PARADIGM pathway analysis of mRNA expression and copy number data
Breast Invasive Carcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1WD3XK6
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNA expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1WD3XK6
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 52 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 mediated by p38-alpha and p38-beta 249
Signaling events mediated by Stem cell factor receptor (c-Kit) 223
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 157
Endothelins 147
EGFR-dependent Endothelin signaling events 145
Class IB PI3K non-lipid kinase events 126
IGF1 pathway 119
Arf6 signaling events 104
FOXM1 transcription factor network 102
Nongenotropic Androgen signaling 98
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 526 . Pathway is significant if Significance.Ratio > 0.05 .

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

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

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

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

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

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

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

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

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

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 526 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Signaling mediated by p38-alpha and p38-beta 0.4734 249 10966 44 -0.6 0.034 1000 -1000 -0.007 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.4240 223 17416 78 -1 0.32 1000 -1000 -0.016 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2985 157 10676 68 -0.88 0.45 1000 -1000 -0.056 -1000
Endothelins 0.2795 147 14135 96 -0.81 0.17 1000 -1000 -0.02 -1000
EGFR-dependent Endothelin signaling events 0.2757 145 3060 21 -0.31 0.048 1000 -1000 -0.034 -1000
Class IB PI3K non-lipid kinase events 0.2395 126 378 3 -0.11 -1000 1000 -1000 -0.013 -1000
IGF1 pathway 0.2262 119 6787 57 -0.27 0.11 1000 -1000 -0.03 -1000
Arf6 signaling events 0.1977 104 6508 62 -0.31 0.081 1000 -1000 0 -1000
FOXM1 transcription factor network 0.1939 102 5251 51 -0.12 0.71 1000 -1000 0.013 -1000
Nongenotropic Androgen signaling 0.1863 98 5107 52 -0.57 0.3 1000 -1000 -0.024 -1000
Glucocorticoid receptor regulatory network 0.1578 83 9470 114 -0.95 0.29 1000 -1000 -0.045 -1000
Signaling events mediated by PTP1B 0.1502 79 6010 76 -0.37 0.19 1000 -1000 -0.034 -1000
S1P1 pathway 0.1464 77 2786 36 -0.62 0.045 1000 -1000 -0.024 -1000
Calcium signaling in the CD4+ TCR pathway 0.1407 74 2310 31 -0.35 0.039 1000 -1000 -0.027 -1000
PDGFR-alpha signaling pathway 0.1331 70 3106 44 -0.7 0.063 1000 -1000 -0.02 -1000
HIF-1-alpha transcription factor network 0.1312 69 5258 76 -0.4 0.07 1000 -1000 -0.014 -1000
Ephrin B reverse signaling 0.1312 69 3325 48 -0.18 0.061 1000 -1000 -0.029 -1000
BMP receptor signaling 0.1293 68 5586 81 -0.4 0.11 1000 -1000 -0.03 -1000
Ras signaling in the CD4+ TCR pathway 0.1255 66 1126 17 -0.2 0.033 1000 -1000 -0.005 -1000
Plasma membrane estrogen receptor signaling 0.1084 57 4948 86 -0.25 0.17 1000 -1000 -0.047 -1000
IL4-mediated signaling events 0.1065 56 5103 91 -0.51 0.14 1000 -1000 -0.11 -1000
FAS signaling pathway (CD95) 0.1065 56 2641 47 -0.88 0.06 1000 -1000 -0.03 -1000
IL6-mediated signaling events 0.1027 54 4097 75 -0.37 0.073 1000 -1000 -0.025 -1000
E-cadherin signaling in keratinocytes 0.1027 54 2335 43 -0.27 0.035 1000 -1000 -0.017 -1000
EPHB forward signaling 0.1008 53 4546 85 -0.18 0.15 1000 -1000 -0.058 -1000
PLK1 signaling events 0.0989 52 4434 85 -0.035 0.17 1000 -1000 -0.026 -1000
Integrins in angiogenesis 0.0989 52 4430 84 -0.39 0.13 1000 -1000 -0.029 -1000
IL23-mediated signaling events 0.0970 51 3103 60 -0.79 0.065 1000 -1000 -0.004 -1000
Aurora B signaling 0.0913 48 3222 67 -0.38 0.24 1000 -1000 -0.028 -1000
Fc-epsilon receptor I signaling in mast cells 0.0875 46 4558 97 -0.36 0.04 1000 -1000 -0.047 -1000
Glypican 1 network 0.0779 41 2012 48 -0.39 0.07 1000 -1000 -0.026 -1000
Insulin Pathway 0.0760 40 3003 74 -0.28 0.091 1000 -1000 -0.028 -1000
Signaling events mediated by the Hedgehog family 0.0741 39 2050 52 -0.14 0.067 1000 -1000 -0.02 -1000
S1P5 pathway 0.0741 39 679 17 -0.17 0.067 1000 -1000 -0.004 -1000
p75(NTR)-mediated signaling 0.0722 38 4827 125 -0.13 0.093 1000 -1000 -0.034 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0703 37 2761 74 -0.27 0.074 1000 -1000 -0.055 -1000
Visual signal transduction: Rods 0.0703 37 1942 52 -0.43 0.074 1000 -1000 -0.024 -1000
Presenilin action in Notch and Wnt signaling 0.0684 36 2205 61 -0.38 0.1 1000 -1000 -0.022 -1000
TCGA08_retinoblastoma 0.0684 36 293 8 -0.022 0.057 1000 -1000 -0.004 -1000
Nectin adhesion pathway 0.0665 35 2244 63 -0.075 0.054 1000 -1000 -0.033 -1000
LPA receptor mediated events 0.0665 35 3629 102 -0.35 0.094 1000 -1000 -0.065 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0627 33 2833 85 -0.54 0.046 1000 -1000 -0.027 -1000
S1P4 pathway 0.0627 33 841 25 -0.17 0.045 1000 -1000 -0.014 -1000
ErbB2/ErbB3 signaling events 0.0589 31 2051 65 -0.35 0.047 1000 -1000 -0.052 -1000
IL27-mediated signaling events 0.0589 31 1629 51 -0.37 0.065 1000 -1000 -0.034 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0589 31 3787 120 -0.25 0.12 1000 -1000 -0.038 -1000
ErbB4 signaling events 0.0570 30 2089 69 -0.36 0.14 1000 -1000 -0.022 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0551 29 1512 52 -0.38 0.1 1000 -1000 -0.012 -1000
Syndecan-3-mediated signaling events 0.0551 29 1031 35 -0.37 0.074 1000 -1000 -0.018 -1000
TCGA08_rtk_signaling 0.0551 29 776 26 -0.27 0.042 1000 -1000 -0.024 -1000
Signaling events regulated by Ret tyrosine kinase 0.0532 28 2349 82 -0.1 0.11 1000 -1000 -0.049 -1000
TCR signaling in naïve CD8+ T cells 0.0513 27 2540 93 -0.04 0.082 1000 -1000 -0.039 -1000
mTOR signaling pathway 0.0494 26 1395 53 -0.051 0.044 1000 -1000 -0.029 -1000
amb2 Integrin signaling 0.0494 26 2133 82 -0.53 0.13 1000 -1000 -0.021 -1000
Syndecan-4-mediated signaling events 0.0494 26 1746 67 -0.39 0.15 1000 -1000 -0.025 -1000
Regulation of nuclear SMAD2/3 signaling 0.0475 25 3468 136 -0.37 0.075 1000 -1000 -0.034 -1000
FOXA2 and FOXA3 transcription factor networks 0.0475 25 1177 46 -0.74 0.05 1000 -1000 -0.011 -1000
IL12-mediated signaling events 0.0456 24 2096 87 -0.83 0.088 1000 -1000 -0.027 -1000
Reelin signaling pathway 0.0456 24 1347 56 -0.056 0.084 1000 -1000 -0.022 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0456 24 2121 88 -0.39 0.13 1000 -1000 -0.056 -1000
Syndecan-1-mediated signaling events 0.0437 23 786 34 -0.042 0.11 1000 -1000 -0.016 -1000
Osteopontin-mediated events 0.0437 23 885 38 -0.35 0.14 1000 -1000 -0.004 -1000
Syndecan-2-mediated signaling events 0.0437 23 1621 69 -0.32 0.13 1000 -1000 -0.03 -1000
IL1-mediated signaling events 0.0437 23 1446 62 -0.051 0.067 1000 -1000 -0.029 -1000
S1P3 pathway 0.0437 23 984 42 -0.17 0.062 1000 -1000 -0.024 -1000
Canonical Wnt signaling pathway 0.0418 22 1140 51 -0.38 0.16 1000 -1000 -0.034 -1000
Coregulation of Androgen receptor activity 0.0399 21 1608 76 -0.23 0.053 1000 -1000 -0.009 -1000
Thromboxane A2 receptor signaling 0.0399 21 2307 105 -0.27 0.066 1000 -1000 -0.037 -1000
HIF-2-alpha transcription factor network 0.0399 21 924 43 -0.22 0.26 1000 -1000 -0.091 -1000
Ceramide signaling pathway 0.0380 20 1555 76 -0.25 0.083 1000 -1000 -0.016 -1000
Regulation of p38-alpha and p38-beta 0.0380 20 1089 54 -0.32 0.071 1000 -1000 -0.043 -1000
Regulation of Telomerase 0.0380 20 2111 102 -0.35 0.087 1000 -1000 -0.015 -1000
Regulation of Androgen receptor activity 0.0380 20 1456 70 -0.43 0.078 1000 -1000 -0.033 -1000
Signaling mediated by p38-gamma and p38-delta 0.0342 18 279 15 -0.006 0.034 1000 -1000 -0.02 -1000
IL2 signaling events mediated by PI3K 0.0342 18 1098 58 -0.12 0.049 1000 -1000 -0.027 -1000
E-cadherin signaling in the nascent adherens junction 0.0342 18 1420 76 -0.042 0.059 1000 -1000 -0.043 -1000
Circadian rhythm pathway 0.0323 17 374 22 -0.021 0.1 1000 -1000 -0.01 -1000
Noncanonical Wnt signaling pathway 0.0323 17 455 26 -0.016 0.04 1000 -1000 -0.021 -1000
E-cadherin signaling events 0.0323 17 87 5 0.006 0.034 1000 -1000 0.021 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0304 16 747 45 -0.007 0.06 1000 -1000 -0.017 -1000
Wnt signaling 0.0304 16 112 7 -0.016 0.04 1000 -1000 -0.01 -1000
Signaling events mediated by PRL 0.0304 16 576 34 -0.31 0.051 1000 -1000 -0.025 -1000
Cellular roles of Anthrax toxin 0.0285 15 614 39 -0.063 0.038 1000 -1000 -0.015 -1000
Hedgehog signaling events mediated by Gli proteins 0.0285 15 1008 65 -0.17 0.077 1000 -1000 -0.037 -1000
ceramide signaling pathway 0.0228 12 628 49 -0.072 0.053 1000 -1000 -0.014 -1000
FoxO family signaling 0.0228 12 807 64 0 0.15 1000 -1000 -0.014 -1000
BCR signaling pathway 0.0228 12 1216 99 -0.15 0.093 1000 -1000 -0.043 -1000
PLK2 and PLK4 events 0.0209 11 33 3 0.016 0.055 1000 -1000 0 -1000
IFN-gamma pathway 0.0209 11 756 68 -0.02 0.099 1000 -1000 -0.033 -1000
Class I PI3K signaling events mediated by Akt 0.0209 11 792 68 -0.15 0.06 1000 -1000 -0.02 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0209 11 1465 125 -0.38 0.075 1000 -1000 -0.029 -1000
VEGFR1 specific signals 0.0209 11 622 56 -0.38 0.075 1000 -1000 -0.029 -1000
Caspase cascade in apoptosis 0.0190 10 813 74 -0.16 0.049 1000 -1000 -0.024 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0190 10 284 28 -0.17 0.053 1000 -1000 -0.012 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0190 10 564 54 -0.041 0.082 1000 -1000 -0.019 -1000
EPO signaling pathway 0.0190 10 562 55 -0.091 0.068 1000 -1000 -0.017 -1000
JNK signaling in the CD4+ TCR pathway 0.0152 8 142 17 -0.04 0.089 1000 -1000 -0.018 -1000
Signaling events mediated by HDAC Class III 0.0152 8 320 40 -0.061 0.062 1000 -1000 -0.03 -1000
TRAIL signaling pathway 0.0152 8 407 48 -0.002 0.046 1000 -1000 -0.019 -1000
Signaling events mediated by HDAC Class II 0.0133 7 592 75 -0.058 0.066 1000 -1000 -0.029 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0133 7 587 83 -0.072 0.066 1000 -1000 -0.011 -1000
Retinoic acid receptors-mediated signaling 0.0133 7 422 58 -0.055 0.08 1000 -1000 -0.024 -1000
Arf6 trafficking events 0.0133 7 514 71 -0.26 0.056 1000 -1000 -0.024 -1000
PDGFR-beta signaling pathway 0.0133 7 711 97 -0.035 0.08 1000 -1000 -0.034 -1000
Arf6 downstream pathway 0.0114 6 279 43 -0.09 0.092 1000 -1000 -0.032 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0114 6 248 37 -0.02 0.085 1000 -1000 -0.015 -1000
Paxillin-dependent events mediated by a4b1 0.0114 6 244 36 -0.07 0.075 1000 -1000 -0.029 -1000
p38 MAPK signaling pathway 0.0114 6 304 44 -0.016 0.066 1000 -1000 -0.011 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0095 5 178 34 -0.047 0.083 1000 -1000 -0.028 -1000
BARD1 signaling events 0.0095 5 334 57 -0.075 0.12 1000 -1000 -0.037 -1000
Visual signal transduction: Cones 0.0095 5 192 38 0 0.069 1000 -1000 0 -1000
Insulin-mediated glucose transport 0.0095 5 181 32 -0.099 0.053 1000 -1000 -0.016 -1000
Signaling events mediated by HDAC Class I 0.0095 5 535 104 -0.21 0.082 1000 -1000 -0.036 -1000
Class I PI3K signaling events 0.0095 5 426 73 -0.008 0.059 1000 -1000 -0.022 -1000
Canonical NF-kappaB pathway 0.0076 4 180 39 0 0.074 1000 -1000 -0.015 -1000
Atypical NF-kappaB pathway 0.0076 4 154 31 -0.02 0.048 1000 -1000 -0.009 -1000
IL2 signaling events mediated by STAT5 0.0076 4 101 22 -0.02 0.081 1000 -1000 -0.007 -1000
Aurora A signaling 0.0057 3 193 60 0 0.12 1000 -1000 -0.01 -1000
Aurora C signaling 0.0057 3 23 7 0 0.078 1000 -1000 -0.012 -1000
TCGA08_p53 0.0057 3 22 7 -0.009 0.028 1000 -1000 -0.008 -1000
LPA4-mediated signaling events 0.0038 2 28 12 -0.01 0.035 1000 -1000 -0.022 -1000
Effects of Botulinum toxin 0.0038 2 73 26 0 0.07 1000 -1000 -0.002 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0019 1 25 23 -0.007 0.064 1000 -1000 -0.022 -1000
Ephrin A reverse signaling 0.0019 1 7 7 0 0.044 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0019 1 27 27 0 0.078 1000 -1000 -0.025 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0019 1 55 33 0 0.075 1000 -1000 -0.022 -1000
Arf1 pathway 0.0019 1 55 54 -0.001 0.062 1000 -1000 -0.013 -1000
a4b1 and a4b7 Integrin signaling 0.0000 0 0 5 0.033 0.054 1000 -1000 0.018 -1000
Glypican 2 network 0.0000 0 0 4 0 0.032 1000 -1000 0 -1000
Rapid glucocorticoid signaling 0.0000 0 17 20 0 0.043 1000 -1000 0 -1000
Alternative NF-kappaB pathway 0.0000 0 2 13 0 0.094 1000 -1000 0 -1000
Total NA 4385 266046 7203 -30 -990 131000 -131000 -3.1 -131000
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.6 0.54 0.4 4 -1 306 310
MKNK1 0.034 0.006 -10000 0 -10000 0 0
MAPK14 -0.2 0.2 -10000 0 -0.36 306 306
ATF2/c-Jun -0.26 0.32 -10000 0 -0.69 144 144
MAPK11 -0.19 0.2 -10000 0 -0.36 286 286
MITF -0.24 0.23 -10000 0 -0.42 308 308
MAPKAPK5 -0.23 0.22 -10000 0 -0.41 308 308
KRT8 -0.22 0.22 -10000 0 -0.39 304 304
MAPKAPK3 0.034 0.012 -10000 0 -10000 0 0
MAPKAPK2 0.028 0.016 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.31 0.32 -10000 0 -0.55 309 309
CEBPB -0.22 0.23 0.3 1 -0.41 283 284
SLC9A1 -0.24 0.23 -10000 0 -0.42 304 304
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.24 0.24 -10000 0 -0.42 306 306
p38alpha-beta/MNK1 -0.25 0.28 -10000 0 -0.45 306 306
JUN -0.26 0.31 -10000 0 -0.68 144 144
PPARGC1A -0.28 0.29 0.28 1 -0.48 314 315
USF1 -0.21 0.22 0.33 4 -0.39 292 296
RAB5/GDP/GDI1 -0.17 0.18 -10000 0 -0.31 301 301
NOS2 -0.24 0.22 -10000 0 -0.41 308 308
DDIT3 -0.23 0.22 -10000 0 -0.41 306 306
RAB5A 0.034 0.005 -10000 0 -10000 0 0
HSPB1 -0.19 0.18 -10000 0 -0.34 270 270
p38alpha-beta/HBP1 -0.25 0.28 -10000 0 -0.45 307 307
CREB1 -0.25 0.24 -10000 0 -0.43 305 305
RAB5/GDP 0.025 0.004 -10000 0 -10000 0 0
EIF4E -0.24 0.24 -10000 0 -0.42 293 293
RPS6KA4 -0.23 0.23 -10000 0 -0.42 304 304
PLA2G4A -0.36 0.27 -10000 0 -0.52 356 356
GDI1 -0.23 0.22 -10000 0 -0.41 308 308
TP53 -0.31 0.3 -10000 0 -0.54 297 297
RPS6KA5 -0.25 0.23 -10000 0 -0.42 315 315
ESR1 -0.29 0.27 0.32 1 -0.43 358 359
HBP1 0.034 0.005 -10000 0 -10000 0 0
MEF2C -0.26 0.26 -10000 0 -0.44 313 313
MEF2A -0.23 0.23 0.3 1 -0.41 304 305
EIF4EBP1 -0.25 0.25 -10000 0 -0.44 300 300
KRT19 -0.22 0.23 0.33 1 -0.4 298 299
ELK4 -0.21 0.22 0.33 2 -0.4 287 289
ATF6 -0.22 0.22 0.33 4 -0.39 295 299
ATF1 -0.25 0.24 -10000 0 -0.43 307 307
p38alpha-beta/MAPKAPK2 -0.22 0.24 -10000 0 -0.42 288 288
p38alpha-beta/MAPKAPK3 -0.25 0.28 -10000 0 -0.45 307 307
Signaling events mediated by Stem cell factor receptor (c-Kit)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.3 0.16 -10000 0 -0.38 377 377
CRKL -0.32 0.17 -10000 0 -0.4 397 397
HRAS -0.23 0.15 -10000 0 -0.34 218 218
mol:PIP3 -0.27 0.17 0.29 1 -0.39 298 299
SPRED1 0.031 0.037 -10000 0 -0.54 2 2
SPRED2 0.034 0.005 -10000 0 -10000 0 0
GAB1 -0.33 0.18 -10000 0 -0.42 401 401
FOXO3 -0.27 0.16 -10000 0 -0.38 240 240
AKT1 -0.3 0.18 -10000 0 -0.4 274 274
BAD -0.28 0.16 -10000 0 -0.38 246 246
megakaryocyte differentiation -0.32 0.17 -10000 0 -0.41 402 402
GSK3B -0.28 0.16 -10000 0 -0.38 245 245
RAF1 -0.19 0.13 -10000 0 -0.32 54 54
SHC1 0.027 0.014 -10000 0 -10000 0 0
STAT3 -0.33 0.18 -10000 0 -0.42 399 399
STAT1 -0.81 0.43 -10000 0 -0.99 421 421
HRAS/SPRED1 -0.19 0.14 -10000 0 -0.32 57 57
cell proliferation -0.33 0.17 -10000 0 -0.41 403 403
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
TEC 0.034 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.32 0.18 -10000 0 -0.4 401 401
HRAS/SPRED2 -0.19 0.14 -10000 0 -0.32 55 55
LYN/TEC/p62DOK -0.29 0.18 -10000 0 -0.4 341 341
MAPK3 -0.13 0.098 -10000 0 -0.28 14 14
STAP1 -0.32 0.18 -10000 0 -0.41 402 402
GRAP2 0.034 0.019 -10000 0 -10000 0 0
JAK2 -0.68 0.37 -10000 0 -0.83 423 423
STAT1 (dimer) -0.79 0.42 -10000 0 -0.97 421 421
mol:Gleevec 0.013 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.28 0.19 -10000 0 -0.4 329 329
actin filament polymerization -0.33 0.17 -10000 0 -0.41 405 405
LYN 0.03 0.015 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.47 0.26 -10000 0 -0.58 409 409
PIK3R1 -0.021 0.17 -10000 0 -0.55 47 47
CBL/CRKL/GRB2 -0.28 0.17 -10000 0 -0.38 348 348
PI3K -0.32 0.2 -10000 0 -0.42 384 384
PTEN 0.026 0.067 -10000 0 -0.54 7 7
SCF/KIT/EPO/EPOR -0.95 0.51 -10000 0 -1.2 403 403
MAPK8 -0.33 0.18 -10000 0 -0.42 403 403
STAT3 (dimer) -0.33 0.17 -10000 0 -0.41 399 399
positive regulation of transcription -0.11 0.083 -10000 0 -0.24 10 10
mol:GDP -0.24 0.16 -10000 0 -0.36 230 230
PIK3C2B -0.3 0.18 -10000 0 -0.42 327 327
CBL/CRKL -0.3 0.16 -10000 0 -0.38 392 392
FER -0.33 0.18 -10000 0 -0.42 401 401
SH2B3 -0.33 0.18 -10000 0 -0.42 403 403
PDPK1 -0.24 0.17 -10000 0 -0.37 269 269
SNAI2 -0.34 0.2 -10000 0 -0.45 373 373
positive regulation of cell proliferation -0.58 0.3 -10000 0 -0.72 419 419
KITLG -0.011 0.07 -10000 0 -0.56 2 2
cell motility -0.58 0.3 -10000 0 -0.72 419 419
PTPN6 0.05 0.021 0.2 4 -10000 0 4
EPOR -0.23 0.19 -10000 0 -1.1 13 13
STAT5A (dimer) -0.48 0.26 -10000 0 -0.6 409 409
SOCS1 0.032 0.012 -10000 0 -10000 0 0
cell migration 0.32 0.17 0.41 401 -10000 0 401
SOS1 0.034 0.004 -10000 0 -10000 0 0
EPO 0.01 0.064 -10000 0 -10000 0 0
VAV1 0.038 0.025 -10000 0 -10000 0 0
GRB10 -0.34 0.18 -10000 0 -0.42 403 403
PTPN11 0.047 0.009 -10000 0 -10000 0 0
SCF/KIT -0.35 0.19 -10000 0 -0.44 405 405
GO:0007205 0.018 0.009 -10000 0 -10000 0 0
MAP2K1 -0.15 0.11 -10000 0 -0.28 22 22
CBL 0.03 0.011 -10000 0 -10000 0 0
KIT -1 0.53 -10000 0 -1.3 404 404
MAP2K2 -0.15 0.11 -10000 0 -0.28 22 22
SHC/Grb2/SOS1 -0.27 0.18 -10000 0 -0.4 294 294
STAT5A -0.5 0.26 -10000 0 -0.61 409 409
GRB2 0.034 0.018 -10000 0 -10000 0 0
response to radiation -0.34 0.2 0.27 2 -0.44 373 375
SHC/GRAP2 0.039 0.026 -10000 0 -10000 0 0
PTPRO -0.33 0.18 -10000 0 -0.42 402 402
SH2B2 -0.33 0.18 -10000 0 -0.42 405 405
DOK1 0.036 0.016 -10000 0 -10000 0 0
MATK -0.33 0.18 -10000 0 -0.42 403 403
CREBBP -0.082 0.075 -10000 0 -0.19 63 63
BCL2 -0.43 0.51 -10000 0 -1.4 111 111
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.047 0.031 0.21 4 -10000 0 4
NFATC2 -0.081 0.23 0.47 5 -0.55 55 60
NFATC3 -0.15 0.17 0.32 1 -0.32 238 239
CD40LG -0.67 0.53 0.75 5 -1 344 349
ITCH -0.064 0.14 -10000 0 -0.52 1 1
CBLB -0.067 0.14 -10000 0 -0.86 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.24 0.31 0.74 7 -0.69 71 78
JUNB 0.031 0.044 -10000 0 -0.54 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.077 0.17 -10000 0 -0.3 190 190
T cell anergy -0.13 0.21 -10000 0 -0.4 180 180
TLE4 -0.065 0.2 -10000 0 -0.6 36 36
Jun/NFAT1-c-4/p21SNFT -0.58 0.55 0.69 3 -0.94 327 330
AP-1/NFAT1-c-4 -0.8 0.68 0.92 5 -1.2 345 350
IKZF1 -0.044 0.17 0.46 10 -0.43 36 46
T-helper 2 cell differentiation -0.12 0.28 0.51 2 -0.74 53 55
AP-1/NFAT1 -0.3 0.3 0.53 6 -0.5 307 313
CALM1 -0.036 0.11 -10000 0 -0.31 1 1
EGR2 -0.8 0.76 0.7 4 -1.4 276 280
EGR3 -0.88 0.76 0.68 4 -1.4 344 348
NFAT1/FOXP3 -0.03 0.18 0.45 10 -0.4 48 58
EGR1 -0.43 0.23 -10000 0 -0.54 414 414
JUN -0.067 0.22 0.26 1 -0.54 89 90
EGR4 0.001 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.055 0.089 -10000 0 -0.17 186 186
GBP3 -0.078 0.24 0.44 2 -0.69 50 52
FOSL1 0.035 0.01 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 -0.54 0.53 0.67 3 -0.9 327 330
DGKA -0.051 0.16 0.47 1 -0.43 38 39
CREM 0.033 0.008 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.76 0.55 -10000 0 -1.1 350 350
CTLA4 -0.023 0.16 0.42 15 -0.39 28 43
NFAT1-c-4 (dimer)/EGR1 -0.78 0.57 -10000 0 -1.1 352 352
NFAT1-c-4 (dimer)/EGR4 -0.56 0.52 0.67 1 -0.9 335 336
FOS -0.35 0.27 0.26 1 -0.54 344 345
IFNG -0.096 0.3 0.56 8 -0.76 50 58
T cell activation -0.39 0.34 0.69 3 -0.67 252 255
MAF -0.008 0.14 -10000 0 -0.54 33 33
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.45 0.41 0.72 333 -0.63 4 337
TNF -0.67 0.48 -10000 0 -0.96 351 351
FASLG -0.88 0.78 0.82 4 -1.4 332 336
TBX21 0.028 0.15 0.29 12 -0.54 30 42
BATF3 0 0.001 -10000 0 -10000 0 0
PRKCQ 0.043 0.036 0.24 6 -10000 0 6
PTPN1 -0.047 0.16 0.42 1 -0.46 27 28
NFAT1-c-4/ICER1 -0.55 0.53 0.61 1 -0.91 330 331
GATA3 0.035 0.16 -10000 0 -0.54 33 33
T-helper 1 cell differentiation -0.094 0.3 0.56 8 -0.74 50 58
IL2RA -0.25 0.31 0.74 6 -0.66 86 92
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.051 0.16 -10000 0 -0.43 35 35
E2F1 0.055 0.048 0.25 1 -10000 0 1
PPARG -0.38 0.26 -10000 0 -0.54 369 369
SLC3A2 -0.049 0.16 -10000 0 -0.43 37 37
IRF4 0.039 0.028 -10000 0 -10000 0 0
PTGS2 -0.77 0.57 0.73 4 -1.1 364 368
CSF2 -0.67 0.53 0.79 4 -1 343 347
JunB/Fra1/NFAT1-c-4 -0.53 0.52 0.6 2 -0.88 323 325
IL4 -0.12 0.29 0.52 1 -0.77 53 54
IL5 -0.68 0.52 0.7 5 -1 346 351
IL2 -0.39 0.35 0.69 3 -0.68 248 251
IL3 -0.088 0.15 -10000 0 -0.91 13 13
RNF128 -0.21 0.33 0.28 12 -0.63 191 203
NFATC1 -0.45 0.41 0.63 4 -0.72 332 336
CDK4 0.28 0.28 0.55 160 -0.64 2 162
PTPRK -0.087 0.24 -10000 0 -0.65 60 60
IL8 -0.66 0.53 0.74 5 -0.99 340 345
POU2F1 0.033 0.015 -10000 0 -10000 0 0
Endothelins

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
AKT1 -0.1 0.17 -10000 0 -0.35 140 140
PTK2B 0.027 0.014 -10000 0 -10000 0 0
mol:Ca2+ -0.17 0.29 -10000 0 -0.7 85 85
EDN1 -0.16 0.25 -10000 0 -0.54 153 153
EDN3 -0.39 0.25 -10000 0 -0.54 375 375
EDN2 0.098 0.078 -10000 0 -0.54 1 1
HRAS/GDP -0.25 0.23 -10000 0 -0.5 183 183
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.13 0.18 -10000 0 -0.4 114 114
ADCY4 -0.083 0.15 0.34 2 -0.3 145 147
ADCY5 -0.08 0.15 0.35 1 -0.3 142 143
ADCY6 -0.081 0.15 0.34 2 -0.3 142 144
ADCY7 -0.077 0.15 0.34 2 -0.29 139 141
ADCY1 -0.081 0.15 -10000 0 -0.3 141 141
ADCY2 -0.082 0.16 0.32 3 -0.3 144 147
ADCY3 -0.081 0.15 0.35 1 -0.3 142 143
ADCY8 -0.067 0.14 0.35 1 -0.3 106 107
ADCY9 -0.075 0.14 -10000 0 -0.3 125 125
arachidonic acid secretion -0.52 0.34 -10000 0 -0.69 377 377
ETB receptor/Endothelin-1/Gq/GTP -0.21 0.21 -10000 0 -0.38 267 267
GNAO1 0.03 0.012 -10000 0 -10000 0 0
HRAS 0.032 0.013 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.092 0.16 -10000 0 -0.32 144 144
ETA receptor/Endothelin-1/Gs/GTP -0.088 0.15 -10000 0 -0.31 146 146
mol:GTP -0.007 0.008 -10000 0 -10000 0 0
COL3A1 -0.1 0.17 0.32 1 -0.35 140 141
EDNRB -0.21 0.29 -10000 0 -0.54 224 224
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.099 0.17 -10000 0 -0.35 141 141
CYSLTR1 -0.1 0.18 0.38 2 -0.35 142 144
SLC9A1 -0.068 0.12 -10000 0 -0.24 112 112
mol:GDP -0.27 0.25 -10000 0 -0.5 221 221
SLC9A3 -0.39 0.39 -10000 0 -0.74 235 235
RAF1 -0.36 0.27 -10000 0 -0.52 328 328
JUN -0.25 0.43 -10000 0 -1 109 109
JAK2 -0.1 0.17 -10000 0 -0.35 142 142
mol:IP3 -0.21 0.22 -10000 0 -0.44 180 180
ETA receptor/Endothelin-1 -0.12 0.2 -10000 0 -0.4 147 147
PLCB1 -0.048 0.2 -10000 0 -0.55 70 70
PLCB2 0.024 0.014 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.29 0.19 -10000 0 -0.4 376 376
FOS -0.68 0.43 -10000 0 -0.95 366 366
Gai/GDP -0.2 0.36 -10000 0 -0.95 83 83
CRK 0.031 0.01 -10000 0 -10000 0 0
mol:Ca ++ -0.26 0.26 -10000 0 -0.54 197 197
BCAR1 0.029 0.013 -10000 0 -10000 0 0
PRKCB1 -0.21 0.21 -10000 0 -0.43 191 191
GNAQ -0.008 0.009 -10000 0 -10000 0 0
GNAZ 0.026 0.063 -10000 0 -0.54 6 6
GNAL 0.03 0.045 -10000 0 -0.54 3 3
Gs family/GDP -0.24 0.22 -10000 0 -0.49 184 184
ETA receptor/Endothelin-1/Gq/GTP -0.097 0.15 -10000 0 -0.35 84 84
MAPK14 -0.22 0.22 -10000 0 -0.42 235 235
TRPC6 -0.18 0.31 -10000 0 -0.77 79 79
GNAI2 0.033 0.01 -10000 0 -10000 0 0
GNAI3 0.034 0.005 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 183 183
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.23 0.23 -10000 0 -0.43 246 246
ETB receptor/Endothelin-2 -0.11 0.22 -10000 0 -0.34 222 222
ETB receptor/Endothelin-3 -0.42 0.27 -10000 0 -0.53 414 414
ETB receptor/Endothelin-1 -0.27 0.28 -10000 0 -0.48 297 297
MAPK3 -0.61 0.39 -10000 0 -0.84 369 369
MAPK1 -0.62 0.41 -10000 0 -0.86 370 370
Rac1/GDP -0.25 0.23 -10000 0 -0.5 181 181
cAMP biosynthetic process -0.031 0.15 0.4 5 -0.34 30 35
MAPK8 -0.18 0.3 -10000 0 -0.67 109 109
SRC 0.032 0.008 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.28 0.29 -10000 0 -0.55 231 231
p130Cas/CRK/Src/PYK2 -0.27 0.29 -10000 0 -0.58 196 196
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.25 0.23 -10000 0 -0.5 185 185
COL1A2 -0.23 0.27 0.43 1 -0.48 219 220
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.071 0.077 0.26 3 -0.4 3 6
mol:DAG -0.21 0.22 -10000 0 -0.44 181 181
MAP2K2 -0.47 0.32 -10000 0 -0.64 371 371
MAP2K1 -0.47 0.32 0.36 1 -0.64 371 372
EDNRA 0.006 0.057 -10000 0 -0.44 3 3
positive regulation of muscle contraction -0.091 0.14 -10000 0 -0.31 138 138
Gq family/GDP -0.21 0.22 -10000 0 -0.45 168 168
HRAS/GTP -0.26 0.24 -10000 0 -0.46 238 238
PRKCH -0.21 0.21 -10000 0 -0.45 170 170
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCA -0.2 0.21 -10000 0 -0.44 163 163
PRKCB -0.21 0.21 -10000 0 -0.43 194 194
PRKCE -0.21 0.21 -10000 0 -0.45 167 167
PRKCD -0.21 0.21 -10000 0 -0.45 170 170
PRKCG -0.21 0.21 0.3 1 -0.45 176 177
regulation of vascular smooth muscle contraction -0.81 0.51 -10000 0 -1.1 367 367
PRKCQ -0.2 0.21 -10000 0 -0.46 162 162
PLA2G4A -0.59 0.4 -10000 0 -0.78 378 378
GNA14 0.026 0.073 -10000 0 -0.55 4 4
GNA15 0.021 0.031 -10000 0 -10000 0 0
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA11 0.019 0.024 -10000 0 -10000 0 0
Rac1/GTP -0.092 0.16 -10000 0 -0.32 143 143
MMP1 0.17 0.15 0.41 84 -10000 0 84
EGFR-dependent Endothelin signaling events

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
HRAS 0.034 0.013 -9999 0 -10000 0 0
EGFR -0.27 0.29 -9999 0 -0.54 269 269
EGF/EGFR -0.3 0.26 -9999 0 -0.44 366 366
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.19 0.21 -9999 0 -0.36 263 263
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.032 0.038 -9999 0 -0.54 2 2
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.15 0.27 -9999 0 -0.54 164 164
EGF/EGFR dimer/SHC -0.23 0.23 -9999 0 -0.41 285 285
mol:GDP -0.19 0.21 -9999 0 -0.36 267 267
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.14 0.26 -9999 0 -0.54 153 153
GRB2/SOS1 0.048 0.019 -9999 0 -10000 0 0
HRAS/GTP -0.18 0.19 -9999 0 -0.34 259 259
SHC1 0.027 0.014 -9999 0 -10000 0 0
HRAS/GDP -0.18 0.2 -9999 0 -0.35 259 259
FRAP1 -0.2 0.17 -9999 0 -0.35 262 262
EGF/EGFR dimer -0.31 0.26 -9999 0 -0.47 357 357
SOS1 0.034 0.004 -9999 0 -10000 0 0
GRB2 0.034 0.018 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.088 0.21 -9999 0 -0.4 154 154
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.11 0.25 0.54 126 -10000 0 126
PI3K Class IB/PDE3B -0.11 0.25 -10000 0 -0.54 126 126
PDE3B -0.11 0.25 -10000 0 -0.54 126 126
IGF1 pathway

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
NCK2 0.034 0.007 -10000 0 -10000 0 0
PTK2 0.027 0.014 -10000 0 -10000 0 0
CRKL -0.17 0.2 -10000 0 -0.34 256 256
GRB2/SOS1/SHC 0.051 0.034 -10000 0 -10000 0 0
HRAS 0.034 0.013 -10000 0 -10000 0 0
IRS1/Crk -0.16 0.21 -10000 0 -0.34 259 259
IGF-1R heterotetramer/IGF1/PTP1B -0.13 0.21 -10000 0 -0.36 221 221
AKT1 -0.16 0.19 0.23 1 -0.47 96 97
BAD -0.16 0.18 0.22 1 -0.45 91 92
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.17 0.2 -10000 0 -0.35 247 247
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.16 0.21 -10000 0 -0.35 246 246
RAF1 -0.12 0.18 -10000 0 -0.45 74 74
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.12 0.22 -10000 0 -0.34 219 219
YWHAZ 0.026 0.018 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.17 0.23 -10000 0 -0.37 259 259
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
RPS6KB1 -0.15 0.18 0.23 1 -0.35 199 200
GNB2L1 0.034 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.099 0.16 0.3 2 -0.39 64 66
PXN 0.034 0.003 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.048 0.019 -10000 0 -10000 0 0
HRAS/GTP -0.11 0.18 -10000 0 -0.33 168 168
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.07 0.18 -10000 0 -0.3 159 159
IGF-1R heterotetramer -0.049 0.14 -10000 0 -0.64 21 21
IGF-1R heterotetramer/IGF1/IRS/Nck -0.15 0.22 -10000 0 -0.34 257 257
Crk/p130 Cas/Paxillin -0.13 0.21 -10000 0 -0.33 238 238
IGF1R -0.049 0.14 -10000 0 -0.65 21 21
IGF1 -0.27 0.3 -10000 0 -0.57 253 253
IRS2/Crk -0.22 0.26 -10000 0 -0.42 267 267
PI3K -0.15 0.24 -10000 0 -0.37 242 242
apoptosis 0.11 0.15 0.39 66 -0.28 2 68
HRAS/GDP 0.025 0.009 -10000 0 -10000 0 0
PRKCD -0.18 0.23 -10000 0 -0.4 234 234
RAF1/14-3-3 E -0.096 0.17 0.34 1 -0.39 73 74
BAD/14-3-3 -0.12 0.16 0.29 2 -0.42 66 68
PRKCZ -0.16 0.19 0.22 1 -0.35 224 225
Crk/p130 Cas/Paxillin/FAK1 -0.1 0.17 -10000 0 -0.4 79 79
PTPN1 0.037 0.03 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.19 0.23 -10000 0 -0.41 244 244
BCAR1 0.029 0.013 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.094 0.19 -10000 0 -0.33 181 181
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.034 0.004 -10000 0 -10000 0 0
IRS1/NCK2 -0.15 0.21 -10000 0 -0.34 257 257
GRB10 0.03 0.051 -10000 0 -0.54 4 4
PTPN11 -0.17 0.2 -10000 0 -0.35 246 246
IRS1 -0.18 0.22 -10000 0 -0.37 259 259
IRS2 -0.23 0.26 -10000 0 -0.44 274 274
IGF-1R heterotetramer/IGF1 -0.2 0.26 -10000 0 -0.45 247 247
GRB2 0.034 0.018 -10000 0 -10000 0 0
PDPK1 -0.16 0.21 -10000 0 -0.36 225 225
YWHAE 0.031 0.01 -10000 0 -10000 0 0
PRKD1 -0.22 0.28 -10000 0 -0.52 193 193
SHC1 0.027 0.014 -10000 0 -10000 0 0
Arf6 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
CENTA1/KIF3B 0.018 0.018 -10000 0 -0.34 1 1
ARNO/beta Arrestin1-2 -0.11 0.14 -10000 0 -0.26 245 245
EGFR -0.27 0.29 -10000 0 -0.54 269 269
EPHA2 0.026 0.062 -10000 0 -0.54 6 6
USP6 0.032 0.018 -10000 0 -10000 0 0
IQSEC1 0.033 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.31 0.26 -10000 0 -0.47 357 357
ARRB2 0.015 0.029 -10000 0 -0.33 3 3
mol:GTP 0.013 0.029 0.12 26 -10000 0 26
ARRB1 0.03 0.027 -10000 0 -0.54 1 1
FBXO8 0.033 0.007 -10000 0 -10000 0 0
TSHR 0.029 0.045 -10000 0 -0.54 3 3
EGF -0.15 0.27 -10000 0 -0.54 164 164
somatostatin receptor activity 0 0 -10000 0 -0.001 217 217
ARAP2 0 0 -10000 0 0 223 223
mol:GDP -0.14 0.14 -10000 0 -0.27 215 215
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 216 216
ITGA2B 0.033 0.012 -10000 0 -10000 0 0
ARF6 0.034 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.057 0.059 -10000 0 -0.32 6 6
ADAP1 0 0 -10000 0 0 135 135
KIF13B 0.027 0.029 -10000 0 -0.54 1 1
HGF/MET 0.006 0.13 -10000 0 -0.4 51 51
PXN 0.034 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.14 0.12 -10000 0 -0.26 214 214
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.26 0.24 -10000 0 -0.41 349 349
ADRB2 -0.26 0.29 -10000 0 -0.54 263 263
receptor agonist activity 0 0 -10000 0 0 208 208
actin filament binding 0 0 -10000 0 0 252 252
SRC 0.032 0.008 -10000 0 -10000 0 0
ITGB3 0.035 0.019 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -0.001 147 147
EFA6/PI-4-5-P2 0 0 -10000 0 -0.001 148 148
ARF6/GDP -0.03 0.084 -10000 0 -0.27 29 29
ARF6/GDP/GULP/ACAP1 -0.16 0.18 -10000 0 -0.35 200 200
alphaIIb/beta3 Integrin/paxillin/GIT1 0.081 0.031 -10000 0 -10000 0 0
ACAP1 0 0 -10000 0 -10000 0 0
ACAP2 0 0 -10000 0 0 237 237
LHCGR/beta Arrestin2 0.022 0.048 -10000 0 -0.47 3 3
EFNA1 0.028 0.016 -10000 0 -10000 0 0
HGF 0.034 0.01 -10000 0 -10000 0 0
CYTH3 0 0 -10000 0 -0.001 206 206
CYTH2 -0.002 0.002 -10000 0 -0.004 245 245
NCK1 0.034 0.005 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 0 138 138
endosomal lumen acidification 0 0 0.001 4 0 151 155
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.072 0.22 -10000 0 -0.54 94 94
GNAQ/ARNO -0.003 0.003 -10000 0 -0.007 140 140
mol:Phosphatidic acid 0 0 -10000 0 0 237 237
PIP3-E 0 0 -10000 0 0 307 307
MET -0.023 0.17 -10000 0 -0.54 50 50
GNA14 0.043 0.068 -10000 0 -0.54 4 4
GNA15 0.036 0.019 -10000 0 -10000 0 0
GIT1 0.032 0.011 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -0.001 175 175
GNA11 0.033 0.006 -10000 0 -10000 0 0
LHCGR 0.032 0.046 -10000 0 -0.54 3 3
AGTR1 -0.18 0.3 -10000 0 -0.54 207 207
desensitization of G-protein coupled receptor protein signaling pathway 0.022 0.048 -10000 0 -0.46 3 3
IPCEF1/ARNO -0.21 0.18 -10000 0 -0.32 355 355
alphaIIb/beta3 Integrin 0.05 0.019 -10000 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 0.57 0.46 1.1 106 -1.3 1 107
PLK1 0.23 0.2 0.65 41 -10000 0 41
BIRC5 0.37 0.25 0.69 123 -0.66 3 126
HSPA1B 0.57 0.46 1.1 136 -1.1 2 138
MAP2K1 0.17 0.13 0.34 129 -10000 0 129
BRCA2 0.6 0.49 1.2 121 -1.3 1 122
FOXM1 0.62 0.61 1.4 142 -1.4 2 144
XRCC1 0.57 0.47 1.2 104 -1.3 1 105
FOXM1B/p19 0.079 0.3 0.98 5 -1.1 3 8
Cyclin D1/CDK4 0.49 0.46 1 105 -0.94 7 112
CDC2 0.63 0.52 1.2 142 -1.1 2 144
TGFA 0.45 0.52 1 119 -0.96 18 137
SKP2 0.58 0.47 1.2 109 -1.3 1 110
CCNE1 0.087 0.063 0.23 45 -10000 0 45
CKS1B 0.62 0.5 1.2 144 -1 2 146
RB1 0.28 0.35 0.74 126 -0.85 6 132
FOXM1C/SP1 0.5 0.45 1 94 -1.2 4 98
AURKB 0.21 0.31 0.68 55 -0.83 20 75
CENPF 0.7 0.53 1.3 163 -1.3 1 164
CDK4 0.092 0.061 0.24 18 -10000 0 18
MYC 0.32 0.44 0.97 82 -0.87 10 92
CHEK2 0.17 0.13 0.35 123 -10000 0 123
ONECUT1 0.5 0.48 1.1 130 -0.98 4 134
CDKN2A -0.017 0.078 -10000 0 -0.23 17 17
LAMA4 0.56 0.48 1.1 110 -1.2 3 113
FOXM1B/HNF6 0.5 0.5 1.1 111 -1.2 4 115
FOS -0.12 0.65 1.1 45 -1 72 117
SP1 0.031 0.033 -10000 0 -0.2 6 6
CDC25B 0.58 0.47 1.2 115 -1.3 1 116
response to radiation 0.12 0.094 0.24 135 -10000 0 135
CENPB 0.57 0.46 1.1 111 -1.3 1 112
CENPA 0.64 0.51 1.2 140 -1.3 1 141
NEK2 0.71 0.52 1.3 170 -1.2 1 171
HIST1H2BA 0.57 0.46 1.1 108 -1.3 1 109
CCNA2 0.11 0.077 0.23 86 -10000 0 86
EP300 0.032 0.009 -10000 0 -10000 0 0
CCNB1/CDK1 0.61 0.52 1.3 116 -1.7 1 117
CCNB2 0.63 0.51 1.2 147 -1.3 1 148
CCNB1 0.64 0.54 1.3 134 -1.4 1 135
ETV5 0.54 0.52 1.1 110 -1.1 10 120
ESR1 0.38 0.61 1.2 94 -1 13 107
CCND1 0.51 0.51 1.1 138 -0.97 7 145
GSK3A 0.14 0.1 0.31 80 -10000 0 80
Cyclin A-E1/CDK1-2 0.21 0.13 0.38 133 -10000 0 133
CDK2 0.071 0.036 0.24 6 -10000 0 6
G2/M transition of mitotic cell cycle 0.14 0.12 0.27 179 -10000 0 179
FOXM1B/Cbp/p300 0.3 0.38 0.88 9 -1.2 2 11
GAS1 0.28 0.71 1.1 91 -1.1 53 144
MMP2 0.56 0.48 1.1 114 -1.2 5 119
RB1/FOXM1C 0.46 0.46 1 112 -1 6 118
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
Nongenotropic Androgen signaling

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
PTK2 0.006 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.011 0.13 -10000 0 -0.32 66 66
regulation of S phase of mitotic cell cycle -0.045 0.13 -10000 0 -0.3 91 91
GNAO1 0.029 0.012 -10000 0 -10000 0 0
HRAS 0.032 0.013 -10000 0 -10000 0 0
SHBG/T-DHT 0.021 0.008 -10000 0 -10000 0 0
PELP1 0.029 0.01 -10000 0 -10000 0 0
AKT1 0.011 0.014 -10000 0 -10000 0 0
MAP2K1 -0.11 0.11 -10000 0 -0.36 61 61
T-DHT/AR -0.033 0.14 -10000 0 -0.4 67 67
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.005 0.003 -10000 0 -0.007 363 363
GNAI2 0.033 0.01 -10000 0 -10000 0 0
GNAI3 0.033 0.005 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 183 183
mol:GDP -0.079 0.16 -10000 0 -0.47 67 67
cell proliferation -0.3 0.21 -10000 0 -0.43 334 334
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
FOS -0.57 0.37 -10000 0 -0.8 365 365
mol:Ca2+ -0.037 0.038 -10000 0 -0.075 231 231
MAPK3 -0.21 0.16 -10000 0 -0.33 280 280
MAPK1 -0.16 0.15 -10000 0 -0.39 84 84
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 -0.003 0.002 -10000 0 -0.004 344 344
cAMP biosynthetic process 0.018 0.027 -10000 0 -10000 0 0
GNG2 0.032 0.026 -10000 0 -0.54 1 1
potassium channel inhibitor activity -0.003 0.002 -10000 0 -0.004 344 344
HRAS/GTP -0.059 0.12 -10000 0 -0.33 64 64
actin cytoskeleton reorganization 0.015 0.095 -10000 0 -0.28 44 44
SRC 0.03 0.008 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.003 0.002 -10000 0 -0.004 344 344
PI3K 0.007 0.11 -10000 0 -0.31 51 51
apoptosis 0.3 0.22 0.42 361 -10000 0 361
T-DHT/AR/PELP1 -0.014 0.13 -10000 0 -0.35 66 66
HRAS/GDP -0.069 0.17 -10000 0 -0.46 66 66
CREB1 -0.32 0.23 -10000 0 -0.46 361 361
RAC1-CDC42/GTP 0.025 0.1 -10000 0 -0.29 44 44
AR -0.043 0.2 -10000 0 -0.55 66 66
GNB1 0.034 0.011 -10000 0 -10000 0 0
RAF1 -0.086 0.11 -10000 0 -0.34 61 61
RAC1-CDC42/GDP -0.032 0.17 -10000 0 -0.44 66 66
T-DHT/AR/PELP1/Src -0.004 0.13 -10000 0 -0.33 65 65
MAP2K2 -0.12 0.11 -10000 0 -0.36 61 61
T-DHT/AR/PELP1/Src/PI3K -0.046 0.13 -10000 0 -0.3 91 91
GNAZ 0.025 0.062 -10000 0 -0.54 6 6
SHBG 0.03 0.011 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.11 0.19 -10000 0 -0.47 78 78
mol:T-DHT -0.001 0.002 -10000 0 -0.004 86 86
RAC1 0.034 0.005 -10000 0 -10000 0 0
GNRH1 -0.001 0.056 0.14 1 -0.4 10 11
Gi family/GTP -0.1 0.14 -10000 0 -0.26 187 187
CDC42 0.033 0.007 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.11 0.11 0.52 5 -10000 0 5
SMARCC2 0.034 0.004 -10000 0 -10000 0 0
SMARCC1 0.035 0.019 -10000 0 -10000 0 0
TBX21 -0.12 0.22 0.41 1 -0.84 31 32
SUMO2 0.001 0.025 -10000 0 -10000 0 0
STAT1 (dimer) 0.072 0.069 0.28 25 -10000 0 25
FKBP4 0.037 0.026 -10000 0 -10000 0 0
FKBP5 0.025 0.082 -10000 0 -0.54 10 10
GR alpha/HSP90/FKBP51/HSP90 0.13 0.14 0.31 62 -0.34 5 67
PRL -0.06 0.11 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.21 0.26 0.52 176 -10000 0 176
RELA -0.096 0.12 0.32 1 -0.27 28 29
FGG 0.23 0.23 0.46 195 -10000 0 195
GR beta/TIF2 0.11 0.14 0.3 106 -0.33 4 110
IFNG -0.39 0.34 0.48 3 -0.69 237 240
apoptosis -0.25 0.18 -10000 0 -0.55 37 37
CREB1 0.058 0.041 -10000 0 -10000 0 0
histone acetylation 0.036 0.14 0.4 38 -0.32 10 48
BGLAP -0.092 0.14 -10000 0 -0.59 2 2
GR/PKAc 0.15 0.14 0.35 43 -0.31 3 46
NF kappa B1 p50/RelA -0.16 0.2 0.48 3 -0.34 140 143
SMARCD1 0.034 0.004 -10000 0 -10000 0 0
MDM2 0.12 0.1 0.22 188 -10000 0 188
GATA3 0.043 0.16 -10000 0 -0.54 33 33
AKT1 0.028 0.024 -10000 0 -10000 0 0
CSF2 -0.008 0.11 -10000 0 -10000 0 0
GSK3B 0.001 0.027 -10000 0 -10000 0 0
NR1I3 -0.19 0.16 -10000 0 -0.58 6 6
CSN2 0.19 0.19 0.38 199 -10000 0 199
BRG1/BAF155/BAF170/BAF60A 0.084 0.027 -10000 0 -10000 0 0
NFATC1 0.037 0.038 -10000 0 -0.54 2 2
POU2F1 0.033 0.015 -10000 0 -10000 0 0
CDKN1A 0.022 0.12 -10000 0 -1.4 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.011 0.006 -10000 0 -10000 0 0
SFN 0.032 0.04 -10000 0 -0.54 2 2
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.14 0.14 0.35 28 -0.33 4 32
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.65 0.33 -10000 0 -0.8 426 426
JUN -0.21 0.24 0.38 2 -0.49 158 160
IL4 -0.12 0.15 -10000 0 -0.47 16 16
CDK5R1 0.028 0.014 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.35 0.24 -10000 0 -0.5 331 331
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.15 0.14 0.35 33 -0.33 4 37
cortisol/GR alpha (monomer) 0.29 0.31 0.58 227 -10000 0 227
NCOA2 0.028 0.015 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.42 0.26 -10000 0 -0.58 361 361
AP-1/NFAT1-c-4 -0.58 0.41 -10000 0 -0.82 348 348
AFP -0.18 0.2 -10000 0 -0.58 27 27
SUV420H1 0.032 0.01 -10000 0 -10000 0 0
IRF1 0.21 0.18 0.5 52 -10000 0 52
TP53 0.046 0.034 -10000 0 -0.51 1 1
PPP5C 0.036 0.017 -10000 0 -10000 0 0
KRT17 -0.9 0.65 -10000 0 -1.4 326 326
KRT14 -0.82 0.63 -10000 0 -1.3 324 324
TBP 0.039 0.011 -10000 0 -10000 0 0
CREBBP 0.18 0.15 0.3 288 -0.29 1 289
HDAC1 0.028 0.012 -10000 0 -10000 0 0
HDAC2 0.029 0.022 -10000 0 -10000 0 0
AP-1 -0.58 0.41 -10000 0 -0.82 349 349
MAPK14 0.01 0.023 -10000 0 -10000 0 0
MAPK10 -0.011 0.082 -10000 0 -0.55 10 10
MAPK11 -0.001 0.025 -10000 0 -10000 0 0
KRT5 -0.95 0.63 -10000 0 -1.4 353 353
interleukin-1 receptor activity -0.003 0.006 -10000 0 -10000 0 0
NCOA1 0.036 0.027 -10000 0 -0.54 1 1
STAT1 0.072 0.069 0.28 25 -10000 0 25
CGA -0.084 0.16 0.42 1 -0.48 10 11
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.15 0.19 0.37 103 -0.36 1 104
MAPK3 0 0.024 -10000 0 -10000 0 0
MAPK1 0.008 0.023 -10000 0 -10000 0 0
ICAM1 -0.26 0.25 0.59 2 -0.6 80 82
NFKB1 -0.095 0.11 0.28 3 -0.25 30 33
MAPK8 -0.15 0.19 0.57 1 -0.37 140 141
MAPK9 0.009 0.024 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.26 0.19 -10000 0 -0.58 39 39
BAX 0.028 0.076 -10000 0 -10000 0 0
POMC -0.14 0.19 0.57 1 -0.72 13 14
EP300 0.18 0.14 0.29 281 -10000 0 281
cortisol/GR alpha (dimer)/p53 0.24 0.26 0.52 188 -10000 0 188
proteasomal ubiquitin-dependent protein catabolic process 0.09 0.11 0.3 63 -10000 0 63
SGK1 0.23 0.17 0.36 302 -0.43 1 303
IL13 -0.29 0.25 0.5 1 -0.6 114 115
IL6 -0.75 0.48 0.62 1 -1 376 377
PRKACG 0.033 0.026 -10000 0 -0.54 1 1
IL5 -0.24 0.2 -10000 0 -0.65 32 32
IL2 -0.42 0.32 -10000 0 -0.68 275 275
CDK5 0.032 0.024 -10000 0 -10000 0 0
PRKACB 0.035 0.082 -10000 0 -0.54 8 8
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
IL8 -0.24 0.26 0.5 5 -0.5 186 191
CDK5R1/CDK5 0.037 0.022 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.096 0.18 0.43 3 -0.39 33 36
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.25 0.25 0.51 200 -10000 0 200
SMARCA4 0.035 0.012 -10000 0 -10000 0 0
chromatin remodeling 0.17 0.16 0.34 186 -10000 0 186
NF kappa B1 p50/RelA/Cbp -0.005 0.19 0.48 25 -0.35 5 30
JUN (dimer) -0.21 0.24 0.38 2 -0.49 158 160
YWHAH 0.033 0.014 -10000 0 -10000 0 0
VIPR1 -0.11 0.16 -10000 0 -0.54 26 26
NR3C1 0.19 0.2 0.39 185 -0.43 6 191
NR4A1 0.014 0.12 -10000 0 -0.55 24 24
TIF2/SUV420H1 0.039 0.023 -10000 0 -10000 0 0
MAPKKK cascade -0.25 0.18 -10000 0 -0.55 37 37
cortisol/GR alpha (dimer)/Src-1 0.27 0.26 0.52 219 -10000 0 219
PBX1 0.043 0.041 -10000 0 -10000 0 0
POU1F1 0.038 0.026 -10000 0 -0.54 1 1
SELE -0.26 0.35 0.52 4 -0.7 128 132
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.17 0.16 0.34 186 -10000 0 186
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.25 0.25 0.51 200 -10000 0 200
mol:cortisol 0.18 0.17 0.33 239 -10000 0 239
MMP1 -0.023 0.35 -10000 0 -0.94 53 53
Signaling events mediated by PTP1B

