10000 0 -0.74 43 43
DAPP1 -0.14 0.29 -10000 0 -0.88 38 38
cytokine secretion -0.07 0.16 -10000 0 -0.39 54 54
mol:DAG -0.051 0.13 0.21 5 -0.43 23 28
PLCG2 0 0.076 -10000 0 -0.48 9 9
MAP2K1 -0.026 0.11 0.21 1 -0.41 12 13
B-cell antigen/BCR complex/FcgammaRIIB -0.097 0.19 -10000 0 -0.36 119 119
mol:PI-3-4-5-P3 -0.11 0.13 0.21 2 -0.32 76 78
ETS1 -0.025 0.1 0.23 1 -0.38 15 16
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.074 0.17 -10000 0 -0.35 79 79
B-cell antigen/BCR complex/LYN -0.1 0.18 -10000 0 -0.41 74 74
MALT1 0.006 0.053 -10000 0 -0.45 5 5
TRAF6 0.012 0 -10000 0 -10000 0 0
RAC1 -0.1 0.21 -10000 0 -0.52 54 54
B-cell antigen/BCR complex/LYN/SYK -0.15 0.21 -10000 0 -0.52 65 65
CARD11 -0.071 0.15 -10000 0 -0.4 48 48
FCGR2B -0.015 0.12 -10000 0 -0.52 19 19
PPP3CA 0.006 0.057 -10000 0 -0.54 4 4
BCL10 0.012 0 -10000 0 -10000 0 0
IKK complex -0.004 0.034 -10000 0 -10000 0 0
PTPRC -0.032 0.15 -10000 0 -0.51 31 31
PDPK1 -0.058 0.1 0.19 1 -0.23 53 54
PPP3CB 0.012 0 -10000 0 -10000 0 0
PPP3CC 0 0.08 -10000 0 -0.54 8 8
POU2F2 0.005 0.025 -10000 0 -0.094 6 6
IGF1 pathway

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
NCK2 0.011 0.029 -10000 0 -0.54 1 1
PTK2 0.012 0 -10000 0 -10000 0 0
CRKL -0.045 0.14 -10000 0 -0.34 55 55
GRB2/SOS1/SHC 0.025 0 -10000 0 -10000 0 0
HRAS 0.011 0.024 -10000 0 -0.45 1 1
IRS1/Crk -0.045 0.14 -10000 0 -0.34 55 55
IGF-1R heterotetramer/IGF1/PTP1B -0.048 0.14 -10000 0 -0.35 55 55
AKT1 -0.038 0.14 -10000 0 -0.44 26 26
BAD -0.03 0.14 -10000 0 -0.41 26 26
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.045 0.14 -10000 0 -0.34 55 55
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.045 0.14 -10000 0 -0.34 55 55
RAF1 -0.023 0.13 -10000 0 -0.4 23 23
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.035 0.14 -10000 0 -0.32 55 55
YWHAZ 0.012 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.056 0.15 -10000 0 -0.31 84 84
PIK3CA 0.01 0.034 -10000 0 -0.45 2 2
RPS6KB1 -0.038 0.14 -10000 0 -0.44 26 26
GNB2L1 0.012 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.021 0.11 -10000 0 -0.34 23 23
PXN 0.012 0 -10000 0 -10000 0 0
PIK3R1 -0.018 0.12 -10000 0 -0.52 21 21
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.018 0 -10000 0 -10000 0 0
HRAS/GTP -0.052 0.11 -10000 0 -0.44 16 16
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.022 0.12 -10000 0 -0.38 16 16
IGF-1R heterotetramer -0.042 0.16 -10000 0 -0.58 28 28
IGF-1R heterotetramer/IGF1/IRS/Nck -0.044 0.14 -10000 0 -0.34 56 56
Crk/p130 Cas/Paxillin -0.029 0.13 -10000 0 -0.47 16 16
IGF1R -0.042 0.16 -10000 0 -0.58 28 28
IGF1 -0.075 0.19 -10000 0 -0.52 57 57
IRS2/Crk -0.06 0.15 -10000 0 -0.34 64 64
PI3K -0.051 0.16 -10000 0 -0.44 35 35
apoptosis 0.019 0.12 0.36 23 -10000 0 23
HRAS/GDP 0.008 0.017 -10000 0 -0.32 1 1
PRKCD -0.037 0.16 -10000 0 -0.43 39 39
RAF1/14-3-3 E -0.013 0.12 -10000 0 -0.34 22 22
BAD/14-3-3 -0.021 0.13 -10000 0 -0.39 23 23
PRKCZ -0.039 0.14 -10000 0 -0.45 26 26
Crk/p130 Cas/Paxillin/FAK1 -0.054 0.11 -10000 0 -0.39 22 22
PTPN1 0.012 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.044 0.16 -10000 0 -0.4 55 55
BCAR1 0.011 0.029 -10000 0 -0.54 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.04 0.14 -10000 0 -0.32 60 60
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.012 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.045 0.14 -10000 0 -0.34 56 56
GRB10 0 0.08 -10000 0 -0.54 8 8
PTPN11 -0.045 0.14 -10000 0 -0.34 55 55
IRS1 -0.056 0.15 -10000 0 -0.35 61 61
IRS2 -0.07 0.16 -10000 0 -0.33 84 84
IGF-1R heterotetramer/IGF1 -0.075 0.18 -10000 0 -0.41 78 78
GRB2 0.012 0 -10000 0 -10000 0 0
PDPK1 -0.045 0.15 -10000 0 -0.47 26 26
YWHAE 0.012 0 -10000 0 -10000 0 0
PRKD1 -0.049 0.17 -10000 0 -0.45 42 42
SHC1 0.012 0 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.012 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.028 0.095 -10000 0 -0.3 15 15
NT3 (dimer)/TRKC -0.1 0.2 -10000 0 -0.4 106 106
NT3 (dimer)/TRKB -0.13 0.21 -10000 0 -0.35 155 155
SHC/Grb2/SOS1/GAB1/PI3K 0.017 0.06 -10000 0 -10000 0 0
RAPGEF1 0.012 0 -10000 0 -10000 0 0
BDNF -0.087 0.2 -10000 0 -0.48 74 74
PIK3CA 0.01 0.034 -10000 0 -0.45 2 2
DYNLT1 0.012 0 -10000 0 -10000 0 0
NTRK1 -0.043 0.16 -10000 0 -0.5 40 40
NTRK2 -0.076 0.19 -10000 0 -0.49 65 65
NTRK3 -0.079 0.2 -10000 0 -0.5 66 66
NT-4/5 (dimer)/TRKB -0.13 0.2 -10000 0 -0.34 159 159
neuron apoptosis 0.12 0.19 0.42 74 -0.2 2 76
SHC 2-3/Grb2 -0.13 0.21 0.21 2 -0.46 73 75
SHC1 0.012 0 -10000 0 -10000 0 0
SHC2 -0.12 0.18 0.2 4 -0.45 53 57
SHC3 -0.14 0.22 0.2 3 -0.48 75 78
STAT3 (dimer) 0.003 0.073 -10000 0 -0.34 15 15
NT3 (dimer)/TRKA -0.11 0.2 -10000 0 -0.36 131 131
RIN/GDP -0.02 0.076 -10000 0 -0.24 6 6
GIPC1 0.012 0 -10000 0 -10000 0 0
KRAS 0.012 0 -10000 0 -10000 0 0
DNAJA3 -0.069 0.15 0.23 4 -0.36 52 56
RIN/GTP 0.002 0.004 -10000 0 -10000 0 0
CCND1 -0.009 0.16 -10000 0 -0.71 18 18
MAGED1 0.002 0.075 -10000 0 -0.54 7 7
PTPN11 0.012 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.068 0.18 -10000 0 -0.49 57 57
SHC/GRB2/SOS1 0.025 0 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.064 0.17 -10000 0 -0.34 90 90
TRKA/NEDD4-2 -0.023 0.12 -10000 0 -0.35 41 41
ELMO1 0.007 0.053 -10000 0 -0.5 4 4
RhoG/GTP/ELMO1/DOCK1 0.013 0.032 -10000 0 -0.3 4 4
NGF -0.045 0.16 -10000 0 -0.5 41 41
HRAS 0.011 0.024 -10000 0 -0.45 1 1
DOCK1 0.012 0 -10000 0 -10000 0 0
GAB2 0.01 0.034 -10000 0 -0.45 2 2
RIT2 0.002 0.005 -10000 0 -10000 0 0
RIT1 0.011 0.029 -10000 0 -0.54 1 1
FRS2 0.012 0 -10000 0 -10000 0 0
DNM1 -0.012 0.11 -10000 0 -0.48 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.012 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.07 0.15 0.22 4 -0.35 55 59
mol:GDP -0.031 0.11 -10000 0 -0.32 14 14
NGF (dimer) -0.045 0.16 -10000 0 -0.5 41 41
RhoG/GDP 0.005 0.038 -10000 0 -0.36 4 4
RIT1/GDP -0.017 0.077 -10000 0 -0.24 6 6
TIAM1 0 0.08 -10000 0 -0.54 8 8
PIK3R1 -0.018 0.12 -10000 0 -0.52 21 21
BDNF (dimer)/TRKB -0.089 0.17 -10000 0 -0.31 126 126
KIDINS220/CRKL/C3G 0.018 0 -10000 0 -10000 0 0
SHC/RasGAP 0.018 0 -10000 0 -10000 0 0
FRS2 family/SHP2 0.024 0.018 -10000 0 -0.32 1 1
SHC/GRB2/SOS1/GAB1 0.031 0.016 -10000 0 -0.28 1 1
RIT1/GTP 0.008 0.021 -10000 0 -0.39 1 1
NT3 (dimer) -0.067 0.18 -10000 0 -0.48 59 59
RAP1/GDP -0.031 0.051 -10000 0 -0.24 2 2
KIDINS220/CRKL 0.012 0 -10000 0 -10000 0 0
BDNF (dimer) -0.087 0.2 -10000 0 -0.48 74 74
ubiquitin-dependent protein catabolic process -0.045 0.14 -10000 0 -0.32 75 75
Schwann cell development -0.038 0.032 -10000 0 -10000 0 0
EHD4 0.012 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.031 0.016 -10000 0 -0.28 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.034 0.017 -10000 0 -10000 0 0
RAP1B 0.012 0 -10000 0 -10000 0 0
RAP1A 0.012 0 -10000 0 -10000 0 0
CDC42/GTP -0.15 0.18 -10000 0 -0.48 67 67
ABL1 0.012 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.018 0 -10000 0 -10000 0 0
Rap1/GTP -0.004 0.071 -10000 0 -10000 0 0
STAT3 0.003 0.073 -10000 0 -0.34 15 15
axon guidance -0.15 0.17 -10000 0 -0.46 67 67
MAPK3 -0.053 0.15 -10000 0 -0.34 61 61
MAPK1 -0.053 0.15 -10000 0 -0.34 60 60
CDC42/GDP -0.016 0.076 -10000 0 -0.23 7 7
NTF3 -0.067 0.18 -10000 0 -0.48 59 59
NTF4 -0.068 0.18 -10000 0 -0.49 57 57
NGF (dimer)/TRKA/FAIM -0.045 0.14 -10000 0 -0.32 75 75
PI3K -0.006 0.093 -10000 0 -0.37 23 23
FRS3 0.011 0.029 -10000 0 -0.54 1 1
FAIM 0.011 0.029 -10000 0 -0.54 1 1
GAB1 0.011 0.029 -10000 0 -0.54 1 1
RASGRF1 -0.14 0.19 0.23 4 -0.41 88 92
SOS1 0.012 0 -10000 0 -10000 0 0
MCF2L -0.092 0.18 -10000 0 -0.35 115 115
RGS19 0.009 0.04 -10000 0 -0.54 2 2
CDC42 0.012 0 -10000 0 -10000 0 0
RAS family/GTP -0.013 0.073 -10000 0 -10000 0 0
Rac1/GDP -0.016 0.076 -10000 0 -0.24 6 6
NGF (dimer)/TRKA/GRIT -0.052 0.14 -10000 0 -0.33 74 74
neuron projection morphogenesis -0.063 0.15 -10000 0 -0.42 29 29
NGF (dimer)/TRKA/NEDD4-2 -0.045 0.14 -10000 0 -0.32 75 75
MAP2K1 0.032 0.015 -10000 0 -10000 0 0
NGFR -0.081 0.2 -10000 0 -0.49 69 69
NGF (dimer)/TRKA/GIPC/GAIP -0.026 0.12 -10000 0 -0.4 13 13
RAS family/GTP/PI3K 0.008 0.077 -10000 0 -0.64 2 2
FRS2 family/SHP2/GRB2/SOS1 0.036 0.015 -10000 0 -0.26 1 1
NRAS 0.005 0.064 -10000 0 -0.54 5 5
GRB2/SOS1 0.018 0 -10000 0 -10000 0 0
PRKCI 0.008 0.044 -10000 0 -0.48 3 3
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCZ 0.009 0.04 -10000 0 -0.54 2 2
MAPKKK cascade -0.1 0.2 -10000 0 -0.59 48 48
RASA1 0.012 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.022 0.12 -10000 0 -0.35 40 40
SQSTM1 0.011 0.024 -10000 0 -0.45 1 1
BDNF (dimer)/TRKB/GIPC -0.073 0.16 -10000 0 -0.35 51 51
NGF (dimer)/TRKA/p62/Atypical PKCs -0.028 0.13 -10000 0 -0.3 49 49
MATK -0.022 0.13 -10000 0 -0.49 25 25
NEDD4L 0.011 0.029 -10000 0 -0.54 1 1
RAS family/GDP -0.029 0.05 -10000 0 -0.22 3 3
NGF (dimer)/TRKA -0.09 0.15 0.25 4 -0.34 79 83
Rac1/GTP -0.1 0.11 -10000 0 -0.3 59 59
FRS2 family/SHP2/CRK family 0.036 0.015 -10000 0 -0.26 1 1
LPA receptor mediated events

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
GNB1/GNG2 -0.016 0.11 -9999 0 -0.35 23 23
NF kappa B1 p50/RelA/I kappa B alpha -0.04 0.13 -9999 0 -0.39 12 12
AP1 -0.1 0.14 -9999 0 -0.46 27 27
mol:PIP3 -0.097 0.14 -9999 0 -0.47 28 28
AKT1 0.006 0.1 -9999 0 -0.39 11 11
PTK2B -0.019 0.088 -9999 0 -0.3 18 18
RHOA 0.012 0.043 -9999 0 -10000 0 0
PIK3CB 0.012 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.043 0.13 -9999 0 -0.36 20 20
MAGI3 0.011 0.029 -9999 0 -0.54 1 1
RELA 0.012 0 -9999 0 -10000 0 0
apoptosis -0.081 0.16 -9999 0 -0.33 82 82
HRAS/GDP 0.008 0.017 -9999 0 -0.32 1 1
positive regulation of microtubule depolymerization -0.015 0.094 -9999 0 -0.44 5 5
NF kappa B1 p50/RelA -0.086 0.14 -9999 0 -0.43 27 27
endothelial cell migration -0.049 0.19 -9999 0 -0.5 51 51
ADCY4 -0.025 0.14 -9999 0 -0.46 22 22
ADCY5 -0.05 0.16 -9999 0 -0.46 32 32
ADCY6 -0.023 0.14 -9999 0 -0.46 22 22
ADCY7 -0.024 0.14 -9999 0 -0.46 22 22
ADCY1 -0.047 0.15 -9999 0 -0.5 26 26
ADCY2 -0.046 0.16 -9999 0 -0.46 34 34
ADCY3 -0.023 0.14 -9999 0 -0.46 22 22
ADCY8 -0.03 0.14 -9999 0 -0.45 26 26
ADCY9 -0.031 0.15 -9999 0 -0.45 28 28
GSK3B -0.012 0.084 -9999 0 -0.3 12 12
arachidonic acid secretion -0.019 0.13 -9999 0 -0.41 24 24
GNG2 -0.002 0.084 -9999 0 -0.48 11 11
TRIP6 0.007 0.064 -9999 0 -0.39 9 9
GNAO1 -0.033 0.13 -9999 0 -0.32 52 52
HRAS 0.011 0.024 -9999 0 -0.45 1 1
NFKBIA -0.052 0.15 -9999 0 -0.39 25 25
GAB1 0.011 0.029 -9999 0 -0.54 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly 0.001 0.14 -9999 0 -0.88 9 9
JUN 0.009 0.037 -9999 0 -0.5 2 2
LPA/LPA2/NHERF2 0.008 0.04 -9999 0 -0.33 3 3
TIAM1 -0.022 0.16 -9999 0 -1 9 9
PIK3R1 -0.018 0.12 -9999 0 -0.52 21 21
mol:IP3 -0.044 0.13 -9999 0 -0.36 20 20
PLCB3 0.014 0.036 -9999 0 -0.29 3 3
FOS -0.019 0.12 -9999 0 -0.47 24 24
positive regulation of mitosis -0.019 0.13 -9999 0 -0.41 24 24
LPA/LPA1-2-3 -0.085 0.16 -9999 0 -0.34 82 82
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.011 0.029 -9999 0 -0.54 1 1
stress fiber formation -0.036 0.11 -9999 0 -0.35 19 19
GNAZ -0.028 0.13 -9999 0 -0.32 46 46
EGFR/PI3K-beta/Gab1 -0.1 0.15 -9999 0 -0.49 28 28
positive regulation of dendritic cell cytokine production -0.086 0.16 -9999 0 -0.33 82 82
LPA/LPA2/MAGI-3 0.01 0.031 -9999 0 -0.32 1 1
ARHGEF1 -0.002 0.096 -9999 0 -0.5 5 5
GNAI2 -0.018 0.11 -9999 0 -0.32 35 35
GNAI3 -0.018 0.11 -9999 0 -0.32 35 35
GNAI1 -0.028 0.12 -9999 0 -0.33 46 46
LPA/LPA3 -0.097 0.17 -9999 0 -0.38 96 96
LPA/LPA2 0.002 0.032 -9999 0 -10000 0 0
LPA/LPA1 -0.031 0.13 -9999 0 -0.34 51 51
HB-EGF/EGFR -0.044 0.13 -9999 0 -0.3 76 76
HBEGF -0.046 0.14 -9999 0 -0.35 65 65
mol:DAG -0.044 0.13 -9999 0 -0.36 20 20
cAMP biosynthetic process -0.036 0.15 -9999 0 -0.46 26 26
NFKB1 0.012 0 -9999 0 -10000 0 0
SRC 0.009 0.04 -9999 0 -0.54 2 2
GNB1 0.012 0.001 -9999 0 -10000 0 0
LYN -0.055 0.15 -9999 0 -0.38 31 31
GNAQ -0.058 0.12 -9999 0 -0.29 71 71
LPAR2 0.012 0 -9999 0 -10000 0 0
LPAR3 -0.12 0.23 -9999 0 -0.52 96 96
LPAR1 -0.027 0.13 -9999 0 -0.58 18 18
IL8 -0.11 0.19 -9999 0 -0.46 56 56
PTK2 -0.074 0.16 -9999 0 -0.31 82 82
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
CASP3 -0.082 0.16 -9999 0 -0.33 82 82
EGFR -0.004 0.092 -9999 0 -0.53 11 11
PLCG1 -0.063 0.14 -9999 0 -0.31 79 79
PLD2 -0.075 0.16 -9999 0 -0.32 75 75
G12/G13 -0.007 0.1 -9999 0 -0.35 18 18
PI3K-beta -0.041 0.097 -9999 0 -0.46 11 11
cell migration -0.014 0.079 -9999 0 -0.26 12 12
SLC9A3R2 0.008 0.047 -9999 0 -0.51 3 3
PXN -0.036 0.11 -9999 0 -0.35 19 19
HRAS/GTP -0.02 0.13 -9999 0 -0.42 24 24
RAC1 0.012 0 -9999 0 -10000 0 0
MMP9 -0.076 0.2 -9999 0 -0.5 64 64
PRKCE 0.011 0.029 -9999 0 -0.54 1 1
PRKCD -0.038 0.12 -9999 0 -0.35 20 20
Gi(beta/gamma) -0.021 0.13 -9999 0 -0.42 24 24
mol:LPA -0.012 0.049 -9999 0 -0.18 17 17
TRIP6/p130 Cas/FAK1/Paxillin -0.054 0.15 -9999 0 -0.45 21 21
MAPKKK cascade -0.019 0.13 -9999 0 -0.41 24 24
contractile ring contraction involved in cytokinesis 0.012 0.043 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.065 0.13 -9999 0 -0.3 79 79
GNA15 -0.067 0.14 -9999 0 -0.32 74 74
GNA12 0.012 0 -9999 0 -10000 0 0
GNA13 0.012 0 -9999 0 -10000 0 0
MAPT -0.016 0.096 -9999 0 -0.5 4 4
GNA11 -0.064 0.14 -9999 0 -0.3 75 75
Rac1/GTP 0.001 0.15 -9999 0 -0.94 9 9
MMP2 -0.049 0.19 -9999 0 -0.51 51 51
Canonical Wnt signaling pathway

