PARADIGM pathway analysis of mRNASeq expression and copy number data
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 69 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
FOXM1 transcription factor network 189
Aurora B signaling 110
Glypican 2 network 103
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 85
Signaling mediated by p38-alpha and p38-beta 82
Endothelins 81
Signaling events regulated by Ret tyrosine kinase 79
IGF1 pathway 73
Signaling events mediated by the Hedgehog family 71
IL23-mediated signaling events 70
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 408 . 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 ( 408 ).

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
FOXM1 transcription factor network 0.4632 189 9658 51 0.023 0.91 1000 -1000 -0.006 -1000
Aurora B signaling 0.2696 110 7422 67 -0.14 0.29 1000 -1000 -0.021 -1000
Glypican 2 network 0.2525 103 415 4 0.04 0.12 1000 -1000 0.016 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2083 85 5801 68 -0.58 0.31 1000 -1000 -0.032 -1000
Signaling mediated by p38-alpha and p38-beta 0.2010 82 3626 44 -0.19 0.026 1000 -1000 -0.009 -1000
Endothelins 0.1985 81 7806 96 -0.38 0.2 1000 -1000 -0.014 -1000
Signaling events regulated by Ret tyrosine kinase 0.1936 79 6534 82 -0.16 0.026 1000 -1000 -0.039 -1000
IGF1 pathway 0.1789 73 4178 57 -0.13 0.052 1000 -1000 -0.022 -1000
Signaling events mediated by the Hedgehog family 0.1740 71 3697 52 -0.089 0.089 1000 -1000 -0.014 -1000
IL23-mediated signaling events 0.1716 70 4241 60 -0.29 0.11 1000 -1000 -0.024 -1000
PLK1 signaling events 0.1667 68 5864 85 -0.063 0.24 1000 -1000 -0.026 -1000
Nongenotropic Androgen signaling 0.1642 67 3519 52 -0.25 0.14 1000 -1000 -0.019 -1000
Syndecan-1-mediated signaling events 0.1618 66 2265 34 -0.044 0.18 1000 -1000 -0.01 -1000
TCGA08_retinoblastoma 0.1593 65 523 8 -0.066 0.16 1000 -1000 -0.009 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1520 62 4909 78 -0.26 0.097 1000 -1000 -0.031 -1000
IL4-mediated signaling events 0.1495 61 5552 91 -0.59 0.38 1000 -1000 -0.042 -1000
Reelin signaling pathway 0.1495 61 3430 56 -0.096 0.079 1000 -1000 -0.012 -1000
Thromboxane A2 receptor signaling 0.1446 59 6241 105 -0.22 0.054 1000 -1000 -0.026 -1000
p75(NTR)-mediated signaling 0.1324 54 6780 125 -0.094 0.078 1000 -1000 -0.042 -1000
TCR signaling in naïve CD8+ T cells 0.1275 52 4880 93 -0.1 0.064 1000 -1000 -0.029 -1000
Aurora C signaling 0.1250 51 362 7 0 0.16 1000 -1000 -0.007 -1000
HIF-1-alpha transcription factor network 0.1225 50 3823 76 -0.079 0.35 1000 -1000 -0.01 -1000
Plasma membrane estrogen receptor signaling 0.1225 50 4332 86 -0.25 0.14 1000 -1000 -0.031 -1000
Fc-epsilon receptor I signaling in mast cells 0.1201 49 4795 97 -0.11 0.028 1000 -1000 -0.035 -1000
Ephrin A reverse signaling 0.1176 48 339 7 -0.038 0.015 1000 -1000 -0.003 -1000
LPA receptor mediated events 0.1152 47 4811 102 -0.19 0.091 1000 -1000 -0.057 -1000
Integrins in angiogenesis 0.1103 45 3812 84 -0.18 0.14 1000 -1000 -0.022 -1000
S1P4 pathway 0.1103 45 1128 25 -0.082 0.045 1000 -1000 -0.005 -1000
BMP receptor signaling 0.1078 44 3588 81 -0.18 0.078 1000 -1000 -0.009 -1000
amb2 Integrin signaling 0.1054 43 3556 82 -0.24 0.091 1000 -1000 -0.017 -1000
Rapid glucocorticoid signaling 0.1054 43 873 20 -0.12 0.072 1000 -1000 -0.012 -1000
Calcium signaling in the CD4+ TCR pathway 0.1029 42 1318 31 -0.077 0.025 1000 -1000 -0.024 -1000
Ras signaling in the CD4+ TCR pathway 0.1029 42 718 17 -0.11 0.025 1000 -1000 -0.006 -1000
Glucocorticoid receptor regulatory network 0.1005 41 4686 114 -0.43 0.19 1000 -1000 -0.04 -1000
IL12-mediated signaling events 0.0980 40 3557 87 -0.36 0.072 1000 -1000 -0.032 -1000
FOXA2 and FOXA3 transcription factor networks 0.0980 40 1876 46 -0.095 0.33 1000 -1000 -0.012 -1000
S1P1 pathway 0.0980 40 1453 36 -0.28 0.025 1000 -1000 -0.014 -1000
Osteopontin-mediated events 0.0956 39 1485 38 -0.081 0.15 1000 -1000 -0.018 -1000
Glypican 1 network 0.0956 39 1882 48 -0.12 0.057 1000 -1000 -0.018 -1000
S1P5 pathway 0.0931 38 659 17 -0.081 0.065 1000 -1000 -0.011 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0931 38 4565 120 -0.16 0.14 1000 -1000 -0.03 -1000
PDGFR-alpha signaling pathway 0.0907 37 1659 44 -0.26 0.037 1000 -1000 -0.025 -1000
IL6-mediated signaling events 0.0907 37 2808 75 -0.18 0.078 1000 -1000 -0.018 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0882 36 1891 52 -0.17 0.039 1000 -1000 -0.024 -1000
Aurora A signaling 0.0858 35 2100 60 -0.14 0.23 1000 -1000 -0.017 -1000
JNK signaling in the CD4+ TCR pathway 0.0833 34 590 17 -0.16 0.038 1000 -1000 -0.011 -1000
TCGA08_p53 0.0833 34 244 7 -0.043 0.026 1000 -1000 -0.007 -1000
S1P3 pathway 0.0784 32 1346 42 -0.095 0.037 1000 -1000 -0.02 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0784 32 2870 88 -0.11 0.064 1000 -1000 -0.047 -1000
Coregulation of Androgen receptor activity 0.0760 31 2410 76 -0.14 0.15 1000 -1000 -0.015 -1000
LPA4-mediated signaling events 0.0711 29 356 12 -0.091 0 1000 -1000 -0.015 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0711 29 1005 34 -0.016 0.046 1000 -1000 -0.028 -1000
Syndecan-2-mediated signaling events 0.0711 29 2021 69 -0.022 0.076 1000 -1000 -0.028 -1000
BCR signaling pathway 0.0711 29 2968 99 -0.078 0.033 1000 -1000 -0.042 -1000
Visual signal transduction: Cones 0.0686 28 1089 38 -0.047 0.085 1000 -1000 -0.015 -1000
Arf6 signaling events 0.0686 28 1789 62 -0.12 0.055 1000 -1000 -0.016 -1000
Presenilin action in Notch and Wnt signaling 0.0662 27 1653 61 -0.081 0.15 1000 -1000 -0.022 -1000
ErbB2/ErbB3 signaling events 0.0637 26 1695 65 -0.12 0.037 1000 -1000 -0.042 -1000
IL27-mediated signaling events 0.0637 26 1349 51 -0.12 0.098 1000 -1000 -0.034 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0613 25 1357 54 -0.096 0.079 1000 -1000 -0.025 -1000
Wnt signaling 0.0613 25 177 7 -0.004 0.042 1000 -1000 -0.006 -1000
Visual signal transduction: Rods 0.0588 24 1248 52 -0.047 0.15 1000 -1000 -0.01 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0564 23 2016 85 -0.22 0.036 1000 -1000 -0.036 -1000
FAS signaling pathway (CD95) 0.0564 23 1100 47 -0.49 0.042 1000 -1000 -0.025 -1000
Canonical Wnt signaling pathway 0.0564 23 1200 51 -0.053 0.15 1000 -1000 -0.02 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0539 22 617 28 -0.081 0.066 1000 -1000 -0.016 -1000
Noncanonical Wnt signaling pathway 0.0539 22 588 26 -0.051 0.042 1000 -1000 -0.019 -1000
Ephrin B reverse signaling 0.0515 21 1011 48 -0.043 0.047 1000 -1000 -0.031 -1000
Class IB PI3K non-lipid kinase events 0.0515 21 63 3 -0.006 0.006 1000 -1000 -0.019 -1000
FoxO family signaling 0.0490 20 1300 64 0.001 0.25 1000 -1000 -0.02 -1000
Effects of Botulinum toxin 0.0490 20 545 26 -0.008 0.075 1000 -1000 -0.009 -1000
Syndecan-4-mediated signaling events 0.0490 20 1378 67 -0.083 0.09 1000 -1000 -0.026 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0490 20 685 33 -0.15 0.15 1000 -1000 -0.017 -1000
Regulation of Androgen receptor activity 0.0490 20 1458 70 -0.15 0.031 1000 -1000 -0.023 -1000
Hedgehog signaling events mediated by Gli proteins 0.0466 19 1245 65 -0.085 0.062 1000 -1000 -0.015 -1000
ceramide signaling pathway 0.0466 19 934 49 -0.007 0.051 1000 -1000 -0.014 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0466 19 1467 74 -0.12 0.059 1000 -1000 -0.043 -1000
Caspase cascade in apoptosis 0.0392 16 1208 74 -0.031 0.051 1000 -1000 -0.027 -1000
Nectin adhesion pathway 0.0392 16 1047 63 -0.042 0.053 1000 -1000 -0.026 -1000
Insulin Pathway 0.0392 16 1195 74 -0.13 0.064 1000 -1000 -0.032 -1000
Cellular roles of Anthrax toxin 0.0368 15 606 39 -0.05 0.041 1000 -1000 -0.013 -1000
Ceramide signaling pathway 0.0368 15 1158 76 -0.12 0.067 1000 -1000 -0.019 -1000
IL1-mediated signaling events 0.0368 15 953 62 -0.033 0.067 1000 -1000 -0.035 -1000
IL2 signaling events mediated by PI3K 0.0368 15 927 58 -0.065 0.12 1000 -1000 -0.024 -1000
Regulation of Telomerase 0.0368 15 1570 102 -0.073 0.21 1000 -1000 -0.013 -1000
EGFR-dependent Endothelin signaling events 0.0368 15 322 21 -0.02 0.072 1000 -1000 -0.026 -1000
PDGFR-beta signaling pathway 0.0368 15 1456 97 -0.071 0.066 1000 -1000 -0.037 -1000
Signaling events mediated by PTP1B 0.0343 14 1095 76 -0.1 0.05 1000 -1000 -0.023 -1000
HIF-2-alpha transcription factor network 0.0343 14 609 43 -0.11 0.11 1000 -1000 -0.063 -1000
EPHB forward signaling 0.0343 14 1261 85 -0.038 0.071 1000 -1000 -0.041 -1000
IL2 signaling events mediated by STAT5 0.0343 14 327 22 -0.034 0.1 1000 -1000 -0.01 -1000
ErbB4 signaling events 0.0319 13 955 69 -0.12 0.045 1000 -1000 -0.012 -1000
Regulation of nuclear SMAD2/3 signaling 0.0294 12 1763 136 -0.14 0.094 1000 -1000 -0.043 -1000
BARD1 signaling events 0.0294 12 712 57 -0.049 0.13 1000 -1000 -0.037 -1000
IFN-gamma pathway 0.0294 12 880 68 -0.082 0.08 1000 -1000 -0.031 -1000
Signaling events mediated by HDAC Class III 0.0294 12 495 40 -0.12 0.049 1000 -1000 -0.039 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0294 12 1043 83 -0.19 0.047 1000 -1000 -0.012 -1000
Regulation of p38-alpha and p38-beta 0.0294 12 689 54 -0.065 0.057 1000 -1000 -0.034 -1000
EPO signaling pathway 0.0270 11 653 55 -0.009 0.064 1000 -1000 -0.009 -1000
Class I PI3K signaling events mediated by Akt 0.0270 11 798 68 -0.093 0.052 1000 -1000 -0.015 -1000
E-cadherin signaling in the nascent adherens junction 0.0270 11 878 76 -0.04 0.051 1000 -1000 -0.04 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0245 10 374 37 -0.022 0.055 1000 -1000 -0.014 -1000
Signaling mediated by p38-gamma and p38-delta 0.0245 10 150 15 -0.016 0.025 1000 -1000 -0.016 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0245 10 462 45 -0.024 0.061 1000 -1000 -0.03 -1000
a4b1 and a4b7 Integrin signaling 0.0221 9 49 5 0.016 0.029 1000 -1000 0.018 -1000
mTOR signaling pathway 0.0221 9 518 53 -0.035 0.029 1000 -1000 -0.023 -1000
Arf6 trafficking events 0.0221 9 678 71 -0.2 0.046 1000 -1000 -0.037 -1000
Syndecan-3-mediated signaling events 0.0196 8 290 35 -0.028 0.059 1000 -1000 -0.005 -1000
Signaling events mediated by PRL 0.0196 8 283 34 -0.043 0.039 1000 -1000 -0.027 -1000
E-cadherin signaling events 0.0196 8 42 5 0.014 0.038 1000 -1000 0.015 -1000
PLK2 and PLK4 events 0.0172 7 22 3 -0.01 0.033 1000 -1000 -0.015 -1000
E-cadherin signaling in keratinocytes 0.0172 7 343 43 -0.016 0.038 1000 -1000 -0.013 -1000
Paxillin-dependent events mediated by a4b1 0.0147 6 226 36 -0.04 0.043 1000 -1000 -0.03 -1000
Class I PI3K signaling events 0.0147 6 475 73 -0.032 0.046 1000 -1000 -0.019 -1000
Insulin-mediated glucose transport 0.0123 5 160 32 -0.12 0.047 1000 -1000 -0.017 -1000
TRAIL signaling pathway 0.0123 5 257 48 -0.017 0.057 1000 -1000 -0.017 -1000
Retinoic acid receptors-mediated signaling 0.0123 5 330 58 -0.039 0.054 1000 -1000 -0.022 -1000
TCGA08_rtk_signaling 0.0123 5 155 26 -0.029 0.049 1000 -1000 -0.017 -1000
p38 MAPK signaling pathway 0.0123 5 240 44 -0.005 0.062 1000 -1000 -0.017 -1000
Canonical NF-kappaB pathway 0.0098 4 177 39 -0.013 0.061 1000 -1000 -0.012 -1000
Signaling events mediated by HDAC Class II 0.0098 4 331 75 -0.031 0.059 1000 -1000 -0.024 -1000
Arf6 downstream pathway 0.0098 4 185 43 -0.045 0.046 1000 -1000 -0.031 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0074 3 420 125 -0.046 0.062 1000 -1000 -0.035 -1000
Circadian rhythm pathway 0.0049 2 49 22 -0.006 0.052 1000 -1000 -0.021 -1000
Signaling events mediated by HDAC Class I 0.0049 2 265 104 -0.048 0.062 1000 -1000 -0.042 -1000
Atypical NF-kappaB pathway 0.0049 2 83 31 -0.014 0.034 1000 -1000 -0.015 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0049 2 80 27 -0.018 0.056 1000 -1000 -0.028 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0025 1 35 23 0 0.047 1000 -1000 -0.009 -1000
VEGFR1 specific signals 0.0025 1 107 56 -0.048 0.063 1000 -1000 -0.019 -1000
Arf1 pathway 0.0000 0 47 54 -0.008 0.046 1000 -1000 -0.01 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.068 1000 -1000 0 -1000
Total NA 3901 228624 7203 -13 12 131000 -131000 -2.8 -131000
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.7 0.6 1.1 225 -0.95 5 230
PLK1 0.41 0.35 0.77 177 -0.74 1 178
BIRC5 0.52 0.35 0.77 239 -1.3 1 240
HSPA1B 0.7 0.6 1.1 224 -1 4 228
MAP2K1 0.23 0.18 0.37 228 -10000 0 228
BRCA2 0.72 0.62 1.2 219 -1 4 223
FOXM1 0.91 0.83 1.5 234 -1.2 5 239
XRCC1 0.7 0.6 1.2 222 -1 4 226
FOXM1B/p19 0.14 0.43 0.96 63 -0.81 15 78
Cyclin D1/CDK4 0.56 0.52 0.98 206 -0.85 6 212
CDC2 0.8 0.69 1.3 233 -1 5 238
TGFA 0.59 0.53 1 222 -0.89 4 226
SKP2 0.75 0.65 1.2 224 -1 4 228
CCNE1 0.088 0.11 0.37 43 -10000 0 43
CKS1B 0.69 0.59 1.1 233 -0.87 7 240
RB1 0.33 0.4 0.77 161 -0.64 3 164
FOXM1C/SP1 0.58 0.55 1 211 -0.91 10 221
AURKB 0.4 0.43 0.73 206 -0.91 14 220
CENPF 0.83 0.69 1.3 242 -1 4 246
CDK4 0.099 0.075 0.18 122 -10000 0 122
MYC 0.48 0.54 0.97 196 -0.9 5 201
CHEK2 0.22 0.18 0.37 219 -10000 0 219
ONECUT1 0.61 0.56 1 216 -0.92 5 221
CDKN2A 0.03 0.15 0.26 94 -0.2 69 163
LAMA4 0.68 0.61 1.1 218 -1.2 7 225
FOXM1B/HNF6 0.61 0.57 1.1 208 -1.1 5 213
FOS 0.4 0.71 1.2 147 -1.1 22 169
SP1 0.023 0.027 -10000 0 -0.16 5 5
CDC25B 0.72 0.62 1.2 224 -1 4 228
response to radiation 0.15 0.12 0.25 218 -10000 0 218
CENPB 0.71 0.61 1.2 220 -1.1 3 223
CENPA 0.84 0.69 1.3 245 -1.1 3 248
NEK2 0.83 0.69 1.3 245 -1.1 3 248
HIST1H2BA 0.71 0.62 1.2 219 -1.1 3 222
CCNA2 0.13 0.15 0.38 102 -10000 0 102
EP300 0.025 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.77 0.68 1.3 218 -1.1 5 223
CCNB2 0.83 0.69 1.3 244 -1 4 248
CCNB1 0.84 0.74 1.4 229 -1.1 4 233
ETV5 0.71 0.62 1.2 223 -1 5 228
ESR1 0.54 0.7 1.2 191 -1.1 23 214
CCND1 0.62 0.57 1.1 224 -0.86 6 230
GSK3A 0.17 0.13 0.29 197 -10000 0 197
Cyclin A-E1/CDK1-2 0.23 0.19 0.4 194 -10000 0 194
CDK2 0.063 0.046 0.15 3 -10000 0 3
G2/M transition of mitotic cell cycle 0.21 0.16 0.32 243 -10000 0 243
FOXM1B/Cbp/p300 0.12 0.36 0.77 35 -0.87 10 45
GAS1 0.52 0.78 1.2 204 -1.1 45 249
MMP2 0.62 0.66 1.1 215 -1 11 226
RB1/FOXM1C 0.48 0.53 0.97 184 -0.92 6 190
CREBBP 0.025 0.007 -10000 0 -10000 0 0
Aurora B signaling

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
Condensin I complex 0.14 0.14 0.27 188 -0.18 5 193
STMN1 0.098 0.12 0.22 186 -10000 0 186
Aurora B/RasGAP/Survivin 0.23 0.16 0.34 259 -0.19 1 260
Chromosomal passenger complex/Cul3 protein complex 0.075 0.13 0.23 119 -0.26 15 134
BIRC5 0.24 0.14 0.33 279 -0.33 1 280
DES -0.14 0.28 -10000 0 -0.55 97 97
Aurora C/Aurora B/INCENP 0.12 0.095 0.23 172 -10000 0 172
Aurora B/TACC1 0.089 0.091 0.21 142 -0.14 2 144
Aurora B/PP2A 0.12 0.1 0.24 169 -10000 0 169
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.037 0.039 0.18 6 -10000 0 6
mitotic metaphase/anaphase transition -0.004 0.006 -10000 0 -10000 0 0
NDC80 0.15 0.18 0.3 201 -10000 0 201
Cul3 protein complex -0.007 0.093 -10000 0 -0.19 83 83
KIF2C 0.19 0.13 0.28 243 -10000 0 243
PEBP1 0.03 0.006 -10000 0 -10000 0 0
KIF20A 0.24 0.14 0.32 287 -10000 0 287
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.12 0.1 0.24 167 -10000 0 167
SEPT1 0.027 0.031 0.33 3 -0.32 1 4
SMC2 0.024 0.017 0.33 1 -10000 0 1
SMC4 0.025 0.006 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.099 0.21 0.29 133 -0.48 30 163
PSMA3 0.026 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.007 0.008 -10000 0 -10000 0 0
H3F3B 0.076 0.076 0.16 176 -10000 0 176
AURKB 0.16 0.15 0.33 176 -10000 0 176
AURKC 0.035 0.053 0.33 13 -10000 0 13
CDCA8 0.11 0.13 0.34 101 -10000 0 101
cytokinesis 0.17 0.18 0.35 179 -10000 0 179
Aurora B/Septin1 0.22 0.19 0.39 190 -0.23 6 196
AURKA 0.093 0.14 0.32 109 -10000 0 109
INCENP 0.038 0.018 0.34 1 -10000 0 1
KLHL13 -0.047 0.14 -10000 0 -0.32 85 85
BUB1 0.068 0.12 0.32 74 -10000 0 74
hSgo1/Aurora B/Survivin 0.29 0.21 0.4 277 -0.17 1 278
EVI5 0.032 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.24 0.18 0.38 223 -10000 0 223
SGOL1 0.14 0.15 0.33 151 -10000 0 151
CENPA 0.22 0.17 0.33 257 -0.16 7 264
NCAPG 0.16 0.15 0.33 176 -10000 0 176
Aurora B/HC8 Proteasome 0.12 0.1 0.24 173 -10000 0 173
NCAPD2 0.025 0.005 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.12 0.1 0.24 174 -10000 0 174
RHOA 0.025 0.006 -10000 0 -10000 0 0
NCAPH 0.2 0.15 0.33 240 -10000 0 240
NPM1 0.072 0.15 0.22 128 -0.36 21 149
RASA1 0.025 0.005 -10000 0 -10000 0 0
KLHL9 0.021 0.011 -10000 0 -10000 0 0
mitotic prometaphase 0.004 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.12 0.1 0.24 173 -10000 0 173
PPP1CC 0.026 0.004 -10000 0 -10000 0 0
Centraspindlin 0.27 0.19 0.41 236 -10000 0 236
RhoA/GDP 0.019 0.004 -10000 0 -10000 0 0
NSUN2 0.084 0.14 0.24 130 -0.31 15 145
MYLK 0.007 0.13 0.16 115 -0.22 58 173
KIF23 0.18 0.15 0.34 196 -10000 0 196
VIM 0.085 0.11 0.2 175 -0.23 2 177
RACGAP1 0.041 0.033 0.35 4 -10000 0 4
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.07 0.16 0.23 74 -0.43 19 93
Chromosomal passenger complex 0.21 0.16 0.31 261 -0.16 1 262
Chromosomal passenger complex/EVI5 0.28 0.19 0.43 232 -0.17 1 233
TACC1 0.021 0.026 -10000 0 -0.32 2 2
PPP2R5D 0.026 0.004 -10000 0 -10000 0 0
CUL3 0.024 0.007 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Glypican 2 network

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
MDK 0.04 0.067 0.33 21 -9999 0 21
GPC2 0.12 0.14 0.33 132 -9999 0 132
GPC2/Midkine 0.11 0.11 0.26 131 -9999 0 131
neuron projection morphogenesis 0.1 0.11 0.26 131 -9999 0 131
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.042 0.078 0.41 14 -0.13 2 16
NFATC2 -0.079 0.24 0.45 5 -0.5 62 67
NFATC3 -0.089 0.15 -10000 0 -0.27 134 134
CD40LG -0.37 0.5 0.52 6 -0.86 180 186
ITCH -0.003 0.068 0.42 1 -0.19 41 42
CBLB -0.002 0.067 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.23 0.45 0.62 18 -0.92 83 101
JUNB 0.022 0.038 -10000 0 -0.32 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.084 0.27 4 -0.23 42 46
T cell anergy -0.033 0.11 0.28 2 -0.32 41 43
TLE4 -0.056 0.18 -10000 0 -0.44 42 42
Jun/NFAT1-c-4/p21SNFT -0.33 0.52 0.58 7 -0.84 181 188
AP-1/NFAT1-c-4 -0.4 0.58 0.69 10 -0.97 178 188
IKZF1 -0.061 0.18 0.44 4 -0.42 47 51
T-helper 2 cell differentiation -0.19 0.33 -10000 0 -0.8 66 66
AP-1/NFAT1 -0.083 0.21 0.4 10 -0.36 96 106
CALM1 0.014 0.057 -10000 0 -0.15 16 16
EGR2 -0.42 0.61 -10000 0 -1.3 113 113
EGR3 -0.58 0.69 0.5 2 -1.2 200 202
NFAT1/FOXP3 -0.034 0.21 0.5 20 -0.38 55 75
EGR1 -0.05 0.15 -10000 0 -0.32 91 91
JUN 0.013 0.071 -10000 0 -0.32 14 14
EGR4 0.023 0.069 0.33 7 -0.32 10 17
mol:Ca2+ -0.007 0.044 0.14 2 -0.13 42 44
GBP3 -0.062 0.17 0.37 1 -0.38 54 55
FOSL1 0.002 0.086 -10000 0 -0.32 27 27
NFAT1-c-4/MAF/IRF4 -0.32 0.5 0.54 2 -0.82 181 183
DGKA -0.059 0.16 -10000 0 -0.39 36 36
CREM 0.025 0.006 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.35 0.48 0.53 1 -0.83 178 179
CTLA4 -0.04 0.19 0.48 17 -0.38 41 58
NFAT1-c-4 (dimer)/EGR1 -0.36 0.54 0.58 4 -0.89 187 191
NFAT1-c-4 (dimer)/EGR4 -0.33 0.51 0.57 5 -0.84 181 186
FOS -0.069 0.15 -10000 0 -0.32 107 107
IFNG -0.087 0.32 0.46 27 -0.66 59 86
T cell activation -0.18 0.28 -10000 0 -0.61 60 60
MAF 0.017 0.054 -10000 0 -0.32 10 10
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.31 0.43 0.73 178 -10000 0 178
TNF -0.33 0.47 0.52 14 -0.8 184 198
FASLG -0.58 0.75 -10000 0 -1.3 203 203
TBX21 0.037 0.1 0.18 53 -0.32 21 74
BATF3 0.025 0.049 0.33 4 -0.32 5 9
PRKCQ -0.002 0.098 0.33 3 -0.31 32 35
PTPN1 -0.06 0.16 -10000 0 -0.39 38 38
NFAT1-c-4/ICER1 -0.34 0.5 0.53 1 -0.84 181 182
GATA3 0.003 0.081 -10000 0 -0.32 24 24
T-helper 1 cell differentiation -0.084 0.32 0.46 27 -0.64 59 86
IL2RA -0.23 0.44 0.62 17 -0.83 96 113
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.057 0.16 -10000 0 -0.44 22 22
E2F1 0.08 0.12 0.33 73 -10000 0 73
PPARG 0.001 0.083 -10000 0 -0.32 25 25
SLC3A2 -0.06 0.16 -10000 0 -0.39 36 36
IRF4 0.007 0.085 0.33 3 -0.32 23 26
PTGS2 -0.38 0.51 0.53 5 -0.88 180 185
CSF2 -0.33 0.52 0.59 23 -0.84 174 197
JunB/Fra1/NFAT1-c-4 -0.33 0.49 0.52 1 -0.82 183 184
IL4 -0.2 0.34 -10000 0 -0.86 64 64
IL5 -0.36 0.48 0.57 6 -0.84 179 185
IL2 -0.18 0.29 -10000 0 -0.63 58 58
IL3 -0.069 0.13 -10000 0 -0.81 9 9
RNF128 -0.024 0.14 0.35 4 -0.43 42 46
NFATC1 -0.31 0.44 -10000 0 -0.74 178 178
CDK4 0.21 0.29 0.56 124 -10000 0 124
PTPRK -0.058 0.16 -10000 0 -0.41 32 32
IL8 -0.37 0.5 0.52 7 -0.86 179 186
POU2F1 0.023 0.009 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.19 0.4 0.34 1 -0.89 98 99
MKNK1 0.026 0.004 -10000 0 -10000 0 0
MAPK14 -0.037 0.15 -10000 0 -0.29 97 97
ATF2/c-Jun -0.055 0.15 -10000 0 -0.29 99 99
MAPK11 -0.035 0.15 -10000 0 -0.3 91 91
MITF -0.073 0.19 -10000 0 -0.36 107 107
MAPKAPK5 -0.053 0.17 0.34 1 -0.34 93 94
KRT8 -0.061 0.18 -10000 0 -0.36 96 96
MAPKAPK3 0.025 0.006 -10000 0 -10000 0 0
MAPKAPK2 0.026 0.004 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.057 0.22 -10000 0 -0.41 102 102
CEBPB -0.05 0.16 -10000 0 -0.34 86 86
SLC9A1 -0.056 0.17 -10000 0 -0.34 96 96
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.056 0.17 0.3 1 -0.35 94 95
p38alpha-beta/MNK1 -0.032 0.18 -10000 0 -0.33 102 102
JUN -0.057 0.15 -10000 0 -0.28 99 99
PPARGC1A -0.16 0.22 -10000 0 -0.34 200 200
USF1 -0.038 0.15 0.34 1 -0.34 73 74
RAB5/GDP/GDI1 -0.033 0.12 -10000 0 -0.25 86 86
NOS2 -0.044 0.22 0.39 26 -0.59 20 46
DDIT3 -0.056 0.17 -10000 0 -0.34 95 95
RAB5A 0.025 0.006 -10000 0 -10000 0 0
HSPB1 -0.05 0.13 0.26 4 -0.28 90 94
p38alpha-beta/HBP1 -0.029 0.18 -10000 0 -0.33 98 98
CREB1 -0.067 0.18 -10000 0 -0.38 97 97
RAB5/GDP 0.018 0.005 -10000 0 -10000 0 0
EIF4E -0.073 0.14 0.2 6 -0.31 88 94
RPS6KA4 -0.058 0.17 -10000 0 -0.34 97 97
PLA2G4A -0.082 0.15 0.23 2 -0.33 93 95
GDI1 -0.055 0.17 -10000 0 -0.34 95 95
TP53 -0.085 0.2 -10000 0 -0.41 101 101
RPS6KA5 -0.062 0.18 -10000 0 -0.35 98 98
ESR1 -0.1 0.21 -10000 0 -0.36 136 136
HBP1 0.026 0.003 -10000 0 -10000 0 0
MEF2C -0.064 0.17 -10000 0 -0.35 100 100
MEF2A -0.058 0.17 -10000 0 -0.34 97 97
EIF4EBP1 -0.066 0.18 0.25 1 -0.37 95 96
KRT19 -0.066 0.18 -10000 0 -0.36 99 99
ELK4 -0.055 0.17 0.34 1 -0.34 95 96
ATF6 -0.04 0.15 0.34 1 -0.34 75 76
ATF1 -0.064 0.18 -10000 0 -0.37 96 96
p38alpha-beta/MAPKAPK2 -0.031 0.18 -10000 0 -0.33 102 102
p38alpha-beta/MAPKAPK3 -0.031 0.18 -10000 0 -0.34 95 95
Endothelins

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
AKT1 -0.094 0.12 0.3 2 -0.34 52 54
PTK2B 0.022 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.13 0.23 -10000 0 -0.64 51 51
EDN1 -0.045 0.082 0.26 4 -0.23 22 26
EDN3 0.002 0.044 0.33 6 -10000 0 6
EDN2 0.025 0.11 0.33 27 -0.32 22 49
HRAS/GDP -0.17 0.21 -10000 0 -0.42 129 129
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.094 0.15 -10000 0 -0.35 82 82
ADCY4 -0.12 0.15 0.28 7 -0.3 111 118
ADCY5 -0.19 0.18 0.21 2 -0.34 186 188
ADCY6 -0.12 0.15 0.28 7 -0.3 109 116
ADCY7 -0.12 0.15 0.28 7 -0.3 111 118
ADCY1 -0.12 0.15 0.3 7 -0.3 110 117
ADCY2 -0.15 0.17 0.22 3 -0.32 157 160
ADCY3 -0.12 0.15 0.28 7 -0.3 109 116
ADCY8 -0.11 0.15 0.28 5 -0.31 95 100
ADCY9 -0.12 0.16 0.28 7 -0.3 116 123
arachidonic acid secretion -0.21 0.26 0.39 1 -0.46 174 175
ETB receptor/Endothelin-1/Gq/GTP -0.061 0.13 -10000 0 -0.3 75 75
GNAO1 -0.081 0.16 -10000 0 -0.32 124 124
HRAS 0.023 0.007 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.071 0.13 0.38 2 -0.32 48 50
ETA receptor/Endothelin-1/Gs/GTP -0.13 0.15 0.36 2 -0.31 117 119
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
COL3A1 -0.096 0.15 0.43 3 -0.39 48 51
EDNRB -0.019 0.11 -10000 0 -0.32 44 44
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.085 0.14 0.3 10 -0.36 46 56
CYSLTR1 -0.1 0.15 0.33 3 -0.41 50 53
SLC9A1 -0.057 0.078 0.22 2 -0.22 47 49
mol:GDP -0.18 0.23 -10000 0 -0.45 129 129
SLC9A3 -0.1 0.22 -10000 0 -0.59 54 54
RAF1 -0.19 0.26 0.33 4 -0.44 168 172
JUN -0.16 0.28 -10000 0 -0.77 54 54
JAK2 -0.085 0.13 0.3 2 -0.35 47 49
mol:IP3 -0.12 0.18 -10000 0 -0.4 96 96
ETA receptor/Endothelin-1 -0.099 0.16 0.45 2 -0.37 62 64
PLCB1 0.006 0.058 -10000 0 -0.32 11 11
PLCB2 0.009 0.033 -10000 0 -0.32 2 2
ETA receptor/Endothelin-3 -0.05 0.11 0.24 1 -0.26 57 58
FOS -0.32 0.41 -10000 0 -0.83 144 144
Gai/GDP -0.29 0.4 -10000 0 -0.8 145 145
CRK 0.024 0.008 -10000 0 -10000 0 0
mol:Ca ++ -0.15 0.19 0.29 2 -0.41 110 112
BCAR1 0.025 0.006 -10000 0 -10000 0 0
PRKCB1 -0.12 0.18 -10000 0 -0.37 111 111
GNAQ 0.01 0.023 -10000 0 -10000 0 0
GNAZ -0.049 0.14 -10000 0 -0.32 87 87
GNAL -0.12 0.17 -10000 0 -0.32 163 163
Gs family/GDP -0.21 0.23 -10000 0 -0.45 155 155
ETA receptor/Endothelin-1/Gq/GTP -0.084 0.14 0.22 2 -0.33 74 76
MAPK14 -0.067 0.13 0.19 2 -0.34 59 61
TRPC6 -0.14 0.24 -10000 0 -0.67 51 51
GNAI2 0.025 0.006 -10000 0 -10000 0 0
GNAI3 0.026 0.003 -10000 0 -10000 0 0
GNAI1 0.023 0.03 -10000 0 -0.32 3 3
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.061 0.13 -10000 0 -0.33 63 63
ETB receptor/Endothelin-2 0.006 0.11 0.24 22 -0.23 56 78
ETB receptor/Endothelin-3 0.002 0.087 0.24 6 -0.23 43 49
ETB receptor/Endothelin-1 -0.047 0.1 0.33 2 -0.25 61 63
MAPK3 -0.3 0.38 0.36 1 -0.74 153 154
MAPK1 -0.3 0.38 0.36 1 -0.74 153 154
Rac1/GDP -0.16 0.21 -10000 0 -0.42 126 126
cAMP biosynthetic process -0.18 0.19 0.25 5 -0.37 160 165
MAPK8 -0.16 0.29 -10000 0 -0.68 74 74
SRC 0.024 0.007 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.12 0.16 -10000 0 -0.31 135 135
p130Cas/CRK/Src/PYK2 -0.16 0.23 0.36 1 -0.48 103 104
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.16 0.21 -10000 0 -0.43 123 123
COL1A2 -0.13 0.21 0.53 2 -0.5 68 70
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.052 0.13 0.24 5 -0.26 80 85
mol:DAG -0.12 0.18 -10000 0 -0.4 96 96
MAP2K2 -0.24 0.3 0.34 4 -0.56 168 172
MAP2K1 -0.24 0.3 0.33 3 -0.56 167 170
EDNRA -0.087 0.14 0.24 2 -0.36 63 65
positive regulation of muscle contraction -0.083 0.11 0.21 7 -0.31 46 53
Gq family/GDP -0.15 0.21 -10000 0 -0.42 118 118
HRAS/GTP -0.18 0.22 -10000 0 -0.44 132 132
PRKCH -0.12 0.17 -10000 0 -0.38 103 103
RAC1 0.025 0.006 -10000 0 -10000 0 0
PRKCA -0.12 0.18 -10000 0 -0.38 106 106
PRKCB -0.16 0.2 -10000 0 -0.39 140 140
PRKCE -0.12 0.18 -10000 0 -0.38 106 106
PRKCD -0.12 0.18 -10000 0 -0.38 102 102
PRKCG -0.12 0.18 -10000 0 -0.38 106 106
regulation of vascular smooth muscle contraction -0.38 0.48 -10000 0 -0.99 144 144
PRKCQ -0.12 0.19 0.25 2 -0.38 111 113
PLA2G4A -0.23 0.29 0.39 1 -0.5 174 175
GNA14 -0.028 0.11 -10000 0 -0.32 45 45
GNA15 0.014 0.035 -10000 0 -0.32 3 3
GNA12 0.025 0.006 -10000 0 -10000 0 0
GNA11 0.016 0.025 -10000 0 -0.32 1 1
Rac1/GTP -0.071 0.13 0.38 2 -0.32 49 51
MMP1 0.2 0.2 0.37 215 -0.59 1 216
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.021 0.075 -10000 0 -0.38 14 14
Crk/p130 Cas/Paxillin -0.11 0.11 -10000 0 -0.23 156 156
JUN -0.085 0.1 0.17 2 -0.28 25 27
HRAS 0.024 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.055 0.12 0.24 5 -0.18 176 181
RAP1A 0.026 0.003 -10000 0 -10000 0 0
FRS2 0.024 0.008 -10000 0 -10000 0 0
RAP1A/GDP 0.019 0.002 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.053 0.12 0.23 6 -0.18 177 183
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.024 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.06 0.1 -10000 0 -0.17 183 183
RHOA 0.025 0.006 -10000 0 -10000 0 0
RAP1A/GTP -0.05 0.11 -10000 0 -0.17 176 176
GRB7 0.02 0.05 0.33 2 -0.32 7 9
RET51/GFRalpha1/GDNF -0.057 0.12 0.24 5 -0.18 183 188
MAPKKK cascade -0.076 0.11 -10000 0 -0.2 162 162
BCAR1 0.025 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.063 0.1 -10000 0 -0.17 187 187
lamellipodium assembly -0.099 0.11 -10000 0 -0.22 152 152
RET51/GFRalpha1/GDNF/SHC -0.052 0.12 0.24 5 -0.18 173 178
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.055 0.1 -10000 0 -0.17 169 169
RET9/GFRalpha1/GDNF/Shank3 -0.06 0.1 -10000 0 -0.17 183 183
MAPK3 -0.068 0.094 0.26 3 -0.29 4 7
DOK1 0.026 0.016 0.33 1 -10000 0 1
DOK6 -0.089 0.16 -10000 0 -0.32 132 132
PXN 0.026 0.004 -10000 0 -10000 0 0
neurite development -0.083 0.099 0.27 2 -0.22 69 71
DOK5 -0.004 0.097 0.33 2 -0.32 33 35
GFRA1 -0.16 0.17 -10000 0 -0.32 216 216
MAPK8 -0.081 0.097 0.18 1 -0.29 14 15
HRAS/GTP -0.071 0.12 -10000 0 -0.21 165 165
tube development -0.055 0.1 0.2 7 -0.16 179 186
MAPK1 -0.067 0.096 0.26 3 -0.29 5 8
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.072 0.097 0.14 2 -0.18 168 170
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
SRC 0.025 0.007 -10000 0 -10000 0 0
PDLIM7 0.025 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.096 0.15 0.24 4 -0.22 199 203
SHC1 0.024 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.056 0.12 0.24 5 -0.18 182 187
RET51/GFRalpha1/GDNF/Dok5 -0.064 0.13 0.24 7 -0.19 186 193
PRKCA 0.022 0.035 -10000 0 -0.32 4 4
HRAS/GDP 0.018 0.006 -10000 0 -10000 0 0
CREB1 -0.088 0.12 -10000 0 -0.24 102 102
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.071 0.098 -10000 0 -0.19 160 160
RET51/GFRalpha1/GDNF/Grb7 -0.055 0.12 0.24 5 -0.18 176 181
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.021 0.069 0.33 7 -0.32 11 18
DOK4 0.026 0.004 -10000 0 -10000 0 0
JNK cascade -0.084 0.098 -10000 0 -0.28 25 25
RET9/GFRalpha1/GDNF/FRS2 -0.059 0.1 -10000 0 -0.17 174 174
SHANK3 0.025 0.006 -10000 0 -10000 0 0
RASA1 0.025 0.005 -10000 0 -10000 0 0
NCK1 0.025 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.067 0.096 -10000 0 -0.18 160 160
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.073 0.11 0.23 2 -0.19 170 172
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.074 0.11 0.2 1 -0.19 167 168
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.072 0.11 0.2 1 -0.36 11 12
PI3K -0.14 0.16 -10000 0 -0.3 159 159
SOS1 0.026 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.052 0.1 -10000 0 -0.16 179 179
GRB10 0.021 0.039 -10000 0 -0.32 5 5
activation of MAPKK activity -0.062 0.1 0.2 2 -0.18 168 170
RET51/GFRalpha1/GDNF/FRS2 -0.055 0.12 0.26 5 -0.18 174 179
GAB1 0.025 0.006 -10000 0 -10000 0 0
IRS1 0.018 0.045 -10000 0 -0.32 7 7
IRS2 0.013 0.063 -10000 0 -0.32 14 14
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.073 0.11 0.2 1 -0.34 15 16
RET51/GFRalpha1/GDNF/PKC alpha -0.056 0.12 0.24 5 -0.18 177 182
GRB2 0.025 0.005 -10000 0 -10000 0 0
PRKACA 0.026 0.003 -10000 0 -10000 0 0
GDNF 0.004 0.026 0.33 1 -10000 0 1
RAC1 0.025 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.059 0.12 0.24 5 -0.18 185 190
Rac1/GTP -0.11 0.13 -10000 0 -0.26 151 151
RET9/GFRalpha1/GDNF -0.072 0.1 -10000 0 -0.19 183 183
GFRalpha1/GDNF -0.089 0.12 -10000 0 -0.22 184 184
IGF1 pathway

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
NCK2 0.026 0.004 -10000 0 -10000 0 0
PTK2 0.023 0.008 -10000 0 -10000 0 0
CRKL -0.081 0.084 0.16 2 -0.18 168 170
GRB2/SOS1/SHC 0.046 0.018 -10000 0 -10000 0 0
HRAS 0.024 0.008 -10000 0 -10000 0 0
IRS1/Crk -0.065 0.097 -10000 0 -0.17 175 175
IGF-1R heterotetramer/IGF1/PTP1B -0.05 0.12 -10000 0 -0.19 162 162
AKT1 -0.071 0.086 0.18 12 -0.17 126 138
BAD -0.072 0.082 0.16 12 -0.26 6 18
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.074 0.082 -10000 0 -0.18 150 150
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.06 0.1 0.2 4 -0.18 174 178
RAF1 -0.053 0.091 0.28 1 -0.5 4 5
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.043 0.11 -10000 0 -0.17 170 170
YWHAZ 0.02 0.011 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.065 0.11 -10000 0 -0.19 178 178
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
RPS6KB1 -0.069 0.085 0.18 11 -0.27 6 17
GNB2L1 0.025 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.041 0.088 0.26 1 -0.38 4 5
PXN 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.037 0.01 -10000 0 -10000 0 0
HRAS/GTP -0.048 0.092 -10000 0 -0.16 148 148
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.021 0.11 -10000 0 -0.16 147 147
IGF-1R heterotetramer -0.014 0.052 -10000 0 -0.36 2 2
IGF-1R heterotetramer/IGF1/IRS/Nck -0.052 0.11 -10000 0 -0.18 174 174
Crk/p130 Cas/Paxillin -0.042 0.11 -10000 0 -0.17 158 158
IGF1R -0.014 0.053 -10000 0 -0.36 2 2
IGF1 -0.13 0.18 -10000 0 -0.34 174 174
IRS2/Crk -0.065 0.1 -10000 0 -0.18 158 158
PI3K -0.04 0.11 -10000 0 -0.17 163 163
apoptosis 0.052 0.072 0.23 5 -0.21 2 7
HRAS/GDP 0.018 0.006 -10000 0 -10000 0 0
PRKCD -0.11 0.14 0.19 2 -0.28 156 158
RAF1/14-3-3 E -0.035 0.092 0.28 1 -0.41 5 6
BAD/14-3-3 -0.055 0.076 0.22 2 -0.24 5 7
PRKCZ -0.072 0.087 0.17 13 -0.28 8 21
Crk/p130 Cas/Paxillin/FAK1 -0.068 0.072 -10000 0 -0.25 4 4
PTPN1 0.024 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.12 0.16 -10000 0 -0.29 174 174
BCAR1 0.025 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.031 0.11 -10000 0 -0.17 150 150
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.026 0.004 -10000 0 -10000 0 0
IRS1/NCK2 -0.061 0.1 -10000 0 -0.18 174 174
GRB10 0.021 0.039 -10000 0 -0.32 5 5
PTPN11 -0.084 0.083 -10000 0 -0.18 174 174
IRS1 -0.066 0.1 -10000 0 -0.19 154 154
IRS2 -0.085 0.091 -10000 0 -0.19 167 167
IGF-1R heterotetramer/IGF1 -0.086 0.14 -10000 0 -0.24 177 177
GRB2 0.025 0.005 -10000 0 -10000 0 0
PDPK1 -0.07 0.085 0.18 9 -0.17 128 137
YWHAE 0.024 0.008 -10000 0 -10000 0 0
PRKD1 -0.12 0.16 0.19 1 -0.3 169 170
SHC1 0.024 0.007 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 0.004 0.2 0.34 42 -0.48 47 89
IHH 0.06 0.098 0.28 43 -0.13 28 71
SHH Np/Cholesterol/GAS1 -0.076 0.1 -10000 0 -0.18 184 184
LRPAP1 0.025 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.075 0.1 0.18 184 -10000 0 184
SMO/beta Arrestin2 -0.019 0.15 0.29 1 -0.36 41 42
SMO -0.026 0.15 0.31 1 -0.37 41 42
AKT1 -0.011 0.14 -10000 0 -0.49 19 19
ARRB2 0.024 0.008 -10000 0 -10000 0 0
BOC -0.004 0.098 0.33 1 -0.32 35 36
ADRBK1 0.026 0.004 -10000 0 -10000 0 0
heart looping -0.026 0.15 0.28 2 -0.37 41 43
STIL -0.039 0.12 0.26 8 -0.28 31 39
DHH N/PTCH2 0.014 0.077 -10000 0 -0.23 36 36
DHH N/PTCH1 0.013 0.13 0.31 1 -0.26 49 50
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
DHH 0.006 0.073 -10000 0 -0.32 19 19
PTHLH -0.03 0.29 0.4 40 -0.74 47 87
determination of left/right symmetry -0.026 0.15 0.28 2 -0.37 41 43
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
skeletal system development -0.029 0.29 0.4 40 -0.73 47 87
IHH N/Hhip -0.018 0.14 0.21 23 -0.24 99 122
DHH N/Hhip -0.037 0.12 0.23 1 -0.23 109 110
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.026 0.15 0.28 2 -0.37 41 43
pancreas development -0.063 0.15 0.33 1 -0.32 97 98
HHAT 0.026 0.004 -10000 0 -10000 0 0
PI3K 0.034 0.018 -10000 0 -0.22 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.031 0.13 0.33 2 -0.32 66 68
somite specification -0.026 0.15 0.28 2 -0.37 41 43
SHH Np/Cholesterol/PTCH1 -0.047 0.12 0.27 1 -0.26 56 57
SHH Np/Cholesterol/PTCH2 -0.054 0.098 -10000 0 -0.18 151 151
SHH Np/Cholesterol/Megalin -0.022 0.11 0.2 44 -0.17 106 150
SHH -0.088 0.099 -10000 0 -0.22 140 140
catabolic process 0.015 0.13 0.27 40 -0.28 48 88
SMO/Vitamin D3 -0.05 0.15 0.33 1 -0.33 50 51
SHH Np/Cholesterol/Hhip -0.089 0.11 -10000 0 -0.2 196 196
LRP2 0.079 0.12 0.33 78 -10000 0 78
receptor-mediated endocytosis -0.05 0.14 0.26 5 -0.34 40 45
SHH Np/Cholesterol/BOC -0.056 0.099 0.2 1 -0.18 155 156
SHH Np/Cholesterol/CDO -0.068 0.1 -10000 0 -0.18 176 176
mesenchymal cell differentiation 0.089 0.11 0.2 196 -10000 0 196
mol:Vitamin D3 -0.039 0.13 0.33 1 -0.28 45 46
IHH N/PTCH2 0.038 0.089 0.21 29 -0.23 23 52
CDON -0.016 0.11 -10000 0 -0.32 48 48
IHH N/PTCH1 0.032 0.15 0.3 39 -0.28 49 88
Megalin/LRPAP1 0.073 0.081 0.24 76 -10000 0 76
PTCH2 0.01 0.073 -10000 0 -0.32 19 19
SHH Np/Cholesterol -0.056 0.081 -10000 0 -0.17 141 141
PTCH1 0.015 0.13 0.27 40 -0.28 48 88
HHIP -0.063 0.15 0.33 1 -0.32 97 98
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.056 0.68 0.92 44 -1.2 70 114
IL23A -0.001 0.63 1 40 -1.1 53 93
NF kappa B1 p50/RelA/I kappa B alpha -0.1 0.54 0.68 13 -1.1 67 80
positive regulation of T cell mediated cytotoxicity -0.007 0.72 1.1 52 -1.2 60 112
ITGA3 -0.012 0.6 0.88 45 -1.1 57 102
IL17F 0.002 0.43 0.67 52 -0.71 56 108
IL12B 0.069 0.14 0.35 57 -10000 0 57
STAT1 (dimer) -0.05 0.64 0.82 45 -1.2 63 108
CD4 -0.01 0.62 0.94 43 -1.1 56 99
IL23 -0.019 0.58 0.88 36 -1.1 51 87
IL23R 0.1 0.24 0.68 36 -0.78 1 37
IL1B -0.017 0.66 0.99 45 -1.2 58 103
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.009 0.64 1 50 -1.1 55 105
TYK2 0.041 0.085 0.23 34 -10000 0 34
STAT4 0.008 0.075 -10000 0 -0.32 20 20
STAT3 0.026 0.005 -10000 0 -10000 0 0
IL18RAP 0.012 0.077 -10000 0 -0.32 20 20
IL12RB1 0.05 0.14 0.31 51 -0.35 10 61
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.058 0.13 0.29 58 -0.26 9 67
IL23R/JAK2 0.11 0.25 0.62 44 -0.68 1 45
positive regulation of chronic inflammatory response -0.007 0.72 1.1 52 -1.2 60 112
natural killer cell activation -0.009 0.023 -10000 0 -0.061 39 39
JAK2 0.058 0.12 0.31 46 -10000 0 46
PIK3R1 0.024 0.019 -10000 0 -0.32 1 1
NFKB1 0.023 0.023 -10000 0 -10000 0 0
RELA 0.022 0.023 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.01 0.56 0.86 39 -1 51 90
ALOX12B -0.001 0.62 0.95 47 -1.1 55 102
CXCL1 -0.035 0.69 0.99 50 -1.2 71 121
T cell proliferation -0.007 0.72 1.1 52 -1.2 60 112
NFKBIA 0.023 0.023 -10000 0 -10000 0 0
IL17A 0.042 0.38 0.63 57 -0.54 54 111
PI3K -0.087 0.57 0.74 20 -1.1 61 81
IFNG 0.05 0.1 0.22 87 -0.12 5 92
STAT3 (dimer) -0.088 0.54 0.7 17 -1.1 60 77
IL18R1 0.027 0.03 -10000 0 -0.32 2 2
IL23/IL23R/JAK2/TYK2/SOCS3 0.034 0.48 0.77 58 -0.76 50 108
IL18/IL18R 0.055 0.093 0.21 19 -0.19 26 45
macrophage activation 0.006 0.042 0.077 73 -0.046 3 76
TNF -0.002 0.64 0.99 46 -1.1 55 101
STAT3/STAT4 -0.088 0.58 0.72 27 -1.1 66 93
STAT4 (dimer) -0.06 0.64 0.82 42 -1.2 67 109
IL18 0.023 0.046 -10000 0 -0.32 6 6
IL19 -0.002 0.61 0.94 45 -1.1 55 100
STAT5A (dimer) -0.049 0.63 0.82 43 -1.2 62 105
STAT1 0.028 0.03 0.33 4 -10000 0 4
SOCS3 -0.009 0.1 -10000 0 -0.32 40 40
CXCL9 0.015 0.67 0.96 65 -1.1 61 126
MPO -0.007 0.61 0.92 43 -1.1 56 99
positive regulation of humoral immune response -0.007 0.72 1.1 52 -1.2 60 112
IL23/IL23R/JAK2/TYK2 -0.018 0.75 1.1 52 -1.3 60 112
IL6 -0.29 0.79 0.9 38 -1.2 157 195
STAT5A 0.025 0.018 -10000 0 -0.32 1 1
IL2 0.024 0.05 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein -0.009 0.023 -10000 0 -0.061 39 39
CD3E -0.057 0.67 0.91 44 -1.2 70 114
keratinocyte proliferation -0.007 0.72 1.1 52 -1.2 60 112
NOS2 -0.004 0.63 0.94 49 -1.1 57 106
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.063 0.067 0.12 3 -0.14 173 176
BUB1B 0.077 0.088 0.18 147 -0.14 2 149
PLK1 0.038 0.046 0.1 101 -0.078 2 103
PLK1S1 0.025 0.033 0.12 9 -0.15 4 13
KIF2A 0.029 0.041 0.12 20 -10000 0 20
regulation of mitotic centrosome separation 0.038 0.045 0.1 101 -0.078 2 103
GOLGA2 0.024 0.008 -10000 0 -10000 0 0
Hec1/SPC24 0.18 0.17 0.34 181 -10000 0 181
WEE1 0.027 0.1 0.2 1 -0.31 27 28
cytokinesis 0.13 0.1 0.22 195 -0.24 3 198
PP2A-alpha B56 0.081 0.1 0.38 1 -0.51 6 7
AURKA 0.054 0.062 0.14 121 -0.18 1 122
PICH/PLK1 0.083 0.12 0.22 145 -10000 0 145
CENPE 0.049 0.067 0.16 82 -10000 0 82
RhoA/GTP 0.019 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.029 0.041 0.12 18 -10000 0 18
PPP2CA 0.025 0.005 -10000 0 -10000 0 0
FZR1 0.025 0.005 -10000 0 -10000 0 0
TPX2 0.084 0.069 0.14 218 -10000 0 218
PAK1 0.024 0.018 -10000 0 -0.33 1 1
SPC24 0.14 0.14 0.33 148 -10000 0 148
FBXW11 0.025 0.006 -10000 0 -10000 0 0
CLSPN 0.073 0.074 0.16 150 -0.2 1 151
GORASP1 0.025 0.006 -10000 0 -10000 0 0
metaphase 0.001 0.003 0.014 16 -0.011 1 17
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.018 0.022 0.053 71 -10000 0 71
G2 phase of mitotic cell cycle 0.002 0.005 0.012 42 -10000 0 42
STAG2 0.026 0.004 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.013 0.074 -10000 0 -0.52 7 7
spindle elongation 0.038 0.045 0.1 101 -0.078 2 103
ODF2 0.025 0.01 -10000 0 -10000 0 0
BUB1 0.063 0.11 0.44 1 -0.55 6 7
TPT1 0.011 0.051 -10000 0 -0.16 29 29
CDC25C 0.11 0.1 0.18 230 -0.26 11 241
CDC25B 0.032 0.04 0.34 6 -10000 0 6
SGOL1 0.063 0.067 0.14 173 -0.12 3 176
RHOA 0.025 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.09 0.1 0.23 130 -10000 0 130
CDC14B -0.004 0.013 -10000 0 -0.22 1 1
CDC20 0.19 0.15 0.33 220 -10000 0 220
PLK1/PBIP1 0.031 0.042 0.11 56 -10000 0 56
mitosis -0.002 0.006 0.024 2 -0.014 2 4
FBXO5 0.026 0.04 0.12 14 -0.12 1 15
CDC2 0.005 0.006 0.013 138 -0.009 1 139
NDC80 0.1 0.14 0.33 109 -10000 0 109
metaphase plate congression 0.031 0.038 -10000 0 -0.22 4 4
ERCC6L 0.083 0.12 0.22 137 -10000 0 137
NLP/gamma Tubulin 0.021 0.024 0.075 22 -10000 0 22
microtubule cytoskeleton organization 0.011 0.051 -10000 0 -0.15 29 29
G2/M transition DNA damage checkpoint 0 0.002 0.014 2 -10000 0 2
PPP1R12A 0.027 0.005 -10000 0 -10000 0 0
interphase 0 0.002 0.014 2 -10000 0 2
PLK1/PRC1-2 0.21 0.15 0.29 280 -10000 0 280
GRASP65/GM130/RAB1/GTP/PLK1 0.06 0.04 -10000 0 -10000 0 0
RAB1A 0.025 0.005 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.033 0.042 0.091 115 -10000 0 115
mitotic prometaphase 0.001 0.003 0.022 4 -10000 0 4
proteasomal ubiquitin-dependent protein catabolic process 0.055 0.062 0.2 2 -0.24 4 6
microtubule-based process 0.18 0.11 0.25 287 -10000 0 287
Golgi organization 0.038 0.045 0.1 101 -0.078 2 103
Cohesin/SA2 0.045 0.038 0.12 18 -10000 0 18
PPP1CB/MYPT1 0.039 0.011 -10000 0 -10000 0 0
KIF20A 0.24 0.14 0.33 287 -10000 0 287
APC/C/CDC20 0.15 0.12 0.26 224 -10000 0 224
PPP2R1A 0.025 0.005 -10000 0 -10000 0 0
chromosome segregation 0.03 0.041 0.11 53 -10000 0 53
PRC1 0.082 0.12 0.33 76 -10000 0 76
ECT2 0.05 0.078 0.2 67 -10000 0 67
C13orf34 0.032 0.039 0.086 105 -10000 0 105
NUDC 0.031 0.038 -10000 0 -0.22 4 4
regulation of attachment of spindle microtubules to kinetochore 0.077 0.088 0.18 147 -0.14 2 149
spindle assembly 0.029 0.035 0.086 66 -10000 0 66
spindle stabilization 0.025 0.032 0.12 9 -0.15 4 13
APC/C/HCDH1 0.02 0.013 -10000 0 -0.18 1 1
MKLP2/PLK1 0.19 0.11 0.25 287 -10000 0 287
CCNB1 0.13 0.14 0.33 142 -10000 0 142
PPP1CB 0.027 0.006 -10000 0 -10000 0 0
BTRC 0.025 0.005 -10000 0 -10000 0 0
ROCK2 0.027 0.069 0.18 2 -0.31 10 12
TUBG1 0.024 0.024 0.14 1 -0.14 1 2
G2/M transition of mitotic cell cycle 0.05 0.081 0.16 115 -10000 0 115
MLF1IP 0.005 0.037 0.19 15 -10000 0 15
INCENP 0.027 0.015 0.33 1 -10000 0 1
Nongenotropic Androgen signaling