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
PDGFRB 0.034 0.006 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.24 0.21 -10000 0 -0.4 259 259
PTP1B/AKT1 -0.16 0.15 0.25 1 -0.29 210 211
FYN 0.03 0.037 -10000 0 -0.54 2 2
p210 bcr-abl/PTP1B -0.19 0.16 0.25 1 -0.31 264 265
EGFR -0.29 0.28 -10000 0 -0.56 269 269
EGF/EGFR -0.36 0.26 -10000 0 -0.5 359 359
CSF1 0.034 0.008 -10000 0 -10000 0 0
AKT1 0.035 0.017 -10000 0 -10000 0 0
INSR 0.033 0.006 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.16 0.17 0.34 1 -0.31 209 210
Insulin Receptor/Insulin -0.11 0.13 -10000 0 -0.38 33 33
HCK 0.036 0.022 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
TYK2 -0.18 0.16 0.33 2 -0.31 221 223
EGF -0.18 0.26 -10000 0 -0.56 164 164
YES1 0.032 0.027 -10000 0 -0.54 1 1
CAV1 -0.37 0.23 -10000 0 -0.49 364 364
TXN 0.028 0.012 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.19 0.18 -10000 0 -0.41 133 133
cell migration 0.19 0.16 0.31 264 -0.25 1 265
STAT3 0.031 0.007 -10000 0 -10000 0 0
PRLR 0.074 0.064 0.19 2 -10000 0 2
ITGA2B 0.032 0.011 -10000 0 -10000 0 0
CSF1R 0.034 0.006 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.082 0.049 -10000 0 -10000 0 0
FGR 0.033 0.008 -10000 0 -10000 0 0
PTP1B/p130 Cas -0.17 0.16 0.24 1 -0.31 239 240
Crk/p130 Cas -0.17 0.16 -10000 0 -0.31 212 212
DOK1 -0.15 0.14 0.27 1 -0.34 95 96
JAK2 -0.081 0.14 -10000 0 -0.52 32 32
Jak2/Leptin Receptor/Leptin -0.25 0.2 -10000 0 -0.44 220 220
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
PTPN1 -0.19 0.16 0.25 1 -0.31 264 265
LYN 0.03 0.015 -10000 0 -10000 0 0
CDH2 0.057 0.055 -10000 0 -10000 0 0
SRC -0.051 0.12 -10000 0 -0.67 15 15
ITGB3 0.033 0.018 -10000 0 -10000 0 0
CAT1/PTP1B -0.14 0.18 0.36 1 -0.42 89 90
CAPN1 0.031 0.014 -10000 0 -10000 0 0
CSK 0.034 0.011 -10000 0 -10000 0 0
PI3K -0.12 0.16 -10000 0 -0.42 59 59
mol:H2O2 -0.005 0.006 -10000 0 -10000 0 0
STAT3 (dimer) -0.22 0.19 -10000 0 -0.4 203 203
negative regulation of transcription -0.08 0.14 0.24 1 -0.52 32 33
FCGR2A 0.03 0.025 -10000 0 -10000 0 0
FER 0.027 0.008 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.045 0.018 -10000 0 -10000 0 0
BLK 0.039 0.044 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.051 0.03 -10000 0 -10000 0 0
RHOA 0.029 0.007 -10000 0 -10000 0 0
LEPR -0.33 0.28 -10000 0 -0.54 321 321
BCAR1 0.029 0.013 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.034 0.018 -10000 0 -10000 0 0
mol:NADPH -0.006 0.004 -10000 0 -10000 0 0
TRPV6 -0.006 0.15 0.42 2 -0.4 41 43
PRL 0.037 0.009 -10000 0 -10000 0 0
SOCS3 0 0.25 -10000 0 -1.3 17 17
SPRY2 -0.32 0.28 -10000 0 -0.55 304 304
Insulin Receptor/Insulin/IRS1 0.015 0.13 -10000 0 -0.35 59 59
CSF1/CSF1R -0.17 0.16 -10000 0 -0.3 215 215
Ras protein signal transduction 0.09 0.18 0.66 39 -10000 0 39
IRS1 -0.034 0.19 -10000 0 -0.54 60 60
INS 0.033 0.007 -10000 0 -10000 0 0
LEP -0.24 0.29 -10000 0 -0.55 237 237
STAT5B -0.14 0.16 0.26 1 -0.35 99 100
STAT5A -0.14 0.16 0.26 1 -0.35 101 102
GRB2 0.034 0.018 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.18 0.16 0.24 1 -0.31 237 238
CSN2 0.079 0.062 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
LAT -0.035 0.076 -10000 0 -0.64 3 3
YBX1 0.044 0.028 -10000 0 -10000 0 0
LCK 0.048 0.044 -10000 0 -10000 0 0
SHC1 0.027 0.014 -10000 0 -10000 0 0
NOX4 0.051 0.055 -10000 0 -10000 0 0
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.051 0.038 -10000 0 -10000 0 0
PDGFRB 0.029 0.007 -10000 0 -10000 0 0
SPHK1 -0.042 0.14 -10000 0 -0.9 11 11
mol:S1P -0.045 0.14 0.3 1 -0.82 11 12
S1P1/S1P/Gi -0.29 0.29 0.33 5 -0.49 305 310
GNAO1 0.003 0.028 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.25 0.26 0.41 3 -0.45 289 292
PLCG1 -0.27 0.27 0.34 5 -0.47 292 297
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.029 0.007 -10000 0 -10000 0 0
GNAI2 0.004 0.029 -10000 0 -10000 0 0
GNAI3 0.005 0.029 -10000 0 -10000 0 0
GNAI1 -0.19 0.27 -10000 0 -0.56 183 183
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.004 0.04 -10000 0 -10000 0 0
S1P1/S1P -0.066 0.13 0.28 8 -0.66 11 19
negative regulation of cAMP metabolic process -0.28 0.28 0.33 5 -0.48 305 310
MAPK3 -0.37 0.35 0.36 9 -0.63 312 321
calcium-dependent phospholipase C activity -0.005 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
KDR 0.029 0.011 -10000 0 -10000 0 0
PLCB2 -0.055 0.12 0.32 6 -0.57 11 17
RAC1 0.034 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.065 0.1 -10000 0 -0.54 11 11
receptor internalization -0.065 0.12 0.24 5 -0.6 11 16
PTGS2 -0.62 0.53 0.43 4 -1 315 319
Rac1/GTP -0.064 0.1 -10000 0 -0.54 11 11
RHOA 0.033 0.007 -10000 0 -10000 0 0
VEGFA 0.045 0.048 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.28 0.28 0.33 5 -0.48 305 310
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.002 0.067 -10000 0 -0.56 6 6
MAPK1 -0.4 0.38 0.37 5 -0.67 317 322
S1P1/S1P/PDGFB-D/PDGFRB -0.08 0.14 0.34 8 -0.62 11 19
ABCC1 0.032 0.023 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.008 0.058 0.26 9 -0.35 2 11
NFATC2 0.009 0.055 0.26 9 -0.34 1 10
NFATC3 0.012 0.052 0.26 9 -10000 0 9
CD40LG -0.22 0.29 0.6 15 -0.51 191 206
PTGS2 -0.32 0.36 0.58 15 -0.61 271 286
JUNB 0.031 0.044 -10000 0 -0.54 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.013 0.032 -10000 0 -10000 0 0
CaM/Ca2+ 0.013 0.032 -10000 0 -10000 0 0
CALM1 0.033 0.019 -10000 0 -10000 0 0
JUN -0.067 0.22 -10000 0 -0.54 89 89
mol:Ca2+ -0.003 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.023 0.012 0.13 1 -10000 0 1
FOSL1 0.034 0.01 -10000 0 -10000 0 0
CREM 0.033 0.007 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.033 0.17 0.45 15 -0.35 57 72
FOS -0.35 0.27 0.19 1 -0.54 344 345
IFNG -0.2 0.31 0.64 18 -0.51 186 204
AP-1/NFAT1-c-4 -0.26 0.34 0.71 11 -0.58 201 212
FASLG -0.19 0.29 0.64 17 -0.48 182 199
NFAT1-c-4/ICER1 0.015 0.098 0.41 9 -0.28 1 10
IL2RA -0.21 0.3 0.62 16 -0.51 187 203
FKBP12/FK506 0.025 0.008 -10000 0 -10000 0 0
CSF2 -0.22 0.3 0.62 16 -0.51 190 206
JunB/Fra1/NFAT1-c-4 0.039 0.11 0.41 9 -0.29 4 13
IL4 -0.22 0.29 0.58 15 -0.51 192 207
IL2 -0.009 0.14 -10000 0 -0.97 11 11
IL3 -0.009 0.13 -10000 0 -0.74 13 13
FKBP1A 0.033 0.012 -10000 0 -10000 0 0
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.033 0.015 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

Figure S15.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S15.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.09 0.18 -10000 0 -0.58 61 61
PDGF/PDGFRA/CRKL -0.054 0.14 -10000 0 -0.4 64 64
positive regulation of JUN kinase activity 0.015 0.12 -10000 0 -0.32 44 44
CRKL 0.033 0.008 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.055 0.14 -10000 0 -0.41 65 65
AP1 -0.7 0.45 -10000 0 -0.97 366 366
mol:IP3 -0.085 0.14 -10000 0 -0.45 56 56
PLCG1 -0.085 0.14 -10000 0 -0.45 56 56
PDGF/PDGFRA/alphaV Integrin -0.055 0.14 -10000 0 -0.41 64 64
RAPGEF1 0.034 0.006 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.084 0.13 -10000 0 -0.45 56 56
CAV3 0.031 0.037 -10000 0 -0.54 2 2
CAV1 -0.38 0.26 -10000 0 -0.54 365 365
SHC/Grb2/SOS1 0.017 0.12 -10000 0 -0.33 44 44
PDGF/PDGFRA/Shf -0.053 0.14 -10000 0 -0.4 64 64
FOS -0.69 0.44 -10000 0 -0.95 366 366
JUN -0.13 0.16 -10000 0 -0.46 86 86
oligodendrocyte development -0.055 0.14 -10000 0 -0.41 64 64
GRB2 0.034 0.018 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:DAG -0.085 0.14 -10000 0 -0.45 56 56
PDGF/PDGFRA -0.09 0.18 -10000 0 -0.58 61 61
actin cytoskeleton reorganization -0.052 0.14 -10000 0 -0.4 64 64
SRF 0.031 0.014 -10000 0 -10000 0 0
SHC1 0.027 0.014 -10000 0 -10000 0 0
PI3K -0.028 0.18 -10000 0 -0.42 82 82
PDGF/PDGFRA/Crk/C3G 0.002 0.14 -10000 0 -0.36 61 61
JAK1 -0.065 0.13 -10000 0 -0.41 60 60
ELK1/SRF -0.065 0.12 0.33 1 -0.36 55 56
SHB 0.035 0.018 -10000 0 -10000 0 0
SHF 0.034 0.013 -10000 0 -10000 0 0
CSNK2A1 0.063 0.025 -10000 0 -10000 0 0
GO:0007205 -0.092 0.14 -10000 0 -0.46 62 62
SOS1 0.034 0.004 -10000 0 -10000 0 0
Ras protein signal transduction 0.015 0.12 -10000 0 -0.32 44 44
PDGF/PDGFRA/SHB -0.052 0.14 -10000 0 -0.4 64 64
PDGF/PDGFRA/Caveolin-1 -0.34 0.24 -10000 0 -0.46 376 376
ITGAV 0.033 0.028 -10000 0 -0.54 1 1
ELK1 -0.11 0.13 0.23 2 -0.44 60 62
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.054 0.14 -10000 0 -0.41 63 63
JAK-STAT cascade -0.065 0.13 -10000 0 -0.41 60 60
cell proliferation -0.053 0.14 -10000 0 -0.4 64 64
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 0.005 0.43 0.81 1 -0.73 77 78
HDAC7 0.007 0.015 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.003 0.37 0.83 4 -0.71 46 50
SMAD4 0.033 0.027 -10000 0 -0.54 1 1
ID2 0.002 0.43 -10000 0 -0.73 75 75
AP1 -0.33 0.27 -10000 0 -0.48 358 358
ABCG2 -0.014 0.44 -10000 0 -0.74 83 83
HIF1A 0.022 0.13 0.32 5 -0.29 15 20
TFF3 -0.049 0.44 -10000 0 -0.75 87 87
GATA2 0.021 0.049 -10000 0 -10000 0 0
AKT1 0.02 0.13 0.34 3 -0.22 7 10
response to hypoxia -0.004 0.11 0.24 20 -0.16 68 88
MCL1 -0.029 0.39 -10000 0 -0.73 74 74
NDRG1 -0.017 0.4 0.88 1 -0.74 69 70
SERPINE1 0.012 0.44 0.83 9 -0.73 76 85
FECH -0.002 0.42 -10000 0 -0.73 77 77
FURIN 0.006 0.43 -10000 0 -0.73 77 77
NCOA2 0.035 0.024 -10000 0 -10000 0 0
EP300 0.033 0.17 0.45 15 -0.3 29 44
HMOX1 0.009 0.44 0.83 7 -0.73 77 84
BHLHE40 -0.053 0.4 0.72 4 -0.73 77 81
BHLHE41 -0.053 0.4 0.72 4 -0.73 77 81
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.042 0.16 -10000 0 -0.39 3 3
ENG 0.045 0.14 0.46 1 -0.41 2 3
JUN -0.075 0.22 -10000 0 -0.55 89 89
RORA -0.006 0.43 -10000 0 -0.74 81 81
ABCB1 -0.29 0.47 -10000 0 -0.94 162 162
TFRC 0.007 0.43 0.85 6 -0.73 76 82
CXCR4 0.01 0.43 0.8 4 -0.73 76 80
TF -0.006 0.44 -10000 0 -0.76 79 79
CITED2 -0.005 0.43 -10000 0 -0.74 78 78
HIF1A/ARNT -0.069 0.44 0.9 4 -0.87 62 66
LDHA -0.01 0.13 -10000 0 -0.74 13 13
ETS1 -0.002 0.43 -10000 0 -0.73 77 77
PGK1 0.007 0.43 0.82 4 -0.73 77 81
NOS2 -0.053 0.4 0.72 4 -0.73 77 81
ITGB2 0.007 0.43 0.82 8 -0.73 76 84
ALDOA 0.004 0.42 -10000 0 -0.73 74 74
Cbp/p300/CITED2 -0.012 0.43 0.82 2 -0.81 60 62
FOS -0.36 0.27 -10000 0 -0.55 344 344
HK2 0.003 0.43 -10000 0 -0.73 77 77
SP1 -0.019 0.094 -10000 0 -0.2 69 69
GCK 0.065 0.22 0.7 1 -10000 0 1
HK1 0.004 0.43 -10000 0 -0.73 77 77
NPM1 0.001 0.43 -10000 0 -0.74 75 75
EGLN1 -0.023 0.4 -10000 0 -0.72 75 75
CREB1 0.04 0.01 -10000 0 -10000 0 0
PGM1 0 0.43 -10000 0 -0.73 76 76
SMAD3 0.034 0.01 -10000 0 -10000 0 0
EDN1 -0.4 0.6 0.62 1 -1.2 163 164
IGFBP1 0.002 0.43 -10000 0 -0.73 77 77
VEGFA 0.068 0.36 0.8 20 -0.61 44 64
HIF1A/JAB1 0.04 0.1 0.31 5 -0.41 4 9
CP -0.063 0.51 0.83 6 -0.79 119 125
CXCL12 -0.087 0.48 -10000 0 -0.8 115 115
COPS5 0.034 0.02 -10000 0 -10000 0 0
SMAD3/SMAD4 0.048 0.028 -10000 0 -0.4 1 1
BNIP3 -0.001 0.43 0.85 1 -0.73 78 79
EGLN3 0.02 0.44 0.83 12 -0.73 75 87
CA9 0.015 0.44 0.84 7 -0.73 77 84
TERT -0.012 0.42 -10000 0 -0.73 76 76
ENO1 0.003 0.43 -10000 0 -0.73 76 76
PFKL 0.002 0.43 -10000 0 -0.73 76 76
NCOA1 0.035 0.027 -10000 0 -0.54 1 1
ADM -0.1 0.5 -10000 0 -0.77 135 135
ARNT 0.02 0.098 -10000 0 -10000 0 0
HNF4A 0.036 0.009 -10000 0 -10000 0 0
ADFP -0.053 0.4 0.72 4 -0.73 77 81
SLC2A1 0.07 0.36 0.81 16 -0.6 45 61
LEP -0.14 0.48 -10000 0 -0.8 131 131
HIF1A/ARNT/Cbp/p300 -0.02 0.36 0.82 2 -0.73 46 48
EPO 0.069 0.32 0.82 10 -0.7 14 24
CREBBP 0.04 0.16 0.44 17 -0.28 14 31
HIF1A/ARNT/Cbp/p300/HDAC7 -0.012 0.35 0.79 6 -0.7 44 50
PFKFB3 -0.005 0.42 -10000 0 -0.74 75 75
NT5E -0.004 0.44 -10000 0 -0.76 76 76
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.026 0.058 -10000 0 -0.54 5 5
EPHB2 0.042 0.037 -10000 0 -10000 0 0
EFNB1 0.015 0.028 -10000 0 -0.4 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.049 0.18 -10000 0 -0.28 180 180
Ephrin B2/EPHB1-2 -0.075 0.19 -10000 0 -0.31 191 191
neuron projection morphogenesis -0.061 0.16 -10000 0 -0.27 180 180
Ephrin B1/EPHB1-2/Tiam1 -0.06 0.18 -10000 0 -0.3 186 186
DNM1 0.034 0.008 -10000 0 -10000 0 0
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.057 0.18 -10000 0 -0.57 56 56
YES1 -0.069 0.26 -10000 0 -0.79 56 56
Ephrin B1/EPHB1-2/NCK2 -0.06 0.18 -10000 0 -0.3 188 188
PI3K -0.045 0.22 -10000 0 -0.51 80 80
mol:GDP -0.06 0.18 -10000 0 -0.29 186 186
ITGA2B 0.033 0.012 -10000 0 -10000 0 0
endothelial cell proliferation 0.038 0.046 -10000 0 -0.34 6 6
FYN -0.071 0.26 -10000 0 -0.79 56 56
MAP3K7 -0.058 0.19 -10000 0 -0.6 56 56
FGR -0.065 0.26 -10000 0 -0.79 56 56
TIAM1 0.035 0.012 0.18 3 -10000 0 3
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
RGS3 0.034 0.005 -10000 0 -10000 0 0
cell adhesion -0.047 0.2 -10000 0 -0.55 56 56
LYN -0.065 0.25 -10000 0 -0.78 56 56
Ephrin B1/EPHB1-2/Src Family Kinases -0.07 0.24 -10000 0 -0.73 57 57
Ephrin B1/EPHB1-2 -0.061 0.21 -10000 0 -0.64 56 56
SRC -0.064 0.25 -10000 0 -0.78 57 57
ITGB3 0.035 0.019 -10000 0 -10000 0 0
EPHB1 -0.18 0.28 -10000 0 -0.54 192 192
EPHB4 0.035 0.032 -10000 0 -0.54 1 1
RAC1 0.034 0.005 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.038 0.046 -10000 0 -0.34 6 6
alphaIIb/beta3 Integrin 0.05 0.019 -10000 0 -10000 0 0
BLK -0.078 0.26 -10000 0 -0.8 56 56
HCK -0.064 0.25 -10000 0 -0.78 56 56
regulation of stress fiber formation 0.061 0.18 0.29 188 -10000 0 188
MAPK8 -0.056 0.18 -10000 0 -0.55 56 56
Ephrin B1/EPHB1-2/RGS3 -0.061 0.18 -10000 0 -0.3 183 183
endothelial cell migration -0.051 0.17 0.26 1 -0.51 58 59
NCK2 0.034 0.007 0.18 1 -10000 0 1
PTPN13 -0.027 0.2 -10000 0 -0.65 47 47
regulation of focal adhesion formation 0.061 0.18 0.29 188 -10000 0 188
chemotaxis 0.061 0.18 0.3 183 -10000 0 183
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
Rac1/GTP -0.054 0.17 -10000 0 -0.28 180 180
angiogenesis -0.061 0.2 -10000 0 -0.64 56 56
LCK -0.061 0.26 -10000 0 -0.78 57 57
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.11 0.079 -9999 0 -0.3 3 3
SMAD6-7/SMURF1 0.064 0.02 -9999 0 -10000 0 0
NOG 0.031 0.031 -9999 0 -0.54 1 1
SMAD9 -0.088 0.24 -9999 0 -0.66 64 64
SMAD4 0.032 0.026 -9999 0 -0.54 1 1
SMAD5 -0.1 0.19 -9999 0 -0.42 90 90
BMP7/USAG1 -0.24 0.2 -9999 0 -0.39 309 309
SMAD5/SKI -0.094 0.19 -9999 0 -0.42 83 83
SMAD1 0.004 0.09 -9999 0 -0.44 10 10
BMP2 -0.23 0.29 -9999 0 -0.54 230 230
SMAD1/SMAD1/SMAD4 0.03 0.087 -9999 0 -0.43 6 6
BMPR1A 0.031 0.044 -9999 0 -0.54 3 3
BMPR1B 0.088 0.071 -9999 0 -10000 0 0
BMPR1A-1B/BAMBI 0.081 0.13 -9999 0 -0.3 38 38
AHSG 0.033 0.007 -9999 0 -10000 0 0
CER1 0.032 0.011 -9999 0 -10000 0 0
BMP2-4/CER1 -0.17 0.23 -9999 0 -0.38 261 261
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.1 0.18 -9999 0 -0.4 93 93
BMP2-4 (homodimer) -0.21 0.25 -9999 0 -0.44 266 266
RGMB 0.033 0.007 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.02 0.19 -9999 0 -0.28 168 168
RGMA -0.053 0.2 -9999 0 -0.54 76 76
SMURF1 0.034 0.005 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.11 0.18 -9999 0 -0.4 112 112
BMP2-4/USAG1 -0.4 0.27 -9999 0 -0.51 408 408
SMAD6/SMURF1/SMAD5 -0.095 0.19 -9999 0 -0.43 80 80
SOSTDC1 -0.37 0.26 -9999 0 -0.54 359 359
BMP7/BMPR2/BMPR1A-1B 0.11 0.072 -9999 0 -0.32 3 3
SKI 0.033 0.007 -9999 0 -10000 0 0
BMP6 (homodimer) -0.16 0.27 -9999 0 -0.54 168 168
HFE2 0.031 0.038 -9999 0 -0.54 2 2
ZFYVE16 0.033 0.007 -9999 0 -10000 0 0
MAP3K7 0.032 0.009 -9999 0 -10000 0 0
BMP2-4/CHRD -0.17 0.23 -9999 0 -0.38 261 261
SMAD5/SMAD5/SMAD4 -0.096 0.19 -9999 0 -0.44 79 79
MAPK1 0.032 0.008 -9999 0 -10000 0 0
TAK1/TAB family -0.089 0.17 -9999 0 -0.36 99 99
BMP7 (homodimer) 0.043 0.043 -9999 0 -10000 0 0
NUP214 0.034 0.005 -9999 0 -10000 0 0
BMP6/FETUA -0.098 0.21 -9999 0 -0.39 171 171
SMAD1/SKI 0.015 0.095 -9999 0 -0.41 10 10
SMAD6 0.033 0.007 -9999 0 -10000 0 0
CTDSP2 0.034 0.006 -9999 0 -10000 0 0
BMP2-4/FETUA -0.17 0.23 -9999 0 -0.38 261 261
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 0.048 0.046 -9999 0 -10000 0 0
BMPR2 (homodimer) 0.034 0.005 -9999 0 -10000 0 0
GADD34/PP1CA 0.06 0.038 -9999 0 -0.34 2 2
BMPR1A-1B (homodimer) 0.084 0.063 -9999 0 -0.4 3 3
CHRDL1 -0.3 0.28 -9999 0 -0.54 301 301
ENDOFIN/SMAD1 0.015 0.097 -9999 0 -0.43 10 10
SMAD6-7/SMURF1/SMAD1 0.048 0.1 -9999 0 -0.48 6 6
SMAD6/SMURF1 0.034 0.005 -9999 0 -10000 0 0
BAMBI 0.017 0.16 -9999 0 -0.54 36 36
SMURF2 0.031 0.013 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.36 0.31 -9999 0 -0.54 354 354
BMP2-4/GREM1 -0.16 0.24 -9999 0 -0.37 266 266
SMAD7 0.033 0.007 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.078 0.23 -9999 0 -0.63 65 65
SMAD1/SMAD6 0.015 0.098 -9999 0 -0.43 10 10
TAK1/SMAD6 0.047 0.015 -9999 0 -10000 0 0
BMP7 0.043 0.043 -9999 0 -10000 0 0
BMP6 -0.16 0.27 -9999 0 -0.54 168 168
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.11 0.19 -9999 0 -0.41 102 102
PPM1A 0.033 0.006 -9999 0 -10000 0 0
SMAD1/SMURF2 0.012 0.093 -9999 0 -0.46 8 8
SMAD7/SMURF1 0.048 0.013 -9999 0 -10000 0 0
CTDSPL 0.031 0.036 -9999 0 -0.54 2 2
PPP1CA 0.034 0.021 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.034 0.005 -9999 0 -10000 0 0
PPP1R15A 0.032 0.036 -9999 0 -0.54 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.11 0.18 -9999 0 -0.4 104 104
CHRD 0.036 0.021 -9999 0 -10000 0 0
BMPR2 0.034 0.005 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.13 0.21 -9999 0 -0.45 114 114
BMP4 -0.04 0.2 -9999 0 -0.54 67 67
FST 0.032 0.039 -9999 0 -0.54 2 2
BMP2-4/NOG -0.16 0.22 -9999 0 -0.38 246 246
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.11 0.075 -9999 0 -0.3 3 3
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.2 0.19 -10000 0 -0.35 217 217
MAP3K8 -0.048 0.19 -10000 0 -0.55 65 65
FOS -0.098 0.12 -10000 0 -0.37 26 26
PRKCA -0.006 0.028 -10000 0 -10000 0 0
PTPN7 -0.002 0.044 -10000 0 -10000 0 0
HRAS 0.032 0.013 -10000 0 -10000 0 0
PRKCB -0.013 0.009 -10000 0 -0.018 364 364
NRAS 0.033 0.016 -10000 0 -10000 0 0
RAS family/GTP 0.029 0.038 -10000 0 -10000 0 0
MAPK3 -0.029 0.075 -10000 0 -0.61 3 3
MAP2K1 -0.055 0.089 -10000 0 -0.28 42 42
ELK1 -0.015 0.037 -10000 0 -10000 0 0
BRAF -0.016 0.037 -10000 0 -0.25 6 6
mol:GTP -0.004 0.003 -10000 0 -0.006 365 365
MAPK1 -0.051 0.12 -10000 0 -0.45 28 28
RAF1 -0.016 0.035 -10000 0 -0.25 5 5
KRAS 0.032 0.018 0.18 5 -10000 0 5
Plasma membrane estrogen receptor 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
GNB1/GNG2 0.009 0.16 -10000 0 -0.3 104 104
ER alpha/Gai/GDP/Gbeta gamma -0.16 0.24 -10000 0 -0.44 160 160
AKT1 -0.18 0.37 -10000 0 -0.78 134 134
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.18 0.38 -10000 0 -0.8 132 132
mol:Ca2+ -0.032 0.12 0.26 3 -0.42 18 21
IGF1R 0.011 0.12 -10000 0 -0.54 21 21
E2/ER alpha (dimer)/Striatin -0.018 0.17 0.23 1 -0.34 104 105
SHC1 0.027 0.014 -10000 0 -10000 0 0
apoptosis 0.17 0.35 0.74 134 -10000 0 134
RhoA/GTP -0.024 0.12 -10000 0 -0.27 81 81
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.13 0.23 0.31 1 -0.45 138 139
regulation of stress fiber formation 0.016 0.12 -10000 0 -0.25 20 20
E2/ERA-ERB (dimer) -0.021 0.17 -10000 0 -0.34 106 106
KRAS 0.034 0.018 0.18 6 -10000 0 6
G13/GTP -0.018 0.15 -10000 0 -0.3 102 102
pseudopodium formation -0.016 0.12 0.25 20 -10000 0 20
E2/ER alpha (dimer)/PELP1 -0.024 0.17 -10000 0 -0.34 107 107
GRB2 0.034 0.018 -10000 0 -10000 0 0
GNG2 0.032 0.026 -10000 0 -0.54 1 1
GNAO1 0.03 0.012 -10000 0 -10000 0 0
HRAS 0.034 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.14 0.25 -10000 0 -0.5 140 140
E2/ER beta (dimer) 0.024 0.005 -10000 0 -10000 0 0
mol:GDP -0.045 0.18 0.23 12 -0.39 105 117
mol:NADP -0.14 0.25 -10000 0 -0.5 140 140
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 -0.035 0.12 0.26 3 -0.43 18 21
IGF-1R heterotetramer 0.011 0.12 -10000 0 -0.54 21 21
PLCB1 -0.036 0.13 -10000 0 -0.33 47 47
PLCB2 0.002 0.087 -10000 0 -0.49 7 7
IGF1 -0.25 0.29 -10000 0 -0.54 252 252
mol:L-citrulline -0.14 0.25 -10000 0 -0.5 140 140
RHOA 0.033 0.007 -10000 0 -10000 0 0
Gai/GDP -0.14 0.28 -10000 0 -0.73 81 81
JNK cascade 0.024 0.005 -10000 0 -10000 0 0
BCAR1 0.029 0.013 -10000 0 -10000 0 0
ESR2 0.033 0.007 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -10000 0 0
ESR1 -0.058 0.26 -10000 0 -0.54 106 106
Gq family/GDP/Gbeta gamma 0.008 0.16 -10000 0 -0.82 15 15
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.029 0.14 -10000 0 -0.54 13 13
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.12 0.22 0.31 1 -0.45 109 110
GNAZ 0.026 0.063 -10000 0 -0.54 6 6
E2/ER alpha (dimer) -0.044 0.18 -10000 0 -0.39 110 110
STRN 0.034 0.027 -10000 0 -0.54 1 1
GNAL 0.03 0.045 -10000 0 -0.54 3 3
PELP1 0.031 0.01 -10000 0 -10000 0 0
MAPK11 0.016 0.006 -10000 0 -10000 0 0
GNAI2 0.033 0.01 -10000 0 -10000 0 0
GNAI3 0.034 0.005 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 183 183
HBEGF -0.11 0.23 0.37 7 -0.56 59 66
cAMP biosynthetic process -0.02 0.13 -10000 0 -0.28 102 102
SRC -0.14 0.23 0.3 4 -0.43 146 150
PI3K 0.005 0.13 -10000 0 -0.37 51 51
GNB1 0.034 0.011 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.02 0.18 -10000 0 -0.37 88 88
SOS1 0.034 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.21 0.21 -10000 0 -0.42 212 212
Gs family/GTP -0.011 0.14 -10000 0 -0.28 102 102
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.061 0.025 -10000 0 -10000 0 0
vasodilation -0.14 0.24 -10000 0 -0.48 140 140
mol:DAG -0.035 0.12 0.26 3 -0.43 18 21
Gs family/GDP/Gbeta gamma -0.04 0.16 -10000 0 -0.35 86 86
MSN -0.018 0.12 0.26 20 -10000 0 20
Gq family/GTP 0.003 0.093 -10000 0 -0.43 10 10
mol:PI-3-4-5-P3 -0.18 0.36 -10000 0 -0.76 132 132
NRAS 0.036 0.016 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.14 0.24 0.48 140 -10000 0 140
GRB2/SOS1 0.048 0.019 -10000 0 -10000 0 0
RhoA/GDP -0.026 0.19 -10000 0 -0.37 104 104
NOS3 -0.15 0.26 -10000 0 -0.53 140 140
GNA11 0.033 0.006 -10000 0 -10000 0 0
MAPKKK cascade -0.13 0.27 -10000 0 -0.57 130 130
E2/ER alpha (dimer)/PELP1/Src -0.14 0.24 0.32 2 -0.47 138 140
ruffle organization -0.016 0.12 0.25 20 -10000 0 20
ROCK2 -0.016 0.13 0.34 6 -10000 0 6
GNA14 0.043 0.068 -10000 0 -0.54 4 4
GNA15 0.036 0.019 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
MMP9 -0.097 0.22 0.39 8 -0.55 56 64
MMP2 -0.14 0.22 0.3 6 -0.55 61 67
IL4-mediated signaling events

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
BCL2L1 -0.14 0.62 0.93 3 -1.1 100 103
STAT6 (cleaved dimer) -0.23 0.54 -10000 0 -1.1 107 107
IGHG1 0.026 0.3 0.62 17 -0.6 10 27
IGHG3 -0.15 0.58 0.78 3 -1.1 107 110
AKT1 -0.026 0.35 0.65 1 -0.69 41 42
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.028 0.28 0.57 6 -0.83 14 20
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.024 0.37 0.64 6 -0.75 38 44
THY1 -0.14 0.62 1 5 -1.1 98 103
MYB -0.006 0.16 -10000 0 -0.54 40 40
HMGA1 0.037 0.022 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.003 0.4 0.72 14 -0.63 62 76
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP 0.001 0.34 0.63 6 -0.74 22 28
SP1 0.057 0.044 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.007 0.057 -10000 0 -0.55 1 1
STAT6 (dimer)/ETS1 -0.16 0.59 0.84 1 -1.1 105 106
SOCS1 -0.06 0.41 0.76 1 -0.72 81 82
SOCS3 -0.015 0.39 0.7 1 -1.1 21 22
FCER2 -0.14 0.52 0.87 6 -0.86 90 96
PARP14 0.042 0.032 -10000 0 -10000 0 0
CCL17 -0.12 0.64 1 10 -1.1 102 112
GRB2 0.034 0.018 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.03 0.29 0.59 9 -0.69 14 23
T cell proliferation -0.18 0.62 -10000 0 -1.1 108 108
IL4R/JAK1 -0.15 0.61 -10000 0 -1.1 96 96
EGR2 -0.51 0.86 0.98 4 -1.3 251 255
JAK2 0.03 0.089 0.27 1 -10000 0 1
JAK3 0.035 0.019 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
JAK1 0.035 0.047 -10000 0 -10000 0 0
COL1A2 0.038 0.31 0.67 8 -1.1 10 18
CCL26 -0.14 0.62 1.1 5 -1.1 102 107
IL4R -0.14 0.68 1.1 7 -1.2 97 104
PTPN6 0.015 0.044 0.19 3 -10000 0 3
IL13RA2 -0.15 0.63 0.97 4 -1.1 104 108
IL13RA1 0.031 0.091 0.27 1 -10000 0 1
IRF4 0.064 0.21 0.71 3 -0.68 7 10
ARG1 0.048 0.26 0.72 4 -1.1 4 8
CBL -0.015 0.36 0.66 6 -0.6 60 66
GTF3A 0.1 0.066 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
IL13RA1/JAK2 0.05 0.13 0.37 4 -10000 0 4
IRF4/BCL6 0.028 0.21 -10000 0 -0.66 9 9
CD40LG 0.048 0.033 0.31 2 -10000 0 2
MAPK14 -0.014 0.38 0.66 6 -0.65 57 63
mitosis -0.02 0.34 0.61 3 -0.65 40 43
STAT6 -0.15 0.76 1.2 15 -1.3 106 121
SPI1 0.043 0.033 -10000 0 -0.24 1 1
RPS6KB1 -0.003 0.33 0.65 5 -0.64 35 40
STAT6 (dimer) -0.15 0.76 1.2 15 -1.3 106 121
STAT6 (dimer)/PARP14 -0.17 0.64 -10000 0 -1.2 107 107
mast cell activation -0.006 0.027 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.018 0.36 0.62 8 -0.7 45 53
FRAP1 -0.026 0.35 0.65 1 -0.69 41 42
LTA -0.14 0.62 0.93 3 -1.1 102 105
FES 0.031 0.037 -10000 0 -0.54 2 2
T-helper 1 cell differentiation 0.14 0.74 1.2 107 -1.2 15 122
CCL11 -0.11 0.61 0.9 4 -1.1 96 100
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.01 0.34 0.62 8 -0.8 21 29
IL2RG 0.044 0.042 0.22 10 -10000 0 10
IL10 -0.1 0.63 1.1 7 -1.1 84 91
IRS1 -0.034 0.19 -10000 0 -0.54 60 60
IRS2 -0.1 0.24 -10000 0 -0.54 117 117
IL4 0.045 0.3 0.77 8 -1 14 22
IL5 -0.14 0.62 1 4 -1.1 97 101
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.061 0.55 0.98 14 -0.86 97 111
COL1A1 0.12 0.4 0.85 16 -1.1 18 34
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.16 0.62 -10000 0 -1.2 90 90
IL2R gamma/JAK3 0.063 0.039 -10000 0 -10000 0 0
TFF3 -0.27 0.73 0.93 3 -1.3 141 144
ALOX15 -0.14 0.62 0.93 3 -1.1 101 104
MYBL1 0.049 0.054 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.094 0.54 0.81 7 -0.91 100 107
SHC1 0.027 0.014 -10000 0 -10000 0 0
CEBPB 0.035 0.034 -10000 0 -0.39 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.042 0.36 0.62 6 -0.68 47 53
mol:PI-3-4-5-P3 -0.025 0.35 0.66 1 -0.69 41 42
PI3K -0.032 0.37 0.66 1 -0.74 41 42
DOK2 0.025 0.039 -10000 0 -0.54 2 2
ETS1 0.002 0.06 -10000 0 -0.51 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.039 0.28 0.57 9 -0.62 14 23
ITGB3 -0.14 0.62 0.97 4 -1.1 102 106
PIGR -0.39 0.84 1 11 -1.3 210 221
IGHE -0.042 0.1 0.18 11 -0.28 21 32
MAPKKK cascade 0.04 0.27 0.57 9 -0.61 14 23
BCL6 -0.026 0.17 -10000 0 -0.55 51 51
OPRM1 -0.14 0.62 0.93 3 -1.1 97 100
RETNLB -0.14 0.62 0.93 3 -1.1 96 99
SELP -0.29 0.82 0.98 10 -1.4 160 170
AICDA -0.14 0.59 0.88 2 -1.1 105 107
FAS signaling pathway (CD95)

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
SPTAN1 0.02 0.093 0.21 72 -10000 0 72
RFC1 0.02 0.088 0.21 74 -10000 0 74
PRKDC 0.04 0.11 0.23 107 -10000 0 107
RIPK1 0.04 0.009 -10000 0 -10000 0 0
CASP7 -0.04 0.11 -10000 0 -0.75 9 9
FASLG/FAS/FADD/FAF1 -0.024 0.091 0.26 9 -0.32 16 25
MAP2K4 -0.18 0.19 -10000 0 -0.45 89 89
mol:ceramide -0.075 0.12 0.27 1 -0.37 32 33
GSN -0.058 0.17 0.22 56 -0.34 107 163
FASLG/FAS/FADD/FAF1/Caspase 8 -0.032 0.097 0.32 3 -0.32 15 18
FAS -0.047 0.14 -10000 0 -0.56 33 33
BID -0.022 0.021 -10000 0 -10000 0 0
MAP3K1 -0.093 0.14 0.28 1 -0.47 23 24
MAP3K7 0.025 0.01 -10000 0 -10000 0 0
RB1 0.021 0.086 0.21 67 -10000 0 67
CFLAR 0.04 0.026 -10000 0 -0.52 1 1
HGF/MET -0.01 0.17 -10000 0 -0.36 90 90
ARHGDIB 0.023 0.096 0.22 72 -10000 0 72
FADD -0.008 0.028 -10000 0 -10000 0 0
actin filament polymerization 0.058 0.17 0.34 108 -0.22 56 164
NFKB1 -0.1 0.12 -10000 0 -0.65 8 8
MAPK8 -0.32 0.25 -10000 0 -0.46 359 359
DFFA 0.02 0.088 0.21 63 -10000 0 63
DNA fragmentation during apoptosis 0.019 0.089 0.21 70 -10000 0 70
FAS/FADD/MET -0.031 0.15 -10000 0 -0.39 66 66
CFLAR/RIP1 0.06 0.027 -10000 0 -0.37 1 1
FAIM3 0.034 0.029 -10000 0 -10000 0 0
FAF1 -0.017 0.033 -10000 0 -10000 0 0
PARP1 0.025 0.1 0.24 73 -10000 0 73
DFFB 0.019 0.089 0.21 70 -10000 0 70
CHUK -0.1 0.11 -10000 0 -0.61 8 8
FASLG 0.001 0.061 -10000 0 -0.55 1 1
FAS/FADD -0.033 0.1 -10000 0 -0.39 32 32
HGF 0.035 0.01 -10000 0 -10000 0 0
LMNA 0.022 0.1 0.42 15 -10000 0 15
CASP6 0.021 0.09 0.21 72 -10000 0 72
CASP10 -0.012 0.03 -10000 0 -10000 0 0
CASP3 0.02 0.1 0.26 68 -0.22 17 85
PTPN13 -0.019 0.17 -10000 0 -0.54 47 47
CASP8 -0.027 0.021 -10000 0 -10000 0 0
IL6 -0.88 0.56 -10000 0 -1.2 380 380
MET -0.022 0.17 -10000 0 -0.54 50 50
ICAD/CAD 0.011 0.075 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.076 0.13 0.27 1 -0.38 32 33
activation of caspase activity by cytochrome c -0.022 0.021 -10000 0 -10000 0 0
PAK2 0.017 0.099 0.23 74 -10000 0 74
BCL2 -0.07 0.22 -10000 0 -0.54 93 93
IL6-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
BCL2L1 -0.023 0.3 0.67 4 -0.72 32 36
CRP 0.002 0.32 0.68 10 -0.73 30 40
cell cycle arrest -0.052 0.34 0.65 7 -0.74 54 61
TIMP1 -0.012 0.28 0.66 9 -0.64 27 36
IL6ST 0.038 0.084 -10000 0 -0.54 9 9
Rac1/GDP -0.088 0.22 0.41 9 -0.44 80 89
AP1 -0.16 0.24 0.55 2 -0.56 72 74
GAB2 0.033 0.015 -10000 0 -10000 0 0
TNFSF11 -0.005 0.32 0.7 7 -0.73 28 35
HSP90B1 0.043 0.14 -10000 0 -0.89 7 7
GAB1 0.035 0.027 -10000 0 -0.54 1 1
MAPK14 -0.13 0.2 0.32 1 -0.54 61 62
AKT1 0.032 0.092 0.34 1 -0.49 3 4
FOXO1 0.005 0.13 -10000 0 -0.44 15 15
MAP2K6 -0.12 0.2 0.36 3 -0.45 86 89
mol:GTP 0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.055 0.24 0.47 11 -0.48 67 78
MITF -0.11 0.21 0.34 8 -0.42 98 106
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.034 0.005 -10000 0 -10000 0 0
A2M -0.16 0.49 -10000 0 -1.3 74 74
CEBPB 0.038 0.03 -10000 0 -0.54 1 1
GRB2/SOS1/GAB family/SHP2 -0.001 0.14 0.4 1 -0.48 21 22
STAT3 -0.071 0.36 0.65 7 -0.81 54 61
STAT1 0.035 0.12 -10000 0 -0.85 7 7
CEBPD -0.08 0.44 0.67 5 -1 71 76
PIK3CA 0.034 0.009 -10000 0 -10000 0 0
PI3K 0.007 0.13 -10000 0 -0.37 51 51
JUN -0.067 0.22 -10000 0 -0.54 89 89
PIAS3/MITF -0.1 0.2 0.36 3 -0.43 78 81
MAPK11 -0.12 0.2 0.32 1 -0.54 60 61
STAT3 (dimer)/FOXO1 -0.086 0.33 0.6 8 -0.67 72 80
GRB2/SOS1/GAB family -0.082 0.18 0.37 2 -0.45 44 46
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.14 0.19 0.3 5 -0.41 99 104
GRB2 0.036 0.019 -10000 0 -10000 0 0
JAK2 0.032 0.011 -10000 0 -10000 0 0
LBP 0.01 0.28 0.64 16 -0.62 23 39
PIK3R1 -0.019 0.17 -10000 0 -0.54 47 47
JAK1 0.038 0.013 -10000 0 -10000 0 0
MYC -0.014 0.38 0.7 12 -0.94 45 57
FGG -0.025 0.3 0.7 3 -0.74 29 32
macrophage differentiation -0.052 0.34 0.65 7 -0.74 54 61
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.15 0.19 -10000 0 -0.32 221 221
JUNB -0.03 0.3 0.66 2 -0.78 25 27
FOS -0.35 0.27 -10000 0 -0.54 344 344
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.12 0.22 0.35 12 -0.44 100 112
STAT1/PIAS1 -0.073 0.23 0.42 11 -0.43 78 89
GRB2/SOS1/GAB family/SHP2/PI3K 0.029 0.097 -10000 0 -0.41 10 10
STAT3 (dimer) -0.069 0.35 0.65 7 -0.8 54 61
PRKCD -0.033 0.26 0.54 12 -0.54 55 67
IL6R 0.03 0.031 -10000 0 -0.55 1 1
SOCS3 -0.15 0.24 -10000 0 -0.92 27 27
gp130 (dimer)/JAK1/JAK1/LMO4 0.073 0.12 0.31 2 -0.32 30 32
Rac1/GTP -0.077 0.23 0.43 10 -0.45 76 86
HCK 0.037 0.022 -10000 0 -10000 0 0
MAPKKK cascade 0.022 0.16 -10000 0 -0.57 24 24
bone resorption -0.002 0.31 0.68 9 -0.68 29 38
IRF1 -0.023 0.31 0.7 5 -0.74 28 33
mol:GDP -0.1 0.21 0.38 11 -0.42 95 106
SOS1 0.038 0.009 -10000 0 -10000 0 0
VAV1 -0.1 0.22 0.38 12 -0.42 97 109
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.15 0.2 -10000 0 -0.57 62 62
PTPN11 0.021 0.093 -10000 0 -0.81 5 5
IL6/IL6RA -0.23 0.2 -10000 0 -0.39 290 290
gp130 (dimer)/TYK2/TYK2/LMO4 0.067 0.11 0.29 1 -0.33 27 28
gp130 (dimer)/JAK2/JAK2/LMO4 0.063 0.11 0.29 1 -0.32 30 31
IL6 -0.37 0.27 0.22 1 -0.54 365 366
PIAS3 0.033 0.008 -10000 0 -10000 0 0
PTPRE 0.004 0.043 -10000 0 -0.52 1 1
PIAS1 0.033 0.007 -10000 0 -10000 0 0
RAC1 0.036 0.006 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.14 0.17 0.29 3 -0.37 103 106
LMO4 0.029 0.12 0.24 3 -0.54 21 24
STAT3 (dimer)/PIAS3 -0.066 0.33 0.62 6 -0.72 58 64
MCL1 0.07 0.12 0.52 2 -10000 0 2
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.025 0.12 0.24 1 -0.33 46 47
adherens junction organization -0.026 0.13 0.23 1 -0.32 55 56
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.14 0.18 0.32 3 -0.38 103 106
FMN1 -0.025 0.12 -10000 0 -0.31 54 54
mol:IP3 -0.025 0.1 -10000 0 -0.29 44 44
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.024 0.12 -10000 0 -0.32 54 54
CTNNB1 0.03 0.051 -10000 0 -0.54 4 4
AKT1 -0.021 0.11 -10000 0 -0.29 47 47
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.028 0.18 -10000 0 -0.51 42 42
CTNND1 0.033 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.021 0.11 0.26 1 -0.32 42 43
VASP -0.021 0.12 0.24 1 -0.32 45 46
ZYX -0.026 0.12 -10000 0 -0.31 54 54
JUB -0.025 0.12 -10000 0 -0.31 54 54
EGFR(dimer) -0.16 0.2 -10000 0 -0.32 265 265
E-cadherin/beta catenin-gamma catenin 0.035 0.091 -10000 0 -0.32 25 25
mol:PI-3-4-5-P3 -0.007 0.13 -10000 0 -0.3 52 52
PIK3CA 0.032 0.011 -10000 0 -10000 0 0
PI3K -0.007 0.13 -10000 0 -0.3 52 52
FYN -0.025 0.11 0.24 1 -0.38 24 25
mol:Ca2+ -0.024 0.099 -10000 0 -0.28 44 44
JUP 0.034 0.011 -10000 0 -10000 0 0
PIK3R1 -0.019 0.17 -10000 0 -0.54 47 47
mol:DAG -0.025 0.1 -10000 0 -0.29 44 44
CDH1 0.006 0.12 -10000 0 -0.54 22 22
RhoA/GDP -0.14 0.18 0.32 3 -0.38 103 106
establishment of polarity of embryonic epithelium -0.021 0.12 0.24 1 -0.31 45 46
SRC 0.033 0.008 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
EGFR -0.27 0.29 -10000 0 -0.54 269 269
CASR -0.023 0.099 0.24 2 -0.27 43 45
RhoA/GTP -0.006 0.1 0.24 1 -0.27 43 44
AKT2 -0.022 0.11 -10000 0 -0.29 49 49
actin cable formation -0.021 0.12 0.25 3 -0.31 45 48
apoptosis 0.018 0.12 0.32 47 -0.26 4 51
CTNNA1 0.034 0.007 -10000 0 -10000 0 0
mol:GDP -0.16 0.18 -10000 0 -0.32 248 248
PIP5K1A -0.023 0.11 -10000 0 -0.32 42 42
PLCG1 -0.025 0.1 -10000 0 -0.3 44 44
Rac1/GTP -0.14 0.19 -10000 0 -0.39 116 116
homophilic cell adhesion -0.001 0.004 -10000 0 -10000 0 0
EPHB forward signaling

Figure S25.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S25.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.048 0.033 0.23 2 -0.34 1 3
cell-cell adhesion 0.11 0.12 0.27 176 -10000 0 176
Ephrin B/EPHB2/RasGAP 0.081 0.067 -10000 0 -0.3 7 7
ITSN1 0.034 0.005 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
SHC1 0.027 0.014 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.044 0.027 -10000 0 -0.34 2 2
Ephrin B1/EPHB1 -0.1 0.19 -10000 0 -0.34 194 194
HRAS/GDP -0.083 0.16 -10000 0 -0.38 48 48
Ephrin B/EPHB1/GRB7 -0.056 0.18 -10000 0 -0.31 159 159
Endophilin/SYNJ1 0.018 0.05 0.26 1 -0.28 7 8
KRAS 0.034 0.018 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.056 0.19 -10000 0 -0.31 174 174
endothelial cell migration 0.026 0.11 -10000 0 -0.3 47 47
GRB2 0.034 0.018 -10000 0 -10000 0 0
GRB7 0.029 0.013 -10000 0 -10000 0 0
PAK1 0.008 0.064 0.3 5 -0.29 5 10
HRAS 0.034 0.013 -10000 0 -10000 0 0
RRAS 0.017 0.048 0.26 1 -0.28 6 7
DNM1 0.034 0.008 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.095 0.16 0.36 2 -0.29 190 192
lamellipodium assembly -0.11 0.12 -10000 0 -0.27 176 176
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.063 0.15 -10000 0 -0.41 37 37
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
EPHB2 0.043 0.037 -10000 0 -10000 0 0
EPHB3 0.035 0.016 -10000 0 -10000 0 0
EPHB1 -0.18 0.28 -10000 0 -0.54 192 192
EPHB4 0.035 0.032 -10000 0 -0.54 1 1
mol:GDP -0.084 0.14 -10000 0 -0.39 46 46
Ephrin B/EPHB2 0.067 0.059 -10000 0 -0.3 7 7
Ephrin B/EPHB3 0.061 0.054 -10000 0 -0.3 7 7
JNK cascade -0.092 0.16 0.39 4 -0.3 183 187
Ephrin B/EPHB1 -0.071 0.18 -10000 0 -0.3 190 190
RAP1/GDP -0.062 0.14 -10000 0 -0.36 41 41
EFNB2 0.026 0.058 -10000 0 -0.54 5 5
EFNB3 0.031 0.011 -10000 0 -10000 0 0
EFNB1 0.032 0.036 -10000 0 -0.54 2 2
Ephrin B2/EPHB1-2 -0.077 0.19 -10000 0 -0.32 191 191
RAP1B 0.033 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.062 0.17 -10000 0 -0.35 44 44
Rap1/GTP -0.075 0.15 -10000 0 -0.28 145 145
axon guidance 0.048 0.033 0.23 2 -0.34 1 3
MAPK3 -0.047 0.14 0.26 1 -0.38 32 33
MAPK1 -0.054 0.14 -10000 0 -0.38 33 33
Rac1/GDP -0.075 0.14 -10000 0 -0.37 44 44
actin cytoskeleton reorganization -0.077 0.12 -10000 0 -0.32 30 30
CDC42/GDP -0.074 0.14 -10000 0 -0.38 42 42
PI3K 0.031 0.12 -10000 0 -0.31 47 47
EFNA5 0.033 0.029 -10000 0 -0.54 1 1
Ephrin B2/EPHB4 0.038 0.046 -10000 0 -0.34 6 6
Ephrin B/EPHB2/Intersectin/N-WASP 0.019 0.068 -10000 0 -0.3 8 8
CDC42 0.033 0.007 -10000 0 -10000 0 0
RAS family/GTP -0.077 0.14 -10000 0 -0.27 153 153
PTK2 0.15 0.27 0.67 104 -10000 0 104
MAP4K4 -0.093 0.16 0.39 4 -0.3 183 187
SRC 0.033 0.008 -10000 0 -10000 0 0
KALRN 0.034 0.005 -10000 0 -10000 0 0
Intersectin/N-WASP 0.048 0.022 -10000 0 -0.4 1 1
neuron projection morphogenesis -0.055 0.14 0.45 5 -0.39 8 13
MAP2K1 -0.06 0.14 -10000 0 -0.4 33 33
WASL 0.033 0.026 -10000 0 -0.54 1 1
Ephrin B1/EPHB1-2/NCK1 -0.062 0.2 -10000 0 -0.32 191 191
cell migration -0.065 0.17 0.32 5 -0.44 35 40
NRAS 0.036 0.016 -10000 0 -10000 0 0
SYNJ1 0.018 0.051 0.26 1 -0.28 7 8
PXN 0.034 0.003 -10000 0 -10000 0 0
TF -0.014 0.068 0.25 1 -0.28 22 23
HRAS/GTP -0.062 0.17 -10000 0 -0.28 178 178
Ephrin B1/EPHB1-2 -0.073 0.19 -10000 0 -0.31 191 191
cell adhesion mediated by integrin -0.009 0.049 0.26 7 -0.2 11 18
RAC1 0.034 0.005 -10000 0 -10000 0 0
mol:GTP -0.062 0.18 -10000 0 -0.29 181 181
RAC1-CDC42/GTP -0.088 0.14 -10000 0 -0.27 164 164
RASA1 0.034 0.012 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.064 0.14 -10000 0 -0.36 42 42
ruffle organization -0.097 0.14 0.41 3 -0.47 8 11
NCK1 0.034 0.005 -10000 0 -10000 0 0
receptor internalization -0.006 0.05 0.25 1 -0.27 7 8
Ephrin B/EPHB2/KALRN 0.082 0.066 -10000 0 -0.3 7 7
ROCK1 0.024 0.038 0.19 17 -0.31 2 19
RAS family/GDP -0.085 0.095 -10000 0 -0.32 28 28
Rac1/GTP -0.089 0.15 -10000 0 -0.28 176 176
Ephrin B/EPHB1/Src/Paxillin -0.087 0.16 -10000 0 -0.29 177 177
PLK1 signaling events

