PARADIGM pathway analysis of mRNA expression data
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C16Q1VKH
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNA expression data. Broad Institute of MIT and Harvard. doi:10.7908/C16Q1VKH
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 62 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 390
PLK2 and PLK4 events 246
PLK1 signaling events 212
TCGA08_retinoblastoma 209
Aurora B signaling 164
Signaling events regulated by Ret tyrosine kinase 119
Osteopontin-mediated events 116
Circadian rhythm pathway 115
S1P3 pathway 108
IL2 signaling events mediated by STAT5 99
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 570 . 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 ( 570 ).

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 0.6842 390 19898 51 -0.022 2.1 1000 -1000 -0.14 -1000
PLK2 and PLK4 events 0.4316 246 739 3 0.057 0.14 1000 -1000 -0.007 -1000
PLK1 signaling events 0.3719 212 18043 85 -0.13 0.29 1000 -1000 -0.026 -1000
TCGA08_retinoblastoma 0.3667 209 1673 8 -0.13 0.14 1000 -1000 -0.001 -1000
Aurora B signaling 0.2877 164 11023 67 -0.3 0.36 1000 -1000 -0.027 -1000
Signaling events regulated by Ret tyrosine kinase 0.2088 119 9810 82 -0.22 0.085 1000 -1000 -0.047 -1000
Osteopontin-mediated events 0.2035 116 4410 38 -0.14 0.18 1000 -1000 -0.029 -1000
Circadian rhythm pathway 0.2018 115 2550 22 -0.082 0.24 1000 -1000 -0.042 -1000
S1P3 pathway 0.1895 108 4575 42 -0.63 0.009 1000 -1000 -0.019 -1000
IL2 signaling events mediated by STAT5 0.1737 99 2191 22 -0.5 0.19 1000 -1000 -0.034 -1000
HIF-1-alpha transcription factor network 0.1684 96 7317 76 -0.064 0.41 1000 -1000 -0.042 -1000
Nongenotropic Androgen signaling 0.1649 94 4904 52 -0.2 0.16 1000 -1000 -0.019 -1000
TCGA08_p53 0.1544 88 620 7 -0.073 0.015 1000 -1000 -0.004 -1000
IGF1 pathway 0.1544 88 5038 57 -0.12 0.083 1000 -1000 -0.046 -1000
PDGFR-alpha signaling pathway 0.1421 81 3583 44 -0.18 0.056 1000 -1000 -0.015 -1000
Endothelins 0.1333 76 7299 96 -0.23 0.11 1000 -1000 -0.028 -1000
LPA receptor mediated events 0.1316 75 7653 102 -0.094 0.036 1000 -1000 -0.039 -1000
TCGA08_rtk_signaling 0.1298 74 1931 26 -0.22 0.099 1000 -1000 -0.004 -1000
Thromboxane A2 receptor signaling 0.1281 73 7697 105 -0.2 0.035 1000 -1000 -0.042 -1000
mTOR signaling pathway 0.1281 73 3880 53 -0.17 0.055 1000 -1000 -0.032 -1000
Insulin Pathway 0.1281 73 5433 74 -0.21 0.056 1000 -1000 -0.046 -1000
Aurora A signaling 0.1263 72 4371 60 -0.3 0.29 1000 -1000 -0.014 -1000
IL4-mediated signaling events 0.1263 72 6593 91 -0.89 0.29 1000 -1000 -0.14 -1000
Syndecan-1-mediated signaling events 0.1175 67 2297 34 -0.081 0.049 1000 -1000 -0.024 -1000
Coregulation of Androgen receptor activity 0.1140 65 4948 76 -0.52 0.13 1000 -1000 -0.024 -1000
Ephrin B reverse signaling 0.1123 64 3075 48 -0.17 0.056 1000 -1000 -0.017 -1000
Integrins in angiogenesis 0.1035 59 5005 84 -0.21 0.15 1000 -1000 -0.039 -1000
IL23-mediated signaling events 0.1035 59 3595 60 -0.18 0.12 1000 -1000 -0.11 -1000
Ras signaling in the CD4+ TCR pathway 0.1018 58 996 17 -0.051 0.098 1000 -1000 -0.011 -1000
Cellular roles of Anthrax toxin 0.0965 55 2181 39 -0.25 0.023 1000 -1000 -0.013 -1000
Reelin signaling pathway 0.0947 54 3068 56 -0.056 0.056 1000 -1000 -0.022 -1000
Signaling events mediated by PRL 0.0930 53 1820 34 -0.11 0.13 1000 -1000 -0.017 -1000
BARD1 signaling events 0.0912 52 2981 57 -0.045 0.2 1000 -1000 -0.032 -1000
FAS signaling pathway (CD95) 0.0895 51 2434 47 -0.091 0.061 1000 -1000 -0.016 -1000
Signaling mediated by p38-alpha and p38-beta 0.0842 48 2135 44 -0.09 0.014 1000 -1000 -0.019 -1000
IL1-mediated signaling events 0.0807 46 2855 62 -0.081 0.12 1000 -1000 -0.036 -1000
Effects of Botulinum toxin 0.0807 46 1203 26 -0.16 0.016 1000 -1000 -0.018 -1000
amb2 Integrin signaling 0.0789 45 3756 82 -0.13 0.074 1000 -1000 -0.025 -1000
Plasma membrane estrogen receptor signaling 0.0789 45 3933 86 -0.13 0.099 1000 -1000 -0.043 -1000
Syndecan-2-mediated signaling events 0.0772 44 3047 69 -0.081 0.074 1000 -1000 -0.01 -1000
TRAIL signaling pathway 0.0772 44 2120 48 -0.16 0.012 1000 -1000 -0.024 -1000
HIF-2-alpha transcription factor network 0.0754 43 1890 43 -0.14 0.19 1000 -1000 -0.049 -1000
Nectin adhesion pathway 0.0702 40 2562 63 -0.13 0.056 1000 -1000 -0.041 -1000
Insulin-mediated glucose transport 0.0667 38 1245 32 -0.27 0.12 1000 -1000 -0.018 -1000
Retinoic acid receptors-mediated signaling 0.0667 38 2209 58 -0.29 0.2 1000 -1000 -0.034 -1000
Signaling events mediated by the Hedgehog family 0.0632 36 1911 52 -0.038 0.13 1000 -1000 -0.029 -1000
Signaling events mediated by PTP1B 0.0632 36 2752 76 -0.21 0.084 1000 -1000 -0.036 -1000
p75(NTR)-mediated signaling 0.0632 36 4556 125 -0.23 0.12 1000 -1000 -0.04 -1000
Fc-epsilon receptor I signaling in mast cells 0.0632 36 3567 97 -0.12 0.054 1000 -1000 -0.038 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0632 36 1895 52 -0.23 0.074 1000 -1000 -0.025 -1000
IL6-mediated signaling events 0.0632 36 2758 75 -0.29 0.096 1000 -1000 -0.025 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0614 35 2993 85 -0.13 0.056 1000 -1000 -0.027 -1000
Regulation of Androgen receptor activity 0.0614 35 2476 70 -0.63 0.019 1000 -1000 -0.035 -1000
Aurora C signaling 0.0579 33 235 7 -0.004 0.049 1000 -1000 -0.01 -1000
FoxO family signaling 0.0579 33 2134 64 -0.011 0.32 1000 -1000 -0.023 -1000
TCR signaling in naïve CD8+ T cells 0.0544 31 2924 93 -0.065 0.099 1000 -1000 -0.036 -1000
PDGFR-beta signaling pathway 0.0544 31 3093 97 -0.097 0.12 1000 -1000 -0.037 -1000
IL2 signaling events mediated by PI3K 0.0526 30 1759 58 -0.13 0.052 1000 -1000 -0.043 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0509 29 674 23 -0.029 0.19 1000 -1000 -0.02 -1000
Arf6 signaling events 0.0509 29 1818 62 -0.13 0.032 1000 -1000 -0.014 -1000
Signaling mediated by p38-gamma and p38-delta 0.0509 29 443 15 -0.094 0.021 1000 -1000 -0.012 -1000
Wnt signaling 0.0509 29 205 7 0.006 0.034 1000 -1000 -0.009 -1000
Glucocorticoid receptor regulatory network 0.0491 28 3263 114 -0.31 0.14 1000 -1000 -0.046 -1000
ErbB4 signaling events 0.0474 27 1918 69 -0.27 0.22 1000 -1000 -0.035 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0474 27 2006 74 -0.14 0.032 1000 -1000 -0.049 -1000
Regulation of Telomerase 0.0474 27 2818 102 -0.27 0.068 1000 -1000 -0.064 -1000
LPA4-mediated signaling events 0.0456 26 313 12 -0.088 0 1000 -1000 -0.013 -1000
Caspase cascade in apoptosis 0.0456 26 1931 74 -0.076 0.1 1000 -1000 -0.022 -1000
EPHB forward signaling 0.0456 26 2273 85 -0.038 0.099 1000 -1000 -0.042 -1000
Glypican 1 network 0.0439 25 1246 48 -0.24 0.045 1000 -1000 -0.014 -1000
IL12-mediated signaling events 0.0421 24 2169 87 -0.25 0.12 1000 -1000 -0.091 -1000
IFN-gamma pathway 0.0421 24 1680 68 -0.07 0.065 1000 -1000 -0.043 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0421 24 918 37 -0.038 0.056 1000 -1000 -0.02 -1000
ceramide signaling pathway 0.0421 24 1196 49 -0.078 0.007 1000 -1000 -0.029 -1000
Syndecan-3-mediated signaling events 0.0421 24 845 35 -0.039 0.027 1000 -1000 -0.018 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0421 24 1116 45 -0.1 0.018 1000 -1000 -0.052 -1000
Syndecan-4-mediated signaling events 0.0421 24 1631 67 -0.083 0.087 1000 -1000 -0.026 -1000
E-cadherin signaling in keratinocytes 0.0404 23 1013 43 -0.037 0.052 1000 -1000 -0.021 -1000
Paxillin-dependent events mediated by a4b1 0.0386 22 796 36 -0.038 0.056 1000 -1000 -0.026 -1000
Canonical Wnt signaling pathway 0.0386 22 1130 51 -0.34 0.13 1000 -1000 -0.029 -1000
EGFR-dependent Endothelin signaling events 0.0386 22 471 21 -0.03 0.014 1000 -1000 -0.016 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0386 22 2712 120 -0.16 0.12 1000 -1000 -0.033 -1000
Regulation of nuclear SMAD2/3 signaling 0.0368 21 2865 136 -0.17 0.13 1000 -1000 -0.019 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0368 21 1136 54 -0.046 0.019 1000 -1000 -0.048 -1000
Ceramide signaling pathway 0.0368 21 1632 76 -0.076 0.044 1000 -1000 -0.028 -1000
Presenilin action in Notch and Wnt signaling 0.0351 20 1249 61 -0.32 0.029 1000 -1000 -0.037 -1000
BMP receptor signaling 0.0351 20 1700 81 -0.18 0.047 1000 -1000 -0.047 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0351 20 1693 83 -0.15 0.19 1000 -1000 -0.03 -1000
S1P1 pathway 0.0351 20 725 36 -0.086 0.015 1000 -1000 -0.034 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0351 20 1371 68 -0.15 0.017 1000 -1000 -0.06 -1000
Class I PI3K signaling events 0.0351 20 1484 73 -0.039 0.094 1000 -1000 -0.023 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0351 20 1594 78 -0.12 0.056 1000 -1000 -0.041 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0333 19 538 28 -0.13 0.017 1000 -1000 -0.014 -1000
IL27-mediated signaling events 0.0333 19 1013 51 -0.08 0.12 1000 -1000 -0.035 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0333 19 627 33 -0.045 0.13 1000 -1000 -0.023 -1000
ErbB2/ErbB3 signaling events 0.0316 18 1219 65 -0.063 0.099 1000 -1000 -0.035 -1000
E-cadherin signaling in the nascent adherens junction 0.0316 18 1397 76 -0.068 0.056 1000 -1000 -0.042 -1000
Canonical NF-kappaB pathway 0.0298 17 693 39 -0.023 0.065 1000 -1000 -0.038 -1000
Noncanonical Wnt signaling pathway 0.0298 17 466 26 -0.003 0.035 1000 -1000 -0.017 -1000
Atypical NF-kappaB pathway 0.0298 17 544 31 -0.038 0.056 1000 -1000 -0.012 -1000
Calcium signaling in the CD4+ TCR pathway 0.0298 17 532 31 -0.097 0.007 1000 -1000 -0.033 -1000
BCR signaling pathway 0.0298 17 1698 99 -0.057 0.056 1000 -1000 -0.042 -1000
Arf6 downstream pathway 0.0281 16 712 43 -0.021 0.021 1000 -1000 -0.015 -1000
Regulation of p38-alpha and p38-beta 0.0281 16 902 54 -0.12 0.028 1000 -1000 -0.03 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0281 16 2004 125 -0.098 0.056 1000 -1000 -0.054 -1000
E-cadherin signaling events 0.0263 15 79 5 -0.005 0.007 1000 -1000 -0.007 -1000
Arf1 pathway 0.0228 13 727 54 -0.021 0.009 1000 -1000 -0.014 -1000
Ephrin A reverse signaling 0.0211 12 90 7 -0.027 0.007 1000 -1000 -0.009 -1000
Signaling events mediated by HDAC Class III 0.0211 12 505 40 -0.034 0.019 1000 -1000 -0.008 -1000
EPO signaling pathway 0.0175 10 566 55 -0.06 0.037 1000 -1000 -0.035 -1000
FOXA2 and FOXA3 transcription factor networks 0.0158 9 445 46 -0.008 0.19 1000 -1000 -0.045 -1000
S1P5 pathway 0.0158 9 154 17 -0.005 0.017 1000 -1000 -0.01 -1000
VEGFR1 specific signals 0.0158 9 507 56 -0.062 0.056 1000 -1000 -0.034 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0158 9 828 88 -0.042 0.074 1000 -1000 -0.068 -1000
a4b1 and a4b7 Integrin signaling 0.0140 8 42 5 0.003 0.017 1000 -1000 -0.007 -1000
Class I PI3K signaling events mediated by Akt 0.0140 8 573 68 -0.16 0.048 1000 -1000 -0.026 -1000
Signaling events mediated by HDAC Class I 0.0140 8 886 104 -0.016 0.027 1000 -1000 -0.025 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0123 7 269 34 -0.016 0.026 1000 -1000 -0.012 -1000
Hedgehog signaling events mediated by Gli proteins 0.0123 7 468 65 -0.05 0.024 1000 -1000 -0.04 -1000
S1P4 pathway 0.0123 7 193 25 -0.014 0.017 1000 -1000 -0.014 -1000
p38 MAPK signaling pathway 0.0123 7 348 44 -0.014 0.024 1000 -1000 -0.035 -1000
Signaling events mediated by HDAC Class II 0.0105 6 455 75 -0.036 0.026 1000 -1000 -0.023 -1000
JNK signaling in the CD4+ TCR pathway 0.0105 6 112 17 -0.013 0.009 1000 -1000 -0.014 -1000
Class IB PI3K non-lipid kinase events 0.0105 6 18 3 -0.009 0.009 1000 -1000 -0.004 -1000
Arf6 trafficking events 0.0070 4 301 71 -0.009 0.014 1000 -1000 -0.02 -1000
Alternative NF-kappaB pathway 0.0053 3 49 13 -0.001 0.02 1000 -1000 -0.005 -1000
Visual signal transduction: Rods 0.0035 2 152 52 -0.013 0.017 1000 -1000 -0.025 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0018 1 51 27 -0.004 0.02 1000 -1000 -0.03 -1000
Rapid glucocorticoid signaling 0.0018 1 27 20 -0.002 0.007 1000 -1000 -0.007 -1000
Visual signal transduction: Cones 0.0000 0 36 38 -0.004 0.016 1000 -1000 -0.009 -1000
Glypican 2 network 0.0000 0 2 4 0.006 0.009 1000 -1000 -0.005 -1000
Total NA 5586 303901 7203 -16 13 131000 -131000 -3.9 -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 1.2 0.34 1.3 504 -10000 0 504
PLK1 0.43 0.27 0.7 200 -10000 0 200
BIRC5 0.43 0.27 0.67 238 -10000 0 238
HSPA1B 1.2 0.34 1.3 517 -0.91 1 518
MAP2K1 0.44 0.15 0.47 523 -10000 0 523
BRCA2 1.4 0.46 1.5 506 -0.91 1 507
FOXM1 2.1 0.88 2.3 514 -1.1 1 515
XRCC1 1.2 0.34 1.3 503 -10000 0 503
FOXM1B/p19 0.75 0.57 1.2 345 -0.91 1 346
Cyclin D1/CDK4 0.7 0.48 1 357 -1.2 1 358
CDC2 1.8 0.6 2 518 -0.96 1 519
TGFA 0.74 0.51 1.1 361 -0.96 1 362
SKP2 1.3 0.44 1.5 505 -10000 0 505
CCNE1 0.25 0.065 0.27 512 -10000 0 512
CKS1B 1.4 0.5 1.6 504 -0.91 1 505
RB1 -0.001 0.023 -10000 0 -10000 0 0
FOXM1C/SP1 0.9 0.41 1.1 440 -1 1 441
AURKB 0.46 0.3 0.72 253 -10000 0 253
CENPF 1.6 0.49 1.7 514 -0.91 1 515
CDK4 0.11 0.069 0.31 10 -10000 0 10
MYC 0.88 0.4 1.1 445 -0.82 1 446
CHEK2 0.47 0.16 0.5 527 -10000 0 527
ONECUT1 0.78 0.53 1.2 362 -1.1 1 363
CDKN2A 0.054 0.14 0.22 199 -0.27 44 243
LAMA4 1.1 0.58 1.3 448 -1.1 2 450
FOXM1B/HNF6 0.79 0.54 1.2 356 -1.3 1 357
FOS 1 0.61 1.3 410 -1.4 1 411
SP1 -0.022 0.091 -10000 0 -0.29 59 59
CDC25B 1.2 0.35 1.3 504 -0.91 1 505
response to radiation 0.22 0.068 0.24 512 -10000 0 512
CENPB 1.2 0.35 1.3 504 -0.91 1 505
CENPA 1.2 0.36 1.3 504 -0.91 1 505
NEK2 1.5 0.51 1.7 507 -10000 0 507
HIST1H2BA 1.2 0.34 1.3 505 -0.91 1 506
CCNA2 0.24 0.083 0.27 473 -10000 0 473
EP300 0.003 0.037 -10000 0 -0.38 5 5
CCNB1/CDK1 1.7 0.55 1.8 505 -1 1 506
CCNB2 1.6 0.48 1.8 515 -10000 0 515
CCNB1 1.8 0.61 1.9 513 -0.96 1 514
ETV5 1.3 0.39 1.4 509 -0.91 1 510
ESR1 1.1 0.52 1.3 449 -1.1 3 452
CCND1 0.79 0.54 1.2 362 -1.2 1 363
GSK3A 0.23 0.078 0.25 473 -0.35 2 475
Cyclin A-E1/CDK1-2 0.24 0.23 0.44 301 -10000 0 301
CDK2 0.18 0.097 0.28 255 -10000 0 255
G2/M transition of mitotic cell cycle 0.42 0.15 0.46 525 -10000 0 525
FOXM1B/Cbp/p300 -0.004 0.057 -10000 0 -0.97 1 1
GAS1 1.1 0.49 1.3 459 -1.2 1 460
MMP2 1 0.61 1.4 426 -1.1 5 431
RB1/FOXM1C 0.76 0.53 1.1 373 -1.1 1 374
CREBBP 0.001 0.046 -10000 0 -0.38 8 8
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.057 0.098 0.22 139 -0.38 3 142
PLK4 0.1 0.11 0.22 259 -10000 0 259
regulation of centriole replication 0.14 0.14 0.24 337 -0.27 1 338
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.13 0.048 -10000 0 -0.15 493 493
BUB1B 0.22 0.07 0.24 505 -10000 0 505
PLK1 0.1 0.036 0.11 514 -10000 0 514
PLK1S1 0.051 0.021 0.06 429 -10000 0 429
KIF2A 0.087 0.035 0.12 195 -0.15 2 197
regulation of mitotic centrosome separation 0.1 0.036 0.11 514 -10000 0 514
GOLGA2 0.006 0 -10000 0 -10000 0 0
Hec1/SPC24 0.24 0.098 0.26 506 -10000 0 506
WEE1 0.14 0.045 0.17 403 -10000 0 403
cytokinesis 0.24 0.094 0.28 468 -10000 0 468
PP2A-alpha B56 0.035 0.063 -10000 0 -10000 0 0
AURKA 0.13 0.036 0.14 539 -10000 0 539
PICH/PLK1 0.27 0.098 0.28 527 -10000 0 527
CENPE 0.099 0.056 0.15 206 -10000 0 206
RhoA/GTP 0.004 0.016 -10000 0 -0.27 2 2
positive regulation of microtubule depolymerization 0.087 0.034 0.12 195 -0.15 2 197
PPP2CA 0.006 0.016 -10000 0 -0.38 1 1
FZR1 0.006 0 -10000 0 -10000 0 0
TPX2 0.15 0.031 0.16 554 -10000 0 554
PAK1 0.014 0.04 0.22 18 -0.39 1 19
SPC24 0.066 0.097 0.22 158 -10000 0 158
FBXW11 0.006 0 -10000 0 -10000 0 0
CLSPN 0.07 0.04 0.16 74 -10000 0 74
GORASP1 0.006 0 -10000 0 -10000 0 0
metaphase 0.001 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.051 0.021 0.06 429 -10000 0 429
G2 phase of mitotic cell cycle 0.007 0.002 0.009 106 -10000 0 106
STAG2 0.016 0.049 0.22 27 -0.38 1 28
GRASP65/GM130/RAB1/GTP 0 0.001 -10000 0 -10000 0 0
spindle elongation 0.1 0.036 0.11 514 -10000 0 514
ODF2 0.013 0.002 -10000 0 -10000 0 0
BUB1 0.005 0.026 -10000 0 -10000 0 0
TPT1 0.052 0.024 0.098 31 -0.18 1 32
CDC25C 0.11 0.07 0.19 214 -10000 0 214
CDC25B 0.027 0.02 0.23 5 -10000 0 5
SGOL1 0.13 0.048 0.15 493 -10000 0 493
RHOA 0.005 0.023 -10000 0 -0.38 2 2
CCNB1/CDK1 0.12 0.14 0.28 236 -10000 0 236
CDC14B 0.005 0.002 -10000 0 -10000 0 0
CDC20 0.17 0.092 0.22 434 -10000 0 434
PLK1/PBIP1 0.009 0.037 0.18 21 -10000 0 21
mitosis 0 0 -10000 0 -10000 0 0
FBXO5 0.15 0.078 0.19 430 -10000 0 430
CDC2 0.21 0.055 0.22 530 -10000 0 530
NDC80 0.2 0.07 0.22 503 -10000 0 503
metaphase plate congression 0.064 0.024 0.11 30 -0.17 1 31
ERCC6L 0.26 0.096 0.3 430 -10000 0 430
NLP/gamma Tubulin 0.052 0.024 0.08 198 -10000 0 198
microtubule cytoskeleton organization 0.052 0.023 0.098 31 -0.18 1 32
G2/M transition DNA damage checkpoint 0.001 0.001 0.021 1 -10000 0 1
PPP1R12A 0.009 0.001 -10000 0 -10000 0 0
interphase 0.001 0.001 0.021 1 -10000 0 1
PLK1/PRC1-2 0.29 0.12 0.32 490 -10000 0 490
GRASP65/GM130/RAB1/GTP/PLK1 0.049 0.032 -10000 0 -10000 0 0
RAB1A 0.006 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.12 0.069 0.14 428 -10000 0 428
mitotic prometaphase 0.003 0.002 0.034 1 -10000 0 1
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.033 -10000 0 -10000 0 0
microtubule-based process 0.2 0.078 0.24 464 -10000 0 464
Golgi organization 0.1 0.036 0.11 514 -10000 0 514
Cohesin/SA2 0.057 0.05 0.16 62 -0.11 1 63
PPP1CB/MYPT1 0.015 0.012 -10000 0 -0.27 1 1
KIF20A 0.18 0.087 0.22 455 -10000 0 455
APC/C/CDC20 0.2 0.081 0.24 442 -10000 0 442
PPP2R1A 0.006 0 -10000 0 -10000 0 0
chromosome segregation 0.007 0.032 0.17 18 -10000 0 18
PRC1 0.16 0.099 0.22 399 -10000 0 399
ECT2 0.23 0.064 0.24 525 -10000 0 525
C13orf34 0.11 0.069 0.14 419 -10000 0 419
NUDC 0.065 0.024 0.11 30 -0.17 1 31
regulation of attachment of spindle microtubules to kinetochore 0.22 0.07 0.24 505 -10000 0 505
spindle assembly 0.077 0.031 0.09 420 -10000 0 420
spindle stabilization 0.051 0.021 0.06 429 -10000 0 429
APC/C/HCDH1 0.009 0.001 -10000 0 -10000 0 0
MKLP2/PLK1 0.2 0.078 0.24 464 -10000 0 464
CCNB1 0.17 0.093 0.22 420 -10000 0 420
PPP1CB 0.008 0.017 -10000 0 -0.39 1 1
BTRC 0.006 0 -10000 0 -10000 0 0
ROCK2 0.072 0.027 0.2 3 -10000 0 3
TUBG1 0.054 0.024 0.11 35 -10000 0 35
G2/M transition of mitotic cell cycle 0.25 0.08 0.27 514 -10000 0 514
MLF1IP 0.01 0.041 0.2 24 -10000 0 24
INCENP 0.012 0.013 0.22 2 -10000 0 2
TCGA08_retinoblastoma

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
CDKN2B -0.032 0.019 -10000 0 -10000 0 0
CDKN2C 0.001 0.052 0.21 26 -10000 0 26
CDKN2A 0.14 0.11 0.24 317 -10000 0 317
CCND2 -0.13 0.082 -10000 0 -0.2 261 261
RB1 0.12 0.083 0.2 271 -10000 0 271
CDK4 -0.094 0.094 -10000 0 -0.18 259 259
CDK6 -0.1 0.1 -10000 0 -0.2 268 268
G1/S progression -0.12 0.082 -10000 0 -0.19 271 271
Aurora B signaling

Figure S5.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S5.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.36 0.16 0.4 503 -10000 0 503
STMN1 0.08 0.13 0.26 161 -10000 0 161
Aurora B/RasGAP/Survivin 0.046 0.052 0.16 88 -0.22 2 90
Chromosomal passenger complex/Cul3 protein complex 0.006 0.11 0.21 55 -0.17 38 93
BIRC5 0.047 0.068 0.23 69 -10000 0 69
DES -0.079 0.17 -10000 0 -0.44 103 103
Aurora C/Aurora B/INCENP 0.053 0.05 0.15 110 -10000 0 110
Aurora B/TACC1 -0.15 0.1 -10000 0 -0.22 345 345
Aurora B/PP2A 0.027 0.042 0.16 51 -10000 0 51
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.019 0.039 0.16 12 -0.14 6 18
mitotic metaphase/anaphase transition -0.008 0.005 -10000 0 -10000 0 0
NDC80 0.23 0.12 0.26 504 -10000 0 504
Cul3 protein complex -0.056 0.11 -10000 0 -0.23 164 164
KIF2C 0.21 0.085 0.24 485 -10000 0 485
PEBP1 0.018 0.004 -10000 0 -10000 0 0
KIF20A 0.17 0.086 0.22 455 -10000 0 455
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.026 0.047 0.16 51 -0.27 3 54
SEPT1 0.006 0 -10000 0 -10000 0 0
SMC2 0.063 0.095 0.22 149 -10000 0 149
SMC4 0.2 0.058 0.22 525 -10000 0 525
NSUN2/NPM1/Nucleolin 0.045 0.096 0.26 91 -10000 0 91
PSMA3 0.006 0.019 0.22 1 -0.38 1 2
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B 0.033 0.065 0.15 112 -0.27 6 118
AURKB 0.057 0.083 0.22 113 -10000 0 113
AURKC 0.006 0 -10000 0 -10000 0 0
CDCA8 0.043 0.063 0.23 58 -10000 0 58
cytokinesis 0.01 0.059 0.33 16 -10000 0 16
Aurora B/Septin1 0.092 0.15 0.34 128 -10000 0 128
AURKA 0.21 0.049 0.22 539 -10000 0 539
INCENP 0.024 0.014 0.23 2 -10000 0 2
KLHL13 -0.1 0.18 0.22 9 -0.38 161 170
BUB1 0.2 0.059 0.22 520 -10000 0 520
hSgo1/Aurora B/Survivin 0.095 0.079 0.17 312 -10000 0 312
EVI5 0.012 0.025 0.22 1 -0.37 2 3
RhoA/GTP 0.011 0.045 0.2 27 -10000 0 27
SGOL1 0.19 0.074 0.22 493 -10000 0 493
CENPA 0.2 0.086 0.22 509 -10000 0 509
NCAPG 0.2 0.071 0.22 500 -10000 0 500
Aurora B/HC8 Proteasome 0.027 0.044 0.16 51 -0.27 1 52
NCAPD2 0.12 0.11 0.22 289 -10000 0 289
Aurora B/PP1-gamma 0.027 0.044 0.16 50 -0.27 1 51
RHOA 0.005 0.023 -10000 0 -0.38 2 2
NCAPH 0.13 0.11 0.22 335 -10000 0 335
NPM1 0 0 -10000 0 -10000 0 0
RASA1 0.004 0.028 -10000 0 -0.38 3 3
KLHL9 0.004 0.028 -10000 0 -0.38 3 3
mitotic prometaphase 0.011 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.044 0.16 51 -0.27 1 52
PPP1CC 0.007 0.023 0.22 3 -0.38 1 4
Centraspindlin 0.35 0.14 0.39 508 -10000 0 508
RhoA/GDP 0.004 0.016 -10000 0 -0.27 2 2
NSUN2 0.001 0.021 0.35 2 -10000 0 2
MYLK 0.005 0.1 0.15 95 -0.27 56 151
KIF23 0.22 0.053 0.23 535 -10000 0 535
VIM -0.008 0.13 0.19 77 -0.27 85 162
RACGAP1 0.19 0.082 0.23 470 -10000 0 470
mitosis 0 0 -10000 0 -10000 0 0
NCL 0 0 -10000 0 -10000 0 0
Chromosomal passenger complex 0.22 0.096 0.24 481 -10000 0 481
Chromosomal passenger complex/EVI5 0.01 0.024 -10000 0 -0.19 1 1
TACC1 -0.3 0.16 -10000 0 -0.38 440 440
PPP2R5D 0.006 0 -10000 0 -10000 0 0
CUL3 0.006 0 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.008 0.064 -10000 0 -0.46 2 2
Crk/p130 Cas/Paxillin -0.17 0.12 -10000 0 -0.3 234 234
JUN -0.06 0.1 0.22 2 -0.32 2 4
HRAS 0.006 0 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.063 0.11 -10000 0 -0.2 210 210
RAP1A 0.007 0.009 0.22 1 -10000 0 1
FRS2 0.013 0.038 0.22 18 -10000 0 18
RAP1A/GDP 0.005 0 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.064 0.11 -10000 0 -0.2 212 212
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.006 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.006 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.068 0.11 0.14 9 -0.2 217 226
RHOA 0.005 0.023 -10000 0 -0.38 2 2
RAP1A/GTP -0.059 0.095 -10000 0 -0.18 210 210
GRB7 0.006 0.035 0.22 5 -0.38 3 8
RET51/GFRalpha1/GDNF -0.063 0.11 -10000 0 -0.2 211 211
MAPKKK cascade -0.071 0.1 -10000 0 -0.2 196 196
BCAR1 0.004 0.028 -10000 0 -0.38 3 3
RET9/GFRalpha1/GDNF/IRS1 -0.18 0.15 0.14 8 -0.26 400 408
lamellipodium assembly -0.16 0.12 -10000 0 -0.28 229 229
RET51/GFRalpha1/GDNF/SHC -0.063 0.11 -10000 0 -0.2 211 211
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
RET9/GFRalpha1/GDNF/SHC -0.067 0.11 0.14 9 -0.2 215 224
RET9/GFRalpha1/GDNF/Shank3 -0.067 0.11 0.14 9 -0.2 215 224
MAPK3 -0.082 0.1 0.23 1 -0.2 232 233
DOK1 0.006 0.016 -10000 0 -0.38 1 1
DOK6 0.006 0 -10000 0 -10000 0 0
PXN -0.002 0.056 -10000 0 -0.38 12 12
neurite development -0.088 0.12 0.23 1 -0.35 50 51
DOK5 0.085 0.14 0.22 241 -0.38 18 259
GFRA1 -0.14 0.19 0.22 9 -0.38 215 224
MAPK8 -0.061 0.1 0.22 2 -0.2 197 199
HRAS/GTP -0.073 0.11 -10000 0 -0.22 196 196
tube development -0.064 0.1 0.14 9 -0.19 215 224
MAPK1 -0.067 0.087 0.23 1 -0.18 209 210
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.07 0.11 0.21 1 -0.21 207 208
Rac1/GDP 0.004 0.011 -10000 0 -0.27 1 1
SRC 0.006 0 -10000 0 -10000 0 0
PDLIM7 0.004 0.028 -10000 0 -0.38 3 3
RET51/GFRalpha1/GDNF/Dok6 -0.058 0.11 -10000 0 -0.19 211 211
SHC1 0.006 0 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.063 0.11 -10000 0 -0.2 211 211
RET51/GFRalpha1/GDNF/Dok5 -0.015 0.13 -10000 0 -0.22 133 133
PRKCA 0.005 0.044 0.22 7 -0.38 5 12
HRAS/GDP 0.005 0 -10000 0 -10000 0 0
CREB1 -0.083 0.12 0.22 1 -0.25 199 200
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.076 0.11 -10000 0 -0.21 215 215
RET51/GFRalpha1/GDNF/Grb7 -0.063 0.11 -10000 0 -0.2 210 210
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.01 0.028 0.22 10 -10000 0 10
DOK4 0.006 0 -10000 0 -10000 0 0
JNK cascade -0.059 0.099 0.22 2 -0.31 2 4
RET9/GFRalpha1/GDNF/FRS2 -0.064 0.11 0.14 17 -0.2 207 224
SHANK3 0.006 0 -10000 0 -10000 0 0
RASA1 0.004 0.028 -10000 0 -0.38 3 3
NCK1 0.024 0.059 0.22 47 -10000 0 47
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.07 0.11 0.22 1 -0.21 203 204
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.068 0.11 0.22 2 -0.21 203 205
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.064 0.11 0.22 1 -0.21 199 200
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.067 0.11 0.21 2 -0.21 199 201
PI3K -0.22 0.18 0.23 1 -0.4 229 230
SOS1 0.014 0.04 0.22 20 -10000 0 20
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.062 0.1 -10000 0 -0.19 215 215
GRB10 0.007 0.009 0.22 1 -10000 0 1
activation of MAPKK activity -0.065 0.1 0.19 2 -0.2 203 205
RET51/GFRalpha1/GDNF/FRS2 -0.06 0.11 -10000 0 -0.2 203 203
GAB1 0.004 0.033 -10000 0 -0.38 4 4
IRS1 -0.21 0.2 -10000 0 -0.38 311 311
IRS2 0.006 0 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.073 0.11 0.21 1 -0.21 211 212
RET51/GFRalpha1/GDNF/PKC alpha -0.064 0.11 -10000 0 -0.21 213 213
GRB2 0.006 0.016 -10000 0 -0.38 1 1
PRKACA 0.006 0 -10000 0 -10000 0 0
GDNF 0.006 0 -10000 0 -10000 0 0
RAC1 0.006 0.016 -10000 0 -0.38 1 1
RET51/GFRalpha1/GDNF/IRS1 -0.18 0.15 -10000 0 -0.26 396 396
Rac1/GTP -0.18 0.14 -10000 0 -0.33 229 229
RET9/GFRalpha1/GDNF -0.08 0.11 -10000 0 -0.22 215 215
GFRalpha1/GDNF -0.096 0.14 -10000 0 -0.27 215 215
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.12 0.17 0.32 177 -0.24 22 199
NF kappa B1 p50/RelA/I kappa B alpha 0.089 0.19 0.36 136 -0.36 23 159
alphaV/beta3 Integrin/Osteopontin/Src 0 0.034 0.21 2 -0.34 4 6
AP1 0.066 0.27 0.43 141 -0.41 59 200
ILK 0.099 0.16 0.28 157 -0.47 3 160
bone resorption 0.009 0.17 0.22 131 -0.32 55 186
PTK2B 0.005 0.023 -10000 0 -0.38 2 2
PYK2/p130Cas 0.097 0.14 0.25 166 -0.25 23 189
ITGAV 0.028 0.065 0.23 35 -0.39 3 38
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.097 0.14 -10000 0 -0.27 216 216
alphaV/beta3 Integrin/Osteopontin 0.03 0.12 0.25 8 -0.25 48 56
MAP3K1 0.098 0.16 0.28 164 -0.27 22 186
JUN 0.008 0.041 0.22 9 -0.39 3 12
MAPK3 0.13 0.22 0.43 163 -0.37 12 175
MAPK1 0.15 0.22 0.43 177 -0.44 3 180
Rac1/GDP 0.004 0.011 -10000 0 -0.27 1 1
NFKB1 -0.001 0.054 -10000 0 -0.38 11 11
MAPK8 0.097 0.16 0.29 164 -0.27 20 184
ITGB3 -0.034 0.15 0.24 13 -0.39 82 95
NFKBIA 0.14 0.23 0.43 173 -0.36 17 190
FOS -0.066 0.16 0.23 8 -0.39 110 118
CD44 -0.14 0.19 -10000 0 -0.38 218 218
CHUK 0.011 0.031 0.22 12 -10000 0 12
PLAU 0.18 0.31 0.64 157 -0.44 4 161
NF kappa B1 p50/RelA 0.093 0.2 0.41 130 -0.36 17 147
BCAR1 0.004 0.028 -10000 0 -0.38 3 3
RELA 0.005 0.023 -10000 0 -0.38 2 2
alphaV beta3 Integrin -0.015 0.12 0.22 3 -0.28 83 86
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.095 0.15 0.26 166 -0.26 22 188
VAV3 0.1 0.16 0.27 192 -0.39 4 196
MAP3K14 0.13 0.19 0.37 173 -0.26 22 195
ROCK2 0.007 0.016 0.22 3 -10000 0 3
SPP1 0.15 0.11 0.23 381 -0.39 3 384
RAC1 0.006 0.016 -10000 0 -0.38 1 1
Rac1/GTP 0.023 0.098 0.22 32 -0.26 10 42
MMP2 0.024 0.28 0.37 137 -0.47 72 209
Circadian rhythm 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
chromatin modification 0.089 0.1 0.38 7 -10000 0 7
CLOCK 0.031 0.039 0.23 13 -10000 0 13
TIMELESS/CRY2 0.17 0.18 0.38 253 -10000 0 253
DEC1/BMAL1 0.024 0.019 0.18 1 -10000 0 1
ATR 0.071 0.099 0.22 170 -10000 0 170
NR1D1 0.12 0.23 -10000 0 -0.95 14 14
ARNTL 0.027 0.029 0.23 3 -10000 0 3
TIMELESS 0.24 0.27 0.53 254 -10000 0 254
NPAS2 0.03 0.046 0.23 14 -0.35 2 16
CRY2 0.006 0 -10000 0 -10000 0 0
mol:CO -0.082 0.093 0.14 3 -0.18 254 257
CHEK1 0.2 0.063 0.22 516 -10000 0 516
mol:HEME 0.082 0.093 0.18 254 -0.14 3 257
PER1 0.006 0.016 -10000 0 -0.38 1 1
BMAL/CLOCK/NPAS2 0.1 0.1 0.22 253 -0.23 1 254
BMAL1/CLOCK 0.13 0.18 0.4 6 -0.8 4 10
S phase of mitotic cell cycle 0.089 0.1 0.38 7 -10000 0 7
TIMELESS/CHEK1/ATR 0.091 0.11 0.39 7 -10000 0 7
mol:NADPH 0.082 0.093 0.18 254 -0.14 3 257
PER1/TIMELESS 0.17 0.18 0.38 253 -10000 0 253
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.006 0 -10000 0 -10000 0 0
S1P3 pathway

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
PDGFRB -0.01 0.079 -10000 0 -0.38 24 24
mol:S1P -0.017 0.016 0.055 4 -0.03 335 339
S1P1/S1P/Gi -0.067 0.086 0.2 5 -0.3 26 31
GNAO1 -0.019 0.043 0.22 6 -0.4 3 9
S1P/S1P3/G12/G13 -0.017 0.025 0.11 1 -0.2 1 2
AKT1 -0.073 0.12 -10000 0 -0.53 24 24
AKT3 -0.63 0.54 0.55 4 -1.1 337 341
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.01 0.079 -10000 0 -0.38 24 24
GNAI2 -0.019 0.023 -10000 0 -10000 0 0
GNAI3 -0.006 0.055 0.21 29 -10000 0 29
GNAI1 -0.023 0.066 0.2 7 -0.4 13 20
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 -0.02 0.019 0.066 4 -0.034 337 341
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 -0.003 0.058 -10000 0 -0.38 13 13
mol:Ca2+ -0.14 0.14 0.34 4 -0.26 322 326
MAPK3 -0.15 0.15 0.3 4 -0.27 325 329
MAPK1 -0.14 0.14 0.3 4 -0.25 321 325
JAK2 -0.14 0.14 0.3 4 -0.25 307 311
CXCR4 -0.13 0.14 0.3 4 -0.25 308 312
FLT1 -0.024 0.028 -10000 0 -10000 0 0
RhoA/GDP 0.004 0.016 -10000 0 -0.27 2 2
Rac1/GDP 0.004 0.011 -10000 0 -0.27 1 1
SRC -0.14 0.13 0.3 4 -0.25 321 325
S1P/S1P3/Gi -0.14 0.14 0.34 4 -0.26 322 326
RAC1 0.006 0.016 -10000 0 -0.38 1 1
RhoA/GTP -0.13 0.13 0.27 4 -0.24 321 325
VEGFA -0.018 0.044 0.22 11 -10000 0 11
S1P/S1P2/Gi -0.083 0.094 0.22 5 -0.29 22 27
VEGFR1 homodimer/VEGFA homodimer -0.033 0.046 0.25 4 -10000 0 4
RHOA 0.005 0.023 -10000 0 -0.38 2 2
S1P/S1P3/Gq -0.094 0.12 -10000 0 -0.24 200 200
GNAQ -0.005 0.065 -10000 0 -0.38 16 16
GNAZ -0.021 0.045 -10000 0 -0.4 6 6
G12/G13 0.009 0.012 -10000 0 -0.27 1 1
GNA14 0.006 0.026 0.22 2 -0.38 2 4
GNA15 0.003 0.037 -10000 0 -0.38 5 5
GNA12 0.006 0 -10000 0 -10000 0 0
GNA13 0.006 0.016 -10000 0 -0.38 1 1
GNA11 -0.13 0.18 -10000 0 -0.38 193 193
Rac1/GTP -0.13 0.13 0.27 4 -0.24 321 325
IL2 signaling events mediated by STAT5

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
GAB2 0.003 0.069 0.22 16 -0.38 13 29
ELF1 0.005 0.046 0.18 4 -0.39 7 11
CCNA2 0.19 0.081 0.22 473 -10000 0 473
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
JAK3 0.006 0 -10000 0 -10000 0 0
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
JAK1 0.004 0.028 -10000 0 -0.38 3 3
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0 0.087 -10000 0 -0.46 1 1
SHC1 0.006 0 -10000 0 -10000 0 0
SP1 -0.24 0.14 -10000 0 -0.32 446 446
IL2RA 0.004 0.045 0.41 4 -0.27 7 11
IL2RB 0.001 0.046 -10000 0 -0.38 8 8
SOS1 0.014 0.04 0.22 20 -10000 0 20
IL2RG -0.007 0.11 0.22 31 -0.38 37 68
G1/S transition of mitotic cell cycle -0.37 0.27 0.34 9 -0.51 446 455
PTPN11 0.006 0 -10000 0 -10000 0 0
CCND2 -0.5 0.27 0.41 5 -0.64 446 451
LCK 0.006 0 -10000 0 -10000 0 0
GRB2 0.006 0.016 -10000 0 -0.38 1 1
IL2 0.006 0 -10000 0 -10000 0 0
CDK6 0.004 0.057 0.22 10 -0.38 9 19
CCND3 0.001 0.08 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 0.25 0.44 0.82 100 -0.89 21 121
HDAC7 0.011 0.036 0.16 14 -10000 0 14
HIF1A/ARNT/Cbp/p300/Src-1 0.009 0.26 0.78 25 -0.72 14 39
SMAD4 0.004 0.012 -10000 0 -10000 0 0
ID2 0.25 0.44 0.81 100 -0.89 21 121
AP1 -0.042 0.12 0.17 10 -0.27 111 121
ABCG2 0.22 0.44 0.8 100 -0.89 25 125
HIF1A 0.083 0.14 0.3 99 -0.46 2 101
TFF3 -0.011 0.37 0.86 26 -0.89 38 64
GATA2 0.008 0.037 0.19 6 -0.38 3 9
AKT1 0.11 0.15 0.35 91 -10000 0 91
response to hypoxia 0.071 0.14 0.32 120 -10000 0 120
MCL1 0.25 0.44 0.8 110 -0.89 21 131
NDRG1 0.26 0.45 0.83 113 -0.92 22 135
SERPINE1 0.28 0.46 0.87 117 -0.89 21 138
FECH 0.25 0.44 0.81 101 -0.89 21 122
FURIN 0.25 0.44 0.81 100 -0.9 22 122
NCOA2 0.007 0.013 0.22 2 -10000 0 2
EP300 0.21 0.24 0.56 139 -0.31 1 140
HMOX1 0.25 0.44 0.81 110 -0.9 23 133
BHLHE40 0.22 0.44 0.78 131 -0.89 21 152
BHLHE41 0.22 0.44 0.78 131 -0.89 21 152
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.012 0.1 0.41 16 -0.3 4 20
ENG 0.11 0.16 0.37 26 -0.39 8 34
JUN 0.01 0.037 0.22 9 -0.38 2 11
RORA 0.25 0.44 0.81 100 -0.89 21 121
ABCB1 -0.015 0.076 0.68 4 -10000 0 4
TFRC 0.3 0.47 0.88 130 -0.89 21 151
CXCR4 0.26 0.44 0.82 112 -0.89 21 133
TF 0.25 0.44 0.82 102 -0.89 21 123
CITED2 0.24 0.44 0.82 97 -0.93 21 118
HIF1A/ARNT -0.064 0.24 0.76 4 -0.98 22 26
LDHA 0.044 0.19 0.64 50 -10000 0 50
ETS1 0.25 0.44 0.81 110 -0.89 21 131
PGK1 0.32 0.49 0.91 152 -0.9 20 172
NOS2 0.22 0.44 0.78 131 -0.89 21 152
ITGB2 0.25 0.44 0.81 110 -0.92 23 133
ALDOA 0.25 0.44 0.81 100 -0.89 21 121
Cbp/p300/CITED2 0.2 0.43 0.83 91 -0.93 20 111
FOS -0.064 0.16 0.22 8 -0.38 110 118
HK2 0.25 0.44 0.82 100 -0.89 21 121
SP1 0.007 0.022 0.21 4 -10000 0 4
GCK 0.26 0.3 0.76 89 -10000 0 89
HK1 0.25 0.44 0.81 100 -0.89 21 121
NPM1 0.25 0.44 0.82 95 -0.89 21 116
EGLN1 0.25 0.44 0.81 101 -0.89 21 122
CREB1 0.05 0.086 0.22 112 -10000 0 112
PGM1 0.26 0.45 0.83 119 -0.89 21 140
SMAD3 0 0.038 -10000 0 -0.39 5 5
EDN1 0.15 0.23 0.72 26 -1.2 1 27
IGFBP1 0.25 0.44 0.81 101 -0.89 21 122
VEGFA 0.29 0.4 0.83 115 -0.64 14 129
HIF1A/JAB1 -0.001 0.046 0.22 11 -0.33 2 13
CP 0.41 0.48 0.92 175 -0.93 23 198
CXCL12 0.21 0.45 0.81 101 -0.9 27 128
COPS5 0.021 0.053 0.22 37 -10000 0 37
SMAD3/SMAD4 0.003 0.032 -10000 0 -0.23 7 7
BNIP3 0.27 0.46 0.88 105 -0.88 22 127
EGLN3 0.26 0.46 0.84 107 -0.9 25 132
CA9 0.28 0.46 0.87 117 -0.89 21 138
TERT 0.25 0.44 0.81 100 -0.89 21 121
ENO1 0.25 0.44 0.81 100 -0.89 21 121
PFKL 0.25 0.44 0.82 100 -0.89 21 121
NCOA1 0.004 0.028 -10000 0 -0.38 3 3
ADM 0.26 0.46 0.89 103 -0.89 21 124
ARNT 0.085 0.13 0.3 99 -10000 0 99
HNF4A 0.007 0.009 0.22 1 -10000 0 1
ADFP 0.3 0.48 0.91 123 -0.89 21 144
SLC2A1 0.3 0.41 0.87 106 -0.64 14 120
LEP 0.25 0.44 0.81 100 -0.89 21 121
HIF1A/ARNT/Cbp/p300 0.015 0.28 0.84 28 -0.75 14 42
EPO 0.26 0.34 0.74 85 -0.82 1 86
CREBBP 0.21 0.25 0.58 131 -10000 0 131
HIF1A/ARNT/Cbp/p300/HDAC7 0.003 0.25 0.72 23 -0.72 14 37
PFKFB3 0.23 0.45 0.8 108 -0.91 25 133
NT5E 0.25 0.47 0.85 116 -0.93 27 143
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 0.018 0.06 0.2 57 -10000 0 57
GNB1/GNG2 -0.086 0.11 -10000 0 -0.21 252 252
regulation of S phase of mitotic cell cycle -0.086 0.13 -10000 0 -0.23 223 223
GNAO1 0.006 0.036 0.22 6 -0.38 3 9
HRAS 0.004 0.006 -10000 0 -10000 0 0
SHBG/T-DHT 0.004 0 -10000 0 -10000 0 0
PELP1 0.004 0.006 -10000 0 -10000 0 0
AKT1 -0.001 0.008 0.2 1 -10000 0 1
MAP2K1 -0.094 0.095 0.2 5 -0.27 49 54
T-DHT/AR -0.12 0.14 -10000 0 -0.27 251 251
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 0.007 8 -0.006 82 90
GNAI2 0.006 0 -10000 0 -10000 0 0
GNAI3 0.017 0.047 0.22 29 -10000 0 29
GNAI1 0 0.064 0.22 7 -0.39 13 20
mol:GDP -0.16 0.18 -10000 0 -0.34 262 262
cell proliferation -0.2 0.19 0.28 7 -0.43 185 192
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
FOS -0.2 0.29 0.43 8 -0.78 111 119
mol:Ca2+ -0.018 0.021 0.042 5 -0.056 62 67
MAPK3 -0.18 0.16 0.33 2 -0.36 198 200
MAPK1 -0.087 0.095 0.22 7 -0.26 76 83
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
mol:IP3 -0.001 0.002 0.012 8 -0.004 62 70
cAMP biosynthetic process 0.012 0.016 -10000 0 -10000 0 0
GNG2 0.004 0.034 0.22 1 -0.38 4 5
potassium channel inhibitor activity -0.001 0.002 0.012 8 -0.004 62 70
HRAS/GTP -0.083 0.099 0.13 5 -0.19 248 253
actin cytoskeleton reorganization -0.013 0.057 -10000 0 -0.18 57 57
SRC 0.004 0.006 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 0.012 8 -0.004 62 70
PI3K -0.017 0.069 -10000 0 -0.22 56 56
apoptosis 0.16 0.18 0.48 111 -0.33 7 118
T-DHT/AR/PELP1 -0.097 0.12 -10000 0 -0.23 251 251
HRAS/GDP -0.15 0.17 -10000 0 -0.33 251 251
CREB1 -0.17 0.19 0.42 2 -0.5 120 122
RAC1-CDC42/GTP -0.012 0.058 -10000 0 -0.18 57 57
AR -0.17 0.19 -10000 0 -0.39 251 251
GNB1 0.006 0.016 -10000 0 -0.38 1 1
RAF1 -0.092 0.092 0.16 5 -0.19 248 253
RAC1-CDC42/GDP -0.15 0.17 -10000 0 -0.32 251 251
T-DHT/AR/PELP1/Src -0.088 0.11 -10000 0 -0.21 251 251
MAP2K2 -0.16 0.12 0.23 2 -0.32 148 150
T-DHT/AR/PELP1/Src/PI3K -0.087 0.13 -10000 0 -0.23 223 223
GNAZ 0.002 0.04 -10000 0 -0.38 6 6
SHBG 0.006 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.032 0.067 -10000 0 -0.29 14 14
mol:T-DHT 0 0.001 -10000 0 -10000 0 0
RAC1 0.006 0.016 -10000 0 -0.38 1 1
GNRH1 -0.002 0.001 -10000 0 -10000 0 0
Gi family/GTP -0.052 0.074 -10000 0 -0.25 19 19
CDC42 0.006 0 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A 0.11 0.099 0.2 317 -10000 0 317
TP53 0 0.1 0.22 1 -0.22 91 92
Senescence 0.001 0.1 0.22 1 -0.22 91 92
Apoptosis 0.001 0.1 0.22 1 -0.22 91 92
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.073 0.067 0.22 3 -0.27 1 4
MDM4 0.015 0.043 0.22 23 -10000 0 23
IGF1 pathway