Figure S12.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S12.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.007 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.035 0.11 -10000 0 -0.18 148 148
regulation of S phase of mitotic cell cycle -0.054 0.097 -10000 0 -0.2 125 125
GNAO1 -0.081 0.16 -10000 0 -0.32 124 124
HRAS 0.021 0.012 -10000 0 -10000 0 0
SHBG/T-DHT 0.016 0.005 -10000 0 -10000 0 0
PELP1 0.022 0.011 -10000 0 -10000 0 0
AKT1 -0.008 0.002 -10000 0 -10000 0 0
MAP2K1 -0.081 0.093 0.18 2 -0.26 44 46
T-DHT/AR -0.071 0.11 -10000 0 -0.22 145 145
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.006 128 128
GNAI2 0.025 0.006 -10000 0 -10000 0 0
GNAI3 0.026 0.003 -10000 0 -10000 0 0
GNAI1 0.023 0.03 -10000 0 -0.32 3 3
mol:GDP -0.12 0.14 -10000 0 -0.31 144 144
cell proliferation -0.16 0.19 0.27 1 -0.42 124 125
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
FOS -0.25 0.34 -10000 0 -0.73 130 130
mol:Ca2+ -0.034 0.036 -10000 0 -0.071 171 171
MAPK3 -0.12 0.15 0.24 3 -0.33 109 112
MAPK1 -0.072 0.11 -10000 0 -0.26 47 47
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
mol:IP3 -0.001 0.002 -10000 0 -0.004 123 123
cAMP biosynthetic process 0.017 0.032 0.16 5 -10000 0 5
GNG2 0.02 0.042 -10000 0 -0.32 6 6
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 123 123
HRAS/GTP -0.049 0.097 -10000 0 -0.17 131 131
actin cytoskeleton reorganization 0.033 0.019 -10000 0 -0.16 1 1
SRC 0.023 0.009 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 123 123
PI3K 0.031 0.016 -10000 0 -0.19 1 1
apoptosis 0.14 0.2 0.42 131 -10000 0 131
T-DHT/AR/PELP1 -0.052 0.1 -10000 0 -0.19 142 142
HRAS/GDP -0.1 0.15 -10000 0 -0.3 144 144
CREB1 -0.16 0.21 -10000 0 -0.44 131 131
RAC1-CDC42/GTP 0.041 0.023 -10000 0 -0.16 1 1
AR -0.1 0.16 -10000 0 -0.32 145 145
GNB1 0.026 0.003 -10000 0 -10000 0 0
RAF1 -0.069 0.086 0.19 2 -0.23 44 46
RAC1-CDC42/GDP -0.087 0.15 -10000 0 -0.29 138 138
T-DHT/AR/PELP1/Src -0.044 0.098 -10000 0 -0.18 131 131
MAP2K2 -0.081 0.093 0.18 2 -0.26 44 46
T-DHT/AR/PELP1/Src/PI3K -0.054 0.098 -10000 0 -0.2 125 125
GNAZ -0.05 0.14 -10000 0 -0.32 87 87
SHBG 0.022 0.011 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.14 0.18 -10000 0 -0.37 135 135
mol:T-DHT 0 0.001 -10000 0 -0.005 22 22
RAC1 0.025 0.006 -10000 0 -10000 0 0
GNRH1 -0.007 0.003 -10000 0 -10000 0 0
Gi family/GTP -0.12 0.14 -10000 0 -0.28 133 133
CDC42 0.026 0.003 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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
TGFB1 0.026 0.004 -10000 0 -10000 0 0
CCL5 0.02 0.091 0.33 13 -0.32 18 31
SDCBP 0.024 0.008 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.11 0.12 0.24 145 -0.24 6 151
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 0.095 0.12 0.26 60 -0.31 3 63
Syndecan-1/Syntenin 0.097 0.12 0.27 58 -0.31 3 61
MAPK3 0.088 0.11 0.24 63 -0.34 2 65
HGF/MET -0.015 0.11 0.24 7 -0.22 86 93
TGFB1/TGF beta receptor Type II 0.026 0.004 -10000 0 -10000 0 0
BSG 0.026 0.004 -10000 0 -10000 0 0
keratinocyte migration 0.095 0.11 0.26 60 -0.3 3 63
Syndecan-1/RANTES 0.11 0.13 0.29 70 -0.29 10 80
Syndecan-1/CD147 0.11 0.12 0.27 63 -0.35 2 65
Syndecan-1/Syntenin/PIP2 0.09 0.11 0.25 57 -0.3 3 60
LAMA5 0.025 0.007 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.088 0.11 0.24 57 -0.29 3 60
MMP7 0.06 0.14 0.33 71 -0.32 20 91
HGF -0.044 0.15 0.33 7 -0.32 86 93
Syndecan-1/CASK 0.083 0.11 0.2 136 -0.3 3 139
Syndecan-1/HGF/MET 0.079 0.15 0.28 57 -0.29 17 74
regulation of cell adhesion 0.072 0.11 0.23 62 -0.34 2 64
HPSE 0.049 0.09 0.33 35 -0.32 3 38
positive regulation of cell migration 0.11 0.12 0.24 145 -0.24 6 151
SDC1 0.11 0.12 0.24 142 -0.25 6 148
Syndecan-1/Collagen 0.11 0.12 0.24 145 -0.24 6 151
PPIB 0.026 0.004 -10000 0 -10000 0 0
MET 0.026 0.004 -10000 0 -10000 0 0
PRKACA 0.026 0.003 -10000 0 -10000 0 0
MMP9 0.091 0.14 0.33 96 -0.32 5 101
MAPK1 0.088 0.11 0.24 62 -0.34 2 64
homophilic cell adhesion 0.11 0.12 0.24 146 -0.38 2 148
MMP1 0.18 0.15 0.33 210 -0.32 1 211
TCGA08_retinoblastoma