Figure S26.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S26.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.035 0.043 0.12 4 -0.11 44 48
BUB1B 0.094 0.063 0.17 111 -10000 0 111
PLK1 0.046 0.035 0.11 54 -10000 0 54
PLK1S1 0.023 0.019 0.059 49 -10000 0 49
KIF2A 0.038 0.037 0.27 4 -10000 0 4
regulation of mitotic centrosome separation 0.046 0.035 0.11 54 -10000 0 54
GOLGA2 0.034 0.008 -10000 0 -10000 0 0
Hec1/SPC24 0.1 0.062 0.17 197 -10000 0 197
WEE1 0.049 0.077 0.22 1 -0.32 14 15
cytokinesis 0.13 0.082 0.21 159 -0.39 1 160
PP2A-alpha B56 0.14 0.11 -10000 0 -0.45 8 8
AURKA 0.051 0.04 0.14 9 -0.16 2 11
PICH/PLK1 0.13 0.095 0.24 171 -10000 0 171
CENPE 0.084 0.067 0.17 119 -10000 0 119
RhoA/GTP 0.024 0.006 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.039 0.037 0.27 4 -10000 0 4
PPP2CA 0.033 0.006 -10000 0 -10000 0 0
FZR1 0.034 0.009 -10000 0 -10000 0 0
TPX2 0.08 0.039 0.14 29 -10000 0 29
PAK1 0.043 0.044 -10000 0 -10000 0 0
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.033 0.007 -10000 0 -10000 0 0
CLSPN 0.044 0.054 0.15 10 -0.2 12 22
GORASP1 0.033 0.006 -10000 0 -10000 0 0
metaphase 0.001 0.004 0.015 39 -10000 0 39
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.023 0.019 0.059 49 -10000 0 49
G2 phase of mitotic cell cycle 0.001 0.003 0.016 7 -10000 0 7
STAG2 0.034 0.003 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.021 0.092 -10000 0 -0.5 15 15
spindle elongation 0.046 0.035 0.11 54 -10000 0 54
ODF2 0.037 0.015 -10000 0 -10000 0 0
BUB1 0.12 0.12 -10000 0 -0.47 10 10
TPT1 0.014 0.059 0.13 1 -0.17 41 42
CDC25C 0.083 0.067 0.17 7 -0.22 11 18
CDC25B 0.048 0.041 -10000 0 -10000 0 0
SGOL1 0.035 0.043 0.11 44 -0.12 4 48
RHOA 0.033 0.007 -10000 0 -10000 0 0
CCNB1/CDK1 0.091 0.067 0.24 27 -10000 0 27
CDC14B -0.002 0.065 -10000 0 -0.4 13 13
CDC20 0.083 0.069 0.18 175 -10000 0 175
PLK1/PBIP1 0.074 0.055 0.14 179 -10000 0 179
mitosis -0.001 0.003 0.033 2 -10000 0 2
FBXO5 0.038 0.044 0.16 22 -10000 0 22
CDC2 0.005 0.004 0.016 32 -10000 0 32
NDC80 0.11 0.074 -10000 0 -10000 0 0
metaphase plate congression 0.027 0.057 -10000 0 -0.21 24 24
ERCC6L 0.12 0.094 0.24 162 -10000 0 162
NLP/gamma Tubulin 0.025 0.025 0.092 11 -0.094 2 13
microtubule cytoskeleton organization 0.014 0.059 0.13 1 -0.17 42 43
G2/M transition DNA damage checkpoint 0 0.003 0.013 10 -10000 0 10
PPP1R12A 0.035 0.005 -10000 0 -10000 0 0
interphase 0 0.003 0.013 10 -10000 0 10
PLK1/PRC1-2 0.17 0.099 0.27 224 -10000 0 224
GRASP65/GM130/RAB1/GTP/PLK1 0.083 0.034 -10000 0 -10000 0 0
RAB1A 0.034 0.005 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.04 0.033 0.098 65 -10000 0 65
mitotic prometaphase 0.001 0.005 0.021 25 -10000 0 25
proteasomal ubiquitin-dependent protein catabolic process 0.051 0.045 -10000 0 -10000 0 0
microtubule-based process 0.12 0.066 0.17 307 -10000 0 307
Golgi organization 0.046 0.035 0.11 54 -10000 0 54
Cohesin/SA2 0.055 0.027 0.16 2 -10000 0 2
PPP1CB/MYPT1 0.051 0.01 -10000 0 -10000 0 0
KIF20A 0.13 0.071 0.18 328 -10000 0 328
APC/C/CDC20 0.094 0.066 0.18 169 -10000 0 169
PPP2R1A 0.034 0.006 -10000 0 -10000 0 0
chromosome segregation 0.073 0.054 0.14 179 -10000 0 179
PRC1 0.1 0.074 -10000 0 -10000 0 0
ECT2 0.072 0.074 0.18 121 -10000 0 121
C13orf34 0.039 0.031 0.096 53 -10000 0 53
NUDC 0.027 0.057 -10000 0 -0.21 23 23
regulation of attachment of spindle microtubules to kinetochore 0.093 0.063 0.16 150 -10000 0 150
spindle assembly 0.036 0.03 0.11 24 -10000 0 24
spindle stabilization 0.023 0.019 0.059 49 -10000 0 49
APC/C/HCDH1 0.021 0.059 -10000 0 -0.34 13 13
MKLP2/PLK1 0.12 0.066 0.17 307 -10000 0 307
CCNB1 0.087 0.07 -10000 0 -10000 0 0
PPP1CB 0.035 0.004 -10000 0 -10000 0 0
BTRC 0.037 0.021 -10000 0 -10000 0 0
ROCK2 0.04 0.05 0.21 1 -0.31 5 6
TUBG1 0.027 0.039 -10000 0 -0.17 12 12
G2/M transition of mitotic cell cycle 0.061 0.064 0.21 26 -10000 0 26
MLF1IP 0.071 0.066 0.14 247 -10000 0 247
INCENP 0.047 0.04 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.06 0.035 -10000 0 -10000 0 0
alphaV beta3 Integrin -0.23 0.18 -10000 0 -0.34 367 367
PTK2 -0.047 0.12 0.4 2 -0.47 7 9
IGF1R 0.011 0.12 -10000 0 -0.54 21 21
PI4KB 0.028 0.014 -10000 0 -10000 0 0
MFGE8 0.007 0.13 -10000 0 -0.54 25 25
SRC 0.033 0.008 -10000 0 -10000 0 0
CDKN1B -0.1 0.13 -10000 0 -0.57 27 27
VEGFA 0.05 0.047 -10000 0 -10000 0 0
ILK -0.087 0.096 -10000 0 -0.47 16 16
ROCK1 0.034 0.006 -10000 0 -10000 0 0
AKT1 -0.082 0.089 -10000 0 -0.45 15 15
PTK2B 0.027 0.051 0.3 6 -0.3 1 7
alphaV/beta3 Integrin/JAM-A -0.16 0.17 -10000 0 -0.3 271 271
CBL 0.03 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.064 0.031 -10000 0 -0.34 1 1
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.16 0.25 -10000 0 -0.39 252 252
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.039 0.06 -10000 0 -0.35 5 5
alphaV/beta3 Integrin/Syndecan-1 0.089 0.053 0.25 3 -0.34 1 4
PI4KA 0.033 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.3 0.25 -10000 0 -0.49 273 273
PI4 Kinase 0.039 0.022 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.1 0.068 0.25 8 -0.34 4 12
RPS6KB1 -0.28 0.23 0.59 1 -0.5 206 207
TLN1 0.033 0.006 -10000 0 -10000 0 0
MAPK3 -0.36 0.29 -10000 0 -0.56 328 328
GPR124 0.008 0.1 -10000 0 -0.54 17 17
MAPK1 -0.38 0.29 -10000 0 -0.56 345 345
PXN 0.034 0.003 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
alphaV/beta3 Integrin/Tumstatin 0.066 0.029 -10000 0 -0.34 1 1
cell adhesion 0.034 0.093 -10000 0 -0.3 31 31
ANGPTL3 0.033 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.072 0.038 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.011 0.12 -10000 0 -0.54 21 21
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
TGFBR2 -0.004 0.14 -10000 0 -0.54 34 34
ITGB3 0.035 0.019 -10000 0 -10000 0 0
IGF1 -0.25 0.29 -10000 0 -0.54 252 252
RAC1 0.034 0.005 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.039 0.08 -10000 0 -0.34 18 18
apoptosis 0.033 0.027 -10000 0 -0.54 1 1
CD47 0.022 0.08 -10000 0 -0.54 10 10
alphaV/beta3 Integrin/CD47 0.057 0.064 -10000 0 -0.34 11 11
VCL 0.034 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.056 0.096 0.25 2 -0.34 23 25
CSF1 0.034 0.008 -10000 0 -10000 0 0
PIK3C2A -0.084 0.091 -10000 0 -0.46 13 13
PI4 Kinase/Pyk2 -0.15 0.13 -10000 0 -0.27 229 229
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.089 0.045 -10000 0 -0.32 1 1
FAK1/Vinculin -0.033 0.11 0.41 2 -0.38 7 9
alphaV beta3/Integrin/ppsTEM5 0.04 0.081 -10000 0 -0.34 18 18
RHOA 0.033 0.007 -10000 0 -10000 0 0
VTN 0.032 0.011 -10000 0 -10000 0 0
BCAR1 0.029 0.013 -10000 0 -10000 0 0
FGF2 -0.39 0.25 -10000 0 -0.54 380 380
F11R -0.23 0.2 -10000 0 -0.4 295 295
alphaV/beta3 Integrin/Lactadherin 0.047 0.089 0.25 1 -0.34 22 23
alphaV/beta3 Integrin/TGFBR2 0.039 0.1 0.25 1 -0.34 33 34
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.069 0.041 -10000 0 -0.32 1 1
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.061 0.028 -10000 0 -0.31 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.13 0.068 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 0.056 0.048 0.29 1 -0.3 1 2
SDC1 0.073 0.065 -10000 0 -10000 0 0
VAV3 0.012 0.071 -10000 0 -0.3 20 20
PTPN11 0.034 0.004 -10000 0 -10000 0 0
IRS1 -0.034 0.19 -10000 0 -0.54 60 60
FAK1/Paxillin -0.032 0.12 0.38 3 -0.38 7 10
cell migration -0.033 0.1 0.36 3 -0.36 6 9
ITGAV 0.033 0.028 -10000 0 -0.54 1 1
PI3K -0.17 0.18 -10000 0 -0.31 269 269
SPP1 0.091 0.087 -10000 0 -0.54 3 3
KDR 0.034 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.033 0.027 -10000 0 -0.54 1 1
COL4A3 0.034 0.006 -10000 0 -10000 0 0
angiogenesis -0.37 0.28 0.31 1 -0.56 323 324
Rac1/GTP 0.031 0.068 -10000 0 -0.28 18 18
EDIL3 0.024 0.13 -10000 0 -0.54 22 22
cell proliferation 0.038 0.1 0.25 1 -0.34 33 34
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.28 0.53 0.97 6 -1.2 65 71
IL23A -0.24 0.48 1.1 6 -1 49 55
NF kappa B1 p50/RelA/I kappa B alpha -0.25 0.46 0.76 2 -1 63 65
positive regulation of T cell mediated cytotoxicity -0.27 0.52 1.1 8 -1.1 65 73
ITGA3 -0.23 0.47 0.96 6 -1 55 61
IL17F -0.18 0.35 0.68 11 -0.66 70 81
IL12B 0.007 0.082 0.3 8 -10000 0 8
STAT1 (dimer) -0.26 0.5 0.89 6 -1.1 63 69
CD4 -0.24 0.47 0.96 5 -1 57 62
IL23 -0.24 0.46 0.93 6 -1 49 55
IL23R -0.019 0.21 0.82 3 -1.1 10 13
IL1B -0.25 0.49 1 8 -1.1 52 60
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.21 0.47 0.93 8 -0.99 54 62
TYK2 0.003 0.06 0.27 3 -10000 0 3
STAT4 0.027 0.069 -10000 0 -0.54 7 7
STAT3 0.033 0.008 -10000 0 -10000 0 0
IL18RAP -0.006 0.16 -10000 0 -0.54 42 42
IL12RB1 0.004 0.06 0.27 3 -10000 0 3
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.009 0.074 0.27 5 -10000 0 5
IL23R/JAK2 -0.023 0.22 0.69 3 -1 10 13
positive regulation of chronic inflammatory response -0.27 0.52 1.1 8 -1.1 65 73
natural killer cell activation 0.001 0.014 0.08 2 -0.061 6 8
JAK2 0.004 0.076 0.32 4 -10000 0 4
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
NFKB1 0.034 0.009 -10000 0 -10000 0 0
RELA 0.034 0.009 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.23 0.44 0.9 7 -0.96 49 56
ALOX12B -0.24 0.46 1 4 -1 54 58
CXCL1 -0.64 0.73 1 8 -1.2 296 304
T cell proliferation -0.27 0.52 1.1 8 -1.1 65 73
NFKBIA 0.033 0.01 -10000 0 -10000 0 0
IL17A -0.12 0.3 0.65 13 -0.53 52 65
PI3K -0.28 0.47 0.78 2 -1 82 84
IFNG 0.022 0.074 0.18 64 -0.12 7 71
STAT3 (dimer) -0.26 0.46 0.77 2 -0.96 78 80
IL18R1 0.04 0.03 0.2 2 -0.54 1 3
IL23/IL23R/JAK2/TYK2/SOCS3 -0.13 0.34 0.77 11 -0.69 39 50
IL18/IL18R 0.065 0.14 0.29 22 -0.34 42 64
macrophage activation -0.013 0.028 0.076 20 -0.044 19 39
TNF -0.25 0.48 1.1 6 -1 56 62
STAT3/STAT4 -0.26 0.48 0.77 4 -1 66 70
STAT4 (dimer) -0.27 0.5 0.86 6 -1.1 68 74
IL18 0.047 0.046 -10000 0 -10000 0 0
IL19 -0.2 0.47 0.92 9 -0.99 53 62
STAT5A (dimer) -0.27 0.49 0.86 5 -1.1 66 71
STAT1 0.059 0.055 -10000 0 -10000 0 0
SOCS3 0.018 0.087 -10000 0 -0.54 12 12
CXCL9 -0.22 0.5 1.1 7 -1.1 58 65
MPO -0.23 0.47 1 5 -0.99 57 62
positive regulation of humoral immune response -0.27 0.52 1.1 8 -1.1 65 73
IL23/IL23R/JAK2/TYK2 -0.28 0.54 1.1 8 -1.2 65 73
IL6 -0.79 0.67 0.94 6 -1.2 363 369
STAT5A 0.032 0.026 -10000 0 -0.54 1 1
IL2 0.049 0.039 0.25 1 -0.52 1 2
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.014 0.08 2 -0.061 6 8
CD3E -0.24 0.46 0.99 5 -1 58 63
keratinocyte proliferation -0.27 0.52 1.1 8 -1.1 65 73
NOS2 -0.25 0.46 0.88 8 -0.95 68 76
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.049 0.077 0.25 33 -10000 0 33
STMN1 0.054 0.084 0.29 45 -10000 0 45
Aurora B/RasGAP/Survivin 0.11 0.077 0.27 1 -10000 0 1
Chromosomal passenger complex/Cul3 protein complex -0.071 0.13 0.21 27 -0.28 44 71
BIRC5 0.12 0.076 -10000 0 -10000 0 0
DES -0.012 0.13 -10000 0 -0.56 24 24
Aurora C/Aurora B/INCENP 0.075 0.052 0.23 14 -10000 0 14
Aurora B/TACC1 0.025 0.087 -10000 0 -0.32 24 24
Aurora B/PP2A 0.058 0.042 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.019 0.022 0.14 3 -10000 0 3
mitotic metaphase/anaphase transition -0.003 0.004 -10000 0 -10000 0 0
NDC80 0.1 0.1 0.28 84 -10000 0 84
Cul3 protein complex -0.23 0.18 -10000 0 -0.35 364 364
KIF2C 0.14 0.1 0.23 257 -10000 0 257
PEBP1 0.039 0.027 -10000 0 -0.55 1 1
KIF20A 0.12 0.07 0.18 328 -10000 0 328
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.056 0.041 -10000 0 -10000 0 0
SEPT1 0.035 0.023 -10000 0 -10000 0 0
SMC2 0.04 0.03 -10000 0 -10000 0 0
SMC4 0.046 0.042 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.063 0.16 0.32 11 -0.43 31 42
PSMA3 0.033 0.006 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.005 -10000 0 -10000 0 0
H3F3B 0.031 0.037 -10000 0 -10000 0 0
AURKB 0.05 0.054 0.2 1 -10000 0 1
AURKC 0.036 0.019 -10000 0 -10000 0 0
CDCA8 0.11 0.074 -10000 0 -10000 0 0
cytokinesis 0.18 0.15 0.35 200 -10000 0 200
Aurora B/Septin1 0.18 0.15 0.38 128 -10000 0 128
AURKA 0.077 0.068 -10000 0 -10000 0 0
INCENP 0.053 0.041 -10000 0 -10000 0 0
KLHL13 -0.38 0.26 -10000 0 -0.54 370 370
BUB1 0.15 0.053 0.2 13 -10000 0 13
hSgo1/Aurora B/Survivin 0.13 0.099 0.3 70 -10000 0 70
EVI5 0.036 0.026 -10000 0 -0.53 1 1
RhoA/GTP 0.22 0.14 0.35 213 -10000 0 213
SGOL1 0.073 0.065 -10000 0 -10000 0 0
CENPA 0.14 0.12 0.28 186 -10000 0 186
NCAPG 0 0 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.058 0.042 -10000 0 -10000 0 0
NCAPD2 0.035 0.021 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.059 0.041 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
NCAPH 0.079 0.067 -10000 0 -10000 0 0
NPM1 0.026 0.11 -10000 0 -0.76 4 4
RASA1 0.034 0.012 -10000 0 -10000 0 0
KLHL9 0.032 0.009 -10000 0 -10000 0 0
mitotic prometaphase 0.005 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.057 0.041 -10000 0 -10000 0 0
PPP1CC 0.034 0.004 -10000 0 -10000 0 0
Centraspindlin 0.24 0.15 0.37 247 -10000 0 247
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
NSUN2 0.027 0.093 0.26 1 -0.75 2 3
MYLK -0.071 0.17 -10000 0 -0.34 139 139
KIF23 0.12 0.075 0.2 1 -10000 0 1
VIM -0.007 0.13 -10000 0 -0.39 47 47
RACGAP1 0.081 0.066 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.025 0.11 -10000 0 -0.48 12 12
Chromosomal passenger complex 0.16 0.13 0.28 245 -10000 0 245
Chromosomal passenger complex/EVI5 0.14 0.11 0.36 25 -10000 0 25
TACC1 0.001 0.12 -10000 0 -0.54 24 24
PPP2R5D 0.034 0.006 -10000 0 -10000 0 0
CUL3 0.032 0.036 -10000 0 -0.54 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.036 0.19 -10000 0 -0.54 61 61
LAT2 -0.029 0.13 -10000 0 -0.35 49 49
AP1 -0.19 0.23 -10000 0 -0.46 150 150
mol:PIP3 0.006 0.19 0.37 23 -0.42 45 68
IKBKB 0.022 0.14 0.29 42 -0.27 33 75
AKT1 -0.006 0.2 0.33 75 -0.46 29 104
IKBKG 0.004 0.13 0.27 23 -0.26 36 59
MS4A2 -0.056 0.21 -10000 0 -0.53 83 83
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
MAP3K1 0.011 0.15 0.36 11 -0.4 26 37
mol:Ca2+ 0.014 0.16 0.31 32 -0.35 32 64
LYN 0.032 0.018 -10000 0 -10000 0 0
CBLB -0.029 0.13 -10000 0 -0.36 44 44
SHC1 0.027 0.014 -10000 0 -10000 0 0
RasGAP/p62DOK -0.091 0.18 -10000 0 -0.31 204 204
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.011 0.2 0.34 66 -0.34 90 156
PTPN13 -0.038 0.19 -10000 0 -0.59 27 27
PTPN11 0.033 0.022 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.002 0.16 0.35 20 -0.35 28 48
SYK 0.04 0.027 -10000 0 -10000 0 0
GRB2 0.034 0.018 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.039 0.15 -10000 0 -0.42 49 49
LAT -0.026 0.12 0.21 2 -0.34 47 49
PAK2 0.009 0.16 0.35 13 -0.42 27 40
NFATC2 -0.011 0.057 -10000 0 -0.69 1 1
HRAS 0.005 0.16 0.3 13 -0.44 29 42
GAB2 0.03 0.012 -10000 0 -10000 0 0
PLA2G1B 0.009 0.11 -10000 0 -0.83 7 7
Fc epsilon R1 -0.036 0.19 -10000 0 -0.42 94 94
Antigen/IgE/Fc epsilon R1 -0.031 0.17 0.23 1 -0.38 94 95
mol:GDP -0.023 0.15 0.28 2 -0.45 28 30
JUN -0.067 0.22 -10000 0 -0.54 89 89
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.55 47 47
FOS -0.36 0.27 -10000 0 -0.54 344 344
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.026 0.13 -10000 0 -0.35 53 53
CHUK 0.004 0.13 0.28 23 -0.27 36 59
KLRG1 -0.024 0.12 -10000 0 -0.32 45 45
VAV1 -0.028 0.13 0.22 2 -0.34 51 53
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.028 0.12 -10000 0 -0.35 48 48
negative regulation of mast cell degranulation -0.027 0.11 -10000 0 -0.3 44 44
BTK -0.024 0.15 -10000 0 -0.5 24 24
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.047 0.17 -10000 0 -0.37 92 92
GAB2/PI3K/SHP2 -0.062 0.15 -10000 0 -0.36 74 74
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.032 0.13 -10000 0 -0.35 52 52
RAF1 0.008 0.12 -10000 0 -0.9 7 7
Fc epsilon R1/FcgammaRIIB/SHIP -0.019 0.18 -10000 0 -0.36 94 94
FCER1G 0.031 0.021 -10000 0 -10000 0 0
FCER1A -0.044 0.19 -10000 0 -0.55 63 63
Antigen/IgE/Fc epsilon R1/Fyn -0.02 0.17 -10000 0 -0.36 92 92
MAPK3 0.01 0.11 -10000 0 -0.86 7 7
MAPK1 0.004 0.11 -10000 0 -0.82 7 7
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 -0.016 0.2 -10000 0 -0.63 31 31
DUSP1 -0.2 0.28 -10000 0 -0.54 208 208
NF-kappa-B/RelA 0.014 0.082 0.18 12 -0.18 21 33
actin cytoskeleton reorganization -0.013 0.18 -10000 0 -0.58 22 22
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.012 0.17 -10000 0 -0.44 39 39
FER -0.028 0.12 -10000 0 -0.35 48 48
RELA 0.034 0.005 -10000 0 -10000 0 0
ITK -0.002 0.069 -10000 0 -0.34 14 14
SOS1 0.034 0.004 -10000 0 -10000 0 0
PLCG1 0 0.16 0.31 8 -0.46 26 34
cytokine secretion -0.005 0.046 -10000 0 -10000 0 0
SPHK1 -0.026 0.12 -10000 0 -0.36 42 42
PTK2 -0.015 0.18 -10000 0 -0.62 22 22
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.039 0.16 -10000 0 -0.44 50 50
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.029 0.22 0.36 19 -0.5 54 73
MAP2K2 0.004 0.11 -10000 0 -0.84 7 7
MAP2K1 0.004 0.11 -10000 0 -0.84 7 7
MAP2K7 0.034 0.005 -10000 0 -10000 0 0
KLRG1/SHP2 -0.013 0.11 0.24 1 -0.37 23 24
MAP2K4 -0.076 0.32 -10000 0 -0.87 70 70
Fc epsilon R1/FcgammaRIIB -0.019 0.19 -10000 0 -0.38 94 94
mol:Choline -0.011 0.2 0.34 66 -0.34 90 156
SHC/Grb2/SOS1 0.01 0.14 -10000 0 -0.39 25 25
FYN 0.03 0.037 -10000 0 -0.54 2 2
DOK1 0.036 0.016 -10000 0 -10000 0 0
PXN -0.015 0.17 -10000 0 -0.56 21 21
HCLS1 -0.028 0.13 0.21 2 -0.35 48 50
PRKCB -0.003 0.16 0.3 26 -0.33 55 81
FCGR2B 0.026 0.039 -10000 0 -0.54 2 2
IGHE 0.001 0.008 -10000 0 -10000 0 0
KLRG1/SHIP -0.028 0.11 -10000 0 -0.3 44 44
LCP2 0.037 0.023 -10000 0 -10000 0 0
PLA2G4A -0.16 0.2 -10000 0 -0.35 219 219
RASA1 0.034 0.012 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.011 0.2 0.34 66 -0.34 90 156
IKK complex 0.023 0.12 0.28 37 -0.22 17 54
WIPF1 0.037 0.022 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.22 0.18 -10000 0 -0.35 325 325
fibroblast growth factor receptor signaling pathway -0.22 0.18 -10000 0 -0.35 325 325
LAMA1 0.033 0.01 -10000 0 -10000 0 0
PRNP 0.017 0.094 -10000 0 -0.54 14 14
GPC1/SLIT2 -0.009 0.15 -10000 0 -0.39 68 68
SMAD2 -0.001 0.084 0.28 1 -0.31 32 33
GPC1/PrPc/Cu2+ 0.033 0.064 -10000 0 -0.34 14 14
GPC1/Laminin alpha1 0.048 0.017 -10000 0 -10000 0 0
TDGF1 0.033 0.007 -10000 0 -10000 0 0
CRIPTO/GPC1 0.048 0.015 -10000 0 -10000 0 0
APP/GPC1 0.045 0.048 -10000 0 -0.4 5 5
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.019 0.019 -10000 0 -0.34 1 1
FLT1 0.032 0.013 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.04 0.1 -10000 0 -0.34 34 34
SERPINC1 0.031 0.024 -10000 0 -10000 0 0
FYN 0.018 0.025 -10000 0 -0.34 2 2
FGR 0.02 0.01 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.024 0.084 0.28 3 -0.36 10 13
SLIT2 -0.039 0.19 -10000 0 -0.54 64 64
GPC1/NRG -0.002 0.13 -10000 0 -0.33 62 62
NRG1 -0.019 0.16 -10000 0 -0.54 43 43
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.07 0.039 0.25 1 -10000 0 1
LYN 0.018 0.013 -10000 0 -10000 0 0
mol:Spermine 0.009 0.01 -10000 0 -10000 0 0
cell growth -0.22 0.18 -10000 0 -0.35 325 325
BMP signaling pathway -0.034 0.013 -10000 0 -10000 0 0
SRC 0.019 0.009 -10000 0 -10000 0 0
TGFBR1 0.036 0.016 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.033 0.2 -10000 0 -0.54 66 66
GPC1 0.034 0.013 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.035 0.016 -10000 0 -10000 0 0
VEGFA 0.05 0.047 -10000 0 -10000 0 0
BLK 0.025 0.032 -10000 0 -10000 0 0
HCK 0.022 0.018 -10000 0 -10000 0 0
FGF2 -0.39 0.25 -10000 0 -0.54 380 380
FGFR1 0.018 0.076 -10000 0 -0.54 9 9
VEGFR1 homodimer 0.032 0.013 -10000 0 -10000 0 0
TGFBR2 -0.004 0.14 -10000 0 -0.54 34 34
cell death 0.045 0.048 -10000 0 -0.4 5 5
ATIII/GPC1 0.043 0.026 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.006 0.16 -10000 0 -0.38 74 74
LCK 0.031 0.033 -10000 0 -10000 0 0
neuron differentiation -0.002 0.13 -10000 0 -0.33 62 62
PrPc/Cu2+ 0.013 0.069 -10000 0 -0.4 14 14
APP 0.03 0.06 -10000 0 -0.54 5 5
TGFBR2 (dimer) -0.004 0.14 -10000 0 -0.54 34 34
Insulin Pathway

Figure S32.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S32.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.16 0.2 -10000 0 -0.32 285 285
TC10/GTP -0.13 0.16 -10000 0 -0.28 274 274
Insulin Receptor/Insulin/IRS1/Shp2 0.04 0.14 -10000 0 -0.32 59 59
HRAS 0.034 0.013 -10000 0 -10000 0 0
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 0 0.19 -10000 0 -0.54 52 52
FOXO3 -0.031 0.16 -10000 0 -0.6 33 33
AKT1 -0.046 0.16 0.3 12 -0.45 22 34
INSR 0.039 0.014 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.091 0.073 0.36 23 -10000 0 23
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.03 0.051 -10000 0 -0.54 4 4
SORBS1 -0.28 0.29 -10000 0 -0.54 279 279
CRK 0.031 0.01 -10000 0 -10000 0 0
PTPN1 0.019 0.054 0.28 19 -10000 0 19
CAV1 -0.24 0.18 -10000 0 -0.33 368 368
CBL/APS/CAP/Crk-II/C3G -0.13 0.18 -10000 0 -0.3 278 278
Insulin Receptor/Insulin/IRS1/NCK2 0.041 0.13 -10000 0 -0.32 57 57
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.003 0.15 -10000 0 -0.3 93 93
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.017 0.097 0.36 1 -0.4 6 7
RPS6KB1 -0.04 0.14 0.27 15 -0.41 21 36
PARD6A 0.031 0.019 -10000 0 -10000 0 0
CBL 0.03 0.011 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.017 0.061 -10000 0 -0.56 5 5
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.012 0.15 0.26 1 -0.42 20 21
HRAS/GTP -0.009 0.077 -10000 0 -0.26 37 37
Insulin Receptor 0.039 0.014 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.038 0.12 -10000 0 -0.3 40 40
PRKCI 0.01 0.086 -10000 0 -0.5 7 7
Insulin Receptor/Insulin/GRB14/PDK1 -0.045 0.16 -10000 0 -0.31 113 113
SHC1 0.027 0.014 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.057 0.058 -10000 0 -0.48 5 5
PI3K 0.007 0.15 -10000 0 -0.3 93 93
NCK2 0.034 0.007 0.18 1 -10000 0 1
RHOQ 0.033 0.026 -10000 0 -0.54 1 1
mol:H2O2 0.001 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.025 0.009 -10000 0 -10000 0 0
AKT2 -0.047 0.16 0.28 15 -0.34 50 65
PRKCZ -0.007 0.081 -10000 0 -0.4 15 15
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.01 0.09 -10000 0 -0.28 45 45
F2RL2 0.046 0.065 -10000 0 -0.54 3 3
TRIP10 0.033 0.026 -10000 0 -0.54 1 1
Insulin Receptor/Insulin/Shc 0.055 0.036 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.043 0.026 -10000 0 -0.34 2 2
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.076 0.055 -10000 0 -10000 0 0
RAPGEF1 0.034 0.006 -10000 0 -10000 0 0
RASA1 0.034 0.012 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.14 0.18 -10000 0 -0.31 279 279
TC10/GDP 0.024 0.019 -10000 0 -0.4 1 1
Insulin Receptor/Insulin/SHC/GRB10 0.069 0.057 -10000 0 -0.32 4 4
INPP5D -0.037 0.096 -10000 0 -0.3 59 59
SOS1 0.034 0.004 -10000 0 -10000 0 0
SGK1 -0.009 0.012 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.034 0.004 -10000 0 -10000 0 0
IRS1 -0.034 0.19 -10000 0 -0.54 60 60
p62DOK/RasGAP 0.058 0.058 -10000 0 -0.48 5 5
INS 0.039 0.014 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.037 0.095 -10000 0 -0.29 59 59
GRB2 0.034 0.018 -10000 0 -10000 0 0
EIF4EBP1 -0.044 0.14 0.3 6 -0.4 21 27
PTPRA 0.038 0.013 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.043 0.026 -10000 0 -0.34 2 2
PDPK1 0.031 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.001 0.087 -10000 0 -0.25 41 41
Insulin Receptor/Insulin/IRS1 0.022 0.13 -10000 0 -0.32 59 59
Insulin Receptor/Insulin/IRS3 0.057 0.024 -10000 0 -10000 0 0
Par3/Par6 0.072 0.058 -10000 0 -0.3 5 5
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.045 0.24 0.59 2 -0.56 73 75
IHH 0.021 0.075 -10000 0 -10000 0 0
SHH Np/Cholesterol/GAS1 -0.068 0.15 -10000 0 -0.31 126 126
LRPAP1 0.033 0.007 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.067 0.15 0.31 126 -10000 0 126
SMO/beta Arrestin2 -0.002 0.19 0.41 2 -0.49 28 30
SMO -0.016 0.18 0.44 2 -0.5 29 31
AKT1 -0.021 0.19 -10000 0 -0.6 36 36
ARRB2 0.031 0.01 -10000 0 -10000 0 0
BOC -0.091 0.24 -10000 0 -0.54 111 111
ADRBK1 0.032 0.01 -10000 0 -10000 0 0
heart looping -0.016 0.18 0.44 2 -0.5 29 31
STIL 0.042 0.15 0.34 32 -0.34 7 39
DHH N/PTCH2 0.049 0.01 -10000 0 -10000 0 0
DHH N/PTCH1 0.006 0.16 0.38 2 -0.44 24 26
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
DHH 0.034 0.004 -10000 0 -10000 0 0
PTHLH -0.11 0.39 0.52 6 -0.9 94 100
determination of left/right symmetry -0.016 0.18 0.44 2 -0.5 29 31
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
skeletal system development -0.11 0.39 0.52 6 -0.89 94 100
IHH N/Hhip 0.038 0.053 -10000 0 -10000 0 0
DHH N/Hhip 0.05 0.011 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.016 0.18 0.44 2 -0.5 29 31
pancreas development 0.034 0.011 -10000 0 -10000 0 0
HHAT 0.024 0.059 -10000 0 -0.54 5 5
PI3K 0.005 0.13 -10000 0 -0.37 51 51
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.14 0.27 -10000 0 -0.54 158 158
somite specification -0.016 0.18 0.44 2 -0.5 29 31
SHH Np/Cholesterol/PTCH1 -0.01 0.12 -10000 0 -0.37 9 9
SHH Np/Cholesterol/PTCH2 0.024 0.037 -10000 0 -0.31 5 5
SHH Np/Cholesterol/Megalin -0.056 0.14 -10000 0 -0.32 110 110
SHH 0.01 0.043 -10000 0 -0.4 5 5
catabolic process -0.009 0.18 0.47 2 -0.36 82 84
SMO/Vitamin D3 0.01 0.17 0.41 16 -0.46 12 28
SHH Np/Cholesterol/Hhip 0.024 0.038 -10000 0 -0.31 5 5
LRP2 -0.12 0.26 -10000 0 -0.54 136 136
receptor-mediated endocytosis -0.061 0.2 0.35 9 -0.51 37 46
SHH Np/Cholesterol/BOC -0.038 0.13 -10000 0 -0.31 86 86
SHH Np/Cholesterol/CDO 0.019 0.049 -10000 0 -0.35 7 7
mesenchymal cell differentiation -0.024 0.038 0.31 5 -10000 0 5
mol:Vitamin D3 0.027 0.16 0.41 17 -0.37 9 26
IHH N/PTCH2 0.038 0.052 -10000 0 -10000 0 0
CDON 0.027 0.045 -10000 0 -0.54 3 3
IHH N/PTCH1 -0.001 0.18 0.47 2 -0.36 82 84
Megalin/LRPAP1 -0.071 0.2 -10000 0 -0.4 137 137
PTCH2 0.034 0.005 -10000 0 -10000 0 0
SHH Np/Cholesterol 0.014 0.034 -10000 0 -0.31 5 5
PTCH1 -0.009 0.18 0.47 2 -0.36 82 84
HHIP 0.034 0.011 -10000 0 -10000 0 0
S1P5 pathway

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:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.067 0.14 0.31 59 -10000 0 59
GNAI2 0.033 0.01 -10000 0 -10000 0 0
S1P/S1P5/G12 0.023 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.012 -10000 0 -10000 0 0
RhoA/GTP -0.067 0.14 -10000 0 -0.32 59 59
negative regulation of cAMP metabolic process -0.08 0.14 -10000 0 -0.25 186 186
GNAZ 0.026 0.063 -10000 0 -0.54 6 6
GNAI3 0.034 0.005 -10000 0 -10000 0 0
GNA12 0.034 0.005 -10000 0 -10000 0 0
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.081 0.14 -10000 0 -0.25 186 186
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 183 183
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.049 0.011 -10000 0 -10000 0 0
Necdin/E2F1 -0.045 0.18 -10000 0 -0.38 111 111
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.003 0.15 -10000 0 -0.31 89 89
NGF (dimer)/p75(NTR)/BEX1 -0.006 0.14 -10000 0 -0.33 75 75
NT-4/5 (dimer)/p75(NTR) -0.04 0.15 -10000 0 -0.38 79 79
IKBKB 0.028 0.013 -10000 0 -10000 0 0
AKT1 -0.032 0.16 0.33 3 -0.32 96 99
IKBKG 0.034 0.003 -10000 0 -10000 0 0
BDNF 0.038 0.047 -10000 0 -0.54 2 2
MGDIs/NGR/p75(NTR)/LINGO1 0.014 0.15 0.25 4 -0.34 72 76
FURIN 0.036 0.023 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.001 0.15 -10000 0 -0.34 75 75
LINGO1 0.056 0.052 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.033 0.029 -10000 0 -0.28 1 1
proBDNF (dimer) 0.038 0.047 -10000 0 -0.54 2 2
NTRK1 0.03 0.022 -10000 0 -10000 0 0
RTN4R 0.041 0.035 -10000 0 -10000 0 0
neuron apoptosis -0.012 0.16 0.41 4 -0.48 14 18
IRAK1 0.036 0.015 -10000 0 -10000 0 0
SHC1 -0.023 0.1 -10000 0 -0.34 50 50
ARHGDIA 0.033 0.011 -10000 0 -10000 0 0
RhoA/GTP 0.024 0.006 -10000 0 -10000 0 0
Gamma Secretase 0.074 0.054 -10000 0 -0.3 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.008 0.14 -10000 0 -0.33 82 82
MAGEH1 0.018 0.094 -10000 0 -0.54 14 14
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.078 0.2 -10000 0 -0.37 149 149
Mammalian IAPs/DIABLO 0.045 0.078 -10000 0 -0.31 17 17
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.044 0.036 -10000 0 -10000 0 0
APP 0.03 0.06 -10000 0 -0.54 5 5
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.033 0.007 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.01 0.12 -10000 0 -0.29 73 73
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.036 0.11 0.21 31 -0.27 74 105
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.016 0.094 -10000 0 -0.26 57 57
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.018 0.14 -10000 0 -0.34 75 75
NCSTN 0.028 0.014 -10000 0 -10000 0 0
mol:GTP -0.018 0.15 -10000 0 -0.35 78 78
PSENEN 0.035 0.015 -10000 0 -10000 0 0
mol:ceramide -0.021 0.13 -10000 0 -0.31 74 74
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.012 0.077 -10000 0 -0.21 56 56
p75(NTR)/beta APP -0.025 0.16 -10000 0 -0.4 76 76
BEX1 0.054 0.05 -10000 0 -10000 0 0
mol:GDP -0.053 0.12 -10000 0 -0.34 75 75
NGF (dimer) 0.004 0.13 -10000 0 -0.31 65 65
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.028 0.15 -10000 0 -0.31 70 70
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
RAC1/GTP -0.013 0.12 -10000 0 -0.29 74 74
MYD88 0.034 0.011 -10000 0 -10000 0 0
CHUK 0.034 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.017 0.15 -10000 0 -0.36 78 78
RHOB 0.032 0.037 -10000 0 -0.54 2 2
RHOA 0.033 0.007 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.058 0.036 -10000 0 -10000 0 0
NT3 (dimer) -0.12 0.26 -10000 0 -0.54 134 134
TP53 -0.028 0.13 0.37 8 -0.29 70 78
PRDM4 -0.017 0.13 -10000 0 -0.31 74 74
BDNF (dimer) 0.055 0.17 -10000 0 -0.31 70 70
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
SORT1 0.034 0.006 -10000 0 -10000 0 0
activation of caspase activity -0.007 0.14 -10000 0 -0.31 89 89
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0 0.13 -10000 0 -0.31 74 74
RHOC 0.034 0.005 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.029 0.14 0.31 5 -0.33 67 72
DIABLO 0.034 0.003 -10000 0 -10000 0 0
SMPD2 -0.022 0.13 -10000 0 -0.31 74 74
APH1B 0.032 0.027 -10000 0 -0.54 1 1
APH1A 0.031 0.028 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.017 0.14 -10000 0 -0.34 74 74
PSEN1 0.033 0.007 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.049 0.012 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.13 0.23 -10000 0 -0.44 171 171
MAPK8 -0.026 0.14 0.3 7 -0.33 65 72
MAPK9 -0.025 0.13 0.28 6 -0.32 64 70
APAF1 0.034 0.003 -10000 0 -10000 0 0
NTF3 -0.12 0.26 -10000 0 -0.54 134 134
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.099 0.24 -10000 0 -0.54 117 117
RAC1/GDP 0.025 0.004 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.009 0.14 -10000 0 -0.3 71 71
p75 CTF/Sortilin/TRAF6/NRIF 0.08 0.027 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.018 0.15 -10000 0 -0.35 78 78
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.027 0.14 -10000 0 -0.3 71 71
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.017 0.14 -10000 0 -0.31 75 75
PRKACB 0.035 0.082 -10000 0 -0.54 8 8
proBDNF (dimer)/p75 ECD 0.052 0.037 -10000 0 -0.4 2 2
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.016 0.11 -10000 0 -0.54 17 17
BIRC2 0.031 0.011 -10000 0 -10000 0 0
neuron projection morphogenesis -0.1 0.16 -10000 0 -0.4 99 99
BAD -0.025 0.15 0.43 7 -0.33 65 72
RIPK2 0.029 0.021 -10000 0 -10000 0 0
NGFR -0.054 0.2 -10000 0 -0.54 75 75
CYCS -0.008 0.13 0.26 7 -0.29 72 79
ADAM17 0.034 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.003 0.12 -10000 0 -0.31 61 61
BCL2L11 -0.025 0.15 0.42 8 -0.33 65 73
BDNF (dimer)/p75(NTR) -0.02 0.16 -10000 0 -0.4 76 76
PI3K -0.03 0.16 -10000 0 -0.34 99 99
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0 0.13 -10000 0 -0.31 74 74
NDNL2 0.033 0.007 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
PRKCI 0.035 0.017 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.04 0.15 -10000 0 -0.38 79 79
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.005 0.13 -10000 0 -0.31 74 74
TRAF6 0.034 0.006 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.031 0.027 -10000 0 -0.54 1 1
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.027 0.13 -10000 0 -0.33 74 74
SQSTM1 0.034 0.009 -10000 0 -10000 0 0
NGFRAP1 0.009 0.12 -10000 0 -0.54 22 22
CASP3 -0.023 0.14 0.39 9 -0.31 66 75
E2F1 0.05 0.047 -10000 0 -10000 0 0
CASP9 0.033 0.008 -10000 0 -10000 0 0
IKK complex 0.03 0.084 -10000 0 -0.3 1 1
NGF (dimer)/TRKA 0.022 0.016 -10000 0 -10000 0 0
MMP7 -0.042 0.19 -10000 0 -0.54 64 64
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.012 0.13 -10000 0 -0.3 73 73
MMP3 0.093 0.099 -10000 0 -0.54 5 5
APAF-1/Caspase 9 -0.033 0.1 -10000 0 -0.26 75 75
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.011 0.091 -10000 0 -0.26 46 46
epithelial cell differentiation 0.04 0.086 -10000 0 -0.29 26 26
CYFIP2 0.05 0.047 -10000 0 -10000 0 0
ENAH -0.008 0.071 0.28 5 -0.3 2 7
EGFR -0.27 0.29 -10000 0 -0.54 269 269
EPHA2 0.026 0.062 -10000 0 -0.54 6 6
MYO6 0 0.074 -10000 0 -0.28 25 25
CTNNB1 0.029 0.052 -10000 0 -0.54 4 4
ABI1/Sra1/Nap1 0.074 0.035 -10000 0 -10000 0 0
AQP5 -0.14 0.24 -10000 0 -0.49 151 151
CTNND1 0.033 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.002 0.072 -10000 0 -0.28 25 25
regulation of calcium-dependent cell-cell adhesion -0.024 0.1 -10000 0 -0.29 63 63
EGF -0.15 0.27 -10000 0 -0.54 164 164
NCKAP1 0.034 0.005 -10000 0 -10000 0 0
AQP3 -0.053 0.18 -10000 0 -0.49 64 64
cortical microtubule organization 0.04 0.086 -10000 0 -0.29 26 26
GO:0000145 -0.022 0.064 -10000 0 -0.27 25 25
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.045 0.089 -10000 0 -0.29 26 26
MLLT4 0.029 0.046 -10000 0 -0.54 3 3
ARF6/GDP -0.03 0.059 -10000 0 -0.27 25 25
ARF6 0.034 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.057 0.059 -10000 0 -0.32 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.002 0.069 -10000 0 -0.26 23 23
PVRL2 0.039 0.027 -10000 0 -10000 0 0
ZYX -0.003 0.073 -10000 0 -0.28 26 26
ARF6/GTP 0.062 0.061 -10000 0 -0.3 6 6
CDH1 0.006 0.12 -10000 0 -0.54 22 22
EGFR/EGFR/EGF/EGF -0.23 0.2 -10000 0 -0.35 357 357
RhoA/GDP 0.04 0.084 -10000 0 -0.28 25 25
actin cytoskeleton organization -0.022 0.067 -10000 0 -0.28 25 25
IGF-1R heterotetramer 0.011 0.12 -10000 0 -0.54 21 21
GIT1 0.032 0.011 -10000 0 -10000 0 0
IGF1R 0.011 0.12 -10000 0 -0.54 21 21
IGF1 -0.25 0.29 -10000 0 -0.54 252 252
DIAPH1 0.057 0.12 -10000 0 -0.56 7 7
Wnt receptor signaling pathway -0.04 0.086 0.29 26 -10000 0 26
RHOA 0.033 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.03 0.059 -10000 0 -0.27 25 25
CTNNA1 0.033 0.006 -10000 0 -10000 0 0
VCL -0.022 0.069 -10000 0 -0.28 25 25
EFNA1 0.028 0.016 -10000 0 -10000 0 0
LPP -0.024 0.066 -10000 0 -0.28 25 25
Ephrin A1/EPHA2 0.022 0.084 -10000 0 -0.29 26 26
SEC6/SEC8 -0.007 0.068 -10000 0 -0.27 26 26
MGAT3 -0.024 0.11 -10000 0 -0.29 63 63
HGF/MET 0.004 0.13 -10000 0 -0.29 73 73
HGF 0.035 0.01 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.011 0.092 -10000 0 -0.26 46 46
actin cable formation 0.054 0.11 0.34 17 -0.29 1 18
KIAA1543 -0.022 0.065 -10000 0 -0.27 25 25
KIFC3 0 0.07 -10000 0 -0.28 25 25
NCK1 0.034 0.005 -10000 0 -10000 0 0
EXOC3 0.032 0.008 -10000 0 -10000 0 0
ACTN1 -0.002 0.072 -10000 0 -0.28 25 25
NCK1/GIT1 0.046 0.016 -10000 0 -10000 0 0
mol:GDP 0.04 0.086 -10000 0 -0.29 26 26
EXOC4 0.034 0.005 -10000 0 -10000 0 0
STX4 -0.002 0.071 -10000 0 -0.28 25 25
PIP5K1C -0.002 0.072 -10000 0 -0.28 25 25
LIMA1 0.013 0.11 -10000 0 -0.54 19 19
ABI1 0.033 0.006 -10000 0 -10000 0 0
ROCK1 0.014 0.1 0.3 13 -0.34 2 15
adherens junction assembly -0.032 0.13 0.3 1 -0.64 13 14
IGF-1R heterotetramer/IGF1 -0.13 0.18 -10000 0 -0.3 250 250
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.045 0.048 -10000 0 -0.25 9 9
MET -0.022 0.17 -10000 0 -0.54 50 50
PLEKHA7 -0.002 0.072 -10000 0 -0.28 25 25
mol:GTP 0.055 0.058 -10000 0 -0.31 6 6
establishment of epithelial cell apical/basal polarity -0.013 0.087 0.36 5 -0.35 1 6
cortical actin cytoskeleton stabilization -0.011 0.091 -10000 0 -0.26 46 46
regulation of cell-cell adhesion -0.022 0.067 -10000 0 -0.28 25 25
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.011 0.092 -10000 0 -0.26 46 46
Visual signal transduction: Rods

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
mol:K + 0.033 0.006 -10000 0 -10000 0 0
GNAT1/GTP 0.024 0.005 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.058 0.04 -10000 0 -0.24 2 2
PDE6G/GNAT1/GTP 0.042 0.016 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.033 0.007 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel -0.09 0.17 -10000 0 -0.29 205 205
mol:Na + -0.09 0.17 -10000 0 -0.49 8 8
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.049 0.1 -10000 0 -0.32 28 28
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.084 0.19 -10000 0 -0.54 7 7
CNGB1 0.029 0.012 -10000 0 -10000 0 0
RDH5 -0.43 0.23 -10000 0 -0.54 412 412
SAG 0.055 0.06 -10000 0 -0.54 1 1
mol:Ca2+ -0.12 0.15 0.36 6 -0.51 7 13
Na + (4 Units) -0.091 0.16 -10000 0 -0.49 7 7
RGS9 0.001 0.13 -10000 0 -0.54 27 27
GNB1/GNGT1 0.071 0.045 0.26 1 -10000 0 1
GNAT1/GDP 0.057 0.092 -10000 0 -0.27 28 28
GUCY2D 0.031 0.011 -10000 0 -10000 0 0
GNGT1 0.067 0.061 -10000 0 -10000 0 0
GUCY2F 0.033 0.038 -10000 0 -0.54 2 2
GNB5 0.032 0.026 -10000 0 -0.54 1 1
mol:GMP (4 units) 0.025 0.052 -10000 0 -0.3 11 11
mol:11-cis-retinal -0.43 0.23 -10000 0 -0.54 412 412
mol:cGMP 0.055 0.073 -10000 0 -0.34 13 13
GNB1 0.034 0.011 -10000 0 -10000 0 0
Rhodopsin -0.31 0.18 -10000 0 -0.4 412 412
SLC24A1 0.033 0.006 -10000 0 -10000 0 0
CNGA1 -0.21 0.29 -10000 0 -0.54 219 219
Metarhodopsin II 0.022 0.003 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.067 0.072 -10000 0 -0.34 12 12
RGS9BP 0.054 0.065 -10000 0 -0.54 2 2
Metarhodopsin II/Transducin 0.037 0.038 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.055 0.064 -10000 0 -0.34 12 12
PDE6A/B 0.038 0.071 -10000 0 -0.37 14 14
mol:Pi 0.048 0.1 -10000 0 -0.32 28 28
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.079 0.043 0.24 1 -10000 0 1
PDE6B 0.021 0.089 -10000 0 -0.54 12 12
PDE6A 0.034 0.009 0.18 1 -10000 0 1
PDE6G 0.033 0.014 -10000 0 -10000 0 0
RHO 0.034 0.005 -10000 0 -10000 0 0
PDE6 0.066 0.11 -10000 0 -0.3 25 25
GUCA1A 0.024 0.077 -10000 0 -0.54 9 9
GC2/GCAP Family 0.074 0.076 -10000 0 -0.36 13 13
GUCA1C 0.031 0.046 -10000 0 -0.54 3 3
GUCA1B 0.033 0.027 -10000 0 -0.54 1 1
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.036 0.085 -10000 0 -0.41 14 14
HDAC1 0.023 0.028 -10000 0 -10000 0 0
AES 0.033 0.008 -10000 0 -10000 0 0
FBXW11 0.033 0.007 -10000 0 -10000 0 0
DTX1 0.031 0.044 -10000 0 -0.54 3 3
LRP6/FZD1 0.047 0.024 -10000 0 -0.4 1 1
TLE1 0.016 0.098 -10000 0 -0.55 15 15
AP1 -0.22 0.19 -10000 0 -0.34 338 338
NCSTN 0.028 0.014 -10000 0 -10000 0 0
ADAM10 0.034 0.013 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.02 0.14 -10000 0 -0.69 10 10
NICD/RBPSUH 0.055 0.092 -10000 0 -0.41 14 14
WIF1 -0.38 0.26 -10000 0 -0.54 370 370
NOTCH1 0.019 0.072 -10000 0 -0.42 12 12
PSENEN 0.035 0.015 -10000 0 -10000 0 0
KREMEN2 0.1 0.076 -10000 0 -10000 0 0
DKK1 0.007 0.18 -10000 0 -0.54 44 44
beta catenin/beta TrCP1 0.01 0.094 -10000 0 -0.43 9 9
APH1B 0.032 0.027 -10000 0 -0.54 1 1
APH1A 0.031 0.028 -10000 0 -10000 0 0
AXIN1 0.016 0.07 -10000 0 -0.6 4 4
CtBP/CBP/TCF1/TLE1/AES 0.001 0.08 0.28 3 -0.36 8 11
PSEN1 0.033 0.007 -10000 0 -10000 0 0
FOS -0.36 0.27 -10000 0 -0.54 344 344
JUN -0.067 0.22 -10000 0 -0.54 89 89
MAP3K7 0.03 0.011 -10000 0 -10000 0 0
CTNNB1 -0.002 0.091 -10000 0 -0.42 11 11
MAPK3 0.032 0.009 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.1 0.07 -10000 0 -0.31 3 3
HNF1A 0.034 0.013 -10000 0 -10000 0 0
CTBP1 0.032 0.009 -10000 0 -10000 0 0
MYC -0.052 0.32 -10000 0 -1.3 31 31
NKD1 0.031 0.021 -10000 0 -10000 0 0
FZD1 0.033 0.026 -10000 0 -0.54 1 1
NOTCH1 precursor/Deltex homolog 1 0.056 0.095 -10000 0 -0.41 14 14
apoptosis -0.22 0.19 -10000 0 -0.34 338 338
Delta 1/NOTCHprecursor 0.053 0.092 -10000 0 -0.41 14 14
DLL1 0.032 0.009 -10000 0 -10000 0 0
PPARD 0.024 0.11 -10000 0 -0.8 7 7
Gamma Secretase 0.075 0.054 -10000 0 -0.3 1 1
APC 0.006 0.1 -10000 0 -0.51 14 14
DVL1 -0.039 0.094 -10000 0 -0.36 28 28
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.006 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.081 0.13 -10000 0 -0.29 41 41
LRP6 0.033 0.008 -10000 0 -10000 0 0
CSNK1A1 0.034 0.006 -10000 0 -10000 0 0
NLK 0.015 0.025 -10000 0 -10000 0 0
CCND1 0.037 0.23 -10000 0 -1.3 12 12
WNT1 0.034 0.005 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.019 0.12 0.37 1 -0.47 14 15
DKK2 0.031 0.054 -10000 0 -0.54 4 4
NOTCH1 precursor/DVL1 -0.015 0.12 -10000 0 -0.65 12 12
GSK3B 0.034 0.008 -10000 0 -10000 0 0
FRAT1 0.034 0.008 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.036 0.087 -10000 0 -0.41 14 14
PPP2R5D -0.002 0.064 -10000 0 -0.39 9 9
MAPK1 0.032 0.008 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.2 0.18 -10000 0 -0.32 356 356
RBPJ 0.033 0.008 -10000 0 -10000 0 0
CREBBP 0.033 0.03 -10000 0 -0.55 1 1
TCGA08_retinoblastoma

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
CDKN2B 0.035 0.033 -10000 0 -10000 0 0
CDKN2C -0.022 0.15 -10000 0 -0.52 41 41
CDKN2A 0.057 0.055 -10000 0 -10000 0 0
CCND2 -0.007 0.06 0.18 28 -0.2 15 43
RB1 0.005 0.072 0.22 14 -0.2 31 45
CDK4 -0.003 0.073 0.21 35 -0.21 13 48
CDK6 -0.005 0.073 0.21 33 -0.22 16 49
G1/S progression 0.003 0.087 0.21 52 -0.23 15 67
Nectin adhesion 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
PDGFRB 0.034 0.006 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.049 0.027 -10000 0 -0.4 1 1
PTK2 -0.053 0.17 -10000 0 -0.44 67 67
positive regulation of JNK cascade -0.025 0.15 -10000 0 -0.33 71 71
CDC42/GDP -0.019 0.2 0.46 1 -0.44 77 78
Rac1/GDP -0.019 0.2 -10000 0 -0.43 78 78
RAP1B 0.033 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.005 -10000 0 -10000 0 0
CTNNB1 0.029 0.052 -10000 0 -0.54 4 4
CDC42/GTP -0.023 0.18 -10000 0 -0.41 69 69
nectin-3/I-afadin -0.024 0.17 -10000 0 -0.41 79 79
RAPGEF1 -0.043 0.2 0.47 1 -0.46 79 80
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.055 0.22 -10000 0 -0.52 79 79
PDGFB-D/PDGFRB 0.034 0.006 -10000 0 -10000 0 0
TLN1 -0.039 0.12 -10000 0 -0.51 19 19
Rap1/GTP -0.03 0.14 -10000 0 -0.34 67 67
IQGAP1 0.033 0.008 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.054 0.041 -10000 0 -0.31 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.024 0.17 -10000 0 -0.41 79 79
PVR 0.035 0.015 -10000 0 -10000 0 0
Necl-5(dimer) 0.035 0.015 -10000 0 -10000 0 0
mol:GDP -0.045 0.24 0.47 1 -0.53 79 80
MLLT4 0.029 0.046 -10000 0 -0.54 3 3
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
PI3K -0.004 0.18 -10000 0 -0.34 104 104
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.038 0.046 -10000 0 -0.26 8 8
positive regulation of lamellipodium assembly -0.021 0.16 -10000 0 -0.34 76 76
PVRL1 0.031 0.015 -10000 0 -10000 0 0
PVRL3 -0.053 0.21 -10000 0 -0.54 77 77
PVRL2 0.039 0.027 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
CDH1 0.006 0.12 -10000 0 -0.54 22 22
CLDN1 -0.003 0.16 -10000 0 -0.54 41 41
JAM-A/CLDN1 -0.007 0.17 -10000 0 -0.36 81 81
SRC -0.075 0.24 -10000 0 -0.57 81 81
ITGB3 0.035 0.019 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin 0.038 0.046 -10000 0 -0.26 8 8
FARP2 -0.045 0.24 0.48 1 -0.6 45 46
RAC1 0.034 0.005 -10000 0 -10000 0 0
CTNNA1 0.033 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.001 0.15 -10000 0 -0.35 79 79
nectin-1/I-afadin 0.038 0.046 -10000 0 -0.26 8 8
nectin-2/I-afadin 0.045 0.048 -10000 0 -0.25 9 9
RAC1/GTP/IQGAP1/filamentous actin 0.044 0.011 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.005 0.15 -10000 0 -0.35 79 79
CDC42/GTP/IQGAP1/filamentous actin 0.043 0.013 -10000 0 -10000 0 0
F11R 0.028 0.017 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.025 0.15 -10000 0 -0.33 71 71
alphaV/beta3 Integrin/Talin -0.005 0.13 0.3 1 -0.5 17 18
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.045 0.048 -10000 0 -0.25 9 9
nectin-2(dimer)/I-afadin/I-afadin 0.045 0.048 -10000 0 -0.25 9 9
PIP5K1C -0.037 0.12 -10000 0 -0.49 23 23
VAV2 -0.042 0.24 0.46 1 -0.54 74 75
RAP1/GDP -0.015 0.19 -10000 0 -0.4 72 72
ITGAV 0.033 0.028 -10000 0 -0.54 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.001 0.15 -10000 0 -0.34 79 79
nectin-3(dimer)/I-afadin/I-afadin -0.024 0.17 -10000 0 -0.41 79 79
Rac1/GTP -0.022 0.19 -10000 0 -0.41 76 76
PTPRM -0.035 0.14 -10000 0 -0.29 83 83
E-cadherin/beta catenin/alpha catenin 0.052 0.1 -10000 0 -0.29 26 26
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.033 0.007 -10000 0 -10000 0 0
LPA receptor mediated events