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
HDAC1 0.018 0.025 -10000 0 -10000 0 0
AES 0.015 0.036 -10000 0 -0.54 1 1
FBXW11 0.012 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.016 0.032 -10000 0 -0.34 3 3
SMAD4 0.011 0.029 -10000 0 -0.54 1 1
DKK2 -0.087 0.2 -10000 0 -0.5 72 72
TLE1 0.014 0.046 -10000 0 -0.54 2 2
MACF1 0.013 0.001 -10000 0 -10000 0 0
CTNNB1 0.068 0.087 0.27 13 -10000 0 13
WIF1 -0.25 0.25 -10000 0 -0.49 193 193
beta catenin/RanBP3 0.052 0.14 0.44 31 -10000 0 31
KREMEN2 -0.053 0.17 -10000 0 -0.48 49 49
DKK1 -0.18 0.24 -10000 0 -0.48 142 142
beta catenin/beta TrCP1 0.071 0.082 0.27 11 -10000 0 11
FZD1 0.009 0.044 -10000 0 -0.48 3 3
AXIN2 -0.055 0.26 -10000 0 -1.3 12 12
AXIN1 0.013 0.001 -10000 0 -10000 0 0
RAN 0.013 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.033 0.036 0.25 1 -10000 0 1
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.005 0.14 -10000 0 -0.43 14 14
Axin1/APC/GSK3 0.052 0.057 0.24 6 -10000 0 6
Axin1/APC/GSK3/beta catenin/Macf1 0.056 0.052 0.3 1 -0.38 1 2
HNF1A -0.093 0.22 -10000 0 -0.53 74 74
CTBP1 0.017 0.021 -10000 0 -10000 0 0
MYC -0.024 0.22 -10000 0 -1.4 9 9
RANBP3 0.013 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.075 0.16 -10000 0 -0.32 108 108
NKD1 -0.093 0.2 -10000 0 -0.46 82 82
TCF4 0.009 0.065 -10000 0 -0.51 5 5
TCF3 0.015 0.033 -10000 0 -0.47 1 1
WNT1/LRP6/FZD1/Axin1 0.023 0.053 -10000 0 -0.51 1 1
Ran/GTP 0.01 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.008 0.16 0.43 17 -0.41 10 27
LEF1 -0.057 0.18 -10000 0 -0.52 50 50
DVL1 0.062 0.044 0.21 2 -10000 0 2
CSNK2A1 0.013 0.001 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.014 0.16 -10000 0 -0.48 17 17
DKK1/LRP6/Kremen 2 -0.13 0.17 -10000 0 -0.3 173 173
LRP6 0.013 0.001 -10000 0 -10000 0 0
CSNK1A1 0.018 0.025 -10000 0 -10000 0 0
NLK 0.011 0.004 -10000 0 -10000 0 0
CCND1 -0.043 0.28 -10000 0 -1.4 15 15
WNT1 -0.003 0.078 -10000 0 -0.45 11 11
GSK3A 0.013 0.001 -10000 0 -10000 0 0
GSK3B 0.012 0.001 -10000 0 -10000 0 0
FRAT1 0.007 0.049 -10000 0 -0.54 3 3
PPP2R5D 0.079 0.092 0.24 81 -10000 0 81
APC 0.025 0.049 -10000 0 -0.47 1 1
WNT1/LRP6/FZD1 0.1 0.09 0.23 87 -10000 0 87
CREBBP 0.017 0.021 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.012 0 -9999 0 -10000 0 0
GNAT1/GTP -0.003 0.05 -9999 0 -0.32 9 9
Metarhodopsin II/Arrestin 0.002 0.04 -9999 0 -0.26 8 8
PDE6G/GNAT1/GTP -0.04 0.12 -9999 0 -0.3 62 62
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.004 0.071 -9999 0 -0.45 9 9
GRK1 -0.008 0.07 -9999 0 -0.45 9 9
CNG Channel -0.14 0.18 -9999 0 -0.5 54 54
mol:Na + -0.082 0.14 -9999 0 -0.46 27 27
mol:ADP -0.008 0.07 -9999 0 -0.45 9 9
RGS9-1/Gbeta5/R9AP -0.039 0.14 -9999 0 -0.33 66 66
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.082 0.15 -9999 0 -0.48 27 27
CNGB1 -0.058 0.17 -9999 0 -0.49 51 51
RDH5 -0.015 0.11 -9999 0 -0.47 21 21
SAG 0.002 0.041 -9999 0 -0.45 3 3
mol:Ca2+ -0.054 0.15 -9999 0 -0.45 27 27
Na + (4 Units) -0.077 0.13 -9999 0 -0.43 27 27
RGS9 -0.054 0.17 -9999 0 -0.49 49 49
GNB1/GNGT1 -0.015 0.11 -9999 0 -0.38 30 30
GNAT1/GDP -0.035 0.13 -9999 0 -0.37 34 34
GUCY2D -0.008 0.088 -9999 0 -0.45 14 14
GNGT1 -0.033 0.15 -9999 0 -0.54 30 30
GUCY2F 0.003 0.034 -9999 0 -0.45 2 2
GNB5 0.006 0.057 -9999 0 -0.54 4 4
mol:GMP (4 units) -0.078 0.16 -9999 0 -0.35 71 71
mol:11-cis-retinal -0.015 0.11 -9999 0 -0.47 21 21
mol:cGMP -0.015 0.1 -9999 0 -0.36 13 13
GNB1 0.012 0 -9999 0 -10000 0 0
Rhodopsin -0.011 0.09 -9999 0 -0.34 25 25
SLC24A1 0.012 0 -9999 0 -10000 0 0
CNGA1 -0.044 0.16 -9999 0 -0.51 40 40
Metarhodopsin II -0.004 0.047 -9999 0 -0.24 14 14
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.017 0.11 -9999 0 -0.36 16 16
RGS9BP -0.022 0.12 -9999 0 -0.45 26 26
Metarhodopsin II/Transducin -0.011 0.078 -9999 0 -0.26 31 31
GCAP Family/Ca ++ -0.014 0.087 -9999 0 -0.27 36 36
PDE6A/B -0.063 0.15 -9999 0 -0.34 83 83
mol:Pi -0.039 0.14 -9999 0 -0.33 66 66
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.011 0.093 -9999 0 -0.28 39 39
PDE6B -0.098 0.21 -9999 0 -0.48 82 82
PDE6A 0.01 0.034 -9999 0 -0.45 2 2
PDE6G -0.063 0.18 -9999 0 -0.48 56 56
RHO -0.001 0.053 -9999 0 -0.45 5 5
PDE6 -0.11 0.2 -9999 0 -0.5 52 52
GUCA1A -0.009 0.088 -9999 0 -0.45 14 14
GC2/GCAP Family -0.011 0.089 -9999 0 -0.32 13 13
GUCA1C -0.005 0.052 -9999 0 -0.45 5 5
GUCA1B -0.014 0.12 -9999 0 -0.51 19 19
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.038 0.15 -10000 0 -0.42 32 32
CRKL -0.038 0.15 -10000 0 -0.43 34 34
HRAS -0.033 0.15 -10000 0 -0.43 26 26
mol:PIP3 -0.047 0.15 0.23 1 -0.42 36 37
SPRED1 0.012 0 -10000 0 -10000 0 0
SPRED2 0.012 0 -10000 0 -10000 0 0
GAB1 -0.046 0.16 -10000 0 -0.45 35 35
FOXO3 -0.033 0.14 -10000 0 -0.42 31 31
AKT1 -0.042 0.15 -10000 0 -0.43 36 36
BAD -0.033 0.14 -10000 0 -0.42 31 31
megakaryocyte differentiation -0.056 0.17 -10000 0 -0.44 43 43
GSK3B -0.033 0.14 -10000 0 -0.42 31 31
RAF1 -0.019 0.13 -10000 0 -0.35 23 23
SHC1 0.012 0 -10000 0 -10000 0 0
STAT3 -0.045 0.16 -10000 0 -0.44 36 36
STAT1 -0.1 0.33 -10000 0 -0.87 46 46
HRAS/SPRED1 -0.02 0.13 -10000 0 -0.36 21 21
cell proliferation -0.045 0.16 -10000 0 -0.44 36 36
PIK3CA 0.01 0.034 -10000 0 -0.45 2 2
TEC 0.002 0.073 -10000 0 -0.53 7 7
RPS6KB1 -0.046 0.16 -10000 0 -0.45 36 36
HRAS/SPRED2 -0.02 0.13 -10000 0 -0.35 23 23
LYN/TEC/p62DOK -0.037 0.16 -10000 0 -0.47 32 32
MAPK3 -0.003 0.096 -10000 0 -0.26 16 16
STAP1 -0.059 0.16 -10000 0 -0.45 39 39
GRAP2 -0.028 0.14 -10000 0 -0.5 29 29
JAK2 -0.091 0.29 -10000 0 -0.76 46 46
STAT1 (dimer) -0.1 0.32 -10000 0 -0.85 46 46
mol:Gleevec 0.001 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.045 0.16 -10000 0 -0.44 38 38
actin filament polymerization -0.048 0.16 -10000 0 -0.44 35 35
LYN 0.008 0.049 -10000 0 -0.54 3 3
STAP1/STAT5A (dimer) -0.07 0.21 -10000 0 -0.59 39 39
PIK3R1 -0.018 0.12 -10000 0 -0.52 21 21
CBL/CRKL/GRB2 -0.022 0.14 -10000 0 -0.4 30 30
PI3K -0.048 0.17 -10000 0 -0.48 36 36
PTEN 0.002 0.075 -10000 0 -0.54 7 7
SCF/KIT/EPO/EPOR -0.12 0.38 -10000 0 -1.2 31 31
MAPK8 -0.047 0.16 -10000 0 -0.45 36 36
STAT3 (dimer) -0.044 0.15 -10000 0 -0.44 36 36
positive regulation of transcription 0.001 0.082 -10000 0 -0.22 11 11
mol:GDP -0.04 0.16 -10000 0 -0.42 38 38
PIK3C2B -0.045 0.16 -10000 0 -0.45 36 36
CBL/CRKL -0.029 0.14 -10000 0 -0.42 30 30
FER -0.047 0.16 -10000 0 -0.46 35 35
SH2B3 -0.045 0.16 -10000 0 -0.44 36 36
PDPK1 -0.039 0.14 0.22 1 -0.4 32 33
SNAI2 -0.055 0.17 -10000 0 -0.46 41 41
positive regulation of cell proliferation -0.075 0.25 -10000 0 -0.66 46 46
KITLG -0.037 0.16 -10000 0 -0.51 35 35
cell motility -0.075 0.25 -10000 0 -0.66 46 46
PTPN6 0.009 0.05 -10000 0 -0.53 3 3
EPOR -0.033 0.2 -10000 0 -1.2 7 7
STAT5A (dimer) -0.062 0.21 -10000 0 -0.58 41 41
SOCS1 0.004 0.066 -10000 0 -0.51 6 6
cell migration 0.06 0.16 0.44 42 -10000 0 42
SOS1 0.012 0 -10000 0 -10000 0 0
EPO -0.017 0.1 -10000 0 -0.45 20 20
VAV1 -0.009 0.1 -10000 0 -0.52 15 15
GRB10 -0.051 0.16 -10000 0 -0.45 39 39
PTPN11 0.013 0.006 -10000 0 -10000 0 0
SCF/KIT -0.054 0.16 -10000 0 -0.42 48 48
GO:0007205 0.002 0.008 -10000 0 -10000 0 0
MAP2K1 -0.007 0.1 -10000 0 -0.29 16 16
CBL 0.012 0 -10000 0 -10000 0 0
KIT -0.085 0.33 -10000 0 -1.3 23 23
MAP2K2 -0.007 0.1 -10000 0 -0.29 16 16
SHC/Grb2/SOS1 -0.031 0.15 -10000 0 -0.44 30 30
STAT5A -0.064 0.22 -10000 0 -0.61 38 38
GRB2 0.012 0 -10000 0 -10000 0 0
response to radiation -0.053 0.17 -10000 0 -0.45 41 41
SHC/GRAP2 -0.011 0.1 -10000 0 -0.36 29 29
PTPRO -0.058 0.17 -10000 0 -0.45 43 43
SH2B2 -0.049 0.16 -10000 0 -0.45 35 35
DOK1 0.012 0 -10000 0 -10000 0 0
MATK -0.062 0.17 -10000 0 -0.44 42 42
CREBBP 0.019 0.034 -10000 0 -10000 0 0
BCL2 -0.052 0.28 -10000 0 -1.2 17 17
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.019 0.11 -10000 0 -0.28 52 52
ER alpha/Gai/GDP/Gbeta gamma -0.034 0.15 -10000 0 -0.38 51 51
AKT1 -0.082 0.28 -10000 0 -0.78 48 48
PIK3CA 0.01 0.034 -10000 0 -0.45 2 2
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.086 0.28 -10000 0 -0.79 48 48
mol:Ca2+ -0.018 0.14 -10000 0 -0.42 29 29
IGF1R -0.029 0.15 -10000 0 -0.54 28 28
E2/ER alpha (dimer)/Striatin -0.032 0.12 -10000 0 -0.33 52 52
SHC1 0.012 0 -10000 0 -10000 0 0
apoptosis 0.077 0.26 0.74 48 -10000 0 48
RhoA/GTP -0.034 0.087 -10000 0 -0.48 3 3
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.067 0.14 -10000 0 -0.41 51 51
regulation of stress fiber formation -0.009 0.084 0.37 4 -10000 0 4
E2/ERA-ERB (dimer) -0.03 0.12 -10000 0 -0.32 51 51
KRAS 0.012 0 -10000 0 -10000 0 0
G13/GTP -0.025 0.1 -10000 0 -0.3 48 48
pseudopodium formation 0.009 0.084 -10000 0 -0.37 4 4
E2/ER alpha (dimer)/PELP1 -0.028 0.12 -10000 0 -0.33 48 48
GRB2 0.012 0 -10000 0 -10000 0 0
GNG2 -0.002 0.084 -10000 0 -0.48 11 11
GNAO1 -0.014 0.11 -10000 0 -0.47 20 20
HRAS 0.011 0.024 -10000 0 -0.45 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.041 0.18 -10000 0 -0.47 51 51
E2/ER beta (dimer) 0.006 0.032 -10000 0 -0.34 3 3
mol:GDP -0.053 0.13 -10000 0 -0.39 49 49
mol:NADP -0.041 0.18 -10000 0 -0.47 51 51
PIK3R1 -0.018 0.12 -10000 0 -0.52 21 21
mol:IP3 -0.019 0.14 -10000 0 -0.44 29 29
IGF-1R heterotetramer -0.029 0.14 -10000 0 -0.54 28 28
PLCB1 -0.019 0.13 -10000 0 -0.46 23 23
PLCB2 -0.014 0.13 -10000 0 -0.48 18 18
IGF1 -0.067 0.19 -10000 0 -0.5 57 57
mol:L-citrulline -0.041 0.18 -10000 0 -0.47 51 51
RHOA 0.012 0 -10000 0 -10000 0 0
Gai/GDP -0.003 0.1 -10000 0 -0.57 8 8
JNK cascade 0.006 0.032 -10000 0 -0.34 3 3
BCAR1 0.011 0.029 -10000 0 -0.54 1 1
ESR2 0.008 0.044 -10000 0 -0.48 3 3
GNAQ 0.011 0.029 -10000 0 -0.54 1 1
ESR1 -0.059 0.18 -10000 0 -0.54 48 48
Gq family/GDP/Gbeta gamma -0.001 0.12 -10000 0 -0.5 16 16
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.005 0.096 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.067 0.14 -10000 0 -0.41 50 50
GNAZ -0.005 0.094 -10000 0 -0.52 12 12
E2/ER alpha (dimer) -0.043 0.14 -10000 0 -0.39 48 48
STRN 0.006 0.057 -10000 0 -0.54 4 4
GNAL -0.01 0.1 -10000 0 -0.48 17 17
PELP1 0.012 0 -10000 0 -10000 0 0
MAPK11 0.011 0.038 -10000 0 -0.28 6 6
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 -0.005 0.095 -10000 0 -0.52 12 12
HBEGF -0.054 0.16 -10000 0 -0.46 29 29
cAMP biosynthetic process -0.046 0.1 -10000 0 -0.27 63 63
SRC -0.028 0.14 -10000 0 -0.35 50 50
PI3K -0.006 0.093 -10000 0 -0.37 23 23
GNB1 0.012 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.052 0.12 -10000 0 -0.35 49 49
SOS1 0.012 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.092 0.16 -10000 0 -0.42 55 55
Gs family/GTP -0.046 0.1 -10000 0 -0.27 63 63
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.019 0.039 -10000 0 -0.28 6 6
vasodilation -0.038 0.17 -10000 0 -0.45 51 51
mol:DAG -0.019 0.14 -10000 0 -0.44 29 29
Gs family/GDP/Gbeta gamma -0.057 0.12 -10000 0 -0.35 50 50
MSN 0.008 0.089 -10000 0 -0.4 4 4
Gq family/GTP -0.015 0.12 -10000 0 -0.55 14 14
mol:PI-3-4-5-P3 -0.081 0.27 -10000 0 -0.76 48 48
NRAS 0.005 0.064 -10000 0 -0.54 5 5
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.038 0.17 0.45 51 -10000 0 51
GRB2/SOS1 0.018 0 -10000 0 -10000 0 0
RhoA/GDP -0.05 0.12 -10000 0 -0.37 48 48
NOS3 -0.044 0.19 -10000 0 -0.49 51 51
GNA11 -0.001 0.082 -10000 0 -0.52 9 9
MAPKKK cascade -0.041 0.2 -10000 0 -0.55 49 49
E2/ER alpha (dimer)/PELP1/Src -0.07 0.15 -10000 0 -0.43 50 50
ruffle organization 0.009 0.084 -10000 0 -0.37 4 4
ROCK2 0.003 0.093 -10000 0 -0.44 3 3
GNA14 -0.003 0.089 -10000 0 -0.54 10 10
GNA15 -0.005 0.093 -10000 0 -0.51 12 12
GNA13 0.012 0 -10000 0 -10000 0 0
MMP9 -0.062 0.17 -10000 0 -0.49 27 27
MMP2 -0.045 0.16 -10000 0 -0.49 23 23
Caspase cascade in apoptosis

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
TOP1 -0.026 0.13 0.19 1 -0.33 41 42
ACTA1 -0.042 0.16 0.23 4 -0.4 47 51
NUMA1 -0.026 0.13 0.19 1 -0.33 41 42
SPTAN1 -0.037 0.16 0.22 4 -0.4 42 46
LIMK1 -0.037 0.16 0.22 4 -0.4 43 47
BIRC3 -0.047 0.16 -10000 0 -0.51 42 42
BIRC2 0.009 0.04 -10000 0 -0.54 2 2
BAX 0.012 0 -10000 0 -10000 0 0
CASP10 -0.06 0.17 -10000 0 -0.37 79 79
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.012 0 -10000 0 -10000 0 0
PTK2 -0.026 0.13 0.19 1 -0.33 41 42
DIABLO 0.012 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.036 0.16 0.22 4 -0.4 42 46
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.012 0 -10000 0 -10000 0 0
GSN -0.038 0.16 0.23 4 -0.41 43 47
MADD 0.012 0 -10000 0 -10000 0 0
TFAP2A -0.1 0.24 -10000 0 -0.58 65 65
BID -0.023 0.091 -10000 0 -0.22 55 55
MAP3K1 -0.008 0.061 -10000 0 -0.21 8 8
TRADD 0.009 0.04 -10000 0 -0.54 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.018 0.017 -10000 0 -0.31 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.037 0.16 0.22 4 -0.41 43 47
CASP9 0.011 0.024 -10000 0 -0.45 1 1
DNA repair -0.005 0.053 -10000 0 -0.18 13 13
neuron apoptosis 0.012 0.027 -10000 0 -0.31 1 1
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.029 0.15 0.21 4 -0.39 41 45
APAF1 0.012 0 -10000 0 -10000 0 0
CASP6 -0.01 0.087 -10000 0 -0.42 3 3
TRAF2 0.012 0 -10000 0 -10000 0 0
ICAD/CAD -0.03 0.15 0.22 4 -0.39 41 45
CASP7 0.023 0.09 0.28 33 -0.33 2 35
KRT18 0.002 0.06 -10000 0 -0.72 2 2
apoptosis -0.032 0.14 0.24 3 -0.41 21 24
DFFA -0.037 0.16 0.22 4 -0.4 43 47
DFFB -0.037 0.16 0.22 4 -0.4 43 47
PARP1 0.005 0.053 0.18 13 -10000 0 13
actin filament polymerization 0.029 0.15 0.38 39 -0.22 4 43
TNF -0.069 0.19 -10000 0 -0.49 60 60
CYCS -0.017 0.071 -10000 0 -0.21 24 24
SATB1 -0.027 0.11 -10000 0 -0.42 7 7
SLK -0.038 0.16 0.23 3 -0.41 41 44
p15 BID/BAX -0.014 0.082 -10000 0 -0.3 9 9
CASP2 -0.003 0.092 -10000 0 -0.38 9 9
JNK cascade 0.007 0.06 0.21 8 -10000 0 8
CASP3 -0.045 0.17 0.24 4 -0.42 46 50
LMNB2 0.002 0.071 -10000 0 -0.35 3 3
RIPK1 0.012 0 -10000 0 -10000 0 0
CASP4 0.005 0.064 -10000 0 -0.54 5 5
Mammalian IAPs/DIABLO -0.003 0.099 -10000 0 -0.3 28 28
negative regulation of DNA binding -0.1 0.23 -10000 0 -0.58 65 65
stress fiber formation -0.037 0.16 0.22 4 -0.4 41 45
GZMB -0.072 0.19 -10000 0 -0.44 73 73
CASP1 -0.002 0.077 -10000 0 -0.3 20 20
LMNB1 0.001 0.072 -10000 0 -0.32 4 4
APP 0.012 0.027 -10000 0 -0.32 1 1
TNFRSF1A 0.011 0.029 -10000 0 -0.54 1 1
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.009 0.021 -10000 0 -0.39 1 1
VIM -0.035 0.14 0.22 9 -0.34 40 49
LMNA 0.002 0.071 -10000 0 -0.35 3 3
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.009 0.097 -10000 0 -0.41 9 9
LRDD 0.011 0.029 -10000 0 -0.54 1 1
SREBF1 -0.038 0.16 0.22 4 -0.4 42 46
APAF-1/Caspase 9 0.004 0.047 0.44 1 -10000 0 1
nuclear fragmentation during apoptosis -0.025 0.13 0.19 1 -0.33 41 42
CFL2 -0.03 0.15 0.22 4 -0.39 39 43
GAS2 -0.07 0.18 0.22 3 -0.43 49 52
positive regulation of apoptosis 0.004 0.072 -10000 0 -0.33 4 4
PRF1 -0.03 0.14 -10000 0 -0.49 31 31
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.043 0.14 0.36 58 -10000 0 58
KIRREL -0.047 0.16 -10000 0 -0.51 41 41
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.043 0.14 -10000 0 -0.36 58 58
PLCG1 0.012 0 -10000 0 -10000 0 0
ARRB2 0.012 0 -10000 0 -10000 0 0
WASL 0.012 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.032 0.12 -10000 0 -0.32 40 40
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.008 0.084 -10000 0 -0.25 27 27
FYN -0.024 0.097 -10000 0 -0.29 30 30
mol:Ca2+ -0.023 0.1 -10000 0 -0.3 30 30
mol:DAG -0.022 0.1 -10000 0 -0.3 30 30
NPHS2 -0.008 0.045 -10000 0 -0.46 3 3
mol:IP3 -0.022 0.1 -10000 0 -0.3 30 30
regulation of endocytosis -0.015 0.092 -10000 0 -0.26 30 30
Nephrin/NEPH1/podocin/Cholesterol -0.03 0.1 -10000 0 -0.27 55 55
establishment of cell polarity -0.043 0.14 -10000 0 -0.36 58 58
Nephrin/NEPH1/podocin/NCK1-2 -0.013 0.097 -10000 0 -0.35 5 5
Nephrin/NEPH1/beta Arrestin2 -0.014 0.094 -10000 0 -0.27 30 30
NPHS1 -0.019 0.1 -10000 0 -0.45 19 19
Nephrin/NEPH1/podocin -0.024 0.098 -10000 0 -0.29 30 30
TJP1 0.012 0 -10000 0 -10000 0 0
NCK1 0.012 0 -10000 0 -10000 0 0
NCK2 0.011 0.029 -10000 0 -0.54 1 1
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.022 0.1 -10000 0 -0.3 30 30
CD2AP -0.004 0.093 -10000 0 -0.54 11 11
Nephrin/NEPH1/podocin/GRB2 -0.022 0.1 -10000 0 -0.3 30 30
GRB2 0.012 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.046 0.12 -10000 0 -0.29 49 49
cytoskeleton organization -0.009 0.096 -10000 0 -0.33 4 4
Nephrin/NEPH1 -0.028 0.097 -10000 0 -0.25 58 58
Nephrin/NEPH1/ZO-1 -0.025 0.11 -10000 0 -0.32 30 30
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.013 0.099 -9999 0 -0.29 42 42
EPHB2 -0.051 0.17 -9999 0 -0.51 45 45
Syndecan-2/TACI -0.021 0.11 -9999 0 -0.29 48 48
LAMA1 -0.14 0.24 -9999 0 -0.52 102 102
Syndecan-2/alpha2 ITGB1 -0.022 0.13 -9999 0 -0.3 58 58
HRAS 0.011 0.024 -9999 0 -0.45 1 1
Syndecan-2/CASK -0.002 0.069 -9999 0 -0.32 17 17
ITGA5 0.01 0.037 -9999 0 -0.5 2 2
BAX 0.018 0.066 -9999 0 -10000 0 0
EPB41 0.012 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0.006 0.063 -9999 0 -0.28 17 17
LAMA3 -0.027 0.14 -9999 0 -0.53 27 27
EZR 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.008 0.049 -9999 0 -0.54 3 3
Syndecan-2/MMP2 -0.026 0.12 -9999 0 -0.3 54 54
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.013 0.11 -9999 0 -0.37 30 30
dendrite morphogenesis -0.032 0.12 -9999 0 -0.31 61 61
Syndecan-2/GM-CSF -0.003 0.084 -9999 0 -0.32 23 23
determination of left/right symmetry -0.001 0.082 -9999 0 -0.38 17 17
Syndecan-2/PKC delta 0.005 0.074 -9999 0 -0.31 19 19
GNB2L1 0.012 0 -9999 0 -10000 0 0
MAPK3 0.004 0.078 -9999 0 -0.28 24 24
MAPK1 0.004 0.078 -9999 0 -0.28 23 23
Syndecan-2/RACK1 0.013 0.061 -9999 0 -0.26 18 18
NF1 0.008 0.049 -9999 0 -0.54 3 3
FGFR/FGF/Syndecan-2 -0.001 0.082 -9999 0 -0.38 17 17
ITGA2 -0.031 0.15 -9999 0 -0.52 30 30
MAPK8 0.011 0.074 -9999 0 -0.31 19 19
Syndecan-2/alpha2/beta1 Integrin -0.08 0.16 -9999 0 -0.3 113 113
Syndecan-2/Kininogen -0.011 0.09 -9999 0 -0.28 36 36
ITGB1 0.012 0 -9999 0 -10000 0 0
SRC 0.016 0.064 -9999 0 -0.26 16 16
Syndecan-2/CASK/Protein 4.1 0.006 0.063 -9999 0 -0.28 17 17
extracellular matrix organization 0.005 0.072 -9999 0 -0.3 19 19
actin cytoskeleton reorganization -0.013 0.099 -9999 0 -0.29 42 42
Syndecan-2/Caveolin-2/Ras 0.011 0.073 -9999 0 -0.29 20 20
Syndecan-2/Laminin alpha3 -0.018 0.11 -9999 0 -0.33 42 42
Syndecan-2/RasGAP 0.019 0.059 -9999 0 -0.25 15 15
alpha5/beta1 Integrin 0.016 0.027 -9999 0 -0.35 2 2
PRKCD 0.009 0.04 -9999 0 -0.54 2 2
Syndecan-2 dimer -0.033 0.12 -9999 0 -0.31 61 61
GO:0007205 0.003 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.023 0.063 -9999 0 -0.5 1 1
RHOA 0.012 0 -9999 0 -10000 0 0
SDCBP 0.012 0 -9999 0 -10000 0 0
TNFRSF13B -0.034 0.14 -9999 0 -0.46 34 34
RASA1 0.012 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.013 0.11 -9999 0 -0.37 30 30
Syndecan-2/Synbindin 0.007 0.07 -9999 0 -0.31 17 17
TGFB1 0.01 0.034 -9999 0 -0.45 2 2
CASP3 0.012 0.067 -9999 0 -0.28 19 19
FN1 -0.02 0.12 -9999 0 -0.47 25 25
Syndecan-2/IL8 -0.042 0.14 -9999 0 -0.31 70 70
SDC2 -0.001 0.082 -9999 0 -0.38 17 17
KNG1 -0.017 0.1 -9999 0 -0.45 19 19
Syndecan-2/Neurofibromin 0.004 0.078 -9999 0 -0.33 19 19
TRAPPC4 0.012 0 -9999 0 -10000 0 0
CSF2 -0.003 0.067 -9999 0 -0.45 8 8
Syndecan-2/TGFB1 0.005 0.073 -9999 0 -0.31 19 19
Syndecan-2/Syntenin/PI-4-5-P2 0.006 0.063 -9999 0 -0.28 17 17
Syndecan-2/Ezrin 0.014 0.064 -9999 0 -0.28 17 17
PRKACA 0.011 0.071 -9999 0 -0.29 19 19
angiogenesis -0.041 0.14 -9999 0 -0.31 70 70
MMP2 -0.04 0.16 -9999 0 -0.5 38 38
IL8 -0.067 0.18 -9999 0 -0.5 58 58
calcineurin-NFAT signaling pathway -0.021 0.11 -9999 0 -0.29 48 48
PDGFR-alpha 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
PDGFRA -0.042 0.16 -9999 0 -0.52 37 37
PDGF/PDGFRA/CRKL -0.02 0.11 -9999 0 -0.36 37 37
positive regulation of JUN kinase activity 0.002 0.087 -9999 0 -0.27 30 30
CRKL 0.012 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.029 0.12 -9999 0 -0.36 39 39
AP1 -0.056 0.15 -9999 0 -0.82 8 8
mol:IP3 -0.02 0.12 -9999 0 -0.37 37 37
PLCG1 -0.02 0.12 -9999 0 -0.37 37 37
PDGF/PDGFRA/alphaV Integrin -0.024 0.13 -9999 0 -0.38 40 40
RAPGEF1 0.012 0 -9999 0 -10000 0 0
CRK 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ -0.02 0.12 -9999 0 -0.37 37 37
CAV3 0 0.034 -9999 0 -0.45 2 2
CAV1 0.006 0.056 -9999 0 -0.47 5 5
SHC/Grb2/SOS1 0.003 0.088 -9999 0 -0.27 30 30
PDGF/PDGFRA/Shf -0.026 0.13 -9999 0 -0.38 42 42
FOS -0.024 0.16 -9999 0 -0.81 8 8
JUN -0.007 0.03 -9999 0 -0.38 2 2
oligodendrocyte development -0.024 0.12 -9999 0 -0.38 40 40
GRB2 0.012 0 -9999 0 -10000 0 0
PIK3R1 -0.018 0.12 -9999 0 -0.52 21 21
mol:DAG -0.02 0.12 -9999 0 -0.37 37 37
PDGF/PDGFRA -0.041 0.16 -9999 0 -0.52 37 37
actin cytoskeleton reorganization -0.021 0.12 -9999 0 -0.36 38 38
SRF 0.019 0.006 -9999 0 -10000 0 0
SHC1 0.012 0 -9999 0 -10000 0 0
PI3K -0.027 0.13 -9999 0 -0.34 49 49
PDGF/PDGFRA/Crk/C3G -0.007 0.097 -9999 0 -0.3 37 37
JAK1 -0.024 0.12 -9999 0 -0.36 42 42
ELK1/SRF 0.003 0.089 -9999 0 -0.28 30 30
SHB 0.011 0.029 -9999 0 -0.54 1 1
SHF 0.002 0.072 -9999 0 -0.51 7 7
CSNK2A1 0.012 0.011 -9999 0 -10000 0 0
GO:0007205 -0.021 0.12 -9999 0 -0.39 37 37
SOS1 0.012 0 -9999 0 -10000 0 0
Ras protein signal transduction 0.002 0.087 -9999 0 -0.27 30 30
PDGF/PDGFRA/SHB -0.021 0.12 -9999 0 -0.36 38 38
PDGF/PDGFRA/Caveolin-1 -0.024 0.12 -9999 0 -0.36 41 41
ITGAV 0.005 0.062 -9999 0 -0.52 5 5
ELK1 -0.012 0.11 -9999 0 -0.33 37 37
PIK3CA 0.01 0.034 -9999 0 -0.45 2 2
PDGF/PDGFRA/Crk -0.02 0.11 -9999 0 -0.36 37 37
JAK-STAT cascade -0.024 0.12 -9999 0 -0.36 42 42
cell proliferation -0.026 0.13 -9999 0 -0.38 42 42
Nectin adhesion pathway