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
CDKN2B 0.03 0.074 0.33 20 -0.29 1 21
CDKN2C -0.017 0.037 0.32 2 -10000 0 2
CDKN2A 0.16 0.16 0.33 184 -10000 0 184
CCND2 -0.06 0.082 0.16 1 -0.24 41 42
RB1 0.064 0.084 0.24 43 -0.17 1 44
CDK4 -0.066 0.086 0.17 1 -0.25 39 40
CDK6 -0.066 0.087 0.18 1 -0.26 41 42
G1/S progression -0.019 0.14 0.18 104 -0.24 44 148
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.077 0.17 0.25 3 -0.38 83 86
CRKL -0.088 0.17 0.25 1 -0.4 87 88
HRAS -0.079 0.17 -10000 0 -0.37 86 86
mol:PIP3 -0.077 0.17 -10000 0 -0.37 94 94
SPRED1 0.025 0.005 -10000 0 -10000 0 0
SPRED2 0.025 0.005 -10000 0 -10000 0 0
GAB1 -0.093 0.18 0.25 2 -0.41 91 93
FOXO3 -0.079 0.17 -10000 0 -0.37 90 90
AKT1 -0.081 0.18 -10000 0 -0.39 91 91
BAD -0.078 0.17 -10000 0 -0.37 87 87
megakaryocyte differentiation -0.09 0.18 0.25 2 -0.4 93 95
GSK3B -0.074 0.18 0.3 2 -0.37 87 89
RAF1 -0.06 0.14 0.25 5 -0.31 71 76
SHC1 0.024 0.007 -10000 0 -10000 0 0
STAT3 -0.093 0.18 0.25 2 -0.41 92 94
STAT1 -0.22 0.42 0.47 1 -0.94 95 96
HRAS/SPRED1 -0.058 0.15 -10000 0 -0.31 81 81
cell proliferation -0.091 0.18 0.25 2 -0.41 91 93
PIK3CA 0.024 0.006 -10000 0 -10000 0 0
TEC 0.026 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.08 0.19 0.28 1 -0.4 93 94
HRAS/SPRED2 -0.057 0.15 -10000 0 -0.31 80 80
LYN/TEC/p62DOK -0.053 0.18 -10000 0 -0.39 81 81
MAPK3 -0.037 0.12 0.25 7 -0.26 33 40
STAP1 -0.096 0.19 0.25 2 -0.42 95 97
GRAP2 -0.012 0.11 -10000 0 -0.32 43 43
JAK2 -0.19 0.37 0.42 1 -0.81 95 96
STAT1 (dimer) -0.21 0.41 0.47 1 -0.92 95 96
mol:Gleevec 0.002 0.008 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.061 0.2 -10000 0 -0.4 89 89
actin filament polymerization -0.088 0.18 0.27 3 -0.4 91 94
LYN 0.024 0.007 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.13 0.26 0.34 1 -0.57 95 96
PIK3R1 0.023 0.018 -10000 0 -0.32 1 1
CBL/CRKL/GRB2 -0.062 0.18 0.28 1 -0.37 85 86
PI3K -0.06 0.19 -10000 0 -0.39 85 85
PTEN 0.025 0.007 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.22 0.49 -10000 0 -1.1 90 90
MAPK8 -0.093 0.18 0.25 2 -0.41 91 93
STAT3 (dimer) -0.091 0.18 0.25 2 -0.4 92 94
positive regulation of transcription -0.028 0.1 0.22 9 -0.21 29 38
mol:GDP -0.076 0.17 -10000 0 -0.38 85 85
PIK3C2B -0.093 0.18 0.25 2 -0.41 93 95
CBL/CRKL -0.071 0.17 0.27 1 -0.38 87 88
FER -0.094 0.18 0.25 2 -0.41 93 95
SH2B3 -0.09 0.18 0.25 2 -0.41 92 94
PDPK1 -0.073 0.16 -10000 0 -0.34 93 93
SNAI2 -0.09 0.18 0.25 2 -0.41 86 88
positive regulation of cell proliferation -0.16 0.31 0.4 1 -0.69 96 97
KITLG 0.007 0.05 -10000 0 -0.34 5 5
cell motility -0.16 0.31 0.4 1 -0.69 96 97
PTPN6 0.029 0.021 0.33 1 -10000 0 1
EPOR -0.074 0.24 -10000 0 -0.94 15 15
STAT5A (dimer) -0.13 0.26 0.36 1 -0.57 95 96
SOCS1 0.026 0.016 0.33 1 -10000 0 1
cell migration 0.097 0.19 0.41 96 -0.25 2 98
SOS1 0.026 0.004 -10000 0 -10000 0 0
EPO 0.034 0.083 0.32 29 -10000 0 29
VAV1 0.013 0.071 0.33 2 -0.32 16 18
GRB10 -0.094 0.18 0.24 3 -0.41 90 93
PTPN11 0.027 0.012 -10000 0 -10000 0 0
SCF/KIT -0.092 0.19 0.28 2 -0.42 94 96
GO:0007205 0.004 0.01 -10000 0 -10000 0 0
MAP2K1 -0.043 0.12 0.25 8 -0.25 67 75
CBL 0.025 0.006 -10000 0 -10000 0 0
KIT -0.26 0.51 -10000 0 -1.2 95 95
MAP2K2 -0.041 0.12 0.25 9 -0.25 65 74
SHC/Grb2/SOS1 -0.052 0.18 -10000 0 -0.39 79 79
STAT5A -0.13 0.26 0.36 1 -0.59 94 95
GRB2 0.025 0.005 -10000 0 -10000 0 0
response to radiation -0.088 0.18 0.26 3 -0.4 86 89
SHC/GRAP2 0.012 0.075 -10000 0 -0.22 36 36
PTPRO -0.092 0.18 0.25 2 -0.41 93 95
SH2B2 -0.09 0.18 0.27 3 -0.41 91 94
DOK1 0.026 0.016 0.33 1 -10000 0 1
MATK -0.099 0.19 0.25 2 -0.42 96 98
CREBBP 0.004 0.069 0.21 6 -0.18 7 13
BCL2 -0.13 0.35 -10000 0 -0.94 49 49
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.33 0.62 0.88 7 -1.2 103 110
STAT6 (cleaved dimer) -0.41 0.6 -10000 0 -1.2 128 128
IGHG1 -0.072 0.26 0.54 15 -0.7 3 18
IGHG3 -0.34 0.58 0.7 3 -1.1 119 122
AKT1 -0.17 0.36 0.65 3 -0.8 48 51
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.12 0.32 0.56 6 -0.8 36 42
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.17 0.38 0.63 5 -0.82 48 53
THY1 -0.35 0.62 0.83 4 -1.2 102 106
MYB 0.059 0.1 0.33 48 -0.32 1 49
HMGA1 0.032 0.042 0.33 8 -10000 0 8
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.21 0.45 0.68 12 -0.82 85 97
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.17 0.38 0.63 5 -0.81 51 56
SP1 0.021 0.035 0.19 2 -0.17 1 3
INPP5D 0.019 0.042 -10000 0 -0.32 6 6
SOCS5 0.021 0.044 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.38 0.62 0.71 2 -1.2 120 122
SOCS1 -0.23 0.4 0.65 4 -0.74 95 99
SOCS3 -0.24 0.47 0.67 2 -1.1 60 62
FCER2 -0.58 0.75 0.87 6 -1.3 184 190
PARP14 0.009 0.037 -10000 0 -0.19 3 3
CCL17 -0.33 0.64 0.94 10 -1.2 102 112
GRB2 0.025 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.12 0.31 0.58 5 -0.68 38 43
T cell proliferation -0.37 0.62 0.76 2 -1.2 112 114
IL4R/JAK1 -0.36 0.61 -10000 0 -1.2 109 109
EGR2 -0.52 0.75 0.84 5 -1.4 143 148
JAK2 0 0.074 0.22 4 -10000 0 4
JAK3 0.02 0.035 0.39 2 -10000 0 2
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
JAK1 0.007 0.042 -10000 0 -10000 0 0
COL1A2 -0.14 0.4 0.57 3 -1.4 28 31
CCL26 -0.36 0.62 0.82 3 -1.2 97 100
IL4R -0.37 0.67 0.88 11 -1.3 104 115
PTPN6 0.022 0.036 0.27 1 -10000 0 1
IL13RA2 -0.36 0.63 0.89 5 -1.2 99 104
IL13RA1 -0.003 0.077 0.22 4 -10000 0 4
IRF4 -0.2 0.47 0.78 3 -1.1 66 69
ARG1 -0.047 0.25 0.59 9 -0.59 20 29
CBL -0.21 0.41 0.62 7 -0.76 89 96
GTF3A 0.027 0.028 0.19 5 -10000 0 5
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
IL13RA1/JAK2 0.007 0.11 0.3 11 -10000 0 11
IRF4/BCL6 -0.16 0.42 0.55 1 -0.99 66 67
CD40LG -0.026 0.11 0.31 3 -0.32 43 46
MAPK14 -0.23 0.45 0.68 4 -0.9 77 81
mitosis -0.16 0.34 0.62 4 -0.74 48 52
STAT6 -0.41 0.76 0.99 12 -1.4 111 123
SPI1 0.033 0.053 0.29 7 -0.32 3 10
RPS6KB1 -0.15 0.33 0.6 4 -0.73 44 48
STAT6 (dimer) -0.4 0.76 0.99 12 -1.4 111 123
STAT6 (dimer)/PARP14 -0.43 0.67 0.73 4 -1.2 134 138
mast cell activation 0.005 0.022 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.18 0.38 0.62 5 -0.83 55 60
FRAP1 -0.17 0.36 0.65 3 -0.8 48 51
LTA -0.36 0.63 0.9 4 -1.2 108 112
FES 0.026 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.38 0.72 1.3 111 -0.99 12 123
CCL11 -0.38 0.63 0.74 1 -1.2 111 112
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.16 0.37 0.62 5 -0.83 44 49
IL2RG 0.017 0.074 0.34 9 -0.32 9 18
IL10 -0.37 0.64 0.86 5 -1.2 107 112
IRS1 0.018 0.045 -10000 0 -0.32 7 7
IRS2 0.013 0.063 -10000 0 -0.32 14 14
IL4 -0.052 0.26 0.64 6 -1.1 10 16
IL5 -0.36 0.62 0.9 4 -1.2 102 106
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.27 0.54 0.82 14 -0.96 98 112
COL1A1 -0.096 0.35 0.67 4 -1.4 14 18
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.38 0.62 -10000 0 -1.2 100 100
IL2R gamma/JAK3 0.028 0.067 0.31 9 -0.23 9 18
TFF3 -0.46 0.74 0.96 4 -1.4 133 137
ALOX15 -0.32 0.64 0.9 11 -1.2 98 109
MYBL1 0.026 0.031 0.33 4 -10000 0 4
T-helper 2 cell differentiation -0.3 0.54 0.71 9 -0.97 116 125
SHC1 0.024 0.007 -10000 0 -10000 0 0
CEBPB 0.031 0.035 -10000 0 -0.32 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.15 0.36 0.6 5 -0.77 45 50
mol:PI-3-4-5-P3 -0.17 0.36 0.65 3 -0.8 48 51
PI3K -0.18 0.38 0.71 2 -0.87 48 50
DOK2 0.017 0.053 0.33 2 -0.32 8 10
ETS1 0.015 0.044 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.11 0.28 0.55 5 -0.64 29 34
ITGB3 -0.41 0.67 0.82 3 -1.3 118 121
PIGR -0.59 0.74 0.89 9 -1.3 187 196
IGHE 0.02 0.086 0.18 19 -0.24 13 32
MAPKKK cascade -0.1 0.28 0.55 5 -0.63 29 34
BCL6 0.029 0.018 -10000 0 -10000 0 0
OPRM1 -0.36 0.61 0.82 3 -1.2 102 105
RETNLB -0.35 0.62 0.81 4 -1.2 101 105
SELP -0.45 0.72 0.85 6 -1.3 137 143
AICDA -0.34 0.58 0.8 3 -1.1 103 106
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.045 0.042 0.24 17 -10000 0 17
VLDLR 0.014 0.054 -10000 0 -0.32 10 10
CRKL 0.027 0.022 0.33 2 -10000 0 2
LRPAP1 0.025 0.005 -10000 0 -10000 0 0
FYN 0.022 0.03 -10000 0 -0.32 3 3
ITGA3 0.03 0.037 0.33 6 -10000 0 6
RELN/VLDLR/Fyn -0.037 0.12 0.23 4 -0.19 142 146
MAPK8IP1/MKK7/MAP3K11/JNK1 0.059 0.042 -10000 0 -0.17 4 4
AKT1 -0.068 0.11 0.19 2 -0.21 135 137
MAP2K7 0.026 0.004 -10000 0 -10000 0 0
RAPGEF1 0.024 0.008 -10000 0 -10000 0 0
DAB1 0 0.12 0.33 23 -0.32 33 56
RELN/LRP8/DAB1 -0.013 0.14 0.23 48 -0.18 118 166
LRPAP1/LRP8 0.07 0.075 0.24 66 -10000 0 66
RELN/LRP8/DAB1/Fyn -0.009 0.13 0.23 44 -0.18 120 164
DAB1/alpha3/beta1 Integrin -0.019 0.12 0.28 5 -0.18 108 113
long-term memory -0.035 0.16 0.35 6 -0.21 138 144
DAB1/LIS1 -0.01 0.13 0.36 3 -0.18 96 99
DAB1/CRLK/C3G -0.016 0.12 0.28 4 -0.18 85 89
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
DAB1/NCK2 -0.008 0.13 0.36 3 -0.18 111 114
ARHGEF2 0.024 0.007 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.051 0.14 0.33 3 -0.32 81 84
CDK5R1 0.037 0.061 0.33 17 -10000 0 17
RELN -0.096 0.16 0.33 4 -0.32 139 143
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
RELN/LRP8/Fyn -0.009 0.13 0.24 39 -0.19 111 150
GRIN2A/RELN/LRP8/DAB1/Fyn -0.039 0.16 0.26 14 -0.22 145 159
MAPK8 0.023 0.03 -10000 0 -0.32 3 3
RELN/VLDLR/DAB1 -0.039 0.12 0.22 15 -0.18 151 166
ITGB1 0.025 0.006 -10000 0 -10000 0 0
MAP1B -0.069 0.12 0.2 13 -0.21 131 144
RELN/LRP8 -0.006 0.13 0.24 39 -0.19 107 146
GRIN2B/RELN/LRP8/DAB1/Fyn -0.001 0.14 0.25 35 -0.18 116 151
PI3K 0.034 0.018 -10000 0 -0.22 1 1
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.038 0.025 0.24 5 -10000 0 5
RAP1A -0.045 0.11 0.28 12 -0.28 9 21
PAFAH1B1 0.024 0.008 -10000 0 -10000 0 0
MAPK8IP1 0.024 0.024 0.33 1 -0.32 1 2
CRLK/C3G 0.035 0.02 0.24 2 -10000 0 2
GRIN2B 0.007 0.059 0.33 12 -10000 0 12
NCK2 0.026 0.004 -10000 0 -10000 0 0
neuron differentiation -0.035 0.11 0.21 6 -0.28 31 37
neuron adhesion -0.039 0.11 0.32 9 -0.29 7 16
LRP8 0.079 0.12 0.33 72 -10000 0 72
GSK3B -0.068 0.1 0.18 1 -0.2 132 133
RELN/VLDLR/DAB1/Fyn -0.032 0.12 0.22 15 -0.18 153 168
MAP3K11 0.026 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.066 0.12 0.2 2 -0.22 142 144
CDK5 0.026 0.003 -10000 0 -10000 0 0
MAPT -0.003 0.14 0.75 9 -0.28 29 38
neuron migration -0.073 0.14 0.29 10 -0.27 92 102
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.034 0.11 0.21 6 -0.28 31 37
RELN/VLDLR 0 0.13 0.25 35 -0.18 105 140
Thromboxane A2 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
TGM2 0.019 0.068 0.33 6 -0.32 11 17
GNB1/GNG2 -0.079 0.089 -10000 0 -0.18 166 166
AKT1 -0.065 0.13 0.4 6 -0.25 23 29
EGF 0.039 0.073 0.33 24 -10000 0 24
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.017 0.057 0.27 1 -0.24 1 2
mol:Ca2+ -0.1 0.18 0.47 7 -0.29 158 165
LYN -0.015 0.054 0.27 1 -0.24 1 2
RhoA/GTP -0.045 0.074 0.18 4 -0.13 132 136
mol:PGI2 0 0.001 -10000 0 -10000 0 0
SYK -0.12 0.2 0.48 7 -0.34 161 168
GNG2 0.02 0.042 -10000 0 -0.32 6 6
ARRB2 0.024 0.008 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.036 0.13 -10000 0 -0.45 24 24
G beta5/gamma2 -0.1 0.12 -10000 0 -0.24 164 164
PRKCH -0.12 0.2 0.47 7 -0.34 161 168
DNM1 0.018 0.042 -10000 0 -0.32 6 6
TXA2/TP beta/beta Arrestin3 0 0.072 -10000 0 -0.55 6 6
mol:GTP 0 0.003 -10000 0 -10000 0 0
PTGDR 0.006 0.072 -10000 0 -0.32 18 18
G12 family/GTP -0.11 0.15 -10000 0 -0.3 157 157
ADRBK1 0.026 0.004 -10000 0 -10000 0 0
ADRBK2 0.024 0.018 -10000 0 -0.32 1 1
RhoA/GTP/ROCK1 0.032 0.01 -10000 0 -10000 0 0
mol:GDP 0.054 0.12 0.3 23 -0.36 6 29
mol:NADP 0.026 0.015 0.32 1 -10000 0 1
RAB11A 0.026 0.004 -10000 0 -10000 0 0
PRKG1 -0.051 0.14 -10000 0 -0.32 87 87
mol:IP3 -0.13 0.22 0.53 6 -0.36 165 171
cell morphogenesis 0.031 0.01 -10000 0 -10000 0 0
PLCB2 -0.18 0.28 0.56 6 -0.49 169 175
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.016 0.069 0.27 1 -0.21 3 4
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.016 0.06 0.28 2 -0.23 5 7
RHOA 0.025 0.006 -10000 0 -10000 0 0
PTGIR 0.025 0.018 -10000 0 -0.32 1 1
PRKCB1 -0.13 0.21 0.48 7 -0.36 163 170
GNAQ 0.023 0.008 -10000 0 -10000 0 0
mol:L-citrulline 0.026 0.015 0.32 1 -10000 0 1
TXA2/TXA2-R family -0.19 0.29 0.57 6 -0.51 167 173
LCK -0.016 0.06 0.27 1 -0.24 3 4
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.014 0.047 -10000 0 -0.17 16 16
TXA2-R family/G12 family/GDP/G beta/gamma 0.016 0.058 -10000 0 -0.39 6 6
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.017 0.047 -10000 0 -0.16 15 15
MAPK14 -0.079 0.14 0.4 7 -0.23 154 161
TGM2/GTP -0.15 0.24 0.58 6 -0.42 147 153
MAPK11 -0.079 0.14 0.4 7 -0.23 153 160
ARHGEF1 -0.061 0.11 0.35 6 -0.18 138 144
GNAI2 0.025 0.006 -10000 0 -10000 0 0
JNK cascade -0.13 0.22 0.51 7 -0.38 165 172
RAB11/GDP 0.025 0.008 -10000 0 -10000 0 0
ICAM1 -0.094 0.17 0.45 8 -0.28 159 167
cAMP biosynthetic process -0.12 0.2 0.5 6 -0.34 153 159
Gq family/GTP/EBP50 -0.02 0.077 0.2 2 -0.17 74 76
actin cytoskeleton reorganization 0.031 0.01 -10000 0 -10000 0 0
SRC -0.017 0.055 0.27 1 -0.24 1 2
GNB5 0.026 0.004 -10000 0 -10000 0 0
GNB1 0.026 0.003 -10000 0 -10000 0 0
EGF/EGFR 0.002 0.077 0.22 15 -0.24 7 22
VCAM1 -0.1 0.18 0.46 7 -0.29 162 169
TP beta/Gq family/GDP/G beta5/gamma2 -0.036 0.13 -10000 0 -0.45 24 24
platelet activation -0.1 0.18 0.47 7 -0.3 155 162
PGI2/IP 0.018 0.012 -10000 0 -0.22 1 1
PRKACA 0.004 0.041 -10000 0 -0.18 19 19
Gq family/GDP/G beta5/gamma2 -0.035 0.12 -10000 0 -0.42 24 24
TXA2/TP beta/beta Arrestin2 -0.017 0.099 -10000 0 -0.38 25 25
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.01 0.039 0.19 1 -0.18 17 18
mol:DAG -0.15 0.24 0.54 6 -0.41 164 170
EGFR 0.017 0.051 -10000 0 -0.32 9 9
TXA2/TP alpha -0.17 0.27 0.56 6 -0.46 159 165
Gq family/GTP -0.021 0.077 0.22 2 -0.2 54 56
YES1 -0.014 0.056 0.27 1 -0.24 1 2
GNAI2/GTP -0.007 0.047 -10000 0 -0.17 17 17
PGD2/DP 0.006 0.049 -10000 0 -0.22 18 18
SLC9A3R1 0.04 0.065 0.33 20 -10000 0 20
FYN -0.016 0.057 0.27 1 -0.26 2 3
mol:NO 0.026 0.015 0.32 1 -10000 0 1
GNA15 0.023 0.03 -10000 0 -0.32 3 3
PGK/cGMP -0.014 0.091 0.21 1 -0.19 86 87
RhoA/GDP 0.025 0.009 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.027 0.073 -10000 0 -0.28 8 8
NOS3 0.026 0.015 0.33 1 -10000 0 1
RAC1 0.025 0.006 -10000 0 -10000 0 0
PRKCA -0.12 0.2 0.47 7 -0.34 151 158
PRKCB -0.15 0.22 0.51 5 -0.38 161 166
PRKCE -0.12 0.2 0.5 7 -0.34 153 160
PRKCD -0.14 0.22 0.48 7 -0.38 164 171
PRKCG -0.13 0.22 0.5 7 -0.38 158 165
muscle contraction -0.18 0.27 0.57 6 -0.47 165 171
PRKCZ -0.12 0.2 0.48 7 -0.34 161 168
ARR3 -0.009 0.017 -10000 0 -10000 0 0
TXA2/TP beta 0.005 0.054 -10000 0 -0.18 18 18
PRKCQ -0.12 0.22 0.5 8 -0.36 155 163
MAPKKK cascade -0.16 0.25 0.54 6 -0.44 166 172
SELE -0.13 0.21 0.46 7 -0.36 165 172
TP beta/GNAI2/GDP/G beta/gamma 0.031 0.057 -10000 0 -0.22 3 3
ROCK1 0.025 0.005 -10000 0 -10000 0 0
GNA14 -0.015 0.11 -10000 0 -0.32 45 45
chemotaxis -0.22 0.32 0.6 6 -0.59 165 171
GNA12 0.025 0.006 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
GNA11 0.025 0.018 -10000 0 -0.32 1 1
Rac1/GTP 0.018 0.005 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.036 0.011 -10000 0 -10000 0 0
Necdin/E2F1 0.039 0.11 0.24 58 -0.22 30 88
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.004 0.13 0.24 4 -0.19 114 118
NGF (dimer)/p75(NTR)/BEX1 -0.039 0.14 0.24 9 -0.23 131 140
NT-4/5 (dimer)/p75(NTR) -0.032 0.12 0.24 3 -0.24 102 105
IKBKB 0.023 0.008 -10000 0 -10000 0 0
AKT1 -0.054 0.1 0.19 21 -0.26 29 50
IKBKG 0.026 0.004 -10000 0 -10000 0 0
BDNF -0.033 0.13 -10000 0 -0.32 67 67
MGDIs/NGR/p75(NTR)/LINGO1 0.031 0.13 0.26 59 -0.19 76 135
FURIN 0.026 0.015 0.33 1 -10000 0 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.035 0.13 0.23 4 -0.21 131 135
LINGO1 0.039 0.062 0.33 18 -10000 0 18
Sortilin/TRAF6/NRIF 0.023 0.02 -10000 0 -10000 0 0
proBDNF (dimer) -0.033 0.13 -10000 0 -0.32 67 67
NTRK1 0.024 0.04 0.33 6 -10000 0 6
RTN4R 0.067 0.1 0.33 56 -10000 0 56
neuron apoptosis -0.05 0.15 0.3 6 -0.36 40 46
IRAK1 0.026 0.004 -10000 0 -10000 0 0
SHC1 -0.064 0.095 0.15 4 -0.22 98 102
ARHGDIA 0.025 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.019 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.059 0.035 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.011 0.13 0.24 4 -0.2 116 120
MAGEH1 0.024 0.024 -10000 0 -0.32 2 2
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.032 0.14 0.24 3 -0.22 136 139
Mammalian IAPs/DIABLO 0.051 0.053 -10000 0 -0.18 18 18
proNGF (dimer) -0.021 0.12 -10000 0 -0.32 53 53
MAGED1 0.026 0.003 -10000 0 -10000 0 0
APP 0.025 0.018 -10000 0 -0.32 1 1
NT-4/5 (dimer) 0.002 0.086 -10000 0 -0.32 27 27
ZNF274 0.025 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.03 0.1 -10000 0 -0.19 113 113
NGF -0.021 0.12 -10000 0 -0.32 53 53
cell cycle arrest -0.052 0.089 0.24 11 -0.28 21 32
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.042 0.11 0.2 1 -0.23 94 95
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.013 0.11 0.23 3 -0.2 98 101
NCSTN 0.022 0.009 -10000 0 -10000 0 0
mol:GTP -0.027 0.13 0.23 4 -0.22 117 121
PSENEN 0.025 0.006 -10000 0 -10000 0 0
mol:ceramide -0.063 0.094 0.18 9 -0.2 106 115
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.041 0.1 -10000 0 -0.32 30 30
p75(NTR)/beta APP -0.016 0.11 0.24 4 -0.22 84 88
BEX1 -0.004 0.1 0.33 6 -0.32 32 38
mol:GDP -0.068 0.1 0.14 5 -0.21 116 121
NGF (dimer) 0.045 0.12 0.23 68 -0.18 61 129
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.041 0.13 0.25 57 -0.18 73 130
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
RAC1/GTP -0.019 0.11 0.2 4 -0.18 113 117
MYD88 0.025 0.006 -10000 0 -10000 0 0
CHUK 0.025 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.026 0.13 0.23 4 -0.22 117 121
RHOB 0.025 0.005 -10000 0 -10000 0 0
RHOA 0.025 0.006 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.067 0.078 0.24 67 -10000 0 67
NT3 (dimer) -0.037 0.13 0.33 1 -0.32 72 73
TP53 -0.057 0.096 0.3 4 -0.3 16 20
PRDM4 -0.067 0.097 0.18 10 -0.2 115 125
BDNF (dimer) 0.02 0.16 0.25 77 -0.21 98 175
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
SORT1 0.026 0.002 -10000 0 -10000 0 0
activation of caspase activity -0.008 0.12 0.22 4 -0.19 114 118
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.012 0.12 0.24 4 -0.2 114 118
RHOC 0.026 0.002 -10000 0 -10000 0 0
XIAP 0.026 0.003 -10000 0 -10000 0 0
MAPK10 -0.093 0.14 0.32 2 -0.3 88 90
DIABLO 0.026 0.004 -10000 0 -10000 0 0
SMPD2 -0.063 0.095 0.18 9 -0.2 106 115
APH1B 0.026 0.004 -10000 0 -10000 0 0
APH1A 0.023 0.008 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.025 0.13 0.23 4 -0.22 115 119
PSEN1 0.025 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.007 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.057 0.14 0.24 3 -0.25 132 135
MAPK8 -0.08 0.13 0.36 4 -0.28 86 90
MAPK9 -0.08 0.14 0.38 4 -0.29 86 90
APAF1 0.026 0.003 -10000 0 -10000 0 0
NTF3 -0.037 0.13 0.33 1 -0.32 72 73
NTF4 0.002 0.086 -10000 0 -0.32 27 27
NDN -0.012 0.11 -10000 0 -0.32 43 43
RAC1/GDP 0.019 0.004 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.007 0.12 -10000 0 -0.19 110 110
p75 CTF/Sortilin/TRAF6/NRIF 0.058 0.024 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.027 0.13 0.23 4 -0.22 117 121
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.011 0.12 0.24 4 -0.19 120 124
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.021 0.12 0.24 4 -0.19 130 134
PRKACB 0.024 0.025 -10000 0 -0.32 2 2
proBDNF (dimer)/p75 ECD -0.007 0.095 -10000 0 -0.22 64 64
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.008 0.073 -10000 0 -0.32 19 19
BIRC2 0.025 0.007 -10000 0 -10000 0 0
neuron projection morphogenesis -0.075 0.11 0.18 1 -0.24 102 103
BAD -0.089 0.14 0.33 4 -0.3 88 92
RIPK2 0.022 0.009 -10000 0 -10000 0 0
NGFR -0.045 0.15 0.33 4 -0.32 86 90
CYCS -0.063 0.092 0.19 12 -0.31 18 30
ADAM17 0.025 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.008 0.11 0.24 3 -0.2 95 98
BCL2L11 -0.088 0.14 0.33 4 -0.3 87 91
BDNF (dimer)/p75(NTR) -0.056 0.14 0.24 4 -0.25 133 137
PI3K -0.011 0.12 0.24 3 -0.2 106 109
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.011 0.13 0.24 4 -0.2 115 119
NDNL2 0.025 0.005 -10000 0 -10000 0 0
YWHAE 0.024 0.008 -10000 0 -10000 0 0
PRKCI 0.025 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.046 0.14 0.24 4 -0.26 116 120
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.012 0.13 0.24 3 -0.2 115 118
TRAF6 0.024 0.007 -10000 0 -10000 0 0
RAC1 0.025 0.006 -10000 0 -10000 0 0
PRKCZ 0.023 0.03 -10000 0 -0.32 3 3
PLG -0.004 0.041 0.33 5 -10000 0 5
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.094 0.12 0.15 5 -0.24 151 156
SQSTM1 0.025 0.006 -10000 0 -10000 0 0
NGFRAP1 0.024 0.024 -10000 0 -0.32 2 2
CASP3 -0.084 0.14 0.3 4 -0.29 88 92
E2F1 0.078 0.12 0.33 73 -10000 0 73
CASP9 0.026 0.003 -10000 0 -10000 0 0
IKK complex -0.009 0.13 0.25 3 -0.32 33 36
NGF (dimer)/TRKA 0.009 0.087 0.24 6 -0.22 45 51
MMP7 0.06 0.14 0.33 71 -0.32 20 91
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.003 0.12 0.24 4 -0.19 109 113
MMP3 0.003 0.14 0.33 28 -0.32 48 76
APAF-1/Caspase 9 -0.079 0.074 -10000 0 -0.28 24 24
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.029 0.21 0.28 20 -0.43 70 90
FYN -0.073 0.27 0.29 18 -0.55 79 97
LAT/GRAP2/SLP76 -0.046 0.22 0.27 13 -0.44 80 93
IKBKB 0.023 0.008 -10000 0 -10000 0 0
AKT1 -0.048 0.18 0.25 18 -0.37 80 98
B2M 0.024 0.014 -10000 0 -10000 0 0
IKBKG -0.014 0.058 0.12 14 -0.12 50 64
MAP3K8 0.023 0.025 -10000 0 -0.32 2 2
mol:Ca2+ -0.015 0.021 0.034 33 -0.055 27 60
integrin-mediated signaling pathway 0.032 0.023 -10000 0 -0.18 4 4
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.076 0.26 0.29 17 -0.53 82 99
TRPV6 -0.003 0.18 1.1 5 -10000 0 5
CD28 0.013 0.072 0.33 2 -0.32 16 18
SHC1 -0.059 0.25 0.27 29 -0.52 75 104
receptor internalization -0.078 0.26 0.29 6 -0.51 84 90
PRF1 -0.08 0.32 0.47 11 -0.8 49 60
KRAS 0.025 0.006 -10000 0 -10000 0 0
GRB2 0.025 0.005 -10000 0 -10000 0 0
COT/AKT1 -0.028 0.15 0.24 16 -0.31 74 90
LAT -0.065 0.25 0.26 20 -0.5 79 99
EntrezGene:6955 0 0.007 0.038 6 -10000 0 6
CD3D -0.001 0.1 0.35 3 -0.33 32 35
CD3E -0.009 0.11 -10000 0 -0.33 39 39
CD3G -0.012 0.11 -10000 0 -0.32 42 42
RASGRP2 -0.037 0.076 -10000 0 -0.16 104 104
RASGRP1 -0.039 0.19 0.26 17 -0.39 71 88
HLA-A 0 0.007 0.037 7 -10000 0 7
RASSF5 0.022 0.034 -10000 0 -0.32 4 4
RAP1A/GTP/RAPL 0.032 0.023 -10000 0 -0.19 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.002 0.072 0.16 24 -0.13 41 65
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.034 0.078 -10000 0 -0.18 75 75
PRKCA -0.026 0.11 0.19 16 -0.23 69 85
GRAP2 -0.012 0.11 -10000 0 -0.32 43 43
mol:IP3 -0.041 0.17 0.2 34 -0.34 79 113
EntrezGene:6957 0 0.007 0.038 3 -10000 0 3
TCR/CD3/MHC I/CD8 -0.072 0.23 0.27 11 -0.51 67 78
ORAI1 -0.01 0.14 0.36 6 -0.94 5 11
CSK -0.07 0.26 0.27 19 -0.52 78 97
B7 family/CD28 -0.017 0.27 0.41 22 -0.5 70 92
CHUK 0.025 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.088 0.29 0.3 9 -0.59 79 88
PTPN6 -0.072 0.25 0.26 19 -0.51 80 99
VAV1 -0.073 0.26 0.27 18 -0.53 78 96
Monovalent TCR/CD3 -0.038 0.16 0.19 5 -0.36 61 66
CBL 0.025 0.006 -10000 0 -10000 0 0
LCK -0.071 0.27 0.29 16 -0.54 78 94
PAG1 -0.063 0.26 0.26 22 -0.52 77 99
RAP1A 0.026 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.085 0.28 0.3 10 -0.57 80 90
CD80 0.064 0.1 0.33 54 -10000 0 54
CD86 0.023 0.038 0.33 1 -0.32 4 5
PDK1/CARD11/BCL10/MALT1 -0.032 0.099 -10000 0 -0.22 74 74
HRAS 0.024 0.008 -10000 0 -10000 0 0
GO:0035030 -0.044 0.21 0.29 21 -0.41 73 94
CD8A -0.007 0.11 0.36 1 -0.33 39 40
CD8B -0.001 0.11 0.34 7 -0.33 35 42
PTPRC -0.011 0.11 0.33 2 -0.32 44 46
PDK1/PKC theta -0.057 0.22 0.28 15 -0.45 80 95
CSK/PAG1 -0.058 0.25 0.27 27 -0.5 77 104
SOS1 0.026 0.004 -10000 0 -10000 0 0
peptide-MHC class I 0.017 0.018 -10000 0 -10000 0 0
GRAP2/SLP76 -0.058 0.26 0.29 13 -0.51 83 96
STIM1 -0.008 0.045 -10000 0 -0.38 1 1
RAS family/GTP 0.008 0.091 0.19 19 -0.17 45 64
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.085 0.27 0.29 6 -0.55 84 90
mol:DAG -0.056 0.13 0.093 2 -0.3 81 83
RAP1A/GDP 0.003 0.035 0.091 11 -0.063 34 45
PLCG1 0.024 0.007 -10000 0 -10000 0 0
CD247 0.019 0.047 0.32 1 -0.33 6 7
cytotoxic T cell degranulation -0.074 0.3 0.47 11 -0.76 49 60
RAP1A/GTP -0.015 0.029 -10000 0 -0.062 103 103
mol:PI-3-4-5-P3 -0.057 0.22 0.28 18 -0.44 81 99
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.05 0.22 0.29 13 -0.43 79 92
NRAS 0.026 0.002 -10000 0 -10000 0 0
ZAP70 0.014 0.065 0.33 1 -0.32 14 15
GRB2/SOS1 0.037 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.056 0.21 0.25 7 -0.43 79 86
MALT1 0.025 0.006 -10000 0 -10000 0 0
TRAF6 0.024 0.007 -10000 0 -10000 0 0
CD8 heterodimer -0.001 0.13 0.3 7 -0.3 53 60
CARD11 0.02 0.045 0.33 1 -0.32 6 7
PRKCB -0.049 0.13 0.19 11 -0.26 80 91
PRKCE -0.026 0.11 0.19 16 -0.23 67 83
PRKCQ -0.066 0.25 0.28 19 -0.51 81 100
LCP2 0.022 0.03 -10000 0 -0.32 3 3
BCL10 0.026 0.003 -10000 0 -10000 0 0
regulation of survival gene product expression -0.038 0.16 0.24 18 -0.32 79 97
IKK complex -0.006 0.065 0.16 19 -0.11 45 64
RAS family/GDP -0.006 0.014 -10000 0 -0.04 14 14
MAP3K14 -0.023 0.12 0.2 16 -0.24 72 88
PDPK1 -0.045 0.18 0.25 17 -0.36 79 96
TCR/CD3/MHC I/CD8/Fyn -0.1 0.31 0.31 6 -0.65 80 86
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.027 0.015 0.33 1 -9999 0 1
Aurora C/Aurora B/INCENP 0.12 0.095 0.22 172 -9999 0 172
metaphase 0 0 -10000 0 -9999 0 0
mitosis 0 0 -10000 0 -9999 0 0
H3F3B 0.022 0.018 -10000 0 -9999 0 0
AURKB 0.16 0.15 0.33 176 -9999 0 176
AURKC 0.035 0.053 0.33 13 -9999 0 13
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 0.18 0.27 0.61 52 -0.47 11 63
HDAC7 0.027 0.006 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.19 0.33 0.75 44 -0.51 14 58
SMAD4 0.025 0.007 -10000 0 -10000 0 0
ID2 0.22 0.28 0.65 43 -0.49 12 55
AP1 -0.046 0.13 -10000 0 -0.24 120 120
ABCG2 0.22 0.28 0.65 51 -0.48 12 63
HIF1A 0.088 0.099 0.26 44 -0.19 2 46
TFF3 0.2 0.31 0.7 49 -0.53 14 63
GATA2 0.03 0.067 0.32 12 -0.32 6 18
AKT1 0.077 0.11 0.28 31 -0.2 5 36
response to hypoxia 0.057 0.096 0.22 59 -0.14 16 75
MCL1 0.2 0.26 0.66 34 -0.5 6 40
NDRG1 0.21 0.27 0.64 51 -0.48 8 59
SERPINE1 0.23 0.28 0.66 44 -0.52 10 54
FECH 0.21 0.27 0.63 48 -0.48 11 59
FURIN 0.23 0.28 0.65 44 -0.48 11 55
NCOA2 0.011 0.078 -10000 0 -0.32 20 20
EP300 0.092 0.15 0.34 50 -0.27 22 72
HMOX1 0.22 0.28 0.66 53 -0.48 11 64
BHLHE40 0.21 0.28 0.64 49 -0.48 11 60
BHLHE41 0.22 0.28 0.63 54 -0.53 11 65
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.12 0.14 0.42 19 -10000 0 19
ENG 0.083 0.11 0.31 11 -10000 0 11
JUN 0.014 0.064 -10000 0 -0.32 14 14
RORA 0.22 0.28 0.64 50 -0.5 12 62
ABCB1 -0.063 0.22 0.51 2 -0.69 42 44
TFRC 0.22 0.28 0.64 49 -0.48 11 60
CXCR4 0.22 0.28 0.63 53 -0.49 12 65
TF 0.24 0.3 0.7 58 -0.5 10 68
CITED2 0.22 0.28 0.63 54 -0.49 9 63
HIF1A/ARNT 0.26 0.39 0.94 48 -0.63 3 51
LDHA -0.002 0.13 0.47 2 -0.56 15 17
ETS1 0.22 0.27 0.65 39 -0.5 8 47
PGK1 0.23 0.27 0.66 41 -0.48 11 52
NOS2 0.24 0.3 0.7 58 -0.5 11 69
ITGB2 0.23 0.28 0.67 45 -0.51 9 54
ALDOA 0.22 0.27 0.63 54 -0.48 11 65
Cbp/p300/CITED2 0.19 0.32 0.68 43 -0.54 17 60
FOS -0.079 0.16 -10000 0 -0.32 123 123
HK2 0.22 0.28 0.67 41 -0.49 9 50
SP1 0.006 0.064 -10000 0 -0.17 42 42
GCK 0.083 0.35 0.6 10 -1.1 27 37
HK1 0.23 0.27 0.65 45 -0.48 11 56
NPM1 0.22 0.27 0.64 50 -0.48 11 61
EGLN1 0.22 0.27 0.65 44 -0.49 9 53
CREB1 0.028 0.006 -10000 0 -10000 0 0
PGM1 0.22 0.28 0.65 46 -0.48 11 57
SMAD3 0.026 0.004 -10000 0 -10000 0 0
EDN1 0.042 0.2 0.56 5 -0.59 15 20
IGFBP1 0.24 0.29 0.69 56 -0.48 10 66
VEGFA 0.18 0.26 0.57 46 -0.45 17 63
HIF1A/JAB1 0.082 0.078 0.25 26 -10000 0 26
CP 0.2 0.32 0.71 57 -0.56 13 70
CXCL12 0.17 0.3 0.63 49 -0.56 15 64
COPS5 0.027 0.016 -10000 0 -10000 0 0
SMAD3/SMAD4 0.036 0.011 -10000 0 -10000 0 0
BNIP3 0.22 0.28 0.65 43 -0.48 11 54
EGLN3 0.22 0.28 0.63 53 -0.5 10 63
CA9 0.35 0.32 0.73 109 -0.48 5 114
TERT 0.27 0.33 0.71 95 -0.48 9 104
ENO1 0.23 0.28 0.65 44 -0.48 10 54
PFKL 0.23 0.27 0.65 42 -0.49 9 51
NCOA1 0.027 0.008 -10000 0 -10000 0 0
ADM 0.22 0.27 0.65 42 -0.49 9 51
ARNT 0.077 0.092 0.31 15 -10000 0 15
HNF4A 0.041 0.097 0.32 37 -0.15 8 45
ADFP 0.18 0.27 0.61 52 -0.47 11 63
SLC2A1 0.18 0.27 0.57 47 -0.45 17 64
LEP 0.22 0.3 0.68 46 -0.53 10 56
HIF1A/ARNT/Cbp/p300 0.19 0.34 0.77 44 -0.52 15 59
EPO 0.19 0.26 0.68 36 -0.5 3 39
CREBBP 0.091 0.15 0.34 50 -0.27 21 71
HIF1A/ARNT/Cbp/p300/HDAC7 0.2 0.33 0.76 41 -0.52 12 53
PFKFB3 0.2 0.27 0.63 46 -0.48 10 56
NT5E 0.21 0.29 0.66 43 -0.53 14 57
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.021 0.087 0.22 2 -0.17 67 69
ER alpha/Gai/GDP/Gbeta gamma -0.17 0.26 -10000 0 -0.52 120 120
AKT1 -0.15 0.34 -10000 0 -0.8 82 82
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.15 0.34 -10000 0 -0.82 82 82
mol:Ca2+ -0.047 0.13 -10000 0 -0.33 58 58
IGF1R 0.024 0.025 -10000 0 -0.32 2 2
E2/ER alpha (dimer)/Striatin -0.002 0.08 -10000 0 -0.18 64 64
SHC1 0.024 0.007 -10000 0 -10000 0 0
apoptosis 0.14 0.32 0.76 82 -10000 0 82
RhoA/GTP -0.04 0.046 -10000 0 -0.15 56 56
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.12 0.23 0.24 1 -0.44 115 116
regulation of stress fiber formation 0.033 0.06 0.24 2 -0.29 1 3
E2/ERA-ERB (dimer) -0.001 0.083 0.21 2 -0.18 66 68
KRAS 0.025 0.006 -10000 0 -10000 0 0
G13/GTP -0.001 0.072 -10000 0 -0.17 64 64
pseudopodium formation -0.033 0.06 0.29 1 -0.24 2 3
E2/ER alpha (dimer)/PELP1 -0.003 0.08 -10000 0 -0.18 65 65
GRB2 0.025 0.005 -10000 0 -10000 0 0
GNG2 0.02 0.042 -10000 0 -0.32 6 6
GNAO1 -0.081 0.16 -10000 0 -0.32 124 124
HRAS 0.024 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.14 0.25 -10000 0 -0.58 86 86
E2/ER beta (dimer) 0.02 0.014 0.22 2 -10000 0 2
mol:GDP -0.037 0.11 -10000 0 -0.28 67 67
mol:NADP -0.14 0.25 -10000 0 -0.58 86 86
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
mol:IP3 -0.056 0.12 -10000 0 -0.34 58 58
IGF-1R heterotetramer 0.024 0.025 -10000 0 -0.32 2 2
PLCB1 -0.051 0.13 -10000 0 -0.35 59 59
PLCB2 -0.05 0.13 -10000 0 -0.34 60 60
IGF1 -0.12 0.17 -10000 0 -0.32 176 176
mol:L-citrulline -0.14 0.25 -10000 0 -0.58 86 86
RHOA 0.025 0.006 -10000 0 -10000 0 0
Gai/GDP -0.25 0.36 -10000 0 -0.71 145 145
JNK cascade 0.02 0.014 0.22 2 -10000 0 2
BCAR1 0.025 0.006 -10000 0 -10000 0 0
ESR2 0.027 0.022 0.33 2 -10000 0 2
GNAQ 0.023 0.008 -10000 0 -10000 0 0
ESR1 -0.031 0.13 -10000 0 -0.32 66 66
Gq family/GDP/Gbeta gamma -0.027 0.15 -10000 0 -0.67 16 16
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.019 0.093 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.12 0.22 0.24 1 -0.43 113 114
GNAZ -0.049 0.14 -10000 0 -0.32 87 87
E2/ER alpha (dimer) -0.02 0.087 -10000 0 -0.22 66 66
STRN 0.026 0.004 -10000 0 -10000 0 0
GNAL -0.12 0.17 -10000 0 -0.32 163 163
PELP1 0.024 0.008 -10000 0 -10000 0 0
MAPK11 -0.011 0.011 0.13 2 -10000 0 2
GNAI2 0.025 0.006 -10000 0 -10000 0 0
GNAI3 0.026 0.003 -10000 0 -10000 0 0
GNAI1 0.023 0.03 -10000 0 -0.32 3 3
HBEGF -0.14 0.26 0.33 10 -0.48 117 127
cAMP biosynthetic process -0.069 0.11 0.14 1 -0.18 188 189
SRC -0.16 0.25 0.33 1 -0.49 116 117
PI3K 0.034 0.018 -10000 0 -0.22 1 1
GNB1 0.026 0.003 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.01 0.12 -10000 0 -0.28 54 54
SOS1 0.026 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.15 0.2 -10000 0 -0.38 145 145
Gs family/GTP -0.066 0.11 0.17 1 -0.18 188 189
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.043 0.018 -10000 0 -10000 0 0
vasodilation -0.13 0.24 -10000 0 -0.55 86 86
mol:DAG -0.056 0.12 -10000 0 -0.34 58 58
Gs family/GDP/Gbeta gamma -0.082 0.13 -10000 0 -0.3 78 78
MSN -0.035 0.063 0.3 1 -0.25 2 3
Gq family/GTP -0.043 0.14 -10000 0 -0.35 60 60
mol:PI-3-4-5-P3 -0.14 0.33 -10000 0 -0.79 82 82
NRAS 0.026 0.002 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.13 0.24 0.55 86 -10000 0 86
GRB2/SOS1 0.037 0.01 -10000 0 -10000 0 0
RhoA/GDP -0.024 0.12 -10000 0 -0.29 58 58
NOS3 -0.15 0.27 -10000 0 -0.61 86 86
GNA11 0.025 0.018 -10000 0 -0.32 1 1
MAPKKK cascade -0.12 0.26 -10000 0 -0.61 80 80
E2/ER alpha (dimer)/PELP1/Src -0.13 0.24 0.26 1 -0.45 115 116
ruffle organization -0.033 0.06 0.29 1 -0.24 2 3
ROCK2 -0.031 0.07 0.32 2 -0.26 1 3
GNA14 -0.015 0.11 -10000 0 -0.32 45 45
GNA15 0.023 0.03 -10000 0 -0.32 3 3
GNA13 0.025 0.005 -10000 0 -10000 0 0
MMP9 -0.12 0.26 0.38 10 -0.47 110 120
MMP2 -0.16 0.24 0.28 3 -0.47 126 129
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.023 0.025 -10000 0 -0.32 2 2
LAT2 -0.063 0.12 0.27 1 -0.27 85 86
AP1 -0.11 0.2 -10000 0 -0.44 74 74
mol:PIP3 -0.067 0.16 0.29 8 -0.32 82 90
IKBKB -0.047 0.12 0.25 11 -0.24 64 75
AKT1 -0.015 0.14 0.29 34 -0.26 21 55
IKBKG -0.054 0.11 0.23 7 -0.23 71 78
MS4A2 -0.062 0.14 -10000 0 -0.32 96 96
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.024 0.006 -10000 0 -10000 0 0
MAP3K1 -0.062 0.15 0.23 10 -0.34 59 69
mol:Ca2+ -0.049 0.13 0.26 8 -0.25 81 89
LYN 0.025 0.013 -10000 0 -10000 0 0
CBLB -0.063 0.12 0.18 1 -0.27 79 80
SHC1 0.024 0.007 -10000 0 -10000 0 0
RasGAP/p62DOK -0.007 0.094 -10000 0 -0.17 97 97
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.019 0.042 -10000 0 -0.32 6 6
PLD2 -0.023 0.14 0.22 66 -0.23 54 120
PTPN13 -0.063 0.15 -10000 0 -0.5 13 13
PTPN11 0.014 0.025 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.032 0.12 0.3 11 -0.28 19 30
SYK 0.021 0.037 -10000 0 -0.33 4 4
GRB2 0.025 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.074 0.15 -10000 0 -0.32 85 85
LAT -0.061 0.12 0.27 1 -0.27 78 79
PAK2 -0.068 0.16 0.25 8 -0.37 62 70
NFATC2 -0.073 0.16 -10000 0 -0.48 53 53
HRAS -0.075 0.17 0.25 3 -0.39 66 69
GAB2 0.024 0.018 -10000 0 -0.32 1 1
PLA2G1B 0.006 0.079 -10000 0 -0.82 3 3
Fc epsilon R1 -0.036 0.13 0.23 6 -0.22 119 125
Antigen/IgE/Fc epsilon R1 -0.03 0.12 0.22 6 -0.19 119 125
mol:GDP -0.079 0.18 0.22 1 -0.42 63 64
JUN 0.014 0.063 -10000 0 -0.32 14 14
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.023 0.019 -10000 0 -0.32 1 1
FOS -0.081 0.16 -10000 0 -0.32 124 124
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.06 0.13 0.18 2 -0.28 84 86
CHUK -0.056 0.11 0.25 5 -0.23 69 74
KLRG1 -0.051 0.11 0.18 2 -0.22 98 100
VAV1 -0.064 0.12 0.18 1 -0.28 79 80
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.06 0.12 0.18 1 -0.28 74 75
negative regulation of mast cell degranulation -0.041 0.12 0.18 1 -0.27 52 53
BTK -0.084 0.19 -10000 0 -0.48 56 56
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.072 0.15 -10000 0 -0.32 85 85
GAB2/PI3K/SHP2 -0.063 0.075 -10000 0 -0.21 56 56
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.057 0.13 0.19 1 -0.24 108 109
RAF1 0.01 0.088 -10000 0 -0.91 3 3
Fc epsilon R1/FcgammaRIIB/SHIP -0.027 0.13 0.23 6 -0.21 119 125
FCER1G 0.028 0.065 0.33 13 -0.31 3 16
FCER1A -0.046 0.14 0.32 1 -0.33 79 80
Antigen/IgE/Fc epsilon R1/Fyn -0.024 0.12 0.22 6 -0.19 115 121
MAPK3 0.006 0.08 -10000 0 -0.83 3 3
MAPK1 0.005 0.08 -10000 0 -0.83 3 3
NFKB1 0.026 0.003 -10000 0 -10000 0 0
MAPK8 -0.06 0.22 -10000 0 -0.62 43 43
DUSP1 -0.065 0.15 -10000 0 -0.32 105 105
NF-kappa-B/RelA -0.028 0.074 0.13 1 -0.16 56 57
actin cytoskeleton reorganization -0.064 0.15 -10000 0 -0.53 12 12
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.059 0.16 0.31 1 -0.32 78 79
FER -0.062 0.12 0.18 1 -0.28 78 79
RELA 0.026 0.004 -10000 0 -10000 0 0
ITK -0.048 0.12 -10000 0 -0.36 46 46
SOS1 0.026 0.004 -10000 0 -10000 0 0
PLCG1 -0.074 0.18 0.3 3 -0.36 84 87
cytokine secretion -0.024 0.051 -10000 0 -0.14 14 14
SPHK1 -0.05 0.13 0.2 12 -0.28 73 85
PTK2 -0.066 0.16 -10000 0 -0.55 12 12
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.074 0.16 -10000 0 -0.33 87 87
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.068 0.16 0.3 5 -0.32 85 90
MAP2K2 0.002 0.081 -10000 0 -0.85 3 3
MAP2K1 0.002 0.081 -10000 0 -0.85 3 3
MAP2K7 0.026 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 -0.043 0.1 0.18 4 -0.22 70 74
MAP2K4 -0.072 0.3 -10000 0 -0.89 46 46
Fc epsilon R1/FcgammaRIIB -0.032 0.14 0.23 7 -0.22 123 130
mol:Choline -0.023 0.13 0.22 66 -0.22 54 120
SHC/Grb2/SOS1 -0.03 0.14 -10000 0 -0.27 68 68
FYN 0.022 0.03 -10000 0 -0.32 3 3
DOK1 0.026 0.016 0.33 1 -10000 0 1
PXN -0.063 0.15 -10000 0 -0.51 12 12
HCLS1 -0.062 0.12 0.18 1 -0.27 77 78
PRKCB -0.075 0.15 0.27 6 -0.29 93 99
FCGR2B 0.003 0.084 0.33 2 -0.32 24 26
IGHE 0 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.041 0.12 0.18 1 -0.28 52 53
LCP2 0.022 0.03 -10000 0 -0.32 3 3
PLA2G4A -0.069 0.13 0.18 1 -0.28 85 86
RASA1 0.025 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.023 0.13 0.22 66 -0.22 54 120
IKK complex -0.035 0.097 0.25 11 -0.19 49 60
WIPF1 0.015 0.059 -10000 0 -0.32 12 12
Ephrin A reverse 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
MAPKKK cascade -0.004 0.084 0.21 3 -0.19 64 67
EFNA5 0.015 0.063 0.33 1 -0.32 13 14
FYN -0.038 0.065 0.18 5 -0.18 64 69
neuron projection morphogenesis -0.004 0.084 0.21 3 -0.19 64 67
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.003 0.084 0.21 3 -0.19 64 67
EPHA5 -0.037 0.11 0.33 2 -0.32 53 55
LPA receptor mediated 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
GNB1/GNG2 0.013 0.087 -10000 0 -0.19 57 57
NF kappa B1 p50/RelA/I kappa B alpha -0.032 0.099 0.27 1 -0.26 21 22
AP1 -0.065 0.13 -10000 0 -0.21 154 154
mol:PIP3 -0.051 0.069 -10000 0 -0.19 65 65
AKT1 -0.026 0.08 0.24 4 -0.25 12 16
PTK2B -0.06 0.11 0.19 1 -0.27 62 63
RHOA -0.012 0.065 0.23 2 -0.26 15 17
PIK3CB 0.025 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.028 0.067 0.21 4 -0.22 14 18
MAGI3 0.026 0.003 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
apoptosis -0.036 0.097 0.17 1 -0.22 77 78
HRAS/GDP 0.018 0.006 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.063 0.12 0.3 3 -0.3 43 46
NF kappa B1 p50/RelA -0.037 0.1 -10000 0 -0.24 53 53
endothelial cell migration -0.034 0.12 -10000 0 -0.32 53 53
ADCY4 -0.1 0.16 -10000 0 -0.34 109 109
ADCY5 -0.19 0.22 -10000 0 -0.42 157 157
ADCY6 -0.1 0.16 -10000 0 -0.34 108 108
ADCY7 -0.1 0.16 -10000 0 -0.34 107 107
ADCY1 -0.1 0.16 -10000 0 -0.33 106 106
ADCY2 -0.14 0.2 -10000 0 -0.38 135 135
ADCY3 -0.1 0.16 -10000 0 -0.34 107 107
ADCY8 -0.097 0.16 -10000 0 -0.34 99 99
ADCY9 -0.11 0.17 -10000 0 -0.35 109 109
GSK3B -0.057 0.11 0.19 7 -0.29 46 53
arachidonic acid secretion -0.12 0.17 -10000 0 -0.35 121 121
GNG2 0.02 0.042 -10000 0 -0.32 6 6
TRIP6 0.013 0.016 -10000 0 -10000 0 0
GNAO1 -0.066 0.12 -10000 0 -0.23 126 126
HRAS 0.024 0.008 -10000 0 -10000 0 0
NFKBIA -0.048 0.093 0.27 1 -0.25 35 36
GAB1 0.025 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.017 0.15 -10000 0 -0.81 13 13
JUN 0.014 0.063 -10000 0 -0.32 14 14
LPA/LPA2/NHERF2 0.027 0.032 0.21 1 -0.081 22 23
TIAM1 0.001 0.17 -10000 0 -0.95 13 13
PIK3R1 0.024 0.019 -10000 0 -0.32 1 1
mol:IP3 -0.027 0.067 0.21 4 -0.2 29 33
PLCB3 -0.017 0.026 0.19 3 -10000 0 3
FOS -0.081 0.16 -10000 0 -0.32 124 124
positive regulation of mitosis -0.12 0.17 -10000 0 -0.35 121 121
LPA/LPA1-2-3 -0.001 0.1 0.22 4 -0.2 78 82
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.025 0.006 -10000 0 -10000 0 0
stress fiber formation -0.038 0.097 0.28 1 -0.3 25 26
GNAZ -0.055 0.11 -10000 0 -0.22 111 111
EGFR/PI3K-beta/Gab1 -0.024 0.086 -10000 0 -0.2 64 64
positive regulation of dendritic cell cytokine production -0.002 0.1 0.22 4 -0.2 78 82
LPA/LPA2/MAGI-3 0.027 0.032 0.21 1 -10000 0 1
ARHGEF1 -0.02 0.082 0.18 29 -0.23 14 43
GNAI2 -0.02 0.073 -10000 0 -0.2 52 52
GNAI3 -0.022 0.076 -10000 0 -0.2 56 56
GNAI1 -0.022 0.076 -10000 0 -0.2 56 56
LPA/LPA3 -0.006 0.073 0.2 4 -0.17 54 58
LPA/LPA2 0.012 0.031 0.22 1 -0.093 23 24
LPA/LPA1 -0.015 0.093 -10000 0 -0.24 56 56
HB-EGF/EGFR 0.034 0.082 0.15 88 -0.22 19 107
HBEGF 0.029 0.1 0.19 101 -0.25 13 114
mol:DAG -0.027 0.067 0.21 4 -0.2 29 33
cAMP biosynthetic process -0.13 0.17 0.27 1 -0.35 129 130
NFKB1 0.026 0.003 -10000 0 -10000 0 0
SRC 0.025 0.007 -10000 0 -10000 0 0
GNB1 0.026 0.005 -10000 0 -10000 0 0
LYN -0.039 0.095 0.25 3 -0.25 32 35
GNAQ -0.011 0.061 0.17 1 -0.2 33 34
LPAR2 0.027 0.015 0.33 1 -10000 0 1
LPAR3 -0.001 0.1 0.33 4 -0.32 33 37
LPAR1 -0.012 0.1 -10000 0 -0.25 53 53
IL8 -0.08 0.2 0.34 3 -0.46 72 75
PTK2 -0.037 0.081 0.2 10 -0.22 38 48
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
CASP3 -0.036 0.097 0.17 1 -0.22 77 78
EGFR 0.016 0.051 -10000 0 -0.32 9 9
PLCG1 -0.021 0.074 0.19 6 -0.21 40 46
PLD2 -0.042 0.083 0.2 10 -0.23 30 40
G12/G13 0.013 0.082 -10000 0 -0.19 51 51
PI3K-beta -0.017 0.078 -10000 0 -0.25 19 19
cell migration -0.005 0.065 0.19 1 -0.26 12 13
SLC9A3R2 0.025 0.005 -10000 0 -10000 0 0
PXN -0.039 0.098 0.28 1 -0.31 25 26
HRAS/GTP -0.12 0.18 -10000 0 -0.36 120 120
RAC1 0.025 0.006 -10000 0 -10000 0 0
MMP9 0.091 0.14 0.33 96 -0.32 5 101
PRKCE 0.025 0.005 -10000 0 -10000 0 0
PRKCD -0.032 0.07 0.29 1 -0.26 7 8
Gi(beta/gamma) -0.1 0.16 -10000 0 -0.32 112 112
mol:LPA -0.009 0.035 -10000 0 -0.13 27 27
TRIP6/p130 Cas/FAK1/Paxillin -0.019 0.1 0.29 1 -0.3 23 24
MAPKKK cascade -0.12 0.17 -10000 0 -0.35 121 121
contractile ring contraction involved in cytokinesis -0.012 0.065 0.23 2 -0.26 15 17
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.032 0.086 0.17 1 -0.21 73 74
GNA15 -0.01 0.062 0.17 1 -0.2 35 36
GNA12 0.025 0.006 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
MAPT -0.065 0.12 0.31 3 -0.31 43 46
GNA11 -0.009 0.062 0.17 1 -0.2 32 33
Rac1/GTP 0.017 0.16 -10000 0 -0.86 13 13
MMP2 -0.034 0.12 -10000 0 -0.33 53 53
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 0.036 0.016 -10000 0 -0.22 1 1
alphaV beta3 Integrin -0.044 0.14 -10000 0 -0.23 131 131
PTK2 -0.063 0.16 0.28 7 -0.4 49 56
IGF1R 0.024 0.025 -10000 0 -0.32 2 2
PI4KB 0.023 0.009 -10000 0 -10000 0 0
MFGE8 0.024 0.025 -10000 0 -0.32 2 2
SRC 0.025 0.007 -10000 0 -10000 0 0
CDKN1B -0.08 0.18 0.19 6 -0.48 61 67
VEGFA 0.025 0.005 -10000 0 -10000 0 0
ILK -0.088 0.19 0.19 6 -0.47 71 77
ROCK1 0.025 0.005 -10000 0 -10000 0 0
AKT1 -0.089 0.18 -10000 0 -0.44 73 73
PTK2B -0.023 0.062 0.18 18 -0.31 1 19
alphaV/beta3 Integrin/JAM-A -0.047 0.14 0.24 6 -0.22 134 140
CBL 0.025 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.023 0.077 0.23 3 -0.19 43 46
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.044 0.12 -10000 0 -0.18 176 176
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.032 0.095 -10000 0 -0.31 23 23
alphaV/beta3 Integrin/Syndecan-1 0.02 0.077 -10000 0 -0.19 46 46
PI4KA 0.025 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.096 0.18 -10000 0 -0.28 176 176
PI4 Kinase 0.033 0.014 -10000 0 -10000 0 0
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.09 0.13 0.23 149 -0.19 38 187
RPS6KB1 -0.13 0.14 0.19 1 -0.33 108 109
TLN1 0.023 0.008 -10000 0 -10000 0 0
MAPK3 -0.17 0.26 -10000 0 -0.52 131 131
GPR124 -0.006 0.093 -10000 0 -0.32 32 32
MAPK1 -0.18 0.26 -10000 0 -0.52 137 137
PXN 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
alphaV/beta3 Integrin/Tumstatin -0.035 0.13 0.23 4 -0.21 129 133
cell adhesion 0.013 0.077 -10000 0 -0.21 40 40
ANGPTL3 0.018 0.04 0.33 5 -10000 0 5
VEGFR2 homodimer/VEGFA homodimer/Src 0.046 0.021 -10000 0 -0.19 1 1
IGF-1R heterotetramer 0.024 0.025 -10000 0 -0.32 2 2
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
TGFBR2 0.023 0.025 -10000 0 -0.32 2 2
ITGB3 -0.012 0.11 -10000 0 -0.32 44 44
IGF1 -0.12 0.17 -10000 0 -0.32 176 176
RAC1 0.025 0.006 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.003 0.098 -10000 0 -0.23 55 55
apoptosis 0.025 0.005 -10000 0 -10000 0 0
CD47 0.025 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.023 0.074 -10000 0 -0.19 41 41
VCL 0.025 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.006 0.12 -10000 0 -0.24 76 76
CSF1 0.013 0.065 -10000 0 -0.32 15 15
PIK3C2A -0.087 0.19 0.19 6 -0.48 70 76
PI4 Kinase/Pyk2 -0.052 0.12 -10000 0 -0.23 102 102
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.035 0.076 -10000 0 -0.18 41 41
FAK1/Vinculin -0.041 0.15 0.3 9 -0.33 46 55
alphaV beta3/Integrin/ppsTEM5 0.003 0.099 -10000 0 -0.23 55 55
RHOA 0.025 0.006 -10000 0 -10000 0 0
VTN -0.022 0.13 0.33 7 -0.32 60 67
BCAR1 0.025 0.006 -10000 0 -10000 0 0
FGF2 -0.083 0.16 -10000 0 -0.32 127 127
F11R -0.066 0.094 -10000 0 -0.23 102 102
alphaV/beta3 Integrin/Lactadherin 0.022 0.077 -10000 0 -0.19 45 45
alphaV/beta3 Integrin/TGFBR2 0.022 0.075 -10000 0 -0.2 41 41
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.049 0.05 -10000 0 -0.18 15 15
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.021 0.066 -10000 0 -0.17 41 41
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.035 0.095 0.33 26 -0.32 11 37
alphaV/beta3 Integrin/Pyk2 0.015 0.068 -10000 0 -0.17 41 41
SDC1 0.02 0.042 -10000 0 -0.32 6 6
VAV3 -0.018 0.06 0.36 3 -10000 0 3
PTPN11 0.025 0.005 -10000 0 -10000 0 0
IRS1 0.018 0.045 -10000 0 -0.32 7 7
FAK1/Paxillin -0.041 0.15 0.3 9 -0.33 48 57
cell migration -0.042 0.14 0.27 12 -0.3 46 58
ITGAV 0.025 0.005 -10000 0 -10000 0 0
PI3K -0.024 0.14 0.3 1 -0.22 110 111
SPP1 0.14 0.15 0.33 161 -10000 0 161
KDR 0.024 0.025 -10000 0 -0.32 2 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.025 0.005 -10000 0 -10000 0 0
COL4A3 -0.064 0.15 0.33 4 -0.32 102 106
angiogenesis -0.16 0.28 0.27 2 -0.52 133 135
Rac1/GTP -0.019 0.058 0.32 3 -10000 0 3
EDIL3 -0.022 0.12 -10000 0 -0.32 55 55
cell proliferation 0.022 0.075 -10000 0 -0.19 41 41
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.081 0.16 -10000 0 -0.32 124 124
CDC42/GTP -0.071 0.14 -10000 0 -0.25 122 122
PLCG1 -0.077 0.13 -10000 0 -0.26 111 111
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.025 0.006 -10000 0 -10000 0 0
GNAI3 0.026 0.003 -10000 0 -10000 0 0
G12/G13 0.035 0.012 -10000 0 -10000 0 0
cell migration -0.07 0.14 -10000 0 -0.24 122 122
S1PR5 0.032 0.055 0.33 11 -0.32 2 13
S1PR4 0.025 0.04 0.33 3 -0.32 3 6
MAPK3 -0.077 0.13 -10000 0 -0.26 115 115
MAPK1 -0.082 0.13 -10000 0 -0.26 119 119
S1P/S1P5/Gi -0.071 0.14 -10000 0 -0.24 144 144
GNAI1 0.023 0.03 -10000 0 -0.32 3 3
CDC42/GDP 0.019 0.002 -10000 0 -10000 0 0
S1P/S1P5/G12 0.036 0.034 0.21 10 -0.19 2 12
RHOA -0.004 0.057 0.19 29 -0.16 2 31
S1P/S1P4/Gi -0.074 0.14 -10000 0 -0.27 114 114
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ -0.049 0.14 -10000 0 -0.32 87 87
S1P/S1P4/G12/G13 0.045 0.027 0.22 3 -0.17 2 5
GNA12 0.025 0.006 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
CDC42 0.026 0.003 -10000 0 -10000 0 0
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS -0.015 0.13 0.24 24 -0.18 126 150
SMAD6-7/SMURF1 0.049 0.025 0.23 3 -0.19 1 4
NOG 0.04 0.081 0.33 29 -10000 0 29
SMAD9 -0.13 0.24 -10000 0 -0.48 120 120
SMAD4 0.025 0.007 -10000 0 -10000 0 0
SMAD5 -0.024 0.11 -10000 0 -0.34 23 23
BMP7/USAG1 -0.12 0.16 0.24 3 -0.26 207 210
SMAD5/SKI -0.019 0.12 -10000 0 -0.35 24 24
SMAD1 0.013 0.049 -10000 0 -0.25 6 6
BMP2 -0.009 0.1 -10000 0 -0.32 40 40
SMAD1/SMAD1/SMAD4 0.024 0.06 -10000 0 -0.25 10 10
BMPR1A 0.025 0.005 -10000 0 -10000 0 0
BMPR1B 0.058 0.11 0.33 54 -0.32 6 60
BMPR1A-1B/BAMBI 0.049 0.089 0.23 45 -0.19 24 69
AHSG 0.031 0.1 0.33 42 -10000 0 42
CER1 -0.007 0.017 -10000 0 -10000 0 0
BMP2-4/CER1 0.009 0.083 0.23 4 -0.19 53 57
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.041 0.12 0.19 1 -0.3 38 39
BMP2-4 (homodimer) 0.003 0.093 0.24 4 -0.23 54 58
RGMB 0.025 0.006 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.078 0.071 0.24 52 -0.18 6 58
RGMA -0.072 0.16 -10000 0 -0.32 114 114
SMURF1 0.026 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.038 0.12 0.18 4 -0.31 36 40
BMP2-4/USAG1 -0.048 0.13 0.23 8 -0.21 150 158
SMAD6/SMURF1/SMAD5 -0.019 0.12 -10000 0 -0.36 22 22
SOSTDC1 -0.088 0.16 0.33 6 -0.32 125 131
BMP7/BMPR2/BMPR1A-1B -0.012 0.12 0.24 28 -0.18 120 148
SKI 0.026 0.003 -10000 0 -10000 0 0
BMP6 (homodimer) 0.026 0.028 0.33 2 -0.32 1 3
HFE2 0.004 0.038 0.33 4 -10000 0 4
ZFYVE16 0.025 0.006 -10000 0 -10000 0 0
MAP3K7 0.025 0.006 -10000 0 -10000 0 0
BMP2-4/CHRD 0 0.11 0.23 5 -0.21 74 79
SMAD5/SMAD5/SMAD4 -0.018 0.12 -10000 0 -0.36 22 22
MAPK1 0.025 0.005 -10000 0 -10000 0 0
TAK1/TAB family -0.026 0.11 -10000 0 -0.29 28 28
BMP7 (homodimer) -0.097 0.16 -10000 0 -0.32 141 141
NUP214 0.024 0.008 -10000 0 -10000 0 0
BMP6/FETUA 0.052 0.064 0.24 41 -10000 0 41
SMAD1/SKI 0.024 0.069 -10000 0 -0.27 11 11
SMAD6 0.027 0.031 0.33 3 -0.32 1 4
CTDSP2 0.026 0.004 -10000 0 -10000 0 0
BMP2-4/FETUA 0.029 0.099 0.23 35 -0.2 45 80
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.023 0.17 0.33 61 -0.32 55 116
BMPR2 (homodimer) 0.025 0.005 -10000 0 -10000 0 0
GADD34/PP1CA 0.049 0.016 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.058 0.077 0.24 52 -0.22 6 58
CHRDL1 -0.18 0.16 -10000 0 -0.32 229 229
ENDOFIN/SMAD1 0.025 0.068 -10000 0 -0.28 9 9
SMAD6-7/SMURF1/SMAD1 0.045 0.074 -10000 0 -0.28 7 7
SMAD6/SMURF1 0.026 0.004 -10000 0 -10000 0 0
BAMBI 0.005 0.099 0.33 7 -0.32 29 36
SMURF2 0.025 0.006 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.11 0.13 -10000 0 -0.21 237 237
BMP2-4/GREM1 0.011 0.14 0.23 60 -0.2 101 161
SMAD7 0.025 0.006 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.13 0.23 -10000 0 -0.45 124 124
SMAD1/SMAD6 0.025 0.069 -10000 0 -0.27 11 11
TAK1/SMAD6 0.036 0.01 -10000 0 -10000 0 0
BMP7 -0.097 0.16 -10000 0 -0.32 141 141
BMP6 0.026 0.028 0.33 2 -0.32 1 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.038 0.12 -10000 0 -0.32 36 36
PPM1A 0.026 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.024 0.068 -10000 0 -0.28 10 10
SMAD7/SMURF1 0.036 0.011 -10000 0 -10000 0 0
CTDSPL 0.025 0.006 -10000 0 -10000 0 0
PPP1CA 0.026 0.004 -10000 0 -10000 0 0
XIAP 0.026 0.003 -10000 0 -10000 0 0
CTDSP1 0.025 0.006 -10000 0 -10000 0 0
PPP1R15A 0.026 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.049 0.14 0.2 4 -0.34 45 49
CHRD -0.004 0.098 0.33 1 -0.32 35 36
BMPR2 0.025 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.048 0.12 0.18 4 -0.33 34 38
BMP4 0.015 0.078 0.33 5 -0.32 17 22
FST 0.015 0.091 0.33 10 -0.32 21 31
BMP2-4/NOG 0.026 0.095 0.25 21 -0.19 45 66
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.006 0.12 0.24 26 -0.17 117 143
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.021 0.11 0.25 8 -0.25 47 55
alphaM/beta2 Integrin/GPIbA -0.003 0.1 0.27 13 -0.25 21 34
alphaM/beta2 Integrin/proMMP-9 0.039 0.15 0.26 81 -0.28 20 101
PLAUR 0.026 0.004 -10000 0 -10000 0 0
HMGB1 -0.008 0.042 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.007 0.092 0.24 10 -0.24 21 31
AGER -0.004 0.058 0.31 6 -10000 0 6
RAP1A 0.026 0.003 -10000 0 -10000 0 0
SELPLG 0.021 0.05 0.33 2 -0.32 7 9
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.04 0.15 0.42 1 -0.21 152 153
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.091 0.14 0.33 96 -0.32 5 101
CYR61 -0.072 0.16 -10000 0 -0.32 114 114
TLN1 0.023 0.008 -10000 0 -10000 0 0
Rap1/GTP 0.004 0.12 -10000 0 -0.36 24 24
RHOA 0.025 0.006 -10000 0 -10000 0 0
P-selectin oligomer -0.039 0.13 -10000 0 -0.32 73 73
MYH2 -0.008 0.11 0.2 5 -0.34 22 27
MST1R 0.018 0.075 0.33 7 -0.32 14 21
leukocyte activation during inflammatory response -0.035 0.11 0.24 8 -0.2 85 93
APOB -0.027 0.12 0.33 6 -0.32 56 62
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.001 0.092 -10000 0 -0.32 31 31
JAM3 0.003 0.083 -10000 0 -0.32 25 25
GP1BA 0.025 0.048 0.33 8 -0.32 1 9
alphaM/beta2 Integrin/CTGF -0.039 0.13 0.25 8 -0.26 82 90
alphaM/beta2 Integrin -0.011 0.13 0.19 12 -0.38 28 40
JAM3 homodimer 0.003 0.083 -10000 0 -0.32 25 25
ICAM2 0.024 0.018 -10000 0 -0.32 1 1
ICAM1 0.031 0.048 0.33 9 -0.32 1 10
phagocytosis triggered by activation of immune response cell surface activating receptor -0.012 0.13 0.19 12 -0.38 28 40
cell adhesion -0.003 0.099 0.27 13 -0.24 21 34
NFKB1 -0.12 0.2 0.32 22 -0.33 156 178
THY1 0.027 0.027 0.33 3 -10000 0 3
RhoA/GDP 0.019 0.004 -10000 0 -10000 0 0
Lipoprotein(a) -0.011 0.098 0.21 10 -0.2 78 88
alphaM/beta2 Integrin/LRP/tPA -0.007 0.1 0.28 7 -0.23 35 42
IL6 -0.24 0.31 0.43 5 -0.57 176 181
ITGB2 -0.008 0.077 0.32 8 -0.34 7 15
elevation of cytosolic calcium ion concentration 0.024 0.12 0.25 42 -0.23 19 61
alphaM/beta2 Integrin/JAM2/JAM3 -0.051 0.15 0.26 7 -0.25 112 119
JAM2 -0.063 0.15 -10000 0 -0.32 103 103
alphaM/beta2 Integrin/ICAM1 0.017 0.11 0.25 20 -0.21 29 49
alphaM/beta2 Integrin/uPA/Plg 0.025 0.12 0.25 42 -0.23 20 62
RhoA/GTP -0.009 0.12 0.21 9 -0.35 25 34
positive regulation of phagocytosis -0.007 0.13 0.31 5 -0.35 30 35
Ron/MSP 0.041 0.075 0.25 26 -0.22 15 41
alphaM/beta2 Integrin/uPAR/uPA 0.025 0.12 0.26 42 -0.24 19 61
alphaM/beta2 Integrin/uPAR -0.007 0.093 0.25 9 -0.24 21 30
PLAU 0.063 0.1 0.33 51 -10000 0 51
PLAT 0.009 0.069 -10000 0 -0.32 17 17
actin filament polymerization -0.009 0.11 0.2 7 -0.33 24 31
MST1 0.039 0.068 0.33 20 -0.32 1 21
alphaM/beta2 Integrin/lipoprotein(a) -0.033 0.11 0.26 8 -0.2 84 92
TNF -0.11 0.19 0.4 21 -0.44 16 37
RAP1B 0.024 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.018 0.12 0.25 45 -0.25 21 66
fibrinolysis 0.023 0.12 0.24 42 -0.23 20 62
HCK 0.018 0.064 0.33 5 -0.32 10 15
dendritic cell antigen processing and presentation -0.012 0.13 0.19 12 -0.38 28 40
VTN -0.022 0.13 0.33 7 -0.32 60 67
alphaM/beta2 Integrin/CYR61 -0.056 0.15 0.26 6 -0.26 113 119
LPA -0.01 0.099 0.33 6 -0.32 31 37
LRP1 0.022 0.034 -10000 0 -0.32 4 4
cell migration 0.01 0.13 0.25 23 -0.26 38 61
FN1 0.035 0.095 0.33 26 -0.32 11 37
alphaM/beta2 Integrin/Thy1 -0.005 0.095 0.24 11 -0.24 22 33
MPO 0.021 0.027 0.33 2 -10000 0 2
KNG1 -0.016 0.004 -10000 0 -10000 0 0
RAP1/GDP 0.033 0.01 -10000 0 -10000 0 0
ROCK1 -0.006 0.12 0.2 7 -0.34 25 32
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.004 0.041 0.33 5 -10000 0 5
CTGF -0.04 0.14 -10000 0 -0.32 76 76
alphaM/beta2 Integrin/Hck -0.005 0.11 0.3 10 -0.27 24 34
ITGAM -0.021 0.086 0.32 3 -0.34 18 21
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.03 0.12 0.29 7 -0.23 74 81
HP 0.048 0.1 0.33 43 -0.32 2 45
leukocyte adhesion -0.088 0.17 0.4 1 -0.34 85 86
SELP -0.039 0.13 -10000 0 -0.32 73 73
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.041 0.1 -10000 0 -0.16 162 162
MAPK9 0.005 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion 0.042 0.096 0.2 106 -0.22 6 112
GNB1/GNG2 0.031 0.028 -10000 0 -0.19 6 6
GNB1 0.026 0.003 -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 0.005 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.056 0.086 -10000 0 -0.16 163 163
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 0.02 0.022 0.047 163 -10000 0 163
GNAL -0.12 0.17 -10000 0 -0.32 163 163
GNG2 0.02 0.042 -10000 0 -0.32 6 6
CRH 0.072 0.14 0.33 89 -0.32 6 95
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.003 0.022 -10000 0 -0.25 3 3
MAPK11 0.005 0.001 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.005 0.065 0.17 9 -0.21 18 27
NFATC2 -0.011 0.085 0.15 18 -0.2 52 70
NFATC3 0.013 0.048 0.15 20 -0.11 1 21
CD40LG -0.061 0.24 0.44 23 -0.42 76 99
PTGS2 -0.077 0.25 0.44 22 -0.43 93 115
JUNB 0.022 0.038 -10000 0 -0.32 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.016 0.033 0.13 3 -10000 0 3
CaM/Ca2+ 0.016 0.033 0.13 3 -10000 0 3
CALM1 0.018 0.028 -10000 0 -10000 0 0
JUN 0.007 0.067 -10000 0 -0.32 13 13
mol:Ca2+ 0.001 0.013 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.018 0.012 -10000 0 -10000 0 0
FOSL1 0.002 0.086 -10000 0 -0.32 27 27
CREM 0.025 0.006 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.017 0.18 0.4 22 -0.3 46 68
FOS -0.076 0.15 -10000 0 -0.32 112 112
IFNG -0.008 0.27 0.48 57 -0.38 67 124
AP-1/NFAT1-c-4 -0.026 0.28 0.61 18 -0.44 70 88
FASLG -0.043 0.23 0.47 26 -0.4 70 96
NFAT1-c-4/ICER1 0 0.13 0.29 18 -0.26 33 51
IL2RA -0.04 0.25 0.5 28 -0.42 66 94
FKBP12/FK506 0.019 0.004 -10000 0 -10000 0 0
CSF2 -0.012 0.26 0.47 51 -0.38 70 121
JunB/Fra1/NFAT1-c-4 0.003 0.14 0.29 19 -0.26 44 63
IL4 -0.054 0.22 0.44 19 -0.38 70 89
IL2 -0.011 0.13 -10000 0 -0.92 8 8
IL3 -0.016 0.12 -10000 0 -0.68 12 12
FKBP1A 0.025 0.006 -10000 0 -10000 0 0
BATF3 0.024 0.049 0.33 4 -0.32 5 9
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.023 0.009 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.11 0.19 -10000 0 -0.45 61 61
MAP3K8 0.014 0.03 -10000 0 -0.32 2 2
FOS -0.082 0.15 -10000 0 -0.36 61 61
PRKCA 0.006 0.041 -10000 0 -0.32 4 4
PTPN7 0.007 0.059 0.31 5 -0.32 6 11
HRAS 0.023 0.007 -10000 0 -10000 0 0
PRKCB -0.082 0.15 -10000 0 -0.32 112 112
NRAS 0.025 0.002 -10000 0 -10000 0 0
RAS family/GTP 0.024 0.036 -10000 0 -10000 0 0
MAPK3 -0.043 0.12 -10000 0 -0.52 14 14
MAP2K1 -0.094 0.17 -10000 0 -0.36 110 110
ELK1 0.007 0.029 -10000 0 -10000 0 0
BRAF -0.085 0.15 -10000 0 -0.33 106 106
mol:GTP -0.001 0.002 -10000 0 -0.004 128 128
MAPK1 -0.045 0.12 -10000 0 -0.52 16 16
RAF1 -0.075 0.15 -10000 0 -0.33 93 93
KRAS 0.024 0.006 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 0.02 0.1 0.32 1 -0.34 1 2
SMARCC2 0.022 0.021 -10000 0 -10000 0 0
SMARCC1 0.022 0.02 -10000 0 -10000 0 0
TBX21 -0.007 0.16 0.55 1 -0.54 23 24
SUMO2 0.015 0.022 -10000 0 -10000 0 0
STAT1 (dimer) 0.032 0.03 0.33 4 -10000 0 4
FKBP4 0.025 0.006 -10000 0 -10000 0 0
FKBP5 0.011 0.069 -10000 0 -0.32 17 17
GR alpha/HSP90/FKBP51/HSP90 0.031 0.12 0.26 13 -0.21 6 19
PRL -0.006 0.11 0.58 2 -10000 0 2
cortisol/GR alpha (dimer)/TIF2 0.017 0.25 0.46 34 -0.5 23 57
RELA -0.12 0.13 -10000 0 -0.23 206 206
FGG 0.06 0.26 0.48 46 -0.5 21 67
GR beta/TIF2 0.018 0.13 0.26 18 -0.27 12 30
IFNG -0.001 0.33 0.58 55 -0.53 36 91
apoptosis -0.047 0.18 0.56 1 -0.56 8 9
CREB1 0.034 0.033 0.2 1 -10000 0 1
histone acetylation -0.11 0.13 -10000 0 -0.37 43 43
BGLAP -0.011 0.12 0.41 1 -0.38 1 2
GR/PKAc 0.035 0.11 0.28 6 -10000 0 6
NF kappa B1 p50/RelA -0.22 0.23 0.35 1 -0.4 230 231
SMARCD1 0.022 0.023 -10000 0 -10000 0 0
MDM2 0.031 0.091 0.19 43 -0.15 5 48
GATA3 0.006 0.084 0.28 1 -0.32 24 25
AKT1 0.023 0.011 -10000 0 -0.19 1 1
CSF2 -0.046 0.13 -10000 0 -0.45 8 8
GSK3B 0.015 0.022 -10000 0 -10000 0 0
NR1I3 -0.011 0.18 0.53 4 -0.54 3 7
CSN2 0.027 0.21 0.36 33 -0.45 24 57
BRG1/BAF155/BAF170/BAF60A 0.054 0.061 -10000 0 -0.24 14 14
NFATC1 0.009 0.071 -10000 0 -0.32 18 18
POU2F1 0.026 0.019 -10000 0 -10000 0 0
CDKN1A -0.002 0.11 0.72 1 -1.2 2 3
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.002 0.007 -10000 0 -10000 0 0
SFN 0.047 0.087 0.33 32 -0.32 3 35
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.051 0.12 0.27 13 -0.2 2 15
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.14 0.32 0.5 1 -0.69 96 97
JUN 0.049 0.25 0.5 55 -0.37 25 80
IL4 -0.031 0.14 -10000 0 -0.46 12 12
CDK5R1 0.03 0.064 0.32 17 -10000 0 17
PRKACA 0.026 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.049 0.08 0.23 1 -0.26 31 32
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.038 0.12 0.27 10 -0.2 3 13
cortisol/GR alpha (monomer) 0.026 0.28 0.52 39 -0.56 24 63
NCOA2 0.006 0.075 -10000 0 -0.32 20 20
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.025 0.2 0.33 38 -0.34 88 126
AP-1/NFAT1-c-4 0 0.35 0.59 61 -0.49 71 132
AFP 0.018 0.2 0.56 10 -10000 0 10
SUV420H1 0.025 0.005 -10000 0 -10000 0 0
IRF1 0.04 0.15 0.4 4 -10000 0 4
TP53 0.029 0.039 -10000 0 -0.5 2 2
PPP5C 0.026 0.004 -10000 0 -10000 0 0
KRT17 -0.046 0.4 0.63 46 -0.76 50 96
KRT14 0.14 0.28 0.5 87 -1.1 4 91
TBP 0.03 0.013 -10000 0 -10000 0 0
CREBBP -0.066 0.1 0.29 4 -0.29 19 23
HDAC1 0.024 0.015 -10000 0 -0.15 3 3
HDAC2 0.013 0.025 -10000 0 -10000 0 0
AP-1 0 0.35 0.59 61 -0.49 71 132
MAPK14 0.015 0.022 -10000 0 -10000 0 0
MAPK10 -0.015 0.097 -10000 0 -0.32 35 35
MAPK11 0.014 0.023 -10000 0 -10000 0 0
KRT5 -0.19 0.55 0.65 43 -0.95 119 162
interleukin-1 receptor activity -0.005 0.01 -10000 0 -10000 0 0
NCOA1 0.026 0.006 -10000 0 -10000 0 0
STAT1 0.032 0.03 0.33 4 -10000 0 4
CGA -0.005 0.14 0.44 7 -0.39 1 8
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.16 0.21 -10000 0 -0.47 95 95
MAPK3 0.014 0.022 -10000 0 -10000 0 0
MAPK1 0.014 0.022 -10000 0 -10000 0 0
ICAM1 -0.15 0.24 0.45 5 -0.48 99 104
NFKB1 -0.12 0.13 -10000 0 -0.23 211 211
MAPK8 0.04 0.2 0.43 49 -0.3 26 75
MAPK9 0.015 0.022 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.05 0.18 0.56 1 -0.59 8 9
BAX 0.001 0.061 -10000 0 -10000 0 0
POMC -0.15 0.26 0.55 2 -0.95 13 15
EP300 -0.068 0.1 0.25 3 -0.27 21 24
cortisol/GR alpha (dimer)/p53 0.023 0.24 0.48 28 -0.5 20 48
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.074 0.18 14 -10000 0 14
SGK1 -0.11 0.27 -10000 0 -1.1 21 21
IL13 -0.04 0.24 0.49 20 -0.58 22 42
IL6 -0.43 0.49 -10000 0 -0.93 187 187
PRKACG -0.01 0.015 -10000 0 -10000 0 0
IL5 -0.034 0.22 0.51 9 -0.56 11 20
IL2 -0.049 0.28 0.54 26 -0.55 36 62
CDK5 0.017 0.019 -10000 0 -10000 0 0
PRKACB 0.024 0.025 -10000 0 -0.32 2 2
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
IL8 -0.24 0.37 0.55 1 -0.72 114 115
CDK5R1/CDK5 0.034 0.05 0.24 17 -10000 0 17
NF kappa B1 p50/RelA/PKAc -0.14 0.2 0.31 1 -0.32 196 197
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.044 0.24 0.46 35 -0.47 20 55
SMARCA4 0.022 0.021 -10000 0 -0.11 1 1
chromatin remodeling 0.024 0.17 0.33 24 -0.4 10 34
NF kappa B1 p50/RelA/Cbp -0.26 0.2 -10000 0 -0.43 187 187
JUN (dimer) 0.048 0.24 0.5 55 -0.36 25 80
YWHAH 0.025 0.005 -10000 0 -10000 0 0
VIPR1 -0.008 0.17 0.38 3 -0.65 15 18
NR3C1 0.033 0.17 0.36 26 -0.32 12 38
NR4A1 -0.16 0.18 -10000 0 -0.32 219 219
TIF2/SUV420H1 0.02 0.058 -10000 0 -0.22 20 20
MAPKKK cascade -0.047 0.18 0.56 1 -0.56 8 9
cortisol/GR alpha (dimer)/Src-1 0.03 0.25 0.46 38 -0.49 22 60
PBX1 0.012 0.07 -10000 0 -0.32 16 16
POU1F1 0.009 0.039 0.33 3 -10000 0 3
SELE -0.39 0.48 0.43 2 -0.89 179 181
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.024 0.17 0.33 24 -0.4 10 34
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.044 0.24 0.46 35 -0.47 20 55
mol:cortisol 0.019 0.16 0.29 46 -0.28 21 67
MMP1 0.19 0.27 0.46 140 -0.74 7 147
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.021 0.15 0.35 27 -0.28 27 54
TBX21 -0.11 0.49 0.83 8 -1.1 63 71
B2M 0.023 0.018 -10000 0 -10000 0 0
TYK2 0.013 0.049 0.21 3 -10000 0 3
IL12RB1 0.02 0.11 0.39 20 -0.36 10 30
GADD45B -0.075 0.4 0.72 7 -0.97 48 55
IL12RB2 0.055 0.14 0.34 62 -0.34 6 68
GADD45G -0.084 0.4 0.7 8 -0.93 51 59
natural killer cell activation 0 0.032 0.13 11 -0.05 25 36
RELB 0.026 0.004 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
IL18 0.017 0.048 -10000 0 -0.32 6 6
IL2RA 0.022 0.097 0.33 19 -0.32 17 36
IFNG 0.072 0.12 0.33 75 -10000 0 75
STAT3 (dimer) -0.07 0.37 0.64 9 -0.8 61 70
HLA-DRB5 -0.006 0.011 -10000 0 -0.025 81 81
FASLG -0.1 0.49 0.89 9 -1.1 61 70
NF kappa B2 p52/RelB -0.11 0.44 -10000 0 -1 63 63
CD4 0.006 0.036 -10000 0 -0.32 2 2
SOCS1 0.026 0.016 0.33 1 -10000 0 1
EntrezGene:6955 -0.008 0.015 0.033 4 -0.029 104 108
CD3D -0.019 0.099 0.32 3 -0.33 32 35
CD3E -0.026 0.1 -10000 0 -0.32 39 39
CD3G -0.03 0.11 -10000 0 -0.33 42 42
IL12Rbeta2/JAK2 0.048 0.11 0.27 55 -0.25 6 61
CCL3 -0.11 0.49 0.87 9 -1.1 57 66
CCL4 -0.13 0.52 0.83 8 -1.2 60 68
HLA-A 0 0.009 0.032 7 -0.04 14 21
IL18/IL18R 0.048 0.095 0.31 2 -0.21 24 26
NOS2 -0.073 0.43 0.8 8 -0.99 52 60
IL12/IL12R/TYK2/JAK2/SPHK2 0.021 0.15 0.35 26 -0.28 26 52
IL1R1 -0.095 0.45 0.8 8 -1 60 68
IL4 -0.003 0.046 -10000 0 -0.2 3 3
JAK2 0.013 0.046 0.21 3 -10000 0 3
EntrezGene:6957 -0.007 0.014 0.032 4 -0.027 89 93
TCR/CD3/MHC I/CD8 -0.12 0.3 0.29 4 -0.64 73 77
RAB7A -0.05 0.34 0.65 8 -0.75 51 59
lysosomal transport -0.044 0.32 0.65 8 -0.71 51 59
FOS -0.36 0.57 0.67 3 -1.1 145 148
STAT4 (dimer) -0.073 0.4 0.68 8 -0.86 64 72
STAT5A (dimer) -0.07 0.48 0.63 25 -1 63 88
GZMA -0.13 0.52 0.82 9 -1.2 59 68
GZMB -0.11 0.5 0.8 12 -1.1 61 73
HLX 0.026 0.015 0.33 1 -10000 0 1
LCK -0.12 0.5 0.77 9 -1.1 63 72
TCR/CD3/MHC II/CD4 -0.1 0.18 -10000 0 -0.31 133 133
IL2/IL2R 0.048 0.09 0.26 24 -0.21 24 48
MAPK14 -0.08 0.41 0.71 7 -0.93 55 62
CCR5 -0.079 0.42 0.74 7 -0.98 51 58
IL1B 0.009 0.11 0.33 14 -0.34 18 32
STAT6 0.005 0.17 0.48 11 -0.62 6 17
STAT4 0.008 0.075 -10000 0 -0.32 20 20
STAT3 0.026 0.004 -10000 0 -10000 0 0
STAT1 0.028 0.03 0.33 4 -10000 0 4
NFKB1 0.026 0.003 -10000 0 -10000 0 0
NFKB2 0.025 0.005 -10000 0 -10000 0 0
IL12B 0.02 0.079 0.34 16 -10000 0 16
CD8A -0.009 0.1 0.36 1 -0.32 39 40
CD8B -0.001 0.11 0.34 7 -0.32 35 42
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.021 0.15 0.28 27 -0.35 27 54
IL2RB 0.022 0.041 0.33 1 -0.32 5 6
proteasomal ubiquitin-dependent protein catabolic process -0.058 0.37 0.65 9 -0.78 63 72
IL2RG 0.025 0.068 0.33 9 -0.32 9 18
IL12 0.031 0.089 0.28 24 -10000 0 24
STAT5A 0.025 0.018 -10000 0 -0.32 1 1
CD247 0.001 0.052 0.33 1 -0.32 6 7
IL2 -0.005 0.019 -10000 0 -10000 0 0
SPHK2 0.027 0.015 0.33 1 -10000 0 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.017 0.064 0.31 9 -10000 0 9
IL12/IL12R/TYK2/JAK2 -0.13 0.58 0.93 10 -1.2 63 73
MAP2K3 -0.092 0.42 0.69 8 -0.97 56 64
RIPK2 0.022 0.009 -10000 0 -10000 0 0
MAP2K6 -0.078 0.4 0.69 8 -0.91 56 64
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.007 0.012 -10000 0 -0.027 101 101
IL18RAP 0.006 0.079 -10000 0 -0.32 20 20
IL12Rbeta1/TYK2 0.027 0.098 0.31 20 -0.28 9 29
EOMES -0.069 0.27 -10000 0 -1 26 26
STAT1 (dimer) -0.03 0.39 0.66 22 -0.79 58 80
T cell proliferation -0.049 0.3 0.56 7 -0.63 60 67
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.021 0.034 -10000 0 -0.33 2 2
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.088 0.28 -10000 0 -0.66 63 63
ATF2 -0.073 0.37 0.66 7 -0.85 55 62
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.19 0.21 0.64 31 -10000 0 31
PCK1 0.21 0.22 0.68 45 -10000 0 45
HNF4A 0.26 0.29 0.83 53 -10000 0 53
KCNJ11 0.19 0.28 0.63 34 -0.72 18 52
AKT1 0.15 0.16 0.45 38 -0.57 1 39
response to starvation 0.019 0.039 0.18 13 -10000 0 13
DLK1 0.18 0.29 0.65 38 -0.68 16 54
NKX2-1 0.21 0.18 0.45 101 -10000 0 101
ACADM 0.19 0.21 0.64 30 -10000 0 30
TAT 0.2 0.21 0.64 46 -10000 0 46
CEBPB 0.039 0.037 0.21 9 -10000 0 9
CEBPA 0.051 0.072 0.3 18 -0.32 2 20
TTR 0.21 0.3 0.76 60 -10000 0 60
PKLR 0.23 0.25 0.68 53 -10000 0 53
APOA1 0.28 0.32 0.98 43 -10000 0 43
CPT1C 0.2 0.22 0.64 36 -0.73 1 37
ALAS1 0.17 0.17 0.61 11 -10000 0 11
TFRC 0.26 0.25 0.72 58 -10000 0 58
FOXF1 -0.095 0.16 -10000 0 -0.32 140 140
NF1 0.028 0.007 -10000 0 -10000 0 0
HNF1A (dimer) 0.094 0.084 0.3 26 -10000 0 26
CPT1A 0.2 0.22 0.65 37 -0.73 1 38
HMGCS1 0.22 0.23 0.65 48 -10000 0 48
NR3C1 0.039 0.072 0.25 8 -0.32 9 17
CPT1B 0.19 0.21 0.63 32 -0.73 1 33
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.079 0.064 -10000 0 -10000 0 0
GCK 0.16 0.29 0.63 33 -0.67 22 55
CREB1 0.041 0.04 0.23 4 -10000 0 4
IGFBP1 0.17 0.19 0.64 31 -10000 0 31
PDX1 0.29 0.27 0.65 101 -10000 0 101
UCP2 0.2 0.21 0.64 35 -10000 0 35
ALDOB 0.23 0.28 0.82 42 -10000 0 42
AFP 0.063 0.13 0.38 25 -10000 0 25
BDH1 0.2 0.22 0.65 32 -10000 0 32
HADH 0.22 0.23 0.67 29 -10000 0 29
F2 0.28 0.32 0.94 42 -10000 0 42
HNF1A 0.094 0.084 0.3 26 -10000 0 26
G6PC 0.12 0.15 0.56 30 -10000 0 30
SLC2A2 0.23 0.24 0.68 48 -10000 0 48
INS -0.033 0.038 -10000 0 -0.17 2 2
FOXA1 0.038 0.14 0.3 25 -0.32 37 62
FOXA3 0.15 0.16 0.39 106 -10000 0 106
FOXA2 0.33 0.36 0.98 56 -10000 0 56
ABCC8 0.21 0.22 0.66 30 -10000 0 30
ALB 0.079 0.15 0.36 63 -10000 0 63
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.025 0.03 -10000 0 -0.23 1 1
PDGFRB 0.009 0.054 -10000 0 -0.33 9 9
SPHK1 0.01 0.096 -10000 0 -0.8 2 2
mol:S1P 0.001 0.097 0.37 2 -0.71 2 4
S1P1/S1P/Gi -0.17 0.23 -10000 0 -0.42 149 149
GNAO1 -0.09 0.16 -10000 0 -0.32 124 124
PDGFB-D/PDGFRB/PLCgamma1 -0.14 0.21 0.27 3 -0.39 142 145
PLCG1 -0.16 0.21 0.28 1 -0.41 140 141
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.009 0.054 -10000 0 -0.33 9 9
GNAI2 0.012 0.024 -10000 0 -10000 0 0
GNAI3 0.013 0.024 -10000 0 -10000 0 0
GNAI1 0.01 0.037 -10000 0 -0.33 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.016 0.015 -10000 0 -0.19 1 1
S1P1/S1P -0.019 0.093 0.23 5 -0.31 5 10
negative regulation of cAMP metabolic process -0.16 0.22 -10000 0 -0.41 149 149
MAPK3 -0.21 0.28 0.28 3 -0.54 145 148
calcium-dependent phospholipase C activity -0.003 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.004 -10000 0 -10000 0 0
KDR 0.016 0.03 -10000 0 -0.32 2 2
PLCB2 -0.011 0.096 0.26 5 -0.44 2 7
RAC1 0.025 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.03 0.065 -10000 0 -0.23 8 8
receptor internalization -0.021 0.084 0.17 2 -0.25 8 10
PTGS2 -0.28 0.41 0.34 1 -0.91 108 109
Rac1/GTP -0.03 0.065 -10000 0 -0.22 10 10
RHOA 0.025 0.006 -10000 0 -10000 0 0
VEGFA 0.017 0.019 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.16 0.22 -10000 0 -0.41 149 149
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.06 0.14 -10000 0 -0.32 87 87
MAPK1 -0.21 0.28 -10000 0 -0.54 145 145
S1P1/S1P/PDGFB-D/PDGFRB -0.024 0.11 0.24 7 -0.26 23 30
ABCC1 0.014 0.026 0.32 1 -10000 0 1
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.061 0.11 0.26 38 -0.18 5 43
NF kappa B1 p50/RelA/I kappa B alpha 0.071 0.12 0.29 44 -10000 0 44
alphaV/beta3 Integrin/Osteopontin/Src 0.12 0.1 0.25 158 -10000 0 158
AP1 0 0.16 0.32 18 -0.33 41 59
ILK 0.036 0.099 0.28 4 -10000 0 4
bone resorption 0.022 0.1 0.28 10 -0.28 4 14
PTK2B 0.022 0.01 -10000 0 -10000 0 0
PYK2/p130Cas 0.088 0.13 0.3 30 -0.18 1 31
ITGAV 0.03 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.024 0.053 -10000 0 -0.22 17 17
alphaV/beta3 Integrin/Osteopontin 0.11 0.14 0.26 146 -0.19 37 183
MAP3K1 0.035 0.1 0.2 46 -0.2 5 51
JUN 0.013 0.064 -10000 0 -0.32 14 14
MAPK3 0.042 0.12 0.26 62 -10000 0 62
MAPK1 0.043 0.12 0.27 56 -10000 0 56
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
NFKB1 0.026 0.003 -10000 0 -10000 0 0
MAPK8 0.024 0.094 0.18 45 -0.2 6 51
ITGB3 -0.007 0.11 -10000 0 -0.32 44 44
NFKBIA 0.045 0.12 0.28 55 -10000 0 55
FOS -0.081 0.16 -10000 0 -0.32 124 124
CD44 0.015 0.056 -10000 0 -0.32 11 11
CHUK 0.025 0.005 -10000 0 -10000 0 0
PLAU 0.071 0.16 0.45 36 -10000 0 36
NF kappa B1 p50/RelA 0.086 0.12 0.32 54 -10000 0 54
BCAR1 0.025 0.006 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.017 0.087 -10000 0 -0.22 44 44
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.035 0.098 0.2 44 -0.19 6 50
VAV3 0.026 0.09 0.2 19 -0.18 1 20
MAP3K14 0.044 0.12 0.25 45 -0.19 6 51
ROCK2 0.019 0.045 -10000 0 -0.32 7 7
SPP1 0.15 0.15 0.33 161 -10000 0 161
RAC1 0.025 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.021 0.089 0.23 7 -10000 0 7
MMP2 -0.039 0.15 0.32 3 -0.41 31 34
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.053 0.14 0.23 1 -0.25 133 134
fibroblast growth factor receptor signaling pathway -0.053 0.14 0.23 1 -0.25 133 134
LAMA1 0.057 0.13 0.33 61 -0.32 14 75
PRNP 0.017 0.051 -10000 0 -0.32 9 9
GPC1/SLIT2 -0.072 0.13 -10000 0 -0.22 168 168
SMAD2 -0.014 0.032 0.18 9 -0.18 2 11
GPC1/PrPc/Cu2+ 0.026 0.035 0.21 1 -0.18 9 10
GPC1/Laminin alpha1 0.055 0.093 0.24 60 -0.22 14 74
TDGF1 0.009 0.035 0.33 3 -10000 0 3
CRIPTO/GPC1 0.033 0.022 0.24 3 -10000 0 3
APP/GPC1 0.035 0.02 0.24 1 -0.2 1 2
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.015 0.013 0.13 2 -10000 0 2
FLT1 0.025 0.005 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.041 0.027 -10000 0 -0.19 2 2
SERPINC1 0.038 0.079 0.33 27 -10000 0 27
FYN -0.017 0.019 0.13 3 -0.19 2 5
FGR -0.017 0.019 0.13 3 -0.19 2 5
positive regulation of MAPKKK cascade -0.005 0.094 0.23 12 -0.29 14 26
SLIT2 -0.12 0.17 -10000 0 -0.32 168 168
GPC1/NRG 0.003 0.1 0.24 17 -0.22 56 73
NRG1 -0.015 0.14 0.33 16 -0.32 56 72
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.046 0.021 0.23 1 -10000 0 1
LYN -0.015 0.013 0.13 2 -10000 0 2
mol:Spermine -0.007 0.01 0.18 1 -10000 0 1
cell growth -0.053 0.14 0.23 1 -0.25 133 134
BMP signaling pathway -0.025 0.017 -10000 0 -0.33 1 1
SRC -0.015 0.015 0.13 3 -10000 0 3
TGFBR1 0.023 0.008 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.12 0.18 0.33 3 -0.32 178 181
GPC1 0.025 0.017 0.33 1 -10000 0 1
TGFBR1 (dimer) 0.023 0.008 -10000 0 -10000 0 0
VEGFA 0.025 0.005 -10000 0 -10000 0 0
BLK -0.017 0.058 0.18 17 -0.19 23 40
HCK -0.015 0.037 0.16 8 -0.19 8 16
FGF2 -0.083 0.16 -10000 0 -0.32 127 127
FGFR1 -0.04 0.13 -10000 0 -0.32 73 73
VEGFR1 homodimer 0.025 0.005 -10000 0 -10000 0 0
TGFBR2 0.023 0.025 -10000 0 -0.32 2 2
cell death 0.035 0.02 0.24 1 -0.2 1 2
ATIII/GPC1 0.042 0.048 0.24 21 -10000 0 21
PLA2G2A/GPC1 -0.077 0.13 0.24 3 -0.22 178 181
LCK -0.017 0.025 0.15 5 -0.19 3 8
neuron differentiation 0.003 0.1 0.24 17 -0.22 56 73
PrPc/Cu2+ 0.013 0.035 -10000 0 -0.22 9 9
APP 0.025 0.018 -10000 0 -0.32 1 1
TGFBR2 (dimer) 0.023 0.025 -10000 0 -0.32 2 2
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.065 0.13 0.3 66 -10000 0 66
GNAI2 0.025 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.036 0.034 0.21 10 -0.19 2 12
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.081 0.16 -10000 0 -0.32 124 124
RhoA/GTP -0.066 0.14 -10000 0 -0.31 66 66
negative regulation of cAMP metabolic process -0.071 0.14 -10000 0 -0.24 144 144
GNAZ -0.049 0.14 -10000 0 -0.32 87 87
GNAI3 0.026 0.003 -10000 0 -10000 0 0
GNA12 0.025 0.006 -10000 0 -10000 0 0
S1PR5 0.032 0.055 0.33 11 -0.32 2 13
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.071 0.14 -10000 0 -0.24 144 144
RhoA/GDP 0.019 0.004 -10000 0 -10000 0 0
RHOA 0.025 0.006 -10000 0 -10000 0 0
GNAI1 0.023 0.03 -10000 0 -0.32 3 3
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.027 0.022 0.33 2 -10000 0 2
RAS family/GTP/Tiam1 -0.066 0.083 -10000 0 -0.2 70 70
NT3 (dimer)/TRKC -0.12 0.16 0.24 1 -0.26 215 216
NT3 (dimer)/TRKB -0.099 0.17 0.23 6 -0.26 189 195
SHC/Grb2/SOS1/GAB1/PI3K 0.012 0.031 -10000 0 -10000 0 0
RAPGEF1 0.024 0.008 -10000 0 -10000 0 0
BDNF -0.033 0.13 -10000 0 -0.32 67 67
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
DYNLT1 0.025 0.005 -10000 0 -10000 0 0
NTRK1 0.024 0.04 0.33 6 -10000 0 6
NTRK2 -0.084 0.17 0.33 7 -0.32 131 138
NTRK3 -0.14 0.17 -10000 0 -0.32 189 189
NT-4/5 (dimer)/TRKB -0.079 0.16 0.26 8 -0.24 177 185
neuron apoptosis 0.14 0.2 0.4 114 -10000 0 114
SHC 2-3/Grb2 -0.15 0.21 -10000 0 -0.43 114 114
SHC1 0.024 0.007 -10000 0 -10000 0 0
SHC2 -0.15 0.22 -10000 0 -0.48 104 104
SHC3 -0.16 0.22 -10000 0 -0.45 120 120
STAT3 (dimer) 0.033 0.063 0.27 14 -0.3 7 21
NT3 (dimer)/TRKA -0.03 0.13 0.26 6 -0.21 122 128
RIN/GDP -0.042 0.097 0.24 4 -0.23 19 23
GIPC1 0.026 0.003 -10000 0 -10000 0 0
KRAS 0.025 0.006 -10000 0 -10000 0 0
DNAJA3 -0.061 0.12 0.18 3 -0.26 89 92
RIN/GTP 0.013 0.011 0.22 1 -10000 0 1
CCND1 0.018 0.12 0.5 14 -0.59 7 21
MAGED1 0.026 0.003 -10000 0 -10000 0 0
PTPN11 0.025 0.005 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.002 0.086 -10000 0 -0.32 27 27
SHC/GRB2/SOS1 0.046 0.018 -10000 0 -10000 0 0
GRB2 0.025 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.015 0.099 0.23 10 -0.21 57 67
TRKA/NEDD4-2 0.036 0.026 0.24 5 -10000 0 5
ELMO1 0.023 0.03 -10000 0 -0.32 3 3
RhoG/GTP/ELMO1/DOCK1 0.03 0.028 -10000 0 -0.22 4 4
NGF -0.021 0.12 -10000 0 -0.32 53 53
HRAS 0.024 0.008 -10000 0 -10000 0 0
DOCK1 0.023 0.025 -10000 0 -0.32 2 2
GAB2 0.024 0.018 -10000 0 -0.32 1 1
RIT2 -0.012 0.021 0.33 1 -10000 0 1
RIT1 0.024 0.007 -10000 0 -10000 0 0
FRS2 0.024 0.008 -10000 0 -10000 0 0
DNM1 0.018 0.042 -10000 0 -0.32 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.024 0.008 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.041 0.13 0.23 2 -0.25 96 98
mol:GDP -0.065 0.13 0.3 3 -0.32 24 27
NGF (dimer) -0.021 0.12 -10000 0 -0.32 53 53
RhoG/GDP 0.017 0.021 -10000 0 -0.22 3 3
RIT1/GDP -0.042 0.094 0.25 3 -0.23 19 22
TIAM1 0.023 0.03 -10000 0 -0.32 3 3
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
BDNF (dimer)/TRKB -0.061 0.14 0.23 7 -0.22 167 174
KIDINS220/CRKL/C3G 0.035 0.02 0.24 2 -10000 0 2
SHC/RasGAP 0.034 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2 0.047 0.018 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.056 0.026 -10000 0 -10000 0 0
RIT1/GTP 0.018 0.005 -10000 0 -10000 0 0
NT3 (dimer) -0.037 0.13 0.33 1 -0.32 72 73
RAP1/GDP -0.043 0.077 -10000 0 -0.2 20 20
KIDINS220/CRKL 0.027 0.022 0.33 2 -10000 0 2
BDNF (dimer) -0.033 0.13 -10000 0 -0.32 67 67
ubiquitin-dependent protein catabolic process 0.022 0.078 0.23 5 -0.19 43 48
Schwann cell development -0.038 0.027 -10000 0 -10000 0 0
EHD4 0.025 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.056 0.026 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.01 0.058 0.2 1 -0.21 12 13
RAP1B 0.024 0.007 -10000 0 -10000 0 0
RAP1A 0.026 0.003 -10000 0 -10000 0 0
CDC42/GTP -0.15 0.16 -10000 0 -0.26 237 237
ABL1 0.023 0.008 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.037 0.01 -10000 0 -10000 0 0
Rap1/GTP -0.035 0.088 -10000 0 -0.29 16 16
STAT3 0.033 0.063 0.27 14 -0.3 7 21
axon guidance -0.15 0.15 -10000 0 -0.26 230 230
MAPK3 -0.032 0.076 0.18 15 -0.19 52 67
MAPK1 -0.032 0.079 0.18 16 -0.2 50 66
CDC42/GDP -0.042 0.098 0.25 3 -0.23 18 21
NTF3 -0.037 0.13 0.33 1 -0.32 72 73
NTF4 0.002 0.086 -10000 0 -0.32 27 27
NGF (dimer)/TRKA/FAIM 0.022 0.081 0.23 6 -0.19 45 51
PI3K 0.034 0.018 -10000 0 -0.22 1 1
FRS3 0.026 0.004 -10000 0 -10000 0 0
FAIM 0.025 0.006 -10000 0 -10000 0 0
GAB1 0.025 0.006 -10000 0 -10000 0 0
RASGRF1 -0.049 0.13 0.21 7 -0.26 90 97
SOS1 0.026 0.004 -10000 0 -10000 0 0
MCF2L -0.13 0.12 0.13 1 -0.23 210 211
RGS19 0.025 0.016 0.33 1 -10000 0 1
CDC42 0.026 0.003 -10000 0 -10000 0 0
RAS family/GTP 0.026 0.086 0.28 1 -0.39 4 5
Rac1/GDP -0.04 0.096 0.25 3 -0.23 19 22
NGF (dimer)/TRKA/GRIT 0.01 0.074 0.21 6 -0.19 45 51
neuron projection morphogenesis -0.047 0.14 -10000 0 -0.55 5 5
NGF (dimer)/TRKA/NEDD4-2 0.022 0.078 0.23 5 -0.19 43 48
MAP2K1 0.005 0.078 0.19 55 -10000 0 55
NGFR -0.045 0.15 0.33 4 -0.32 86 90
NGF (dimer)/TRKA/GIPC/GAIP -0.014 0.085 -10000 0 -0.23 41 41
RAS family/GTP/PI3K 0.015 0.02 -10000 0 -0.22 2 2
FRS2 family/SHP2/GRB2/SOS1 0.067 0.033 -10000 0 -10000 0 0
NRAS 0.026 0.002 -10000 0 -10000 0 0
GRB2/SOS1 0.037 0.01 -10000 0 -10000 0 0
PRKCI 0.025 0.006 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.025 0.006 -10000 0 -10000 0 0
PRKCZ 0.023 0.03 -10000 0 -0.32 3 3
MAPKKK cascade -0.078 0.22 -10000 0 -0.61 54 54
RASA1 0.025 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.034 0.027 0.24 5 -10000 0 5
SQSTM1 0.025 0.006 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.047 0.14 0.24 6 -0.2 165 171
NGF (dimer)/TRKA/p62/Atypical PKCs 0.039 0.083 0.24 6 -0.17 44 50
MATK 0.009 0.088 0.33 5 -0.32 23 28
NEDD4L 0.024 0.007 -10000 0 -10000 0 0
RAS family/GDP -0.053 0.059 -10000 0 -0.16 37 37
NGF (dimer)/TRKA -0.057 0.13 0.21 3 -0.27 97 100
Rac1/GTP -0.066 0.096 -10000 0 -0.21 96 96
FRS2 family/SHP2/CRK family 0.062 0.039 0.24 2 -10000 0 2
PDGFR-alpha signaling pathway