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
GNB1/GNG2 0.047 0.035 -10000 0 -0.25 5 5
NF kappa B1 p50/RelA/I kappa B alpha 0.06 0.061 0.28 3 -0.24 2 5
AP1 -0.22 0.19 -10000 0 -0.33 345 345
mol:PIP3 -0.15 0.16 -10000 0 -0.29 277 277
AKT1 0.005 0.091 -10000 0 -0.33 7 7
PTK2B -0.015 0.081 -10000 0 -0.18 88 88
RHOA 0.009 0.066 -10000 0 -0.28 17 17
PIK3CB 0.034 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.026 0.058 0.19 45 -0.27 1 46
MAGI3 0.04 0.042 -10000 0 -0.54 1 1
RELA 0.034 0.005 -10000 0 -10000 0 0
apoptosis 0.017 0.022 -10000 0 -0.19 5 5
HRAS/GDP 0.025 0.009 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.015 0.079 0.23 5 -0.28 6 11
NF kappa B1 p50/RelA 0.02 0.04 -10000 0 -0.31 1 1
endothelial cell migration 0.016 0.053 0.27 2 -0.47 5 7
ADCY4 -0.048 0.096 -10000 0 -0.23 45 45
ADCY5 -0.047 0.094 -10000 0 -0.22 45 45
ADCY6 -0.047 0.094 -10000 0 -0.22 44 44
ADCY7 -0.037 0.091 -10000 0 -0.27 19 19
ADCY1 -0.046 0.093 -10000 0 -0.22 44 44
ADCY2 -0.05 0.1 0.18 1 -0.24 48 49
ADCY3 -0.046 0.094 -10000 0 -0.22 43 43
ADCY8 -0.041 0.087 -10000 0 -0.23 31 31
ADCY9 -0.043 0.09 -10000 0 -0.22 36 36
GSK3B -0.015 0.079 0.25 4 -0.22 18 22
arachidonic acid secretion -0.054 0.1 -10000 0 -0.24 61 61
GNG2 0.032 0.026 -10000 0 -0.54 1 1
TRIP6 0.023 0.02 -10000 0 -0.39 1 1
GNAO1 0.019 0.021 0.15 2 -0.26 2 4
HRAS 0.034 0.013 -10000 0 -10000 0 0
NFKBIA 0.027 0.061 0.25 4 -0.24 4 8
GAB1 0.033 0.027 -10000 0 -0.54 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.05 0.11 -10000 0 -0.85 7 7
JUN -0.067 0.22 -10000 0 -0.54 89 89
LPA/LPA2/NHERF2 0.024 0.017 -10000 0 -0.11 3 3
TIAM1 0.031 0.12 -10000 0 -1 7 7
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 0.026 0.056 0.2 45 -10000 0 45
PLCB3 0.036 0.05 0.19 42 -10000 0 42
FOS -0.35 0.27 -10000 0 -0.54 344 344
positive regulation of mitosis -0.054 0.1 -10000 0 -0.24 61 61
LPA/LPA1-2-3 0.007 0.02 -10000 0 -0.18 5 5
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.029 0.013 -10000 0 -10000 0 0
stress fiber formation 0.016 0.059 -10000 0 -0.27 7 7
GNAZ 0.015 0.044 -10000 0 -0.28 10 10
EGFR/PI3K-beta/Gab1 -0.15 0.17 -10000 0 -0.3 277 277
positive regulation of dendritic cell cytokine production 0.007 0.019 -10000 0 -0.18 5 5
LPA/LPA2/MAGI-3 0.029 0.03 -10000 0 -0.2 3 3
ARHGEF1 0.037 0.055 -10000 0 -0.22 2 2
GNAI2 0.02 0.025 -10000 0 -0.21 5 5
GNAI3 0.02 0.023 0.15 2 -0.22 4 6
GNAI1 -0.11 0.17 -10000 0 -0.34 184 184
LPA/LPA3 0.002 0.01 -10000 0 -0.093 5 5
LPA/LPA2 0.002 0.01 -10000 0 -0.093 5 5
LPA/LPA1 0.007 0.026 -10000 0 -0.25 5 5
HB-EGF/EGFR -0.12 0.2 -10000 0 -0.31 249 249
HBEGF 0.066 0.077 -10000 0 -0.4 4 4
mol:DAG 0.026 0.056 0.2 45 -10000 0 45
cAMP biosynthetic process -0.056 0.1 0.24 1 -0.28 27 28
NFKB1 0.034 0.005 -10000 0 -10000 0 0
SRC 0.033 0.008 -10000 0 -10000 0 0
GNB1 0.034 0.012 -10000 0 -10000 0 0
LYN 0.04 0.069 0.26 20 -0.28 1 21
GNAQ 0.003 0.009 0.057 2 -0.075 5 7
LPAR2 0 0.001 -10000 0 -10000 0 0
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 0.003 0.016 0.075 2 -0.15 5 7
IL8 -0.19 0.22 0.35 13 -0.38 264 277
PTK2 0.02 0.021 -10000 0 -0.16 4 4
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
CASP3 0.017 0.022 -10000 0 -0.19 5 5
EGFR -0.27 0.29 -10000 0 -0.54 269 269
PLCG1 0.017 0.018 -10000 0 -0.11 2 2
PLD2 0.022 0.025 -10000 0 -0.2 5 5
G12/G13 0.044 0.03 -10000 0 -0.19 5 5
PI3K-beta -0.01 0.089 -10000 0 -0.37 8 8
cell migration 0.027 0.044 -10000 0 -0.25 7 7
SLC9A3R2 0.032 0.015 -10000 0 -10000 0 0
PXN 0.015 0.059 -10000 0 -0.28 7 7
HRAS/GTP -0.054 0.1 -10000 0 -0.25 61 61
RAC1 0.034 0.005 -10000 0 -10000 0 0
MMP9 0.094 0.074 -10000 0 -10000 0 0
PRKCE 0.034 0.004 -10000 0 -10000 0 0
PRKCD 0.024 0.059 0.21 10 -0.26 1 11
Gi(beta/gamma) -0.051 0.11 -10000 0 -0.26 54 54
mol:LPA 0.003 0.016 0.075 2 -0.15 5 7
TRIP6/p130 Cas/FAK1/Paxillin 0.03 0.052 -10000 0 -0.24 4 4
MAPKKK cascade -0.054 0.1 -10000 0 -0.24 61 61
contractile ring contraction involved in cytokinesis 0.008 0.068 -10000 0 -0.27 19 19
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.021 0.039 -10000 0 -0.31 4 4
GNA15 0.016 0.014 -10000 0 -10000 0 0
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
MAPT -0.015 0.08 0.23 5 -0.29 6 11
GNA11 0.015 0.009 -10000 0 -10000 0 0
Rac1/GTP 0.051 0.11 -10000 0 -0.91 7 7
MMP2 0.016 0.053 0.27 2 -0.47 5 7
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.005 0.13 -10000 0 -0.39 50 50
CRKL -0.002 0.11 0.37 1 -0.39 17 18
mol:PIP3 0.009 0.064 0.49 7 -10000 0 7
AKT1 0.021 0.08 0.39 11 -10000 0 11
PTK2B 0.027 0.014 -10000 0 -10000 0 0
RAPGEF1 -0.003 0.11 0.35 1 -0.43 10 11
RANBP10 0.03 0.012 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.023 0.12 -10000 0 -0.34 50 50
MAP3K5 -0.013 0.13 0.37 1 -0.41 24 25
HGF/MET/CIN85/CBL/ENDOPHILINS 0.037 0.12 -10000 0 -0.32 51 51
AP1 -0.29 0.24 -10000 0 -0.44 346 346
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.027 0.014 -10000 0 -10000 0 0
apoptosis -0.54 0.38 -10000 0 -0.77 367 367
STAT3 (dimer) -0.007 0.11 -10000 0 -0.42 16 16
GAB1/CRKL/SHP2/PI3K 0.01 0.14 -10000 0 -0.44 16 16
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.014 0.11 0.36 1 -0.42 10 11
PTPN11 0.034 0.004 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.032 0.008 -10000 0 -10000 0 0
PTEN 0.026 0.067 -10000 0 -0.54 7 7
ELK1 -0.019 0.084 0.27 11 -0.21 8 19
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.006 0.064 -10000 0 -0.26 5 5
PAK1 0.046 0.099 0.43 13 -10000 0 13
HGF/MET/RANBP10 0.021 0.12 -10000 0 -0.34 50 50
HRAS -0.032 0.2 -10000 0 -0.58 58 58
DOCK1 -0.004 0.11 0.43 2 -0.44 10 12
GAB1 -0.003 0.12 -10000 0 -0.41 17 17
CRK -0.003 0.11 0.37 1 -0.45 10 11
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.022 0.18 -10000 0 -0.53 55 55
JUN -0.067 0.22 -10000 0 -0.54 89 89
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.013 0.087 -10000 0 -0.27 51 51
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
cell morphogenesis -0.018 0.15 0.41 6 -0.44 18 24
GRB2/SHC 0.02 0.081 -10000 0 -0.25 31 31
FOS -0.36 0.27 -10000 0 -0.54 344 344
GLMN 0.004 0.004 -10000 0 -10000 0 0
cell motility -0.019 0.084 0.27 11 -0.21 8 19
HGF/MET/MUC20 0.008 0.12 -10000 0 -0.34 51 51
cell migration 0.019 0.08 -10000 0 -0.24 31 31
GRB2 0.034 0.018 -10000 0 -10000 0 0
CBL 0.03 0.011 -10000 0 -10000 0 0
MET/RANBP10 0.001 0.13 -10000 0 -0.39 52 52
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.012 0.097 -10000 0 -0.38 14 14
MET/MUC20 -0.017 0.13 -10000 0 -0.39 52 52
RAP1B 0.002 0.11 0.32 2 -0.41 9 11
RAP1A -0.004 0.1 0.51 1 -0.42 9 10
HGF/MET/RANBP9 0.027 0.12 -10000 0 -0.34 48 48
RAF1 -0.025 0.19 -10000 0 -0.55 58 58
STAT3 -0.007 0.11 -10000 0 -0.42 16 16
cell proliferation 0.025 0.15 0.34 10 -0.39 31 41
RPS6KB1 0.001 0.061 -10000 0 -0.32 10 10
MAPK3 -0.037 0.081 0.62 3 -10000 0 3
MAPK1 -0.004 0.17 0.65 29 -10000 0 29
RANBP9 0.034 0.009 -10000 0 -10000 0 0
MAPK8 -0.004 0.13 0.45 1 -0.43 11 12
SRC -0.006 0.096 -10000 0 -0.36 14 14
PI3K -0.01 0.13 -10000 0 -0.28 86 86
MET/Glomulin -0.013 0.11 -10000 0 -0.35 50 50
SOS1 0.034 0.004 -10000 0 -10000 0 0
MAP2K1 -0.022 0.18 0.48 1 -0.52 56 57
MET -0.022 0.17 -10000 0 -0.54 50 50
MAP4K1 0.002 0.12 0.39 1 -0.44 15 16
PTK2 0.027 0.014 -10000 0 -10000 0 0
MAP2K2 -0.022 0.18 0.48 1 -0.52 57 58
BAD 0.018 0.074 0.38 8 -10000 0 8
MAP2K4 -0.013 0.12 0.35 1 -0.39 21 22
SHP2/GRB2/SOS1/GAB1 0.02 0.14 -10000 0 -0.36 51 51
INPPL1 0.032 0.01 -10000 0 -10000 0 0
PXN 0.034 0.003 -10000 0 -10000 0 0
SH3KBP1 0.033 0.027 -10000 0 -0.54 1 1
HGS -0.015 0.077 -10000 0 -0.25 44 44
PLCgamma1/PKC 0.024 0.006 -10000 0 -10000 0 0
HGF 0.035 0.01 -10000 0 -10000 0 0
RASA1 0.034 0.012 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
PTPRJ 0.035 0.017 -10000 0 -10000 0 0
NCK/PLCgamma1 0.026 0.093 -10000 0 -0.24 48 48
PDPK1 0.024 0.087 0.47 8 -10000 0 8
HGF/MET/SHIP 0.008 0.12 -10000 0 -0.34 51 51
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.012 -10000 0 -10000 0 0
CDC42/GTP -0.067 0.14 -10000 0 -0.32 59 59
PLCG1 -0.073 0.13 -10000 0 -0.33 54 54
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.033 0.01 -10000 0 -10000 0 0
GNAI3 0.034 0.005 -10000 0 -10000 0 0
G12/G13 0.045 0.017 -10000 0 -10000 0 0
cell migration -0.067 0.14 -10000 0 -0.31 59 59
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.07 0.13 -10000 0 -0.34 49 49
MAPK1 -0.077 0.13 -10000 0 -0.33 56 56
S1P/S1P5/Gi -0.081 0.14 -10000 0 -0.25 186 186
GNAI1 -0.17 0.28 -10000 0 -0.54 183 183
CDC42/GDP 0.024 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.023 0.004 -10000 0 -10000 0 0
RHOA 0.034 0.051 0.2 3 -10000 0 3
S1P/S1P4/Gi -0.081 0.14 -10000 0 -0.25 186 186
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.026 0.063 -10000 0 -0.54 6 6
S1P/S1P4/G12/G13 0.039 0.014 -10000 0 -10000 0 0
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
CDC42 0.033 0.007 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.005 0.015 -10000 0 -10000 0 0
RAS family/GTP -0.006 0.1 -10000 0 -0.28 15 15
NFATC4 -0.028 0.08 0.28 3 -0.25 16 19
ERBB2IP 0.034 0.008 -10000 0 -10000 0 0
HSP90 (dimer) 0.033 0.006 -10000 0 -10000 0 0
mammary gland morphogenesis -0.036 0.087 -10000 0 -0.3 27 27
JUN -0.055 0.071 -10000 0 -10000 0 0
HRAS 0.033 0.013 -10000 0 -10000 0 0
DOCK7 -0.036 0.09 0.26 2 -0.29 27 29
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.02 0.098 -10000 0 -0.3 25 25
AKT1 0.007 0.016 -10000 0 -10000 0 0
BAD -0.005 0.014 -10000 0 -10000 0 0
MAPK10 -0.022 0.07 0.26 4 -0.26 7 11
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.037 0.093 -10000 0 -0.32 27 27
RAF1 -0.038 0.096 -10000 0 -0.3 17 17
ErbB2/ErbB3/neuregulin 2 -0.18 0.17 -10000 0 -0.33 272 272
STAT3 0.01 0.16 -10000 0 -0.84 18 18
cell migration -0.015 0.071 0.29 5 -0.26 3 8
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.26 0.28 -10000 0 -0.65 124 124
FOS -0.33 0.26 -10000 0 -0.49 366 366
NRAS 0.034 0.016 -10000 0 -10000 0 0
mol:Ca2+ -0.036 0.087 -10000 0 -0.3 27 27
MAPK3 -0.16 0.21 -10000 0 -0.51 90 90
MAPK1 -0.18 0.24 -10000 0 -0.54 113 113
JAK2 -0.033 0.089 0.26 2 -0.29 27 29
NF2 0.003 0.069 -10000 0 -0.68 5 5
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0 0.08 -10000 0 -0.28 24 24
NRG1 -0.021 0.16 -10000 0 -0.55 43 43
GRB2/SOS1 0.047 0.019 -10000 0 -10000 0 0
MAPK8 -0.038 0.1 -10000 0 -0.29 30 30
MAPK9 -0.02 0.064 0.26 3 -10000 0 3
ERBB2 -0.022 0.013 -10000 0 -10000 0 0
ERBB3 0.036 0.025 -10000 0 -10000 0 0
SHC1 0.026 0.014 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
apoptosis 0.02 0.027 -10000 0 -0.18 2 2
STAT3 (dimer) 0.011 0.16 -10000 0 -0.82 18 18
RNF41 -0.009 0.014 -10000 0 -10000 0 0
FRAP1 -0.002 0.013 0.11 3 -10000 0 3
RAC1-CDC42/GTP -0.037 0.06 -10000 0 -0.22 27 27
ErbB2/ErbB2/HSP90 (dimer) -0.008 0.023 -10000 0 -10000 0 0
CHRNA1 -0.12 0.17 -10000 0 -0.38 90 90
myelination -0.022 0.089 0.33 6 -10000 0 6
PPP3CB -0.033 0.086 0.25 2 -0.27 26 28
KRAS 0.033 0.018 0.18 6 -10000 0 6
RAC1-CDC42/GDP 0.035 0.1 -10000 0 -0.27 8 8
NRG2 -0.35 0.27 -10000 0 -0.54 339 339
mol:GDP 0 0.08 -10000 0 -0.28 24 24
SOS1 0.033 0.004 -10000 0 -10000 0 0
MAP2K2 -0.054 0.1 -10000 0 -0.31 22 22
SRC 0.033 0.008 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.033 0.092 0.27 2 -0.29 27 29
MAP2K1 -0.17 0.21 -10000 0 -0.59 53 53
heart morphogenesis -0.036 0.087 -10000 0 -0.3 27 27
RAS family/GDP 0.029 0.11 -10000 0 -0.28 13 13
GRB2 0.033 0.018 -10000 0 -10000 0 0
PRKACA 0.004 0.082 -10000 0 -0.68 7 7
CHRNE -0.006 0.018 -10000 0 -10000 0 0
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
activation of caspase activity -0.007 0.016 -10000 0 -10000 0 0
nervous system development -0.036 0.087 -10000 0 -0.3 27 27
CDC42 0.033 0.007 -10000 0 -10000 0 0
IL27-mediated signaling events

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
TGFB1 0.042 0.009 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response -0.01 0.22 0.7 24 -0.45 13 37
IL27/IL27R/JAK1 0.032 0.28 0.65 17 -1 19 36
TBX21 0.024 0.26 0.53 41 -0.59 39 80
IL12B 0.042 0.027 0.2 9 -10000 0 9
IL12A 0.005 0.061 0.14 6 -0.4 11 17
IL6ST 0.034 0.08 0.24 1 -0.54 8 9
IL27RA/JAK1 0.003 0.24 0.47 5 -1.2 18 23
IL27 -0.019 0.18 0.33 1 -0.54 51 52
TYK2 0.043 0.026 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.19 0.14 -10000 0 -0.78 2 2
T-helper 2 cell differentiation -0.01 0.22 0.7 24 -0.45 13 37
T cell proliferation during immune response -0.01 0.22 0.7 24 -0.45 13 37
MAPKKK cascade 0.01 0.22 0.45 13 -0.7 24 37
STAT3 0.033 0.007 -10000 0 -10000 0 0
STAT2 0.034 0.004 -10000 0 -10000 0 0
STAT1 0.061 0.057 0.23 1 -10000 0 1
IL12RB1 0.036 0.007 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.05 0.25 0.55 48 -0.63 23 71
IL27/IL27R/JAK2/TYK2 0.009 0.22 0.47 12 -0.71 24 36
positive regulation of T cell mediated cytotoxicity 0.01 0.22 0.45 13 -0.7 24 37
STAT1 (dimer) 0.037 0.33 0.8 23 -1 22 45
JAK2 0.039 0.023 0.24 1 -10000 0 1
JAK1 0.036 0.013 -10000 0 -10000 0 0
STAT2 (dimer) 0.025 0.21 0.46 8 -0.67 24 32
T cell proliferation -0.18 0.25 0.5 5 -0.58 80 85
IL12/IL12R/TYK2/JAK2 0.065 0.19 0.53 2 -0.77 15 17
IL17A -0.19 0.14 -10000 0 -0.78 2 2
mast cell activation -0.01 0.22 0.7 24 -0.45 13 37
IFNG 0.033 0.066 0.14 102 -0.1 11 113
T cell differentiation 0 0.009 0.019 31 -0.024 20 51
STAT3 (dimer) 0.023 0.21 0.47 7 -0.67 23 30
STAT5A (dimer) 0.023 0.21 0.47 7 -0.65 25 32
STAT4 (dimer) 0.021 0.21 0.48 7 -0.67 25 32
STAT4 0.027 0.069 -10000 0 -0.54 7 7
T cell activation -0.005 0.028 0.12 17 -0.12 9 26
IL27R/JAK2/TYK2 0.052 0.25 0.55 3 -1.1 18 21
GATA3 -0.013 0.37 0.73 12 -1.3 33 45
IL18 0.019 0.036 0.14 27 -10000 0 27
positive regulation of mast cell cytokine production 0.024 0.2 0.46 7 -0.65 23 30
IL27/EBI3 0.015 0.14 0.34 3 -0.39 50 53
IL27RA -0.016 0.25 0.52 5 -1.3 18 23
IL6 -0.37 0.26 -10000 0 -0.54 365 365
STAT5A 0.032 0.026 -10000 0 -0.54 1 1
monocyte differentiation 0.002 0.003 -10000 0 -10000 0 0
IL2 -0.009 0.12 0.47 18 -0.82 2 20
IL1B 0.009 0.044 0.14 3 -0.4 5 8
EBI3 0.041 0.026 0.25 1 -10000 0 1
TNF 0.013 0.02 0.14 4 -10000 0 4
Neurotrophic factor-mediated Trk receptor signaling

Figure S46.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S46.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.033 0.008 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.028 0.095 -10000 0 -0.27 17 17
NT3 (dimer)/TRKC -0.082 0.21 -10000 0 -0.41 142 142
NT3 (dimer)/TRKB -0.25 0.29 -10000 0 -0.48 280 280
SHC/Grb2/SOS1/GAB1/PI3K 0.002 0.073 -10000 0 -0.24 26 26
RAPGEF1 0.034 0.006 -10000 0 -10000 0 0
BDNF 0.038 0.047 -10000 0 -0.54 2 2
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
DYNLT1 0.032 0.009 -10000 0 -10000 0 0
NTRK1 0.03 0.022 -10000 0 -10000 0 0
NTRK2 -0.23 0.29 -10000 0 -0.54 237 237
NTRK3 0.015 0.1 -10000 0 -0.54 16 16
NT-4/5 (dimer)/TRKB -0.17 0.23 -10000 0 -0.4 234 234
neuron apoptosis 0.12 0.21 0.46 102 -10000 0 102
SHC 2-3/Grb2 -0.13 0.23 -10000 0 -0.51 102 102
SHC1 0.027 0.014 -10000 0 -10000 0 0
SHC2 -0.14 0.24 -10000 0 -0.56 104 104
SHC3 -0.12 0.21 -10000 0 -0.49 93 93
STAT3 (dimer) 0.054 0.077 -10000 0 -0.36 10 10
NT3 (dimer)/TRKA -0.084 0.2 -10000 0 -0.38 134 134
RIN/GDP 0.006 0.11 0.28 3 -0.28 16 19
GIPC1 0.034 0.011 -10000 0 -10000 0 0
KRAS 0.034 0.018 0.18 6 -10000 0 6
DNAJA3 -0.054 0.13 -10000 0 -0.34 71 71
RIN/GTP 0.024 0.019 -10000 0 -0.4 1 1
CCND1 0.015 0.12 -10000 0 -0.78 10 10
MAGED1 0.044 0.036 -10000 0 -10000 0 0
PTPN11 0.034 0.004 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.051 0.034 -10000 0 -10000 0 0
GRB2 0.034 0.018 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.04 0.027 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.032 0.067 -10000 0 -0.3 15 15
ELMO1 0.034 0.005 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.042 0.032 -10000 0 -0.34 3 3
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.034 0.013 -10000 0 -10000 0 0
DOCK1 0.03 0.044 -10000 0 -0.54 3 3
GAB2 0.03 0.012 -10000 0 -10000 0 0
RIT2 0.032 0.026 -10000 0 -0.54 1 1
RIT1 0.028 0.014 -10000 0 -10000 0 0
FRS2 0.032 0.029 -10000 0 -0.54 1 1
DNM1 0.034 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.035 0.15 -10000 0 -0.33 79 79
mol:GDP -0.008 0.15 0.34 6 -0.43 18 24
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.025 0.003 -10000 0 -10000 0 0
RIT1/GDP -0.005 0.097 0.29 1 -0.29 14 15
TIAM1 0.035 0.012 0.18 3 -10000 0 3
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
BDNF (dimer)/TRKB -0.12 0.2 -10000 0 -0.34 234 234
KIDINS220/CRKL/C3G 0.047 0.014 -10000 0 -10000 0 0
SHC/RasGAP 0.039 0.023 -10000 0 -10000 0 0
FRS2 family/SHP2 0.064 0.028 -10000 0 -0.34 1 1
SHC/GRB2/SOS1/GAB1 0.063 0.043 -10000 0 -10000 0 0
RIT1/GTP 0.021 0.01 -10000 0 -10000 0 0
NT3 (dimer) -0.12 0.26 -10000 0 -0.54 134 134
RAP1/GDP 0.002 0.09 -10000 0 -0.25 14 14
KIDINS220/CRKL 0.033 0.008 -10000 0 -10000 0 0
BDNF (dimer) 0.038 0.047 -10000 0 -0.54 2 2
ubiquitin-dependent protein catabolic process 0.029 0.057 -10000 0 -0.32 10 10
Schwann cell development -0.037 0.032 -10000 0 -10000 0 0
EHD4 0.033 0.007 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.076 0.039 -10000 0 -0.32 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.026 0.067 -10000 0 -0.3 7 7
RAP1B 0.033 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.17 0.22 -10000 0 -0.35 271 271
ABL1 0.034 0.005 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.048 0.019 -10000 0 -10000 0 0
Rap1/GTP -0.041 0.12 -10000 0 -0.43 23 23
STAT3 0.054 0.077 -10000 0 -0.36 10 10
axon guidance -0.17 0.2 -10000 0 -0.34 271 271
MAPK3 0.048 0.067 0.28 4 -10000 0 4
MAPK1 0.052 0.069 0.28 5 -10000 0 5
CDC42/GDP 0.008 0.11 0.29 6 -0.29 14 20
NTF3 -0.12 0.26 -10000 0 -0.54 134 134
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.038 0.022 -10000 0 -10000 0 0
PI3K 0.005 0.13 -10000 0 -0.37 51 51
FRS3 0.033 0.006 -10000 0 -10000 0 0
FAIM 0.033 0.006 -10000 0 -10000 0 0
GAB1 0.033 0.027 -10000 0 -0.54 1 1
RASGRF1 -0.052 0.14 -10000 0 -0.34 76 76
SOS1 0.034 0.004 -10000 0 -10000 0 0
MCF2L -0.083 0.17 -10000 0 -0.35 140 140
RGS19 0.034 0.022 -10000 0 -10000 0 0
CDC42 0.033 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.048 0.099 0.36 1 -0.43 5 6
Rac1/GDP 0.007 0.11 0.27 5 -0.3 13 18
NGF (dimer)/TRKA/GRIT 0.02 0.014 -10000 0 -10000 0 0
neuron projection morphogenesis -0.025 0.22 0.42 1 -0.73 28 29
NGF (dimer)/TRKA/NEDD4-2 0.03 0.058 -10000 0 -0.32 10 10
MAP2K1 0.064 0.088 0.36 14 -10000 0 14
NGFR -0.054 0.2 -10000 0 -0.54 75 75
NGF (dimer)/TRKA/GIPC/GAIP 0.024 0.025 -10000 0 -10000 0 0
RAS family/GTP/PI3K 0 0.085 -10000 0 -0.26 40 40
FRS2 family/SHP2/GRB2/SOS1 0.087 0.044 -10000 0 -0.3 1 1
NRAS 0.036 0.016 -10000 0 -10000 0 0
GRB2/SOS1 0.048 0.019 -10000 0 -10000 0 0
PRKCI 0.035 0.017 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade -0.018 0.072 -10000 0 -0.56 4 4
RASA1 0.034 0.012 -10000 0 -10000 0 0
TRKA/c-Abl 0.042 0.024 -10000 0 -10000 0 0
SQSTM1 0.034 0.009 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.099 0.2 -10000 0 -0.31 232 232
NGF (dimer)/TRKA/p62/Atypical PKCs 0.049 0.03 -10000 0 -10000 0 0
MATK 0.038 0.028 -10000 0 -10000 0 0
NEDD4L 0.018 0.095 -10000 0 -0.54 14 14
RAS family/GDP -0.033 0.057 -10000 0 -0.22 16 16
NGF (dimer)/TRKA -0.059 0.14 -10000 0 -0.36 81 81
Rac1/GTP -0.05 0.098 -10000 0 -0.28 40 40
FRS2 family/SHP2/CRK family 0.082 0.046 -10000 0 -0.3 1 1
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.035 0.11 0.31 7 -0.34 6 13
epithelial cell differentiation 0.087 0.091 -10000 0 -10000 0 0
ITCH 0.047 0.025 -10000 0 -10000 0 0
WWP1 0.05 0.15 0.53 29 -10000 0 29
FYN 0.03 0.037 -10000 0 -0.54 2 2
EGFR -0.27 0.29 -10000 0 -0.54 269 269
PRL 0.033 0.006 -10000 0 -10000 0 0
neuron projection morphogenesis 0.028 0.12 0.37 10 -0.38 4 14
PTPRZ1 -0.36 0.27 -10000 0 -0.54 354 354
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.016 0.1 -10000 0 -0.38 6 6
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.011 0.11 0.28 1 -0.32 34 35
ADAM17 0.047 0.025 -10000 0 -10000 0 0
ErbB4/ErbB4 0.031 0.12 0.43 25 -0.38 3 28
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.036 0.11 0.32 8 -0.34 3 11
NCOR1 0.031 0.011 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.004 0.11 -10000 0 -0.39 7 7
GRIN2B -0.017 0.1 -10000 0 -0.37 7 7
ErbB4/ErbB2/betacellulin 0.028 0.097 -10000 0 -0.36 4 4
STAT1 0.059 0.055 -10000 0 -10000 0 0
HBEGF 0.029 0.051 -10000 0 -0.54 4 4
PRLR 0.071 0.064 -10000 0 -10000 0 0
E4ICDs/ETO2 -0.005 0.14 0.32 3 -0.39 41 44
axon guidance 0.12 0.14 0.45 31 -10000 0 31
NEDD4 0.04 0.06 -10000 0 -0.52 5 5
Prolactin receptor/Prolactin receptor/Prolactin 0.074 0.047 -10000 0 -10000 0 0
CBFA2T3 -0.023 0.17 -10000 0 -0.54 47 47
ErbB4/ErbB2/HBEGF 0.037 0.086 -10000 0 -0.33 3 3
MAPK3 0.029 0.12 0.37 8 -0.38 4 12
STAT1 (dimer) 0.055 0.11 0.35 11 -0.36 2 13
MAPK1 0.034 0.12 0.4 10 -0.38 4 14
JAK2 0.032 0.011 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta 0.003 0.11 -10000 0 -0.38 7 7
NRG1 -0.015 0.12 -10000 0 -0.4 41 41
NRG3 0.035 0.043 -10000 0 -0.54 2 2
NRG2 -0.35 0.27 -10000 0 -0.54 339 339
NRG4 0.034 0.013 -10000 0 -10000 0 0
heart development 0.12 0.14 0.45 31 -10000 0 31
neural crest cell migration 0.003 0.11 -10000 0 -0.38 7 7
ERBB2 0.021 0.028 0.3 1 -0.37 1 2
WWOX/E4ICDs 0.028 0.1 0.34 6 -0.34 3 9
SHC1 0.027 0.014 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.13 0.16 -10000 0 -0.36 22 22
apoptosis -0.037 0.095 0.31 4 -0.31 24 28
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.19 0.17 -10000 0 -0.32 255 255
ErbB4/ErbB2/epiregulin 0.047 0.093 0.36 4 -0.34 1 5
ErbB4/ErbB4/betacellulin/betacellulin 0.022 0.12 0.31 6 -0.35 17 23
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.087 0.12 0.38 9 -0.32 2 11
MDM2 0.029 0.11 0.35 28 -0.36 2 30
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.001 0.1 -10000 0 -0.3 34 34
STAT5A 0.11 0.12 0.41 31 -10000 0 31
ErbB4/EGFR/neuregulin 1 beta -0.15 0.18 -10000 0 -0.46 60 60
DLG4 0.031 0.011 -10000 0 -10000 0 0
GRB2/SHC 0.039 0.026 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.024 0.09 -10000 0 -0.33 2 2
STAT5A (dimer) 0.14 0.12 0.4 23 -10000 0 23
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.13 0.12 0.4 28 -0.36 1 29
LRIG1 0.014 0.1 -10000 0 -0.54 17 17
EREG 0.045 0.049 -10000 0 -0.54 1 1
BTC 0.011 0.12 -10000 0 -0.54 21 21
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.11 0.13 0.46 30 -10000 0 30
ERBB4 0.031 0.12 0.43 25 -0.38 3 28
STAT5B 0.033 0.01 -10000 0 -10000 0 0
YAP1 -0.002 0.12 0.26 6 -0.43 26 32
GRB2 0.034 0.018 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.038 0.081 -10000 0 -10000 0 0
glial cell differentiation -0.023 0.089 0.33 2 -10000 0 2
WWOX 0.034 0.03 -10000 0 -10000 0 0
cell proliferation 0.052 0.14 0.43 10 -0.42 5 15
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 0.039 0.11 1 1 -10000 0 1
VDR 0.032 0.037 -10000 0 -0.54 2 2
FAM120B 0.032 0.009 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.062 0.077 0.29 14 -10000 0 14
RXRs/LXRs/DNA/Oxysterols 0.089 0.09 -10000 0 -0.37 2 2
MED1 0.029 0.012 -10000 0 -10000 0 0
mol:9cRA 0.01 0.014 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.032 0.13 -10000 0 -0.27 101 101
RXRs/NUR77 0.07 0.093 -10000 0 -0.3 18 18
RXRs/PPAR -0.15 0.14 -10000 0 -0.26 262 262
NCOR2 0.034 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.024 0.027 -10000 0 -0.4 2 2
RARs/VDR/DNA/Vit D3 0.015 0.14 -10000 0 -0.3 74 74
RARA 0.031 0.012 -10000 0 -10000 0 0
NCOA1 0.033 0.026 -10000 0 -0.54 1 1
VDR/VDR/DNA 0.032 0.037 -10000 0 -0.54 2 2
RARs/RARs/DNA/9cRA 0.006 0.13 -10000 0 -0.29 75 75
RARG 0.034 0.004 -10000 0 -10000 0 0
RPS6KB1 0.063 0.17 0.56 52 -10000 0 52
RARs/THRs/DNA/SMRT -0.031 0.13 -10000 0 -0.27 101 101
THRA -0.002 0.13 -10000 0 -0.54 28 28
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.024 0.027 -10000 0 -0.4 2 2
RXRs/PPAR/9cRA/PGJ2/DNA 0.075 0.07 -10000 0 -0.3 4 4
NR1H4 0.035 0.009 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.1 0.088 -10000 0 -0.28 5 5
NR1H2 0.043 0.016 -10000 0 -10000 0 0
NR1H3 0.043 0.031 -10000 0 -0.54 1 1
RXRs/VDR/DNA/Vit D3 0.077 0.062 -10000 0 -0.29 4 4
NR4A1 0.007 0.12 -10000 0 -0.54 24 24
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.057 0.057 -10000 0 -10000 0 0
RXRG 0.031 0.055 -10000 0 -0.54 4 4
RXR alpha/CCPG 0.052 0.02 -10000 0 -10000 0 0
RXRA 0.042 0.015 -10000 0 -10000 0 0
RXRB 0.044 0.017 -10000 0 -10000 0 0
THRB 0.028 0.057 -10000 0 -0.54 5 5
PPARG -0.38 0.26 -10000 0 -0.54 369 369
PPARD 0.034 0.01 -10000 0 -10000 0 0
TNF 0.082 0.09 -10000 0 -10000 0 0
mol:Oxysterols 0.009 0.013 -10000 0 -10000 0 0
cholesterol transport 0.089 0.089 -10000 0 -0.37 2 2
PPARA 0.031 0.027 -10000 0 -0.54 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.057 0.21 -10000 0 -0.54 80 80
RXRs/NUR77/BCL2 -0.028 0.12 -10000 0 -0.26 75 75
SREBF1 0.083 0.1 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.075 0.07 -10000 0 -0.3 4 4
ABCA1 0.077 0.11 -10000 0 -1 2 2
RARs/THRs 0.004 0.16 -10000 0 -0.32 98 98
RXRs/FXR 0.084 0.065 -10000 0 -0.31 4 4
BCL2 -0.072 0.22 -10000 0 -0.54 93 93
Syndecan-3-mediated signaling events

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
CTTN 0.028 0.013 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.13 0.17 -9999 0 -0.56 19 19
Syndecan-3/Neurocan 0.043 0.1 -9999 0 -0.47 16 16
POMC 0.035 0.031 -9999 0 -0.54 1 1
EGFR -0.27 0.29 -9999 0 -0.54 269 269
Syndecan-3/EGFR -0.12 0.18 -9999 0 -0.3 191 191
AGRP 0.03 0.015 -9999 0 -10000 0 0
NCSTN 0.028 0.014 -9999 0 -10000 0 0
PSENEN 0.035 0.015 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.032 0.027 -9999 0 -0.54 1 1
APH1A 0.031 0.028 -9999 0 -10000 0 0
NCAN 0.039 0.028 -9999 0 -10000 0 0
long-term memory 0.041 0.096 -9999 0 -0.45 13 13
Syndecan-3/IL8 0.049 0.11 -9999 0 -0.47 16 16
PSEN1 0.033 0.007 -9999 0 -10000 0 0
Src/Cortactin 0.04 0.021 -9999 0 -10000 0 0
FYN 0.03 0.037 -9999 0 -0.54 2 2
limb bud formation -0.001 0.089 -9999 0 -0.48 16 16
MC4R 0.034 0.013 -9999 0 -10000 0 0
SRC 0.033 0.008 -9999 0 -10000 0 0
PTN -0.37 0.27 -9999 0 -0.54 355 355
FGFR/FGF/Syndecan-3 -0.001 0.09 -9999 0 -0.49 16 16
neuron projection morphogenesis -0.12 0.16 -9999 0 -0.55 19 19
Syndecan-3/AgRP 0.034 0.1 -9999 0 -0.47 16 16
Syndecan-3/AgRP/MC4R 0.05 0.1 -9999 0 -0.46 15 15
Fyn/Cortactin 0.038 0.03 -9999 0 -0.28 2 2
SDC3 -0.002 0.091 -9999 0 -0.49 16 16
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.048 0.11 -9999 0 -0.46 16 16
IL8 0.048 0.053 -9999 0 -0.54 1 1
Syndecan-3/Fyn/Cortactin 0.043 0.099 -9999 0 -0.46 13 13
Syndecan-3/CASK -0.003 0.087 -9999 0 -0.47 16 16
alpha-MSH/MC4R 0.049 0.027 -9999 0 -0.4 1 1
Gamma Secretase 0.074 0.054 -9999 0 -0.3 1 1
TCGA08_rtk_signaling