Figure S41.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S41.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0 0.078 -9999 0 -0.49 9 9
alphaV beta3 Integrin -0.044 0.14 -9999 0 -0.35 63 63
PTK2 -0.046 0.16 -9999 0 -0.46 37 37
positive regulation of JNK cascade -0.035 0.093 -9999 0 -0.3 38 38
CDC42/GDP -0.012 0.14 -9999 0 -0.41 39 39
Rac1/GDP -0.011 0.14 -9999 0 -0.41 39 39
RAP1B 0.012 0 -9999 0 -10000 0 0
RAP1A 0.012 0 -9999 0 -10000 0 0
CTNNB1 0.011 0.029 -9999 0 -0.54 1 1
CDC42/GTP -0.043 0.12 -9999 0 -0.38 38 38
nectin-3/I-afadin -0.03 0.13 -9999 0 -0.37 46 46
RAPGEF1 -0.022 0.15 -9999 0 -0.46 38 38
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.034 0.17 -9999 0 -0.53 38 38
PDGFB-D/PDGFRB 0 0.078 -9999 0 -0.49 9 9
TLN1 -0.032 0.13 -9999 0 -0.35 39 39
Rap1/GTP -0.037 0.099 -9999 0 -0.32 38 38
IQGAP1 0.012 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.023 0.016 -9999 0 -0.29 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.03 0.13 -9999 0 -0.37 46 46
PVR 0.012 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.012 0 -9999 0 -10000 0 0
mol:GDP -0.024 0.17 -9999 0 -0.51 39 39
MLLT4 0.011 0.029 -9999 0 -0.54 1 1
PIK3CA 0.01 0.034 -9999 0 -0.45 2 2
PI3K -0.023 0.13 -9999 0 -0.51 9 9
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.014 0.04 -9999 0 -0.37 4 4
positive regulation of lamellipodium assembly -0.039 0.1 -9999 0 -0.33 40 40
PVRL1 0.008 0.047 -9999 0 -0.51 3 3
PVRL3 -0.053 0.18 -9999 0 -0.52 45 45
PVRL2 0.011 0.029 -9999 0 -0.54 1 1
PIK3R1 -0.018 0.12 -9999 0 -0.52 21 21
CDH1 0.002 0.075 -9999 0 -0.54 7 7
CLDN1 -0.062 0.18 -9999 0 -0.51 53 53
JAM-A/CLDN1 -0.05 0.15 -9999 0 -0.32 69 69
SRC -0.045 0.19 -9999 0 -0.59 38 38
ITGB3 -0.068 0.18 -9999 0 -0.48 60 60
nectin-1(dimer)/I-afadin/I-afadin 0.014 0.04 -9999 0 -0.37 4 4
FARP2 -0.026 0.16 -9999 0 -0.5 38 38
RAC1 0.012 0 -9999 0 -10000 0 0
CTNNA1 0.012 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.016 0.11 -9999 0 -0.31 46 46
nectin-1/I-afadin 0.014 0.04 -9999 0 -0.37 4 4
nectin-2/I-afadin 0.016 0.03 -9999 0 -0.38 2 2
RAC1/GTP/IQGAP1/filamentous actin 0.017 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.019 0.12 -9999 0 -0.31 48 48
CDC42/GTP/IQGAP1/filamentous actin 0.017 0 -9999 0 -10000 0 0
F11R 0.008 0.049 -9999 0 -0.54 3 3
positive regulation of filopodium formation -0.035 0.093 -9999 0 -0.3 38 38
alphaV/beta3 Integrin/Talin -0.058 0.16 -9999 0 -0.48 25 25
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.016 0.03 -9999 0 -0.38 2 2
nectin-2(dimer)/I-afadin/I-afadin 0.016 0.03 -9999 0 -0.38 2 2
PIP5K1C -0.041 0.13 -9999 0 -0.38 39 39
VAV2 -0.032 0.18 -9999 0 -0.53 40 40
RAP1/GDP -0.042 0.12 -9999 0 -0.38 39 39
ITGAV 0.005 0.062 -9999 0 -0.52 5 5
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.017 0.11 -9999 0 -0.31 47 47
nectin-3(dimer)/I-afadin/I-afadin -0.03 0.13 -9999 0 -0.37 46 46
Rac1/GTP -0.047 0.12 -9999 0 -0.4 40 40
PTPRM -0.052 0.15 -9999 0 -0.32 74 74
E-cadherin/beta catenin/alpha catenin 0.027 0.055 -9999 0 -0.51 1 1
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.012 0 -9999 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.009 0.021 -9999 0 -0.39 1 1
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.001 0.069 -9999 0 -0.31 17 17
STXBP1 -0.006 0.098 -9999 0 -0.52 13 13
ACh/CHRNA1 -0.066 0.14 -9999 0 -0.33 74 74
RAB3GAP2/RIMS1/UNC13B 0.009 0.058 -9999 0 -0.26 17 17
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 -0.014 0.096 -9999 0 -0.45 17 17
mol:ACh -0.013 0.041 -9999 0 -0.12 29 29
RAB3GAP2 0.012 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.035 0.072 -9999 0 -0.31 10 10
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.066 0.14 -9999 0 -0.33 74 74
UNC13B 0.012 0 -9999 0 -10000 0 0
CHRNA1 -0.089 0.2 -9999 0 -0.49 74 74
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.078 0.14 -9999 0 -0.33 88 88
SNAP25 -0.039 0.092 -9999 0 -0.21 79 79
VAMP2 0.006 0 -9999 0 -10000 0 0
SYT1 -0.11 0.22 -9999 0 -0.49 88 88
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.004 0.063 -9999 0 -0.31 14 14
STX1A/SNAP25 fragment 1/VAMP2 -0.035 0.072 -9999 0 -0.31 10 10
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.039 0.28 -10000 0 -0.83 35 35
NCK1/PAK1/Dok-R -0.052 0.12 -10000 0 -0.4 35 35
NCK1/Dok-R -0.057 0.3 -10000 0 -0.94 35 35
PIK3CA 0.01 0.034 -10000 0 -0.45 2 2
mol:beta2-estradiol 0.011 0.063 0.24 24 -10000 0 24
RELA 0.012 0 -10000 0 -10000 0 0
SHC1 0.013 0.002 -10000 0 -10000 0 0
Rac/GDP 0.009 0 -10000 0 -10000 0 0
F2 -0.022 0.15 0.24 23 -0.46 32 55
TNIP2 0.012 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.052 0.28 -10000 0 -0.89 35 35
FN1 -0.02 0.12 -10000 0 -0.47 25 25
PLD2 -0.06 0.31 -10000 0 -0.98 35 35
PTPN11 0.012 0 -10000 0 -10000 0 0
GRB14 -0.11 0.22 -10000 0 -0.5 85 85
ELK1 -0.046 0.28 -10000 0 -0.89 35 35
GRB7 -0.014 0.11 -10000 0 -0.47 20 20
PAK1 0.012 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.07 0.3 -10000 0 -0.95 35 35
CDKN1A -0.022 0.25 -10000 0 -0.66 39 39
ITGA5 0.01 0.037 -10000 0 -0.5 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.057 0.3 -10000 0 -0.94 35 35
CRK 0.012 0 -10000 0 -10000 0 0
mol:NO -0.019 0.22 -10000 0 -0.62 35 35
PLG -0.1 0.32 -10000 0 -1 35 35
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.033 0.26 -10000 0 -0.8 35 35
GRB2 0.012 0 -10000 0 -10000 0 0
PIK3R1 -0.018 0.12 -10000 0 -0.52 21 21
ANGPT2 -0.009 0.18 -10000 0 -1 6 6
BMX -0.099 0.32 -10000 0 -1 35 35
ANGPT1 -0.077 0.31 -10000 0 -1.2 25 25
tube development -0.015 0.23 -10000 0 -0.62 35 35
ANGPT4 -0.011 0.088 -10000 0 -0.45 14 14
response to hypoxia -0.005 0.021 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.12 0.33 -10000 0 -1.1 36 36
alpha5/beta1 Integrin 0.016 0.027 -10000 0 -0.35 2 2
FGF2 -0.027 0.14 -10000 0 -0.5 28 28
STAT5A (dimer) -0.024 0.27 -10000 0 -0.74 34 34
mol:L-citrulline -0.019 0.22 -10000 0 -0.62 35 35
AGTR1 -0.003 0.071 -10000 0 -0.45 9 9
MAPK14 -0.055 0.31 -10000 0 -0.98 35 35
Tie2/SHP2 -0.018 0.19 -10000 0 -0.95 12 12
TEK -0.024 0.21 -10000 0 -1 12 12
RPS6KB1 -0.034 0.26 -10000 0 -0.8 35 35
Angiotensin II/AT1 0 0.051 -10000 0 -0.32 9 9
Tie2/Ang1/GRB2 -0.062 0.31 -10000 0 -1 35 35
MAPK3 -0.05 0.29 -10000 0 -0.91 35 35
MAPK1 -0.05 0.29 -10000 0 -0.91 35 35
Tie2/Ang1/GRB7 -0.074 0.32 -10000 0 -1 35 35
NFKB1 0.012 0 -10000 0 -10000 0 0
MAPK8 -0.061 0.31 -10000 0 -0.98 35 35
PI3K -0.051 0.31 -10000 0 -0.94 35 35
FES -0.057 0.31 -10000 0 -0.97 35 35
Crk/Dok-R -0.057 0.3 -10000 0 -0.94 35 35
Tie2/Ang1/ABIN2 -0.062 0.31 -10000 0 -1 35 35
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.031 0.25 -10000 0 -0.74 35 35
STAT5A 0.011 0.024 -10000 0 -0.45 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.033 0.26 -10000 0 -0.8 35 35
Tie2/Ang2 -0.039 0.29 -10000 0 -0.85 33 33
Tie2/Ang1 -0.07 0.33 -10000 0 -1 35 35
FOXO1 -0.031 0.26 -10000 0 -0.73 39 39
ELF1 0.016 0.019 -10000 0 -10000 0 0
ELF2 -0.062 0.3 -10000 0 -0.97 35 35
mol:Choline -0.056 0.3 -10000 0 -0.94 35 35
cell migration -0.033 0.069 -10000 0 -0.23 35 35
FYN -0.022 0.25 -10000 0 -0.71 34 34
DOK2 0 0.078 -10000 0 -0.49 9 9
negative regulation of cell cycle -0.015 0.23 -10000 0 -0.58 43 43
ETS1 0 0.068 -10000 0 -0.41 2 2
PXN -0.017 0.23 -10000 0 -0.66 35 35
ITGB1 0.012 0 -10000 0 -10000 0 0
NOS3 -0.027 0.24 -10000 0 -0.71 35 35
RAC1 0.012 0 -10000 0 -10000 0 0
TNF -0.08 0.19 -10000 0 -0.42 83 83
MAPKKK cascade -0.056 0.3 -10000 0 -0.94 35 35
RASA1 0.012 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.061 0.32 -10000 0 -1 35 35
NCK1 0.012 0 -10000 0 -10000 0 0
vasculogenesis -0.013 0.2 -10000 0 -0.56 35 35
mol:Phosphatidic acid -0.056 0.3 -10000 0 -0.94 35 35
mol:Angiotensin II 0.001 0.005 -10000 0 -10000 0 0
mol:NADP -0.019 0.22 -10000 0 -0.62 35 35
Rac1/GTP -0.089 0.22 -10000 0 -0.74 35 35
MMP2 -0.085 0.32 -10000 0 -1 36 36
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.013 0.11 -10000 0 -0.49 18 18
GNB1/GNG2 -0.052 0.068 -10000 0 -0.19 53 53
AKT1 -0.026 0.092 -10000 0 -0.21 38 38
EGF -0.065 0.18 -10000 0 -0.48 57 57
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.009 0.078 -10000 0 -0.37 5 5
mol:Ca2+ -0.052 0.13 -10000 0 -0.3 57 57
LYN 0.014 0.067 -10000 0 -0.39 2 2
RhoA/GTP -0.031 0.045 -10000 0 -0.13 27 27
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.061 0.15 -10000 0 -0.34 55 55
GNG2 -0.002 0.084 -10000 0 -0.48 11 11
ARRB2 0.012 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0 0.12 -10000 0 -0.42 19 19
G beta5/gamma2 -0.064 0.091 -10000 0 -0.25 54 54
PRKCH -0.058 0.15 -10000 0 -0.35 51 51
DNM1 -0.012 0.11 -10000 0 -0.48 18 18
TXA2/TP beta/beta Arrestin3 -0.011 0.038 -10000 0 -0.22 6 6
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.029 0.14 -10000 0 -0.52 28 28
G12 family/GTP -0.077 0.11 -10000 0 -0.3 53 53
ADRBK1 0.011 0.024 -10000 0 -0.45 1 1
ADRBK2 0.003 0.07 -10000 0 -0.54 6 6
RhoA/GTP/ROCK1 0.016 0.001 -10000 0 -10000 0 0
mol:GDP 0.032 0.099 0.33 16 -10000 0 16
mol:NADP 0.002 0.071 -10000 0 -0.47 8 8
RAB11A 0.012 0 -10000 0 -10000 0 0
PRKG1 -0.033 0.15 -10000 0 -0.51 32 32
mol:IP3 -0.067 0.16 -10000 0 -0.37 57 57
cell morphogenesis 0.016 0.001 -10000 0 -10000 0 0
PLCB2 -0.094 0.21 -10000 0 -0.51 54 54
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.024 0.1 -10000 0 -0.36 13 13
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.006 0.085 -10000 0 -0.38 8 8
RHOA 0.012 0 -10000 0 -10000 0 0
PTGIR 0.005 0.058 -10000 0 -0.49 5 5
PRKCB1 -0.065 0.15 -10000 0 -0.37 56 56
GNAQ 0.011 0.029 -10000 0 -0.54 1 1
mol:L-citrulline 0.002 0.071 -10000 0 -0.47 8 8
TXA2/TXA2-R family -0.098 0.21 -10000 0 -0.53 54 54
LCK 0.003 0.084 -10000 0 -0.37 5 5
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.004 0.064 -10000 0 -0.45 1 1
TXA2-R family/G12 family/GDP/G beta/gamma 0.019 0.03 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.013 0.065 -10000 0 -0.45 1 1
MAPK14 -0.034 0.1 -10000 0 -0.23 51 51
TGM2/GTP -0.082 0.18 -10000 0 -0.43 57 57
MAPK11 -0.036 0.1 -10000 0 -0.23 51 51
ARHGEF1 -0.025 0.08 -10000 0 -0.18 37 37
GNAI2 0.012 0 -10000 0 -10000 0 0
JNK cascade -0.07 0.16 -10000 0 -0.39 54 54
RAB11/GDP 0.013 0.001 -10000 0 -10000 0 0
ICAM1 -0.047 0.12 -10000 0 -0.29 51 51
cAMP biosynthetic process -0.07 0.15 -10000 0 -0.36 56 56
Gq family/GTP/EBP50 0.003 0.08 -10000 0 -0.31 17 17
actin cytoskeleton reorganization 0.016 0.001 -10000 0 -10000 0 0
SRC 0.014 0.064 -10000 0 -0.35 1 1
GNB5 0.006 0.057 -10000 0 -0.54 4 4
GNB1 0.012 0 -10000 0 -10000 0 0
EGF/EGFR -0.008 0.091 -10000 0 -0.31 12 12
VCAM1 -0.061 0.14 -10000 0 -0.35 54 54
TP beta/Gq family/GDP/G beta5/gamma2 0 0.12 -10000 0 -0.42 19 19
platelet activation -0.046 0.14 -10000 0 -0.3 52 52
PGI2/IP 0.004 0.042 -10000 0 -0.35 5 5
PRKACA -0.005 0.073 -10000 0 -0.26 25 25
Gq family/GDP/G beta5/gamma2 -0.001 0.11 -10000 0 -0.4 19 19
TXA2/TP beta/beta Arrestin2 -0.015 0.068 -10000 0 -0.5 6 6
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.001 0.073 -10000 0 -0.25 25 25
mol:DAG -0.073 0.17 -10000 0 -0.41 55 55
EGFR -0.004 0.092 -10000 0 -0.53 11 11
TXA2/TP alpha -0.095 0.2 -10000 0 -0.49 56 56
Gq family/GTP -0.014 0.066 -10000 0 -0.25 23 23
YES1 0.015 0.063 -10000 0 -0.35 1 1
GNAI2/GTP -0.019 0.058 -10000 0 -0.41 1 1
PGD2/DP -0.021 0.1 -10000 0 -0.38 28 28
SLC9A3R1 0.005 0.06 -10000 0 -0.5 5 5
FYN 0.015 0.063 -10000 0 -0.35 1 1
mol:NO 0.002 0.071 -10000 0 -0.47 8 8
GNA15 -0.005 0.093 -10000 0 -0.51 12 12
PGK/cGMP -0.018 0.1 -10000 0 -0.31 39 39
RhoA/GDP 0.013 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.002 0.092 -10000 0 -0.41 4 4
NOS3 0.002 0.071 -10000 0 -0.47 8 8
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCA -0.064 0.15 -10000 0 -0.36 54 54
PRKCB -0.065 0.16 -10000 0 -0.36 59 59
PRKCE -0.054 0.14 -10000 0 -0.35 51 51
PRKCD -0.061 0.16 -10000 0 -0.38 51 51
PRKCG -0.093 0.18 -10000 0 -0.41 58 58
muscle contraction -0.092 0.2 -10000 0 -0.49 55 55
PRKCZ -0.058 0.15 -10000 0 -0.34 53 53
ARR3 0.003 0.034 -10000 0 -0.45 2 2
TXA2/TP beta 0.004 0.074 -10000 0 -0.46 1 1
PRKCQ -0.084 0.17 -10000 0 -0.37 64 64
MAPKKK cascade -0.086 0.19 -10000 0 -0.46 57 57
SELE -0.063 0.15 -10000 0 -0.34 57 57
TP beta/GNAI2/GDP/G beta/gamma 0.014 0.075 -10000 0 -0.44 1 1
ROCK1 0.012 0 -10000 0 -10000 0 0
GNA14 -0.003 0.089 -10000 0 -0.54 10 10
chemotaxis -0.11 0.24 -10000 0 -0.6 55 55
GNA12 0.012 0 -10000 0 -10000 0 0
GNA13 0.012 0 -10000 0 -10000 0 0
GNA11 -0.001 0.082 -10000 0 -0.52 9 9
Rac1/GTP 0.008 0.003 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.014 0.04 -9999 0 -0.33 5 5
alphaV beta3 Integrin -0.052 0.14 -9999 0 -0.3 89 89
PTK2 -0.031 0.14 -9999 0 -0.48 13 13
IGF1R -0.029 0.15 -9999 0 -0.54 28 28
PI4KB 0.011 0.024 -9999 0 -0.45 1 1
MFGE8 0.003 0.07 -9999 0 -0.5 7 7
SRC 0.009 0.04 -9999 0 -0.54 2 2
CDKN1B -0.041 0.14 -9999 0 -0.5 22 22
VEGFA 0.009 0.042 -9999 0 -0.45 3 3
ILK -0.018 0.074 -9999 0 -0.32 6 6
ROCK1 0.012 0 -9999 0 -10000 0 0
AKT1 -0.009 0.07 -9999 0 -0.32 4 4
PTK2B -0.017 0.11 -9999 0 -0.57 3 3
alphaV/beta3 Integrin/JAM-A -0.044 0.14 -9999 0 -0.52 9 9
CBL 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.035 0.13 -9999 0 -0.3 64 64
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.049 0.16 -9999 0 -0.36 61 61
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.001 0.078 -9999 0 -0.33 5 5
alphaV/beta3 Integrin/Syndecan-1 -0.039 0.13 -9999 0 -0.29 75 75
PI4KA 0.012 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.13 0.18 -9999 0 -0.52 46 46
PI4 Kinase 0.017 0.017 -9999 0 -0.31 1 1
PIK3CA 0.01 0.034 -9999 0 -0.45 2 2
alphaV/beta3 Integrin/Osteopontin -0.054 0.16 -9999 0 -0.33 82 82
RPS6KB1 -0.093 0.19 -9999 0 -0.49 46 46
TLN1 0.012 0 -9999 0 -10000 0 0
MAPK3 -0.074 0.18 -9999 0 -0.51 44 44
GPR124 -0.001 0.083 -9999 0 -0.5 10 10
MAPK1 -0.074 0.18 -9999 0 -0.51 44 44
PXN 0.012 0 -9999 0 -10000 0 0
PIK3R1 -0.018 0.12 -9999 0 -0.52 21 21
alphaV/beta3 Integrin/Tumstatin -0.07 0.16 -9999 0 -0.33 99 99
cell adhesion -0.027 0.12 -9999 0 -0.36 27 27
ANGPTL3 0.002 0.041 -9999 0 -0.45 3 3
VEGFR2 homodimer/VEGFA homodimer/Src 0.019 0.042 -9999 0 -0.32 3 3
IGF-1R heterotetramer -0.029 0.14 -9999 0 -0.54 28 28
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
TGFBR2 0.009 0.04 -9999 0 -0.54 2 2
ITGB3 -0.068 0.18 -9999 0 -0.48 60 60
IGF1 -0.067 0.19 -9999 0 -0.5 57 57
RAC1 0.012 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.036 0.14 -9999 0 -0.31 68 68
apoptosis 0.005 0.061 -9999 0 -0.52 5 5
CD47 0.007 0.05 -9999 0 -0.47 4 4
alphaV/beta3 Integrin/CD47 -0.032 0.12 -9999 0 -0.29 67 67
VCL 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.067 0.16 -9999 0 -0.38 53 53
CSF1 0.002 0.073 -9999 0 -0.53 7 7
PIK3C2A -0.018 0.074 -9999 0 -0.32 6 6
PI4 Kinase/Pyk2 -0.057 0.1 -9999 0 -0.43 9 9
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.021 0.12 -9999 0 -0.31 26 26
FAK1/Vinculin -0.018 0.12 -9999 0 -0.38 13 13
alphaV beta3/Integrin/ppsTEM5 -0.036 0.14 -9999 0 -0.31 68 68
RHOA 0.012 0 -9999 0 -10000 0 0
VTN -0.009 0.095 -9999 0 -0.46 16 16
BCAR1 0.011 0.029 -9999 0 -0.54 1 1
FGF2 -0.027 0.14 -9999 0 -0.5 28 28
F11R -0.012 0.11 -9999 0 -0.37 30 30
alphaV/beta3 Integrin/Lactadherin -0.034 0.13 -9999 0 -0.31 66 66
alphaV/beta3 Integrin/TGFBR2 -0.03 0.12 -9999 0 -0.29 64 64
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.021 0.057 -9999 0 -0.28 11 11
HSP90AA1 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.025 0.11 -9999 0 -0.26 63 63
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.02 0.12 -9999 0 -0.47 25 25
alphaV/beta3 Integrin/Pyk2 -0.015 0.11 -9999 0 -0.57 3 3
SDC1 -0.005 0.095 -9999 0 -0.52 12 12
VAV3 0.001 0.095 -9999 0 -0.54 2 2
PTPN11 0.012 0 -9999 0 -10000 0 0
IRS1 -0.011 0.11 -9999 0 -0.53 16 16
FAK1/Paxillin -0.018 0.12 -9999 0 -0.38 13 13
cell migration -0.01 0.11 -9999 0 -0.36 9 9
ITGAV 0.005 0.062 -9999 0 -0.52 5 5
PI3K -0.075 0.13 -9999 0 -0.46 19 19
SPP1 -0.032 0.14 -9999 0 -0.5 32 32
KDR 0.01 0.037 -9999 0 -0.5 2 2
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.005 0.062 -9999 0 -0.52 5 5
COL4A3 -0.057 0.17 -9999 0 -0.49 50 50
angiogenesis -0.07 0.19 -9999 0 -0.51 44 44
Rac1/GTP 0.008 0.088 -9999 0 -0.49 2 2
EDIL3 -0.051 0.17 -9999 0 -0.52 44 44
cell proliferation -0.03 0.12 -9999 0 -0.29 64 64
LPA4-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
ADCY4 0.009 0.047 -9999 0 -0.28 9 9
ADCY5 -0.038 0.12 -9999 0 -0.31 61 61
ADCY6 0.014 0.025 -9999 0 -0.33 2 2
ADCY7 0.013 0.029 -9999 0 -0.31 3 3
ADCY1 -0.042 0.12 -9999 0 -0.29 71 71
ADCY2 -0.034 0.12 -9999 0 -0.3 59 59
ADCY3 0.015 0.018 -9999 0 -0.33 1 1
ADCY8 -0.002 0.057 -9999 0 -0.27 16 16
PRKCE 0.009 0.021 -9999 0 -0.39 1 1
ADCY9 -0.001 0.071 -9999 0 -0.29 21 21
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.028 0.076 -9999 0 -0.26 15 15
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.012 0.069 -10000 0 -0.58 4 4
HDAC1 0.011 0.009 -10000 0 -10000 0 0
AES 0.011 0.029 -10000 0 -0.54 1 1
FBXW11 0.012 0 -10000 0 -10000 0 0
DTX1 -0.008 0.1 -10000 0 -0.52 14 14
LRP6/FZD1 0.015 0.032 -10000 0 -0.34 3 3
TLE1 0.009 0.04 -10000 0 -0.54 2 2
AP1 -0.03 0.09 -10000 0 -0.28 19 19
NCSTN 0.012 0 -10000 0 -10000 0 0
ADAM10 0.006 0.057 -10000 0 -0.54 4 4
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.021 0.12 -10000 0 -0.48 9 9
NICD/RBPSUH 0.021 0.065 -10000 0 -0.56 4 4
WIF1 -0.25 0.25 -10000 0 -0.49 193 193
NOTCH1 -0.008 0.064 -10000 0 -0.6 4 4
PSENEN 0.011 0.029 -10000 0 -0.54 1 1
KREMEN2 -0.053 0.17 -10000 0 -0.48 49 49
DKK1 -0.18 0.24 -10000 0 -0.48 142 142
beta catenin/beta TrCP1 0.033 0.06 0.23 1 -0.3 1 2
APH1B 0.006 0.057 -10000 0 -0.54 4 4
APH1A 0.011 0.024 -10000 0 -0.45 1 1
AXIN1 -0.006 0.038 0.25 3 -0.24 2 5
CtBP/CBP/TCF1/TLE1/AES -0.026 0.11 0.22 1 -0.5 2 3
PSEN1 0.012 0 -10000 0 -10000 0 0
FOS -0.019 0.12 -10000 0 -0.47 24 24
JUN 0.01 0.037 -10000 0 -0.5 2 2
MAP3K7 0.012 0.004 -10000 0 -10000 0 0
CTNNB1 0.028 0.064 0.22 3 -0.32 1 4
MAPK3 0.011 0.024 -10000 0 -0.45 1 1
DKK2/LRP6/Kremen 2 -0.075 0.16 -10000 0 -0.32 108 108
HNF1A -0.097 0.22 -10000 0 -0.54 74 74
CTBP1 0.012 0.003 -10000 0 -10000 0 0
MYC -0.016 0.21 -10000 0 -1.3 9 9
NKD1 -0.093 0.2 -10000 0 -0.46 82 82
FZD1 0.008 0.044 -10000 0 -0.48 3 3
NOTCH1 precursor/Deltex homolog 1 0.011 0.087 -10000 0 -0.63 4 4
apoptosis -0.03 0.09 -10000 0 -0.28 19 19
Delta 1/NOTCHprecursor 0.016 0.073 -10000 0 -0.56 4 4
DLL1 0.002 0.072 -10000 0 -0.51 7 7
PPARD 0.019 0.023 -10000 0 -10000 0 0
Gamma Secretase 0.032 0.037 -10000 0 -0.26 5 5
APC -0.006 0.038 0.25 3 -0.24 2 5
DVL1 -0.009 0.043 -10000 0 -0.48 1 1
CSNK2A1 0.012 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.004 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.13 0.17 -10000 0 -0.3 174 174
LRP6 0.012 0 -10000 0 -10000 0 0
CSNK1A1 0.012 0.001 -10000 0 -10000 0 0
NLK 0.014 0.01 -10000 0 -10000 0 0
CCND1 -0.036 0.27 -10000 0 -1.3 15 15
WNT1 -0.004 0.078 -10000 0 -0.45 11 11
Axin1/APC/beta catenin 0.022 0.052 0.26 3 -0.35 1 4
DKK2 -0.087 0.2 -10000 0 -0.5 72 72
NOTCH1 precursor/DVL1 -0.012 0.061 -10000 0 -0.5 5 5
GSK3B 0.012 0.001 -10000 0 -10000 0 0
FRAT1 0.008 0.049 -10000 0 -0.54 3 3
NOTCH/Deltex homolog 1 -0.017 0.082 -10000 0 -0.64 4 4
PPP2R5D 0.038 0.092 0.21 81 -10000 0 81
MAPK1 0.011 0.024 -10000 0 -0.45 1 1
WNT1/LRP6/FZD1 -0.13 0.15 -10000 0 -0.3 94 94
RBPJ 0.011 0.024 -10000 0 -0.45 1 1
CREBBP 0.014 0.004 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.014 0.04 -9999 0 -10000 0 0
VDR 0.006 0.057 -9999 0 -0.54 4 4
FAM120B 0.012 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.042 0.14 -9999 0 -0.43 20 20
RXRs/LXRs/DNA/Oxysterols -0.048 0.17 -9999 0 -0.45 43 43
MED1 0.012 0 -9999 0 -10000 0 0
mol:9cRA -0.002 0.018 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.033 0.12 -9999 0 -0.5 7 7
RXRs/NUR77 -0.057 0.15 -9999 0 -0.32 60 60
RXRs/PPAR -0.073 0.14 -9999 0 -0.36 38 38
NCOR2 0.012 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0.005 0.041 -9999 0 -0.39 4 4
RARs/VDR/DNA/Vit D3 0.012 0.067 -9999 0 -0.27 14 14
RARA 0.012 0 -9999 0 -10000 0 0
NCOA1 0.012 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.006 0.057 -9999 0 -0.54 4 4
RARs/RARs/DNA/9cRA 0.007 0.06 -9999 0 -0.25 19 19
RARG 0.007 0.053 -9999 0 -0.5 4 4
RPS6KB1 0.023 0.047 -9999 0 -0.52 1 1
RARs/THRs/DNA/SMRT -0.033 0.12 -9999 0 -0.5 7 7
THRA 0.008 0.044 -9999 0 -0.48 3 3
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0.005 0.041 -9999 0 -0.39 4 4
RXRs/PPAR/9cRA/PGJ2/DNA -0.054 0.14 -9999 0 -0.32 53 53
NR1H4 -0.018 0.095 -9999 0 -0.45 17 17
RXRs/LXRs/DNA -0.038 0.14 -9999 0 -0.39 19 19
NR1H2 0.012 0.014 -9999 0 -10000 0 0
NR1H3 0.01 0.028 -9999 0 -0.44 1 1
RXRs/VDR/DNA/Vit D3 -0.044 0.13 -9999 0 -0.29 56 56
NR4A1 -0.014 0.11 -9999 0 -0.46 21 21
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.036 0.1 -9999 0 -0.32 19 19
RXRG -0.12 0.22 -9999 0 -0.5 92 92
RXR alpha/CCPG 0.017 0.024 -9999 0 -0.4 1 1
RXRA 0.01 0.032 -9999 0 -0.55 1 1
RXRB 0.011 0.016 -9999 0 -10000 0 0
THRB -0.1 0.22 -9999 0 -0.53 77 77
PPARG -0.095 0.21 -9999 0 -0.51 76 76
PPARD 0.012 0 -9999 0 -10000 0 0
TNF -0.1 0.31 -9999 0 -0.94 37 37
mol:Oxysterols -0.002 0.016 -9999 0 -10000 0 0
cholesterol transport -0.047 0.17 -9999 0 -0.44 43 43
PPARA 0.009 0.04 -9999 0 -0.54 2 2
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.008 0.1 -9999 0 -0.5 15 15
RXRs/NUR77/BCL2 -0.053 0.14 -9999 0 -0.32 59 59
SREBF1 -0.038 0.17 -9999 0 -0.57 15 15
RXRs/RXRs/DNA/9cRA -0.053 0.14 -9999 0 -0.32 53 53
ABCA1 -0.053 0.22 -9999 0 -0.78 20 20
RARs/THRs -0.04 0.14 -9999 0 -0.53 7 7
RXRs/FXR -0.06 0.15 -9999 0 -0.34 54 54
BCL2 -0.015 0.12 -9999 0 -0.52 19 19
Retinoic acid receptors-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
HDAC1 0.012 0 -10000 0 -10000 0 0
HDAC3 0.012 0 -10000 0 -10000 0 0
VDR 0.006 0.057 -10000 0 -0.54 4 4
Cbp/p300/PCAF 0.018 0.05 -10000 0 -0.32 8 8
EP300 0.012 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0 0.075 -10000 0 -0.35 8 8
KAT2B 0 0.08 -10000 0 -0.54 8 8
MAPK14 0.012 0 -10000 0 -10000 0 0
AKT1 0.006 0.094 0.21 29 -0.28 11 40
RAR alpha/9cRA/Cyclin H -0.054 0.096 -10000 0 -0.47 8 8
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.004 0.083 -10000 0 -0.36 11 11
CDC2 0 0.002 -10000 0 -10000 0 0
response to UV 0 0.003 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.038 0.096 -10000 0 -0.42 9 9
NCOR2 0.012 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.005 0.041 -10000 0 -0.39 4 4
RXRs/RARs/NRIP1/9cRA -0.082 0.21 -10000 0 -0.52 54 54
NCOA2 -0.008 0.1 -10000 0 -0.52 14 14
NCOA3 0.012 0 -10000 0 -10000 0 0
NCOA1 0.012 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.006 0.057 -10000 0 -0.54 4 4
RARG 0.007 0.053 -10000 0 -0.5 4 4
RAR gamma1/9cRA 0.014 0.033 -10000 0 -0.3 4 4
MAPK3 0.011 0.024 -10000 0 -0.45 1 1
MAPK1 0.011 0.024 -10000 0 -0.45 1 1
MAPK8 0.01 0.041 -10000 0 -0.55 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.094 0.2 -10000 0 -0.48 59 59
RARA -0.046 0.11 -10000 0 -0.27 54 54
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.012 0.095 -10000 0 -0.35 15 15
PRKCA -0.011 0.11 -10000 0 -0.53 17 17
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.098 0.22 -10000 0 -0.53 59 59
RXRG -0.14 0.2 -10000 0 -0.4 105 105
RXRA -0.037 0.1 -10000 0 -0.3 21 21
RXRB -0.072 0.15 -10000 0 -0.36 54 54
VDR/Vit D3/DNA 0.005 0.041 -10000 0 -0.39 4 4
RBP1 -0.076 0.2 -10000 0 -0.52 61 61
CRBP1/9-cic-RA -0.055 0.14 -10000 0 -0.38 61 61
RARB -0.007 0.1 -10000 0 -0.5 15 15
PRKCG -0.14 0.23 -10000 0 -0.48 116 116
MNAT1 0.012 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.07 0.21 -10000 0 -0.5 51 51
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.062 0.18 -10000 0 -0.43 50 50
proteasomal ubiquitin-dependent protein catabolic process -0.02 0.1 -10000 0 -0.37 15 15
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.098 0.22 -10000 0 -0.53 59 59
positive regulation of DNA binding -0.051 0.091 -10000 0 -0.44 8 8
NRIP1 -0.1 0.26 -10000 0 -0.92 23 23
RXRs/RARs -0.099 0.21 -10000 0 -0.5 61 61
RXRs/RXRs/DNA/9cRA -0.1 0.2 -10000 0 -0.5 57 57
PRKACA 0.012 0 -10000 0 -10000 0 0
CDK7 0.011 0.029 -10000 0 -0.54 1 1
TFIIH 0.024 0.018 -10000 0 -0.32 1 1
RAR alpha/9cRA -0.035 0.064 -10000 0 -0.39 4 4
CCNH 0.012 0 -10000 0 -10000 0 0
CREBBP 0.012 0 -10000 0 -10000 0 0
RAR gamma2/9cRA -0.003 0.025 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.006 0.061 -9999 0 -0.36 8 8
NFATC2 -0.019 0.086 -9999 0 -0.34 22 22
NFATC3 0.002 0.03 -9999 0 -10000 0 0
CD40LG -0.12 0.26 -9999 0 -0.61 53 53
PTGS2 -0.16 0.29 -9999 0 -0.58 87 87
JUNB 0.006 0.057 -9999 0 -0.54 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.003 0.017 -9999 0 -10000 0 0
CaM/Ca2+ -0.003 0.017 -9999 0 -10000 0 0
CALM1 0.008 0.009 -9999 0 -10000 0 0
JUN 0.005 0.039 -9999 0 -0.51 2 2
mol:Ca2+ -0.008 0.012 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.006 0.006 -9999 0 -10000 0 0
FOSL1 -0.024 0.13 -9999 0 -0.49 27 27
CREM 0.012 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.055 0.16 -9999 0 -0.42 28 28
FOS -0.024 0.12 -9999 0 -0.47 24 24
IFNG -0.12 0.25 -9999 0 -0.57 61 61
AP-1/NFAT1-c-4 -0.12 0.26 -9999 0 -0.6 54 54
FASLG -0.13 0.27 -9999 0 -0.65 51 51
NFAT1-c-4/ICER1 -0.036 0.1 -9999 0 -0.35 18 18
IL2RA -0.12 0.25 -9999 0 -0.6 47 47
FKBP12/FK506 0.009 0 -9999 0 -10000 0 0
CSF2 -0.11 0.23 -9999 0 -0.56 40 40
JunB/Fra1/NFAT1-c-4 -0.04 0.13 -9999 0 -0.36 28 28
IL4 -0.11 0.22 -9999 0 -0.54 41 41
IL2 -0.019 0.074 -9999 0 -10000 0 0
IL3 -0.019 0.031 -9999 0 -10000 0 0
FKBP1A 0.012 0 -9999 0 -10000 0 0
BATF3 -0.005 0.092 -9999 0 -0.48 13 13
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.001 0.071 -9999 0 -0.45 9 9
EGFR-dependent Endothelin signaling events