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
PDGFRA -0.044 0.12 -10000 0 -0.34 55 55
PDGF/PDGFRA/CRKL -0.016 0.089 -10000 0 -0.23 52 52
positive regulation of JUN kinase activity 0.027 0.075 -10000 0 -0.18 44 44
CRKL 0.027 0.022 0.33 2 -10000 0 2
PDGF/PDGFRA/Caveolin-3 -0.02 0.087 0.24 1 -0.23 50 51
AP1 -0.26 0.35 -10000 0 -0.75 128 128
mol:IP3 -0.058 0.079 -10000 0 -0.25 51 51
PLCG1 -0.058 0.079 -10000 0 -0.25 51 51
PDGF/PDGFRA/alphaV Integrin -0.018 0.09 -10000 0 -0.23 55 55
RAPGEF1 0.024 0.008 -10000 0 -10000 0 0
CRK 0.024 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.058 0.079 -10000 0 -0.25 51 51
CAV3 -0.004 0.029 0.33 2 -10000 0 2
CAV1 0.01 0.071 -10000 0 -0.32 18 18
SHC/Grb2/SOS1 0.028 0.076 -10000 0 -0.18 44 44
PDGF/PDGFRA/Shf -0.022 0.097 -10000 0 -0.24 58 58
FOS -0.26 0.34 -10000 0 -0.75 127 127
JUN -0.047 0.054 -10000 0 -0.28 14 14
oligodendrocyte development -0.018 0.09 -10000 0 -0.23 55 55
GRB2 0.025 0.005 -10000 0 -10000 0 0
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
mol:DAG -0.058 0.079 -10000 0 -0.25 51 51
PDGF/PDGFRA -0.043 0.12 -10000 0 -0.34 55 55
actin cytoskeleton reorganization -0.017 0.087 -10000 0 -0.23 52 52
SRF 0.001 0.021 -10000 0 -10000 0 0
SHC1 0.024 0.007 -10000 0 -10000 0 0
PI3K 0.001 0.08 -10000 0 -0.19 49 49
PDGF/PDGFRA/Crk/C3G -0.001 0.08 -10000 0 -0.19 53 53
JAK1 -0.049 0.073 -10000 0 -0.23 55 55
ELK1/SRF -0.045 0.077 0.16 6 -0.22 50 56
SHB 0.023 0.009 -10000 0 -10000 0 0
SHF 0.021 0.042 -10000 0 -0.32 6 6
CSNK2A1 0.037 0.023 -10000 0 -10000 0 0
GO:0007205 -0.058 0.091 -10000 0 -0.28 51 51
SOS1 0.026 0.004 -10000 0 -10000 0 0
Ras protein signal transduction 0.027 0.075 -10000 0 -0.18 44 44
PDGF/PDGFRA/SHB -0.017 0.087 -10000 0 -0.23 52 52
PDGF/PDGFRA/Caveolin-1 -0.026 0.11 -10000 0 -0.26 60 60
ITGAV 0.025 0.005 -10000 0 -10000 0 0
ELK1 -0.064 0.085 -10000 0 -0.26 50 50
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.018 0.088 -10000 0 -0.23 53 53
JAK-STAT cascade -0.049 0.073 -10000 0 -0.23 55 55
cell proliferation -0.022 0.096 -10000 0 -0.24 58 58
IL6-mediated signaling events

Figure S43.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S43.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.042 0.25 0.63 16 -0.7 7 23
CRP 0.046 0.26 0.73 21 -0.72 6 27
cell cycle arrest 0.019 0.26 0.62 25 -0.67 14 39
TIMP1 0.038 0.24 0.62 17 -0.62 8 25
IL6ST -0.016 0.12 0.18 1 -0.32 54 55
Rac1/GDP -0.053 0.21 0.37 16 -0.42 62 78
AP1 0.031 0.16 0.41 9 -0.47 6 15
GAB2 0.027 0.019 -10000 0 -0.32 1 1
TNFSF11 0.025 0.27 0.66 18 -0.79 10 28
HSP90B1 0.047 0.098 -10000 0 -0.55 3 3
GAB1 0.027 0.007 -10000 0 -10000 0 0
MAPK14 -0.12 0.23 -10000 0 -0.57 69 69
AKT1 0.031 0.045 -10000 0 -0.32 2 2
FOXO1 0.028 0.052 -10000 0 -0.31 2 2
MAP2K6 -0.096 0.21 0.28 9 -0.45 77 86
mol:GTP 0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.029 0.22 0.42 24 -0.46 44 68
MITF -0.079 0.2 0.33 13 -0.4 79 92
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.026 0.004 -10000 0 -10000 0 0
A2M -0.1 0.38 -10000 0 -1.2 41 41
CEBPB 0.03 0.022 -10000 0 -0.32 1 1
GRB2/SOS1/GAB family/SHP2 0.019 0.11 0.3 8 -0.48 4 12
STAT3 0.01 0.27 0.62 25 -0.71 14 39
STAT1 0.008 0.13 0.39 1 -0.75 9 10
CEBPD 0.036 0.25 0.64 18 -0.8 7 25
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
PI3K 0.035 0.019 -10000 0 -0.23 1 1
JUN 0.015 0.063 -10000 0 -0.32 14 14
PIAS3/MITF -0.065 0.19 0.32 11 -0.39 69 80
MAPK11 -0.12 0.23 -10000 0 -0.56 69 69
STAT3 (dimer)/FOXO1 -0.002 0.25 0.58 23 -0.59 16 39
GRB2/SOS1/GAB family -0.039 0.18 0.29 5 -0.38 54 59
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.078 0.18 0.25 8 -0.39 72 80
GRB2 0.027 0.006 -10000 0 -10000 0 0
JAK2 0.022 0.009 -10000 0 -10000 0 0
LBP 0.078 0.26 0.64 32 -0.58 5 37
PIK3R1 0.024 0.019 -10000 0 -0.32 1 1
JAK1 0.024 0.022 -10000 0 -10000 0 0
MYC 0.024 0.31 0.64 20 -0.92 19 39
FGG 0.037 0.26 0.69 24 -0.7 7 31
macrophage differentiation 0.019 0.26 0.62 25 -0.67 14 39
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.049 0.15 -10000 0 -0.32 56 56
JUNB 0.016 0.25 0.61 15 -0.8 10 25
FOS -0.08 0.16 -10000 0 -0.32 124 124
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.07 0.21 0.34 22 -0.41 74 96
STAT1/PIAS1 -0.029 0.2 0.39 24 -0.44 37 61
GRB2/SOS1/GAB family/SHP2/PI3K 0.037 0.043 -10000 0 -0.29 2 2
STAT3 (dimer) 0.013 0.27 0.62 25 -0.7 14 39
PRKCD -0.009 0.23 0.49 24 -0.5 33 57
IL6R -0.001 0.091 -10000 0 -0.32 29 29
SOCS3 -0.18 0.34 -10000 0 -1 52 52
gp130 (dimer)/JAK1/JAK1/LMO4 0.028 0.11 0.26 7 -0.19 52 59
Rac1/GTP -0.044 0.22 0.37 24 -0.43 61 85
HCK 0.019 0.064 0.33 5 -0.32 10 15
MAPKKK cascade 0.042 0.11 0.4 1 -0.52 5 6
bone resorption 0.028 0.26 0.65 19 -0.74 10 29
IRF1 0.023 0.24 0.64 15 -0.7 7 22
mol:GDP -0.07 0.21 0.32 22 -0.41 73 95
SOS1 0.028 0.008 -10000 0 -10000 0 0
VAV1 -0.073 0.21 0.33 22 -0.41 74 96
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.14 0.27 0.44 1 -0.61 77 78
PTPN11 0.022 0.056 -10000 0 -0.7 1 1
IL6/IL6RA -0.069 0.15 -10000 0 -0.24 158 158
gp130 (dimer)/TYK2/TYK2/LMO4 0.024 0.095 0.26 2 -0.19 54 56
gp130 (dimer)/JAK2/JAK2/LMO4 0.017 0.093 0.31 1 -0.19 54 55
IL6 -0.11 0.17 -10000 0 -0.32 166 166
PIAS3 0.023 0.009 -10000 0 -10000 0 0
PTPRE 0.004 0.048 0.33 2 -0.18 5 7
PIAS1 0.026 0.004 -10000 0 -10000 0 0
RAC1 0.027 0.007 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.085 0.18 0.25 6 -0.38 70 76
LMO4 0.029 0.036 0.18 1 -0.33 1 2
STAT3 (dimer)/PIAS3 -0.004 0.24 0.58 18 -0.7 11 29
MCL1 0.049 0.081 0.39 2 -10000 0 2
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.013 0.078 0.4 7 -10000 0 7
VDR 0.024 0.025 -10000 0 -0.32 2 2
FAM120B 0.025 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.017 0.11 0.26 17 -0.3 15 32
RXRs/LXRs/DNA/Oxysterols 0.002 0.12 0.32 17 -0.34 6 23
MED1 0.025 0.006 -10000 0 -10000 0 0
mol:9cRA 0.006 0.013 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.008 0.079 -10000 0 -0.21 46 46
RXRs/NUR77 -0.093 0.14 -10000 0 -0.21 213 213
RXRs/PPAR -0.044 0.1 -10000 0 -0.2 99 99
NCOR2 0.026 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.017 -10000 0 -0.22 2 2
RARs/VDR/DNA/Vit D3 0.037 0.066 -10000 0 -0.17 34 34
RARA 0.026 0.004 -10000 0 -10000 0 0
NCOA1 0.025 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.024 0.024 -10000 0 -0.32 2 2
RARs/RARs/DNA/9cRA 0.028 0.057 -10000 0 -0.16 33 33
RARG 0.026 0.003 -10000 0 -10000 0 0
RPS6KB1 0.021 0.1 0.6 12 -10000 0 12
RARs/THRs/DNA/SMRT -0.009 0.081 -10000 0 -0.36 7 7
THRA 0.025 0.005 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.018 0.017 -10000 0 -0.22 2 2
RXRs/PPAR/9cRA/PGJ2/DNA 0.002 0.1 0.25 13 -0.17 78 91
NR1H4 -0.038 0.15 0.33 16 -0.32 72 88
RXRs/LXRs/DNA 0.02 0.11 0.29 13 -10000 0 13
NR1H2 0.031 0.013 -10000 0 -10000 0 0
NR1H3 0.03 0.014 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.006 0.097 0.29 1 -0.16 87 88
NR4A1 -0.17 0.17 -10000 0 -0.32 224 224
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.046 0.13 0.21 10 -0.21 125 135
RXRG -0.058 0.14 -10000 0 -0.32 95 95
RXR alpha/CCPG 0.037 0.017 -10000 0 -10000 0 0
RXRA 0.028 0.015 -10000 0 -10000 0 0
RXRB 0.032 0.013 -10000 0 -10000 0 0
THRB 0.004 0.082 -10000 0 -0.32 24 24
PPARG 0.001 0.083 -10000 0 -0.32 25 25
PPARD 0.026 0.003 -10000 0 -10000 0 0
TNF 0.001 0.13 0.41 19 -10000 0 19
mol:Oxysterols 0.005 0.012 -10000 0 -10000 0 0
cholesterol transport 0.002 0.12 0.32 17 -0.34 6 23
PPARA 0.024 0.025 -10000 0 -0.32 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.004 0.096 -10000 0 -0.32 34 34
RXRs/NUR77/BCL2 -0.13 0.15 -10000 0 -0.24 228 228
SREBF1 -0.002 0.1 0.39 1 -10000 0 1
RXRs/RXRs/DNA/9cRA 0.003 0.1 0.25 14 -0.17 78 92
ABCA1 0.005 0.098 -10000 0 -10000 0 0
RARs/THRs 0.039 0.089 -10000 0 -0.19 48 48
RXRs/FXR -0.025 0.13 0.26 6 -0.2 126 132
BCL2 0.012 0.065 -10000 0 -0.32 15 15
Aurora A signaling

Figure S45.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S45.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.017 0.064 0.19 2 -0.16 5 7
BIRC5 0.23 0.14 0.33 279 -0.32 1 280
NFKBIA 0 0.051 0.21 5 -10000 0 5
CPEB1 -0.14 0.16 -10000 0 -0.32 189 189
AKT1 0 0.052 0.22 5 -10000 0 5
NDEL1 0.024 0.008 -10000 0 -10000 0 0
Aurora A/BRCA1 0.013 0.057 0.2 3 -0.14 5 8
NDEL1/TACC3 0.031 0.075 0.26 14 -10000 0 14
GADD45A 0.026 0.002 -10000 0 -10000 0 0
GSK3B -0.019 0.032 -10000 0 -10000 0 0
PAK1/Aurora A 0.015 0.062 0.19 2 -0.16 4 6
MDM2 0.024 0.008 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.1 0.11 0.2 214 -10000 0 214
TP53 0.007 0.07 0.21 5 -0.21 23 28
DLG7 0.005 0.048 0.16 4 -10000 0 4
AURKAIP1 0.027 0.015 0.33 1 -10000 0 1
ARHGEF7 0.025 0.006 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.033 0.079 0.28 14 -10000 0 14
G2/M transition of mitotic cell cycle 0.013 0.056 0.2 3 -0.14 5 8
AURKA 0.012 0.066 0.22 6 -10000 0 6
AURKB 0.11 0.098 0.19 205 -0.15 14 219
CDC25B 0.015 0.053 0.19 14 -10000 0 14
G2/M transition checkpoint 0.002 0.043 0.15 2 -0.13 5 7
mRNA polyadenylation -0.069 0.086 -10000 0 -0.18 108 108
Aurora A/CPEB -0.069 0.087 -10000 0 -0.18 108 108
Aurora A/TACC1/TRAP/chTOG 0.023 0.067 -10000 0 -0.2 1 1
BRCA1 0.026 0.015 0.33 1 -10000 0 1
centrosome duplication 0.015 0.062 0.19 2 -0.16 4 6
regulation of centrosome cycle 0.03 0.073 0.26 14 -10000 0 14
spindle assembly 0.022 0.066 -10000 0 -0.2 1 1
TDRD7 0.024 0.008 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.16 0.1 0.26 151 -0.15 1 152
CENPA 0.13 0.095 0.2 253 -0.24 1 254
Aurora A/PP2A 0.016 0.063 0.19 2 -0.16 5 7
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.013 0.05 0.17 5 -0.18 2 7
negative regulation of DNA binding 0.008 0.072 0.21 5 -0.21 24 29
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.035 0.012 -10000 0 -10000 0 0
RASA1 0.025 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A 0.002 0.044 0.15 2 -0.13 5 7
mitotic prometaphase -0.01 0.029 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.066 0.22 6 -10000 0 6
TACC1 0.021 0.026 -10000 0 -0.32 2 2
TACC3 0.041 0.069 0.33 22 -10000 0 22
Aurora A/Antizyme1 0.025 0.066 -10000 0 -0.15 1 1
Aurora A/RasGAP 0.017 0.062 0.19 2 -0.15 4 6
OAZ1 0.025 0.005 -10000 0 -10000 0 0
RAN 0.025 0.005 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.02 0.032 -10000 0 -10000 0 0
GIT1 0.025 0.006 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.045 0.022 -10000 0 -0.19 1 1
Importin alpha/Importin beta/TPX2 0.1 0.11 0.2 214 -10000 0 214
PPP2R5D 0.026 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.074 0.1 0.21 123 -10000 0 123
PAK1 0.024 0.018 -10000 0 -0.32 1 1
CKAP5 0.025 0.007 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.031 0.086 0.24 4 -0.19 44 48
MAP4K1 0.018 0.06 0.33 3 -0.32 10 13
MAP3K8 0.023 0.025 -10000 0 -0.32 2 2
PRKCB -0.071 0.15 -10000 0 -0.32 112 112
DBNL 0.026 0.004 -10000 0 -10000 0 0
CRKL 0.027 0.022 0.33 2 -10000 0 2
MAP3K1 -0.012 0.087 -10000 0 -0.33 16 16
JUN -0.16 0.28 -10000 0 -0.56 126 126
MAP3K7 -0.011 0.086 -10000 0 -0.32 16 16
GRAP2 -0.012 0.11 -10000 0 -0.32 43 43
CRK 0.024 0.008 -10000 0 -10000 0 0
MAP2K4 -0.016 0.1 -10000 0 -0.35 20 20
LAT 0.026 0.016 0.33 1 -10000 0 1
LCP2 0.022 0.03 -10000 0 -0.32 3 3
MAPK8 -0.16 0.29 -10000 0 -0.58 127 127
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.004 0.095 -10000 0 -0.34 16 16
LAT/GRAP2/SLP76/HPK1/HIP-55 0.038 0.085 0.24 4 -0.18 41 45
TCGA08_p53

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
CDKN2A 0.087 0.096 0.19 190 -10000 0 190
TP53 0.027 0.042 0.16 3 -0.2 3 6
Senescence 0.024 0.053 0.16 3 -0.18 12 15
Apoptosis 0.024 0.053 0.16 3 -0.18 12 15
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.043 0.091 0.27 18 -10000 0 18
MDM4 0.026 0.003 -10000 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.018 0.051 -10000 0 -0.32 9 9
mol:S1P 0 0.004 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.085 0.14 -10000 0 -0.24 155 155
GNAO1 -0.081 0.16 -10000 0 -0.32 124 124
S1P/S1P3/G12/G13 0.037 0.033 -10000 0 -0.18 4 4
AKT1 -0.045 0.15 -10000 0 -0.54 29 29
AKT3 -0.063 0.22 -10000 0 -1 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.018 0.051 -10000 0 -0.32 9 9
GNAI2 0.023 0.013 -10000 0 -10000 0 0
GNAI3 0.024 0.012 -10000 0 -10000 0 0
GNAI1 0.022 0.032 -10000 0 -0.32 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.019 0.037 -10000 0 -0.32 4 4
S1PR2 0.026 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.078 0.16 -10000 0 -0.38 67 67
MAPK3 -0.085 0.15 -10000 0 -0.35 77 77
MAPK1 -0.089 0.15 -10000 0 -0.35 79 79
JAK2 -0.095 0.17 0.21 1 -0.38 85 86
CXCR4 -0.091 0.15 -10000 0 -0.36 79 79
FLT1 0.024 0.015 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
SRC -0.082 0.15 -10000 0 -0.35 75 75
S1P/S1P3/Gi -0.078 0.16 -10000 0 -0.38 67 67
RAC1 0.025 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.08 0.15 -10000 0 -0.33 82 82
VEGFA 0.024 0.015 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.075 0.14 -10000 0 -0.27 116 116
VEGFR1 homodimer/VEGFA homodimer 0.036 0.022 -10000 0 -10000 0 0
RHOA 0.025 0.006 -10000 0 -10000 0 0
S1P/S1P3/Gq -0.01 0.074 -10000 0 -0.2 50 50
GNAQ 0.023 0.008 -10000 0 -10000 0 0
GNAZ -0.05 0.14 -10000 0 -0.32 87 87
G12/G13 0.035 0.012 -10000 0 -10000 0 0
GNA14 -0.015 0.11 -10000 0 -0.32 45 45
GNA15 0.023 0.03 -10000 0 -0.32 3 3
GNA12 0.025 0.006 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
GNA11 0.025 0.018 -10000 0 -0.32 1 1
Rac1/GTP -0.077 0.15 -10000 0 -0.33 79 79
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.062 0.25 -10000 0 -0.76 42 42
NCK1/PAK1/Dok-R -0.056 0.12 -10000 0 -0.39 42 42
NCK1/Dok-R -0.057 0.28 -10000 0 -0.86 42 42
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
mol:beta2-estradiol 0.015 0.065 0.23 34 -0.12 2 36
RELA 0.026 0.004 -10000 0 -10000 0 0
SHC1 0.024 0.007 -10000 0 -10000 0 0
Rac/GDP 0.019 0.004 -10000 0 -10000 0 0
F2 0.035 0.11 0.3 56 -10000 0 56
TNIP2 0.025 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.037 0.28 -10000 0 -0.82 42 42
FN1 0.035 0.095 0.33 26 -0.32 11 37
PLD2 -0.074 0.28 -10000 0 -0.88 42 42
PTPN11 0.025 0.005 -10000 0 -10000 0 0
GRB14 0.064 0.1 0.33 53 -10000 0 53
ELK1 -0.063 0.26 -10000 0 -0.81 42 42
GRB7 0.02 0.05 0.33 2 -0.32 7 9
PAK1 0.024 0.018 -10000 0 -0.32 1 1
Tie2/Ang1/alpha5/beta1 Integrin -0.041 0.3 -10000 0 -0.88 42 42
CDKN1A -0.063 0.19 -10000 0 -0.56 38 38
ITGA5 0.013 0.065 -10000 0 -0.32 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.057 0.28 -10000 0 -0.86 42 42
CRK 0.024 0.008 -10000 0 -10000 0 0
mol:NO -0.046 0.2 -10000 0 -0.58 42 42
PLG -0.075 0.28 -10000 0 -0.88 42 42
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.062 0.24 -10000 0 -0.74 42 42
GRB2 0.025 0.005 -10000 0 -10000 0 0
PIK3R1 0.024 0.019 -10000 0 -0.32 1 1
ANGPT2 -0.11 0.2 0.39 1 -0.58 40 41
BMX -0.098 0.29 -10000 0 -0.93 42 42
ANGPT1 -0.079 0.31 0.35 2 -1.1 34 36
tube development -0.075 0.2 -10000 0 -0.59 44 44
ANGPT4 0.021 0.044 0.33 7 -10000 0 7
response to hypoxia -0.005 0.02 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.041 0.3 -10000 0 -0.89 42 42
alpha5/beta1 Integrin 0.026 0.05 -10000 0 -0.22 15 15
FGF2 -0.083 0.16 -10000 0 -0.32 127 127
STAT5A (dimer) -0.076 0.23 -10000 0 -0.66 44 44
mol:L-citrulline -0.046 0.2 -10000 0 -0.58 42 42
AGTR1 -0.11 0.17 -10000 0 -0.32 161 161
MAPK14 -0.075 0.29 -10000 0 -0.91 42 42
Tie2/SHP2 -0.044 0.2 -10000 0 -0.85 18 18
TEK -0.052 0.22 -10000 0 -0.95 18 18
RPS6KB1 -0.06 0.25 -10000 0 -0.74 42 42
Angiotensin II/AT1 -0.075 0.12 0.11 1 -0.22 161 162
Tie2/Ang1/GRB2 -0.062 0.29 -10000 0 -0.9 42 42
MAPK3 -0.069 0.26 -10000 0 -0.82 42 42
MAPK1 -0.071 0.26 -10000 0 -0.83 42 42
Tie2/Ang1/GRB7 -0.064 0.29 -10000 0 -0.9 42 42
NFKB1 0.026 0.003 -10000 0 -10000 0 0
MAPK8 -0.075 0.28 -10000 0 -0.88 42 42
PI3K -0.074 0.28 -10000 0 -0.86 42 42
FES -0.083 0.3 -10000 0 -0.9 43 43
Crk/Dok-R -0.056 0.28 -10000 0 -0.86 42 42
Tie2/Ang1/ABIN2 -0.062 0.3 -10000 0 -0.9 42 42
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.054 0.23 -10000 0 -0.69 42 42
STAT5A 0.025 0.018 -10000 0 -0.32 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.05 0.25 -10000 0 -0.73 42 42
Tie2/Ang2 -0.096 0.25 -10000 0 -0.76 43 43
Tie2/Ang1 -0.072 0.3 -10000 0 -0.93 42 42
FOXO1 -0.052 0.23 -10000 0 -0.69 42 42
ELF1 0.023 0.028 -10000 0 -0.12 5 5
ELF2 -0.067 0.28 -10000 0 -0.87 42 42
mol:Choline -0.071 0.27 -10000 0 -0.85 42 42
cell migration -0.027 0.073 -10000 0 -0.22 42 42
FYN -0.083 0.22 -10000 0 -0.66 44 44
DOK2 0.017 0.053 0.33 2 -0.32 8 10
negative regulation of cell cycle -0.057 0.18 -10000 0 -0.51 38 38
ETS1 0.007 0.075 -10000 0 -0.24 32 32
PXN -0.041 0.22 0.41 2 -0.62 42 44
ITGB1 0.025 0.006 -10000 0 -10000 0 0
NOS3 -0.054 0.22 -10000 0 -0.66 42 42
RAC1 0.025 0.006 -10000 0 -10000 0 0
TNF 0.022 0.1 0.33 20 -0.24 33 53
MAPKKK cascade -0.071 0.27 -10000 0 -0.85 42 42
RASA1 0.025 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.062 0.29 -10000 0 -0.88 42 42
NCK1 0.025 0.006 -10000 0 -10000 0 0
vasculogenesis -0.04 0.18 -10000 0 -0.52 42 42
mol:Phosphatidic acid -0.071 0.27 -10000 0 -0.85 42 42
mol:Angiotensin II 0.001 0.002 -10000 0 -10000 0 0
mol:NADP -0.046 0.2 -10000 0 -0.58 42 42
Rac1/GTP -0.055 0.23 -10000 0 -0.7 42 42
MMP2 -0.081 0.29 -10000 0 -0.91 42 42
Coregulation of Androgen receptor activity

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
NRIP1 0.023 0.022 -10000 0 -10000 0 0
SVIL 0.02 0.032 -10000 0 -0.31 2 2
ZNF318 0.028 0.038 0.19 16 -10000 0 16
JMJD2C 0.02 0.05 0.17 41 -10000 0 41
T-DHT/AR/Ubc9 -0.048 0.12 0.21 3 -0.2 144 147
CARM1 0.024 0.012 -10000 0 -10000 0 0
PRDX1 0.026 0.004 -10000 0 -10000 0 0
PELP1 0.022 0.013 -10000 0 -10000 0 0
CTNNB1 0.023 0.019 -10000 0 -10000 0 0
AKT1 0.025 0.015 -10000 0 -10000 0 0
PTK2B 0.019 0.018 -10000 0 -10000 0 0
MED1 0.024 0.016 -10000 0 -10000 0 0
MAK 0.032 0.054 0.24 21 -10000 0 21
response to oxidative stress 0 0.002 -10000 0 -10000 0 0
HIP1 0.021 0.033 -10000 0 -0.25 3 3
GSN 0.018 0.036 -10000 0 -0.32 3 3
NCOA2 0.004 0.075 -10000 0 -0.32 20 20
NCOA6 0.021 0.022 -10000 0 -0.13 1 1
DNA-PK 0.045 0.04 0.21 7 -10000 0 7
NCOA4 0.024 0.009 -10000 0 -10000 0 0
PIAS3 0.021 0.019 -10000 0 -10000 0 0
cell proliferation 0.003 0.07 0.28 7 -0.45 4 11
XRCC5 0.023 0.015 -10000 0 -10000 0 0
UBE3A 0.022 0.028 -10000 0 -0.12 2 2
T-DHT/AR/SNURF -0.06 0.13 0.21 3 -0.21 153 156
FHL2 -0.019 0.096 -10000 0 -0.6 6 6
RANBP9 0.022 0.021 -10000 0 -0.097 2 2
JMJD1A -0.013 0.057 0.17 12 -0.12 68 80
CDK6 0.017 0.054 -10000 0 -0.32 10 10
TGFB1I1 0.012 0.065 -10000 0 -0.32 13 13
T-DHT/AR/CyclinD1 -0.043 0.12 0.25 4 -0.2 123 127
XRCC6 0.024 0.014 -10000 0 -10000 0 0
T-DHT/AR -0.044 0.14 0.26 25 -0.21 154 179
CTDSP1 0.023 0.013 -10000 0 -10000 0 0
CTDSP2 0.026 0.025 -10000 0 -10000 0 0
BRCA1 0.023 0.028 0.35 1 -10000 0 1
TCF4 0.019 0.047 -10000 0 -0.32 6 6
CDKN2A 0.15 0.16 0.33 184 -10000 0 184
SRF 0.027 0.021 -10000 0 -10000 0 0
NKX3-1 -0.053 0.1 0.19 9 -0.23 74 83
KLK3 -0.036 0.26 0.39 12 -1.3 16 28
TMF1 0.023 0.012 -10000 0 -10000 0 0
HNRNPA1 0.025 0.017 -10000 0 -10000 0 0
AOF2 -0.001 0.015 -10000 0 -0.072 16 16
APPL1 -0.012 0.023 0.11 3 -10000 0 3
T-DHT/AR/Caspase 8 -0.046 0.12 0.19 3 -0.2 142 145
AR -0.094 0.17 -10000 0 -0.33 132 132
UBA3 0.022 0.014 -10000 0 -10000 0 0
PATZ1 0.024 0.016 -10000 0 -10000 0 0
PAWR 0.023 0.02 -10000 0 -0.32 1 1
PRKDC 0.023 0.015 -10000 0 -10000 0 0
PA2G4 0.025 0.02 -10000 0 -10000 0 0
UBE2I 0.025 0.005 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.038 0.11 0.18 3 -0.18 139 142
RPS6KA3 0.023 0.023 -10000 0 -0.091 8 8
T-DHT/AR/ARA70 -0.047 0.12 0.22 3 -0.2 141 144
LATS2 0.024 0.024 -10000 0 -0.32 1 1
T-DHT/AR/PRX1 -0.039 0.11 0.17 2 -0.18 142 144
Cyclin D3/CDK11 p58 0.019 0.005 -10000 0 -10000 0 0
VAV3 0.025 0.047 0.32 5 -0.31 3 8
KLK2 0.007 0.13 0.35 40 -0.36 2 42
CASP8 0.024 0.012 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.043 0.12 0.24 2 -0.2 132 134
TMPRSS2 -0.14 0.31 0.38 12 -0.78 72 84
CCND1 0.016 0.05 0.33 1 -0.32 7 8
PIAS1 0.022 0.028 -10000 0 -0.13 1 1
mol:T-DHT -0.001 0.023 0.051 26 -0.056 26 52
CDC2L1 0 0.001 -10000 0 -10000 0 0
PIAS4 0.021 0.039 -10000 0 -0.18 14 14
T-DHT/AR/CDK6 -0.05 0.12 0.2 3 -0.2 147 150
CMTM2 0.028 0.035 0.33 5 -10000 0 5
SNURF -0.003 0.086 -10000 0 -0.32 27 27
ZMIZ1 0.018 0.035 -10000 0 -10000 0 0
CCND3 0.026 0.005 -10000 0 -10000 0 0
TGIF1 0.023 0.017 -10000 0 -10000 0 0
FKBP4 0.022 0.022 -10000 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.012 0.009 -10000 0 -0.19 1 1
ADCY5 -0.091 0.087 -10000 0 -0.19 184 184
ADCY6 -0.012 0.003 -10000 0 -10000 0 0
ADCY7 -0.012 0.003 -10000 0 -10000 0 0
ADCY1 -0.009 0.024 0.14 9 -0.19 1 10
ADCY2 -0.062 0.081 -10000 0 -0.19 120 120
ADCY3 -0.012 0.003 -10000 0 -10000 0 0
ADCY8 -0.01 0.018 0.15 4 -10000 0 4
PRKCE -0.008 0.002 -10000 0 -10000 0 0
ADCY9 -0.015 0.023 -10000 0 -0.19 7 7
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.019 0.1 0.24 26 -0.2 4 30
Nephrin/Neph1 signaling in the kidney podocyte

Figure S52.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S52.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity -0.01 0.086 0.24 40 -0.23 6 46
KIRREL -0.008 0.11 -10000 0 -0.33 40 40
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.01 0.086 0.23 6 -0.24 40 46
PLCG1 0.024 0.007 -10000 0 -10000 0 0
ARRB2 0.024 0.008 -10000 0 -10000 0 0
WASL 0.026 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.038 0.082 0.23 17 -0.18 36 53
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.003 0.064 -10000 0 -0.19 32 32
FYN -0.003 0.09 0.19 44 -0.18 34 78
mol:Ca2+ 0.035 0.079 0.24 6 -0.18 33 39
mol:DAG 0.036 0.079 0.24 6 -0.18 33 39
NPHS2 0.012 0.071 0.32 18 -10000 0 18
mol:IP3 0.036 0.079 0.24 6 -0.18 33 39
regulation of endocytosis 0.024 0.07 0.2 6 -0.17 35 41
Nephrin/NEPH1/podocin/Cholesterol 0.026 0.076 0.21 18 -0.17 36 54
establishment of cell polarity 0.01 0.086 0.23 6 -0.24 40 46
Nephrin/NEPH1/podocin/NCK1-2 0.046 0.081 0.28 2 -0.17 33 35
Nephrin/NEPH1/beta Arrestin2 0.026 0.072 0.21 6 -0.17 35 41
NPHS1 0.005 0.049 0.32 6 -10000 0 6
Nephrin/NEPH1/podocin 0.024 0.076 0.2 18 -0.18 37 55
TJP1 0.025 0.005 -10000 0 -10000 0 0
NCK1 0.025 0.006 -10000 0 -10000 0 0
NCK2 0.026 0.004 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.037 0.08 0.24 6 -0.18 33 39
CD2AP 0.026 0.003 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.038 0.081 0.23 17 -0.18 34 51
GRB2 0.025 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.005 0.089 0.2 41 -0.17 35 76
cytoskeleton organization -0.016 0.069 0.21 8 -0.21 31 39
Nephrin/NEPH1 0.012 0.061 0.19 6 -0.16 40 46
Nephrin/NEPH1/ZO-1 0.023 0.075 0.22 6 -0.19 40 46
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.017 0.08 0.24 25 -0.19 30 55
EPHB2 0.047 0.076 0.33 28 -10000 0 28
Syndecan-2/TACI -0.001 0.072 0.22 7 -0.19 44 51
LAMA1 0.057 0.13 0.33 61 -0.32 14 75
Syndecan-2/alpha2 ITGB1 0.033 0.094 0.25 32 -0.17 40 72
HRAS 0.024 0.008 -10000 0 -10000 0 0
Syndecan-2/CASK -0.006 0.043 -10000 0 -0.18 24 24
ITGA5 0.013 0.065 -10000 0 -0.32 15 15
BAX -0.017 0.036 -10000 0 -10000 0 0
EPB41 0.026 0.002 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.008 0.043 -10000 0 -0.16 23 23
LAMA3 0.023 0.13 0.33 34 -0.32 32 66
EZR 0.025 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.022 0.034 -10000 0 -0.32 4 4
Syndecan-2/MMP2 -0.003 0.074 -10000 0 -0.22 39 39
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.036 0.025 0.24 3 -0.22 1 4
dendrite morphogenesis 0.023 0.077 0.25 26 -0.18 23 49
Syndecan-2/GM-CSF 0.046 0.1 0.24 71 -0.18 21 92
determination of left/right symmetry -0.007 0.052 -10000 0 -0.21 24 24
Syndecan-2/PKC delta 0.008 0.047 -10000 0 -0.18 23 23
GNB2L1 0.025 0.006 -10000 0 -10000 0 0
MAPK3 0.034 0.096 0.2 61 -0.17 16 77
MAPK1 0.034 0.099 0.2 62 -0.17 20 82
Syndecan-2/RACK1 0.018 0.046 -10000 0 -0.15 24 24
NF1 0.025 0.006 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.007 0.052 -10000 0 -0.21 24 24
ITGA2 0.027 0.035 0.33 4 -0.32 1 5
MAPK8 -0.016 0.041 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.047 0.098 0.24 55 -0.17 29 84
Syndecan-2/Kininogen 0.004 0.045 -10000 0 -0.18 21 21
ITGB1 0.025 0.006 -10000 0 -10000 0 0
SRC 0.003 0.074 0.18 53 -10000 0 53
Syndecan-2/CASK/Protein 4.1 0.008 0.044 -10000 0 -0.16 24 24
extracellular matrix organization 0.008 0.049 -10000 0 -0.18 24 24
actin cytoskeleton reorganization 0.017 0.08 0.23 25 -0.19 30 55
Syndecan-2/Caveolin-2/Ras 0.017 0.053 -10000 0 -0.17 26 26
Syndecan-2/Laminin alpha3 0.014 0.094 0.24 33 -0.19 42 75
Syndecan-2/RasGAP 0.026 0.049 -10000 0 -0.15 22 22
alpha5/beta1 Integrin 0.026 0.05 -10000 0 -0.22 15 15
PRKCD 0.025 0.006 -10000 0 -10000 0 0
Syndecan-2 dimer 0.023 0.078 0.25 26 -0.18 23 49
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.01 0.042 -10000 0 -10000 0 0
RHOA 0.025 0.006 -10000 0 -10000 0 0
SDCBP 0.024 0.008 -10000 0 -10000 0 0
TNFRSF13B -0.002 0.097 0.33 7 -0.32 28 35
RASA1 0.025 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.036 0.025 0.24 3 -0.22 1 4
Syndecan-2/Synbindin 0.007 0.048 -10000 0 -0.18 24 24
TGFB1 0.026 0.004 -10000 0 -10000 0 0
CASP3 0.008 0.081 0.19 58 -0.17 19 77
FN1 0.035 0.095 0.33 26 -0.32 11 37
Syndecan-2/IL8 -0.013 0.08 0.22 1 -0.2 61 62
SDC2 -0.007 0.052 -10000 0 -0.22 24 24
KNG1 -0.016 0.004 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.008 0.049 -10000 0 -0.18 24 24
TRAPPC4 0.025 0.006 -10000 0 -10000 0 0
CSF2 0.076 0.12 0.33 74 -10000 0 74
Syndecan-2/TGFB1 0.008 0.049 -10000 0 -0.18 24 24
Syndecan-2/Syntenin/PI-4-5-P2 0.008 0.043 -10000 0 -0.16 23 23
Syndecan-2/Ezrin 0.02 0.049 -10000 0 -0.16 23 23
PRKACA 0.008 0.084 0.19 61 -0.17 24 85
angiogenesis -0.013 0.08 0.22 1 -0.2 61 62
MMP2 -0.001 0.092 -10000 0 -0.32 31 31
IL8 -0.022 0.12 0.33 1 -0.32 56 57
calcineurin-NFAT signaling pathway -0.001 0.072 0.22 7 -0.19 44 51
BCR signaling pathway

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
JUN -0.047 0.15 0.27 7 -0.35 44 51
IKBKB -0.018 0.1 0.26 2 -0.29 22 24
AKT1 -0.03 0.1 0.26 16 -0.21 33 49
IKBKG -0.015 0.098 0.26 2 -0.29 24 26
CALM1 -0.03 0.13 0.32 2 -0.4 26 28
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
MAP3K1 -0.064 0.2 0.32 7 -0.49 46 53
MAP3K7 0.025 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.027 0.13 0.34 2 -0.42 26 28
DOK1 0.026 0.016 0.33 1 -10000 0 1
AP-1 -0.038 0.097 0.21 3 -0.25 25 28
LYN 0.024 0.007 -10000 0 -10000 0 0
BLNK 0.014 0.061 -10000 0 -0.32 13 13
SHC1 0.024 0.007 -10000 0 -10000 0 0
BCR complex -0.003 0.13 0.35 14 -0.25 69 83
CD22 -0.065 0.19 0.39 7 -0.45 58 65
CAMK2G -0.027 0.12 0.3 2 -0.38 26 28
CSNK2A1 0.025 0.006 -10000 0 -10000 0 0
INPP5D 0.019 0.042 -10000 0 -0.32 6 6
SHC/GRB2/SOS1 -0.017 0.08 0.16 6 -0.3 10 16
GO:0007205 -0.028 0.14 0.34 2 -0.42 26 28
SYK 0.02 0.035 -10000 0 -0.32 4 4
ELK1 -0.029 0.13 0.41 2 -0.4 26 28
NFATC1 -0.075 0.19 0.26 9 -0.4 70 79
B-cell antigen/BCR complex -0.003 0.13 0.35 14 -0.25 69 83
PAG1/CSK 0.033 0.014 -10000 0 -10000 0 0
NFKBIB 0.01 0.042 0.15 2 -0.13 7 9
HRAS -0.031 0.13 0.29 3 -0.38 27 30
NFKBIA 0.01 0.041 0.15 2 -0.12 6 8
NF-kappa-B/RelA/I kappa B beta 0.014 0.037 0.15 2 -10000 0 2
RasGAP/Csk 0.019 0.12 0.31 13 -0.23 62 75
mol:GDP -0.029 0.13 0.34 2 -0.4 29 31
PTEN 0.025 0.007 -10000 0 -10000 0 0
CD79B 0.017 0.077 0.33 7 -0.32 15 22
NF-kappa-B/RelA/I kappa B alpha 0.014 0.037 0.15 2 -10000 0 2
GRB2 0.025 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.078 0.2 0.45 7 -0.45 61 68
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
mol:IP3 -0.031 0.14 0.34 2 -0.42 27 29
CSK 0.026 0.004 -10000 0 -10000 0 0
FOS -0.069 0.14 0.37 1 -0.42 29 30
CHUK -0.022 0.11 0.26 2 -0.3 36 38
IBTK 0.025 0.006 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.008 0.13 0.27 2 -0.37 23 25
PTPN6 -0.07 0.18 0.36 7 -0.43 60 67
RELA 0.026 0.004 -10000 0 -10000 0 0
BCL2A1 0.008 0.031 0.17 1 -10000 0 1
VAV2 -0.074 0.2 0.34 8 -0.46 62 70
ubiquitin-dependent protein catabolic process 0.011 0.042 0.15 2 -0.12 7 9
BTK -0.034 0.25 -10000 0 -1 24 24
CD19 -0.058 0.18 0.33 11 -0.46 49 60
MAP4K1 0.018 0.06 0.33 3 -0.32 10 13
CD72 0.033 0.054 0.33 13 -10000 0 13
PAG1 0.023 0.009 -10000 0 -10000 0 0
MAPK14 -0.055 0.17 0.3 7 -0.43 43 50
SH3BP5 0.024 0.018 -10000 0 -0.32 1 1
PIK3AP1 -0.036 0.15 0.37 3 -0.47 26 29
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.061 0.23 0.34 6 -0.5 57 63
RAF1 -0.014 0.13 0.26 11 -0.38 22 33
RasGAP/p62DOK/SHIP 0.016 0.12 0.36 7 -0.24 55 62
CD79A -0.023 0.14 0.33 14 -0.32 69 83
re-entry into mitotic cell cycle -0.038 0.096 0.21 3 -0.25 25 28
RASA1 0.025 0.005 -10000 0 -10000 0 0
MAPK3 -0.01 0.11 0.25 11 -0.34 18 29
MAPK1 -0.013 0.12 0.26 14 -0.36 16 30
CD72/SHP1 -0.039 0.2 0.36 19 -0.41 59 78
NFKB1 0.026 0.003 -10000 0 -10000 0 0
MAPK8 -0.055 0.17 0.3 9 -0.42 45 54
actin cytoskeleton organization -0.062 0.18 0.3 11 -0.4 59 70
NF-kappa-B/RelA 0.03 0.071 0.28 2 -0.19 5 7
Calcineurin -0.012 0.12 0.29 2 -0.37 23 25
PI3K -0.075 0.14 -10000 0 -0.34 68 68
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.03 0.14 0.36 2 -0.41 32 34
SOS1 0.026 0.004 -10000 0 -10000 0 0
Bam32/HPK1 -0.061 0.24 0.52 2 -0.67 43 45
DAPP1 -0.077 0.26 -10000 0 -0.73 44 44
cytokine secretion -0.069 0.17 0.26 9 -0.38 68 77
mol:DAG -0.031 0.14 0.34 2 -0.42 27 29
PLCG2 0.026 0.036 0.33 3 -0.32 2 5
MAP2K1 -0.014 0.12 0.25 10 -0.36 21 31
B-cell antigen/BCR complex/FcgammaRIIB 0.003 0.13 0.32 14 -0.25 64 78
mol:PI-3-4-5-P3 -0.051 0.12 0.24 16 -0.26 56 72
ETS1 -0.027 0.12 0.26 4 -0.35 25 29
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.02 0.12 0.32 14 -0.2 69 83
B-cell antigen/BCR complex/LYN -0.039 0.18 0.34 7 -0.48 41 48
MALT1 0.025 0.006 -10000 0 -10000 0 0
TRAF6 0.024 0.007 -10000 0 -10000 0 0
RAC1 -0.065 0.19 0.31 10 -0.43 59 69
B-cell antigen/BCR complex/LYN/SYK -0.033 0.19 0.46 7 -0.4 57 64
CARD11 -0.025 0.14 0.32 3 -0.39 30 33
FCGR2B 0.003 0.084 0.33 2 -0.32 24 26
PPP3CA 0.026 0.003 -10000 0 -10000 0 0
BCL10 0.026 0.003 -10000 0 -10000 0 0
IKK complex 0 0.051 0.15 7 -0.13 16 23
PTPRC -0.011 0.11 0.33 2 -0.32 44 46
PDPK1 -0.034 0.092 0.21 19 -0.19 52 71
PPP3CB 0.025 0.005 -10000 0 -10000 0 0
PPP3CC 0.022 0.01 -10000 0 -10000 0 0
POU2F2 0.01 0.031 0.16 3 -10000 0 3
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.041 0.032 0.2 4 -0.16 6 10
RGS9BP 0.012 0.063 0.33 1 -0.32 13 14
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 -0.012 0.021 0.33 1 -10000 0 1
mol:Na + 0.045 0.093 0.21 74 -0.15 32 106
mol:ADP -0.016 0.018 0.22 2 -10000 0 2
GNAT2 0.02 0.032 0.33 3 -10000 0 3
RGS9-1/Gbeta5/R9AP -0.008 0.1 0.23 1 -0.2 90 91
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.03 0.021 0.21 5 -10000 0 5
GRK7 0.017 0.017 -10000 0 -10000 0 0
CNGB3 0.085 0.13 0.33 87 -10000 0 87
Cone Metarhodopsin II/X-Arrestin 0.014 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0.023 0.096 0.21 62 -0.17 20 82
Cone PDE6 0.004 0.1 0.23 2 -0.18 88 90
Cone Metarhodopsin II 0.025 0.012 0.2 1 -10000 0 1
Na + (4 Units) 0.047 0.098 0.24 59 -0.17 20 79
GNAT2/GDP 0.003 0.097 0.22 4 -0.17 90 94
GNB5 0.026 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.012 0.033 0.18 10 -10000 0 10
Cone Transducin 0.044 0.034 0.22 4 -0.17 6 10
SLC24A2 0.027 0.072 0.33 21 -10000 0 21
GNB3/GNGT2 0.033 0.035 0.24 1 -0.22 6 7
GNB3 0.023 0.034 0.33 1 -0.32 3 4
GNAT2/GTP 0.019 0.018 0.22 3 -10000 0 3
CNGA3 -0.021 0.099 -10000 0 -0.32 39 39
ARR3 -0.009 0.017 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.046 0.094 0.21 74 -0.15 32 106
mol:Pi -0.009 0.1 0.23 1 -0.2 90 91
Cone CNG Channel 0.052 0.085 -10000 0 -0.16 22 22
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.027 0.072 0.33 21 -10000 0 21
RGS9 -0.047 0.14 -10000 0 -0.32 84 84
PDE6C -0.009 0.017 -10000 0 -10000 0 0
GNGT2 0.022 0.035 -10000 0 -0.32 4 4
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H -0.008 0.029 0.33 2 -10000 0 2
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.027 0.023 -10000 0 -0.18 3 3
ARNO/beta Arrestin1-2 0.01 0.079 -10000 0 -0.78 2 2
EGFR 0.017 0.051 -10000 0 -0.32 9 9
EPHA2 0.022 0.038 -10000 0 -0.32 5 5
USP6 0.024 0.008 -10000 0 -10000 0 0
IQSEC1 0.023 0.009 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.041 0.063 0.24 23 -0.22 9 32
ARRB2 0.008 0.011 0.16 2 -10000 0 2
mol:GTP 0.013 0.047 0.13 32 -0.14 7 39
ARRB1 0.022 0.035 -10000 0 -0.32 4 4
FBXO8 0.025 0.006 -10000 0 -10000 0 0
TSHR 0.02 0.045 0.33 7 -10000 0 7
EGF 0.039 0.073 0.33 24 -10000 0 24
somatostatin receptor activity 0 0 0.001 2 -0.001 74 76
ARAP2 0.024 0.025 -10000 0 -0.32 2 2
mol:GDP -0.062 0.12 0.19 2 -0.25 90 92
mol:PI-3-4-5-P3 0 0 0.001 4 -0.001 50 54
ITGA2B 0.047 0.08 0.33 30 -10000 0 30
ARF6 0.025 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.055 0.037 0.24 2 -0.18 4 6
ADAP1 0.022 0.03 -10000 0 -0.32 3 3
KIF13B 0.022 0.01 -10000 0 -10000 0 0
HGF/MET -0.015 0.11 0.24 7 -0.22 86 93
PXN 0.026 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.057 0.12 0.21 4 -0.25 81 85
EGFR/EGFR/EGF/EGF/ARFGEP100 0.049 0.058 0.23 23 -0.19 7 30
ADRB2 -0.017 0.11 -10000 0 -0.32 49 49
receptor agonist activity 0 0 0 2 0 74 76
actin filament binding 0 0 0 2 0 81 83
SRC 0.025 0.007 -10000 0 -10000 0 0
ITGB3 -0.012 0.11 -10000 0 -0.32 44 44
GNAQ 0.023 0.008 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 0.001 5 -0.001 52 57
ARF6/GDP -0.027 0.14 0.27 6 -0.39 36 42
ARF6/GDP/GULP/ACAP1 -0.062 0.15 0.24 4 -0.3 88 92
alphaIIb/beta3 Integrin/paxillin/GIT1 0.046 0.086 0.24 23 -0.18 38 61
ACAP1 0.018 0.062 0.33 4 -0.32 10 14
ACAP2 0.025 0.006 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.013 0.027 0.26 2 -10000 0 2
EFNA1 0.026 0.022 0.33 2 -10000 0 2
HGF -0.044 0.15 0.33 7 -0.32 86 93
CYTH3 -0.008 0.002 -10000 0 -10000 0 0
CYTH2 0.013 0.07 -10000 0 -0.97 2 2
NCK1 0.025 0.006 -10000 0 -10000 0 0
fibronectin binding 0 0 0 9 0 55 64
endosomal lumen acidification 0 0 0 12 0 74 86
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.025 0.12 -10000 0 -0.32 59 59
GNAQ/ARNO 0.025 0.067 -10000 0 -0.9 2 2
mol:Phosphatidic acid 0 0 0 1 -10000 0 1
PIP3-E 0 0 0 3 0 8 11
MET 0.025 0.004 -10000 0 -10000 0 0
GNA14 -0.015 0.11 -10000 0 -0.32 45 45
GNA15 0.023 0.03 -10000 0 -0.32 3 3
GIT1 0.025 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 5 -0.001 61 66
GNA11 0.025 0.018 -10000 0 -0.32 1 1
LHCGR -0.004 0.03 0.33 2 -10000 0 2
AGTR1 -0.12 0.17 -10000 0 -0.32 161 161
desensitization of G-protein coupled receptor protein signaling pathway 0.013 0.027 0.26 2 -10000 0 2
IPCEF1/ARNO 0.04 0.078 -10000 0 -0.83 2 2
alphaIIb/beta3 Integrin 0.023 0.096 0.24 25 -0.21 44 69
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.007 0.14 -10000 0 -0.39 44 44
HDAC1 0.024 0.016 -10000 0 -10000 0 0
AES 0.025 0.007 -10000 0 -10000 0 0
FBXW11 0.025 0.006 -10000 0 -10000 0 0
DTX1 0.019 0.072 0.33 6 -0.32 13 19
LRP6/FZD1 0.037 0.019 0.24 1 -0.23 1 2
TLE1 0.022 0.02 -10000 0 -0.32 1 1
AP1 -0.058 0.12 -10000 0 -0.24 109 109
NCSTN 0.022 0.009 -10000 0 -10000 0 0
ADAM10 0.025 0.005 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.025 0.18 -10000 0 -0.64 27 27
NICD/RBPSUH 0 0.14 -10000 0 -0.39 44 44
WIF1 -0.054 0.14 0.33 9 -0.32 77 86
NOTCH1 -0.024 0.13 -10000 0 -0.41 41 41
PSENEN 0.025 0.006 -10000 0 -10000 0 0
KREMEN2 0.14 0.15 0.33 151 -10000 0 151
DKK1 -0.011 0.13 0.33 14 -0.32 55 69
beta catenin/beta TrCP1 0.033 0.062 -10000 0 -10000 0 0
APH1B 0.026 0.004 -10000 0 -10000 0 0
APH1A 0.023 0.008 -10000 0 -10000 0 0
AXIN1 -0.011 0.088 -10000 0 -0.36 13 13
CtBP/CBP/TCF1/TLE1/AES 0.003 0.062 0.28 2 -0.28 2 4
PSEN1 0.025 0.005 -10000 0 -10000 0 0
FOS -0.081 0.16 -10000 0 -0.32 124 124
JUN 0.014 0.063 -10000 0 -0.32 14 14
MAP3K7 0.024 0.011 -10000 0 -10000 0 0
CTNNB1 0.023 0.067 0.29 4 -10000 0 4
MAPK3 0.025 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.15 0.13 0.27 188 -0.19 1 189
HNF1A 0.029 0.034 0.33 5 -10000 0 5
CTBP1 0.025 0.008 -10000 0 -10000 0 0
MYC -0.04 0.26 -10000 0 -1.2 19 19
NKD1 0.01 0.086 0.33 5 -0.32 22 27
FZD1 0.026 0.023 0.33 1 -0.32 1 2
NOTCH1 precursor/Deltex homolog 1 -0.001 0.15 0.31 2 -0.41 42 44
apoptosis -0.058 0.12 -10000 0 -0.24 109 109
Delta 1/NOTCHprecursor -0.002 0.14 -10000 0 -0.39 44 44
DLL1 0.024 0.037 0.33 2 -0.32 3 5
PPARD 0.016 0.047 -10000 0 -0.76 1 1
Gamma Secretase 0.059 0.035 -10000 0 -10000 0 0
APC -0.013 0.1 -10000 0 -0.48 12 12
DVL1 0.003 0.03 -10000 0 -0.24 3 3
CSNK2A1 0.025 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0.005 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.081 0.13 0.24 129 -0.19 30 159
LRP6 0.025 0.005 -10000 0 -10000 0 0
CSNK1A1 0.025 0.007 -10000 0 -10000 0 0
NLK 0.009 0.011 -10000 0 -10000 0 0
CCND1 -0.003 0.2 -10000 0 -1.2 10 10
WNT1 0.018 0.032 0.33 3 -10000 0 3
Axin1/APC/beta catenin 0.013 0.1 0.28 3 -0.4 8 11
DKK2 0.089 0.13 0.33 88 -0.32 1 89
NOTCH1 precursor/DVL1 -0.014 0.13 -10000 0 -0.39 38 38
GSK3B 0.025 0.005 -10000 0 -10000 0 0
FRAT1 0.025 0.008 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.006 0.15 -10000 0 -0.41 42 42
PPP2R5D 0.02 0.053 0.24 3 -0.32 3 6
MAPK1 0.025 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.019 0.099 0.24 11 -0.18 72 83
RBPJ 0.025 0.005 -10000 0 -10000 0 0
CREBBP 0.025 0.011 -10000 0 -10000 0 0
ErbB2/ErbB3 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
USP8 -0.013 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.01 0.11 0.29 5 -0.24 9 14
NFATC4 -0.034 0.08 0.22 11 -0.29 4 15
ERBB2IP 0.024 0.009 -10000 0 -10000 0 0
HSP90 (dimer) 0.025 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.038 0.087 0.25 5 -0.2 51 56
JUN -0.009 0.094 0.31 7 -0.3 1 8
HRAS 0.024 0.008 -10000 0 -10000 0 0
DOCK7 -0.039 0.086 0.26 7 -0.2 50 57
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.01 0.09 0.22 14 -0.18 50 64
AKT1 -0.007 0.007 -10000 0 -10000 0 0
BAD -0.013 0.004 -10000 0 -10000 0 0
MAPK10 -0.028 0.072 0.18 14 -0.19 8 22
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.038 0.094 0.27 5 -0.21 51 56
RAF1 -0.002 0.1 0.29 8 -0.26 8 16
ErbB2/ErbB3/neuregulin 2 -0.063 0.098 0.19 3 -0.19 146 149
STAT3 0.022 0.063 -10000 0 -0.84 2 2
cell migration -0.027 0.071 0.22 8 -0.18 12 20
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.044 0.24 0.47 10 -0.61 23 33
FOS -0.099 0.26 0.42 10 -0.43 131 141
NRAS 0.026 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.038 0.087 0.25 5 -0.2 51 56
MAPK3 -0.012 0.19 0.44 10 -0.51 17 27
MAPK1 -0.014 0.19 0.44 10 -0.54 17 27
JAK2 -0.038 0.081 0.26 4 -0.2 48 52
NF2 -0.001 0.065 -10000 0 -0.62 4 4
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.009 0.085 0.19 7 -0.21 50 57
NRG1 -0.015 0.14 0.32 16 -0.32 56 72
GRB2/SOS1 0.037 0.01 -10000 0 -10000 0 0
MAPK8 -0.04 0.11 0.24 5 -0.24 55 60
MAPK9 -0.023 0.063 0.18 14 -0.17 2 16
ERBB2 -0.014 0.049 0.25 13 -10000 0 13
ERBB3 0.016 0.054 -10000 0 -0.32 10 10
SHC1 0.024 0.007 -10000 0 -10000 0 0
RAC1 0.025 0.006 -10000 0 -10000 0 0
apoptosis 0.015 0.011 -10000 0 -10000 0 0
STAT3 (dimer) 0.022 0.061 -10000 0 -0.82 2 2
RNF41 -0.017 0.009 -10000 0 -10000 0 0
FRAP1 -0.007 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.043 0.052 -10000 0 -0.16 49 49
ErbB2/ErbB2/HSP90 (dimer) -0.013 0.038 0.19 11 -10000 0 11
CHRNA1 0.014 0.18 0.42 32 -0.39 16 48
myelination -0.028 0.086 0.24 15 -0.27 4 19
PPP3CB -0.035 0.081 0.24 7 -0.2 13 20
KRAS 0.025 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.009 0.096 0.23 2 -0.19 44 46
NRG2 -0.12 0.17 -10000 0 -0.32 164 164
mol:GDP -0.009 0.084 0.19 7 -0.21 50 57
SOS1 0.026 0.005 -10000 0 -10000 0 0
MAP2K2 -0.007 0.11 0.32 13 -0.3 8 21
SRC 0.025 0.007 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.039 0.085 0.25 6 -0.2 51 57
MAP2K1 -0.039 0.19 0.41 7 -0.57 14 21
heart morphogenesis -0.038 0.087 0.25 5 -0.2 51 56
RAS family/GDP 0.01 0.1 0.25 1 -0.24 8 9
GRB2 0.026 0.005 -10000 0 -10000 0 0
PRKACA 0.002 0.072 -10000 0 -0.64 5 5
CHRNE 0.003 0.031 0.16 6 -0.16 1 7
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.007 0.007 -10000 0 -10000 0 0
nervous system development -0.038 0.087 0.25 5 -0.2 51 56
CDC42 0.026 0.003 -10000 0 -10000 0 0
IL27-mediated signaling events