Figure S14.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S14.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.006 0 -10000 0 -10000 0 0
PTK2 0.028 0.065 0.22 57 -10000 0 57
CRKL -0.12 0.13 -10000 0 -0.32 135 135
GRB2/SOS1/SHC 0.012 0.01 -10000 0 -0.23 1 1
HRAS 0.006 0 -10000 0 -10000 0 0
IRS1/Crk -0.12 0.13 -10000 0 -0.32 135 135
IGF-1R heterotetramer/IGF1/PTP1B -0.07 0.11 -10000 0 -0.26 135 135
AKT1 -0.097 0.13 -10000 0 -0.29 131 131
BAD -0.093 0.12 -10000 0 -0.3 110 110
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.12 0.13 -10000 0 -0.32 135 135
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.12 0.13 -10000 0 -0.32 135 135
RAF1 -0.085 0.12 -10000 0 -0.29 89 89
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.1 0.13 -10000 0 -0.3 135 135
YWHAZ 0.006 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.12 0.14 -10000 0 -0.22 339 339
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
RPS6KB1 -0.095 0.13 0.24 1 -0.29 129 130
GNB2L1 0.006 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.076 0.1 -10000 0 -0.26 89 89
PXN -0.002 0.056 -10000 0 -0.38 12 12
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.009 0.012 -10000 0 -0.27 1 1
HRAS/GTP -0.099 0.12 -10000 0 -0.28 135 135
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.047 0.094 -10000 0 -0.21 131 131
IGF-1R heterotetramer -0.11 0.17 -10000 0 -0.44 121 121
IGF-1R heterotetramer/IGF1/IRS/Nck -0.11 0.13 -10000 0 -0.32 135 135
Crk/p130 Cas/Paxillin -0.11 0.13 -10000 0 -0.3 146 146
IGF1R -0.11 0.17 -10000 0 -0.44 121 121
IGF1 -0.042 0.077 0.18 4 -0.42 16 20
IRS2/Crk -0.11 0.12 -10000 0 -0.3 135 135
PI3K -0.1 0.15 -10000 0 -0.28 178 178
apoptosis 0.083 0.11 0.26 110 -10000 0 110
HRAS/GDP 0.005 0 -10000 0 -10000 0 0
PRKCD -0.099 0.13 -10000 0 -0.32 134 134
RAF1/14-3-3 E -0.074 0.11 -10000 0 -0.26 89 89
BAD/14-3-3 -0.088 0.12 -10000 0 -0.28 110 110
PRKCZ -0.097 0.13 -10000 0 -0.29 131 131
Crk/p130 Cas/Paxillin/FAK1 -0.094 0.11 -10000 0 -0.28 105 105
PTPN1 0.006 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.1 0.14 -10000 0 -0.33 134 134
BCAR1 0.004 0.028 -10000 0 -0.38 3 3
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.058 0.097 0.15 1 -0.22 135 136
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.014 0.04 0.22 20 -10000 0 20
IRS1/NCK2 -0.12 0.13 -10000 0 -0.32 135 135
GRB10 0.007 0.009 0.22 1 -10000 0 1
PTPN11 -0.12 0.13 -10000 0 -0.32 135 135
IRS1 -0.08 0.15 -10000 0 -0.34 135 135
IRS2 -0.12 0.13 -10000 0 -0.32 135 135
IGF-1R heterotetramer/IGF1 -0.096 0.14 -10000 0 -0.34 135 135
GRB2 0.006 0.016 -10000 0 -0.38 1 1
PDPK1 -0.1 0.14 -10000 0 -0.28 174 174
YWHAE 0.006 0.016 -10000 0 -0.38 1 1
PRKD1 -0.097 0.13 -10000 0 -0.32 128 128
SHC1 0.006 0 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.075 0.16 0.21 6 -0.4 108 114
PDGF/PDGFRA/CRKL -0.049 0.11 -10000 0 -0.27 110 110
positive regulation of JUN kinase activity -0.026 0.087 -10000 0 -0.2 103 103
CRKL 0.006 0 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.05 0.11 -10000 0 -0.27 111 111
AP1 -0.18 0.34 0.52 8 -0.83 112 120
mol:IP3 -0.061 0.11 0.18 9 -0.29 106 115
PLCG1 -0.061 0.11 0.19 9 -0.29 106 115
PDGF/PDGFRA/alphaV Integrin -0.05 0.11 -10000 0 -0.27 109 109
RAPGEF1 0.006 0 -10000 0 -10000 0 0
CRK 0.006 0 -10000 0 -10000 0 0
mol:Ca2+ -0.061 0.11 0.18 9 -0.28 106 115
CAV3 0.006 0.016 -10000 0 -0.38 1 1
CAV1 -0.062 0.15 0.22 3 -0.38 101 104
SHC/Grb2/SOS1 -0.025 0.088 -10000 0 -0.2 103 103
PDGF/PDGFRA/Shf -0.049 0.11 -10000 0 -0.27 110 110
FOS -0.18 0.33 0.56 6 -0.82 112 118
JUN -0.018 0.046 0.22 9 -0.31 3 12
oligodendrocyte development -0.05 0.11 -10000 0 -0.27 109 109
GRB2 0.006 0.016 -10000 0 -0.38 1 1
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
mol:DAG -0.061 0.11 0.18 9 -0.29 106 115
PDGF/PDGFRA -0.075 0.16 0.21 6 -0.4 108 114
actin cytoskeleton reorganization -0.049 0.11 -10000 0 -0.27 110 110
SRF 0 0.03 -10000 0 -0.27 6 6
SHC1 0.006 0 -10000 0 -10000 0 0
PI3K -0.057 0.12 -10000 0 -0.27 125 125
PDGF/PDGFRA/Crk/C3G -0.038 0.092 -10000 0 -0.22 108 108
JAK1 -0.057 0.11 0.18 6 -0.27 110 116
ELK1/SRF -0.053 0.089 -10000 0 -0.23 110 110
SHB 0.006 0 -10000 0 -10000 0 0
SHF 0.006 0 -10000 0 -10000 0 0
CSNK2A1 0.016 0.019 -10000 0 -10000 0 0
GO:0007205 -0.066 0.13 0.2 9 -0.31 108 117
SOS1 0.014 0.04 0.22 20 -10000 0 20
Ras protein signal transduction -0.026 0.087 -10000 0 -0.2 103 103
PDGF/PDGFRA/SHB -0.049 0.11 -10000 0 -0.27 110 110
PDGF/PDGFRA/Caveolin-1 -0.095 0.16 -10000 0 -0.32 176 176
ITGAV 0.017 0.06 0.22 35 -0.38 3 38
ELK1 -0.065 0.11 0.2 6 -0.28 108 114
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
PDGF/PDGFRA/Crk -0.049 0.11 -10000 0 -0.27 110 110
JAK-STAT cascade -0.057 0.11 0.18 6 -0.27 110 116
cell proliferation -0.049 0.11 -10000 0 -0.27 110 110
Endothelins

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
AKT1 0.022 0.2 0.39 88 -0.36 18 106
PTK2B 0.005 0.023 -10000 0 -0.39 2 2
mol:Ca2+ -0.017 0.16 0.43 8 -0.46 8 16
EDN1 0.02 0.15 0.3 90 -0.29 11 101
EDN3 0.008 0.018 0.22 4 -10000 0 4
EDN2 0.011 0.031 0.22 12 -10000 0 12
HRAS/GDP -0.024 0.18 0.31 19 -0.38 38 57
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.038 0.15 0.3 12 -0.32 55 67
ADCY4 0.039 0.17 0.27 148 -0.3 18 166
ADCY5 0.039 0.17 0.27 148 -0.3 18 166
ADCY6 0.038 0.17 0.27 148 -0.3 18 166
ADCY7 0.038 0.17 0.27 148 -0.3 18 166
ADCY1 0.038 0.17 0.27 148 -0.3 18 166
ADCY2 0.038 0.17 0.27 148 -0.3 18 166
ADCY3 0.039 0.17 0.27 148 -0.3 18 166
ADCY8 -0.037 0.18 0.27 75 -0.34 62 137
ADCY9 0.022 0.18 0.27 144 -0.32 40 184
arachidonic acid secretion -0.15 0.26 0.43 9 -0.52 131 140
ETB receptor/Endothelin-1/Gq/GTP -0.023 0.15 0.23 16 -0.28 72 88
GNAO1 0.006 0.036 0.22 6 -0.38 3 9
HRAS 0.004 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.016 0.18 0.37 92 -0.33 19 111
ETA receptor/Endothelin-1/Gs/GTP 0.015 0.17 0.36 86 -0.32 18 104
mol:GTP 0 0.009 -10000 0 -10000 0 0
COL3A1 0.11 0.31 0.54 169 -0.59 14 183
EDNRB 0.053 0.078 0.17 163 -10000 0 163
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.031 0.28 0.39 89 -0.49 114 203
CYSLTR1 0.036 0.23 0.43 110 -0.42 10 120
SLC9A1 0.009 0.13 0.27 87 -0.23 13 100
mol:GDP -0.026 0.19 0.33 17 -0.4 38 55
SLC9A3 0.049 0.16 0.36 9 -0.41 5 14
RAF1 -0.048 0.21 0.38 12 -0.4 87 99
JUN -0.02 0.18 0.52 8 -0.68 8 16
JAK2 0.02 0.2 0.39 88 -0.37 20 108
mol:IP3 -0.034 0.16 0.26 62 -0.34 48 110
ETA receptor/Endothelin-1 0.013 0.23 0.45 92 -0.3 108 200
PLCB1 0.023 0.061 0.22 49 -10000 0 49
PLCB2 0.003 0.008 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 0.007 0.092 0.19 86 -0.17 13 99
FOS -0.18 0.38 0.56 8 -0.91 110 118
Gai/GDP 0.007 0.073 -10000 0 -0.66 3 3
CRK 0.006 0.001 -10000 0 -10000 0 0
mol:Ca ++ 0.004 0.23 0.36 115 -0.39 51 166
BCAR1 0.004 0.028 -10000 0 -0.38 3 3
PRKCB1 -0.03 0.16 0.29 17 -0.36 35 52
GNAQ -0.007 0.066 -10000 0 -0.39 16 16
GNAZ 0.002 0.04 -10000 0 -0.38 6 6
GNAL 0.006 0 -10000 0 -10000 0 0
Gs family/GDP -0.07 0.12 -10000 0 -0.35 47 47
ETA receptor/Endothelin-1/Gq/GTP -0.049 0.17 0.26 62 -0.36 62 124
MAPK14 -0.016 0.13 0.23 9 -0.3 32 41
TRPC6 -0.019 0.17 0.46 5 -0.49 7 12
GNAI2 0.006 0 -10000 0 -10000 0 0
GNAI3 0.017 0.047 0.22 29 -10000 0 29
GNAI1 0 0.063 0.22 7 -0.38 13 20
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.017 0.14 0.24 12 -0.28 47 59
ETB receptor/Endothelin-2 0.037 0.053 0.14 22 -10000 0 22
ETB receptor/Endothelin-3 0.038 0.052 0.14 22 -10000 0 22
ETB receptor/Endothelin-1 0.036 0.15 0.35 92 -0.26 10 102
MAPK3 -0.17 0.36 0.52 8 -0.8 121 129
MAPK1 -0.15 0.33 0.52 8 -0.75 113 121
Rac1/GDP -0.024 0.18 0.31 16 -0.39 36 52
cAMP biosynthetic process -0.013 0.17 0.26 51 -0.31 61 112
MAPK8 -0.027 0.18 0.44 7 -0.46 24 31
SRC 0.006 0.001 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.044 0.099 0.19 100 -0.26 3 103
p130Cas/CRK/Src/PYK2 -0.022 0.18 0.39 11 -0.43 27 38
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.023 0.18 0.31 16 -0.39 35 51
COL1A2 0.08 0.3 0.63 109 -0.72 11 120
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.006 0.091 0.19 83 -0.17 13 96
mol:DAG -0.034 0.16 0.26 62 -0.34 48 110
MAP2K2 -0.15 0.28 0.44 8 -0.59 128 136
MAP2K1 -0.075 0.25 0.48 9 -0.51 109 118
EDNRA 0.01 0.14 0.27 87 -0.23 21 108
positive regulation of muscle contraction 0.014 0.17 0.32 88 -0.32 18 106
Gq family/GDP -0.11 0.15 0.28 5 -0.4 78 83
HRAS/GTP -0.026 0.18 0.3 19 -0.36 53 72
PRKCH -0.031 0.16 0.29 15 -0.36 36 51
RAC1 0.006 0.016 -10000 0 -0.38 1 1
PRKCA -0.031 0.16 0.3 16 -0.37 36 52
PRKCB -0.031 0.15 0.24 68 -0.33 50 118
PRKCE -0.03 0.16 0.29 16 -0.38 30 46
PRKCD -0.032 0.16 0.29 17 -0.37 35 52
PRKCG -0.031 0.16 0.29 17 -0.33 49 66
regulation of vascular smooth muscle contraction -0.23 0.44 0.54 8 -1.1 110 118
PRKCQ -0.033 0.16 0.28 18 -0.37 39 57
PLA2G4A -0.17 0.28 0.43 9 -0.58 131 140
GNA14 0.003 0.028 0.22 2 -0.39 2 4
GNA15 0.001 0.038 -10000 0 -0.39 5 5
GNA12 0.006 0 -10000 0 -10000 0 0
GNA11 -0.13 0.18 -10000 0 -0.39 193 193
Rac1/GTP 0.016 0.18 0.37 92 -0.33 19 111
MMP1 0.05 0.11 0.42 38 -10000 0 38
LPA receptor mediated events

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
GNB1/GNG2 -0.029 0.081 -10000 0 -0.2 105 105
NF kappa B1 p50/RelA/I kappa B alpha -0.051 0.097 -10000 0 -0.26 62 62
AP1 -0.05 0.12 0.16 37 -0.2 175 212
mol:PIP3 -0.065 0.1 -10000 0 -0.21 171 171
AKT1 -0.034 0.091 -10000 0 -0.28 26 26
PTK2B -0.037 0.079 0.16 16 -0.19 103 119
RHOA -0.014 0.055 -10000 0 -0.4 2 2
PIK3CB 0.021 0.059 0.22 41 -0.38 1 42
mol:Ca2+ -0.051 0.072 -10000 0 -0.2 72 72
MAGI3 0.011 0.03 0.22 11 -10000 0 11
RELA 0.005 0.023 -10000 0 -0.38 2 2
apoptosis -0.025 0.087 0.18 24 -0.2 99 123
HRAS/GDP 0.005 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.035 0.07 0.15 11 -0.17 97 108
NF kappa B1 p50/RelA -0.054 0.11 0.18 39 -0.21 133 172
endothelial cell migration -0.072 0.2 0.42 16 -0.49 101 117
ADCY4 -0.032 0.1 0.21 17 -0.23 96 113
ADCY5 -0.032 0.1 0.21 17 -0.23 96 113
ADCY6 -0.033 0.1 0.21 17 -0.23 96 113
ADCY7 -0.033 0.1 0.21 17 -0.23 96 113
ADCY1 -0.033 0.1 0.21 17 -0.23 96 113
ADCY2 -0.033 0.1 0.21 17 -0.23 96 113
ADCY3 -0.032 0.1 0.21 17 -0.23 96 113
ADCY8 -0.094 0.12 0.21 7 -0.21 248 255
ADCY9 -0.048 0.12 0.21 17 -0.27 102 119
GSK3B -0.037 0.075 0.15 16 -0.18 103 119
arachidonic acid secretion -0.032 0.097 0.2 16 -0.22 98 114
GNG2 0.004 0.034 0.22 1 -0.38 4 5
TRIP6 -0.007 0.031 -10000 0 -0.34 3 3
GNAO1 -0.032 0.098 0.22 21 -0.22 102 123
HRAS 0.006 0 -10000 0 -10000 0 0
NFKBIA -0.058 0.097 -10000 0 -0.27 61 61
GAB1 0.004 0.033 -10000 0 -0.38 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.01 0.038 -10000 0 -0.86 1 1
JUN 0.008 0.039 0.22 9 -0.38 3 12
LPA/LPA2/NHERF2 -0.021 0.06 -10000 0 -0.12 119 119
TIAM1 0.007 0.044 -10000 0 -1 1 1
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
mol:IP3 -0.052 0.073 -10000 0 -0.2 72 72
PLCB3 -0.021 0.055 -10000 0 -0.22 28 28
FOS -0.066 0.16 0.22 8 -0.38 110 118
positive regulation of mitosis -0.032 0.097 0.2 16 -0.22 98 114
LPA/LPA1-2-3 -0.031 0.076 -10000 0 -0.19 101 101
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -10000 0 0
BCAR1 0.004 0.028 -10000 0 -0.38 3 3
stress fiber formation -0.03 0.092 0.19 16 -0.22 53 69
GNAZ -0.035 0.097 0.24 16 -0.22 106 122
EGFR/PI3K-beta/Gab1 -0.066 0.11 -10000 0 -0.21 171 171
positive regulation of dendritic cell cytokine production -0.031 0.076 -10000 0 -0.19 101 101
LPA/LPA2/MAGI-3 -0.01 0.032 -10000 0 -10000 0 0
ARHGEF1 -0.03 0.08 0.2 16 -0.18 102 118
GNAI2 -0.033 0.095 0.24 16 -0.22 101 117
GNAI3 -0.025 0.1 0.19 42 -0.22 98 140
GNAI1 -0.036 0.1 0.22 21 -0.23 106 127
LPA/LPA3 -0.017 0.038 -10000 0 -0.099 101 101
LPA/LPA2 -0.017 0.038 -10000 0 -0.098 101 101
LPA/LPA1 -0.044 0.1 -10000 0 -0.26 101 101
HB-EGF/EGFR 0.007 0.086 0.19 16 -0.23 47 63
HBEGF 0.025 0.072 0.2 79 -10000 0 79
mol:DAG -0.052 0.073 -10000 0 -0.2 72 72
cAMP biosynthetic process -0.043 0.1 0.19 17 -0.24 100 117
NFKB1 -0.001 0.054 -10000 0 -0.38 11 11
SRC 0.006 0 -10000 0 -10000 0 0
GNB1 0.005 0.017 -10000 0 -0.38 1 1
LYN -0.06 0.097 -10000 0 -0.26 67 67
GNAQ -0.015 0.051 0.1 16 -0.23 16 32
LPAR2 0 0.001 -10000 0 -10000 0 0
LPAR3 0 0.001 -10000 0 -10000 0 0
LPAR1 -0.024 0.064 0.13 16 -0.15 101 117
IL8 -0.018 0.2 0.48 46 -0.37 52 98
PTK2 -0.009 0.092 0.16 63 -0.18 93 156
Rac1/GDP 0.004 0.011 -10000 0 -0.27 1 1
CASP3 -0.025 0.088 0.18 24 -0.2 99 123
EGFR -0.03 0.12 0.23 1 -0.38 54 55
PLCG1 -0.049 0.07 0.1 11 -0.13 189 200
PLD2 -0.023 0.08 0.2 16 -0.18 101 117
G12/G13 -0.027 0.08 -10000 0 -0.2 102 102
PI3K-beta -0.044 0.089 -10000 0 -0.31 28 28
cell migration -0.006 0.05 0.19 2 -0.27 1 3
SLC9A3R2 -0.013 0.085 -10000 0 -0.38 28 28
PXN -0.03 0.093 0.19 16 -0.23 52 68
HRAS/GTP -0.033 0.098 0.2 16 -0.22 98 114
RAC1 0.006 0.016 -10000 0 -0.38 1 1
MMP9 0.036 0.074 0.22 77 -10000 0 77
PRKCE 0.007 0.009 0.22 1 -10000 0 1
PRKCD -0.05 0.071 -10000 0 -0.2 71 71
Gi(beta/gamma) -0.031 0.1 0.21 17 -0.22 96 113
mol:LPA -0.024 0.064 0.13 16 -0.15 101 117
TRIP6/p130 Cas/FAK1/Paxillin -0.02 0.098 0.2 16 -0.2 89 105
MAPKKK cascade -0.032 0.097 0.2 16 -0.22 98 114
contractile ring contraction involved in cytokinesis -0.014 0.055 -10000 0 -0.4 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.009 0.039 0.1 17 -0.082 97 114
GNA15 -0.011 0.043 0.1 16 -0.25 5 21
GNA12 0.006 0 -10000 0 -10000 0 0
GNA13 0.006 0.016 -10000 0 -0.39 1 1
MAPT -0.036 0.071 0.15 11 -0.17 97 108
GNA11 -0.082 0.11 0.1 11 -0.23 188 199
Rac1/GTP 0.01 0.04 -10000 0 -0.92 1 1
MMP2 -0.072 0.2 0.42 16 -0.49 101 117
TCGA08_rtk_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
PDGFRA -0.067 0.16 0.22 6 -0.38 110 116
HRAS 0.006 0 -10000 0 -10000 0 0
EGFR -0.03 0.12 0.22 1 -0.38 54 55
AKT -0.11 0.16 0.21 12 -0.27 219 231
FOXO3 0.001 0.046 -10000 0 -0.38 8 8
AKT1 0.007 0.009 0.22 1 -10000 0 1
FOXO1 0 0.049 -10000 0 -0.38 9 9
AKT3 -0.22 0.2 0.22 4 -0.38 337 341
FOXO4 0.006 0 -10000 0 -10000 0 0
MET -0.013 0.12 0.22 32 -0.38 45 77
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
PIK3CB 0.021 0.058 0.22 41 -0.38 1 42
NRAS 0.099 0.11 0.22 245 -10000 0 245
PIK3CG 0.013 0.037 0.22 17 -10000 0 17
PIK3R3 0.061 0.094 0.22 144 -10000 0 144
PIK3R2 0.007 0.013 0.22 2 -10000 0 2
NF1 -0.01 0.079 0.22 1 -0.38 24 25
RAS 0.015 0.11 0.18 54 -0.28 30 84
ERBB2 0.005 0.039 0.22 5 -0.38 4 9
proliferation/survival/translation 0.065 0.11 0.21 126 -0.18 7 133
PI3K 0.009 0.12 0.19 60 -0.28 42 102
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
KRAS 0.03 0.067 0.22 62 -10000 0 62
FOXO 0.019 0.043 0.18 15 -10000 0 15
AKT2 0.009 0.024 0.22 7 -10000 0 7
PTEN -0.001 0.054 -10000 0 -0.38 11 11
Thromboxane A2 receptor 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
TGM2 -0.2 0.2 0.22 2 -0.39 295 297
GNB1/GNG2 -0.06 0.071 -10000 0 -0.19 94 94
AKT1 -0.022 0.19 0.36 86 -10000 0 86
EGF 0.009 0.024 0.22 7 -10000 0 7
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.008 0.034 -10000 0 -10000 0 0
mol:Ca2+ -0.062 0.25 0.44 86 -0.36 67 153
LYN -0.013 0.047 -10000 0 -0.31 2 2
RhoA/GTP -0.053 0.058 -10000 0 -0.13 106 106
mol:PGI2 0 0.001 -10000 0 -10000 0 0
SYK -0.061 0.26 0.45 86 -0.37 88 174
GNG2 0.004 0.034 0.22 1 -0.38 4 5
ARRB2 0.006 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.11 0.16 -10000 0 -0.33 198 198
G beta5/gamma2 -0.062 0.11 0.17 40 -0.26 88 128
PRKCH -0.073 0.27 0.45 87 -0.4 88 175
DNM1 0.006 0 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 0.03 0.03 -10000 0 -10000 0 0
mol:GTP 0.001 0.005 -10000 0 -10000 0 0
PTGDR 0.006 0.016 -10000 0 -0.38 1 1
G12 family/GTP -0.12 0.13 -10000 0 -0.25 270 270
ADRBK1 0.006 0 -10000 0 -10000 0 0
ADRBK2 -0.006 0.071 0.22 1 -0.38 19 20
RhoA/GTP/ROCK1 0.007 0.014 -10000 0 -0.23 2 2
mol:GDP 0.035 0.18 0.46 15 -0.31 85 100
mol:NADP 0.006 0.001 -10000 0 -10000 0 0
RAB11A 0.006 0 -10000 0 -10000 0 0
PRKG1 0.007 0.009 0.22 1 -10000 0 1
mol:IP3 -0.089 0.29 0.46 86 -0.43 87 173
cell morphogenesis 0.007 0.014 -10000 0 -0.23 2 2
PLCB2 -0.14 0.35 0.49 84 -0.61 88 172
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.007 0.035 -10000 0 -10000 0 0
mol:PDG2 0 0.001 -10000 0 -10000 0 0
HCK -0.007 0.035 -10000 0 -10000 0 0
RHOA 0.005 0.023 -10000 0 -0.38 2 2
PTGIR 0.005 0.023 -10000 0 -0.38 2 2
PRKCB1 -0.082 0.28 0.46 86 -0.43 87 173
GNAQ -0.005 0.065 -10000 0 -0.38 16 16
mol:L-citrulline 0.006 0.001 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.11 0.34 0.51 86 -0.58 87 173
LCK -0.008 0.034 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.006 0.017 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.004 0.024 -10000 0 -0.46 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.006 0.017 -10000 0 -10000 0 0
MAPK14 -0.03 0.2 0.38 86 -0.25 63 149
TGM2/GTP -0.13 0.33 0.49 84 -0.43 269 353
MAPK11 -0.03 0.2 0.38 86 -0.25 58 144
ARHGEF1 -0.029 0.16 0.3 84 -0.2 8 92
GNAI2 0.006 0 -10000 0 -10000 0 0
JNK cascade -0.071 0.28 0.48 86 -0.42 87 173
RAB11/GDP 0.004 0.01 -10000 0 -10000 0 0
ICAM1 -0.033 0.24 0.44 86 -0.32 64 150
cAMP biosynthetic process -0.1 0.27 0.43 84 -0.39 97 181
Gq family/GTP/EBP50 -0.14 0.17 -10000 0 -0.29 276 276
actin cytoskeleton reorganization 0.007 0.014 -10000 0 -0.23 2 2
SRC -0.008 0.034 -10000 0 -10000 0 0
GNB5 0.002 0.043 -10000 0 -0.38 7 7
GNB1 0.006 0.016 -10000 0 -0.38 1 1
EGF/EGFR -0.023 0.058 -10000 0 -0.22 17 17
VCAM1 -0.04 0.26 0.47 87 -0.39 88 175
TP beta/Gq family/GDP/G beta5/gamma2 -0.11 0.16 -10000 0 -0.33 198 198
platelet activation -0.056 0.24 0.44 86 -0.34 64 150
PGI2/IP 0.004 0.016 -10000 0 -0.27 2 2
PRKACA 0.001 0.016 -10000 0 -0.2 3 3
Gq family/GDP/G beta5/gamma2 -0.1 0.15 -10000 0 -0.3 198 198
TXA2/TP beta/beta Arrestin2 0.028 0.03 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.002 0.016 -10000 0 -0.19 3 3
mol:DAG -0.096 0.3 0.48 84 -0.49 87 171
EGFR -0.03 0.12 0.22 1 -0.38 54 55
TXA2/TP alpha -0.15 0.34 0.49 84 -0.54 107 191
Gq family/GTP -0.064 0.097 -10000 0 -0.19 200 200
YES1 -0.005 0.039 -10000 0 -10000 0 0
GNAI2/GTP -0.006 0.035 -10000 0 -0.17 7 7
PGD2/DP 0.004 0.012 -10000 0 -0.27 1 1
SLC9A3R1 -0.097 0.17 -10000 0 -0.38 151 151
FYN -0.025 0.066 -10000 0 -0.3 10 10
mol:NO 0.006 0.001 -10000 0 -10000 0 0
GNA15 0.003 0.037 -10000 0 -0.38 5 5
PGK/cGMP 0.007 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.002 0.024 -10000 0 -0.38 2 2
TP alpha/TGM2/GDP/G beta/gamma -0.087 0.09 -10000 0 -0.34 3 3
NOS3 0.006 0.001 -10000 0 -10000 0 0
RAC1 0.006 0.016 -10000 0 -0.38 1 1
PRKCA -0.072 0.27 0.45 86 -0.4 90 176
PRKCB -0.07 0.27 0.45 87 -0.4 87 174
PRKCE -0.069 0.27 0.46 86 -0.4 87 173
PRKCD -0.074 0.28 0.46 86 -0.42 88 174
PRKCG -0.083 0.28 0.46 86 -0.44 87 173
muscle contraction -0.11 0.32 0.49 86 -0.54 87 173
PRKCZ -0.06 0.26 0.45 86 -0.37 87 173
ARR3 0.006 0 -10000 0 -10000 0 0
TXA2/TP beta -0.001 0.04 -10000 0 -10000 0 0
PRKCQ -0.071 0.27 0.45 87 -0.4 93 180
MAPKKK cascade -0.11 0.32 0.48 86 -0.52 88 174
SELE -0.038 0.23 0.43 86 -0.31 64 150
TP beta/GNAI2/GDP/G beta/gamma 0.007 0.022 -10000 0 -10000 0 0
ROCK1 0.007 0.009 0.22 1 -10000 0 1
GNA14 0.006 0.026 0.22 2 -0.38 2 4
chemotaxis -0.11 0.36 0.53 86 -0.62 87 173
GNA12 0.006 0 -10000 0 -10000 0 0
GNA13 0.006 0.016 -10000 0 -0.38 1 1
GNA11 -0.13 0.18 -10000 0 -0.38 193 193
Rac1/GTP 0.001 0.013 -10000 0 -0.27 1 1
mTOR signaling pathway

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
GBL 0.006 0 -10000 0 -10000 0 0
MKNK1 0.006 0 -10000 0 -10000 0 0
mol:PIP3 -0.13 0.14 0.2 1 -0.26 254 255
FRAP1 -0.012 0.036 -10000 0 -10000 0 0
AKT1 -0.11 0.12 0.17 1 -0.23 251 252
INSR -0.02 0.098 -10000 0 -0.38 38 38
Insulin Receptor/Insulin -0.007 0.058 -10000 0 -0.22 38 38
mol:GTP -0.086 0.1 -10000 0 -0.19 207 207
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.036 0.039 -10000 0 -10000 0 0
TSC2 0.006 0 -10000 0 -10000 0 0
RHEB/GDP -0.079 0.082 -10000 0 -0.27 30 30
TSC1 0.006 0.016 -10000 0 -0.38 1 1
Insulin Receptor/IRS1 -0.17 0.16 -10000 0 -0.31 320 320
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.039 0.044 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.006 0 -10000 0 -10000 0 0
RPS6KB1 -0.048 0.073 0.18 1 -0.21 23 24
MAP3K5 -0.002 0.036 0.23 1 -0.32 7 8
PIK3R1 -0.038 0.12 -10000 0 -0.39 64 64
apoptosis -0.002 0.036 0.23 1 -0.32 7 8
mol:LY294002 -0.001 0.001 -10000 0 -0.001 311 311
EIF4B -0.044 0.067 0.17 1 -10000 0 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.04 0.065 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 -0.013 0.022 -10000 0 -10000 0 0
KIAA1303 0.006 0 -10000 0 -10000 0 0
PI3K -0.14 0.16 0.14 1 -0.25 341 342
mTOR/RHEB/GTP/Raptor/GBL -0.024 0.055 0.18 1 -10000 0 1
FKBP1A 0.005 0.003 -10000 0 -10000 0 0
RHEB/GTP -0.076 0.085 -10000 0 -0.27 30 30
mol:Amino Acids -0.001 0.001 -10000 0 -0.001 311 311
FKBP12/Rapamycin 0.004 0.004 -10000 0 -10000 0 0
PDPK1 -0.12 0.13 0.18 1 -0.24 254 255
EIF4E 0.006 0 -10000 0 -10000 0 0
ASK1/PP5C -0.007 0.069 -10000 0 -0.58 7 7
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.014 0.028 -10000 0 -10000 0 0
TSC1/TSC2 -0.091 0.11 -10000 0 -0.21 207 207
tumor necrosis factor receptor activity 0.001 0.001 0.001 311 -10000 0 311
RPS6 0.006 0 -10000 0 -10000 0 0
PPP5C 0.007 0.009 0.22 1 -10000 0 1
EIF4G1 0.006 0 -10000 0 -10000 0 0
IRS1 -0.17 0.16 -10000 0 -0.32 311 311
INS 0.006 0 -10000 0 -10000 0 0
PTEN -0.001 0.054 -10000 0 -0.38 11 11
PDK2 -0.12 0.13 0.18 1 -0.24 255 256
EIF4EBP1 0.008 0.009 -10000 0 -10000 0 0
PIK3CA 0.055 0.091 0.22 131 -10000 0 131
PPP2R5D -0.012 0.034 -10000 0 -10000 0 0
peptide biosynthetic process -0.024 0.06 -10000 0 -0.21 55 55
RHEB 0.017 0.047 0.22 28 -10000 0 28
EIF4A1 0.006 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.002 11 -10000 0 11
EEF2 -0.024 0.06 -10000 0 -0.21 55 55
eIF4E/4E-BP1 0.011 0.006 -10000 0 -10000 0 0
Insulin Pathway

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
CBL/APS/CAP -0.12 0.12 -10000 0 -0.21 342 342
TC10/GTP -0.006 0.052 -10000 0 -0.18 49 49
Insulin Receptor/Insulin/IRS1/Shp2 -0.12 0.13 -10000 0 -0.23 320 320
HRAS 0.006 0 -10000 0 -10000 0 0
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 0.015 0.042 0.22 22 -10000 0 22
FOXO3 -0.03 0.089 -10000 0 -0.74 8 8
AKT1 -0.093 0.11 0.22 1 -0.32 50 51
INSR -0.02 0.098 -10000 0 -0.39 38 38
Insulin Receptor/Insulin 0.002 0.05 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.007 0.009 0.22 1 -10000 0 1
SORBS1 -0.027 0.11 -10000 0 -0.38 49 49
CRK 0.006 0 -10000 0 -10000 0 0
PTPN1 -0.017 0.044 -10000 0 -10000 0 0
CAV1 -0.15 0.13 0.14 3 -0.23 367 370
CBL/APS/CAP/Crk-II/C3G -0.003 0.058 -10000 0 -0.19 49 49
Insulin Receptor/Insulin/IRS1/NCK2 -0.12 0.13 -10000 0 -0.23 320 320
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.11 0.12 -10000 0 -0.22 273 273
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.12 0.15 -10000 0 -0.55 39 39
RPS6KB1 -0.085 0.11 0.22 2 -0.3 45 47
PARD6A 0.006 0.016 -10000 0 -0.38 1 1
CBL 0.006 0 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.005 0.031 -10000 0 -0.73 1 1
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.1 0.095 -10000 0 -0.3 55 55
HRAS/GTP -0.1 0.09 -10000 0 -0.18 301 301
Insulin Receptor -0.02 0.098 -10000 0 -0.39 38 38
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.11 0.12 -10000 0 -0.21 321 321
PRKCI 0.042 0.074 0.22 1 -10000 0 1
Insulin Receptor/Insulin/GRB14/PDK1 -0.1 0.11 -10000 0 -0.21 258 258
SHC1 0.006 0 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.022 0.049 -10000 0 -0.63 1 1
PI3K -0.11 0.12 -10000 0 -0.22 273 273
NCK2 0.006 0 -10000 0 -10000 0 0
RHOQ 0.007 0.016 0.22 3 -10000 0 3
mol:H2O2 -0.003 0.006 -10000 0 -10000 0 0
HRAS/GDP 0.005 0 -10000 0 -10000 0 0
AKT2 -0.091 0.12 0.23 2 -0.31 55 57
PRKCZ -0.028 0.034 -10000 0 -10000 0 0
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.11 0.1 -10000 0 -0.2 320 320
F2RL2 0.006 0 -10000 0 -10000 0 0
TRIP10 0.006 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc -0.001 0.051 -10000 0 -0.19 38 38
TC10/GTP/CIP4/Exocyst 0.009 0.001 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.01 0.055 -10000 0 -0.18 37 37
RAPGEF1 0.006 0 -10000 0 -10000 0 0
RASA1 0.004 0.028 -10000 0 -0.38 3 3
NCK1 0.024 0.059 0.22 47 -10000 0 47
CBL/APS/CAP/Crk-II -0.006 0.061 -10000 0 -0.2 49 49
TC10/GDP 0.005 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.003 0.053 -10000 0 -0.19 38 38
INPP5D -0.12 0.11 -10000 0 -0.21 320 320
SOS1 0.014 0.04 0.22 20 -10000 0 20
SGK1 -0.012 0.011 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.006 0 -10000 0 -10000 0 0
IRS1 -0.21 0.2 -10000 0 -0.38 311 311
p62DOK/RasGAP 0.023 0.049 -10000 0 -0.64 1 1
INS 0.004 0.009 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.12 0.11 -10000 0 -0.21 320 320
GRB2 0.006 0.016 -10000 0 -0.38 1 1
EIF4EBP1 -0.087 0.11 0.21 1 -0.3 46 47
PTPRA 0.004 0.012 0.2 1 -10000 0 1
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
TC10/GTP/CIP4 0.009 0.001 -10000 0 -10000 0 0
PDPK1 0.006 0 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.12 0.12 -10000 0 -0.35 38 38
Insulin Receptor/Insulin/IRS1 -0.12 0.12 -10000 0 -0.23 320 320
Insulin Receptor/Insulin/IRS3 -0.009 0.071 -10000 0 -0.27 38 38
Par3/Par6 0.015 0.012 -10000 0 -0.19 1 1
Aurora A signaling

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
Aurora A/GADD45A 0.11 0.052 0.26 44 -10000 0 44
BIRC5 0.032 0.07 0.22 69 -10000 0 69
NFKBIA 0.11 0.037 -10000 0 -10000 0 0
CPEB1 0.006 0 -10000 0 -10000 0 0
AKT1 0.11 0.033 0.32 1 -10000 0 1
NDEL1 0.006 0 -10000 0 -10000 0 0
Aurora A/BRCA1 0 0.001 -10000 0 -10000 0 0
NDEL1/TACC3 0.051 0.046 -10000 0 -10000 0 0
GADD45A 0.024 0.059 0.22 46 -10000 0 46
GSK3B 0.007 0.004 -10000 0 -10000 0 0
PAK1/Aurora A 0.1 0.039 0.27 17 -10000 0 17
MDM2 0.007 0.024 0.22 4 -0.38 1 5
JUB 0.021 0.054 0.22 38 -10000 0 38
TPX2 0.19 0.033 0.2 554 -10000 0 554
TP53 0.053 0.098 0.23 7 -0.24 6 13
DLG7 0.29 0.07 0.31 527 -10000 0 527
AURKAIP1 -0.005 0.067 -10000 0 -0.38 17 17
ARHGEF7 0.007 0.009 0.22 1 -10000 0 1
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.14 0.076 0.24 219 -10000 0 219
G2/M transition of mitotic cell cycle 0 0.001 -10000 0 -10000 0 0
AURKA 0.14 0.04 -10000 0 -10000 0 0
AURKB 0.06 0.043 0.14 112 -10000 0 112
CDC25B 0.11 0.036 0.19 40 -10000 0 40
G2/M transition checkpoint 0.001 0.006 0.14 1 -10000 0 1
mRNA polyadenylation 0 0.001 -10000 0 -10000 0 0
Aurora A/CPEB 0 0.001 -10000 0 -10000 0 0
Aurora A/TACC1/TRAP/chTOG -0.038 0.097 0.23 26 -0.2 20 46
BRCA1 0.018 0.048 0.22 30 -10000 0 30
centrosome duplication 0.1 0.039 0.26 17 -10000 0 17
regulation of centrosome cycle 0.002 0.013 -10000 0 -10000 0 0
spindle assembly -0.049 0.078 -10000 0 -0.19 21 21
TDRD7 0.007 0.038 0.22 8 -0.38 3 11
Aurora A/RasGAP/Survivin 0.07 0.037 -10000 0 -10000 0 0
CENPA 0.076 0.032 0.13 115 -10000 0 115
Aurora A/PP2A 0.097 0.026 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.15 0.085 0.22 274 -10000 0 274
negative regulation of DNA binding 0.053 0.098 0.23 7 -0.24 6 13
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.009 0.001 -10000 0 -10000 0 0
RASA1 0.004 0.028 -10000 0 -0.38 3 3
Ajuba/Aurora A 0.001 0.006 0.14 1 -10000 0 1
mitotic prometaphase 0 0 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.14 0.04 -10000 0 -10000 0 0
TACC1 -0.3 0.16 -10000 0 -0.38 440 440
TACC3 0.095 0.11 0.22 233 -10000 0 233
Aurora A/Antizyme1 0.007 0.11 -10000 0 -0.26 21 21
Aurora A/RasGAP 0.096 0.027 -10000 0 -10000 0 0
OAZ1 -0.14 0.19 -10000 0 -0.38 219 219
RAN 0.006 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.007 0.004 -10000 0 -10000 0 0
GIT1 0.007 0.009 0.22 1 -10000 0 1
GIT1/beta-PIX/PAK1 0.012 0.01 -10000 0 -0.23 1 1
Importin alpha/Importin beta/TPX2 0.19 0.033 0.2 554 -10000 0 554
PPP2R5D 0.006 0 -10000 0 -10000 0 0
Aurora A/TPX2 0.24 0.04 0.25 533 -10000 0 533
PAK1 0.012 0.041 0.22 18 -0.38 1 19
CKAP5 0.05 0.087 0.22 115 -10000 0 115
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.26 0.62 0.92 3 -1.3 100 103
STAT6 (cleaved dimer) -0.41 0.53 -10000 0 -1.2 160 160
IGHG1 -0.052 0.28 0.6 24 -1.2 4 28
IGHG3 -0.26 0.58 0.77 3 -1.2 105 108
AKT1 -0.16 0.37 0.57 2 -0.94 46 48
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.12 0.35 0.52 5 -1.1 39 44
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.25 0.41 0.62 2 -0.93 88 90
THY1 -0.22 0.66 1.1 23 -1.3 90 113
MYB -0.025 0.11 0.22 1 -0.38 46 47
HMGA1 0.007 0.032 0.22 6 -0.38 2 8
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.14 0.42 0.67 24 -0.91 48 72
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.15 0.41 0.61 5 -1.2 38 43
SP1 0.073 0.11 0.24 169 -10000 0 169
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.003 0.033 0.22 3 -10000 0 3
STAT6 (dimer)/ETS1 -0.31 0.62 -10000 0 -1.3 124 124
SOCS1 -0.19 0.41 -10000 0 -0.8 108 108
SOCS3 -0.13 0.37 -10000 0 -1 29 29
FCER2 -0.15 0.45 0.89 4 -0.88 56 60
PARP14 0.053 0.096 0.22 128 -0.38 3 131
CCL17 -0.27 0.62 0.92 3 -1.3 100 103
GRB2 0.006 0.016 -10000 0 -0.38 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.098 0.31 0.54 8 -0.76 35 43
T cell proliferation -0.34 0.68 -10000 0 -1.4 128 128
IL4R/JAK1 -0.36 0.7 -10000 0 -1.5 132 132
EGR2 -0.26 0.62 1 3 -1.3 100 103
JAK2 0.002 0.079 0.2 23 -0.4 4 27
JAK3 0.006 0.011 -10000 0 -10000 0 0
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
JAK1 0.005 0.041 -10000 0 -0.38 3 3
COL1A2 0.024 0.36 0.63 60 -1.3 9 69
CCL26 -0.27 0.62 0.92 3 -1.3 100 103
IL4R -0.36 0.79 0.99 13 -1.6 128 141
PTPN6 0.004 0.026 -10000 0 -10000 0 0
IL13RA2 -0.26 0.62 0.95 4 -1.3 95 99
IL13RA1 -0.006 0.097 0.23 3 -0.42 15 18
IRF4 -0.019 0.17 -10000 0 -10000 0 0
ARG1 -0.035 0.24 0.6 3 -0.86 7 10
CBL -0.14 0.39 0.63 8 -0.86 48 56
GTF3A 0.11 0.12 0.24 246 -10000 0 246
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
IL13RA1/JAK2 0.009 0.12 0.29 26 -0.31 18 44
IRF4/BCL6 -0.028 0.15 -10000 0 -10000 0 0
CD40LG 0.008 0.014 0.25 2 -10000 0 2
MAPK14 -0.14 0.39 0.65 5 -0.98 38 43
mitosis -0.15 0.35 0.56 3 -0.86 46 49
STAT6 -0.31 0.75 1.1 24 -1.5 101 125
SPI1 0.003 0.041 0.2 1 -0.38 6 7
RPS6KB1 -0.15 0.34 0.58 3 -0.85 42 45
STAT6 (dimer) -0.31 0.75 1.1 24 -1.5 101 125
STAT6 (dimer)/PARP14 -0.28 0.65 0.87 2 -1.4 106 108
mast cell activation 0.001 0.023 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.14 0.4 0.62 5 -1.1 43 48
FRAP1 -0.16 0.37 0.57 2 -0.94 46 48
LTA -0.27 0.62 0.92 3 -1.3 100 103
FES 0.006 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.29 0.72 1.5 101 -1.1 24 125
CCL11 -0.25 0.6 0.88 15 -1.2 100 115
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.14 0.4 0.6 5 -1.1 43 48
IL2RG -0.007 0.11 0.23 31 -0.37 37 68
IL10 -0.27 0.62 0.92 3 -1.3 100 103
IRS1 -0.21 0.2 -10000 0 -0.38 311 311
IRS2 0.006 0 -10000 0 -10000 0 0
IL4 -0.007 0.23 0.7 13 -10000 0 13
IL5 -0.27 0.62 0.92 3 -1.3 100 103
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.2 0.57 0.93 24 -1 99 123
COL1A1 0.11 0.42 0.81 75 -1.5 5 80
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.38 0.71 -10000 0 -1.5 128 128
IL2R gamma/JAK3 -0.008 0.067 0.26 1 -0.26 37 38
TFF3 -0.89 0.6 0.92 2 -1.3 290 292
ALOX15 -0.27 0.62 0.92 3 -1.3 100 103
MYBL1 0.034 0.072 0.22 72 -10000 0 72
T-helper 2 cell differentiation -0.22 0.54 0.79 8 -1 113 121
SHC1 0.006 0 -10000 0 -10000 0 0
CEBPB 0.005 0.035 0.21 2 -0.38 4 6
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.14 0.4 0.6 5 -1.2 37 42
mol:PI-3-4-5-P3 -0.16 0.37 0.57 2 -0.94 46 48
PI3K -0.18 0.4 0.58 2 -1 50 52
DOK2 0.007 0.009 0.22 1 -10000 0 1
ETS1 0 0.043 0.23 4 -0.35 1 5
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.092 0.3 0.53 8 -0.74 36 44
ITGB3 -0.34 0.72 1.1 5 -1.4 128 133
PIGR -0.48 0.75 0.99 6 -1.4 174 180
IGHE -0.027 0.093 -10000 0 -0.26 41 41
MAPKKK cascade -0.09 0.3 0.53 8 -0.73 35 43
BCL6 -0.004 0.063 -10000 0 -0.38 15 15
OPRM1 -0.27 0.62 0.92 3 -1.3 100 103
RETNLB -0.27 0.62 0.92 3 -1.3 100 103
SELP -0.31 0.66 0.95 4 -1.3 118 122
AICDA -0.26 0.58 -10000 0 -1.2 100 100
Syndecan-1-mediated signaling events

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
TGFB1 -0.081 0.16 -10000 0 -0.38 127 127
CCL5 -0.037 0.13 0.22 6 -0.38 66 72
SDCBP 0.006 0.026 0.22 2 -0.38 2 4
FGFR/FGF2/Syndecan-1 -0.042 0.17 0.22 44 -0.42 52 96
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 -0.041 0.16 0.2 42 -0.4 52 94
Syndecan-1/Syntenin -0.041 0.16 0.2 41 -0.4 52 93
MAPK3 -0.053 0.16 0.26 5 -0.38 66 71
HGF/MET -0.013 0.075 -10000 0 -0.27 45 45
TGFB1/TGF beta receptor Type II -0.081 0.16 -10000 0 -0.38 127 127
BSG 0.006 0 -10000 0 -10000 0 0
keratinocyte migration -0.04 0.16 0.2 42 -0.4 52 94
Syndecan-1/RANTES -0.06 0.19 0.2 43 -0.44 76 119
Syndecan-1/CD147 -0.041 0.15 -10000 0 -0.39 52 52
Syndecan-1/Syntenin/PIP2 -0.055 0.14 -10000 0 -0.39 52 52
LAMA5 0.007 0.013 0.22 2 -10000 0 2
positive regulation of cell-cell adhesion -0.054 0.14 -10000 0 -0.38 52 52
MMP7 -0.069 0.2 0.22 69 -0.38 148 217
HGF 0.008 0.018 0.22 4 -10000 0 4
Syndecan-1/CASK -0.044 0.16 0.19 44 -0.4 52 96
Syndecan-1/HGF/MET -0.047 0.17 0.25 15 -0.39 69 84
regulation of cell adhesion -0.054 0.15 0.26 5 -0.37 66 71
HPSE 0.012 0.036 0.22 16 -10000 0 16
positive regulation of cell migration -0.042 0.17 0.22 44 -0.42 52 96
SDC1 -0.038 0.17 0.22 44 -0.42 52 96
Syndecan-1/Collagen -0.042 0.17 0.22 44 -0.42 52 96
PPIB 0.006 0 -10000 0 -10000 0 0
MET -0.013 0.12 0.22 32 -0.38 45 77
PRKACA 0.006 0 -10000 0 -10000 0 0
MMP9 0.035 0.074 0.22 77 -10000 0 77
MAPK1 -0.039 0.15 0.26 5 -0.37 52 57
homophilic cell adhesion -0.042 0.17 0.22 44 -0.42 52 96
MMP1 0.049 0.086 0.22 114 -10000 0 114
Coregulation of Androgen receptor activity