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
HRAS 0.011 0.024 -9999 0 -0.45 1 1
EGFR -0.004 0.092 -9999 0 -0.53 11 11
EGF/EGFR -0.042 0.12 -9999 0 -0.29 47 47
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.013 0.11 -9999 0 -0.28 32 32
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.002 0.084 -9999 0 -0.48 11 11
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.065 0.18 -9999 0 -0.48 57 57
EGF/EGFR dimer/SHC -0.032 0.13 -9999 0 -0.3 65 65
mol:GDP -0.015 0.11 -9999 0 -0.28 32 32
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.012 0.11 -9999 0 -0.52 17 17
GRB2/SOS1 0.018 0 -9999 0 -10000 0 0
HRAS/GTP -0.039 0.087 -9999 0 -0.44 3 3
SHC1 0.012 0 -9999 0 -10000 0 0
HRAS/GDP -0.04 0.089 -9999 0 -0.45 3 3
FRAP1 -0.017 0.1 -9999 0 -0.27 32 32
EGF/EGFR dimer -0.049 0.15 -9999 0 -0.36 65 65
SOS1 0.012 0 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.01 0.1 -9999 0 -0.36 28 28
Signaling events mediated by PTP1B

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
PDGFRB 0 0.078 -10000 0 -0.49 9 9
Jak2/Leptin Receptor -0.04 0.14 0.19 2 -0.42 31 33
PTP1B/AKT1 -0.004 0.078 -10000 0 -0.29 12 12
FYN 0.011 0.024 -10000 0 -0.45 1 1
p210 bcr-abl/PTP1B -0.01 0.085 0.18 4 -0.32 14 18
EGFR -0.005 0.094 -10000 0 -0.54 11 11
EGF/EGFR -0.039 0.13 -10000 0 -0.35 37 37
CSF1 0.002 0.073 -10000 0 -0.53 7 7
AKT1 0.011 0.024 -10000 0 -0.45 1 1
INSR 0.012 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.08 0.16 -10000 0 -0.33 79 79
Insulin Receptor/Insulin -0.019 0.053 -10000 0 -0.3 3 3
HCK -0.012 0.11 -10000 0 -0.51 17 17
CRK 0.012 0 -10000 0 -10000 0 0
TYK2 -0.003 0.081 -10000 0 -0.3 13 13
EGF -0.065 0.18 -10000 0 -0.49 57 57
YES1 0.011 0.029 -10000 0 -0.54 1 1
CAV1 -0.009 0.092 0.18 4 -0.34 11 15
TXN 0.011 0.024 -10000 0 -0.45 1 1
PTP1B/IRS1/GRB2 -0.009 0.099 -10000 0 -0.33 21 21
cell migration 0.01 0.085 0.32 14 -0.18 4 18
STAT3 0.012 0.001 -10000 0 -10000 0 0
PRLR -0.068 0.19 -10000 0 -0.52 55 55
ITGA2B -0.039 0.15 -10000 0 -0.51 36 36
CSF1R -0.009 0.1 -10000 0 -0.51 15 15
Prolactin Receptor/Prolactin -0.065 0.16 -10000 0 -0.37 76 76
FGR -0.004 0.091 -10000 0 -0.5 12 12
PTP1B/p130 Cas -0.004 0.081 -10000 0 -0.3 13 13
Crk/p130 Cas 0.001 0.077 -10000 0 -0.34 7 7
DOK1 0 0.082 -10000 0 -0.36 8 8
JAK2 -0.042 0.14 -10000 0 -0.42 30 30
Jak2/Leptin Receptor/Leptin -0.051 0.12 -10000 0 -0.43 25 25
PIK3R1 -0.018 0.12 -10000 0 -0.52 21 21
PTPN1 -0.01 0.085 0.18 4 -0.32 14 18
LYN 0.008 0.049 -10000 0 -0.54 3 3
CDH2 -0.14 0.24 -10000 0 -0.5 111 111
SRC 0.009 0.049 -10000 0 -0.48 2 2
ITGB3 -0.068 0.18 -10000 0 -0.48 60 60
CAT1/PTP1B -0.064 0.16 -10000 0 -0.44 34 34
CAPN1 0.011 0.029 -10000 0 -0.55 1 1
CSK 0.012 0 -10000 0 -10000 0 0
PI3K -0.029 0.073 -10000 0 -0.34 5 5
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.047 0.12 -10000 0 -0.43 24 24
negative regulation of transcription -0.041 0.14 -10000 0 -0.42 30 30
FCGR2A 0.004 0.066 -10000 0 -0.51 6 6
FER 0.008 0.047 -10000 0 -0.51 3 3
alphaIIb/beta3 Integrin -0.076 0.17 -10000 0 -0.36 92 92
BLK -0.071 0.18 -10000 0 -0.49 60 60
Insulin Receptor/Insulin/Shc 0.017 0.014 -10000 0 -10000 0 0
RHOA 0.013 0.003 -10000 0 -10000 0 0
LEPR 0.003 0.069 -10000 0 -0.49 7 7
BCAR1 0.011 0.029 -10000 0 -0.54 1 1
p210 bcr-abl/Grb2 0.012 0 -10000 0 -10000 0 0
mol:NADPH 0 0.003 -10000 0 -10000 0 0
TRPV6 -0.071 0.16 -10000 0 -0.46 33 33
PRL -0.023 0.12 -10000 0 -0.45 25 25
SOCS3 -0.029 0.23 -10000 0 -1.3 11 11
SPRY2 -0.019 0.12 -10000 0 -0.51 22 22
Insulin Receptor/Insulin/IRS1 0.002 0.071 -10000 0 -0.32 17 17
CSF1/CSF1R -0.013 0.1 -10000 0 -0.38 14 14
Ras protein signal transduction 0.015 0.025 -10000 0 -10000 0 0
IRS1 -0.011 0.11 -10000 0 -0.53 16 16
INS 0 0.024 -10000 0 -0.45 1 1
LEP -0.007 0.078 -10000 0 -0.45 11 11
STAT5B -0.019 0.092 -10000 0 -0.27 26 26
STAT5A -0.019 0.092 -10000 0 -0.27 27 27
GRB2 0.012 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.009 0.094 -10000 0 -0.36 14 14
CSN2 -0.026 0.08 -10000 0 -10000 0 0
PIK3CA 0.01 0.034 -10000 0 -0.45 2 2
LAT -0.001 0.084 -10000 0 -0.5 8 8
YBX1 0.018 0.028 -10000 0 -0.52 1 1
LCK -0.017 0.12 -10000 0 -0.5 21 21
SHC1 0.012 0 -10000 0 -10000 0 0
NOX4 -0.011 0.11 -10000 0 -0.51 16 16
FAS signaling pathway (CD95)

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
SPTAN1 0.014 0.056 0.23 19 -0.21 1 20
RFC1 0.014 0.056 0.23 20 -0.21 1 21
PRKDC 0.012 0.061 0.23 20 -0.28 3 23
RIPK1 0.013 0.002 -10000 0 -10000 0 0
CASP7 -0.012 0.068 0.24 1 -0.8 2 3
FASLG/FAS/FADD/FAF1 -0.009 0.093 0.21 26 -0.26 22 48
MAP2K4 -0.002 0.1 -10000 0 -0.36 4 4
mol:ceramide -0.012 0.11 -10000 0 -0.31 25 25
GSN 0.013 0.059 0.23 20 -0.26 2 22
FASLG/FAS/FADD/FAF1/Caspase 8 0.002 0.1 -10000 0 -0.3 20 20
FAS 0 0.079 -10000 0 -0.53 8 8
BID 0.013 0.041 0.29 6 -0.33 1 7
MAP3K1 0.008 0.075 0.2 1 -0.52 2 3
MAP3K7 0.012 0.003 -10000 0 -10000 0 0
RB1 0.002 0.083 0.23 20 -0.3 15 35
CFLAR 0.013 0.002 -10000 0 -10000 0 0
HGF/MET -0.071 0.17 -10000 0 -0.34 98 98
ARHGDIB 0.013 0.057 0.23 19 -10000 0 19
FADD 0.01 0.024 -10000 0 -0.45 1 1
actin filament polymerization -0.013 0.059 0.26 2 -0.23 20 22
NFKB1 -0.024 0.049 -10000 0 -10000 0 0
MAPK8 -0.007 0.13 -10000 0 -0.41 17 17
DFFA 0.014 0.056 0.23 20 -0.21 1 21
DNA fragmentation during apoptosis 0.014 0.056 0.23 20 -0.21 1 21
FAS/FADD/MET -0.014 0.11 -10000 0 -0.31 42 42
CFLAR/RIP1 0.016 0.006 -10000 0 -10000 0 0
FAIM3 0 0.081 -10000 0 -0.51 9 9
FAF1 0.012 0.006 -10000 0 -10000 0 0
PARP1 0.014 0.056 0.23 19 -10000 0 19
DFFB 0.014 0.056 0.23 20 -0.21 1 21
CHUK -0.02 0.042 -10000 0 -10000 0 0
FASLG -0.047 0.16 -10000 0 -0.5 42 42
FAS/FADD 0.008 0.06 -10000 0 -0.37 9 9
HGF -0.043 0.16 -10000 0 -0.5 40 40
LMNA 0.024 0.049 0.22 15 -10000 0 15
CASP6 0.014 0.056 0.23 19 -10000 0 19
CASP10 0.002 0.07 -10000 0 -0.5 7 7
CASP3 0.017 0.067 0.26 24 -0.25 1 25
PTPN13 -0.041 0.16 -10000 0 -0.52 37 37
CASP8 0.007 0.055 0.32 9 -0.4 1 10
IL6 -0.053 0.25 -10000 0 -1.2 13 13
MET -0.035 0.15 -10000 0 -0.52 33 33
ICAD/CAD 0.013 0.052 0.22 15 -10000 0 15
FASLG/FAS/FADD/FAF1/Caspase 10 -0.012 0.11 -10000 0 -0.32 25 25
activation of caspase activity by cytochrome c 0.013 0.041 0.29 6 -0.33 1 7
PAK2 0.013 0.058 0.23 19 -0.23 2 21
BCL2 -0.015 0.12 -10000 0 -0.52 19 19
Coregulation of Androgen receptor activity

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
NRIP1 -0.005 0.089 -9999 0 -0.54 10 10
SVIL -0.003 0.085 -9999 0 -0.54 9 9
ZNF318 0.019 0.025 -9999 0 -10000 0 0
JMJD2C -0.004 0.029 -9999 0 -0.086 40 40
T-DHT/AR/Ubc9 -0.043 0.13 -9999 0 -0.34 56 56
CARM1 0.012 0.001 -9999 0 -10000 0 0
PRDX1 0.013 0.002 -9999 0 -10000 0 0
PELP1 0.013 0.004 -9999 0 -10000 0 0
CTNNB1 0.009 0.029 -9999 0 -0.54 1 1
AKT1 0.013 0.025 -9999 0 -0.45 1 1
PTK2B 0.008 0.041 -9999 0 -0.54 2 2
MED1 0.014 0.008 -9999 0 -10000 0 0
MAK -0.031 0.15 -9999 0 -0.49 37 37
response to oxidative stress 0 0.002 -9999 0 -10000 0 0
HIP1 0.007 0.041 -9999 0 -0.54 2 2
GSN 0.008 0.031 -9999 0 -0.54 1 1
NCOA2 -0.008 0.1 -9999 0 -0.52 14 14
NCOA6 0.011 0.008 -9999 0 -10000 0 0
DNA-PK 0.029 0.036 -9999 0 -0.32 2 2
NCOA4 0.011 0.024 -9999 0 -0.45 1 1
PIAS3 0.011 0.008 -9999 0 -10000 0 0
cell proliferation -0.052 0.16 -9999 0 -0.7 18 18
XRCC5 0.014 0.006 -9999 0 -10000 0 0
UBE3A 0.009 0.016 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.097 0.17 -9999 0 -0.34 109 109
FHL2 -0.023 0.19 -9999 0 -1.1 11 11
RANBP9 0.011 0.008 -9999 0 -10000 0 0
JMJD1A -0.01 0.054 -9999 0 -0.13 58 58
CDK6 -0.014 0.12 -9999 0 -0.5 19 19
TGFB1I1 0.001 0.065 -9999 0 -0.46 7 7
T-DHT/AR/CyclinD1 -0.061 0.15 -9999 0 -0.35 71 71
XRCC6 0.014 0.006 -9999 0 -10000 0 0
T-DHT/AR -0.049 0.16 -9999 0 -0.36 61 61
CTDSP1 0.011 0.003 -9999 0 -10000 0 0
CTDSP2 0.017 0.017 -9999 0 -10000 0 0
BRCA1 0.007 0.041 -9999 0 -0.54 2 2
TCF4 0.008 0.065 -9999 0 -0.54 5 5
CDKN2A -0.11 0.21 -9999 0 -0.47 91 91
SRF 0.017 0.023 -9999 0 -10000 0 0
NKX3-1 -0.085 0.27 -9999 0 -0.8 37 37
KLK3 -0.03 0.18 -9999 0 -1.3 4 4
TMF1 0.011 0.003 -9999 0 -10000 0 0
HNRNPA1 0.015 0.009 -9999 0 -10000 0 0
AOF2 -0.003 0.011 -9999 0 -0.072 4 4
APPL1 0.021 0.032 -9999 0 -0.35 2 2
T-DHT/AR/Caspase 8 -0.042 0.14 -9999 0 -0.34 56 56
AR -0.077 0.2 -9999 0 -0.54 55 55
UBA3 0.011 0.003 -9999 0 -10000 0 0
PATZ1 0.015 0.009 -9999 0 -10000 0 0
PAWR 0.011 0.003 -9999 0 -10000 0 0
PRKDC 0.011 0.041 -9999 0 -0.54 2 2
PA2G4 0.014 0.025 -9999 0 -0.42 1 1
UBE2I 0.012 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.037 0.12 -9999 0 -0.31 56 56
RPS6KA3 0.01 0.011 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.045 0.14 -9999 0 -0.34 57 57
LATS2 0.015 0.009 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.036 0.12 -9999 0 -0.31 55 55
Cyclin D3/CDK11 p58 0.01 0.002 -9999 0 -10000 0 0
VAV3 -0.03 0.14 -9999 0 -0.54 27 27
KLK2 -0.054 0.15 -9999 0 -0.42 40 40
CASP8 0.012 0.029 -9999 0 -0.54 1 1
T-DHT/AR/TIF2/CARM1 -0.044 0.14 -9999 0 -0.34 57 57
TMPRSS2 -0.098 0.3 -9999 0 -1 33 33
CCND1 -0.015 0.12 -9999 0 -0.52 18 18
PIAS1 0.009 0.016 -9999 0 -10000 0 0
mol:T-DHT -0.01 0.03 -9999 0 -0.074 43 43
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.006 0.024 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.058 0.16 -9999 0 -0.36 70 70
CMTM2 -0.005 0.094 -9999 0 -0.52 12 12
SNURF -0.075 0.19 -9999 0 -0.5 60 60
ZMIZ1 0.004 0.027 -9999 0 -10000 0 0
CCND3 0.012 0.001 -9999 0 -10000 0 0
TGIF1 0.015 0.009 -9999 0 -10000 0 0
FKBP4 0.011 0.008 -9999 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.024 0.14 -9999 0 -0.44 16 16
NF kappa B1 p50/RelA/I kappa B alpha -0.002 0.13 -9999 0 -0.44 9 9
alphaV/beta3 Integrin/Osteopontin/Src -0.014 0.11 -9999 0 -0.36 36 36
AP1 -0.037 0.18 -9999 0 -0.48 27 27
ILK -0.034 0.14 -9999 0 -0.46 17 17
bone resorption -0.023 0.14 -9999 0 -0.43 22 22
PTK2B 0.009 0.04 -9999 0 -0.54 2 2
PYK2/p130Cas -0.025 0.14 -9999 0 -0.44 19 19
ITGAV 0.007 0.061 -9999 0 -0.52 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.003 0.077 -9999 0 -0.38 14 14
alphaV/beta3 Integrin/Osteopontin -0.044 0.16 -9999 0 -0.37 54 54
MAP3K1 -0.036 0.15 -9999 0 -0.46 19 19
JUN 0.009 0.037 -9999 0 -0.49 2 2
MAPK3 -0.024 0.14 -9999 0 -0.43 19 19
MAPK1 -0.024 0.14 -9999 0 -0.43 19 19
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 -0.03 0.14 -9999 0 -0.43 20 20
ITGB3 -0.065 0.18 -9999 0 -0.48 60 60
NFKBIA -0.015 0.14 -9999 0 -0.43 16 16
FOS -0.019 0.12 -9999 0 -0.47 24 24
CD44 -0.009 0.1 -9999 0 -0.54 14 14
CHUK 0.012 0 -9999 0 -10000 0 0
PLAU -0.024 0.2 -9999 0 -0.89 10 10
NF kappa B1 p50/RelA -0.049 0.1 -9999 0 -0.44 9 9
BCAR1 0.011 0.029 -9999 0 -0.54 1 1
RELA 0.012 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.039 0.14 -9999 0 -0.34 63 63
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.041 0.15 -9999 0 -0.45 22 22
VAV3 -0.053 0.16 -9999 0 -0.46 28 28
MAP3K14 -0.033 0.15 -9999 0 -0.43 21 21
ROCK2 0.012 0 -9999 0 -10000 0 0
SPP1 -0.029 0.14 -9999 0 -0.5 32 32
RAC1 0.012 0 -9999 0 -10000 0 0
Rac1/GTP -0.043 0.15 -9999 0 -0.43 27 27
MMP2 -0.049 0.2 -9999 0 -0.56 28 28
Arf6 signaling events