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
PDGFRA -0.035 0.19 -10000 0 -0.54 61 61
HRAS 0.034 0.013 -10000 0 -10000 0 0
EGFR -0.27 0.29 -10000 0 -0.54 269 269
AKT -0.018 0.12 0.37 5 -0.26 39 44
FOXO3 0.032 0.01 -10000 0 -10000 0 0
AKT1 0.035 0.017 -10000 0 -10000 0 0
FOXO1 -0.023 0.17 -10000 0 -0.54 48 48
AKT3 0.028 0.019 -10000 0 -10000 0 0
FOXO4 0.034 0.002 -10000 0 -10000 0 0
MET -0.022 0.17 -10000 0 -0.54 50 50
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
PIK3CB 0.033 0.006 -10000 0 -10000 0 0
NRAS 0.036 0.016 -10000 0 -10000 0 0
PIK3CG 0.037 0.022 -10000 0 -10000 0 0
PIK3R3 0.042 0.035 -10000 0 -10000 0 0
PIK3R2 0.035 0.017 -10000 0 -10000 0 0
NF1 0.032 0.009 -10000 0 -10000 0 0
RAS -0.077 0.14 0.24 1 -0.33 86 87
ERBB2 0.028 0.029 -10000 0 -0.54 1 1
proliferation/survival/translation -0.016 0.098 0.3 26 -0.27 2 28
PI3K -0.068 0.16 0.32 9 -0.31 102 111
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
KRAS 0.034 0.018 0.18 6 -10000 0 6
FOXO 0.034 0.081 0.32 7 -0.17 10 17
AKT2 0.034 0.006 -10000 0 -10000 0 0
PTEN 0.026 0.067 -10000 0 -0.54 7 7
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.028 0.081 -10000 0 -0.49 7 7
Crk/p130 Cas/Paxillin -0.082 0.14 -10000 0 -0.38 71 71
JUN -0.002 0.15 0.28 3 -0.43 21 24
HRAS 0.034 0.013 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.11 0.17 -10000 0 -0.29 61 61
RAP1A 0.034 0.005 -10000 0 -10000 0 0
FRS2 0.032 0.029 -10000 0 -0.54 1 1
RAP1A/GDP 0.025 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.11 0.17 0.35 3 -0.3 58 61
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.034 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.055 0.14 -10000 0 -0.31 61 61
RHOA 0.033 0.007 -10000 0 -10000 0 0
RAP1A/GTP 0.076 0.15 -10000 0 -0.29 47 47
GRB7 0.029 0.013 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF 0.11 0.17 -10000 0 -0.3 59 59
MAPKKK cascade 0.057 0.14 0.25 8 -0.29 42 50
BCAR1 0.029 0.013 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.015 0.2 -10000 0 -0.38 93 93
lamellipodium assembly -0.044 0.16 -10000 0 -0.35 72 72
RET51/GFRalpha1/GDNF/SHC 0.091 0.16 -10000 0 -0.3 45 45
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC 0.044 0.13 -10000 0 -0.31 46 46
RET9/GFRalpha1/GDNF/Shank3 0.049 0.14 -10000 0 -0.31 62 62
MAPK3 0.042 0.13 0.28 3 -10000 0 3
DOK1 0.036 0.016 -10000 0 -10000 0 0
DOK6 0.032 0.049 -10000 0 -0.54 3 3
PXN 0.034 0.003 -10000 0 -10000 0 0
neurite development 0.043 0.12 0.33 1 -0.37 1 2
DOK5 0.012 0.11 -10000 0 -0.54 18 18
GFRA1 0.028 0.23 -10000 0 -0.54 65 65
MAPK8 0.053 0.12 0.27 4 -0.37 8 12
HRAS/GTP 0.092 0.16 0.3 4 -0.32 44 48
tube development 0.055 0.14 0.31 13 -0.3 58 71
MAPK1 0.044 0.13 0.38 2 -10000 0 2
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.02 0.11 -10000 0 -0.26 59 59
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
SRC 0.033 0.008 -10000 0 -10000 0 0
PDLIM7 0.034 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.11 0.17 0.35 2 -0.31 44 46
SHC1 0.027 0.014 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.09 0.17 -10000 0 -0.3 60 60
RET51/GFRalpha1/GDNF/Dok5 0.087 0.18 -10000 0 -0.3 65 65
PRKCA 0.031 0.013 -10000 0 -10000 0 0
HRAS/GDP 0.025 0.009 -10000 0 -10000 0 0
CREB1 0.042 0.12 -10000 0 -0.28 33 33
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.018 0.097 -10000 0 -0.25 41 41
RET51/GFRalpha1/GDNF/Grb7 0.099 0.16 -10000 0 -0.3 45 45
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.1 0.073 -10000 0 -10000 0 0
DOK4 0.03 0.012 -10000 0 -10000 0 0
JNK cascade -0.001 0.15 0.28 3 -0.42 21 24
RET9/GFRalpha1/GDNF/FRS2 0.05 0.15 -10000 0 -0.31 63 63
SHANK3 0.032 0.009 -10000 0 -10000 0 0
RASA1 0.034 0.012 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.019 0.099 -10000 0 -0.25 41 41
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.054 0.13 0.26 7 -0.39 5 12
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.06 0.13 0.25 4 -0.27 47 51
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.047 0.11 0.25 6 -0.38 3 9
PI3K -0.039 0.26 0.34 3 -0.54 76 79
SOS1 0.034 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.058 0.14 -10000 0 -0.3 58 58
GRB10 0.03 0.051 -10000 0 -0.54 4 4
activation of MAPKK activity 0.056 0.12 0.26 7 -0.38 2 9
RET51/GFRalpha1/GDNF/FRS2 0.1 0.17 0.35 1 -0.3 61 62
GAB1 0.033 0.027 -10000 0 -0.54 1 1
IRS1 -0.034 0.19 -10000 0 -0.54 60 60
IRS2 -0.1 0.24 -10000 0 -0.54 117 117
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.046 0.12 0.25 6 -0.25 33 39
RET51/GFRalpha1/GDNF/PKC alpha 0.098 0.17 -10000 0 -0.3 57 57
GRB2 0.034 0.018 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
GDNF 0.034 0.009 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.071 0.23 -10000 0 -0.38 87 87
Rac1/GTP -0.033 0.2 -10000 0 -0.42 72 72
RET9/GFRalpha1/GDNF 0.038 0.15 -10000 0 -0.34 62 62
GFRalpha1/GDNF 0.039 0.17 -10000 0 -0.4 62 62
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.089 0.16 0.34 70 -0.4 11 81
FYN 0.062 0.16 0.42 23 -0.41 17 40
LAT/GRAP2/SLP76 0.071 0.16 0.46 22 -0.41 11 33
IKBKB 0.028 0.013 -10000 0 -10000 0 0
AKT1 0.059 0.16 0.37 47 -0.31 29 76
B2M 0.037 0.011 -10000 0 -10000 0 0
IKBKG 0.034 0.071 0.19 51 -10000 0 51
MAP3K8 -0.04 0.19 -10000 0 -0.54 65 65
mol:Ca2+ -0.011 0.017 0.032 9 -0.089 12 21
integrin-mediated signaling pathway 0.037 0.023 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.053 0.18 0.5 22 -0.41 28 50
TRPV6 0.013 0.22 1.3 10 -0.54 17 27
CD28 0.028 0.084 -10000 0 -0.55 10 10
SHC1 0.072 0.18 0.34 74 -0.42 19 93
receptor internalization 0.024 0.19 0.36 25 -0.39 65 90
PRF1 0.037 0.16 0.54 10 -0.74 7 17
KRAS 0.034 0.018 0.18 6 -10000 0 6
GRB2 0.034 0.018 -10000 0 -10000 0 0
COT/AKT1 0.036 0.16 0.35 42 -0.31 34 76
LAT 0.055 0.17 0.42 27 -0.44 17 44
EntrezGene:6955 0.001 0.004 -10000 0 -10000 0 0
CD3D 0.04 0.036 0.21 8 -10000 0 8
CD3E 0.034 0.016 0.22 1 -10000 0 1
CD3G 0.038 0.073 -10000 0 -0.54 5 5
RASGRP2 0.009 0.049 0.17 10 -0.16 28 38
RASGRP1 0.065 0.16 0.43 31 -0.33 15 46
HLA-A 0.041 0.025 0.22 2 -10000 0 2
RASSF5 0.03 0.023 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.038 0.023 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.067 0.098 0.22 92 -0.13 2 94
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.01 0.048 -10000 0 -0.18 15 15
PRKCA 0.041 0.1 0.33 25 -0.22 6 31
GRAP2 0.034 0.019 -10000 0 -10000 0 0
mol:IP3 0.002 0.091 0.29 10 -0.33 10 20
EntrezGene:6957 0.003 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.025 0.13 0.32 20 -0.3 48 68
ORAI1 -0.02 0.17 -10000 0 -1.1 10 10
CSK 0.046 0.16 0.41 19 -0.43 16 35
B7 family/CD28 0.082 0.17 0.48 23 -0.44 13 36
CHUK 0.034 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.042 0.17 0.41 21 -0.39 35 56
PTPN6 0.044 0.16 0.37 25 -0.39 21 46
VAV1 0.043 0.16 0.46 17 -0.41 21 38
Monovalent TCR/CD3 0.023 0.1 0.28 21 -0.37 21 42
CBL 0.03 0.011 -10000 0 -10000 0 0
LCK 0.062 0.16 0.4 28 -0.41 14 42
PAG1 0.061 0.17 0.39 30 -0.46 13 43
RAP1A 0.034 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.04 0.17 0.39 23 -0.42 24 47
CD80 0.045 0.038 0.19 1 -10000 0 1
CD86 0.036 0.013 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1 0.01 0.067 -10000 0 -0.22 10 10
HRAS 0.034 0.013 -10000 0 -10000 0 0
GO:0035030 0.042 0.14 0.38 26 -0.38 14 40
CD8A 0.003 0.006 0.048 1 -10000 0 1
CD8B 0.041 0.026 0.22 2 -10000 0 2
PTPRC 0.035 0.035 -10000 0 -10000 0 0
PDK1/PKC theta 0.071 0.19 0.42 56 -0.36 23 79
CSK/PAG1 0.064 0.16 0.39 28 -0.46 11 39
SOS1 0.034 0.004 -10000 0 -10000 0 0
peptide-MHC class I 0.057 0.024 -10000 0 -10000 0 0
GRAP2/SLP76 0.065 0.17 0.47 18 -0.42 16 34
STIM1 0.004 0.1 1.2 3 -10000 0 3
RAS family/GTP 0.076 0.11 0.28 55 -0.18 10 65
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.021 0.19 0.36 26 -0.41 65 91
mol:DAG -0.016 0.068 0.14 1 -0.28 13 14
RAP1A/GDP 0.036 0.048 0.13 51 -10000 0 51
PLCG1 0.032 0.008 -10000 0 -10000 0 0
CD247 0.022 0.11 0.2 10 -0.55 15 25
cytotoxic T cell degranulation 0.038 0.16 0.53 10 -0.71 7 17
RAP1A/GTP 0.002 0.016 -10000 0 -0.061 26 26
mol:PI-3-4-5-P3 0.055 0.17 0.46 24 -0.36 28 52
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.023 0.12 0.33 9 -0.41 10 19
NRAS 0.036 0.016 -10000 0 -10000 0 0
ZAP70 0.038 0.024 -10000 0 -10000 0 0
GRB2/SOS1 0.048 0.019 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.045 0.13 0.33 7 -0.4 11 18
MALT1 0.033 0.01 -10000 0 -10000 0 0
TRAF6 0.034 0.006 -10000 0 -10000 0 0
CD8 heterodimer 0.033 0.022 0.19 5 -10000 0 5
CARD11 0.038 0.027 -10000 0 -10000 0 0
PRKCB -0.013 0.051 0.16 4 -0.2 13 17
PRKCE 0.046 0.11 0.32 29 -0.22 9 38
PRKCQ 0.059 0.18 0.48 28 -0.4 24 52
LCP2 0.036 0.023 -10000 0 -10000 0 0
BCL10 0.033 0.007 -10000 0 -10000 0 0
regulation of survival gene product expression 0.059 0.15 0.34 54 -0.27 29 83
IKK complex 0.056 0.093 0.23 71 -10000 0 71
RAS family/GDP 0 0.009 -10000 0 -10000 0 0
MAP3K14 0.029 0.14 0.28 49 -0.26 27 76
PDPK1 0.063 0.16 0.39 52 -0.3 25 77
TCR/CD3/MHC I/CD8/Fyn 0.014 0.17 0.4 13 -0.54 18 31
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.034 0.006 -10000 0 -10000 0 0
mol:PIP3 -0.048 0.13 0.24 4 -0.3 95 99
FRAP1 -0.014 0.11 0.34 1 -0.5 18 19
AKT1 -0.041 0.12 0.25 5 -0.29 69 74
INSR 0.034 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.044 0.011 -10000 0 -10000 0 0
mol:GTP -0.004 0.12 0.27 3 -0.28 34 37
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.007 0.057 -10000 0 -0.22 10 10
TSC2 0.031 0.01 -10000 0 -10000 0 0
RHEB/GDP -0.013 0.094 -10000 0 -0.26 32 32
TSC1 0.034 0.006 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.019 0.13 -10000 0 -0.33 72 72
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.004 0.072 -10000 0 -0.25 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.034 0.006 -10000 0 -10000 0 0
RPS6KB1 -0.009 0.1 0.3 4 -0.32 26 30
MAP3K5 -0.019 0.097 0.2 5 -0.29 51 56
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
apoptosis -0.019 0.097 0.2 5 -0.29 51 56
mol:LY294002 0 0.001 0.001 2 -0.002 61 63
EIF4B -0.008 0.096 0.28 5 -0.32 15 20
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.016 0.098 0.24 3 -0.3 15 18
eIF4E/eIF4G1/eIF4A1 -0.002 0.069 -10000 0 -0.3 18 18
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.026 0.15 -10000 0 -0.31 104 104
mTOR/RHEB/GTP/Raptor/GBL 0.008 0.077 0.25 12 -0.21 12 24
FKBP1A 0.034 0.012 -10000 0 -10000 0 0
RHEB/GTP 0.005 0.1 0.26 2 -0.32 11 13
mol:Amino Acids 0 0.001 0.001 2 -0.002 61 63
FKBP12/Rapamycin 0.025 0.009 -10000 0 -10000 0 0
PDPK1 -0.051 0.12 0.22 7 -0.29 88 95
EIF4E 0.034 0.005 -10000 0 -10000 0 0
ASK1/PP5C -0.04 0.21 -10000 0 -0.57 61 61
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.009 0.049 -10000 0 -10000 0 0
TSC1/TSC2 -0.003 0.12 0.29 3 -0.3 34 37
tumor necrosis factor receptor activity 0 0.001 0.002 61 -0.001 2 63
RPS6 0.032 0.026 -10000 0 -0.54 1 1
PPP5C 0.036 0.017 -10000 0 -10000 0 0
EIF4G1 0.033 0.007 -10000 0 -10000 0 0
IRS1 -0.041 0.13 -10000 0 -0.35 73 73
INS 0.033 0.007 -10000 0 -10000 0 0
PTEN 0.025 0.067 -10000 0 -0.54 7 7
PDK2 -0.046 0.12 0.22 9 -0.29 75 84
EIF4EBP1 -0.033 0.25 -10000 0 -1 29 29
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
PPP2R5D -0.012 0.1 0.35 3 -0.44 18 21
peptide biosynthetic process 0.019 0.016 0.19 4 -10000 0 4
RHEB 0.034 0.009 -10000 0 -10000 0 0
EIF4A1 0.031 0.011 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.005 15 -0.003 9 24
EEF2 0.02 0.016 0.19 3 -10000 0 3
eIF4E/4E-BP1 -0.016 0.24 -10000 0 -0.97 29 29
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.021 0.077 -10000 0 -0.28 5 5
alphaM/beta2 Integrin/GPIbA -0.016 0.079 0.27 3 -10000 0 3
alphaM/beta2 Integrin/proMMP-9 0.042 0.098 0.26 15 -10000 0 15
PLAUR 0.068 0.062 -10000 0 -10000 0 0
HMGB1 -0.03 0.045 -10000 0 -0.23 2 2
alphaM/beta2 Integrin/Talin -0.02 0.072 -10000 0 -10000 0 0
AGER -0.035 0.051 -10000 0 -0.59 1 1
RAP1A 0.034 0.005 -10000 0 -10000 0 0
SELPLG 0.034 0.028 -10000 0 -0.54 1 1
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.1 0.14 -10000 0 -0.37 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.094 0.074 -10000 0 -10000 0 0
CYR61 -0.13 0.26 -10000 0 -0.54 143 143
TLN1 0.033 0.006 -10000 0 -10000 0 0
Rap1/GTP 0.06 0.087 -10000 0 -0.34 8 8
RHOA 0.033 0.007 -10000 0 -10000 0 0
P-selectin oligomer -0.1 0.24 -10000 0 -0.54 117 117
MYH2 0.064 0.094 0.32 3 -0.5 4 7
MST1R 0.043 0.038 -10000 0 -10000 0 0
leukocyte activation during inflammatory response -0.013 0.067 -10000 0 -10000 0 0
APOB 0.034 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.028 0.039 -10000 0 -0.54 2 2
JAM3 -0.008 0.14 -10000 0 -0.54 34 34
GP1BA 0.036 0.029 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CTGF -0.033 0.1 -10000 0 -0.36 21 21
alphaM/beta2 Integrin 0.048 0.083 0.25 2 -0.36 8 10
JAM3 homodimer -0.008 0.14 -10000 0 -0.54 34 34
ICAM2 0.021 0.076 -10000 0 -0.54 9 9
ICAM1 0.039 0.029 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor 0.045 0.087 0.25 2 -0.37 9 11
cell adhesion -0.016 0.078 0.27 3 -10000 0 3
NFKB1 -0.22 0.19 0.4 1 -0.36 301 302
THY1 0.034 0.025 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
Lipoprotein(a) 0.043 0.013 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA -0.062 0.13 -10000 0 -0.33 72 72
IL6 -0.53 0.36 0.38 1 -0.74 374 375
ITGB2 -0.022 0.063 0.2 2 -10000 0 2
elevation of cytosolic calcium ion concentration 0.032 0.11 0.31 8 -10000 0 8
alphaM/beta2 Integrin/JAM2/JAM3 -0.11 0.2 -10000 0 -0.42 122 122
JAM2 -0.12 0.25 -10000 0 -0.54 132 132
alphaM/beta2 Integrin/ICAM1 0.008 0.092 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA/Plg 0.01 0.091 -10000 0 -0.36 1 1
RhoA/GTP 0.043 0.1 -10000 0 -0.41 12 12
positive regulation of phagocytosis 0.036 0.083 0.28 3 -0.35 3 6
Ron/MSP 0.056 0.028 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA 0.033 0.11 0.32 8 -10000 0 8
alphaM/beta2 Integrin/uPAR 0.01 0.095 0.26 12 -10000 0 12
PLAU 0.057 0.053 -10000 0 -10000 0 0
PLAT -0.064 0.21 -10000 0 -0.54 82 82
actin filament polymerization 0.065 0.097 0.31 8 -0.44 5 13
MST1 0.033 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/lipoprotein(a) -0.011 0.071 -10000 0 -10000 0 0
TNF -0.21 0.18 0.41 3 -0.6 7 10
RAP1B 0.033 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.003 0.085 0.26 1 -10000 0 1
fibrinolysis 0.009 0.089 -10000 0 -0.36 1 1
HCK 0.036 0.022 -10000 0 -10000 0 0
dendritic cell antigen processing and presentation 0.045 0.087 0.25 2 -0.37 9 11
VTN 0.032 0.011 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 -0.11 0.18 -10000 0 -0.38 134 134
LPA 0.032 0.009 -10000 0 -10000 0 0
LRP1 0.034 0.004 -10000 0 -10000 0 0
cell migration 0.029 0.091 0.24 15 -0.36 2 17
FN1 0.13 0.068 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 -0.017 0.075 0.26 1 -10000 0 1
MPO 0.031 0.016 -10000 0 -10000 0 0
KNG1 0.033 0.007 -10000 0 -10000 0 0
RAP1/GDP 0.044 0.012 -10000 0 -10000 0 0
ROCK1 0.063 0.11 0.29 5 -0.42 10 15
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.031 0.027 -10000 0 -0.54 1 1
CTGF 0.011 0.11 -10000 0 -0.54 19 19
alphaM/beta2 Integrin/Hck -0.017 0.076 0.27 5 -10000 0 5
ITGAM -0.028 0.044 -10000 0 -10000 0 0
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.073 0.16 -10000 0 -0.36 99 99
HP 0.029 0.012 -10000 0 -10000 0 0
leukocyte adhesion -0.17 0.2 -10000 0 -0.47 121 121
SELP -0.1 0.24 -10000 0 -0.54 117 117
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.12 0.12 0.3 2 -0.63 4 6
Syndecan-4/Syndesmos 0.13 0.12 0.39 5 -0.72 4 9
positive regulation of JNK cascade 0.062 0.18 0.39 2 -0.62 7 9
Syndecan-4/ADAM12 0.15 0.13 0.4 7 -0.76 4 11
CCL5 0.029 0.06 -10000 0 -0.54 5 5
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
DNM2 0.034 0.005 -10000 0 -10000 0 0
ITGA5 0.034 0.008 -10000 0 -10000 0 0
SDCBP 0.028 0.028 -10000 0 -0.54 1 1
PLG 0.012 0.041 -10000 0 -0.54 1 1
ADAM12 0.057 0.061 -10000 0 -0.54 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.032 0.012 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha 0.008 0.023 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.13 0.12 0.39 3 -0.72 4 7
Syndecan-4/CXCL12/CXCR4 0.066 0.19 0.4 2 -0.67 7 9
Syndecan-4/Laminin alpha3 0.054 0.16 0.4 3 -0.75 5 8
MDK 0.044 0.037 -10000 0 -10000 0 0
Syndecan-4/FZD7 0.062 0.17 0.39 2 -0.62 7 9
Syndecan-4/Midkine 0.14 0.12 0.38 8 -0.7 4 12
FZD7 -0.13 0.26 -10000 0 -0.54 145 145
Syndecan-4/FGFR1/FGF -0.066 0.16 0.4 1 -0.51 15 16
THBS1 0.038 0.025 -10000 0 -10000 0 0
integrin-mediated signaling pathway 0.14 0.12 0.39 4 -0.72 4 8
positive regulation of MAPKKK cascade 0.062 0.18 0.39 2 -0.62 7 9
Syndecan-4/TACI 0.13 0.12 0.39 4 -0.76 4 8
CXCR4 0.044 0.037 -10000 0 -10000 0 0
cell adhesion 0.091 0.071 0.27 50 -10000 0 50
Syndecan-4/Dynamin 0.14 0.12 0.39 3 -0.76 4 7
Syndecan-4/TSP1 0.14 0.12 0.42 4 -0.76 4 8
Syndecan-4/GIPC 0.14 0.12 0.4 5 -0.76 4 9
Syndecan-4/RANTES 0.13 0.13 0.39 2 -0.76 4 6
ITGB1 0.033 0.006 -10000 0 -10000 0 0
LAMA1 0.033 0.01 -10000 0 -10000 0 0
LAMA3 -0.15 0.27 -10000 0 -0.54 161 161
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCA 0.03 0.22 0.7 49 -10000 0 49
Syndecan-4/alpha-Actinin 0.14 0.12 0.39 3 -0.76 4 7
TFPI -0.19 0.28 -10000 0 -0.54 198 198
F2 0.039 0.02 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.049 0.012 -10000 0 -10000 0 0
positive regulation of cell adhesion 0.044 0.15 0.38 2 -0.69 5 7
ACTN1 0.033 0.007 -10000 0 -10000 0 0
TNC 0.037 0.036 -10000 0 -0.54 1 1
Syndecan-4/CXCL12 0.056 0.19 0.4 2 -0.56 12 14
FGF6 0.03 0.037 -10000 0 -0.54 2 2
RHOA 0.033 0.007 -10000 0 -10000 0 0
CXCL12 -0.14 0.26 -10000 0 -0.54 152 152
TNFRSF13B 0.032 0.014 -10000 0 -10000 0 0
FGF2 -0.39 0.25 -10000 0 -0.54 380 380
FGFR1 0.018 0.076 -10000 0 -0.54 9 9
Syndecan-4/PI-4-5-P2 0.096 0.12 0.31 2 -0.76 4 6
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.13 0.076 0.18 298 -10000 0 298
cell migration -0.013 0.008 -10000 0 -10000 0 0
PRKCD 0.016 0.035 -10000 0 -10000 0 0
vasculogenesis 0.14 0.12 0.4 5 -0.72 4 9
SDC4 0.11 0.12 0.34 3 -0.81 4 7
Syndecan-4/Tenascin C 0.14 0.12 0.39 4 -0.76 4 8
Syndecan-4/PI-4-5-P2/PKC alpha -0.005 0.014 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.12 0.12 0.38 3 -0.76 4 7
MMP9 0.094 0.078 0.2 2 -10000 0 2
Rac1/GTP 0.092 0.072 0.27 50 -10000 0 50
cytoskeleton organization 0.13 0.12 0.39 5 -0.69 4 9
GIPC1 0.034 0.011 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.036 0.19 0.38 5 -0.58 11 16
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.035 0.016 -10000 0 -10000 0 0
HSPA8 0.029 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.073 0.19 0.33 1 -0.4 107 108
AKT1 0.038 0.02 -10000 0 -10000 0 0
GSC -0.095 0.4 -10000 0 -1.3 46 46
NKX2-5 0.045 0.05 -10000 0 -10000 0 0
muscle cell differentiation 0 0.12 0.49 15 -10000 0 15
SMAD2-3/SMAD4/SP1 0.053 0.12 -10000 0 -0.31 13 13
SMAD4 -0.028 0.084 -10000 0 -0.29 17 17
CBFB 0.03 0.014 -10000 0 -10000 0 0
SAP18 0.032 0.009 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.16 0.2 -10000 0 -0.34 275 275
SMAD3/SMAD4/VDR 0.052 0.095 -10000 0 -0.35 6 6
MYC -0.006 0.12 -10000 0 -0.55 25 25
CDKN2B -0.05 0.2 -10000 0 -0.85 14 14
AP1 -0.26 0.29 -10000 0 -0.66 129 129
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.015 0.11 -10000 0 -0.39 20 20
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.01 0.11 -10000 0 -0.37 21 21
SP3 0.035 0.008 -10000 0 -10000 0 0
CREB1 0.034 0.006 -10000 0 -10000 0 0
FOXH1 0.018 0.041 -10000 0 -0.19 1 1
SMAD3/SMAD4/GR -0.045 0.14 -10000 0 -0.39 51 51
GATA3 0.038 0.16 -10000 0 -0.53 33 33
SKI/SIN3/HDAC complex/NCoR1 0.017 0.083 -10000 0 -0.38 15 15
MEF2C/TIF2 0.008 0.15 0.34 3 -0.54 24 27
endothelial cell migration -0.058 0.11 0.6 5 -10000 0 5
MAX 0.025 0.024 -10000 0 -10000 0 0
RBBP7 0.037 0.022 -10000 0 -10000 0 0
RBBP4 0.033 0.006 -10000 0 -10000 0 0
RUNX2 0.036 0.019 -10000 0 -10000 0 0
RUNX3 -0.006 0.15 -10000 0 -0.54 36 36
RUNX1 0.018 0.098 -10000 0 -0.54 15 15
CTBP1 0.033 0.008 -10000 0 -10000 0 0
NR3C1 -0.019 0.16 -10000 0 -0.55 40 40
VDR 0.032 0.037 -10000 0 -0.54 2 2
CDKN1A 0.004 0.11 -10000 0 -1.1 3 3
KAT2B 0.001 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.026 0.11 -10000 0 -0.34 27 27
DCP1A 0.033 0.008 -10000 0 -10000 0 0
SKI 0.033 0.007 -10000 0 -10000 0 0
SERPINE1 0.058 0.11 -10000 0 -0.61 5 5
SMAD3/SMAD4/ATF2 0.004 0.092 -10000 0 -0.29 10 10
SMAD3/SMAD4/ATF3 -0.09 0.2 -10000 0 -0.41 132 132
SAP30 0.033 0.009 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.062 0.04 -10000 0 -10000 0 0
JUN -0.26 0.28 -10000 0 -0.67 122 122
SMAD3/SMAD4/IRF7 0.021 0.094 -10000 0 -0.29 9 9
TFE3 0.03 0.046 -10000 0 -0.18 8 8
COL1A2 0.075 0.13 0.39 10 -0.71 5 15
mesenchymal cell differentiation -0.005 0.093 0.29 9 -10000 0 9
DLX1 0.043 0.036 -10000 0 -10000 0 0
TCF3 0.035 0.017 -10000 0 -10000 0 0
FOS -0.37 0.28 -10000 0 -0.56 346 346
SMAD3/SMAD4/Max -0.018 0.089 -10000 0 -0.29 9 9
Cbp/p300/SNIP1 0.06 0.033 -10000 0 -0.32 1 1
ZBTB17 0.027 0.022 -10000 0 -10000 0 0
LAMC1 -0.038 0.15 -10000 0 -0.6 27 27
TGIF2/HDAC complex/SMAD3/SMAD4 0.005 0.091 -10000 0 -0.29 10 10
IRF7 0.039 0.024 0.22 1 -10000 0 1
ESR1 -0.068 0.25 0.23 3 -0.55 106 109
HNF4A 0.033 0.008 -10000 0 -10000 0 0
MEF2C 0.015 0.17 0.42 9 -0.55 28 37
SMAD2-3/SMAD4 0.009 0.11 -10000 0 -0.31 19 19
Cbp/p300/Src-1 0.062 0.039 -10000 0 -0.32 2 2
IGHV3OR16-13 -0.007 0.07 -10000 0 -0.45 10 10
TGIF2/HDAC complex 0.033 0.01 -10000 0 -10000 0 0
CREBBP 0.032 0.028 -10000 0 -0.52 1 1
SKIL 0.045 0.042 -10000 0 -10000 0 0
HDAC1 0.033 0.005 -10000 0 -10000 0 0
HDAC2 0.033 0.017 -10000 0 -10000 0 0
SNIP1 0.033 0.006 -10000 0 -10000 0 0
GCN5L2 0.003 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.019 0.13 -10000 0 -0.38 30 30
MSG1/HSC70 -0.21 0.22 -10000 0 -0.4 297 297
SMAD2 0.02 0.053 -10000 0 -0.23 1 1
SMAD3 -0.015 0.063 -10000 0 -0.22 2 2
SMAD3/E2F4-5/DP1/p107/SMAD4 0.005 0.07 -10000 0 -0.31 6 6
SMAD2/SMAD2/SMAD4 0.01 0.053 0.22 6 -0.3 2 8
NCOR1 0.031 0.011 -10000 0 -10000 0 0
NCOA2 0.028 0.015 -10000 0 -10000 0 0
NCOA1 0.033 0.026 -10000 0 -0.54 1 1
MYOD/E2A 0.049 0.035 -10000 0 -0.4 2 2
SMAD2-3/SMAD4/SP1/MIZ-1 0.074 0.12 -10000 0 -0.32 8 8
IFNB1 -0.012 0.072 0.32 3 -0.3 1 4
SMAD3/SMAD4/MEF2C 0.022 0.18 0.41 1 -0.56 29 30
CITED1 -0.3 0.29 -10000 0 -0.54 296 296
SMAD2-3/SMAD4/ARC105 0.025 0.11 -10000 0 -0.3 12 12
RBL1 0.04 0.032 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.001 0.11 -10000 0 -0.44 12 12
RUNX1-3/PEBPB2 0.02 0.13 -10000 0 -0.35 49 49
SMAD7 -0.18 0.22 -10000 0 -0.51 96 96
MYC/MIZ-1 0.008 0.098 -10000 0 -0.41 25 25
SMAD3/SMAD4 0.032 0.097 0.33 10 -0.38 3 13
IL10 -0.006 0.12 0.4 1 -0.39 21 22
PIASy/HDAC complex 0.026 0.028 -10000 0 -10000 0 0
PIAS3 0.034 0.009 -10000 0 -10000 0 0
CDK2 0.04 0.023 0.22 1 -10000 0 1
IL5 -0.002 0.12 0.4 1 -0.38 26 27
CDK4 0.036 0.011 -10000 0 -10000 0 0
PIAS4 0.026 0.028 -10000 0 -10000 0 0
ATF3 -0.12 0.25 -10000 0 -0.54 128 128
SMAD3/SMAD4/SP1 0.039 0.1 -10000 0 -0.3 11 11
FOXG1 0.042 0.037 -10000 0 -10000 0 0
FOXO3 0.021 0.02 -10000 0 -10000 0 0
FOXO1 -0.019 0.12 -10000 0 -0.39 48 48
FOXO4 0.022 0.02 -10000 0 -10000 0 0
heart looping 0.015 0.17 0.42 9 -0.55 28 37
CEBPB 0.031 0.029 -10000 0 -0.54 1 1
SMAD3/SMAD4/DLX1 0.013 0.094 -10000 0 -0.29 7 7
MYOD1 0.033 0.041 -10000 0 -0.54 2 2
SMAD3/SMAD4/HNF4 0.006 0.091 -10000 0 -0.29 9 9
SMAD3/SMAD4/GATA3 0.027 0.15 -10000 0 -0.41 32 32
SnoN/SIN3/HDAC complex/NCoR1 0.045 0.041 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.006 0.15 -10000 0 -0.36 48 48
SMAD3/SMAD4/SP1-3 0.061 0.11 -10000 0 -0.34 4 4
MED15 0.033 0.008 -10000 0 -10000 0 0
SP1 0.047 0.024 -10000 0 -10000 0 0
SIN3B 0.035 0.014 -10000 0 -10000 0 0
SIN3A 0.033 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.045 0.12 -10000 0 -0.37 23 23
ITGB5 -0.003 0.084 0.33 1 -0.41 4 5
TGIF/SIN3/HDAC complex/CtBP 0.024 0.07 -10000 0 -0.33 12 12
SMAD3/SMAD4/AR -0.044 0.16 -10000 0 -0.39 71 71
AR -0.04 0.19 -10000 0 -0.54 66 66
negative regulation of cell growth -0.022 0.12 -10000 0 -0.37 24 24
SMAD3/SMAD4/MYOD 0.004 0.096 -10000 0 -0.3 11 11
E2F5 0.035 0.036 -10000 0 -10000 0 0
E2F4 0.03 0.012 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.05 0.11 -10000 0 -0.37 9 9
SMAD2-3/SMAD4/FOXO1-3a-4 -0.007 0.11 -10000 0 -0.37 20 20
TFDP1 0.033 0.021 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.25 0.3 -10000 0 -0.69 122 122
SMAD3/SMAD4/RUNX2 0.006 0.093 -10000 0 -0.29 9 9
TGIF2 0.033 0.01 -10000 0 -10000 0 0
TGIF1 0.031 0.027 -10000 0 -0.54 1 1
ATF2 0.034 0.005 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.017 0.18 -10000 0 -0.75 3 3
PCK1 -0.74 0.54 -10000 0 -1 387 387
HNF4A 0.033 0.2 0.73 1 -0.75 3 4
KCNJ11 0.038 0.24 0.75 3 -0.76 3 6
AKT1 0.012 0.15 -10000 0 -0.5 4 4
response to starvation 0.005 0.002 -10000 0 -10000 0 0
DLK1 0.028 0.22 0.88 1 -0.81 3 4
NKX2-1 0.034 0.12 0.64 1 -10000 0 1
ACADM 0.015 0.21 -10000 0 -0.86 8 8
TAT -0.058 0.2 -10000 0 -0.72 16 16
CEBPB 0.034 0.028 -10000 0 -0.54 1 1
CEBPA 0.035 0.045 -10000 0 -0.54 3 3
TTR -0.033 0.26 0.59 1 -0.65 44 45
PKLR 0.035 0.19 -10000 0 -0.79 2 2
APOA1 0.022 0.22 -10000 0 -0.88 3 3
CPT1C 0.028 0.2 0.71 1 -0.76 3 4
ALAS1 0.031 0.14 -10000 0 -10000 0 0
TFRC -0.017 0.2 0.7 2 -10000 0 2
FOXF1 0.025 0.021 -10000 0 -10000 0 0
NF1 0.038 0.01 -10000 0 -10000 0 0
HNF1A (dimer) 0.05 0.022 -10000 0 -0.22 1 1
CPT1A 0.025 0.21 0.72 3 -0.7 3 6
HMGCS1 0.023 0.2 0.75 2 -0.76 3 5
NR3C1 0 0.16 -10000 0 -0.51 43 43
CPT1B 0.018 0.19 -10000 0 -0.75 3 3
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.041 0.015 -10000 0 -10000 0 0
GCK 0.023 0.19 -10000 0 -0.76 3 3
CREB1 -0.18 0.14 -10000 0 -0.27 334 334
IGFBP1 0.015 0.14 -10000 0 -0.66 4 4
PDX1 0.043 0.16 -10000 0 -1.1 2 2
UCP2 0.026 0.2 0.66 2 -0.7 3 5
ALDOB 0.023 0.22 -10000 0 -0.81 3 3
AFP -0.052 0.14 0.39 1 -0.39 12 13
BDH1 0.025 0.19 0.67 2 -0.76 3 5
HADH 0.018 0.23 -10000 0 -0.93 5 5
F2 0.038 0.22 -10000 0 -0.82 3 3
HNF1A 0.05 0.022 -10000 0 -0.22 1 1
G6PC -0.098 0.12 -10000 0 -10000 0 0
SLC2A2 0.047 0.16 -10000 0 -0.84 2 2
INS 0.022 0.015 0.25 1 -10000 0 1
FOXA1 -0.003 0.23 0.32 7 -0.53 73 80
FOXA3 -0.12 0.14 -10000 0 -0.29 67 67
FOXA2 0.03 0.27 -10000 0 -0.92 3 3
ABCC8 -0.066 0.42 0.9 1 -0.93 85 86
ALB -0.054 0.15 0.39 1 -0.56 8 9
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.011 0.096 0.35 8 -0.31 9 17
TBX21 -0.13 0.37 0.74 5 -1.2 37 42
B2M 0.038 0.013 0.2 1 -10000 0 1
TYK2 0.017 0.036 -10000 0 -10000 0 0
IL12RB1 0.017 0.036 -10000 0 -10000 0 0
GADD45B -0.071 0.28 0.7 2 -0.85 31 33
IL12RB2 0.03 0.076 0.26 6 -0.55 1 7
GADD45G -0.062 0.26 0.67 4 -0.69 42 46
natural killer cell activation -0.008 0.022 -10000 0 -10000 0 0
RELB 0.036 0.02 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
IL18 0.045 0.046 0.24 2 -10000 0 2
IL2RA 0.041 0.035 -10000 0 -10000 0 0
IFNG 0.063 0.066 -10000 0 -0.54 1 1
STAT3 (dimer) -0.062 0.24 0.6 8 -0.59 47 55
HLA-DRB5 -0.008 0.032 -10000 0 -10000 0 0
FASLG -0.061 0.26 0.73 7 -0.82 16 23
NF kappa B2 p52/RelB -0.082 0.25 0.54 6 -0.59 62 68
CD4 -0.008 0.031 -10000 0 -10000 0 0
SOCS1 0.032 0.012 -10000 0 -10000 0 0
EntrezGene:6955 -0.014 0.015 -10000 0 -10000 0 0
CD3D 0.003 0.05 0.21 5 -10000 0 5
CD3E -0.001 0.033 0.21 1 -10000 0 1
CD3G 0.004 0.081 -10000 0 -0.56 5 5
IL12Rbeta2/JAK2 0.028 0.075 0.3 7 -0.41 1 8
CCL3 -0.087 0.25 0.71 2 -0.8 19 21
CCL4 -0.087 0.25 0.79 1 -0.8 19 20
HLA-A 0.043 0.026 0.21 1 -10000 0 1
IL18/IL18R 0.058 0.14 0.4 11 -0.36 42 53
NOS2 -0.086 0.26 0.6 9 -0.59 67 76
IL12/IL12R/TYK2/JAK2/SPHK2 0.008 0.099 0.35 8 -0.32 9 17
IL1R1 -0.17 0.43 0.71 2 -1.2 63 65
IL4 0.038 0.03 -10000 0 -10000 0 0
JAK2 0.016 0.037 0.25 1 -10000 0 1
EntrezGene:6957 -0.011 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.003 0.15 0.34 22 -0.37 28 50
RAB7A -0.045 0.24 0.64 4 -0.7 26 30
lysosomal transport -0.042 0.24 0.62 5 -0.65 28 33
FOS -0.83 0.6 0.57 1 -1.2 367 368
STAT4 (dimer) -0.034 0.27 0.63 9 -0.67 41 50
STAT5A (dimer) -0.061 0.26 0.58 8 -0.61 55 63
GZMA -0.093 0.25 0.57 7 -0.59 63 70
GZMB -0.092 0.26 0.71 6 -0.85 19 25
HLX 0.025 0.038 -10000 0 -0.54 2 2
LCK -0.086 0.27 0.69 9 -0.63 62 71
TCR/CD3/MHC II/CD4 -0.12 0.16 0.28 5 -0.44 61 66
IL2/IL2R 0.088 0.056 0.37 4 -0.32 1 5
MAPK14 -0.06 0.28 0.63 8 -0.75 42 50
CCR5 -0.068 0.28 0.71 10 -0.74 41 51
IL1B 0.014 0.071 0.26 1 -0.55 5 6
STAT6 -0.039 0.18 0.39 7 -0.66 27 34
STAT4 0.027 0.069 -10000 0 -0.54 7 7
STAT3 0.033 0.007 -10000 0 -10000 0 0
STAT1 0.059 0.055 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
NFKB2 0.035 0.012 -10000 0 -10000 0 0
IL12B 0.01 0.048 0.25 2 -10000 0 2
CD8A 0.005 0.009 -10000 0 -10000 0 0
CD8B 0.042 0.027 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.011 0.096 0.3 9 -0.35 8 17
IL2RB 0.035 0.022 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.028 0.26 0.61 10 -0.62 40 50
IL2RG 0.043 0.035 -10000 0 -10000 0 0
IL12 0.007 0.089 0.28 4 -0.41 11 15
STAT5A 0.032 0.026 -10000 0 -0.54 1 1
CD247 -0.003 0.11 0.21 8 -0.55 15 23
IL2 0.033 0.027 -10000 0 -0.54 1 1
SPHK2 0.034 0.005 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.006 0.093 0.23 2 -0.56 11 13
IL12/IL12R/TYK2/JAK2 -0.1 0.27 0.68 8 -0.66 63 71
MAP2K3 -0.071 0.29 0.62 8 -0.75 50 58
RIPK2 0.029 0.021 -10000 0 -10000 0 0
MAP2K6 -0.063 0.27 0.63 8 -0.72 44 52
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.012 0.034 -10000 0 -10000 0 0
IL18RAP -0.009 0.16 -10000 0 -0.55 42 42
IL12Rbeta1/TYK2 0.029 0.047 0.25 1 -10000 0 1
EOMES 0.042 0.1 -10000 0 -0.56 5 5
STAT1 (dimer) -0.013 0.26 0.67 15 -0.6 37 52
T cell proliferation -0.031 0.22 0.54 9 -0.54 42 51
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.037 0.031 0.2 2 -0.56 1 3
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.022 0.23 0.52 2 -0.61 40 42
ATF2 -0.057 0.26 0.6 7 -0.7 41 48
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.049 0.023 -10000 0 -10000 0 0
VLDLR -0.041 0.19 -10000 0 -0.54 65 65
CRKL 0.033 0.008 -10000 0 -10000 0 0
LRPAP1 0.033 0.007 -10000 0 -10000 0 0
FYN 0.03 0.037 -10000 0 -0.54 2 2
ITGA3 0.03 0.028 -10000 0 -0.54 1 1
RELN/VLDLR/Fyn -0.011 0.16 -10000 0 -0.36 82 82
MAPK8IP1/MKK7/MAP3K11/JNK1 0.078 0.047 -10000 0 -10000 0 0
AKT1 -0.056 0.14 -10000 0 -0.3 108 108
MAP2K7 0.034 0.005 -10000 0 -10000 0 0
RAPGEF1 0.034 0.006 -10000 0 -10000 0 0
DAB1 0.034 0.006 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.07 0.084 0.24 2 -0.29 20 22
LRPAP1/LRP8 0.073 0.047 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn 0.075 0.088 -10000 0 -0.28 22 22
DAB1/alpha3/beta1 Integrin 0.018 0.13 -10000 0 -0.3 58 58
long-term memory 0.081 0.11 -10000 0 -0.33 20 20
DAB1/LIS1 0.034 0.15 -10000 0 -0.31 64 64
DAB1/CRLK/C3G 0.019 0.14 -10000 0 -0.3 64 64
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
DAB1/NCK2 0.039 0.15 -10000 0 -0.31 64 64
ARHGEF2 0.03 0.022 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.032 0.012 -10000 0 -10000 0 0
CDK5R1 0.033 0.014 -10000 0 -10000 0 0
RELN 0.012 0.11 -10000 0 -0.54 20 20
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
RELN/LRP8/Fyn 0.066 0.095 0.25 1 -0.32 22 23
GRIN2A/RELN/LRP8/DAB1/Fyn 0.084 0.095 -10000 0 -0.3 14 14
MAPK8 0.033 0.026 -10000 0 -0.54 1 1
RELN/VLDLR/DAB1 -0.005 0.15 -10000 0 -0.33 80 80
ITGB1 0.033 0.006 -10000 0 -10000 0 0
MAP1B -0.037 0.16 0.28 8 -0.34 92 100
RELN/LRP8 0.07 0.091 0.25 1 -0.32 20 21
GRIN2B/RELN/LRP8/DAB1/Fyn 0.08 0.11 -10000 0 -0.31 29 29
PI3K 0.005 0.13 -10000 0 -0.37 51 51
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.043 0.027 -10000 0 -0.4 1 1
RAP1A -0.029 0.12 0.35 3 -0.48 5 8
PAFAH1B1 0.032 0.01 -10000 0 -10000 0 0
MAPK8IP1 0.034 0.005 -10000 0 -10000 0 0
CRLK/C3G 0.047 0.014 -10000 0 -10000 0 0
GRIN2B 0.021 0.085 -10000 0 -0.54 11 11
NCK2 0.034 0.007 -10000 0 -10000 0 0
neuron differentiation 0.049 0.069 0.24 3 -0.55 1 4
neuron adhesion -0.012 0.13 0.38 5 -0.46 4 9
LRP8 0.072 0.064 -10000 0 -10000 0 0
GSK3B -0.051 0.14 -10000 0 -0.5 24 24
RELN/VLDLR/DAB1/Fyn 0.005 0.15 -10000 0 -0.31 82 82
MAP3K11 0.034 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.055 0.16 -10000 0 -0.31 114 114
CDK5 0.037 0.023 -10000 0 -10000 0 0
MAPT 0.014 0.12 0.79 10 -0.5 3 13
neuron migration -0.027 0.15 0.33 7 -0.38 35 42
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.048 0.068 -10000 0 -0.55 1 1
RELN/VLDLR 0.029 0.16 -10000 0 -0.31 80 80
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.007 0.23 -10000 0 -0.9 24 24
NCK1/PAK1/Dok-R -0.034 0.093 -10000 0 -0.41 24 24
NCK1/Dok-R 0.017 0.24 -10000 0 -1 23 23
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
mol:beta2-estradiol -0.001 0.04 0.23 14 -10000 0 14
RELA 0.034 0.005 -10000 0 -10000 0 0
SHC1 0.028 0.014 -10000 0 -10000 0 0
Rac/GDP 0.025 0.004 -10000 0 -10000 0 0
F2 0.018 0.047 0.28 12 -10000 0 12
TNIP2 0.034 0.013 -10000 0 -10000 0 0
NF kappa B/RelA 0.043 0.23 -10000 0 -0.94 23 23
FN1 0.13 0.068 -10000 0 -10000 0 0
PLD2 -0.004 0.23 -10000 0 -1 23 23
PTPN11 0.034 0.004 -10000 0 -10000 0 0
GRB14 0 0.19 -10000 0 -0.54 52 52
ELK1 0.005 0.21 -10000 0 -0.94 23 23
GRB7 0.029 0.013 -10000 0 -10000 0 0
PAK1 0.043 0.046 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.096 0.25 -10000 0 -0.96 23 23
CDKN1A -0.003 0.19 -10000 0 -0.66 21 21
ITGA5 0.034 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.016 0.24 -10000 0 -1 23 23
CRK 0.031 0.01 -10000 0 -10000 0 0
mol:NO 0.016 0.18 -10000 0 -0.65 24 24
PLG -0.004 0.23 -10000 0 -1 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.002 0.21 -10000 0 -0.84 24 24
GRB2 0.034 0.018 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
ANGPT2 -0.075 0.23 -10000 0 -0.66 35 35
BMX -0.16 0.28 -10000 0 -1.3 23 23
ANGPT1 -0.012 0.21 -10000 0 -1.2 14 14
tube development -0.012 0.2 -10000 0 -0.73 21 21
ANGPT4 0.032 0.008 -10000 0 -10000 0 0
response to hypoxia -0.001 0.015 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.002 0.28 -10000 0 -1.1 23 23
alpha5/beta1 Integrin 0.049 0.012 -10000 0 -10000 0 0
FGF2 -0.39 0.25 -10000 0 -0.54 380 380
STAT5A (dimer) -0.002 0.23 -10000 0 -0.85 21 21
mol:L-citrulline 0.016 0.18 -10000 0 -0.65 24 24
AGTR1 -0.18 0.3 -10000 0 -0.54 207 207
MAPK14 -0.003 0.26 -10000 0 -1 26 26
Tie2/SHP2 0.001 0.21 -10000 0 -0.99 16 16
TEK -0.004 0.22 -10000 0 -1.1 16 16
RPS6KB1 0.021 0.23 -10000 0 -0.86 24 24
Angiotensin II/AT1 -0.13 0.22 -10000 0 -0.39 209 209
Tie2/Ang1/GRB2 0.011 0.24 -10000 0 -1.1 23 23
MAPK3 0.005 0.22 -10000 0 -0.93 23 23
MAPK1 -0.005 0.21 -10000 0 -0.96 23 23
Tie2/Ang1/GRB7 0.005 0.24 -10000 0 -1.1 23 23
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 -0.004 0.23 -10000 0 -1 23 23
PI3K -0.005 0.26 -10000 0 -1 24 24
FES -0.01 0.26 -10000 0 -1.1 26 26
Crk/Dok-R 0.017 0.24 -10000 0 -1 23 23
Tie2/Ang1/ABIN2 0.013 0.25 -10000 0 -1.1 23 23
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.013 0.21 -10000 0 -0.8 24 24
STAT5A 0.032 0.027 -10000 0 -0.54 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.033 0.23 -10000 0 -0.82 24 24
Tie2/Ang2 -0.027 0.25 -10000 0 -1 21 21
Tie2/Ang1 0.001 0.25 -10000 0 -1.1 23 23
FOXO1 0.006 0.22 -10000 0 -0.82 25 25
ELF1 0.035 0.027 -10000 0 -10000 0 0
ELF2 0.002 0.23 -10000 0 -1 23 23
mol:Choline -0.002 0.22 -10000 0 -0.99 23 23
cell migration -0.015 0.053 -10000 0 -0.23 24 24
FYN -0.018 0.22 -10000 0 -0.84 21 21
DOK2 0.025 0.039 -10000 0 -0.54 2 2
negative regulation of cell cycle 0.002 0.17 -10000 0 -0.59 21 21
ETS1 0.031 0.056 -10000 0 -0.29 11 11
PXN 0.038 0.2 -10000 0 -0.68 24 24
ITGB1 0.033 0.006 -10000 0 -10000 0 0
NOS3 0.012 0.2 -10000 0 -0.74 24 24
RAC1 0.034 0.005 -10000 0 -10000 0 0
TNF 0.038 0.054 0.26 1 -0.25 13 14
MAPKKK cascade -0.002 0.22 -10000 0 -0.99 23 23
RASA1 0.034 0.012 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.003 0.24 -10000 0 -1 22 22
NCK1 0.034 0.005 -10000 0 -10000 0 0
vasculogenesis 0.019 0.16 -10000 0 -0.58 24 24
mol:Phosphatidic acid -0.002 0.22 -10000 0 -0.99 23 23
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.016 0.18 -10000 0 -0.65 24 24
Rac1/GTP 0.014 0.21 -10000 0 -0.8 24 24
MMP2 -0.003 0.24 -10000 0 -1 23 23
Syndecan-1-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
TGFB1 0.034 0.008 -10000 0 -10000 0 0
CCL5 0.029 0.06 -10000 0 -0.54 5 5
SDCBP 0.028 0.028 -10000 0 -0.54 1 1
FGFR/FGF2/Syndecan-1 0.087 0.14 0.32 31 -0.34 8 39
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 0.069 0.14 0.29 17 -0.34 9 26
Syndecan-1/Syntenin 0.071 0.14 0.3 23 -0.34 9 32
MAPK3 0.071 0.13 0.28 28 -0.33 7 35
HGF/MET 0.006 0.13 -10000 0 -0.4 51 51
TGFB1/TGF beta receptor Type II 0.034 0.008 -10000 0 -10000 0 0
BSG 0.034 0.015 -10000 0 -10000 0 0
keratinocyte migration 0.069 0.14 0.29 17 -0.34 9 26
Syndecan-1/RANTES 0.076 0.15 0.3 28 -0.37 11 39
Syndecan-1/CD147 0.093 0.15 0.36 12 -0.34 8 20
Syndecan-1/Syntenin/PIP2 0.066 0.13 0.29 18 -0.32 9 27
LAMA5 0.032 0.012 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.064 0.13 0.28 18 -0.32 9 27
MMP7 -0.042 0.19 -10000 0 -0.54 64 64
HGF 0.035 0.01 -10000 0 -10000 0 0
Syndecan-1/CASK 0.058 0.13 0.25 24 -0.32 11 35
Syndecan-1/HGF/MET 0.063 0.18 0.33 11 -0.38 32 43
regulation of cell adhesion 0.061 0.12 0.3 10 -0.33 6 16
HPSE 0.045 0.04 -10000 0 -10000 0 0
positive regulation of cell migration 0.087 0.14 0.32 31 -0.34 8 39
SDC1 0.087 0.13 0.26 93 -0.27 10 103
Syndecan-1/Collagen 0.087 0.14 0.32 31 -0.34 8 39
PPIB 0.034 0.009 -10000 0 -10000 0 0
MET -0.022 0.17 -10000 0 -0.54 50 50
PRKACA 0.034 0.005 -10000 0 -10000 0 0
MMP9 0.094 0.074 -10000 0 -10000 0 0
MAPK1 0.071 0.13 0.29 24 -0.34 6 30
homophilic cell adhesion 0.085 0.14 0.32 31 -0.34 8 39
MMP1 0.11 0.077 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.099 0.077 0.31 6 -0.29 4 10
NF kappa B1 p50/RelA/I kappa B alpha 0.11 0.1 0.38 12 -10000 0 12
alphaV/beta3 Integrin/Osteopontin/Src 0.099 0.072 0.26 2 -0.39 4 6
AP1 -0.14 0.22 0.49 1 -0.46 90 91
ILK 0.077 0.073 0.31 7 -0.3 4 11
bone resorption 0.059 0.071 -10000 0 -10000 0 0
PTK2B 0.027 0.014 -10000 0 -10000 0 0
PYK2/p130Cas 0.1 0.09 0.33 2 -0.28 4 6
ITGAV 0.04 0.029 -10000 0 -0.54 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.047 0.031 -10000 0 -0.4 2 2
alphaV/beta3 Integrin/Osteopontin 0.12 0.078 0.32 3 -0.33 4 7
MAP3K1 0.079 0.078 0.3 12 -0.3 5 17
JUN -0.066 0.22 -10000 0 -0.54 89 89
MAPK3 0.079 0.096 0.31 30 -0.28 3 33
MAPK1 0.078 0.093 0.33 15 -0.28 4 19
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 0.064 0.077 0.29 12 -0.29 6 18
ITGB3 0.041 0.021 0.2 3 -10000 0 3
NFKBIA 0.077 0.099 0.35 22 -10000 0 22
FOS -0.35 0.27 -10000 0 -0.54 344 344
CD44 0.033 0.028 -10000 0 -0.54 1 1
CHUK 0.034 0.005 -10000 0 -10000 0 0
PLAU 0.084 0.15 0.48 14 -0.53 1 15
NF kappa B1 p50/RelA 0.14 0.1 0.42 16 -10000 0 16
BCAR1 0.029 0.013 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.061 0.033 -10000 0 -0.39 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.08 0.075 0.3 11 -0.3 4 15
VAV3 0.063 0.096 0.29 16 -0.29 12 28
MAP3K14 0.087 0.083 0.3 15 -0.3 4 19
ROCK2 0.033 0.026 -10000 0 -0.54 1 1
SPP1 0.096 0.088 -10000 0 -0.54 3 3
RAC1 0.034 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.072 0.088 0.28 11 -0.27 10 21
MMP2 -0.13 0.17 0.47 1 -0.41 73 74
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.071 0.094 0.23 3 -0.32 16 19
EPHB2 0.043 0.037 -10000 0 -10000 0 0
Syndecan-2/TACI 0.016 0.066 -10000 0 -0.33 16 16
LAMA1 0.033 0.01 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 -0.058 0.17 -10000 0 -0.32 133 133
HRAS 0.034 0.013 -10000 0 -10000 0 0
Syndecan-2/CASK -0.001 0.06 -10000 0 -0.33 16 16
ITGA5 0.034 0.008 -10000 0 -10000 0 0
BAX 0 0.063 0.49 2 -10000 0 2
EPB41 0.033 0.007 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.015 0.059 -10000 0 -0.3 16 16
LAMA3 -0.15 0.27 -10000 0 -0.54 161 161
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.32 0.28 -10000 0 -0.54 318 318
Syndecan-2/MMP2 0.013 0.073 -10000 0 -0.37 16 16
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.033 0.081 -10000 0 -0.4 16 16
dendrite morphogenesis 0.022 0.07 -10000 0 -0.33 16 16
Syndecan-2/GM-CSF 0.02 0.068 -10000 0 -0.33 16 16
determination of left/right symmetry 0 0.071 -10000 0 -0.39 16 16
Syndecan-2/PKC delta 0.017 0.066 -10000 0 -0.33 16 16
GNB2L1 0.034 0.006 -10000 0 -10000 0 0
MAPK3 0.042 0.094 0.28 4 -0.3 15 19
MAPK1 0.047 0.097 0.28 4 -0.3 16 20
Syndecan-2/RACK1 0.03 0.062 -10000 0 -0.28 16 16
NF1 0.032 0.009 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0 0.071 -10000 0 -0.39 16 16
ITGA2 0.014 0.1 -10000 0 -0.54 17 17
MAPK8 0.001 0.067 0.34 3 -0.33 17 20
Syndecan-2/alpha2/beta1 Integrin 0.035 0.091 -10000 0 -0.33 22 22
Syndecan-2/Kininogen 0.017 0.065 -10000 0 -0.33 16 16
ITGB1 0.033 0.006 -10000 0 -10000 0 0
SRC 0.042 0.089 0.3 6 -0.28 15 21
Syndecan-2/CASK/Protein 4.1 0.015 0.06 -10000 0 -0.3 16 16
extracellular matrix organization 0.017 0.065 -10000 0 -0.33 16 16
actin cytoskeleton reorganization 0.07 0.094 0.23 3 -0.32 16 19
Syndecan-2/Caveolin-2/Ras -0.15 0.18 -10000 0 -0.32 237 237
Syndecan-2/Laminin alpha3 -0.082 0.17 -10000 0 -0.35 132 132
Syndecan-2/RasGAP 0.042 0.066 -10000 0 -0.28 15 15
alpha5/beta1 Integrin 0.049 0.012 -10000 0 -10000 0 0
PRKCD 0.035 0.017 -10000 0 -10000 0 0
Syndecan-2 dimer 0.022 0.071 -10000 0 -0.33 16 16
GO:0007205 0.003 0.005 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.027 0.058 -10000 0 -0.27 15 15
RHOA 0.033 0.007 -10000 0 -10000 0 0
SDCBP 0.028 0.028 -10000 0 -0.54 1 1
TNFRSF13B 0.032 0.014 -10000 0 -10000 0 0
RASA1 0.034 0.012 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.033 0.081 -10000 0 -0.4 16 16
Syndecan-2/Synbindin 0.015 0.065 -10000 0 -0.33 16 16
TGFB1 0.034 0.008 -10000 0 -10000 0 0
CASP3 0.042 0.095 0.24 8 -0.3 16 24
FN1 0.13 0.068 -10000 0 -10000 0 0
Syndecan-2/IL8 0.024 0.074 0.23 1 -0.34 16 17
SDC2 0 0.071 -10000 0 -0.39 16 16
KNG1 0.033 0.007 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.016 0.065 -10000 0 -0.33 16 16
TRAPPC4 0.03 0.011 -10000 0 -10000 0 0
CSF2 0.039 0.028 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.017 0.066 -10000 0 -0.33 16 16
Syndecan-2/Syntenin/PI-4-5-P2 0.016 0.06 -10000 0 -0.3 16 16
Syndecan-2/Ezrin 0.015 0.059 -10000 0 -0.3 16 16
PRKACA 0.043 0.096 0.23 5 -0.3 16 21
angiogenesis 0.024 0.073 0.23 1 -0.33 16 17
MMP2 0.028 0.039 -10000 0 -0.54 2 2
IL8 0.048 0.053 -10000 0 -0.54 1 1
calcineurin-NFAT signaling pathway 0.016 0.065 -10000 0 -0.33 16 16
IL1-mediated signaling events

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
UBC13/UEV1A 0.025 0.004 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.033 0.013 0.18 2 -10000 0 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.005 0.1 -10000 0 -0.38 19 19
IRAK/TOLLIP 0.038 0.014 -10000 0 -10000 0 0
IKBKB 0.028 0.013 -10000 0 -10000 0 0
IKBKG 0.034 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.054 0.044 0.26 1 -0.4 3 4
IL1A 0.036 0.016 -10000 0 -10000 0 0
IL1B -0.017 0.12 -10000 0 -0.42 41 41
IRAK/TRAF6/p62/Atypical PKCs 0.064 0.027 -10000 0 -10000 0 0
IL1R2 0.038 0.055 -10000 0 -0.54 3 3
IL1R1 -0.031 0.18 -10000 0 -0.54 58 58
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.031 0.13 -10000 0 -0.43 30 30
TOLLIP 0.033 0.007 -10000 0 -10000 0 0
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.031 0.011 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.022 0.006 -10000 0 -10000 0 0
IKK complex/ELKS 0.038 0.067 -10000 0 -0.35 1 1
JUN -0.051 0.1 -10000 0 -0.27 83 83
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.026 0.2 -10000 0 -0.37 112 112
IL1 alpha/IL1R1/IL1RAP/MYD88 0.039 0.13 -10000 0 -0.32 58 58
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.052 0.13 -10000 0 -0.3 57 57
IL1 beta fragment/IL1R1/IL1RAP -0.024 0.16 -10000 0 -0.35 91 91
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 -0.01 0.05 -10000 0 -0.27 11 11
IRAK1 0.019 0.011 -10000 0 -10000 0 0
IL1RN/IL1R1 0.014 0.15 -10000 0 -0.39 58 58
IRAK4 0.034 0.005 -10000 0 -10000 0 0
PRKCI 0.035 0.017 -10000 0 -10000 0 0
TRAF6 0.034 0.006 -10000 0 -10000 0 0
PI3K 0.005 0.13 -10000 0 -0.37 51 51
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.022 0.14 -10000 0 -0.42 31 31
CHUK 0.034 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.024 0.16 -10000 0 -0.35 91 91
IL1 beta/IL1R2 0.007 0.12 -10000 0 -0.36 44 44
IRAK/TRAF6/TAK1/TAB1/TAB2 0.046 0.019 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.035 0.18 -10000 0 -0.35 112 112
IRAK3 0.035 0.033 -10000 0 -0.54 1 1
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.008 0.16 -10000 0 -0.33 88 88
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.001 0.1 -10000 0 -0.39 12 12
IL1 alpha/IL1R1/IL1RAP 0.022 0.13 -10000 0 -0.34 58 58
RELA 0.034 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.034 0.009 -10000 0 -10000 0 0
MYD88 0.034 0.011 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.053 0.028 -10000 0 -10000 0 0
IL1RAP 0.033 0.006 -10000 0 -10000 0 0
UBE2N 0.034 0.005 -10000 0 -10000 0 0
IRAK/TRAF6 -0.023 0.13 -10000 0 -0.29 79 79
CASP1 -0.013 0.15 -10000 0 -0.54 38 38
IL1RN/IL1R2 0.067 0.056 0.26 6 -0.4 3 9
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.006 0.16 -10000 0 -0.34 89 89
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.005 0.13 -10000 0 -0.35 57 57
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
IL1RN 0.054 0.05 -10000 0 -10000 0 0
TRAF6/TAK1/TAB1/TAB2 0.045 0.016 -10000 0 -10000 0 0
MAP2K6 0.014 0.053 0.36 1 -0.28 10 11
S1P3 pathway

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
PDGFRB 0.034 0.006 -10000 0 -10000 0 0
mol:S1P 0.001 0.003 0.031 6 -10000 0 6
S1P1/S1P/Gi -0.091 0.16 -10000 0 -0.28 187 187
GNAO1 0.031 0.013 -10000 0 -10000 0 0
S1P/S1P3/G12/G13 0.041 0.016 -10000 0 -10000 0 0
AKT1 -0.011 0.11 -10000 0 -0.51 16 16
AKT3 -0.015 0.12 -10000 0 -0.58 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.034 0.006 -10000 0 -10000 0 0
GNAI2 0.035 0.011 -10000 0 -10000 0 0
GNAI3 0.035 0.007 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 183 183
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.002 0.004 0.036 6 -10000 0 6
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.07 0.14 0.24 2 -0.34 57 59
MAPK3 -0.062 0.13 0.23 1 -0.33 48 49
MAPK1 -0.068 0.13 0.23 1 -0.33 55 56
JAK2 -0.062 0.15 0.33 1 -0.34 61 62
CXCR4 -0.063 0.14 0.25 2 -0.33 52 54
FLT1 0.035 0.015 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
SRC -0.066 0.13 0.32 2 -0.33 54 56
S1P/S1P3/Gi -0.071 0.14 0.26 1 -0.34 57 58
RAC1 0.034 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.059 0.14 -10000 0 -0.32 57 57
VEGFA 0.052 0.047 0.22 1 -10000 0 1
S1P/S1P2/Gi -0.074 0.14 -10000 0 -0.34 58 58
VEGFR1 homodimer/VEGFA homodimer 0.062 0.039 0.27 1 -10000 0 1
RHOA 0.033 0.007 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.026 0.038 -10000 0 -0.29 4 4
GNAQ 0 0 -10000 0 -10000 0 0
GNAZ 0.027 0.063 -10000 0 -0.54 6 6
G12/G13 0.045 0.017 -10000 0 -10000 0 0
GNA14 0.043 0.068 -10000 0 -0.54 4 4
GNA15 0.036 0.019 -10000 0 -10000 0 0
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
GNA11 0.033 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.059 0.14 -10000 0 -0.32 57 57
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.043 0.24 8 -10000 0 8
AES 0.026 0.036 0.22 4 -10000 0 4
FBXW11 0.033 0.007 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.048 0.024 -10000 0 -0.4 1 1
SMAD4 0.032 0.026 -10000 0 -0.54 1 1
DKK2 0.031 0.054 -10000 0 -0.54 4 4
TLE1 0.01 0.1 0.27 1 -0.55 15 16
MACF1 0.034 0.006 -10000 0 -10000 0 0
CTNNB1 0.15 0.11 0.36 26 -0.41 3 29
WIF1 -0.38 0.26 -10000 0 -0.54 370 370
beta catenin/RanBP3 0.041 0.15 0.5 40 -0.43 2 42
KREMEN2 0.1 0.076 -10000 0 -10000 0 0
DKK1 0.007 0.18 -10000 0 -0.54 44 44
beta catenin/beta TrCP1 0.16 0.1 0.36 22 -0.41 2 24
FZD1 0.034 0.026 -10000 0 -0.54 1 1
AXIN2 0.029 0.29 0.65 47 -1.1 15 62
AXIN1 0.032 0.01 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.07 0.086 -10000 0 -0.54 8 8
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.091 0.15 0.35 9 -0.6 12 21
Axin1/APC/GSK3 0.065 0.059 0.32 1 -10000 0 1
Axin1/APC/GSK3/beta catenin/Macf1 0.06 0.076 0.37 1 -0.54 1 2
HNF1A 0.027 0.041 0.25 6 -10000 0 6
CTBP1 0.025 0.038 0.24 4 -10000 0 4
MYC 0.097 0.44 0.62 136 -1.3 29 165
RANBP3 0.033 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.1 0.07 -10000 0 -0.31 3 3
NKD1 0.031 0.021 -10000 0 -10000 0 0
TCF4 0.018 0.076 0.23 6 -0.54 7 13
TCF3 0.027 0.042 0.26 5 -10000 0 5
WNT1/LRP6/FZD1/Axin1 0.077 0.039 -10000 0 -0.32 1 1
Ran/GTP 0.025 0.005 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0 0.21 0.55 32 -0.52 15 47
LEF1 0.054 0.068 0.27 8 -10000 0 8
DVL1 0.079 0.058 0.25 3 -10000 0 3
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.097 0.17 0.32 7 -0.59 15 22
DKK1/LRP6/Kremen 2 0.082 0.13 0.26 1 -0.29 41 42
LRP6 0.033 0.008 -10000 0 -10000 0 0
CSNK1A1 0.027 0.042 0.26 5 -10000 0 5
NLK 0.036 0.031 -10000 0 -10000 0 0
CCND1 0.12 0.38 0.76 91 -1.2 14 105
WNT1 0.035 0.005 -10000 0 -10000 0 0
GSK3A 0.035 0.005 -10000 0 -10000 0 0
GSK3B 0.034 0.008 -10000 0 -10000 0 0
FRAT1 0.035 0.008 -10000 0 -10000 0 0
PPP2R5D 0.055 0.058 -10000 0 -0.39 3 3
APC 0.038 0.062 0.38 4 -0.3 1 5
WNT1/LRP6/FZD1 0.16 0.1 0.27 58 -0.3 1 59
CREBBP 0.023 0.044 0.22 5 -0.55 1 6
Coregulation of Androgen receptor activity