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
NRIP1 -0.11 0.18 -10000 0 -0.38 165 165
SVIL -0.005 0.067 0.22 1 -0.38 17 18
ZNF318 0.006 0.009 0.22 1 -10000 0 1
JMJD2C 0.007 0.021 0.22 2 -0.39 1 3
T-DHT/AR/Ubc9 -0.15 0.12 -10000 0 -0.27 251 251
CARM1 0.007 0.009 0.22 1 -10000 0 1
PRDX1 0.006 0 -10000 0 -10000 0 0
PELP1 0.006 0 -10000 0 -10000 0 0
CTNNB1 0.007 0.009 0.22 1 -10000 0 1
AKT1 0.007 0.009 0.22 1 -10000 0 1
PTK2B 0.005 0.023 -10000 0 -0.38 2 2
MED1 0.007 0.013 0.22 2 -10000 0 2
MAK -0.083 0.16 0.22 2 -0.39 130 132
response to oxidative stress 0 0 -10000 0 -10000 0 0
HIP1 0.007 0.009 0.22 1 -10000 0 1
GSN -0.032 0.12 -10000 0 -0.38 56 56
NCOA2 0.007 0.013 0.22 2 -10000 0 2
NCOA6 0.007 0.009 0.22 1 -10000 0 1
DNA-PK 0.009 0.005 -10000 0 -10000 0 0
NCOA4 0.006 0 -10000 0 -10000 0 0
PIAS3 0.007 0.009 0.22 1 -10000 0 1
cell proliferation -0.2 0.29 0.22 1 -0.72 130 131
XRCC5 0.029 0.066 0.22 60 -10000 0 60
UBE3A 0.006 0 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.15 0.12 -10000 0 -0.28 251 251
FHL2 -0.093 0.073 0.44 1 -0.52 6 7
RANBP9 0.007 0.013 0.22 2 -10000 0 2
JMJD1A -0.028 0.11 0.22 66 -10000 0 66
CDK6 0.004 0.057 0.22 10 -0.38 9 19
TGFB1I1 -0.03 0.11 -10000 0 -0.38 53 53
T-DHT/AR/CyclinD1 -0.21 0.15 -10000 0 -0.32 324 324
XRCC6 0.006 0 -10000 0 -10000 0 0
T-DHT/AR -0.21 0.13 -10000 0 -0.3 325 325
CTDSP1 0.004 0.028 -10000 0 -0.38 3 3
CTDSP2 0.005 0.023 -10000 0 -0.39 2 2
BRCA1 0.018 0.048 0.22 30 -10000 0 30
TCF4 0.004 0.028 -10000 0 -0.38 3 3
CDKN2A 0.13 0.11 0.22 317 -10000 0 317
SRF 0.003 0.041 0.24 1 -0.39 6 7
NKX3-1 -0.12 0.13 -10000 0 -10000 0 0
KLK3 -0.011 0.063 -10000 0 -10000 0 0
TMF1 0.007 0.013 0.22 2 -10000 0 2
HNRNPA1 0.006 0 -10000 0 -10000 0 0
AOF2 0.007 0.009 0.22 1 -10000 0 1
APPL1 -0.004 0.008 0.2 1 -10000 0 1
T-DHT/AR/Caspase 8 -0.15 0.12 -10000 0 -0.27 251 251
AR -0.21 0.19 -10000 0 -0.42 251 251
UBA3 0 0 -10000 0 -10000 0 0
PATZ1 0.007 0.009 0.22 1 -10000 0 1
PAWR 0.006 0 -10000 0 -10000 0 0
PRKDC 0.048 0.085 0.22 110 -10000 0 110
PA2G4 0.007 0.009 0.22 1 -10000 0 1
UBE2I 0.006 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.14 0.11 -10000 0 -0.25 251 251
RPS6KA3 0.004 0.039 0.22 2 -0.38 5 7
T-DHT/AR/ARA70 -0.15 0.12 -10000 0 -0.27 251 251
LATS2 0.006 0 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.14 0.11 -10000 0 -0.25 251 251
Cyclin D3/CDK11 p58 0.005 0 -10000 0 -10000 0 0
VAV3 0.03 0.068 0.22 63 -10000 0 63
KLK2 -0.089 0.058 -10000 0 -0.57 1 1
CASP8 0.006 0 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.14 0.11 -10000 0 -0.25 251 251
TMPRSS2 -0.52 0.41 -10000 0 -0.83 356 356
CCND1 -0.093 0.17 0.22 1 -0.38 145 146
PIAS1 0.007 0.009 0.22 1 -10000 0 1
mol:T-DHT -0.037 0.031 -10000 0 -0.07 212 212
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.007 0 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.15 0.12 -10000 0 -0.28 252 252
CMTM2 0.006 0 -10000 0 -10000 0 0
SNURF 0.006 0.016 -10000 0 -0.38 1 1
ZMIZ1 -0.039 0.049 0.21 1 -0.39 5 6
CCND3 0.006 0 -10000 0 -10000 0 0
TGIF1 0.006 0 -10000 0 -10000 0 0
FKBP4 0.023 0.057 0.22 43 -10000 0 43
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 -0.013 0.1 0.22 15 -0.38 36 51
EPHB2 0.01 0.027 0.22 9 -10000 0 9
EFNB1 -0.003 0.026 -10000 0 -0.27 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.021 0.034 0.24 3 -0.18 5 8
Ephrin B2/EPHB1-2 0.007 0.062 0.15 14 -0.2 36 50
neuron projection morphogenesis 0.01 0.021 -10000 0 -0.17 7 7
Ephrin B1/EPHB1-2/Tiam1 0.02 0.037 0.27 3 -0.19 6 9
DNM1 0.007 0.002 -10000 0 -10000 0 0
cell-cell signaling 0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.11 0.23 0.24 1 -0.52 131 132
YES1 -0.16 0.32 0.23 1 -0.75 127 128
Ephrin B1/EPHB1-2/NCK2 0.02 0.035 0.27 3 -0.18 5 8
PI3K -0.098 0.26 0.23 10 -0.47 160 170
mol:GDP 0.02 0.036 0.26 3 -0.18 6 9
ITGA2B 0.006 0 -10000 0 -10000 0 0
endothelial cell proliferation -0.006 0.057 -10000 0 -0.22 36 36
FYN -0.17 0.33 -10000 0 -0.78 127 127
MAP3K7 -0.12 0.24 0.21 2 -0.56 127 129
FGR -0.16 0.32 -10000 0 -0.75 127 127
TIAM1 0.006 0.021 0.22 2 -0.38 1 3
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
RGS3 0.006 0 -10000 0 -10000 0 0
cell adhesion -0.12 0.25 0.24 12 -0.53 136 148
LYN -0.16 0.32 -10000 0 -0.76 127 127
Ephrin B1/EPHB1-2/Src Family Kinases -0.15 0.3 -10000 0 -0.7 127 127
Ephrin B1/EPHB1-2 -0.13 0.26 -10000 0 -0.61 127 127
SRC -0.16 0.32 -10000 0 -0.75 127 127
ITGB3 -0.045 0.14 0.22 13 -0.38 82 95
EPHB1 0.012 0.033 0.22 14 -10000 0 14
EPHB4 0.006 0 -10000 0 -10000 0 0
RAC1 0.006 0.016 -10000 0 -0.38 1 1
Ephrin B2/EPHB4 -0.006 0.057 -10000 0 -0.22 36 36
alphaIIb/beta3 Integrin -0.031 0.098 -10000 0 -0.27 82 82
BLK -0.16 0.32 -10000 0 -0.75 127 127
HCK -0.16 0.32 -10000 0 -0.75 127 127
regulation of stress fiber formation -0.019 0.034 0.18 5 -0.26 3 8
MAPK8 -0.11 0.22 0.22 1 -0.5 131 132
Ephrin B1/EPHB1-2/RGS3 0.02 0.035 0.27 3 -0.19 4 7
endothelial cell migration -0.11 0.21 0.22 1 -0.44 149 150
NCK2 0.006 0 -10000 0 -10000 0 0
PTPN13 -0.094 0.22 0.21 34 -0.5 127 161
regulation of focal adhesion formation -0.019 0.034 0.18 5 -0.26 3 8
chemotaxis -0.019 0.034 0.19 4 -0.26 3 7
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
Rac1/GTP 0.013 0.022 -10000 0 -0.17 7 7
angiogenesis -0.13 0.26 -10000 0 -0.6 127 127
LCK -0.16 0.32 -10000 0 -0.75 127 127
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 0.009 0.002 -10000 0 -10000 0 0
alphaV beta3 Integrin -0.024 0.087 -10000 0 -0.23 83 83
PTK2 -0.012 0.13 0.25 14 -0.31 72 86
IGF1R -0.077 0.16 -10000 0 -0.38 121 121
PI4KB 0.008 0.018 0.22 4 -10000 0 4
MFGE8 -0.004 0.086 0.22 15 -0.38 23 38
SRC 0.006 0 -10000 0 -10000 0 0
CDKN1B -0.012 0.052 -10000 0 -0.45 3 3
VEGFA 0.018 0.048 0.22 30 -10000 0 30
ILK -0.012 0.039 -10000 0 -10000 0 0
ROCK1 0.007 0.009 0.22 1 -10000 0 1
AKT1 -0.013 0.035 -10000 0 -10000 0 0
PTK2B -0.016 0.09 0.28 6 -0.2 82 88
alphaV/beta3 Integrin/JAM-A -0.006 0.088 0.27 3 -0.2 82 85
CBL 0.006 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.023 0.086 -10000 0 -0.23 82 82
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.15 0.16 -10000 0 -0.26 339 339
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.011 0.084 0.21 6 -0.4 4 10
alphaV/beta3 Integrin/Syndecan-1 -0.024 0.086 -10000 0 -0.23 82 82
PI4KA 0.007 0.016 0.22 3 -10000 0 3
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.14 -10000 0 -0.26 280 280
PI4 Kinase 0.009 0.001 -10000 0 -10000 0 0
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
alphaV/beta3 Integrin/Osteopontin -0.022 0.073 -10000 0 -0.24 48 48
RPS6KB1 -0.11 0.16 0.23 10 -0.32 135 145
TLN1 0.005 0.023 -10000 0 -0.38 2 2
MAPK3 -0.11 0.17 -10000 0 -0.46 86 86
GPR124 -0.012 0.082 -10000 0 -0.38 26 26
MAPK1 -0.093 0.16 -10000 0 -0.45 82 82
PXN -0.002 0.056 -10000 0 -0.38 12 12
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
alphaV/beta3 Integrin/Tumstatin -0.024 0.087 -10000 0 -0.23 83 83
cell adhesion -0.023 0.1 0.29 2 -0.24 92 94
ANGPTL3 0.007 0.009 0.22 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.012 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer -0.077 0.16 -10000 0 -0.38 121 121
Rac1/GDP 0.004 0.011 -10000 0 -0.27 1 1
TGFBR2 -0.003 0.058 -10000 0 -0.38 13 13
ITGB3 -0.045 0.14 0.22 13 -0.38 82 95
IGF1 -0.003 0.067 0.22 4 -0.38 16 20
RAC1 0.006 0.016 -10000 0 -0.38 1 1
regulation of cell-matrix adhesion -0.034 0.1 -10000 0 -0.24 101 101
apoptosis 0.017 0.059 0.22 35 -0.38 3 38
CD47 0.02 0.056 0.22 37 -0.38 1 38
alphaV/beta3 Integrin/CD47 -0.024 0.085 -10000 0 -0.23 80 80
VCL 0.007 0.016 0.22 3 -10000 0 3
alphaV/beta3 Integrin/Del1 -0.025 0.086 -10000 0 -0.23 80 80
CSF1 -0.01 0.079 0.22 1 -0.38 24 25
PIK3C2A -0.01 0.041 -10000 0 -10000 0 0
PI4 Kinase/Pyk2 -0.033 0.06 -10000 0 -0.33 2 2
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.002 0.094 -10000 0 -0.21 80 80
FAK1/Vinculin -0.005 0.11 0.23 14 -0.26 72 86
alphaV beta3/Integrin/ppsTEM5 -0.034 0.1 -10000 0 -0.24 101 101
RHOA 0.005 0.023 -10000 0 -0.38 2 2
VTN 0.006 0 -10000 0 -10000 0 0
BCAR1 0.004 0.028 -10000 0 -0.38 3 3
FGF2 0.006 0 -10000 0 -10000 0 0
F11R -0.004 0.008 0.2 1 -10000 0 1
alphaV/beta3 Integrin/Lactadherin -0.032 0.098 -10000 0 -0.24 96 96
alphaV/beta3 Integrin/TGFBR2 -0.028 0.095 -10000 0 -0.24 88 88
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.013 0.06 -10000 0 -0.21 28 28
HSP90AA1 0.006 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.011 0.09 0.14 42 -0.21 84 126
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.074 0.12 0.22 201 -0.38 13 214
alphaV/beta3 Integrin/Pyk2 -0.003 0.094 0.29 6 -0.2 82 88
SDC1 0.007 0.016 0.22 3 -10000 0 3
VAV3 0.008 0.073 0.27 8 -0.2 25 33
PTPN11 0.006 0 -10000 0 -10000 0 0
IRS1 -0.21 0.2 -10000 0 -0.38 311 311
FAK1/Paxillin -0.008 0.11 0.23 14 -0.26 73 87
cell migration -0.009 0.11 0.23 14 -0.24 72 86
ITGAV 0.017 0.06 0.22 35 -0.38 3 38
PI3K -0.009 0.11 -10000 0 -0.2 108 108
SPP1 0.15 0.11 0.22 381 -0.38 3 384
KDR 0.007 0.013 0.22 2 -10000 0 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.017 0.059 0.22 35 -0.38 3 38
COL4A3 0.006 0 -10000 0 -10000 0 0
angiogenesis -0.095 0.18 -10000 0 -0.49 83 83
Rac1/GTP 0.006 0.067 0.24 8 -0.18 26 34
EDIL3 0.032 0.073 0.22 69 -0.38 1 70
cell proliferation -0.028 0.095 -10000 0 -0.24 88 88
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.013 0.54 1.1 40 -1.3 35 75
IL23A -0.003 0.47 0.99 32 -1.1 21 53
NF kappa B1 p50/RelA/I kappa B alpha -0.16 0.32 -10000 0 -0.92 60 60
positive regulation of T cell mediated cytotoxicity 0.004 0.53 1.1 47 -0.98 58 105
ITGA3 -0.062 0.53 0.9 33 -1.2 48 81
IL17F -0.003 0.35 0.68 44 -0.72 23 67
IL12B 0.036 0.095 0.29 47 -10000 0 47
STAT1 (dimer) 0.045 0.48 0.86 56 -0.97 44 100
CD4 -0.001 0.47 0.99 35 -1.1 22 57
IL23 -0.015 0.44 0.92 18 -1.1 20 38
IL23R 0.056 0.2 0.61 44 -10000 0 44
IL1B 0 0.48 1 32 -1.1 21 53
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.004 0.46 0.93 32 -1.1 21 53
TYK2 0.022 0.064 0.25 18 -10000 0 18
STAT4 0.007 0.013 0.22 2 -10000 0 2
STAT3 -0.002 0.056 -10000 0 -0.39 12 12
IL18RAP 0.005 0.014 -10000 0 -10000 0 0
IL12RB1 0.022 0.064 0.25 18 -10000 0 18
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
IL12Rbeta1/TYK2 0.026 0.072 0.22 36 -10000 0 36
IL23R/JAK2 0.061 0.22 0.59 48 -10000 0 48
positive regulation of chronic inflammatory response 0.004 0.53 1.1 47 -0.98 58 105
natural killer cell activation -0.005 0.019 -10000 0 -0.068 22 22
JAK2 0.034 0.1 0.29 49 -0.41 4 53
PIK3R1 -0.038 0.12 -10000 0 -0.39 64 64
NFKB1 -0.003 0.056 -10000 0 -0.39 11 11
RELA 0.003 0.026 -10000 0 -0.39 2 2
positive regulation of dendritic cell antigen processing and presentation -0.011 0.43 0.84 32 -1 20 52
ALOX12B -0.004 0.46 0.93 32 -1.1 21 53
CXCL1 -0.18 0.68 0.97 34 -1.2 134 168
T cell proliferation 0.004 0.53 1.1 47 -0.98 58 105
NFKBIA -0.006 0.067 -10000 0 -0.39 16 16
IL17A 0.015 0.31 0.63 45 -0.56 22 67
PI3K -0.13 0.34 0.5 24 -0.9 59 83
IFNG 0.027 0.072 0.26 37 -10000 0 37
STAT3 (dimer) -0.15 0.31 -10000 0 -0.91 50 50
IL18R1 0.006 0.016 0.22 1 -10000 0 1
IL23/IL23R/JAK2/TYK2/SOCS3 0.03 0.35 0.77 48 -0.77 8 56
IL18/IL18R 0.02 0.059 0.26 29 -10000 0 29
macrophage activation -0.008 0.017 0.048 13 -10000 0 13
TNF -0.004 0.48 0.98 32 -1.1 21 53
STAT3/STAT4 -0.16 0.31 -10000 0 -0.91 59 59
STAT4 (dimer) -0.027 0.46 0.81 32 -0.95 57 89
IL18 0.045 0.085 0.22 103 -10000 0 103
IL19 -0.003 0.46 0.95 32 -1.1 21 53
STAT5A (dimer) -0.03 0.46 0.81 32 -0.95 58 90
STAT1 0.12 0.11 0.22 297 -10000 0 297
SOCS3 0.001 0.051 0.22 2 -0.38 9 11
CXCL9 0.032 0.51 0.99 58 -1.1 21 79
MPO -0.004 0.46 0.93 32 -1.1 21 53
positive regulation of humoral immune response 0.004 0.53 1.1 47 -0.98 58 105
IL23/IL23R/JAK2/TYK2 -0.004 0.54 1.1 47 -1 58 105
IL6 -0.054 0.54 0.91 34 -1.3 53 87
STAT5A 0 0.049 -10000 0 -0.38 9 9
IL2 0.009 0.035 0.15 25 -10000 0 25
positive regulation of tyrosine phosphorylation of STAT protein -0.005 0.019 -10000 0 -0.068 22 22
CD3E -0.013 0.49 0.97 32 -1.2 28 60
keratinocyte proliferation 0.004 0.53 1.1 47 -0.98 58 105
NOS2 -0.005 0.46 0.87 47 -0.87 58 105
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.051 0.16 0.42 8 -0.33 108 116
MAP3K8 0.003 0.008 -10000 0 -10000 0 0
FOS -0.03 0.11 0.34 8 -0.3 34 42
PRKCA 0.001 0.045 0.22 7 -0.39 5 12
PTPN7 0.001 0.016 -10000 0 -10000 0 0
HRAS 0.003 0.006 -10000 0 -10000 0 0
PRKCB -0.002 0.009 0.049 8 -0.016 109 117
NRAS 0.098 0.11 0.22 245 -10000 0 245
RAS family/GTP 0.051 0.065 0.14 187 -10000 0 187
MAPK3 -0.038 0.14 0.22 8 -0.44 51 59
MAP2K1 0.01 0.056 0.2 11 -0.33 5 16
ELK1 0 0.015 -10000 0 -10000 0 0
BRAF -0.002 0.039 0.29 2 -0.31 5 7
mol:GTP -0.001 0.003 0.008 8 -0.006 110 118
MAPK1 0.002 0.05 0.22 8 -0.38 1 9
RAF1 -0.002 0.038 0.29 1 -0.31 5 6
KRAS 0.027 0.068 0.22 62 -10000 0 62
Cellular roles of Anthrax toxin

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
ANTXR1 -0.001 0.064 0.22 5 -0.38 14 19
ANTXR2 -0.021 0.1 0.22 2 -0.38 41 43
negative regulation of myeloid dendritic cell antigen processing and presentation -0.005 0.016 -10000 0 -0.057 49 49
monocyte activation -0.034 0.15 0.26 1 -0.39 82 83
MAP2K2 -0.25 0.33 -10000 0 -0.69 207 207
MAP2K1 -0.006 0.016 0.13 1 -0.081 6 7
MAP2K7 -0.006 0.015 -10000 0 -0.081 6 6
MAP2K6 0.007 0.045 0.13 57 -0.081 6 63
CYAA -0.019 0.063 0.12 7 -0.21 49 56
MAP2K4 -0.009 0.026 -10000 0 -0.14 13 13
IL1B -0.003 0.044 0.13 36 -0.12 8 44
Channel -0.012 0.068 -10000 0 -0.23 49 49
NLRP1 -0.006 0.015 0.085 1 -10000 0 1
CALM1 -0.006 0.068 -10000 0 -0.38 18 18
negative regulation of phagocytosis -0.019 0.087 -10000 0 -0.49 18 18
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.005 0.016 0.057 49 -10000 0 49
MAPK3 -0.023 0.055 -10000 0 -0.18 57 57
MAPK1 -0.006 0.018 0.13 1 -0.19 1 2
PGR -0.18 0.059 -10000 0 -0.19 512 512
PA/Cellular Receptors -0.014 0.075 -10000 0 -0.25 49 49
apoptosis -0.005 0.016 -10000 0 -0.057 49 49
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.01 0.067 0.13 7 -0.22 49 56
macrophage activation -0.023 0.054 0.12 1 -0.19 52 53
TNF 0.007 0.009 0.22 1 -10000 0 1
VCAM1 -0.034 0.15 0.26 1 -0.39 82 83
platelet activation -0.019 0.087 -10000 0 -0.49 18 18
MAPKKK cascade 0.023 0.036 0.067 189 -10000 0 189
IL18 0.012 0.06 0.13 96 -0.12 8 104
negative regulation of macrophage activation -0.005 0.016 -10000 0 -0.057 49 49
LEF -0.005 0.016 -10000 0 -0.057 49 49
CASP1 -0.012 0.027 -10000 0 -0.082 62 62
mol:cAMP -0.019 0.087 -10000 0 -0.49 18 18
necrosis -0.005 0.016 -10000 0 -0.057 49 49
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.009 0.066 0.13 7 -0.21 49 56
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Reelin signaling pathway

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
CDK5R1/CDK5 0.008 0.003 -10000 0 -10000 0 0
VLDLR -0.002 0.072 0.22 8 -0.38 17 25
CRKL 0.006 0 -10000 0 -10000 0 0
LRPAP1 0.006 0.028 0.22 3 -0.38 2 5
FYN -0.039 0.13 0.22 1 -0.38 67 68
ITGA3 -0.025 0.11 0.22 4 -0.38 48 52
RELN/VLDLR/Fyn -0.056 0.12 -10000 0 -0.24 151 151
MAPK8IP1/MKK7/MAP3K11/JNK1 0.02 0.017 -10000 0 -0.19 1 1
AKT1 -0.025 0.11 0.2 7 -0.22 117 124
MAP2K7 0.006 0 -10000 0 -10000 0 0
RAPGEF1 0.006 0 -10000 0 -10000 0 0
DAB1 0.006 0 -10000 0 -10000 0 0
RELN/LRP8/DAB1 -0.012 0.085 0.14 32 -0.2 84 116
LRPAP1/LRP8 0.008 0.017 -10000 0 -0.27 2 2
RELN/LRP8/DAB1/Fyn -0.033 0.1 -10000 0 -0.2 140 140
DAB1/alpha3/beta1 Integrin -0.036 0.087 -10000 0 -0.19 135 135
long-term memory -0.024 0.1 0.26 2 -0.2 133 135
DAB1/LIS1 -0.019 0.077 -10000 0 -0.19 97 97
DAB1/CRLK/C3G -0.021 0.074 -10000 0 -0.18 98 98
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
DAB1/NCK2 -0.012 0.084 -10000 0 -0.19 98 98
ARHGEF2 0.007 0.013 0.22 2 -10000 0 2
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.018 0.048 0.22 30 -10000 0 30
CDK5R1 0.006 0 -10000 0 -10000 0 0
RELN -0.041 0.15 0.22 27 -0.38 84 111
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
RELN/LRP8/Fyn -0.05 0.11 -10000 0 -0.24 140 140
GRIN2A/RELN/LRP8/DAB1/Fyn -0.024 0.11 -10000 0 -0.2 133 133
MAPK8 0.008 0.02 0.22 5 -10000 0 5
RELN/VLDLR/DAB1 -0.02 0.089 0.14 27 -0.2 99 126
ITGB1 0.007 0.016 0.22 3 -10000 0 3
MAP1B -0.052 0.11 0.28 3 -0.22 145 148
RELN/LRP8 -0.024 0.086 -10000 0 -0.23 85 85
GRIN2B/RELN/LRP8/DAB1/Fyn -0.029 0.11 -10000 0 -0.2 140 140
PI3K -0.022 0.083 -10000 0 -0.27 56 56
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin -0.014 0.078 -10000 0 -0.27 48 48
RAP1A -0.029 0.076 0.25 4 -0.33 1 5
PAFAH1B1 0.007 0.009 0.22 1 -10000 0 1
MAPK8IP1 0.007 0.013 0.22 2 -10000 0 2
CRLK/C3G 0.009 0 -10000 0 -10000 0 0
GRIN2B 0.007 0.016 0.22 3 -10000 0 3
NCK2 0.006 0 -10000 0 -10000 0 0
neuron differentiation -0.033 0.089 0.18 2 -0.37 10 12
neuron adhesion -0.042 0.085 0.25 4 -0.32 6 10
LRP8 0.01 0.027 0.22 9 -10000 0 9
GSK3B -0.027 0.11 0.19 7 -0.35 14 21
RELN/VLDLR/DAB1/Fyn -0.039 0.11 -10000 0 -0.21 151 151
MAP3K11 0.006 0.016 -10000 0 -0.38 1 1
RELN/VLDLR/DAB1/P13K -0.025 0.12 0.22 7 -0.23 117 124
CDK5 0.031 0.069 0.22 65 -10000 0 65
MAPT 0.005 0.013 -10000 0 -10000 0 0
neuron migration -0.038 0.13 0.24 8 -0.28 77 85
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.033 0.089 0.18 2 -0.37 10 12
RELN/VLDLR -0.015 0.093 -10000 0 -0.21 98 98
Signaling events mediated by PRL

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
CCNE1 0.2 0.065 0.22 512 -10000 0 512
mol:Halofuginone -0.001 0.022 -10000 0 -0.2 7 7
ITGA1 0.036 0.074 0.22 78 -10000 0 78
CDKN1A -0.063 0.12 -10000 0 -0.46 42 42
PRL-3/alpha Tubulin 0.006 0.031 -10000 0 -0.27 7 7
mol:Ca2+ -0.019 0.074 0.31 7 -0.27 33 40
AGT -0.016 0.091 -10000 0 -0.38 33 33
CCNA2 0.047 0.12 0.27 2 -0.74 7 9
TUBA1B 0.006 0 -10000 0 -10000 0 0
EGR1 -0.11 0.14 0.2 4 -0.27 233 237
CDK2/Cyclin E1 0.13 0.13 0.28 107 -0.34 24 131
MAPK3 -0.028 0.087 0.2 8 -0.28 56 64
PRL-2 /Rab GGTase beta 0.006 0.005 -10000 0 -10000 0 0
MAPK1 -0.005 0.04 0.2 9 -0.27 8 17
PTP4A1 -0.09 0.13 -10000 0 -0.79 7 7
PTP4A3 0.004 0.05 0.22 8 -0.38 7 15
PTP4A2 0.006 0 -10000 0 -10000 0 0
ITGB1 -0.003 0.038 0.2 10 -0.27 6 16
SRC 0.006 0 -10000 0 -10000 0 0
RAC1 -0.041 0.082 -10000 0 -0.41 15 15
Rab GGTase beta/Rab GGTase alpha 0.006 0.005 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.081 0.12 -10000 0 -0.75 7 7
RABGGTA 0.006 0 -10000 0 -10000 0 0
BCAR1 -0.005 0.044 0.31 7 -0.27 3 10
RHOC -0.041 0.08 -10000 0 -0.4 15 15
RHOA -0.042 0.081 -10000 0 -0.4 16 16
cell motility -0.043 0.082 -10000 0 -0.41 14 14
PRL-1/alpha Tubulin -0.081 0.12 -10000 0 -0.75 7 7
PRL-3/alpha1 Integrin 0.005 0.031 -10000 0 -0.27 7 7
ROCK1 -0.043 0.082 -10000 0 -0.41 14 14
RABGGTB 0.095 0.11 0.22 235 -10000 0 235
CDK2 0.1 0.11 0.22 255 -10000 0 255
mitosis -0.089 0.12 -10000 0 -0.78 7 7
ATF5 0.006 0.021 0.22 2 -0.38 1 3
BARD1 signaling events

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
BARD1/CSTF1 0.008 0.004 -10000 0 -10000 0 0
ATM 0.014 0.04 0.22 20 -10000 0 20
UBE2D3 0.006 0 -10000 0 -10000 0 0
PRKDC 0.048 0.085 0.22 110 -10000 0 110
ATR 0.071 0.099 0.22 170 -10000 0 170
UBE2L3 0.006 0 -10000 0 -10000 0 0
FANCD2 0.12 0.12 0.34 109 -10000 0 109
protein ubiquitination 0.059 0.062 -10000 0 -10000 0 0
XRCC5 0.029 0.066 0.22 60 -10000 0 60
XRCC6 0.006 0 -10000 0 -10000 0 0
M/R/N Complex 0.008 0.015 -10000 0 -0.23 2 2
MRE11A 0.058 0.092 0.22 136 -10000 0 136
DNA-PK 0.009 0.006 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.001 0.011 -10000 0 -10000 0 0
FANCF 0.006 0 -10000 0 -10000 0 0
BRCA1 0.018 0.048 0.22 30 -10000 0 30
CCNE1 0.2 0.065 0.22 512 -10000 0 512
CDK2/Cyclin E1 0.001 0.002 -10000 0 -10000 0 0
FANCG 0.007 0.009 0.22 1 -10000 0 1
BRCA1/BACH1/BARD1 0.007 0.004 -10000 0 -10000 0 0
FANCE 0.006 0 -10000 0 -10000 0 0
FANCC 0.008 0.02 0.22 5 -10000 0 5
NBN 0.019 0.055 0.22 35 -0.38 1 36
FANCA 0.012 0.035 0.22 15 -10000 0 15
DNA repair 0.18 0.18 0.34 267 -10000 0 267
BRCA1/BARD1/ubiquitin 0.007 0.004 -10000 0 -10000 0 0
BARD1/DNA-PK 0.046 0.056 -10000 0 -10000 0 0
FANCL 0.02 0.053 0.22 36 -10000 0 36
mRNA polyadenylation -0.008 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.075 0.097 0.25 105 -0.2 1 106
BRCA1/BACH1/BARD1/TopBP1 0.006 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.028 0.092 -10000 0 -0.2 44 44
BARD1/CSTF1/BRCA1 0.01 0.005 -10000 0 -10000 0 0
BRCA1/BACH1 0.018 0.048 0.22 30 -10000 0 30
BARD1 0.045 0.083 0.22 103 -10000 0 103
PCNA 0.042 0.081 0.22 95 -10000 0 95
BRCA1/BARD1/UbcH5C 0.01 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.01 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.051 0.061 -10000 0 -10000 0 0
BARD1/DNA-PK/P53 0.02 0.082 -10000 0 -0.19 45 45
BRCA1/BARD1/Ubiquitin 0.007 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP 0.046 0.064 0.28 9 -10000 0 9
FA complex 0.042 0.055 0.21 21 -10000 0 21
BARD1/EWS 0.008 0.004 -10000 0 -10000 0 0
RBBP8 0.038 0.084 0.2 116 -10000 0 116
TP53 -0.045 0.13 0.22 3 -0.38 76 79
TOPBP1 0.11 0.11 0.22 284 -10000 0 284
G1/S transition of mitotic cell cycle -0.027 0.09 0.2 44 -10000 0 44
BRCA1/BARD1 0.065 0.068 -10000 0 -10000 0 0
CSTF1 0.009 0.025 0.22 8 -10000 0 8
BARD1/EWS-Fli1 0.004 0.002 -10000 0 -10000 0 0
CDK2 0.1 0.11 0.22 255 -10000 0 255
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.093 0.11 0.22 230 -10000 0 230
RAD50 0.006 0.021 0.22 2 -0.38 1 3
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.007 0.004 -10000 0 -10000 0 0
EWSR1 0.006 0 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.022 0.067 0.18 78 -0.21 3 81
RFC1 0.03 0.076 0.19 94 -10000 0 94
PRKDC 0.054 0.094 0.22 82 -10000 0 82
RIPK1 0.007 0.005 -10000 0 -10000 0 0
CASP7 0 0.034 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 0.024 0.091 0.17 112 -0.22 18 130
MAP2K4 -0.017 0.094 0.29 4 -0.29 41 45
mol:ceramide -0.012 0.07 0.25 4 -0.36 6 10
GSN 0.004 0.085 0.18 66 -0.21 41 107
FASLG/FAS/FADD/FAF1/Caspase 8 0.015 0.082 0.26 3 -0.28 6 9
FAS -0.01 0.075 0.22 1 -0.39 21 22
BID -0.003 0.027 0.24 7 -10000 0 7
MAP3K1 -0.002 0.062 0.21 4 -0.26 4 8
MAP3K7 0.009 0.029 0.22 10 -10000 0 10
RB1 0.026 0.076 0.19 79 -0.21 6 85
CFLAR 0.006 0.017 -10000 0 -0.38 1 1
HGF/MET -0.059 0.12 -10000 0 -0.25 151 151
ARHGDIB 0.009 0.087 0.18 74 -0.22 37 111
FADD 0.004 0.009 -10000 0 -10000 0 0
actin filament polymerization -0.004 0.084 0.21 41 -0.18 66 107
NFKB1 -0.023 0.12 0.29 4 -0.79 11 15
MAPK8 -0.029 0.13 0.36 4 -0.44 46 50
DFFA 0.023 0.065 0.18 79 -10000 0 79
DNA fragmentation during apoptosis 0.023 0.065 0.18 79 -10000 0 79
FAS/FADD/MET -0.017 0.083 0.2 1 -0.25 60 61
CFLAR/RIP1 0.01 0.014 -10000 0 -0.27 1 1
FAIM3 0.002 0.04 -10000 0 -0.38 6 6
FAF1 0.006 0.023 0.22 5 -10000 0 5
PARP1 0.037 0.081 0.2 79 -10000 0 79
DFFB 0.023 0.065 0.18 79 -10000 0 79
CHUK -0.02 0.12 0.25 4 -0.74 11 15
FASLG 0.004 0.01 -10000 0 -10000 0 0
FAS/FADD -0.004 0.054 -10000 0 -0.27 21 21
HGF 0.008 0.018 0.22 4 -10000 0 4
LMNA 0.051 0.093 0.22 75 -0.19 4 79
CASP6 0.061 0.1 0.2 180 -10000 0 180
CASP10 0.004 0.031 0.22 4 -0.38 2 6
CASP3 0.03 0.079 0.22 79 -0.18 2 81
PTPN13 -0.068 0.18 0.22 34 -0.38 127 161
CASP8 -0.003 0.033 0.31 6 -10000 0 6
IL6 -0.091 0.33 0.54 4 -1.1 48 52
MET -0.013 0.12 0.22 32 -0.38 45 77
ICAD/CAD 0.02 0.058 0.16 67 -10000 0 67
FASLG/FAS/FADD/FAF1/Caspase 10 -0.012 0.071 0.25 4 -0.37 6 10
activation of caspase activity by cytochrome c -0.003 0.027 0.24 7 -10000 0 7
PAK2 0.024 0.066 0.18 79 -10000 0 79
BCL2 -0.043 0.13 0.22 2 -0.38 73 75
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.072 0.28 0.47 6 -0.95 50 56
MKNK1 0.006 0 -10000 0 -10000 0 0
MAPK14 -0.014 0.089 0.19 7 -0.29 50 57
ATF2/c-Jun -0.009 0.096 0.43 9 -0.52 3 12
MAPK11 -0.015 0.088 -10000 0 -0.29 50 50
MITF -0.022 0.1 -10000 0 -0.34 50 50
MAPKAPK5 -0.022 0.1 -10000 0 -0.34 50 50
KRT8 -0.022 0.1 -10000 0 -0.34 51 51
MAPKAPK3 0.006 0 -10000 0 -10000 0 0
MAPKAPK2 0.006 0.016 -10000 0 -0.38 1 1
p38alpha-beta/CK2 -0.022 0.13 0.26 6 -0.42 50 56
CEBPB -0.023 0.11 0.22 6 -0.34 53 59
SLC9A1 -0.022 0.1 -10000 0 -0.34 50 50
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.018 0.11 0.3 9 -0.33 49 58
p38alpha-beta/MNK1 -0.013 0.1 0.22 6 -0.33 50 56
JUN -0.01 0.095 0.44 9 -0.52 3 12
PPARGC1A -0.02 0.1 0.22 6 -0.34 50 56
USF1 -0.021 0.1 -10000 0 -0.34 50 50
RAB5/GDP/GDI1 -0.016 0.075 -10000 0 -0.25 50 50
NOS2 -0.022 0.1 0.22 6 -0.34 50 56
DDIT3 0 0.12 0.38 3 -0.34 43 46
RAB5A 0.006 0 -10000 0 -10000 0 0
HSPB1 -0.024 0.089 -10000 0 -0.28 56 56
p38alpha-beta/HBP1 -0.013 0.1 0.22 6 -0.33 49 55
CREB1 -0.024 0.11 -10000 0 -0.37 50 50
RAB5/GDP 0.005 0 -10000 0 -10000 0 0
EIF4E -0.028 0.086 -10000 0 -0.3 50 50
RPS6KA4 -0.022 0.1 -10000 0 -0.34 50 50
PLA2G4A -0.09 0.14 0.31 2 -0.27 196 198
GDI1 -0.022 0.1 0.22 6 -0.34 52 58
TP53 -0.054 0.14 0.24 6 -0.45 50 56
RPS6KA5 -0.022 0.1 -10000 0 -0.34 51 51
ESR1 -0.051 0.14 -10000 0 -0.32 105 105
HBP1 0.014 0.041 0.22 21 -10000 0 21
MEF2C -0.03 0.12 -10000 0 -0.35 62 62
MEF2A -0.022 0.1 -10000 0 -0.34 50 50
EIF4EBP1 -0.024 0.11 -10000 0 -0.37 50 50
KRT19 -0.042 0.14 0.22 6 -0.37 78 84
ELK4 -0.022 0.1 -10000 0 -0.34 50 50
ATF6 -0.022 0.1 -10000 0 -0.34 50 50
ATF1 -0.024 0.11 -10000 0 -0.37 50 50
p38alpha-beta/MAPKAPK2 -0.013 0.1 0.22 6 -0.33 51 57
p38alpha-beta/MAPKAPK3 -0.013 0.1 0.22 6 -0.33 50 56
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.004 0.011 -10000 0 -0.27 1 1
PRKCZ 0.006 0 -10000 0 -10000 0 0
MAP3K7IP2 0.005 0.025 0.22 1 -0.38 2 3
ERC1 0.008 0.029 0.22 7 -0.38 1 8
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.011 0.066 0.22 15 -0.23 17 32
IRAK/TOLLIP 0.006 0.01 0.14 1 -0.2 1 2
IKBKB 0.007 0.016 0.22 3 -10000 0 3
IKBKG 0.006 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.006 0.031 -10000 0 -0.27 7 7
IL1A 0.011 0.031 0.22 12 -10000 0 12
IL1B -0.011 0.11 0.21 52 -0.27 57 109
IRAK/TRAF6/p62/Atypical PKCs 0.075 0.056 -10000 0 -10000 0 0
IL1R2 0.007 0.055 0.22 14 -0.38 7 21
IL1R1 -0.081 0.16 0.22 1 -0.38 127 128
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.017 0.13 0.19 8 -0.26 85 93
TOLLIP 0.006 0 -10000 0 -10000 0 0
TICAM2 0.006 0.019 0.22 1 -0.38 1 2
MAP3K3 0.006 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.012 0.014 -10000 0 -0.23 2 2
IKK complex/ELKS 0.008 0.032 -10000 0 -0.3 1 1
JUN 0.007 0.048 0.22 5 -10000 0 5
MAP3K7 0.01 0.028 0.22 10 -10000 0 10
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.013 0.16 0.26 64 -0.24 116 180
IL1 alpha/IL1R1/IL1RAP/MYD88 0.02 0.12 -10000 0 -0.2 84 84
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.021 0.11 -10000 0 -0.19 82 82
IL1 beta fragment/IL1R1/IL1RAP -0.001 0.14 -10000 0 -0.24 107 107
NFKB1 -0.001 0.054 -10000 0 -0.38 11 11
MAPK8 0.008 0.046 0.24 3 -0.17 3 6
IRAK1 -0.003 0.012 0.16 1 -0.22 1 2
IL1RN/IL1R1 -0.053 0.12 -10000 0 -0.27 126 126
IRAK4 0.017 0.047 0.22 28 -10000 0 28
PRKCI 0.12 0.11 0.22 306 -10000 0 306
TRAF6 0.007 0.013 0.22 2 -10000 0 2
PI3K -0.022 0.083 -10000 0 -0.27 56 56
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.002 0.12 0.2 35 -0.31 23 58
CHUK 0.011 0.031 0.22 12 -10000 0 12
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.001 0.14 -10000 0 -0.24 107 107
IL1 beta/IL1R2 -0.012 0.083 0.17 24 -0.23 64 88
IRAK/TRAF6/TAK1/TAB1/TAB2 0.017 0.022 -10000 0 -0.18 3 3
NF kappa B1 p50/RelA -0.054 0.11 -10000 0 -0.34 49 49
IRAK3 0.015 0.042 0.22 22 -10000 0 22
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.016 0.14 0.25 31 -0.22 106 137
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.008 0.11 0.22 19 -0.21 82 101
IL1 alpha/IL1R1/IL1RAP -0.034 0.083 -10000 0 -0.23 83 83
RELA 0.005 0.023 -10000 0 -0.38 2 2
MAP3K7IP1 0.006 0 -10000 0 -10000 0 0
SQSTM1 0.006 0 -10000 0 -10000 0 0
MYD88 0.006 0.016 -10000 0 -0.38 1 1
IRAK/TRAF6/MEKK3 0.011 0.013 -10000 0 -0.19 1 1
IL1RAP 0.095 0.11 0.22 235 -0.38 1 236
UBE2N 0.006 0.016 -10000 0 -0.38 1 1
IRAK/TRAF6 -0.045 0.077 -10000 0 -0.3 22 22
CASP1 -0.026 0.12 0.22 17 -0.38 57 74
IL1RN/IL1R2 0.005 0.031 -10000 0 -0.27 7 7
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.01 0.14 0.26 17 -0.22 107 124
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.021 0.14 -10000 0 -0.3 81 81
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
IL1RN 0.012 0.035 0.22 15 -10000 0 15
TRAF6/TAK1/TAB1/TAB2 0.014 0.015 -10000 0 -0.18 3 3
MAP2K6 0.009 0.047 0.25 1 -0.18 3 4
Effects of Botulinum toxin