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
TGFB1 0.027 0.005 -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 -0.033 0.16 0.37 8 -0.37 27 35
IL27/IL27R/JAK1 0.089 0.18 0.53 27 -10000 0 27
TBX21 0.041 0.19 0.42 46 -0.36 17 63
IL12B 0.035 0.064 0.35 14 -10000 0 14
IL12A 0.002 0.031 0.2 8 -10000 0 8
IL6ST -0.014 0.12 0.18 1 -0.32 54 55
IL27RA/JAK1 0.037 0.064 0.4 2 -10000 0 2
IL27 0.042 0.08 0.35 23 -10000 0 23
TYK2 0.039 0.027 0.17 1 -10000 0 1
T-helper cell lineage commitment -0.083 0.12 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.033 0.16 0.37 8 -0.37 27 35
T cell proliferation during immune response -0.033 0.16 0.37 8 -0.37 27 35
MAPKKK cascade 0.033 0.16 0.37 27 -0.37 8 35
STAT3 0.026 0.004 -10000 0 -10000 0 0
STAT2 0.026 0.004 -10000 0 -10000 0 0
STAT1 0.031 0.032 0.33 4 -10000 0 4
IL12RB1 0.035 0.088 0.34 20 -0.32 10 30
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.069 0.22 0.52 50 -0.39 8 58
IL27/IL27R/JAK2/TYK2 0.033 0.16 0.37 27 -0.37 8 35
positive regulation of T cell mediated cytotoxicity 0.033 0.16 0.37 27 -0.37 8 35
STAT1 (dimer) 0.098 0.24 0.61 44 -0.4 9 53
JAK2 0.031 0.023 -10000 0 -10000 0 0
JAK1 0.028 0.01 -10000 0 -10000 0 0
STAT2 (dimer) 0.036 0.15 0.36 20 -0.36 8 28
T cell proliferation -0.03 0.18 0.35 23 -0.32 54 77
IL12/IL12R/TYK2/JAK2 0.051 0.23 0.51 13 -0.75 20 33
IL17A -0.081 0.12 -10000 0 -10000 0 0
mast cell activation -0.033 0.16 0.37 8 -0.37 27 35
IFNG 0.034 0.076 0.18 74 -0.098 4 78
T cell differentiation 0.001 0.008 0.018 56 -0.016 2 58
STAT3 (dimer) 0.036 0.15 0.36 20 -0.36 8 28
STAT5A (dimer) 0.035 0.15 0.36 20 -0.36 8 28
STAT4 (dimer) 0.03 0.16 0.37 17 -0.34 15 32
STAT4 0.008 0.075 -10000 0 -0.32 20 20
T cell activation -0.006 0.014 -10000 0 -0.14 4 4
IL27R/JAK2/TYK2 0.051 0.12 0.42 5 -10000 0 5
GATA3 -0.026 0.36 0.58 42 -1.2 26 68
IL18 -0.007 0.027 -10000 0 -0.22 6 6
positive regulation of mast cell cytokine production 0.036 0.15 0.36 20 -0.35 8 28
IL27/EBI3 0.064 0.08 0.3 29 -0.23 3 32
IL27RA 0.024 0.06 0.41 2 -10000 0 2
IL6 -0.12 0.17 -10000 0 -0.32 170 170
STAT5A 0.025 0.018 -10000 0 -0.32 1 1
monocyte differentiation 0.002 0.003 0.014 2 -10000 0 2
IL2 -0.024 0.047 -10000 0 -0.39 1 1
IL1B -0.006 0.06 0.2 15 -0.22 18 33
EBI3 0.037 0.055 0.32 8 -0.32 3 11
TNF 0.006 0.044 0.19 21 -10000 0 21
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.026 0.004 -10000 0 -10000 0 0
VLDLR 0.014 0.054 -10000 0 -0.32 10 10
LRPAP1 0.025 0.005 -10000 0 -10000 0 0
NUDC 0.026 0.003 -10000 0 -10000 0 0
RELN/LRP8 -0.006 0.13 0.24 39 -0.19 107 146
CaM/Ca2+ 0.019 0.003 -10000 0 -10000 0 0
KATNA1 0.025 0.005 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.043 0.09 0.2 10 -10000 0 10
IQGAP1/CaM 0.037 0.008 -10000 0 -10000 0 0
DAB1 0 0.12 0.33 23 -0.32 33 56
IQGAP1 0.026 0.004 -10000 0 -10000 0 0
PLA2G7 0.064 0.1 0.33 51 -10000 0 51
CALM1 0.026 0.004 -10000 0 -10000 0 0
DYNLT1 0.025 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.07 0.075 0.24 66 -10000 0 66
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.026 0.004 -10000 0 -10000 0 0
CDK5R1 0.037 0.061 0.33 17 -10000 0 17
LIS1/Poliovirus Protein 3A -0.011 0.004 -10000 0 -10000 0 0
CDK5R2 0.033 0.078 0.33 25 -10000 0 25
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.045 0.13 0.23 15 -0.2 151 166
YWHAE 0.024 0.008 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.037 0.092 0.31 5 -0.22 2 7
MAP1B -0.018 0.067 -10000 0 -0.22 40 40
RAC1 0.008 0.004 -10000 0 -10000 0 0
p35/CDK5 -0.036 0.095 0.21 23 -10000 0 23
RELN -0.096 0.16 0.33 4 -0.32 139 143
PAFAH/LIS1 0.047 0.068 0.22 51 -10000 0 51
LIS1/CLIP170 0.021 0.009 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.044 0.074 0.18 2 -10000 0 2
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.068 0.14 0.22 5 -0.33 59 64
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.034 0.088 0.29 4 -0.21 15 19
LIS1/IQGAP1 0.022 0.009 -10000 0 -10000 0 0
RHOA 0.008 0.004 -10000 0 -10000 0 0
PAFAH1B1 -0.014 0.006 -10000 0 -10000 0 0
PAFAH1B3 0.039 0.062 0.33 18 -10000 0 18
PAFAH1B2 0.025 0.006 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain -0.002 0.056 -10000 0 -0.15 32 32
NDEL1/Katanin 60/Dynein heavy chain -0.025 0.098 0.3 4 -0.23 1 5
LRP8 0.079 0.12 0.33 72 -10000 0 72
NDEL1/Katanin 60 -0.039 0.091 0.3 4 -0.23 3 7
P39/CDK5 -0.039 0.1 0.22 24 -10000 0 24
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.022 0.009 -10000 0 -10000 0 0
CDK5 -0.045 0.082 0.18 10 -10000 0 10
PPP2R5D 0.026 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.019 0.008 -10000 0 -10000 0 0
CSNK2A1 0.025 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.034 0.12 0.23 13 -0.18 140 153
RELN/VLDLR 0 0.13 0.25 35 -0.18 105 140
CDC42 0.008 0.004 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD -0.004 0.11 0.22 18 -0.36 14 32
FZD6 0.021 0.01 -10000 0 -10000 0 0
WNT6 0.042 0.1 0.33 36 -0.32 10 46
WNT4 0.007 0.088 0.33 3 -0.32 25 28
FZD3 0.02 0.026 -10000 0 -0.32 2 2
WNT5A 0.026 0.066 0.33 10 -0.32 7 17
WNT11 0.032 0.11 0.33 32 -0.32 20 52
Visual signal transduction: Rods

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
mol:K + 0.026 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.018 0.021 0.22 4 -10000 0 4
Metarhodopsin II/Arrestin 0.022 0.008 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.037 0.037 0.21 16 -10000 0 16
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.013 0.037 0.33 4 -10000 0 4
GRK1 -0.012 0.021 0.33 1 -10000 0 1
CNG Channel 0.071 0.099 0.27 24 -0.16 24 48
mol:Na + 0.087 0.099 0.28 32 -0.17 14 46
mol:ADP -0.012 0.021 0.33 1 -10000 0 1
RGS9-1/Gbeta5/R9AP -0.008 0.1 0.23 1 -0.2 90 91
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.11 0.11 0.33 32 -0.17 14 46
CNGB1 0.15 0.15 0.33 172 -10000 0 172
RDH5 0.025 0.018 -10000 0 -0.32 1 1
SAG -0.016 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.032 0.094 0.3 20 -10000 0 20
Na + (4 Units) 0.061 0.08 0.21 30 -0.16 14 44
RGS9 -0.047 0.14 -10000 0 -0.32 84 84
GNB1/GNGT1 0.045 0.04 0.24 16 -10000 0 16
GNAT1/GDP 0.002 0.094 0.22 3 -0.17 88 91
GUCY2D 0.045 0.093 0.33 39 -10000 0 39
GNGT1 0.033 0.063 0.33 17 -10000 0 17
GUCY2F -0.012 0.014 -10000 0 -10000 0 0
GNB5 0.026 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) 0.006 0.052 0.15 22 -0.16 14 36
mol:11-cis-retinal 0.025 0.018 -10000 0 -0.32 1 1
mol:cGMP 0.056 0.055 0.23 20 -0.16 1 21
GNB1 0.026 0.003 -10000 0 -10000 0 0
Rhodopsin 0.031 0.015 -10000 0 -0.23 1 1
SLC24A1 0.026 0.004 -10000 0 -10000 0 0
CNGA1 0.023 0.11 0.33 25 -0.32 25 50
Metarhodopsin II 0.022 0.011 0.2 1 -10000 0 1
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.074 0.07 0.24 55 -0.16 1 56
RGS9BP 0.012 0.063 0.33 1 -0.32 13 14
Metarhodopsin II/Transducin 0.016 0.026 0.14 3 -0.17 1 4
GCAP Family/Ca ++ 0.049 0.042 0.21 21 -0.18 1 22
PDE6A/B 0.029 0.054 0.24 5 -0.22 15 20
mol:Pi -0.009 0.1 0.23 1 -0.2 90 91
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.051 0.038 0.22 17 -10000 0 17
PDE6B 0.013 0.067 0.33 1 -0.32 15 16
PDE6A 0.026 0.036 0.33 5 -10000 0 5
PDE6G 0.034 0.054 0.33 13 -10000 0 13
RHO -0.007 0.018 -10000 0 -10000 0 0
PDE6 0.009 0.12 0.37 1 -0.18 94 95
GUCA1A 0.03 0.07 0.33 20 -10000 0 20
GC2/GCAP Family 0.06 0.043 0.23 21 -0.18 1 22
GUCA1C -0.013 0.02 0.33 1 -10000 0 1
GUCA1B 0.025 0.018 -10000 0 -0.32 1 1
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.035 0.012 -10000 0 -10000 0 0
CRKL -0.025 0.13 0.29 4 -0.49 14 18
mol:PIP3 0.005 0.062 -10000 0 -0.86 2 2
AKT1 -0.005 0.057 -10000 0 -0.77 2 2
PTK2B 0.022 0.01 -10000 0 -10000 0 0
RAPGEF1 -0.025 0.12 0.31 2 -0.5 12 14
RANBP10 0.025 0.006 -10000 0 -10000 0 0
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.004 0.1 0.23 7 -0.19 79 86
MAP3K5 -0.025 0.13 0.34 2 -0.45 16 18
HGF/MET/CIN85/CBL/ENDOPHILINS 0.014 0.1 0.24 7 -0.17 85 92
AP1 -0.053 0.11 0.18 1 -0.22 116 117
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.024 0.007 -10000 0 -10000 0 0
apoptosis -0.22 0.36 -10000 0 -0.73 133 133
STAT3 (dimer) -0.031 0.097 -10000 0 -0.28 22 22
GAB1/CRKL/SHP2/PI3K -0.001 0.13 0.38 1 -0.5 11 12
INPP5D 0.019 0.042 -10000 0 -0.32 6 6
CBL/CRK -0.016 0.12 0.27 1 -0.46 14 15
PTPN11 0.025 0.005 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.024 0.007 -10000 0 -10000 0 0
PTEN 0.025 0.007 -10000 0 -10000 0 0
ELK1 0.002 0.088 0.35 17 -0.2 1 18
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.021 0.071 -10000 0 -0.23 20 20
PAK1 -0.002 0.066 0.27 1 -0.73 2 3
HGF/MET/RANBP10 0.002 0.1 0.23 7 -0.19 84 91
HRAS -0.033 0.12 -10000 0 -0.47 18 18
DOCK1 -0.028 0.12 0.32 4 -0.45 15 19
GAB1 -0.028 0.13 0.24 1 -0.5 15 16
CRK -0.028 0.12 0.26 2 -0.48 15 17
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.06 0.18 -10000 0 -0.4 82 82
JUN 0.014 0.063 -10000 0 -0.32 14 14
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.028 0.072 -10000 0 -0.16 86 86
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
cell morphogenesis -0.025 0.13 0.34 9 -0.34 17 26
GRB2/SHC -0.003 0.081 -10000 0 -0.21 13 13
FOS -0.081 0.16 -10000 0 -0.32 124 124
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility 0.002 0.087 0.34 17 -0.2 1 18
HGF/MET/MUC20 -0.01 0.095 0.21 7 -0.18 86 93
cell migration -0.004 0.079 -10000 0 -0.21 13 13
GRB2 0.025 0.005 -10000 0 -10000 0 0
CBL 0.025 0.006 -10000 0 -10000 0 0
MET/RANBP10 0.036 0.01 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.029 0.092 -10000 0 -0.21 74 74
MET/MUC20 0.019 0.003 -10000 0 -10000 0 0
RAP1B -0.016 0.12 0.35 3 -0.49 11 14
RAP1A -0.028 0.11 0.37 1 -0.49 11 12
HGF/MET/RANBP9 0.006 0.098 0.23 7 -0.19 75 82
RAF1 -0.014 0.13 0.29 2 -0.44 17 19
STAT3 -0.03 0.096 -10000 0 -0.29 19 19
cell proliferation -0.037 0.14 0.26 8 -0.3 68 76
RPS6KB1 -0.004 0.032 -10000 0 -10000 0 0
MAPK3 -0.005 0.093 0.57 7 -10000 0 7
MAPK1 -0.001 0.11 0.65 8 -10000 0 8
RANBP9 0.024 0.007 -10000 0 -10000 0 0
MAPK8 -0.018 0.12 0.29 4 -0.42 18 22
SRC -0.034 0.083 -10000 0 -0.26 20 20
PI3K -0.003 0.081 -10000 0 -0.21 15 15
MET/Glomulin 0.016 0.025 -10000 0 -10000 0 0
SOS1 0.026 0.004 -10000 0 -10000 0 0
MAP2K1 -0.013 0.13 0.28 3 -0.42 17 20
MET 0.026 0.004 -10000 0 -10000 0 0
MAP4K1 -0.025 0.13 0.37 1 -0.48 16 17
PTK2 0.023 0.008 -10000 0 -10000 0 0
MAP2K2 -0.011 0.13 0.28 4 -0.41 17 21
BAD -0.007 0.06 0.38 1 -0.73 2 3
MAP2K4 -0.021 0.12 0.32 3 -0.42 15 18
SHP2/GRB2/SOS1/GAB1 -0.007 0.12 -10000 0 -0.48 11 11
INPPL1 0.025 0.006 -10000 0 -10000 0 0
PXN 0.026 0.004 -10000 0 -10000 0 0
SH3KBP1 0.026 0.004 -10000 0 -10000 0 0
HGS -0.033 0.064 0.13 2 -0.15 82 84
PLCgamma1/PKC 0.018 0.005 -10000 0 -10000 0 0
HGF -0.044 0.15 0.33 7 -0.32 86 93
RASA1 0.025 0.005 -10000 0 -10000 0 0
NCK1 0.025 0.006 -10000 0 -10000 0 0
PTPRJ 0.025 0.006 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.001 0.087 -10000 0 -0.17 75 75
PDPK1 -0.001 0.058 -10000 0 -0.81 2 2
HGF/MET/SHIP -0.002 0.11 0.23 7 -0.2 88 95
FAS signaling pathway (CD95)

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
SPTAN1 -0.012 0.04 -10000 0 -0.19 11 11
RFC1 -0.011 0.046 0.21 2 -0.19 12 14
PRKDC 0.005 0.076 0.22 33 -0.19 9 42
RIPK1 0.029 0.009 -10000 0 -10000 0 0
CASP7 -0.036 0.13 -10000 0 -0.68 14 14
FASLG/FAS/FADD/FAF1 -0.021 0.066 -10000 0 -0.24 16 16
MAP2K4 -0.12 0.18 -10000 0 -0.41 63 63
mol:ceramide -0.052 0.11 -10000 0 -0.32 25 25
GSN -0.011 0.042 0.22 1 -0.19 11 12
FASLG/FAS/FADD/FAF1/Caspase 8 -0.034 0.088 -10000 0 -0.29 19 19
FAS -0.004 0.047 -10000 0 -0.33 5 5
BID -0.023 0.037 0.23 6 -0.2 4 10
MAP3K1 -0.068 0.14 -10000 0 -0.46 22 22
MAP3K7 0.006 0.024 -10000 0 -10000 0 0
RB1 -0.01 0.045 0.21 2 -0.21 8 10
CFLAR 0.029 0.008 -10000 0 -10000 0 0
HGF/MET -0.002 0.11 0.23 7 -0.19 90 97
ARHGDIB -0.008 0.054 0.24 6 -0.19 12 18
FADD 0 0.029 -10000 0 -10000 0 0
actin filament polymerization 0.011 0.042 0.19 8 -0.22 1 9
NFKB1 -0.063 0.13 -10000 0 -0.51 10 10
MAPK8 -0.2 0.26 -10000 0 -0.47 179 179
DFFA -0.011 0.049 0.4 1 -0.19 9 10
DNA fragmentation during apoptosis -0.011 0.05 0.31 2 -0.19 13 15
FAS/FADD/MET 0.01 0.049 -10000 0 -0.21 5 5
CFLAR/RIP1 0.042 0.016 -10000 0 -10000 0 0
FAIM3 0.027 0.046 0.33 4 -0.32 4 8
FAF1 -0.002 0.033 -10000 0 -10000 0 0
PARP1 -0.012 0.045 -10000 0 -0.19 10 10
DFFB -0.011 0.05 0.21 6 -0.19 13 19
CHUK -0.063 0.11 -10000 0 -0.5 7 7
FASLG -0.009 0.081 0.32 7 -0.33 15 22
FAS/FADD 0 0.047 -10000 0 -0.24 5 5
HGF -0.044 0.15 0.33 7 -0.32 86 93
LMNA -0.004 0.063 0.22 19 -10000 0 19
CASP6 -0.011 0.045 0.22 1 -0.19 9 10
CASP10 0 0.03 -10000 0 -10000 0 0
CASP3 -0.006 0.049 0.19 13 -0.21 10 23
PTPN13 0.019 0.045 -10000 0 -0.32 7 7
CASP8 -0.024 0.039 0.29 4 -0.23 4 8
IL6 -0.49 0.58 -10000 0 -1.1 182 182
MET 0.026 0.004 -10000 0 -10000 0 0
ICAD/CAD -0.014 0.052 0.39 2 -10000 0 2
FASLG/FAS/FADD/FAF1/Caspase 10 -0.053 0.11 -10000 0 -0.32 25 25
activation of caspase activity by cytochrome c -0.023 0.037 0.23 6 -0.2 4 10
PAK2 -0.003 0.06 0.2 21 -0.19 8 29
BCL2 0.013 0.065 -10000 0 -0.32 15 15
Canonical Wnt signaling 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
HDAC1 0.03 0.03 0.2 2 -10000 0 2
AES 0.028 0.026 0.19 1 -10000 0 1
FBXW11 0.025 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.037 0.019 0.24 1 -0.22 1 2
SMAD4 0.025 0.007 -10000 0 -10000 0 0
DKK2 0.089 0.13 0.33 88 -0.32 1 89
TLE1 0.025 0.03 0.16 2 -0.32 1 3
MACF1 0.025 0.006 -10000 0 -10000 0 0
CTNNB1 0.06 0.09 0.26 8 -0.35 3 11
WIF1 -0.051 0.14 0.33 9 -0.32 77 86
beta catenin/RanBP3 0.056 0.14 0.4 42 -0.34 3 45
KREMEN2 0.14 0.15 0.33 151 -10000 0 151
DKK1 -0.011 0.13 0.33 14 -0.32 55 69
beta catenin/beta TrCP1 0.069 0.086 0.27 5 -0.34 2 7
FZD1 0.026 0.023 0.33 1 -0.32 1 2
AXIN2 -0.053 0.33 0.62 17 -1.2 25 42
AXIN1 0.026 0.005 -10000 0 -10000 0 0
RAN 0.026 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.02 0.11 -10000 0 -0.48 15 15
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.004 0.16 -10000 0 -0.52 23 23
Axin1/APC/GSK3 0.026 0.057 0.25 3 -0.28 1 4
Axin1/APC/GSK3/beta catenin/Macf1 0.022 0.065 0.37 1 -0.3 5 6
HNF1A 0.032 0.042 0.27 8 -10000 0 8
CTBP1 0.028 0.027 0.2 2 -10000 0 2
MYC 0.021 0.35 0.57 56 -1.3 18 74
RANBP3 0.026 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.15 0.13 0.27 188 -0.19 1 189
NKD1 0.01 0.086 0.33 5 -0.32 22 27
TCF4 0.022 0.047 0.18 1 -0.3 6 7
TCF3 0.028 0.028 0.18 3 -10000 0 3
WNT1/LRP6/FZD1/Axin1 0.062 0.028 0.24 3 -0.17 1 4
Ran/GTP 0.019 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.01 0.16 0.44 32 -0.48 8 40
LEF1 0.034 0.045 0.27 10 -10000 0 10
DVL1 0.023 0.051 -10000 0 -0.25 2 2
CSNK2A1 0.025 0.006 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.002 0.14 0.28 1 -0.48 19 20
DKK1/LRP6/Kremen 2 0.081 0.13 0.24 129 -0.19 31 160
LRP6 0.026 0.005 -10000 0 -10000 0 0
CSNK1A1 0.029 0.029 0.2 2 -10000 0 2
NLK 0.021 0.016 -10000 0 -10000 0 0
CCND1 0.04 0.3 0.68 45 -1.3 7 52
WNT1 0.021 0.031 0.33 3 -10000 0 3
GSK3A 0.026 0.005 -10000 0 -10000 0 0
GSK3B 0.025 0.005 -10000 0 -10000 0 0
FRAT1 0.026 0.005 -10000 0 -10000 0 0
PPP2R5D 0.034 0.062 0.25 9 -0.27 1 10
APC -0.014 0.049 0.21 14 -10000 0 14
WNT1/LRP6/FZD1 0.038 0.071 0.21 11 -0.19 2 13
CREBBP 0.026 0.026 0.17 2 -10000 0 2
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.027 0.015 0.33 1 -10000 0 1
SPHK1 0.066 0.11 0.33 56 -0.32 1 57
GNAI2 0.025 0.006 -10000 0 -10000 0 0
mol:S1P 0.028 0.049 0.14 59 -0.22 1 60
GNAO1 -0.081 0.16 -10000 0 -0.32 124 124
mol:Sphinganine-1-P 0.013 0.071 0.19 57 -0.22 1 58
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.06 0.045 -10000 0 -0.18 2 2
GNAI3 0.026 0.003 -10000 0 -10000 0 0
G12/G13 0.035 0.012 -10000 0 -10000 0 0
S1PR3 0.02 0.035 -10000 0 -0.32 4 4
S1PR2 0.026 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.016 0.036 -10000 0 -0.2 2 2
S1PR5 0.032 0.055 0.33 11 -0.32 2 13
S1PR4 0.025 0.04 0.33 3 -0.32 3 6
GNAI1 0.023 0.03 -10000 0 -0.32 3 3
S1P/S1P5/G12 0.055 0.055 0.25 10 -0.17 4 14
S1P/S1P3/Gq -0.028 0.13 -10000 0 -0.28 73 73
S1P/S1P4/Gi -0.062 0.14 0.19 1 -0.34 62 63
GNAQ 0.023 0.008 -10000 0 -10000 0 0
GNAZ -0.049 0.14 -10000 0 -0.32 87 87
GNA14 -0.015 0.11 -10000 0 -0.32 45 45
GNA15 0.023 0.03 -10000 0 -0.32 3 3
GNA12 0.025 0.006 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
GNA11 0.025 0.018 -10000 0 -0.32 1 1
ABCC1 0.026 0.016 0.33 1 -10000 0 1
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.033 0.13 -10000 0 -0.32 65 65
GNB1/GNG2 0.015 0.12 0.28 3 -0.33 15 18
mol:DAG -0.006 0.1 0.23 3 -0.32 14 17
PLCG1 -0.006 0.1 0.23 3 -0.32 14 17
YES1 -0.009 0.098 0.2 18 -0.37 12 30
FZD3 0.02 0.026 -10000 0 -0.32 2 2
FZD6 0.021 0.01 -10000 0 -10000 0 0
G protein 0.019 0.12 0.28 10 -0.34 13 23
MAP3K7 -0.048 0.11 0.32 3 -0.27 38 41
mol:Ca2+ -0.005 0.1 0.23 3 -0.31 14 17
mol:IP3 -0.006 0.1 0.23 3 -0.32 14 17
NLK 0.007 0.042 -10000 0 -0.81 1 1
GNB1 0.026 0.003 -10000 0 -10000 0 0
CAMK2A -0.051 0.11 0.21 3 -0.28 42 45
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.004 0.11 0.22 18 -0.36 14 32
CSNK1A1 0.025 0.005 -10000 0 -10000 0 0
GNAS -0.011 0.1 0.21 19 -0.35 13 32
GO:0007205 -0.011 0.098 0.22 3 -0.31 14 17
WNT6 0.042 0.1 0.33 36 -0.32 10 46
WNT4 0.007 0.088 0.33 3 -0.32 25 28
NFAT1/CK1 alpha -0.014 0.12 0.26 4 -0.34 19 23
GNG2 0.02 0.042 -10000 0 -0.32 6 6
WNT5A 0.026 0.066 0.33 10 -0.32 7 17
WNT11 0.032 0.11 0.33 32 -0.32 20 52
CDC42 -0.002 0.1 0.19 30 -0.36 12 42
Ephrin B reverse 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
EFNB2 0.026 0.016 0.33 1 -10000 0 1
EPHB2 0.047 0.076 0.32 28 -10000 0 28
EFNB1 -0.015 0.028 -10000 0 -0.22 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.044 0.078 -10000 0 -0.18 25 25
Ephrin B2/EPHB1-2 0.047 0.074 0.22 31 -0.17 23 54
neuron projection morphogenesis 0.026 0.064 -10000 0 -0.17 27 27
Ephrin B1/EPHB1-2/Tiam1 0.04 0.081 0.23 27 -0.18 27 54
DNM1 0.019 0.042 -10000 0 -0.32 6 6
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.014 0.084 0.23 2 -0.44 14 16
YES1 -0.012 0.13 -10000 0 -0.66 15 15
Ephrin B1/EPHB1-2/NCK2 0.043 0.081 0.23 30 -0.18 27 57
PI3K 0.022 0.093 -10000 0 -0.44 15 15
mol:GDP 0.039 0.079 0.22 27 -0.18 28 55
ITGA2B 0.047 0.08 0.33 30 -10000 0 30
endothelial cell proliferation 0.033 0.013 0.21 1 -10000 0 1
FYN -0.013 0.13 -10000 0 -0.69 14 14
MAP3K7 -0.014 0.088 -10000 0 -0.47 14 14
FGR -0.01 0.13 -10000 0 -0.66 16 16
TIAM1 0.023 0.03 -10000 0 -0.32 3 3
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
RGS3 0.024 0.008 -10000 0 -10000 0 0
cell adhesion -0.001 0.097 -10000 0 -0.4 14 14
LYN -0.009 0.12 -10000 0 -0.66 14 14
Ephrin B1/EPHB1-2/Src Family Kinases -0.016 0.12 -10000 0 -0.6 16 16
Ephrin B1/EPHB1-2 -0.012 0.095 -10000 0 -0.51 14 14
SRC -0.009 0.13 -10000 0 -0.65 16 16
ITGB3 -0.012 0.11 -10000 0 -0.32 44 44
EPHB1 0.007 0.089 0.32 4 -0.32 25 29
EPHB4 0.026 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.006 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.034 0.013 0.21 1 -10000 0 1
alphaIIb/beta3 Integrin 0.023 0.096 0.24 25 -0.21 44 69
BLK -0.028 0.14 -10000 0 -0.67 16 16
HCK -0.014 0.13 -10000 0 -0.65 16 16
regulation of stress fiber formation -0.042 0.079 0.18 27 -0.22 30 57
MAPK8 -0.016 0.092 0.31 2 -0.44 15 17
Ephrin B1/EPHB1-2/RGS3 0.045 0.079 0.23 30 -0.18 22 52
endothelial cell migration -0.009 0.081 0.21 12 -0.38 14 26
NCK2 0.026 0.004 -10000 0 -10000 0 0
PTPN13 0.017 0.06 -10000 0 -0.43 7 7
regulation of focal adhesion formation -0.042 0.079 0.18 27 -0.22 30 57
chemotaxis -0.043 0.078 0.18 22 -0.22 30 52
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.035 0.071 -10000 0 -0.17 26 26
angiogenesis -0.012 0.094 -10000 0 -0.51 14 14
LCK -0.01 0.13 -10000 0 -0.65 16 16
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.006 0.076 0.32 21 -10000 0 21
PI3K Class IB/PDE3B 0.006 0.077 -10000 0 -0.32 21 21
PDE3B 0.006 0.077 -10000 0 -0.32 21 21
FoxO family signaling

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
G6PC 0.029 0.1 0.4 18 -10000 0 18
PLK1 0.25 0.29 0.67 107 -10000 0 107
CDKN1B 0.17 0.18 0.43 76 -0.36 2 78
FOXO3 0.23 0.26 0.6 103 -0.42 1 104
KAT2B 0.063 0.056 0.17 8 -0.32 1 9
FOXO1/SIRT1 0.017 0.063 0.24 10 -10000 0 10
CAT 0.21 0.24 0.57 81 -10000 0 81
CTNNB1 0.025 0.005 -10000 0 -10000 0 0
AKT1 0.07 0.053 0.18 14 -10000 0 14
FOXO1 0.026 0.083 0.31 19 -10000 0 19
MAPK10 0.028 0.044 0.2 13 -0.15 6 19
mol:GTP 0.001 0 -10000 0 -10000 0 0
FOXO4 0.048 0.069 -10000 0 -10000 0 0
response to oxidative stress 0.046 0.049 0.12 93 -10000 0 93
FOXO3A/SIRT1 0.2 0.21 0.51 90 -10000 0 90
XPO1 0.026 0.005 -10000 0 -10000 0 0
EP300 0.03 0.013 -10000 0 -10000 0 0
BCL2L11 0.07 0.11 -10000 0 -0.71 4 4
FOXO1/SKP2 0.03 0.068 0.26 16 -10000 0 16
mol:GDP 0.046 0.049 0.12 93 -10000 0 93
RAN 0.026 0.005 -10000 0 -10000 0 0
GADD45A 0.16 0.15 0.45 12 -0.48 1 13
YWHAQ 0.025 0.006 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.038 0.1 -10000 0 -0.48 8 8
MST1 0.078 0.081 0.33 22 -10000 0 22
CSNK1D 0.025 0.005 -10000 0 -10000 0 0
CSNK1E 0.025 0.005 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.033 0.087 -10000 0 -0.45 5 5
YWHAB 0.024 0.008 -10000 0 -10000 0 0
MAPK8 0.034 0.041 0.21 15 -0.16 1 16
MAPK9 0.034 0.039 0.21 14 -10000 0 14
YWHAG 0.026 0.003 -10000 0 -10000 0 0
YWHAE 0.024 0.008 -10000 0 -10000 0 0
YWHAZ 0.02 0.011 -10000 0 -10000 0 0
SIRT1 0.007 0.035 0.19 2 -10000 0 2
SOD2 0.17 0.18 0.5 17 -0.56 1 18
RBL2 0.17 0.23 0.49 64 -0.58 9 73
RAL/GDP 0.063 0.037 -10000 0 -10000 0 0
CHUK 0.065 0.053 0.19 2 -10000 0 2
Ran/GTP 0.02 0.004 -10000 0 -10000 0 0
CSNK1G2 0.025 0.005 -10000 0 -10000 0 0
RAL/GTP 0.064 0.034 -10000 0 -10000 0 0
CSNK1G1 0.026 0.004 -10000 0 -10000 0 0
FASLG 0.027 0.29 0.56 5 -1.2 20 25
SKP2 0.026 0.035 0.33 5 -10000 0 5
USP7 0.025 0.007 -10000 0 -10000 0 0
IKBKB 0.059 0.053 0.18 7 -10000 0 7
CCNB1 0.25 0.29 0.67 99 -10000 0 99
FOXO1-3a-4/beta catenin 0.16 0.16 0.48 22 -10000 0 22
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.067 0.25 16 -10000 0 16
CSNK1A1 0.025 0.005 -10000 0 -10000 0 0
SGK1 0.052 0.082 -10000 0 -0.31 12 12
CSNK1G3 0.025 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.036 0.01 -10000 0 -10000 0 0
ZFAND5 0.043 0.065 -10000 0 -10000 0 0
SFN 0.047 0.087 0.33 32 -0.32 3 35
CDK2 0.027 0.022 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.082 0.1 0.28 33 -0.46 2 35
CREBBP 0.025 0.022 -10000 0 -10000 0 0
FBXO32 0.23 0.26 0.59 98 -0.68 1 99
BCL6 0.19 0.19 0.55 17 -10000 0 17
RALB 0.026 0.004 -10000 0 -10000 0 0
RALA 0.026 0.005 -10000 0 -10000 0 0
YWHAH 0.025 0.005 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A -0.006 0.021 0.2 4 -10000 0 4
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.024 0.048 0.24 1 -0.22 13 14
STXBP1 0.015 0.054 -10000 0 -0.32 10 10
ACh/CHRNA1 0.051 0.094 0.24 69 -0.089 25 94
RAB3GAP2/RIMS1/UNC13B 0.036 0.046 0.23 1 -0.19 13 14
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 -0.001 0.064 0.33 1 -0.32 13 14
mol:ACh -0.004 0.038 0.077 25 -0.11 27 52
RAB3GAP2 0.026 0.004 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.015 0.071 0.3 1 -0.18 23 24
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.051 0.094 0.24 69 -0.089 25 94
UNC13B 0.023 0.008 -10000 0 -10000 0 0
CHRNA1 0.075 0.12 0.33 69 -10000 0 69
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.002 0.078 0.27 8 -0.2 36 44
SNAP25 -0.008 0.059 0.13 10 -0.22 25 35
VAMP2 0.003 0.001 -10000 0 -10000 0 0
SYT1 0.003 0.1 0.33 8 -0.32 33 41
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.016 0.033 0.15 3 -0.19 9 12
STX1A/SNAP25 fragment 1/VAMP2 0.015 0.071 0.3 1 -0.18 23 24
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.013 0.13 0.29 3 -0.45 19 22
Syndecan-4/Syndesmos 0.056 0.15 0.35 5 -0.64 7 12
positive regulation of JNK cascade 0.02 0.17 0.34 5 -0.52 13 18
Syndecan-4/ADAM12 0.074 0.17 0.38 24 -0.64 7 31
CCL5 0.02 0.091 0.33 13 -0.32 18 31
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
DNM2 0.026 0.004 -10000 0 -10000 0 0
ITGA5 0.013 0.065 -10000 0 -0.32 15 15
SDCBP 0.024 0.008 -10000 0 -10000 0 0
PLG 0.004 0.044 0.33 5 -10000 0 5
ADAM12 0.055 0.09 0.33 40 -10000 0 40
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.025 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.025 0.022 0.069 1 -10000 0 1
Syndecan-4/Laminin alpha1 0.074 0.18 0.39 26 -0.67 7 33
Syndecan-4/CXCL12/CXCR4 0.021 0.18 0.38 3 -0.56 13 16
Syndecan-4/Laminin alpha3 0.061 0.17 0.38 24 -0.61 8 32
MDK 0.04 0.067 0.33 21 -10000 0 21
Syndecan-4/FZD7 0.055 0.15 0.38 3 -0.6 8 11
Syndecan-4/Midkine 0.067 0.16 0.36 8 -0.67 6 14
FZD7 0.011 0.069 -10000 0 -0.32 17 17
Syndecan-4/FGFR1/FGF -0.013 0.18 0.35 2 -0.51 19 21
THBS1 0.015 0.059 -10000 0 -0.32 12 12
integrin-mediated signaling pathway 0.054 0.16 0.37 11 -0.66 7 18
positive regulation of MAPKKK cascade 0.02 0.17 0.34 5 -0.52 13 18
Syndecan-4/TACI 0.05 0.16 0.35 10 -0.55 10 20
CXCR4 0.019 0.048 -10000 0 -0.32 8 8
cell adhesion 0.011 0.074 0.2 15 -0.29 11 26
Syndecan-4/Dynamin 0.057 0.15 0.38 3 -0.68 6 9
Syndecan-4/TSP1 0.056 0.15 0.38 3 -0.63 8 11
Syndecan-4/GIPC 0.057 0.15 0.38 3 -0.64 7 10
Syndecan-4/RANTES 0.058 0.16 0.37 12 -0.59 10 22
ITGB1 0.025 0.006 -10000 0 -10000 0 0
LAMA1 0.057 0.13 0.33 61 -0.32 14 75
LAMA3 0.023 0.13 0.33 34 -0.32 32 66
RAC1 0.025 0.006 -10000 0 -10000 0 0
PRKCA 0.006 0.16 0.74 17 -10000 0 17
Syndecan-4/alpha-Actinin 0.058 0.15 0.38 3 -0.63 7 10
TFPI 0.019 0.048 -10000 0 -0.32 8 8
F2 0.047 0.08 0.34 27 -10000 0 27
alpha5/beta1 Integrin 0.026 0.05 -10000 0 -0.22 15 15
positive regulation of cell adhesion 0.056 0.17 0.41 18 -0.66 7 25
ACTN1 0.025 0.005 -10000 0 -10000 0 0
TNC 0.009 0.096 0.33 9 -0.32 25 34
Syndecan-4/CXCL12 0.032 0.17 0.35 5 -0.56 13 18
FGF6 -0.016 0.006 -10000 0 -10000 0 0
RHOA 0.025 0.006 -10000 0 -10000 0 0
CXCL12 -0.067 0.15 -10000 0 -0.32 108 108
TNFRSF13B -0.002 0.097 0.33 7 -0.32 28 35
FGF2 -0.083 0.16 -10000 0 -0.32 127 127
FGFR1 -0.04 0.13 -10000 0 -0.32 73 73
Syndecan-4/PI-4-5-P2 0.031 0.14 0.34 4 -0.63 7 11
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.026 0.097 0.33 26 -0.3 11 37
cell migration -0.018 0.013 -10000 0 -10000 0 0
PRKCD 0.014 0.025 -10000 0 -10000 0 0
vasculogenesis 0.056 0.15 0.38 3 -0.6 8 11
SDC4 0.045 0.15 0.38 4 -0.68 7 11
Syndecan-4/Tenascin C 0.055 0.16 0.39 9 -0.7 7 16
Syndecan-4/PI-4-5-P2/PKC alpha -0.023 0.014 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.053 0.15 0.35 5 -0.68 6 11
MMP9 0.09 0.14 0.33 96 -0.32 5 101
Rac1/GTP 0.011 0.075 0.2 15 -0.3 11 26
cytoskeleton organization 0.056 0.15 0.35 5 -0.6 7 12
GIPC1 0.026 0.003 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.056 0.16 0.38 3 -0.65 7 10
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.15 0.17 -10000 0 -0.32 198 198
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.026 0.016 0.33 1 -10000 0 1
TCEB1 0.023 0.009 -10000 0 -10000 0 0
HIF1A/p53 0.012 0.058 -10000 0 -0.28 13 13
HIF1A 0.001 0.048 -10000 0 -0.28 10 10
COPS5 0.024 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.055 0.038 0.24 1 -10000 0 1
FIH (dimer) 0.025 0.005 -10000 0 -10000 0 0
CDKN2A 0.15 0.16 0.33 184 -10000 0 184
ARNT/IPAS -0.083 0.13 -10000 0 -0.22 177 177
HIF1AN 0.025 0.005 -10000 0 -10000 0 0
GNB2L1 0.025 0.006 -10000 0 -10000 0 0
HIF1A/ARNT 0.011 0.05 -10000 0 -0.28 8 8
CUL2 0.025 0.006 -10000 0 -10000 0 0
OS9 0.026 0.004 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.043 0.024 0.23 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.013 0.058 -10000 0 -0.28 13 13
PHD1-3/OS9 0.055 0.04 -10000 0 -0.18 8 8
HIF1A/RACK1/Elongin B/Elongin C 0.029 0.062 -10000 0 -0.27 12 12
VHL 0.023 0.008 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.011 0.057 -10000 0 -0.28 12 12
EGLN3 0.018 0.048 -10000 0 -0.32 8 8
EGLN2 0.025 0.005 -10000 0 -10000 0 0
EGLN1 0.026 0.004 -10000 0 -10000 0 0
TP53 0.024 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.025 0.065 -10000 0 -0.49 6 6
ARNT 0.023 0.009 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.025 0.005 -10000 0 -10000 0 0
HIF1A/p19ARF 0.084 0.11 0.26 21 -0.23 12 33
Regulation of Androgen receptor activity

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
HDAC1 -0.014 0.009 -10000 0 -10000 0 0
SMARCC1 0.002 0.038 -10000 0 -0.7 1 1
REL 0.021 0.037 0.34 1 -0.32 3 4
HDAC7 -0.064 0.11 0.22 6 -0.29 53 59
JUN 0.013 0.064 -10000 0 -0.32 14 14
EP300 0.025 0.005 -10000 0 -10000 0 0
KAT2B 0.024 0.018 -10000 0 -0.32 1 1
KAT5 0.026 0.004 -10000 0 -10000 0 0
MAPK14 -0.016 0.033 0.18 1 -0.23 4 5
FOXO1 0.023 0.019 -10000 0 -0.32 1 1
T-DHT/AR -0.042 0.13 0.31 6 -0.29 54 60
MAP2K6 0.011 0.048 0.32 1 -0.32 5 6
BRM/BAF57 0.031 0.023 -10000 0 -10000 0 0
MAP2K4 0.014 0.025 -10000 0 -10000 0 0
SMARCA2 0.021 0.015 -10000 0 -10000 0 0
PDE9A -0.12 0.33 -10000 0 -0.91 55 55
NCOA2 0.008 0.075 -10000 0 -0.32 20 20
CEBPA 0.028 0.05 0.32 8 -0.32 2 10
EHMT2 0.025 0.009 -10000 0 -10000 0 0
cell proliferation -0.017 0.17 0.4 19 -0.36 27 46
NR0B1 0.024 0.091 0.33 32 -10000 0 32
EGR1 -0.054 0.14 -10000 0 -0.32 92 92
RXRs/9cRA -0.013 0.089 -10000 0 -0.17 93 93
AR/RACK1/Src -0.01 0.12 0.3 24 -0.24 5 29
AR/GR -0.067 0.12 0.2 1 -0.22 129 130
GNB2L1 0.026 0.007 -10000 0 -10000 0 0
PKN1 0.025 0.018 -10000 0 -0.32 1 1
RCHY1 0.026 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0.001 0.004 0.016 9 -10000 0 9
MAPK8 -0.014 0.029 -10000 0 -0.22 3 3
T-DHT/AR/TIF2/CARM1 -0.014 0.12 0.29 14 -0.26 15 29
SRC -0.018 0.06 0.19 16 -0.17 7 23
NR3C1 0.016 0.056 -10000 0 -0.32 11 11
KLK3 -0.067 0.25 0.39 16 -1 18 34
APPBP2 0.013 0.025 -10000 0 -10000 0 0
TRIM24 0.027 0.029 0.32 3 -10000 0 3
T-DHT/AR/TIP60 -0.039 0.081 0.24 4 -0.23 9 13
TMPRSS2 -0.15 0.38 0.52 2 -0.92 75 77
RXRG -0.075 0.14 -10000 0 -0.32 95 95
mol:9cRA 0 0.002 -10000 0 -10000 0 0
RXRA 0.024 0.008 -10000 0 -10000 0 0
RXRB 0.026 0.003 -10000 0 -10000 0 0
CARM1 0.027 0.006 -10000 0 -10000 0 0
NR2C2 0.023 0.019 -10000 0 -0.32 1 1
KLK2 0.005 0.14 0.39 33 -0.37 3 36
AR -0.069 0.12 0.18 3 -0.23 125 128
SENP1 0.026 0.005 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
MDM2 0.022 0.017 -10000 0 -10000 0 0
SRY -0.001 0.009 0.028 16 -0.034 19 35
GATA2 0.029 0.067 0.33 12 -0.32 6 18
MYST2 0 0.002 -10000 0 -10000 0 0
HOXB13 -0.017 0.13 0.34 8 -0.32 54 62
T-DHT/AR/RACK1/Src -0.02 0.1 0.31 10 -0.25 5 15
positive regulation of transcription 0.029 0.067 0.33 12 -0.32 6 18
DNAJA1 0.013 0.025 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.025 0.16 12 -10000 0 12
NCOA1 0.029 0.019 -10000 0 -10000 0 0
SPDEF 0.012 0.15 0.33 34 -0.32 46 80
T-DHT/AR/TIF2 -0.027 0.094 0.27 2 -0.28 20 22
T-DHT/AR/Hsp90 -0.038 0.082 0.24 4 -0.22 10 14
GSK3B 0.022 0.015 -10000 0 -10000 0 0
NR2C1 0.023 0.012 -10000 0 -10000 0 0
mol:T-DHT -0.024 0.049 0.2 5 -0.18 7 12
SIRT1 0.026 0.004 -10000 0 -10000 0 0
ZMIZ2 0.023 0.018 -10000 0 -10000 0 0
POU2F1 0.001 0.07 0.2 7 -0.18 22 29
T-DHT/AR/DAX-1 -0.025 0.1 0.3 11 -0.23 9 20
CREBBP 0.025 0.007 -10000 0 -10000 0 0
SMARCE1 0.024 0.013 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

Figure S75.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S75.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.026 0.002 -10000 0 -10000 0 0
HDAC2 0.024 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.036 0.063 -10000 0 -0.2 26 26
forebrain development -0.072 0.23 -10000 0 -0.56 55 55
GNAO1 -0.08 0.16 -10000 0 -0.32 124 124
SMO/beta Arrestin2 0.026 0.06 -10000 0 -0.22 21 21
SMO 0.01 0.077 -10000 0 -0.32 21 21
ARRB2 0.025 0.009 -10000 0 -10000 0 0
GLI3/SPOP 0.024 0.083 0.28 1 -0.33 7 8
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
GSK3B 0.025 0.005 -10000 0 -10000 0 0
GNAI2 0.026 0.007 -10000 0 -10000 0 0
SIN3/HDAC complex 0.06 0.019 -10000 0 -10000 0 0
GNAI1 0.024 0.03 -10000 0 -0.32 3 3
XPO1 0.03 0.012 -10000 0 -10000 0 0
GLI1/Su(fu) -0.056 0.22 -10000 0 -0.66 34 34
SAP30 0.025 0.006 -10000 0 -10000 0 0
mol:GDP 0.01 0.077 -10000 0 -0.32 21 21
MIM/GLI2A 0.046 0.062 0.21 50 -10000 0 50
IFT88 0.025 0.006 -10000 0 -10000 0 0
GNAI3 0.027 0.003 -10000 0 -10000 0 0
GLI2 -0.015 0.087 0.2 2 -0.29 18 20
GLI3 0.012 0.082 0.26 2 -0.34 7 9
CSNK1D 0.025 0.005 -10000 0 -10000 0 0
CSNK1E 0.025 0.005 -10000 0 -10000 0 0
SAP18 0.025 0.005 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.025 0.006 -10000 0 -10000 0 0
GNG2 0.02 0.042 -10000 0 -0.32 6 6
Gi family/GTP -0.077 0.15 -10000 0 -0.28 114 114
SIN3B 0.026 0.003 -10000 0 -10000 0 0
SIN3A 0.025 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.012 0.089 -10000 0 -0.4 10 10
GLI2/Su(fu) -0.015 0.11 -10000 0 -0.32 32 32
FOXA2 0.062 0.16 0.41 43 -0.66 3 46
neural tube patterning -0.072 0.23 -10000 0 -0.56 55 55
SPOP 0.026 0.004 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.01 0.069 -10000 0 -0.31 5 5
GNB1 0.026 0.003 -10000 0 -10000 0 0
CSNK1G2 0.025 0.005 -10000 0 -10000 0 0
CSNK1G3 0.025 0.005 -10000 0 -10000 0 0
MTSS1 0.046 0.062 0.21 50 -10000 0 50
embryonic limb morphogenesis -0.072 0.23 -10000 0 -0.56 55 55
SUFU 0.01 0.047 -10000 0 -0.34 4 4
LGALS3 0.025 0.018 -10000 0 -0.32 1 1
catabolic process 0.006 0.11 -10000 0 -0.36 19 19
GLI3A/CBP -0.014 0.12 -10000 0 -0.3 54 54
KIF3A 0.025 0.005 -10000 0 -10000 0 0
GLI1 -0.076 0.24 -10000 0 -0.58 55 55
RAB23 0.025 0.018 -10000 0 -0.32 1 1
CSNK1A1 0.025 0.005 -10000 0 -10000 0 0
IFT172 0.025 0.005 -10000 0 -10000 0 0
RBBP7 0.025 0.004 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.011 0.068 -10000 0 -0.31 5 5
GNAZ -0.048 0.14 -10000 0 -0.32 87 87
RBBP4 0.026 0.002 -10000 0 -10000 0 0
CSNK1G1 0.026 0.004 -10000 0 -10000 0 0
PIAS1 0.026 0.004 -10000 0 -10000 0 0
PRKACA 0.026 0.003 -10000 0 -10000 0 0
GLI2/SPOP -0.007 0.092 -10000 0 -0.3 19 19
STK36 0.029 0.012 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.085 0.15 -10000 0 -0.36 72 72
PTCH1 -0.066 0.21 -10000 0 -0.65 29 29
MIM/GLI1 -0.041 0.24 0.36 24 -0.55 50 74
CREBBP -0.014 0.12 -10000 0 -0.3 54 54
Su(fu)/SIN3/HDAC complex 0.008 0.057 -10000 0 -0.34 6 6
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.007 0.11 0.22 4 -0.41 12 16
BAG4 0.022 0.01 -10000 0 -10000 0 0
BAD 0.002 0.05 0.17 6 -0.14 12 18
NFKBIA 0.025 0.005 -10000 0 -10000 0 0
BIRC3 0.008 0.073 -10000 0 -0.32 19 19
BAX 0.003 0.05 0.17 5 -0.15 8 13
EnzymeConsortium:3.1.4.12 0.004 0.031 0.082 9 -0.087 12 21
IKBKB 0.005 0.12 0.28 11 -0.38 12 23
MAP2K2 0.018 0.084 0.2 49 -0.17 2 51
MAP2K1 0.018 0.084 0.2 51 -0.17 2 53
SMPD1 0 0.042 0.1 1 -0.14 20 21
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.01 0.12 0.27 11 -0.36 15 26
MAP2K4 0.004 0.048 0.21 6 -0.15 4 10
protein ubiquitination -0.001 0.11 0.37 2 -0.4 12 14
EnzymeConsortium:2.7.1.37 0.019 0.087 0.2 51 -0.17 2 53
response to UV 0 0.001 0.003 32 -10000 0 32
RAF1 0.021 0.087 0.21 51 -0.16 4 55
CRADD 0.026 0.004 -10000 0 -10000 0 0
mol:ceramide 0.005 0.049 0.12 11 -0.13 22 33
I-kappa-B-alpha/RELA/p50/ubiquitin 0.033 0.009 -10000 0 -10000 0 0
MADD 0.025 0.007 -10000 0 -10000 0 0
MAP3K1 0.003 0.049 0.13 11 -0.14 8 19
TRADD 0.025 0.006 -10000 0 -10000 0 0
RELA/p50 0.026 0.004 -10000 0 -10000 0 0
MAPK3 0.021 0.084 0.2 51 -0.17 3 54
MAPK1 0.021 0.084 0.2 52 -0.17 2 54
p50/RELA/I-kappa-B-alpha 0.037 0.009 -10000 0 -10000 0 0
FADD 0.004 0.11 0.26 8 -0.38 12 20
KSR1 0.009 0.062 0.19 21 -0.14 10 31
MAPK8 0.001 0.056 0.21 12 -0.16 2 14
TRAF2 0.023 0.008 -10000 0 -10000 0 0
response to radiation 0 0.001 0.002 18 -10000 0 18
CHUK -0.005 0.11 0.32 2 -0.39 12 14
TNF R/SODD 0.032 0.015 -10000 0 -10000 0 0
TNF 0.041 0.067 0.33 21 -10000 0 21
CYCS 0.008 0.055 0.16 19 -0.14 6 25
IKBKG -0.003 0.11 0.29 4 -0.4 12 16
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.006 0.11 0.22 1 -0.31 31 32
RELA 0.026 0.004 -10000 0 -10000 0 0
RIPK1 0.025 0.006 -10000 0 -10000 0 0
AIFM1 0.007 0.053 0.15 16 -0.14 7 23
TNF/TNF R/SODD 0.051 0.046 0.23 19 -10000 0 19
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
response to heat 0 0.001 0.002 18 -10000 0 18
CASP8 -0.001 0.14 -10000 0 -0.55 21 21
NSMAF 0.003 0.12 0.25 9 -0.33 21 30
response to hydrogen peroxide 0 0.001 0.003 32 -10000 0 32
BCL2 0.012 0.065 -10000 0 -0.32 15 15
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.008 0.041 -10000 0 -0.18 18 18
epithelial cell differentiation 0.042 0.042 -10000 0 -0.16 13 13
CYFIP2 0.017 0.054 -10000 0 -0.32 10 10
ENAH -0.005 0.086 0.29 17 -0.21 1 18
EGFR 0.017 0.051 -10000 0 -0.32 9 9
EPHA2 0.022 0.038 -10000 0 -0.32 5 5
MYO6 -0.014 0.056 0.18 25 -10000 0 25
CTNNB1 0.025 0.005 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.041 0.041 -10000 0 -0.19 10 10
AQP5 0.003 0.061 0.32 1 -0.28 2 3
CTNND1 0.026 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.013 0.058 0.18 26 -10000 0 26
regulation of calcium-dependent cell-cell adhesion -0.007 0.072 0.19 40 -10000 0 40
EGF 0.039 0.073 0.33 24 -10000 0 24
NCKAP1 0.026 0.004 -10000 0 -10000 0 0
AQP3 -0.087 0.16 -10000 0 -0.37 94 94
cortical microtubule organization 0.042 0.042 -10000 0 -0.16 13 13
GO:0000145 -0.013 0.054 0.17 26 -10000 0 26
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.047 0.044 -10000 0 -0.16 13 13
MLLT4 0.025 0.006 -10000 0 -10000 0 0
ARF6/GDP -0.035 0.031 -10000 0 -0.17 13 13
ARF6 0.025 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.055 0.037 0.24 2 -0.18 4 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.008 0.047 0.26 2 -0.21 1 3
PVRL2 0.026 0.004 -10000 0 -10000 0 0
ZYX -0.013 0.058 0.18 26 -10000 0 26
ARF6/GTP 0.059 0.039 0.23 2 -0.17 4 6
CDH1 0.014 0.061 -10000 0 -0.32 13 13
EGFR/EGFR/EGF/EGF 0.034 0.057 -10000 0 -0.17 19 19
RhoA/GDP 0.042 0.043 -10000 0 -0.16 13 13
actin cytoskeleton organization -0.017 0.05 0.16 22 -10000 0 22
IGF-1R heterotetramer 0.024 0.025 -10000 0 -0.32 2 2
GIT1 0.025 0.006 -10000 0 -10000 0 0
IGF1R 0.024 0.025 -10000 0 -0.32 2 2
IGF1 -0.12 0.17 -10000 0 -0.32 176 176
DIAPH1 0.005 0.15 -10000 0 -0.56 17 17
Wnt receptor signaling pathway -0.042 0.042 0.16 13 -10000 0 13
RHOA 0.025 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.035 0.031 -10000 0 -0.17 13 13
CTNNA1 0.025 0.005 -10000 0 -10000 0 0
VCL -0.017 0.051 0.16 22 -10000 0 22
EFNA1 0.026 0.022 0.33 2 -10000 0 2
LPP -0.02 0.049 0.17 18 -10000 0 18
Ephrin A1/EPHA2 0.033 0.046 -10000 0 -0.17 15 15
SEC6/SEC8 -0.029 0.026 -10000 0 -0.16 9 9
MGAT3 -0.007 0.073 0.19 40 -10000 0 40
HGF/MET -0.003 0.088 -10000 0 -0.16 91 91
HGF -0.044 0.15 0.33 7 -0.32 86 93
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.008 0.042 -10000 0 -0.18 18 18
actin cable formation 0.015 0.092 0.31 18 -10000 0 18
KIAA1543 -0.014 0.054 0.16 25 -0.28 1 26
KIFC3 -0.015 0.057 0.18 23 -10000 0 23
NCK1 0.025 0.006 -10000 0 -10000 0 0
EXOC3 0.022 0.009 -10000 0 -10000 0 0
ACTN1 -0.015 0.055 0.18 24 -10000 0 24
NCK1/GIT1 0.035 0.012 -10000 0 -10000 0 0
mol:GDP 0.042 0.042 -10000 0 -0.16 13 13
EXOC4 0.025 0.005 -10000 0 -10000 0 0
STX4 -0.014 0.056 0.18 23 -10000 0 23
PIP5K1C -0.013 0.058 0.18 26 -10000 0 26
LIMA1 0.026 0.004 -10000 0 -10000 0 0
ABI1 0.025 0.006 -10000 0 -10000 0 0
ROCK1 -0.001 0.095 0.32 18 -0.24 1 19
adherens junction assembly -0.013 0.07 0.26 5 -0.26 7 12
IGF-1R heterotetramer/IGF1 -0.048 0.1 -10000 0 -0.16 176 176
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.036 0.011 -10000 0 -10000 0 0
MET 0.026 0.004 -10000 0 -10000 0 0
PLEKHA7 -0.014 0.057 0.18 25 -0.3 1 26
mol:GTP 0.053 0.036 0.23 2 -0.18 4 6
establishment of epithelial cell apical/basal polarity 0.007 0.1 0.33 18 -10000 0 18
cortical actin cytoskeleton stabilization 0.008 0.041 -10000 0 -0.18 18 18
regulation of cell-cell adhesion -0.017 0.05 0.16 22 -10000 0 22
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.008 0.042 -10000 0 -0.18 18 18
Caspase cascade in apoptosis