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
NRIP1 0.029 0.064 -10000 0 -0.54 6 6
SVIL 0.022 0.084 -10000 0 -0.54 11 11
ZNF318 0.03 0.008 -10000 0 -10000 0 0
JMJD2C 0.007 0.01 0.12 4 -10000 0 4
T-DHT/AR/Ubc9 -0.036 0.14 -10000 0 -0.31 80 80
CARM1 0.035 0.014 -10000 0 -10000 0 0
PRDX1 0.035 0.015 -10000 0 -10000 0 0
PELP1 0.031 0.01 -10000 0 -10000 0 0
CTNNB1 0.03 0.052 -10000 0 -0.54 4 4
AKT1 0.034 0.018 -10000 0 -10000 0 0
PTK2B 0.028 0.014 -10000 0 -10000 0 0
MED1 0.028 0.012 -10000 0 -10000 0 0
MAK 0.037 0.032 -10000 0 -10000 0 0
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.036 0.008 -10000 0 -10000 0 0
GSN -0.11 0.25 -10000 0 -0.54 132 132
NCOA2 0.028 0.015 -10000 0 -10000 0 0
NCOA6 0.034 0.008 -10000 0 -10000 0 0
DNA-PK 0.053 0.03 -10000 0 -10000 0 0
NCOA4 0.033 0.026 -10000 0 -0.54 1 1
PIAS3 0.033 0.008 -10000 0 -10000 0 0
cell proliferation 0 0.066 -10000 0 -0.45 5 5
XRCC5 0.033 0.006 -10000 0 -10000 0 0
UBE3A 0.034 0.009 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.052 0.13 -10000 0 -0.31 85 85
FHL2 -0.11 0.32 -10000 0 -0.99 58 58
RANBP9 0.035 0.009 -10000 0 -10000 0 0
JMJD1A -0.027 0.061 -10000 0 -0.14 122 122
CDK6 0.028 0.064 -10000 0 -0.54 6 6
TGFB1I1 0.029 0.045 -10000 0 -0.54 3 3
T-DHT/AR/CyclinD1 -0.037 0.15 -10000 0 -0.38 68 68
XRCC6 0.031 0.009 -10000 0 -10000 0 0
T-DHT/AR -0.057 0.17 -10000 0 -0.36 83 83
CTDSP1 0.034 0.006 -10000 0 -10000 0 0
CTDSP2 0.031 0.008 -10000 0 -10000 0 0
BRCA1 0.037 0.022 -10000 0 -10000 0 0
TCF4 0.024 0.067 -10000 0 -0.55 7 7
CDKN2A 0.051 0.054 -10000 0 -10000 0 0
SRF 0.02 0.058 -10000 0 -10000 0 0
NKX3-1 -0.072 0.11 -10000 0 -0.22 173 173
KLK3 0.012 0.056 -10000 0 -10000 0 0
TMF1 0.033 0.007 -10000 0 -10000 0 0
HNRNPA1 0.033 0.006 -10000 0 -10000 0 0
AOF2 0.001 0.002 0.021 1 -10000 0 1
APPL1 0.015 0.014 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.04 0.14 -10000 0 -0.36 65 65
AR -0.069 0.2 -10000 0 -0.56 66 66
UBA3 0 0.001 -10000 0 -10000 0 0
PATZ1 0.031 0.01 -10000 0 -10000 0 0
PAWR 0.034 0.03 -10000 0 -0.54 1 1
PRKDC 0.031 0.019 -10000 0 -10000 0 0
PA2G4 0.032 0.006 -10000 0 -10000 0 0
UBE2I 0.031 0.01 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.032 0.13 -10000 0 -0.32 63 63
RPS6KA3 0.034 0.037 -10000 0 -0.54 2 2
T-DHT/AR/ARA70 -0.039 0.14 -10000 0 -0.36 66 66
LATS2 0.02 0.076 -10000 0 -0.54 9 9
T-DHT/AR/PRX1 -0.034 0.13 -10000 0 -0.33 66 66
Cyclin D3/CDK11 p58 0.025 0.004 -10000 0 -10000 0 0
VAV3 0.03 0.12 0.19 1 -0.54 19 20
KLK2 -0.018 0.069 -10000 0 -0.42 1 1
CASP8 0.033 0.005 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.019 0.13 -10000 0 -0.32 54 54
TMPRSS2 -0.23 0.42 -10000 0 -0.97 122 122
CCND1 0.024 0.088 -10000 0 -0.54 10 10
PIAS1 0.035 0.007 -10000 0 -10000 0 0
mol:T-DHT -0.017 0.035 0.049 1 -0.071 141 142
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.037 0.016 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.043 0.14 -10000 0 -0.35 71 71
CMTM2 0.029 0.012 -10000 0 -10000 0 0
SNURF 0 0 -10000 0 -10000 0 0
ZMIZ1 0.004 0.053 -10000 0 -10000 0 0
CCND3 0.033 0.006 -10000 0 -10000 0 0
TGIF1 0.03 0.027 -10000 0 -0.54 1 1
FKBP4 0.038 0.026 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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
TGM2 0.046 0.042 -10000 0 -10000 0 0
GNB1/GNG2 -0.019 0.054 -10000 0 -0.18 45 45
AKT1 0.059 0.13 0.4 20 -0.36 5 25
EGF -0.15 0.27 -10000 0 -0.54 164 164
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.029 0.053 0.26 2 -10000 0 2
mol:Ca2+ 0.06 0.16 0.49 16 -0.33 15 31
LYN 0.026 0.052 0.26 3 -10000 0 3
RhoA/GTP 0.025 0.067 0.19 15 -0.14 4 19
mol:PGI2 0 0.001 -10000 0 -10000 0 0
SYK 0.058 0.17 0.54 14 -0.34 40 54
GNG2 0.033 0.026 -10000 0 -0.54 1 1
ARRB2 0.031 0.01 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.012 0.12 -10000 0 -0.63 14 14
G beta5/gamma2 -0.014 0.075 -10000 0 -0.24 45 45
PRKCH 0.053 0.18 0.55 12 -0.36 41 53
DNM1 0.034 0.008 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 0.015 0.029 -10000 0 -0.53 1 1
mol:GTP 0.001 0.003 -10000 0 -10000 0 0
PTGDR 0.03 0.06 -10000 0 -0.54 5 5
G12 family/GTP 0.004 0.11 -10000 0 -0.3 41 41
ADRBK1 0.032 0.01 -10000 0 -10000 0 0
ADRBK2 0.03 0.037 -10000 0 -0.54 2 2
RhoA/GTP/ROCK1 0.044 0.012 -10000 0 -10000 0 0
mol:GDP -0.042 0.13 0.38 14 -0.44 10 24
mol:NADP 0.034 0.006 -10000 0 -10000 0 0
RAB11A 0.033 0.006 -10000 0 -10000 0 0
PRKG1 0.034 0.005 -10000 0 -10000 0 0
mol:IP3 0.059 0.18 0.64 9 -0.38 35 44
cell morphogenesis 0.044 0.012 -10000 0 -10000 0 0
PLCB2 0.051 0.22 0.71 8 -0.51 39 47
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.03 0.055 0.25 4 -10000 0 4
mol:PDG2 0 0.001 -10000 0 -10000 0 0
HCK 0.029 0.056 0.26 2 -10000 0 2
RHOA 0.033 0.007 -10000 0 -10000 0 0
PTGIR 0.034 0.005 -10000 0 -10000 0 0
PRKCB1 0.055 0.18 0.64 9 -0.37 44 53
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.034 0.006 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.053 0.23 0.73 8 -0.52 45 53
LCK 0.038 0.061 0.25 6 -10000 0 6
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.044 0.042 -10000 0 -0.23 4 4
TXA2-R family/G12 family/GDP/G beta/gamma 0.024 0.098 -10000 0 -0.4 23 23
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.04 0.042 -10000 0 -0.23 5 5
MAPK14 0.052 0.13 0.41 19 -0.25 10 29
TGM2/GTP 0.056 0.2 0.68 9 -0.45 16 25
MAPK11 0.05 0.13 0.42 19 -0.25 8 27
ARHGEF1 0.046 0.11 0.36 16 -0.2 6 22
GNAI2 0.033 0.01 -10000 0 -10000 0 0
JNK cascade 0.059 0.19 0.53 16 -0.38 45 61
RAB11/GDP 0.031 0.01 -10000 0 -10000 0 0
ICAM1 0.058 0.15 0.46 19 -0.31 12 31
cAMP biosynthetic process 0.054 0.17 0.58 10 -0.38 16 26
Gq family/GTP/EBP50 0.033 0.048 -10000 0 -0.22 6 6
actin cytoskeleton reorganization 0.044 0.012 -10000 0 -10000 0 0
SRC 0.027 0.053 0.26 2 -10000 0 2
GNB5 0.032 0.026 -10000 0 -0.54 1 1
GNB1 0.034 0.011 -10000 0 -10000 0 0
EGF/EGFR -0.064 0.11 0.26 3 -0.29 42 45
VCAM1 0.053 0.16 0.47 17 -0.31 45 62
TP beta/Gq family/GDP/G beta5/gamma2 0.012 0.12 -10000 0 -0.63 14 14
platelet activation 0.063 0.16 0.5 17 -0.32 14 31
PGI2/IP 0.026 0.004 -10000 0 -10000 0 0
PRKACA 0.023 0.031 -10000 0 -0.27 5 5
Gq family/GDP/G beta5/gamma2 0.015 0.11 -10000 0 -0.55 14 14
TXA2/TP beta/beta Arrestin2 -0.004 0.061 -10000 0 -0.39 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.013 0.031 -10000 0 -0.25 5 5
mol:DAG 0.057 0.2 0.66 9 -0.42 44 53
EGFR -0.27 0.29 -10000 0 -0.54 269 269
TXA2/TP alpha 0.058 0.21 0.71 8 -0.47 36 44
Gq family/GTP 0.009 0.052 0.22 1 -0.22 18 19
YES1 0.029 0.057 0.26 2 -0.43 1 3
GNAI2/GTP 0.03 0.04 -10000 0 -0.24 2 2
PGD2/DP 0.023 0.044 -10000 0 -0.4 5 5
SLC9A3R1 0.059 0.058 0.18 96 -10000 0 96
FYN 0.026 0.055 0.27 1 -0.29 2 3
mol:NO 0.034 0.006 -10000 0 -10000 0 0
GNA15 0.036 0.019 -10000 0 -10000 0 0
PGK/cGMP 0.045 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.031 0.011 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.066 0.056 0.29 1 -0.35 1 2
NOS3 0.034 0.006 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCA 0.064 0.18 0.56 12 -0.35 39 51
PRKCB 0.053 0.17 0.55 12 -0.35 46 58
PRKCE 0.055 0.17 0.58 11 -0.36 40 51
PRKCD 0.054 0.18 0.6 10 -0.38 45 55
PRKCG 0.056 0.18 0.61 10 -0.38 45 55
muscle contraction 0.054 0.22 0.68 9 -0.48 45 54
PRKCZ 0.057 0.17 0.5 16 -0.34 44 60
ARR3 0.035 0.002 -10000 0 -10000 0 0
TXA2/TP beta 0.044 0.049 -10000 0 -0.25 5 5
PRKCQ 0.06 0.18 0.51 18 -0.35 44 62
MAPKKK cascade 0.054 0.2 0.66 9 -0.45 40 49
SELE 0.049 0.18 0.46 19 -0.38 48 67
TP beta/GNAI2/GDP/G beta/gamma 0.062 0.049 -10000 0 -0.35 1 1
ROCK1 0.034 0.006 -10000 0 -10000 0 0
GNA14 0.043 0.068 -10000 0 -0.54 4 4
chemotaxis 0.05 0.25 0.76 8 -0.6 48 56
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
GNA11 0.033 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.026 0.005 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 0.037 0.1 0.46 3 -0.63 5 8
oxygen homeostasis 0.026 0.03 0.2 3 -10000 0 3
TCEB2 0.031 0.01 -10000 0 -10000 0 0
TCEB1 0.028 0.013 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.13 0.14 0.45 20 -0.32 5 25
EPO 0.22 0.25 0.71 47 -0.52 1 48
FIH (dimer) 0.056 0.031 0.26 1 -10000 0 1
APEX1 0.058 0.038 0.23 3 -10000 0 3
SERPINE1 0.26 0.25 0.72 43 -0.51 3 46
FLT1 -0.016 0.17 -10000 0 -0.67 22 22
ADORA2A 0.26 0.25 0.7 59 -0.5 3 62
germ cell development 0.25 0.23 0.7 35 -0.52 2 37
SLC11A2 0.26 0.24 0.73 34 -0.51 3 37
BHLHE40 0.18 0.23 0.68 36 -0.49 4 40
HIF1AN 0.056 0.031 0.26 1 -10000 0 1
HIF2A/ARNT/SIRT1 0.17 0.19 0.55 39 -0.4 2 41
ETS1 0.041 0.034 -10000 0 -0.54 1 1
CITED2 0.005 0.15 -10000 0 -0.78 14 14
KDR -0.006 0.15 -10000 0 -0.62 21 21
PGK1 0.26 0.24 0.72 40 -0.51 3 43
SIRT1 0.036 0.008 -10000 0 -10000 0 0
response to hypoxia 0.002 0.006 -10000 0 -10000 0 0
HIF2A/ARNT 0.23 0.26 0.78 21 -0.56 4 25
EPAS1 0.16 0.18 0.52 46 -0.33 8 54
SP1 0.047 0.029 -10000 0 -10000 0 0
ABCG2 0.24 0.26 0.71 36 -0.62 10 46
EFNA1 0.18 0.22 0.67 17 -0.51 3 20
FXN 0.25 0.24 0.7 40 -0.57 1 41
POU5F1 0.25 0.24 0.71 34 -0.54 2 36
neuron apoptosis -0.22 0.26 0.55 4 -0.77 22 26
EP300 0.032 0.009 -10000 0 -10000 0 0
EGLN3 0.08 0.074 0.25 28 -0.54 1 29
EGLN2 0.059 0.035 0.25 1 -10000 0 1
EGLN1 0.045 0.034 0.26 1 -10000 0 1
VHL/Elongin B/Elongin C 0.053 0.033 -10000 0 -10000 0 0
VHL 0.036 0.018 -10000 0 -10000 0 0
ARNT 0.045 0.038 -10000 0 -10000 0 0
SLC2A1 0.25 0.24 0.69 50 -0.5 3 53
TWIST1 0.21 0.29 0.69 39 -0.56 27 66
ELK1 0.04 0.019 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.14 0.18 0.55 21 -0.36 5 26
VEGFA 0.26 0.25 0.73 43 -0.51 3 46
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.021 0.12 -10000 0 -0.4 46 46
MAP4K4 0.003 0.084 -10000 0 -0.3 19 19
BAG4 0.028 0.016 -10000 0 -10000 0 0
PKC zeta/ceramide -0.013 0.067 0.15 4 -0.28 8 12
NFKBIA 0.033 0.007 -10000 0 -10000 0 0
BIRC3 0.016 0.11 -10000 0 -0.54 17 17
BAX 0.008 0.049 -10000 0 -0.35 5 5
RIPK1 0.033 0.006 -10000 0 -10000 0 0
AKT1 0.008 0.075 0.72 5 -10000 0 5
BAD -0.013 0.07 0.2 1 -0.34 5 6
SMPD1 0.018 0.064 0.23 7 -0.25 10 17
RB1 -0.013 0.068 -10000 0 -0.34 5 5
FADD/Caspase 8 0.031 0.12 0.29 10 -0.42 8 18
MAP2K4 -0.014 0.071 -10000 0 -0.35 6 6
NSMAF 0.028 0.028 -10000 0 -0.54 1 1
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.008 0.074 0.28 4 -0.35 4 8
EGF -0.15 0.27 -10000 0 -0.54 164 164
mol:ceramide -0.012 0.074 0.16 13 -0.3 8 21
MADD 0.034 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.024 0.12 -10000 0 -0.41 47 47
ASAH1 0.027 0.042 -10000 0 -0.54 2 2
negative regulation of cell cycle -0.014 0.068 -10000 0 -0.34 5 5
cell proliferation -0.11 0.14 -10000 0 -0.3 87 87
BID -0.014 0.19 -10000 0 -0.66 35 35
MAP3K1 -0.011 0.073 0.2 1 -0.34 6 7
EIF2A -0.005 0.073 0.27 7 -0.29 1 8
TRADD 0.03 0.012 -10000 0 -10000 0 0
CRADD 0.034 0.005 -10000 0 -10000 0 0
MAPK3 -0.003 0.072 0.27 5 -0.32 5 10
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.008 0.078 0.27 5 -0.36 4 9
Cathepsin D/ceramide 0.011 0.08 -10000 0 -0.26 8 8
FADD 0.028 0.1 0.28 2 -0.31 14 16
KSR1 -0.006 0.073 0.21 6 -0.36 4 10
MAPK8 -0.008 0.07 -10000 0 -0.29 8 8
PRKRA -0.012 0.071 0.2 1 -0.34 5 6
PDGFA -0.019 0.16 -10000 0 -0.54 46 46
TRAF2 0.035 0.012 -10000 0 -10000 0 0
IGF1 -0.25 0.29 -10000 0 -0.54 252 252
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.012 0.074 0.16 13 -0.3 8 21
CTSD 0.046 0.043 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.049 0.01 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.11 0.15 -10000 0 -0.32 86 86
PRKCD 0.035 0.017 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.024 0.12 -10000 0 -0.41 47 47
RelA/NF kappa B1 0.049 0.01 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.034 0.03 -10000 0 -0.54 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.007 0.091 -10000 0 -0.32 20 20
TNFR1A/BAG4/TNF-alpha 0.053 0.035 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.021 0.12 -10000 0 -0.4 46 46
MAP2K1 -0.008 0.072 0.29 4 -0.34 4 8
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
CYCS 0.027 0.082 0.24 19 -0.25 6 25
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.023 -10000 0 -10000 0 0
EIF2AK2 -0.008 0.07 0.22 5 -0.3 5 10
TNF-alpha/TNFR1A/FAN 0.057 0.036 -10000 0 -0.33 1 1
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.022 0.093 -10000 0 -0.41 16 16
MAP2K2 -0.007 0.073 0.29 4 -0.33 4 8
SMPD3 -0.002 0.12 0.24 3 -0.3 58 61
TNF 0.038 0.023 -10000 0 -10000 0 0
PKC zeta/PAR4 0.025 0.021 -10000 0 -0.4 1 1
mol:PHOSPHOCHOLINE 0.083 0.12 0.24 172 -0.22 3 175
NF kappa B1/RelA/I kappa B alpha 0.075 0.031 -10000 0 -0.3 1 1
AIFM1 0.026 0.082 0.23 22 -0.24 7 29
BCL2 -0.072 0.22 -10000 0 -0.54 93 93
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.04 0.016 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.033 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.02 0.081 -10000 0 -0.54 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.03 0.012 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.11 0.12 -10000 0 -0.23 241 241
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.032 0.027 -10000 0 -0.54 1 1
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.031 0.011 -10000 0 -10000 0 0
FYN 0.03 0.037 -10000 0 -0.54 2 2
MAP3K12 0.034 0.004 -10000 0 -10000 0 0
FGR 0.033 0.008 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.04 0.093 -10000 0 -0.32 37 37
PRKG1 0.034 0.005 -10000 0 -10000 0 0
DUSP8 0.033 0.007 -10000 0 -10000 0 0
PGK/cGMP/p38 alpha 0.012 0.12 -10000 0 -0.36 25 25
apoptosis -0.039 0.089 -10000 0 -0.3 37 37
RAL/GTP 0.045 0.01 -10000 0 -10000 0 0
LYN 0.03 0.015 -10000 0 -10000 0 0
DUSP1 -0.2 0.28 -10000 0 -0.54 208 208
PAK1 0.043 0.046 -10000 0 -10000 0 0
SRC 0.033 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.071 0.036 -10000 0 -10000 0 0
TRAF6 0.034 0.006 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.034 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.044 0.012 -10000 0 -10000 0 0
MAPK11 0.001 0.13 0.4 2 -0.39 27 29
BLK 0.039 0.044 -10000 0 -10000 0 0
HCK 0.036 0.022 -10000 0 -10000 0 0
MAP2K3 0.031 0.01 -10000 0 -10000 0 0
DUSP16 0.033 0.012 -10000 0 -10000 0 0
DUSP10 0.028 0.032 -10000 0 -0.54 1 1
TRAF6/MEKK3 0.038 0.016 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.006 0.13 0.39 2 -0.36 31 33
positive regulation of innate immune response 0.001 0.16 0.47 2 -0.44 30 32
LCK 0.048 0.044 -10000 0 -10000 0 0
p38alpha-beta/MKP7 0.014 0.15 0.58 1 -0.42 29 30
p38alpha-beta/MKP5 0.009 0.15 0.58 1 -0.42 28 29
PGK/cGMP 0.025 0.004 -10000 0 -10000 0 0
PAK2 0.033 0.007 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.086 0.2 -10000 0 -0.44 64 64
CDC42 0.033 0.007 -10000 0 -10000 0 0
RALB 0.034 0.005 -10000 0 -10000 0 0
RALA 0.034 0.006 -10000 0 -10000 0 0
PAK3 -0.32 0.28 -10000 0 -0.54 310 310
Regulation of Telomerase

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
Telomerase catalytic core complex 0.002 0.18 -10000 0 -0.85 8 8
RAD9A 0.031 0.01 -10000 0 -10000 0 0
AP1 -0.31 0.27 -10000 0 -0.47 356 356
IFNAR2 0.038 0.012 -10000 0 -10000 0 0
AKT1 -0.004 0.12 -10000 0 -0.38 13 13
ER alpha/Oestrogen -0.041 0.19 -10000 0 -0.39 110 110
NFX1/SIN3/HDAC complex 0.035 0.074 -10000 0 -0.34 12 12
EGF -0.15 0.27 -10000 0 -0.54 164 164
SMG5 0.029 0.016 -10000 0 -10000 0 0
SMG6 0.031 0.01 -10000 0 -10000 0 0
SP3/HDAC2 0.056 0.025 -10000 0 -10000 0 0
TERT/c-Abl 0.011 0.17 -10000 0 -0.78 8 8
SAP18 0.033 0.01 -10000 0 -10000 0 0
MRN complex 0.049 0.033 -10000 0 -10000 0 0
WT1 0.087 0.07 0.2 16 -10000 0 16
WRN 0.028 0.015 -10000 0 -10000 0 0
SP1 0.041 0.016 -10000 0 -10000 0 0
SP3 0.036 0.007 -10000 0 -10000 0 0
TERF2IP 0.029 0.013 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.028 0.16 -10000 0 -0.7 8 8
Mad/Max 0.055 0.018 -10000 0 -10000 0 0
TERT -0.006 0.18 -10000 0 -0.89 8 8
CCND1 0.034 0.26 0.57 9 -1.1 13 22
MAX 0.035 0.01 -10000 0 -10000 0 0
RBBP7 0.038 0.022 -10000 0 -10000 0 0
RBBP4 0.034 0.006 -10000 0 -10000 0 0
TERF2 0.027 0.028 -10000 0 -0.49 1 1
PTGES3 0.033 0.026 -10000 0 -0.54 1 1
SIN3A 0.034 0.006 -10000 0 -10000 0 0
Telomerase/911 0.04 0.057 -10000 0 -0.45 2 2
CDKN1B 0.043 0.11 0.31 1 -0.61 10 11
RAD1 0.034 0.009 -10000 0 -10000 0 0
XRCC5 0.034 0.005 -10000 0 -10000 0 0
XRCC6 0.032 0.009 -10000 0 -10000 0 0
SAP30 0.035 0.009 -10000 0 -10000 0 0
TRF2/PARP2 0.042 0.029 -10000 0 -0.39 1 1
UBE3A 0.035 0.009 -10000 0 -10000 0 0
JUN -0.066 0.22 -10000 0 -0.54 89 89
E6 0.002 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.029 0.012 -10000 0 -10000 0 0
FOS -0.35 0.27 -10000 0 -0.54 344 344
IFN-gamma/IRF1 0.082 0.083 0.27 28 -0.32 10 38
PARP2 0.034 0.006 -10000 0 -10000 0 0
BLM 0.073 0.066 -10000 0 -10000 0 0
Telomerase 0.006 0.093 -10000 0 -0.63 5 5
IRF1 0.045 0.048 -10000 0 -0.18 8 8
ESR1 -0.057 0.26 -10000 0 -0.54 106 106
KU/TER 0.047 0.014 -10000 0 -10000 0 0
ATM/TRF2 0.037 0.033 -10000 0 -0.29 1 1
ubiquitin-dependent protein catabolic process 0.043 0.067 -10000 0 -0.36 6 6
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.044 0.068 -10000 0 -0.36 6 6
HDAC1 0.035 0.006 -10000 0 -10000 0 0
HDAC2 0.039 0.021 -10000 0 -10000 0 0
ATM 0.017 0.021 0.21 1 -10000 0 1
SMAD3 0.009 0.017 -10000 0 -10000 0 0
ABL1 0.034 0.005 -10000 0 -10000 0 0
MXD1 0.037 0.009 -10000 0 -10000 0 0
MRE11A 0.03 0.011 -10000 0 -10000 0 0
HUS1 0.034 0.01 -10000 0 -10000 0 0
RPS6KB1 0.03 0.012 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.025 0.18 -10000 0 -0.76 10 10
NR2F2 0.007 0.094 -10000 0 -0.55 13 13
MAPK3 0.019 0.022 -10000 0 -0.4 1 1
MAPK1 0.019 0.022 -10000 0 -0.4 1 1
TGFB1/TGF beta receptor Type II 0.033 0.009 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
HNRNPC 0.034 0.006 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.017 0.021 0.21 1 -10000 0 1
NBN 0.028 0.016 -10000 0 -10000 0 0
EGFR -0.27 0.29 -10000 0 -0.54 269 269
mol:Oestrogen 0.001 0.003 -10000 0 -10000 0 0
EGF/EGFR -0.31 0.26 -10000 0 -0.46 354 354
MYC -0.002 0.12 -10000 0 -0.54 25 25
IL2 0.04 0.031 -10000 0 -0.54 1 1
KU 0.047 0.014 -10000 0 -10000 0 0
RAD50 0.033 0.006 -10000 0 -10000 0 0
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
TGFB1 0.033 0.009 -10000 0 -10000 0 0
TRF2/BLM 0.065 0.056 -10000 0 -0.39 1 1
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.023 0.18 -10000 0 -0.78 8 8
SP1/HDAC2 0.061 0.032 -10000 0 -10000 0 0
PINX1 0.027 0.014 -10000 0 -10000 0 0
Telomerase/EST1A 0.022 0.16 -10000 0 -0.7 8 8
Smad3/Myc 0.005 0.081 -10000 0 -0.34 25 25
911 complex 0.061 0.026 -10000 0 -10000 0 0
IFNG 0.065 0.073 -10000 0 -0.22 9 9
Telomerase/PinX1 0.011 0.16 -10000 0 -0.7 8 8
Telomerase/AKT1/mTOR/p70S6K 0.022 0.12 0.3 1 -0.49 15 16
SIN3B 0.036 0.014 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
Telomerase/EST1B 0.028 0.16 -10000 0 -0.72 7 7
response to DNA damage stimulus -0.001 0.03 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.061 0.051 -10000 0 -0.31 1 1
TRF2/WRN 0.036 0.03 -10000 0 -0.39 1 1
Telomerase/hnRNP C1/C2 0.028 0.16 -10000 0 -0.73 7 7
E2F1 0.054 0.048 -10000 0 -10000 0 0
ZNFX1 0.033 0.017 -10000 0 -10000 0 0
PIF1 0.039 0.028 -10000 0 -10000 0 0
NCL 0.034 0.006 -10000 0 -10000 0 0
DKC1 0.035 0.011 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.017 0.003 -10000 0 -10000 0 0
SMARCC1 0.017 0.054 -10000 0 -0.68 1 1
REL 0.036 0.024 -10000 0 -10000 0 0
HDAC7 -0.052 0.12 -10000 0 -0.33 42 42
JUN -0.067 0.22 -10000 0 -0.54 89 89
EP300 0.032 0.009 -10000 0 -10000 0 0
KAT2B 0 0 0.003 2 -10000 0 2
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.003 0.063 -10000 0 -0.41 10 10
FOXO1 -0.023 0.17 -10000 0 -0.54 48 48
T-DHT/AR -0.027 0.14 -10000 0 -0.35 42 42
MAP2K6 0.008 0.084 -10000 0 -0.55 10 10
BRM/BAF57 0.046 0.018 -10000 0 -10000 0 0
MAP2K4 0.018 0.027 -10000 0 -10000 0 0
SMARCA2 0.033 0.009 -10000 0 -10000 0 0
PDE9A -0.059 0.26 -10000 0 -1 31 31
NCOA2 0.029 0.015 -10000 0 -10000 0 0
CEBPA 0.03 0.044 -10000 0 -0.54 3 3
EHMT2 0.035 0.004 -10000 0 -10000 0 0
cell proliferation 0.037 0.15 0.43 13 -0.46 3 16
NR0B1 -0.094 0.25 -10000 0 -0.54 120 120
EGR1 -0.43 0.23 -10000 0 -0.54 414 414
RXRs/9cRA 0.051 0.043 -10000 0 -0.31 4 4
AR/RACK1/Src 0.003 0.1 0.34 5 -0.36 5 10
AR/GR -0.04 0.14 -10000 0 -0.33 54 54
GNB2L1 0.034 0.006 -10000 0 -10000 0 0
PKN1 0.034 0.01 -10000 0 -10000 0 0
RCHY1 0.029 0.051 -10000 0 -0.54 4 4
epidermal growth factor receptor activity 0 0.001 0.009 4 -10000 0 4
MAPK8 0.003 0.033 -10000 0 -0.44 1 1
T-DHT/AR/TIF2/CARM1 0.006 0.095 0.35 1 -0.37 6 7
SRC -0.011 0.072 -10000 0 -0.33 7 7
NR3C1 -0.012 0.16 -10000 0 -0.54 40 40
KLK3 -0.042 0.097 0.45 1 -10000 0 1
APPBP2 0.018 0.027 -10000 0 -10000 0 0
TRIM24 0.035 0.013 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.036 0.072 -10000 0 -0.36 11 11
TMPRSS2 -0.22 0.45 -10000 0 -1 123 123
RXRG 0.024 0.053 -10000 0 -0.54 4 4
mol:9cRA 0 0 0.003 2 -10000 0 2
RXRA 0.034 0.006 -10000 0 -10000 0 0
RXRB 0.034 0.005 -10000 0 -10000 0 0
CARM1 0.035 0.014 -10000 0 -10000 0 0
NR2C2 0.035 0.014 -10000 0 -10000 0 0
KLK2 0.013 0.078 0.34 3 -10000 0 3
AR -0.025 0.1 -10000 0 -0.28 58 58
SENP1 0.034 0.004 -10000 0 -10000 0 0
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
MDM2 0.032 0.011 -10000 0 -10000 0 0
SRY -0.001 0.002 -10000 0 -0.025 4 4
GATA2 0.042 0.033 0.18 28 -10000 0 28
MYST2 0 0.001 -10000 0 -0.006 4 4
HOXB13 0.078 0.07 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src 0 0.1 0.36 5 -0.36 6 11
positive regulation of transcription 0.042 0.033 0.18 28 -10000 0 28
DNAJA1 0.019 0.03 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.032 -10000 0 -0.33 4 4
NCOA1 0.041 0.033 -10000 0 -0.57 1 1
SPDEF -0.019 0.17 -10000 0 -0.54 50 50
T-DHT/AR/TIF2 0.017 0.079 0.38 2 -0.3 5 7
T-DHT/AR/Hsp90 -0.011 0.098 0.36 2 -0.36 11 13
GSK3B 0.033 0.01 -10000 0 -10000 0 0
NR2C1 0.033 0.026 -10000 0 -0.54 1 1
mol:T-DHT -0.019 0.072 0.22 15 -0.36 10 25
SIRT1 0.034 0.005 -10000 0 -10000 0 0
ZMIZ2 0.032 0.008 -10000 0 -10000 0 0
POU2F1 0.003 0.065 -10000 0 -0.18 7 7
T-DHT/AR/DAX-1 -0.072 0.17 0.36 2 -0.34 109 111
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
SMARCE1 0.033 0.009 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.006 0.029 0.36 1 -0.34 1 2
SNTA1 0.032 0.026 -10000 0 -0.54 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.011 0.058 0.33 6 -0.34 1 7
MAPK12 0.008 0.086 0.21 40 -0.28 24 64
CCND1 0.009 0.083 0.21 2 -0.5 10 12
p38 gamma/SNTA1 0.027 0.086 0.39 1 -0.26 22 23
MAP2K3 0.031 0.01 -10000 0 -10000 0 0
PKN1 0.034 0.01 -10000 0 -10000 0 0
G2/M transition checkpoint 0.008 0.086 0.21 40 -0.27 24 64
MAP2K6 0.015 0.098 0.25 45 -0.3 25 70
MAPT 0.013 0.067 0.27 8 -0.26 10 18
MAPK13 0.017 0.027 -10000 0 -0.4 1 1
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.062 -10000 0 -0.33 17 17
IL2 signaling events mediated by PI3K

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
BCL2L1 0.02 0.091 -10000 0 -0.44 3 3
UGCG 0.029 0.11 -10000 0 -0.64 11 11
AKT1/mTOR/p70S6K/Hsp90/TERT 0 0.18 0.33 1 -0.4 43 44
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide 0.03 0.11 -10000 0 -0.64 11 11
mol:DAG 0.005 0.11 -10000 0 -0.85 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.02 0.22 0.35 1 -0.42 73 74
FRAP1 -0.036 0.24 0.38 1 -0.47 84 85
FOXO3 0.005 0.18 0.38 3 -0.51 30 33
AKT1 0.002 0.2 0.38 1 -0.54 33 34
GAB2 0.027 0.014 -10000 0 -10000 0 0
SMPD1 0.009 0.12 -10000 0 -0.66 15 15
SGMS1 0.019 0.083 -10000 0 -0.62 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP -0.028 0.097 -10000 0 -0.34 44 44
CALM1 0.033 0.006 -10000 0 -10000 0 0
cell proliferation 0.049 0.12 0.34 2 -0.44 11 13
EIF3A 0.034 0.006 -10000 0 -10000 0 0
PI3K 0.004 0.13 -10000 0 -0.37 51 51
RPS6KB1 0 0.13 -10000 0 -0.83 8 8
mol:sphingomyelin 0.005 0.11 -10000 0 -0.85 7 7
natural killer cell activation -0.002 0.005 -10000 0 -0.02 3 3
JAK3 0.033 0.009 -10000 0 -10000 0 0
PIK3R1 -0.021 0.17 -10000 0 -0.54 47 47
JAK1 0.033 0.01 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MYC 0.023 0.27 0.45 3 -0.92 31 34
MYB -0.047 0.34 -10000 0 -1.2 42 42
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.028 0.13 0.31 2 -0.38 15 17
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.035 0.13 -10000 0 -0.71 9 9
mol:PI-3-4-5-P3 0.03 0.13 0.31 2 -0.37 15 17
Rac1/GDP -0.011 0.096 -10000 0 -0.31 44 44
T cell proliferation 0.028 0.12 0.31 1 -0.35 15 16
SHC1 0.025 0.016 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.028 0.094 25 -0.068 41 66
PRKCZ 0.027 0.12 0.31 1 -0.36 15 16
NF kappa B1 p50/RelA -0.008 0.22 0.37 1 -0.49 46 47
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.021 0.097 0.3 1 -0.35 12 13
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
IL2RA 0.039 0.035 -10000 0 -10000 0 0
IL2RB 0.035 0.023 -10000 0 -10000 0 0
TERT 0.032 0.028 -10000 0 -0.54 1 1
E2F1 0.013 0.14 0.34 1 -0.4 46 47
SOS1 0.032 0.01 -10000 0 -10000 0 0
RPS6 0.032 0.026 -10000 0 -0.54 1 1
mol:cAMP -0.002 0.014 0.032 41 -0.05 24 65
PTPN11 0.031 0.011 -10000 0 -10000 0 0
IL2RG 0.042 0.037 -10000 0 -10000 0 0
actin cytoskeleton organization 0.028 0.12 0.31 1 -0.35 15 16
GRB2 0.032 0.02 -10000 0 -10000 0 0
IL2 0.032 0.029 -10000 0 -0.54 1 1
PIK3CA 0.032 0.012 -10000 0 -10000 0 0
Rac1/GTP 0.014 0.1 -10000 0 -0.29 44 44
LCK 0.047 0.045 -10000 0 -10000 0 0
BCL2 -0.12 0.38 0.52 1 -0.83 104 105
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.038 0.15 -10000 0 -0.43 46 46
KLHL20 0.042 0.12 0.31 41 -0.26 14 55
CYFIP2 0.05 0.047 -10000 0 -10000 0 0
Rac1/GDP 0.001 0.12 0.31 7 -0.3 25 32
ENAH -0.033 0.14 -10000 0 -0.41 43 43
AP1M1 0.034 0.006 -10000 0 -10000 0 0
RAP1B 0.033 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.005 -10000 0 -10000 0 0
CTNNB1 0.029 0.052 -10000 0 -0.54 4 4
CDC42/GTP 0.009 0.076 -10000 0 -0.29 2 2
ABI1/Sra1/Nap1 -0.016 0.04 -10000 0 -0.18 13 13
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.049 0.095 -10000 0 -0.31 26 26
RAPGEF1 -0.031 0.14 0.3 3 -0.4 40 43
CTNND1 0.033 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.032 0.16 -10000 0 -0.44 51 51
CRK -0.028 0.14 0.31 2 -0.41 46 48
E-cadherin/gamma catenin/alpha catenin 0.037 0.089 -10000 0 -0.34 21 21
alphaE/beta7 Integrin 0.046 0.016 -10000 0 -10000 0 0
IQGAP1 0.033 0.008 -10000 0 -10000 0 0
NCKAP1 0.034 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.055 0.042 -10000 0 -0.31 3 3
DLG1 -0.042 0.16 -10000 0 -0.43 52 52
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.021 0.061 -10000 0 -0.2 14 14
MLLT4 0.029 0.046 -10000 0 -0.54 3 3
ARF6/GTP/NME1/Tiam1 0.058 0.025 -10000 0 -10000 0 0
PI3K -0.022 0.081 -10000 0 -0.26 14 14
ARF6 0.034 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.02 0.095 -10000 0 -0.32 33 33
TIAM1 0.035 0.012 0.18 3 -10000 0 3
E-cadherin(dimer)/Ca2+ 0.046 0.089 -10000 0 -0.29 26 26
AKT1 -0.007 0.057 -10000 0 -0.2 1 1
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
CDH1 0.006 0.12 -10000 0 -0.54 22 22
RhoA/GDP 0 0.12 0.3 7 -0.3 25 32
actin cytoskeleton organization 0.037 0.094 0.26 42 -0.19 13 55
CDC42/GDP 0 0.12 0.3 7 -0.3 25 32
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.004 0.067 -10000 0 -0.22 38 38
ITGB7 0.034 0.004 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.05 0.096 -10000 0 -0.31 26 26
E-cadherin/Ca2+/beta catenin/alpha catenin 0.032 0.082 -10000 0 -0.29 26 26
mol:GDP -0.019 0.12 0.31 7 -0.34 35 42
CDC42/GTP/IQGAP1 0.043 0.013 -10000 0 -10000 0 0
JUP 0.033 0.01 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.006 0.12 0.34 3 -0.31 24 27
RAC1/GTP/IQGAP1 0.044 0.012 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.049 0.012 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
CDC42 0.033 0.007 -10000 0 -10000 0 0
CTNNA1 0.034 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.016 0.068 0.21 23 -0.23 11 34
NME1 0.031 0.011 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.038 0.16 -10000 0 -0.44 49 49
regulation of cell-cell adhesion -0.001 0.061 -10000 0 -0.24 3 3
WASF2 0.02 0.044 0.12 32 -0.11 4 36
Rap1/GTP 0.012 0.087 0.28 1 -0.31 3 4
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.059 0.092 -10000 0 -0.3 21 21
CCND1 0.017 0.08 0.25 20 -0.28 11 31
VAV2 -0.02 0.19 0.39 3 -0.52 40 43
RAP1/GDP 0.009 0.1 0.31 3 -0.34 5 8
adherens junction assembly -0.035 0.16 -10000 0 -0.42 49 49
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.033 0.006 -10000 0 -10000 0 0
PIP5K1C 0.034 0.009 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.044 0.089 -10000 0 -0.29 24 24
E-cadherin/beta catenin -0.007 0.089 -10000 0 -0.34 33 33
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.039 0.16 -10000 0 -0.43 50 50
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.14 0.28 59 -0.41 19 78
E-cadherin/beta catenin/alpha catenin 0.036 0.096 -10000 0 -0.34 26 26
ITGAE 0.031 0.01 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.033 0.17 -10000 0 -0.45 51 51
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.1 0.086 -10000 0 -10000 0 0
CLOCK 0.039 0.01 -10000 0 -10000 0 0
TIMELESS/CRY2 0.069 0.069 -10000 0 -10000 0 0
DEC1/BMAL1 0.052 0.025 -10000 0 -0.4 1 1
ATR 0.034 0.006 -10000 0 -10000 0 0
NR1D1 0.04 0.053 -10000 0 -10000 0 0
ARNTL 0.037 0.028 -10000 0 -0.54 1 1
TIMELESS 0.059 0.091 -10000 0 -10000 0 0
NPAS2 0.042 0.02 -10000 0 -10000 0 0
CRY2 0.034 0.005 -10000 0 -10000 0 0
mol:CO -0.021 0.03 -10000 0 -0.11 54 54
CHEK1 0.087 0.075 0.18 202 -10000 0 202
mol:HEME 0.021 0.03 0.11 54 -10000 0 54
PER1 0.024 0.063 -10000 0 -0.54 6 6
BMAL/CLOCK/NPAS2 0.088 0.044 -10000 0 -0.34 1 1
BMAL1/CLOCK 0.057 0.073 -10000 0 -0.38 1 1
S phase of mitotic cell cycle 0.1 0.086 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.1 0.087 -10000 0 -10000 0 0
mol:NADPH 0.021 0.03 0.11 54 -10000 0 54
PER1/TIMELESS 0.059 0.074 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.035 0.01 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.03 0.027 -10000 0 -0.54 1 1
GNB1/GNG2 0.024 0.15 -10000 0 -0.44 27 27
mol:DAG 0.005 0.13 -10000 0 -0.41 26 26
PLCG1 0.004 0.13 -10000 0 -0.42 26 26
YES1 -0.003 0.13 0.25 1 -0.48 24 25
FZD3 0.014 0.091 -10000 0 -0.54 13 13
FZD6 0.007 0.11 -10000 0 -0.54 18 18
G protein 0.035 0.15 0.35 4 -0.42 25 29
MAP3K7 -0.006 0.11 0.25 1 -0.37 22 23
mol:Ca2+ 0.005 0.12 -10000 0 -0.4 26 26
mol:IP3 0.005 0.13 -10000 0 -0.41 26 26
NLK 0.004 0.13 -10000 0 -0.81 12 12
GNB1 0.034 0.011 -10000 0 -10000 0 0
CAMK2A -0.001 0.12 0.26 1 -0.38 25 26
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.016 0.13 -10000 0 -0.38 45 45
CSNK1A1 0.034 0.006 -10000 0 -10000 0 0
GNAS -0.006 0.13 0.25 1 -0.45 24 25
GO:0007205 -0.001 0.12 0.26 1 -0.41 26 27
WNT6 0.033 0.04 -10000 0 -0.54 2 2
WNT4 0.04 0.033 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.016 0.14 -10000 0 -0.45 21 21
GNG2 0.032 0.026 -10000 0 -0.54 1 1
WNT5A 0.01 0.13 -10000 0 -0.54 25 25
WNT11 0.024 0.079 -10000 0 -0.54 9 9
CDC42 -0.004 0.13 -10000 0 -0.46 22 22
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.034 0.094 -9999 0 -0.34 25 25
E-cadherin/beta catenin 0.018 0.1 -9999 0 -0.33 36 36
CTNNB1 0.029 0.052 -9999 0 -0.54 4 4
JUP 0.033 0.01 -9999 0 -10000 0 0
CDH1 0.006 0.12 -9999 0 -0.54 22 22
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.028 0.016 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.047 0.14 -10000 0 -0.45 16 16
NEF 0.011 0.022 -10000 0 -10000 0 0
NFKBIA 0.029 0.037 -10000 0 -0.35 1 1
BIRC3 0.008 0.14 0.29 19 -0.44 33 52
CYCS 0.033 0.13 0.27 17 -0.42 16 33
RIPK1 0.033 0.006 -10000 0 -10000 0 0
CD247 0.029 0.11 0.23 17 -0.55 15 32
MAP2K7 0.038 0.19 0.35 1 -0.71 18 19
protein ubiquitination 0.014 0.11 0.37 2 -0.39 15 17
CRADD 0.034 0.005 -10000 0 -10000 0 0
DAXX 0.034 0.008 -10000 0 -10000 0 0
FAS -0.003 0.14 -10000 0 -0.54 33 33
BID 0.031 0.13 0.25 9 -0.43 17 26
NF-kappa-B/RelA/I kappa B alpha 0.06 0.087 -10000 0 -0.26 25 25
TRADD 0.03 0.012 -10000 0 -10000 0 0
MAP3K5 0.003 0.13 -10000 0 -0.54 26 26
CFLAR 0.033 0.026 -10000 0 -0.54 1 1
FADD 0.028 0.015 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.06 0.087 -10000 0 -0.27 25 25
MAPK8 0.037 0.17 0.48 2 -0.68 16 18
APAF1 0.034 0.003 -10000 0 -10000 0 0
TRAF1 0.035 0.015 -10000 0 -10000 0 0
TRAF2 0.035 0.012 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.036 0.14 0.26 8 -0.33 38 46
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.012 0.14 -10000 0 -0.49 17 17
CHUK 0.012 0.12 0.38 2 -0.43 15 17
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.038 0.12 -10000 0 -0.33 41 41
TCRz/NEF 0.031 0.093 0.24 17 -0.41 15 32
TNF 0.038 0.023 -10000 0 -10000 0 0
FASLG 0.036 0.11 0.31 43 -0.37 15 58
NFKB1 0.03 0.035 -10000 0 -0.17 1 1
TNFR1A/BAG4/TNF-alpha 0.053 0.035 -10000 0 -10000 0 0
CASP6 0.053 0.15 -10000 0 -0.52 18 18
CASP7 0.019 0.19 0.4 16 -0.47 42 58
RELA 0.03 0.034 -10000 0 -0.17 1 1
CASP2 0.033 0.006 -10000 0 -10000 0 0
CASP3 0.016 0.19 0.4 15 -0.47 43 58
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.023 -10000 0 -10000 0 0
CASP8 0.034 0.005 -10000 0 -10000 0 0
CASP9 0.033 0.008 -10000 0 -10000 0 0
MAP3K14 0.015 0.13 0.36 1 -0.46 17 18
APAF-1/Caspase 9 0.02 0.13 0.26 2 -0.36 31 33
BCL2 -0.007 0.18 0.52 4 -0.57 21 25
Wnt signaling

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
Noncanonical Wnts/FZD -0.016 0.13 -9999 0 -0.38 45 45
FZD6 0.007 0.11 -9999 0 -0.54 18 18
WNT6 0.033 0.04 -9999 0 -0.54 2 2
WNT4 0.04 0.033 -9999 0 -10000 0 0
FZD3 0.014 0.091 -9999 0 -0.54 13 13
WNT5A 0.01 0.13 -9999 0 -0.54 25 25
WNT11 0.024 0.079 -9999 0 -0.54 9 9
Signaling events mediated by PRL

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
CCNE1 0.058 0.056 -10000 0 -10000 0 0
mol:Halofuginone 0.003 0.004 -10000 0 -10000 0 0
ITGA1 0.031 0.037 -10000 0 -0.54 2 2
CDKN1A -0.08 0.1 -10000 0 -0.53 17 17
PRL-3/alpha Tubulin 0.042 0.027 -10000 0 -10000 0 0
mol:Ca2+ -0.005 0.042 -10000 0 -10000 0 0
AGT 0.042 0.048 0.18 53 -10000 0 53
CCNA2 -0.18 0.12 -10000 0 -10000 0 0
TUBA1B 0.035 0.012 -10000 0 -10000 0 0
EGR1 -0.31 0.16 -10000 0 -0.39 412 412
CDK2/Cyclin E1 -0.042 0.11 -10000 0 -0.47 16 16
MAPK3 0.015 0.018 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.051 0.017 -10000 0 -10000 0 0
MAPK1 0.015 0.019 -10000 0 -10000 0 0
PTP4A1 -0.22 0.13 -10000 0 -10000 0 0
PTP4A3 0.03 0.025 -10000 0 -10000 0 0
PTP4A2 0.036 0.021 -10000 0 -10000 0 0
ITGB1 0.015 0.019 -10000 0 -10000 0 0
SRC 0.033 0.008 -10000 0 -10000 0 0
RAC1 -0.058 0.079 -10000 0 -0.52 7 7
Rab GGTase beta/Rab GGTase alpha 0.049 0.011 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.21 0.12 -10000 0 -10000 0 0
RABGGTA 0.033 0.006 -10000 0 -10000 0 0
BCAR1 -0.019 0.018 -10000 0 -10000 0 0
RHOC -0.059 0.084 -10000 0 -0.53 9 9
RHOA -0.064 0.1 -10000 0 -0.56 14 14
cell motility -0.084 0.095 -10000 0 -0.4 23 23
PRL-1/alpha Tubulin -0.21 0.12 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.04 0.034 -10000 0 -0.4 1 1
ROCK1 -0.082 0.095 -10000 0 -0.4 22 22
RABGGTB 0.034 0.006 -10000 0 -10000 0 0
CDK2 0.037 0.021 -10000 0 -10000 0 0
mitosis -0.22 0.13 -10000 0 -10000 0 0
ATF5 0.034 0.011 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.035 0.031 -10000 0 -0.54 1 1
ANTXR2 0.022 0.08 -10000 0 -0.54 10 10
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.01 -10000 0 -0.073 11 11
monocyte activation 0.013 0.085 -10000 0 -0.35 25 25
MAP2K2 0.004 0.097 -10000 0 -0.57 14 14
MAP2K1 -0.005 0.01 -10000 0 -10000 0 0
MAP2K7 -0.005 0.01 -10000 0 -10000 0 0
MAP2K6 -0.01 0.042 -10000 0 -0.3 10 10
CYAA -0.011 0.043 -10000 0 -0.29 11 11
MAP2K4 -0.005 0.012 -10000 0 -0.18 1 1
IL1B -0.013 0.05 0.24 1 -0.26 11 12
Channel 0.036 0.053 -10000 0 -0.31 11 11
NLRP1 -0.007 0.028 -10000 0 -0.27 5 5
CALM1 0.033 0.006 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.002 0.075 -10000 0 -0.4 16 16
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.01 0.073 11 -10000 0 11
MAPK3 -0.005 0.01 -10000 0 -10000 0 0
MAPK1 -0.005 0.01 -10000 0 -10000 0 0
PGR -0.063 0.14 0.086 114 -0.29 143 257
PA/Cellular Receptors 0.038 0.058 -10000 0 -0.34 11 11
apoptosis -0.002 0.01 -10000 0 -0.073 11 11
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.035 0.05 -10000 0 -0.29 11 11
macrophage activation 0.007 0.049 0.18 37 -10000 0 37
TNF 0.038 0.023 -10000 0 -10000 0 0
VCAM1 0.012 0.086 -10000 0 -0.35 25 25
platelet activation 0.002 0.075 -10000 0 -0.4 16 16
MAPKKK cascade -0.003 0.03 0.12 3 -0.14 6 9
IL18 -0.001 0.04 0.14 1 -0.25 3 4
negative regulation of macrophage activation -0.002 0.01 -10000 0 -0.073 11 11
LEF -0.002 0.01 -10000 0 -0.073 11 11
CASP1 -0.006 0.033 -10000 0 -0.11 35 35
mol:cAMP 0.002 0.075 -10000 0 -0.41 16 16
necrosis -0.002 0.01 -10000 0 -0.073 11 11
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.035 0.05 -10000 0 -0.29 11 11
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.034 0.005 -10000 0 -10000 0 0
HDAC2 0.033 0.017 -10000 0 -10000 0 0
GNB1/GNG2 0.048 0.088 -10000 0 -0.34 23 23
forebrain development -0.043 0.2 -10000 0 -0.58 46 46
GNAO1 0.03 0.012 -10000 0 -10000 0 0
SMO/beta Arrestin2 0.029 0.093 -10000 0 -0.4 22 22
SMO 0.012 0.12 -10000 0 -0.54 22 22
ARRB2 0.032 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.03 0.11 0.29 1 -0.44 11 12
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
GSK3B 0.034 0.008 -10000 0 -10000 0 0
GNAI2 0.034 0.01 -10000 0 -10000 0 0
SIN3/HDAC complex 0.077 0.032 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 183 183
XPO1 0.036 0.006 -10000 0 -10000 0 0
GLI1/Su(fu) -0.033 0.19 -10000 0 -0.66 26 26
SAP30 0.033 0.009 -10000 0 -10000 0 0
mol:GDP 0.012 0.12 -10000 0 -0.54 22 22
MIM/GLI2A 0.033 0.029 0.31 1 -10000 0 1
IFT88 0.031 0.027 -10000 0 -0.54 1 1
GNAI3 0.034 0.006 -10000 0 -10000 0 0
GLI2 0.016 0.084 -10000 0 -0.37 14 14
GLI3 0.017 0.11 0.3 1 -0.43 14 15
CSNK1D 0.032 0.008 -10000 0 -10000 0 0
CSNK1E 0.032 0.009 -10000 0 -10000 0 0
SAP18 0.032 0.009 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.031 0.027 -10000 0 -0.54 1 1
GNG2 0.032 0.026 -10000 0 -0.54 1 1
Gi family/GTP -0.083 0.16 -10000 0 -0.37 72 72
SIN3B 0.035 0.014 -10000 0 -10000 0 0
SIN3A 0.033 0.006 -10000 0 -10000 0 0
GLI3/Su(fu) 0.025 0.11 -10000 0 -0.45 15 15
GLI2/Su(fu) 0.019 0.11 -10000 0 -0.45 13 13
FOXA2 0.016 0.12 -10000 0 -0.76 8 8
neural tube patterning -0.043 0.2 -10000 0 -0.58 46 46
SPOP 0.031 0.011 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.027 0.064 -10000 0 -0.35 1 1
GNB1 0.034 0.011 -10000 0 -10000 0 0
CSNK1G2 0.033 0.007 -10000 0 -10000 0 0
CSNK1G3 0.033 0.007 -10000 0 -10000 0 0
MTSS1 0.033 0.029 0.31 1 -10000 0 1
embryonic limb morphogenesis -0.043 0.2 -10000 0 -0.58 46 46
SUFU 0.019 0.049 -10000 0 -0.38 1 1
LGALS3 -0.03 0.18 -10000 0 -0.54 56 56
catabolic process 0.037 0.13 0.32 1 -0.56 14 15
GLI3A/CBP 0.001 0.12 -10000 0 -0.36 49 49
KIF3A 0.033 0.006 -10000 0 -10000 0 0
GLI1 -0.045 0.21 -10000 0 -0.59 46 46
RAB23 0.035 0.014 -10000 0 -10000 0 0
CSNK1A1 0.034 0.006 -10000 0 -10000 0 0
IFT172 0.033 0.026 -10000 0 -0.54 1 1
RBBP7 0.037 0.022 -10000 0 -10000 0 0
Su(fu)/Galectin3 -0.009 0.13 -10000 0 -0.33 59 59
GNAZ 0.026 0.063 -10000 0 -0.54 6 6
RBBP4 0.033 0.006 -10000 0 -10000 0 0
CSNK1G1 0.033 0.007 -10000 0 -10000 0 0
PIAS1 0.033 0.007 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
GLI2/SPOP 0.028 0.088 -10000 0 -0.46 9 9
STK36 0.035 0.026 -10000 0 -0.54 1 1
Gi family/GNB1/GNG2/GDP -0.083 0.17 -10000 0 -0.4 70 70
PTCH1 -0.038 0.18 -10000 0 -0.71 16 16
MIM/GLI1 -0.024 0.18 -10000 0 -0.66 23 23
CREBBP 0.002 0.12 -10000 0 -0.36 49 49
Su(fu)/SIN3/HDAC complex 0.015 0.1 -10000 0 -0.46 16 16
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.004 0.13 0.28 1 -0.46 21 22
BAG4 0.028 0.016 -10000 0 -10000 0 0
BAD 0.007 0.047 0.18 3 -0.18 8 11
NFKBIA 0.033 0.007 -10000 0 -10000 0 0
BIRC3 0.016 0.11 -10000 0 -0.54 17 17
BAX 0.007 0.052 0.26 3 -0.18 8 11
EnzymeConsortium:3.1.4.12 0.003 0.032 0.09 4 -0.097 21 25
IKBKB 0.013 0.13 0.35 1 -0.45 15 16
MAP2K2 0.011 0.059 0.23 10 -0.22 2 12
MAP2K1 0.011 0.06 0.23 11 -0.22 2 13
SMPD1 0.004 0.04 0.2 1 -0.16 11 12
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.031 0.14 0.36 4 -0.44 20 24
MAP2K4 0.007 0.052 0.2 2 -0.24 5 7
protein ubiquitination 0.002 0.13 0.36 3 -0.44 20 23
EnzymeConsortium:2.7.1.37 0.01 0.063 0.24 10 -0.24 2 12
response to UV 0 0.001 0.003 12 -0.002 1 13
RAF1 0.011 0.06 0.21 18 -0.21 3 21
CRADD 0.034 0.005 -10000 0 -10000 0 0
mol:ceramide 0.008 0.05 0.16 3 -0.15 21 24
I-kappa-B-alpha/RELA/p50/ubiquitin 0.043 0.014 -10000 0 -0.14 1 1
MADD 0.034 0.005 -10000 0 -10000 0 0
MAP3K1 0.007 0.054 0.2 2 -0.22 8 10
TRADD 0.03 0.012 -10000 0 -10000 0 0
RELA/p50 0.034 0.005 -10000 0 -10000 0 0
MAPK3 0.014 0.06 0.23 11 -0.22 2 13
MAPK1 0.01 0.068 0.23 11 -0.22 8 19
p50/RELA/I-kappa-B-alpha 0.048 0.016 -10000 0 -0.17 1 1
FADD 0.026 0.14 0.3 8 -0.46 18 26
KSR1 0.011 0.057 0.2 14 -0.18 7 21
MAPK8 0.004 0.056 0.28 3 -0.24 5 8
TRAF2 0.035 0.012 -10000 0 -10000 0 0
response to radiation 0 0 0.003 2 -10000 0 2
CHUK -0.007 0.12 -10000 0 -0.46 18 18
TNF R/SODD 0.038 0.023 -10000 0 -10000 0 0
TNF 0.038 0.023 -10000 0 -10000 0 0
CYCS 0.025 0.07 0.19 21 -0.18 7 28
IKBKG -0.007 0.13 0.45 1 -0.46 18 19
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.003 0.14 -10000 0 -0.46 24 24
RELA 0.034 0.005 -10000 0 -10000 0 0
RIPK1 0.034 0.006 -10000 0 -10000 0 0
AIFM1 0.024 0.069 0.19 19 -0.18 8 27
TNF/TNF R/SODD 0.053 0.035 -10000 0 -10000 0 0
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
response to heat 0 0 0.003 2 -10000 0 2
CASP8 0.018 0.13 -10000 0 -0.65 16 16
NSMAF 0.015 0.14 0.28 5 -0.45 19 24
response to hydrogen peroxide 0 0.001 0.003 12 -0.002 1 13
BCL2 -0.072 0.22 -10000 0 -0.54 93 93
FoxO family signaling