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
CENTA1/KIF3B 0.005 0.063 -9999 0 -0.33 13 13
ARNO/beta Arrestin1-2 -0.016 0.083 -9999 0 -10000 0 0
EGFR -0.004 0.092 -9999 0 -0.53 11 11
EPHA2 -0.003 0.088 -9999 0 -0.51 11 11
USP6 0.011 0.024 -9999 0 -0.45 1 1
IQSEC1 0.011 0.029 -9999 0 -0.54 1 1
EGFR/EGFR/EGF/EGF -0.049 0.15 -9999 0 -0.36 65 65
ARRB2 0.006 0.018 -9999 0 -0.19 3 3
mol:GTP 0.005 0.041 -9999 0 -0.17 12 12
ARRB1 0.007 0.053 -9999 0 -0.5 4 4
FBXO8 0.01 0.034 -9999 0 -0.45 2 2
TSHR -0.04 0.14 -9999 0 -0.45 40 40
EGF -0.065 0.18 -9999 0 -0.48 57 57
somatostatin receptor activity 0 0 -9999 0 -0.001 18 18
ARAP2 -0.009 0.1 -9999 0 -0.54 14 14
mol:GDP -0.019 0.07 -9999 0 -0.25 14 14
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 8 8
ITGA2B -0.038 0.15 -9999 0 -0.51 36 36
ARF6 0.012 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.016 0.068 -9999 0 -0.27 20 20
ADAP1 -0.004 0.093 -9999 0 -0.54 11 11
KIF13B 0.009 0.04 -9999 0 -0.54 2 2
HGF/MET -0.056 0.16 -9999 0 -0.38 69 69
PXN 0.012 0 -9999 0 -10000 0 0
ARF6/GTP -0.024 0.082 -9999 0 -0.25 18 18
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.033 0.13 -9999 0 -0.3 66 66
ADRB2 -0.064 0.18 -9999 0 -0.48 57 57
receptor agonist activity 0 0 -9999 0 0 20 20
actin filament binding 0 0 -9999 0 0 19 19
SRC 0.009 0.04 -9999 0 -0.54 2 2
ITGB3 -0.068 0.18 -9999 0 -0.48 60 60
GNAQ 0.011 0.029 -9999 0 -0.54 1 1
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 12 12
ARF6/GDP 0.012 0.077 -9999 0 -0.4 5 5
ARF6/GDP/GULP/ACAP1 -0.026 0.12 -9999 0 -0.38 27 27
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.042 0.13 -9999 0 -0.3 44 44
ACAP1 -0.001 0.08 -9999 0 -0.48 10 10
ACAP2 0.011 0.029 -9999 0 -0.54 1 1
LHCGR/beta Arrestin2 -0.001 0.024 -9999 0 -0.26 3 3
EFNA1 -0.001 0.082 -9999 0 -0.52 9 9
HGF -0.043 0.16 -9999 0 -0.5 40 40
CYTH3 0.009 0.017 -9999 0 -0.32 1 1
CYTH2 0.009 0.001 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 19 19
endosomal lumen acidification 0 0 0 1 0 17 18
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.032 0.15 -9999 0 -0.54 30 30
GNAQ/ARNO 0.014 0.015 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 5 5
MET -0.035 0.15 -9999 0 -0.52 33 33
GNA14 -0.003 0.089 -9999 0 -0.54 10 10
GNA15 -0.005 0.093 -9999 0 -0.51 12 12
GIT1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 12 12
GNA11 -0.001 0.082 -9999 0 -0.52 9 9
LHCGR -0.003 0.041 -9999 0 -0.45 3 3
AGTR1 -0.003 0.071 -9999 0 -0.45 9 9
desensitization of G-protein coupled receptor protein signaling pathway -0.001 0.024 -9999 0 -0.26 3 3
IPCEF1/ARNO -0.023 0.097 -9999 0 -0.44 3 3
alphaIIb/beta3 Integrin -0.075 0.17 -9999 0 -0.36 92 92
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.01 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.029 0.12 -10000 0 -0.28 65 65
regulation of S phase of mitotic cell cycle -0.025 0.11 -10000 0 -0.42 11 11
GNAO1 -0.014 0.11 -10000 0 -0.47 20 20
HRAS 0.011 0.024 -10000 0 -0.45 1 1
SHBG/T-DHT -0.014 0.082 -10000 0 -0.33 24 24
PELP1 0.012 0.001 -10000 0 -10000 0 0
AKT1 0.009 0.017 -10000 0 -0.32 1 1
MAP2K1 -0.003 0.093 -10000 0 -0.31 3 3
T-DHT/AR -0.048 0.14 -10000 0 -0.38 55 55
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.005 22 22
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 -0.005 0.095 -10000 0 -0.52 12 12
mol:GDP -0.068 0.16 -10000 0 -0.47 44 44
cell proliferation 0.003 0.11 -10000 0 -0.39 8 8
PIK3CA 0.01 0.034 -10000 0 -0.45 2 2
FOS 0.001 0.13 -10000 0 -0.66 8 8
mol:Ca2+ -0.01 0.021 -10000 0 -0.069 23 23
MAPK3 0.001 0.1 -10000 0 -0.36 4 4
MAPK1 0.007 0.056 -10000 0 -0.26 1 1
PIK3R1 -0.018 0.12 -10000 0 -0.52 21 21
mol:IP3 0 0.001 -10000 0 -0.003 24 24
cAMP biosynthetic process -0.01 0.08 -10000 0 -0.3 24 24
GNG2 -0.002 0.084 -10000 0 -0.48 11 11
potassium channel inhibitor activity 0 0.001 -10000 0 -0.003 24 24
HRAS/GTP -0.018 0.098 -10000 0 -0.26 46 46
actin cytoskeleton reorganization -0.015 0.058 -10000 0 -0.25 17 17
SRC 0.009 0.041 -10000 0 -0.54 2 2
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.003 24 24
PI3K -0.004 0.079 -10000 0 -0.31 23 23
apoptosis -0.006 0.091 0.38 8 -10000 0 8
T-DHT/AR/PELP1 -0.032 0.12 -10000 0 -0.31 55 55
HRAS/GDP -0.064 0.15 -10000 0 -0.44 44 44
CREB1 0.005 0.096 -10000 0 -0.41 8 8
RAC1-CDC42/GTP -0.014 0.059 -10000 0 -0.26 17 17
AR -0.067 0.19 -10000 0 -0.52 55 55
GNB1 0.012 0 -10000 0 -10000 0 0
RAF1 -0.009 0.096 -10000 0 -0.3 3 3
RAC1-CDC42/GDP -0.059 0.14 -10000 0 -0.42 44 44
T-DHT/AR/PELP1/Src -0.023 0.11 -10000 0 -0.28 57 57
MAP2K2 -0.003 0.093 -10000 0 -0.31 3 3
T-DHT/AR/PELP1/Src/PI3K -0.025 0.12 -10000 0 -0.42 11 11
GNAZ -0.005 0.094 -10000 0 -0.52 12 12
SHBG -0.023 0.13 -10000 0 -0.53 24 24
Gi family/GNB1/GNG2/GDP -0.002 0.088 -10000 0 -0.33 13 13
mol:T-DHT 0 0 -10000 0 -0.002 18 18
RAC1 0.012 0 -10000 0 -10000 0 0
GNRH1 -0.006 0.078 -10000 0 -0.39 15 15
Gi family/GTP -0.018 0.089 -10000 0 -0.33 12 12
CDC42 0.012 0 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.016 0.099 -9999 0 -0.27 47 47
RGS9BP -0.022 0.12 -9999 0 -0.45 26 26
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.008 0.07 -9999 0 -0.45 9 9
mol:Na + -0.004 0.058 -9999 0 -0.26 17 17
mol:ADP -0.003 0.06 -9999 0 -0.32 13 13
GNAT2 0.007 0.042 -9999 0 -0.45 3 3
RGS9-1/Gbeta5/R9AP -0.039 0.14 -9999 0 -0.33 66 66
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.006 0.029 -9999 0 -0.27 4 4
GRK7 0.003 0.048 -9999 0 -0.45 4 4
CNGB3 -0.008 0.078 -9999 0 -0.45 11 11
Cone Metarhodopsin II/X-Arrestin 0.002 0.024 -9999 0 -0.32 2 2
mol:Ca2+ -0.006 0.061 -9999 0 -0.24 24 24
Cone PDE6 -0.031 0.12 -9999 0 -0.35 31 31
Cone Metarhodopsin II -0.002 0.046 -9999 0 -0.24 13 13
Na + (4 Units) -0.005 0.061 -9999 0 -0.23 24 24
GNAT2/GDP -0.029 0.12 -9999 0 -0.35 32 32
GNB5 0.006 0.057 -9999 0 -0.54 4 4
mol:GMP (4 units) 0.006 0.034 -9999 0 -0.24 7 7
Cone Transducin -0.016 0.1 -9999 0 -0.28 47 47
SLC24A2 -0.004 0.062 -9999 0 -0.45 7 7
GNB3/GNGT2 -0.029 0.13 -9999 0 -0.36 46 46
GNB3 -0.037 0.15 -9999 0 -0.5 35 35
GNAT2/GTP 0.005 0.03 -9999 0 -0.32 3 3
CNGA3 0 0.058 -9999 0 -0.45 6 6
ARR3 0.003 0.034 -9999 0 -0.45 2 2
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.004 0.058 -9999 0 -0.27 17 17
mol:Pi -0.039 0.14 -9999 0 -0.33 66 66
Cone CNG Channel -0.009 0.059 -9999 0 -0.42 3 3
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.004 0.062 -9999 0 -0.45 7 7
RGS9 -0.054 0.17 -9999 0 -0.49 49 49
PDE6C 0.001 0.041 -9999 0 -0.45 3 3
GNGT2 -0.004 0.091 -9999 0 -0.5 12 12
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.001 0.024 -9999 0 -0.45 1 1
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.016 0.11 -10000 0 -0.37 33 33
CRKL -0.01 0.1 -10000 0 -0.37 9 9
mol:PIP3 -0.007 0.068 0.48 7 -10000 0 7
AKT1 0.007 0.048 0.34 7 -0.23 1 8
PTK2B 0.009 0.04 -10000 0 -0.54 2 2
RAPGEF1 -0.004 0.096 -10000 0 -0.37 7 7
RANBP10 0.012 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.034 -10000 0 -0.45 2 2
HGF/MET/SHIP2 -0.039 0.14 -10000 0 -0.32 69 69
MAP3K5 -0.004 0.11 -10000 0 -0.42 10 10
HGF/MET/CIN85/CBL/ENDOPHILINS -0.029 0.13 -10000 0 -0.31 49 49
AP1 -0.014 0.088 -10000 0 -0.31 25 25
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.012 0 -10000 0 -10000 0 0
apoptosis -0.011 0.12 -10000 0 -0.87 6 6
STAT3 (dimer) -0.01 0.11 -10000 0 -0.47 6 6
GAB1/CRKL/SHP2/PI3K -0.008 0.12 -10000 0 -0.41 15 15
INPP5D -0.002 0.088 -10000 0 -0.53 10 10
CBL/CRK -0.003 0.096 -10000 0 -0.36 8 8
PTPN11 0.012 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.012 0 -10000 0 -10000 0 0
PTEN 0.002 0.075 -10000 0 -0.54 7 7
ELK1 -0.018 0.055 -10000 0 -0.19 33 33
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.003 0.068 -10000 0 -0.28 7 7
PAK1 0.012 0.044 0.32 7 -10000 0 7
HGF/MET/RANBP10 -0.039 0.14 -10000 0 -0.32 69 69
HRAS -0.041 0.18 -10000 0 -0.62 28 28
DOCK1 -0.004 0.096 -10000 0 -0.36 8 8
GAB1 -0.017 0.1 -10000 0 -0.3 31 31
CRK -0.01 0.1 -10000 0 -0.37 9 9
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.051 0.19 -10000 0 -0.54 47 47
JUN 0.01 0.037 -10000 0 -0.5 2 2
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.029 0.096 -10000 0 -0.26 47 47
PIK3R1 -0.018 0.12 -10000 0 -0.52 21 21
cell morphogenesis -0.004 0.13 -10000 0 -0.47 14 14
GRB2/SHC -0.011 0.087 -10000 0 -0.36 6 6
FOS -0.019 0.12 -10000 0 -0.47 24 24
GLMN -0.01 0.049 -10000 0 -0.26 14 14
cell motility -0.018 0.055 -10000 0 -0.19 33 33
HGF/MET/MUC20 -0.047 0.14 -10000 0 -0.32 69 69
cell migration -0.011 0.085 -10000 0 -0.36 6 6
GRB2 0.012 0 -10000 0 -10000 0 0
CBL 0.012 0 -10000 0 -10000 0 0
MET/RANBP10 -0.016 0.11 -10000 0 -0.37 33 33
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.015 0.11 -10000 0 -0.49 5 5
MET/MUC20 -0.025 0.11 -10000 0 -0.38 33 33
RAP1B 0.002 0.091 -10000 0 -0.36 6 6
RAP1A 0.002 0.091 -10000 0 -0.36 6 6
HGF/MET/RANBP9 -0.039 0.14 -10000 0 -0.32 69 69
RAF1 -0.033 0.17 -10000 0 -0.57 28 28
STAT3 -0.01 0.11 -10000 0 -0.47 6 6
cell proliferation -0.017 0.14 -10000 0 -0.37 47 47
RPS6KB1 -0.01 0.049 -10000 0 -0.24 5 5
MAPK3 -0.021 0.05 -10000 0 -10000 0 0
MAPK1 -0.021 0.05 -10000 0 -10000 0 0
RANBP9 0.012 0 -10000 0 -10000 0 0
MAPK8 0.007 0.1 -10000 0 -0.41 10 10
SRC -0.009 0.1 -10000 0 -0.47 6 6
PI3K -0.028 0.12 -10000 0 -0.38 23 23
MET/Glomulin -0.027 0.11 -10000 0 -0.3 45 45
SOS1 0.012 0 -10000 0 -10000 0 0
MAP2K1 -0.024 0.16 -10000 0 -0.53 28 28
MET -0.035 0.15 -10000 0 -0.52 33 33
MAP4K1 -0.007 0.1 -10000 0 -0.35 11 11
PTK2 0.012 0 -10000 0 -10000 0 0
MAP2K2 -0.024 0.16 -10000 0 -0.53 28 28
BAD 0.012 0.044 0.32 7 -0.21 1 8
MAP2K4 0.002 0.1 -10000 0 -0.38 10 10
SHP2/GRB2/SOS1/GAB1 -0.042 0.1 -10000 0 -0.36 29 29
INPPL1 0.012 0 -10000 0 -10000 0 0
PXN 0.012 0 -10000 0 -10000 0 0
SH3KBP1 0.008 0.047 -10000 0 -0.51 3 3
HGS -0.021 0.089 -10000 0 -0.27 29 29
PLCgamma1/PKC 0.009 0 -10000 0 -10000 0 0
HGF -0.043 0.16 -10000 0 -0.5 40 40
RASA1 0.012 0 -10000 0 -10000 0 0
NCK1 0.012 0 -10000 0 -10000 0 0
PTPRJ 0.007 0.048 -10000 0 -0.45 4 4
NCK/PLCgamma1 -0.011 0.09 -10000 0 -0.25 29 29
PDPK1 0 0.053 0.38 7 -10000 0 7
HGF/MET/SHIP -0.047 0.15 -10000 0 -0.33 76 76
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.072 0.21 -9999 0 -0.71 8 8
CRP -0.082 0.22 -9999 0 -0.73 10 10
cell cycle arrest -0.091 0.24 -9999 0 -0.71 18 18
TIMP1 -0.067 0.21 -9999 0 -0.76 11 11
IL6ST -0.036 0.15 -9999 0 -0.52 33 33
Rac1/GDP -0.049 0.15 -9999 0 -0.44 27 27
AP1 -0.006 0.096 -9999 0 -0.39 2 2
GAB2 0.01 0.034 -9999 0 -0.45 2 2
TNFSF11 -0.17 0.37 -9999 0 -1 47 47
HSP90B1 0.011 0.044 -9999 0 -10000 0 0
GAB1 0.011 0.029 -9999 0 -0.54 1 1
MAPK14 -0.046 0.18 -9999 0 -0.54 28 28
AKT1 0.031 0.052 -9999 0 -10000 0 0
FOXO1 0.035 0.051 -9999 0 -10000 0 0
MAP2K6 -0.054 0.16 -9999 0 -0.48 30 30
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
MAP2K4 -0.052 0.16 -9999 0 -0.48 20 20
MITF -0.049 0.15 -9999 0 -0.46 24 24
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.012 0 -9999 0 -10000 0 0
A2M 0.01 0.1 -9999 0 -1.3 2 2
CEBPB 0.016 0.006 -9999 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.003 0.063 -9999 0 -10000 0 0
STAT3 -0.095 0.25 -9999 0 -0.75 18 18
STAT1 -0.004 0.019 -9999 0 -10000 0 0
CEBPD -0.079 0.23 -9999 0 -0.8 14 14
PIK3CA 0.011 0.034 -9999 0 -0.45 2 2
PI3K -0.003 0.093 -9999 0 -0.36 23 23
JUN 0.009 0.037 -9999 0 -0.5 2 2
PIAS3/MITF -0.04 0.14 -9999 0 -0.45 21 21
MAPK11 -0.048 0.18 -9999 0 -0.56 27 27
STAT3 (dimer)/FOXO1 -0.043 0.2 -9999 0 -0.56 12 12
GRB2/SOS1/GAB family -0.051 0.11 -9999 0 -0.43 17 17
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.049 0.15 -9999 0 -0.42 31 31
GRB2 0.013 0.001 -9999 0 -10000 0 0
JAK2 -0.001 0.085 -9999 0 -0.54 9 9
LBP -0.17 0.34 -9999 0 -0.85 56 56
PIK3R1 -0.017 0.12 -9999 0 -0.52 21 21
JAK1 0.004 0.065 -9999 0 -0.55 5 5
MYC -0.087 0.25 -9999 0 -0.92 15 15
FGG -0.083 0.22 -9999 0 -0.72 10 10
macrophage differentiation -0.091 0.24 -9999 0 -0.71 18 18
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.05 0.16 -9999 0 -0.47 23 23
JUNB -0.075 0.22 -9999 0 -0.72 14 14
FOS -0.019 0.12 -9999 0 -0.47 24 24
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.053 0.15 -9999 0 -0.44 29 29
STAT1/PIAS1 -0.045 0.14 -9999 0 -0.41 21 21
GRB2/SOS1/GAB family/SHP2/PI3K 0.021 0.053 -9999 0 -10000 0 0
STAT3 (dimer) -0.094 0.25 -9999 0 -0.75 18 18
PRKCD -0.057 0.19 -9999 0 -0.56 17 17
IL6R -0.021 0.13 -9999 0 -0.52 23 23
SOCS3 -0.053 0.24 -9999 0 -1.1 14 14
gp130 (dimer)/JAK1/JAK1/LMO4 -0.014 0.11 -9999 0 -0.33 37 37
Rac1/GTP -0.053 0.16 -9999 0 -0.45 26 26
HCK -0.012 0.11 -9999 0 -0.51 17 17
MAPKKK cascade 0.006 0.058 -9999 0 -10000 0 0
bone resorption -0.15 0.34 -9999 0 -0.93 47 47
IRF1 -0.072 0.21 -9999 0 -0.71 9 9
mol:GDP -0.056 0.16 -9999 0 -0.44 33 33
SOS1 0.012 0.002 -9999 0 -10000 0 0
VAV1 -0.056 0.16 -9999 0 -0.44 33 33
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.052 0.2 -9999 0 -0.56 35 35
PTPN11 -0.003 0.015 -9999 0 -10000 0 0
IL6/IL6RA -0.049 0.15 -9999 0 -0.36 64 64
gp130 (dimer)/TYK2/TYK2/LMO4 -0.01 0.1 -9999 0 -0.32 32 32
gp130 (dimer)/JAK2/JAK2/LMO4 -0.018 0.12 -9999 0 -0.34 39 39
IL6 -0.047 0.16 -9999 0 -0.48 44 44
PIAS3 0.012 0 -9999 0 -10000 0 0
PTPRE 0.006 0.06 -9999 0 -0.45 6 6
PIAS1 0.012 0 -9999 0 -10000 0 0
RAC1 0.012 0.001 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.043 0.13 -9999 0 -0.41 21 21
LMO4 0.007 0.051 -9999 0 -0.55 3 3
STAT3 (dimer)/PIAS3 -0.085 0.23 -9999 0 -0.72 15 15
MCL1 0.036 0.048 -9999 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A -0.027 0.11 -9999 0 -0.34 41 41
PRKCZ 0.009 0.04 -9999 0 -0.54 2 2
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.012 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.002 0.067 -9999 0 -0.31 6 6
IRAK/TOLLIP -0.005 0.086 -9999 0 -0.28 17 17
IKBKB 0.012 0 -9999 0 -10000 0 0
IKBKG 0.012 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.076 0.17 -9999 0 -0.36 92 92
IL1A -0.055 0.17 -9999 0 -0.47 51 51
IL1B -0.019 0.13 -9999 0 -0.39 35 35
IRAK/TRAF6/p62/Atypical PKCs 0.009 0.082 -9999 0 -0.44 1 1
IL1R2 -0.052 0.17 -9999 0 -0.52 45 45
IL1R1 -0.001 0.083 -9999 0 -0.53 9 9
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.006 0.083 -9999 0 -0.39 5 5
TOLLIP 0.012 0 -9999 0 -10000 0 0
TICAM2 -0.007 0.097 -9999 0 -0.54 12 12
MAP3K3 0.012 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0.008 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.031 0.065 -9999 0 -10000 0 0
JUN -0.001 0.09 -9999 0 -0.42 4 4
MAP3K7 0.012 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.018 0.13 -9999 0 -0.53 10 10
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.023 0.11 -9999 0 -0.3 25 25
PIK3R1 -0.018 0.12 -9999 0 -0.52 21 21
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.014 0.11 -9999 0 -0.34 5 5
IL1 beta fragment/IL1R1/IL1RAP -0.017 0.12 -9999 0 -0.34 32 32
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 -0.006 0.094 -9999 0 -0.45 4 4
IRAK1 -0.014 0.095 -9999 0 -0.32 17 17
IL1RN/IL1R1 -0.031 0.13 -9999 0 -0.37 47 47
IRAK4 0.012 0 -9999 0 -10000 0 0
PRKCI 0.008 0.044 -9999 0 -0.48 3 3
TRAF6 0.012 0 -9999 0 -10000 0 0
PI3K -0.006 0.093 -9999 0 -0.37 23 23
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.004 0.083 -9999 0 -0.37 6 6
CHUK 0.012 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.017 0.12 -9999 0 -0.34 32 32
IL1 beta/IL1R2 -0.049 0.16 -9999 0 -0.35 72 72
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0.075 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.046 0.1 -9999 0 -0.48 10 10
IRAK3 -0.023 0.13 -9999 0 -0.48 27 27
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.012 0.13 -9999 0 -0.53 11 11
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.005 0.081 -9999 0 -0.32 2 2
IL1 alpha/IL1R1/IL1RAP -0.034 0.12 -9999 0 -0.28 70 70
RELA 0.012 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.011 0.024 -9999 0 -0.45 1 1
MYD88 0.012 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.003 0.082 -9999 0 -10000 0 0
IL1RAP -0.004 0.09 -9999 0 -0.5 12 12
UBE2N 0.012 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.056 0.11 -9999 0 -0.46 16 16
CASP1 -0.01 0.1 -9999 0 -0.5 16 16
IL1RN/IL1R2 -0.067 0.17 -9999 0 -0.39 77 77
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.008 0.12 -9999 0 -0.57 6 6
TMEM189-UBE2V1 -0.05 0.16 -9999 0 -0.49 41 41
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.009 0.086 -9999 0 -0.34 10 10
PIK3CA 0.01 0.034 -9999 0 -0.45 2 2
IL1RN -0.043 0.16 -9999 0 -0.5 40 40
TRAF6/TAK1/TAB1/TAB2 -0.017 0.075 -9999 0 -0.26 17 17
MAP2K6 -0.011 0.095 -9999 0 -0.47 3 3
FOXM1 transcription factor network