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
TOP1 -0.003 0.11 -10000 0 -0.4 19 19
ACTA1 -0.02 0.12 0.21 9 -0.35 30 39
NUMA1 -0.005 0.12 0.2 9 -0.42 21 30
SPTAN1 -0.022 0.12 0.2 9 -0.37 26 35
LIMK1 -0.022 0.12 0.2 9 -0.37 26 35
BIRC3 0.008 0.073 -10000 0 -0.32 19 19
BIRC2 0.025 0.007 -10000 0 -10000 0 0
BAX 0.026 0.004 -10000 0 -10000 0 0
CASP10 -0.017 0.081 0.16 34 -0.25 26 60
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.026 0.003 -10000 0 -10000 0 0
PTK2 -0.005 0.12 -10000 0 -0.45 17 17
DIABLO 0.026 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes -0.022 0.12 0.2 9 -0.37 26 35
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.026 0.004 -10000 0 -10000 0 0
GSN -0.023 0.12 0.2 9 -0.38 27 36
MADD 0.025 0.007 -10000 0 -10000 0 0
TFAP2A 0.036 0.11 0.38 3 -0.63 7 10
BID -0.002 0.057 0.17 10 -0.18 25 35
MAP3K1 -0.015 0.1 -10000 0 -0.38 23 23
TRADD 0.025 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.007 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.02 0.12 0.21 10 -0.36 29 39
CASP9 0.026 0.003 -10000 0 -10000 0 0
DNA repair -0.004 0.049 0.19 3 -10000 0 3
neuron apoptosis 0.005 0.095 -10000 0 -0.62 7 7
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.015 0.13 0.2 9 -0.44 22 31
APAF1 0.026 0.003 -10000 0 -10000 0 0
CASP6 -0.003 0.14 -10000 0 -0.91 7 7
TRAF2 0.023 0.008 -10000 0 -10000 0 0
ICAD/CAD -0.026 0.12 -10000 0 -0.38 25 25
CASP7 0 0.084 0.26 11 -0.29 6 17
KRT18 0.018 0.061 -10000 0 -0.47 3 3
apoptosis -0.012 0.12 0.26 2 -0.42 22 24
DFFA -0.023 0.12 0.2 9 -0.37 27 36
DFFB -0.023 0.12 0.2 9 -0.36 29 38
PARP1 0.004 0.049 -10000 0 -0.2 3 3
actin filament polymerization 0.023 0.11 0.38 22 -10000 0 22
TNF 0.041 0.067 0.33 21 -10000 0 21
CYCS 0 0.051 0.17 1 -0.17 14 15
SATB1 -0.002 0.14 -10000 0 -0.85 7 7
SLK -0.022 0.12 0.2 9 -0.38 25 34
p15 BID/BAX 0.006 0.067 -10000 0 -0.22 19 19
CASP2 -0.002 0.069 0.2 5 -0.25 10 15
JNK cascade 0.015 0.1 0.38 23 -10000 0 23
CASP3 -0.019 0.13 0.22 9 -0.37 30 39
LMNB2 0.005 0.1 -10000 0 -0.39 14 14
RIPK1 0.025 0.006 -10000 0 -10000 0 0
CASP4 0.025 0.006 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.051 0.053 -10000 0 -0.18 18 18
negative regulation of DNA binding 0.036 0.11 0.38 3 -0.62 7 10
stress fiber formation -0.022 0.12 0.2 9 -0.37 25 34
GZMB -0.012 0.11 0.24 34 -0.28 28 62
CASP1 0.005 0.038 -10000 0 -0.24 9 9
LMNB1 0.006 0.11 -10000 0 -0.42 17 17
APP 0.005 0.096 -10000 0 -0.63 7 7
TNFRSF1A 0.025 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.008 0.002 -10000 0 -10000 0 0
VIM -0.008 0.12 0.27 2 -0.42 22 24
LMNA 0.012 0.078 -10000 0 -0.31 9 9
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.002 0.071 0.18 6 -0.24 12 18
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.019 0.12 0.23 10 -0.38 25 35
APAF-1/Caspase 9 0.021 0.058 -10000 0 -0.6 2 2
nuclear fragmentation during apoptosis -0.005 0.12 0.2 9 -0.41 21 30
CFL2 -0.024 0.11 -10000 0 -0.39 22 22
GAS2 -0.031 0.12 0.2 9 -0.37 28 37
positive regulation of apoptosis 0.011 0.1 -10000 0 -0.4 12 12
PRF1 0.02 0.085 0.33 11 -0.32 16 27
Nectin adhesion pathway

Figure S79.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S79.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.018 0.051 -10000 0 -0.32 9 9
alphaV beta3 Integrin 0.008 0.082 -10000 0 -0.22 44 44
PTK2 -0.018 0.11 -10000 0 -0.37 26 26
positive regulation of JNK cascade -0.016 0.12 -10000 0 -0.32 34 34
CDC42/GDP -0.014 0.16 -10000 0 -0.4 38 38
Rac1/GDP -0.015 0.16 -10000 0 -0.4 39 39
RAP1B 0.024 0.007 -10000 0 -10000 0 0
RAP1A 0.026 0.003 -10000 0 -10000 0 0
CTNNB1 0.025 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.015 0.15 -10000 0 -0.39 34 34
nectin-3/I-afadin 0.019 0.067 0.24 2 -0.22 27 29
RAPGEF1 -0.015 0.14 0.31 3 -0.41 30 33
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.022 0.14 -10000 0 -0.44 35 35
PDGFB-D/PDGFRB 0.018 0.051 -10000 0 -0.32 9 9
TLN1 -0.016 0.037 -10000 0 -0.27 4 4
Rap1/GTP -0.01 0.099 -10000 0 -0.3 31 31
IQGAP1 0.026 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.044 0.018 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.019 0.067 0.24 2 -0.22 27 29
PVR 0.026 0.004 -10000 0 -10000 0 0
Necl-5(dimer) 0.026 0.004 -10000 0 -10000 0 0
mol:GDP -0.033 0.18 -10000 0 -0.48 39 39
MLLT4 0.025 0.006 -10000 0 -10000 0 0
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
PI3K 0.044 0.073 0.24 2 -0.17 32 34
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.034 0.018 -10000 0 -0.22 1 1
positive regulation of lamellipodium assembly -0.021 0.12 -10000 0 -0.32 34 34
PVRL1 0.024 0.018 -10000 0 -0.32 1 1
PVRL3 0.004 0.089 0.33 2 -0.32 27 29
PVRL2 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
CDH1 0.014 0.061 -10000 0 -0.32 13 13
CLDN1 0.015 0.079 0.33 6 -0.32 17 23
JAM-A/CLDN1 0.03 0.074 0.24 5 -0.18 35 40
SRC -0.025 0.16 -10000 0 -0.48 37 37
ITGB3 -0.012 0.11 -10000 0 -0.32 44 44
nectin-1(dimer)/I-afadin/I-afadin 0.034 0.018 -10000 0 -0.22 1 1
FARP2 -0.035 0.2 -10000 0 -0.51 44 44
RAC1 0.025 0.006 -10000 0 -10000 0 0
CTNNA1 0.025 0.005 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.032 0.063 0.23 2 -0.19 27 29
nectin-1/I-afadin 0.034 0.018 -10000 0 -0.22 1 1
nectin-2/I-afadin 0.036 0.011 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.033 0.01 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.031 0.064 0.23 2 -0.19 28 30
CDC42/GTP/IQGAP1/filamentous actin 0.034 0.007 -10000 0 -10000 0 0
F11R 0.02 0.02 -10000 0 -0.32 1 1
positive regulation of filopodium formation -0.016 0.12 -10000 0 -0.32 34 34
alphaV/beta3 Integrin/Talin 0.003 0.088 0.26 3 -0.28 14 17
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.036 0.011 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.036 0.011 -10000 0 -10000 0 0
PIP5K1C -0.014 0.042 -10000 0 -0.28 5 5
VAV2 -0.042 0.2 -10000 0 -0.52 34 34
RAP1/GDP -0.007 0.14 -10000 0 -0.37 29 29
ITGAV 0.025 0.005 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.032 0.062 0.23 2 -0.19 26 28
nectin-3(dimer)/I-afadin/I-afadin 0.019 0.067 0.24 2 -0.22 27 29
Rac1/GTP -0.022 0.15 -10000 0 -0.39 34 34
PTPRM -0.005 0.055 -10000 0 -0.18 29 29
E-cadherin/beta catenin/alpha catenin 0.053 0.054 -10000 0 -0.18 12 12
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.026 0.003 -10000 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.044 0.1 -10000 0 -0.16 167 167
TC10/GTP -0.042 0.098 -10000 0 -0.16 156 156
Insulin Receptor/Insulin/IRS1/Shp2 0.051 0.041 -10000 0 -0.17 7 7
HRAS 0.024 0.008 -10000 0 -10000 0 0
APS homodimer 0.029 0.033 0.33 5 -10000 0 5
GRB14 0.064 0.1 0.33 53 -10000 0 53
FOXO3 -0.034 0.18 -10000 0 -0.55 42 42
AKT1 -0.001 0.066 0.3 6 -10000 0 6
INSR 0.029 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.048 0.034 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.021 0.039 -10000 0 -0.32 5 5
SORBS1 -0.13 0.17 -10000 0 -0.32 180 180
CRK 0.024 0.008 -10000 0 -10000 0 0
PTPN1 -0.009 0.024 -10000 0 -10000 0 0
CAV1 -0.019 0.04 0.17 3 -0.18 14 17
CBL/APS/CAP/Crk-II/C3G -0.033 0.12 0.24 5 -0.17 160 165
Insulin Receptor/Insulin/IRS1/NCK2 0.052 0.04 -10000 0 -0.17 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.037 0.036 -10000 0 -0.15 7 7
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.019 0.062 -10000 0 -0.36 7 7
RPS6KB1 -0.007 0.061 0.28 6 -10000 0 6
PARD6A 0.024 0.018 -10000 0 -0.32 1 1
CBL 0.025 0.006 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.017 0.04 0.29 1 -0.49 2 3
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.009 0.054 0.19 2 -10000 0 2
HRAS/GTP -0.026 0.027 -10000 0 -0.16 4 4
Insulin Receptor 0.029 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.055 0.045 -10000 0 -0.16 6 6
PRKCI 0.024 0.048 -10000 0 -0.44 1 1
Insulin Receptor/Insulin/GRB14/PDK1 0.027 0.038 -10000 0 -0.15 5 5
SHC1 0.024 0.007 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.042 0.04 -10000 0 -0.42 2 2
PI3K 0.046 0.041 -10000 0 -0.15 7 7
NCK2 0.026 0.004 -10000 0 -10000 0 0
RHOQ 0.025 0.005 -10000 0 -10000 0 0
mol:H2O2 -0.001 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.018 0.006 -10000 0 -10000 0 0
AKT2 -0.001 0.066 0.28 7 -10000 0 7
PRKCZ 0.02 0.065 -10000 0 -0.39 5 5
SH2B2 0.029 0.033 0.33 5 -10000 0 5
SHC/SHIP -0.016 0.035 0.19 2 -10000 0 2
F2RL2 0.02 0.085 0.33 12 -0.32 15 27
TRIP10 0.025 0.018 -10000 0 -0.32 1 1
Insulin Receptor/Insulin/Shc 0.041 0.022 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.033 0.013 -10000 0 -0.17 1 1
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.061 0.035 -10000 0 -10000 0 0
RAPGEF1 0.024 0.008 -10000 0 -10000 0 0
RASA1 0.025 0.005 -10000 0 -10000 0 0
NCK1 0.025 0.006 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.04 0.12 0.24 5 -0.17 174 179
TC10/GDP 0.019 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.052 0.035 -10000 0 -0.18 3 3
INPP5D -0.015 0.034 0.17 4 -0.17 7 11
SOS1 0.026 0.004 -10000 0 -10000 0 0
SGK1 -0.039 0.19 -10000 0 -0.69 30 30
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.005 -10000 0 -10000 0 0
IRS1 0.018 0.045 -10000 0 -0.32 7 7
p62DOK/RasGAP 0.042 0.041 -10000 0 -0.42 2 2
INS -0.011 0.019 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.015 0.034 0.17 4 -0.17 7 11
GRB2 0.025 0.005 -10000 0 -10000 0 0
EIF4EBP1 -0.007 0.054 0.25 4 -10000 0 4
PTPRA 0.026 0.008 -10000 0 -10000 0 0
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.033 0.013 -10000 0 -0.17 1 1
PDPK1 0.025 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.008 0.042 -10000 0 -0.21 4 4
Insulin Receptor/Insulin/IRS1 0.038 0.034 -10000 0 -0.17 7 7
Insulin Receptor/Insulin/IRS3 0.035 0.017 -10000 0 -10000 0 0
Par3/Par6 0.049 0.055 0.22 11 -0.16 15 26
Cellular roles of Anthrax toxin

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
ANTXR1 0.022 0.035 -10000 0 -0.32 4 4
ANTXR2 0.004 0.083 -10000 0 -0.32 25 25
negative regulation of myeloid dendritic cell antigen processing and presentation -0.005 0.011 -10000 0 -0.046 26 26
monocyte activation 0.009 0.086 -10000 0 -0.35 18 18
MAP2K2 -0.003 0.095 -10000 0 -0.57 11 11
MAP2K1 -0.009 0.01 -10000 0 -0.074 1 1
MAP2K7 -0.009 0.01 -10000 0 -0.074 1 1
MAP2K6 -0.011 0.021 0.14 1 -0.15 6 7
CYAA -0.019 0.037 -10000 0 -0.16 26 26
MAP2K4 -0.008 0.009 -10000 0 -0.074 1 1
IL1B -0.012 0.046 0.16 5 -0.16 22 27
Channel 0.019 0.051 -10000 0 -0.17 26 26
NLRP1 -0.011 0.022 -10000 0 -0.15 8 8
CALM1 0.026 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis 0 0.053 -10000 0 -0.39 7 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.005 0.011 0.046 26 -10000 0 26
MAPK3 -0.009 0.01 -10000 0 -0.074 1 1
MAPK1 -0.009 0.01 -10000 0 -0.074 1 1
PGR -0.05 0.069 -10000 0 -0.16 114 114
PA/Cellular Receptors 0.019 0.056 -10000 0 -0.19 26 26
apoptosis -0.005 0.011 -10000 0 -0.046 26 26
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.018 0.049 -10000 0 -0.17 26 26
macrophage activation -0.011 0.019 0.14 5 -10000 0 5
TNF 0.041 0.067 0.33 21 -10000 0 21
VCAM1 0.01 0.085 -10000 0 -0.36 17 17
platelet activation 0 0.053 -10000 0 -0.39 7 7
MAPKKK cascade 0.004 0.025 0.085 2 -0.097 8 10
IL18 -0.01 0.033 0.11 2 -0.19 9 11
negative regulation of macrophage activation -0.005 0.011 -10000 0 -0.046 26 26
LEF -0.005 0.011 -10000 0 -0.047 26 26
CASP1 -0.007 0.024 -10000 0 -0.11 16 16
mol:cAMP 0 0.053 -10000 0 -0.39 7 7
necrosis -0.005 0.011 -10000 0 -0.046 26 26
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.019 0.048 -10000 0 -0.16 26 26
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.014 0.018 0.22 2 -10000 0 2
MAP4K4 0.002 0.074 0.2 6 -0.27 8 14
BAG4 0.022 0.01 -10000 0 -10000 0 0
PKC zeta/ceramide 0.011 0.05 -10000 0 -0.18 23 23
NFKBIA 0.025 0.005 -10000 0 -10000 0 0
BIRC3 0.008 0.073 -10000 0 -0.32 19 19
BAX 0.007 0.041 -10000 0 -0.4 3 3
RIPK1 0.025 0.006 -10000 0 -10000 0 0
AKT1 -0.008 0.058 0.66 3 -10000 0 3
BAD -0.007 0.047 0.19 3 -0.18 22 25
SMPD1 0.006 0.068 0.16 11 -0.21 21 32
RB1 -0.008 0.043 0.2 1 -0.18 22 23
FADD/Caspase 8 0.01 0.093 0.26 11 -0.28 11 22
MAP2K4 -0.009 0.046 0.18 5 -0.18 22 27
NSMAF 0.024 0.008 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.018 0.079 0.21 47 -0.18 10 57
EGF 0.039 0.073 0.33 24 -10000 0 24
mol:ceramide -0.004 0.048 -10000 0 -0.19 23 23
MADD 0.025 0.007 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.012 0.015 0.26 1 -10000 0 1
ASAH1 0.022 0.01 -10000 0 -10000 0 0
negative regulation of cell cycle -0.008 0.043 0.2 1 -0.18 22 23
cell proliferation -0.033 0.095 0.29 4 -0.22 11 15
BID 0.001 0.12 -10000 0 -0.55 12 12
MAP3K1 -0.008 0.047 0.2 2 -0.18 23 25
EIF2A -0.003 0.068 0.2 26 -0.18 19 45
TRADD 0.025 0.005 -10000 0 -10000 0 0
CRADD 0.026 0.004 -10000 0 -10000 0 0
MAPK3 0.015 0.075 0.2 45 -0.18 9 54
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.015 0.074 0.19 46 -0.17 9 55
Cathepsin D/ceramide 0.012 0.049 -10000 0 -0.18 23 23
FADD 0.01 0.076 0.21 17 -0.26 5 22
KSR1 -0.001 0.056 0.19 14 -0.18 20 34
MAPK8 -0.005 0.056 -10000 0 -0.19 8 8
PRKRA -0.008 0.045 0.22 1 -0.18 22 23
PDGFA 0.025 0.006 -10000 0 -10000 0 0
TRAF2 0.023 0.008 -10000 0 -10000 0 0
IGF1 -0.12 0.17 -10000 0 -0.32 176 176
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.004 0.047 -10000 0 -0.19 23 23
CTSD 0.024 0.007 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.037 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.034 0.1 0.31 4 -0.26 8 12
PRKCD 0.025 0.006 -10000 0 -10000 0 0
PRKCZ 0.023 0.03 -10000 0 -0.32 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.012 0.015 0.26 1 -10000 0 1
RelA/NF kappa B1 0.037 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.025 0.018 -10000 0 -0.32 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.001 0.068 0.19 6 -0.29 6 12
TNFR1A/BAG4/TNF-alpha 0.051 0.046 0.23 19 -10000 0 19
mol:Sphingosine-1-phosphate -0.014 0.018 0.22 2 -10000 0 2
MAP2K1 0.012 0.075 0.19 47 -0.18 10 57
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
CYCS 0.01 0.042 0.14 6 -0.16 3 9
TNFRSF1A 0.025 0.005 -10000 0 -10000 0 0
NFKB1 0.026 0.003 -10000 0 -10000 0 0
TNFR1A/BAG4 0.032 0.015 -10000 0 -10000 0 0
EIF2AK2 -0.007 0.052 0.22 8 -0.18 20 28
TNF-alpha/TNFR1A/FAN 0.055 0.044 0.23 20 -10000 0 20
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.011 0.087 -10000 0 -0.37 15 15
MAP2K2 0.013 0.074 0.2 46 -0.18 9 55
SMPD3 0.013 0.057 0.19 3 -0.26 6 9
TNF 0.041 0.067 0.33 21 -10000 0 21
PKC zeta/PAR4 0.035 0.027 -10000 0 -0.22 4 4
mol:PHOSPHOCHOLINE -0.007 0.046 -10000 0 -0.14 20 20
NF kappa B1/RelA/I kappa B alpha 0.067 0.035 -10000 0 -0.17 4 4
AIFM1 0.008 0.045 0.14 11 -0.17 4 15
BCL2 0.012 0.065 -10000 0 -0.32 15 15
IL1-mediated signaling events

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
UBC13/UEV1A 0.019 0.003 -10000 0 -10000 0 0
PRKCZ 0.023 0.03 -10000 0 -0.32 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.025 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.015 0.042 -10000 0 -0.2 5 5
IRAK/TOLLIP 0.024 0.009 -10000 0 -10000 0 0
IKBKB 0.023 0.008 -10000 0 -10000 0 0
IKBKG 0.026 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.048 0.12 0.26 66 -0.22 39 105
IL1A 0.025 0.14 0.33 38 -0.32 34 72
IL1B -0.021 0.067 0.19 14 -0.23 25 39
IRAK/TRAF6/p62/Atypical PKCs 0.05 0.035 -10000 0 -0.16 3 3
IL1R2 0.046 0.099 0.33 36 -0.32 7 43
IL1R1 0.025 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.003 0.063 0.22 1 -0.24 6 7
TOLLIP 0.024 0.007 -10000 0 -10000 0 0
TICAM2 0.024 0.019 -10000 0 -0.32 1 1
MAP3K3 0.025 0.006 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.017 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.01 0.064 -10000 0 -0.32 1 1
JUN -0.023 0.039 0.15 10 -0.15 6 16
MAP3K7 0.025 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.048 0.07 0.33 1 -0.17 23 24
IL1 alpha/IL1R1/IL1RAP/MYD88 0.059 0.093 0.24 44 -0.18 32 76
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.067 0.093 0.24 43 -0.17 32 75
IL1 beta fragment/IL1R1/IL1RAP 0.031 0.065 0.23 9 -0.18 23 32
NFKB1 0.026 0.003 -10000 0 -10000 0 0
MAPK8 -0.016 0.037 0.16 12 -10000 0 12
IRAK1 -0.012 0.002 -10000 0 -10000 0 0
IL1RN/IL1R1 0.041 0.041 0.24 11 -0.22 3 14
IRAK4 0.026 0.004 -10000 0 -10000 0 0
PRKCI 0.025 0.006 -10000 0 -10000 0 0
TRAF6 0.024 0.007 -10000 0 -10000 0 0
PI3K 0.034 0.018 -10000 0 -0.22 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.016 0.053 0.22 3 -0.23 6 9
CHUK 0.025 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.031 0.065 0.23 9 -0.18 23 32
IL1 beta/IL1R2 0.031 0.09 0.23 34 -0.21 29 63
IRAK/TRAF6/TAK1/TAB1/TAB2 0.03 0.013 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.034 0.059 0.22 1 -0.17 20 21
IRAK3 0.016 0.056 -10000 0 -0.32 11 11
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.051 0.068 0.3 2 -0.17 21 23
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.009 0.077 0.22 4 -0.18 32 36
IL1 alpha/IL1R1/IL1RAP 0.049 0.094 0.24 44 -0.19 32 76
RELA 0.026 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.025 0.006 -10000 0 -10000 0 0
MYD88 0.025 0.006 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.039 0.023 -10000 0 -10000 0 0
IL1RAP 0.032 0.045 0.33 9 -10000 0 9
UBE2N 0.026 0.004 -10000 0 -10000 0 0
IRAK/TRAF6 -0.033 0.041 0.12 8 -10000 0 8
CASP1 0.017 0.051 -10000 0 -0.32 9 9
IL1RN/IL1R2 0.055 0.083 0.25 45 -0.24 9 54
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.042 0.066 0.24 10 -0.18 22 32
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.01 0.075 0.21 1 -0.31 6 7
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
IL1RN 0.031 0.058 0.33 11 -0.32 3 14
TRAF6/TAK1/TAB1/TAB2 0.034 0.013 -10000 0 -10000 0 0
MAP2K6 -0.01 0.039 0.17 14 -0.15 5 19
IL2 signaling events mediated by PI3K

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
BCL2L1 0.028 0.083 0.58 1 -0.63 1 2
UGCG -0.065 0.22 -10000 0 -0.58 59 59
AKT1/mTOR/p70S6K/Hsp90/TERT 0.08 0.12 0.32 21 -0.28 10 31
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.062 0.22 -10000 0 -0.57 59 59
mol:DAG 0.008 0.11 -10000 0 -0.77 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 0.033 0.14 0.33 2 -0.41 27 29
FRAP1 0.025 0.16 0.36 2 -0.46 27 29
FOXO3 0.022 0.13 0.33 2 -0.41 24 26
AKT1 0.026 0.14 0.34 2 -0.42 26 28
GAB2 0.022 0.021 -10000 0 -0.32 1 1
SMPD1 -0.019 0.16 -10000 0 -0.57 29 29
SGMS1 0.012 0.083 -10000 0 -0.57 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 -0.009 0.013 -10000 0 -0.18 1 1
CALM1 0.026 0.004 -10000 0 -10000 0 0
cell proliferation -0.01 0.18 0.31 2 -0.45 34 36
EIF3A 0.025 0.005 -10000 0 -10000 0 0
PI3K 0.033 0.025 -10000 0 -0.22 1 1
RPS6KB1 0.047 0.064 -10000 0 -10000 0 0
mol:sphingomyelin 0.008 0.11 -10000 0 -0.77 7 7
natural killer cell activation 0 0.003 -10000 0 -10000 0 0
JAK3 0.027 0.024 0.33 2 -10000 0 2
PIK3R1 0.023 0.022 -10000 0 -0.32 1 1
JAK1 0.025 0.011 -10000 0 -10000 0 0
NFKB1 0.026 0.003 -10000 0 -10000 0 0
MYC 0.026 0.23 0.46 2 -0.84 20 22
MYB 0.1 0.16 0.5 36 -0.98 1 37
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.028 0.11 0.28 3 -0.37 14 17
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.059 0.058 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.028 0.11 0.28 3 -0.37 13 16
Rac1/GDP 0.014 0.018 -10000 0 -0.17 1 1
T cell proliferation 0.025 0.11 0.32 4 -0.38 11 15
SHC1 0.023 0.012 -10000 0 -10000 0 0
RAC1 0.025 0.006 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.021 0.049 0.14 56 -0.085 1 57
PRKCZ 0.023 0.11 0.29 4 -0.39 11 15
NF kappa B1 p50/RelA 0.042 0.15 0.39 1 -0.4 26 27
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.014 0.069 0.34 2 -0.4 5 7
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
IL2RA 0.021 0.097 0.33 19 -0.32 17 36
IL2RB 0.021 0.043 0.33 1 -0.32 5 6
TERT 0.12 0.15 0.33 136 -10000 0 136
E2F1 0.1 0.14 0.4 56 -10000 0 56
SOS1 0.024 0.012 -10000 0 -10000 0 0
RPS6 0.022 0.009 -10000 0 -10000 0 0
mol:cAMP -0.011 0.024 0.034 1 -0.071 56 57
PTPN11 0.023 0.013 -10000 0 -10000 0 0
IL2RG 0.024 0.07 0.33 9 -0.32 9 18
actin cytoskeleton organization 0.025 0.11 0.32 4 -0.38 11 15
GRB2 0.023 0.012 -10000 0 -10000 0 0
IL2 0.018 0.014 -10000 0 -10000 0 0
PIK3CA 0.024 0.013 -10000 0 -10000 0 0
Rac1/GTP 0.04 0.032 -10000 0 -0.16 1 1
LCK 0.023 0.042 0.33 2 -0.32 4 6
BCL2 0.009 0.19 0.36 3 -0.66 24 27
Regulation of Telomerase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Telomerase catalytic core complex 0.21 0.22 0.47 133 -0.49 2 135
RAD9A 0.029 0.034 0.33 5 -10000 0 5
AP1 -0.03 0.14 -10000 0 -0.23 120 120
IFNAR2 0.043 0.022 -10000 0 -10000 0 0
AKT1 0.019 0.07 0.18 4 -0.15 34 38
ER alpha/Oestrogen -0.01 0.089 -10000 0 -0.21 66 66
NFX1/SIN3/HDAC complex 0.046 0.048 -10000 0 -0.24 2 2
EGF 0.049 0.072 0.33 24 -10000 0 24
SMG5 0.024 0.007 -10000 0 -10000 0 0
SMG6 0.024 0.008 -10000 0 -10000 0 0
SP3/HDAC2 0.063 0.038 0.18 5 -10000 0 5
TERT/c-Abl 0.16 0.19 0.42 93 -0.46 2 95
SAP18 0.028 0.007 -10000 0 -10000 0 0
MRN complex 0.042 0.022 -10000 0 -10000 0 0
WT1 0.073 0.1 0.34 48 -10000 0 48
WRN 0.022 0.009 -10000 0 -10000 0 0
SP1 0.051 0.03 -10000 0 -10000 0 0
SP3 0.034 0.012 -10000 0 -10000 0 0
TERF2IP 0.025 0.006 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.056 0.11 -10000 0 -0.41 3 3
Mad/Max 0.057 0.03 0.27 1 -10000 0 1
TERT 0.21 0.22 0.47 130 -0.5 2 132
CCND1 0.2 0.26 0.54 69 -0.89 7 76
MAX 0.034 0.012 -10000 0 -10000 0 0
RBBP7 0.029 0.006 -10000 0 -10000 0 0
RBBP4 0.029 0.004 -10000 0 -10000 0 0
TERF2 0.023 0.012 -10000 0 -10000 0 0
PTGES3 0.026 0.003 -10000 0 -10000 0 0
SIN3A 0.029 0.006 -10000 0 -10000 0 0
Telomerase/911 0.089 0.08 0.27 17 -10000 0 17
CDKN1B 0.036 0.065 0.24 6 -10000 0 6
RAD1 0.023 0.009 -10000 0 -10000 0 0
XRCC5 0.025 0.006 -10000 0 -10000 0 0
XRCC6 0.025 0.005 -10000 0 -10000 0 0
SAP30 0.028 0.007 -10000 0 -10000 0 0
TRF2/PARP2 0.036 0.013 -10000 0 -10000 0 0
UBE3A 0.033 0.012 -10000 0 -10000 0 0
JUN 0.02 0.064 -10000 0 -0.31 14 14
E6 0.008 0.009 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.037 0.022 -10000 0 -10000 0 0
FOS -0.073 0.16 -10000 0 -0.31 124 124
IFN-gamma/IRF1 0.093 0.088 0.27 73 -10000 0 73
PARP2 0.025 0.005 -10000 0 -10000 0 0
BLM 0.034 0.049 0.33 11 -10000 0 11
Telomerase 0.052 0.087 0.25 18 -0.34 3 21
IRF1 0.036 0.014 -10000 0 -10000 0 0
ESR1 -0.027 0.13 -10000 0 -0.31 66 66
KU/TER 0.036 0.01 -10000 0 -10000 0 0
ATM/TRF2 0.033 0.02 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.047 0.054 -10000 0 -0.27 2 2
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.047 0.055 -10000 0 -0.28 2 2
HDAC1 0.029 0.004 -10000 0 -10000 0 0
HDAC2 0.045 0.027 -10000 0 -10000 0 0
ATM 0.011 0.01 -10000 0 -10000 0 0
SMAD3 -0.025 0.013 -10000 0 -10000 0 0
ABL1 0.023 0.008 -10000 0 -10000 0 0
MXD1 0.034 0.02 0.34 1 -10000 0 1
MRE11A 0.025 0.005 -10000 0 -10000 0 0
HUS1 0.025 0.005 -10000 0 -10000 0 0
RPS6KB1 0.025 0.006 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.17 0.2 0.45 63 -0.42 3 66
NR2F2 -0.008 0.04 -10000 0 -0.32 1 1
MAPK3 0.008 0.028 -10000 0 -10000 0 0
MAPK1 0.007 0.028 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.003 0.027 -10000 0 -10000 0 0
NFKB1 0.026 0.003 -10000 0 -10000 0 0
HNRNPC 0.025 0.005 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.011 0.009 -10000 0 -10000 0 0
NBN 0.022 0.01 -10000 0 -10000 0 0
EGFR 0.023 0.051 -10000 0 -0.31 9 9
mol:Oestrogen 0.004 0.005 -10000 0 -10000 0 0
EGF/EGFR 0.054 0.066 0.26 23 -0.2 9 32
MYC 0.015 0.073 -10000 0 -0.31 18 18
IL2 0.043 0.031 -10000 0 -10000 0 0
KU 0.036 0.01 -10000 0 -10000 0 0
RAD50 0.025 0.005 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
TGFB1 0.003 0.027 -10000 0 -10000 0 0
TRF2/BLM 0.041 0.034 0.23 11 -10000 0 11
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.19 0.2 0.45 94 -0.45 2 96
SP1/HDAC2 0.081 0.057 0.26 5 -10000 0 5
PINX1 0.022 0.01 -10000 0 -10000 0 0
Telomerase/EST1A 0.057 0.11 -10000 0 -0.41 3 3
Smad3/Myc -0.01 0.048 -10000 0 -0.19 18 18
911 complex 0.046 0.029 0.23 5 -10000 0 5
IFNG 0.088 0.12 0.34 75 -10000 0 75
Telomerase/PinX1 0.047 0.11 -10000 0 -0.44 2 2
Telomerase/AKT1/mTOR/p70S6K 0.095 0.11 0.29 26 -0.28 3 29
SIN3B 0.029 0.005 -10000 0 -10000 0 0
YWHAE 0.024 0.008 -10000 0 -10000 0 0
Telomerase/EST1B 0.056 0.11 -10000 0 -0.45 2 2
response to DNA damage stimulus 0.001 0.024 -10000 0 -0.12 1 1
MRN complex/TRF2/Rap1 0.055 0.034 -10000 0 -10000 0 0
TRF2/WRN 0.032 0.017 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.06 0.11 -10000 0 -0.41 3 3
E2F1 0.093 0.12 0.35 73 -10000 0 73
ZNFX1 0.027 0.009 -10000 0 -10000 0 0
PIF1 0.049 0.084 0.33 33 -0.32 1 34
NCL 0.024 0.007 -10000 0 -10000 0 0
DKC1 0.026 0.004 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.024 0.008 -10000 0 -10000 0 0
EGFR 0.017 0.051 -10000 0 -0.32 9 9
EGF/EGFR 0.022 0.081 0.19 21 -0.16 53 74
EGF/EGFR dimer/SHC/GRB2/SOS1 0.072 0.055 0.24 20 -0.17 3 23
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA -0.02 0.12 -10000 0 -0.32 52 52
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.039 0.073 0.33 24 -10000 0 24
EGF/EGFR dimer/SHC 0.051 0.057 0.24 21 -0.19 7 28
mol:GDP 0.063 0.05 0.31 1 -0.17 3 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.024 0.037 0.33 2 -0.32 3 5
GRB2/SOS1 0.037 0.01 -10000 0 -10000 0 0
HRAS/GTP 0.039 0.037 -10000 0 -0.16 3 3
SHC1 0.024 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.055 0.049 0.27 1 -0.16 3 4
FRAP1 -0.013 0.035 0.17 8 -0.16 3 11
EGF/EGFR dimer 0.041 0.063 0.24 23 -0.22 9 32
SOS1 0.026 0.004 -10000 0 -10000 0 0
GRB2 0.025 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 0.002 0.09 0.24 2 -0.23 51 53
PDGFR-beta 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
S1P1/Sphingosine-1-phosphate 0.035 0.12 0.24 23 -0.35 20 43
PDGFB-D/PDGFRB/SLAP 0.021 0.067 0.24 1 -0.27 18 19
PDGFB-D/PDGFRB/APS/CBL 0.045 0.044 0.23 5 -0.19 9 14
AKT1 0.009 0.093 0.31 15 -10000 0 15
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.041 0.14 0.29 13 -0.38 21 34
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
FGR 0.011 0.083 0.34 2 -0.38 5 7
mol:Ca2+ 0.014 0.12 0.25 18 -0.41 22 40
MYC 0.019 0.2 0.36 13 -0.68 21 34
SHC1 0.024 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.024 0.059 0.18 1 -0.17 4 5
LRP1/PDGFRB/PDGFB 0.042 0.045 0.24 1 -0.19 12 13
GRB10 0.021 0.039 -10000 0 -0.32 5 5
PTPN11 0.025 0.005 -10000 0 -10000 0 0
GO:0007205 0.013 0.13 0.25 18 -0.41 22 40
PTEN 0.025 0.007 -10000 0 -10000 0 0
GRB2 0.025 0.005 -10000 0 -10000 0 0
GRB7 0.02 0.05 0.33 2 -0.32 7 9
PDGFB-D/PDGFRB/SHP2 0.032 0.038 -10000 0 -0.23 8 8
PDGFB-D/PDGFRB/GRB10 0.028 0.049 -10000 0 -0.23 14 14
cell cycle arrest 0.021 0.067 0.24 1 -0.27 18 19
HRAS 0.024 0.008 -10000 0 -10000 0 0
HIF1A 0.004 0.087 0.28 17 -10000 0 17
GAB1 0.015 0.12 0.34 4 -0.39 20 24
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.016 0.12 0.3 9 -0.36 17 26
PDGFB-D/PDGFRB 0.037 0.045 -10000 0 -0.2 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.032 0.036 -10000 0 -0.23 7 7
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.024 0.11 0.26 10 -0.35 13 23
positive regulation of MAPKKK cascade 0.032 0.038 -10000 0 -0.23 8 8
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
mol:IP3 0.013 0.13 0.25 18 -0.42 22 40
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.023 0.011 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.027 0.055 0.24 2 -0.23 16 18
SHB 0.023 0.009 -10000 0 -10000 0 0
BLK -0.071 0.2 -10000 0 -0.43 82 82
PTPN2 0.023 0.013 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.032 0.04 -10000 0 -0.23 9 9
BCAR1 0.025 0.006 -10000 0 -10000 0 0
VAV2 0.014 0.14 0.31 9 -0.41 20 29
CBL 0.025 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.031 0.04 -10000 0 -0.22 9 9
LCK 0.009 0.098 0.34 2 -0.47 7 9
PDGFRB 0.018 0.053 -10000 0 -0.33 9 9
ACP1 0.025 0.006 -10000 0 -10000 0 0
HCK -0.001 0.12 0.34 1 -0.6 12 13
ABL1 0.012 0.11 0.25 17 -0.34 19 36
PDGFB-D/PDGFRB/CBL 0.008 0.14 0.33 4 -0.46 22 26
PTPN1 0.022 0.013 -10000 0 -10000 0 0
SNX15 0.026 0.004 -10000 0 -10000 0 0
STAT3 0.026 0.004 -10000 0 -10000 0 0
STAT1 0.028 0.03 0.33 4 -10000 0 4
cell proliferation 0.022 0.18 0.34 16 -0.59 22 38
SLA 0.013 0.063 0.33 1 -0.32 13 14
actin cytoskeleton reorganization 0.009 0.088 0.32 9 -10000 0 9
SRC 0.01 0.067 0.33 1 -0.38 1 2
PI3K -0.027 0.028 -10000 0 -0.17 8 8
PDGFB-D/PDGFRB/GRB7/SHC 0.038 0.05 0.23 2 -0.19 14 16
SH2B2 0.029 0.033 0.33 5 -10000 0 5
PLCgamma1/SPHK1 0.041 0.14 0.3 12 -0.39 21 33
LYN 0.011 0.076 0.32 1 -0.53 2 3
LRP1 0.022 0.034 -10000 0 -0.32 4 4
SOS1 0.026 0.004 -10000 0 -10000 0 0
STAT5B 0.026 0.004 -10000 0 -10000 0 0
STAT5A 0.025 0.018 -10000 0 -0.32 1 1
NCK1-2/p130 Cas 0.051 0.052 -10000 0 -0.18 7 7
SPHK1 0.066 0.11 0.33 56 -0.33 1 57
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.013 0.13 0.25 18 -0.42 22 40
PLCG1 0.013 0.13 0.27 12 -0.42 22 34
NHERF/PDGFRB 0.051 0.056 0.23 18 -0.19 9 27
YES1 -0.002 0.098 0.35 1 -0.5 9 10
cell migration 0.05 0.055 0.23 18 -0.19 9 27
SHC/Grb2/SOS1 0.052 0.051 -10000 0 -0.18 6 6
SLC9A3R2 0.025 0.005 -10000 0 -10000 0 0
SLC9A3R1 0.04 0.065 0.33 20 -10000 0 20
NHERF1-2/PDGFRB/PTEN 0.059 0.055 0.24 15 -0.18 9 24
FYN -0.015 0.13 -10000 0 -0.44 24 24
DOK1 0.002 0.069 0.18 48 -0.18 7 55
HRAS/GTP 0.018 0.006 -10000 0 -10000 0 0
PDGFB 0.026 0.016 0.33 1 -10000 0 1
RAC1 0.011 0.15 0.34 9 -0.41 30 39
PRKCD 0.001 0.068 0.18 47 -0.19 8 55
FER -0.001 0.068 0.17 45 -0.19 9 54
MAPKKK cascade 0.014 0.091 0.38 8 -10000 0 8
RASA1 0 0.067 0.18 44 -0.19 7 51
NCK1 0.025 0.006 -10000 0 -10000 0 0
NCK2 0.026 0.004 -10000 0 -10000 0 0
p62DOK/Csk 0.009 0.067 0.22 4 -10000 0 4
PDGFB-D/PDGFRB/SHB 0.029 0.039 -10000 0 -0.22 8 8
chemotaxis 0.012 0.11 0.25 17 -0.33 19 36
STAT1-3-5/STAT1-3-5 0.043 0.05 -10000 0 -0.17 9 9
Bovine Papilomavirus E5/PDGFRB 0.014 0.037 -10000 0 -0.22 9 9
PTPRJ 0.025 0.006 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.018 0.051 -10000 0 -0.32 9 9
Jak2/Leptin Receptor 0.011 0.15 0.29 8 -0.37 38 46
PTP1B/AKT1 0.022 0.079 -10000 0 -0.29 7 7
FYN 0.022 0.03 -10000 0 -0.32 3 3
p210 bcr-abl/PTP1B 0.014 0.081 -10000 0 -0.31 7 7
EGFR 0.017 0.053 -10000 0 -0.32 9 9
EGF/EGFR 0.032 0.089 0.25 8 -0.29 6 14
CSF1 0.013 0.065 -10000 0 -0.32 15 15
AKT1 0.025 0.007 -10000 0 -10000 0 0
INSR 0.026 0.006 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.04 0.1 0.28 24 -0.31 6 30
Insulin Receptor/Insulin 0.033 0.076 -10000 0 -0.28 6 6
HCK 0.018 0.064 0.33 5 -0.32 10 15
CRK 0.024 0.008 -10000 0 -10000 0 0
TYK2 0.011 0.08 0.3 3 -0.31 6 9
EGF 0.042 0.072 0.33 24 -10000 0 24
YES1 0.024 0.008 -10000 0 -10000 0 0
CAV1 0.016 0.087 0.21 1 -0.27 12 13
TXN 0.026 0.023 0.33 2 -10000 0 2
PTP1B/IRS1/GRB2 0.03 0.083 -10000 0 -0.28 6 6
cell migration -0.014 0.081 0.31 7 -10000 0 7
STAT3 0.026 0.004 -10000 0 -10000 0 0
PRLR 0.021 0.095 0.33 17 -0.32 17 34
ITGA2B 0.047 0.079 0.32 30 -10000 0 30
CSF1R 0.01 0.077 0.33 2 -0.32 19 21
Prolactin Receptor/Prolactin 0.028 0.069 0.24 18 -0.23 15 33
FGR 0.024 0.024 -10000 0 -0.32 2 2
PTP1B/p130 Cas 0.023 0.08 -10000 0 -0.3 7 7
Crk/p130 Cas 0.029 0.082 -10000 0 -0.3 6 6
DOK1 0.009 0.09 0.24 1 -0.29 15 16
JAK2 0.001 0.15 0.27 5 -0.37 43 48
Jak2/Leptin Receptor/Leptin -0.008 0.14 0.27 3 -0.34 30 33
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
PTPN1 0.014 0.081 -10000 0 -0.31 7 7
LYN 0.024 0.007 -10000 0 -10000 0 0
CDH2 0.05 0.094 0.33 38 -0.32 3 41
SRC 0.023 0.076 -10000 0 -0.44 8 8
ITGB3 -0.012 0.11 -10000 0 -0.32 44 44
CAT1/PTP1B 0.009 0.12 0.3 9 -0.34 14 23
CAPN1 0.026 0.005 -10000 0 -10000 0 0
CSK 0.026 0.004 -10000 0 -10000 0 0
PI3K 0.034 0.076 -10000 0 -0.28 5 5
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.011 0.14 0.26 2 -0.32 38 40
negative regulation of transcription 0.002 0.15 0.27 5 -0.36 43 48
FCGR2A 0.029 0.051 0.33 10 -0.32 1 11
FER 0.024 0.025 -10000 0 -0.32 2 2
alphaIIb/beta3 Integrin 0.023 0.097 0.24 25 -0.21 44 69
BLK 0.003 0.11 0.33 15 -0.32 30 45
Insulin Receptor/Insulin/Shc 0.04 0.018 -10000 0 -10000 0 0
RHOA 0.026 0.006 -10000 0 -10000 0 0
LEPR 0.013 0.068 -10000 0 -0.31 17 17
BCAR1 0.025 0.006 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.025 0.005 -10000 0 -10000 0 0
mol:NADPH 0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.014 0.13 0.23 11 -0.32 30 41
PRL 0.009 0.041 0.33 5 -10000 0 5
SOCS3 -0.1 0.36 -10000 0 -1.1 43 43
SPRY2 0.019 0.046 -10000 0 -0.32 7 7
Insulin Receptor/Insulin/IRS1 0.037 0.035 -10000 0 -0.19 7 7
CSF1/CSF1R 0.022 0.1 0.28 1 -0.29 15 16
Ras protein signal transduction 0.003 0.11 0.53 14 -10000 0 14
IRS1 0.018 0.045 -10000 0 -0.32 7 7
INS 0.009 0.015 -10000 0 -10000 0 0
LEP -0.001 0.12 0.33 15 -0.32 35 50
STAT5B 0.018 0.1 0.22 5 -0.31 17 22
STAT5A 0.018 0.11 0.22 4 -0.32 16 20
GRB2 0.025 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.022 0.085 -10000 0 -0.27 11 11
CSN2 0.027 0.07 -10000 0 -10000 0 0
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
LAT 0.035 0.06 -10000 0 -0.4 3 3
YBX1 0.031 0.006 -10000 0 -10000 0 0
LCK 0.024 0.04 0.33 2 -0.32 4 6
SHC1 0.024 0.007 -10000 0 -10000 0 0
NOX4 0.048 0.079 0.33 30 -10000 0 30
HIF-2-alpha transcription factor network

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
MMP14 0.02 0.078 0.42 1 -0.57 5 6
oxygen homeostasis 0.008 0.015 -10000 0 -10000 0 0
TCEB2 0.026 0.016 0.33 1 -10000 0 1
TCEB1 0.023 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.052 0.091 0.32 8 -0.24 3 11
EPO 0.1 0.19 0.54 34 -0.39 2 36
FIH (dimer) 0.027 0.026 -10000 0 -10000 0 0
APEX1 0.028 0.031 -10000 0 -10000 0 0
SERPINE1 0.084 0.18 0.51 27 -0.46 3 30
FLT1 0.007 0.11 -10000 0 -0.59 9 9
ADORA2A 0.08 0.17 0.48 26 -0.39 2 28
germ cell development 0.11 0.21 0.52 53 -0.38 4 57
SLC11A2 0.082 0.17 0.51 22 -0.39 1 23
BHLHE40 0.072 0.17 0.51 20 -0.4 2 22
HIF1AN 0.027 0.026 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.076 0.13 0.43 20 -0.27 3 23
ETS1 0.03 0.012 -10000 0 -10000 0 0
CITED2 0.014 0.089 -10000 0 -0.58 6 6
KDR 0.004 0.13 -10000 0 -0.61 15 15
PGK1 0.081 0.17 0.51 21 -0.4 2 23
SIRT1 0.027 0.006 -10000 0 -10000 0 0
response to hypoxia 0.001 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.11 0.2 0.64 14 -0.45 2 16
EPAS1 0.039 0.092 0.3 19 -0.25 3 22
SP1 0.029 0.009 0.2 1 -10000 0 1
ABCG2 0.076 0.18 0.54 20 -0.39 10 30
EFNA1 0.077 0.17 0.53 17 -0.4 2 19
FXN 0.08 0.17 0.48 26 -0.39 2 28
POU5F1 0.11 0.21 0.53 52 -0.39 4 56
neuron apoptosis -0.11 0.19 0.44 2 -0.63 14 16
EP300 0.025 0.005 -10000 0 -10000 0 0
EGLN3 0.021 0.055 -10000 0 -0.32 8 8
EGLN2 0.027 0.026 -10000 0 -10000 0 0
EGLN1 0.028 0.026 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.041 0.025 0.23 1 -10000 0 1
VHL 0.023 0.008 -10000 0 -10000 0 0
ARNT 0.025 0.029 -10000 0 -10000 0 0
SLC2A1 0.081 0.17 0.47 28 -0.39 2 30
TWIST1 0.05 0.2 0.48 24 -0.39 36 60
ELK1 0.029 0.004 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.067 0.12 0.41 8 -10000 0 8
VEGFA 0.081 0.17 0.51 22 -0.4 2 24
CREBBP 0.025 0.007 -10000 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.039 0.062 0.21 28 -0.19 13 41
cell-cell adhesion 0.034 0.035 0.16 20 -10000 0 20
Ephrin B/EPHB2/RasGAP 0.071 0.068 0.24 31 -0.17 8 39
ITSN1 0.026 0.004 -10000 0 -10000 0 0
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
SHC1 0.024 0.007 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.038 0.037 0.21 13 -0.19 2 15
Ephrin B1/EPHB1 0.021 0.056 0.21 3 -0.18 25 28
HRAS/GDP 0.004 0.075 -10000 0 -0.22 15 15
Ephrin B/EPHB1/GRB7 0.048 0.082 0.25 11 -0.17 33 44
Endophilin/SYNJ1 -0.006 0.056 0.19 19 -10000 0 19
KRAS 0.025 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.045 0.075 0.25 8 -0.17 29 37
endothelial cell migration 0.047 0.024 -10000 0 -0.16 1 1
GRB2 0.025 0.005 -10000 0 -10000 0 0
GRB7 0.02 0.05 0.33 2 -0.32 7 9
PAK1 -0.006 0.066 0.26 5 -10000 0 5
HRAS 0.024 0.008 -10000 0 -10000 0 0
RRAS -0.008 0.055 0.18 17 -10000 0 17
DNM1 0.018 0.042 -10000 0 -0.32 6 6
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.014 0.067 0.31 3 -10000 0 3
lamellipodium assembly -0.034 0.035 -10000 0 -0.16 20 20
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.003 0.07 0.3 1 -0.28 5 6
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
EPHB2 0.047 0.076 0.33 28 -10000 0 28
EPHB3 0.033 0.059 0.33 13 -0.32 2 15
EPHB1 0.006 0.089 0.33 4 -0.32 25 29
EPHB4 0.026 0.004 -10000 0 -10000 0 0
mol:GDP -0.012 0.057 0.3 1 -0.23 10 11
Ephrin B/EPHB2 0.061 0.062 0.23 31 -0.16 8 39
Ephrin B/EPHB3 0.051 0.053 0.22 15 -0.16 9 24
JNK cascade -0.008 0.089 0.3 21 -0.31 1 22
Ephrin B/EPHB1 0.037 0.067 0.22 8 -0.16 30 38
RAP1/GDP 0.006 0.083 0.36 3 -0.24 8 11
EFNB2 0.026 0.016 0.33 1 -10000 0 1
EFNB3 0.021 0.069 0.33 8 -0.32 10 18
EFNB1 0.026 0.004 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.047 0.074 0.23 31 -0.17 23 54
RAP1B 0.024 0.007 -10000 0 -10000 0 0
RAP1A 0.026 0.003 -10000 0 -10000 0 0
CDC42/GTP 0.032 0.076 0.28 2 -0.2 10 12
Rap1/GTP -0.03 0.045 0.14 1 -10000 0 1
axon guidance 0.038 0.061 0.21 28 -0.18 13 41
MAPK3 -0.008 0.066 0.22 6 -0.27 5 11
MAPK1 -0.007 0.067 0.19 8 -0.27 5 13
Rac1/GDP -0.02 0.077 0.24 6 -0.24 10 16
actin cytoskeleton reorganization -0.035 0.046 -10000 0 -0.19 9 9
CDC42/GDP -0.019 0.081 0.28 7 -0.24 10 17
PI3K 0.051 0.026 -10000 0 -0.16 1 1
EFNA5 0.015 0.063 0.33 1 -0.32 13 14
Ephrin B2/EPHB4 0.034 0.013 0.21 1 -10000 0 1
Ephrin B/EPHB2/Intersectin/N-WASP 0.015 0.057 0.25 2 -0.18 8 10
CDC42 0.026 0.003 -10000 0 -10000 0 0
RAS family/GTP -0.032 0.043 0.11 1 -10000 0 1
PTK2 0.044 0.17 0.55 39 -10000 0 39
MAP4K4 -0.008 0.089 0.3 21 -0.31 1 22
SRC 0.025 0.007 -10000 0 -10000 0 0
KALRN 0.026 0.039 0.33 4 -0.32 2 6
Intersectin/N-WASP 0.037 0.008 -10000 0 -10000 0 0
neuron projection morphogenesis -0.008 0.09 0.26 21 -0.27 1 22
MAP2K1 -0.004 0.065 0.26 1 -0.27 5 6
WASL 0.026 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.06 0.078 0.24 29 -0.18 25 54
cell migration 0.003 0.095 0.25 8 -0.31 6 14
NRAS 0.026 0.002 -10000 0 -10000 0 0
SYNJ1 -0.006 0.057 0.19 19 -10000 0 19
PXN 0.026 0.004 -10000 0 -10000 0 0
TF -0.001 0.065 0.18 21 -10000 0 21
HRAS/GTP 0.032 0.066 0.24 2 -0.16 19 21
Ephrin B1/EPHB1-2 0.046 0.073 0.22 30 -0.17 25 55
cell adhesion mediated by integrin 0.006 0.045 0.16 7 -0.19 12 19
RAC1 0.025 0.006 -10000 0 -10000 0 0
mol:GTP 0.037 0.072 0.23 8 -0.16 22 30
RAC1-CDC42/GTP -0.034 0.041 -10000 0 -0.16 20 20
RASA1 0.025 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.004 0.081 0.42 1 -0.24 10 11
ruffle organization -0.011 0.082 0.29 9 -10000 0 9
NCK1 0.025 0.006 -10000 0 -10000 0 0
receptor internalization -0.012 0.056 0.17 17 -0.29 1 18
Ephrin B/EPHB2/KALRN 0.07 0.072 0.24 34 -0.17 10 44
ROCK1 -0.001 0.052 0.18 23 -0.17 2 25
RAS family/GDP -0.038 0.04 -10000 0 -0.18 12 12
Rac1/GTP -0.03 0.045 0.12 1 -0.16 21 22
Ephrin B/EPHB1/Src/Paxillin -0.002 0.07 0.24 3 -0.26 6 9
IL2 signaling events mediated by STAT5