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
STX1A -0.002 0 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.009 0 -10000 0 -10000 0 0
STXBP1 -0.038 0.12 -10000 0 -0.38 65 65
ACh/CHRNA1 -0.04 0.05 0.13 26 -10000 0 26
RAB3GAP2/RIMS1/UNC13B 0.013 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.006 0 -10000 0 -10000 0 0
mol:ACh -0.065 0.042 0.069 1 -0.092 400 401
RAB3GAP2 0.009 0.024 0.22 7 -10000 0 7
STX1A/SNAP25/VAMP2 -0.12 0.091 -10000 0 -0.28 65 65
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.04 0.05 0.13 26 -10000 0 26
UNC13B 0.006 0 -10000 0 -10000 0 0
CHRNA1 0.016 0.045 0.22 26 -10000 0 26
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.041 0.047 0.12 21 -10000 0 21
SNAP25 0.003 0.016 0.14 8 -10000 0 8
VAMP2 -0.16 0.099 -10000 0 -0.22 407 407
SYT1 0.014 0.041 0.22 21 -10000 0 21
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 -0.021 0.073 -10000 0 -0.22 65 65
STX1A/SNAP25 fragment 1/VAMP2 -0.12 0.091 -10000 0 -0.28 65 65
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.039 0.098 -10000 0 -0.24 108 108
alphaM/beta2 Integrin/GPIbA 0.003 0.035 -10000 0 -0.23 9 9
alphaM/beta2 Integrin/proMMP-9 0.002 0.035 -10000 0 -0.23 9 9
PLAUR 0.011 0.032 0.22 13 -10000 0 13
HMGB1 0.002 0.016 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.002 0.038 -10000 0 -0.23 11 11
AGER 0.002 0.016 -10000 0 -10000 0 0
RAP1A 0.007 0.009 0.22 1 -10000 0 1
SELPLG -0.009 0.075 -10000 0 -0.38 22 22
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.001 0.062 -10000 0 -0.19 51 51
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.035 0.074 0.22 77 -10000 0 77
CYR61 -0.028 0.12 0.22 7 -0.38 54 61
TLN1 0.005 0.023 -10000 0 -0.38 2 2
Rap1/GTP -0.063 0.091 -10000 0 -0.33 31 31
RHOA 0.005 0.023 -10000 0 -0.38 2 2
P-selectin oligomer -0.02 0.099 0.22 1 -0.38 39 40
MYH2 -0.049 0.16 0.2 41 -0.39 31 72
MST1R 0.008 0.018 0.22 4 -10000 0 4
leukocyte activation during inflammatory response 0.005 0.03 -10000 0 -0.19 9 9
APOB 0.006 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.057 0.16 0.22 16 -0.38 101 117
JAM3 0.007 0.013 0.22 2 -10000 0 2
GP1BA 0.006 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CTGF -0.043 0.1 -10000 0 -0.24 117 117
alphaM/beta2 Integrin -0.034 0.14 0.19 50 -0.38 31 81
JAM3 homodimer 0.007 0.013 0.22 2 -10000 0 2
ICAM2 0.001 0.043 -10000 0 -0.38 7 7
ICAM1 0.015 0.089 0.22 49 -0.38 15 64
phagocytosis triggered by activation of immune response cell surface activating receptor -0.034 0.14 0.19 50 -0.37 31 81
cell adhesion 0.003 0.035 -10000 0 -0.23 9 9
NFKB1 -0.034 0.1 0.38 5 -0.34 46 51
THY1 0.073 0.1 0.22 177 -0.38 1 178
RhoA/GDP 0.004 0.016 -10000 0 -0.27 2 2
Lipoprotein(a) 0.009 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA -0.038 0.1 -10000 0 -0.22 128 128
IL6 -0.057 0.18 0.48 5 -0.63 46 51
ITGB2 -0.003 0.053 0.22 2 -0.39 9 11
elevation of cytosolic calcium ion concentration 0.039 0.068 -10000 0 -0.2 9 9
alphaM/beta2 Integrin/JAM2/JAM3 -0.068 0.11 -10000 0 -0.21 206 206
JAM2 -0.13 0.19 0.22 1 -0.38 204 205
alphaM/beta2 Integrin/ICAM1 0.015 0.062 -10000 0 -0.23 20 20
alphaM/beta2 Integrin/uPA/Plg 0.037 0.077 -10000 0 -0.21 18 18
RhoA/GTP -0.05 0.17 0.21 49 -0.25 180 229
positive regulation of phagocytosis -0.052 0.082 0.17 1 -0.3 30 31
Ron/MSP 0.009 0.001 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA 0.041 0.07 -10000 0 -0.2 9 9
alphaM/beta2 Integrin/uPAR 0.003 0.035 -10000 0 -0.23 9 9
PLAU 0.066 0.097 0.22 158 -10000 0 158
PLAT -0.071 0.16 0.22 7 -0.38 116 123
actin filament polymerization -0.046 0.16 0.2 41 -0.38 31 72
MST1 0.007 0.009 0.22 1 -10000 0 1
alphaM/beta2 Integrin/lipoprotein(a) 0.008 0.033 -10000 0 -0.19 9 9
TNF -0.032 0.097 0.39 5 -0.4 4 9
RAP1B 0.007 0.026 0.22 5 -0.38 1 6
alphaM/beta2 Integrin/uPA 0 0.035 -10000 0 -0.23 9 9
fibrinolysis 0.036 0.075 -10000 0 -0.21 18 18
HCK 0.007 0.009 0.22 1 -10000 0 1
dendritic cell antigen processing and presentation -0.034 0.14 0.19 50 -0.37 31 81
VTN 0.006 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 -0.019 0.079 -10000 0 -0.24 60 60
LPA 0.006 0 -10000 0 -10000 0 0
LRP1 -0.001 0.054 -10000 0 -0.38 11 11
cell migration -0.018 0.1 -10000 0 -0.22 99 99
FN1 0.074 0.12 0.22 201 -0.38 13 214
alphaM/beta2 Integrin/Thy1 0.003 0.033 0.12 1 -0.23 6 7
MPO 0.006 0 -10000 0 -10000 0 0
KNG1 0.007 0.009 0.22 1 -10000 0 1
RAP1/GDP 0.008 0.01 -10000 0 -0.22 1 1
ROCK1 -0.048 0.16 0.2 41 -0.32 55 96
ELA2 0.006 0 -10000 0 -10000 0 0
PLG -0.001 0.054 -10000 0 -0.38 11 11
CTGF -0.071 0.16 -10000 0 -0.38 112 112
alphaM/beta2 Integrin/Hck 0.003 0.035 -10000 0 -0.23 9 9
ITGAM 0.004 0.022 0.22 3 -10000 0 3
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.014 0.084 -10000 0 -0.24 62 62
HP -0.13 0.24 0.22 93 -0.38 254 347
leukocyte adhesion -0.038 0.13 0.26 1 -0.3 36 37
SELP -0.02 0.099 0.22 1 -0.38 39 40
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.009 0.067 -10000 0 -0.2 64 64
ER alpha/Gai/GDP/Gbeta gamma -0.025 0.11 -10000 0 -0.31 56 56
AKT1 -0.064 0.23 -10000 0 -0.7 61 61
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.063 0.24 -10000 0 -0.7 61 61
mol:Ca2+ -0.069 0.11 -10000 0 -0.36 36 36
IGF1R -0.077 0.16 -10000 0 -0.38 121 121
E2/ER alpha (dimer)/Striatin -0.016 0.072 -10000 0 -0.22 61 61
SHC1 0.006 0 -10000 0 -10000 0 0
apoptosis 0.06 0.22 0.66 61 -10000 0 61
RhoA/GTP -0.014 0.035 -10000 0 -0.17 22 22
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.031 0.11 -10000 0 -0.33 60 60
regulation of stress fiber formation -0.032 0.079 0.24 6 -0.21 28 34
E2/ERA-ERB (dimer) -0.016 0.072 -10000 0 -0.22 61 61
KRAS 0.03 0.067 0.22 62 -10000 0 62
G13/GTP -0.015 0.065 -10000 0 -0.2 62 62
pseudopodium formation 0.032 0.079 0.21 28 -0.24 6 34
E2/ER alpha (dimer)/PELP1 -0.016 0.072 -10000 0 -0.22 61 61
GRB2 0.006 0.016 -10000 0 -0.38 1 1
GNG2 0.004 0.034 0.22 1 -0.38 4 5
GNAO1 0.006 0.036 0.22 6 -0.38 3 9
HRAS 0.006 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.035 0.14 -10000 0 -0.41 60 60
E2/ER beta (dimer) 0.005 0 -10000 0 -10000 0 0
mol:GDP -0.023 0.078 -10000 0 -0.25 56 56
mol:NADP -0.035 0.14 -10000 0 -0.41 60 60
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
mol:IP3 -0.071 0.12 -10000 0 -0.38 36 36
IGF-1R heterotetramer -0.077 0.16 -10000 0 -0.38 121 121
PLCB1 -0.071 0.12 -10000 0 -0.38 36 36
PLCB2 -0.082 0.12 -10000 0 -0.38 38 38
IGF1 -0.003 0.067 0.22 4 -0.38 16 20
mol:L-citrulline -0.035 0.14 -10000 0 -0.41 60 60
RHOA 0.005 0.023 -10000 0 -0.38 2 2
Gai/GDP 0.005 0.065 -10000 0 -0.65 3 3
JNK cascade 0.005 0 -10000 0 -10000 0 0
BCAR1 0.004 0.028 -10000 0 -0.38 3 3
ESR2 0.006 0 -10000 0 -10000 0 0
GNAQ -0.005 0.065 -10000 0 -0.38 16 16
ESR1 -0.036 0.12 -10000 0 -0.38 61 61
Gq family/GDP/Gbeta gamma -0.12 0.19 -10000 0 -0.37 194 194
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.013 0.077 -10000 0 -0.5 1 1
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.03 0.11 -10000 0 -0.33 60 60
GNAZ 0.002 0.04 -10000 0 -0.38 6 6
E2/ER alpha (dimer) -0.025 0.084 -10000 0 -0.27 61 61
STRN 0.007 0.013 0.22 2 -10000 0 2
GNAL 0.006 0 -10000 0 -10000 0 0
PELP1 0.006 0 -10000 0 -10000 0 0
MAPK11 -0.003 0 -10000 0 -10000 0 0
GNAI2 0.006 0 -10000 0 -10000 0 0
GNAI3 0.017 0.047 0.22 29 -10000 0 29
GNAI1 0 0.063 0.22 7 -0.38 13 20
HBEGF -0.029 0.1 -10000 0 -0.29 46 46
cAMP biosynthetic process -0.013 0.058 -10000 0 -0.18 61 61
SRC -0.026 0.1 -10000 0 -0.3 55 55
PI3K -0.022 0.083 -10000 0 -0.27 56 56
GNB1 0.006 0.016 -10000 0 -0.38 1 1
G13/GDP/Gbeta gamma -0.018 0.073 -10000 0 -0.23 56 56
SOS1 0.014 0.04 0.22 20 -10000 0 20
IGF-1R heterotetramer/IGF1 -0.063 0.11 -10000 0 -0.31 64 64
Gs family/GTP -0.011 0.059 -10000 0 -0.18 61 61
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.067 0.064 0.14 245 -10000 0 245
vasodilation -0.033 0.13 -10000 0 -0.4 60 60
mol:DAG -0.071 0.12 -10000 0 -0.38 36 36
Gs family/GDP/Gbeta gamma -0.02 0.071 -10000 0 -0.22 56 56
MSN 0.032 0.083 0.21 28 -0.26 6 34
Gq family/GTP -0.084 0.13 -10000 0 -0.4 38 38
mol:PI-3-4-5-P3 -0.06 0.23 -10000 0 -0.68 61 61
NRAS 0.099 0.11 0.22 245 -10000 0 245
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.033 0.13 0.4 60 -10000 0 60
GRB2/SOS1 0.009 0.012 -10000 0 -0.27 1 1
RhoA/GDP -0.021 0.076 -10000 0 -0.24 56 56
NOS3 -0.037 0.14 -10000 0 -0.43 60 60
GNA11 -0.13 0.18 -10000 0 -0.38 193 193
MAPKKK cascade -0.044 0.16 -10000 0 -0.5 61 61
E2/ER alpha (dimer)/PELP1/Src -0.028 0.12 -10000 0 -0.34 60 60
ruffle organization 0.032 0.079 0.21 28 -0.24 6 34
ROCK2 0.036 0.081 0.22 28 -10000 0 28
GNA14 0.006 0.026 0.22 2 -0.38 2 4
GNA15 0.003 0.037 -10000 0 -0.38 5 5
GNA13 0.006 0.016 -10000 0 -0.38 1 1
MMP9 -0.009 0.1 0.21 4 -0.29 42 46
MMP2 -0.051 0.12 -10000 0 -0.31 57 57
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.049 0.097 0.16 205 -0.23 28 233
EPHB2 0.01 0.027 0.22 9 -10000 0 9
Syndecan-2/TACI 0.001 0.042 0.14 7 -0.22 17 24
LAMA1 0.045 0.083 0.22 102 -10000 0 102
Syndecan-2/alpha2 ITGB1 -0.03 0.099 -10000 0 -0.22 115 115
HRAS 0.006 0 -10000 0 -10000 0 0
Syndecan-2/CASK -0.004 0.041 0.14 7 -0.22 17 24
ITGA5 0.008 0.018 0.22 4 -10000 0 4
BAX -0.004 0.04 -10000 0 -10000 0 0
EPB41 0.016 0.045 0.22 26 -10000 0 26
positive regulation of cell-cell adhesion -0.001 0.04 0.14 2 -0.21 18 20
LAMA3 -0.02 0.1 0.22 6 -0.38 42 48
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.013 0.089 0.22 3 -0.38 30 33
Syndecan-2/MMP2 -0.035 0.11 0.15 23 -0.24 107 130
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 -0.026 0.093 -10000 0 -0.27 72 72
dendrite morphogenesis 0.003 0.046 0.15 16 -0.22 17 33
Syndecan-2/GM-CSF 0.001 0.042 0.14 7 -0.22 17 24
determination of left/right symmetry -0.004 0.051 0.2 7 -0.27 17 24
Syndecan-2/PKC delta 0 0.044 0.14 7 -0.22 19 26
GNB2L1 0.006 0 -10000 0 -10000 0 0
MAPK3 -0.026 0.071 -10000 0 -0.22 62 62
MAPK1 -0.008 0.039 -10000 0 -0.2 18 18
Syndecan-2/RACK1 0.005 0.037 0.13 7 -0.19 17 24
NF1 -0.01 0.079 0.22 1 -0.38 24 25
FGFR/FGF/Syndecan-2 -0.004 0.051 0.2 7 -0.27 17 24
ITGA2 -0.044 0.13 0.22 2 -0.38 74 76
MAPK8 -0.005 0.045 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.006 0.092 0.27 1 -0.2 66 67
Syndecan-2/Kininogen 0.001 0.043 0.14 8 -0.22 17 25
ITGB1 0.007 0.016 0.22 3 -10000 0 3
SRC -0.008 0.033 -10000 0 -0.18 17 17
Syndecan-2/CASK/Protein 4.1 0.005 0.044 0.14 24 -0.2 15 39
extracellular matrix organization -0.05 0.11 0.14 6 -0.23 136 142
actin cytoskeleton reorganization 0.049 0.096 0.16 205 -0.23 28 233
Syndecan-2/Caveolin-2/Ras -0.005 0.065 0.14 3 -0.22 42 45
Syndecan-2/Laminin alpha3 -0.014 0.076 0.15 13 -0.23 58 71
Syndecan-2/RasGAP 0.007 0.038 -10000 0 -0.18 20 20
alpha5/beta1 Integrin 0.009 0.001 -10000 0 -10000 0 0
PRKCD 0.005 0.023 -10000 0 -0.38 2 2
Syndecan-2 dimer 0.003 0.047 0.15 16 -0.22 17 33
GO:0007205 0 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.002 0.037 -10000 0 -0.18 20 20
RHOA 0.005 0.023 -10000 0 -0.38 2 2
SDCBP 0.006 0.026 0.22 2 -0.38 2 4
TNFRSF13B 0.006 0 -10000 0 -10000 0 0
RASA1 0.004 0.028 -10000 0 -0.38 3 3
alpha2/beta1 Integrin -0.026 0.093 -10000 0 -0.27 72 72
Syndecan-2/Synbindin 0.011 0.058 0.16 44 -0.22 16 60
TGFB1 -0.081 0.16 -10000 0 -0.38 127 127
CASP3 -0.006 0.043 -10000 0 -0.2 18 18
FN1 0.074 0.12 0.22 201 -0.38 13 214
Syndecan-2/IL8 0.013 0.06 0.16 52 -0.22 16 68
SDC2 -0.004 0.051 0.2 7 -0.27 17 24
KNG1 0.007 0.009 0.22 1 -10000 0 1
Syndecan-2/Neurofibromin -0.008 0.06 0.15 6 -0.22 39 45
TRAPPC4 0.021 0.055 0.22 40 -10000 0 40
CSF2 0.006 0 -10000 0 -10000 0 0
Syndecan-2/TGFB1 -0.05 0.11 0.14 6 -0.24 136 142
Syndecan-2/Syntenin/PI-4-5-P2 -0.001 0.04 0.14 2 -0.21 18 20
Syndecan-2/Ezrin -0.001 0.037 -10000 0 -0.2 19 19
PRKACA -0.016 0.053 -10000 0 -0.2 39 39
angiogenesis 0.013 0.06 0.16 52 -0.22 16 68
MMP2 -0.057 0.16 0.22 16 -0.38 101 117
IL8 0.024 0.059 0.22 47 -10000 0 47
calcineurin-NFAT signaling pathway 0.001 0.042 0.14 7 -0.22 17 24
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.004 0.13 0.22 60 -0.38 48 108
positive regulation of NF-kappaB transcription factor activity -0.016 0.079 -10000 0 -0.27 48 48
MAP2K4 -0.009 0.077 -10000 0 -0.28 7 7
IKBKB 0.007 0.016 0.22 3 -10000 0 3
TNFRSF10B 0.007 0.009 0.22 1 -10000 0 1
TNFRSF10A 0.007 0.016 0.22 3 -10000 0 3
SMPD1 -0.012 0.048 -10000 0 -0.17 49 49
IKBKG 0.006 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.006 0.019 0.22 1 -0.38 1 2
TRAIL/TRAILR2 -0.015 0.077 -10000 0 -0.27 48 48
TRAIL/TRAILR3 -0.13 0.15 -10000 0 -0.29 257 257
TRAIL/TRAILR1 -0.015 0.077 -10000 0 -0.27 48 48
TRAIL/TRAILR4 -0.016 0.079 -10000 0 -0.28 48 48
TRAIL/TRAILR1/DAP3/GTP 0.009 0.076 -10000 0 -0.2 47 47
IKK complex -0.003 0.037 -10000 0 -10000 0 0
RIPK1 0.006 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.005 0 -10000 0 -10000 0 0
MAPK3 -0.028 0.12 0.2 53 -0.28 90 143
MAP3K1 -0.006 0.078 -10000 0 -0.28 6 6
TRAILR4 (trimer) 0.006 0.019 0.22 1 -0.38 1 2
TRADD 0.002 0.04 -10000 0 -0.38 6 6
TRAILR1 (trimer) 0.007 0.016 0.22 3 -10000 0 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.003 0.075 -10000 0 -0.21 53 53
CFLAR 0.006 0.016 -10000 0 -0.38 1 1
MAPK1 -0.005 0.1 0.2 61 -0.27 49 110
TRAIL/TRAILR1/FADD/TRADD/RIP 0.012 0.077 -10000 0 -0.2 53 53
mol:ceramide -0.012 0.047 -10000 0 -0.17 49 49
FADD 0.006 0 -10000 0 -10000 0 0
MAPK8 -0.009 0.073 -10000 0 -0.26 7 7
TRAF2 0.006 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.16 0.2 0.22 1 -0.38 249 250
CHUK 0.011 0.031 0.22 12 -10000 0 12
TRAIL/TRAILR1/FADD -0.009 0.066 -10000 0 -0.23 48 48
DAP3 0.007 0.016 0.22 3 -10000 0 3
CASP10 -0.009 0.086 -10000 0 -0.25 48 48
JNK cascade -0.016 0.079 -10000 0 -0.27 48 48
TRAIL (trimer) -0.004 0.13 0.22 60 -0.38 48 108
TNFRSF10C -0.16 0.2 0.22 1 -0.38 249 250
TRAIL/TRAILR1/DAP3/GTP/FADD 0.011 0.072 -10000 0 -0.19 47 47
TRAIL/TRAILR2/FADD -0.009 0.066 -10000 0 -0.23 48 48
cell death -0.012 0.047 -10000 0 -0.16 49 49
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.003 0.074 -10000 0 -0.21 53 53
TRAILR2 (trimer) 0.007 0.009 0.22 1 -10000 0 1
CASP8 0.001 0.036 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.012 0.076 -10000 0 -0.2 53 53
HIF-2-alpha transcription factor network

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
MMP14 0.005 0.1 0.53 16 -1 1 17
oxygen homeostasis 0.029 0.048 0.19 18 -10000 0 18
TCEB2 0.006 0 -10000 0 -10000 0 0
TCEB1 0.006 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.015 0.12 -10000 0 -0.33 20 20
EPO 0.14 0.31 0.71 82 -10000 0 82
FIH (dimer) 0.033 0.047 0.2 16 -10000 0 16
APEX1 0.052 0.077 0.23 75 -10000 0 75
SERPINE1 0.16 0.36 0.81 88 -0.56 3 91
FLT1 -0.009 0.036 -10000 0 -0.74 1 1
ADORA2A 0.15 0.32 0.71 86 -0.55 3 89
germ cell development 0.14 0.34 0.75 82 -0.62 4 86
SLC11A2 0.14 0.34 0.76 84 -0.56 3 87
BHLHE40 0.14 0.33 0.74 81 -0.56 3 84
HIF1AN 0.033 0.047 0.2 16 -10000 0 16
HIF2A/ARNT/SIRT1 0.007 0.17 0.48 7 -0.41 10 17
ETS1 0.01 0.028 0.23 6 -0.38 1 7
CITED2 -0.039 0.17 -10000 0 -0.93 20 20
KDR -0.008 0.045 0.62 1 -0.74 1 2
PGK1 0.19 0.38 0.81 106 -0.56 3 109
SIRT1 0.006 0 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.15 0.34 0.78 71 -0.64 3 74
EPAS1 0.078 0.26 0.57 78 -0.36 20 98
SP1 0.018 0.052 0.24 28 -10000 0 28
ABCG2 0.11 0.35 0.74 78 -0.64 15 93
EFNA1 0.15 0.34 0.76 86 -0.56 3 89
FXN 0.15 0.32 0.72 83 -0.55 3 86
POU5F1 0.14 0.34 0.75 82 -0.64 4 86
neuron apoptosis -0.14 0.33 0.63 3 -0.77 71 74
EP300 0.003 0.037 -10000 0 -0.38 5 5
EGLN3 0.027 0.11 0.24 45 -0.38 25 70
EGLN2 0.035 0.049 0.2 17 -10000 0 17
EGLN1 0.033 0.047 0.2 16 -10000 0 16
VHL/Elongin B/Elongin C 0.013 0.001 -10000 0 -10000 0 0
VHL 0.007 0.016 0.22 3 -10000 0 3
ARNT 0.03 0.046 0.2 17 -10000 0 17
SLC2A1 0.16 0.34 0.76 88 -0.55 3 91
TWIST1 0.15 0.32 0.71 86 -0.55 3 89
ELK1 0.003 0.021 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.009 0.17 0.48 7 -0.42 11 18
VEGFA 0.15 0.34 0.76 88 -0.56 3 91
CREBBP 0.001 0.046 -10000 0 -0.38 8 8
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.01 0.079 -10000 0 -0.38 24 24
alphaV beta3 Integrin -0.033 0.1 -10000 0 -0.28 83 83
PTK2 -0.044 0.12 0.28 2 -0.46 27 29
positive regulation of JNK cascade -0.022 0.068 -10000 0 -0.31 27 27
CDC42/GDP -0.012 0.1 -10000 0 -0.42 27 27
Rac1/GDP -0.012 0.1 -10000 0 -0.42 27 27
RAP1B 0.007 0.026 0.22 5 -0.38 1 6
RAP1A 0.007 0.009 0.22 1 -10000 0 1
CTNNB1 0.007 0.009 0.22 1 -10000 0 1
CDC42/GTP -0.025 0.085 -10000 0 -0.38 27 27
nectin-3/I-afadin -0.005 0.062 -10000 0 -0.28 27 27
RAPGEF1 -0.02 0.11 0.23 1 -0.47 27 28
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.022 0.13 -10000 0 -0.53 27 27
PDGFB-D/PDGFRB -0.01 0.079 -10000 0 -0.38 24 24
TLN1 -0.11 0.15 -10000 0 -0.29 212 212
Rap1/GTP -0.027 0.074 -10000 0 -0.34 27 27
IQGAP1 0.005 0.025 0.22 1 -0.38 2 3
Rap1/GTP/I-afadin 0.006 0.041 0.14 6 -0.2 19 25
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.005 0.062 -10000 0 -0.28 27 27
PVR 0.006 0 -10000 0 -10000 0 0
Necl-5(dimer) 0.006 0 -10000 0 -10000 0 0
mol:GDP -0.018 0.12 -10000 0 -0.52 27 27
MLLT4 -0.006 0.068 -10000 0 -0.38 18 18
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
PI3K 0.011 0.11 -10000 0 -0.21 87 87
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.001 0.049 -10000 0 -0.27 18 18
positive regulation of lamellipodium assembly -0.024 0.074 -10000 0 -0.33 29 29
PVRL1 0.007 0.009 0.22 1 -10000 0 1
PVRL3 0.022 0.088 0.22 61 -0.38 11 72
PVRL2 0.006 0.019 0.22 1 -0.38 1 2
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
CDH1 -0.005 0.067 -10000 0 -0.38 17 17
CLDN1 -0.078 0.16 0.22 5 -0.38 125 130
JAM-A/CLDN1 -0.028 0.11 -10000 0 -0.22 127 127
SRC -0.026 0.14 -10000 0 -0.59 27 27
ITGB3 -0.045 0.14 0.22 13 -0.38 82 95
nectin-1(dimer)/I-afadin/I-afadin 0.001 0.049 -10000 0 -0.27 18 18
FARP2 -0.016 0.12 -10000 0 -0.5 27 27
RAC1 0.006 0.016 -10000 0 -0.38 1 1
CTNNA1 0.005 0.023 -10000 0 -0.38 2 2
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0 0.053 -10000 0 -0.23 27 27
nectin-1/I-afadin 0.001 0.049 -10000 0 -0.27 18 18
nectin-2/I-afadin 0 0.05 -10000 0 -0.27 19 19
RAC1/GTP/IQGAP1/filamentous actin 0.007 0.017 -10000 0 -0.22 3 3
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0 0.053 -10000 0 -0.23 27 27
CDC42/GTP/IQGAP1/filamentous actin 0.008 0.014 -10000 0 -0.22 2 2
F11R 0.007 0.009 0.22 1 -10000 0 1
positive regulation of filopodium formation -0.022 0.068 -10000 0 -0.31 27 27
alphaV/beta3 Integrin/Talin -0.12 0.16 0.22 7 -0.3 207 214
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0.05 -10000 0 -0.27 19 19
nectin-2(dimer)/I-afadin/I-afadin 0 0.05 -10000 0 -0.27 19 19
PIP5K1C -0.11 0.16 -10000 0 -0.31 210 210
VAV2 -0.018 0.13 -10000 0 -0.52 29 29
RAP1/GDP -0.019 0.092 -10000 0 -0.4 27 27
ITGAV 0.017 0.06 0.22 35 -0.38 3 38
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.001 0.054 -10000 0 -0.23 28 28
nectin-3(dimer)/I-afadin/I-afadin -0.005 0.062 -10000 0 -0.28 27 27
Rac1/GTP -0.026 0.091 -10000 0 -0.4 29 29
PTPRM -0.13 0.17 -10000 0 -0.33 219 219
E-cadherin/beta catenin/alpha catenin 0.006 0.054 -10000 0 -0.2 34 34
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.006 0 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.1 0.1 0.2 1 -0.28 9 10
CaM/Ca2+ -0.004 0.048 -10000 0 -0.27 18 18
AKT1 0.007 0.009 0.22 1 -10000 0 1
AKT2 0.009 0.024 0.22 7 -10000 0 7
STXBP4 0.007 0.013 0.22 2 -10000 0 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.031 0.068 -10000 0 -0.26 1 1
YWHAZ 0.006 0 -10000 0 -10000 0 0
CALM1 -0.006 0.068 -10000 0 -0.38 18 18
YWHAQ 0.006 0 -10000 0 -10000 0 0
TBC1D4 -0.003 0.015 0.2 3 -10000 0 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.005 0.03 0.22 1 -0.38 3 4
YWHAB 0.007 0.009 0.22 1 -10000 0 1
SNARE/Synip -0.16 0.11 -10000 0 -0.23 405 405
YWHAG 0.004 0.033 -10000 0 -0.38 4 4
ASIP 0.005 0.03 0.22 1 -0.38 3 4
PRKCI 0.12 0.11 0.22 306 -10000 0 306
AS160/CaM/Ca2+ -0.004 0.048 -10000 0 -0.27 18 18
RHOQ 0.007 0.016 0.22 3 -10000 0 3
GYS1 0.001 0.015 -10000 0 -10000 0 0
PRKCZ 0.006 0 -10000 0 -10000 0 0
TRIP10 0.006 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.009 0.001 -10000 0 -10000 0 0
AS160/14-3-3 0.005 0.029 -10000 0 -10000 0 0
VAMP2 -0.27 0.18 -10000 0 -0.38 407 407
SLC2A4 -0.034 0.072 -10000 0 -0.28 1 1
STX4 0.006 0 -10000 0 -10000 0 0
GSK3B 0.006 0.018 -10000 0 -10000 0 0
SFN 0.013 0.039 0.22 19 -10000 0 19
LNPEP 0.009 0.037 0.22 10 -0.38 2 12
YWHAE 0.006 0.016 -10000 0 -0.38 1 1
Retinoic acid receptors-mediated 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
HDAC1 0.017 0.047 0.22 28 -10000 0 28
HDAC3 0.006 0 -10000 0 -10000 0 0
VDR 0.007 0.013 0.22 2 -10000 0 2
Cbp/p300/PCAF 0.003 0.039 -10000 0 -0.26 11 11
EP300 0.003 0.037 -10000 0 -0.38 5 5
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.011 0.05 0.18 2 -0.28 7 9
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0.009 0.22 1 -10000 0 1
AKT1 0.036 0.085 0.22 14 -10000 0 14
RAR alpha/9cRA/Cyclin H -0.052 0.084 -10000 0 -0.31 29 29
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.015 0.053 0.19 1 -0.24 13 14
CDC2 0.2 0.055 0.22 530 -10000 0 530
response to UV -0.007 0.012 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.019 0.046 0.18 4 -0.17 5 9
NCOR2 0 0.049 -10000 0 -0.38 9 9
VDR/VDR/Vit D3 0.005 0 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.12 0.26 -10000 0 -0.51 159 159
NCOA2 0.007 0.013 0.22 2 -10000 0 2
NCOA3 0.01 0.028 0.22 10 -10000 0 10
NCOA1 0.004 0.028 -10000 0 -0.38 3 3
VDR/VDR/DNA 0.007 0.013 0.22 2 -10000 0 2
RARG 0.008 0.042 0.21 22 -10000 0 22
RAR gamma1/9cRA 0.003 0.008 -10000 0 -10000 0 0
MAPK3 -0.037 0.11 -10000 0 -0.39 51 51
MAPK1 0.006 0.019 0.22 1 -0.38 1 2
MAPK8 -0.002 0.026 0.22 5 -10000 0 5
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.046 0.16 -10000 0 -0.39 35 35
RARA -0.024 0.05 -10000 0 -0.22 5 5
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.013 0.052 0.19 1 -0.26 10 11
PRKCA -0.015 0.049 0.22 3 -0.38 5 8
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.13 0.27 -10000 0 -0.55 165 165
RXRG -0.023 0.061 -10000 0 -0.27 7 7
RXRA 0.013 0.12 0.2 3 -0.32 30 33
RXRB -0.025 0.051 -10000 0 -0.27 5 5
VDR/Vit D3/DNA 0.005 0 -10000 0 -10000 0 0
RBP1 -0.11 0.18 -10000 0 -0.38 174 174
CRBP1/9-cic-RA -0.079 0.13 -10000 0 -0.27 174 174
RARB 0.002 0.038 0.22 14 -10000 0 14
PRKCG -0.012 0.03 -10000 0 -10000 0 0
MNAT1 0.006 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.02 0.19 0.3 2 -0.42 24 26
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.045 0.15 -10000 0 -0.4 34 34
proteasomal ubiquitin-dependent protein catabolic process -0.021 0.058 -10000 0 -0.26 6 6
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.13 0.27 -10000 0 -0.55 165 165
positive regulation of DNA binding -0.05 0.079 -10000 0 -0.28 35 35
NRIP1 -0.29 0.51 -10000 0 -1.1 165 165
RXRs/RARs -0.091 0.2 -10000 0 -0.4 166 166
RXRs/RXRs/DNA/9cRA -0.048 0.16 -10000 0 -0.4 35 35
PRKACA 0.006 0 -10000 0 -10000 0 0
CDK7 0.014 0.04 0.22 20 -10000 0 20
TFIIH 0.012 0.002 -10000 0 -10000 0 0
RAR alpha/9cRA -0.005 0.044 -10000 0 -10000 0 0
CCNH 0.007 0.009 0.22 1 -10000 0 1
CREBBP 0.001 0.046 -10000 0 -0.38 8 8
RAR gamma2/9cRA 0.005 0.01 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 0.085 0.21 0.46 117 -0.47 15 132
IHH 0.023 0.074 -10000 0 -0.42 7 7
SHH Np/Cholesterol/GAS1 -0.016 0.066 -10000 0 -0.21 57 57
LRPAP1 0.006 0.028 0.22 3 -0.38 2 5
dorsoventral neural tube patterning 0.016 0.065 0.21 57 -10000 0 57
SMO/beta Arrestin2 0.039 0.13 -10000 0 -0.5 10 10
SMO 0.04 0.14 -10000 0 -0.52 10 10
AKT1 0.023 0.12 -10000 0 -10000 0 0
ARRB2 0.006 0 -10000 0 -10000 0 0
BOC -0.033 0.12 0.22 1 -0.38 58 59
ADRBK1 0.006 0 -10000 0 -10000 0 0
heart looping 0.04 0.14 -10000 0 -0.51 10 10
STIL 0.13 0.13 0.32 116 -10000 0 116
DHH N/PTCH2 0.009 0 -10000 0 -10000 0 0
DHH N/PTCH1 -0.005 0.066 -10000 0 -0.37 15 15
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
DHH 0.006 0 -10000 0 -10000 0 0
PTHLH 0.074 0.2 -10000 0 -0.51 15 15
determination of left/right symmetry 0.04 0.14 -10000 0 -0.51 10 10
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
skeletal system development 0.074 0.2 -10000 0 -0.5 15 15
IHH N/Hhip 0.02 0.045 0.24 1 -0.24 6 7
DHH N/Hhip 0.009 0.001 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.04 0.14 -10000 0 -0.51 10 10
pancreas development 0.008 0.02 0.22 5 -10000 0 5
HHAT 0.001 0.046 -10000 0 -0.38 8 8
PI3K -0.022 0.083 -10000 0 -0.27 56 56
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.029 0.11 -10000 0 -0.38 51 51
somite specification 0.04 0.14 -10000 0 -0.51 10 10
SHH Np/Cholesterol/PTCH1 -0.008 0.062 -10000 0 -0.38 10 10
SHH Np/Cholesterol/PTCH2 0.003 0.025 -10000 0 -0.2 8 8
SHH Np/Cholesterol/Megalin 0.038 0.065 0.14 148 -0.2 6 154
SHH -0.007 0.032 0.2 1 -0.27 8 9
catabolic process 0.055 0.15 0.31 117 -0.41 15 132
SMO/Vitamin D3 0.038 0.12 -10000 0 -0.46 10 10
SHH Np/Cholesterol/Hhip 0.004 0.028 0.14 5 -0.2 8 13
LRP2 0.063 0.095 0.22 151 -10000 0 151
receptor-mediated endocytosis 0.038 0.13 0.32 28 -0.47 10 38
SHH Np/Cholesterol/BOC -0.018 0.068 0.14 1 -0.21 65 66
SHH Np/Cholesterol/CDO 0.005 0.034 0.14 12 -0.2 10 22
mesenchymal cell differentiation -0.004 0.028 0.2 8 -0.14 5 13
mol:Vitamin D3 0.041 0.12 0.24 115 -0.38 10 125
IHH N/PTCH2 0.02 0.046 -10000 0 -0.24 7 7
CDON 0.009 0.039 0.22 12 -0.38 2 14
IHH N/PTCH1 0.054 0.14 0.29 117 -0.41 15 132
Megalin/LRPAP1 0.006 0.017 -10000 0 -0.27 2 2
PTCH2 0.006 0 -10000 0 -10000 0 0
SHH Np/Cholesterol 0 0.024 -10000 0 -0.2 8 8
PTCH1 0.055 0.15 0.31 117 -0.41 15 132
HHIP 0.008 0.02 0.22 5 -10000 0 5
Signaling events mediated by PTP1B

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
PDGFRB -0.01 0.079 -10000 0 -0.38 24 24
Jak2/Leptin Receptor -0.001 0.076 0.21 3 -0.38 7 10
PTP1B/AKT1 -0.017 0.091 -10000 0 -0.3 11 11
FYN -0.039 0.13 0.22 1 -0.38 67 68
p210 bcr-abl/PTP1B -0.018 0.099 -10000 0 -0.28 26 26
EGFR -0.032 0.12 0.22 1 -0.39 54 55
EGF/EGFR -0.045 0.094 0.19 3 -0.32 34 37
CSF1 -0.01 0.079 0.22 1 -0.38 24 25
AKT1 0.004 0.011 0.22 1 -10000 0 1
INSR -0.021 0.098 -10000 0 -0.39 38 38
PTP1B/N-cadherin -0.009 0.13 0.22 33 -0.31 45 78
Insulin Receptor/Insulin -0.027 0.09 -10000 0 -0.32 21 21
HCK 0.007 0.009 0.22 1 -10000 0 1
CRK 0.006 0 -10000 0 -10000 0 0
TYK2 -0.018 0.094 -10000 0 -0.26 26 26
EGF 0.005 0.025 0.22 7 -10000 0 7
YES1 0.011 0.031 0.22 12 -10000 0 12
CAV1 -0.047 0.12 -10000 0 -0.32 46 46
TXN -0.017 0.09 -10000 0 -0.39 31 31
PTP1B/IRS1/GRB2 -0.11 0.13 -10000 0 -0.31 100 100
cell migration 0.018 0.099 0.28 26 -10000 0 26
STAT3 -0.003 0.056 -10000 0 -0.39 12 12
PRLR 0.014 0.039 0.22 19 -10000 0 19
ITGA2B 0.004 0.005 -10000 0 -10000 0 0
CSF1R -0.014 0.09 0.22 3 -0.38 31 34
Prolactin Receptor/Prolactin 0.011 0.015 0.21 3 -10000 0 3
FGR 0.006 0 -10000 0 -10000 0 0
PTP1B/p130 Cas -0.017 0.095 -10000 0 -0.26 27 27
Crk/p130 Cas -0.015 0.093 -10000 0 -0.26 27 27
DOK1 -0.028 0.098 -10000 0 -0.31 20 20
JAK2 -0.004 0.073 -10000 0 -0.42 5 5
Jak2/Leptin Receptor/Leptin -0.026 0.093 -10000 0 -0.33 20 20
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
PTPN1 -0.018 0.1 -10000 0 -0.28 26 26
LYN -0.007 0.07 -10000 0 -0.38 19 19
CDH2 -0.001 0.17 0.22 118 -0.38 76 194
SRC 0 0.041 -10000 0 -10000 0 0
ITGB3 -0.046 0.14 0.22 13 -0.39 82 95
CAT1/PTP1B -0.03 0.11 -10000 0 -0.31 22 22
CAPN1 0.001 0.033 -10000 0 -0.39 4 4
CSK 0.006 0 -10000 0 -10000 0 0
PI3K -0.036 0.1 -10000 0 -0.31 34 34
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.025 0.09 0.22 1 -0.37 15 16
negative regulation of transcription -0.004 0.072 -10000 0 -0.42 5 5
FCGR2A -0.002 0.066 0.22 5 -0.38 15 20
FER 0.004 0.011 0.22 1 -10000 0 1
alphaIIb/beta3 Integrin -0.032 0.099 -10000 0 -0.27 82 82
BLK 0.007 0.009 0.22 1 -10000 0 1
Insulin Receptor/Insulin/Shc -0.004 0.06 -10000 0 -0.23 38 38
RHOA 0.003 0.024 -10000 0 -0.39 2 2
LEPR 0.007 0.031 0.22 5 -0.38 2 7
BCAR1 0.004 0.028 -10000 0 -0.38 3 3
p210 bcr-abl/Grb2 0.006 0.016 -10000 0 -0.38 1 1
mol:NADPH -0.001 0.002 -10000 0 -10000 0 0
TRPV6 -0.023 0.079 -10000 0 -0.23 31 31
PRL 0.007 0.01 0.22 1 -10000 0 1
SOCS3 -0.014 0.15 0.55 2 -1.2 9 11
SPRY2 -0.048 0.16 0.22 37 -0.39 91 128
Insulin Receptor/Insulin/IRS1 -0.13 0.14 -10000 0 -0.25 320 320
CSF1/CSF1R -0.029 0.12 0.24 1 -0.32 51 52
Ras protein signal transduction 0 0.034 -10000 0 -0.32 1 1
IRS1 -0.21 0.2 -10000 0 -0.38 311 311
INS 0.004 0.006 -10000 0 -10000 0 0
LEP 0.005 0.017 -10000 0 -0.38 1 1
STAT5B -0.014 0.089 -10000 0 -0.24 30 30
STAT5A -0.013 0.087 -10000 0 -0.23 29 29
GRB2 0.006 0.016 -10000 0 -0.38 1 1
PDGFB-D/PDGFRB -0.023 0.1 -10000 0 -0.28 33 33
CSN2 0.008 0.035 0.52 1 -10000 0 1
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
LAT -0.012 0.1 -10000 0 -0.56 15 15
YBX1 0.007 0.006 -10000 0 -10000 0 0
LCK 0.006 0 -10000 0 -10000 0 0
SHC1 0.006 0 -10000 0 -10000 0 0
NOX4 0.084 0.1 0.22 212 -10000 0 212
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.009 0.001 -10000 0 -10000 0 0
Necdin/E2F1 -0.16 0.14 -10000 0 -0.27 342 342
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.015 0.021 -10000 0 -0.19 4 4
NGF (dimer)/p75(NTR)/BEX1 -0.045 0.098 -10000 0 -0.22 130 130
NT-4/5 (dimer)/p75(NTR) 0.005 0 -10000 0 -10000 0 0
IKBKB 0.007 0.016 0.22 3 -10000 0 3
AKT1 0.005 0.084 -10000 0 -0.19 55 55
IKBKG 0.006 0 -10000 0 -10000 0 0
BDNF 0.006 0 -10000 0 -10000 0 0
MGDIs/NGR/p75(NTR)/LINGO1 0.013 0.001 -10000 0 -10000 0 0
FURIN 0.002 0.04 -10000 0 -0.38 6 6
proBDNF (dimer)/p75(NTR)/Sortilin 0.013 0.001 -10000 0 -10000 0 0
LINGO1 0.009 0.022 0.22 6 -10000 0 6
Sortilin/TRAF6/NRIF -0.028 0.054 -10000 0 -0.18 65 65
proBDNF (dimer) 0.006 0 -10000 0 -10000 0 0
NTRK1 0.006 0 -10000 0 -10000 0 0
RTN4R 0.007 0.009 0.22 1 -10000 0 1
neuron apoptosis -0.003 0.076 -10000 0 -10000 0 0
IRAK1 0.007 0.009 0.22 1 -10000 0 1
SHC1 -0.003 0.007 0.15 1 -10000 0 1
ARHGDIA -0.079 0.16 -10000 0 -0.38 124 124
RhoA/GTP 0.004 0.016 -10000 0 -0.27 2 2
Gamma Secretase -0.005 0.07 -10000 0 -0.2 66 66
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.009 0.031 0.14 5 -0.2 10 15
MAGEH1 -0.001 0.054 -10000 0 -0.38 11 11
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.12 0.11 -10000 0 -0.2 337 337
Mammalian IAPs/DIABLO 0.021 0.11 -10000 0 -0.2 68 68
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.006 0.028 0.22 3 -0.38 2 5
APP 0 0.049 -10000 0 -0.38 9 9
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.006 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.035 0.084 -10000 0 -0.19 125 125
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest 0.021 0.048 0.17 6 -10000 0 6
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.034 0.048 0.21 1 -0.21 1 2
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.009 0.001 -10000 0 -10000 0 0
NCSTN 0.007 0.009 0.22 1 -10000 0 1
mol:GTP 0.008 0.001 -10000 0 -10000 0 0
PSENEN -0.006 0.068 -10000 0 -0.38 18 18
mol:ceramide -0.004 0.02 0.14 6 -0.2 3 9
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.079 0.064 0.19 98 -10000 0 98
p75(NTR)/beta APP 0.005 0.035 -10000 0 -0.27 9 9
BEX1 -0.067 0.18 0.22 43 -0.38 130 173
mol:GDP -0.001 0.006 0.15 1 -10000 0 1
NGF (dimer) -0.035 0.12 -10000 0 -0.21 158 158
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.031 0.093 -10000 0 -0.2 124 124
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
RAC1/GTP 0.007 0.008 -10000 0 -0.19 1 1
MYD88 0.006 0.016 -10000 0 -0.38 1 1
CHUK 0.011 0.031 0.22 12 -10000 0 12
NGF (dimer)/p75(NTR)/PKA 0.008 0.001 -10000 0 -10000 0 0
RHOB -0.012 0.082 -10000 0 -0.38 26 26
RHOA 0.005 0.023 -10000 0 -0.38 2 2
MAGE-G1/E2F1 0.008 0.017 -10000 0 -0.27 2 2
NT3 (dimer) 0.037 0.075 0.22 81 -10000 0 81
TP53 -0.028 0.064 -10000 0 -10000 0 0
PRDM4 -0.003 0.014 0.14 6 -10000 0 6
BDNF (dimer) -0.029 0.12 -10000 0 -0.21 154 154
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
SORT1 0.008 0.02 0.22 5 -10000 0 5
activation of caspase activity 0.012 0.017 -10000 0 -0.19 4 4
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.014 0.015 0.14 8 -10000 0 8
RHOC 0.006 0.016 -10000 0 -0.38 1 1
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.011 0.04 -10000 0 -10000 0 0
DIABLO 0.1 0.11 0.22 248 -10000 0 248
SMPD2 -0.004 0.02 0.14 6 -0.2 3 9
APH1B -0.027 0.11 -10000 0 -0.38 49 49
APH1A 0.007 0.009 0.22 1 -10000 0 1
proNGF (dimer)/p75(NTR)/Sortilin 0.008 0.001 -10000 0 -10000 0 0
PSEN1 0.007 0.009 0.22 1 -10000 0 1
APAF-1/Pro-Caspase 9 0.009 0.001 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.008 0.003 -10000 0 -10000 0 0
MAPK8 -0.004 0.028 -10000 0 -10000 0 0
MAPK9 -0.005 0.028 -10000 0 -10000 0 0
APAF1 0.01 0.03 0.22 11 -10000 0 11
NTF3 0.037 0.075 0.22 81 -10000 0 81
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.23 0.19 -10000 0 -0.38 342 342
RAC1/GDP 0.004 0.011 -10000 0 -0.27 1 1
RhoA-B-C/GDP 0.004 0.042 -10000 0 -0.18 29 29
p75 CTF/Sortilin/TRAF6/NRIF 0.043 0.053 -10000 0 -10000 0 0
RhoA-B-C/GTP 0.008 0.001 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.02 0.014 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.018 0.015 -10000 0 -10000 0 0
PRKACB 0.01 0.027 0.22 9 -10000 0 9
proBDNF (dimer)/p75 ECD 0.007 0.004 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.076 0.17 0.22 13 -0.38 127 140
BIRC2 0.037 0.075 0.22 81 -10000 0 81
neuron projection morphogenesis -0.048 0.085 0.16 3 -0.25 19 22
BAD -0.007 0.031 -10000 0 -10000 0 0
RIPK2 0.065 0.096 0.22 156 -10000 0 156
NGFR 0.007 0.009 0.22 1 -10000 0 1
CYCS -0.003 0.021 0.14 1 -0.19 2 3
ADAM17 0.051 0.088 0.22 118 -10000 0 118
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.048 0.058 0.14 159 -10000 0 159
BCL2L11 -0.007 0.031 -10000 0 -10000 0 0
BDNF (dimer)/p75(NTR) 0.009 0 -10000 0 -10000 0 0
PI3K 0.018 0.091 -10000 0 -0.2 56 56
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.013 0.018 -10000 0 -0.2 2 2
NDNL2 0.005 0.023 -10000 0 -0.38 2 2
YWHAE 0.006 0.016 -10000 0 -0.38 1 1
PRKCI 0.12 0.11 0.22 306 -10000 0 306
NGF (dimer)/p75(NTR) 0.005 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.013 0.021 0.14 9 -0.2 2 11
TRAF6 0.007 0.013 0.22 2 -10000 0 2
RAC1 0.006 0.016 -10000 0 -0.38 1 1
PRKCZ 0.006 0 -10000 0 -10000 0 0
PLG -0.001 0.054 -10000 0 -0.38 11 11
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.034 0.054 0.26 1 -10000 0 1
SQSTM1 0.006 0 -10000 0 -10000 0 0
NGFRAP1 0.004 0.028 -10000 0 -0.38 3 3
CASP3 -0.006 0.03 -10000 0 -10000 0 0
E2F1 0.006 0 -10000 0 -10000 0 0
CASP9 0.007 0.009 0.22 1 -10000 0 1
IKK complex 0.004 0.006 -10000 0 -10000 0 0
NGF (dimer)/TRKA 0.005 0 -10000 0 -10000 0 0
MMP7 -0.069 0.2 0.22 69 -0.38 148 217
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.017 0.014 -10000 0 -10000 0 0
MMP3 0.009 0.025 0.22 8 -10000 0 8
APAF-1/Caspase 9 -0.029 0.052 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.006 0.019 0.22 1 -0.38 1 2
LAT2 -0.016 0.088 -10000 0 -0.28 47 47
AP1 -0.037 0.12 0.25 4 -0.36 36 40
mol:PIP3 -0.02 0.11 0.19 1 -0.33 48 49
IKBKB -0.009 0.064 0.14 7 -0.21 30 37
AKT1 -0.025 0.11 0.21 11 -0.31 32 43
IKBKG -0.01 0.063 0.14 7 -0.2 42 49
MS4A2 0.006 0.007 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.054 0.091 0.22 131 -10000 0 131
MAP3K1 -0.011 0.089 0.19 6 -0.3 28 34
mol:Ca2+ -0.014 0.084 0.16 7 -0.26 48 55
LYN -0.008 0.073 -10000 0 -0.4 19 19
CBLB -0.014 0.088 0.2 1 -0.27 47 48
SHC1 0.006 0 -10000 0 -10000 0 0
RasGAP/p62DOK -0.057 0.1 -10000 0 -0.2 183 183
positive regulation of cell migration -0.008 0.04 -10000 0 -0.27 13 13
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.033 0.083 -10000 0 -0.2 79 79
PTPN13 -0.032 0.13 -10000 0 -0.42 25 25
PTPN11 0.004 0.008 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.009 0.1 0.19 28 -0.26 25 53
SYK 0.001 0.044 0.22 3 -0.39 6 9
GRB2 0.005 0.017 -10000 0 -0.39 1 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.03 0.098 -10000 0 -0.33 48 48
LAT -0.015 0.087 -10000 0 -0.27 47 47
PAK2 -0.01 0.096 0.19 7 -0.3 41 48
NFATC2 -0.015 0.078 -10000 0 -0.5 13 13
HRAS -0.011 0.1 0.2 7 -0.32 41 48
GAB2 0.003 0.069 0.22 16 -0.38 13 29
PLA2G1B -0.048 0.068 -10000 0 -10000 0 0
Fc epsilon R1 -0.008 0.062 -10000 0 -0.21 47 47
Antigen/IgE/Fc epsilon R1 -0.001 0.061 0.14 21 -0.19 47 68
mol:GDP -0.011 0.11 0.21 16 -0.33 41 57
JUN 0.008 0.039 0.22 9 -0.38 3 12
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 -0.038 0.12 -10000 0 -0.39 64 64
FOS -0.066 0.16 0.22 8 -0.38 110 118
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.014 0.091 -10000 0 -0.28 48 48
CHUK -0.008 0.065 0.14 8 -0.2 41 49
KLRG1 -0.011 0.078 -10000 0 -0.24 44 44
VAV1 -0.015 0.089 0.23 1 -0.28 47 48
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.015 0.087 -10000 0 -0.27 47 47
negative regulation of mast cell degranulation -0.012 0.072 -10000 0 -0.22 44 44
BTK -0.016 0.1 0.22 15 -0.36 28 43
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK 0 0.071 0.2 21 -0.19 20 41
GAB2/PI3K/SHP2 -0.054 0.092 -10000 0 -0.22 103 103
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.016 0.095 -10000 0 -0.26 57 57
RAF1 0.005 0.012 -10000 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP 0.003 0.061 -10000 0 -0.18 47 47
FCER1G -0.015 0.12 0.21 33 -0.39 47 80
FCER1A 0.006 0.016 0.22 3 -10000 0 3
Antigen/IgE/Fc epsilon R1/Fyn -0.018 0.094 -10000 0 -0.2 103 103
MAPK3 -0.053 0.08 -10000 0 -0.31 27 27
MAPK1 -0.038 0.057 -10000 0 -0.31 1 1
NFKB1 -0.001 0.054 -10000 0 -0.38 11 11
MAPK8 0.004 0.057 -10000 0 -0.4 7 7
DUSP1 -0.12 0.18 0.22 1 -0.38 179 180
NF-kappa-B/RelA -0.01 0.044 -10000 0 -0.18 23 23
actin cytoskeleton reorganization -0.001 0.11 -10000 0 -0.4 16 16
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.007 0.13 0.22 7 -0.37 31 38
FER -0.015 0.087 -10000 0 -0.27 47 47
RELA 0.005 0.023 -10000 0 -0.38 2 2
ITK -0.002 0.032 0.15 12 -10000 0 12
SOS1 0.014 0.04 0.22 20 -10000 0 20
PLCG1 -0.012 0.1 0.21 7 -0.32 41 48
cytokine secretion -0.01 0.031 -10000 0 -0.16 11 11
SPHK1 -0.015 0.087 -10000 0 -0.27 47 47
PTK2 -0.002 0.11 -10000 0 -0.42 16 16
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.029 0.1 -10000 0 -0.34 49 49
EDG1 -0.008 0.04 -10000 0 -0.27 13 13
mol:DAG -0.018 0.11 0.19 1 -0.34 42 43
MAP2K2 -0.07 0.097 -10000 0 -10000 0 0
MAP2K1 0.003 0.012 -10000 0 -10000 0 0
MAP2K7 0.006 0 -10000 0 -10000 0 0
KLRG1/SHP2 -0.012 0.064 -10000 0 -0.28 18 18
MAP2K4 -0.002 0.095 -10000 0 -0.85 7 7
Fc epsilon R1/FcgammaRIIB 0.003 0.066 -10000 0 -0.19 47 47
mol:Choline -0.032 0.082 -10000 0 -0.2 79 79
SHC/Grb2/SOS1 -0.003 0.088 -10000 0 -0.27 42 42
FYN -0.039 0.13 0.22 1 -0.38 67 68
DOK1 0.006 0.016 -10000 0 -0.38 1 1
PXN -0.006 0.1 -10000 0 -0.4 15 15
HCLS1 -0.014 0.099 0.23 5 -0.29 48 53
PRKCB -0.014 0.083 0.16 7 -0.25 48 55
FCGR2B 0.019 0.055 0.22 36 -0.38 1 37
IGHE -0.001 0.003 -10000 0 -10000 0 0
KLRG1/SHIP -0.012 0.073 -10000 0 -0.23 44 44
LCP2 -0.013 0.085 -10000 0 -0.39 28 28
PLA2G4A -0.069 0.13 -10000 0 -0.29 76 76
RASA1 0.004 0.028 -10000 0 -0.38 3 3
mol:Phosphatidic acid -0.032 0.082 -10000 0 -0.2 79 79
IKK complex -0.005 0.052 0.13 8 -0.17 22 30
WIPF1 0.006 0.016 -10000 0 -0.38 1 1
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.23 0.44 -10000 0 -1.1 127 127
VDR 0.007 0.013 0.22 2 -10000 0 2
FAM120B 0.004 0.028 -10000 0 -0.38 3 3
RXRs/LXRs/DNA/9cRA 0.023 0.11 0.33 38 -0.4 3 41
RXRs/LXRs/DNA/Oxysterols 0.026 0.13 0.41 38 -0.41 7 45
MED1 0.007 0.013 0.22 2 -10000 0 2
mol:9cRA 0.01 0.023 0.1 2 -10000 0 2
RARs/THRs/DNA/Src-1 -0.022 0.095 0.21 2 -0.21 96 98
RXRs/NUR77 -0.041 0.13 0.26 4 -0.22 135 139
RXRs/PPAR 0.015 0.056 0.24 2 -10000 0 2
NCOR2 0 0.049 -10000 0 -0.38 9 9
VDR/VDR/Vit D3 0.005 0 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.023 0.031 -10000 0 -10000 0 0
RARA 0.006 0 -10000 0 -10000 0 0
NCOA1 0.004 0.028 -10000 0 -0.38 3 3
VDR/VDR/DNA 0.007 0.013 0.22 2 -10000 0 2
RARs/RARs/DNA/9cRA 0.025 0.033 0.14 37 -10000 0 37
RARG 0.015 0.042 0.22 22 -10000 0 22
RPS6KB1 -0.085 0.18 0.36 9 -0.41 125 134
RARs/THRs/DNA/SMRT -0.024 0.099 0.21 2 -0.22 100 102
THRA -0.065 0.15 -10000 0 -0.38 104 104
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.005 0 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.074 0.12 0.31 45 -10000 0 45
NR1H4 0.008 0.02 0.22 5 -10000 0 5
RXRs/LXRs/DNA 0.043 0.1 0.32 38 -0.36 3 41
NR1H2 -0.002 0.073 -10000 0 -0.38 19 19
NR1H3 0.01 0.037 -10000 0 -0.38 3 3
RXRs/VDR/DNA/Vit D3 0.04 0.073 0.25 5 -0.19 15 20
NR4A1 -0.13 0.19 0.22 5 -0.38 201 206
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.019 0.059 0.22 2 -10000 0 2
RXRG 0.02 0.047 0.22 17 -0.35 2 19
RXR alpha/CCPG 0.003 0.06 -10000 0 -0.26 26 26
RXRA 0 0.08 -10000 0 -0.38 23 23
RXRB 0.016 0.023 -10000 0 -10000 0 0
THRB 0.018 0.049 0.22 31 -10000 0 31
PPARG 0.009 0.022 0.22 6 -10000 0 6
PPARD 0.006 0 -10000 0 -10000 0 0
TNF 0.025 0.12 0.49 2 -0.49 1 3
mol:Oxysterols 0.005 0.021 -10000 0 -10000 0 0
cholesterol transport 0.026 0.12 0.41 38 -0.41 7 45
PPARA 0.006 0 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.013 0.038 0.22 18 -10000 0 18
RXRs/NUR77/BCL2 -0.095 0.14 0.22 1 -0.24 222 223
SREBF1 0.015 0.16 0.45 1 -0.89 9 10
RXRs/RXRs/DNA/9cRA 0.072 0.12 0.31 45 -10000 0 45
ABCA1 0.035 0.15 0.53 37 -0.49 1 38
RARs/THRs -0.006 0.092 -10000 0 -0.19 95 95
RXRs/FXR 0.044 0.079 0.25 8 -0.2 15 23
BCL2 -0.043 0.13 0.22 2 -0.38 73 75
IL6-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
BCL2L1 -0.18 0.29 -10000 0 -0.82 64 64
CRP -0.18 0.29 -10000 0 -0.82 64 64
cell cycle arrest -0.22 0.35 -10000 0 -0.92 82 82
TIMP1 -0.19 0.31 -10000 0 -0.82 79 79
IL6ST -0.021 0.085 -10000 0 -0.39 28 28
Rac1/GDP -0.062 0.13 0.38 1 -0.41 39 40
AP1 -0.032 0.13 0.53 2 -0.56 14 16
GAB2 0.005 0.07 0.22 16 -0.38 13 29
TNFSF11 -0.18 0.29 -10000 0 -0.82 64 64
HSP90B1 -0.029 0.094 -10000 0 -1 4 4
GAB1 0.005 0.033 -10000 0 -0.39 4 4
MAPK14 -0.031 0.13 0.49 1 -0.59 17 18
AKT1 0.004 0.083 0.6 1 -10000 0 1
FOXO1 -0.001 0.082 0.56 1 -10000 0 1
MAP2K6 -0.037 0.12 0.46 1 -0.47 23 24
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
MAP2K4 -0.093 0.16 0.47 1 -0.49 40 41
MITF -0.057 0.12 0.37 1 -0.39 39 40
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.006 0 -10000 0 -10000 0 0
A2M -0.086 0.32 0.53 2 -1.2 41 43
CEBPB 0.005 0.034 0.22 1 -0.38 4 5
GRB2/SOS1/GAB family/SHP2 -0.012 0.092 -10000 0 -0.44 11 11
STAT3 -0.23 0.39 -10000 0 -0.97 88 88
STAT1 0.096 0.1 -10000 0 -10000 0 0
CEBPD -0.2 0.33 -10000 0 -0.95 67 67
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
PI3K -0.021 0.084 0.26 1 -0.27 56 57
JUN 0.007 0.039 0.22 9 -0.38 3 12
PIAS3/MITF -0.052 0.11 0.33 1 -0.37 38 39
MAPK11 -0.031 0.13 0.49 1 -0.59 17 18
STAT3 (dimer)/FOXO1 -0.18 0.29 -10000 0 -0.75 75 75
GRB2/SOS1/GAB family -0.021 0.1 0.25 2 -0.36 17 19
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.038 0.1 0.27 1 -0.32 40 41
GRB2 0.007 0.017 -10000 0 -0.38 1 1
JAK2 0.004 0.035 0.22 2 -0.38 4 6
LBP -0.14 0.23 0.56 1 -0.67 38 39
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
JAK1 -0.004 0.031 -10000 0 -0.39 3 3
MYC -0.23 0.37 -10000 0 -0.98 89 89
FGG -0.18 0.29 -10000 0 -0.82 60 60
macrophage differentiation -0.22 0.35 -10000 0 -0.92 82 82
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.027 0.092 0.2 1 -0.24 71 72
JUNB -0.29 0.44 -10000 0 -0.98 156 156
FOS -0.067 0.16 0.22 8 -0.38 110 118
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.058 0.13 0.41 1 -0.4 41 42
STAT1/PIAS1 -0.06 0.12 -10000 0 -0.42 27 27
GRB2/SOS1/GAB family/SHP2/PI3K 0.006 0.086 0.5 1 -0.27 3 4
STAT3 (dimer) -0.23 0.38 -10000 0 -0.98 85 85
PRKCD -0.13 0.21 0.53 1 -0.57 54 55
IL6R -0.002 0.023 0.22 1 -0.4 1 2
SOCS3 -0.027 0.16 0.54 1 -1.1 9 10
gp130 (dimer)/JAK1/JAK1/LMO4 -0.014 0.065 0.22 1 -0.26 27 28
Rac1/GTP -0.073 0.14 0.41 1 -0.44 41 42
HCK 0.007 0.009 0.22 1 -10000 0 1
MAPKKK cascade -0.008 0.11 0.42 1 -0.54 13 14
bone resorption -0.17 0.28 -10000 0 -0.76 64 64
IRF1 -0.2 0.33 -10000 0 -0.92 65 65
mol:GDP -0.06 0.12 0.4 1 -0.39 41 42
SOS1 0.015 0.041 0.23 20 -10000 0 20
VAV1 -0.061 0.12 0.4 1 -0.4 41 42
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.021 0.11 0.44 1 -0.52 17 18
PTPN11 -0.004 0.021 -10000 0 -10000 0 0
IL6/IL6RA -0.024 0.081 0.15 1 -0.29 46 47
gp130 (dimer)/TYK2/TYK2/LMO4 -0.01 0.055 -10000 0 -0.23 28 28
gp130 (dimer)/JAK2/JAK2/LMO4 -0.011 0.06 0.16 1 -0.24 30 31
IL6 -0.032 0.11 0.22 4 -0.39 46 50
PIAS3 0.007 0.009 0.22 1 -10000 0 1
PTPRE 0.012 0.015 -10000 0 -10000 0 0
PIAS1 0.007 0.009 0.22 1 -10000 0 1
RAC1 0.001 0.018 -10000 0 -0.39 1 1
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.038 0.095 -10000 0 -0.3 40 40
LMO4 0.001 0.037 0.22 10 -0.39 1 11
STAT3 (dimer)/PIAS3 -0.21 0.34 -10000 0 -0.86 91 91
MCL1 0.004 0.079 0.7 1 -10000 0 1
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.013 0.075 -10000 0 -0.27 45 45
CRKL -0.009 0.08 -10000 0 -0.25 44 44
mol:PIP3 0.01 0.051 0.36 11 -10000 0 11
AKT1 0.005 0.036 0.25 11 -10000 0 11
PTK2B 0.005 0.023 -10000 0 -0.38 2 2
RAPGEF1 -0.01 0.076 -10000 0 -0.24 44 44
RANBP10 0.006 0.016 -10000 0 -0.38 1 1
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
HGF/MET/SHIP2 -0.007 0.064 -10000 0 -0.23 45 45
MAP3K5 -0.009 0.076 -10000 0 -0.32 10 10
HGF/MET/CIN85/CBL/ENDOPHILINS 0.007 0.07 -10000 0 -0.2 45 45
AP1 -0.038 0.1 0.15 7 -0.23 112 119
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.006 0 -10000 0 -10000 0 0
apoptosis -0.13 0.29 0.33 1 -0.71 112 113
STAT3 (dimer) -0.005 0.084 0.21 7 -0.23 52 59
GAB1/CRKL/SHP2/PI3K 0.004 0.11 0.21 9 -0.34 16 25
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.006 0.077 -10000 0 -0.24 44 44
PTPN11 0.006 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.009 0.022 0.22 6 -10000 0 6
PTEN -0.001 0.054 -10000 0 -0.38 11 11
ELK1 0.016 0.086 0.21 74 -10000 0 74
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.006 0.043 -10000 0 -0.16 5 5
PAK1 0.007 0.041 0.23 11 -0.2 1 12
HGF/MET/RANBP10 -0.007 0.064 -10000 0 -0.23 45 45
HRAS -0.028 0.15 -10000 0 -0.54 45 45
DOCK1 -0.01 0.078 0.21 1 -0.24 44 45
GAB1 -0.008 0.084 0.18 1 -0.26 44 45
CRK -0.009 0.08 -10000 0 -0.25 44 44
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.022 0.14 -10000 0 -0.48 45 45
JUN 0.008 0.039 0.22 9 -0.38 3 12
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.008 0.067 0.12 33 -0.22 45 78
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
cell morphogenesis -0.003 0.11 0.21 23 -0.38 13 36
GRB2/SHC -0.001 0.061 -10000 0 -0.19 46 46
FOS -0.066 0.16 0.22 8 -0.38 110 118
GLMN 0.022 0.048 0.13 94 -10000 0 94
cell motility 0.015 0.086 0.21 74 -10000 0 74
HGF/MET/MUC20 -0.01 0.063 -10000 0 -0.22 45 45
cell migration -0.001 0.06 -10000 0 -0.19 46 46
GRB2 0.006 0.016 -10000 0 -0.38 1 1
CBL 0.006 0 -10000 0 -10000 0 0
MET/RANBP10 -0.014 0.076 -10000 0 -0.27 46 46
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0 0.084 0.22 7 -0.22 52 59
MET/MUC20 -0.017 0.074 -10000 0 -0.27 45 45
RAP1B -0.01 0.073 -10000 0 -0.32 8 8
RAP1A -0.01 0.073 -10000 0 -0.32 8 8
HGF/MET/RANBP9 -0.007 0.064 -10000 0 -0.23 45 45
RAF1 -0.027 0.15 -10000 0 -0.51 45 45
STAT3 -0.005 0.085 0.21 7 -0.23 52 59
cell proliferation -0.015 0.1 0.2 8 -0.33 45 53
RPS6KB1 0.011 0.041 0.13 12 -10000 0 12
MAPK3 0.054 0.2 0.67 51 -10000 0 51
MAPK1 -0.005 0.057 0.68 1 -10000 0 1
RANBP9 0.007 0.013 0.22 2 -10000 0 2
MAPK8 -0.005 0.074 -10000 0 -0.26 16 16
SRC -0.003 0.079 0.2 7 -0.38 4 11
PI3K 0.008 0.11 0.22 9 -0.2 85 94
MET/Glomulin 0.009 0.08 0.19 32 -0.23 38 70
SOS1 0.014 0.04 0.22 20 -10000 0 20
MAP2K1 -0.026 0.14 0.25 1 -0.48 45 46
MET -0.013 0.12 0.22 32 -0.38 45 77
MAP4K1 -0.007 0.076 -10000 0 -0.24 43 43
PTK2 0.028 0.065 0.22 57 -10000 0 57
MAP2K2 -0.085 0.15 -10000 0 -0.52 45 45
BAD 0.003 0.034 0.23 11 -10000 0 11
MAP2K4 -0.011 0.073 -10000 0 -0.3 11 11
SHP2/GRB2/SOS1/GAB1 -0.018 0.085 -10000 0 -0.3 46 46
INPPL1 0.007 0.013 0.22 2 -10000 0 2
PXN -0.002 0.056 -10000 0 -0.38 12 12
SH3KBP1 0.007 0.009 0.22 1 -10000 0 1
HGS -0.01 0.062 0.21 1 -0.2 45 46
PLCgamma1/PKC 0.005 0 -10000 0 -10000 0 0
HGF 0.008 0.018 0.22 4 -10000 0 4
RASA1 0.004 0.028 -10000 0 -0.38 3 3
NCK1 0.024 0.059 0.22 47 -10000 0 47
PTPRJ 0.007 0.016 0.22 3 -10000 0 3
NCK/PLCgamma1 0.012 0.074 0.15 53 -0.19 45 98
PDPK1 0.007 0.041 0.29 11 -10000 0 11
HGF/MET/SHIP -0.01 0.063 -10000 0 -0.22 45 45
Regulation of Androgen receptor activity