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
NFATC3 0.024 0.37 -9999 0 -1.2 13 13
PLK1 0.029 0.14 -9999 0 -1.4 3 3
BIRC5 -0.006 0.27 -9999 0 -1.4 13 13
HSPA1B 0.017 0.38 -9999 0 -1.2 15 15
MAP2K1 0.028 0.033 -9999 0 -10000 0 0
BRCA2 0.003 0.41 -9999 0 -1.2 21 21
FOXM1 -0.004 0.47 -9999 0 -1.6 15 15
XRCC1 0.024 0.37 -9999 0 -1.2 13 13
FOXM1B/p19 -0.16 0.32 -9999 0 -1.1 24 24
Cyclin D1/CDK4 -0.009 0.39 -9999 0 -1 21 21
CDC2 0.017 0.38 -9999 0 -1.2 15 15
TGFA -0.02 0.4 -9999 0 -0.98 29 29
SKP2 0.024 0.37 -9999 0 -1.2 13 13
CCNE1 -0.011 0.11 -9999 0 -0.5 19 19
CKS1B 0.023 0.37 -9999 0 -1.2 13 13
RB1 -0.094 0.2 -9999 0 -0.96 13 13
FOXM1C/SP1 0.005 0.4 -9999 0 -1.3 16 16
AURKB 0.024 0.17 -9999 0 -1.4 5 5
CENPF 0.013 0.4 -9999 0 -1.3 15 15
CDK4 0.017 0.014 -9999 0 -10000 0 0
MYC 0.021 0.35 -9999 0 -1 17 17
CHEK2 0.025 0.052 -9999 0 -0.52 2 2
ONECUT1 -0.004 0.38 -9999 0 -1.1 18 18
CDKN2A -0.11 0.21 -9999 0 -0.48 91 91
LAMA4 0.022 0.37 -9999 0 -1.2 12 12
FOXM1B/HNF6 -0.02 0.43 -9999 0 -1.3 20 20
FOS 0.007 0.39 -9999 0 -1.2 17 17
SP1 0.013 0.004 -9999 0 -10000 0 0
CDC25B 0.023 0.37 -9999 0 -1.2 13 13
response to radiation 0.013 0.03 -9999 0 -10000 0 0
CENPB 0.024 0.37 -9999 0 -1.2 13 13
CENPA 0.015 0.39 -9999 0 -1.2 15 15
NEK2 0.02 0.38 -9999 0 -1.2 14 14
HIST1H2BA 0.016 0.37 -9999 0 -1.2 13 13
CCNA2 0.007 0.066 -9999 0 -0.55 5 5
EP300 0.012 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.008 0.41 -9999 0 -1.4 15 15
CCNB2 0.023 0.37 -9999 0 -1.2 13 13
CCNB1 0.019 0.38 -9999 0 -1.2 15 15
ETV5 -0.01 0.43 -9999 0 -1.2 26 26
ESR1 -0.072 0.52 -9999 0 -1.1 58 58
CCND1 -0.008 0.4 -9999 0 -1.1 22 22
GSK3A 0.026 0.028 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.017 0.091 -9999 0 -0.31 22 22
CDK2 0.015 0.008 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.015 0.035 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.13 0.3 -9999 0 -1.2 15 15
GAS1 -0.061 0.48 -9999 0 -1.1 42 42
MMP2 -0.024 0.45 -9999 0 -1.2 32 32
RB1/FOXM1C -0.014 0.4 -9999 0 -1.1 21 21
CREBBP 0.012 0 -9999 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.002 0.075 -10000 0 -0.54 7 7
ANTXR2 -0.01 0.11 -10000 0 -0.53 15 15
negative regulation of myeloid dendritic cell antigen processing and presentation -0.004 0.017 -10000 0 -0.075 19 19
monocyte activation -0.063 0.17 -10000 0 -0.46 48 48
MAP2K2 -0.002 0.007 -10000 0 -10000 0 0
MAP2K1 -0.003 0.014 -10000 0 -10000 0 0
MAP2K7 -0.003 0.014 -10000 0 -10000 0 0
MAP2K6 -0.016 0.064 -10000 0 -0.3 17 17
CYAA -0.005 0.076 -10000 0 -0.32 19 19
MAP2K4 -0.005 0.025 -10000 0 -0.28 2 2
IL1B -0.011 0.075 -10000 0 -0.27 24 24
Channel -0.002 0.081 -10000 0 -0.34 19 19
NLRP1 -0.01 0.044 -10000 0 -0.27 9 9
CALM1 0.012 0 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.007 0.022 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.004 0.017 0.075 19 -10000 0 19
MAPK3 -0.004 0.018 -10000 0 -0.23 1 1
MAPK1 -0.004 0.018 -10000 0 -0.23 1 1
PGR -0.074 0.12 -10000 0 -0.29 94 94
PA/Cellular Receptors -0.003 0.089 -10000 0 -0.37 19 19
apoptosis -0.004 0.017 -10000 0 -0.075 19 19
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.001 0.077 -10000 0 -0.32 19 19
macrophage activation 0.011 0.023 -10000 0 -0.21 2 2
TNF -0.069 0.19 -10000 0 -0.49 60 60
VCAM1 -0.063 0.17 -10000 0 -0.46 48 48
platelet activation 0.007 0.022 -10000 0 -10000 0 0
MAPKKK cascade -0.005 0.027 0.14 7 -10000 0 7
IL18 -0.008 0.072 -10000 0 -0.26 24 24
negative regulation of macrophage activation -0.004 0.017 -10000 0 -0.075 19 19
LEF -0.004 0.017 -10000 0 -0.075 19 19
CASP1 -0.008 0.028 -10000 0 -0.14 12 12
mol:cAMP -0.004 0.019 -10000 0 -10000 0 0
necrosis -0.004 0.017 -10000 0 -0.075 19 19
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.002 0.077 -10000 0 -0.32 19 19
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.019 0.016 -10000 0 -10000 0 0
HSPA8 0.005 0.057 -10000 0 -0.54 4 4
SMAD3/SMAD4/ER alpha -0.047 0.13 0.2 3 -0.36 47 50
AKT1 0.01 0.029 -10000 0 -0.46 1 1
GSC -0.26 0.54 -10000 0 -1.4 71 71
NKX2-5 -0.052 0.16 -10000 0 -0.45 49 49
muscle cell differentiation 0.053 0.078 0.39 6 -10000 0 6
SMAD2-3/SMAD4/SP1 0.018 0.087 -10000 0 -0.36 3 3
SMAD4 -0.006 0.059 -10000 0 -0.59 1 1
CBFB 0.012 0 -10000 0 -10000 0 0
SAP18 0.012 0.002 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.002 0.1 -10000 0 -0.28 35 35
SMAD3/SMAD4/VDR 0.034 0.063 -10000 0 -0.3 1 1
MYC -0.005 0.095 -10000 0 -0.5 13 13
CDKN2B -0.025 0.24 -10000 0 -1.2 12 12
AP1 0.019 0.085 -10000 0 -0.49 3 3
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.036 0.041 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.037 0.12 -10000 0 -0.38 15 15
SP3 0.014 0.004 -10000 0 -10000 0 0
CREB1 0.012 0 -10000 0 -10000 0 0
FOXH1 -0.053 0.15 -10000 0 -0.52 33 33
SMAD3/SMAD4/GR 0.007 0.081 -10000 0 -0.36 8 8
GATA3 -0.043 0.15 -10000 0 -0.5 32 32
SKI/SIN3/HDAC complex/NCoR1 0.033 0.022 -10000 0 -10000 0 0
MEF2C/TIF2 -0.059 0.15 -10000 0 -0.44 23 23
endothelial cell migration 0.021 0.23 1.3 10 -10000 0 10
MAX 0.013 0.01 -10000 0 -10000 0 0
RBBP7 0.01 0.024 -10000 0 -0.45 1 1
RBBP4 0.012 0.002 -10000 0 -10000 0 0
RUNX2 -0.051 0.16 -10000 0 -0.47 48 48
RUNX3 -0.03 0.14 -10000 0 -0.51 30 30
RUNX1 0.003 0.07 -10000 0 -0.54 6 6
CTBP1 0.012 0 -10000 0 -10000 0 0
NR3C1 -0.002 0.087 -10000 0 -0.5 11 11
VDR 0.006 0.057 -10000 0 -0.54 4 4
CDKN1A 0.006 0.26 -10000 0 -1.2 16 16
KAT2B 0.002 0.081 -10000 0 -0.54 8 8
SMAD2/SMAD2/SMAD4/FOXH1 -0.047 0.14 -10000 0 -0.35 37 37
DCP1A 0.012 0 -10000 0 -10000 0 0
SKI 0.012 0.002 -10000 0 -10000 0 0
SERPINE1 -0.022 0.23 -10000 0 -1.3 10 10
SMAD3/SMAD4/ATF2 0.019 0.055 -10000 0 -0.32 1 1
SMAD3/SMAD4/ATF3 -0.004 0.1 -10000 0 -0.34 20 20
SAP30 0.009 0.04 -10000 0 -0.54 2 2
Cbp/p300/PIAS3 0.042 0.039 -10000 0 -10000 0 0
JUN 0.017 0.083 -10000 0 -0.49 3 3
SMAD3/SMAD4/IRF7 0.007 0.085 -10000 0 -0.35 11 11
TFE3 0.014 0.018 -10000 0 -10000 0 0
COL1A2 -0.015 0.16 -10000 0 -0.68 17 17
mesenchymal cell differentiation 0.022 0.13 0.34 38 -10000 0 38
DLX1 -0.039 0.14 -10000 0 -0.45 38 38
TCF3 0.011 0.029 -10000 0 -0.54 1 1
FOS -0.016 0.12 -10000 0 -0.47 24 24
SMAD3/SMAD4/Max 0.017 0.056 -10000 0 -0.33 1 1
Cbp/p300/SNIP1 0.03 0.014 -10000 0 -10000 0 0
ZBTB17 0.012 0.01 -10000 0 -10000 0 0
LAMC1 0.021 0.077 -10000 0 -0.46 6 6
TGIF2/HDAC complex/SMAD3/SMAD4 0.016 0.063 -10000 0 -0.32 4 4
IRF7 -0.005 0.098 -10000 0 -0.52 13 13
ESR1 -0.059 0.18 -10000 0 -0.53 48 48
HNF4A -0.15 0.24 -10000 0 -0.5 117 117
MEF2C -0.058 0.15 -10000 0 -0.45 21 21
SMAD2-3/SMAD4 0.004 0.07 -10000 0 -0.38 1 1
Cbp/p300/Src-1 0.035 0.023 -10000 0 -10000 0 0
IGHV3OR16-13 -0.007 0.022 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.008 0.047 -10000 0 -0.51 3 3
CREBBP 0.016 0.011 -10000 0 -10000 0 0
SKIL 0.009 0.04 -10000 0 -0.54 2 2
HDAC1 0.012 0.002 -10000 0 -10000 0 0
HDAC2 0.012 0.002 -10000 0 -10000 0 0
SNIP1 0.011 0.003 -10000 0 -10000 0 0
GCN5L2 0.005 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.027 0.065 -10000 0 -0.32 3 3
MSG1/HSC70 -0.029 0.12 -10000 0 -0.35 44 44
SMAD2 -0.005 0.043 -10000 0 -10000 0 0
SMAD3 0.009 0.044 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.027 0.043 -10000 0 -0.3 1 1
SMAD2/SMAD2/SMAD4 0 0.059 -10000 0 -0.34 9 9
NCOR1 0.012 0.002 -10000 0 -10000 0 0
NCOA2 -0.008 0.1 -10000 0 -0.52 14 14
NCOA1 0.012 0 -10000 0 -10000 0 0
MYOD/E2A -0.014 0.088 -10000 0 -0.32 29 29
SMAD2-3/SMAD4/SP1/MIZ-1 0.03 0.083 -10000 0 -0.35 2 2
IFNB1 0.007 0.073 -10000 0 -0.34 4 4
SMAD3/SMAD4/MEF2C -0.048 0.14 -10000 0 -0.45 16 16
CITED1 -0.043 0.16 -10000 0 -0.48 41 41
SMAD2-3/SMAD4/ARC105 0.014 0.063 -10000 0 -0.34 1 1
RBL1 0.009 0.04 -10000 0 -0.54 2 2
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.021 0.1 -10000 0 -0.48 11 11
RUNX1-3/PEBPB2 -0.007 0.1 -10000 0 -0.32 34 34
SMAD7 0.035 0.083 -10000 0 -0.46 1 1
MYC/MIZ-1 0.005 0.072 -10000 0 -0.37 11 11
SMAD3/SMAD4 0.04 0.13 0.27 58 -0.39 8 66
IL10 -0.049 0.2 -10000 0 -0.5 49 49
PIASy/HDAC complex 0.008 0.011 -10000 0 -10000 0 0
PIAS3 0.014 0.005 -10000 0 -10000 0 0
CDK2 0.016 0.011 -10000 0 -10000 0 0
IL5 -0.021 0.12 -10000 0 -0.52 7 7
CDK4 0.017 0.012 -10000 0 -10000 0 0
PIAS4 0.008 0.011 -10000 0 -10000 0 0
ATF3 -0.023 0.12 -10000 0 -0.47 27 27
SMAD3/SMAD4/SP1 0.021 0.082 -10000 0 -0.39 2 2
FOXG1 -0.17 0.25 -10000 0 -0.52 129 129
FOXO3 0.018 0.026 -10000 0 -0.32 1 1
FOXO1 0.017 0.031 -10000 0 -0.32 2 2
FOXO4 0.018 0.026 -10000 0 -0.32 1 1
heart looping -0.058 0.15 -10000 0 -0.44 21 21
CEBPB 0.012 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.014 0.11 -10000 0 -0.36 18 18
MYOD1 -0.031 0.12 -10000 0 -0.45 28 28
SMAD3/SMAD4/HNF4 -0.089 0.17 -10000 0 -0.34 88 88
SMAD3/SMAD4/GATA3 -0.024 0.14 -10000 0 -0.5 11 11
SnoN/SIN3/HDAC complex/NCoR1 0.009 0.04 -10000 0 -0.54 2 2
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.004 0.1 -10000 0 -0.38 11 11
SMAD3/SMAD4/SP1-3 0.034 0.077 -10000 0 -0.37 3 3
MED15 0.012 0 -10000 0 -10000 0 0
SP1 0.01 0.035 -10000 0 -10000 0 0
SIN3B 0.012 0.002 -10000 0 -10000 0 0
SIN3A 0.012 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.065 0.15 -10000 0 -0.4 30 30
ITGB5 0.03 0.074 -10000 0 -0.48 3 3
TGIF/SIN3/HDAC complex/CtBP 0.038 0.016 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.033 0.14 -10000 0 -0.36 49 49
AR -0.067 0.19 -10000 0 -0.52 55 55
negative regulation of cell growth 0.025 0.057 -10000 0 -0.32 1 1
SMAD3/SMAD4/MYOD -0.009 0.095 -10000 0 -0.34 10 10
E2F5 0.01 0.034 -10000 0 -0.45 2 2
E2F4 0.012 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.018 0.11 -10000 0 -0.37 13 13
SMAD2-3/SMAD4/FOXO1-3a-4 0.02 0.078 -10000 0 -0.32 12 12
TFDP1 0.012 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.022 0.088 -10000 0 -0.5 3 3
SMAD3/SMAD4/RUNX2 -0.022 0.13 -10000 0 -0.35 38 38
TGIF2 0.008 0.047 -10000 0 -0.51 3 3
TGIF1 0.012 0 -10000 0 -10000 0 0
ATF2 0.012 0 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.012 0 -9999 0 -10000 0 0
VLDLR -0.004 0.093 -9999 0 -0.54 11 11
LRPAP1 0.012 0 -9999 0 -10000 0 0
NUDC 0.012 0 -9999 0 -10000 0 0
RELN/LRP8 -0.076 0.15 -9999 0 -0.3 116 116
CaM/Ca2+ 0.009 0 -9999 0 -10000 0 0
KATNA1 0.012 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.063 0.14 -9999 0 -0.3 57 57
IQGAP1/CaM 0.018 0 -9999 0 -10000 0 0
DAB1 -0.03 0.13 -9999 0 -0.45 31 31
IQGAP1 0.012 0 -9999 0 -10000 0 0
PLA2G7 -0.018 0.12 -9999 0 -0.49 22 22
CALM1 0.012 0 -9999 0 -10000 0 0
DYNLT1 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 0.013 0.045 -9999 0 -0.34 6 6
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.012 0 -9999 0 -10000 0 0
CDK5R1 0.001 0.074 -9999 0 -0.5 8 8
LIS1/Poliovirus Protein 3A 0.014 0 -9999 0 -10000 0 0
CDK5R2 -0.033 0.13 -9999 0 -0.45 33 33
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.11 0.17 -9999 0 -0.31 142 142
YWHAE 0.012 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.042 0.12 -9999 0 -0.38 6 6
MAP1B -0.021 0.072 -9999 0 -0.29 21 21
RAC1 0.019 0 -9999 0 -10000 0 0
p35/CDK5 -0.048 0.12 -9999 0 -0.42 5 5
RELN -0.14 0.23 -9999 0 -0.49 114 114
PAFAH/LIS1 0.005 0.073 -9999 0 -0.28 22 22
LIS1/CLIP170 0.024 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.054 0.075 -9999 0 -0.33 3 3
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.051 0.11 -9999 0 -0.4 4 4
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.052 0.12 -9999 0 -0.35 15 15
LIS1/IQGAP1 0.024 0 -9999 0 -10000 0 0
RHOA 0.019 0 -9999 0 -10000 0 0
PAFAH1B1 0.019 0 -9999 0 -10000 0 0
PAFAH1B3 0.011 0.024 -9999 0 -0.45 1 1
PAFAH1B2 0.009 0.04 -9999 0 -0.54 2 2
MAP1B/LIS1/Dynein heavy chain 0.008 0.05 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.036 0.12 -9999 0 -0.36 6 6
LRP8 0.004 0.062 -9999 0 -0.48 6 6
NDEL1/Katanin 60 -0.042 0.12 -9999 0 -0.38 6 6
P39/CDK5 -0.065 0.14 -9999 0 -0.43 14 14
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.024 0 -9999 0 -10000 0 0
CDK5 -0.052 0.13 -9999 0 -0.45 4 4
PPP2R5D 0.012 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.02 0 -9999 0 -10000 0 0
CSNK2A1 0.012 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.077 0.15 -9999 0 -0.44 14 14
RELN/VLDLR -0.07 0.14 -9999 0 -0.3 68 68
CDC42 0.019 0 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin 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
ITGB1 0.012 0 -9999 0 -10000 0 0
ITGB7 0.001 0.077 -9999 0 -0.52 8 8
ITGA4 -0.013 0.11 -9999 0 -0.5 18 18
alpha4/beta7 Integrin -0.008 0.099 -9999 0 -0.37 25 25
alpha4/beta1 Integrin 0 0.08 -9999 0 -0.35 18 18
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.01 0.037 -10000 0 -0.5 2 2
LAT2 -0.018 0.11 -10000 0 -0.37 16 16
AP1 -0.058 0.13 -10000 0 -0.48 21 21
mol:PIP3 -0.023 0.15 -10000 0 -0.48 21 21
IKBKB -0.005 0.091 0.15 2 -0.28 17 19
AKT1 -0.022 0.12 -10000 0 -0.39 15 15
IKBKG -0.005 0.091 0.15 1 -0.28 17 18
MS4A2 -0.018 0.11 -10000 0 -0.46 21 21
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.034 -10000 0 -0.45 2 2
MAP3K1 -0.007 0.12 -10000 0 -0.43 15 15
mol:Ca2+ -0.014 0.12 -10000 0 -0.35 21 21
LYN 0.007 0.05 -10000 0 -0.55 3 3
CBLB -0.016 0.1 -10000 0 -0.36 15 15
SHC1 0.012 0 -10000 0 -10000 0 0
RasGAP/p62DOK 0.016 0.043 -10000 0 -0.23 11 11
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D -0.002 0.088 -10000 0 -0.53 10 10
PLD2 -0.031 0.12 -10000 0 -0.36 21 21
PTPN13 -0.032 0.13 -10000 0 -0.43 16 16
PTPN11 0.011 0.007 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.001 0.1 -10000 0 -0.31 9 9
SYK 0 0.08 -10000 0 -0.54 8 8
GRB2 0.012 0 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.065 0.14 -10000 0 -0.5 21 21
LAT -0.022 0.11 -10000 0 -0.41 15 15
PAK2 -0.014 0.13 -10000 0 -0.45 17 17
NFATC2 -0.048 0.12 -10000 0 -0.49 22 22
HRAS -0.021 0.14 -10000 0 -0.49 18 18
GAB2 0.01 0.034 -10000 0 -0.45 2 2
PLA2G1B 0.025 0.015 -10000 0 -10000 0 0
Fc epsilon R1 -0.056 0.15 -10000 0 -0.32 80 80
Antigen/IgE/Fc epsilon R1 -0.049 0.14 -10000 0 -0.29 80 80
mol:GDP -0.03 0.15 -10000 0 -0.52 21 21
JUN 0.01 0.037 -10000 0 -0.5 2 2
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 -0.018 0.12 -10000 0 -0.52 21 21
FOS -0.019 0.12 -10000 0 -0.47 24 24
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.024 0.11 -10000 0 -0.36 19 19
CHUK -0.005 0.091 0.15 2 -0.28 17 19
KLRG1 -0.023 0.11 -10000 0 -0.39 14 14
VAV1 -0.027 0.12 -10000 0 -0.43 19 19
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.016 0.1 -10000 0 -0.36 15 15
negative regulation of mast cell degranulation -0.022 0.12 -10000 0 -0.41 18 18
BTK -0.033 0.16 -10000 0 -0.59 19 19
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.035 0.14 -10000 0 -0.48 19 19
GAB2/PI3K/SHP2 -0.061 0.11 -10000 0 -0.43 14 14
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.024 0.11 -10000 0 -0.32 25 25
RAF1 0.015 0.019 -10000 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.053 0.16 -10000 0 -0.43 37 37
FCER1G -0.005 0.094 -10000 0 -0.52 12 12
FCER1A -0.068 0.19 -10000 0 -0.51 56 56
Antigen/IgE/Fc epsilon R1/Fyn -0.039 0.13 -10000 0 -0.32 44 44
MAPK3 0.023 0.016 -10000 0 -10000 0 0
MAPK1 0.023 0.016 -10000 0 -10000 0 0
NFKB1 0.012 0 -10000 0 -10000 0 0
MAPK8 0.008 0.067 -10000 0 -0.5 4 4
DUSP1 -0.001 0.079 -10000 0 -0.45 11 11
NF-kappa-B/RelA -0.022 0.043 -10000 0 -0.21 2 2
actin cytoskeleton reorganization -0.013 0.1 -10000 0 -0.48 5 5
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.06 0.12 -10000 0 -0.48 18 18
FER -0.018 0.1 -10000 0 -0.36 15 15
RELA 0.012 0 -10000 0 -10000 0 0
ITK -0.035 0.1 -10000 0 -0.37 26 26
SOS1 0.012 0 -10000 0 -10000 0 0
PLCG1 -0.025 0.15 -10000 0 -0.51 20 20
cytokine secretion -0.016 0.031 -10000 0 -10000 0 0
SPHK1 -0.025 0.11 -10000 0 -0.35 20 20
PTK2 -0.014 0.1 -10000 0 -0.51 5 5
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.063 0.13 -10000 0 -0.51 19 19
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.019 0.14 -10000 0 -0.46 20 20
MAP2K2 0.02 0.016 -10000 0 -10000 0 0
MAP2K1 0.02 0.016 -10000 0 -10000 0 0
MAP2K7 0.012 0 -10000 0 -10000 0 0
KLRG1/SHP2 -0.021 0.1 -10000 0 -0.39 13 13
MAP2K4 0.013 0.068 -10000 0 -0.9 2 2
Fc epsilon R1/FcgammaRIIB -0.055 0.16 -10000 0 -0.37 55 55
mol:Choline -0.03 0.12 -10000 0 -0.36 21 21
SHC/Grb2/SOS1 -0.004 0.098 -10000 0 -0.43 6 6
FYN 0.011 0.024 -10000 0 -0.45 1 1
DOK1 0.012 0 -10000 0 -10000 0 0
PXN -0.007 0.098 -10000 0 -0.47 5 5
HCLS1 -0.026 0.12 -10000 0 -0.38 23 23
PRKCB -0.018 0.12 -10000 0 -0.36 25 25
FCGR2B -0.015 0.12 -10000 0 -0.52 19 19
IGHE -0.001 0.005 -10000 0 -10000 0 0
KLRG1/SHIP -0.022 0.12 -10000 0 -0.42 18 18
LCP2 0 0.079 -10000 0 -0.5 9 9
PLA2G4A -0.063 0.14 -10000 0 -0.37 37 37
RASA1 0.012 0 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.03 0.12 -10000 0 -0.36 21 21
IKK complex 0.009 0.072 0.15 2 -0.23 11 13
WIPF1 0.008 0.047 -10000 0 -0.51 3 3
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.005 0.084 -9999 0 -0.34 16 16
CRKL 0.012 0 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
DOCK1 0.012 0 -9999 0 -10000 0 0
ITGA4 -0.013 0.11 -9999 0 -0.5 18 18
alpha4/beta7 Integrin/MAdCAM1 -0.023 0.12 -9999 0 -0.3 35 35
EPO -0.016 0.1 -9999 0 -0.45 20 20
alpha4/beta7 Integrin -0.008 0.099 -9999 0 -0.37 25 25
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.012 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0 0.08 -9999 0 -0.35 18 18
EPO/EPOR (dimer) -0.02 0.11 -9999 0 -0.34 37 37
lamellipodium assembly 0.013 0.067 -9999 0 -0.3 1 1
PIK3CA 0.01 0.034 -9999 0 -0.45 2 2
PI3K -0.006 0.093 -9999 0 -0.37 23 23
ARF6 0.012 0 -9999 0 -10000 0 0
JAK2 -0.012 0.11 -9999 0 -0.41 14 14
PXN 0.012 0 -9999 0 -10000 0 0
PIK3R1 -0.018 0.12 -9999 0 -0.52 21 21
MADCAM1 -0.049 0.16 -9999 0 -0.49 44 44
cell adhesion -0.024 0.12 -9999 0 -0.3 35 35
CRKL/CBL 0.018 0 -9999 0 -10000 0 0
ITGB1 0.012 0 -9999 0 -10000 0 0
SRC -0.018 0.12 -9999 0 -0.33 33 33
ITGB7 0.001 0.077 -9999 0 -0.52 8 8
RAC1 0.012 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.024 0.13 -9999 0 -0.33 52 52
p130Cas/Crk/Dock1 0.003 0.1 -9999 0 -0.46 6 6
VCAM1 -0.044 0.16 -9999 0 -0.5 40 40
RHOA 0.012 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.018 0.063 -9999 0 -0.28 10 10
BCAR1 -0.011 0.11 -9999 0 -0.51 6 6
EPOR -0.013 0.11 -9999 0 -0.48 19 19
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.012 0 -9999 0 -10000 0 0
GIT1 0.012 0 -9999 0 -10000 0 0
Rac1/GTP 0.013 0.068 -9999 0 -0.31 1 1
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.01 0.042 -9999 0 -0.34 5 5
PDGFRB -0.001 0.078 -9999 0 -0.49 9 9
SPHK1 -0.024 0.077 -9999 0 -0.79 3 3
mol:S1P -0.027 0.071 -9999 0 -0.7 3 3
S1P1/S1P/Gi -0.051 0.16 -9999 0 -0.37 50 50
GNAO1 -0.017 0.11 -9999 0 -0.48 20 20
PDGFB-D/PDGFRB/PLCgamma1 -0.044 0.15 -9999 0 -0.45 17 17
PLCG1 -0.045 0.15 -9999 0 -0.35 50 50
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.001 0.078 -9999 0 -0.49 9 9
GNAI2 0.01 0.006 -9999 0 -10000 0 0
GNAI3 0.01 0.006 -9999 0 -10000 0 0
GNAI1 -0.008 0.096 -9999 0 -0.53 12 12
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.006 0.036 -9999 0 -0.29 5 5
S1P1/S1P -0.01 0.082 -9999 0 -0.44 5 5
negative regulation of cAMP metabolic process -0.049 0.16 -9999 0 -0.36 50 50
MAPK3 -0.076 0.22 -9999 0 -0.54 52 52
calcium-dependent phospholipase C activity -0.002 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
KDR 0.008 0.038 -9999 0 -0.5 2 2
PLCB2 -0.009 0.086 -9999 0 -0.34 11 11
RAC1 0.012 0 -9999 0 -10000 0 0
RhoA/GTP -0.028 0.059 -9999 0 -0.37 5 5
receptor internalization -0.032 0.066 -9999 0 -0.38 6 6
PTGS2 -0.15 0.36 -9999 0 -0.98 50 50
Rac1/GTP -0.028 0.059 -9999 0 -0.37 5 5
RHOA 0.012 0 -9999 0 -10000 0 0
VEGFA 0.007 0.042 -9999 0 -0.46 3 3
negative regulation of T cell proliferation -0.049 0.16 -9999 0 -0.36 50 50
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.007 0.095 -9999 0 -0.52 12 12
MAPK1 -0.076 0.21 -9999 0 -0.54 49 49
S1P1/S1P/PDGFB-D/PDGFRB -0.012 0.096 -9999 0 -0.4 7 7
ABCC1 0.011 0.003 -9999 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.009 0.038 -10000 0 -0.45 2 2
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.025 0.15 0.61 9 -10000 0 9
IL27/IL27R/JAK1 -0.034 0.2 -10000 0 -0.8 11 11
TBX21 -0.047 0.21 -10000 0 -0.62 27 27
IL12B 0.001 0.054 -10000 0 -0.45 5 5
IL12A -0.037 0.12 -10000 0 -0.35 47 47
IL6ST -0.035 0.15 -10000 0 -0.52 33 33
IL27RA/JAK1 -0.004 0.15 -10000 0 -1.2 5 5
IL27 -0.003 0.077 -10000 0 -0.46 10 10
TYK2 0.013 0.009 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.019 0.083 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.025 0.15 0.61 9 -10000 0 9
T cell proliferation during immune response 0.025 0.15 0.61 9 -10000 0 9
MAPKKK cascade -0.025 0.15 -10000 0 -0.61 9 9
STAT3 0.012 0 -10000 0 -10000 0 0
STAT2 0.012 0 -10000 0 -10000 0 0
STAT1 0.01 0.034 -10000 0 -0.45 2 2
IL12RB1 -0.024 0.13 -10000 0 -0.5 26 26
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.046 0.21 -10000 0 -0.59 29 29
IL27/IL27R/JAK2/TYK2 -0.025 0.15 -10000 0 -0.62 9 9
positive regulation of T cell mediated cytotoxicity -0.025 0.15 -10000 0 -0.61 9 9
STAT1 (dimer) -0.086 0.23 0.46 7 -0.83 17 24
JAK2 0 0.086 -10000 0 -0.54 9 9
JAK1 0.005 0.063 -10000 0 -0.54 5 5
STAT2 (dimer) -0.018 0.14 -10000 0 -0.58 9 9
T cell proliferation -0.047 0.16 -10000 0 -0.55 15 15
IL12/IL12R/TYK2/JAK2 -0.027 0.11 -10000 0 -0.57 3 3
IL17A -0.02 0.082 -10000 0 -10000 0 0
mast cell activation 0.025 0.15 0.61 9 -10000 0 9
IFNG -0.007 0.038 -10000 0 -0.11 26 26
T cell differentiation -0.003 0.008 0.015 14 -0.022 32 46
STAT3 (dimer) -0.018 0.14 -10000 0 -0.58 9 9
STAT5A (dimer) -0.019 0.14 -10000 0 -0.61 8 8
STAT4 (dimer) -0.027 0.16 -10000 0 -0.6 12 12
STAT4 -0.006 0.096 -10000 0 -0.5 13 13
T cell activation -0.006 0.016 0.1 7 -10000 0 7
IL27R/JAK2/TYK2 -0.021 0.17 -10000 0 -0.96 7 7
GATA3 -0.041 0.23 -10000 0 -1.3 11 11
IL18 -0.009 0.084 -10000 0 -0.38 18 18
positive regulation of mast cell cytokine production -0.018 0.14 -10000 0 -0.57 9 9
IL27/EBI3 -0.014 0.11 -10000 0 -0.37 31 31
IL27RA -0.008 0.16 -10000 0 -1.3 5 5
IL6 -0.047 0.16 -10000 0 -0.48 44 44
STAT5A 0.011 0.024 -10000 0 -0.45 1 1
monocyte differentiation 0 0.002 -10000 0 -10000 0 0
IL2 -0.001 0.084 0.48 5 -10000 0 5
IL1B -0.014 0.092 -10000 0 -0.37 23 23
EBI3 -0.019 0.12 -10000 0 -0.5 23 23
TNF -0.049 0.13 -10000 0 -0.35 60 60
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.16 0.24 -9999 0 -0.48 125 125
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.012 0 -9999 0 -10000 0 0
TCEB1 0.012 0 -9999 0 -10000 0 0
HIF1A/p53 0.012 0.056 -9999 0 -0.24 15 15
HIF1A 0.017 0.02 -9999 0 -10000 0 0
COPS5 0.012 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.036 0.015 -9999 0 -0.26 1 1
FIH (dimer) 0.012 0 -9999 0 -10000 0 0
CDKN2A -0.11 0.21 -9999 0 -0.48 91 91
ARNT/IPAS -0.1 0.17 -9999 0 -0.34 125 125
HIF1AN 0.012 0 -9999 0 -10000 0 0
GNB2L1 0.012 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.023 0.02 -9999 0 -10000 0 0
CUL2 0.012 0 -9999 0 -10000 0 0
OS9 0.012 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.025 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.023 0.02 -9999 0 -10000 0 0
PHD1-3/OS9 0.016 0.069 -9999 0 -0.28 17 17
HIF1A/RACK1/Elongin B/Elongin C 0.033 0.019 -9999 0 -10000 0 0
VHL 0.011 0.029 -9999 0 -0.54 1 1
HSP90AA1 0.012 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.023 0.02 -9999 0 -10000 0 0
EGLN3 -0.016 0.12 -9999 0 -0.53 19 19
EGLN2 0.012 0 -9999 0 -10000 0 0
EGLN1 0.012 0 -9999 0 -10000 0 0
TP53 -0.01 0.11 -9999 0 -0.54 15 15
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.031 0.029 -9999 0 -0.52 1 1
ARNT 0.012 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.012 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.034 0.1 -9999 0 -0.26 31 31
Regulation of Androgen receptor activity