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
GAB2 0.024 0.018 -10000 0 -0.32 1 1
ELF1 0.023 0.078 0.2 19 -0.31 16 35
CCNA2 0.1 0.13 0.33 102 -10000 0 102
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
JAK3 0.028 0.021 0.33 2 -10000 0 2
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
JAK1 0.026 0.003 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.032 0.093 0.3 3 -0.45 5 8
SHC1 0.025 0.007 -10000 0 -10000 0 0
SP1 0.005 0.088 -10000 0 -0.3 31 31
IL2RA 0.004 0.14 0.36 19 -0.59 15 34
IL2RB 0.022 0.041 0.33 1 -0.32 5 6
SOS1 0.026 0.005 -10000 0 -10000 0 0
IL2RG 0.025 0.068 0.33 9 -0.32 9 18
G1/S transition of mitotic cell cycle -0.004 0.21 0.36 5 -0.6 35 40
PTPN11 0.026 0.005 -10000 0 -10000 0 0
CCND2 -0.034 0.16 -10000 0 -0.59 31 31
LCK 0.025 0.04 0.33 2 -0.32 4 6
GRB2 0.026 0.005 -10000 0 -10000 0 0
IL2 0.016 0.012 -10000 0 -10000 0 0
CDK6 0.017 0.054 -10000 0 -0.32 10 10
CCND3 0.036 0.091 -10000 0 -0.53 2 2
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.035 0.054 -10000 0 -0.29 3 3
epithelial cell differentiation 0.008 0.08 0.28 1 -0.3 3 4
ITCH 0.023 0.02 -10000 0 -10000 0 0
WWP1 0.027 0.058 -10000 0 -10000 0 0
FYN 0.022 0.03 -10000 0 -0.32 3 3
EGFR 0.017 0.051 -10000 0 -0.32 9 9
PRL 0.001 0.041 0.33 5 -10000 0 5
neuron projection morphogenesis 0.009 0.093 0.27 14 -0.3 1 15
PTPRZ1 -0.028 0.18 0.33 41 -0.32 89 130
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.025 0.081 -10000 0 -0.32 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.002 0.07 -10000 0 -0.24 4 4
ADAM17 0.022 0.02 -10000 0 -10000 0 0
ErbB4/ErbB4 0.025 0.04 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.04 0.063 0.3 4 -0.24 2 6
NCOR1 0.023 0.008 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.008 0.075 0.25 1 -0.29 2 3
GRIN2B -0.002 0.076 0.26 4 -0.28 2 6
ErbB4/ErbB2/betacellulin 0.02 0.069 0.27 2 -0.25 1 3
STAT1 0.028 0.03 0.33 4 -10000 0 4
HBEGF 0.015 0.059 -10000 0 -0.32 12 12
PRLR 0.02 0.094 0.33 17 -0.32 17 34
E4ICDs/ETO2 0.036 0.049 -10000 0 -0.24 2 2
axon guidance 0.013 0.091 0.3 2 -0.3 2 4
NEDD4 0.019 0.026 -10000 0 -0.3 1 1
Prolactin receptor/Prolactin receptor/Prolactin 0.025 0.067 0.24 18 -0.23 15 33
CBFA2T3 0.015 0.059 -10000 0 -0.32 12 12
ErbB4/ErbB2/HBEGF 0.033 0.054 0.27 2 -0.34 1 3
MAPK3 0.004 0.086 0.27 6 -0.3 1 7
STAT1 (dimer) 0.041 0.051 -10000 0 -0.23 2 2
MAPK1 0.008 0.087 0.27 7 -0.3 1 8
JAK2 0.022 0.009 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta 0.001 0.071 0.25 2 -0.34 1 3
NRG1 -0.029 0.092 0.2 19 -0.23 54 73
NRG3 0.014 0.061 0.33 13 -10000 0 13
NRG2 -0.12 0.17 -10000 0 -0.32 164 164
NRG4 -0.007 0.1 -10000 0 -0.32 37 37
heart development 0.013 0.091 0.3 2 -0.3 2 4
neural crest cell migration 0.001 0.07 0.25 2 -0.34 1 3
ERBB2 -0.001 0.053 0.27 14 -10000 0 14
WWOX/E4ICDs 0.034 0.047 -10000 0 -0.24 2 2
SHC1 0.024 0.007 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.027 0.075 -10000 0 -0.26 6 6
apoptosis -0.028 0.07 0.3 6 -0.34 1 7
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.012 0.067 -10000 0 -0.26 14 14
ErbB4/ErbB2/epiregulin 0.045 0.099 0.3 10 -0.3 1 11
ErbB4/ErbB4/betacellulin/betacellulin 0.031 0.054 -10000 0 -0.26 4 4
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.039 0.076 0.32 1 -0.36 1 2
MDM2 0.036 0.078 0.28 32 -10000 0 32
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.004 0.068 -10000 0 -0.26 1 1
STAT5A 0.013 0.093 0.32 6 -0.29 2 8
ErbB4/EGFR/neuregulin 1 beta 0.006 0.075 0.25 1 -0.3 2 3
DLG4 0.024 0.008 -10000 0 -10000 0 0
GRB2/SHC 0.035 0.012 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.029 0.043 -10000 0 -0.22 1 1
STAT5A (dimer) 0.018 0.096 0.32 1 -0.35 2 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.029 0.097 0.32 2 -0.29 2 4
LRIG1 -0.004 0.094 -10000 0 -0.32 33 33
EREG 0.016 0.17 0.33 52 -0.32 55 107
BTC -0.018 0.11 -10000 0 -0.32 49 49
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.01 0.086 0.3 2 -0.3 1 3
ERBB4 0.017 0.03 -10000 0 -10000 0 0
STAT5B 0.026 0.004 -10000 0 -10000 0 0
YAP1 0.011 0.078 0.25 1 -0.46 9 10
GRB2 0.025 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.025 0.061 0.25 1 -0.3 1 2
glial cell differentiation -0.029 0.043 0.22 1 -10000 0 1
WWOX 0.022 0.019 -10000 0 -0.32 1 1
cell proliferation -0.026 0.13 0.3 10 -0.37 16 26
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.02 0.019 -10000 0 -10000 0 0
HSPA8 0.025 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.006 0.11 0.28 1 -0.22 62 63
AKT1 0.027 0.022 -10000 0 -0.1 1 1
GSC 0.034 0.1 0.43 7 -10000 0 7
NKX2-5 -0.001 0.01 -10000 0 -10000 0 0
muscle cell differentiation -0.006 0.098 0.38 9 -10000 0 9
SMAD2-3/SMAD4/SP1 0.052 0.096 -10000 0 -0.28 12 12
SMAD4 0.007 0.051 -10000 0 -0.17 7 7
CBFB 0.025 0.005 -10000 0 -10000 0 0
SAP18 0.025 0.005 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.044 0.038 0.23 6 -10000 0 6
SMAD3/SMAD4/VDR 0.048 0.066 -10000 0 -0.22 3 3
MYC 0.001 0.076 -10000 0 -0.32 18 18
CDKN2B -0.14 0.3 0.4 11 -0.79 31 42
AP1 -0.037 0.12 -10000 0 -0.4 20 20
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.005 0.073 -10000 0 -0.28 12 12
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.004 0.088 0.22 5 -0.34 13 18
SP3 0.026 0.004 -10000 0 -10000 0 0
CREB1 0.025 0.005 -10000 0 -10000 0 0
FOXH1 0.08 0.12 0.33 74 -10000 0 74
SMAD3/SMAD4/GR 0.014 0.079 -10000 0 -0.23 14 14
GATA3 -0.001 0.085 -10000 0 -0.31 25 25
SKI/SIN3/HDAC complex/NCoR1 0.003 0.063 -10000 0 -0.34 6 6
MEF2C/TIF2 0.023 0.085 0.31 2 -0.35 8 10
endothelial cell migration -0.015 0.15 1.1 6 -0.4 3 9
MAX 0.023 0.016 -10000 0 -10000 0 0
RBBP7 0.026 0.004 -10000 0 -10000 0 0
RBBP4 0.026 0.002 -10000 0 -10000 0 0
RUNX2 0.028 0.035 0.33 4 -0.32 1 5
RUNX3 0.014 0.063 -10000 0 -0.32 14 14
RUNX1 0.025 0.005 -10000 0 -10000 0 0
CTBP1 0.025 0.005 -10000 0 -10000 0 0
NR3C1 0.014 0.058 -10000 0 -0.32 11 11
VDR 0.024 0.025 -10000 0 -0.32 2 2
CDKN1A -0.012 0.1 -10000 0 -0.82 4 4
KAT2B 0.02 0.022 -10000 0 -0.32 1 1
SMAD2/SMAD2/SMAD4/FOXH1 0.08 0.092 0.26 44 -0.19 2 46
DCP1A 0.025 0.006 -10000 0 -10000 0 0
SKI 0.026 0.003 -10000 0 -10000 0 0
SERPINE1 0.015 0.15 0.4 3 -1.1 6 9
SMAD3/SMAD4/ATF2 0.023 0.067 -10000 0 -0.18 5 5
SMAD3/SMAD4/ATF3 -0.012 0.12 -10000 0 -0.23 72 72
SAP30 0.025 0.006 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.038 0.033 -10000 0 -10000 0 0
JUN -0.048 0.11 -10000 0 -0.4 20 20
SMAD3/SMAD4/IRF7 0.03 0.082 0.33 4 -0.23 3 7
TFE3 0.027 0.016 -10000 0 -0.18 1 1
COL1A2 -0.019 0.2 0.38 2 -0.74 27 29
mesenchymal cell differentiation -0.025 0.07 0.18 6 -0.25 2 8
DLX1 0.051 0.093 0.33 41 -10000 0 41
TCF3 0.025 0.005 -10000 0 -10000 0 0
FOS -0.077 0.16 -10000 0 -0.33 113 113
SMAD3/SMAD4/Max 0.019 0.068 -10000 0 -0.2 3 3
Cbp/p300/SNIP1 0.044 0.023 -10000 0 -10000 0 0
ZBTB17 0.02 0.025 -10000 0 -0.12 1 1
LAMC1 -0.003 0.049 -10000 0 -0.37 1 1
TGIF2/HDAC complex/SMAD3/SMAD4 0.023 0.064 -10000 0 -0.18 5 5
IRF7 0.034 0.058 0.33 13 -0.32 1 14
ESR1 -0.023 0.12 -10000 0 -0.32 57 57
HNF4A 0.042 0.092 0.33 37 -10000 0 37
MEF2C 0.031 0.087 0.29 3 -0.35 8 11
SMAD2-3/SMAD4 0.029 0.076 -10000 0 -0.21 8 8
Cbp/p300/Src-1 0.041 0.029 -10000 0 -10000 0 0
IGHV3OR16-13 -0.006 0.065 -10000 0 -0.36 13 13
TGIF2/HDAC complex 0.024 0.007 -10000 0 -10000 0 0
CREBBP 0.02 0.017 -10000 0 -10000 0 0
SKIL 0.025 0.006 -10000 0 -10000 0 0
HDAC1 0.026 0.002 -10000 0 -10000 0 0
HDAC2 0.025 0.006 -10000 0 -10000 0 0
SNIP1 0.026 0.004 -10000 0 -10000 0 0
GCN5L2 -0.001 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.029 0.072 -10000 0 -0.2 4 4
MSG1/HSC70 0.041 0.03 0.24 8 -10000 0 8
SMAD2 0.027 0.027 -10000 0 -0.12 2 2
SMAD3 0.004 0.05 -10000 0 -0.17 3 3
SMAD3/E2F4-5/DP1/p107/SMAD4 0.005 0.045 -10000 0 -0.19 3 3
SMAD2/SMAD2/SMAD4 0.002 0.059 0.2 6 -0.19 8 14
NCOR1 0.023 0.008 -10000 0 -10000 0 0
NCOA2 0.006 0.075 -10000 0 -0.32 20 20
NCOA1 0.025 0.005 -10000 0 -10000 0 0
MYOD/E2A 0.029 0.009 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.063 0.1 -10000 0 -0.29 11 11
IFNB1 -0.004 0.066 0.38 7 -0.25 1 8
SMAD3/SMAD4/MEF2C 0.049 0.1 0.31 1 -0.37 8 9
CITED1 0.031 0.042 0.33 8 -10000 0 8
SMAD2-3/SMAD4/ARC105 0.046 0.073 -10000 0 -0.21 5 5
RBL1 0.025 0.016 0.33 1 -10000 0 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.003 0.11 0.26 4 -0.53 11 15
RUNX1-3/PEBPB2 0.041 0.045 -10000 0 -0.19 13 13
SMAD7 -0.04 0.13 -10000 0 -0.4 24 24
MYC/MIZ-1 0.012 0.067 0.18 1 -0.18 38 39
SMAD3/SMAD4 -0.015 0.092 -10000 0 -0.41 10 10
IL10 -0.007 0.12 0.37 1 -0.39 18 19
PIASy/HDAC complex 0.025 0.012 -10000 0 -10000 0 0
PIAS3 0.021 0.013 -10000 0 -10000 0 0
CDK2 0.02 0.017 -10000 0 -10000 0 0
IL5 -0.01 0.094 0.36 2 -0.25 9 11
CDK4 0.02 0.017 -10000 0 -10000 0 0
PIAS4 0.025 0.012 -10000 0 -10000 0 0
ATF3 -0.034 0.13 -10000 0 -0.32 70 70
SMAD3/SMAD4/SP1 0.022 0.089 -10000 0 -0.26 15 15
FOXG1 0.035 0.11 0.33 50 -10000 0 50
FOXO3 -0.01 0.025 -10000 0 -10000 0 0
FOXO1 -0.011 0.027 -10000 0 -0.24 1 1
FOXO4 -0.01 0.028 0.19 1 -10000 0 1
heart looping 0.03 0.086 0.29 3 -0.34 8 11
CEBPB 0.024 0.024 -10000 0 -0.32 1 1
SMAD3/SMAD4/DLX1 0.041 0.091 0.26 23 -0.19 4 27
MYOD1 -0.016 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.039 0.087 0.26 23 -0.2 3 26
SMAD3/SMAD4/GATA3 0.005 0.095 0.28 2 -0.22 38 40
SnoN/SIN3/HDAC complex/NCoR1 0.025 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.046 0.075 -10000 0 -0.24 8 8
SMAD3/SMAD4/SP1-3 0.048 0.084 -10000 0 -0.26 9 9
MED15 0.025 0.005 -10000 0 -10000 0 0
SP1 0.019 0.04 -10000 0 -0.14 5 5
SIN3B 0.026 0.003 -10000 0 -10000 0 0
SIN3A 0.026 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.077 0.092 0.32 9 -0.22 6 15
ITGB5 -0.016 0.058 -10000 0 -0.26 4 4
TGIF/SIN3/HDAC complex/CtBP 0.016 0.052 -10000 0 -0.33 4 4
SMAD3/SMAD4/AR -0.059 0.12 -10000 0 -0.21 140 140
AR -0.1 0.16 -10000 0 -0.32 145 145
negative regulation of cell growth -0.01 0.086 -10000 0 -0.28 14 14
SMAD3/SMAD4/MYOD 0.016 0.064 -10000 0 -0.18 4 4
E2F5 0.023 0.029 0.33 2 -0.32 1 3
E2F4 0.025 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.094 0.09 0.34 7 -0.17 1 8
SMAD2-3/SMAD4/FOXO1-3a-4 0.007 0.083 0.24 1 -0.36 12 13
TFDP1 0.025 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.019 0.13 -10000 0 -0.4 20 20
SMAD3/SMAD4/RUNX2 0.025 0.07 0.25 2 -0.19 6 8
TGIF2 0.024 0.007 -10000 0 -10000 0 0
TGIF1 0.024 0.008 -10000 0 -10000 0 0
ATF2 0.026 0.004 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.028 0.04 -10000 0 -0.22 9 9
ATM 0.025 0.006 -10000 0 -10000 0 0
UBE2D3 0.026 0.003 -10000 0 -10000 0 0
PRKDC 0.024 0.008 -10000 0 -10000 0 0
ATR 0.025 0.006 -10000 0 -10000 0 0
UBE2L3 0.025 0.005 -10000 0 -10000 0 0
FANCD2 0.015 0.019 0.2 4 -10000 0 4
protein ubiquitination 0.063 0.065 0.22 36 -0.17 7 43
XRCC5 0.025 0.006 -10000 0 -10000 0 0
XRCC6 0.025 0.005 -10000 0 -10000 0 0
M/R/N Complex 0.042 0.022 -10000 0 -10000 0 0
MRE11A 0.025 0.005 -10000 0 -10000 0 0
DNA-PK 0.045 0.02 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.008 0.14 -10000 0 -0.53 22 22
FANCF 0.024 0.024 0.33 1 -0.32 1 2
BRCA1 0.026 0.015 0.33 1 -10000 0 1
CCNE1 0.056 0.094 0.33 43 -10000 0 43
CDK2/Cyclin E1 0.055 0.063 0.24 41 -10000 0 41
FANCG 0.024 0.008 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.031 0.039 0.24 1 -0.22 8 9
FANCE 0.027 0.015 0.33 1 -10000 0 1
FANCC 0.024 0.017 0.33 1 -10000 0 1
NBN 0.022 0.01 -10000 0 -10000 0 0
FANCA 0.044 0.073 0.33 25 -10000 0 25
DNA repair 0.031 0.11 0.29 18 -0.38 11 29
BRCA1/BARD1/ubiquitin 0.031 0.039 0.24 1 -0.22 8 9
BARD1/DNA-PK 0.053 0.039 -10000 0 -0.18 7 7
FANCL 0.026 0.016 0.33 1 -10000 0 1
mRNA polyadenylation -0.028 0.04 0.22 9 -10000 0 9
BRCA1/BARD1/CTIP/M/R/N Complex 0.018 0.05 -10000 0 -0.23 3 3
BRCA1/BACH1/BARD1/TopBP1 0.043 0.039 0.23 1 -0.19 8 9
BRCA1/BARD1/P53 0.05 0.043 0.24 1 -0.18 8 9
BARD1/CSTF1/BRCA1 0.042 0.039 0.23 1 -0.19 8 9
BRCA1/BACH1 0.026 0.015 0.33 1 -10000 0 1
BARD1 0.017 0.051 -10000 0 -0.32 9 9
PCNA 0.026 0.016 0.33 1 -10000 0 1
BRCA1/BARD1/UbcH5C 0.045 0.038 0.23 1 -0.19 8 9
BRCA1/BARD1/UbcH7 0.043 0.038 0.23 1 -0.19 8 9
BRCA1/BARD1/RAD51/PCNA 0.11 0.095 0.24 124 -0.18 6 130
BARD1/DNA-PK/P53 0.055 0.046 -10000 0 -0.17 7 7
BRCA1/BARD1/Ubiquitin 0.031 0.039 0.24 1 -0.22 8 9
BRCA1/BARD1/CTIP 0.03 0.034 0.22 1 -0.18 8 9
FA complex 0.011 0.076 0.23 6 -0.25 14 20
BARD1/EWS 0.029 0.04 -10000 0 -0.22 9 9
RBBP8 -0.014 0.005 -10000 0 -10000 0 0
TP53 0.024 0.008 -10000 0 -10000 0 0
TOPBP1 0.025 0.005 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.049 0.042 0.18 8 -0.23 1 9
BRCA1/BARD1 0.077 0.071 0.24 36 -0.17 7 43
CSTF1 0.025 0.007 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.013 0.035 -10000 0 -0.22 9 9
CDK2 0.025 0.005 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.13 0.14 0.33 143 -10000 0 143
RAD50 0.025 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.031 0.039 0.24 1 -0.22 8 9
EWSR1 0.025 0.006 -10000 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.075 0.077 0.23 67 -10000 0 67
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.027 0.022 0.33 2 -10000 0 2
STAT1 (dimer)/Cbp/p300 0.057 0.063 0.27 9 -10000 0 9
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.052 0.03 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.008 0.053 -10000 0 -0.21 5 5
CaM/Ca2+ 0.071 0.07 0.32 2 -10000 0 2
RAP1A 0.026 0.003 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.036 0.06 0.25 8 -10000 0 8
AKT1 0.022 0.082 0.26 21 -10000 0 21
MAP2K1 0.012 0.065 0.24 12 -10000 0 12
MAP3K11 0.016 0.068 0.21 20 -10000 0 20
IFNGR1 0.029 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.056 0.16 -10000 0 -0.31 95 95
Rap1/GTP -0.014 0.029 0.11 1 -10000 0 1
CRKL/C3G 0.035 0.02 0.24 2 -10000 0 2
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.08 0.078 0.33 2 -10000 0 2
CEBPB 0.035 0.11 0.31 3 -0.53 6 9
STAT3 0.026 0.004 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.072 0.12 0.44 1 -0.67 7 8
STAT1 0.018 0.071 0.25 15 -10000 0 15
CALM1 0.026 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.072 0.12 0.32 75 -10000 0 75
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.021 0.078 0.25 17 -10000 0 17
CEBPB/PTGES2/Cbp/p300 0.031 0.063 -10000 0 -0.36 5 5
mol:Ca2+ 0.071 0.074 0.22 67 -10000 0 67
MAPK3 0.024 0.099 -10000 0 -0.71 4 4
STAT1 (dimer) 0 0.077 -10000 0 -0.29 4 4
MAPK1 0.021 0.11 -10000 0 -0.75 5 5
JAK2 0.026 0.012 -10000 0 -10000 0 0
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
JAK1 0.03 0.008 -10000 0 -10000 0 0
CAMK2D 0.024 0.025 -10000 0 -0.32 2 2
DAPK1 0.03 0.091 0.34 3 -0.5 6 9
SMAD7 0.003 0.047 0.19 4 -10000 0 4
CBL/CRKL/C3G 0.051 0.059 0.26 11 -10000 0 11
PI3K 0.061 0.064 0.28 2 -10000 0 2
IFNG 0.073 0.12 0.32 75 -10000 0 75
apoptosis 0.023 0.094 0.31 2 -0.39 13 15
CAMK2G 0.025 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.026 0.004 -10000 0 -10000 0 0
CAMK2A -0.082 0.15 -10000 0 -0.32 119 119
CAMK2B 0.054 0.091 0.33 40 -10000 0 40
FRAP1 0.018 0.075 0.25 21 -10000 0 21
PRKCD 0.021 0.081 0.26 20 -10000 0 20
RAP1B 0.024 0.007 -10000 0 -10000 0 0
negative regulation of cell growth -0.008 0.053 -10000 0 -0.21 5 5
PTPN2 0.024 0.007 -10000 0 -10000 0 0
EP300 0.025 0.005 -10000 0 -10000 0 0
IRF1 0.009 0.054 0.23 5 -10000 0 5
STAT1 (dimer)/PIASy 0.02 0.078 0.25 17 -10000 0 17
SOCS1 0.004 0.14 -10000 0 -1 7 7
mol:GDP 0.04 0.061 0.24 11 -10000 0 11
CASP1 0 0.051 0.2 2 -0.22 6 8
PTGES2 0.024 0.008 -10000 0 -10000 0 0
IRF9 0.019 0.035 -10000 0 -0.17 2 2
mol:PI-3-4-5-P3 0.044 0.05 0.22 2 -10000 0 2
RAP1/GDP 0.025 0.043 0.17 3 -10000 0 3
CBL 0.015 0.067 0.23 15 -10000 0 15
MAP3K1 0.015 0.066 0.23 15 -10000 0 15
PIAS1 0.026 0.004 -10000 0 -10000 0 0
PIAS4 0.025 0.005 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.008 0.053 -10000 0 -0.21 5 5
PTPN11 0.017 0.064 0.23 11 -10000 0 11
CREBBP 0.025 0.007 -10000 0 -10000 0 0
RAPGEF1 0.024 0.008 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.025 0.005 -10000 0 -10000 0 0
HDAC4 0.024 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 -0.002 0.064 -10000 0 -0.22 31 31
CDKN1A -0.013 0.039 -10000 0 -0.56 2 2
KAT2B 0.024 0.018 -10000 0 -0.32 1 1
BAX 0.026 0.004 -10000 0 -10000 0 0
FOXO3 -0.004 0.003 -10000 0 -10000 0 0
FOXO1 0.023 0.019 -10000 0 -0.32 1 1
FOXO4 0.01 0.007 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.025 0.005 -10000 0 -10000 0 0
TAT 0.023 0.067 0.33 17 -10000 0 17
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.017 0.012 -10000 0 -0.23 1 1
PPARGC1A -0.12 0.17 0.33 1 -0.32 164 165
FHL2 0.023 0.03 -10000 0 -0.32 3 3
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.036 0.012 -10000 0 -10000 0 0
HIST2H4A 0.002 0.064 0.22 31 -10000 0 31
SIRT1/FOXO3a 0.018 0.022 -10000 0 -10000 0 0
SIRT1 0.025 0.012 0.19 2 -10000 0 2
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.045 0.021 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.023 0.052 -10000 0 -0.21 5 5
apoptosis -0.049 0.015 -10000 0 -10000 0 0
SIRT1/PGC1A -0.057 0.11 0.21 1 -0.19 164 165
p53/SIRT1 0.032 0.025 0.36 2 -10000 0 2
SIRT1/FOXO4 0.012 0.048 -10000 0 -0.21 7 7
FOXO1/FHL2/SIRT1 0.042 0.026 -10000 0 -0.17 3 3
HIST1H1E 0.02 0.037 0.14 34 -10000 0 34
SIRT1/p300 0.036 0.012 -10000 0 -10000 0 0
muscle cell differentiation -0.028 0.019 0.19 1 -0.22 1 2
TP53 0.023 0.014 0.19 2 -10000 0 2
KU70/SIRT1/BAX 0.049 0.015 -10000 0 -10000 0 0
CREBBP 0.025 0.007 -10000 0 -10000 0 0
MEF2D 0.025 0.006 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.041 0.042 0.24 16 -10000 0 16
ACSS2 -0.014 0.018 0.17 3 -10000 0 3
SIRT1/PCAF/MYOD 0.029 0.019 0.22 1 -0.19 1 2
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.023 0.009 -10000 0 -10000 0 0
NFATC1 -0.004 0.092 0.29 2 -0.3 15 17
NFATC2 -0.036 0.068 -10000 0 -0.2 24 24
NFATC3 0.003 0.028 -10000 0 -0.3 3 3
YWHAE 0.024 0.008 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.033 0.12 0.26 7 -0.32 34 41
Exportin 1/Ran/NUP214 0.042 0.019 -10000 0 -10000 0 0
mol:DAG -0.002 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.025 0.12 0.26 1 -0.31 32 33
BCL2/BAX 0.026 0.05 -10000 0 -0.22 15 15
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.004 0.021 -10000 0 -10000 0 0
CaM/Ca2+ -0.004 0.021 -10000 0 -10000 0 0
BAX 0.026 0.004 -10000 0 -10000 0 0
MAPK14 0.023 0.007 -10000 0 -10000 0 0
BAD 0.026 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D -0.023 0.12 0.25 4 -0.32 30 34
Calcineurin A alpha-beta B1/BCL2 0.012 0.065 -10000 0 -0.32 15 15
FKBP8 0.026 0.003 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.023 0.11 0.31 30 -0.25 4 34
KPNB1 0.026 0.004 -10000 0 -10000 0 0
KPNA2 0.028 0.026 0.33 3 -10000 0 3
XPO1 0.025 0.005 -10000 0 -10000 0 0
SFN 0.047 0.087 0.33 32 -0.32 3 35
MAP3K8 0.019 0.026 -10000 0 -0.32 2 2
NFAT4/CK1 alpha -0.009 0.034 -10000 0 -0.16 3 3
MEF2D/NFAT1/Cbp/p300 -0.1 0.14 -10000 0 -0.24 179 179
CABIN1 -0.033 0.12 0.26 7 -0.32 34 41
CALM1 0.001 0.023 -10000 0 -10000 0 0
RAN 0.025 0.005 -10000 0 -10000 0 0
MAP3K1 0.025 0.006 -10000 0 -10000 0 0
CAMK4 0.018 0.051 0.33 1 -0.32 8 9
mol:Ca2+ -0.006 0.006 -10000 0 -10000 0 0
MAPK3 0.025 0.005 -10000 0 -10000 0 0
YWHAH 0.025 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.038 0.021 0.24 4 -10000 0 4
YWHAB 0.024 0.008 -10000 0 -10000 0 0
MAPK8 0.016 0.032 -10000 0 -0.32 3 3
MAPK9 0.025 0.006 -10000 0 -10000 0 0
YWHAG 0.026 0.003 -10000 0 -10000 0 0
FKBP1A 0.025 0.006 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.015 0.099 0.32 1 -0.31 16 17
PRKCH 0.025 0.005 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.004 0.037 -10000 0 -10000 0 0
CASP3 0.022 0.008 -10000 0 -10000 0 0
PIM1 0.026 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.002 0.014 -10000 0 -10000 0 0
apoptosis 0.014 0.018 0.16 1 -10000 0 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.028 0.051 0.23 1 -0.26 2 3
PRKCB -0.071 0.15 -10000 0 -0.32 112 112
PRKCE 0.025 0.005 -10000 0 -10000 0 0
JNK2/NFAT4 0.018 0.039 -10000 0 -0.27 3 3
BAD/BCL-XL 0.034 0.014 -10000 0 -10000 0 0
PRKCD 0.025 0.006 -10000 0 -10000 0 0
NUP214 0.023 0.008 -10000 0 -10000 0 0
PRKCZ 0.016 0.032 -10000 0 -0.32 3 3
PRKCA 0.022 0.035 -10000 0 -0.32 4 4
PRKCG 0.013 0.057 0.33 11 -10000 0 11
PRKCQ -0.001 0.096 0.33 3 -0.32 31 34
FKBP38/BCL2 0.027 0.05 -10000 0 -0.22 15 15
EP300 -0.004 0.026 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.025 0.006 -10000 0 -10000 0 0
NFATc/JNK1 0.003 0.093 0.32 1 -0.29 16 17
CaM/Ca2+/FKBP38 0.002 0.029 -10000 0 -10000 0 0
FKBP12/FK506 0.019 0.004 -10000 0 -10000 0 0
CSNK1A1 -0.02 0.01 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.001 0.04 0.2 1 -0.19 8 9
NFATc/ERK1 0.009 0.09 0.29 2 -0.29 13 15
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.022 0.12 -10000 0 -0.3 35 35
NR4A1 -0.19 0.19 -10000 0 -0.35 215 215
GSK3B 0.019 0.013 -10000 0 -10000 0 0
positive T cell selection 0.003 0.028 -10000 0 -0.29 3 3
NFAT1/CK1 alpha -0.031 0.057 -10000 0 -0.19 13 13
RCH1/ KPNB1 0.039 0.019 0.24 3 -10000 0 3
YWHAQ 0.025 0.006 -10000 0 -10000 0 0
PRKACA 0.023 0.007 -10000 0 -10000 0 0
AKAP5 0.029 0.03 0.33 4 -10000 0 4
MEF2D -0.003 0.026 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.02 0.011 -10000 0 -10000 0 0
NFATc/p38 alpha 0.005 0.093 0.32 1 -0.29 15 16
CREBBP -0.004 0.026 -10000 0 -10000 0 0
BCL2 0.012 0.065 -10000 0 -0.32 15 15
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.032 0.011 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.025 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.022 0.041 0.33 1 -0.32 5 6
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.023 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.013 0.021 0.18 2 -0.16 1 3
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.024 0.008 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.025 0.006 -10000 0 -10000 0 0
FYN 0.022 0.03 -10000 0 -0.32 3 3
MAP3K12 0.025 0.018 -10000 0 -0.32 1 1
FGR 0.024 0.024 -10000 0 -0.32 2 2
p38 alpha/TAB1 -0.038 0.08 -10000 0 -0.27 33 33
PRKG1 -0.051 0.14 -10000 0 -0.32 87 87
DUSP8 0.007 0.075 -10000 0 -0.32 20 20
PGK/cGMP/p38 alpha -0.03 0.12 0.19 1 -0.3 42 43
apoptosis -0.037 0.077 -10000 0 -0.26 33 33
RAL/GTP 0.034 0.008 -10000 0 -10000 0 0
LYN 0.024 0.007 -10000 0 -10000 0 0
DUSP1 -0.065 0.15 -10000 0 -0.32 105 105
PAK1 0.024 0.018 -10000 0 -0.32 1 1
SRC 0.025 0.007 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.057 0.027 0.24 1 -10000 0 1
TRAF6 0.024 0.007 -10000 0 -10000 0 0
RAC1 0.025 0.006 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.026 0.016 0.33 1 -10000 0 1
RAC1-CDC42/GTP 0.033 0.009 -10000 0 -10000 0 0
MAPK11 -0.001 0.11 0.27 6 -0.3 19 25
BLK 0.003 0.11 0.33 15 -0.32 30 45
HCK 0.018 0.064 0.33 5 -0.32 10 15
MAP2K3 0.024 0.008 -10000 0 -10000 0 0
DUSP16 0.025 0.005 -10000 0 -10000 0 0
DUSP10 0.03 0.033 0.33 5 -10000 0 5
TRAF6/MEKK3 0.03 0.011 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.005 0.11 0.25 4 -0.31 27 31
positive regulation of innate immune response -0.004 0.13 0.3 5 -0.34 25 30
LCK 0.024 0.04 0.33 2 -0.32 4 6
p38alpha-beta/MKP7 0.005 0.13 0.3 5 -0.33 24 29
p38alpha-beta/MKP5 0.006 0.13 0.29 5 -0.33 24 29
PGK/cGMP -0.033 0.097 -10000 0 -0.22 87 87
PAK2 0.025 0.006 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.021 0.14 0.27 1 -0.35 35 36
CDC42 0.026 0.003 -10000 0 -10000 0 0
RALB 0.026 0.004 -10000 0 -10000 0 0
RALA 0.025 0.005 -10000 0 -10000 0 0
PAK3 0.016 0.058 0.33 12 -10000 0 12
EPO 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
BCL2L1 0.03 0.081 0.38 2 -10000 0 2
CRKL 0 0.06 0.24 9 -10000 0 9
mol:DAG 0.029 0.054 0.22 7 -10000 0 7
HRAS 0.012 0.086 0.3 16 -10000 0 16
MAPK8 0.007 0.068 0.21 28 -0.18 2 30
RAP1A 0 0.061 0.25 8 -10000 0 8
GAB1 0 0.061 0.25 8 -10000 0 8
MAPK14 0.008 0.068 0.2 30 -10000 0 30
EPO 0.039 0.081 0.32 29 -10000 0 29
PLCG1 0.029 0.054 0.22 7 -10000 0 7
EPOR/TRPC2/IP3 Receptors 0.032 0.04 0.32 7 -10000 0 7
RAPGEF1 0.024 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.04 0.088 0.23 28 -0.2 32 60
GAB1/SHC/GRB2/SOS1 0.041 0.054 0.26 4 -10000 0 4
EPO/EPOR (dimer) 0.054 0.058 0.23 35 -10000 0 35
IRS2 -0.005 0.067 0.25 8 -0.23 2 10
STAT1 0.032 0.069 0.24 8 -0.23 9 17
STAT5B 0.03 0.061 0.23 8 -10000 0 8
cell proliferation 0.005 0.076 0.22 32 -0.17 2 34
GAB1/SHIP/PIK3R1/SHP2/SHC 0.027 0.043 -10000 0 -10000 0 0
TEC 0 0.061 0.25 8 -10000 0 8
SOCS3 -0.009 0.1 -10000 0 -0.32 40 40
STAT1 (dimer) 0.032 0.068 0.24 10 -0.23 9 19
JAK2 0.023 0.014 -10000 0 -10000 0 0
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
EPO/EPOR (dimer)/JAK2 0.064 0.064 0.3 1 -10000 0 1
EPO/EPOR 0.054 0.058 0.23 35 -10000 0 35
LYN 0.023 0.013 -10000 0 -10000 0 0
TEC/VAV2 -0.001 0.058 0.23 5 -10000 0 5
elevation of cytosolic calcium ion concentration 0.032 0.04 0.32 7 -10000 0 7
SHC1 0.024 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.061 0.053 0.23 28 -10000 0 28
mol:IP3 0.029 0.054 0.22 7 -10000 0 7
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.029 0.071 0.28 6 -0.24 3 9
SH2B3 0.026 0.012 -10000 0 -10000 0 0
NFKB1 0.008 0.068 0.2 30 -10000 0 30
EPO/EPOR (dimer)/JAK2/SOCS3 0 0.07 0.24 2 -0.2 33 35
PTPN6 0.003 0.061 0.25 9 -10000 0 9
TEC/VAV2/GRB2 0.039 0.054 0.26 4 -10000 0 4
EPOR 0.032 0.041 0.32 7 -10000 0 7
INPP5D 0.019 0.042 -10000 0 -0.32 6 6
mol:GDP 0.04 0.054 0.26 4 -10000 0 4
SOS1 0.026 0.004 -10000 0 -10000 0 0
PLCG2 0.026 0.036 0.33 3 -0.32 2 5
CRKL/CBL/C3G 0.039 0.053 0.25 5 -10000 0 5
VAV2 0 0.059 0.25 7 -10000 0 7
CBL 0 0.059 0.25 7 -10000 0 7
SHC/Grb2/SOS1 0.032 0.041 -10000 0 -10000 0 0
STAT5A 0.029 0.062 0.23 8 -0.22 1 9
GRB2 0.025 0.005 -10000 0 -10000 0 0
STAT5 (dimer) 0.04 0.08 0.34 1 -0.3 10 11
LYN/PLCgamma2 0.034 0.028 0.24 3 -0.22 1 4
PTPN11 0.025 0.005 -10000 0 -10000 0 0
BTK -0.006 0.07 0.25 8 -0.24 3 11
BCL2 0.012 0.16 0.33 3 -0.72 15 18
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.013 0.015 0.26 1 -10000 0 1
BAD/BCL-XL/YWHAZ 0.028 0.021 0.2 1 -10000 0 1
CDKN1B 0.008 0.052 -10000 0 -0.29 9 9
CDKN1A 0.004 0.055 -10000 0 -0.29 11 11
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.024 0.008 -10000 0 -10000 0 0
FOXO3 0.01 0.037 -10000 0 -0.29 4 4
AKT1 0.003 0.053 -10000 0 -0.3 11 11
BAD 0.026 0.003 -10000 0 -10000 0 0
AKT3 0.002 0.047 -10000 0 -0.24 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.006 0.053 -10000 0 -0.29 10 10
AKT1/ASK1 0.03 0.065 -10000 0 -0.28 11 11
BAD/YWHAZ 0.04 0.024 -10000 0 -10000 0 0
RICTOR 0.023 0.009 -10000 0 -10000 0 0
RAF1 0.023 0.009 -10000 0 -10000 0 0
JNK cascade -0.028 0.062 0.27 12 -10000 0 12
TSC1 0.007 0.049 -10000 0 -0.29 8 8
YWHAZ 0.02 0.011 -10000 0 -10000 0 0
AKT1/RAF1 0.029 0.061 -10000 0 -0.29 8 8
EP300 0.025 0.005 -10000 0 -10000 0 0
mol:GDP 0.01 0.056 -10000 0 -0.3 11 11
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.007 0.049 -10000 0 -0.29 9 9
YWHAQ 0.025 0.006 -10000 0 -10000 0 0
TBC1D4 -0.003 0.001 -10000 0 -10000 0 0
MAP3K5 0.024 0.018 -10000 0 -0.32 1 1
MAPKAP1 0.023 0.008 -10000 0 -10000 0 0
negative regulation of cell cycle -0.042 0.066 0.33 2 -0.22 7 9
YWHAH 0.025 0.005 -10000 0 -10000 0 0
AKT1S1 0.006 0.052 -10000 0 -0.29 10 10
CASP9 0.006 0.055 -10000 0 -0.29 11 11
YWHAB 0.024 0.008 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.028 0.068 0.24 1 -0.28 12 13
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.046 0.019 -10000 0 -10000 0 0
YWHAE 0.024 0.008 -10000 0 -10000 0 0
SRC 0.025 0.007 -10000 0 -10000 0 0
AKT2/p21CIP1 0.01 0.056 0.24 3 -0.28 7 10
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.012 0.028 -10000 0 -0.27 2 2
CHUK 0.008 0.044 -10000 0 -0.28 7 7
BAD/BCL-XL 0.025 0.061 0.25 1 -0.28 10 11
mTORC2 0.026 0.014 -10000 0 -10000 0 0
AKT2 0.01 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.044 0.082 0.25 9 -0.34 4 13
PDPK1 0.025 0.006 -10000 0 -10000 0 0
MDM2 0.018 0.071 0.26 2 -0.29 10 12
MAPKKK cascade -0.029 0.06 0.28 8 -10000 0 8
MDM2/Cbp/p300 0.052 0.081 0.3 1 -0.29 7 8
TSC1/TSC2 0.004 0.051 0.23 1 -0.28 9 10
proteasomal ubiquitin-dependent protein catabolic process 0.049 0.078 0.29 1 -0.28 7 8
glucose import -0.092 0.079 0.2 1 -0.16 227 228
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.011 0.04 0.19 3 -0.19 3 6
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.093 0.079 0.2 1 -0.16 227 228
GSK3A 0.009 0.057 -10000 0 -0.29 10 10
FOXO1 0.005 0.053 -10000 0 -0.29 10 10
GSK3B 0.009 0.061 -10000 0 -0.29 11 11
SFN 0.047 0.087 0.33 32 -0.32 3 35
G1/S transition of mitotic cell cycle 0.014 0.071 0.24 4 -0.28 11 15
p27Kip1/14-3-3 family 0.028 0.047 0.28 1 -0.34 1 2
PRKACA 0.026 0.003 -10000 0 -10000 0 0
KPNA1 0.025 0.005 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
YWHAG 0.026 0.003 -10000 0 -10000 0 0
RHEB 0.026 0.003 -10000 0 -10000 0 0
CREBBP 0.025 0.007 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.008 0.093 -10000 0 -0.33 29 29
KLHL20 0.001 0.087 0.27 9 -0.2 29 38
CYFIP2 0.017 0.054 -10000 0 -0.32 10 10
Rac1/GDP 0.009 0.088 0.26 9 -0.23 12 21
ENAH -0.008 0.094 -10000 0 -0.33 30 30
AP1M1 0.026 0.003 -10000 0 -10000 0 0
RAP1B 0.024 0.007 -10000 0 -10000 0 0
RAP1A 0.026 0.003 -10000 0 -10000 0 0
CTNNB1 0.025 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.013 0.047 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.023 0.043 -10000 0 -0.14 36 36
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.046 0.055 -10000 0 -0.18 17 17
RAPGEF1 -0.003 0.093 0.26 4 -0.34 17 21
CTNND1 0.026 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.002 0.097 -10000 0 -0.33 30 30
CRK -0.004 0.091 -10000 0 -0.33 25 25
E-cadherin/gamma catenin/alpha catenin 0.038 0.049 -10000 0 -0.2 14 14
alphaE/beta7 Integrin 0.032 0.031 -10000 0 -0.22 5 5
IQGAP1 0.026 0.004 -10000 0 -10000 0 0
NCKAP1 0.026 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.044 0.018 -10000 0 -10000 0 0
DLG1 -0.007 0.09 -10000 0 -0.33 27 27
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.021 0.024 -10000 0 -0.13 12 12
MLLT4 0.025 0.006 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.045 0.026 0.22 1 -0.17 3 4
PI3K -0.026 0.031 -10000 0 -0.16 12 12
ARF6 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.026 0.052 -10000 0 -0.24 14 14
TIAM1 0.023 0.03 -10000 0 -0.32 3 3
E-cadherin(dimer)/Ca2+ 0.047 0.044 -10000 0 -0.16 13 13
AKT1 -0.006 0.042 0.16 5 -10000 0 5
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
CDH1 0.014 0.061 -10000 0 -0.32 13 13
RhoA/GDP 0.009 0.089 0.27 9 -0.23 14 23
actin cytoskeleton organization 0.003 0.068 0.21 11 -0.15 27 38
CDC42/GDP 0.009 0.09 0.26 10 -0.23 14 24
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.006 0.042 -10000 0 -0.19 16 16
ITGB7 0.022 0.038 -10000 0 -0.32 5 5
RAC1 0.025 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.051 0.048 -10000 0 -0.18 13 13
E-cadherin/Ca2+/beta catenin/alpha catenin 0.035 0.039 -10000 0 -0.16 13 13
mol:GDP -0.004 0.095 0.27 10 -0.26 14 24
CDC42/GTP/IQGAP1 0.034 0.007 -10000 0 -10000 0 0
JUP 0.024 0.025 -10000 0 -0.32 2 2
p120 catenin/RhoA/GDP 0.015 0.088 0.27 7 -0.24 13 20
RAC1/GTP/IQGAP1 0.033 0.01 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.038 0.008 -10000 0 -10000 0 0
RHOA 0.025 0.006 -10000 0 -10000 0 0
CDC42 0.026 0.003 -10000 0 -10000 0 0
CTNNA1 0.025 0.005 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.011 0.066 0.24 16 -0.15 5 21
NME1 0.026 0.016 0.33 1 -10000 0 1
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.005 0.089 -10000 0 -0.34 25 25
regulation of cell-cell adhesion -0.019 0.031 -10000 0 -10000 0 0
WASF2 -0.005 0.034 0.09 6 -0.084 6 12
Rap1/GTP -0.008 0.057 0.21 5 -10000 0 5
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.051 0.061 -10000 0 -0.18 18 18
CCND1 0.012 0.076 0.28 16 -0.19 5 21
VAV2 -0.04 0.2 -10000 0 -0.56 38 38
RAP1/GDP 0.015 0.073 0.27 6 -10000 0 6
adherens junction assembly -0.005 0.087 -10000 0 -0.33 25 25
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.025 0.006 -10000 0 -10000 0 0
PIP5K1C 0.025 0.005 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.036 0.056 -10000 0 -0.18 17 17
E-cadherin/beta catenin 0.001 0.049 -10000 0 -0.28 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.009 0.093 -10000 0 -0.33 29 29
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.017 0.12 0.36 13 -0.31 34 47
E-cadherin/beta catenin/alpha catenin 0.039 0.046 -10000 0 -0.19 13 13
ITGAE 0.024 0.008 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.002 0.099 -10000 0 -0.34 30 30
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.005 0.049 0.17 1 -0.24 14 15
CRKL 0.027 0.022 0.33 2 -10000 0 2
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
DOCK1 0.023 0.025 -10000 0 -0.32 2 2
ITGA4 0.016 0.061 0.33 1 -0.32 12 13
alpha4/beta7 Integrin/MAdCAM1 0.055 0.059 0.24 12 -0.17 15 27
EPO 0.039 0.082 0.33 29 -10000 0 29
alpha4/beta7 Integrin 0.027 0.054 0.24 1 -0.22 17 18
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.024 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.029 0.047 0.24 1 -0.22 12 13
EPO/EPOR (dimer) 0.053 0.058 0.24 35 -10000 0 35
lamellipodium assembly 0.006 0.079 0.24 1 -0.41 9 10
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
PI3K 0.034 0.018 -10000 0 -0.22 1 1
ARF6 0.025 0.005 -10000 0 -10000 0 0
JAK2 0.017 0.05 0.21 1 -0.22 10 11
PXN 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
MADCAM1 0.03 0.058 0.33 14 -10000 0 14
cell adhesion 0.053 0.058 0.23 12 -0.17 15 27
CRKL/CBL 0.036 0.018 0.24 2 -10000 0 2
ITGB1 0.025 0.006 -10000 0 -10000 0 0
SRC -0.021 0.059 0.18 15 -0.21 20 35
ITGB7 0.022 0.038 -10000 0 -0.32 5 5
RAC1 0.025 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.034 0.071 0.23 3 -0.23 23 26
p130Cas/Crk/Dock1 -0.015 0.073 0.34 1 -0.29 4 5
VCAM1 0.013 0.073 0.33 2 -0.32 17 19
RHOA 0.025 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.051 0.047 0.24 1 -0.18 12 13
BCAR1 -0.022 0.059 0.19 15 -0.2 19 34
EPOR 0.031 0.039 0.33 7 -10000 0 7
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.025 0.006 -10000 0 -10000 0 0
GIT1 0.025 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.006 0.082 0.24 1 -0.42 9 10
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.016 0.007 -10000 0 -10000 0 0
SNTA1 0.023 0.008 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.003 0.045 0.13 39 -10000 0 39
MAPK12 -0.009 0.027 0.13 6 -0.17 5 11
CCND1 0.006 0.062 0.18 1 -0.37 8 9
p38 gamma/SNTA1 -0.004 0.048 0.19 17 -0.19 1 18
MAP2K3 0.024 0.008 -10000 0 -10000 0 0
PKN1 0.025 0.018 -10000 0 -0.32 1 1
G2/M transition checkpoint -0.001 0.049 0.2 18 -0.17 5 23
MAP2K6 -0.007 0.022 0.11 1 -0.18 6 7
MAPT -0.015 0.083 0.23 8 -0.25 33 41
MAPK13 -0.015 0.005 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.005 0.012 -10000 0 -0.24 1 1
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.022 0.01 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.027 0.072 -10000 0 -0.3 4 4
NEF -0.004 0.038 -10000 0 -0.16 20 20
NFKBIA 0.021 0.027 -10000 0 -0.13 2 2
BIRC3 -0.024 0.088 0.38 3 -0.38 17 20
CYCS 0.006 0.08 0.22 6 -0.24 15 21
RIPK1 0.025 0.006 -10000 0 -10000 0 0
CD247 0.015 0.057 0.33 1 -0.2 21 22
MAP2K7 0.017 0.13 -10000 0 -0.59 11 11
protein ubiquitination 0.007 0.075 0.22 1 -0.31 3 4
CRADD 0.026 0.004 -10000 0 -10000 0 0
DAXX 0.026 0.003 -10000 0 -10000 0 0
FAS 0.021 0.039 -10000 0 -0.32 5 5
BID 0.011 0.077 0.18 25 -0.25 15 40
NF-kappa-B/RelA/I kappa B alpha 0.044 0.063 0.36 3 -0.22 17 20
TRADD 0.025 0.005 -10000 0 -10000 0 0
MAP3K5 0.024 0.018 -10000 0 -0.32 1 1
CFLAR 0.025 0.005 -10000 0 -10000 0 0
FADD 0.024 0.008 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.044 0.064 0.36 3 -0.22 17 20
MAPK8 0.014 0.12 0.32 1 -0.55 11 12
APAF1 0.026 0.003 -10000 0 -10000 0 0
TRAF1 0.023 0.03 0.33 1 -0.32 2 3
TRAF2 0.023 0.008 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.017 0.082 0.19 24 -0.26 15 39
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.011 0.087 0.23 4 -0.35 7 11
CHUK 0.006 0.078 -10000 0 -0.34 3 3
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.061 0.045 -10000 0 -0.2 4 4
TCRz/NEF 0.011 0.063 0.22 7 -0.23 21 28
TNF 0.041 0.067 0.33 21 -10000 0 21
FASLG -0.002 0.1 0.39 7 -0.43 15 22
NFKB1 0.021 0.027 -10000 0 -0.13 2 2
TNFR1A/BAG4/TNF-alpha 0.051 0.046 0.23 19 -10000 0 19
CASP6 0.018 0.14 -10000 0 -0.51 17 17
CASP7 -0.006 0.13 0.34 4 -0.42 24 28
RELA 0.022 0.025 -10000 0 -10000 0 0
CASP2 0.026 0.003 -10000 0 -10000 0 0
CASP3 -0.005 0.13 0.34 4 -0.41 25 29
TNFRSF1A 0.025 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.032 0.015 -10000 0 -10000 0 0
CASP8 0.025 0.006 -10000 0 -10000 0 0
CASP9 0.026 0.003 -10000 0 -10000 0 0
MAP3K14 0.009 0.085 -10000 0 -0.33 7 7
APAF-1/Caspase 9 0.005 0.085 -10000 0 -0.3 15 15
BCL2 0.006 0.12 0.3 1 -0.52 11 12
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.025 0.006 -10000 0 -10000 0 0
ITGB7 0.022 0.038 -10000 0 -0.32 5 5
ITGA4 0.016 0.061 0.33 1 -0.32 12 13
alpha4/beta7 Integrin 0.027 0.054 0.24 1 -0.22 17 18
alpha4/beta1 Integrin 0.029 0.047 0.24 1 -0.22 12 13
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.026 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.02 0.044 -10000 0 -0.19 24 24
FRAP1 0.012 0.047 -10000 0 -0.38 3 3
AKT1 -0.007 0.055 0.16 18 -0.21 6 24
INSR 0.026 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.027 0.008 -10000 0 -10000 0 0
mol:GTP 0.017 0.058 0.23 4 -0.19 5 9
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.008 0.021 -10000 0 -10000 0 0
TSC2 0.025 0.005 -10000 0 -10000 0 0
RHEB/GDP -0.022 0.033 -10000 0 -0.17 5 5
TSC1 0.023 0.008 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.002 0.069 -10000 0 -0.21 37 37
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.02 0.029 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.025 0.005 -10000 0 -10000 0 0
RPS6KB1 0.016 0.049 0.22 3 -10000 0 3
MAP3K5 0 0.044 0.19 7 -0.19 14 21
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
apoptosis 0 0.044 0.19 7 -0.19 14 21
mol:LY294002 0 0 -10000 0 -0.001 36 36
EIF4B 0.013 0.049 0.24 5 -10000 0 5
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.029 0.044 0.23 1 -10000 0 1
eIF4E/eIF4G1/eIF4A1 0.014 0.029 -10000 0 -0.24 3 3
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.017 0.064 -10000 0 -0.19 32 32
mTOR/RHEB/GTP/Raptor/GBL -0.004 0.044 0.17 9 -10000 0 9
FKBP1A 0.025 0.006 -10000 0 -10000 0 0
RHEB/GTP 0.024 0.053 0.22 3 -0.17 5 8
mol:Amino Acids 0 0 -10000 0 -0.001 36 36
FKBP12/Rapamycin 0.019 0.005 -10000 0 -10000 0 0
PDPK1 -0.016 0.054 0.16 18 -0.18 17 35
EIF4E 0.026 0.003 -10000 0 -10000 0 0
ASK1/PP5C 0.019 0.11 -10000 0 -0.54 15 15
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.009 0.033 -10000 0 -0.23 5 5
TSC1/TSC2 0.02 0.063 0.25 4 -0.2 5 9
tumor necrosis factor receptor activity 0 0 0.001 36 -10000 0 36
RPS6 0.022 0.009 -10000 0 -10000 0 0
PPP5C 0.026 0.004 -10000 0 -10000 0 0
EIF4G1 0.025 0.006 -10000 0 -10000 0 0
IRS1 -0.014 0.067 -10000 0 -0.22 37 37
INS -0.016 0.005 -10000 0 -10000 0 0
PTEN 0.024 0.007 -10000 0 -10000 0 0
PDK2 -0.017 0.053 0.15 16 -0.18 18 34
EIF4EBP1 -0.035 0.26 -10000 0 -1 25 25
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
PPP2R5D 0.012 0.049 -10000 0 -0.35 3 3
peptide biosynthetic process -0.016 0.015 0.18 2 -10000 0 2
RHEB 0.026 0.003 -10000 0 -10000 0 0
EIF4A1 0.024 0.008 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 12 -10000 0 12
EEF2 -0.016 0.015 0.18 2 -10000 0 2
eIF4E/4E-BP1 -0.022 0.24 -10000 0 -0.95 25 25
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.2 0.16 -10000 0 -0.32 259 259
CLTC 0.01 0.07 -10000 0 -0.38 10 10
calcium ion-dependent exocytosis 0.007 0.029 0.2 2 -0.16 6 8
Dynamin 2/GTP 0.021 0.009 0.14 1 -10000 0 1
EXOC4 0.025 0.005 -10000 0 -10000 0 0
CD59 0.006 0.047 -10000 0 -0.32 7 7
CPE -0.017 0.034 0.18 1 -0.19 14 15
CTNNB1 0.025 0.005 -10000 0 -10000 0 0
membrane fusion 0.008 0.016 -10000 0 -10000 0 0
CTNND1 -0.012 0.038 0.18 15 -10000 0 15
DNM2 0.026 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.006 0.051 0.18 2 -0.24 10 12
TSHR -0.009 0.026 0.18 7 -10000 0 7
INS -0.024 0.13 -10000 0 -0.48 30 30
BIN1 -0.016 0.11 -10000 0 -0.32 49 49
mol:Choline 0.008 0.016 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP -0.011 0.01 0.18 1 -10000 0 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.025 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.021 0.009 0.14 1 -10000 0 1
JUP 0.005 0.049 -10000 0 -0.31 8 8
ASAP2/amphiphysin II 0.021 0.07 -10000 0 -0.17 46 46
ARF6/GTP 0.019 0.003 -10000 0 -10000 0 0
CDH1 0.001 0.057 -10000 0 -0.32 8 8
clathrin-independent pinocytosis 0.019 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.027 0.035 0.33 4 -0.32 1 5
positive regulation of endocytosis 0.019 0.003 -10000 0 -10000 0 0
EXOC2 0.025 0.007 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.021 0.046 -10000 0 -0.23 3 3
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.025 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.03 0.069 0.32 9 -0.25 1 10
positive regulation of phagocytosis -0.012 0.003 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.035 0.023 0.21 4 -0.19 1 5
ACAP1 0.01 0.028 -10000 0 -0.17 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.04 0.084 -10000 0 -0.36 9 9
clathrin heavy chain/ACAP1 0.011 0.063 0.24 2 -0.34 8 10
JIP4/KLC1 0.046 0.015 -10000 0 -10000 0 0
EXOC1 0.026 0.003 -10000 0 -10000 0 0
exocyst 0.021 0.047 -10000 0 -0.23 3 3
RALA/GTP 0.019 0.004 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.033 0.009 -10000 0 -10000 0 0
receptor recycling 0.019 0.003 -10000 0 -10000 0 0
CTNNA1 -0.012 0.038 0.18 15 -10000 0 15
NME1 -0.011 0.01 0.18 1 -10000 0 1
clathrin coat assembly 0.013 0.073 0.26 1 -0.38 10 11
IL2RA 0.012 0.061 -10000 0 -0.31 7 7
VAMP3 -0.012 0.003 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.075 0.084 -10000 0 -0.32 12 12
EXOC6 0.025 0.005 -10000 0 -10000 0 0
PLD1 0.008 0.009 -10000 0 -10000 0 0
PLD2 0.009 0.01 -10000 0 -10000 0 0
EXOC5 0.026 0.004 -10000 0 -10000 0 0
PIP5K1C 0.005 0.034 0.19 1 -0.2 8 9
SDC1 0.005 0.05 -10000 0 -0.31 7 7
ARF6/GDP 0.021 0.009 0.15 1 -10000 0 1
EXOC7 0.025 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.032 0.071 0.26 1 -0.33 9 10
mol:Phosphatidic acid 0.008 0.016 -10000 0 -10000 0 0
endocytosis -0.02 0.069 0.17 46 -10000 0 46
SCAMP2 0.026 0.004 -10000 0 -10000 0 0
ADRB2 -0.008 0.078 -10000 0 -0.38 10 10
EXOC3 0.022 0.009 -10000 0 -10000 0 0
ASAP2 0.025 0.005 -10000 0 -10000 0 0
Dynamin 2/GDP 0.025 0.011 0.17 1 -10000 0 1
KLC1 0.025 0.005 -10000 0 -10000 0 0
AVPR2 -0.002 0.087 0.24 1 -0.41 9 10
RALA 0.025 0.005 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.023 0.072 0.28 3 -0.31 9 12
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.024 0.008 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.028 0.095 0.27 6 -0.36 3 9
Syndecan-3/Neurocan 0.029 0.05 0.22 10 -0.38 3 13
POMC 0.028 0.061 0.33 10 -0.32 5 15
EGFR 0.017 0.051 -10000 0 -0.32 9 9
Syndecan-3/EGFR 0.023 0.04 -10000 0 -0.33 3 3
AGRP 0.007 0.031 0.33 2 -10000 0 2
NCSTN 0.022 0.009 -10000 0 -10000 0 0
PSENEN 0.025 0.006 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.026 0.004 -10000 0 -10000 0 0
APH1A 0.023 0.008 -10000 0 -10000 0 0
NCAN 0.014 0.054 0.33 10 -10000 0 10
long-term memory 0.039 0.051 -10000 0 -0.41 3 3
Syndecan-3/IL8 0.008 0.069 0.21 1 -0.47 3 4
PSEN1 0.025 0.005 -10000 0 -10000 0 0
Src/Cortactin 0.033 0.014 -10000 0 -10000 0 0
FYN 0.022 0.03 -10000 0 -0.32 3 3
limb bud formation 0.006 0.034 -10000 0 -0.46 2 2
MC4R 0.002 0.041 0.33 5 -10000 0 5
SRC 0.025 0.007 -10000 0 -10000 0 0
PTN -0.028 0.16 0.33 20 -0.32 80 100
FGFR/FGF/Syndecan-3 0.006 0.034 -10000 0 -0.47 2 2
neuron projection morphogenesis 0.009 0.096 0.3 8 -0.36 3 11
Syndecan-3/AgRP 0.024 0.042 0.21 2 -0.38 3 5
Syndecan-3/AgRP/MC4R 0.042 0.053 0.31 2 -0.37 3 5
Fyn/Cortactin 0.032 0.023 -10000 0 -0.22 2 2
SDC3 0.006 0.034 -10000 0 -0.47 2 2
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.008 0.068 0.21 1 -0.46 3 4
IL8 -0.022 0.12 0.33 1 -0.32 56 57
Syndecan-3/Fyn/Cortactin 0.04 0.052 -10000 0 -0.42 3 3
Syndecan-3/CASK 0.005 0.035 -10000 0 -0.38 3 3
alpha-MSH/MC4R 0.034 0.048 0.24 13 -0.23 5 18
Gamma Secretase 0.059 0.035 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.056 0.094 0.33 43 -10000 0 43
mol:Halofuginone 0.002 0 -10000 0 -10000 0 0
ITGA1 0.025 0.006 -10000 0 -10000 0 0
CDKN1A -0.006 0.059 -10000 0 -0.42 6 6
PRL-3/alpha Tubulin 0.034 0.013 -10000 0 -10000 0 0
mol:Ca2+ -0.043 0.067 0.18 1 -0.23 44 45
AGT -0.013 0.12 0.33 3 -0.32 48 51
CCNA2 -0.013 0.085 0.3 9 -10000 0 9
TUBA1B 0.026 0.003 -10000 0 -10000 0 0
EGR1 -0.041 0.094 -10000 0 -0.21 92 92
CDK2/Cyclin E1 0.039 0.088 0.31 1 -0.36 6 7
MAPK3 -0.014 0.006 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.038 0.006 -10000 0 -10000 0 0
MAPK1 -0.014 0.006 -10000 0 -10000 0 0
PTP4A1 -0.039 0.061 -10000 0 -10000 0 0
PTP4A3 0.023 0.008 -10000 0 -10000 0 0
PTP4A2 0.026 0.001 -10000 0 -10000 0 0
ITGB1 -0.014 0.006 -10000 0 -10000 0 0
SRC 0.025 0.007 -10000 0 -10000 0 0
RAC1 -0.001 0.035 -10000 0 -0.45 1 1
Rab GGTase beta/Rab GGTase alpha 0.037 0.009 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.032 0.074 -10000 0 -10000 0 0
RABGGTA 0.025 0.005 -10000 0 -10000 0 0
BCAR1 -0.02 0.009 -10000 0 -10000 0 0
RHOC 0 0.027 -10000 0 -10000 0 0
RHOA -0.009 0.068 -10000 0 -0.38 11 11
cell motility 0.006 0.067 0.28 2 -0.28 5 7
PRL-1/alpha Tubulin -0.033 0.074 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.033 0.014 -10000 0 -10000 0 0
ROCK1 0.008 0.066 0.28 2 -0.28 5 7
RABGGTB 0.026 0.004 -10000 0 -10000 0 0
CDK2 0.025 0.005 -10000 0 -10000 0 0
mitosis -0.039 0.061 -10000 0 -10000 0 0
ATF5 0.029 0.03 0.33 4 -10000 0 4
E-cadherin 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
E-cadherin/beta catenin-gamma catenin 0.038 0.05 -9999 0 -0.2 14 14
E-cadherin/beta catenin 0.027 0.047 -9999 0 -0.22 13 13
CTNNB1 0.025 0.005 -9999 0 -10000 0 0
JUP 0.024 0.025 -9999 0 -0.32 2 2
CDH1 0.014 0.061 -9999 0 -0.32 13 13
PLK2 and PLK4 events