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
HDAC1 0.017 0.071 0.23 53 -10000 0 53
SMARCC1 -0.012 0.022 -10000 0 -10000 0 0
REL 0.006 0 -10000 0 -10000 0 0
HDAC7 -0.14 0.11 0.23 4 -0.27 174 178
JUN 0.008 0.039 0.22 9 -0.38 3 12
EP300 0.003 0.037 -10000 0 -0.38 5 5
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.002 0.064 0.18 58 -10000 0 58
FOXO1 0 0.049 -10000 0 -0.38 9 9
T-DHT/AR -0.15 0.12 -10000 0 -0.28 173 173
MAP2K6 0.01 0.07 0.22 57 -10000 0 57
BRM/BAF57 -0.054 0.12 -10000 0 -0.27 130 130
MAP2K4 -0.017 0.045 -10000 0 -0.4 7 7
SMARCA2 -0.083 0.16 -10000 0 -0.38 130 130
PDE9A -0.21 0.32 -10000 0 -1.1 64 64
NCOA2 0.007 0.013 0.22 2 -10000 0 2
CEBPA 0.006 0 -10000 0 -10000 0 0
EHMT2 0.007 0.009 0.22 1 -10000 0 1
cell proliferation -0.17 0.12 -10000 0 -0.33 120 120
NR0B1 0.014 0.041 0.22 21 -10000 0 21
EGR1 -0.15 0.19 0.22 4 -0.38 227 231
RXRs/9cRA 0.007 0.048 -10000 0 -0.2 23 23
AR/RACK1/Src -0.074 0.07 -10000 0 -0.31 6 6
AR/GR -0.12 0.12 -10000 0 -0.24 238 238
GNB2L1 0.006 0 -10000 0 -10000 0 0
PKN1 0.009 0.032 0.22 9 -0.38 1 10
RCHY1 0.011 0.032 0.22 13 -10000 0 13
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.024 0.038 0.17 5 -0.29 7 12
T-DHT/AR/TIF2/CARM1 -0.074 0.073 0.25 1 -0.3 6 7
SRC -0.033 0.058 0.22 2 -0.24 6 8
NR3C1 -0.003 0.058 -10000 0 -0.38 13 13
KLK3 -0.06 0.077 -10000 0 -10000 0 0
APPBP2 -0.011 0.03 0.22 5 -0.39 1 6
TRIM24 0.008 0.02 0.22 5 -10000 0 5
T-DHT/AR/TIP60 -0.077 0.073 0.18 1 -0.23 22 23
TMPRSS2 -0.63 0.48 -10000 0 -1 356 356
RXRG 0.011 0.044 0.22 17 -0.38 2 19
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA -0.01 0.077 -10000 0 -0.38 23 23
RXRB 0.006 0 -10000 0 -10000 0 0
CARM1 0.007 0.009 0.22 1 -10000 0 1
NR2C2 0.006 0 -10000 0 -10000 0 0
KLK2 -0.06 0.06 -10000 0 -10000 0 0
AR -0.12 0.13 -10000 0 -0.26 237 237
SENP1 0.018 0.049 0.22 31 -10000 0 31
HSP90AA1 0.006 0 -10000 0 -10000 0 0
MDM2 0.007 0.024 0.22 4 -0.38 1 5
SRY 0.006 0 -10000 0 -10000 0 0
GATA2 0.004 0.034 0.22 1 -0.38 4 5
MYST2 0.006 0.019 0.22 1 -0.38 1 2
HOXB13 0.007 0.009 0.22 1 -10000 0 1
T-DHT/AR/RACK1/Src -0.076 0.072 -10000 0 -0.32 6 6
positive regulation of transcription 0.004 0.034 0.22 1 -0.38 4 5
DNAJA1 -0.01 0.028 0.21 7 -10000 0 7
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.052 0.27 10 -0.29 1 11
NCOA1 0.009 0.032 -10000 0 -0.42 3 3
SPDEF -0.041 0.13 0.22 1 -0.38 69 70
T-DHT/AR/TIF2 -0.053 0.062 0.17 2 -0.26 13 15
T-DHT/AR/Hsp90 -0.077 0.075 0.18 1 -0.23 22 23
GSK3B -0.005 0.009 -10000 0 -10000 0 0
NR2C1 0.012 0.033 0.22 14 -10000 0 14
mol:T-DHT -0.034 0.064 0.24 2 -0.26 6 8
SIRT1 0.006 0 -10000 0 -10000 0 0
ZMIZ2 0.006 0 -10000 0 -10000 0 0
POU2F1 -0.064 0.056 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.072 0.08 0.22 5 -0.33 6 11
CREBBP 0.001 0.046 -10000 0 -0.38 8 8
SMARCE1 0.006 0 -10000 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.007 0.013 0.22 2 -10000 0 2
Aurora C/Aurora B/INCENP 0.038 0.051 0.14 113 -10000 0 113
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B -0.004 0.05 -10000 0 -0.45 7 7
AURKB 0.049 0.086 0.22 113 -10000 0 113
AURKC 0.006 0 -10000 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.055 0.072 -10000 0 -10000 0 0
PLK1 0.24 0.31 0.89 43 -0.77 1 44
CDKN1B 0.16 0.25 0.58 61 -0.48 2 63
FOXO3 0.23 0.31 0.72 66 -0.57 8 74
KAT2B 0.048 0.054 0.14 66 -10000 0 66
FOXO1/SIRT1 0.007 0.056 -10000 0 -0.31 3 3
CAT 0.21 0.31 0.71 41 -1 9 50
CTNNB1 0.006 0.009 0.22 1 -10000 0 1
AKT1 0.053 0.059 0.23 5 -10000 0 5
FOXO1 0.062 0.082 -10000 0 -0.35 2 2
MAPK10 0.014 0.053 0.17 4 -0.18 19 23
mol:GTP 0 0.006 -10000 0 -10000 0 0
FOXO4 0.025 0.13 0.38 26 -0.47 2 28
response to oxidative stress 0.048 0.056 0.15 66 -10000 0 66
FOXO3A/SIRT1 0.096 0.25 0.61 44 -0.51 17 61
XPO1 0.025 0.063 0.22 52 -10000 0 52
EP300 0.002 0.037 -10000 0 -0.39 5 5
BCL2L11 0.07 0.081 0.58 2 -10000 0 2
FOXO1/SKP2 0.085 0.1 0.26 82 -0.32 2 84
mol:GDP 0.048 0.056 0.15 66 -10000 0 66
RAN 0.004 0.007 -10000 0 -10000 0 0
GADD45A 0.16 0.23 0.64 55 -10000 0 55
YWHAQ 0.006 0 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.029 0.035 -10000 0 -10000 0 0
MST1 0.052 0.058 0.18 41 -10000 0 41
CSNK1D 0.006 0 -10000 0 -10000 0 0
CSNK1E 0.006 0 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.01 0.041 -10000 0 -0.27 5 5
YWHAB 0.007 0.009 0.22 1 -10000 0 1
MAPK8 0.021 0.043 0.18 5 -0.2 1 6
MAPK9 0.019 0.042 0.16 6 -0.18 2 8
YWHAG 0.004 0.033 -10000 0 -0.38 4 4
YWHAE 0.006 0.016 -10000 0 -0.38 1 1
YWHAZ 0.006 0 -10000 0 -10000 0 0
SIRT1 -0.002 0.026 -10000 0 -10000 0 0
SOD2 0.031 0.45 0.56 57 -0.79 113 170
RBL2 0.18 0.24 0.59 38 -0.92 1 39
RAL/GDP 0.039 0.045 0.18 6 -0.21 1 7
CHUK 0.056 0.062 0.19 52 -10000 0 52
Ran/GTP 0.004 0.012 -10000 0 -10000 0 0
CSNK1G2 0.006 0 -10000 0 -10000 0 0
RAL/GTP 0.039 0.053 0.18 27 -0.2 1 28
CSNK1G1 0.006 0 -10000 0 -10000 0 0
FASLG 0.069 0.075 -10000 0 -10000 0 0
SKP2 0.056 0.091 0.22 131 -10000 0 131
USP7 0.004 0.02 0.23 1 -0.38 1 2
IKBKB 0.053 0.059 0.19 41 -10000 0 41
CCNB1 0.32 0.34 0.78 74 -0.68 2 76
FOXO1-3a-4/beta catenin 0.12 0.26 0.54 59 -0.44 2 61
proteasomal ubiquitin-dependent protein catabolic process 0.085 0.099 0.26 82 -0.32 2 84
CSNK1A1 0.007 0.009 0.22 1 -10000 0 1
SGK1 0.048 0.054 0.14 66 -10000 0 66
CSNK1G3 0.006 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.009 0.023 0.2 4 -10000 0 4
ZFAND5 0.026 0.12 0.42 5 -0.87 1 6
SFN 0.013 0.039 0.22 19 -10000 0 19
CDK2 0.096 0.11 0.22 255 -10000 0 255
FOXO3A/14-3-3 0.08 0.091 0.26 37 -0.34 2 39
CREBBP -0.011 0.046 -10000 0 -0.39 8 8
FBXO32 0.016 0.56 0.72 42 -0.92 130 172
BCL6 0.16 0.3 0.59 36 -1 15 51
RALB 0.003 0.018 -10000 0 -0.39 1 1
RALA 0.004 0.012 0.22 1 -10000 0 1
YWHAH 0.005 0.03 0.22 1 -0.38 3 4
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.027 0.11 -10000 0 -0.39 31 31
FYN -0.056 0.16 0.29 9 -0.45 51 60
LAT/GRAP2/SLP76 -0.037 0.12 -10000 0 -0.4 42 42
IKBKB 0.007 0.016 0.22 3 -10000 0 3
AKT1 -0.03 0.11 0.24 8 -0.34 42 50
B2M 0 0.041 -10000 0 -0.39 6 6
IKBKG -0.013 0.031 -10000 0 -0.11 24 24
MAP3K8 0.006 0 -10000 0 -10000 0 0
mol:Ca2+ -0.011 0.014 -10000 0 -0.05 46 46
integrin-mediated signaling pathway 0.006 0.022 -10000 0 -0.22 5 5
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.042 0.15 0.27 8 -0.46 42 50
TRPV6 0.006 0.032 0.51 1 -10000 0 1
CD28 0.004 0.005 -10000 0 -10000 0 0
SHC1 -0.036 0.13 0.29 6 -0.46 33 39
receptor internalization -0.03 0.12 0.27 6 -0.42 29 35
PRF1 -0.065 0.25 0.69 1 -1.1 28 29
KRAS 0.03 0.067 0.22 62 -10000 0 62
GRB2 0.006 0.016 -10000 0 -0.38 1 1
COT/AKT1 -0.021 0.09 0.21 8 -0.28 39 47
LAT -0.036 0.13 0.28 6 -0.44 36 42
EntrezGene:6955 -0.001 0.004 0.053 1 -10000 0 1
CD3D -0.056 0.15 0.23 2 -0.39 90 92
CD3E -0.004 0.066 0.23 5 -0.4 14 19
CD3G 0.015 0.055 0.22 33 -0.4 1 34
RASGRP2 -0.002 0.012 0.068 1 -10000 0 1
RASGRP1 -0.05 0.14 0.26 5 -0.35 76 81
HLA-A -0.008 0.066 -10000 0 -0.4 16 16
RASSF5 0.003 0.037 -10000 0 -0.38 5 5
RAP1A/GTP/RAPL 0.006 0.022 -10000 0 -0.22 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.008 0.042 0.14 6 -0.11 37 43
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.021 0.05 -10000 0 -0.17 41 41
PRKCA -0.025 0.062 0.12 4 -0.2 42 46
GRAP2 0.006 0 -10000 0 -10000 0 0
mol:IP3 -0.031 0.091 -10000 0 -0.3 41 41
EntrezGene:6957 -0.001 0.005 0.06 1 -10000 0 1
TCR/CD3/MHC I/CD8 -0.034 0.12 0.36 2 -0.42 29 31
ORAI1 -0.02 0.067 -10000 0 -0.27 38 38
CSK -0.037 0.13 0.28 6 -0.45 36 42
B7 family/CD28 -0.028 0.14 0.36 7 -0.44 37 44
CHUK 0.011 0.031 0.22 12 -10000 0 12
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.042 0.14 0.3 5 -0.49 36 41
PTPN6 -0.038 0.14 0.26 9 -0.46 36 45
VAV1 -0.036 0.13 0.28 6 -0.46 33 39
Monovalent TCR/CD3 -0.031 0.11 0.26 6 -0.25 91 97
CBL 0.006 0 -10000 0 -10000 0 0
LCK -0.041 0.15 0.28 9 -0.44 48 57
PAG1 -0.037 0.13 0.28 6 -0.45 36 42
RAP1A 0.007 0.009 0.22 1 -10000 0 1
TCR/CD3/MHC I/CD8/LCK -0.042 0.15 0.3 5 -0.49 36 41
CD80 0.008 0.028 0.22 9 -10000 0 9
CD86 0.012 0.041 0.22 21 -10000 0 21
PDK1/CARD11/BCL10/MALT1 -0.023 0.06 -10000 0 -0.2 42 42
HRAS 0.006 0 -10000 0 -10000 0 0
GO:0035030 -0.03 0.12 0.3 11 -0.38 37 48
CD8A 0.004 0.007 -10000 0 -10000 0 0
CD8B 0.004 0.017 0.21 3 -10000 0 3
PTPRC -0.008 0.13 0.22 49 -0.39 45 94
PDK1/PKC theta -0.038 0.13 0.29 5 -0.4 42 47
CSK/PAG1 -0.037 0.13 0.28 5 -0.45 33 38
SOS1 0.014 0.04 0.22 20 -10000 0 20
peptide-MHC class I -0.005 0.061 -10000 0 -0.32 19 19
GRAP2/SLP76 -0.041 0.14 -10000 0 -0.44 45 45
STIM1 -0.026 0.094 -10000 0 -0.38 37 37
RAS family/GTP 0.023 0.066 0.16 35 -0.15 14 49
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.031 0.12 0.27 6 -0.43 29 35
mol:DAG -0.032 0.081 -10000 0 -0.27 44 44
RAP1A/GDP -0.003 0.019 0.064 5 -0.055 20 25
PLCG1 0.009 0.022 0.22 6 -10000 0 6
CD247 0.004 0.007 -10000 0 -10000 0 0
cytotoxic T cell degranulation -0.061 0.23 0.68 1 -1 28 29
RAP1A/GTP -0.001 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.035 0.13 0.26 8 -0.39 42 50
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.037 0.11 -10000 0 -0.38 41 41
NRAS 0.099 0.11 0.22 245 -10000 0 245
ZAP70 0.006 0.002 -10000 0 -10000 0 0
GRB2/SOS1 0.009 0.012 -10000 0 -0.27 1 1
LAT/GRAP2/SLP76/VAV1 -0.041 0.11 -10000 0 -0.37 45 45
MALT1 0.017 0.047 0.22 29 -10000 0 29
TRAF6 0.007 0.013 0.22 2 -10000 0 2
CD8 heterodimer 0.005 0.012 -10000 0 -10000 0 0
CARD11 0.007 0.013 0.22 2 -10000 0 2
PRKCB -0.027 0.057 -10000 0 -0.19 44 44
PRKCE -0.025 0.059 -10000 0 -0.2 40 40
PRKCQ -0.041 0.14 0.3 5 -0.44 42 47
LCP2 -0.013 0.085 -10000 0 -0.38 28 28
BCL10 0.006 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.025 0.095 0.22 9 -0.29 41 50
IKK complex -0.004 0.033 0.11 12 -0.096 15 27
RAS family/GDP -0.002 0.007 -10000 0 -0.037 2 2
MAP3K14 -0.018 0.071 0.21 5 -0.21 39 44
PDPK1 -0.029 0.1 0.24 8 -0.32 41 49
TCR/CD3/MHC I/CD8/Fyn -0.044 0.15 0.29 5 -0.52 33 38
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate -0.026 0.093 -10000 0 -0.4 25 25
PDGFB-D/PDGFRB/SLAP -0.005 0.056 -10000 0 -0.27 24 24
PDGFB-D/PDGFRB/APS/CBL -0.003 0.047 -10000 0 -0.22 24 24
AKT1 -0.06 0.1 -10000 0 -0.29 35 35
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.025 0.091 -10000 0 -0.43 24 24
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
FGR -0.015 0.055 -10000 0 -0.26 23 23
mol:Ca2+ -0.027 0.094 -10000 0 -0.45 24 24
MYC -0.095 0.24 -10000 0 -0.76 60 60
SHC1 0.006 0 -10000 0 -10000 0 0
HRAS/GDP -0.008 0.041 -10000 0 -0.19 27 27
LRP1/PDGFRB/PDGFB -0.004 0.058 -10000 0 -0.23 34 34
GRB10 0.007 0.009 0.22 1 -10000 0 1
PTPN11 0.006 0 -10000 0 -10000 0 0
GO:0007205 -0.027 0.095 -10000 0 -0.46 24 24
PTEN -0.001 0.054 -10000 0 -0.38 11 11
GRB2 0.006 0.016 -10000 0 -0.38 1 1
GRB7 0.006 0.035 0.22 5 -0.38 3 8
PDGFB-D/PDGFRB/SHP2 -0.005 0.056 -10000 0 -0.27 24 24
PDGFB-D/PDGFRB/GRB10 -0.005 0.056 -10000 0 -0.27 24 24
cell cycle arrest -0.005 0.056 -10000 0 -0.27 24 24
HRAS 0.006 0 -10000 0 -10000 0 0
HIF1A -0.057 0.094 -10000 0 -0.28 28 28
GAB1 -0.037 0.097 -10000 0 -0.43 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.037 0.092 -10000 0 -0.39 24 24
PDGFB-D/PDGFRB -0.001 0.05 -10000 0 -0.24 24 24
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.005 0.056 -10000 0 -0.27 24 24
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.034 0.097 -10000 0 -0.38 25 25
positive regulation of MAPKKK cascade -0.005 0.056 -10000 0 -0.27 24 24
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
mol:IP3 -0.027 0.096 -10000 0 -0.46 24 24
E5 -0.001 0.001 -10000 0 -10000 0 0
CSK 0.007 0.001 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.006 0.059 -10000 0 -0.27 27 27
SHB 0.006 0 -10000 0 -10000 0 0
BLK -0.015 0.055 -10000 0 -0.26 23 23
PTPN2 0.004 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.005 0.056 -10000 0 -0.27 24 24
BCAR1 0.004 0.028 -10000 0 -0.38 3 3
VAV2 -0.047 0.11 -10000 0 -0.4 30 30
CBL 0.006 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.005 0.056 -10000 0 -0.27 24 24
LCK -0.015 0.055 -10000 0 -0.26 24 24
PDGFRB -0.012 0.08 -10000 0 -0.39 24 24
ACP1 0.024 0.059 0.22 46 -10000 0 46
HCK -0.016 0.055 -10000 0 -0.26 24 24
ABL1 -0.03 0.08 -10000 0 -0.36 24 24
PDGFB-D/PDGFRB/CBL -0.039 0.11 -10000 0 -0.5 24 24
PTPN1 0.004 0.007 -10000 0 -10000 0 0
SNX15 0.006 0 -10000 0 -10000 0 0
STAT3 -0.002 0.056 -10000 0 -0.38 12 12
STAT1 0.12 0.11 0.22 297 -10000 0 297
cell proliferation -0.085 0.21 -10000 0 -0.67 60 60
SLA 0.007 0.013 0.22 2 -10000 0 2
actin cytoskeleton reorganization -0.008 0.052 -10000 0 -0.36 1 1
SRC -0.014 0.055 -10000 0 -0.26 23 23
PI3K -0.077 0.095 -10000 0 -0.22 112 112
PDGFB-D/PDGFRB/GRB7/SHC -0.001 0.051 -10000 0 -0.23 27 27
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 -0.026 0.094 -10000 0 -0.44 24 24
LYN -0.033 0.11 -10000 0 -0.38 42 42
LRP1 -0.001 0.054 -10000 0 -0.38 11 11
SOS1 0.014 0.04 0.22 20 -10000 0 20
STAT5B -0.001 0.054 -10000 0 -0.38 11 11
STAT5A 0 0.049 -10000 0 -0.38 9 9
NCK1-2/p130 Cas 0.014 0.055 -10000 0 -0.2 24 24
SPHK1 0.004 0.011 0.22 1 -10000 0 1
EDG1 -0.005 0.059 -10000 0 -0.39 13 13
mol:DAG -0.027 0.096 -10000 0 -0.46 24 24
PLCG1 -0.028 0.098 -10000 0 -0.47 24 24
NHERF/PDGFRB -0.073 0.13 -10000 0 -0.25 185 185
YES1 -0.013 0.057 -10000 0 -0.26 23 23
cell migration -0.073 0.12 -10000 0 -0.25 185 185
SHC/Grb2/SOS1 0.01 0.047 -10000 0 -0.19 23 23
SLC9A3R2 -0.013 0.085 -10000 0 -0.38 28 28
SLC9A3R1 -0.097 0.17 -10000 0 -0.38 151 151
NHERF1-2/PDGFRB/PTEN -0.068 0.12 -10000 0 -0.22 194 194
FYN -0.072 0.17 -10000 0 -0.45 87 87
DOK1 -0.015 0.042 -10000 0 -0.21 25 25
HRAS/GTP 0.005 0 -10000 0 -10000 0 0
PDGFB 0.006 0 -10000 0 -10000 0 0
RAC1 -0.067 0.15 -10000 0 -0.42 83 83
PRKCD -0.016 0.043 -10000 0 -0.21 26 26
FER -0.015 0.042 0.15 1 -0.21 24 25
MAPKKK cascade -0.012 0.042 -10000 0 -0.19 9 9
RASA1 -0.017 0.043 -10000 0 -0.21 27 27
NCK1 0.024 0.059 0.22 47 -10000 0 47
NCK2 0.006 0 -10000 0 -10000 0 0
p62DOK/Csk -0.013 0.039 -10000 0 -0.19 25 25
PDGFB-D/PDGFRB/SHB -0.005 0.056 -10000 0 -0.27 24 24
chemotaxis -0.03 0.078 -10000 0 -0.35 24 24
STAT1-3-5/STAT1-3-5 -0.008 0.049 -10000 0 -0.19 32 32
Bovine Papilomavirus E5/PDGFRB -0.009 0.055 -10000 0 -0.27 24 24
PTPRJ 0.007 0.016 0.22 3 -10000 0 3
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.01 0.093 0.62 1 -10000 0 1
UGCG -0.009 0.039 -10000 0 -0.6 1 1
AKT1/mTOR/p70S6K/Hsp90/TERT -0.065 0.15 -10000 0 -0.42 47 47
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.008 0.04 -10000 0 -0.59 1 1
mol:DAG -0.012 0.1 -10000 0 -0.88 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.098 0.19 -10000 0 -0.43 116 116
FRAP1 -0.1 0.23 -10000 0 -0.53 94 94
FOXO3 -0.076 0.18 -10000 0 -0.5 60 60
AKT1 -0.078 0.19 -10000 0 -0.51 69 69
GAB2 -0.001 0.07 0.22 16 -0.39 13 29
SMPD1 -0.009 0.042 -10000 0 -0.71 1 1
SGMS1 -0.018 0.088 -10000 0 -0.71 8 8
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 0.004 0.099 0.15 120 -0.23 56 176
CALM1 -0.006 0.068 -10000 0 -0.38 18 18
cell proliferation -0.037 0.11 -10000 0 -0.29 57 57
EIF3A 0.006 0 -10000 0 -10000 0 0
PI3K -0.025 0.084 0.28 1 -0.27 56 57
RPS6KB1 -0.016 0.067 0.38 1 -10000 0 1
mol:sphingomyelin -0.012 0.1 -10000 0 -0.88 8 8
natural killer cell activation -0.002 0.004 -10000 0 -10000 0 0
JAK3 0.002 0.008 -10000 0 -10000 0 0
PIK3R1 -0.042 0.12 -10000 0 -0.39 64 64
JAK1 0 0.029 -10000 0 -0.39 3 3
NFKB1 -0.001 0.054 -10000 0 -0.38 11 11
MYC -0.12 0.3 -10000 0 -0.93 61 61
MYB -0.086 0.31 0.54 1 -1.1 46 47
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.044 0.13 0.29 1 -0.38 34 35
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.012 0.062 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.043 0.13 0.29 1 -0.37 34 35
Rac1/GDP -0.001 0.085 0.19 1 -0.2 57 58
T cell proliferation -0.041 0.12 0.27 1 -0.35 33 34
SHC1 0.002 0.007 -10000 0 -10000 0 0
RAC1 0.005 0.017 -10000 0 -0.38 1 1
positive regulation of cyclin-dependent protein kinase activity -0.004 0.019 0.18 1 -0.064 46 47
PRKCZ -0.043 0.12 0.27 1 -0.36 33 34
NF kappa B1 p50/RelA -0.09 0.2 -10000 0 -0.46 100 100
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.011 0.099 0.5 1 -0.37 8 9
HSP90AA1 0.006 0 -10000 0 -10000 0 0
RELA 0.005 0.023 -10000 0 -0.38 2 2
IL2RA 0.004 0.02 0.22 4 -10000 0 4
IL2RB -0.003 0.046 -10000 0 -0.38 8 8
TERT 0.006 0 -10000 0 -10000 0 0
E2F1 -0.03 0.12 0.48 1 -0.43 46 47
SOS1 0.01 0.041 0.22 20 -10000 0 20
RPS6 0.006 0 -10000 0 -10000 0 0
mol:cAMP 0.002 0.01 0.033 4 -0.13 1 5
PTPN11 0.002 0.008 -10000 0 -10000 0 0
IL2RG -0.011 0.11 0.22 31 -0.39 37 68
actin cytoskeleton organization -0.041 0.12 0.27 1 -0.35 33 34
GRB2 0.001 0.018 -10000 0 -0.38 1 1
IL2 0.002 0.009 -10000 0 -10000 0 0
PIK3CA 0.052 0.092 0.22 131 -10000 0 131
Rac1/GTP 0.004 0.083 0.22 1 -0.19 57 58
LCK 0.002 0.009 -10000 0 -10000 0 0
BCL2 -0.13 0.29 -10000 0 -0.76 90 90
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.006 0 -10000 0 -10000 0 0
SMAD2 0.006 0.041 0.19 2 -0.2 3 5
SMAD3 -0.018 0.062 -10000 0 -0.3 5 5
SMAD3/SMAD4 0.094 0.044 0.22 13 -10000 0 13
SMAD4/Ubc9/PIASy 0.013 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.12 0.054 0.21 61 -10000 0 61
PPM1A 0.006 0 -10000 0 -10000 0 0
CALM1 -0.006 0.068 -10000 0 -0.38 18 18
SMAD2/SMAD4 0.009 0.035 -10000 0 -0.18 3 3
MAP3K1 0.004 0.033 -10000 0 -0.38 4 4
TRAP-1/SMAD4 0.009 0 -10000 0 -10000 0 0
MAPK3 -0.029 0.11 -10000 0 -0.38 51 51
MAPK1 0.006 0.019 0.22 1 -0.38 1 2
NUP214 0.006 0 -10000 0 -10000 0 0
CTDSP1 0.004 0.028 -10000 0 -0.38 3 3
CTDSP2 0.005 0.023 -10000 0 -0.38 2 2
CTDSPL 0.006 0 -10000 0 -10000 0 0
KPNB1 0.006 0 -10000 0 -10000 0 0
TGFBRAP1 0.006 0 -10000 0 -10000 0 0
UBE2I 0.006 0 -10000 0 -10000 0 0
NUP153 0.012 0.036 0.22 16 -10000 0 16
KPNA2 0.19 0.075 0.22 491 -10000 0 491
PIAS4 0.006 0 -10000 0 -10000 0 0
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.029 0.08 -10000 0 -0.22 82 82
ARNO/beta Arrestin1-2 -0.001 0.025 0.12 1 -0.17 11 12
EGFR -0.03 0.12 0.22 1 -0.39 54 55
EPHA2 0.007 0.009 0.22 1 -10000 0 1
USP6 0.006 0 -10000 0 -10000 0 0
IQSEC1 0.006 0 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.017 0.082 -10000 0 -0.27 54 54
ARRB2 0.003 0.011 0.15 3 -10000 0 3
mol:GTP 0.009 0.016 0.063 10 -10000 0 10
ARRB1 -0.001 0.055 0.22 1 -0.38 11 12
FBXO8 0.006 0 -10000 0 -10000 0 0
TSHR 0.013 0.038 0.22 18 -10000 0 18
EGF 0.009 0.024 0.22 7 -10000 0 7
somatostatin receptor activity 0 0 -10000 0 -0.001 32 32
ARAP2 0 0 -10000 0 0 19 19
mol:GDP -0.048 0.079 -10000 0 -0.22 47 47
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 25 25
ITGA2B 0.006 0 -10000 0 -10000 0 0
ARF6 0.006 0.016 -10000 0 -0.39 1 1
Ephrin A1/EPHA2/NCK1/GIT1 0.032 0.042 -10000 0 -10000 0 0
ADAP1 0 0 -10000 0 0 16 16
KIF13B -0.05 0.14 -10000 0 -0.38 82 82
HGF/MET -0.013 0.075 -10000 0 -0.27 45 45
PXN -0.002 0.056 -10000 0 -0.38 12 12
ARF6/GTP -0.046 0.076 -10000 0 -0.25 31 31
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.01 0.07 -10000 0 -0.23 54 54
ADRB2 0.006 0 -10000 0 -10000 0 0
receptor agonist activity 0 0 -10000 0 0 31 31
actin filament binding 0 0 -10000 0 0 40 40
SRC 0.006 0 -10000 0 -10000 0 0
ITGB3 -0.045 0.14 0.22 13 -0.38 82 95
GNAQ -0.005 0.065 -10000 0 -0.39 16 16
EFA6/PI-4-5-P2 0 0 -10000 0 -0.001 22 22
ARF6/GDP -0.004 0.039 -10000 0 -0.26 2 2
ARF6/GDP/GULP/ACAP1 -0.066 0.097 -10000 0 -0.25 74 74
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.017 0.087 -10000 0 -0.21 91 91
ACAP1 0 0 -10000 0 -10000 0 0
ACAP2 0 0 -10000 0 0 21 21
LHCGR/beta Arrestin2 0.007 0.013 0.18 3 -10000 0 3
EFNA1 0.017 0.047 0.22 28 -10000 0 28
HGF 0.008 0.018 0.22 4 -10000 0 4
CYTH3 0 0 -10000 0 -0.001 24 24
CYTH2 -0.001 0.001 -10000 0 -0.004 47 47
NCK1 0.024 0.059 0.22 47 -10000 0 47
fibronectin binding 0 0 -10000 0 0 36 36
endosomal lumen acidification 0 0 -10000 0 0 42 42
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.052 0.14 0.22 3 -0.38 86 89
GNAQ/ARNO -0.004 0.031 -10000 0 -0.18 16 16
mol:Phosphatidic acid 0 0 -10000 0 0 21 21
PIP3-E 0.005 0.023 -10000 0 -0.38 2 2
MET -0.013 0.12 0.22 32 -0.38 45 77
GNA14 0.006 0.027 0.22 2 -0.39 2 4
GNA15 0.003 0.037 -10000 0 -0.39 5 5
GIT1 0.007 0.009 0.22 1 -10000 0 1
mol:PI-4-5-P2 0 0 -10000 0 -0.001 22 22
GNA11 -0.13 0.18 -10000 0 -0.39 193 193
LHCGR 0.007 0.016 0.22 3 -10000 0 3
AGTR1 0.006 0 -10000 0 -10000 0 0
desensitization of G-protein coupled receptor protein signaling pathway 0.007 0.013 0.18 3 -10000 0 3
IPCEF1/ARNO -0.01 0.057 0.17 3 -0.17 56 59
alphaIIb/beta3 Integrin -0.031 0.098 -10000 0 -0.27 82 82
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.006 0.023 0.16 2 -0.23 5 7
SNTA1 0.006 0 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.021 0.064 0.17 89 -0.23 3 92
MAPK12 0.006 0.062 0.26 1 -0.21 21 22
CCND1 -0.094 0.17 -10000 0 -0.38 145 145
p38 gamma/SNTA1 0.003 0.057 0.22 1 -0.2 21 22
MAP2K3 0.003 0.037 -10000 0 -0.38 5 5
PKN1 0.009 0.032 0.22 9 -0.38 1 10
G2/M transition checkpoint 0.006 0.062 0.26 1 -0.21 21 22
MAP2K6 0.009 0.07 0.17 57 -0.23 21 78
MAPT 0.002 0.031 0.17 1 -0.18 4 5
MAPK13 -0.006 0.028 0.2 2 -0.27 5 7
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK -0.006 0.055 0.15 7 -0.27 21 28
Wnt signaling

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
Noncanonical Wnts/FZD 0.034 0.061 0.22 19 -0.21 7 26
FZD6 0.022 0.06 0.22 43 -0.38 1 44
WNT6 0.006 0.016 -10000 0 -0.38 1 1
WNT4 0.006 0 -10000 0 -10000 0 0
FZD3 0.031 0.08 0.22 72 -0.38 4 76
WNT5A 0.006 0.029 0.22 4 -0.38 2 6
WNT11 0.026 0.062 0.22 52 -10000 0 52
Glucocorticoid receptor regulatory network

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
PCK2 -0.048 0.05 -10000 0 -10000 0 0
SMARCC2 0.007 0.009 0.22 1 -10000 0 1
SMARCC1 0.006 0 -10000 0 -10000 0 0
TBX21 0.058 0.06 -10000 0 -10000 0 0
SUMO2 0 0.01 -10000 0 -10000 0 0
STAT1 (dimer) 0.11 0.12 0.22 294 -0.2 5 299
FKBP4 0.023 0.057 0.22 43 -10000 0 43
FKBP5 -0.051 0.14 0.22 2 -0.38 84 86
GR alpha/HSP90/FKBP51/HSP90 -0.075 0.1 -10000 0 -0.28 82 82
PRL 0.035 0.055 0.59 1 -10000 0 1
cortisol/GR alpha (dimer)/TIF2 -0.1 0.14 -10000 0 -0.47 14 14
RELA 0.008 0.08 0.23 14 -0.27 8 22
FGG -0.1 0.13 -10000 0 -0.5 10 10
GR beta/TIF2 -0.053 0.07 -10000 0 -0.32 11 11
IFNG 0.097 0.17 0.58 26 -10000 0 26
apoptosis -0.16 0.22 0.56 2 -0.58 39 41
CREB1 0.008 0 -10000 0 -10000 0 0
histone acetylation 0.035 0.081 -10000 0 -0.37 7 7
BGLAP 0.051 0.065 0.53 2 -10000 0 2
GR/PKAc -0.038 0.055 -10000 0 -0.27 8 8
NF kappa B1 p50/RelA 0.014 0.15 0.41 14 -0.32 63 77
SMARCD1 0.006 0 -10000 0 -10000 0 0
MDM2 -0.031 0.045 -10000 0 -0.28 1 1
GATA3 0.009 0.013 0.22 2 -10000 0 2
AKT1 0.006 0.009 0.22 1 -10000 0 1
CSF2 0.027 0.054 -10000 0 -0.48 1 1
GSK3B 0 0.01 -10000 0 -10000 0 0
NR1I3 -0.14 0.2 0.65 1 -0.52 23 24
CSN2 -0.093 0.12 -10000 0 -0.46 10 10
BRG1/BAF155/BAF170/BAF60A 0.017 0.019 -10000 0 -0.2 2 2
NFATC1 0.007 0.016 -10000 0 -0.39 1 1
POU2F1 0.007 0.006 0.16 1 -10000 0 1
CDKN1A -0.1 0.32 -10000 0 -1.3 35 35
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.008 -10000 0 -10000 0 0
SFN 0.013 0.039 0.22 19 -10000 0 19
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.064 0.095 -10000 0 -0.26 82 82
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.31 0.39 0.56 4 -0.78 227 231
JUN 0.11 0.14 0.47 37 -10000 0 37
IL4 0.05 0.06 -10000 0 -10000 0 0
CDK5R1 0.001 0.009 -10000 0 -10000 0 0
PRKACA 0.006 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.053 0.079 -10000 0 -0.26 51 51
GR alpha/HSP90/FKBP51/HSP90/PP5C -0.068 0.092 -10000 0 -0.26 78 78
cortisol/GR alpha (monomer) -0.12 0.16 -10000 0 -0.54 15 15
NCOA2 0.007 0.013 0.22 2 -10000 0 2
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.011 0.17 0.26 38 -0.37 95 133
AP-1/NFAT1-c-4 0.097 0.2 0.57 35 -0.45 1 36
AFP 0.069 0.1 0.47 2 -10000 0 2
SUV420H1 0.008 0.02 0.22 5 -10000 0 5
IRF1 -0.011 0.22 0.5 4 -0.84 26 30
TP53 -0.072 0.17 -10000 0 -0.43 106 106
PPP5C 0.007 0.009 0.22 1 -10000 0 1
KRT17 0.092 0.18 0.69 23 -10000 0 23
KRT14 0.057 0.11 0.6 16 -10000 0 16
TBP 0.008 0.011 0.2 2 -10000 0 2
CREBBP -0.005 0.054 -10000 0 -0.25 22 22
HDAC1 0.016 0.047 0.22 28 -10000 0 28
HDAC2 0.01 0.036 0.22 13 -0.39 1 14
AP-1 0.097 0.2 0.57 35 -0.45 1 36
MAPK14 0 0.014 0.22 1 -10000 0 1
MAPK10 -0.012 0.069 0.21 1 -0.39 18 19
MAPK11 0 0.01 -10000 0 -10000 0 0
KRT5 0.14 0.24 0.58 108 -10000 0 108
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
NCOA1 0.004 0.028 -10000 0 -0.39 3 3
STAT1 0.11 0.12 0.23 294 -0.2 5 299
CGA 0.05 0.059 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.058 0.088 -10000 0 -0.41 10 10
MAPK3 -0.035 0.11 -10000 0 -0.39 51 51
MAPK1 -0.001 0.021 0.21 1 -0.37 1 2
ICAM1 0.055 0.25 0.58 48 -0.98 15 63
NFKB1 0.001 0.1 0.23 14 -0.34 21 35
MAPK8 0.095 0.12 0.39 37 -10000 0 37
MAPK9 -0.001 0.021 0.24 1 -0.37 1 2
cortisol/GR alpha (dimer) -0.17 0.23 0.56 2 -0.6 42 44
BAX -0.045 0.13 -10000 0 -10000 0 0
POMC -0.014 0.13 -10000 0 -10000 0 0
EP300 -0.003 0.046 -10000 0 -0.35 6 6
cortisol/GR alpha (dimer)/p53 -0.15 0.16 -10000 0 -0.5 32 32
proteasomal ubiquitin-dependent protein catabolic process -0.027 0.041 0.21 3 -0.24 1 4
SGK1 -0.018 0.065 -10000 0 -0.28 25 25
IL13 0.068 0.12 0.49 8 -10000 0 8
IL6 -0.009 0.29 0.57 5 -0.94 46 51
PRKACG 0.006 0 -10000 0 -10000 0 0
IL5 0.054 0.12 -10000 0 -10000 0 0
IL2 0.08 0.15 0.51 17 -10000 0 17
CDK5 0.026 0.07 0.22 65 -10000 0 65
PRKACB 0.01 0.027 0.22 9 -10000 0 9
HSP90AA1 0.006 0 -10000 0 -10000 0 0
IL8 0.074 0.18 0.57 47 -10000 0 47
CDK5R1/CDK5 0.003 0.017 0.18 2 -10000 0 2
NF kappa B1 p50/RelA/PKAc 0.025 0.12 0.33 16 -0.37 10 26
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.083 0.13 0.41 1 -0.47 10 11
SMARCA4 0.007 0.032 0.22 6 -0.38 2 8
chromatin remodeling -0.062 0.086 -10000 0 -0.32 10 10
NF kappa B1 p50/RelA/Cbp 0.009 0.13 0.34 13 -0.43 10 23
JUN (dimer) 0.1 0.14 0.47 37 -10000 0 37
YWHAH 0.005 0.03 0.22 1 -0.38 3 4
VIPR1 0.058 0.06 -10000 0 -10000 0 0
NR3C1 -0.081 0.099 -10000 0 -0.42 13 13
NR4A1 -0.13 0.19 0.22 5 -0.38 200 205
TIF2/SUV420H1 0.009 0.001 -10000 0 -10000 0 0
MAPKKK cascade -0.16 0.22 0.56 2 -0.58 39 41
cortisol/GR alpha (dimer)/Src-1 -0.1 0.13 -10000 0 -0.51 10 10
PBX1 0 0.054 -10000 0 -0.38 11 11
POU1F1 0.007 0.006 -10000 0 -10000 0 0
SELE 0.049 0.12 0.48 3 -10000 0 3
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.063 0.086 -10000 0 -0.32 10 10
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.083 0.13 0.41 1 -0.47 10 11
mol:cortisol -0.069 0.082 -10000 0 -0.28 11 11
MMP1 0.12 0.22 0.55 112 -10000 0 112
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.008 0.076 0.36 1 -0.63 3 4
epithelial cell differentiation -0.003 0.053 -10000 0 -0.59 3 3
ITCH 0.003 0.022 0.19 2 -10000 0 2
WWP1 0.007 0.11 0.53 2 -1.2 3 5
FYN -0.039 0.13 0.22 1 -0.38 67 68
EGFR -0.03 0.12 0.22 1 -0.38 54 55
PRL 0.007 0.009 0.22 1 -10000 0 1
neuron projection morphogenesis -0.001 0.08 0.28 2 -0.34 7 9
PTPRZ1 0.007 0.013 0.22 2 -10000 0 2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.027 0.07 0.24 1 -0.51 3 4
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.024 0.085 0.34 3 -0.57 3 6
ADAM17 0.051 0.085 0.21 119 -10000 0 119
ErbB4/ErbB4 0.011 0.09 0.49 2 -0.7 3 5
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.12 0.13 -10000 0 -0.34 52 52
NCOR1 0.002 0.04 -10000 0 -0.38 6 6
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.001 0.1 0.27 2 -0.37 9 11
GRIN2B -0.001 0.097 0.3 4 -0.35 9 13
ErbB4/ErbB2/betacellulin 0.024 0.081 0.27 3 -0.48 4 7
STAT1 0.12 0.11 0.22 297 -10000 0 297
HBEGF 0.007 0.016 0.22 3 -10000 0 3
PRLR 0.013 0.039 0.22 19 -10000 0 19
E4ICDs/ETO2 0.007 0.074 0.36 1 -0.63 3 4
axon guidance 0.015 0.072 0.36 2 -0.68 3 5
NEDD4 0.004 0.026 0.21 4 -10000 0 4
Prolactin receptor/Prolactin receptor/Prolactin 0.009 0.002 -10000 0 -10000 0 0
CBFA2T3 0.006 0 -10000 0 -10000 0 0
ErbB4/ErbB2/HBEGF 0.024 0.079 0.26 3 -0.55 3 6
MAPK3 0 0.082 0.29 2 -0.35 7 9
STAT1 (dimer) 0.088 0.11 0.31 11 -0.59 3 14
MAPK1 0.013 0.071 0.26 3 -0.49 3 6
JAK2 0.004 0.035 0.22 2 -0.38 4 6
ErbB4/ErbB2/neuregulin 1 beta 0.02 0.082 0.3 3 -0.55 3 6
NRG1 0.038 0.08 0.19 118 -10000 0 118
NRG3 -0.27 0.18 0.22 1 -0.38 407 408
NRG2 0.006 0 -10000 0 -10000 0 0
NRG4 0.009 0.056 0.22 19 -0.38 6 25
heart development 0.015 0.072 0.36 2 -0.68 3 5
neural crest cell migration 0.02 0.081 0.3 3 -0.54 3 6
ERBB2 0.038 0.083 0.19 122 -0.28 3 125
WWOX/E4ICDs 0.007 0.074 0.36 1 -0.63 3 4
SHC1 0.006 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.007 0.094 -10000 0 -0.38 10 10
apoptosis 0.22 0.16 0.33 332 -10000 0 332
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.007 0.074 0.36 1 -0.63 3 4
ErbB4/ErbB2/epiregulin 0.023 0.078 0.23 1 -0.55 3 4
ErbB4/ErbB4/betacellulin/betacellulin 0.009 0.079 0.32 2 -0.56 4 6
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.018 0.071 -10000 0 -0.56 3 3
MDM2 0.007 0.08 0.35 4 -0.63 3 7
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.019 0.067 0.25 3 -0.5 3 6
STAT5A 0.01 0.071 0.32 2 -0.66 3 5
ErbB4/EGFR/neuregulin 1 beta 0.006 0.094 0.24 2 -0.44 5 7
DLG4 0.006 0 -10000 0 -10000 0 0
GRB2/SHC 0.009 0.012 -10000 0 -0.27 1 1
E4ICDs/TAB2/NCoR1 0.006 0.075 -10000 0 -0.66 3 3
STAT5A (dimer) 0.01 0.064 -10000 0 -0.65 3 3
MAP3K7IP2 0.005 0.025 0.22 1 -0.38 2 3
STAT5B (dimer) 0.013 0.071 0.3 2 -0.66 3 5
LRIG1 0.012 0.05 0.22 21 -0.38 3 24
EREG 0.007 0.009 0.22 1 -10000 0 1
BTC 0.007 0.043 0.22 9 -0.38 4 13
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.015 0.072 0.36 2 -0.69 3 5
ERBB4 0.011 0.089 0.65 1 -0.7 3 4
STAT5B -0.001 0.054 -10000 0 -0.38 11 11
YAP1 0.006 0.024 0.23 1 -10000 0 1
GRB2 0.006 0.016 -10000 0 -0.38 1 1
ErbB4/ErbB2/neuregulin 4 0.026 0.083 0.25 2 -0.44 5 7
glial cell differentiation -0.006 0.074 0.65 3 -10000 0 3
WWOX 0.006 0 -10000 0 -10000 0 0
cell proliferation 0.023 0.079 0.3 3 -0.48 4 7
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.016 0.065 -10000 0 -0.21 56 56
epithelial cell differentiation 0.007 0.037 -10000 0 -0.19 19 19
CYFIP2 -0.001 0.051 -10000 0 -0.38 10 10
ENAH -0.001 0.044 0.19 4 -10000 0 4
EGFR -0.03 0.12 0.22 1 -0.38 54 55
EPHA2 0.007 0.009 0.22 1 -10000 0 1
MYO6 -0.011 0.042 -10000 0 -0.19 23 23
CTNNB1 0.007 0.009 0.22 1 -10000 0 1
ABI1/Sra1/Nap1 0.008 0.031 -10000 0 -0.23 10 10
AQP5 0.029 0.067 -10000 0 -10000 0 0
CTNND1 0.006 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.012 0.032 -10000 0 -0.18 19 19
regulation of calcium-dependent cell-cell adhesion -0.014 0.038 -10000 0 -0.18 27 27
EGF 0.009 0.024 0.22 7 -10000 0 7
NCKAP1 0.01 0.028 0.22 10 -10000 0 10
AQP3 -0.14 0.19 -10000 0 -0.42 176 176
cortical microtubule organization 0.007 0.037 -10000 0 -0.19 19 19
GO:0000145 -0.011 0.03 -10000 0 -0.17 19 19
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.008 0.038 -10000 0 -0.19 19 19
MLLT4 -0.006 0.068 -10000 0 -0.38 18 18
ARF6/GDP -0.013 0.028 -10000 0 -10000 0 0
ARF6 0.006 0.016 -10000 0 -0.38 1 1
Ephrin A1/EPHA2/NCK1/GIT1 0.032 0.042 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.048 0.096 -10000 0 -0.25 84 84
PVRL2 0.006 0.019 0.22 1 -0.38 1 2
ZYX -0.038 0.071 -10000 0 -0.19 99 99
ARF6/GTP 0.031 0.038 -10000 0 -0.19 1 1
CDH1 -0.005 0.067 -10000 0 -0.38 17 17
EGFR/EGFR/EGF/EGF -0.013 0.066 -10000 0 -0.19 70 70
RhoA/GDP 0.006 0.037 -10000 0 -0.18 21 21
actin cytoskeleton organization -0.01 0.042 -10000 0 -0.19 19 19
IGF-1R heterotetramer -0.077 0.16 -10000 0 -0.38 121 121
GIT1 0.007 0.009 0.22 1 -10000 0 1
IGF1R -0.077 0.16 -10000 0 -0.38 121 121
IGF1 -0.003 0.067 0.22 4 -0.38 16 20
DIAPH1 0.002 0.08 -10000 0 -0.55 11 11
Wnt receptor signaling pathway -0.007 0.037 0.19 19 -10000 0 19
RHOA 0.005 0.023 -10000 0 -0.38 2 2
RhoA/GTP -0.014 0.029 -10000 0 -10000 0 0
CTNNA1 0.005 0.023 -10000 0 -0.38 2 2
VCL -0.011 0.042 -10000 0 -0.2 19 19
EFNA1 0.017 0.047 0.22 28 -10000 0 28
LPP -0.022 0.053 -10000 0 -0.19 48 48
Ephrin A1/EPHA2 0.005 0.033 -10000 0 -0.18 17 17
SEC6/SEC8 -0.019 0.043 -10000 0 -0.33 3 3
MGAT3 -0.014 0.038 -10000 0 -0.18 27 27
HGF/MET -0.01 0.064 -10000 0 -0.19 58 58
HGF 0.008 0.018 0.22 4 -10000 0 4
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.016 0.066 -10000 0 -0.21 56 56
actin cable formation -0.02 0.066 0.16 4 -0.23 16 20
KIAA1543 -0.013 0.037 -10000 0 -0.19 19 19
KIFC3 -0.012 0.032 -10000 0 -0.18 19 19
NCK1 0.024 0.059 0.22 47 -10000 0 47
EXOC3 0.007 0.009 0.22 1 -10000 0 1
ACTN1 -0.015 0.043 -10000 0 -0.2 29 29
NCK1/GIT1 0.009 0.003 -10000 0 -10000 0 0
mol:GDP 0.007 0.037 -10000 0 -0.19 19 19
EXOC4 0.009 0.024 0.22 7 -10000 0 7
STX4 -0.012 0.032 -10000 0 -0.18 19 19
PIP5K1C -0.012 0.032 -10000 0 -0.18 19 19
LIMA1 -0.02 0.098 -10000 0 -0.38 38 38
ABI1 0.007 0.009 0.22 1 -10000 0 1
ROCK1 -0.001 0.047 0.2 4 -10000 0 4
adherens junction assembly -0.008 0.039 -10000 0 -0.62 1 1
IGF-1R heterotetramer/IGF1 -0.04 0.088 -10000 0 -0.18 150 150
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0.05 -10000 0 -0.27 19 19
MET -0.013 0.12 0.22 32 -0.38 45 77
PLEKHA7 -0.012 0.035 -10000 0 -0.19 19 19
mol:GTP 0.031 0.041 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity -0.018 0.044 -10000 0 -0.32 3 3
cortical actin cytoskeleton stabilization -0.016 0.065 -10000 0 -0.21 56 56
regulation of cell-cell adhesion -0.01 0.042 -10000 0 -0.19 19 19
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.016 0.066 -10000 0 -0.21 56 56
Regulation of Telomerase