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
HDAC1 0.019 0.002 -9999 0 -10000 0 0
SMARCC1 0.005 0.01 -9999 0 -10000 0 0
REL 0.01 0.038 -9999 0 -0.5 2 2
HDAC7 0.01 0.12 -9999 0 -0.47 11 11
JUN 0.009 0.037 -9999 0 -0.49 2 2
EP300 0.012 0 -9999 0 -10000 0 0
KAT2B 0 0.08 -9999 0 -0.54 8 8
KAT5 0.012 0.001 -9999 0 -10000 0 0
MAPK14 0 0.085 -9999 0 -0.38 17 17
FOXO1 0.011 0.024 -9999 0 -0.45 1 1
T-DHT/AR 0.009 0.12 -9999 0 -0.49 11 11
MAP2K6 -0.013 0.11 -9999 0 -0.53 17 17
BRM/BAF57 0.009 0.055 -9999 0 -0.39 7 7
MAP2K4 0.009 0.041 -9999 0 -0.54 2 2
SMARCA2 0.001 0.075 -9999 0 -0.54 7 7
PDE9A -0.075 0.23 -9999 0 -1.1 14 14
NCOA2 -0.008 0.1 -9999 0 -0.52 14 14
CEBPA -0.025 0.14 -9999 0 -0.52 26 26
EHMT2 0.012 0.003 -9999 0 -10000 0 0
cell proliferation -0.018 0.16 -9999 0 -0.5 18 18
NR0B1 -0.025 0.11 -9999 0 -0.45 24 24
EGR1 -0.014 0.11 -9999 0 -0.48 19 19
RXRs/9cRA -0.05 0.13 -9999 0 -0.27 92 92
AR/RACK1/Src 0.001 0.099 -9999 0 -0.42 10 10
AR/GR -0.023 0.12 -9999 0 -0.36 26 26
GNB2L1 0.012 0.002 -9999 0 -10000 0 0
PKN1 0.012 0.001 -9999 0 -10000 0 0
RCHY1 0.012 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.002 -9999 0 -10000 0 0
MAPK8 0.014 0.044 -9999 0 -0.39 4 4
T-DHT/AR/TIF2/CARM1 -0.002 0.11 -9999 0 -0.42 14 14
SRC 0.011 0.079 -9999 0 -0.32 10 10
NR3C1 -0.003 0.088 -9999 0 -0.51 11 11
KLK3 -0.15 0.24 -9999 0 -0.63 46 46
APPBP2 0.012 0.005 -9999 0 -10000 0 0
TRIM24 0.011 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIP60 0.002 0.098 -9999 0 -0.45 10 10
TMPRSS2 -0.13 0.34 -9999 0 -1.2 33 33
RXRG -0.12 0.22 -9999 0 -0.5 92 92
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.011 0.029 -9999 0 -0.54 1 1
RXRB 0.012 0.001 -9999 0 -10000 0 0
CARM1 0.012 0.002 -9999 0 -10000 0 0
NR2C2 0.012 0.001 -9999 0 -10000 0 0
KLK2 -0.021 0.15 -9999 0 -0.55 7 7
AR -0.021 0.12 -9999 0 -0.31 46 46
SENP1 0.012 0.001 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
MDM2 0.011 0.041 -9999 0 -0.54 2 2
SRY 0.001 0.006 -9999 0 -10000 0 0
GATA2 -0.059 0.18 -9999 0 -0.53 49 49
MYST2 0.012 0.001 -9999 0 -10000 0 0
HOXB13 -0.14 0.24 -9999 0 -0.53 99 99
T-DHT/AR/RACK1/Src 0.004 0.098 -9999 0 -0.43 10 10
positive regulation of transcription -0.059 0.18 -9999 0 -0.53 49 49
DNAJA1 0.012 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.025 -9999 0 -0.32 2 2
NCOA1 0.015 0.005 -9999 0 -10000 0 0
SPDEF -0.12 0.24 -9999 0 -0.54 90 90
T-DHT/AR/TIF2 0.009 0.084 -9999 0 -0.32 10 10
T-DHT/AR/Hsp90 0.002 0.098 -9999 0 -0.45 10 10
GSK3B 0.012 0.002 -9999 0 -10000 0 0
NR2C1 0.013 0.001 -9999 0 -10000 0 0
mol:T-DHT 0.008 0.082 -9999 0 -0.32 18 18
SIRT1 0.009 0.04 -9999 0 -0.54 2 2
ZMIZ2 0.013 0.006 -9999 0 -10000 0 0
POU2F1 0.005 0.082 -9999 0 -0.48 9 9
T-DHT/AR/DAX-1 -0.018 0.12 -9999 0 -0.43 16 16
CREBBP 0.012 0.001 -9999 0 -10000 0 0
SMARCE1 0.012 0.003 -9999 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.002 0.068 -10000 0 -0.35 4 4
epithelial cell differentiation -0.062 0.12 -10000 0 -0.44 16 16
ITCH 0.018 0.033 -10000 0 -0.54 1 1
WWP1 0.004 0.061 -10000 0 -10000 0 0
FYN 0.011 0.024 -10000 0 -0.45 1 1
EGFR -0.004 0.092 -10000 0 -0.53 11 11
PRL -0.022 0.12 -10000 0 -0.45 25 25
neuron projection morphogenesis 0.008 0.088 -10000 0 -0.38 1 1
PTPRZ1 -0.038 0.14 -10000 0 -0.45 36 36
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.002 0.094 -10000 0 -0.42 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.022 0.1 -10000 0 -0.37 9 9
ADAM17 0.017 0.043 -10000 0 -0.54 2 2
ErbB4/ErbB4 -0.003 0.077 -10000 0 -0.39 3 3
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.021 0.099 -10000 0 -0.34 16 16
NCOR1 0.012 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.015 0.1 -10000 0 -0.37 8 8
GRIN2B -0.021 0.11 -10000 0 -0.41 9 9
ErbB4/ErbB2/betacellulin -0.011 0.099 -10000 0 -0.37 9 9
STAT1 0.01 0.034 -10000 0 -0.45 2 2
HBEGF 0.011 0.024 -10000 0 -0.45 1 1
PRLR -0.067 0.19 -10000 0 -0.52 55 55
E4ICDs/ETO2 -0.019 0.11 -10000 0 -0.36 19 19
axon guidance 0.001 0.074 -10000 0 -10000 0 0
NEDD4 0.009 0.075 -10000 0 -0.53 7 7
Prolactin receptor/Prolactin receptor/Prolactin -0.063 0.16 -10000 0 -0.37 76 76
CBFA2T3 -0.027 0.13 -10000 0 -0.48 29 29
ErbB4/ErbB2/HBEGF 0.007 0.07 -10000 0 -0.34 5 5
MAPK3 0.003 0.09 -10000 0 -0.4 1 1
STAT1 (dimer) 0.001 0.069 -10000 0 -0.35 4 4
MAPK1 0.003 0.09 -10000 0 -0.4 1 1
JAK2 -0.001 0.085 -10000 0 -0.54 9 9
ErbB4/ErbB2/neuregulin 1 beta -0.022 0.11 -10000 0 -0.37 10 10
NRG1 -0.02 0.12 -10000 0 -0.35 43 43
NRG3 -0.029 0.12 -10000 0 -0.45 29 29
NRG2 -0.048 0.16 -10000 0 -0.5 43 43
NRG4 -0.037 0.15 -10000 0 -0.51 35 35
heart development 0.001 0.074 -10000 0 -10000 0 0
neural crest cell migration -0.022 0.11 -10000 0 -0.36 10 10
ERBB2 0.011 0.067 -10000 0 -0.34 13 13
WWOX/E4ICDs 0.002 0.068 -10000 0 -0.33 4 4
SHC1 0.012 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.025 0.11 -10000 0 -0.39 12 12
apoptosis 0.033 0.076 0.33 5 -10000 0 5
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.032 0.12 -10000 0 -0.43 14 14
ErbB4/ErbB2/epiregulin -0.054 0.13 -10000 0 -0.38 11 11
ErbB4/ErbB4/betacellulin/betacellulin -0.017 0.1 -10000 0 -0.33 25 25
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.041 0.15 -10000 0 -0.44 27 27
MDM2 0.003 0.074 -10000 0 -0.38 5 5
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.015 0.096 -10000 0 -0.33 8 8
STAT5A 0.007 0.071 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.023 0.11 -10000 0 -0.38 14 14
DLG4 0.009 0.04 -10000 0 -0.54 2 2
GRB2/SHC 0.018 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.002 0.06 -10000 0 -0.32 3 3
STAT5A (dimer) -0.065 0.12 -10000 0 -0.48 16 16
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.007 0.069 -10000 0 -10000 0 0
LRIG1 -0.016 0.12 -10000 0 -0.54 19 19
EREG -0.11 0.21 -10000 0 -0.47 90 90
BTC -0.022 0.13 -10000 0 -0.54 23 23
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.001 0.075 -10000 0 -10000 0 0
ERBB4 -0.003 0.078 -10000 0 -0.4 3 3
STAT5B 0.012 0 -10000 0 -10000 0 0
YAP1 0.007 0.024 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.018 0.11 -10000 0 -0.42 10 10
glial cell differentiation -0.002 0.06 0.32 3 -10000 0 3
WWOX 0.011 0.029 -10000 0 -0.54 1 1
cell proliferation -0.03 0.13 -10000 0 -0.46 14 14
Ceramide signaling pathway

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
SPHK2 -0.002 0.086 -10000 0 -0.35 21 21
MAP4K4 -0.009 0.11 -10000 0 -0.51 9 9
BAG4 0.011 0.029 -10000 0 -0.54 1 1
PKC zeta/ceramide -0.002 0.048 0.14 11 -0.35 2 13
NFKBIA 0.012 0 -10000 0 -10000 0 0
BIRC3 -0.047 0.16 -10000 0 -0.51 42 42
BAX 0.003 0.022 -10000 0 -10000 0 0
RIPK1 0.012 0 -10000 0 -10000 0 0
AKT1 0.014 0.024 -10000 0 -0.42 1 1
BAD -0.001 0.042 0.14 20 -10000 0 20
SMPD1 -0.006 0.067 -10000 0 -0.2 27 27
RB1 -0.012 0.068 0.15 10 -0.28 14 24
FADD/Caspase 8 -0.001 0.11 -10000 0 -0.49 10 10
MAP2K4 0.002 0.045 0.16 2 -0.28 2 4
NSMAF 0.012 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0 0.049 0.16 2 -0.27 4 6
EGF -0.065 0.18 -10000 0 -0.48 57 57
mol:ceramide -0.008 0.046 0.14 20 -10000 0 20
MADD 0.012 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.002 0.086 -10000 0 -0.35 21 21
ASAH1 0.012 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.012 0.067 0.15 10 -0.28 14 24
cell proliferation -0.021 0.09 -10000 0 -0.25 33 33
BID -0.001 0.072 -10000 0 -0.32 8 8
MAP3K1 -0.002 0.042 0.15 10 -0.15 1 11
EIF2A 0.007 0.045 0.17 1 -0.24 3 4
TRADD 0.009 0.04 -10000 0 -0.54 2 2
CRADD 0.012 0 -10000 0 -10000 0 0
MAPK3 0.01 0.046 0.17 1 -0.24 4 5
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.01 0.046 0.17 1 -0.24 4 5
Cathepsin D/ceramide -0.002 0.045 0.14 11 -0.26 2 13
FADD -0.01 0.11 -10000 0 -0.51 9 9
KSR1 -0.006 0.051 0.14 12 -0.24 6 18
MAPK8 0.005 0.049 0.15 8 -0.24 5 13
PRKRA -0.001 0.042 0.15 11 -10000 0 11
PDGFA -0.017 0.12 -10000 0 -0.5 21 21
TRAF2 0.012 0 -10000 0 -10000 0 0
IGF1 -0.067 0.19 -10000 0 -0.5 57 57
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.008 0.045 0.14 20 -10000 0 20
CTSD 0.01 0.034 -10000 0 -0.45 2 2
regulation of nitric oxide biosynthetic process 0.018 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.022 0.096 -10000 0 -0.26 33 33
PRKCD 0.009 0.04 -10000 0 -0.54 2 2
PRKCZ 0.009 0.04 -10000 0 -0.54 2 2
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.002 0.086 -10000 0 -0.35 21 21
RelA/NF kappa B1 0.018 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.012 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.016 0.11 -10000 0 -0.54 9 9
TNFR1A/BAG4/TNF-alpha -0.027 0.12 -10000 0 -0.29 61 61
mol:Sphingosine-1-phosphate -0.002 0.086 -10000 0 -0.35 21 21
MAP2K1 0.006 0.047 0.17 1 -0.25 4 5
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.012 0 -10000 0 -10000 0 0
CYCS 0.008 0.044 0.15 14 -0.2 1 15
TNFRSF1A 0.011 0.029 -10000 0 -0.54 1 1
NFKB1 0.012 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0.016 0.03 -10000 0 -0.38 2 2
EIF2AK2 0.002 0.047 0.16 2 -0.25 3 5
TNF-alpha/TNFR1A/FAN -0.026 0.12 -10000 0 -0.29 60 60
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.007 0.071 -10000 0 -0.3 10 10
MAP2K2 0.006 0.047 0.17 1 -0.25 4 5
SMPD3 -0.034 0.12 -10000 0 -0.31 48 48
TNF -0.069 0.19 -10000 0 -0.49 60 60
PKC zeta/PAR4 0.016 0.03 -10000 0 -0.38 2 2
mol:PHOSPHOCHOLINE 0.015 0.076 0.17 55 -0.12 1 56
NF kappa B1/RelA/I kappa B alpha 0.035 0.022 -10000 0 -10000 0 0
AIFM1 0.009 0.042 0.15 14 -10000 0 14
BCL2 -0.015 0.12 -10000 0 -0.52 19 19
Signaling events mediated by HDAC Class III