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
G6PC 0.003 0.098 -10000 0 -10000 0 0
PLK1 0.13 0.22 0.63 19 -0.79 5 24
CDKN1B 0.1 0.18 0.54 6 -0.45 14 20
FOXO3 0.11 0.23 0.54 27 -0.62 16 43
KAT2B 0.02 0.032 0.085 39 -0.054 16 55
FOXO1/SIRT1 0.006 0.1 -10000 0 -0.33 9 9
CAT 0.055 0.36 0.63 11 -1 42 53
CTNNB1 0.029 0.052 -10000 0 -0.54 4 4
AKT1 0.053 0.046 -10000 0 -10000 0 0
FOXO1 0.001 0.11 -10000 0 -0.35 10 10
MAPK10 0.024 0.06 0.22 9 -0.29 10 19
mol:GTP 0 0.004 -10000 0 -10000 0 0
FOXO4 0.044 0.12 0.43 3 -0.4 6 9
response to oxidative stress 0.023 0.033 0.091 39 -0.056 12 51
FOXO3A/SIRT1 0.085 0.2 0.47 15 -0.58 16 31
XPO1 0.034 0.005 -10000 0 -10000 0 0
EP300 0.035 0.01 -10000 0 -10000 0 0
BCL2L11 0.057 0.082 -10000 0 -0.82 3 3
FOXO1/SKP2 0.016 0.1 -10000 0 -0.31 10 10
mol:GDP 0.023 0.033 0.09 39 -0.056 12 51
RAN 0.034 0.005 -10000 0 -10000 0 0
GADD45A 0.082 0.21 0.5 1 -0.78 16 17
YWHAQ 0.034 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.036 0.15 -10000 0 -0.53 21 21
MST1 0.047 0.042 -10000 0 -10000 0 0
CSNK1D 0.032 0.008 -10000 0 -10000 0 0
CSNK1E 0.032 0.009 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.024 0.14 -10000 0 -0.48 25 25
YWHAB 0.032 0.008 -10000 0 -10000 0 0
MAPK8 0.029 0.042 0.22 8 -0.27 1 9
MAPK9 0.029 0.04 0.22 9 -10000 0 9
YWHAG 0.034 0.008 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
YWHAZ 0.026 0.018 -10000 0 -10000 0 0
SIRT1 0.022 0.023 -10000 0 -10000 0 0
SOD2 0.095 0.2 0.56 9 -0.56 11 20
RBL2 0.035 0.32 0.56 2 -0.78 47 49
RAL/GDP 0.057 0.036 -10000 0 -10000 0 0
CHUK 0.048 0.043 -10000 0 -10000 0 0
Ran/GTP 0.024 0.014 -10000 0 -10000 0 0
CSNK1G2 0.033 0.007 -10000 0 -10000 0 0
RAL/GTP 0.057 0.042 -10000 0 -10000 0 0
CSNK1G1 0.033 0.007 -10000 0 -10000 0 0
FASLG 0.075 0.12 -10000 0 -1.4 1 1
SKP2 0.035 0.018 -10000 0 -10000 0 0
USP7 0.032 0.01 -10000 0 -10000 0 0
IKBKB 0.04 0.041 -10000 0 -10000 0 0
CCNB1 0.15 0.24 0.62 20 -0.93 3 23
FOXO1-3a-4/beta catenin 0.096 0.22 0.56 9 -0.4 39 48
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.1 -10000 0 -0.3 10 10
CSNK1A1 0.034 0.006 -10000 0 -10000 0 0
SGK1 0.02 0.032 0.085 39 -0.054 16 55
CSNK1G3 0.033 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.045 0.02 -10000 0 -10000 0 0
ZFAND5 0.044 0.11 0.44 2 -10000 0 2
SFN 0.032 0.04 -10000 0 -0.54 2 2
CDK2 0.039 0.021 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.054 0.13 -10000 0 -0.48 15 15
CREBBP 0.032 0.028 -10000 0 -0.54 1 1
FBXO32 0.12 0.35 0.65 26 -1.1 26 52
BCL6 0.018 0.4 0.55 1 -1.1 55 56
RALB 0.034 0.005 -10000 0 -10000 0 0
RALA 0.034 0.006 -10000 0 -10000 0 0
YWHAH 0.033 0.014 -10000 0 -10000 0 0
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.016 0.15 0.36 6 -0.39 16 22
IKBKB 0.05 0.092 0.35 8 -0.35 2 10
AKT1 0.062 0.12 0.32 46 -0.25 2 48
IKBKG 0.056 0.077 0.33 8 -0.28 3 11
CALM1 0.031 0.086 0.28 8 -0.39 6 14
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
MAP3K1 0.068 0.14 0.45 4 -0.49 12 16
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0.031 0.091 0.29 7 -0.35 10 17
DOK1 0.036 0.016 -10000 0 -10000 0 0
AP-1 -0.073 0.11 0.32 1 -0.24 67 68
LYN 0.03 0.015 -10000 0 -10000 0 0
BLNK 0.039 0.026 -10000 0 -10000 0 0
SHC1 0.027 0.014 -10000 0 -10000 0 0
BCR complex 0.041 0.07 0.26 3 -0.4 10 13
CD22 0.015 0.089 0.31 3 -0.58 6 9
CAMK2G 0.029 0.084 0.26 10 -0.37 6 16
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.023 0.044 -10000 0 -0.28 6 6
GO:0007205 0.032 0.092 0.29 7 -0.36 10 17
SYK 0.038 0.026 -10000 0 -10000 0 0
ELK1 0.033 0.09 0.28 8 -0.38 7 15
NFATC1 0.064 0.11 0.33 9 -0.41 8 17
B-cell antigen/BCR complex 0.041 0.07 0.26 3 -0.4 10 13
PAG1/CSK 0.043 0.028 0.26 1 -10000 0 1
NFKBIB 0.043 0.053 0.21 9 -0.13 9 18
HRAS 0.044 0.095 0.27 14 -0.35 8 22
NFKBIA 0.043 0.052 0.2 10 -0.12 9 19
NF-kappa-B/RelA/I kappa B beta 0.047 0.049 0.21 9 -10000 0 9
RasGAP/Csk 0.064 0.079 0.35 2 -0.39 6 8
mol:GDP 0.032 0.089 0.28 7 -0.38 7 14
PTEN 0.026 0.067 -10000 0 -0.54 7 7
CD79B 0.02 0.081 -10000 0 -0.54 10 10
NF-kappa-B/RelA/I kappa B alpha 0.047 0.048 0.21 9 -10000 0 9
GRB2 0.034 0.018 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.049 0.15 0.42 5 -0.48 14 19
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 0.03 0.09 0.3 6 -0.37 9 15
CSK 0.034 0.011 -10000 0 -10000 0 0
FOS -0.15 0.14 0.27 1 -0.36 60 61
CHUK 0.053 0.084 0.33 8 -0.34 5 13
IBTK 0.033 0.008 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.054 0.09 0.34 1 -0.39 4 5
PTPN6 0.031 0.1 0.32 6 -0.55 6 12
RELA 0.034 0.005 -10000 0 -10000 0 0
BCL2A1 0.042 0.044 0.2 10 -10000 0 10
VAV2 0.045 0.11 0.32 3 -0.57 6 9
ubiquitin-dependent protein catabolic process 0.046 0.052 0.21 9 -0.12 14 23
BTK 0.017 0.09 -10000 0 -0.96 4 4
CD19 0.022 0.093 0.31 3 -0.55 6 9
MAP4K1 0.037 0.021 -10000 0 -10000 0 0
CD72 0.062 0.059 -10000 0 -10000 0 0
PAG1 0.031 0.025 -10000 0 -10000 0 0
MAPK14 0.065 0.13 0.43 6 -0.42 12 18
SH3BP5 0.018 0.094 -10000 0 -0.54 14 14
PIK3AP1 0.029 0.096 0.33 6 -0.41 9 15
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.047 0.095 0.31 4 -0.44 7 11
RAF1 0.042 0.09 0.26 11 -0.34 7 18
RasGAP/p62DOK/SHIP 0.054 0.071 0.3 1 -0.35 7 8
CD79A 0.042 0.034 -10000 0 -10000 0 0
re-entry into mitotic cell cycle -0.071 0.11 0.32 1 -0.24 60 61
RASA1 0.034 0.012 -10000 0 -10000 0 0
MAPK3 0.048 0.092 0.29 17 -0.34 4 21
MAPK1 0.038 0.083 0.3 6 -0.34 4 10
CD72/SHP1 0.093 0.12 0.37 19 -0.52 6 25
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 0.065 0.13 0.44 5 -0.42 12 17
actin cytoskeleton organization 0.071 0.11 0.32 17 -0.49 6 23
NF-kappa-B/RelA 0.093 0.089 0.36 9 -0.22 2 11
Calcineurin 0.042 0.091 -10000 0 -0.38 5 5
PI3K -0.002 0.074 -10000 0 -0.4 7 7
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.032 0.095 0.32 6 -0.42 10 16
SOS1 0.034 0.004 -10000 0 -10000 0 0
Bam32/HPK1 0.065 0.16 -10000 0 -0.64 15 15
DAPP1 0.031 0.16 -10000 0 -0.71 16 16
cytokine secretion 0.063 0.11 0.31 11 -0.38 8 19
mol:DAG 0.03 0.09 0.3 6 -0.37 9 15
PLCG2 0.021 0.073 -10000 0 -0.54 8 8
MAP2K1 0.039 0.087 0.28 6 -0.37 4 10
B-cell antigen/BCR complex/FcgammaRIIB 0.046 0.074 0.28 3 -0.43 7 10
mol:PI-3-4-5-P3 0.031 0.1 0.31 20 -0.3 6 26
ETS1 0.026 0.081 0.3 3 -0.34 7 10
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.075 0.079 0.44 1 -0.3 9 10
B-cell antigen/BCR complex/LYN 0.016 0.084 -10000 0 -0.47 11 11
MALT1 0.033 0.009 -10000 0 -10000 0 0
TRAF6 0.033 0.006 -10000 0 -10000 0 0
RAC1 0.063 0.11 0.33 14 -0.52 6 20
B-cell antigen/BCR complex/LYN/SYK 0.043 0.099 0.36 3 -0.53 6 9
CARD11 0.034 0.094 0.29 11 -0.4 6 17
FCGR2B 0.026 0.039 -10000 0 -0.54 2 2
PPP3CA 0.03 0.051 -10000 0 -0.54 4 4
BCL10 0.033 0.007 -10000 0 -10000 0 0
IKK complex 0.045 0.059 0.18 32 -0.14 1 33
PTPRC 0.035 0.035 -10000 0 -10000 0 0
PDPK1 0.039 0.096 0.27 33 -0.22 4 37
PPP3CB 0.034 0.004 -10000 0 -10000 0 0
PPP3CC 0.024 0.046 -10000 0 -0.54 3 3
POU2F2 0.036 0.039 0.24 5 -10000 0 5
PLK2 and PLK4 events

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
PLK2 0.016 0.1 -9999 0 -0.54 17 17
PLK4 0.055 0.052 -9999 0 -10000 0 0
regulation of centriole replication 0.023 0.086 -9999 0 -0.38 16 16
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.087 0.075 0.31 1 -0.28 5 6
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.033 0.008 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.099 0.11 0.42 30 -10000 0 30
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.063 0.055 -10000 0 -0.34 5 5
antigen processing and presentation of peptide antigen via MHC class I -0.004 0.097 0.17 1 -0.28 36 37
CaM/Ca2+ 0.085 0.071 -10000 0 -0.27 5 5
RAP1A 0.034 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.075 0.089 0.31 24 -0.27 5 29
AKT1 0.018 0.11 0.33 8 -0.35 11 19
MAP2K1 0.026 0.074 0.34 3 -0.27 1 4
MAP3K11 0.043 0.07 0.32 4 -0.27 5 9
IFNGR1 0.03 0.058 -10000 0 -0.54 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.046 0.09 -10000 0 -0.44 7 7
Rap1/GTP 0.018 0.035 -10000 0 -10000 0 0
CRKL/C3G 0.047 0.014 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.095 0.075 -10000 0 -0.3 5 5
CEBPB 0.057 0.14 0.42 6 -0.59 5 11
STAT3 0.033 0.007 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.092 0.1 -10000 0 -0.75 4 4
STAT1 0.059 0.093 0.3 27 -0.27 5 32
CALM1 0.033 0.006 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.061 0.064 -10000 0 -0.55 1 1
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.075 0.09 0.34 10 -10000 0 10
CEBPB/PTGES2/Cbp/p300 0.039 0.085 0.29 3 -0.37 5 8
mol:Ca2+ 0.082 0.072 0.3 1 -0.28 5 6
MAPK3 0.042 0.12 -10000 0 -0.65 8 8
STAT1 (dimer) 0.02 0.15 0.32 3 -0.43 25 28
MAPK1 0.01 0.2 -10000 0 -0.7 33 33
JAK2 0.035 0.016 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
JAK1 0.036 0.013 -10000 0 -10000 0 0
CAMK2D 0.03 0.052 -10000 0 -0.54 4 4
DAPK1 0.058 0.11 0.41 12 -0.35 4 16
SMAD7 0.022 0.071 0.23 8 -0.19 5 13
CBL/CRKL/C3G 0.069 0.069 0.33 3 -0.26 1 4
PI3K 0.048 0.12 -10000 0 -0.31 33 33
IFNG 0.061 0.064 -10000 0 -0.55 1 1
apoptosis 0.048 0.12 0.38 11 -0.46 9 20
CAMK2G 0.034 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.033 0.007 -10000 0 -10000 0 0
CAMK2A 0.034 0.006 -10000 0 -10000 0 0
CAMK2B 0.039 0.069 -10000 0 -0.54 5 5
FRAP1 0.002 0.1 0.3 10 -0.36 7 17
PRKCD 0.018 0.11 0.34 9 -0.32 14 23
RAP1B 0.033 0.007 -10000 0 -10000 0 0
negative regulation of cell growth -0.004 0.097 0.17 1 -0.28 36 37
PTPN2 0.033 0.007 -10000 0 -10000 0 0
EP300 0.033 0.009 -10000 0 -10000 0 0
IRF1 0.066 0.12 0.4 34 -10000 0 34
STAT1 (dimer)/PIASy 0.072 0.091 0.35 9 -10000 0 9
SOCS1 0.018 0.1 -10000 0 -1 5 5
mol:GDP 0.064 0.065 0.31 3 -0.25 2 5
CASP1 0.005 0.11 0.25 10 -0.27 57 67
PTGES2 0.034 0.005 -10000 0 -10000 0 0
IRF9 0.052 0.068 0.27 17 -10000 0 17
mol:PI-3-4-5-P3 0.031 0.1 -10000 0 -0.3 33 33
RAP1/GDP 0.051 0.052 -10000 0 -10000 0 0
CBL 0.041 0.068 0.31 4 -0.27 5 9
MAP3K1 0.045 0.071 0.33 3 -0.27 5 8
PIAS1 0.033 0.007 -10000 0 -10000 0 0
PIAS4 0.034 0.016 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.004 0.097 0.17 1 -0.28 36 37
PTPN11 0.044 0.072 0.33 4 -0.28 5 9
CREBBP 0.031 0.028 -10000 0 -0.54 1 1
RAPGEF1 0.034 0.006 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

Figure S90.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S90.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.016 0.004 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.041 0.028 -10000 0 -10000 0 0
CDKN1B 0.018 0.071 0.31 3 -0.35 7 10
CDKN1A 0.02 0.067 0.28 2 -0.34 9 11
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.031 0.019 -10000 0 -10000 0 0
FOXO3 0.023 0.063 0.28 1 -0.36 6 7
AKT1 0.022 0.064 -10000 0 -0.36 9 9
BAD 0.033 0.007 -10000 0 -10000 0 0
AKT3 0.015 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.019 0.062 -10000 0 -0.34 9 9
AKT1/ASK1 0.033 0.096 -10000 0 -0.35 9 9
BAD/YWHAZ 0.051 0.032 -10000 0 -10000 0 0
RICTOR 0.033 0.006 -10000 0 -10000 0 0
RAF1 0.034 0.006 -10000 0 -10000 0 0
JNK cascade -0.032 0.093 0.34 9 -10000 0 9
TSC1 0.021 0.057 -10000 0 -0.36 6 6
YWHAZ 0.026 0.018 -10000 0 -10000 0 0
AKT1/RAF1 0.055 0.077 0.3 2 -0.34 9 11
EP300 0.032 0.009 -10000 0 -10000 0 0
mol:GDP 0.022 0.063 -10000 0 -0.35 9 9
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.027 0.08 0.28 22 -0.34 9 31
YWHAQ 0.034 0.005 -10000 0 -10000 0 0
TBC1D4 0.002 0.048 0.25 2 -0.32 10 12
MAP3K5 0.003 0.13 -10000 0 -0.54 26 26
MAPKAP1 0.034 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.041 0.079 0.29 7 -0.28 2 9
YWHAH 0.033 0.014 -10000 0 -10000 0 0
AKT1S1 0.023 0.068 -10000 0 -0.34 9 9
CASP9 0.022 0.047 -10000 0 -0.3 4 4
YWHAB 0.032 0.008 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.05 0.084 0.35 2 -0.45 2 4
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.059 0.026 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
SRC 0.033 0.008 -10000 0 -10000 0 0
AKT2/p21CIP1 0.022 0.062 -10000 0 -0.36 5 5
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.054 -10000 0 -0.33 9 9
CHUK 0.02 0.061 -10000 0 -0.34 8 8
BAD/BCL-XL 0.056 0.074 0.31 1 -0.38 4 5
mTORC2 0.042 0.01 -10000 0 -10000 0 0
AKT2 0.017 0.006 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.043 0.11 0.37 4 -0.42 10 14
PDPK1 0.031 0.01 -10000 0 -10000 0 0
MDM2 0.024 0.071 0.28 4 -0.34 9 13
MAPKKK cascade -0.055 0.076 0.34 9 -0.3 2 11
MDM2/Cbp/p300 0.06 0.082 0.36 2 -0.37 4 6
TSC1/TSC2 0.025 0.08 0.35 3 -0.38 4 7
proteasomal ubiquitin-dependent protein catabolic process 0.057 0.078 0.35 2 -0.35 4 6
glucose import -0.15 0.15 0.21 1 -0.3 251 252
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.022 0.055 -10000 0 -0.64 1 1
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.15 0.16 0.21 1 -0.31 237 238
GSK3A 0.021 0.065 -10000 0 -0.34 9 9
FOXO1 -0.006 0.096 -10000 0 -0.43 9 9
GSK3B 0.021 0.062 0.28 1 -0.34 8 9
SFN 0.032 0.04 -10000 0 -0.54 2 2
G1/S transition of mitotic cell cycle 0.031 0.076 0.39 1 -0.62 1 2
p27Kip1/14-3-3 family 0.031 0.044 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
KPNA1 0.034 0.005 -10000 0 -10000 0 0
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
YWHAG 0.034 0.008 -10000 0 -10000 0 0
RHEB 0.034 0.009 -10000 0 -10000 0 0
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
Signaling events mediated by VEGFR1 and VEGFR2

Figure S91.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S91.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin 0.049 0.027 -10000 0 -0.4 1 1
AKT1 0.026 0.14 0.36 3 -0.46 14 17
PTK2B 0.015 0.084 0.36 2 -0.43 1 3
VEGFR2 homodimer/Frs2 0.022 0.087 -10000 0 -0.33 27 27
CAV1 -0.38 0.26 -10000 0 -0.54 365 365
CALM1 0.033 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.049 0.092 -10000 0 -0.3 23 23
endothelial cell proliferation 0.051 0.13 0.39 10 -0.44 8 18
mol:Ca2+ 0.02 0.091 0.37 1 -0.5 4 5
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.068 0.093 -10000 0 -0.45 1 1
RP11-342D11.1 0.002 0.087 0.27 1 -0.43 7 8
CDH5 0.03 0.012 -10000 0 -10000 0 0
VEGFA homodimer 0.07 0.059 -10000 0 -0.29 3 3
SHC1 0.027 0.014 -10000 0 -10000 0 0
SHC2 0.006 0.12 -10000 0 -0.54 24 24
HRAS/GDP 0.031 0.08 -10000 0 -0.41 4 4
SH2D2A 0.043 0.048 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.056 0.12 -10000 0 -0.47 12 12
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.049 0.095 -10000 0 -0.31 19 19
VEGFR1 homodimer 0.032 0.013 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.056 0.1 -10000 0 -0.44 4 4
GRB10 0.017 0.11 -10000 0 -0.61 7 7
PTPN11 0.034 0.004 -10000 0 -10000 0 0
GRB2 0.034 0.018 -10000 0 -10000 0 0
PAK1 0.043 0.046 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.067 0.1 -10000 0 -0.43 1 1
HRAS 0.034 0.013 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.027 0.081 -10000 0 -0.37 8 8
HIF1A 0.031 0.054 -10000 0 -0.54 4 4
FRS2 0.032 0.029 -10000 0 -0.54 1 1
oxygen and reactive oxygen species metabolic process 0.066 0.091 -10000 0 -0.44 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.033 0.006 -10000 0 -10000 0 0
Nck/Pak 0.053 0.037 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.044 0.095 -10000 0 -0.31 26 26
mol:GDP 0.043 0.09 -10000 0 -0.43 4 4
mol:NADP 0.031 0.11 0.59 1 -0.42 14 15
eNOS/Hsp90 0.046 0.11 0.57 1 -0.41 12 13
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 0.02 0.092 0.37 1 -0.5 4 5
HIF1A/ARNT 0.037 0.042 -10000 0 -0.4 3 3
SHB 0.035 0.018 -10000 0 -10000 0 0
VEGFA 0.051 0.048 -10000 0 -10000 0 0
VEGFC 0.021 0.084 -10000 0 -0.54 11 11
FAK1/Vinculin 0.04 0.11 0.37 1 -0.41 4 5
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.067 0.096 -10000 0 -0.29 24 24
PTPN6 0.033 0.015 -10000 0 -10000 0 0
EPAS1 0.01 0.13 -10000 0 -0.54 29 29
mol:L-citrulline 0.031 0.11 0.59 1 -0.42 14 15
ITGAV 0.033 0.028 -10000 0 -0.54 1 1
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.063 0.093 -10000 0 -0.29 20 20
VEGFR2 homodimer/VEGFA homodimer 0.049 0.11 -10000 0 -0.34 27 27
VEGFR2/3 heterodimer 0.022 0.087 -10000 0 -0.34 28 28
VEGFB 0.033 0.007 -10000 0 -10000 0 0
MAPK11 0.002 0.1 -10000 0 -0.46 8 8
VEGFR2 homodimer 0.003 0.096 -10000 0 -0.39 28 28
FLT1 0.032 0.013 -10000 0 -10000 0 0
NEDD4 0.028 0.058 -10000 0 -0.54 5 5
MAPK3 0.016 0.094 0.37 1 -0.45 4 5
MAPK1 0.012 0.093 0.34 2 -0.45 4 6
VEGFA145/NRP2 0.06 0.038 0.26 1 -10000 0 1
VEGFR1/2 heterodimer 0.021 0.087 -10000 0 -0.34 28 28
KDR 0.003 0.096 -10000 0 -0.39 28 28
VEGFA165/NRP1/VEGFR2 homodimer 0.053 0.1 -10000 0 -0.54 4 4
SRC 0.033 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.018 0.098 0.37 2 -0.46 4 6
PI3K 0.018 0.12 -10000 0 -0.5 8 8
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.051 0.092 -10000 0 -0.31 24 24
FES 0.018 0.095 -10000 0 -0.56 4 4
GAB1 0.041 0.1 -10000 0 -0.4 6 6
VEGFR2 homodimer/VEGFA homodimer/Src 0.05 0.089 -10000 0 -0.31 21 21
CTNNB1 0.029 0.052 -10000 0 -0.54 4 4
SOS1 0.034 0.004 -10000 0 -10000 0 0
ARNT 0.027 0.014 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.13 0.16 -10000 0 -0.45 41 41
VEGFR2 homodimer/VEGFA homodimer/Yes 0.048 0.093 -10000 0 -0.31 24 24
PI3K/GAB1 0.03 0.14 0.39 2 -0.45 14 16
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.075 0.096 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.031 0.1 -10000 0 -0.32 38 38
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
CDC42 0.019 0.097 0.37 1 -0.56 4 5
actin cytoskeleton reorganization 0.048 0.094 -10000 0 -0.31 19 19
PTK2 0.023 0.091 -10000 0 -0.4 6 6
EDG1 0.002 0.087 0.27 1 -0.43 7 8
mol:DAG 0.02 0.092 0.37 1 -0.5 4 5
CaM/Ca2+ 0.033 0.088 -10000 0 -0.47 4 4
MAP2K3 0.002 0.086 -10000 0 -0.53 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.046 0.12 -10000 0 -0.63 7 7
PLCG1 0.02 0.092 0.37 1 -0.51 4 5
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.068 0.094 0.37 1 -0.3 21 22
IQGAP1 0.033 0.008 -10000 0 -10000 0 0
YES1 0.032 0.027 -10000 0 -0.54 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.051 0.093 -10000 0 -0.31 24 24
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.049 0.092 -10000 0 -0.31 23 23
cell migration 0.044 0.11 0.39 2 -0.47 2 4
mol:PI-3-4-5-P3 0.018 0.11 -10000 0 -0.47 8 8
FYN 0.03 0.037 -10000 0 -0.54 2 2
VEGFB/NRP1 0.022 0.089 -10000 0 -0.52 4 4
mol:NO 0.031 0.11 0.59 1 -0.42 14 15
PXN 0.034 0.003 -10000 0 -10000 0 0
HRAS/GTP 0.013 0.071 -10000 0 -0.41 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.038 0.11 -10000 0 -0.63 7 7
VHL 0.036 0.018 -10000 0 -10000 0 0
ITGB3 0.035 0.019 -10000 0 -10000 0 0
NOS3 0.03 0.12 0.6 1 -0.48 14 15
VEGFR2 homodimer/VEGFA homodimer/Sck 0.032 0.12 -10000 0 -0.32 38 38
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCA 0.006 0.08 0.37 1 -0.44 4 5
PRKCB 0.005 0.084 0.36 1 -0.48 4 5
VCL 0.034 0.005 -10000 0 -10000 0 0
VEGFA165/NRP1 0.026 0.094 -10000 0 -0.32 25 25
VEGFR1/2 heterodimer/VEGFA homodimer 0.047 0.093 -10000 0 -0.31 24 24
VEGFA165/NRP2 0.06 0.038 0.26 1 -10000 0 1
MAPKKK cascade 0.063 0.12 0.39 7 -0.56 5 12
NRP2 0.035 0.015 -10000 0 -10000 0 0
VEGFC homodimer 0.021 0.084 -10000 0 -0.54 11 11
NCK1 0.034 0.005 -10000 0 -10000 0 0
ROCK1 0.034 0.006 -10000 0 -10000 0 0
FAK1/Paxillin 0.041 0.11 0.44 2 -0.41 4 6
MAP3K13 0.017 0.095 -10000 0 -0.56 4 4
PDPK1 0.004 0.098 -10000 0 -0.42 8 8
VEGFR1 specific signals

Figure S92.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S92.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer 0.037 0.039 -10000 0 -0.34 4 4
VEGFR1 homodimer/NRP1 0.015 0.034 -10000 0 -0.33 4 4
mol:DAG 0.019 0.042 -10000 0 -0.3 4 4
VEGFR1 homodimer/NRP1/VEGFR 121 0.042 0.044 -10000 0 -0.3 3 3
CaM/Ca2+ 0.037 0.041 -10000 0 -10000 0 0
HIF1A 0.039 0.055 -10000 0 -0.54 4 4
GAB1 0.033 0.027 -10000 0 -0.54 1 1
AKT1 -0.008 0.099 -10000 0 -0.36 4 4
PLCG1 0.019 0.042 -10000 0 -0.31 4 4
NOS3 0.019 0.087 -10000 0 -0.49 6 6
CBL 0.03 0.011 -10000 0 -10000 0 0
mol:NO 0.02 0.093 -10000 0 -0.48 7 7
FLT1 0.021 0.043 -10000 0 -0.39 4 4
PGF 0.034 0.011 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2/VEGFR121 0.062 0.051 -10000 0 -0.31 3 3
CALM1 0.033 0.006 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
eNOS/Hsp90 0.036 0.095 -10000 0 -0.46 7 7
endothelial cell proliferation 0.027 0.07 0.4 2 -10000 0 2
mol:Ca2+ 0.019 0.041 -10000 0 -0.3 4 4
MAPK3 -0.006 0.035 0.25 1 -10000 0 1
MAPK1 -0.006 0.037 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
PLGF homodimer 0.034 0.011 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.38 0.26 -10000 0 -0.54 365 365
VEGFA homodimer 0.05 0.047 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.047 0.049 -10000 0 -0.34 3 3
platelet activating factor biosynthetic process 0.019 0.073 0.34 2 -10000 0 2
PI3K 0.037 0.11 -10000 0 -0.3 41 41
PRKCA -0.004 0.04 0.26 1 -10000 0 1
PRKCB -0.002 0.039 -10000 0 -10000 0 0
VEGFR1 homodimer/PLGF homodimer 0.038 0.039 -10000 0 -0.34 4 4
VEGFA 0.05 0.047 -10000 0 -10000 0 0
VEGFB 0.033 0.007 -10000 0 -10000 0 0
mol:IP3 0.019 0.042 -10000 0 -0.3 4 4
RASA1 0.02 0.043 -10000 0 -10000 0 0
NRP2 0.035 0.015 -10000 0 -10000 0 0
VEGFR1 homodimer 0.021 0.043 -10000 0 -0.39 4 4
VEGFB homodimer 0.033 0.007 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.16 0.16 -10000 0 -0.51 21 21
PTPN11 0.034 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.035 0.11 -10000 0 -0.3 42 42
mol:L-citrulline 0.02 0.093 -10000 0 -0.48 7 7
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.075 0.059 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.061 0.05 -10000 0 -0.31 3 3
CD2AP 0.034 0.009 -10000 0 -10000 0 0
PI3K/GAB1 0.047 0.12 -10000 0 -0.54 1 1
PDPK1 -0.001 0.095 -10000 0 -0.36 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.062 0.049 -10000 0 -0.31 3 3
mol:NADP 0.02 0.093 -10000 0 -0.48 7 7
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.072 0.057 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.038 0.04 -10000 0 -0.34 4 4
Caspase cascade in apoptosis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TOP1 0.035 0.074 0.29 2 -0.34 8 10
ACTA1 0.007 0.083 0.26 1 -0.44 2 3
NUMA1 0.027 0.082 0.29 2 -0.38 8 10
SPTAN1 0.02 0.068 0.31 4 -0.48 1 5
LIMK1 0.033 0.074 0.3 7 -0.48 1 8
BIRC3 0.016 0.11 -10000 0 -0.54 17 17
BIRC2 0.03 0.011 -10000 0 -10000 0 0
BAX 0.035 0.012 -10000 0 -10000 0 0
CASP10 -0.003 0.04 0.24 8 -0.35 1 9
CRMA 0 0 -10000 0 -0.001 1 1
XIAP 0 0 0.001 1 -0.001 37 38
PTK2 0.029 0.094 0.28 3 -0.47 9 12
DIABLO 0.034 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes 0.02 0.067 0.3 5 -0.48 1 6
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.034 0.005 -10000 0 -10000 0 0
GSN -0.055 0.14 0.35 1 -0.29 89 90
MADD 0.034 0.005 -10000 0 -10000 0 0
TFAP2A 0.04 0.099 -10000 0 -0.65 8 8
BID 0.013 0.025 0.16 9 -0.2 1 10
MAP3K1 0.011 0.095 -10000 0 -0.38 24 24
TRADD 0.03 0.012 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.049 0.012 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.025 0.07 0.3 5 -0.48 1 6
CASP9 0.033 0.008 -10000 0 -10000 0 0
DNA repair -0.034 0.059 0.32 3 -0.2 17 20
neuron apoptosis 0.008 0.15 -10000 0 -0.68 20 20
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.024 0.074 0.32 1 -0.63 1 2
APAF1 0.034 0.003 -10000 0 -10000 0 0
CASP6 0.023 0.14 -10000 0 -0.85 11 11
TRAF2 0.035 0.012 -10000 0 -10000 0 0
ICAD/CAD 0.017 0.062 0.31 1 -0.47 1 2
CASP7 0.016 0.082 0.27 21 -0.33 3 24
KRT18 0.035 0.095 -10000 0 -0.73 6 6
apoptosis 0.012 0.1 0.31 2 -0.44 9 11
DFFA 0.02 0.065 0.3 2 -0.48 1 3
DFFB 0.02 0.064 0.28 3 -0.48 1 4
PARP1 0.034 0.059 0.2 17 -0.33 3 20
actin filament polymerization 0.016 0.13 0.38 4 -0.31 7 11
TNF 0.038 0.023 -10000 0 -10000 0 0
CYCS 0.023 0.046 0.23 6 -0.22 4 10
SATB1 -0.011 0.16 -10000 0 -0.78 13 13
SLK 0.02 0.068 0.29 4 -0.48 1 5
p15 BID/BAX 0.026 0.051 -10000 0 -0.28 4 4
CASP2 0.004 0.085 0.24 6 -0.31 15 21
JNK cascade -0.011 0.095 0.38 24 -10000 0 24
CASP3 0.024 0.07 0.31 3 -0.5 1 4
LMNB2 0.018 0.13 0.35 2 -0.51 21 23
RIPK1 0.033 0.006 -10000 0 -10000 0 0
CASP4 0.025 0.058 -10000 0 -0.54 5 5
Mammalian IAPs/DIABLO 0.045 0.078 -10000 0 -0.31 17 17
negative regulation of DNA binding 0.041 0.097 -10000 0 -0.64 8 8
stress fiber formation 0.019 0.068 0.29 4 -0.47 1 5
GZMB 0.022 0.046 0.29 7 -0.4 2 9
CASP1 -0.017 0.12 -10000 0 -0.4 41 41
LMNB1 0.042 0.13 0.35 3 -0.57 13 16
APP 0.007 0.15 -10000 0 -0.69 20 20
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
response to stress 0 0 0.001 20 -0.001 28 48
CASP8 0.009 0.001 -10000 0 -10000 0 0
VIM 0.015 0.11 0.31 2 -0.44 10 12
LMNA 0.022 0.082 0.34 2 -0.35 10 12
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.005 0.088 -10000 0 -0.31 18 18
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.027 0.069 0.28 4 -0.41 1 5
APAF-1/Caspase 9 0.018 0.11 -10000 0 -0.6 15 15
nuclear fragmentation during apoptosis 0.027 0.081 0.28 2 -0.37 8 10
CFL2 -0.017 0.13 0.31 7 -0.39 4 11
GAS2 -0.16 0.15 0.3 5 -0.34 40 45
positive regulation of apoptosis 0.035 0.12 0.33 3 -0.47 18 21
PRF1 0.037 0.022 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

Figure S94.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S94.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.034 0.005 -10000 0 -10000 0 0
SPHK1 0.033 0.06 -10000 0 -0.54 4 4
GNAI2 0.033 0.01 -10000 0 -10000 0 0
mol:S1P 0.02 0.034 0.2 2 -0.26 4 6
GNAO1 0.03 0.012 -10000 0 -10000 0 0
mol:Sphinganine-1-P 0.018 0.045 -10000 0 -0.4 4 4
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.053 0.04 -10000 0 -0.21 3 3
GNAI3 0.034 0.005 -10000 0 -10000 0 0
G12/G13 0.045 0.017 -10000 0 -10000 0 0
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.011 0.031 -10000 0 -0.24 4 4
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 183 183
S1P/S1P5/G12 0.042 0.04 -10000 0 -0.22 4 4
S1P/S1P3/Gq 0.036 0.053 -10000 0 -0.29 6 6
S1P/S1P4/Gi -0.067 0.15 0.27 1 -0.34 59 60
GNAQ 0 0 -10000 0 -10000 0 0
GNAZ 0.026 0.063 -10000 0 -0.54 6 6
GNA14 0.043 0.068 -10000 0 -0.54 4 4
GNA15 0.036 0.019 -10000 0 -10000 0 0
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
GNA11 0.033 0.006 -10000 0 -10000 0 0
ABCC1 0.035 0.023 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0.033 0.006 -10000 0 -10000 0 0
VLDLR -0.041 0.19 -10000 0 -0.54 65 65
LRPAP1 0.033 0.007 -10000 0 -10000 0 0
NUDC 0.033 0.007 -10000 0 -10000 0 0
RELN/LRP8 0.07 0.091 0.25 1 -0.32 20 21
CaM/Ca2+ 0.025 0.005 -10000 0 -10000 0 0
KATNA1 0.032 0.009 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.029 0.079 0.28 3 -0.29 20 23
IQGAP1/CaM 0.047 0.014 -10000 0 -10000 0 0
DAB1 0.034 0.006 -10000 0 -10000 0 0
IQGAP1 0.033 0.008 -10000 0 -10000 0 0
PLA2G7 0.043 0.098 -10000 0 -0.54 10 10
CALM1 0.033 0.006 -10000 0 -10000 0 0
DYNLT1 0.032 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.073 0.047 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.035 0.007 -10000 0 -10000 0 0
CDK5R1 0.033 0.014 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.011 0.004 -10000 0 -10000 0 0
CDK5R2 0.034 0.005 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.008 0.16 -10000 0 -0.36 80 80
YWHAE 0.031 0.01 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.041 0.078 0.38 2 -0.32 2 4
MAP1B -0.021 0.089 -10000 0 -0.29 49 49
RAC1 0.016 0.007 -10000 0 -10000 0 0
p35/CDK5 0.035 0.073 0.27 3 -0.28 13 16
RELN 0.012 0.11 0.18 3 -0.54 20 23
PAFAH/LIS1 0.04 0.067 -10000 0 -0.34 10 10
LIS1/CLIP170 0.034 0.014 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.032 0.069 -10000 0 -0.28 2 2
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.008 0.13 -10000 0 -0.3 54 54
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.025 0.073 0.32 4 -0.33 2 6
LIS1/IQGAP1 0.032 0.014 -10000 0 -10000 0 0
RHOA 0.016 0.007 -10000 0 -10000 0 0
PAFAH1B1 0.015 0.006 -10000 0 -10000 0 0
PAFAH1B3 0.082 0.069 -10000 0 -10000 0 0
PAFAH1B2 0.03 0.012 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.005 0.075 -10000 0 -0.36 2 2
NDEL1/Katanin 60/Dynein heavy chain 0.048 0.087 0.36 3 -0.31 2 5
LRP8 0.072 0.064 -10000 0 -10000 0 0
NDEL1/Katanin 60 0.035 0.082 0.38 2 -0.32 2 4
P39/CDK5 0.036 0.072 0.27 2 -0.28 13 15
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.033 0.014 -10000 0 -10000 0 0
CDK5 0.006 0.076 0.28 2 -0.3 13 15
PPP2R5D 0.034 0.006 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.029 0.012 -10000 0 -10000 0 0
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.002 0.15 -10000 0 -0.32 80 80
RELN/VLDLR 0.029 0.16 -10000 0 -0.31 80 80
CDC42 0.016 0.007 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.022 0.14 -10000 0 -10000 0 0
CRKL 0.015 0.067 0.29 4 -10000 0 4
mol:DAG 0.025 0.074 -10000 0 -10000 0 0
HRAS 0.051 0.089 0.32 13 -10000 0 13
MAPK8 0.047 0.075 0.27 12 -0.32 1 13
RAP1A 0.015 0.067 0.3 3 -10000 0 3
GAB1 0.017 0.066 0.3 2 -10000 0 2
MAPK14 0.048 0.073 0.27 12 -10000 0 12
EPO 0.046 0.052 -10000 0 -10000 0 0
PLCG1 0.025 0.074 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.028 0.024 -10000 0 -10000 0 0
RAPGEF1 0.034 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.053 0.079 -10000 0 -0.35 11 11
GAB1/SHC/GRB2/SOS1 0.043 0.064 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.053 0.047 -10000 0 -10000 0 0
IRS2 -0.052 0.14 -10000 0 -0.32 90 90
STAT1 0.042 0.12 -10000 0 -0.36 2 2
STAT5B 0.029 0.099 -10000 0 -10000 0 0
cell proliferation 0.025 0.08 0.26 15 -0.3 1 16
GAB1/SHIP/PIK3R1/SHP2/SHC 0.002 0.086 -10000 0 -0.37 1 1
TEC 0.016 0.067 0.3 3 -10000 0 3
SOCS3 0.018 0.087 -10000 0 -0.54 12 12
STAT1 (dimer) 0.042 0.11 -10000 0 -0.35 2 2
JAK2 0.031 0.018 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
EPO/EPOR (dimer)/JAK2 0.068 0.091 0.32 1 -10000 0 1
EPO/EPOR 0.053 0.047 -10000 0 -10000 0 0
LYN 0.022 0.026 -10000 0 -10000 0 0
TEC/VAV2 0.033 0.072 0.29 4 -10000 0 4
elevation of cytosolic calcium ion concentration 0.028 0.024 -10000 0 -10000 0 0
SHC1 0.027 0.014 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.055 0.058 -10000 0 -10000 0 0
mol:IP3 0.025 0.074 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.069 0.15 -10000 0 -0.31 120 120
SH2B3 0.033 0.016 -10000 0 -10000 0 0
NFKB1 0.048 0.073 0.27 12 -10000 0 12
EPO/EPOR (dimer)/JAK2/SOCS3 0.024 0.055 -10000 0 -0.27 10 10
PTPN6 0.01 0.06 -10000 0 -10000 0 0
TEC/VAV2/GRB2 0.045 0.075 0.3 3 -10000 0 3
EPOR 0.028 0.024 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.041 0.065 -10000 0 -10000 0 0
SOS1 0.034 0.004 -10000 0 -10000 0 0
PLCG2 0.021 0.073 -10000 0 -0.54 8 8
CRKL/CBL/C3G 0.039 0.077 0.3 3 -10000 0 3
VAV2 0.018 0.068 0.3 4 -10000 0 4
CBL 0.014 0.066 0.29 4 -10000 0 4
SHC/Grb2/SOS1 0.03 0.059 -10000 0 -10000 0 0
STAT5A 0.028 0.1 -10000 0 -0.32 1 1
GRB2 0.034 0.018 -10000 0 -10000 0 0
STAT5 (dimer) 0.025 0.15 -10000 0 -0.33 49 49
LYN/PLCgamma2 0.029 0.061 0.25 1 -0.36 10 11
PTPN11 0.034 0.004 -10000 0 -10000 0 0
BTK 0.02 0.071 0.3 3 -10000 0 3
BCL2 -0.091 0.36 -10000 0 -0.82 98 98
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.079 0.055 0.4 6 -10000 0 6
MAP4K1 0.037 0.021 -10000 0 -10000 0 0
MAP3K8 -0.04 0.19 -10000 0 -0.54 65 65
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0.035 0.012 -10000 0 -10000 0 0
CRKL 0.033 0.008 -10000 0 -10000 0 0
MAP3K1 0.031 0.059 0.3 3 -0.31 3 6
JUN -0.04 0.13 -10000 0 -0.43 19 19
MAP3K7 0.029 0.053 0.27 3 -0.27 3 6
GRAP2 0.034 0.019 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
MAP2K4 0.002 0.1 0.28 3 -0.37 16 19
LAT 0.035 0.025 -10000 0 -10000 0 0
LCP2 0.036 0.023 -10000 0 -10000 0 0
MAPK8 0.011 0.08 -10000 0 -0.58 8 8
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.037 0.061 0.3 3 -0.29 4 7
LAT/GRAP2/SLP76/HPK1/HIP-55 0.089 0.06 0.39 6 -10000 0 6
Signaling events mediated by HDAC Class III

Figure S98.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S98.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.032 0.009 -10000 0 -10000 0 0
HDAC4 0.033 0.007 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.005 0.008 -10000 0 -10000 0 0
CDKN1A -0.01 0.043 -10000 0 -0.66 2 2
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.035 0.012 -10000 0 -10000 0 0
FOXO3 -0.006 0.004 -10000 0 -10000 0 0
FOXO1 -0.023 0.17 -10000 0 -0.54 48 48
FOXO4 0.017 0.015 -10000 0 -0.28 1 1
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.032 0.009 -10000 0 -10000 0 0
TAT 0.03 0.043 -10000 0 -0.54 2 2
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.009 0.03 -10000 0 -0.4 2 2
PPARGC1A -0.023 0.17 -10000 0 -0.54 51 51
FHL2 -0.026 0.18 -10000 0 -0.54 55 55
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.044 0.016 -10000 0 -10000 0 0
HIST2H4A -0.005 0.008 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.022 0.032 -10000 0 -0.21 2 2
SIRT1 0.03 0.012 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.053 0.029 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.052 0.053 -10000 0 -0.23 3 3
apoptosis -0.061 0.022 -10000 0 -10000 0 0
SIRT1/PGC1A 0.004 0.12 -10000 0 -0.34 50 50
p53/SIRT1 0.037 0.024 0.42 1 -10000 0 1
SIRT1/FOXO4 0.032 0.045 -10000 0 -0.23 3 3
FOXO1/FHL2/SIRT1 -0.02 0.16 -10000 0 -0.34 91 91
HIST1H1E 0.039 0.043 -10000 0 -0.28 1 1
SIRT1/p300 0.044 0.016 -10000 0 -10000 0 0
muscle cell differentiation -0.018 0.026 0.34 2 -10000 0 2
TP53 0.028 0.017 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.062 0.023 -10000 0 -10000 0 0
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
MEF2D 0.028 0.013 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.04 0.038 -10000 0 -0.33 3 3
ACSS2 0.014 0.008 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.019 0.026 -10000 0 -0.34 2 2
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.011 0.11 -10000 0 -0.54 19 19
positive regulation of NF-kappaB transcription factor activity 0.023 0.085 -10000 0 -0.4 19 19
MAP2K4 0.015 0.085 -10000 0 -0.4 12 12
IKBKB 0.028 0.013 -10000 0 -10000 0 0
TNFRSF10B 0.027 0.016 0.18 1 -10000 0 1
TNFRSF10A 0.028 0.018 -10000 0 -10000 0 0
SMPD1 0.004 0.057 -10000 0 -0.27 18 18
IKBKG 0.034 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.027 0.014 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.022 0.086 -10000 0 -0.38 21 21
TRAIL/TRAILR3 0.023 0.086 -10000 0 -0.4 19 19
TRAIL/TRAILR1 0.023 0.085 -10000 0 -0.39 19 19
TRAIL/TRAILR4 0.023 0.085 -10000 0 -0.4 19 19
TRAIL/TRAILR1/DAP3/GTP 0.031 0.066 -10000 0 -0.31 13 13
IKK complex 0.024 0.074 -10000 0 -0.42 5 5
RIPK1 0.033 0.006 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.021 0.01 -10000 0 -10000 0 0
MAPK3 0 0.078 -10000 0 -0.4 19 19
MAP3K1 0.015 0.1 -10000 0 -0.46 14 14
TRAILR4 (trimer) 0.027 0.014 -10000 0 -10000 0 0
TRADD 0.03 0.012 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.028 0.018 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.002 0.081 -10000 0 -0.4 12 12
CFLAR 0.033 0.026 -10000 0 -0.54 1 1
MAPK1 0.001 0.076 -10000 0 -0.4 18 18
TRAIL/TRAILR1/FADD/TRADD/RIP 0.046 0.079 -10000 0 -0.3 13 13
mol:ceramide 0.004 0.057 -10000 0 -0.26 18 18
FADD 0.028 0.015 -10000 0 -10000 0 0
MAPK8 -0.001 0.1 -10000 0 -0.4 16 16
TRAF2 0.035 0.012 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.027 0.017 -10000 0 -10000 0 0
CHUK 0.034 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.033 0.073 -10000 0 -0.33 14 14
DAP3 0.028 0.014 -10000 0 -10000 0 0
CASP10 0.024 0.077 0.34 3 -0.34 5 8
JNK cascade 0.023 0.085 -10000 0 -0.4 19 19
TRAIL (trimer) 0.011 0.11 -10000 0 -0.54 19 19
TNFRSF10C 0.028 0.017 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.035 0.064 -10000 0 -0.29 9 9
TRAIL/TRAILR2/FADD 0.032 0.074 -10000 0 -0.34 14 14
cell death 0.004 0.056 -10000 0 -0.26 18 18
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.002 0.081 -10000 0 -0.4 12 12
TRAILR2 (trimer) 0.027 0.016 0.18 1 -10000 0 1
CASP8 0.02 0.056 -10000 0 -0.58 3 3
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.046 0.08 -10000 0 -0.3 14 14
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0.073 0.038 -10000 0 -0.32 1 1
HDAC3 0.034 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.01 0.002 -10000 0 -10000 0 0
GATA1/HDAC4 0.049 0.011 -10000 0 -10000 0 0
GATA1/HDAC5 0.049 0.012 -10000 0 -10000 0 0
GATA2/HDAC5 0.053 0.026 -10000 0 -10000 0 0
HDAC5/BCL6/BCoR 0.023 0.12 -10000 0 -0.34 50 50
HDAC9 0.035 0.017 -10000 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.033 0.11 -10000 0 -0.34 40 40
HDAC4/ANKRA2 0.045 0.032 -10000 0 -0.32 3 3
HDAC5/YWHAB 0.046 0.016 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.017 0.02 -10000 0 -0.17 3 3
GATA2 0.042 0.033 0.18 28 -10000 0 28
HDAC4/RFXANK 0.048 0.012 -10000 0 -10000 0 0
BCOR 0.034 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.031 0.028 -10000 0 -0.54 1 1
HDAC5 0.033 0.007 -10000 0 -10000 0 0
GNB1/GNG2 0.048 0.024 -10000 0 -0.4 1 1
Histones 0.023 0.051 -10000 0 -0.28 4 4
ADRBK1 0.032 0.01 -10000 0 -10000 0 0
HDAC4 0.033 0.007 -10000 0 -10000 0 0
XPO1 0.034 0.005 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.045 0.033 -10000 0 -0.4 2 2
HDAC4/Ubc9 0.045 0.017 -10000 0 -10000 0 0
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.045 0.019 -10000 0 -0.17 1 1
TUBA1B 0.035 0.012 -10000 0 -10000 0 0
HDAC6 0.034 0.003 -10000 0 -10000 0 0
HDAC5/RFXANK 0.048 0.013 -10000 0 -10000 0 0
CAMK4 0.035 0.017 -10000 0 -10000 0 0
Tubulin/HDAC6 0.06 0.057 -10000 0 -0.34 9 9
SUMO1 0.034 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.032 0.008 -10000 0 -10000 0 0
GATA1 0.034 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
NR3C1 -0.012 0.16 -10000 0 -0.54 40 40
SUMO1/HDAC4 0.051 0.051 -10000 0 -0.25 3 3
SRF 0.034 0.006 -10000 0 -10000 0 0
HDAC4/YWHAB 0.046 0.015 -10000 0 -10000 0 0
Tubulin 0.042 0.061 -10000 0 -0.4 9 9
HDAC4/14-3-3 E 0.045 0.019 -10000 0 -0.17 1 1
GNB1 0.034 0.011 -10000 0 -10000 0 0
RANGAP1 0.038 0.03 -10000 0 -10000 0 0
BCL6/BCoR 0.004 0.13 -10000 0 -0.4 51 51
HDAC4/HDAC3/SMRT (N-CoR2) 0.066 0.017 -10000 0 -10000 0 0
HDAC4/SRF 0.065 0.022 -10000 0 -10000 0 0
HDAC4/ER alpha -0.027 0.2 -10000 0 -0.39 110 110
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.023 0.05 -10000 0 -0.28 4 4
cell motility 0.059 0.056 -10000 0 -0.34 9 9
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.031 0.01 -10000 0 -10000 0 0
HDAC7/HDAC3 0.025 0.004 -10000 0 -10000 0 0
BCL6 -0.024 0.17 -10000 0 -0.54 51 51
HDAC4/CaMK II delta B 0.033 0.007 -10000 0 -10000 0 0
Hsp90/HDAC6 0.049 0.01 -10000 0 -10000 0 0
ESR1 -0.058 0.26 -10000 0 -0.54 106 106
HDAC6/HDAC11 0.052 0.019 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.051 0.05 -10000 0 -0.26 3 3
NPC 0.02 0.002 -10000 0 -10000 0 0
MEF2C 0.005 0.12 -10000 0 -0.54 25 25
RAN 0.034 0.005 -10000 0 -10000 0 0
HDAC4/MEF2C 0.066 0.092 -10000 0 -0.3 24 24
GNG2 0.032 0.026 -10000 0 -0.54 1 1
NCOR2 0.034 0.004 -10000 0 -10000 0 0
TUBB2A 0.024 0.076 0.18 1 -0.54 9 10
HDAC11 0.038 0.025 -10000 0 -10000 0 0
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
RANBP2 0.034 0.004 -10000 0 -10000 0 0
ANKRA2 0.03 0.037 -10000 0 -0.54 2 2
RFXANK 0.034 0.005 -10000 0 -10000 0 0
nuclear import -0.038 0.02 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.033 0.007 -10000 0 -10000 0 0
NFATC1 0.042 0.086 0.35 3 -0.4 5 8
NFATC2 0.002 0.074 0.29 1 -0.25 16 17
NFATC3 0.013 0.008 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.031 0.062 0.26 2 -0.26 7 9
Exportin 1/Ran/NUP214 0.066 0.017 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.054 0.065 -10000 0 -10000 0 0
BCL2/BAX -0.035 0.17 -10000 0 -0.4 93 93
CaM/Ca2+/Calcineurin A alpha-beta B1 0.023 0.012 -10000 0 -10000 0 0
CaM/Ca2+ 0.023 0.012 -10000 0 -10000 0 0
BAX 0.035 0.012 -10000 0 -10000 0 0
MAPK14 0.034 0.006 -10000 0 -10000 0 0
BAD 0.033 0.007 -10000 0 -10000 0 0
CABIN1/MEF2D 0.037 0.06 -10000 0 -0.26 6 6
Calcineurin A alpha-beta B1/BCL2 -0.072 0.22 -10000 0 -0.54 93 93
FKBP8 0.034 0.009 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.037 0.059 0.26 6 -10000 0 6
KPNB1 0.032 0.009 -10000 0 -10000 0 0
KPNA2 0.058 0.06 -10000 0 -10000 0 0
XPO1 0.034 0.005 -10000 0 -10000 0 0
SFN 0.032 0.04 -10000 0 -0.54 2 2
MAP3K8 -0.04 0.19 -10000 0 -0.54 65 65
NFAT4/CK1 alpha 0.028 0.038 -10000 0 -0.33 1 1
MEF2D/NFAT1/Cbp/p300 0.032 0.1 -10000 0 -0.31 19 19
CABIN1 0.031 0.061 0.26 2 -0.27 7 9
CALM1 0.033 0.008 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
MAP3K1 0.036 0.046 -10000 0 -0.54 2 2
CAMK4 0.035 0.017 -10000 0 -10000 0 0
mol:Ca2+ 0 0.004 -10000 0 -10000 0 0
MAPK3 0.032 0.009 -10000 0 -10000 0 0
YWHAH 0.033 0.014 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.053 0.04 -10000 0 -0.4 2 2
YWHAB 0.032 0.008 -10000 0 -10000 0 0
MAPK8 0.032 0.026 -10000 0 -0.54 1 1
MAPK9 0.034 0.009 0.18 1 -10000 0 1
YWHAG 0.034 0.008 -10000 0 -10000 0 0
FKBP1A 0.033 0.012 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.044 0.099 0.32 1 -0.39 9 10
PRKCH 0.029 0.051 -10000 0 -0.54 4 4
CABIN1/Cbp/p300 0.04 0.031 -10000 0 -0.4 1 1
CASP3 0.033 0.008 -10000 0 -10000 0 0
PIM1 0.035 0.015 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.022 0.009 -10000 0 -10000 0 0
apoptosis -0.003 0.058 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.04 0.047 -10000 0 -10000 0 0
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.034 0.004 -10000 0 -10000 0 0
JNK2/NFAT4 0.01 0.064 -10000 0 -0.17 4 4
BAD/BCL-XL 0.047 0.014 -10000 0 -10000 0 0
PRKCD 0.035 0.017 -10000 0 -10000 0 0
NUP214 0.034 0.005 -10000 0 -10000 0 0
PRKCZ 0 0.002 -10000 0 -10000 0 0
PRKCA 0.031 0.013 -10000 0 -10000 0 0
PRKCG 0.034 0.006 -10000 0 -10000 0 0
PRKCQ 0.039 0.03 -10000 0 -10000 0 0
FKBP38/BCL2 -0.034 0.17 -10000 0 -0.4 90 90
EP300 0.03 0.015 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
NFATc/JNK1 0.057 0.087 0.34 1 -0.38 5 6
CaM/Ca2+/FKBP38 0.043 0.015 -10000 0 -10000 0 0
FKBP12/FK506 0.025 0.008 -10000 0 -10000 0 0
CSNK1A1 0.016 0.012 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.044 0.018 -10000 0 -10000 0 0
NFATc/ERK1 0.054 0.086 0.34 1 -0.38 5 6
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.066 0.063 -10000 0 -10000 0 0
NR4A1 0.024 0.14 -10000 0 -0.48 25 25
GSK3B 0.034 0.01 -10000 0 -10000 0 0
positive T cell selection 0.013 0.007 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.006 0.062 -10000 0 -0.31 5 5
RCH1/ KPNB1 0.062 0.046 -10000 0 -10000 0 0
YWHAQ 0.034 0.005 -10000 0 -10000 0 0
PRKACA 0.034 0.006 -10000 0 -10000 0 0
AKAP5 0.04 0.051 -10000 0 -0.54 2 2
MEF2D 0.027 0.016 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.026 0.018 -10000 0 -10000 0 0
NFATc/p38 alpha 0.057 0.085 0.34 1 -0.38 5 6
CREBBP 0.028 0.029 -10000 0 -0.54 1 1
BCL2 -0.072 0.22 -10000 0 -0.54 93 93
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.034 0.005 -10000 0 -10000 0 0
HDAC3 0.034 0.006 -10000 0 -10000 0 0
VDR 0.032 0.037 -10000 0 -0.54 2 2
Cbp/p300/PCAF 0.039 0.024 -10000 0 -0.34 1 1
EP300 0.032 0.009 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0 0.088 -10000 0 -0.31 16 16
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.034 0.005 -10000 0 -10000 0 0
AKT1 -0.008 0.12 0.27 4 -0.26 53 57
RAR alpha/9cRA/Cyclin H 0.077 0.065 0.28 1 -0.28 2 3
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.001 0.1 -10000 0 -0.24 54 54
CDC2 0 0.003 -10000 0 -10000 0 0
response to UV 0.001 0.004 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.046 0.047 -10000 0 -0.45 1 1
NCOR2 0.034 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.024 0.027 -10000 0 -0.4 2 2
RXRs/RARs/NRIP1/9cRA 0.022 0.12 0.38 1 -0.52 10 11
NCOA2 0.028 0.015 -10000 0 -10000 0 0
NCOA3 0.032 0.01 -10000 0 -10000 0 0
NCOA1 0.033 0.026 -10000 0 -0.54 1 1
VDR/VDR/DNA 0.032 0.037 -10000 0 -0.54 2 2
RARG 0.034 0.008 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.046 0.009 -10000 0 -10000 0 0
MAPK3 0.032 0.013 -10000 0 -10000 0 0
MAPK1 0.032 0.008 -10000 0 -10000 0 0
MAPK8 0.033 0.028 -10000 0 -0.54 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.068 0.066 -10000 0 -0.36 1 1
RARA 0.021 0.023 0.2 1 -0.24 1 2
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0 0.092 -10000 0 -0.24 45 45
PRKCA 0.033 0.019 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.027 0.13 0.41 4 -0.54 9 13
RXRG 0.021 0.033 -10000 0 -0.32 3 3
RXRA 0.039 0.054 0.22 1 -0.28 3 4
RXRB 0.027 0.019 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.024 0.027 -10000 0 -0.4 2 2
RBP1 0.007 0.13 -10000 0 -0.54 26 26
CRBP1/9-cic-RA 0.005 0.094 -10000 0 -0.4 26 26
RARB -0.055 0.21 -10000 0 -0.54 80 80
PRKCG 0.035 0.015 -10000 0 -10000 0 0
MNAT1 0.033 0.006 -10000 0 -10000 0 0
RAR alpha/RXRs 0.009 0.11 -10000 0 -0.49 3 3
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.026 0.11 -10000 0 -0.43 4 4
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.096 0.25 6 -0.31 11 17
RXRs/RARs/NRIP1/9cRA/HDAC3 0.027 0.13 0.41 4 -0.56 9 13
positive regulation of DNA binding 0.059 0.055 -10000 0 -0.27 2 2
NRIP1 0.02 0.19 0.56 2 -1.1 9 11
RXRs/RARs 0.029 0.12 0.35 5 -0.45 9 14
RXRs/RXRs/DNA/9cRA 0.026 0.056 0.27 2 -0.34 2 4
PRKACA 0.034 0.005 -10000 0 -10000 0 0
CDK7 0.033 0.007 -10000 0 -10000 0 0
TFIIH 0.065 0.018 -10000 0 -10000 0 0
RAR alpha/9cRA 0.08 0.05 -10000 0 -10000 0 0
CCNH 0.033 0.007 -10000 0 -10000 0 0
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
RAR gamma2/9cRA 0.063 0.023 -10000 0 -10000 0 0
Arf6 trafficking events