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
Telomerase catalytic core complex -0.12 0.2 0.46 1 -0.56 26 27
RAD9A 0.006 0 -10000 0 -10000 0 0
AP1 -0.052 0.11 -10000 0 -0.28 112 112
IFNAR2 0.001 0.014 0.21 1 -10000 0 1
AKT1 -0.022 0.054 -10000 0 -0.2 14 14
ER alpha/Oestrogen -0.028 0.084 -10000 0 -0.27 61 61
NFX1/SIN3/HDAC complex 0.007 0.038 0.21 2 -0.21 1 3
EGF 0.005 0.025 0.22 7 -10000 0 7
SMG5 0.007 0.016 0.22 3 -10000 0 3
SMG6 0.006 0 -10000 0 -10000 0 0
SP3/HDAC2 0 0.02 -10000 0 -0.29 1 1
TERT/c-Abl -0.12 0.19 -10000 0 -0.5 48 48
SAP18 0.002 0.017 -10000 0 -0.38 1 1
MRN complex 0.008 0.015 -10000 0 -0.23 2 2
WT1 -0.023 0.092 -10000 0 -0.39 34 34
WRN 0.034 0.073 0.22 74 -10000 0 74
SP1 -0.002 0.014 -10000 0 -10000 0 0
SP3 0.001 0.009 -10000 0 -10000 0 0
TERF2IP 0.006 0 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.11 0.17 -10000 0 -0.48 43 43
Mad/Max 0.002 0.013 -10000 0 -10000 0 0
TERT -0.12 0.2 0.46 1 -0.58 22 23
CCND1 -0.27 0.45 0.57 1 -1 145 146
MAX 0.001 0.009 -10000 0 -10000 0 0
RBBP7 0.003 0.02 0.22 1 -0.38 1 2
RBBP4 0.012 0.042 0.22 22 -10000 0 22
TERF2 0.005 0.001 -10000 0 -10000 0 0
PTGES3 -0.03 0.11 0.22 1 -0.38 53 54
SIN3A 0.003 0.006 -10000 0 -10000 0 0
Telomerase/911 0.007 0.084 0.24 3 -0.26 5 8
CDKN1B -0.008 0.079 0.39 7 -0.44 3 10
RAD1 0.015 0.043 0.22 23 -10000 0 23
XRCC5 0.029 0.066 0.22 60 -10000 0 60
XRCC6 0.006 0 -10000 0 -10000 0 0
SAP30 0.003 0.006 -10000 0 -10000 0 0
TRF2/PARP2 0.007 0.004 -10000 0 -10000 0 0
UBE3A 0.002 0.008 -10000 0 -10000 0 0
JUN 0.003 0.04 0.22 9 -0.38 3 12
E6 -0.002 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0 0.009 -10000 0 -10000 0 0
FOS -0.07 0.16 0.22 8 -0.39 110 118
IFN-gamma/IRF1 -0.01 0.06 -10000 0 -0.27 27 27
PARP2 0.032 0.07 0.22 68 -10000 0 68
BLM 0.068 0.098 0.22 163 -10000 0 163
Telomerase 0.009 0.073 0.23 1 -10000 0 1
IRF1 -0.015 0.085 0.22 3 -0.37 28 31
ESR1 -0.039 0.12 -10000 0 -0.39 61 61
KU/TER 0.008 0.003 -10000 0 -10000 0 0
ATM/TRF2 0.014 0.026 0.15 20 -10000 0 20
ubiquitin-dependent protein catabolic process 0.008 0.039 0.25 1 -0.21 1 2
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.008 0.039 0.25 1 -0.21 1 2
HDAC1 0.014 0.048 0.22 28 -10000 0 28
HDAC2 0.003 0.039 0.22 13 -0.4 1 14
ATM 0.009 0.036 0.2 20 -10000 0 20
SMAD3 -0.062 0.11 -10000 0 -0.27 131 131
ABL1 0 0.049 -10000 0 -0.38 9 9
MXD1 0.001 0.009 -10000 0 -10000 0 0
MRE11A 0.058 0.092 0.22 136 -10000 0 136
HUS1 0.006 0 -10000 0 -10000 0 0
RPS6KB1 0.01 0.03 0.22 11 -10000 0 11
TERT/NF kappa B1/14-3-3 -0.12 0.18 -10000 0 -0.52 25 25
NR2F2 0.004 0.049 -10000 0 -0.38 9 9
MAPK3 -0.031 0.076 -10000 0 -0.27 51 51
MAPK1 -0.007 0.015 0.18 1 -0.27 1 2
TGFB1/TGF beta receptor Type II -0.08 0.16 -10000 0 -0.38 127 127
NFKB1 -0.001 0.054 -10000 0 -0.38 11 11
HNRNPC 0.006 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.009 0.036 0.2 20 -10000 0 20
NBN 0.019 0.055 0.22 35 -0.38 1 36
EGFR -0.035 0.12 0.22 1 -0.39 54 55
mol:Oestrogen -0.001 0.003 -10000 0 -10000 0 0
EGF/EGFR -0.023 0.082 -10000 0 -0.28 54 54
MYC -0.039 0.12 -10000 0 -0.39 60 60
IL2 -0.002 0.015 -10000 0 -10000 0 0
KU 0.008 0.003 -10000 0 -10000 0 0
RAD50 0.006 0.021 0.22 2 -0.38 1 3
HSP90AA1 0.006 0 -10000 0 -10000 0 0
TGFB1 -0.08 0.16 -10000 0 -0.38 127 127
TRF2/BLM 0.006 0.004 -10000 0 -10000 0 0
FRAP1 0.006 0 -10000 0 -10000 0 0
KU/TERT -0.1 0.2 -10000 0 -0.49 44 44
SP1/HDAC2 -0.002 0.024 -10000 0 -0.29 1 1
PINX1 0.009 0.025 0.22 8 -10000 0 8
Telomerase/EST1A -0.11 0.17 -10000 0 -0.48 43 43
Smad3/Myc -0.069 0.13 -10000 0 -0.25 167 167
911 complex 0.012 0.003 -10000 0 -10000 0 0
IFNG 0.013 0.052 0.22 28 -0.22 1 29
Telomerase/PinX1 -0.11 0.17 -10000 0 -0.48 42 42
Telomerase/AKT1/mTOR/p70S6K -0.028 0.11 -10000 0 -0.38 17 17
SIN3B 0.003 0.011 0.22 1 -10000 0 1
YWHAE 0.006 0.016 -10000 0 -0.38 1 1
Telomerase/EST1B -0.11 0.17 -10000 0 -0.48 46 46
response to DNA damage stimulus 0.004 0.018 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.041 0.05 -10000 0 -0.19 2 2
TRF2/WRN 0.007 0.004 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.11 0.17 -10000 0 -0.48 42 42
E2F1 0 0.011 -10000 0 -10000 0 0
ZNFX1 0.005 0.023 0.22 6 -10000 0 6
PIF1 0.006 0 -10000 0 -10000 0 0
NCL 0.008 0.018 0.22 4 -10000 0 4
DKC1 0.064 0.096 0.22 152 -10000 0 152
telomeric DNA binding 0 0 -10000 0 -10000 0 0
LPA4-mediated signaling events

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
ADCY4 -0.003 0.01 0.17 2 -10000 0 2
ADCY5 -0.002 0.014 0.17 4 -10000 0 4
ADCY6 -0.003 0.007 0.17 1 -10000 0 1
ADCY7 -0.003 0.007 0.17 1 -10000 0 1
ADCY1 -0.003 0.007 0.17 1 -10000 0 1
ADCY2 -0.003 0.007 0.17 1 -10000 0 1
ADCY3 -0.003 0.01 0.17 2 -10000 0 2
ADCY8 -0.088 0.12 0.17 14 -0.23 228 242
PRKCE -0.002 0.008 0.2 1 -10000 0 1
ADCY9 -0.025 0.067 0.17 1 -0.23 56 57
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.046 0.053 0.14 1 -10000 0 1
Caspase cascade in apoptosis

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
TOP1 0.042 0.071 0.18 32 -0.21 9 41
ACTA1 0.019 0.084 0.19 13 -0.27 12 25
NUMA1 0.042 0.071 0.2 14 -0.23 1 15
SPTAN1 0.026 0.081 0.2 10 -0.25 12 22
LIMK1 0.027 0.079 0.2 10 -0.25 12 22
BIRC3 -0.076 0.17 0.22 13 -0.39 127 140
BIRC2 0.037 0.075 0.22 81 -10000 0 81
BAX 0.006 0 -10000 0 -10000 0 0
CASP10 -0.008 0.061 0.17 24 -0.23 27 51
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0.049 0.074 0.19 41 -0.21 7 48
DIABLO 0.1 0.11 0.22 248 -10000 0 248
apoptotic nuclear changes 0.026 0.08 0.2 10 -0.25 12 22
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.006 0 -10000 0 -10000 0 0
GSN 0.009 0.096 0.2 8 -0.29 17 25
MADD 0.006 0 -10000 0 -10000 0 0
TFAP2A 0.037 0.049 -10000 0 -10000 0 0
BID -0.003 0.039 0.23 1 -0.16 25 26
MAP3K1 0.015 0.056 -10000 0 -0.45 4 4
TRADD 0.002 0.04 -10000 0 -0.38 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.009 0.002 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.014 0.083 0.21 6 -0.26 15 21
CASP9 0.007 0.009 0.22 1 -10000 0 1
DNA repair -0.043 0.07 -10000 0 -0.16 120 120
neuron apoptosis 0.008 0.084 -10000 0 -0.63 9 9
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.041 0.077 0.21 11 -0.24 9 20
APAF1 0.01 0.03 0.22 11 -10000 0 11
CASP6 0.043 0.07 -10000 0 -10000 0 0
TRAF2 0.006 0 -10000 0 -10000 0 0
ICAD/CAD 0.025 0.076 0.19 9 -0.24 12 21
CASP7 0.052 0.1 0.23 127 -0.22 13 140
KRT18 0.017 0.041 -10000 0 -0.54 2 2
apoptosis 0.023 0.097 0.22 24 -0.26 9 33
DFFA 0.027 0.079 0.2 10 -0.25 12 22
DFFB 0.027 0.079 0.2 10 -0.25 12 22
PARP1 0.043 0.07 0.16 120 -10000 0 120
actin filament polymerization -0.023 0.077 0.24 12 -0.19 10 22
TNF 0.007 0.009 0.22 1 -10000 0 1
CYCS -0.005 0.034 0.18 1 -10000 0 1
SATB1 -0.024 0.1 -10000 0 -0.31 3 3
SLK 0.026 0.081 0.21 8 -0.25 12 20
p15 BID/BAX 0.001 0.034 0.17 1 -10000 0 1
CASP2 -0.036 0.086 -10000 0 -0.37 13 13
JNK cascade -0.015 0.055 0.45 4 -10000 0 4
CASP3 0.031 0.085 0.19 40 -0.26 12 52
LMNB2 0.006 0.062 0.18 3 -0.27 4 7
RIPK1 0.006 0 -10000 0 -10000 0 0
CASP4 0.003 0.066 0.22 14 -0.39 12 26
Mammalian IAPs/DIABLO 0.021 0.11 -10000 0 -0.2 68 68
negative regulation of DNA binding 0.037 0.049 -10000 0 -10000 0 0
stress fiber formation 0.026 0.08 0.2 9 -0.25 12 21
GZMB -0.008 0.069 0.21 20 -0.27 25 45
CASP1 -0.023 0.12 0.19 25 -0.33 59 84
LMNB1 0.048 0.07 0.19 17 -0.26 1 18
APP 0.008 0.085 -10000 0 -0.64 9 9
TNFRSF1A -0.011 0.08 -10000 0 -0.38 25 25
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.002 0 -10000 0 -10000 0 0
VIM 0.026 0.1 0.22 27 -0.26 9 36
LMNA 0.004 0.073 0.18 3 -0.37 8 11
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.04 0.09 -10000 0 -0.39 13 13
LRDD 0.006 0 -10000 0 -10000 0 0
SREBF1 0.024 0.084 0.2 9 -0.27 14 23
APAF-1/Caspase 9 -0.001 0.11 -10000 0 -0.29 7 7
nuclear fragmentation during apoptosis 0.042 0.07 0.2 14 -0.22 1 15
CFL2 0.023 0.078 0.19 10 -0.24 12 22
GAS2 0.029 0.083 0.22 16 -0.25 12 28
positive regulation of apoptosis 0.027 0.069 0.19 6 -0.28 6 12
PRF1 -0.011 0.081 0.22 1 -0.38 25 26
EPHB forward signaling

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
Ephrin A5/EPHB2 0.007 0.017 -10000 0 -0.22 3 3
cell-cell adhesion 0.021 0.044 0.32 1 -10000 0 1
Ephrin B/EPHB2/RasGAP 0.007 0.065 -10000 0 -0.2 45 45
ITSN1 0.007 0.009 0.22 1 -10000 0 1
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
SHC1 0.006 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.006 0.022 -10000 0 -0.22 5 5
Ephrin B1/EPHB1 0.006 0.022 -10000 0 -0.22 5 5
HRAS/GDP -0.01 0.064 -10000 0 -0.24 39 39
Ephrin B/EPHB1/GRB7 0.008 0.066 -10000 0 -0.2 44 44
Endophilin/SYNJ1 -0.014 0.055 -10000 0 -0.18 42 42
KRAS 0.03 0.067 0.22 62 -10000 0 62
Ephrin B/EPHB1/Src 0.008 0.064 -10000 0 -0.2 42 42
endothelial cell migration -0.022 0.078 -10000 0 -0.21 78 78
GRB2 0.006 0.016 -10000 0 -0.38 1 1
GRB7 0.006 0.035 0.22 5 -0.38 3 8
PAK1 -0.01 0.063 0.25 4 -0.19 40 44
HRAS 0.006 0 -10000 0 -10000 0 0
RRAS -0.033 0.08 -10000 0 -0.2 93 93
DNM1 0.006 0 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.013 0.057 0.24 1 -0.19 42 43
lamellipodium assembly -0.021 0.044 -10000 0 -0.32 1 1
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.006 0.062 0.21 1 -0.21 36 37
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
EPHB2 0.01 0.027 0.22 9 -10000 0 9
EPHB3 0.012 0.033 0.22 14 -10000 0 14
EPHB1 0.012 0.033 0.22 14 -10000 0 14
EPHB4 0.006 0 -10000 0 -10000 0 0
mol:GDP -0.017 0.074 0.22 1 -0.26 39 40
Ephrin B/EPHB2 0.004 0.062 -10000 0 -0.2 42 42
Ephrin B/EPHB3 0.004 0.062 -10000 0 -0.2 42 42
JNK cascade 0.01 0.051 0.28 5 -0.19 3 8
Ephrin B/EPHB1 0.005 0.063 -10000 0 -0.2 42 42
RAP1/GDP -0.007 0.07 0.23 3 -0.24 35 38
EFNB2 -0.013 0.1 0.22 15 -0.38 36 51
EFNB3 0.005 0.03 0.22 1 -0.38 3 4
EFNB1 0.003 0.037 -10000 0 -0.38 5 5
Ephrin B2/EPHB1-2 0.005 0.061 0.14 30 -0.2 36 66
RAP1B 0.007 0.026 0.22 5 -0.38 1 6
RAP1A 0.007 0.009 0.22 1 -10000 0 1
CDC42/GTP -0.005 0.062 -10000 0 -0.22 42 42
Rap1/GTP -0.022 0.044 -10000 0 -0.32 1 1
axon guidance 0.007 0.017 -10000 0 -0.22 3 3
MAPK3 -0.025 0.077 0.19 1 -0.35 8 9
MAPK1 -0.01 0.056 0.19 1 -0.35 1 2
Rac1/GDP -0.017 0.07 0.21 1 -0.25 39 40
actin cytoskeleton reorganization -0.014 0.038 -10000 0 -0.18 22 22
CDC42/GDP -0.017 0.07 0.21 1 -0.25 39 40
PI3K 0.008 0.1 -10000 0 -0.21 78 78
EFNA5 0.006 0.035 0.22 5 -0.38 3 8
Ephrin B2/EPHB4 -0.006 0.057 -10000 0 -0.22 36 36
Ephrin B/EPHB2/Intersectin/N-WASP -0.006 0.063 -10000 0 -0.21 42 42
CDC42 0.006 0 -10000 0 -10000 0 0
RAS family/GTP -0.014 0.036 -10000 0 -0.32 1 1
PTK2 0.035 0.11 0.38 57 -10000 0 57
MAP4K4 0.01 0.052 0.29 5 -0.19 3 8
SRC 0.006 0 -10000 0 -10000 0 0
KALRN 0.009 0.022 0.22 6 -10000 0 6
Intersectin/N-WASP 0.009 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.011 0.064 0.2 9 -0.33 1 10
MAP2K1 -0.007 0.058 0.2 1 -0.36 1 2
WASL 0.006 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.028 0.043 -10000 0 -0.2 3 3
cell migration -0.02 0.072 0.2 1 -0.32 9 10
NRAS 0.099 0.11 0.22 245 -10000 0 245
SYNJ1 -0.014 0.056 -10000 0 -0.19 42 42
PXN -0.002 0.056 -10000 0 -0.38 12 12
TF -0.012 0.055 -10000 0 -0.34 1 1
HRAS/GTP -0.003 0.051 -10000 0 -0.18 45 45
Ephrin B1/EPHB1-2 0.014 0.03 -10000 0 -0.2 5 5
cell adhesion mediated by integrin 0.016 0.059 0.21 42 -0.14 12 54
RAC1 0.006 0.016 -10000 0 -0.38 1 1
mol:GTP 0.004 0.061 0.24 1 -0.18 45 46
RAC1-CDC42/GTP -0.022 0.045 -10000 0 -0.32 1 1
RASA1 0.004 0.028 -10000 0 -0.38 3 3
RAC1-CDC42/GDP -0.008 0.07 0.2 1 -0.24 36 37
ruffle organization -0.015 0.057 0.22 4 -0.32 1 5
NCK1 0.024 0.059 0.22 47 -10000 0 47
receptor internalization -0.014 0.053 -10000 0 -0.34 1 1
Ephrin B/EPHB2/KALRN 0.009 0.063 -10000 0 -0.2 40 40
ROCK1 -0.002 0.029 0.14 15 -0.2 5 20
RAS family/GDP -0.015 0.041 -10000 0 -0.19 22 22
Rac1/GTP -0.022 0.046 -10000 0 -0.33 1 1
Ephrin B/EPHB1/Src/Paxillin -0.01 0.071 0.21 1 -0.22 53 54
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.007 0.036 -10000 0 -0.23 13 13
fibroblast growth factor receptor signaling pathway 0.007 0.036 -10000 0 -0.23 13 13
LAMA1 0.045 0.083 0.22 102 -10000 0 102
PRNP 0 0.052 0.22 1 -0.38 10 11
GPC1/SLIT2 -0.01 0.07 -10000 0 -0.27 39 39
SMAD2 -0.011 0.032 -10000 0 -0.2 15 15
GPC1/PrPc/Cu2+ 0.004 0.031 -10000 0 -0.22 10 10
GPC1/Laminin alpha1 0.008 0.004 -10000 0 -10000 0 0
TDGF1 0.006 0 -10000 0 -10000 0 0
CRIPTO/GPC1 0.009 0 -10000 0 -10000 0 0
APP/GPC1 0.005 0.035 -10000 0 -0.27 9 9
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.001 0.024 0.16 12 -10000 0 12
FLT1 0.006 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.007 0.036 -10000 0 -0.23 13 13
SERPINC1 0.006 0 -10000 0 -10000 0 0
FYN -0.031 0.072 0.16 1 -0.23 67 68
FGR -0.005 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.018 0.05 -10000 0 -0.26 1 1
SLIT2 -0.01 0.11 0.22 28 -0.38 39 67
GPC1/NRG 0.009 0 -10000 0 -10000 0 0
NRG1 0.007 0.009 0.22 1 -10000 0 1
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.012 0.003 -10000 0 -10000 0 0
LYN -0.012 0.04 -10000 0 -0.23 19 19
mol:Spermine -0.002 0 -10000 0 -10000 0 0
cell growth 0.007 0.036 -10000 0 -0.23 13 13
BMP signaling pathway -0.006 0 -10000 0 -10000 0 0
SRC -0.005 0 -10000 0 -10000 0 0
TGFBR1 0.006 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.24 0.19 0.22 4 -0.38 365 369
GPC1 0.006 0 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.006 0 -10000 0 -10000 0 0
VEGFA 0.018 0.048 0.22 30 -10000 0 30
BLK -0.004 0.007 0.16 1 -10000 0 1
HCK -0.004 0.007 0.16 1 -10000 0 1
FGF2 0.006 0 -10000 0 -10000 0 0
FGFR1 0 0.063 0.22 7 -0.38 13 20
VEGFR1 homodimer 0.006 0 -10000 0 -10000 0 0
TGFBR2 -0.003 0.058 -10000 0 -0.38 13 13
cell death 0.005 0.035 -10000 0 -0.27 9 9
ATIII/GPC1 0.009 0 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.17 0.13 -10000 0 -0.27 365 365
LCK -0.005 0 -10000 0 -10000 0 0
neuron differentiation 0.009 0 -10000 0 -10000 0 0
PrPc/Cu2+ 0 0.036 -10000 0 -0.27 10 10
APP 0 0.049 -10000 0 -0.38 9 9
TGFBR2 (dimer) -0.003 0.058 -10000 0 -0.38 13 13
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.017 0.092 0.33 7 -0.31 9 16
TBX21 -0.067 0.23 0.76 5 -0.83 2 7
B2M 0.002 0.04 -10000 0 -0.38 6 6
TYK2 -0.001 0.028 0.18 1 -10000 0 1
IL12RB1 -0.001 0.028 0.18 1 -10000 0 1
GADD45B -0.032 0.19 0.82 6 -0.58 1 7
IL12RB2 0.002 0.037 0.22 7 -10000 0 7
GADD45G -0.034 0.19 0.78 5 -0.74 2 7
natural killer cell activation -0.004 0.026 0.15 5 -10000 0 5
RELB 0.004 0.028 -10000 0 -0.38 3 3
RELA 0.005 0.023 -10000 0 -0.38 2 2
IL18 0.042 0.085 0.22 103 -10000 0 103
IL2RA 0.008 0.018 0.22 4 -10000 0 4
IFNG 0.017 0.047 0.22 28 -10000 0 28
STAT3 (dimer) -0.058 0.21 0.66 6 -0.63 13 19
HLA-DRB5 0.032 0.11 0.22 110 -0.39 17 127
FASLG -0.067 0.23 0.76 5 -0.83 2 7
NF kappa B2 p52/RelB -0.093 0.18 -10000 0 -0.57 33 33
CD4 0.005 0.041 0.22 12 -0.39 2 14
SOCS1 -0.013 0.085 -10000 0 -0.38 28 28
EntrezGene:6955 -0.003 0.011 -10000 0 -10000 0 0
CD3D -0.059 0.14 0.2 2 -0.39 90 92
CD3E -0.006 0.065 0.21 5 -0.39 14 19
CD3G 0.013 0.054 0.22 33 -0.38 1 34
IL12Rbeta2/JAK2 0 0.05 0.24 6 -0.28 4 10
CCL3 -0.063 0.24 0.78 10 -0.83 2 12
CCL4 -0.068 0.23 0.7 7 -0.57 33 40
HLA-A -0.005 0.065 -10000 0 -0.38 16 16
IL18/IL18R 0.014 0.055 0.35 10 -10000 0 10
NOS2 -0.05 0.21 0.73 7 -0.5 28 35
IL12/IL12R/TYK2/JAK2/SPHK2 -0.006 0.077 0.33 7 -0.28 1 8
IL1R1 -0.22 0.49 0.76 5 -1.1 125 130
IL4 0.008 0.028 -10000 0 -0.19 1 1
JAK2 -0.003 0.045 0.18 5 -0.4 4 9
EntrezGene:6957 -0.003 0.009 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.034 0.097 -10000 0 -0.39 21 21
RAB7A -0.023 0.18 0.76 5 -10000 0 5
lysosomal transport -0.021 0.18 0.75 5 -10000 0 5
FOS -0.25 0.5 0.61 9 -1.2 112 121
STAT4 (dimer) -0.022 0.21 0.75 6 -0.66 2 8
STAT5A (dimer) -0.09 0.19 -10000 0 -0.56 33 33
GZMA -0.071 0.25 0.76 5 -1.3 4 9
GZMB -0.064 0.24 0.76 6 -0.83 2 8
HLX 0.006 0 -10000 0 -10000 0 0
LCK -0.073 0.24 0.7 7 -0.6 33 40
TCR/CD3/MHC II/CD4 -0.093 0.21 0.3 11 -0.5 89 100
IL2/IL2R 0.005 0.072 -10000 0 -0.23 40 40
MAPK14 -0.029 0.2 0.78 6 -10000 0 6
CCR5 -0.035 0.19 0.74 5 -0.58 1 6
IL1B 0.013 0.065 0.24 38 -10000 0 38
STAT6 -0.02 0.12 0.45 7 -0.53 6 13
STAT4 0.007 0.013 0.22 2 -10000 0 2
STAT3 -0.002 0.056 -10000 0 -0.38 12 12
STAT1 0.12 0.11 0.22 297 -10000 0 297
NFKB1 -0.001 0.054 -10000 0 -0.38 11 11
NFKB2 0.006 0 -10000 0 -10000 0 0
IL12B -0.001 0.029 0.2 1 -10000 0 1
CD8A 0.006 0 -10000 0 -10000 0 0
CD8B 0.008 0.016 0.22 3 -10000 0 3
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.016 0.092 0.3 9 -0.33 7 16
IL2RB 0.001 0.046 -10000 0 -0.38 8 8
proteasomal ubiquitin-dependent protein catabolic process -0.019 0.2 0.71 7 -0.61 2 9
IL2RG -0.007 0.11 0.22 31 -0.38 37 68
IL12 0.002 0.047 0.23 8 -0.27 1 9
STAT5A 0 0.049 -10000 0 -0.38 9 9
CD247 0.002 0.012 -10000 0 -10000 0 0
IL2 0.006 0 -10000 0 -10000 0 0
SPHK2 0.006 0 -10000 0 -10000 0 0
FRAP1 0.006 0 -10000 0 -10000 0 0
IL12A 0.012 0.063 0.22 38 -0.39 1 39
IL12/IL12R/TYK2/JAK2 -0.075 0.25 0.82 7 -0.63 32 39
MAP2K3 -0.034 0.2 0.78 6 -0.62 2 8
RIPK2 0.065 0.096 0.22 156 -10000 0 156
MAP2K6 -0.026 0.19 0.78 6 -10000 0 6
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.09 0.17 -10000 0 -0.39 134 134
IL18RAP 0.003 0.013 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0 0.036 0.2 3 -10000 0 3
EOMES -0.004 0.044 -10000 0 -10000 0 0
STAT1 (dimer) 0.02 0.22 0.61 20 -0.58 4 24
T cell proliferation -0.005 0.18 0.66 7 -0.5 1 8
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.004 0.016 0.22 1 -10000 0 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.066 0.12 0.25 1 -0.5 5 6
ATF2 -0.028 0.18 0.73 6 -10000 0 6
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.009 0.066 0.23 4 -0.24 25 29
positive regulation of NF-kappaB transcription factor activity 0 0.002 -10000 0 -10000 0 0
CRKL 0.006 0 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.044 0.13 0.27 27 -0.32 26 53
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.001 0.063 -10000 0 -0.28 25 25
antigen processing and presentation of peptide antigen via MHC class I -0.036 0.082 0.18 2 -0.26 55 57
CaM/Ca2+ 0.001 0.067 0.17 1 -0.21 39 40
RAP1A 0.007 0.009 0.22 1 -10000 0 1
STAT1 (dimer)/SHP2 0.063 0.11 0.24 42 -0.35 8 50
AKT1 -0.001 0.1 0.26 8 -0.32 24 32
MAP2K1 -0.01 0.061 0.23 4 -0.3 9 13
MAP3K11 -0.009 0.062 0.24 4 -0.27 13 17
IFNGR1 -0.01 0.079 -10000 0 -0.4 23 23
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.022 0.089 -10000 0 -0.38 23 23
Rap1/GTP -0.018 0.04 -10000 0 -0.26 9 9
CRKL/C3G 0.009 0 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.013 0.062 0.22 2 -0.23 25 27
CEBPB -0.025 0.1 0.4 3 -0.39 13 16
STAT3 -0.002 0.056 -10000 0 -0.38 12 12
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.058 0.23 -10000 0 -0.98 31 31
STAT1 0.064 0.11 0.24 43 -0.35 8 51
CALM1 -0.006 0.068 -10000 0 -0.38 18 18
IFN-gamma (dimer) 0.014 0.044 0.2 28 -10000 0 28
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
STAT1 (dimer)/PIAS1 0.062 0.1 0.23 43 -0.33 8 51
CEBPB/PTGES2/Cbp/p300 -0.028 0.083 0.42 2 -0.3 15 17
mol:Ca2+ 0.008 0.065 0.21 5 -0.23 25 30
MAPK3 -0.07 0.21 0.34 1 -0.69 54 55
STAT1 (dimer) -0.044 0.12 0.39 7 -0.42 35 42
MAPK1 -0.006 0.071 0.34 1 -0.54 2 3
JAK2 0.003 0.038 0.21 2 -0.42 4 6
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
JAK1 0.003 0.031 -10000 0 -0.4 3 3
CAMK2D -0.01 0.077 -10000 0 -0.39 23 23
DAPK1 -0.016 0.089 0.44 3 -0.57 5 8
SMAD7 0.02 0.086 0.32 17 -0.21 2 19
CBL/CRKL/C3G -0.01 0.055 0.19 1 -0.29 9 10
PI3K -0.017 0.087 0.16 4 -0.25 57 61
IFNG 0.014 0.044 0.2 28 -10000 0 28
apoptosis -0.002 0.079 0.39 4 -0.36 6 10
CAMK2G 0.006 0 -10000 0 -10000 0 0
STAT3 (dimer) -0.002 0.056 -10000 0 -0.38 12 12
CAMK2A 0.006 0 -10000 0 -10000 0 0
CAMK2B 0.006 0 -10000 0 -10000 0 0
FRAP1 -0.002 0.098 0.25 8 -0.3 24 32
PRKCD -0.002 0.1 0.25 9 -0.32 24 33
RAP1B 0.007 0.026 0.22 5 -0.38 1 6
negative regulation of cell growth -0.036 0.082 0.18 2 -0.26 55 57
PTPN2 0.006 0 -10000 0 -10000 0 0
EP300 0.001 0.037 -10000 0 -0.38 5 5
IRF1 0.012 0.14 0.55 5 -0.38 40 45
STAT1 (dimer)/PIASy 0.065 0.11 0.26 43 -0.33 8 51
SOCS1 -0.06 0.27 -10000 0 -1.2 28 28
mol:GDP -0.011 0.051 -10000 0 -0.28 9 9
CASP1 0.012 0.13 0.45 19 -0.26 55 74
PTGES2 0.006 0 -10000 0 -10000 0 0
IRF9 -0.011 0.052 0.3 6 -0.27 3 9
mol:PI-3-4-5-P3 -0.022 0.082 -10000 0 -0.24 60 60
RAP1/GDP -0.017 0.041 -10000 0 -0.25 10 10
CBL -0.008 0.061 0.24 4 -0.26 15 19
MAP3K1 -0.01 0.063 0.24 4 -0.27 14 18
PIAS1 0.007 0.009 0.22 1 -10000 0 1
PIAS4 0.007 0.002 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.036 0.082 0.18 2 -0.26 55 57
PTPN11 -0.008 0.063 0.23 5 -0.24 25 30
CREBBP -0.001 0.046 -10000 0 -0.38 8 8
RAPGEF1 0.006 0 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.023 0.055 0.29 4 -0.22 3 7
CRKL 0.006 0 -10000 0 -10000 0 0
Rac1/GDP 0.004 0.011 -10000 0 -0.27 1 1
DOCK1 0.006 0.026 0.22 2 -0.38 2 4
ITGA4 0.017 0.047 0.22 29 -10000 0 29
alpha4/beta7 Integrin/MAdCAM1 0.02 0.036 -10000 0 -0.2 6 6
EPO 0.006 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.007 0.024 -10000 0 -0.27 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.006 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.009 0.002 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.009 0.001 -10000 0 -10000 0 0
lamellipodium assembly 0.002 0.095 -10000 0 -0.24 56 56
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
PI3K -0.022 0.083 -10000 0 -0.27 56 56
ARF6 0.006 0.016 -10000 0 -0.38 1 1
JAK2 0.01 0.038 0.26 1 -0.29 4 5
PXN -0.002 0.056 -10000 0 -0.38 12 12
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
MADCAM1 0.006 0 -10000 0 -10000 0 0
cell adhesion 0.019 0.035 -10000 0 -0.2 6 6
CRKL/CBL 0.009 0 -10000 0 -10000 0 0
ITGB1 0.007 0.016 0.22 3 -10000 0 3
SRC -0.005 0.1 0.27 12 -0.2 82 94
ITGB7 0.003 0.038 0.22 1 -0.38 5 6
RAC1 0.006 0.016 -10000 0 -0.38 1 1
alpha4/beta1 Integrin/VCAM1 -0.024 0.083 -10000 0 -0.23 82 82
p130Cas/Crk/Dock1 -0.007 0.092 0.24 12 -0.34 1 13
VCAM1 -0.017 0.17 0.22 87 -0.38 82 169
RHOA 0.005 0.023 -10000 0 -0.38 2 2
alpha4/beta1 Integrin/Paxillin/GIT1 0.019 0.042 -10000 0 -0.2 10 10
BCAR1 -0.006 0.099 0.26 12 -0.19 84 96
EPOR 0.007 0.016 0.22 3 -10000 0 3
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.006 0 -10000 0 -10000 0 0
GIT1 0.007 0.009 0.22 1 -10000 0 1
Rac1/GTP 0.001 0.097 -10000 0 -0.24 56 56
ceramide signaling pathway

Figure S74.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S74.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.067 0.13 -10000 0 -0.36 43 43
BAG4 0.006 0 -10000 0 -10000 0 0
BAD -0.026 0.041 -10000 0 -0.16 14 14
NFKBIA -0.005 0.065 -10000 0 -0.38 16 16
BIRC3 -0.076 0.17 0.22 13 -0.38 127 140
BAX -0.026 0.041 -10000 0 -0.16 14 14
EnzymeConsortium:3.1.4.12 -0.018 0.03 -10000 0 -0.083 44 44
IKBKB -0.064 0.12 -10000 0 -0.53 14 14
MAP2K2 -0.078 0.084 -10000 0 -0.18 202 202
MAP2K1 -0.028 0.036 -10000 0 -0.17 6 6
SMPD1 -0.018 0.031 -10000 0 -0.13 14 14
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.066 0.13 -10000 0 -0.56 14 14
MAP2K4 -0.028 0.044 -10000 0 -0.17 25 25
protein ubiquitination -0.064 0.13 -10000 0 -0.54 14 14
EnzymeConsortium:2.7.1.37 -0.053 0.055 -10000 0 -0.2 16 16
response to UV 0 0 -10000 0 -0.002 11 11
RAF1 -0.029 0.038 -10000 0 -0.16 14 14
CRADD 0.006 0.001 -10000 0 -10000 0 0
mol:ceramide -0.026 0.042 -10000 0 -0.16 15 15
I-kappa-B-alpha/RELA/p50/ubiquitin 0.001 0.041 -10000 0 -0.22 18 18
MADD 0.006 0.001 -10000 0 -10000 0 0
MAP3K1 -0.026 0.043 -10000 0 -0.17 18 18
TRADD 0.002 0.04 -10000 0 -0.39 6 6
RELA/p50 0.005 0.023 -10000 0 -0.38 2 2
MAPK3 -0.067 0.073 -10000 0 -0.21 69 69
MAPK1 -0.056 0.06 -10000 0 -0.18 42 42
p50/RELA/I-kappa-B-alpha 0.001 0.049 -10000 0 -0.27 18 18
FADD -0.068 0.13 -10000 0 -0.36 45 45
KSR1 -0.027 0.04 -10000 0 -0.16 14 14
MAPK8 -0.026 0.041 -10000 0 -0.17 15 15
TRAF2 0.007 0.001 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -0.002 1 1
CHUK -0.062 0.13 -10000 0 -0.52 14 14
TNF R/SODD -0.003 0.057 -10000 0 -0.27 25 25
TNF 0.006 0.009 0.22 1 -10000 0 1
CYCS -0.014 0.049 0.13 2 -0.16 12 14
IKBKG -0.065 0.13 -10000 0 -0.53 14 14
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.07 0.14 -10000 0 -0.37 48 48
RELA 0.005 0.023 -10000 0 -0.38 2 2
RIPK1 0.007 0.001 -10000 0 -10000 0 0
AIFM1 -0.004 0.056 0.13 19 -0.16 12 31
TNF/TNF R/SODD 0.002 0.049 -10000 0 -0.23 25 25
TNFRSF1A -0.011 0.08 -10000 0 -0.38 25 25
response to heat 0 0 -10000 0 -0.002 1 1
CASP8 -0.013 0.06 -10000 0 -0.84 2 2
NSMAF -0.066 0.13 -10000 0 -0.35 44 44
response to hydrogen peroxide 0 0 -10000 0 -0.002 11 11
BCL2 -0.043 0.13 0.22 2 -0.38 73 75
Syndecan-3-mediated signaling events