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
EP300 0.012 0 -10000 0 -10000 0 0
HDAC4 0.01 0.034 -10000 0 -0.45 2 2
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.009 0.062 0.31 12 -10000 0 12
CDKN1A -0.026 0.14 -10000 0 -0.7 16 16
KAT2B 0 0.08 -10000 0 -0.54 8 8
BAX 0.012 0 -10000 0 -10000 0 0
FOXO3 0.001 0.008 -10000 0 -10000 0 0
FOXO1 0.011 0.024 -10000 0 -0.45 1 1
FOXO4 0.02 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.012 0 -10000 0 -10000 0 0
TAT 0.001 0.058 -10000 0 -0.45 6 6
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.02 0.1 -10000 0 -0.34 35 35
PPARGC1A -0.13 0.23 -10000 0 -0.49 106 106
FHL2 -0.004 0.093 -10000 0 -0.54 11 11
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.017 0.034 -10000 0 -0.33 2 2
HIST2H4A 0.009 0.062 -10000 0 -0.32 12 12
SIRT1/FOXO3a 0.003 0.031 -10000 0 -0.28 2 2
SIRT1 0.011 0.047 -10000 0 -0.48 2 2
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.023 0.036 -10000 0 -0.28 3 3
SIRT1/Histone H1b 0.009 0.06 -10000 0 -0.24 14 14
apoptosis -0.024 0.029 0.32 1 -10000 0 1
SIRT1/PGC1A -0.074 0.14 -10000 0 -0.3 105 105
p53/SIRT1 -0.004 0.098 0.38 11 -0.39 12 23
SIRT1/FOXO4 0.022 0.031 -10000 0 -0.26 2 2
FOXO1/FHL2/SIRT1 0.013 0.061 -10000 0 -0.29 13 13
HIST1H1E 0.004 0.062 -10000 0 -0.28 14 14
SIRT1/p300 0.017 0.034 -10000 0 -0.33 2 2
muscle cell differentiation 0.01 0.093 0.29 33 -10000 0 33
TP53 -0.008 0.11 -10000 0 -0.5 15 15
KU70/SIRT1/BAX 0.024 0.03 -10000 0 -0.32 1 1
CREBBP 0.012 0 -10000 0 -10000 0 0
MEF2D 0.012 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.008 0.057 -10000 0 -0.36 7 7
ACSS2 0.019 0.033 -10000 0 -0.33 2 2
SIRT1/PCAF/MYOD -0.01 0.093 -10000 0 -0.29 33 33
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.013 0.11 -10000 0 -0.51 18 18
positive regulation of NF-kappaB transcription factor activity -0.023 0.12 -10000 0 -0.38 38 38
MAP2K4 0.022 0.067 -10000 0 -0.38 3 3
IKBKB 0.012 0 -10000 0 -10000 0 0
TNFRSF10B 0.009 0.04 -10000 0 -0.54 2 2
TNFRSF10A -0.001 0.085 -10000 0 -0.54 9 9
SMPD1 0.006 0.046 -10000 0 -0.2 14 14
IKBKG 0.012 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.019 0.12 -10000 0 -0.51 22 22
TRAIL/TRAILR2 -0.002 0.087 -10000 0 -0.36 20 20
TRAIL/TRAILR3 -0.037 0.15 -10000 0 -0.4 49 49
TRAIL/TRAILR1 -0.01 0.11 -10000 0 -0.39 25 25
TRAIL/TRAILR4 -0.023 0.12 -10000 0 -0.38 38 38
TRAIL/TRAILR1/DAP3/GTP 0.002 0.084 -10000 0 -0.3 25 25
IKK complex -0.008 0.03 -10000 0 -10000 0 0
RIPK1 0.012 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.009 0 -10000 0 -10000 0 0
MAPK3 0 0.084 -10000 0 -0.36 19 19
MAP3K1 0.018 0.068 -10000 0 -0.35 5 5
TRAILR4 (trimer) -0.019 0.12 -10000 0 -0.51 22 22
TRADD 0.009 0.04 -10000 0 -0.54 2 2
TRAILR1 (trimer) -0.001 0.085 -10000 0 -0.54 9 9
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.013 0.077 -10000 0 -0.53 3 3
CFLAR 0.012 0 -10000 0 -10000 0 0
MAPK1 0 0.084 -10000 0 -0.36 19 19
TRAIL/TRAILR1/FADD/TRADD/RIP 0.014 0.086 -10000 0 -0.3 20 20
mol:ceramide 0.006 0.045 -10000 0 -0.2 14 14
FADD 0.011 0.024 -10000 0 -0.45 1 1
MAPK8 0.025 0.069 -10000 0 -0.39 4 4
TRAF2 0.012 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.041 0.16 -10000 0 -0.52 37 37
CHUK 0.012 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0 0.093 -10000 0 -0.33 26 26
DAP3 0.012 0 -10000 0 -10000 0 0
CASP10 -0.011 0.096 0.25 12 -0.37 13 25
JNK cascade -0.023 0.12 -10000 0 -0.38 38 38
TRAIL (trimer) -0.013 0.11 -10000 0 -0.51 18 18
TNFRSF10C -0.041 0.16 -10000 0 -0.52 37 37
TRAIL/TRAILR1/DAP3/GTP/FADD 0.008 0.08 -10000 0 -0.3 19 19
TRAIL/TRAILR2/FADD 0.007 0.075 -10000 0 -0.3 21 21
cell death 0.006 0.045 -10000 0 -0.2 14 14
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.018 0.058 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.009 0.04 -10000 0 -0.54 2 2
CASP8 0.003 0.047 -10000 0 -0.77 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.019 0.068 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.011 0.024 -9999 0 -0.45 1 1
Syndecan-3/Src/Cortactin -0.021 0.11 -9999 0 -0.42 2 2
Syndecan-3/Neurocan -0.001 0.058 -9999 0 -0.57 1 1
POMC -0.064 0.18 -9999 0 -0.48 57 57
EGFR -0.004 0.092 -9999 0 -0.53 11 11
Syndecan-3/EGFR 0.011 0.058 -9999 0 -0.29 11 11
AGRP 0.006 0.025 -9999 0 -0.45 1 1
NCSTN 0.012 0 -9999 0 -10000 0 0
PSENEN 0.011 0.029 -9999 0 -0.54 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.006 0.057 -9999 0 -0.54 4 4
APH1A 0.011 0.024 -9999 0 -0.45 1 1
NCAN -0.015 0.099 -9999 0 -0.45 18 18
long-term memory 0.025 0.035 -9999 0 -0.54 1 1
Syndecan-3/IL8 -0.021 0.1 -9999 0 -0.28 29 29
PSEN1 0.012 0 -9999 0 -10000 0 0
Src/Cortactin 0.015 0.034 -9999 0 -0.36 3 3
FYN 0.011 0.024 -9999 0 -0.45 1 1
limb bud formation -0.003 0.033 -9999 0 -0.59 1 1
MC4R -0.022 0.11 -9999 0 -0.45 23 23
SRC 0.009 0.04 -9999 0 -0.54 2 2
PTN -0.094 0.21 -9999 0 -0.5 76 76
FGFR/FGF/Syndecan-3 -0.003 0.033 -9999 0 -0.6 1 1
neuron projection morphogenesis -0.039 0.11 -9999 0 -0.41 5 5
Syndecan-3/AgRP 0.01 0.036 -9999 0 -0.57 1 1
Syndecan-3/AgRP/MC4R 0.003 0.063 -9999 0 -0.36 3 3
Fyn/Cortactin 0.017 0.024 -9999 0 -0.31 2 2
SDC3 -0.003 0.033 -9999 0 -0.61 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.02 0.1 -9999 0 -0.28 29 29
IL8 -0.067 0.18 -9999 0 -0.5 58 58
Syndecan-3/Fyn/Cortactin 0.025 0.036 -9999 0 -0.55 1 1
Syndecan-3/CASK -0.003 0.032 -9999 0 -0.58 1 1
alpha-MSH/MC4R -0.061 0.15 -9999 0 -0.34 77 77
Gamma Secretase 0.032 0.037 -9999 0 -0.26 5 5
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.007 0.14 -10000 0 -0.6 11 11
UGCG -0.007 0.12 -10000 0 -0.73 9 9
AKT1/mTOR/p70S6K/Hsp90/TERT -0.024 0.16 -10000 0 -0.42 31 31
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.007 0.12 -10000 0 -0.72 9 9
mol:DAG -0.004 0.048 -10000 0 -0.93 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.057 0.13 -10000 0 -0.45 30 30
FRAP1 -0.01 0.18 -10000 0 -0.51 33 33
FOXO3 0.002 0.16 -10000 0 -0.49 23 23
AKT1 -0.006 0.17 -10000 0 -0.51 26 26
GAB2 0.01 0.034 -10000 0 -0.45 2 2
SMPD1 0.01 0.031 -10000 0 -10000 0 0
SGMS1 0.009 0.047 -10000 0 -0.65 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP -0.003 0.079 -10000 0 -0.31 23 23
CALM1 0.012 0 -10000 0 -10000 0 0
cell proliferation 0 0.11 -10000 0 -0.42 13 13
EIF3A 0.012 0 -10000 0 -10000 0 0
PI3K -0.002 0.094 -10000 0 -0.36 23 23
RPS6KB1 0.006 0.064 -10000 0 -0.73 1 1
mol:sphingomyelin -0.004 0.048 -10000 0 -0.93 1 1
natural killer cell activation 0 0.002 -10000 0 -0.012 7 7
JAK3 0.003 0.076 -10000 0 -0.51 8 8
PIK3R1 -0.016 0.12 -10000 0 -0.52 21 21
JAK1 0.007 0.064 -10000 0 -0.54 5 5
NFKB1 0.012 0 -10000 0 -10000 0 0
MYC -0.009 0.2 -10000 0 -0.73 19 19
MYB -0.029 0.25 -10000 0 -1.1 18 18
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.006 0.16 -10000 0 -0.52 20 20
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.019 0.061 -10000 0 -0.66 1 1
mol:PI-3-4-5-P3 -0.005 0.15 -10000 0 -0.5 20 20
Rac1/GDP 0.005 0.072 -10000 0 -0.29 17 17
T cell proliferation 0.001 0.15 -10000 0 -0.52 17 17
SHC1 0.012 0.002 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.002 0.014 -10000 0 -0.065 16 16
PRKCZ -0.001 0.15 -10000 0 -0.54 17 17
NF kappa B1 p50/RelA -0.022 0.15 -10000 0 -0.51 20 20
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.016 0.15 -10000 0 -0.51 21 21
HSP90AA1 0.012 0 -10000 0 -10000 0 0
RELA 0.012 0 -10000 0 -10000 0 0
IL2RA -0.022 0.13 -10000 0 -0.51 24 24
IL2RB -0.021 0.13 -10000 0 -0.51 25 25
TERT -0.083 0.2 -10000 0 -0.5 68 68
E2F1 0 0.1 -10000 0 -0.44 18 18
SOS1 0.012 0.003 -10000 0 -10000 0 0
RPS6 0.011 0.029 -10000 0 -0.54 1 1
mol:cAMP -0.001 0.007 0.031 16 -10000 0 16
PTPN11 0.012 0.003 -10000 0 -10000 0 0
IL2RG -0.02 0.13 -10000 0 -0.5 25 25
actin cytoskeleton organization 0.001 0.15 -10000 0 -0.52 17 17
GRB2 0.012 0.003 -10000 0 -10000 0 0
IL2 -0.012 0.09 -10000 0 -0.45 15 15
PIK3CA 0.012 0.034 -10000 0 -0.45 2 2
Rac1/GTP 0.012 0.07 -10000 0 -0.27 17 17
LCK -0.015 0.12 -10000 0 -0.5 21 21
BCL2 -0.016 0.22 -10000 0 -0.72 25 25
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.002 0.12 -9999 0 -0.52 9 9
MAP3K8 0.006 0.057 -9999 0 -0.54 4 4
FOS -0.001 0.12 -9999 0 -0.54 8 8
PRKCA -0.012 0.11 -9999 0 -0.53 17 17
PTPN7 -0.007 0.099 -9999 0 -0.48 15 15
HRAS 0.011 0.024 -9999 0 -0.45 1 1
PRKCB -0.026 0.13 -9999 0 -0.49 28 28
NRAS 0.005 0.064 -9999 0 -0.54 5 5
RAS family/GTP 0.019 0.039 -9999 0 -0.28 6 6
MAPK3 0 0.097 -9999 0 -0.55 7 7
MAP2K1 -0.01 0.13 -9999 0 -0.42 27 27
ELK1 0.012 0.005 -9999 0 -10000 0 0
BRAF -0.015 0.12 -9999 0 -0.43 27 27
mol:GTP 0 0.001 -9999 0 -0.004 24 24
MAPK1 0 0.097 -9999 0 -0.6 6 6
RAF1 -0.015 0.12 -9999 0 -0.43 27 27
KRAS 0.012 0.001 -9999 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 -0.003 0.086 -9999 0 -0.49 11 11
PLK4 0.003 0.07 -9999 0 -0.54 6 6
regulation of centriole replication 0.002 0.08 -9999 0 -0.36 17 17
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 -0.014 0.14 -9999 0 -0.4 31 31
MAP4K1 -0.006 0.095 -9999 0 -0.48 14 14
MAP3K8 0.006 0.057 -9999 0 -0.54 4 4
PRKCB -0.026 0.13 -9999 0 -0.49 28 28
DBNL 0.012 0 -9999 0 -10000 0 0
CRKL 0.012 0 -9999 0 -10000 0 0
MAP3K1 0.008 0.1 -9999 0 -0.5 8 8
JUN -0.005 0.14 -9999 0 -0.63 15 15
MAP3K7 0.008 0.096 -9999 0 -0.47 8 8
GRAP2 -0.028 0.14 -9999 0 -0.5 29 29
CRK 0.012 0 -9999 0 -10000 0 0
MAP2K4 0.012 0.099 -9999 0 -0.45 9 9
LAT 0.001 0.074 -9999 0 -0.5 8 8
LCP2 0 0.079 -9999 0 -0.5 9 9
MAPK8 -0.01 0.14 -9999 0 -0.66 15 15
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.002 0.1 -9999 0 -0.5 8 8
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.006 0.13 -9999 0 -0.65 9 9
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.023 0.11 -9999 0 -0.44 5 5
CRKL 0.006 0.084 -9999 0 -0.34 5 5
mol:DAG 0.01 0.089 -9999 0 -0.32 14 14
HRAS 0.025 0.076 -9999 0 -0.36 2 2
MAPK8 -0.001 0.088 -9999 0 -0.31 15 15
RAP1A 0.006 0.084 -9999 0 -0.34 5 5
GAB1 0.005 0.085 -9999 0 -0.34 5 5
MAPK14 0.001 0.084 -9999 0 -0.3 13 13
EPO -0.016 0.1 -9999 0 -0.45 20 20
PLCG1 0.01 0.091 -9999 0 -0.33 14 14
EPOR/TRPC2/IP3 Receptors -0.013 0.11 -9999 0 -0.48 19 19
RAPGEF1 0.012 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.018 0.11 -9999 0 -0.28 52 52
GAB1/SHC/GRB2/SOS1 -0.023 0.058 -9999 0 -0.37 1 1
EPO/EPOR (dimer) -0.017 0.11 -9999 0 -0.34 37 37
IRS2 -0.017 0.12 -9999 0 -0.37 18 18
STAT1 0.012 0.1 -9999 0 -0.38 8 8
STAT5B 0.011 0.096 -9999 0 -0.41 5 5
cell proliferation 0.006 0.082 -9999 0 -0.34 7 7
GAB1/SHIP/PIK3R1/SHP2/SHC -0.038 0.086 -9999 0 -0.43 7 7
TEC 0.001 0.092 -9999 0 -0.4 5 5
SOCS3 -0.009 0.1 -9999 0 -0.52 15 15
STAT1 (dimer) 0.012 0.1 -9999 0 -0.37 8 8
JAK2 -0.002 0.085 -9999 0 -0.54 9 9
PIK3R1 -0.018 0.12 -9999 0 -0.52 21 21
EPO/EPOR (dimer)/JAK2 0.012 0.093 -9999 0 -0.31 9 9
EPO/EPOR -0.017 0.11 -9999 0 -0.34 37 37
LYN 0.009 0.049 -9999 0 -0.54 3 3
TEC/VAV2 0.006 0.094 -9999 0 -0.39 5 5
elevation of cytosolic calcium ion concentration -0.013 0.11 -9999 0 -0.48 19 19
SHC1 0.012 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.002 0.096 -9999 0 -0.27 40 40
mol:IP3 0.01 0.089 -9999 0 -0.32 14 14
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.025 0.14 -9999 0 -0.46 21 21
SH2B3 0.01 0.009 -9999 0 -10000 0 0
NFKB1 0.001 0.084 -9999 0 -0.3 13 13
EPO/EPOR (dimer)/JAK2/SOCS3 -0.027 0.068 -9999 0 -0.24 21 21
PTPN6 0 0.087 -9999 0 -0.32 8 8
TEC/VAV2/GRB2 0.011 0.092 -9999 0 -0.38 5 5
EPOR -0.013 0.11 -9999 0 -0.48 19 19
INPP5D -0.002 0.088 -9999 0 -0.53 10 10
mol:GDP -0.024 0.059 -9999 0 -0.33 3 3
SOS1 0.012 0 -9999 0 -10000 0 0
PLCG2 0 0.076 -9999 0 -0.48 9 9
CRKL/CBL/C3G 0.019 0.08 -9999 0 -0.35 3 3
VAV2 0.003 0.088 -9999 0 -0.34 6 6
CBL 0.006 0.084 -9999 0 -0.34 5 5
SHC/Grb2/SOS1 -0.025 0.062 -9999 0 -0.35 3 3
STAT5A 0.011 0.096 -9999 0 -0.38 7 7
GRB2 0.012 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.021 0.11 -9999 0 -0.44 5 5
LYN/PLCgamma2 0.007 0.066 -9999 0 -0.35 12 12
PTPN11 0.012 0 -9999 0 -10000 0 0
BTK -0.005 0.1 -9999 0 -0.4 8 8
BCL2 -0.001 0.2 -9999 0 -0.79 18 18
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.011 0.029 -9999 0 -0.54 1 1
Caspase 8 (4 units) 0.004 0.083 -9999 0 -0.39 3 3
NEF -0.012 0.048 -9999 0 -0.19 17 17
NFKBIA 0.003 0.033 -9999 0 -10000 0 0
BIRC3 -0.024 0.18 -9999 0 -0.51 42 42
CYCS 0.004 0.09 -9999 0 -0.44 2 2
RIPK1 0.012 0 -9999 0 -10000 0 0
CD247 -0.04 0.16 -9999 0 -0.59 27 27
MAP2K7 0.006 0.083 -9999 0 -0.51 2 2
protein ubiquitination 0.021 0.078 -9999 0 -0.38 4 4
CRADD 0.012 0 -9999 0 -10000 0 0
DAXX 0.012 0 -9999 0 -10000 0 0
FAS 0.001 0.079 -9999 0 -0.53 8 8
BID -0.001 0.094 -9999 0 -0.4 3 3
NF-kappa-B/RelA/I kappa B alpha 0.002 0.091 -9999 0 -10000 0 0
TRADD 0.009 0.04 -9999 0 -0.54 2 2
MAP3K5 0.004 0.064 -9999 0 -0.5 6 6
CFLAR 0.012 0 -9999 0 -10000 0 0
FADD 0.011 0.024 -9999 0 -0.45 1 1
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.002 0.092 -9999 0 -10000 0 0
MAPK8 0.011 0.082 -9999 0 -0.43 3 3
APAF1 0.012 0 -9999 0 -10000 0 0
TRAF1 0.01 0.037 -9999 0 -0.5 2 2
TRAF2 0.012 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.007 0.098 -9999 0 -0.28 26 26
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.008 0.095 -9999 0 -0.48 5 5
CHUK 0.02 0.083 -9999 0 -0.42 4 4
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.025 0.057 -9999 0 -10000 0 0
TCRz/NEF -0.042 0.16 -9999 0 -0.39 54 54
TNF -0.069 0.19 -9999 0 -0.49 60 60
FASLG -0.061 0.22 -9999 0 -0.58 51 51
NFKB1 0.003 0.033 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.027 0.12 -9999 0 -0.29 61 61
CASP6 0.019 0.071 -9999 0 -0.5 1 1
CASP7 -0.005 0.17 -9999 0 -0.52 31 31
RELA 0.003 0.033 -9999 0 -10000 0 0
CASP2 0.012 0 -9999 0 -10000 0 0
CASP3 -0.004 0.17 -9999 0 -0.51 30 30
TNFRSF1A 0.011 0.029 -9999 0 -0.54 1 1
TNFR1A/BAG4 0.016 0.03 -9999 0 -0.38 2 2
CASP8 0.011 0.029 -9999 0 -0.54 1 1
CASP9 0.011 0.024 -9999 0 -0.45 1 1
MAP3K14 0.015 0.09 -9999 0 -0.47 4 4
APAF-1/Caspase 9 -0.053 0.12 -9999 0 -0.4 31 31
BCL2 0.004 0.1 -9999 0 -0.39 10 10
IL2 signaling events mediated by STAT5

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
GAB2 0.01 0.034 -9999 0 -0.45 2 2
ELF1 -0.001 0.08 -9999 0 -0.34 17 17
CCNA2 0.005 0.064 -9999 0 -0.54 5 5
PIK3CA 0.01 0.034 -9999 0 -0.45 2 2
JAK3 0.002 0.076 -9999 0 -0.5 8 8
PIK3R1 -0.017 0.12 -9999 0 -0.52 21 21
JAK1 0.005 0.064 -9999 0 -0.54 5 5
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.003 0.14 -9999 0 -0.51 17 17
SHC1 0.013 0 -9999 0 -10000 0 0
SP1 0.003 0.066 -9999 0 -0.34 7 7
IL2RA -0.017 0.18 -9999 0 -0.66 24 24
IL2RB -0.022 0.13 -9999 0 -0.51 25 25
SOS1 0.013 0 -9999 0 -10000 0 0
IL2RG -0.022 0.13 -9999 0 -0.5 25 25
G1/S transition of mitotic cell cycle -0.014 0.16 -9999 0 -0.62 15 15
PTPN11 0.013 0 -9999 0 -10000 0 0
CCND2 -0.007 0.14 -9999 0 -0.51 23 23
LCK -0.016 0.12 -9999 0 -0.5 21 21
GRB2 0.013 0 -9999 0 -10000 0 0
IL2 -0.013 0.09 -9999 0 -0.45 15 15
CDK6 -0.014 0.12 -9999 0 -0.51 19 19
CCND3 0.013 0.13 -9999 0 -0.53 9 9
Regulation of Telomerase

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
Telomerase catalytic core complex -0.17 0.38 -9999 0 -1.1 48 48
RAD9A 0.012 0 -9999 0 -10000 0 0
AP1 -0.008 0.092 -9999 0 -0.34 25 25
IFNAR2 0.01 0.029 -9999 0 -0.54 1 1
AKT1 -0.028 0.086 -9999 0 -0.26 16 16
ER alpha/Oestrogen -0.044 0.14 -9999 0 -0.39 48 48
NFX1/SIN3/HDAC complex 0.031 0.026 -9999 0 -10000 0 0
EGF -0.066 0.18 -9999 0 -0.48 57 57
SMG5 0.012 0 -9999 0 -10000 0 0
SMG6 0.012 0 -9999 0 -10000 0 0
SP3/HDAC2 0.015 0.013 -9999 0 -10000 0 0
TERT/c-Abl -0.15 0.35 -9999 0 -1 46 46
SAP18 0.012 0.002 -9999 0 -10000 0 0
MRN complex 0.024 0.018 -9999 0 -0.32 1 1
WT1 -0.13 0.23 -9999 0 -0.5 104 104
WRN 0.012 0 -9999 0 -10000 0 0
SP1 0.01 0.011 -9999 0 -10000 0 0
SP3 0.011 0.005 -9999 0 -10000 0 0
TERF2IP 0.012 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.15 0.3 -9999 0 -0.89 46 46
Mad/Max 0.015 0.019 -9999 0 -0.31 1 1
TERT -0.18 0.4 -9999 0 -1.2 46 46
CCND1 -0.16 0.38 -9999 0 -1 57 57
MAX 0.011 0.005 -9999 0 -10000 0 0
RBBP7 0.01 0.024 -9999 0 -0.45 1 1
RBBP4 0.012 0.002 -9999 0 -10000 0 0
TERF2 0.012 0.004 -9999 0 -10000 0 0
PTGES3 0.012 0 -9999 0 -10000 0 0
SIN3A 0.012 0.002 -9999 0 -10000 0 0
Telomerase/911 0.017 0.039 -9999 0 -10000 0 0
CDKN1B -0.033 0.16 -9999 0 -0.61 20 20
RAD1 0.012 0 -9999 0 -10000 0 0
XRCC5 0.012 0 -9999 0 -10000 0 0
XRCC6 0.012 0 -9999 0 -10000 0 0
SAP30 0.009 0.04 -9999 0 -0.54 2 2
TRF2/PARP2 0.018 0.003 -9999 0 -10000 0 0
UBE3A 0.011 0.005 -9999 0 -10000 0 0
JUN 0.008 0.037 -9999 0 -0.49 2 2
E6 -0.002 0.005 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.007 0.007 -9999 0 -10000 0 0
FOS -0.02 0.12 -9999 0 -0.47 24 24
IFN-gamma/IRF1 -0.03 0.13 -9999 0 -0.33 53 53
PARP2 0.012 0 -9999 0 -10000 0 0
BLM 0.008 0.049 -9999 0 -0.54 3 3
Telomerase -0.004 0.078 -9999 0 -0.46 6 6
IRF1 0.002 0.056 -9999 0 -0.45 3 3
ESR1 -0.06 0.18 -9999 0 -0.54 48 48
KU/TER 0.018 0 -9999 0 -10000 0 0
ATM/TRF2 0.018 0.019 -9999 0 -0.34 1 1
ubiquitin-dependent protein catabolic process 0.035 0.025 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.035 0.025 -9999 0 -10000 0 0
HDAC1 0.012 0.002 -9999 0 -10000 0 0
HDAC2 0.009 0.011 -9999 0 -10000 0 0
ATM -0.001 0.022 -9999 0 -0.42 1 1
SMAD3 0.019 0.025 -9999 0 -0.31 2 2
ABL1 0.012 0 -9999 0 -10000 0 0
MXD1 0.01 0.024 -9999 0 -0.45 1 1
MRE11A 0.012 0 -9999 0 -10000 0 0
HUS1 0.012 0 -9999 0 -10000 0 0
RPS6KB1 0.011 0.029 -9999 0 -0.54 1 1
TERT/NF kappa B1/14-3-3 -0.14 0.35 -9999 0 -0.99 46 46
NR2F2 0.008 0.065 -9999 0 -0.54 5 5
MAPK3 -0.003 0.067 -9999 0 -0.32 16 16
MAPK1 -0.003 0.067 -9999 0 -0.32 16 16
TGFB1/TGF beta receptor Type II 0.011 0.034 -9999 0 -0.45 2 2
NFKB1 0.012 0 -9999 0 -10000 0 0
HNRNPC 0.012 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.001 0.022 -9999 0 -0.41 1 1
NBN 0.011 0.029 -9999 0 -0.54 1 1
EGFR -0.005 0.093 -9999 0 -0.53 11 11
mol:Oestrogen -0.001 0.003 -9999 0 -10000 0 0
EGF/EGFR -0.051 0.15 -9999 0 -0.36 65 65
MYC -0.008 0.097 -9999 0 -0.51 13 13
IL2 -0.017 0.091 -9999 0 -0.46 15 15
KU 0.018 0 -9999 0 -10000 0 0
RAD50 0.012 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
TGFB1 0.011 0.034 -9999 0 -0.45 2 2
TRF2/BLM 0.015 0.034 -9999 0 -0.36 3 3
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.14 0.36 -9999 0 -1 46 46
SP1/HDAC2 0.015 0.019 -9999 0 -10000 0 0
PINX1 0.012 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.15 0.3 -9999 0 -0.89 46 46
Smad3/Myc 0.012 0.064 -9999 0 -0.29 15 15
911 complex 0.025 0 -9999 0 -10000 0 0
IFNG -0.044 0.15 -9999 0 -0.47 36 36
Telomerase/PinX1 -0.15 0.3 -9999 0 -0.89 46 46
Telomerase/AKT1/mTOR/p70S6K -0.017 0.084 -9999 0 -0.34 2 2
SIN3B 0.012 0.002 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.15 0.3 -9999 0 -0.89 46 46
response to DNA damage stimulus 0.003 0.007 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0.035 0.015 -9999 0 -10000 0 0
TRF2/WRN 0.018 0.003 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.15 0.3 -9999 0 -0.89 46 46
E2F1 0.002 0.067 -9999 0 -0.48 7 7
ZNFX1 0.012 0.002 -9999 0 -10000 0 0
PIF1 0.001 0.077 -9999 0 -0.52 8 8
NCL 0.012 0 -9999 0 -10000 0 0
DKC1 0.012 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.02 0.04 -9999 0 -0.32 5 5
SNTA1 0.007 0.05 -9999 0 -0.47 4 4
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.014 0.059 -9999 0 -0.32 11 11
MAPK12 -0.002 0.084 -9999 0 -0.26 34 34
CCND1 -0.012 0.1 -9999 0 -0.47 15 15
p38 gamma/SNTA1 0.003 0.085 -9999 0 -0.28 19 19
MAP2K3 0.012 0 -9999 0 -10000 0 0
PKN1 0.012 0 -9999 0 -10000 0 0
G2/M transition checkpoint -0.001 0.084 -9999 0 -0.26 34 34
MAP2K6 0.004 0.07 -9999 0 -0.3 18 18
MAPT 0.004 0.072 -9999 0 -0.32 13 13
MAPK13 0.014 0.047 -9999 0 -0.38 5 5
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.014 0.018 -9999 0 -0.33 1 1
Signaling events mediated by PRL

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 -0.014 0.11 -10000 0 -0.5 19 19
mol:Halofuginone 0.004 0.012 -10000 0 -0.22 1 1
ITGA1 -0.006 0.095 -10000 0 -0.48 14 14
CDKN1A 0.003 0.1 -10000 0 -0.43 15 15
PRL-3/alpha Tubulin 0.013 0.043 -10000 0 -0.36 5 5
mol:Ca2+ -0.087 0.16 0.32 3 -0.36 92 95
AGT -0.12 0.22 -10000 0 -0.49 93 93
CCNA2 0.014 0.088 -10000 0 -0.6 4 4
TUBA1B 0.012 0 -10000 0 -10000 0 0
EGR1 0.001 0.081 -10000 0 -0.34 20 20
CDK2/Cyclin E1 0.003 0.11 -10000 0 -0.37 17 17
MAPK3 0.013 0.047 -10000 0 -0.35 6 6
PRL-2 /Rab GGTase beta 0.018 0 -10000 0 -10000 0 0
MAPK1 0.013 0.047 -10000 0 -0.35 6 6
PTP4A1 0.013 0.085 -10000 0 -0.68 3 3
PTP4A3 0.005 0.06 -10000 0 -0.5 5 5
PTP4A2 0.012 0 -10000 0 -10000 0 0
ITGB1 0.014 0.044 -10000 0 -0.36 5 5
SRC 0.009 0.04 -10000 0 -0.54 2 2
RAC1 0.017 0.064 -10000 0 -0.48 4 4
Rab GGTase beta/Rab GGTase alpha 0.018 0 -10000 0 -10000 0 0
PRL-1/ATF-5 0.015 0.084 -10000 0 -0.64 3 3
RABGGTA 0.012 0 -10000 0 -10000 0 0
BCAR1 0.003 0.043 0.31 5 -0.4 1 6
RHOC 0.017 0.064 -10000 0 -0.48 4 4
RHOA 0.017 0.064 -10000 0 -0.48 4 4
cell motility 0.02 0.066 -10000 0 -0.43 5 5
PRL-1/alpha Tubulin 0.018 0.08 -10000 0 -0.64 3 3
PRL-3/alpha1 Integrin 0 0.083 -10000 0 -0.36 18 18
ROCK1 0.02 0.066 -10000 0 -0.43 5 5
RABGGTB 0.012 0 -10000 0 -10000 0 0
CDK2 0.012 0 -10000 0 -10000 0 0
mitosis 0.013 0.084 -10000 0 -0.67 3 3
ATF5 0.006 0.054 -10000 0 -0.45 5 5
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.012 0.001 -9999 0 -10000 0 0
HDAC2 0.012 0.001 -9999 0 -10000 0 0
GNB1/GNG2 0.004 0.073 -9999 0 -0.3 20 20
forebrain development -0.058 0.2 -9999 0 -0.53 44 44
GNAO1 -0.014 0.11 -9999 0 -0.47 20 20
SMO/beta Arrestin2 0.007 0.062 -9999 0 -0.38 9 9
SMO -0.002 0.085 -9999 0 -0.54 9 9
ARRB2 0.011 0.005 -9999 0 -10000 0 0
GLI3/SPOP 0.023 0.075 -9999 0 -0.46 1 1
mol:GTP 0 0.003 -9999 0 -10000 0 0
GSK3B 0.012 0 -9999 0 -10000 0 0
GNAI2 0.012 0.003 -9999 0 -10000 0 0
SIN3/HDAC complex 0.031 0.024 -9999 0 -0.28 2 2
GNAI1 -0.006 0.095 -9999 0 -0.52 12 12
XPO1 0.012 0.006 -9999 0 -10000 0 0
GLI1/Su(fu) -0.04 0.17 -9999 0 -0.5 24 24
SAP30 0.01 0.04 -9999 0 -0.54 2 2
mol:GDP -0.002 0.085 -9999 0 -0.54 9 9
MIM/GLI2A -0.017 0.11 -9999 0 -0.54 15 15
IFT88 0.011 0.029 -9999 0 -0.54 1 1
GNAI3 0.012 0.003 -9999 0 -10000 0 0
GLI2 0.03 0.038 -9999 0 -10000 0 0
GLI3 0.017 0.079 -9999 0 -0.38 2 2
CSNK1D 0.012 0 -9999 0 -10000 0 0
CSNK1E 0.012 0 -9999 0 -10000 0 0
SAP18 0.012 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.011 0.029 -9999 0 -0.54 1 1
GNG2 -0.002 0.084 -9999 0 -0.48 11 11
Gi family/GTP -0.004 0.09 -9999 0 -0.3 18 18
SIN3B 0.012 0.001 -9999 0 -10000 0 0
SIN3A 0.012 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.029 0.065 -9999 0 -0.4