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
PLK2 0.026 0.016 0.33 1 -9999 0 1
PLK4 0.033 0.047 0.33 10 -9999 0 10
regulation of centriole replication -0.01 0.033 0.19 11 -9999 0 11
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.006 0.054 0.23 4 -0.23 2 6
adherens junction organization 0.006 0.068 0.22 3 -0.22 15 18
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.067 0.24 7 -0.25 2 9
FMN1 0.009 0.062 0.17 2 -0.22 16 18
mol:IP3 0.002 0.04 -10000 0 -0.27 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.01 0.064 -10000 0 -0.22 18 18
CTNNB1 0.026 0.006 -10000 0 -10000 0 0
AKT1 0.01 0.052 0.17 4 -0.32 1 5
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.012 0.085 0.25 1 -0.3 17 18
CTNND1 0.027 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.003 0.056 -10000 0 -0.21 16 16
VASP 0.004 0.06 -10000 0 -0.22 17 17
ZYX 0.004 0.062 -10000 0 -0.22 18 18
JUB 0.007 0.061 -10000 0 -0.21 18 18
EGFR(dimer) 0.018 0.071 0.21 1 -0.22 17 18
E-cadherin/beta catenin-gamma catenin 0.038 0.047 -10000 0 -0.19 14 14
mol:PI-3-4-5-P3 0.031 0.063 0.21 4 -0.32 1 5
PIK3CA 0.025 0.008 -10000 0 -10000 0 0
PI3K 0.032 0.064 0.21 4 -0.33 1 5
FYN -0.006 0.067 0.25 5 -0.24 12 17
mol:Ca2+ 0.002 0.039 -10000 0 -0.26 1 1
JUP 0.024 0.025 -10000 0 -0.32 2 2
PIK3R1 0.025 0.019 -10000 0 -0.32 1 1
mol:DAG 0.002 0.04 -10000 0 -0.27 1 1
CDH1 0.014 0.061 -10000 0 -0.32 13 13
RhoA/GDP 0.021 0.067 0.24 6 -0.25 2 8
establishment of polarity of embryonic epithelium 0.004 0.06 -10000 0 -0.21 17 17
SRC 0.025 0.007 -10000 0 -10000 0 0
RAC1 0.025 0.006 -10000 0 -10000 0 0
RHOA 0.025 0.006 -10000 0 -10000 0 0
EGFR 0.017 0.051 -10000 0 -0.32 9 9
CASR -0.005 0.051 0.23 5 -0.26 1 6
RhoA/GTP 0.018 0.049 0.21 1 -0.25 1 2
AKT2 0.009 0.052 0.17 3 -0.32 1 4
actin cable formation 0.006 0.062 0.2 1 -0.33 2 3
apoptosis -0.016 0.063 0.2 5 -0.24 7 12
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
mol:GDP -0.007 0.055 0.18 8 -0.26 2 10
PIP5K1A 0.003 0.057 -10000 0 -0.22 16 16
PLCG1 0.002 0.04 -10000 0 -0.28 1 1
Rac1/GTP 0.025 0.071 -10000 0 -0.21 16 16
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.027 0.022 0.33 2 -10000 0 2
Rac1/GDP 0.024 0.014 -10000 0 -10000 0 0
DOCK1 0.023 0.025 -10000 0 -0.32 2 2
ITGA4 0.016 0.061 0.33 1 -0.32 12 13
RAC1 0.025 0.006 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.027 0.054 0.24 1 -0.22 17 18
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.024 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.042 0.045 0.23 1 -0.19 12 13
alpha4/beta7 Integrin/Paxillin 0.03 0.045 0.22 1 -0.18 17 18
lamellipodium assembly 0.001 0.079 -10000 0 -0.37 8 8
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
PI3K 0.034 0.018 -10000 0 -0.22 1 1
ARF6 0.025 0.005 -10000 0 -10000 0 0
TLN1 0.023 0.008 -10000 0 -10000 0 0
PXN -0.016 0.003 -10000 0 -10000 0 0
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
ARF6/GTP 0.039 0.042 0.19 1 -0.16 12 13
cell adhesion 0.038 0.041 0.22 1 -0.16 11 12
CRKL/CBL 0.036 0.018 0.24 2 -10000 0 2
alpha4/beta1 Integrin/Paxillin 0.031 0.039 0.22 1 -0.18 12 13
ITGB1 0.025 0.006 -10000 0 -10000 0 0
ITGB7 0.022 0.038 -10000 0 -0.32 5 5
ARF6/GDP 0.025 0.014 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.036 0.065 0.22 3 -0.21 23 26
p130Cas/Crk/Dock1 0.043 0.026 -10000 0 -0.19 2 2
VCAM1 0.013 0.073 0.33 2 -0.32 17 19
alpha4/beta1 Integrin/Paxillin/Talin 0.04 0.041 0.22 1 -0.16 11 12
alpha4/beta1 Integrin/Paxillin/GIT1 0.041 0.043 0.22 1 -0.17 12 13
BCAR1 0.025 0.006 -10000 0 -10000 0 0
mol:GDP -0.04 0.042 0.17 12 -0.22 1 13
CBL 0.025 0.006 -10000 0 -10000 0 0
PRKACA 0.026 0.003 -10000 0 -10000 0 0
GIT1 0.025 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.04 0.041 0.22 1 -0.16 11 12
Rac1/GTP 0 0.085 -10000 0 -0.41 8 8
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 -0.018 0.054 0.29 3 -10000 0 3
DAPP1 -0.001 0.1 0.26 5 -0.3 16 21
Src family/SYK family/BLNK-LAT/BTK-ITK -0.029 0.15 0.32 1 -0.42 31 32
mol:DAG -0.008 0.08 0.22 10 -0.2 17 27
HRAS 0.025 0.009 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
ARF5/GDP 0.026 0.064 0.21 1 -0.28 6 7
PLCG2 0.026 0.036 0.33 3 -0.32 2 5
PLCG1 0.024 0.007 -10000 0 -10000 0 0
ARF5 0.026 0.003 -10000 0 -10000 0 0
mol:GTP -0.017 0.043 0.22 4 -10000 0 4
ARF1/GTP -0.007 0.045 0.25 4 -10000 0 4
RHOA 0.025 0.006 -10000 0 -10000 0 0
YES1 0.024 0.008 -10000 0 -10000 0 0
RAP1A/GTP -0.018 0.039 0.15 19 -10000 0 19
ADAP1 -0.02 0.042 0.28 2 -10000 0 2
ARAP3 -0.017 0.043 0.22 4 -10000 0 4
INPPL1 0.025 0.006 -10000 0 -10000 0 0
PREX1 0.024 0.007 -10000 0 -10000 0 0
ARHGEF6 0.023 0.03 -10000 0 -0.32 3 3
ARHGEF7 0.025 0.006 -10000 0 -10000 0 0
ARF1 0.026 0.003 -10000 0 -10000 0 0
NRAS 0.027 0.005 -10000 0 -10000 0 0
FYN 0.022 0.03 -10000 0 -0.32 3 3
ARF6 0.025 0.005 -10000 0 -10000 0 0
FGR 0.024 0.024 -10000 0 -0.32 2 2
mol:Ca2+ -0.004 0.053 0.21 8 -0.12 6 14
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.023 0.03 -10000 0 -0.32 3 3
ZAP70 0.014 0.065 0.33 1 -0.32 14 15
mol:IP3 -0.009 0.068 0.24 8 -0.17 11 19
LYN 0.024 0.007 -10000 0 -10000 0 0
ARF1/GDP 0.026 0.065 0.21 1 -0.28 6 7
RhoA/GDP 0.028 0.049 0.22 2 -10000 0 2
PDK1/Src/Hsp90 0.046 0.019 -10000 0 -10000 0 0
BLNK 0.014 0.061 -10000 0 -0.32 13 13
actin cytoskeleton reorganization 0.01 0.07 0.25 4 -0.26 4 8
SRC 0.025 0.007 -10000 0 -10000 0 0
PLEKHA2 -0.016 0.017 -10000 0 -0.19 3 3
RAC1 0.025 0.006 -10000 0 -10000 0 0
PTEN 0.024 0.014 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.021 0.048 0.28 2 -10000 0 2
RhoA/GTP -0.019 0.045 0.29 2 -10000 0 2
Src family/SYK family/BLNK-LAT -0.015 0.1 -10000 0 -0.28 29 29
BLK 0.003 0.11 0.33 15 -0.32 30 45
PDPK1 0.025 0.006 -10000 0 -10000 0 0
CYTH1 -0.021 0.04 0.28 2 -10000 0 2
HCK 0.018 0.064 0.33 5 -0.32 10 15
CYTH3 -0.02 0.041 0.28 2 -10000 0 2
CYTH2 -0.02 0.042 0.28 2 -10000 0 2
KRAS 0.025 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.007 0.085 -10000 0 -0.37 17 17
SGK1 -0.01 0.1 -10000 0 -0.37 24 24
INPP5D 0.019 0.042 -10000 0 -0.32 6 6
mol:GDP 0.013 0.063 0.21 1 -0.29 6 7
SOS1 0.026 0.004 -10000 0 -10000 0 0
SYK 0.02 0.035 -10000 0 -0.32 4 4
ARF6/GDP -0.004 0.053 0.24 4 -10000 0 4
mol:PI-3-4-5-P3 -0.018 0.041 0.28 2 -10000 0 2
ARAP3/RAP1A/GTP -0.018 0.04 0.16 19 -10000 0 19
VAV1 0.013 0.071 0.33 2 -0.32 16 18
mol:PI-3-4-P2 -0.016 0.019 -10000 0 -0.22 3 3
RAS family/GTP/PI3K Class I 0.036 0.04 -10000 0 -10000 0 0
PLEKHA1 -0.017 0.017 -10000 0 -0.19 3 3
Rac1/GDP 0.024 0.063 -10000 0 -0.28 6 6
LAT 0.026 0.016 0.33 1 -10000 0 1
Rac1/GTP 0.01 0.053 -10000 0 -0.28 5 5
ITK -0.032 0.057 0.28 2 -10000 0 2
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.017 0.097 0.23 7 -0.27 20 27
LCK 0.024 0.04 0.33 2 -0.32 4 6
BTK -0.027 0.052 0.28 2 -10000 0 2
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.1 0.12 -10000 0 -0.34 32 32
CaM/Ca2+ 0.019 0.003 -10000 0 -10000 0 0
AKT1 0.025 0.005 -10000 0 -10000 0 0
AKT2 0.025 0.005 -10000 0 -10000 0 0
STXBP4 0.025 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.11 0.12 -10000 0 -0.36 36 36
YWHAZ 0.02 0.011 -10000 0 -10000 0 0
CALM1 0.026 0.004 -10000 0 -10000 0 0
YWHAQ 0.025 0.006 -10000 0 -10000 0 0
TBC1D4 -0.015 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.025 0.005 -10000 0 -10000 0 0
YWHAB 0.024 0.008 -10000 0 -10000 0 0
SNARE/Synip 0.045 0.019 -10000 0 -10000 0 0
YWHAG 0.026 0.003 -10000 0 -10000 0 0
ASIP 0.012 0.034 0.33 3 -10000 0 3
PRKCI 0.025 0.006 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.019 0.003 -10000 0 -10000 0 0
RHOQ 0.025 0.005 -10000 0 -10000 0 0
GYS1 0.004 0.017 0.24 2 -10000 0 2
PRKCZ 0.023 0.03 -10000 0 -0.32 3 3
TRIP10 0.025 0.018 -10000 0 -0.32 1 1
TC10/GTP/CIP4/Exocyst 0.033 0.013 -10000 0 -0.17 1 1
AS160/14-3-3 0.024 0.06 0.2 9 -0.3 2 11
VAMP2 0.024 0.008 -10000 0 -10000 0 0
SLC2A4 -0.12 0.13 -10000 0 -0.4 36 36
STX4 0.026 0.004 -10000 0 -10000 0 0
GSK3B 0.015 0.005 -10000 0 -10000 0 0
SFN 0.047 0.087 0.33 32 -0.32 3 35
LNPEP 0.025 0.005 -10000 0 -10000 0 0
YWHAE 0.024 0.008 -10000 0 -10000 0 0
TRAIL signaling 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
TNFSF10 0.035 0.056 0.33 14 -10000 0 14
positive regulation of NF-kappaB transcription factor activity 0.032 0.043 0.24 9 -0.22 4 13
MAP2K4 0.012 0.05 0.22 3 -0.23 2 5
IKBKB 0.023 0.008 -10000 0 -10000 0 0
TNFRSF10B 0.022 0.01 -10000 0 -10000 0 0
TNFRSF10A 0.021 0.02 -10000 0 -0.32 1 1
SMPD1 0.009 0.013 -10000 0 -10000 0 0
IKBKG 0.026 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.017 0.039 -10000 0 -0.32 5 5
TRAIL/TRAILR2 0.035 0.035 0.24 9 -10000 0 9
TRAIL/TRAILR3 0.037 0.044 0.24 14 -0.22 1 15
TRAIL/TRAILR1 0.034 0.037 0.24 9 -0.22 1 10
TRAIL/TRAILR4 0.032 0.043 0.24 9 -0.22 4 13
TRAIL/TRAILR1/DAP3/GTP 0.041 0.035 0.22 9 -10000 0 9
IKK complex 0.008 0.049 -10000 0 -10000 0 0
RIPK1 0.025 0.006 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.018 0.005 -10000 0 -10000 0 0
MAPK3 -0.006 0.044 0.2 17 -10000 0 17
MAP3K1 0.02 0.038 0.26 1 -0.23 2 3
TRAILR4 (trimer) 0.017 0.039 -10000 0 -0.32 5 5
TRADD 0.025 0.005 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.021 0.02 -10000 0 -0.32 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.001 0.053 -10000 0 -0.18 1 1
CFLAR 0.025 0.005 -10000 0 -10000 0 0
MAPK1 -0.007 0.04 0.2 14 -10000 0 14
TRAIL/TRAILR1/FADD/TRADD/RIP 0.056 0.05 0.24 9 -0.17 1 10
mol:ceramide 0.009 0.013 -10000 0 -10000 0 0
FADD 0.024 0.008 -10000 0 -10000 0 0
MAPK8 0.005 0.057 0.23 3 -0.23 1 4
TRAF2 0.023 0.008 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.025 0.039 0.33 5 -0.32 1 6
CHUK 0.025 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.042 0.039 0.23 9 -0.19 1 10
DAP3 0.024 0.007 -10000 0 -10000 0 0
CASP10 0.015 0.063 0.23 13 -10000 0 13
JNK cascade 0.032 0.043 0.24 9 -0.22 4 13
TRAIL (trimer) 0.035 0.055 0.33 14 -10000 0 14
TNFRSF10C 0.025 0.039 0.33 5 -0.32 1 6
TRAIL/TRAILR1/DAP3/GTP/FADD 0.046 0.04 0.22 9 -10000 0 9
TRAIL/TRAILR2/FADD 0.042 0.037 0.23 9 -10000 0 9
cell death 0.009 0.013 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.001 0.053 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.022 0.01 -10000 0 -10000 0 0
CASP8 -0.017 0.12 -10000 0 -0.55 19 19
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.057 0.049 0.24 9 -10000 0 9
Retinoic acid receptors-mediated signaling

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
HDAC1 0.026 0.002 -10000 0 -10000 0 0
HDAC3 0.025 0.005 -10000 0 -10000 0 0
VDR 0.024 0.025 -10000 0 -0.32 2 2
Cbp/p300/PCAF 0.045 0.023 -10000 0 -0.19 1 1
EP300 0.025 0.005 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.004 0.059 -10000 0 -0.27 8 8
KAT2B 0.024 0.018 -10000 0 -0.32 1 1
MAPK14 0.026 0.003 -10000 0 -10000 0 0
AKT1 0.006 0.074 0.3 3 -0.26 4 7
RAR alpha/9cRA/Cyclin H 0.037 0.061 -10000 0 -0.28 2 2
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.001 0.067 -10000 0 -0.29 8 8
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.028 0.042 -10000 0 -0.33 3 3
NCOR2 0.026 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.017 -10000 0 -0.22 2 2
RXRs/RARs/NRIP1/9cRA 0.004 0.085 0.37 1 -0.43 2 3
NCOA2 0.006 0.075 -10000 0 -0.32 20 20
NCOA3 0.024 0.007 -10000 0 -10000 0 0
NCOA1 0.025 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.024 0.024 -10000 0 -0.32 2 2
RARG 0.026 0.004 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.035 0.006 -10000 0 -10000 0 0
MAPK3 0.025 0.006 -10000 0 -10000 0 0
MAPK1 0.025 0.005 -10000 0 -10000 0 0
MAPK8 0.023 0.03 -10000 0 -0.32 3 3
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.014 0.071 -10000 0 -0.34 3 3
RARA 0.013 0.029 0.16 2 -0.18 4 6
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.01 0.08 -10000 0 -0.34 11 11
PRKCA 0.023 0.034 -10000 0 -0.31 4 4
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.001 0.091 -10000 0 -0.44 2 2
RXRG -0.039 0.11 0.19 3 -0.24 85 88
RXRA 0.017 0.042 0.2 1 -0.19 5 6
RXRB 0.017 0.035 0.17 12 -0.23 3 15
VDR/Vit D3/DNA 0.018 0.017 -10000 0 -0.22 2 2
RBP1 0.008 0.085 0.33 3 -0.32 23 26
CRBP1/9-cic-RA 0.007 0.058 0.22 3 -0.22 23 26
RARB -0.003 0.096 -10000 0 -0.32 34 34
PRKCG 0.03 0.05 0.33 11 -10000 0 11
MNAT1 0.026 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.006 0.079 0.28 1 -0.48 2 3
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.006 0.081 -10000 0 -0.38 3 3
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.079 0.24 6 -0.29 8 14
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.002 0.092 -10000 0 -0.41 3 3
positive regulation of DNA binding 0.027 0.053 -10000 0 -0.27 2 2
NRIP1 -0.001 0.092 -10000 0 -10000 0 0
RXRs/RARs -0.005 0.095 -10000 0 -0.4 5 5
RXRs/RXRs/DNA/9cRA -0.005 0.059 -10000 0 -0.34 3 3
PRKACA 0.026 0.003 -10000 0 -10000 0 0
CDK7 0.025 0.006 -10000 0 -10000 0 0
TFIIH 0.049 0.015 -10000 0 -10000 0 0
RAR alpha/9cRA 0.054 0.043 -10000 0 -0.25 1 1
CCNH 0.025 0.005 -10000 0 -10000 0 0
CREBBP 0.025 0.007 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.046 0.019 -10000 0 -10000 0 0
TCGA08_rtk_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
PDGFRA -0.021 0.12 -10000 0 -0.32 55 55
HRAS 0.024 0.008 -10000 0 -10000 0 0
EGFR 0.017 0.051 -10000 0 -0.32 9 9
AKT 0.021 0.084 0.25 6 -0.24 11 17
FOXO3 0.025 0.007 -10000 0 -10000 0 0
AKT1 0.025 0.005 -10000 0 -10000 0 0
FOXO1 0.023 0.019 -10000 0 -0.32 1 1
AKT3 0.014 0.063 -10000 0 -0.32 14 14
FOXO4 0.027 0.015 0.33 1 -10000 0 1
MET 0.026 0.004 -10000 0 -10000 0 0
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
PIK3CB 0.025 0.006 -10000 0 -10000 0 0
NRAS 0.026 0.002 -10000 0 -10000 0 0
PIK3CG 0.017 0.063 0.33 2 -0.32 12 14
PIK3R3 0.026 0.003 -10000 0 -10000 0 0
PIK3R2 0.026 0.003 -10000 0 -10000 0 0
NF1 0.025 0.006 -10000 0 -10000 0 0
RAS 0.006 0.062 0.21 3 -0.21 9 12
ERBB2 0.025 0.006 -10000 0 -10000 0 0
proliferation/survival/translation -0.029 0.067 0.25 7 -0.23 1 8
PI3K 0.017 0.066 0.24 10 -0.16 7 17
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
KRAS 0.025 0.006 -10000 0 -10000 0 0
FOXO 0.049 0.056 0.24 6 -10000 0 6
AKT2 0.025 0.005 -10000 0 -10000 0 0
PTEN 0.025 0.007 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.013 0.027 -10000 0 -0.22 1 1
TRAF2/ASK1 0.03 0.017 -10000 0 -0.19 1 1
ATM 0.025 0.006 -10000 0 -10000 0 0
MAP2K3 -0.005 0.097 -10000 0 -0.34 19 19
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.002 0.073 0.21 1 -0.27 11 12
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.019 0.039 -10000 0 -0.32 5 5
TXN 0.006 0.011 0.16 2 -10000 0 2
CALM1 0.026 0.004 -10000 0 -10000 0 0
GADD45A 0.026 0.002 -10000 0 -10000 0 0
GADD45B 0.017 0.054 -10000 0 -0.32 10 10
MAP3K1 0.025 0.006 -10000 0 -10000 0 0
MAP3K6 0.026 0.002 -10000 0 -10000 0 0
MAP3K7 0.025 0.006 -10000 0 -10000 0 0
MAP3K4 0.025 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.036 0.016 -10000 0 -0.22 1 1
TAK1/TAB family -0.004 0.016 -10000 0 -10000 0 0
RAC1/OSM/MEKK3 0.046 0.017 0.22 1 -10000 0 1
TRAF2 0.023 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.013 0.085 -10000 0 -0.28 16 16
TRAF6 0.005 0.002 -10000 0 -10000 0 0
RAC1 0.025 0.006 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.054 0.091 0.33 40 -10000 0 40
CCM2 0.026 0.016 0.33 1 -10000 0 1
CaM/Ca2+/CAMKIIB 0.051 0.054 0.21 40 -10000 0 40
MAPK11 0.025 0.006 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.062 0.054 0.22 38 -0.17 1 39
OSM/MEKK3 0.037 0.014 0.24 1 -10000 0 1
TAOK1 0.009 0.013 -10000 0 -0.24 1 1
TAOK2 0.01 0.003 -10000 0 -10000 0 0
TAOK3 0.01 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.026 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.024 0.018 -10000 0 -0.32 1 1
MAP3K10 0.025 0.005 -10000 0 -10000 0 0
MAP3K3 0.025 0.006 -10000 0 -10000 0 0
TRX/ASK1 0.012 0.037 -10000 0 -0.1 36 36
GADD45/MTK1/MTK1 0.045 0.046 -10000 0 -0.17 13 13
Canonical NF-kappaB pathway

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
FBXW11 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.044 0.075 0.28 4 -0.27 6 10
ERC1 0.025 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.042 0.051 0.24 22 -0.22 1 23
NFKBIA -0.013 0.033 0.2 9 -10000 0 9
BIRC2 0.025 0.007 -10000 0 -10000 0 0
IKBKB 0.023 0.008 -10000 0 -10000 0 0
RIPK2 0.022 0.009 -10000 0 -10000 0 0
IKBKG 0.024 0.067 -10000 0 -0.34 6 6
IKK complex/A20 0.061 0.089 0.31 8 -0.33 7 15
NEMO/A20/RIP2 0.022 0.009 -10000 0 -10000 0 0
XPO1 0.025 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.042 0.075 0.26 2 -0.33 8 10
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.025 0.005 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.033 0.009 -10000 0 -10000 0 0
IKK complex/ELKS 0.042 0.069 -10000 0 -0.3 8 8
BCL10/MALT1/TRAF6 0.046 0.019 -10000 0 -10000 0 0
NOD2 0.042 0.076 0.33 24 -0.32 2 26
NFKB1 0.027 0.004 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
MALT1 0.025 0.006 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.036 0.011 -10000 0 -10000 0 0
ATM 0.025 0.006 -10000 0 -10000 0 0
TNF/TNFR1A 0.047 0.046 0.24 21 -10000 0 21
TRAF6 0.024 0.007 -10000 0 -10000 0 0
PRKCA 0.022 0.035 -10000 0 -0.32 4 4
CHUK 0.025 0.005 -10000 0 -10000 0 0
UBE2D3 0.026 0.003 -10000 0 -10000 0 0
TNF 0.041 0.067 0.33 21 -10000 0 21
NF kappa B1 p50/RelA 0.054 0.017 -10000 0 -10000 0 0
BCL10 0.026 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.013 0.033 0.2 9 -10000 0 9
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.025 0.005 -10000 0 -10000 0 0
IKK complex 0.049 0.076 -10000 0 -0.32 8 8
CYLD 0.025 0.005 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.053 0.078 -10000 0 -0.32 7 7
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.059 0.034 -10000 0 -0.18 6 6
HDAC3 0.025 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.015 0.006 -10000 0 -10000 0 0
GATA1/HDAC4 0.033 0.011 -10000 0 -10000 0 0
GATA1/HDAC5 0.035 0.008 -10000 0 -10000 0 0
GATA2/HDAC5 0.038 0.047 0.24 11 -0.22 6 17
HDAC5/BCL6/BCoR 0.049 0.016 -10000 0 -10000 0 0
HDAC9 0.003 0.083 -10000 0 -0.32 25 25
Glucocorticoid receptor/Hsp90/HDAC6 0.043 0.042 -10000 0 -0.19 11 11
HDAC4/ANKRA2 0.034 0.013 -10000 0 -10000 0 0
HDAC5/YWHAB 0.035 0.012 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.008 0.019 -10000 0 -0.37 1 1
GATA2 0.029 0.067 0.33 12 -0.32 6 18
HDAC4/RFXANK 0.036 0.015 0.24 1 -10000 0 1
BCOR 0.026 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.025 0.006 -10000 0 -10000 0 0
HDAC5 0.026 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.034 0.033 -10000 0 -0.22 6 6
Histones -0.002 0.061 -10000 0 -0.21 10 10
ADRBK1 0.026 0.004 -10000 0 -10000 0 0
HDAC4 0.024 0.007 -10000 0 -10000 0 0
XPO1 0.025 0.005 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.036 0.011 -10000 0 -10000 0 0
HDAC4/Ubc9 0.035 0.012 -10000 0 -10000 0 0
HDAC7 0.026 0.004 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.035 0.013 -10000 0 -10000 0 0
TUBA1B 0.026 0.003 -10000 0 -10000 0 0
HDAC6 0.026 0.003 -10000 0 -10000 0 0
HDAC5/RFXANK 0.038 0.013 0.24 1 -10000 0 1
CAMK4 0.018 0.051 0.33 1 -0.32 8 9
Tubulin/HDAC6 0.048 0.022 -10000 0 -0.19 2 2
SUMO1 0.025 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.024 0.008 -10000 0 -10000 0 0
GATA1 0.013 0.02 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.024 0.008 -10000 0 -10000 0 0
NR3C1 0.016 0.056 -10000 0 -0.32 11 11
SUMO1/HDAC4 0.027 0.045 -10000 0 -0.18 12 12
SRF 0.026 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.033 0.015 -10000 0 -10000 0 0
Tubulin 0.035 0.021 -10000 0 -0.22 2 2
HDAC4/14-3-3 E 0.033 0.014 -10000 0 -10000 0 0
GNB1 0.026 0.003 -10000 0 -10000 0 0
RANGAP1 0.025 0.005 -10000 0 -10000 0 0
BCL6/BCoR 0.036 0.01 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.047 0.018 -10000 0 -10000 0 0
HDAC4/SRF 0.041 0.038 -10000 0 -0.19 8 8
HDAC4/ER alpha -0.007 0.096 -10000 0 -0.22 66 66
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.002 0.061 -10000 0 -0.21 10 10
cell motility 0.047 0.022 -10000 0 -0.19 2 2
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.025 0.005 -10000 0 -10000 0 0
HDAC7/HDAC3 0.037 0.009 -10000 0 -10000 0 0
BCL6 0.025 0.006 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.024 0.007 -10000 0 -10000 0 0
Hsp90/HDAC6 0.037 0.008 -10000 0 -10000 0 0
ESR1 -0.031 0.13 -10000 0 -0.32 66 66
HDAC6/HDAC11 0.033 0.025 -10000 0 -0.22 3 3
Ran/GTP/Exportin 1 0.026 0.047 -10000 0 -0.19 11 11
NPC 0.015 0.002 -10000 0 -10000 0 0
MEF2C 0.016 0.056 -10000 0 -0.32 11 11
RAN 0.025 0.005 -10000 0 -10000 0 0
HDAC4/MEF2C 0.059 0.047 -10000 0 -0.17 10 10
GNG2 0.02 0.042 -10000 0 -0.32 6 6
NCOR2 0.026 0.004 -10000 0 -10000 0 0
TUBB2A 0.023 0.025 -10000 0 -0.32 2 2
HDAC11 0.021 0.031 -10000 0 -0.32 3 3
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
RANBP2 0.026 0.004 -10000 0 -10000 0 0
ANKRA2 0.025 0.006 -10000 0 -10000 0 0
RFXANK 0.027 0.015 0.33 1 -10000 0 1
nuclear import -0.024 0.014 -10000 0 -10000 0 0
Arf6 downstream pathway

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
PLAUR 0.014 0.019 -10000 0 -10000 0 0
regulation of axonogenesis -0.003 0.026 0.25 4 -10000 0 4
myoblast fusion -0.022 0.024 -10000 0 -10000 0 0
mol:GTP 0.017 0.029 -10000 0 -0.16 10 10
regulation of calcium-dependent cell-cell adhesion -0.045 0.036 0.18 3 -0.22 1 4
ARF1/GTP 0.032 0.027 -10000 0 -0.12 9 9
mol:GM1 0.005 0.021 -10000 0 -0.13 1 1
mol:Choline -0.008 0.013 -10000 0 -10000 0 0
lamellipodium assembly 0.007 0.056 -10000 0 -0.35 8 8
MAPK3 0.016 0.02 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.046 0.036 0.23 1 -0.18 3 4
ARF1 0.026 0.003 -10000 0 -10000 0 0
ARF6/GDP 0.022 0.024 -10000 0 -10000 0 0
ARF1/GDP 0.023 0.045 -10000 0 -0.2 10 10
ARF6 0.033 0.008 -10000 0 -10000 0 0
RAB11A 0.026 0.004 -10000 0 -10000 0 0
TIAM1 0.023 0.031 -10000 0 -0.32 3 3
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.017 0.018 -10000 0 -10000 0 0
actin filament bundle formation -0.024 0.044 0.2 10 -10000 0 10
KALRN 0.01 0.021 0.15 1 -0.16 2 3
RAB11FIP3/RAB11A 0.037 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.025 0.044 -10000 0 -0.2 10 10
NME1 0.026 0.017 0.33 1 -10000 0 1
Rac1/GDP 0.026 0.044 -10000 0 -0.21 10 10
substrate adhesion-dependent cell spreading 0.017 0.029 -10000 0 -0.16 10 10
cortical actin cytoskeleton organization 0.007 0.056 -10000 0 -0.35 8 8
RAC1 0.025 0.006 -10000 0 -10000 0 0
liver development 0.017 0.029 -10000 0 -0.16 10 10
ARF6/GTP 0.017 0.029 -10000 0 -0.16 10 10
RhoA/GTP 0.031 0.027 -10000 0 -0.12 9 9
mol:GDP 0.005 0.036 -10000 0 -0.22 8 8
ARF6/GTP/RAB11FIP3/RAB11A 0.045 0.028 -10000 0 -10000 0 0
RHOA 0.025 0.006 -10000 0 -10000 0 0
PLD1 0.012 0.022 -10000 0 -0.12 8 8
RAB11FIP3 0.025 0.005 -10000 0 -10000 0 0
tube morphogenesis 0.007 0.056 -10000 0 -0.35 8 8
ruffle organization 0.003 0.026 -10000 0 -0.25 4 4
regulation of epithelial cell migration 0.017 0.029 -10000 0 -0.16 10 10
PLD2 0.014 0.018 -10000 0 -0.14 1 1
PIP5K1A 0.003 0.026 -10000 0 -0.25 4 4
mol:Phosphatidic acid -0.008 0.013 -10000 0 -10000 0 0
Rac1/GTP 0.007 0.056 -10000 0 -0.35 8 8
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.008 0.082 -10000 0 -0.22 44 44
AKT1 0.02 0.073 0.35 2 -0.35 3 5
PTK2B -0.02 0.064 0.33 1 -0.24 3 4
VEGFR2 homodimer/Frs2 0.024 0.017 -10000 0 -0.18 1 1
CAV1 0.01 0.071 -10000 0 -0.32 18 18
CALM1 0.026 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.037 0.023 -10000 0 -10000 0 0
endothelial cell proliferation 0.005 0.1 0.32 8 -0.33 4 12
mol:Ca2+ -0.011 0.045 0.35 1 -0.22 2 3
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.055 0.031 -10000 0 -10000 0 0
RP11-342D11.1 -0.01 0.038 -10000 0 -0.22 2 2
CDH5 0.024 0.025 -10000 0 -0.32 2 2
VEGFA homodimer 0.051 0.03 -10000 0 -10000 0 0
SHC1 0.024 0.007 -10000 0 -10000 0 0
SHC2 0.006 0.083 0.33 1 -0.32 24 25
HRAS/GDP 0.033 0.031 -10000 0 -0.21 1 1
SH2D2A 0.027 0.027 0.33 3 -10000 0 3
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.041 0.069 -10000 0 -0.37 4 4
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.041 0.026 -10000 0 -10000 0 0
VEGFR1 homodimer 0.025 0.005 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.062 0.039 -10000 0 -0.22 1 1
GRB10 -0.016 0.051 0.35 1 -0.4 3 4
PTPN11 0.025 0.005 -10000 0 -10000 0 0
GRB2 0.025 0.005 -10000 0 -10000 0 0
PAK1 0.024 0.018 -10000 0 -0.32 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.062 0.038 -10000 0 -0.22 1 1
HRAS 0.024 0.008 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.002 0.071 -10000 0 -0.27 8 8
HIF1A 0.026 0.016 0.33 1 -10000 0 1
FRS2 0.024 0.008 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.049 0.026 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.024 0.018 -10000 0 -0.32 1 1
Nck/Pak 0.035 0.017 -10000 0 -0.22 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.037 0.029 -10000 0 -10000 0 0
mol:GDP 0.047 0.032 -10000 0 -0.21 1 1
mol:NADP 0.024 0.075 0.31 3 -0.36 4 7
eNOS/Hsp90 0.036 0.073 0.31 3 -0.34 4 7
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
mol:IP3 -0.012 0.045 0.35 1 -0.22 2 3
HIF1A/ARNT 0.033 0.014 -10000 0 -10000 0 0
SHB 0.023 0.009 -10000 0 -10000 0 0
VEGFA 0.025 0.011 -10000 0 -10000 0 0
VEGFC 0.024 0.029 0.33 1 -0.32 2 3
FAK1/Vinculin 0.011 0.086 0.28 2 -0.36 2 4
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.025 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.035 0.074 -10000 0 -0.25 3 3
PTPN6 0.026 0.016 0.33 1 -10000 0 1
EPAS1 0.03 0.009 -10000 0 -10000 0 0
mol:L-citrulline 0.024 0.075 0.31 3 -0.36 4 7
ITGAV 0.025 0.005 -10000 0 -10000 0 0
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.053 0.035 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer 0.042 0.031 -10000 0 -0.23 3 3
VEGFR2/3 heterodimer 0.025 0.022 -10000 0 -0.34 1 1
VEGFB 0.026 0.003 -10000 0 -10000 0 0
MAPK11 0.002 0.057 0.4 2 -10000 0 2
VEGFR2 homodimer 0.012 0.008 -10000 0 -10000 0 0
FLT1 0.025 0.005 -10000 0 -10000 0 0
NEDD4 0.024 0.021 -10000 0 -0.32 1 1
MAPK3 -0.015 0.076 0.25 8 -0.25 3 11
MAPK1 -0.014 0.077 0.24 11 -0.25 3 14
VEGFA145/NRP2 0.024 0.055 -10000 0 -0.22 18 18
VEGFR1/2 heterodimer 0.027 0.015 -10000 0 -10000 0 0
KDR 0.013 0.008 -10000 0 -10000 0 0
VEGFA165/NRP1/VEGFR2 homodimer 0.031 0.051 -10000 0 -0.25 3 3
SRC 0.025 0.007 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.007 0.081 0.25 10 -0.26 3 13
PI3K 0.024 0.044 -10000 0 -0.29 2 2
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.039 0.021 -10000 0 -10000 0 0
FES -0.013 0.044 0.36 1 -0.22 2 3
GAB1 0.025 0.037 -10000 0 -0.32 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.038 0.023 -10000 0 -10000 0 0
CTNNB1 0.025 0.005 -10000 0 -10000 0 0
SOS1 0.026 0.004 -10000 0 -10000 0 0
ARNT 0.023 0.009 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.032 0.068 0.28 1 -0.34 4 5
VEGFR2 homodimer/VEGFA homodimer/Yes 0.037 0.023 -10000 0 -10000 0 0
PI3K/GAB1 0.021 0.066 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.061 0.042 -10000 0 -10000 0 0
PRKACA 0.026 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.037 0.029 0.22 1 -0.31 1 2
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
CDC42 -0.013 0.045 0.36 1 -0.22 2 3
actin cytoskeleton reorganization 0.04 0.026 -10000 0 -10000 0 0
PTK2 -0.005 0.065 -10000 0 -0.33 3 3
EDG1 -0.01 0.038 -10000 0 -0.22 2 2
mol:DAG -0.012 0.045 0.35 1 -0.22 2 3
CaM/Ca2+ 0.026 0.044 0.32 1 -10000 0 1
MAP2K3 -0.009 0.052 0.35 1 -0.22 2 3
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.039 0.052 -10000 0 -0.4 3 3
PLCG1 -0.012 0.045 0.36 1 -0.22 2 3
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.05 0.037 -10000 0 -10000 0 0
IQGAP1 0.026 0.004 -10000 0 -10000 0 0
YES1 0.024 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.039 0.022 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.041 0.024 0.34 1 -10000 0 1
cell migration 0.011 0.084 0.31 2 -0.33 3 5
mol:PI-3-4-5-P3 0.025 0.045 0.25 2 -0.28 2 4
FYN 0.022 0.03 -10000 0 -0.32 3 3
VEGFB/NRP1 -0.013 0.039 -10000 0 -10000 0 0
mol:NO 0.024 0.075 0.31 3 -0.36 4 7
PXN 0.026 0.004 -10000 0 -10000 0 0
HRAS/GTP -0.025 0.017 -10000 0 -0.21 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.027 0.044 -10000 0 -0.4 3 3
VHL 0.023 0.008 -10000 0 -10000 0 0
ITGB3 -0.012 0.11 -10000 0 -0.32 44 44
NOS3 0.024 0.08 0.32 3 -0.4 4 7
VEGFR2 homodimer/VEGFA homodimer/Sck 0.028 0.054 -10000 0 -0.28 1 1
RAC1 0.025 0.006 -10000 0 -10000 0 0
PRKCA -0.011 0.057 0.34 2 -0.29 1 3
PRKCB -0.046 0.076 -10000 0 -0.34 2 2
VCL 0.025 0.005 -10000 0 -10000 0 0
VEGFA165/NRP1 0.023 0.037 -10000 0 -0.22 2 2
VEGFR1/2 heterodimer/VEGFA homodimer 0.04 0.021 -10000 0 -10000 0 0
VEGFA165/NRP2 0.024 0.055 -10000 0 -0.22 18 18
MAPKKK cascade -0.011 0.065 0.34 2 -0.34 2 4
NRP2 0.01 0.071 -10000 0 -0.32 18 18
VEGFC homodimer 0.024 0.029 0.33 1 -0.32 2 3
NCK1 0.025 0.006 -10000 0 -10000 0 0
ROCK1 0.025 0.005 -10000 0 -10000 0 0
FAK1/Paxillin 0.012 0.087 0.28 3 -0.36 2 5
MAP3K13 -0.011 0.045 -10000 0 -0.22 2 2
PDPK1 0 0.052 0.24 6 -0.26 2 8
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.043 0.036 -10000 0 -10000 0 0
CLOCK 0.027 0.004 -10000 0 -10000 0 0
TIMELESS/CRY2 0.031 0.031 -10000 0 -10000 0 0
DEC1/BMAL1 0.034 0.033 0.24 9 -10000 0 9
ATR 0.025 0.006 -10000 0 -10000 0 0
NR1D1 0.013 0.021 -10000 0 -10000 0 0
ARNTL 0.026 0.008 -10000 0 -10000 0 0
TIMELESS 0.014 0.034 0.42 2 -10000 0 2
NPAS2 0.025 0.025 -10000 0 -0.32 2 2
CRY2 0.024 0.007 -10000 0 -10000 0 0
mol:CO -0.006 0.011 -10000 0 -0.14 3 3
CHEK1 0.028 0.03 0.33 4 -10000 0 4
mol:HEME 0.006 0.011 0.14 3 -10000 0 3
PER1 0.014 0.056 -10000 0 -0.32 11 11
BMAL/CLOCK/NPAS2 0.052 0.027 -10000 0 -0.19 2 2
BMAL1/CLOCK 0.02 0.042 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.043 0.036 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.044 0.036 -10000 0 -10000 0 0
mol:NADPH 0.006 0.011 0.14 3 -10000 0 3
PER1/TIMELESS 0.027 0.033 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.001 0.054 0.33 10 -10000 0 10
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.055 0.065 0.24 20 -10000 0 20
Ran/GTP/Exportin 1/HDAC1 -0.016 0.005 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.028 0.061 -10000 0 -0.22 3 3
SUMO1 0.025 0.005 -10000 0 -10000 0 0
ZFPM1 0.025 0.005 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.008 0.019 -10000 0 -0.37 1 1
FKBP3 0.025 0.005 -10000 0 -10000 0 0
Histones 0.053 0.054 -10000 0 -10000 0 0
YY1/LSF 0.016 0.054 -10000 0 -0.21 10 10
SMG5 0.024 0.007 -10000 0 -10000 0 0
RAN 0.025 0.005 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.023 0.023 -10000 0 -10000 0 0
I kappa B alpha/HDAC1 0.026 0.051 -10000 0 -0.17 2 2
SAP18 0.025 0.005 -10000 0 -10000 0 0
RELA 0.023 0.033 0.18 1 -10000 0 1
HDAC1/Smad7 0.049 0.015 -10000 0 -10000 0 0
RANGAP1 0.025 0.005 -10000 0 -10000 0 0
HDAC3/TR2 0.029 0.049 -10000 0 -0.17 11 11
NuRD/MBD3 Complex 0.017 0.047 -10000 0 -0.26 3 3
NF kappa B1 p50/RelA 0.021 0.065 -10000 0 -0.23 10 10
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.029 0.067 0.33 12 -0.32 6 18
GATA1 0.013 0.02 -10000 0 -10000 0 0
Mad/Max 0.037 0.014 0.24 1 -10000 0 1
NuRD/MBD3 Complex/GATA1/Fog1 0.017 0.054 -10000 0 -0.24 5 5
RBBP7 0.026 0.004 -10000 0 -10000 0 0
NPC 0.015 0.002 -10000 0 -10000 0 0
RBBP4 0.026 0.002 -10000 0 -10000 0 0
MAX 0.026 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.025 0.006 -10000 0 -10000 0 0
NFKBIA 0.02 0.019 -10000 0 -10000 0 0
KAT2B 0.024 0.018 -10000 0 -0.32 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.009 0.035 -10000 0 -0.37 1 1
SIN3 complex 0.062 0.02 -10000 0 -10000 0 0
SMURF1 0.026 0.004 -10000 0 -10000 0 0
CHD3 0.024 0.008 -10000 0 -10000 0 0
SAP30 0.025 0.006 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.023 0.008 -10000 0 -10000 0 0
YY1/HDAC3 0.016 0.049 -10000 0 -0.24 3 3
YY1/HDAC2 0.017 0.052 -10000 0 -0.2 10 10
YY1/HDAC1 0.016 0.055 -10000 0 -0.21 10 10
NuRD/MBD2 Complex (MeCP1) 0.013 0.052 -10000 0 -0.29 3 3
PPARG 0.006 0.061 -10000 0 -0.23 16 16
HDAC8/hEST1B 0.049 0.015 -10000 0 -10000 0 0
UBE2I 0.025 0.005 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.025 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.029 0.048 -10000 0 -10000 0 0
MBD3L2 -0.017 0.003 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.048 0.015 -10000 0 -10000 0 0
CREBBP 0.025 0.007 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.017 0.057 -10000 0 -0.29 6 6
HDAC1 0.026 0.002 -10000 0 -10000 0 0
HDAC3 0.021 0.019 -10000 0 -10000 0 0
HDAC2 0.025 0.006 -10000 0 -10000 0 0
YY1 0.011 0.012 -10000 0 -0.21 1 1
HDAC8 0.026 0.003 -10000 0 -10000 0 0
SMAD7 0.025 0.006 -10000 0 -10000 0 0
NCOR2 0.026 0.004 -10000 0 -10000 0 0
MXD1 0.026 0.016 0.33 1 -10000 0 1
STAT3 0.015 0.005 -10000 0 -10000 0 0
NFKB1 0.026 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.026 0.004 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.029 0.056 -10000 0 -0.2 10 10
YY1/SAP30/HDAC1 0.029 0.055 -10000 0 -0.2 9 9
EP300 0.025 0.005 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.015 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.019 -10000 0 -10000 0 0
histone deacetylation 0.013 0.052 -10000 0 -0.29 3 3
STAT3 (dimer non-phopshorylated)/HDAC3 0.021 0.041 -10000 0 -0.21 3 3
nuclear export -0.048 0.015 -10000 0 -10000 0 0
PRKACA 0.026 0.003 -10000 0 -10000 0 0
GATAD2B 0.024 0.008 -10000 0 -10000 0 0
GATAD2A 0.026 0.004 -10000 0 -10000 0 0
GATA2/HDAC3 0.03 0.06 0.22 9 -0.29 1 10
GATA1/HDAC1 0.036 0.006 -10000 0 -10000 0 0
GATA1/HDAC3 0.027 0.048 -10000 0 -10000 0 0
CHD4 0.025 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.047 0.046 0.24 21 -10000 0 21
SIN3/HDAC complex/Mad/Max 0.013 0.05 -10000 0 -0.31 4 4
NuRD Complex 0.015 0.06 -10000 0 -0.25 7 7
positive regulation of chromatin silencing 0.05 0.053 -10000 0 -10000 0 0
SIN3B 0.026 0.003 -10000 0 -10000 0 0
MTA2 0.026 0.003 -10000 0 -10000 0 0
SIN3A 0.026 0.004 -10000 0 -10000 0 0
XPO1 0.025 0.005 -10000 0 -10000 0 0
SUMO1/HDAC1 0.027 0.049 -10000 0 -0.19 12 12
HDAC complex 0.062 0.019 -10000 0 -10000 0 0
GATA1/Fog1 0.035 0.009 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.049 0.015 -10000 0 -10000 0 0
TNF 0.041 0.067 0.33 21 -10000 0 21
negative regulation of cell growth 0.013 0.05 -10000 0 -0.31 4 4
NuRD/MBD2/PRMT5 Complex 0.013 0.052 -10000 0 -0.29 3 3
Ran/GTP/Exportin 1 0.026 0.047 -10000 0 -0.19 11 11
NF kappa B/RelA/I kappa B alpha 0.016 0.046 0.19 1 -0.23 4 5
SIN3/HDAC complex/NCoR1 0.003 0.054 -10000 0 -0.3 5 5
TFCP2 0.026 0.004 -10000 0 -10000 0 0
NR2C1 0.026 0.004 -10000 0 -10000 0 0
MBD3 0.025 0.005 -10000 0 -10000 0 0
MBD2 0.025 0.006 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.036 0.016 -10000 0 -0.22 1 1
FBXW11 0.025 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.02 0.023 0.22 1 -0.19 3 4
NF kappa B1 p50/RelA/I kappa B alpha 0.015 0.051 -10000 0 -0.18 4 4
NFKBIA 0.01 0.038 -10000 0 -0.18 7 7
MAPK14 0.026 0.003 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.021 0.009 -10000 0 -10000 0 0
ARRB2 0.01 0.003 -10000 0 -10000 0 0
REL 0.023 0.034 0.33 1 -0.32 3 4
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.021 0.013 -10000 0 -0.17 1 1
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.022 0.009 -10000 0 -10000 0 0
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.016 0.017 0.25 2 -10000 0 2
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
NFKB1 -0.014 0.005 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.014 0.037 -10000 0 -0.17 7 7
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.013 0.055 -10000 0 -0.19 8 8
SRC 0.025 0.007 -10000 0 -10000 0 0
PI3K 0.034 0.018 -10000 0 -0.22 1 1
NF kappa B1 p50/RelA 0.014 0.037 -10000 0 -0.17 7 7
IKBKB 0.023 0.008 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.006 -10000 0 -10000 0 0
SYK 0.02 0.035 -10000 0 -0.32 4 4
I kappa B alpha/PIK3R1 0.015 0.053 -10000 0 -0.18 13 13
cell death 0.013 0.054 -10000 0 -0.18 8 8
NF kappa B1 p105/c-Rel 0.02 0.023 0.22 1 -0.19 3 4
LCK 0.024 0.04 0.33 2 -0.32 4 6
BCL3 0.025 0.018 -10000 0 -0.32 1 1
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.026 0.002 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.017 0.01 -10000 0 -10000 0 0
MDM2/SUMO1 0.024 0.049 -10000 0 -0.19 12 12
HDAC4 0.024 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.018 0.01 -10000 0 -10000 0 0
SUMO1 0.025 0.005 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.005 0.026 -10000 0 -0.2 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 -0.004 0.031 -10000 0 -0.24 4 4
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.025 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.026 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.027 0.045 -10000 0 -0.18 12 12
SUMO1/HDAC1 0.027 0.049 -10000 0 -0.19 12 12
RANGAP1 0.025 0.005 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.056 0.026 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.008 0.019 -10000 0 -0.37 1 1
Ran/GTP 0.014 0.044 -10000 0 -0.19 11 11
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.024 0.008 -10000 0 -10000 0 0
UBE2I 0.025 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.015 0.052 0.19 12 -0.19 11 23
NPC 0.015 0.002 -10000 0 -10000 0 0
PIAS2 0.025 0.006 -10000 0 -10000 0 0
PIAS1 0.026 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.025 0.007 -10000 0 -10000 0 0
SMAD2 0 0.051 0.23 4 -0.24 7 11
SMAD3 0.011 0.032 -10000 0 -10000 0 0
SMAD3/SMAD4 0.03 0.035 -10000 0 -0.38 1 1
SMAD4/Ubc9/PIASy 0.047 0.017 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.036 0.061 0.28 1 -0.26 2 3
PPM1A 0.026 0.004 -10000 0 -10000 0 0
CALM1 0.026 0.004 -10000 0 -10000 0 0
SMAD2/SMAD4 0.011 0.05 0.23 1 -0.22 8 9
MAP3K1 0.025 0.006 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.034 0.027 -10000 0 -0.22 4 4
MAPK3 0.025 0.005 -10000 0 -10000 0 0
MAPK1 0.025 0.005 -10000 0 -10000 0 0
NUP214 0.024 0.008 -10000 0 -10000 0 0
CTDSP1 0.025 0.006 -10000 0 -10000 0 0
CTDSP2 0.026 0.004 -10000 0 -10000 0 0
CTDSPL 0.025 0.006 -10000 0 -10000 0 0
KPNB1 0.026 0.004 -10000 0 -10000 0 0
TGFBRAP1 0.022 0.034 -10000 0 -0.32 4 4
UBE2I 0.025 0.005 -10000 0 -10000 0 0
NUP153 0.024 0.007 -10000 0 -10000 0 0
KPNA2 0.028 0.026 0.33 3 -10000 0 3
PIAS4 0.026 0.004 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.027 0.01 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 -0.009 0.007 -10000 0 -10000 0 0
mol:DAG -0.008 0.038 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.024 0.01 -10000 0 -10000 0 0
CaM/Ca2+ -0.011 0.039 -10000 0 -10000 0 0
HIF1A 0.031 0.016 0.33 1 -10000 0 1
GAB1 0.025 0.006 -10000 0 -10000 0 0
AKT1 -0.001 0.051 0.22 1 -10000 0 1
PLCG1 -0.009 0.038 -10000 0 -10000 0 0
NOS3 0.019 0.052 0.27 2 -0.36 1 3
CBL 0.025 0.006 -10000 0 -10000 0 0
mol:NO 0.018 0.058 0.27 3 -0.35 1 4
FLT1 0.012 0.009 -10000 0 -10000 0 0
PGF 0.035 0.053 0.33 13 -10000 0 13
VEGFR1 homodimer/NRP2/VEGFR121 0.029 0.047 -10000 0 -10000 0 0
CALM1 0.026 0.004 -10000 0 -10000 0 0
PIK3CA 0.025 0.006 -10000 0 -10000 0 0
eNOS/Hsp90 0.029 0.057 0.27 2 -0.34 1 3
endothelial cell proliferation -0.022 0.089 0.29 6 -0.27 3 9
mol:Ca2+ -0.008 0.038 -10000 0 -10000 0 0
MAPK3 -0.015 0.038 0.24 1 -10000 0 1
MAPK1 -0.015 0.042 0.24 3 -10000 0 3
PIK3R1 0.024 0.018 -10000 0 -0.32 1 1
PLGF homodimer 0.035 0.053 0.33 13 -10000 0 13
PRKACA 0.026 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.01 0.071 -10000 0 -0.32 18 18
VEGFA homodimer 0.025 0.005 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.026 0.011 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.016 0.045 0.25 5 -10000 0 5
PI3K 0.057 0.043 -10000 0 -10000 0 0
PRKCA -0.013 0.039 0.26 1 -10000 0 1
PRKCB -0.048 0.073 0.26 1 -10000 0 1
VEGFR1 homodimer/PLGF homodimer 0.034 0.037 -10000 0 -10000 0 0
VEGFA 0.025 0.005 -10000 0 -10000 0 0
VEGFB 0.026 0.003 -10000 0 -10000 0 0
mol:IP3 -0.008 0.038 -10000 0 -10000 0 0
RASA1 -0.013 0.033 -10000 0 -10000 0 0
NRP2 0.01 0.071 -10000 0 -0.32 18 18
VEGFR1 homodimer 0.012 0.009 -10000 0 -10000 0 0
VEGFB homodimer 0.026 0.003 -10000 0 -10000 0 0
NCK1 0.025 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.025 0.061 0.28 2 -0.34 1 3
PTPN11 0.025 0.005 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.051 0.039 -10000 0 -10000 0 0
mol:L-citrulline 0.018 0.058 0.27 3 -0.35 1 4
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.054 0.027 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.038 0.017 -10000 0 -10000 0 0
CD2AP 0.026 0.003 -10000 0 -10000 0 0
PI3K/GAB1 0.063 0.047 -10000 0 -10000 0 0
PDPK1 -0.004 0.056 0.24 1 -10000 0 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.039 0.016 -10000 0 -10000 0 0
mol:NADP 0.018 0.058 0.27 3 -0.35 1 4
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.048 0.022 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.017 0.046 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.007 0.029 0.14 16 -10000 0 16
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.017 0.026 0.13 2 -10000 0 2
AP2 0.036 0.011 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.029 0.018 -10000 0 -10000 0 0
CLTB 0.025 0.006 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.012 0.008 -10000 0 -10000 0 0
CD4 0.024 0.025 -10000 0 -0.32 2 2
CLTA 0.023 0.008 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
ARFGAP1 -0.008 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.004 0.009 -10000 0 -10000 0 0
ARF1/GTP 0.029 0.014 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.002 0.014 -10000 0 -10000 0 0
mol:Choline 0.003 0.009 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.028 0.006 -10000 0 -10000 0 0
DDEF1 0.002 0.009 -10000 0 -10000 0 0
ARF1/GDP 0.004 0.019 -10000 0 -0.11 1 1
AP2M1 0.025 0.006 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.004 0.014 -10000 0 -10000 0 0
Rac/GTP 0.02 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.034 0.013 -10000 0 -10000 0 0
ARFIP2 0.016 0.019 -10000 0 -10000 0 0
COPA 0.022 0.009 -10000 0 -10000 0 0
RAC1 0.025 0.006 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.017 0.051 0.15 3 -0.19 3 6
ARF1/GTP/ARHGAP10 0.019 0.006 -10000 0 -10000 0 0
GGA3 0.025 0.005 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.023 0.022 -10000 0 -0.23 2 2
AP2A1 0.026 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.002 0.037 -10000 0 -0.22 6 6
ARF1/GDP/Membrin 0.027 0.027 -10000 0 -0.25 2 2
Arfaptin 2/Rac/GDP 0.03 0.012 -10000 0 -10000 0 0
CYTH2 0.028 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.036 0.01 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.019 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 0.015 0.041 -10000 0 -10000 0 0
PLD2 0.003 0.009 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE -0.008 0.002 -10000 0 -10000 0 0
PIP5K1A 0.004 0.009 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.016 0.02 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.003 0.009 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 -0.008 0.002 -10000 0 -10000 0 0
GOSR2 0.007 0.024 -10000 0 -0.31 2 2
USO1 0.008 0.017 -10000 0 -0.31 1 1
GBF1 0.005 0.036 -10000 0 -0.31 5 5
ARF1/GTP/Arfaptin 2 0.034 0.012 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.046 0.024 -10000 0 -0.19 2 2
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 0.037 0.009 -9999 0 -9999 0 0
FBXW11 0.025 0.006 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.006 -9999 0 -9999 0 0
CHUK 0.025 0.005 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.068 0.028 -9999 0 -9999 0 0
NFKB1 0.026 0.003 -9999 0 -9999 0 0
MAP3K14 0.026 0.004 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.037 0.008 -9999 0 -9999 0 0
RELB 0.026 0.004 -9999 0 -9999 0 0
NFKB2 0.025 0.005 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.033 0.009 -9999 0 -9999 0 0
regulation of B cell activation 0.033 0.008 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 404 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.ZF.AA5P TCGA.ZF.AA5N TCGA.ZF.AA5H TCGA.ZF.AA58
109_MAP3K5 0.017 -0.091 0.023 0.047
47_PPARGC1A 0.026 -0.017 -0.32 -0.32
105_BMP4 0.026 0.026 0.026 0.026
105_BMP6 0.026 0.026 0.026 0.026
105_BMP7 0.026 0.026 -0.32 -0.32
105_BMP2 0.026 0.026 0.026 0.026
131_RELN/VLDLR 0.068 0.062 0.068 -0.18
30_TGFB1/TGF beta receptor Type II -0.027 -0.029 -0.03 0.026
84_STAT5B 0.015 -0.1 0.083 0.013
84_STAT5A 0.015 -0.1 0.083 0.013
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BLCA-TP/19437945/BLCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/BLCA-TP/19775025/Gistic2_Analysis_19775625/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.

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)
Made with Nozzle