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
CTTN 0.007 0.013 0.22 2 -10000 0 2
Syndecan-3/Src/Cortactin 0.003 0.12 -10000 0 -0.48 24 24
Syndecan-3/Neurocan -0.019 0.1 -10000 0 -0.54 20 20
POMC 0.007 0.009 0.22 1 -10000 0 1
EGFR -0.03 0.12 0.22 1 -0.38 54 55
Syndecan-3/EGFR -0.036 0.11 -10000 0 -0.29 72 72
AGRP 0.006 0 -10000 0 -10000 0 0
NCSTN 0.007 0.009 0.22 1 -10000 0 1
PSENEN -0.006 0.068 -10000 0 -0.38 18 18
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B -0.027 0.11 -10000 0 -0.38 49 49
APH1A 0.007 0.009 0.22 1 -10000 0 1
NCAN 0.006 0 -10000 0 -10000 0 0
long-term memory -0.035 0.11 -10000 0 -0.44 28 28
Syndecan-3/IL8 -0.007 0.11 -10000 0 -0.53 20 20
PSEN1 0.007 0.009 0.22 1 -10000 0 1
Src/Cortactin 0.009 0.001 -10000 0 -10000 0 0
FYN -0.039 0.13 0.22 1 -0.38 67 68
limb bud formation -0.023 0.1 -10000 0 -0.56 20 20
MC4R 0 0 -10000 0 -10000 0 0
SRC 0.006 0 -10000 0 -10000 0 0
PTN 0.027 0.12 0.22 95 -0.38 22 117
FGFR/FGF/Syndecan-3 -0.023 0.1 -10000 0 -0.56 20 20
neuron projection morphogenesis -0.011 0.11 -10000 0 -0.51 20 20
Syndecan-3/AgRP -0.019 0.1 -10000 0 -0.54 20 20
Syndecan-3/AgRP/MC4R -0.018 0.098 -10000 0 -0.52 20 20
Fyn/Cortactin -0.024 0.09 -10000 0 -0.27 67 67
SDC3 -0.023 0.1 -10000 0 -0.57 20 20
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration -0.007 0.11 -10000 0 -0.52 20 20
IL8 0.024 0.059 0.22 47 -10000 0 47
Syndecan-3/Fyn/Cortactin -0.036 0.12 -10000 0 -0.46 28 28
Syndecan-3/CASK -0.022 0.1 -10000 0 -0.54 20 20
alpha-MSH/MC4R 0.005 0 -10000 0 -10000 0 0
Gamma Secretase -0.005 0.07 -10000 0 -0.2 66 66
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.006 0 -10000 0 -10000 0 0
Caspase 8 (4 units) 0 0.056 -10000 0 -0.49 4 4
NEF -0.001 0 -10000 0 -10000 0 0
NFKBIA -0.024 0.083 -10000 0 -0.44 16 16
BIRC3 -0.1 0.21 0.45 13 -0.47 127 140
CYCS -0.01 0.05 -10000 0 -0.43 4 4
RIPK1 0.006 0 -10000 0 -10000 0 0
CD247 0.007 0 -10000 0 -10000 0 0
MAP2K7 -0.009 0.06 -10000 0 -0.47 5 5
protein ubiquitination -0.022 0.07 -10000 0 -0.28 11 11
CRADD 0.006 0 -10000 0 -10000 0 0
DAXX 0.007 0.013 0.22 2 -10000 0 2
FAS -0.008 0.074 0.22 1 -0.38 21 22
BID -0.008 0.052 -10000 0 -0.45 4 4
NF-kappa-B/RelA/I kappa B alpha -0.054 0.13 -10000 0 -0.28 132 132
TRADD 0.002 0.04 -10000 0 -0.38 6 6
MAP3K5 0.002 0.044 0.22 1 -0.38 7 8
CFLAR 0.006 0.016 -10000 0 -0.38 1 1
FADD 0.006 0 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.054 0.13 -10000 0 -0.28 132 132
MAPK8 -0.009 0.054 -10000 0 -0.4 5 5
APAF1 0.01 0.03 0.22 11 -10000 0 11
TRAF1 0.006 0 -10000 0 -10000 0 0
TRAF2 0.006 0 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.006 0.055 -10000 0 -0.24 24 24
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.028 0.083 -10000 0 -0.33 18 18
CHUK -0.024 0.074 -10000 0 -0.31 11 11
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.009 0.052 -10000 0 -0.22 24 24
TCRz/NEF 0.007 0 -10000 0 -10000 0 0
TNF 0.007 0.009 0.22 1 -10000 0 1
FASLG -0.004 0 -10000 0 -10000 0 0
NFKB1 -0.02 0.075 -10000 0 -0.46 11 11
TNFR1A/BAG4/TNF-alpha 0.002 0.049 -10000 0 -0.23 25 25
CASP6 0.018 0.086 -10000 0 -0.55 4 4
CASP7 -0.1 0.21 0.34 12 -0.48 127 139
RELA -0.014 0.051 -10000 0 -0.47 2 2
CASP2 0.012 0.033 0.22 14 -10000 0 14
CASP3 -0.099 0.21 0.34 12 -0.48 127 139
TNFRSF1A -0.011 0.08 -10000 0 -0.38 25 25
TNFR1A/BAG4 -0.003 0.057 -10000 0 -0.27 25 25
CASP8 0.006 0 -10000 0 -10000 0 0
CASP9 0.007 0.009 0.22 1 -10000 0 1
MAP3K14 -0.028 0.078 -10000 0 -0.3 18 18
APAF-1/Caspase 9 -0.08 0.14 -10000 0 -0.32 126 126
BCL2 -0.03 0.073 -10000 0 -0.38 6 6
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.071 0.12 0.25 60 -0.43 14 74
Syndecan-4/Syndesmos 0.056 0.089 0.33 2 -0.34 1 3
positive regulation of JNK cascade 0.017 0.11 0.35 5 -0.36 8 13
Syndecan-4/ADAM12 0.087 0.12 0.38 28 -10000 0 28
CCL5 -0.037 0.13 0.22 6 -0.38 66 72
Rac1/GDP 0.004 0.011 -10000 0 -0.27 1 1
DNM2 0.007 0.009 0.22 1 -10000 0 1
ITGA5 0.008 0.018 0.22 4 -10000 0 4
SDCBP 0.006 0.026 0.22 2 -0.38 2 4
PLG -0.011 0.053 -10000 0 -0.38 11 11
ADAM12 0.057 0.092 0.22 135 -10000 0 135
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.007 0.009 0.22 1 -10000 0 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.006 0.006 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.079 0.097 0.35 7 -10000 0 7
Syndecan-4/CXCL12/CXCR4 0.033 0.13 0.35 6 -0.37 8 14
Syndecan-4/Laminin alpha3 0.045 0.1 0.33 2 -0.4 4 6
MDK 0.007 0.013 0.22 2 -10000 0 2
Syndecan-4/FZD7 0.06 0.091 0.35 3 -10000 0 3
Syndecan-4/Midkine 0.056 0.089 0.33 2 -0.34 1 3
FZD7 0.014 0.041 0.22 21 -10000 0 21
Syndecan-4/FGFR1/FGF 0.033 0.071 -10000 0 -0.33 2 2
THBS1 -0.04 0.13 0.22 8 -0.38 72 80
integrin-mediated signaling pathway 0.086 0.12 0.35 32 -10000 0 32
positive regulation of MAPKKK cascade 0.017 0.11 0.35 5 -0.36 8 13
Syndecan-4/TACI 0.055 0.089 0.33 2 -0.34 1 3
CXCR4 0.014 0.049 0.22 23 -0.38 2 25
cell adhesion 0.041 0.077 0.19 12 -0.22 19 31
Syndecan-4/Dynamin 0.056 0.089 0.33 2 -0.34 1 3
Syndecan-4/TSP1 0.036 0.12 0.36 4 -0.36 9 13
Syndecan-4/GIPC 0.057 0.09 0.33 2 -0.34 1 3
Syndecan-4/RANTES 0.037 0.12 0.34 7 -0.38 9 16
ITGB1 0.007 0.016 0.22 3 -10000 0 3
LAMA1 0.045 0.083 0.22 102 -10000 0 102
LAMA3 -0.02 0.1 0.22 6 -0.38 42 48
RAC1 0.006 0.016 -10000 0 -0.38 1 1
PRKCA -0.022 0.063 0.37 7 -0.36 5 12
Syndecan-4/alpha-Actinin 0.052 0.095 0.33 2 -0.36 5 7
TFPI -0.083 0.17 0.22 3 -0.38 131 134
F2 0.005 0.015 0.25 1 -10000 0 1
alpha5/beta1 Integrin 0.009 0.001 -10000 0 -10000 0 0
positive regulation of cell adhesion 0.064 0.11 0.36 6 -0.37 2 8
ACTN1 -0.002 0.056 -10000 0 -0.38 12 12
TNC 0.058 0.092 0.22 137 -10000 0 137
Syndecan-4/CXCL12 0.029 0.13 0.35 3 -0.36 9 12
FGF6 0.006 0 -10000 0 -10000 0 0
RHOA 0.005 0.023 -10000 0 -0.38 2 2
CXCL12 -0.055 0.15 0.22 9 -0.38 94 103
TNFRSF13B 0.006 0 -10000 0 -10000 0 0
FGF2 0.006 0 -10000 0 -10000 0 0
FGFR1 0 0.063 0.22 7 -0.38 13 20
Syndecan-4/PI-4-5-P2 0.051 0.088 0.31 3 -0.34 1 4
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.077 0.13 0.23 201 -0.37 13 214
cell migration -0.003 0.004 -10000 0 -10000 0 0
PRKCD -0.005 0.026 -10000 0 -0.37 2 2
vasculogenesis 0.035 0.12 0.35 4 -0.35 9 13
SDC4 0.056 0.095 0.33 3 -0.36 1 4
Syndecan-4/Tenascin C 0.088 0.12 0.36 31 -10000 0 31
Syndecan-4/PI-4-5-P2/PKC alpha -0.005 0.004 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.055 0.09 0.33 2 -0.35 2 4
MMP9 0.032 0.079 0.23 77 -10000 0 77
Rac1/GTP 0.041 0.078 0.19 12 -0.22 19 31
cytoskeleton organization 0.055 0.087 0.33 2 -0.33 1 3
GIPC1 0.009 0.025 0.22 8 -10000 0 8
Syndecan-4/TFPI 0.017 0.13 0.3 4 -0.36 10 14
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.003 0.097 0.2 3 -0.24 55 58
adherens junction organization -0.006 0.073 0.2 1 -0.27 25 26
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.013 0.1 0.22 2 -0.32 18 20
FMN1 -0.012 0.074 -10000 0 -0.26 27 27
mol:IP3 0.002 0.087 0.21 2 -0.31 5 7
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.006 0.072 -10000 0 -0.27 25 25
CTNNB1 0.006 0.01 0.22 1 -10000 0 1
AKT1 0.001 0.088 0.19 2 -0.34 5 7
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.011 0.072 -10000 0 -0.37 17 17
CTNND1 0.005 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.003 0.074 0.18 13 -0.25 24 37
VASP -0.007 0.068 -10000 0 -0.26 25 25
ZYX -0.028 0.093 -10000 0 -0.29 35 35
JUB 0.001 0.077 0.19 6 -0.26 25 31
EGFR(dimer) -0.02 0.09 0.19 1 -0.27 37 38
E-cadherin/beta catenin-gamma catenin 0 0.055 -10000 0 -0.23 29 29
mol:PI-3-4-5-P3 0.007 0.095 0.2 2 -0.35 5 7
PIK3CA 0.052 0.089 0.22 131 -10000 0 131
PI3K 0.007 0.097 0.2 2 -0.36 5 7
FYN -0.032 0.12 0.21 1 -0.32 62 63
mol:Ca2+ 0.002 0.086 0.21 2 -0.3 5 7
JUP -0.005 0.063 -10000 0 -0.38 15 15
PIK3R1 -0.037 0.12 -10000 0 -0.39 64 64
mol:DAG 0.002 0.087 0.21 2 -0.31 5 7
CDH1 -0.006 0.066 -10000 0 -0.38 17 17
RhoA/GDP -0.013 0.1 0.22 2 -0.32 18 20
establishment of polarity of embryonic epithelium -0.007 0.067 -10000 0 -0.26 25 25
SRC 0.006 0 -10000 0 -10000 0 0
RAC1 0.006 0.016 -10000 0 -0.38 1 1
RHOA 0.005 0.023 -10000 0 -0.38 2 2
EGFR -0.03 0.12 0.22 1 -0.38 54 55
CASR -0.002 0.081 0.2 2 -0.29 5 7
RhoA/GTP 0.002 0.079 0.21 1 -0.28 5 6
AKT2 0.002 0.089 0.21 4 -0.34 5 9
actin cable formation -0.014 0.072 -10000 0 -0.25 27 27
apoptosis 0.002 0.092 0.21 55 -0.19 2 57
CTNNA1 0.004 0.024 -10000 0 -0.39 2 2
mol:GDP -0.017 0.1 0.22 3 -0.33 18 21
PIP5K1A 0.003 0.075 0.18 13 -0.25 24 37
PLCG1 0.001 0.088 0.21 2 -0.31 5 7
Rac1/GTP -0.018 0.085 -10000 0 -0.25 36 36
homophilic cell adhesion 0 0.004 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.006 0 -10000 0 -10000 0 0
Rac1/GDP 0.006 0.017 -10000 0 -0.38 1 1
DOCK1 0.006 0.026 0.22 2 -0.38 2 4
ITGA4 0.017 0.047 0.22 29 -10000 0 29
RAC1 0.006 0.016 -10000 0 -0.38 1 1
alpha4/beta7 Integrin 0.007 0.024 -10000 0 -0.27 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.006 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.012 0.003 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.011 0.047 0.28 1 -0.22 13 14
lamellipodium assembly -0.01 0.12 0.23 1 -0.33 56 57
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
PI3K -0.022 0.083 -10000 0 -0.27 56 56
ARF6 0.006 0.016 -10000 0 -0.38 1 1
TLN1 0.005 0.023 -10000 0 -0.38 2 2
PXN -0.01 0.038 -10000 0 -0.27 12 12
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
ARF6/GTP 0.008 0.027 -10000 0 -0.18 11 11
cell adhesion 0.015 0.043 -10000 0 -0.21 11 11
CRKL/CBL 0.009 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.013 0.042 -10000 0 -0.2 10 10
ITGB1 0.007 0.016 0.22 3 -10000 0 3
ITGB7 0.003 0.038 0.22 1 -0.38 5 6
ARF6/GDP 0.006 0.017 -10000 0 -0.38 1 1
alpha4/beta1 Integrin/Paxillin/VCAM1 0.006 0.1 0.27 12 -0.19 90 102
p130Cas/Crk/Dock1 0.011 0.022 -10000 0 -0.23 5 5
VCAM1 -0.017 0.17 0.22 87 -0.38 82 169
alpha4/beta1 Integrin/Paxillin/Talin 0.016 0.044 -10000 0 -0.21 11 11
alpha4/beta1 Integrin/Paxillin/GIT1 0.017 0.041 -10000 0 -0.19 10 10
BCAR1 0.004 0.028 -10000 0 -0.38 3 3
mol:GDP -0.016 0.04 0.19 10 -10000 0 10
CBL 0.006 0 -10000 0 -10000 0 0
PRKACA 0.006 0 -10000 0 -10000 0 0
GIT1 0.007 0.009 0.22 1 -10000 0 1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.016 0.044 -10000 0 -0.21 11 11
Rac1/GTP -0.013 0.13 -10000 0 -0.36 56 56
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.044 0.065 0.23 45 -10000 0 45
AES -0.031 0.14 0.15 14 -0.37 84 98
FBXW11 0.006 0 -10000 0 -10000 0 0
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.007 0.004 -10000 0 -10000 0 0
SMAD4 0.006 0 -10000 0 -10000 0 0
DKK2 0.006 0 -10000 0 -10000 0 0
TLE1 0.031 0.049 0.19 25 -0.34 1 26
MACF1 0.009 0.03 0.22 8 -0.39 1 9
CTNNB1 0.016 0.047 0.24 3 -10000 0 3
WIF1 0.011 0.03 0.22 11 -10000 0 11
beta catenin/RanBP3 0.12 0.18 0.37 186 -10000 0 186
KREMEN2 0.006 0 -10000 0 -10000 0 0
DKK1 0.012 0.036 0.22 16 -10000 0 16
beta catenin/beta TrCP1 0.032 0.047 0.23 3 -10000 0 3
FZD1 0.005 0.003 -10000 0 -10000 0 0
AXIN2 -0.071 0.14 0.54 2 -0.56 17 19
AXIN1 0.007 0.001 -10000 0 -10000 0 0
RAN 0.007 0.002 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.018 0.038 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.001 0.12 0.26 5 -0.29 38 43
Axin1/APC/GSK3 0.017 0.034 0.2 1 -10000 0 1
Axin1/APC/GSK3/beta catenin/Macf1 0.022 0.044 0.24 1 -10000 0 1
HNF1A 0.028 0.044 0.16 13 -0.34 2 15
CTBP1 0.03 0.04 0.17 13 -10000 0 13
MYC -0.18 0.41 -10000 0 -1.3 60 60
RANBP3 0.007 0.002 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.012 0.007 0.16 1 -10000 0 1
NKD1 0.006 0.009 0.22 1 -10000 0 1
TCF4 0.029 0.05 0.17 17 -0.37 3 20
TCF3 0.03 0.039 0.16 14 -10000 0 14
WNT1/LRP6/FZD1/Axin1 0.029 0.039 -10000 0 -10000 0 0
Ran/GTP 0.007 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.13 0.24 0.48 148 -0.45 1 149
LEF1 0.056 0.082 0.23 87 -0.34 1 88
DVL1 0.021 0.029 -10000 0 -10000 0 0
CSNK2A1 0.006 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.088 0.15 -10000 0 -0.45 45 45
DKK1/LRP6/Kremen 2 0.011 0.004 -10000 0 -10000 0 0
LRP6 0.028 0.066 0.22 60 -10000 0 60
CSNK1A1 0.034 0.045 0.19 21 -10000 0 21
NLK 0.001 0.019 0.22 3 -10000 0 3
CCND1 -0.34 0.56 0.53 1 -1.3 145 146
WNT1 0.005 0.003 -10000 0 -10000 0 0
GSK3A 0.001 0.04 -10000 0 -0.39 6 6
GSK3B 0.004 0.005 -10000 0 -10000 0 0
FRAT1 0.004 0.023 -10000 0 -0.38 2 2
PPP2R5D 0.015 0.02 -10000 0 -0.22 1 1
APC 0.008 0.04 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.015 0.04 -10000 0 -10000 0 0
CREBBP 0.024 0.061 0.16 16 -0.37 8 24
EGFR-dependent Endothelin signaling events

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
HRAS 0.006 0 -10000 0 -10000 0 0
EGFR -0.03 0.12 0.22 1 -0.38 54 55
EGF/EGFR -0.007 0.058 -10000 0 -0.18 55 55
EGF/EGFR dimer/SHC/GRB2/SOS1 0.003 0.065 -10000 0 -0.19 50 50
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.008 0.018 0.22 4 -10000 0 4
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.009 0.024 0.22 7 -10000 0 7
EGF/EGFR dimer/SHC -0.01 0.07 -10000 0 -0.23 54 54
mol:GDP 0.002 0.064 -10000 0 -0.19 50 50
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.012 0.039 0.22 16 -0.38 1 17
GRB2/SOS1 0.009 0.012 -10000 0 -0.27 1 1
HRAS/GTP -0.006 0.054 -10000 0 -0.18 50 50
SHC1 0.006 0 -10000 0 -10000 0 0
HRAS/GDP -0.002 0.057 -10000 0 -0.18 50 50
FRAP1 -0.018 0.058 0.24 2 -10000 0 2
EGF/EGFR dimer -0.017 0.082 -10000 0 -0.27 54 54
SOS1 0.014 0.04 0.22 20 -10000 0 20
GRB2 0.006 0.016 -10000 0 -0.38 1 1
ETA receptor/Endothelin-1 0.009 0.012 -10000 0 -0.27 1 1
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.006 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.071 0.07 0.21 74 -10000 0 74
NT3 (dimer)/TRKC 0.008 0.003 -10000 0 -10000 0 0
NT3 (dimer)/TRKB 0.011 0.005 -10000 0 -10000 0 0
SHC/Grb2/SOS1/GAB1/PI3K 0.007 0.089 0.22 8 -0.21 60 68
RAPGEF1 0.006 0 -10000 0 -10000 0 0
BDNF 0.006 0 -10000 0 -10000 0 0
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
DYNLT1 -0.043 0.13 -10000 0 -0.38 72 72
NTRK1 0.006 0 -10000 0 -10000 0 0
NTRK2 0.007 0.016 0.22 3 -10000 0 3
NTRK3 0.007 0.016 0.22 3 -10000 0 3
NT-4/5 (dimer)/TRKB 0.008 0.001 -10000 0 -10000 0 0
neuron apoptosis 0.004 0.069 0.27 13 -10000 0 13
SHC 2-3/Grb2 -0.004 0.073 -10000 0 -0.29 13 13
SHC1 0.006 0 -10000 0 -10000 0 0
SHC2 -0.014 0.1 -10000 0 -0.4 29 29
SHC3 0.008 0.043 -10000 0 -0.23 1 1
STAT3 (dimer) -0.082 0.15 0.18 1 -0.32 157 158
NT3 (dimer)/TRKA 0.011 0.005 -10000 0 -10000 0 0
RIN/GDP 0.038 0.04 0.18 8 -10000 0 8
GIPC1 0.009 0.025 0.22 8 -10000 0 8
KRAS 0.03 0.067 0.22 62 -10000 0 62
DNAJA3 0.002 0.058 0.19 2 -0.31 1 3
RIN/GTP 0.005 0 -10000 0 -10000 0 0
CCND1 -0.16 0.28 0.41 1 -0.61 157 158
MAGED1 0.006 0.028 0.22 3 -0.38 2 5
PTPN11 0.006 0 -10000 0 -10000 0 0
RICS -0.079 0.16 -10000 0 -0.38 124 124
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.012 0.01 -10000 0 -0.23 1 1
GRB2 0.006 0.016 -10000 0 -0.38 1 1
NGF (dimer)/TRKA/MATK 0.009 0 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.009 0.012 -10000 0 -0.27 1 1
ELMO1 0.012 0.033 0.22 14 -10000 0 14
RhoG/GTP/ELMO1/DOCK1 0.007 0.014 -10000 0 -0.22 2 2
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.006 0 -10000 0 -10000 0 0
DOCK1 0.006 0.026 0.22 2 -0.38 2 4
GAB2 0.003 0.069 0.22 16 -0.38 13 29
RIT2 0.006 0 -10000 0 -10000 0 0
RIT1 0.02 0.052 0.22 35 -10000 0 35
FRS2 0.013 0.038 0.22 18 -10000 0 18
DNM1 0.006 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.006 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.004 0.051 0.2 9 -0.3 1 10
mol:GDP 0.046 0.052 0.22 8 -10000 0 8
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.005 0.001 -10000 0 -10000 0 0
RIT1/GDP 0.044 0.047 0.18 20 -10000 0 20
TIAM1 0.006 0.021 0.22 2 -0.38 1 3
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
BDNF (dimer)/TRKB 0.013 0.001 -10000 0 -10000 0 0
KIDINS220/CRKL/C3G 0.009 0 -10000 0 -10000 0 0
SHC/RasGAP 0.008 0.02 -10000 0 -0.27 3 3
FRS2 family/SHP2 0.012 0.002 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.019 0.032 -10000 0 -0.2 5 5
RIT1/GTP 0.004 0.001 -10000 0 -10000 0 0
NT3 (dimer) 0.037 0.075 0.22 81 -10000 0 81
RAP1/GDP 0.007 0.015 -10000 0 -0.22 1 1
KIDINS220/CRKL 0.006 0 -10000 0 -10000 0 0
BDNF (dimer) 0.006 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.008 0.01 -10000 0 -0.22 1 1
Schwann cell development -0.002 0.005 -10000 0 -10000 0 0
EHD4 0.006 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.024 0.033 -10000 0 -0.2 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.006 0.035 0.19 1 -10000 0 1
RAP1B 0.007 0.026 0.22 5 -0.38 1 6
RAP1A 0.007 0.009 0.22 1 -10000 0 1
CDC42/GTP 0.01 0.004 -10000 0 -10000 0 0
ABL1 0 0.049 -10000 0 -0.38 9 9
SH2B family/GRB2/SOS1 0.009 0.012 -10000 0 -0.27 1 1
Rap1/GTP 0.009 0.023 -10000 0 -0.24 1 1
STAT3 -0.082 0.15 0.18 1 -0.32 157 158
axon guidance 0.007 0.003 -10000 0 -10000 0 0
MAPK3 -0.022 0.057 -10000 0 -0.2 51 51
MAPK1 -0.004 0.011 0.15 1 -0.2 1 2
CDC42/GDP 0.038 0.04 0.18 8 -10000 0 8
NTF3 0.037 0.075 0.22 81 -10000 0 81
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.009 0 -10000 0 -10000 0 0
PI3K -0.022 0.083 -10000 0 -0.27 56 56
FRS3 0.006 0 -10000 0 -10000 0 0
FAIM 0.006 0 -10000 0 -10000 0 0
GAB1 0.004 0.033 -10000 0 -0.38 4 4
RASGRF1 0.002 0.057 0.18 1 -0.31 1 2
SOS1 0.014 0.04 0.22 20 -10000 0 20
MCF2L 0.018 0.056 0.15 83 -10000 0 83
RGS19 0.006 0 -10000 0 -10000 0 0
CDC42 0.006 0 -10000 0 -10000 0 0
RAS family/GTP 0.054 0.066 0.27 6 -0.37 1 7
Rac1/GDP 0.037 0.04 0.18 8 -10000 0 8
NGF (dimer)/TRKA/GRIT -0.042 0.096 -10000 0 -0.22 124 124
neuron projection morphogenesis -0.067 0.16 -10000 0 -0.84 12 12
NGF (dimer)/TRKA/NEDD4-2 0.008 0.01 -10000 0 -0.22 1 1
MAP2K1 -0.003 0.031 -10000 0 -0.19 5 5
NGFR 0.007 0.009 0.22 1 -10000 0 1
NGF (dimer)/TRKA/GIPC/GAIP -0.021 0.072 -10000 0 -0.21 72 72
RAS family/GTP/PI3K 0.063 0.11 0.23 89 -0.21 26 115
FRS2 family/SHP2/GRB2/SOS1 0.026 0.031 -10000 0 -0.19 1 1
NRAS 0.099 0.11 0.22 245 -10000 0 245
GRB2/SOS1 0.009 0.012 -10000 0 -0.27 1 1
PRKCI 0.12 0.11 0.22 306 -10000 0 306
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.006 0.016 -10000 0 -0.38 1 1
PRKCZ 0.006 0 -10000 0 -10000 0 0
MAPKKK cascade 0.011 0.032 -10000 0 -10000 0 0
RASA1 0.004 0.028 -10000 0 -0.38 3 3
TRKA/c-Abl 0.005 0.035 -10000 0 -0.27 9 9
SQSTM1 0.006 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.009 0.077 -10000 0 -0.2 72 72
NGF (dimer)/TRKA/p62/Atypical PKCs 0.079 0.06 -10000 0 -10000 0 0
MATK 0.006 0 -10000 0 -10000 0 0
NEDD4L 0.008 0.029 0.22 7 -0.38 1 8
RAS family/GDP -0.001 0.007 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.012 0.045 0.19 1 -0.32 1 2
Rac1/GTP -0.004 0.02 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family 0.023 0.021 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

Figure S83.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S83.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.008 0.039 -10000 0 -0.38 5 5
HSPA8 0.004 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.041 0.091 -10000 0 -0.28 54 54
AKT1 0.006 0.01 0.22 1 -10000 0 1
GSC -0.01 0.021 -10000 0 -10000 0 0
NKX2-5 0.004 0.012 -10000 0 -10000 0 0
muscle cell differentiation -0.007 0.075 0.37 3 -0.23 1 4
SMAD2-3/SMAD4/SP1 0.035 0.1 0.3 11 -0.35 2 13
SMAD4 -0.003 0.051 -10000 0 -10000 0 0
CBFB 0.004 0.028 -10000 0 -0.38 3 3
SAP18 0.004 0.017 -10000 0 -0.38 1 1
Cbp/p300/MSG1 0.016 0.047 0.22 2 -0.26 10 12
SMAD3/SMAD4/VDR 0.014 0.066 0.23 3 -0.27 7 10
MYC -0.035 0.12 -10000 0 -0.39 60 60
CDKN2B 0.007 0.042 -10000 0 -10000 0 0
AP1 -0.029 0.11 0.51 2 -0.32 15 17
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.053 0.062 0.23 12 -10000 0 12
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.002 0.042 -10000 0 -0.29 1 1
SP3 0.009 0.017 -10000 0 -10000 0 0
CREB1 0.006 0 -10000 0 -10000 0 0
FOXH1 0.004 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/GR -0.023 0.064 -10000 0 -0.28 12 12
GATA3 0.007 0.013 0.22 2 -10000 0 2
SKI/SIN3/HDAC complex/NCoR1 0.009 0.041 0.18 11 -10000 0 11
MEF2C/TIF2 -0.013 0.071 -10000 0 -0.38 17 17
endothelial cell migration -0.076 0.17 -10000 0 -0.54 69 69
MAX -0.006 0.034 -10000 0 -10000 0 0
RBBP7 0.004 0.019 0.22 1 -0.39 1 2
RBBP4 0.013 0.042 0.22 22 -10000 0 22
RUNX2 0.007 0.013 0.22 2 -10000 0 2
RUNX3 0.007 0.009 0.22 1 -10000 0 1
RUNX1 0.006 0.016 -10000 0 -0.38 1 1
CTBP1 0.006 0 -10000 0 -10000 0 0
NR3C1 -0.015 0.066 -10000 0 -0.39 13 13
VDR 0.007 0.013 0.22 2 -10000 0 2
CDKN1A -0.034 0.29 -10000 0 -1.1 35 35
KAT2B 0.001 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.006 0.04 -10000 0 -0.24 2 2
DCP1A 0.006 0 -10000 0 -10000 0 0
SKI 0.005 0.004 -10000 0 -10000 0 0
SERPINE1 0.076 0.17 0.54 69 -10000 0 69
SMAD3/SMAD4/ATF2 -0.006 0.048 0.2 4 -0.27 3 7
SMAD3/SMAD4/ATF3 -0.006 0.049 0.2 4 -0.29 4 8
SAP30 0.005 0.004 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.02 0.054 -10000 0 -0.26 11 11
JUN -0.024 0.12 0.52 9 -0.34 12 21
SMAD3/SMAD4/IRF7 -0.004 0.049 0.21 3 -0.31 2 5
TFE3 0.022 0.041 0.18 8 -0.39 1 9
COL1A2 0.13 0.25 0.47 169 -0.8 9 178
mesenchymal cell differentiation 0.006 0.048 0.31 2 -0.2 3 5
DLX1 0.007 0.013 0.22 2 -10000 0 2
TCF3 0.006 0 -10000 0 -10000 0 0
FOS -0.067 0.16 0.22 8 -0.39 110 118
SMAD3/SMAD4/Max -0.019 0.055 -10000 0 -0.3 3 3
Cbp/p300/SNIP1 0.012 0.041 -10000 0 -0.26 11 11
ZBTB17 0.006 0 -10000 0 -10000 0 0
LAMC1 0.034 0.13 0.44 45 -0.31 1 46
TGIF2/HDAC complex/SMAD3/SMAD4 -0.006 0.049 0.21 3 -0.27 4 7
IRF7 0.006 0 -10000 0 -10000 0 0
ESR1 -0.055 0.13 -10000 0 -0.41 61 61
HNF4A 0.007 0.009 0.22 1 -10000 0 1
MEF2C -0.014 0.073 -10000 0 -0.4 17 17
SMAD2-3/SMAD4 -0.007 0.052 0.21 3 -0.28 4 7
Cbp/p300/Src-1 0.014 0.048 -10000 0 -0.25 14 14
IGHV3OR16-13 -0.003 0.01 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.006 0.016 -10000 0 -0.38 1 1
CREBBP 0.004 0.047 -10000 0 -0.38 8 8
SKIL 0.11 0.11 0.22 281 -10000 0 281
HDAC1 0.015 0.047 0.22 28 -10000 0 28
HDAC2 0.009 0.037 0.22 13 -0.38 1 14
SNIP1 0.005 0.014 0.22 2 -10000 0 2
GCN5L2 0.01 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.012 0.071 0.37 5 -0.3 3 8
MSG1/HSC70 0.006 0.008 -10000 0 -10000 0 0
SMAD2 0.002 0.026 -10000 0 -0.39 2 2
SMAD3 -0.004 0.056 0.17 2 -0.47 2 4
SMAD3/E2F4-5/DP1/p107/SMAD4 0.03 0.062 0.22 14 -0.24 1 15
SMAD2/SMAD2/SMAD4 0.002 0.034 0.16 1 -10000 0 1
NCOR1 0.001 0.04 -10000 0 -0.39 6 6
NCOA2 0.007 0.013 0.22 2 -10000 0 2
NCOA1 0.004 0.028 -10000 0 -0.38 3 3
MYOD/E2A 0.009 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.036 0.096 0.3 6 -0.32 2 8
IFNB1 0.001 0.06 -10000 0 -0.31 1 1
SMAD3/SMAD4/MEF2C -0.008 0.084 -10000 0 -0.38 17 17
CITED1 0.011 0.032 0.22 13 -10000 0 13
SMAD2-3/SMAD4/ARC105 -0.001 0.056 0.22 1 -0.25 6 7
RBL1 0.023 0.058 0.22 45 -10000 0 45
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.002 0.049 -10000 0 -0.29 1 1
RUNX1-3/PEBPB2 0.011 0.02 -10000 0 -0.23 4 4
SMAD7 0.002 0.15 0.48 6 -0.5 4 10
MYC/MIZ-1 -0.021 0.086 -10000 0 -0.27 60 60
SMAD3/SMAD4 0.067 0.11 0.35 37 -0.4 2 39
IL10 0.001 0.06 -10000 0 -0.31 1 1
PIASy/HDAC complex 0.001 0.014 -10000 0 -10000 0 0
PIAS3 0.008 0.01 0.22 1 -10000 0 1
CDK2 0.11 0.11 0.22 255 -10000 0 255
IL5 0.001 0.06 -10000 0 -0.31 1 1
CDK4 0.014 0.029 0.22 9 -10000 0 9
PIAS4 0.001 0.014 -10000 0 -10000 0 0
ATF3 0.009 0.033 0.22 10 -0.38 1 11
SMAD3/SMAD4/SP1 0.026 0.1 0.32 6 -0.27 12 18
FOXG1 0.008 0.01 0.22 1 -10000 0 1
FOXO3 -0.008 0.033 0.2 1 -0.27 8 9
FOXO1 -0.008 0.035 0.2 1 -0.27 9 10
FOXO4 -0.004 0.009 0.2 1 -10000 0 1
heart looping -0.014 0.073 -10000 0 -0.4 17 17
CEBPB 0.004 0.034 0.22 1 -0.38 4 5
SMAD3/SMAD4/DLX1 -0.006 0.048 0.21 3 -0.27 3 6
MYOD1 0.006 0 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 -0.006 0.048 0.21 3 -0.27 3 6
SMAD3/SMAD4/GATA3 -0.003 0.05 0.21 3 -0.31 2 5
SnoN/SIN3/HDAC complex/NCoR1 0.11 0.11 0.22 281 -10000 0 281
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.011 0.057 0.21 2 -0.24 6 8
SMAD3/SMAD4/SP1-3 0.036 0.098 0.29 10 -0.35 2 12
MED15 0.005 0.03 0.22 1 -0.38 3 4
SP1 0.026 0.055 0.17 8 -10000 0 8
SIN3B 0.005 0.01 0.22 1 -10000 0 1
SIN3A 0.005 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.009 0.053 -10000 0 -0.24 13 13
ITGB5 0.032 0.12 0.5 20 -0.32 2 22
TGIF/SIN3/HDAC complex/CtBP 0.012 0.035 0.21 2 -10000 0 2
SMAD3/SMAD4/AR -0.11 0.13 -10000 0 -0.26 229 229
AR -0.17 0.19 -10000 0 -0.38 251 251
negative regulation of cell growth 0.023 0.065 0.25 3 -0.31 3 6
SMAD3/SMAD4/MYOD -0.006 0.048 0.19 5 -0.27 3 8
E2F5 0.026 0.063 0.22 53 -10000 0 53
E2F4 0.006 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.016 0.046 -10000 0 -0.2 5 5
SMAD2-3/SMAD4/FOXO1-3a-4 -0.005 0.051 -10000 0 -0.29 2 2
TFDP1 0.012 0.036 0.22 16 -10000 0 16
SMAD3/SMAD4/AP1 -0.022 0.1 -10000 0 -0.33 15 15
SMAD3/SMAD4/RUNX2 -0.005 0.048 0.21 3 -0.31 2 5
TGIF2 0.006 0.016 -10000 0 -0.38 1 1
TGIF1 0.006 0 -10000 0 -10000 0 0
ATF2 0.007 0.016 0.22 3 -10000 0 3
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.007 0.009 0.22 1 -10000 0 1
VLDLR -0.002 0.072 0.22 8 -0.38 17 25
LRPAP1 0.006 0.028 0.22 3 -0.38 2 5
NUDC 0.006 0.016 -10000 0 -0.38 1 1
RELN/LRP8 -0.024 0.086 -10000 0 -0.23 85 85
CaM/Ca2+ -0.004 0.048 -10000 0 -0.27 18 18
KATNA1 0.007 0.013 0.22 2 -10000 0 2
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.029 0.087 0.27 2 -0.21 94 96
IQGAP1/CaM 0 0.051 -10000 0 -0.27 20 20
DAB1 0.006 0 -10000 0 -10000 0 0
IQGAP1 0.005 0.025 0.22 1 -0.38 2 3
PLA2G7 0.019 0.072 0.22 45 -0.38 6 51
CALM1 -0.006 0.068 -10000 0 -0.38 18 18
DYNLT1 -0.043 0.13 -10000 0 -0.38 72 72
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.008 0.017 -10000 0 -0.27 2 2
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.006 0 -10000 0 -10000 0 0
CDK5R1 0.006 0 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A -0.003 0.006 0.14 1 -10000 0 1
CDK5R2 0.006 0 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.03 0.09 -10000 0 -0.23 99 99
YWHAE 0.006 0.016 -10000 0 -0.38 1 1
NDEL1/14-3-3 E -0.012 0.083 0.25 5 -0.32 1 6
MAP1B -0.029 0.081 -10000 0 -0.24 72 72
RAC1 0.001 0.017 -10000 0 -0.22 3 3
p35/CDK5 -0.013 0.089 0.27 5 -0.35 1 6
RELN -0.041 0.15 0.22 27 -0.38 84 111
PAFAH/LIS1 0.016 0.049 0.16 45 -0.23 6 51
LIS1/CLIP170 0.006 0.006 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.046 0.067 -10000 0 -0.3 6 6
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.022 0.09 0.23 5 -0.24 15 20
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.011 0.086 0.26 5 -0.34 1 6
LIS1/IQGAP1 0.006 0.016 0.16 1 -0.23 2 3
RHOA 0 0.023 -10000 0 -0.36 2 2
PAFAH1B1 -0.004 0.008 0.2 1 -10000 0 1
PAFAH1B3 0.018 0.049 0.22 31 -10000 0 31
PAFAH1B2 0.005 0.023 -10000 0 -0.38 2 2
MAP1B/LIS1/Dynein heavy chain -0.014 0.055 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.012 0.08 0.22 4 -0.31 1 5
LRP8 0.01 0.027 0.22 9 -10000 0 9
NDEL1/Katanin 60 -0.011 0.083 0.25 5 -0.32 1 6
P39/CDK5 -0.013 0.089 0.27 5 -0.35 1 6
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.006 0.011 -10000 0 -0.23 1 1
CDK5 -0.012 0.094 0.3 5 -0.19 85 90
PPP2R5D 0.006 0 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.005 0 -10000 0 -10000 0 0
CSNK2A1 0.006 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.015 0.088 0.27 3 -0.19 98 101
RELN/VLDLR -0.015 0.093 -10000 0 -0.21 98 98
CDC42 0.002 0.009 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.017 0.057 -10000 0 -0.27 28 28
MAP4K4 -0.042 0.09 -10000 0 -0.36 13 13
BAG4 0.006 0 -10000 0 -10000 0 0
PKC zeta/ceramide 0.011 0.022 0.14 2 -10000 0 2
NFKBIA -0.005 0.065 -10000 0 -0.38 16 16
BIRC3 -0.076 0.17 0.22 13 -0.38 127 140
BAX 0.006 0.013 -10000 0 -10000 0 0
RIPK1 0.006 0 -10000 0 -10000 0 0
AKT1 -0.003 0.016 0.39 1 -10000 0 1
BAD 0.006 0.024 0.11 28 -10000 0 28
SMPD1 -0.017 0.043 -10000 0 -0.18 25 25
RB1 0.008 0.04 0.15 21 -0.18 6 27
FADD/Caspase 8 -0.043 0.093 -10000 0 -0.39 13 13
MAP2K4 0.001 0.033 0.14 2 -0.18 10 12
NSMAF 0.008 0.02 0.22 5 -10000 0 5
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.004 0.022 0.14 2 -10000 0 2
EGF 0.009 0.024 0.22 7 -10000 0 7
mol:ceramide 0.008 0.026 0.12 28 -10000 0 28
MADD 0.006 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.018 0.059 -10000 0 -0.27 30 30
ASAH1 0.005 0.023 -10000 0 -0.38 2 2
negative regulation of cell cycle 0.008 0.04 0.14 24 -0.18 6 30
cell proliferation -0.041 0.073 -10000 0 -0.23 44 44
BID -0.026 0.072 -10000 0 -0.34 7 7
MAP3K1 0.005 0.027 0.12 6 -0.18 3 9
EIF2A 0.041 0.064 0.22 19 -10000 0 19
TRADD 0.002 0.04 -10000 0 -0.38 6 6
CRADD 0.006 0 -10000 0 -10000 0 0
MAPK3 -0.045 0.071 -10000 0 -0.27 27 27
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.032 0.051 -10000 0 -0.28 1 1
Cathepsin D/ceramide 0.007 0.035 0.14 2 -0.18 11 13
FADD -0.044 0.09 -10000 0 -0.36 13 13
KSR1 0.006 0.024 0.11 28 -10000 0 28
MAPK8 0.006 0.028 0.16 3 -10000 0 3
PRKRA 0.007 0.026 0.11 30 -10000 0 30
PDGFA -0.013 0.085 -10000 0 -0.38 28 28
TRAF2 0.006 0 -10000 0 -10000 0 0
IGF1 -0.003 0.067 0.22 4 -0.38 16 20
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process 0.008 0.026 0.12 28 -10000 0 28
CTSD -0.001 0.054 -10000 0 -0.38 11 11
regulation of nitric oxide biosynthetic process 0.003 0.042 -10000 0 -0.27 13 13
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.043 0.078 -10000 0 -0.24 44 44
PRKCD 0.005 0.023 -10000 0 -0.38 2 2
PRKCZ 0.006 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.018 0.059 -10000 0 -0.27 30 30
RelA/NF kappa B1 0.003 0.042 -10000 0 -0.27 13 13
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.006 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.045 0.096 -10000 0 -0.38 13 13
TNFR1A/BAG4/TNF-alpha 0.002 0.049 -10000 0 -0.23 25 25
mol:Sphingosine-1-phosphate -0.017 0.057 -10000 0 -0.27 28 28
MAP2K1 0.003 0.022 0.13 2 -10000 0 2
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.005 0.023 -10000 0 -0.38 2 2
CYCS 0.022 0.05 0.14 73 -10000 0 73
TNFRSF1A -0.011 0.08 -10000 0 -0.38 25 25
NFKB1 -0.001 0.054 -10000 0 -0.38 11 11
TNFR1A/BAG4 -0.003 0.057 -10000 0 -0.27 25 25
EIF2AK2 0.044 0.066 0.14 176 -10000 0 176
TNF-alpha/TNFR1A/FAN 0.002 0.049 -10000 0 -0.23 25 25
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.029 0.087 -10000 0 -0.48 13 13
MAP2K2 -0.06 0.083 -10000 0 -0.17 192 192
SMPD3 -0.02 0.05 -10000 0 -0.23 14 14
TNF 0.007 0.009 0.22 1 -10000 0 1
PKC zeta/PAR4 0.009 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0 0.029 0.11 21 -0.15 5 26
NF kappa B1/RelA/I kappa B alpha 0.008 0.05 -10000 0 -0.21 26 26
AIFM1 0.037 0.063 0.17 82 -10000 0 82
BCL2 -0.043 0.13 0.22 2 -0.38 73 75
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.01 0.094 -10000 0 -0.54 17 17
HDAC1 0.028 0.051 0.24 28 -10000 0 28
AES -0.051 0.14 -10000 0 -0.38 89 89
FBXW11 0.006 0 -10000 0 -10000 0 0
DTX1 0.006 0 -10000 0 -10000 0 0
LRP6/FZD1 0.008 0.003 -10000 0 -10000 0 0
TLE1 0.011 0.03 0.23 7 -0.37 1 8
AP1 -0.051 0.11 0.22 4 -0.24 130 134
NCSTN 0.006 0.009 0.22 1 -10000 0 1
ADAM10 0.007 0.013 0.22 2 -10000 0 2
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.12 0.16 -10000 0 -0.46 60 60
NICD/RBPSUH -0.011 0.094 -10000 0 -0.54 17 17
WIF1 0.01 0.03 0.22 11 -10000 0 11
NOTCH1 -0.016 0.098 -10000 0 -0.56 17 17
PSENEN -0.006 0.069 -10000 0 -0.39 18 18
KREMEN2 0.006 0 -10000 0 -10000 0 0
DKK1 0.012 0.036 0.22 16 -10000 0 16
beta catenin/beta TrCP1 -0.017 0.041 -10000 0 -10000 0 0
APH1B -0.028 0.11 -10000 0 -0.39 49 49
APH1A 0.006 0.009 0.22 1 -10000 0 1
AXIN1 -0.004 0.033 0.19 2 -0.19 1 3
CtBP/CBP/TCF1/TLE1/AES 0.019 0.11 0.26 28 -10000 0 28
PSEN1 0.006 0.009 0.22 1 -10000 0 1
FOS -0.066 0.16 0.22 8 -0.38 110 118
JUN 0.008 0.039 0.22 9 -0.38 3 12
MAP3K7 0.015 0.029 0.22 10 -10000 0 10
CTNNB1 -0.02 0.04 0.21 1 -10000 0 1
MAPK3 -0.029 0.11 -10000 0 -0.38 51 51
DKK2/LRP6/Kremen 2 0.011 0.004 -10000 0 -10000 0 0
HNF1A 0.009 0.024 -10000 0 -0.38 2 2
CTBP1 0.01 0.008 -10000 0 -10000 0 0
MYC -0.15 0.38 -10000 0 -1.3 60 60
NKD1 0.008 0.009 0.22 1 -10000 0 1
FZD1 0.006 0.001 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.012 0.094 -10000 0 -0.54 17 17
apoptosis -0.05 0.11 0.21 4 -0.24 130 134
Delta 1/NOTCHprecursor -0.012 0.094 -10000 0 -0.54 17 17
DLL1 0.006 0 -10000 0 -10000 0 0
PPARD -0.026 0.042 -10000 0 -10000 0 0
Gamma Secretase -0.014 0.069 -10000 0 -0.2 66 66
APC -0.004 0.033 0.19 2 -10000 0 2
DVL1 -0.001 0.009 -10000 0 -10000 0 0
CSNK2A1 0.002 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0.011 0.008 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.011 0.004 -10000 0 -10000 0 0
LRP6 0.029 0.066 0.22 60 -10000 0 60
CSNK1A1 0.002 0.011 0.22 1 -10000 0 1
NLK 0.019 0.029 0.19 3 -10000 0 3
CCND1 -0.32 0.54 0.53 1 -1.2 145 146
WNT1 0.006 0.001 -10000 0 -10000 0 0
Axin1/APC/beta catenin -0.021 0.046 0.22 1 -10000 0 1
DKK2 0.006 0 -10000 0 -10000 0 0
NOTCH1 precursor/DVL1 -0.012 0.086 -10000 0 -0.49 17 17
GSK3B 0.007 0.002 -10000 0 -10000 0 0
FRAT1 0.007 0.024 -10000 0 -0.38 2 2
NOTCH/Deltex homolog 1 -0.01 0.094 -10000 0 -0.54 17 17
PPP2R5D -0.001 0.01 -10000 0 -10000 0 0
MAPK1 0.006 0.019 0.22 1 -0.38 1 2
WNT1/LRP6/FZD1 0.028 0.042 -10000 0 -10000 0 0
RBPJ 0.007 0.009 0.22 1 -10000 0 1
CREBBP -0.001 0.045 -10000 0 -0.38 8 8
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.012 0.098 -10000 0 -0.21 72 72
SMAD6-7/SMURF1 0.013 0.001 -10000 0 -10000 0 0
NOG 0.006 0.021 0.22 2 -0.38 1 3
SMAD9 -0.01 0.077 -10000 0 -0.46 14 14
SMAD4 0.006 0 -10000 0 -10000 0 0
SMAD5 -0.012 0.062 -10000 0 -0.31 5 5
BMP7/USAG1 -0.014 0.072 -10000 0 -0.28 39 39
SMAD5/SKI -0.008 0.061 -10000 0 -0.29 5 5
SMAD1 -0.002 0.03 -10000 0 -0.31 3 3
BMP2 0.006 0.016 -10000 0 -0.38 1 1
SMAD1/SMAD1/SMAD4 0.004 0.026 -10000 0 -0.26 3 3
BMPR1A 0.005 0.042 0.22 5 -0.38 5 10
BMPR1B -0.014 0.095 0.22 7 -0.38 33 40
BMPR1A-1B/BAMBI -0.003 0.058 -10000 0 -0.23 33 33
AHSG 0.006 0 -10000 0 -10000 0 0
CER1 0.007 0.009 0.22 1 -10000 0 1
BMP2-4/CER1 0.012 0.01 -10000 0 -0.23 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.025 0.08 -10000 0 -0.35 10 10
BMP2-4 (homodimer) 0.009 0.012 -10000 0 -0.27 1 1
RGMB 0.006 0 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.004 0.061 -10000 0 -0.21 38 38
RGMA -0.01 0.077 -10000 0 -0.38 23 23
SMURF1 0.006 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.011 0.062 0.19 1 -0.35 4 5
BMP2-4/USAG1 0.009 0.018 -10000 0 -0.23 3 3
SMAD6/SMURF1/SMAD5 -0.008 0.061 -10000 0 -0.29 5 5
SOSTDC1 0.047 0.089 0.22 111 -0.38 2 113
BMP7/BMPR2/BMPR1A-1B 0.002 0.099 -10000 0 -0.22 72 72
SKI 0.006 0 -10000 0 -10000 0 0
BMP6 (homodimer) 0.007 0.013 0.22 2 -10000 0 2
HFE2 0.006 0 -10000 0 -10000 0 0
ZFYVE16 0.007 0.016 0.22 3 -10000 0 3
MAP3K7 0.01 0.028 0.22 10 -10000 0 10
BMP2-4/CHRD 0.012 0.01 -10000 0 -0.23 1 1
SMAD5/SMAD5/SMAD4 -0.008 0.061 -10000 0 -0.31 4 4
MAPK1 0.006 0.019 0.22 1 -0.38 1 2
TAK1/TAB family 0.002 0.06 -10000 0 -0.31 4 4
BMP7 (homodimer) 0.003 0.13 0.22 69 -0.38 43 112
NUP214 0.006 0 -10000 0 -10000 0 0
BMP6/FETUA 0.009 0.001 -10000 0 -10000 0 0
SMAD1/SKI 0.002 0.029 -10000 0 -0.3 3 3
SMAD6 0.008 0.02 0.22 5 -10000 0 5
CTDSP2 0.005 0.023 -10000 0 -0.38 2 2
BMP2-4/FETUA 0.012 0.01 -10000 0 -0.23 1 1
MAP3K7IP1 0.006 0 -10000 0 -10000 0 0
GREM1 0.013 0.038 0.22 18 -10000 0 18
BMPR2 (homodimer) 0.006 0.016 -10000 0 -0.38 1 1
GADD34/PP1CA -0.01 0.071 -10000 0 -0.23 55 55
BMPR1A-1B (homodimer) -0.009 0.071 -10000 0 -0.28 37 37
CHRDL1 -0.18 0.2 0.22 2 -0.38 270 272
ENDOFIN/SMAD1 0.003 0.031 -10000 0 -0.3 3 3
SMAD6-7/SMURF1/SMAD1 0.009 0.031 -10000 0 -0.28 3 3
SMAD6/SMURF1 0.006 0 -10000 0 -10000 0 0
BAMBI 0.022 0.064 0.22 46 -0.38 2 48
SMURF2 0.007 0.009 0.22 1 -10000 0 1
BMP2-4/CHRDL1 -0.1 0.12 -10000 0 -0.23 266 266
BMP2-4/GREM1 0.012 0.01 -10000 0 -0.23 1 1
SMAD7 0.006 0 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.007 0.074 -10000 0 -0.44 14 14
SMAD1/SMAD6 0.002 0.029 -10000 0 -0.3 3 3
TAK1/SMAD6 0.009 0.001 -10000 0 -10000 0 0
BMP7 0.003 0.13 0.22 69 -0.38 43 112
BMP6 0.007 0.013 0.22 2 -10000 0 2
MAP3K7IP2 0.005 0.025 0.22 1 -0.38 2 3
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.009 0.058 -10000 0 -0.33 4 4
PPM1A 0.006 0 -10000 0 -10000 0 0
SMAD1/SMURF2 0.002 0.03 -10000 0 -0.3 3 3
SMAD7/SMURF1 0.009 0 -10000 0 -10000 0 0
CTDSPL 0.006 0 -10000 0 -10000 0 0
PPP1CA 0.006 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 0.004 0.028 -10000 0 -0.38 3 3
PPP1R15A -0.031 0.12 0.22 1 -0.38 55 56
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.004 0.071 0.19 7 -0.38 4 11
CHRD 0.006 0 -10000 0 -10000 0 0
BMPR2 0.006 0.016 -10000 0 -0.38 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.012 0.066 0.19 1 -0.38 4 5
BMP4 0.011 0.031 0.22 12 -10000 0 12
FST 0.023 0.057 0.22 43 -10000 0 43
BMP2-4/NOG 0.012 0.014 -10000 0 -0.23 2 2
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.005 0.094 -10000 0 -0.21 72 72
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.007 0.009 0.22 1 -10000 0 1
NFATC1 0.062 0.037 -10000 0 -10000 0 0
NFATC2 -0.02 0.046 0.16 5 -0.18 12 17
NFATC3 -0.007 0.03 -10000 0 -10000 0 0
YWHAE 0.006 0.016 -10000 0 -0.38 1 1
Calcineurin A alpha-beta B1/CABIN1 0.001 0.037 -10000 0 -0.34 1 1
Exportin 1/Ran/NUP214 0.005 0.01 -10000 0 -10000 0 0
mol:DAG -0.002 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.007 0.047 -10000 0 -0.2 7 7
BCL2/BAX -0.026 0.093 -10000 0 -0.27 73 73
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.011 0.049 -10000 0 -0.27 18 18
CaM/Ca2+ -0.011 0.049 -10000 0 -0.27 18 18
BAX 0.006 0 -10000 0 -10000 0 0
MAPK14 0.002 0.012 0.22 1 -10000 0 1
BAD 0.006 0 -10000 0 -10000 0 0
CABIN1/MEF2D 0.001 0.036 -10000 0 -0.33 1 1
Calcineurin A alpha-beta B1/BCL2 -0.043 0.13 0.22 2 -0.38 73 75
FKBP8 -0.007 0.072 -10000 0 -0.38 20 20
activation-induced cell death of T cells -0.001 0.035 0.32 1 -10000 0 1
KPNB1 0.006 0 -10000 0 -10000 0 0
KPNA2 0.19 0.075 0.22 491 -10000 0 491
XPO1 0.022 0.063 0.22 52 -10000 0 52
SFN 0.013 0.039 0.22 19 -10000 0 19
MAP3K8 0.001 0.008 -10000 0 -10000 0 0
NFAT4/CK1 alpha -0.012 0.048 -10000 0 -0.23 22 22
MEF2D/NFAT1/Cbp/p300 -0.08 0.14 0.4 5 -0.25 199 204
CABIN1 0.001 0.037 -10000 0 -0.34 1 1
CALM1 -0.012 0.068 -10000 0 -0.39 18 18
RAN 0.002 0.005 -10000 0 -10000 0 0
MAP3K1 0.004 0.033 -10000 0 -0.38 4 4
CAMK4 0.01 0.027 0.22 9 -10000 0 9
mol:Ca2+ -0.004 0.008 -10000 0 -10000 0 0
MAPK3 -0.029 0.11 -10000 0 -0.38 51 51
YWHAH 0.005 0.03 0.22 1 -0.38 3 4
Calcineurin A alpha-beta B1/AKAP79/PKA 0.004 0.008 -10000 0 -10000 0 0
YWHAB 0.007 0.009 0.22 1 -10000 0 1
MAPK8 0.003 0.022 0.22 5 -10000 0 5
MAPK9 0.006 0.019 0.22 1 -0.38 1 2
YWHAG 0.004 0.033 -10000 0 -0.38 4 4
FKBP1A 0.006 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.042 0.055 -10000 0 -10000 0 0
PRKCH 0.005 0.023 -10000 0 -0.38 2 2
CABIN1/Cbp/p300 -0.01 0.048 -10000 0 -0.32 11 11
CASP3 0.005 0.03 0.22 10 -10000 0 10
PIM1 0.007 0.016 0.22 3 -10000 0 3
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.006 -10000 0 -10000 0 0
apoptosis -0.002 0.041 0.16 16 -10000 0 16
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.002 0.04 -10000 0 -0.39 1 1
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.007 0.009 0.22 1 -10000 0 1
JNK2/NFAT4 -0.004 0.03 -10000 0 -0.2 1 1
BAD/BCL-XL 0.009 0 -10000 0 -10000 0 0
PRKCD 0.005 0.023 -10000 0 -0.38 2 2
NUP214 0.002 0.005 -10000 0 -10000 0 0
PRKCZ 0.001 0.008 -10000 0 -10000 0 0
PRKCA 0.005 0.044 0.22 7 -0.38 5 12
PRKCG 0.006 0 -10000 0 -10000 0 0
PRKCQ 0.002 0.06 0.22 8 -0.38 11 19
FKBP38/BCL2 -0.036 0.11 -10000 0 -0.28 89 89
EP300 -0.006 0.038 -10000 0 -0.39 5 5
PRKCB1 0.009 0.022 0.22 6 -10000 0 6
CSNK2A1 0.006 0 -10000 0 -10000 0 0
NFATc/JNK1 0.06 0.039 0.22 3 -10000 0 3
CaM/Ca2+/FKBP38 -0.015 0.059 -10000 0 -0.23 38 38
FKBP12/FK506 0.005 0 -10000 0 -10000 0 0
CSNK1A1 -0.016 0.041 0.16 1 -0.23 18 19
CaM/Ca2+/CAMK IV -0.007 0.041 -10000 0 -0.23 17 17
NFATc/ERK1 0.054 0.047 -10000 0 -0.35 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.004 0.045 -10000 0 -0.3 1 1
NR4A1 -0.15 0.2 0.51 5 -0.41 203 208
GSK3B 0.001 0.008 -10000 0 -10000 0 0
positive T cell selection -0.007 0.03 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.024 0.054 0.14 6 -0.25 18 24
RCH1/ KPNB1 0.001 0.003 -10000 0 -10000 0 0
YWHAQ 0.006 0 -10000 0 -10000 0 0
PRKACA 0.001 0.007 -10000 0 -10000 0 0
AKAP5 0.006 0 -10000 0 -10000 0 0
MEF2D -0.003 0.013 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.006 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.06 0.037 -10000 0 -10000 0 0
CREBBP -0.008 0.047 -10000 0 -0.39 8 8
BCL2 -0.043 0.13 0.22 2 -0.38 73 75
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.002 0.044 0.2 1 -0.27 13 14
PDGFRB -0.012 0.079 -10000 0 -0.39 24 24
SPHK1 -0.004 0.022 -10000 0 -10000 0 0
mol:S1P -0.007 0.032 0.3 1 -10000 0 1
S1P1/S1P/Gi -0.024 0.13 0.41 6 -0.37 45 51
GNAO1 0.004 0.037 0.22 6 -0.39 3 9
PDGFB-D/PDGFRB/PLCgamma1 -0.026 0.12 0.38 6 -0.35 42 48
PLCG1 -0.025 0.12 0.39 6 -0.36 42 48
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.012 0.079 -10000 0 -0.39 24 24
GNAI2 0.004 0.009 -10000 0 -10000 0 0
GNAI3 0.015 0.048 0.22 29 -10000 0 29
GNAI1 -0.002 0.064 0.22 7 -0.39 13 20
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.008 0.084 0.22 1 -0.5 13 14
S1P1/S1P -0.01 0.086 0.33 2 -0.43 13 15
negative regulation of cAMP metabolic process -0.023 0.12 0.41 6 -0.36 45 51
MAPK3 -0.056 0.18 0.47 6 -0.55 54 60
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.004 0.011 -10000 0 -0.27 1 1
RhoA/GDP 0.004 0.016 -10000 0 -0.27 2 2
KDR 0.002 0.029 0.22 2 -0.16 13 15
PLCB2 -0.014 0.079 0.31 2 -0.39 13 15
RAC1 0.006 0.016 -10000 0 -0.38 1 1
RhoA/GTP -0.018 0.066 -10000 0 -0.37 13 13
receptor internalization -0.01 0.081 0.31 2 -0.4 13 15
PTGS2 -0.086 0.29 0.55 6 -0.97 50 56
Rac1/GTP -0.018 0.065 -10000 0 -0.37 13 13
RHOA 0.005 0.023 -10000 0 -0.38 2 2
VEGFA 0.013 0.056 0.22 30 -0.16 13 43
negative regulation of T cell proliferation -0.023 0.12 0.41 6 -0.36 45 51
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0 0.041 -10000 0 -0.39 6 6
MAPK1 -0.04 0.17 0.47 6 -0.51 52 58
S1P1/S1P/PDGFB-D/PDGFRB -0.015 0.1 0.3 6 -0.47 14 20
ABCC1 0.006 0.023 0.22 6 -10000 0 6
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.009 0.022 0.3 2 -10000 0 2
NFATC2 -0.035 0.2 0.45 2 -0.62 24 26
NFATC3 0.017 0.045 0.36 1 -0.26 2 3
CD40LG -0.047 0.2 0.56 3 -0.71 8 11
ITCH -0.007 0.054 0.42 1 -10000 0 1
CBLB -0.006 0.06 0.42 4 -10000 0 4
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.05 0.16 0.64 6 -0.69 10 16
JUNB -0.097 0.17 -10000 0 -0.38 151 151
CaM/Ca2+/Calcineurin A alpha-beta B1 0.002 0.049 -10000 0 -0.28 17 17
T cell anergy -0.01 0.075 0.37 10 -0.35 2 12
TLE4 -0.09 0.26 0.4 1 -0.63 92 93
Jun/NFAT1-c-4/p21SNFT 0.005 0.16 0.51 1 -0.72 4 5
AP-1/NFAT1-c-4 -0.024 0.23 0.7 2 -0.79 8 10
IKZF1 -0.027 0.14 -10000 0 -0.46 20 20
T-helper 2 cell differentiation -0.027 0.14 -10000 0 -0.63 8 8
AP-1/NFAT1 -0.048 0.18 0.38 3 -0.43 53 56
CALM1 -0.002 0.071 -10000 0 -0.39 17 17
EGR2 -0.007 0.14 0.7 2 -0.87 1 3
EGR3 -0.008 0.13 0.73 1 -0.87 1 2
NFAT1/FOXP3 -0.014 0.15 0.46 5 -0.45 23 28
EGR1 -0.15 0.19 0.22 4 -0.39 226 230
JUN 0.01 0.043 0.22 9 -0.36 3 12
EGR4 0.007 0.009 0.22 1 -10000 0 1
mol:Ca2+ 0 0.02 0.13 12 -10000 0 12
GBP3 -0.048 0.23 0.43 21 -0.65 52 73
FOSL1 0.006 0 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 0.002 0.14 -10000 0 -0.69 4 4
DGKA -0.024 0.14 0.42 5 -0.46 20 25
CREM 0.007 0.009 0.22 1 -10000 0 1
NFAT1-c-4/PPARG 0 0.14 -10000 0 -0.72 4 4
CTLA4 -0.03 0.12 0.53 5 -0.4 19 24
NFAT1-c-4 (dimer)/EGR1 -0.088 0.18 -10000 0 -0.66 11 11
NFAT1-c-4 (dimer)/EGR4 0.001 0.15 -10000 0 -0.72 4 4
FOS -0.063 0.16 0.22 8 -0.38 110 118
IFNG -0.026 0.17 0.48 26 -0.58 11 37
T cell activation -0.03 0.14 -10000 0 -0.58 5 5
MAF 0.004 0.028 -10000 0 -0.38 3 3
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.001 0.12 1.3 1 -0.63 1 2
TNF -0.087 0.17 -10000 0 -0.64 7 7
FASLG -0.011 0.14 -10000 0 -0.94 1 1
TBX21 0.017 0.044 0.21 28 -10000 0 28
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.002 0.06 0.22 8 -0.38 11 19
PTPN1 -0.027 0.14 -10000 0 -0.46 20 20
NFAT1-c-4/ICER1 -0.001 0.14 -10000 0 -0.72 4 4
GATA3 0.007 0.013 0.22 2 -10000 0 2
T-helper 1 cell differentiation -0.024 0.17 0.48 26 -0.57 11 37
IL2RA -0.05 0.16 0.69 4 -0.59 20 24
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.023 0.15 0.43 9 -0.46 20 29
E2F1 0.009 0.016 -10000 0 -10000 0 0
PPARG 0.009 0.022 0.22 6 -10000 0 6
SLC3A2 -0.026 0.14 0.42 2 -0.46 20 22
IRF4 0.007 0.013 0.22 2 -10000 0 2
PTGS2 -0.06 0.23 0.67 3 -0.76 14 17
CSF2 -0.047 0.2 0.56 3 -0.71 8 11
JunB/Fra1/NFAT1-c-4 -0.053 0.18 -10000 0 -0.67 10 10
IL4 -0.028 0.15 -10000 0 -0.67 6 6
IL5 -0.047 0.2 0.56 3 -0.71 8 11
IL2 -0.031 0.14 -10000 0 -0.58 5 5
IL3 -0.019 0.033 -10000 0 -10000 0 0
RNF128 -0.005 0.065 0.42 7 -10000 0 7
NFATC1 -0.001 0.12 0.63 1 -1.3 1 2
CDK4 0.014 0.13 0.73 5 -10000 0 5
PTPRK -0.034 0.16 0.4 2 -0.54 28 30
IL8 -0.034 0.23 0.64 7 -0.71 8 15
POU2F1 0.007 0 -10000 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP 0.056 0.07 0.21 41 -10000 0 41
DAPP1 -0.019 0.064 -10000 0 -0.32 1 1
Src family/SYK family/BLNK-LAT/BTK-ITK 0 0.08 -10000 0 -0.31 9 9
mol:DAG 0.027 0.068 0.17 35 -0.16 3 38
HRAS 0.011 0.005 -10000 0 -10000 0 0
RAP1A 0.011 0.01 0.21 1 -10000 0 1
ARF5/GDP 0.033 0.034 0.17 2 -10000 0 2
PLCG2 0.006 0 -10000 0 -10000 0 0
PLCG1 0.009 0.022 0.22 6 -10000 0 6
ARF5 0.006 0 -10000 0 -10000 0 0
mol:GTP 0.058 0.072 0.22 41 -10000 0 41
ARF1/GTP 0.05 0.07 0.22 37 -10000 0 37
RHOA 0.005 0.023 -10000 0 -0.38 2 2
YES1 0.011 0.031 0.22 12 -10000 0 12
RAP1A/GTP 0.058 0.071 0.22 41 -10000 0 41
ADAP1 0.056 0.069 0.22 41 -10000 0 41
ARAP3 0.057 0.071 0.22 41 -10000 0 41
INPPL1 0.007 0.013 0.22 2 -10000 0 2
PREX1 0.006 0.016 -10000 0 -0.38 1 1
ARHGEF6 0.007 0.031 0.22 5 -0.38 2 7
ARHGEF7 0.007 0.009 0.22 1 -10000 0 1
ARF1 -0.02 0.098 -10000 0 -0.38 38 38
NRAS 0.094 0.1 0.21 245 -10000 0 245
FYN -0.039 0.13 0.22 1 -0.38 67 68
ARF6 0.006 0.016 -10000 0 -0.38 1 1
FGR 0.006 0 -10000 0 -10000 0 0
mol:Ca2+ 0.015 0.039 0.14 7 -10000 0 7
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.006 0.021 0.22 2 -0.38 1 3
ZAP70 0.006 0 -10000 0 -10000 0 0
mol:IP3 0.017 0.049 0.15 9 -0.12 1 10
LYN -0.007 0.07 -10000 0 -0.38 19 19
ARF1/GDP 0.027 0.044 0.17 2 -0.17 11 13
RhoA/GDP 0.052 0.056 0.22 12 -0.17 1 13
PDK1/Src/Hsp90 0.013 0 -10000 0 -10000 0 0
BLNK -0.013 0.085 -10000 0 -0.38 28 28
actin cytoskeleton reorganization 0.058 0.067 0.2 47 -10000 0 47
SRC 0.006 0 -10000 0 -10000 0 0
PLEKHA2 -0.003 0.017 0.17 2 -0.23 2 4
RAC1 0.006 0.016 -10000 0 -0.38 1 1
PTEN -0.009 0.05 -10000 0 -0.36 11 11
HSP90AA1 0.006 0 -10000 0 -10000 0 0
ARF6/GTP 0.055 0.07 0.21 41 -0.18 1 42
RhoA/GTP 0.055 0.07 0.21 41 -0.18 1 42
Src family/SYK family/BLNK-LAT -0.027 0.079 -10000 0 -0.37 9 9
BLK 0.007 0.009 0.22 1 -10000 0 1
PDPK1 0.006 0 -10000 0 -10000 0 0
CYTH1 0.056 0.069 0.22 41 -10000 0 41
HCK 0.007 0.009 0.22 1 -10000 0 1
CYTH3 0.056 0.069 0.22 41 -10000 0 41
CYTH2 0.056 0.069 0.22 41 -10000 0 41
KRAS 0.032 0.063 0.21 62 -10000 0 62
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.039 0.047 0.22 5 -10000 0 5
SGK1 0.004 0.025 0.17 11 -10000 0 11
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.031 0.036 0.18 2 -0.16 3 5
SOS1 0.014 0.04 0.22 20 -10000 0 20
SYK 0.003 0.043 0.22 3 -0.38 6 9
ARF6/GDP 0.057 0.068 0.21 41 -10000 0 41
mol:PI-3-4-5-P3 0.059 0.074 0.23 41 -10000 0 41
ARAP3/RAP1A/GTP 0.058 0.071 0.22 41 -10000 0 41
VAV1 0.008 0.018 0.22 4 -10000 0 4
mol:PI-3-4-P2 -0.001 0.012 0.2 2 -10000 0 2
RAS family/GTP/PI3K Class I 0.074 0.072 0.24 41 -10000 0 41
PLEKHA1 -0.001 0.017 0.17 6 -10000 0 6
Rac1/GDP 0.033 0.035 0.17 2 -0.17 1 3
LAT 0.006 0 -10000 0 -10000 0 0
Rac1/GTP 0.018 0.033 -10000 0 -0.25 4 4
ITK 0.058 0.073 0.22 46 -10000 0 46
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.029 0.083 0.2 32 -0.22 3 35
LCK 0.006 0 -10000 0 -10000 0 0
BTK 0.061 0.077 0.22 58 -10000 0 58
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.003 0.1 0.34 19 -0.36 1 20
CRKL 0.004 0.11 0.34 19 -0.38 1 20
HRAS 0.006 0.097 0.32 16 -10000 0 16
mol:PIP3 0.013 0.11 0.34 19 -0.28 3 22
SPRED1 0.003 0.038 0.22 1 -0.38 5 6
SPRED2 0.006 0 -10000 0 -10000 0 0
GAB1 0.005 0.11 0.37 19 -0.31 3 22
FOXO3 0.008 0.1 0.33 18 -0.32 3 21
AKT1 0.011 0.1 0.34 18 -10000 0 18
BAD 0.01 0.099 0.33 18 -10000 0 18
megakaryocyte differentiation 0.008 0.11 0.38 19 -0.28 1 20
GSK3B 0.01 0.099 0.33 18 -10000 0 18
RAF1 0.005 0.085 0.3 16 -10000 0 16
SHC1 0.006 0 -10000 0 -10000 0 0
STAT3 0.002 0.11 0.37 17 -0.3 2 19
STAT1 0.012 0.21 0.57 11 -0.55 27 38
HRAS/SPRED1 0.008 0.086 0.29 16 -0.3 1 17
cell proliferation 0.008 0.11 0.38 19 -0.28 1 20
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
TEC 0.033 0.071 0.22 71 -10000 0 71
RPS6KB1 0.012 0.11 0.36 19 -10000 0 19
HRAS/SPRED2 0.009 0.085 0.29 15 -10000 0 15
LYN/TEC/p62DOK 0.012 0.097 -10000 0 -0.29 4 4
MAPK3 -0.038 0.089 0.24 10 -0.26 28 38
STAP1 0.007 0.11 0.37 19 -0.28 1 20
GRAP2 0.006 0 -10000 0 -10000 0 0
JAK2 -0.001 0.19 0.54 11 -0.46 20 31
STAT1 (dimer) 0.012 0.21 0.57 11 -0.54 27 38
mol:Gleevec -0.001 0.008 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.005 0.093 -10000 0 -0.33 5 5
actin filament polymerization 0.008 0.11 0.36 19 -0.27 2 21
LYN -0.007 0.07 -10000 0 -0.38 19 19
STAP1/STAT5A (dimer) 0.001 0.15 0.41 18 -0.52 4 22
PIK3R1 -0.038 0.12 -10000 0 -0.39 64 64
CBL/CRKL/GRB2 0.005 0.096 0.29 16 -0.35 1 17
PI3K 0.017 0.13 0.34 10 -0.38 7 17
PTEN -0.001 0.054 -10000 0 -0.38 11 11
SCF/KIT/EPO/EPOR 0.01 0.2 0.69 2 -10000 0 2
MAPK8 0.007 0.11 0.38 19 -0.28 2 21
STAT3 (dimer) 0.002 0.11 0.37 17 -0.3 2 19
positive regulation of transcription -0.03 0.076 0.23 10 -0.24 14 24
mol:GDP 0.006 0.1 0.32 16 -0.32 2 18
PIK3C2B 0.007 0.11 0.37 19 -0.28 1 20
CBL/CRKL 0.006 0.1 0.32 19 -0.36 1 20
FER 0.007 0.11 0.37 19 -0.28 2 21
SH2B3 0.006 0.11 0.37 19 -0.28 1 20
PDPK1 0.012 0.1 0.32 19 -0.27 3 22
SNAI2 0 0.12 0.37 18 -0.36 6 24
positive regulation of cell proliferation 0.006 0.18 0.47 17 -0.43 23 40
KITLG 0.01 0.026 0.23 3 -10000 0 3
cell motility 0.006 0.18 0.47 17 -0.43 23 40
PTPN6 0.001 0.014 -10000 0 -10000 0 0
EPOR 0 0.14 0.62 4 -0.64 8 12
STAT5A (dimer) 0.003 0.16 0.43 18 -0.54 4 22
SOCS1 -0.013 0.085 -10000 0 -0.38 28 28
cell migration -0.007 0.11 0.28 1 -0.36 19 20
SOS1 0.014 0.04 0.22 20 -10000 0 20
EPO 0.007 0.013 -10000 0 -10000 0 0
VAV1 0.008 0.018 0.22 4 -10000 0 4
GRB10 0.007 0.11 0.37 19 -0.28 1 20
PTPN11 0.001 0.011 -10000 0 -10000 0 0
SCF/KIT 0.009 0.12 0.4 19 -0.29 2 21
GO:0007205 -0.001 0.01 -10000 0 -10000 0 0
MAP2K1 0.005 0.074 0.27 16 -10000 0 16
CBL 0.006 0 -10000 0 -10000 0 0
KIT 0.009 0.16 0.57 18 -0.58 7 25
MAP2K2 -0.047 0.096 0.26 10 -0.26 29 39
SHC/Grb2/SOS1 0.006 0.088 -10000 0 -0.27 1 1
STAT5A 0.002 0.16 0.44 18 -0.55 4 22
GRB2 0.006 0.016 -10000 0 -0.38 1 1
response to radiation 0 0.12 0.37 18 -0.35 6 24
SHC/GRAP2 0.009 0 -10000 0 -10000 0 0
PTPRO 0.007 0.11 0.38 19 -0.28 1 20
SH2B2 0.007 0.11 0.37 19 -0.27 2 21
DOK1 0.006 0.016 -10000 0 -0.38 1 1
MATK 0.006 0.11 0.37 19 -0.28 1 20
CREBBP 0.001 0.082 0.28 20 -0.4 8 28
BCL2 -0.12 0.41 0.81 2 -1.1 79 81
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.006 0 -10000 0 -10000 0 0
SPHK1 0.007 0.009 0.22 1 -10000 0 1
GNAI2 0.006 0 -10000 0 -10000 0 0
mol:S1P 0.004 0.015 -10000 0 -10000 0 0
GNAO1 0.006 0.036 0.22 6 -0.38 3 9
mol:Sphinganine-1-P -0.004 0.008 0.2 1 -10000 0 1
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.01 0.012 -10000 0 -0.19 1 1
GNAI3 0.017 0.047 0.22 29 -10000 0 29
G12/G13 0.009 0.012 -10000 0 -0.27 1 1
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 -0.003 0.058 -10000 0 -0.38 13 13
S1P1/S1P 0.003 0.035 -10000 0 -0.22 13 13
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 0 0.063 0.22 7 -0.38 13 20
S1P/S1P5/G12 0.006 0.001 -10000 0 -10000 0 0
S1P/S1P3/Gq -0.072 0.12 -10000 0 -0.22 198 198
S1P/S1P4/Gi 0.004 0.045 0.18 1 -0.19 20 21
GNAQ -0.005 0.065 -10000 0 -0.38 16 16
GNAZ 0.002 0.04 -10000 0 -0.38 6 6
GNA14 0.006 0.026 0.22 2 -0.38 2 4
GNA15 0.003 0.037 -10000 0 -0.38 5 5
GNA12 0.006 0 -10000 0 -10000 0 0
GNA13 0.006 0.016 -10000 0 -0.38 1 1
GNA11 -0.13 0.18 -10000 0 -0.38 193 193
ABCC1 0.009 0.022 0.22 6 -10000 0 6
IL27-mediated 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
TGFB1 -0.08 0.16 -10000 0 -0.38 127 127
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response -0.007 0.093 0.51 4 -0.4 2 6
IL27/IL27R/JAK1 0.012 0.099 0.51 1 -0.99 2 3
TBX21 0.047 0.11 0.47 5 -0.59 2 7
IL12B 0.009 0.01 -10000 0 -10000 0 0
IL12A 0.012 0.051 0.2 37 -0.27 1 38
IL6ST -0.011 0.087 -10000 0 -0.39 28 28
IL27RA/JAK1 0.004 0.073 -10000 0 -1.1 2 2
IL27 0.008 0.012 -10000 0 -10000 0 0
TYK2 0.01 0.02 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.074 0.14 -10000 0 -0.55 18 18
T-helper 2 cell differentiation -0.007 0.093 0.51 4 -0.4 2 6
T cell proliferation during immune response -0.007 0.093 0.51 4 -0.4 2 6
MAPKKK cascade 0.007 0.093 0.4 2 -0.51 4 6
STAT3 -0.002 0.056 -10000 0 -0.38 12 12
STAT2 0.031 0.068 0.22 64 -10000 0 64
STAT1 0.12 0.11 0.22 297 -10000 0 297
IL12RB1 0.007 0.005 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.05 0.12 0.5 9 -0.59 2 11
IL27/IL27R/JAK2/TYK2 0.006 0.094 0.4 2 -0.52 4 6
positive regulation of T cell mediated cytotoxicity 0.007 0.093 0.4 2 -0.51 4 6
STAT1 (dimer) 0.053 0.11 0.51 3 -0.84 2 5
JAK2 0.007 0.039 0.25 2 -0.39 4 6
JAK1 0.004 0.028 -10000 0 -0.39 3 3
STAT2 (dimer) 0.024 0.1 0.41 8 -0.46 4 12
T cell proliferation -0.01 0.1 0.44 2 -0.51 6 8
IL12/IL12R/TYK2/JAK2 0.034 0.082 0.44 5 -10000 0 5
IL17A -0.074 0.14 -10000 0 -0.55 18 18
mast cell activation -0.007 0.093 0.51 4 -0.4 2 6
IFNG 0.011 0.048 0.21 28 -10000 0 28
T cell differentiation 0 0.005 0.022 26 -0.024 2 28
STAT3 (dimer) 0.005 0.092 0.35 2 -0.46 7 9
STAT5A (dimer) 0.006 0.089 0.35 2 -0.49 4 6
STAT4 (dimer) 0.009 0.085 0.35 2 -0.46 4 6
STAT4 0.007 0.013 0.22 2 -10000 0 2
T cell activation -0.001 0.013 0.12 2 -0.19 2 4
IL27R/JAK2/TYK2 0.01 0.1 0.4 2 -1 2 4
GATA3 -0.001 0.036 -10000 0 -10000 0 0
IL18 0.035 0.077 0.2 103 -10000 0 103
positive regulation of mast cell cytokine production 0.005 0.091 0.35 2 -0.46 7 9
IL27/EBI3 0.013 0.021 0.16 1 -10000 0 1
IL27RA 0.002 0.078 -10000 0 -1.2 2 2
IL6 -0.023 0.11 0.22 4 -0.38 46 50
STAT5A 0 0.049 -10000 0 -0.38 9 9
monocyte differentiation 0.001 0.003 0.015 3 -10000 0 3
IL2 -0.003 0.042 0.46 2 -0.42 2 4
IL1B 0.012 0.05 0.2 38 -10000 0 38
EBI3 0.008 0.012 -10000 0 -10000 0 0
TNF -0.001 0.009 0.2 1 -10000 0 1
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.008 0.018 0.22 4 -10000 0 4
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.006 0 -10000 0 -10000 0 0
TCEB1 0.006 0 -10000 0 -10000 0 0
HIF1A/p53 -0.017 0.066 -10000 0 -0.23 6 6
HIF1A -0.001 0.024 -10000 0 -0.19 3 3
COPS5 0.02 0.053 0.22 37 -10000 0 37
VHL/Elongin B/Elongin C/RBX1/CUL2 0.03 0.037 -10000 0 -0.19 1 1
FIH (dimer) 0.006 0 -10000 0 -10000 0 0
CDKN2A 0.13 0.11 0.22 317 -10000 0 317
ARNT/IPAS 0.009 0.001 -10000 0 -10000 0 0
HIF1AN 0.006 0 -10000 0 -10000 0 0
GNB2L1 0.006 0 -10000 0 -10000 0 0
HIF1A/ARNT 0.005 0.026 -10000 0 -10000 0 0
CUL2 0.026 0.066 0.22 55 -0.38 1 56
OS9 0.006 0.016 -10000 0 -0.38 1 1
RACK1/Elongin B/Elongin C 0.013 0 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.005 0.026 -10000 0 -10000 0 0
PHD1-3/OS9 0.013 0.056 -10000 0 -0.2 26 26
HIF1A/RACK1/Elongin B/Elongin C 0.011 0.025 -10000 0 -10000 0 0
VHL 0.007 0.016 0.22 3 -10000 0 3
HSP90AA1 0.006 0 -10000 0 -10000 0 0
HIF1A/JAB1 0.014 0.044 0.2 8 -10000 0 8
EGLN3 0 0.096 0.22 30 -0.38 25 55
EGLN2 0.006 0 -10000 0 -10000 0 0
EGLN1 0.006 0 -10000 0 -10000 0 0
TP53 -0.045 0.13 0.22 3 -0.38 76 79
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.018 0.032 -10000 0 -10000 0 0
ARNT 0.007 0.009 0.22 1 -10000 0 1
ARD1A 0.01 0.03 0.22 11 -10000 0 11
RBX1 0.006 0 -10000 0 -10000 0 0
HIF1A/p19ARF 0.079 0.071 0.2 19 -10000 0 19
ErbB2/ErbB3 signaling events