Figure S103.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S103.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.26 0.28 -10000 0 -0.54 253 253
CLTC 0.034 0.056 0.26 1 -0.42 3 4
calcium ion-dependent exocytosis 0.015 0.043 -10000 0 -0.37 2 2
Dynamin 2/GTP 0.03 0.013 -10000 0 -10000 0 0
EXOC4 0.034 0.005 -10000 0 -10000 0 0
CD59 0.02 0.045 -10000 0 -0.32 3 3
CPE -0.042 0.13 -10000 0 -0.34 84 84
CTNNB1 0.029 0.052 -10000 0 -0.54 4 4
membrane fusion 0.012 0.035 -10000 0 -0.35 1 1
CTNND1 0.031 0.055 0.37 1 -10000 0 1
DNM2 0.034 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.022 0.045 0.25 1 -0.29 3 4
TSHR 0.015 0.028 -10000 0 -0.34 3 3
INS 0.008 0.099 -10000 0 -0.5 18 18
BIN1 0.034 0.005 -10000 0 -10000 0 0
mol:Choline 0.012 0.035 -10000 0 -0.35 1 1
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.006 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.034 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.029 0.012 -10000 0 -10000 0 0
JUP 0.022 0.036 -10000 0 -0.29 2 2
ASAP2/amphiphysin II 0.042 0.009 -10000 0 -10000 0 0
ARF6/GTP 0.025 0.004 -10000 0 -10000 0 0
CDH1 0.008 0.066 -10000 0 -0.38 4 4
clathrin-independent pinocytosis 0.025 0.004 -10000 0 -10000 0 0
MAPK8IP3 0.03 0.038 -10000 0 -0.54 2 2
positive regulation of endocytosis 0.025 0.004 -10000 0 -10000 0 0
EXOC2 0.041 0.033 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.036 0.053 -10000 0 -0.36 3 3
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.031 0.011 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.045 0.082 0.35 5 -10000 0 5
positive regulation of phagocytosis 0.017 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.04 0.029 -10000 0 -0.34 2 2
ACAP1 0.011 0.035 -10000 0 -0.23 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.026 0.04 -10000 0 -0.29 2 2
clathrin heavy chain/ACAP1 0.03 0.069 0.29 4 -0.32 6 10
JIP4/KLC1 0.056 0.024 -10000 0 -10000 0 0
EXOC1 0.034 0.005 -10000 0 -10000 0 0
exocyst 0.036 0.054 -10000 0 -0.36 3 3
RALA/GTP 0.025 0.004 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.041 0.016 -10000 0 -10000 0 0
receptor recycling 0.025 0.004 -10000 0 -10000 0 0
CTNNA1 0.032 0.056 0.37 1 -10000 0 1
NME1 0.016 0.006 -10000 0 -10000 0 0
clathrin coat assembly 0.037 0.065 0.29 2 -0.42 3 5
IL2RA 0.027 0.047 -10000 0 -0.36 3 3
VAMP3 0.017 0.005 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.1 0.13 -10000 0 -0.34 17 17
EXOC6 0.033 0.027 -10000 0 -0.54 1 1
PLD1 0.005 0.062 -10000 0 -0.28 21 21
PLD2 0.016 0.016 -10000 0 -0.27 1 1
EXOC5 0.034 0.006 -10000 0 -10000 0 0
PIP5K1C 0.019 0.037 -10000 0 -0.42 1 1
SDC1 0.037 0.051 -10000 0 -0.36 3 3
ARF6/GDP 0.028 0.011 -10000 0 -10000 0 0
EXOC7 0.032 0.009 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.047 0.085 -10000 0 -0.36 5 5
mol:Phosphatidic acid 0.012 0.035 -10000 0 -0.35 1 1
endocytosis -0.041 0.009 -10000 0 -10000 0 0
SCAMP2 0.033 0.007 -10000 0 -10000 0 0
ADRB2 -0.11 0.15 -10000 0 -0.34 30 30
EXOC3 0.032 0.008 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.036 0.022 -10000 0 -10000 0 0
KLC1 0.033 0.006 -10000 0 -10000 0 0
AVPR2 0.032 0.069 0.29 2 -0.38 4 6
RALA 0.034 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.04 0.085 0.34 2 -0.38 3 5
PDGFR-beta signaling pathway

Figure S104.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S104.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.039 0.085 0.34 1 -0.34 6 7
PDGFB-D/PDGFRB/SLAP 0.04 0.027 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/APS/CBL 0.041 0.017 -10000 0 -10000 0 0
AKT1 0.026 0.12 0.39 16 -10000 0 16
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.046 0.094 0.35 3 -0.36 9 12
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
FGR 0.009 0.1 -10000 0 -0.45 17 17
mol:Ca2+ 0.037 0.092 0.34 3 -0.38 10 13
MYC 0.048 0.23 0.39 20 -0.76 30 50
SHC1 0.027 0.014 -10000 0 -10000 0 0
HRAS/GDP 0.049 0.046 0.27 1 -10000 0 1
LRP1/PDGFRB/PDGFB 0.065 0.023 -10000 0 -10000 0 0
GRB10 0.03 0.051 -10000 0 -0.54 4 4
PTPN11 0.034 0.004 -10000 0 -10000 0 0
GO:0007205 0.037 0.093 0.34 3 -0.39 10 13
PTEN 0.026 0.067 -10000 0 -0.54 7 7
GRB2 0.034 0.018 -10000 0 -10000 0 0
GRB7 0.029 0.013 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.05 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.047 0.041 -10000 0 -0.4 4 4
cell cycle arrest 0.04 0.027 -10000 0 -10000 0 0
HRAS 0.034 0.013 -10000 0 -10000 0 0
HIF1A 0.02 0.12 0.37 16 -0.34 1 17
GAB1 0.04 0.1 0.33 4 -0.41 7 11
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.038 0.096 0.36 5 -0.35 6 11
PDGFB-D/PDGFRB 0.06 0.037 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.049 0.018 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.03 0.079 -10000 0 -0.37 4 4
positive regulation of MAPKKK cascade 0.05 0.01 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 0.037 0.094 0.34 3 -0.39 10 13
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.033 0.012 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.043 0.02 -10000 0 -10000 0 0
SHB 0.035 0.018 -10000 0 -10000 0 0
BLK -0.035 0.17 -10000 0 -0.4 73 73
PTPN2 0.034 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.05 0.011 -10000 0 -10000 0 0
BCAR1 0.029 0.013 -10000 0 -10000 0 0
VAV2 0.039 0.11 0.36 4 -0.42 10 14
CBL 0.03 0.011 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.05 0.015 -10000 0 -10000 0 0
LCK 0.025 0.096 -10000 0 -0.54 8 8
PDGFRB 0.035 0.009 -10000 0 -10000 0 0
ACP1 0.034 0.006 -10000 0 -10000 0 0
HCK 0.024 0.076 -10000 0 -0.62 4 4
ABL1 0.033 0.096 0.35 3 -0.39 8 11
PDGFB-D/PDGFRB/CBL 0.033 0.11 0.35 1 -0.44 12 13
PTPN1 0.037 0.03 -10000 0 -10000 0 0
SNX15 0.034 0.005 -10000 0 -10000 0 0
STAT3 0.033 0.007 -10000 0 -10000 0 0
STAT1 0.059 0.055 -10000 0 -10000 0 0
cell proliferation 0.052 0.21 0.37 24 -0.66 31 55
SLA 0.029 0.025 0.18 9 -10000 0 9
actin cytoskeleton reorganization 0.05 0.06 0.42 3 -10000 0 3
SRC 0.021 0.06 -10000 0 -0.62 2 2
PI3K -0.011 0.066 -10000 0 -0.27 20 20
PDGFB-D/PDGFRB/GRB7/SHC 0.046 0.034 -10000 0 -10000 0 0
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.047 0.096 0.35 3 -0.37 9 12
LYN 0.021 0.055 -10000 0 -0.41 3 3
LRP1 0.034 0.004 -10000 0 -10000 0 0
SOS1 0.034 0.004 -10000 0 -10000 0 0
STAT5B 0.033 0.01 -10000 0 -10000 0 0
STAT5A 0.032 0.026 -10000 0 -0.54 1 1
NCK1-2/p130 Cas 0.075 0.053 -10000 0 -10000 0 0
SPHK1 0.034 0.06 -10000 0 -0.55 4 4
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.037 0.094 0.34 3 -0.39 10 13
PLCG1 0.037 0.095 0.34 3 -0.4 10 13
NHERF/PDGFRB 0.074 0.05 -10000 0 -10000 0 0
YES1 0.009 0.11 -10000 0 -0.54 14 14
cell migration 0.073 0.05 -10000 0 -10000 0 0
SHC/Grb2/SOS1 0.066 0.056 -10000 0 -10000 0 0
SLC9A3R2 0.032 0.015 -10000 0 -10000 0 0
SLC9A3R1 0.059 0.058 0.18 96 -10000 0 96
NHERF1-2/PDGFRB/PTEN 0.08 0.07 -10000 0 -0.31 4 4
FYN 0.006 0.1 -10000 0 -0.43 18 18
DOK1 0.036 0.05 -10000 0 -10000 0 0
HRAS/GTP 0.025 0.009 -10000 0 -10000 0 0
PDGFB 0.033 0.015 -10000 0 -10000 0 0
RAC1 0.024 0.16 0.38 2 -0.51 27 29
PRKCD 0.037 0.056 0.34 3 -10000 0 3
FER 0.036 0.055 0.38 2 -10000 0 2
MAPKKK cascade 0.051 0.1 0.35 24 -10000 0 24
RASA1 0.036 0.054 0.38 2 -10000 0 2
NCK1 0.034 0.005 -10000 0 -10000 0 0
NCK2 0.034 0.007 0.18 1 -10000 0 1
p62DOK/Csk 0.054 0.044 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.05 0.019 -10000 0 -10000 0 0
chemotaxis 0.033 0.095 0.33 4 -0.38 8 12
STAT1-3-5/STAT1-3-5 0.079 0.049 -10000 0 -0.29 1 1
Bovine Papilomavirus E5/PDGFRB 0.025 0.007 -10000 0 -10000 0 0
PTPRJ 0.035 0.017 -10000 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.099 0.13 0.42 8 -10000 0 8
regulation of axonogenesis -0.021 0.05 0.24 1 -10000 0 1
myoblast fusion -0.065 0.074 -10000 0 -0.25 9 9
mol:GTP 0.048 0.045 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.09 0.066 -10000 0 -0.25 8 8
ARF1/GTP 0.052 0.044 -10000 0 -10000 0 0
mol:GM1 0.033 0.04 -10000 0 -10000 0 0
mol:Choline 0.017 0.076 -10000 0 -0.32 20 20
lamellipodium assembly 0.056 0.079 0.25 8 -0.33 1 9
MAPK3 0.071 0.078 0.22 16 -10000 0 16
ARF6/GTP/NME1/Tiam1 0.092 0.067 0.25 9 -10000 0 9
ARF1 0.027 0.014 -10000 0 -10000 0 0
ARF6/GDP 0.065 0.074 0.25 9 -10000 0 9
ARF1/GDP 0.056 0.069 -10000 0 -10000 0 0
ARF6 0.054 0.026 -10000 0 -10000 0 0
RAB11A 0.033 0.006 -10000 0 -10000 0 0
TIAM1 0.04 0.014 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.073 0.079 0.22 21 -10000 0 21
actin filament bundle formation -0.075 0.064 -10000 0 -10000 0 0
KALRN 0.042 0.056 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0.045 0.017 -10000 0 -10000 0 0
RhoA/GDP 0.076 0.064 -10000 0 -10000 0 0
NME1 0.035 0.015 -10000 0 -10000 0 0
Rac1/GDP 0.078 0.063 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.048 0.045 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.056 0.079 0.25 8 -0.33 1 9
RAC1 0.034 0.005 -10000 0 -10000 0 0
liver development 0.048 0.045 -10000 0 -10000 0 0
ARF6/GTP 0.048 0.045 -10000 0 -10000 0 0
RhoA/GTP 0.062 0.041 -10000 0 -10000 0 0
mol:GDP 0.051 0.076 0.2 99 -10000 0 99
ARF6/GTP/RAB11FIP3/RAB11A 0.075 0.044 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
PLD1 0.029 0.087 -10000 0 -0.35 20 20
RAB11FIP3 0.031 0.01 -10000 0 -10000 0 0
tube morphogenesis 0.056 0.079 0.25 8 -0.33 1 9
ruffle organization 0.021 0.05 -10000 0 -0.24 1 1
regulation of epithelial cell migration 0.048 0.045 -10000 0 -10000 0 0
PLD2 0.042 0.045 -10000 0 -0.36 1 1
PIP5K1A 0.021 0.05 -10000 0 -0.24 1 1
mol:Phosphatidic acid 0.017 0.076 -10000 0 -0.32 20 20
Rac1/GTP 0.056 0.08 0.25 8 -0.33 1 9
Paxillin-independent events mediated by a4b1 and a4b7

Figure S106.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S106.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.027 0.026 -10000 0 -10000 0 0
CRKL 0.033 0.008 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
DOCK1 0.03 0.044 -10000 0 -0.54 3 3
ITGA4 0.04 0.029 -10000 0 -10000 0 0
alpha4/beta7 Integrin/MAdCAM1 0.085 0.033 -10000 0 -10000 0 0
EPO 0.054 0.05 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.054 0.022 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.053 0.023 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.063 0.037 -10000 0 -10000 0 0
lamellipodium assembly -0.004 0.11 -10000 0 -0.32 42 42
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
PI3K 0.005 0.13 -10000 0 -0.37 51 51
ARF6 0.034 0.005 -10000 0 -10000 0 0
JAK2 0.042 0.034 -10000 0 -10000 0 0
PXN 0.034 0.003 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
MADCAM1 0.034 0.013 -10000 0 -10000 0 0
cell adhesion 0.082 0.032 -10000 0 -10000 0 0
CRKL/CBL 0.044 0.018 -10000 0 -10000 0 0
ITGB1 0.033 0.006 -10000 0 -10000 0 0
SRC 0.021 0.064 0.38 2 -0.31 11 13
ITGB7 0.034 0.004 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.061 0.067 -10000 0 -0.34 11 11
p130Cas/Crk/Dock1 0.039 0.07 0.37 1 -0.28 14 15
VCAM1 0.023 0.086 -10000 0 -0.54 11 11
RHOA 0.033 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.081 0.035 -10000 0 -10000 0 0
BCAR1 -0.007 0.061 0.39 2 -0.3 11 13
EPOR 0.034 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.03 0.011 -10000 0 -10000 0 0
GIT1 0.032 0.011 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.11 -10000 0 -0.33 42 42
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.033 0.008 -9999 0 -10000 0 0
Rac1/GDP 0.03 0.013 -9999 0 -10000 0 0
DOCK1 0.03 0.044 -9999 0 -0.54 3 3
ITGA4 0.04 0.029 -9999 0 -10000 0 0
RAC1 0.034 0.005 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.054 0.022 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.031 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.069 0.025 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.059 0.023 -9999 0 -10000 0 0
lamellipodium assembly -0.032 0.16 -9999 0 -0.43 59 59
PIK3CA 0.033 0.008 -9999 0 -10000 0 0
PI3K 0.005 0.13 -9999 0 -0.37 51 51
ARF6 0.034 0.005 -9999 0 -10000 0 0
TLN1 0.033 0.006 -9999 0 -10000 0 0
PXN 0.017 0.003 -9999 0 -10000 0 0
PIK3R1 -0.02 0.17 -9999 0 -0.54 47 47
ARF6/GTP 0.068 0.033 -9999 0 -10000 0 0
cell adhesion 0.073 0.029 -9999 0 -10000 0 0
CRKL/CBL 0.044 0.018 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.058 0.024 -9999 0 -10000 0 0
ITGB1 0.033 0.006 -9999 0 -10000 0 0
ITGB7 0.034 0.004 -9999 0 -10000 0 0
ARF6/GDP 0.03 0.013 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.069 0.064 -9999 0 -0.3 11 11
p130Cas/Crk/Dock1 0.052 0.043 -9999 0 -0.34 3 3
VCAM1 0.023 0.086 -9999 0 -0.54 11 11
alpha4/beta1 Integrin/Paxillin/Talin 0.075 0.03 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.072 0.034 -9999 0 -10000 0 0
BCAR1 0.029 0.013 -9999 0 -10000 0 0
mol:GDP -0.07 0.033 -9999 0 -10000 0 0
CBL 0.03 0.011 -9999 0 -10000 0 0
PRKACA 0.034 0.005 -9999 0 -10000 0 0
GIT1 0.032 0.011 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.075 0.03 -9999 0 -10000 0 0
Rac1/GTP -0.038 0.18 -9999 0 -0.49 59 59
p38 MAPK signaling pathway

Figure S108.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S108.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.008 0.07 -10000 0 -0.28 26 26
TRAF2/ASK1 0.022 0.087 -10000 0 -0.29 34 34
ATM 0.03 0.012 -10000 0 -10000 0 0
MAP2K3 -0.016 0.14 0.28 1 -0.41 31 32
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.014 0.13 0.32 1 -0.38 35 36
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.036 0.017 -10000 0 -10000 0 0
TXN 0.01 0.006 -10000 0 -10000 0 0
CALM1 0.033 0.006 -10000 0 -10000 0 0
GADD45A 0.025 0.072 -10000 0 -0.54 8 8
GADD45B 0.031 0.037 -10000 0 -0.54 2 2
MAP3K1 0.036 0.046 -10000 0 -0.54 2 2
MAP3K6 0.033 0.008 -10000 0 -10000 0 0
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
MAP3K4 0.032 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.021 0.1 -10000 0 -0.34 34 34
TAK1/TAB family -0.002 0.021 -10000 0 -0.21 1 1
RAC1/OSM/MEKK3 0.057 0.023 -10000 0 -10000 0 0
TRAF2 0.035 0.012 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.008 0.12 -10000 0 -0.34 22 22
TRAF6 0.009 0.002 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.039 0.069 -10000 0 -0.54 5 5
CCM2 0.034 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.047 0.046 -10000 0 -0.34 5 5
MAPK11 0.032 0.009 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.041 0.094 -10000 0 -0.3 31 31
OSM/MEKK3 0.044 0.018 -10000 0 -10000 0 0
TAOK1 0.016 0.013 -10000 0 -10000 0 0
TAOK2 0.015 0.008 -10000 0 -10000 0 0
TAOK3 0.016 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.034 0.005 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.003 0.13 -10000 0 -0.54 26 26
MAP3K10 0.032 0.039 -10000 0 -0.54 2 2
MAP3K3 0.031 0.011 -10000 0 -10000 0 0
TRX/ASK1 0.009 0.082 -10000 0 -0.32 28 28
GADD45/MTK1/MTK1 0.066 0.059 -10000 0 -0.29 10 10
Nephrin/Neph1 signaling in the kidney podocyte

Figure S109.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S109.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity -0.047 0.032 -10000 0 -10000 0 0
KIRREL 0.032 0.018 -10000 0 -10000 0 0
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.047 0.032 -10000 0 -10000 0 0
PLCG1 0.032 0.008 -10000 0 -10000 0 0
ARRB2 0.031 0.01 -10000 0 -10000 0 0
WASL 0.033 0.026 -10000 0 -0.54 1 1
Nephrin/NEPH1/podocin/CD2AP 0.071 0.046 -10000 0 -10000 0 0
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.031 0.027 -10000 0 -0.24 1 1
FYN 0.065 0.096 0.28 71 -0.24 2 73
mol:Ca2+ 0.066 0.047 -10000 0 -10000 0 0
mol:DAG 0.067 0.047 -10000 0 -10000 0 0
NPHS2 0.033 0.017 -10000 0 -10000 0 0
mol:IP3 0.067 0.047 -10000 0 -10000 0 0
regulation of endocytosis 0.053 0.043 -10000 0 -0.22 2 2
Nephrin/NEPH1/podocin/Cholesterol 0.055 0.038 -10000 0 -10000 0 0
establishment of cell polarity 0.047 0.032 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2 0.083 0.053 -10000 0 -10000 0 0
Nephrin/NEPH1/beta Arrestin2 0.055 0.045 -10000 0 -0.23 2 2
NPHS1 0.049 0.032 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin 0.056 0.043 -10000 0 -0.24 2 2
TJP1 0.032 0.026 -10000 0 -0.54 1 1
NCK1 0.034 0.005 -10000 0 -10000 0 0
NCK2 0.034 0.007 0.18 1 -10000 0 1
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.069 0.048 -10000 0 -10000 0 0
CD2AP 0.034 0.009 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.068 0.049 -10000 0 -10000 0 0
GRB2 0.034 0.018 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.056 0.12 0.3 68 -0.3 14 82
cytoskeleton organization 0.033 0.055 0.26 12 -10000 0 12
Nephrin/NEPH1 0.04 0.026 -10000 0 -10000 0 0
Nephrin/NEPH1/ZO-1 0.057 0.042 -10000 0 -0.37 1 1
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.048 0.022 -10000 0 -10000 0 0
ATM 0.03 0.012 -10000 0 -10000 0 0
UBE2D3 0.034 0.005 -10000 0 -10000 0 0
PRKDC 0.031 0.019 -10000 0 -10000 0 0
ATR 0.034 0.006 -10000 0 -10000 0 0
UBE2L3 0.033 0.008 -10000 0 -10000 0 0
FANCD2 0.024 0.015 -10000 0 -10000 0 0
protein ubiquitination 0.089 0.059 0.33 1 -10000 0 1
XRCC5 0.034 0.005 -10000 0 -10000 0 0
XRCC6 0.032 0.009 -10000 0 -10000 0 0
M/R/N Complex 0.049 0.033 -10000 0 -10000 0 0
MRE11A 0.03 0.011 -10000 0 -10000 0 0
DNA-PK 0.056 0.031 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.025 0.11 -10000 0 -0.47 11 11
FANCF 0.033 0.006 -10000 0 -10000 0 0
BRCA1 0.036 0.021 -10000 0 -10000 0 0
CCNE1 0.058 0.056 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.068 0.047 0.26 8 -10000 0 8
FANCG 0.034 0.011 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.052 0.025 -10000 0 -10000 0 0
FANCE 0.033 0.027 -10000 0 -0.54 1 1
FANCC 0.036 0.016 -10000 0 -10000 0 0
NBN 0.028 0.016 -10000 0 -10000 0 0
FANCA 0.061 0.064 -10000 0 -10000 0 0
DNA repair 0.075 0.1 0.32 12 -0.4 2 14
BRCA1/BARD1/ubiquitin 0.052 0.025 -10000 0 -10000 0 0
BARD1/DNA-PK 0.072 0.04 -10000 0 -10000 0 0
FANCL 0.034 0.004 -10000 0 -10000 0 0
mRNA polyadenylation -0.048 0.022 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.024 0.074 -10000 0 -0.31 3 3
BRCA1/BACH1/BARD1/TopBP1 0.068 0.028 0.25 1 -10000 0 1
BRCA1/BARD1/P53 0.078 0.038 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.063 0.032 -10000 0 -10000 0 0
BRCA1/BACH1 0.036 0.021 -10000 0 -10000 0 0
BARD1 0.037 0.023 -10000 0 -10000 0 0
PCNA 0.037 0.026 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.069 0.027 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.067 0.028 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.12 0.071 0.35 2 -10000 0 2
BARD1/DNA-PK/P53 0.077 0.05 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.052 0.025 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP 0.048 0.039 -10000 0 -0.32 2 2
FA complex 0.042 0.054 -10000 0 -0.3 2 2
BARD1/EWS 0.049 0.02 -10000 0 -10000 0 0
RBBP8 0.013 0.028 -10000 0 -0.4 2 2
TP53 0.031 0.014 -10000 0 -10000 0 0
TOPBP1 0.035 0.012 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.075 0.037 -10000 0 -10000 0 0
BRCA1/BARD1 0.097 0.064 0.35 1 -10000 0 1
CSTF1 0.031 0.01 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.027 0.016 -10000 0 -10000 0 0
CDK2 0.037 0.021 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.11 0.074 0.18 286 -10000 0 286
RAD50 0.033 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.052 0.025 -10000 0 -10000 0 0
EWSR1 0.032 0.008 -10000 0 -10000 0 0
Visual signal transduction: Cones

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin 0.047 0.037 -10000 0 -0.3 3 3
RGS9BP 0.054 0.065 -10000 0 -0.54 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.043 0.042 0.23 1 -0.34 2 3
mol:ADP 0.008 0.019 0.14 1 -0.4 1 2
GNAT2 0.031 0.045 -10000 0 -0.54 3 3
RGS9-1/Gbeta5/R9AP 0.049 0.1 -10000 0 -0.32 28 28
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.04 0.039 -10000 0 -0.34 4 4
GRK7 0.033 0.027 -10000 0 -0.54 1 1
CNGB3 0.033 0.03 -10000 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.026 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.056 0.075 0.28 9 -0.31 2 11
Cone PDE6 0.069 0.1 -10000 0 -0.3 21 21
Cone Metarhodopsin II 0.021 0.015 -10000 0 -0.31 1 1
Na + (4 Units) 0.056 0.046 -10000 0 -0.31 2 2
GNAT2/GDP 0.056 0.096 -10000 0 -0.28 30 30
GNB5 0.032 0.026 -10000 0 -0.54 1 1
mol:GMP (4 units) 0.021 0.046 -10000 0 -0.31 5 5
Cone Transducin 0.051 0.04 -10000 0 -0.31 3 3
SLC24A2 0.033 0.01 -10000 0 -10000 0 0
GNB3/GNGT2 0.043 0.02 -10000 0 -10000 0 0
GNB3 0.032 0.011 -10000 0 -10000 0 0
GNAT2/GTP 0.022 0.034 -10000 0 -0.34 4 4
CNGA3 0.042 0.052 -10000 0 -0.54 2 2
ARR3 0.035 0.002 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.044 0.042 0.23 1 -0.34 2 3
mol:Pi 0.048 0.1 -10000 0 -0.32 28 28
Cone CNG Channel 0.063 0.062 -10000 0 -0.29 6 6
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.033 0.01 -10000 0 -10000 0 0
RGS9 0.001 0.13 -10000 0 -0.54 27 27
PDE6C 0.034 0.028 -10000 0 -0.54 1 1
GNGT2 0.031 0.011 -10000 0 -10000 0 0
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.033 0.03 -10000 0 -0.54 1 1
Insulin-mediated glucose transport

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.075 0.14 0.38 1 -0.28 39 40
CaM/Ca2+ 0.025 0.005 -10000 0 -10000 0 0
AKT1 0.035 0.017 -10000 0 -10000 0 0
AKT2 0.034 0.006 -10000 0 -10000 0 0
STXBP4 0.031 0.014 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.09 0.13 0.41 1 -0.28 54 55
YWHAZ 0.026 0.018 -10000 0 -10000 0 0
CALM1 0.033 0.006 -10000 0 -10000 0 0
YWHAQ 0.034 0.005 -10000 0 -10000 0 0
TBC1D4 0.006 0.07 -10000 0 -0.4 14 14
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.033 0.014 -10000 0 -10000 0 0
YWHAB 0.032 0.008 -10000 0 -10000 0 0
SNARE/Synip 0.053 0.031 -10000 0 -10000 0 0
YWHAG 0.034 0.008 -10000 0 -10000 0 0
ASIP 0 0 -10000 0 -10000 0 0
PRKCI 0.035 0.017 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.025 0.005 -10000 0 -10000 0 0
RHOQ 0.033 0.026 -10000 0 -0.54 1 1
GYS1 0.017 0.021 0.25 3 -10000 0 3
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.033 0.026 -10000 0 -0.54 1 1
TC10/GTP/CIP4/Exocyst 0.043 0.026 -10000 0 -0.34 2 2
AS160/14-3-3 0.025 0.077 -10000 0 -0.37 8 8
VAMP2 0.031 0.011 -10000 0 -10000 0 0
SLC2A4 -0.099 0.14 0.42 1 -0.31 54 55
STX4 0.031 0.01 -10000 0 -10000 0 0
GSK3B 0.027 0.014 -10000 0 -10000 0 0
SFN 0.032 0.04 -10000 0 -0.54 2 2
LNPEP 0.035 0.016 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

Figure S113.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S113.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA 0.076 0.054 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.01 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.05 0.064 -10000 0 -0.29 2 2
SUMO1 0.034 0.005 -10000 0 -10000 0 0
ZFPM1 0.029 0.015 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.017 0.02 -10000 0 -0.17 3 3
FKBP3 0.034 0.005 -10000 0 -10000 0 0
Histones 0.076 0.049 -10000 0 -10000 0 0
YY1/LSF 0.031 0.057 -10000 0 -0.26 9 9
SMG5 0.029 0.016 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.031 0.025 -10000 0 -10000 0 0
I kappa B alpha/HDAC1 0.041 0.044 -10000 0 -0.25 1 1
SAP18 0.032 0.009 -10000 0 -10000 0 0
RELA 0.028 0.042 -10000 0 -0.23 8 8
HDAC1/Smad7 0.064 0.019 -10000 0 -10000 0 0
RANGAP1 0.038 0.03 -10000 0 -10000 0 0
HDAC3/TR2 0.044 0.041 -10000 0 -0.29 1 1
NuRD/MBD3 Complex 0.04 0.06 -10000 0 -0.32 5 5
NF kappa B1 p50/RelA 0.042 0.068 0.4 1 -0.33 2 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.042 0.033 0.18 28 -10000 0 28
GATA1 0.034 0.003 -10000 0 -10000 0 0
Mad/Max 0.048 0.013 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.029 0.094 -10000 0 -0.37 13 13
RBBP7 0.037 0.022 -10000 0 -10000 0 0
NPC 0.02 0.002 -10000 0 -10000 0 0
RBBP4 0.033 0.006 -10000 0 -10000 0 0
MAX 0.033 0.007 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.033 0.007 -10000 0 -10000 0 0
NFKBIA 0.028 0.019 -10000 0 -0.27 1 1
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.027 0.054 -10000 0 -0.29 6 6
SIN3 complex 0.078 0.032 -10000 0 -10000 0 0
SMURF1 0.034 0.005 -10000 0 -10000 0 0
CHD3 0.032 0.016 -10000 0 -10000 0 0
SAP30 0.034 0.009 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.031 0.011 -10000 0 -10000 0 0
YY1/HDAC3 0.031 0.051 -10000 0 -0.36 2 2
YY1/HDAC2 0.034 0.047 -10000 0 -0.23 6 6
YY1/HDAC1 0.034 0.051 -10000 0 -0.24 7 7
NuRD/MBD2 Complex (MeCP1) 0.039 0.058 -10000 0 -0.25 5 5
PPARG -0.21 0.16 -10000 0 -0.31 340 340
HDAC8/hEST1B 0.057 0.029 -10000 0 -10000 0 0
UBE2I 0.031 0.01 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.007 -10000 0 -10000 0 0
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.044 0.039 -10000 0 -10000 0 0
MBD3L2 0.033 0.026 -10000 0 -0.54 1 1
ubiquitin-dependent protein catabolic process 0.064 0.019 -10000 0 -10000 0 0
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
NuRD/MBD3/MBD3L2 Complex 0.04 0.081 -10000 0 -0.35 9 9
HDAC1 0.034 0.005 -10000 0 -10000 0 0
HDAC3 0.03 0.013 -10000 0 -10000 0 0
HDAC2 0.033 0.017 -10000 0 -10000 0 0
YY1 0.016 0.015 -10000 0 -0.28 1 1
HDAC8 0.035 0.002 -10000 0 -10000 0 0
SMAD7 0.033 0.007 -10000 0 -10000 0 0
NCOR2 0.034 0.004 -10000 0 -10000 0 0
MXD1 0.034 0.008 -10000 0 -10000 0 0
STAT3 0.023 0.019 -10000 0 -0.33 1 1
NFKB1 0.034 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.034 0.004 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.049 0.058 -10000 0 -0.24 9 9
YY1/SAP30/HDAC1 0.05 0.054 -10000 0 -0.22 7 7
EP300 0.032 0.009 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.023 0.019 -10000 0 -0.32 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.019 -10000 0 -0.27 1 1
histone deacetylation 0.039 0.061 -10000 0 -0.27 6 6
STAT3 (dimer non-phopshorylated)/HDAC3 0.032 0.042 -10000 0 -0.26 1 1
nuclear export -0.056 0.028 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
GATAD2B 0.028 0.014 -10000 0 -10000 0 0
GATAD2A 0.037 0.022 -10000 0 -10000 0 0
GATA2/HDAC3 0.049 0.046 -10000 0 -10000 0 0
GATA1/HDAC1 0.05 0.009 -10000 0 -10000 0 0
GATA1/HDAC3 0.045 0.039 -10000 0 -10000 0 0
CHD4 0.032 0.008 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.05 0.021 -10000 0 -10000 0 0
SIN3/HDAC complex/Mad/Max 0.028 0.063 -10000 0 -0.31 10 10
NuRD Complex 0.04 0.076 -10000 0 -0.31 7 7
positive regulation of chromatin silencing 0.072 0.048 -10000 0 -10000 0 0
SIN3B 0.035 0.014 -10000 0 -10000 0 0
MTA2 0.034 0.006 -10000 0 -10000 0 0
SIN3A 0.033 0.006 -10000 0 -10000 0 0
XPO1 0.034 0.005 -10000 0 -10000 0 0
SUMO1/HDAC1 0.053 0.05 -10000 0 -0.25 3 3
HDAC complex 0.082 0.031 -10000 0 -10000 0 0
GATA1/Fog1 0.042 0.02 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.063 0.023 -10000 0 -10000 0 0
TNF 0.038 0.023 -10000 0 -10000 0 0
negative regulation of cell growth 0.025 0.072 -10000 0 -0.33 14 14
NuRD/MBD2/PRMT5 Complex 0.039 0.058 -10000 0 -0.25 5 5
Ran/GTP/Exportin 1 0.051 0.05 -10000 0 -0.26 3 3
NF kappa B/RelA/I kappa B alpha 0.031 0.048 -10000 0 -0.32 1 1
SIN3/HDAC complex/NCoR1 0.021 0.064 -10000 0 -0.31 11 11
TFCP2 0.032 0.036 -10000 0 -0.54 2 2
NR2C1 0.033 0.026 -10000 0 -0.54 1 1
MBD3 0.033 0.007 -10000 0 -10000 0 0
MBD2 0.034 0.011 -10000 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.005 0.054 0.31 4 -10000 0 4
DAPP1 0.033 0.11 0.28 7 -0.32 20 27
Src family/SYK family/BLNK-LAT/BTK-ITK 0.044 0.14 0.41 10 -0.45 18 28
mol:DAG 0.041 0.095 0.28 31 -0.2 1 32
HRAS 0.035 0.013 -10000 0 -10000 0 0
RAP1A 0.035 0.007 -10000 0 -10000 0 0
ARF5/GDP 0.047 0.078 -10000 0 -0.35 7 7
PLCG2 0.021 0.073 -10000 0 -0.54 8 8
PLCG1 0.032 0.008 -10000 0 -10000 0 0
ARF5 0.034 0.005 -10000 0 -10000 0 0
mol:GTP -0.006 0.055 0.32 7 -10000 0 7
ARF1/GTP 0.003 0.05 0.31 7 -10000 0 7
RHOA 0.033 0.007 -10000 0 -10000 0 0
YES1 0.032 0.027 -10000 0 -0.54 1 1
RAP1A/GTP -0.004 0.055 0.25 10 -10000 0 10
ADAP1 -0.006 0.052 0.3 7 -10000 0 7
ARAP3 -0.006 0.055 0.32 7 -10000 0 7
INPPL1 0.032 0.01 -10000 0 -10000 0 0
PREX1 0.055 0.079 -10000 0 -0.54 4 4
ARHGEF6 0.014 0.11 -10000 0 -0.54 18 18
ARHGEF7 0.031 0.012 -10000 0 -10000 0 0
ARF1 0.027 0.014 -10000 0 -10000 0 0
NRAS 0.037 0.017 -10000 0 -10000 0 0
FYN 0.03 0.037 -10000 0 -0.54 2 2
ARF6 0.034 0.005 -10000 0 -10000 0 0
FGR 0.033 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0.023 0.058 0.21 18 -0.16 1 19
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.035 0.012 0.18 3 -10000 0 3
ZAP70 0.038 0.024 -10000 0 -10000 0 0
mol:IP3 0.026 0.071 0.23 23 -0.23 1 24
LYN 0.03 0.015 -10000 0 -10000 0 0
ARF1/GDP 0.037 0.077 0.43 1 -0.35 7 8
RhoA/GDP 0.05 0.059 0.31 5 -10000 0 5
PDK1/Src/Hsp90 0.059 0.026 -10000 0 -10000 0 0
BLNK 0.039 0.026 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.035 0.083 0.35 8 -0.33 4 12
SRC 0.033 0.008 -10000 0 -10000 0 0
PLEKHA2 -0.005 0.006 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
PTEN 0.024 0.065 -10000 0 -0.52 7 7
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
ARF6/GTP -0.004 0.06 0.3 9 -10000 0 9
RhoA/GTP -0.005 0.057 0.33 6 -10000 0 6
Src family/SYK family/BLNK-LAT 0.042 0.091 0.31 11 -0.36 6 17
BLK 0.039 0.044 -10000 0 -10000 0 0
PDPK1 0.031 0.01 -10000 0 -10000 0 0
CYTH1 -0.006 0.052 0.3 7 -10000 0 7
HCK 0.036 0.022 -10000 0 -10000 0 0
CYTH3 -0.006 0.052 0.3 7 -10000 0 7
CYTH2 -0.006 0.052 0.3 7 -10000 0 7
KRAS 0.035 0.018 0.18 1 -10000 0 1
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.014 0.031 0.26 1 -10000 0 1
SGK1 0.019 0.044 0.38 3 -10000 0 3
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.031 0.079 0.29 3 -0.34 8 11
SOS1 0.034 0.004 -10000 0 -10000 0 0
SYK 0.039 0.026 -10000 0 -10000 0 0
ARF6/GDP 0.033 0.064 0.34 8 -10000 0 8
mol:PI-3-4-5-P3 -0.006 0.059 0.34 8 -10000 0 8
ARAP3/RAP1A/GTP -0.004 0.055 0.25 10 -10000 0 10
VAV1 0.038 0.025 0.18 15 -10000 0 15
mol:PI-3-4-P2 0.008 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.052 0.039 0.29 2 -10000 0 2
PLEKHA1 -0.008 0.021 -10000 0 -0.34 2 2
Rac1/GDP 0.048 0.078 0.22 1 -0.35 7 8
LAT 0.035 0.025 -10000 0 -10000 0 0
Rac1/GTP 0.027 0.082 -10000 0 -0.31 18 18
ITK -0.003 0.06 0.32 6 -0.29 2 8
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.042 0.11 0.34 23 -0.27 2 25
LCK 0.048 0.044 -10000 0 -10000 0 0
BTK -0.002 0.059 0.33 6 -10000 0 6
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.035 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.064 0.12 0.34 6 -0.34 8 14
ERC1 0.033 0.013 0.18 2 -10000 0 2
RIP2/NOD2 0.053 0.051 0.26 3 -10000 0 3
NFKBIA 0.014 0.022 -10000 0 -0.33 1 1
BIRC2 0.031 0.011 -10000 0 -10000 0 0
IKBKB 0.028 0.013 -10000 0 -10000 0 0
RIPK2 0.029 0.021 -10000 0 -10000 0 0
IKBKG 0.019 0.14 -10000 0 -0.39 42 42
IKK complex/A20 0.04 0.15 -10000 0 -0.42 22 22
NEMO/A20/RIP2 0.029 0.021 -10000 0 -10000 0 0
XPO1 0.034 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.03 0.15 -10000 0 -0.41 32 32
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.045 0.009 -10000 0 -10000 0 0
IKK complex/ELKS 0.024 0.13 -10000 0 -0.41 21 21
BCL10/MALT1/TRAF6 0.064 0.021 -10000 0 -10000 0 0
NOD2 0.059 0.061 -10000 0 -10000 0 0
NFKB1 0.036 0.007 -10000 0 -10000 0 0
RELA 0.036 0.007 -10000 0 -10000 0 0
MALT1 0.033 0.01 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.045 0.017 -10000 0 -10000 0 0
ATM 0.03 0.012 -10000 0 -10000 0 0
TNF/TNFR1A 0.05 0.021 -10000 0 -10000 0 0
TRAF6 0.034 0.006 -10000 0 -10000 0 0
PRKCA 0.031 0.013 -10000 0 -10000 0 0
CHUK 0.034 0.005 -10000 0 -10000 0 0
UBE2D3 0.034 0.005 -10000 0 -10000 0 0
TNF 0.038 0.023 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.074 0.023 -10000 0 -10000 0 0
BCL10 0.033 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.022 -10000 0 -0.32 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.009 -10000 0 -10000 0 0
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
IKK complex 0.032 0.15 -10000 0 -0.43 22 22
CYLD 0.03 0.012 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.035 0.14 -10000 0 -0.42 20 20
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.05 0.014 -10000 0 -10000 0 0
FBXW11 0.033 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.033 0.022 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.043 0.052 -10000 0 -0.26 2 2
NFKBIA 0.033 0.037 -10000 0 -0.28 1 1
MAPK14 0.034 0.005 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.03 0.016 -10000 0 -10000 0 0
ARRB2 0.017 0.006 -10000 0 -10000 0 0
REL 0.038 0.023 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.032 0.018 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.031 0.015 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.022 0.015 0.26 1 -10000 0 1
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
NFKB1 0.014 0.007 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.04 0.05 -10000 0 -0.22 3 3
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.041 0.057 -10000 0 -0.29 2 2
SRC 0.033 0.008 -10000 0 -10000 0 0
PI3K 0.005 0.13 -10000 0 -0.37 51 51
NF kappa B1 p50/RelA 0.04 0.05 -10000 0 -0.22 3 3
IKBKB 0.028 0.013 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.007 -10000 0 -10000 0 0
SYK 0.039 0.026 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.017 0.1 -10000 0 -0.27 42 42
cell death 0.04 0.055 -10000 0 -0.28 2 2
NF kappa B1 p105/c-Rel 0.033 0.022 -10000 0 -10000 0 0
LCK 0.048 0.044 -10000 0 -10000 0 0
BCL3 0.035 0.014 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GAB2 0.03 0.012 -10000 0 -10000 0 0
ELF1 0.045 0.029 -10000 0 -10000 0 0
CCNA2 0.081 0.069 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
JAK3 0.034 0.006 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
JAK1 0.034 0.007 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.065 0.11 0.34 3 -0.37 9 12
SHC1 0.028 0.014 -10000 0 -10000 0 0
SP1 0.036 0.049 -10000 0 -0.36 8 8
IL2RA 0.036 0.057 -10000 0 -10000 0 0
IL2RB 0.036 0.022 -10000 0 -10000 0 0
SOS1 0.035 0.004 -10000 0 -10000 0 0
IL2RG 0.044 0.035 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.047 0.15 0.39 2 -0.77 11 13
PTPN11 0.035 0.004 -10000 0 -10000 0 0
CCND2 0.009 0.1 -10000 0 -0.77 9 9
LCK 0.049 0.044 -10000 0 -10000 0 0
GRB2 0.034 0.018 -10000 0 -10000 0 0
IL2 0.033 0.027 -10000 0 -0.54 1 1
CDK6 0.028 0.064 -10000 0 -0.54 6 6
CCND3 0.067 0.11 0.46 4 -0.45 1 5
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.046 0.055 -10000 0 -0.29 8 8
BIRC5 0.12 0.075 -10000 0 -10000 0 0
NFKBIA 0.023 0.041 0.27 5 -10000 0 5
CPEB1 0.019 0.092 -10000 0 -0.54 13 13
AKT1 0.023 0.041 0.3 3 -10000 0 3
NDEL1 0.031 0.011 -10000 0 -10000 0 0
Aurora A/BRCA1 0.04 0.035 -10000 0 -10000 0 0
NDEL1/TACC3 0.095 0.066 -10000 0 -10000 0 0
GADD45A 0.025 0.072 -10000 0 -0.54 8 8
GSK3B 0.003 0.027 -10000 0 -10000 0 0
PAK1/Aurora A 0.056 0.049 -10000 0 -10000 0 0
MDM2 0.033 0.01 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.11 0.059 -10000 0 -10000 0 0
TP53 0.022 0.059 -10000 0 -10000 0 0
DLG7 0.023 0.032 -10000 0 -10000 0 0
AURKAIP1 0.034 0.013 -10000 0 -10000 0 0
ARHGEF7 0.031 0.012 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.1 0.07 0.27 1 -10000 0 1
G2/M transition of mitotic cell cycle 0.04 0.034 -10000 0 -10000 0 0
AURKA 0.032 0.041 -10000 0 -10000 0 0
AURKB 0.044 0.054 -10000 0 -10000 0 0
CDC25B 0.035 0.047 -10000 0 -10000 0 0
G2/M transition checkpoint 0.016 0.028 -10000 0 -10000 0 0
mRNA polyadenylation 0.03 0.059 -10000 0 -0.28 13 13
Aurora A/CPEB 0.031 0.06 -10000 0 -0.28 13 13
Aurora A/TACC1/TRAP/chTOG 0.053 0.089 -10000 0 -0.29 18 18
BRCA1 0.036 0.021 -10000 0 -10000 0 0
centrosome duplication 0.056 0.049 -10000 0 -10000 0 0
regulation of centrosome cycle 0.092 0.064 -10000 0 -10000 0 0
spindle assembly 0.051 0.087 -10000 0 -0.29 18 18
TDRD7 0.034 0.005 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.12 0.072 -10000 0 -10000 0 0
CENPA 0.061 0.056 0.16 64 -0.23 1 65
Aurora A/PP2A 0.052 0.037 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.028 0.036 0.27 1 -10000 0 1
negative regulation of DNA binding 0.022 0.058 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.043 0.02 -10000 0 -10000 0 0
RASA1 0.034 0.012 -10000 0 -10000 0 0
Ajuba/Aurora A 0.016 0.028 -10000 0 -10000 0 0
mitotic prometaphase 0.006 0.024 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.032 0.041 -10000 0 -10000 0 0
TACC1 0.001 0.12 -10000 0 -0.54 24 24
TACC3 0.096 0.073 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.069 0.037 -10000 0 -10000 0 0
Aurora A/RasGAP 0.051 0.037 -10000 0 -10000 0 0
OAZ1 0.033 0.007 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.003 0.027 -10000 0 -10000 0 0
GIT1 0.032 0.011 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.059 0.043 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.11 0.059 -10000 0 -10000 0 0
PPP2R5D 0.034 0.006 -10000 0 -10000 0 0
Aurora A/TPX2 0.1 0.063 0.25 3 -10000 0 3
PAK1 0.043 0.046 -10000 0 -10000 0 0
CKAP5 0.035 0.015 -10000 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.045 0.04 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.078 0.055 0.24 19 -10000 0 19
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.017 0.032 -10000 0 -0.31 4 4
AURKB 0.057 0.058 -10000 0 -10000 0 0
AURKC 0.036 0.019 -10000 0 -10000 0 0
TCGA08_p53

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2A 0.027 0.046 -10000 0 -10000 0 0
TP53 -0.002 0.055 -10000 0 -0.26 1 1
Senescence -0.006 0.06 -10000 0 -0.26 1 1
Apoptosis -0.006 0.06 -10000 0 -0.26 1 1
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.009 0.068 0.3 19 -10000 0 19
MDM4 0.028 0.017 -10000 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.01 0.033 -10000 0 -0.34 5 5
ADCY5 -0.006 0.022 -10000 0 -0.34 1 1
ADCY6 -0.007 0.001 -10000 0 -10000 0 0
ADCY7 -0.003 0.019 -10000 0 -10000 0 0
ADCY1 -0.006 0.009 -10000 0 -10000 0 0
ADCY2 -0.009 0.042 -10000 0 -0.34 7 7
ADCY3 -0.007 0.007 -10000 0 -10000 0 0
ADCY8 -0.004 0.015 -10000 0 -10000 0 0
PRKCE 0.009 0.001 -10000 0 -10000 0 0
ADCY9 -0.004 0.016 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.035 0.07 0.24 15 -10000 0 15
Effects of Botulinum toxin

Figure S122.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S122.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A 0.012 0.019 0.14 12 -10000 0 12
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.053 0.029 -10000 0 -10000 0 0
STXBP1 0.034 0.005 -10000 0 -10000 0 0
ACh/CHRNA1 0.023 0.031 -10000 0 -0.16 1 1
RAB3GAP2/RIMS1/UNC13B 0.057 0.038 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.042 0.035 -10000 0 -10000 0 0
mol:ACh 0 0.032 0.091 13 -0.12 11 24
RAB3GAP2 0.028 0.014 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.041 0.055 -10000 0 -10000 0 0
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.023 0.031 -10000 0 -0.16 1 1
UNC13B 0.034 0.014 -10000 0 -10000 0 0
CHRNA1 0.035 0.01 -10000 0 -10000 0 0
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.053 0.077 0.18 13 -0.33 9 22
SNAP25 0.007 0.035 -10000 0 -0.3 5 5
VAMP2 0.006 0.002 -10000 0 -10000 0 0
SYT1 0.07 0.1 -10000 0 -0.54 8 8
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.033 0.015 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.041 0.055 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.032 0.026 -10000 0 -0.54 1 1
SMAD2 -0.007 0.05 -10000 0 -0.25 8 8
SMAD3 0.027 0.045 0.29 2 -10000 0 2
SMAD3/SMAD4 0.058 0.065 -10000 0 -0.46 3 3
SMAD4/Ubc9/PIASy 0.058 0.034 -10000 0 -0.34 1 1
SMAD2/SMAD2/SMAD4 0.064 0.074 -10000 0 -0.32 1 1
PPM1A 0.033 0.006 -10000 0 -10000 0 0
CALM1 0.033 0.006 -10000 0 -10000 0 0
SMAD2/SMAD4 0.009 0.057 -10000 0 -0.3 4 4
MAP3K1 0.036 0.046 -10000 0 -0.54 2 2
TRAP-1/SMAD4 0.047 0.025 -10000 0 -0.4 1 1
MAPK3 0.032 0.009 -10000 0 -10000 0 0
MAPK1 0.032 0.008 -10000 0 -10000 0 0
NUP214 0.034 0.005 -10000 0 -10000 0 0
CTDSP1 0.034 0.005 -10000 0 -10000 0 0
CTDSP2 0.034 0.006 -10000 0 -10000 0 0
CTDSPL 0.031 0.036 -10000 0 -0.54 2 2
KPNB1 0.032 0.009 -10000 0 -10000 0 0
TGFBRAP1 0.034 0.004 -10000 0 -10000 0 0
UBE2I 0.031 0.01 -10000 0 -10000 0 0
NUP153 0.033 0.006 -10000 0 -10000 0 0
KPNA2 0.058 0.06 -10000 0 -10000 0 0
PIAS4 0.035 0.016 -10000 0 -10000 0 0
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.043 0.022 -9999 0 -0.34 1 1
EFNA5 0.033 0.029 -9999 0 -0.54 1 1
FYN 0.017 0.031 -9999 0 -0.31 3 3
neuron projection morphogenesis 0.043 0.022 -9999 0 -0.34 1 1
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 0.044 0.022 -9999 0 -0.34 1 1
EPHA5 0.034 0.005 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

Figure S125.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S125.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.034 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.006 0.014 -10000 0 -10000 0 0
MDM2/SUMO1 0.049 0.052 -10000 0 -0.25 3 3
HDAC4 0.033 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.006 0.014 -10000 0 -10000 0 0
SUMO1 0.034 0.005 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.016 0.026 -10000 0 -0.29 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.007 0.034 -10000 0 -0.27 3 3
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.034 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.051 0.051 -10000 0 -0.25 3 3
SUMO1/HDAC1 0.053 0.05 -10000 0 -0.25 3 3
RANGAP1 0.038 0.03 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.078 0.03 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.017 0.02 -10000 0 -0.17 3 3
Ran/GTP 0.036 0.047 -10000 0 -0.23 5 5
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.033 0.01 -10000 0 -10000 0 0
UBE2I 0.031 0.01 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0.05 0.26 2 -0.26 3 5
NPC 0.02 0.002 -10000 0 -10000 0 0
PIAS2 0.033 0.007 -10000 0 -10000 0 0
PIAS1 0.033 0.007 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

Figure S126.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S126.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A 0.034 0.004 -10000 0 -10000 0 0
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.031 0.01 -10000 0 -10000 0 0
TCEB1 0.028 0.013 -10000 0 -10000 0 0
HIF1A/p53 0.046 0.06 -10000 0 -0.27 7 7
HIF1A 0.03 0.05 -10000 0 -0.27 6 6
COPS5 0.028 0.013 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.07 0.05 -10000 0 -10000 0 0
FIH (dimer) 0.034 0.005 -10000 0 -10000 0 0
CDKN2A 0.053 0.054 -10000 0 -10000 0 0
ARNT/IPAS 0.04 0.021 -10000 0 -10000 0 0
HIF1AN 0.034 0.005 -10000 0 -10000 0 0
GNB2L1 0.034 0.006 -10000 0 -10000 0 0
HIF1A/ARNT 0.033 0.056 -10000 0 -0.28 7 7
CUL2 0.034 0.009 -10000 0 -10000 0 0
OS9 0.034 0.006 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.052 0.031 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.049 0.059 -10000 0 -0.27 8 8
PHD1-3/OS9 0.075 0.059 -10000 0 -0.32 1 1
HIF1A/RACK1/Elongin B/Elongin C 0.057 0.065 -10000 0 -0.3 2 2
VHL 0.036 0.018 -10000 0 -10000 0 0
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
HIF1A/JAB1 0.04 0.059 -10000 0 -0.27 7 7
EGLN3 0.059 0.064 -10000 0 -0.54 1 1
EGLN2 0.035 0.017 -10000 0 -10000 0 0
EGLN1 0.027 0.014 -10000 0 -10000 0 0
TP53 0.031 0.014 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.044 0.064 -10000 0 -0.47 6 6
ARNT 0.027 0.014 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.032 0.009 -10000 0 -10000 0 0
HIF1A/p19ARF 0.059 0.068 0.26 3 -0.26 7 10
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.015 0.036 -10000 0 -10000 0 0
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.035 0.052 0.17 1 -0.19 2 3
AP2 0.049 0.017 0.26 1 -10000 0 1
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.043 0.015 -10000 0 -10000 0 0
CLTB 0.033 0.007 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.018 0.019 -10000 0 -10000 0 0
CD4 0.032 0.009 -10000 0 -10000 0 0
CLTA 0.033 0.006 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.009 0.008 0.14 2 -10000 0 2
mol:PI-4-5-P2 0.009 0.02 -10000 0 -0.19 1 1
ARF1/GTP 0.015 0.014 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.011 0.022 0.18 5 -10000 0 5
mol:Choline 0.008 0.02 -10000 0 -0.2 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.028 0.015 -10000 0 -10000 0 0
DDEF1 0.007 0.02 -10000 0 -0.2 1 1
ARF1/GDP 0.002 0.022 -10000 0 -10000 0 0
AP2M1 0.034 0.009 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.013 0.008 -10000 0 -10000 0 0
Rac/GTP 0.028 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.033 0.024 -10000 0 -10000 0 0
ARFIP2 0.021 0.026 -10000 0 -10000 0 0
COPA 0.028 0.014 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.016 0.032 -10000 0 -0.21 2 2
ARF1/GTP/ARHGAP10 0.018 0.01 -10000 0 -10000 0 0
GGA3 0.032 0.009 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.016 0.041 -10000 0 -0.23 9 9
AP2A1 0.034 0.013 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.011 0.032 -10000 0 -0.23 5 5
ARF1/GDP/Membrin 0.018 0.049 -10000 0 -0.25 13 13
Arfaptin 2/Rac/GDP 0.041 0.016 -10000 0 -10000 0 0
CYTH2 -0.001 0.002 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.033 0.021 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.025 0.004 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.024 0.032 -10000 0 -10000 0 0
PLD2 0.008 0.02 -10000 0 -0.2 1 1
ARF-GAP1/v-SNARE 0.009 0.008 0.14 2 -10000 0 2
PIP5K1A 0.009 0.02 -10000 0 -0.19 1 1
ARF1/GTP/Membrin/GBF1/p115 0.015 0.024 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.008 0.02 -10000 0 -0.2 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.009 0.008 0.14 2 -10000 0 2
GOSR2 0.013 0.018 -10000 0 -0.26 1 1
USO1 0.012 0.024 -10000 0 -0.31 2 2
GBF1 0.013 0.02 -10000 0 -0.31 1 1
ARF1/GTP/Arfaptin 2 0.036 0.022 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.062 0.026 0.25 1 -10000 0 1
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.033 0.006 -9999 0 -9999 0 0
ITGB7 0.034 0.004 -9999 0 -9999 0 0
ITGA4 0.04 0.029 -9999 0 -9999 0 0
alpha4/beta7 Integrin 0.054 0.022 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0.053 0.023 -9999 0 -9999 0 0
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.044 0.037 -9999 0 -9999 0 0
GPC2 0 0 -9999 0 -9999 0 0
GPC2/Midkine 0.032 0.026 -9999 0 -9999 0 0
neuron projection morphogenesis 0.032 0.026 -9999 0 -9999 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.053 0.036 -10000 0 -0.29 4 4
MAPK9 0.009 0.005 0.11 1 -10000 0 1
adrenocorticotropin secretion 0.01 0.017 -10000 0 -10000 0 0
GNB1/GNG2 0.043 0.021 -10000 0 -0.34 1 1
GNB1 0.034 0.011 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.019 0.025 -10000 0 -0.31 3 3
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.001 0.006 0.08 3 -10000 0 3
GNAL 0.03 0.045 -10000 0 -0.54 3 3
GNG2 0.032 0.026 -10000 0 -0.54 1 1
CRH 0.031 0.024 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.009 0.016 -10000 0 -0.34 1 1
MAPK11 0.009 0.003 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.048 0.015 -10000 0 -9999 0 0
FBXW11 0.033 0.007 -10000 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.007 -10000 0 -9999 0 0
CHUK 0.034 0.005 -10000 0 -9999 0 0
NF kappa B2 p100/RelB 0.094 0.036 -10000 0 -9999 0 0
NFKB1 0.034 0.005 -10000 0 -9999 0 0
MAP3K14 0.033 0.007 -10000 0 -9999 0 0
NF kappa B1 p50/RelB 0.051 0.017 -10000 0 -9999 0 0
RELB 0.036 0.02 -10000 0 -9999 0 0
NFKB2 0.035 0.012 -10000 0 -9999 0 0
NF kappa B2 p52/RelB 0.047 0.018 0.23 1 -9999 0 1
regulation of B cell activation 0.047 0.017 0.23 1 -9999 0 1
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 513 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.E2.A1BD TCGA.E2.A1BC TCGA.E2.A1B6 TCGA.E2.A1B5
109_MAP3K5 0.039 0.039 0.093 0.093
47_PPARGC1A 0.035 0.035 0.035 0.18
105_BMP4 0.035 0.035 0.035 0.035
105_BMP6 0.035 0.035 0.035 0.035
105_BMP7 0.035 0.035 0.035 0.035
105_BMP2 0.035 0.035 0.035 0.035
131_RELN/VLDLR 0.089 0.089 -0.32 0.18
30_TGFB1/TGF beta receptor Type II 0.034 0.034 0.034 0.034
84_STAT5B -0.21 -0.0037 -0.03 -0.21
84_STAT5A -0.21 -0.0037 -0.03 -0.21
Methods & Data
Input

  • Expression Data Normalization = Normal controls were used to median center the expression data used in this analysis.

  • mRNA Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BRCA-TP/3348117/GDAC_MergeDataFiles_3200708/BRCA-TP.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/BRCA-TP/3471814/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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