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
USP8 -0.002 0.015 0.17 4 -10000 0 4
RAS family/GTP 0.058 0.097 0.3 33 -0.22 1 34
NFATC4 -0.013 0.047 0.19 1 -0.27 1 2
ERBB2IP 0.004 0.023 -10000 0 -0.38 2 2
HSP90 (dimer) 0.006 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.01 0.065 0.28 7 -0.23 6 13
JUN 0.001 0.096 0.38 18 -10000 0 18
HRAS 0.005 0.005 -10000 0 -10000 0 0
DOCK7 -0.006 0.064 0.23 8 -0.33 1 9
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.002 0.058 0.19 2 -0.2 32 34
AKT1 -0.002 0.009 0.2 1 -10000 0 1
BAD -0.003 0.007 0.17 1 -10000 0 1
MAPK10 -0.009 0.041 0.17 2 -0.16 5 7
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.011 0.07 0.3 7 -0.26 4 11
RAF1 0.053 0.11 0.37 29 -10000 0 29
ErbB2/ErbB3/neuregulin 2 -0.002 0.058 0.15 10 -0.21 32 42
STAT3 -0.012 0.13 -10000 0 -0.92 12 12
cell migration -0.006 0.044 0.17 6 -0.17 1 7
mol:PI-3-4-5-P3 0 0.001 -10000 0 -10000 0 0
cell proliferation -0.042 0.21 0.57 25 -0.5 14 39
FOS -0.063 0.24 0.53 28 -0.46 110 138
NRAS 0.099 0.11 0.22 245 -10000 0 245
mol:Ca2+ -0.01 0.065 0.28 7 -0.23 6 13
MAPK3 -0.046 0.2 0.52 25 -0.52 26 51
MAPK1 -0.017 0.18 0.51 26 -0.46 5 31
JAK2 -0.015 0.057 0.19 5 -0.25 3 8
NF2 0 0.013 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.003 0.058 -10000 0 -0.22 28 28
NRG1 0.005 0.011 0.23 1 -10000 0 1
GRB2/SOS1 0.009 0.012 -10000 0 -0.27 1 1
MAPK8 -0.01 0.065 0.24 6 -0.24 25 31
MAPK9 -0.007 0.039 0.16 5 -0.18 1 6
ERBB2 -0.004 0.035 0.23 7 -0.27 4 11
ERBB3 -0.011 0.092 0.22 10 -0.39 29 39
SHC1 0.005 0.004 -10000 0 -10000 0 0
RAC1 0.006 0.016 -10000 0 -0.38 1 1
apoptosis 0.003 0.011 -10000 0 -0.19 1 1
STAT3 (dimer) -0.012 0.13 -10000 0 -0.9 12 12
RNF41 -0.003 0.016 0.15 6 -10000 0 6
FRAP1 -0.003 0.007 0.17 1 -10000 0 1
RAC1-CDC42/GTP -0.018 0.034 -10000 0 -0.17 8 8
ErbB2/ErbB2/HSP90 (dimer) -0.005 0.027 0.16 7 -0.23 4 11
CHRNA1 -0.012 0.17 0.53 28 -0.38 1 29
myelination -0.014 0.046 0.19 1 -0.27 1 2
PPP3CB -0.014 0.052 0.18 5 -0.31 1 6
KRAS 0.029 0.068 0.22 62 -10000 0 62
RAC1-CDC42/GDP 0.002 0.052 -10000 0 -0.2 27 27
NRG2 0.006 0 -10000 0 -10000 0 0
mol:GDP -0.003 0.057 -10000 0 -0.22 28 28
SOS1 0.014 0.04 0.22 20 -10000 0 20
MAP2K2 0.004 0.12 0.38 22 -0.32 5 27
SRC 0.006 0 -10000 0 -10000 0 0
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 -0.014 0.054 0.2 2 -0.33 1 3
MAP2K1 0.032 0.16 0.5 26 -0.41 2 28
heart morphogenesis -0.01 0.065 0.28 7 -0.23 6 13
RAS family/GDP 0.076 0.095 0.27 45 -0.21 2 47
GRB2 0.005 0.017 -10000 0 -0.39 1 1
PRKACA 0.002 0.006 -10000 0 -10000 0 0
CHRNE 0.003 0.033 0.28 4 -10000 0 4
HSP90AA1 0.006 0 -10000 0 -10000 0 0
activation of caspase activity 0.002 0.009 -10000 0 -0.2 1 1
nervous system development -0.01 0.065 0.28 7 -0.23 6 13
CDC42 0.006 0 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.013 0.073 -10000 0 -0.4 18 18
KLHL20 -0.044 0.077 0.32 1 -0.29 9 10
CYFIP2 -0.001 0.051 -10000 0 -0.38 10 10
Rac1/GDP -0.015 0.05 -10000 0 -0.25 19 19
ENAH -0.014 0.074 -10000 0 -0.41 17 17
AP1M1 0.007 0.016 0.22 3 -10000 0 3
RAP1B 0.007 0.026 0.22 5 -0.38 1 6
RAP1A 0.007 0.009 0.22 1 -10000 0 1
CTNNB1 0.006 0.009 0.22 1 -10000 0 1
CDC42/GTP -0.018 0.035 -10000 0 -0.21 6 6
ABI1/Sra1/Nap1 -0.035 0.051 -10000 0 -0.15 21 21
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.008 0.045 -10000 0 -0.21 21 21
RAPGEF1 -0.016 0.064 -10000 0 -0.36 17 17
CTNND1 0.006 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.011 0.075 -10000 0 -0.4 19 19
CRK -0.015 0.069 -10000 0 -0.39 17 17
E-cadherin/gamma catenin/alpha catenin -0.002 0.06 -10000 0 -0.25 31 31
alphaE/beta7 Integrin 0.007 0.026 -10000 0 -0.27 5 5
IQGAP1 0.005 0.025 0.22 1 -0.38 2 3
NCKAP1 0.01 0.028 0.22 10 -10000 0 10
Rap1/GTP/I-afadin 0.006 0.041 0.14 6 -0.2 19 25
DLG1 -0.003 0.082 -10000 0 -0.39 19 19
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.023 0.04 -10000 0 -0.17 10 10
MLLT4 -0.006 0.068 -10000 0 -0.38 18 18
ARF6/GTP/NME1/Tiam1 0.018 0.033 0.14 33 -0.2 2 35
PI3K -0.029 0.05 -10000 0 -0.22 10 10
ARF6 0.005 0.016 -10000 0 -0.38 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin -0.006 0.068 -10000 0 -0.29 29 29
TIAM1 0.006 0.021 0.22 2 -0.38 1 3
E-cadherin(dimer)/Ca2+ 0.007 0.037 -10000 0 -0.19 19 19
AKT1 -0.018 0.031 -10000 0 -0.15 4 4
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
CDH1 -0.006 0.067 -10000 0 -0.38 17 17
RhoA/GDP -0.013 0.05 -10000 0 -0.25 19 19
actin cytoskeleton organization -0.032 0.058 0.27 1 -0.22 7 8
CDC42/GDP -0.012 0.049 -10000 0 -0.25 19 19
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.009 0.054 -10000 0 -0.23 31 31
ITGB7 0.003 0.038 0.22 1 -0.38 5 6
RAC1 0.005 0.016 -10000 0 -0.38 1 1
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.008 0.04 -10000 0 -0.2 19 19
E-cadherin/Ca2+/beta catenin/alpha catenin 0.004 0.037 0.13 1 -0.19 19 20
mol:GDP -0.016 0.055 -10000 0 -0.29 19 19
CDC42/GTP/IQGAP1 0.008 0.014 -10000 0 -0.22 2 2
JUP -0.004 0.063 -10000 0 -0.38 15 15
p120 catenin/RhoA/GDP -0.012 0.051 -10000 0 -0.26 18 18
RAC1/GTP/IQGAP1 0.007 0.017 -10000 0 -0.22 3 3
PIP5K1C/AP1M1 0.009 0.001 -10000 0 -10000 0 0
RHOA 0.005 0.023 -10000 0 -0.38 2 2
CDC42 0.006 0 -10000 0 -10000 0 0
CTNNA1 0.005 0.023 -10000 0 -0.38 2 2
positive regulation of S phase of mitotic cell cycle -0.046 0.081 0.37 1 -0.18 144 145
NME1 0.018 0.049 0.22 31 -10000 0 31
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.013 0.073 -10000 0 -0.41 17 17
regulation of cell-cell adhesion -0.016 0.031 -10000 0 -0.19 6 6
WASF2 -0.038 0.045 -10000 0 -0.13 47 47
Rap1/GTP -0.017 0.041 -10000 0 -0.24 6 6
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.004 0.058 -10000 0 -0.21 35 35
CCND1 -0.057 0.1 0.41 1 -0.22 145 146
VAV2 -0.019 0.088 -10000 0 -0.45 20 20
RAP1/GDP -0.011 0.046 -10000 0 -0.22 18 18
adherens junction assembly -0.013 0.071 -10000 0 -0.4 17 17
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.007 0.009 0.22 1 -10000 0 1
PIP5K1C 0.006 0 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0 0.055 -10000 0 -0.26 9 9
E-cadherin/beta catenin -0.006 0.051 -10000 0 -0.29 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.014 0.073 -10000 0 -0.39 19 19
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
Rac1/GTP -0.068 0.12 0.42 1 -0.37 20 21
E-cadherin/beta catenin/alpha catenin 0.004 0.043 -10000 0 -0.23 19 19
ITGAE 0.006 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.012 0.076 -10000 0 -0.41 19 19
Canonical NF-kappaB pathway

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
FBXW11 0.004 0.015 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.032 0.07 0.23 4 -0.31 2 6
ERC1 0.008 0.029 0.22 7 -0.38 1 8
RIP2/NOD2 0.007 0.004 -10000 0 -10000 0 0
NFKBIA -0.023 0.08 -10000 0 -0.47 16 16
BIRC2 0.037 0.075 0.22 81 -10000 0 81
IKBKB 0.007 0.016 0.22 3 -10000 0 3
RIPK2 0.065 0.096 0.22 156 -10000 0 156
IKBKG 0.039 0.053 0.2 1 -10000 0 1
IKK complex/A20 0.03 0.051 0.26 1 -10000 0 1
NEMO/A20/RIP2 0.065 0.096 0.22 156 -10000 0 156
XPO1 0.026 0.062 0.22 52 -10000 0 52
NEMO/ATM 0.051 0.064 0.26 22 -10000 0 22
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.006 0 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.008 0.002 -10000 0 -10000 0 0
IKK complex/ELKS 0.007 0.009 -10000 0 -10000 0 0
BCL10/MALT1/TRAF6 0.012 0.003 -10000 0 -10000 0 0
NOD2 0.007 0.009 0.22 1 -10000 0 1
NFKB1 -0.004 0.059 -10000 0 -0.41 11 11
RELA 0.002 0.028 -10000 0 -0.39 2 2
MALT1 0.017 0.047 0.22 29 -10000 0 29
cIAP1/UbcH5C 0.008 0.003 -10000 0 -10000 0 0
ATM 0.014 0.04 0.22 20 -10000 0 20
TNF/TNFR1A -0.003 0.057 -10000 0 -0.27 25 25
TRAF6 0.007 0.013 0.22 2 -10000 0 2
PRKCA 0.005 0.044 0.22 7 -0.38 5 12
CHUK 0.011 0.031 0.22 12 -10000 0 12
UBE2D3 0.006 0 -10000 0 -10000 0 0
TNF 0.007 0.009 0.22 1 -10000 0 1
NF kappa B1 p50/RelA 0.002 0.059 -10000 0 -0.26 26 26
BCL10 0.006 0 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.023 0.08 -10000 0 -0.46 16 16
beta TrCP1/SCF ubiquitin ligase complex 0.004 0.016 -10000 0 -10000 0 0
TNFRSF1A -0.011 0.08 -10000 0 -0.38 25 25
IKK complex 0.049 0.053 0.23 8 -10000 0 8
CYLD 0.006 0 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.04 0.045 0.28 1 -10000 0 1
Noncanonical Wnt 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
NFATC2 -0.003 0.058 -10000 0 -0.38 13 13
GNB1/GNG2 0.035 0.054 0.19 19 -10000 0 19
mol:DAG 0.027 0.054 0.18 20 -10000 0 20
PLCG1 0.028 0.055 0.18 20 -10000 0 20
YES1 0.032 0.062 0.21 22 -0.2 7 29
FZD3 0.031 0.08 0.22 72 -0.38 4 76
FZD6 0.022 0.06 0.22 43 -0.38 1 44
G protein 0.032 0.053 -10000 0 -10000 0 0
MAP3K7 0.021 0.054 0.18 21 -10000 0 21
mol:Ca2+ 0.027 0.053 0.18 20 -10000 0 20
mol:IP3 0.027 0.054 0.18 20 -10000 0 20
NLK 0.011 0.012 -10000 0 -10000 0 0
GNB1 0.006 0.016 -10000 0 -0.38 1 1
CAMK2A 0.021 0.053 0.17 20 -10000 0 20
MAP3K7IP1 0.006 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD 0.034 0.061 0.22 19 -0.21 7 26
CSNK1A1 0.007 0.009 0.22 1 -10000 0 1
GNAS 0.029 0.058 0.2 19 -0.2 7 26
GO:0007205 0.023 0.055 0.18 20 -10000 0 20
WNT6 0.006 0.016 -10000 0 -0.38 1 1
WNT4 0.006 0 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.031 0.06 0.2 3 -0.34 1 4
GNG2 0.004 0.034 0.22 1 -0.38 4 5
WNT5A 0.006 0.029 0.22 4 -0.38 2 6
WNT11 0.026 0.062 0.22 52 -10000 0 52
CDC42 0.028 0.059 0.2 22 -10000 0 22
Atypical NF-kappaB pathway

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
BCL3/RelA -0.002 0.058 -10000 0 -0.29 21 21
FBXW11 0.006 0 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.002 0.034 -10000 0 -0.23 11 11
NF kappa B1 p50/RelA/I kappa B alpha -0.003 0.048 -10000 0 -0.35 4 4
NFKBIA -0.005 0.039 -10000 0 -0.2 20 20
MAPK14 0.007 0.009 0.22 1 -10000 0 1
NF kappa B1 p105/p50 0.002 0.034 -10000 0 -0.23 11 11
ARRB2 0.003 0.006 0.15 1 -10000 0 1
REL 0.006 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.006 0.055 -10000 0 -0.23 32 32
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.002 0.036 -10000 0 -0.23 13 13
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
NF kappa B1 p50 dimer -0.008 0.039 0.18 3 -0.27 11 14
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
NFKB1 -0.008 0.04 0.2 3 -0.27 11 14
RELA 0.005 0.023 -10000 0 -0.38 2 2
positive regulation of anti-apoptosis -0.001 0.029 -10000 0 -0.18 8 8
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.002 0.047 -10000 0 -0.34 4 4
SRC 0.006 0 -10000 0 -10000 0 0
PI3K -0.022 0.083 -10000 0 -0.27 56 56
NF kappa B1 p50/RelA -0.001 0.029 -10000 0 -0.18 8 8
IKBKB 0.007 0.016 0.22 3 -10000 0 3
beta TrCP1/SCF ubiquitin ligase complex 0.006 0 -10000 0 -10000 0 0
SYK 0.003 0.043 0.22 3 -0.38 6 9
I kappa B alpha/PIK3R1 -0.022 0.071 -10000 0 -0.19 81 81
cell death -0.002 0.046 -10000 0 -0.33 4 4
NF kappa B1 p105/c-Rel 0.002 0.034 -10000 0 -0.23 11 11
LCK 0.006 0 -10000 0 -10000 0 0
BCL3 -0.008 0.074 -10000 0 -0.38 21 21
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.01 0.047 0.25 2 -0.22 18 20
NFATC2 -0.015 0.057 0.25 2 -0.23 28 30
NFATC3 -0.01 0.046 0.25 2 -0.22 17 19
CD40LG -0.055 0.13 0.69 2 -0.5 2 4
PTGS2 -0.068 0.17 0.55 7 -0.55 19 26
JUNB -0.097 0.17 -10000 0 -0.38 151 151
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.007 0.047 -10000 0 -0.26 18 18
CaM/Ca2+ -0.007 0.047 -10000 0 -0.26 18 18
CALM1 -0.007 0.068 -10000 0 -0.38 18 18
JUN 0.007 0.041 0.22 9 -0.39 3 12
mol:Ca2+ -0.001 0.008 0.074 2 -10000 0 2
Calcineurin A alpha-beta B1/FKBP12/FK506 0.004 0.005 -10000 0 -10000 0 0
FOSL1 0.006 0 -10000 0 -10000 0 0
CREM 0.007 0.009 0.22 1 -10000 0 1
Jun/NFAT1-c-4/p21SNFT -0.031 0.055 -10000 0 -0.29 4 4
FOS -0.066 0.16 0.22 8 -0.38 110 118
IFNG -0.05 0.14 0.55 13 -0.5 2 15
AP-1/NFAT1-c-4 -0.032 0.15 -10000 0 -0.43 19 19
FASLG -0.055 0.13 0.69 2 -0.5 2 4
NFAT1-c-4/ICER1 -0.019 0.062 -10000 0 -0.26 4 4
IL2RA -0.054 0.14 0.72 3 -0.5 2 5
FKBP12/FK506 0.005 0 -10000 0 -10000 0 0
CSF2 -0.055 0.13 0.69 2 -0.5 2 4
JunB/Fra1/NFAT1-c-4 -0.064 0.1 -10000 0 -0.3 36 36
IL4 -0.055 0.13 0.69 2 -0.5 2 4
IL2 -0.002 0.009 -10000 0 -10000 0 0
IL3 -0.005 0.015 -10000 0 -10000 0 0
FKBP1A 0.006 0 -10000 0 -10000 0 0
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.007 0 -10000 0 -10000 0 0
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.008 0.067 -10000 0 -0.29 18 18
IKBKB 0.004 0.047 0.19 1 -0.22 2 3
AKT1 -0.019 0.069 0.18 7 -0.19 16 23
IKBKG 0.001 0.041 -10000 0 -0.19 1 1
CALM1 -0.016 0.07 -10000 0 -0.27 25 25
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
MAP3K1 -0.008 0.09 -10000 0 -0.41 17 17
MAP3K7 0.01 0.028 0.22 10 -10000 0 10
mol:Ca2+ -0.01 0.065 -10000 0 -0.28 21 21
DOK1 0.006 0.016 -10000 0 -0.38 1 1
AP-1 -0.023 0.059 0.17 4 -0.2 20 24
LYN -0.007 0.07 -10000 0 -0.38 19 19
BLNK -0.013 0.085 -10000 0 -0.38 28 28
SHC1 0.006 0 -10000 0 -10000 0 0
BCR complex 0.009 0.001 -10000 0 -10000 0 0
CD22 -0.055 0.11 0.2 2 -0.41 23 25
CAMK2G -0.016 0.066 -10000 0 -0.26 25 25
CSNK2A1 0.006 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.023 0.055 -10000 0 -0.21 43 43
GO:0007205 -0.01 0.066 -10000 0 -0.28 21 21
SYK 0.003 0.043 0.22 3 -0.38 6 9
ELK1 -0.01 0.063 -10000 0 -0.27 21 21
NFATC1 -0.012 0.074 0.2 1 -0.31 21 22
B-cell antigen/BCR complex 0.009 0.001 -10000 0 -10000 0 0
PAG1/CSK 0.009 0.001 -10000 0 -10000 0 0
NFKBIB 0.002 0.025 -10000 0 -0.13 13 13
HRAS -0.011 0.061 -10000 0 -0.27 19 19
NFKBIA 0.003 0.023 -10000 0 -0.13 10 10
NF-kappa-B/RelA/I kappa B beta 0.003 0.026 -10000 0 -0.14 13 13
RasGAP/Csk 0.025 0.035 -10000 0 -0.19 4 4
mol:GDP -0.01 0.063 -10000 0 -0.27 21 21
PTEN -0.001 0.054 -10000 0 -0.38 11 11
CD79B 0.006 0 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha 0.003 0.025 -10000 0 -0.13 13 13
GRB2 0.006 0.016 -10000 0 -0.38 1 1
PI3K/BCAP/CD19 -0.044 0.13 -10000 0 -0.37 47 47
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
mol:IP3 -0.01 0.066 -10000 0 -0.29 21 21
CSK 0.006 0 -10000 0 -10000 0 0
FOS -0.041 0.094 -10000 0 -0.3 32 32
CHUK 0.003 0.044 -10000 0 -0.19 2 2
IBTK 0.009 0.024 0.22 7 -10000 0 7
CARD11/BCL10/MALT1/TAK1 0.004 0.063 -10000 0 -0.24 19 19
PTPN6 -0.052 0.11 0.21 3 -0.4 23 26
RELA 0.005 0.023 -10000 0 -0.39 2 2
BCL2A1 0.002 0.021 0.1 1 -0.13 3 4
VAV2 -0.013 0.096 0.24 1 -0.42 21 22
ubiquitin-dependent protein catabolic process 0.002 0.025 -10000 0 -0.13 13 13
BTK 0.009 0.029 -10000 0 -10000 0 0
CD19 -0.015 0.089 0.2 2 -0.42 19 21
MAP4K1 0.007 0.013 0.22 2 -10000 0 2
CD72 0.006 0 -10000 0 -10000 0 0
PAG1 0.007 0.013 0.22 2 -10000 0 2
MAPK14 -0.007 0.08 -10000 0 -0.35 17 17
SH3BP5 0.004 0.028 -10000 0 -0.38 3 3
PIK3AP1 -0.011 0.071 -10000 0 -0.32 21 21
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.011 0.08 -10000 0 -0.33 25 25
RAF1 -0.012 0.058 -10000 0 -0.25 19 19
RasGAP/p62DOK/SHIP 0.013 0.019 -10000 0 -0.18 5 5
CD79A 0.009 0.024 0.22 7 -10000 0 7
re-entry into mitotic cell cycle -0.023 0.058 0.17 4 -0.19 23 27
RASA1 0.004 0.028 -10000 0 -0.38 3 3
MAPK3 -0.026 0.067 -10000 0 -0.29 12 12
MAPK1 -0.012 0.051 -10000 0 -0.28 7 7
CD72/SHP1 -0.049 0.11 0.23 1 -0.38 22 23
NFKB1 -0.001 0.054 -10000 0 -0.39 11 11
MAPK8 -0.007 0.078 -10000 0 -0.34 17 17
actin cytoskeleton organization -0.012 0.086 0.22 1 -0.37 21 22
NF-kappa-B/RelA 0.004 0.058 -10000 0 -0.25 16 16
Calcineurin -0.009 0.065 -10000 0 -0.24 25 25
PI3K -0.057 0.09 -10000 0 -0.28 44 44
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.012 0.073 -10000 0 -0.33 21 21
SOS1 0.014 0.04 0.22 20 -10000 0 20
Bam32/HPK1 -0.004 0.1 -10000 0 -0.49 17 17
DAPP1 -0.011 0.11 -10000 0 -0.55 17 17
cytokine secretion -0.011 0.07 0.2 1 -0.3 21 22
mol:DAG -0.01 0.066 -10000 0 -0.29 21 21
PLCG2 0.006 0 -10000 0 -10000 0 0
MAP2K1 -0.012 0.055 -10000 0 -0.3 8 8
B-cell antigen/BCR complex/FcgammaRIIB 0.012 0.011 -10000 0 -0.23 1 1
mol:PI-3-4-5-P3 -0.036 0.078 0.2 5 -0.23 28 33
ETS1 -0.015 0.064 -10000 0 -0.25 25 25
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.002 0.07 -10000 0 -0.22 46 46
B-cell antigen/BCR complex/LYN -0.013 0.094 0.21 2 -0.44 19 21
MALT1 0.017 0.047 0.22 29 -10000 0 29
TRAF6 0.007 0.013 0.22 2 -10000 0 2
RAC1 -0.014 0.091 0.23 1 -0.39 21 22
B-cell antigen/BCR complex/LYN/SYK -0.05 0.099 -10000 0 -0.34 24 24
CARD11 -0.01 0.063 -10000 0 -0.27 21 21
FCGR2B 0.019 0.055 0.22 36 -0.38 1 37
PPP3CA 0.004 0.033 -10000 0 -0.38 4 4
BCL10 0.006 0 -10000 0 -10000 0 0
IKK complex 0.005 0.025 0.11 4 -10000 0 4
PTPRC -0.006 0.13 0.22 49 -0.38 45 94
PDPK1 -0.021 0.064 0.16 7 -0.17 19 26
PPP3CB 0.006 0 -10000 0 -10000 0 0
PPP3CC 0.006 0 -10000 0 -10000 0 0
POU2F2 0.001 0.019 -10000 0 -0.13 3 3
Arf6 downstream pathway

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
PLAUR -0.001 0.096 0.51 13 -10000 0 13
regulation of axonogenesis -0.021 0.047 0.34 1 -0.17 17 18
myoblast fusion -0.002 0.052 0.33 1 -0.29 13 14
mol:GTP 0.011 0.03 0.18 13 -0.33 1 14
regulation of calcium-dependent cell-cell adhesion -0.012 0.039 0.21 2 -0.24 13 15
ARF1/GTP -0.006 0.063 -10000 0 -0.24 37 37
mol:GM1 0.006 0.027 0.17 13 -0.26 1 14
mol:Choline 0.012 0.045 0.16 49 -0.22 1 50
lamellipodium assembly 0.001 0.053 0.29 13 -0.42 1 14
MAPK3 -0.01 0.088 0.33 13 -0.24 52 65
ARF6/GTP/NME1/Tiam1 0.013 0.039 0.24 13 -0.21 2 15
ARF1 -0.02 0.098 -10000 0 -0.38 38 38
ARF6/GDP 0.002 0.052 0.29 13 -0.33 1 14
ARF1/GDP -0.01 0.068 0.25 11 -0.22 37 48
ARF6 0.011 0.026 -10000 0 -0.49 1 1
RAB11A 0.006 0 -10000 0 -10000 0 0
TIAM1 0.005 0.023 0.22 2 -0.39 1 3
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.013 0.051 0.32 14 -0.24 2 16
actin filament bundle formation 0.003 0.028 0.23 3 -10000 0 3
KALRN -0.003 0.025 0.18 1 -0.3 1 2
RAB11FIP3/RAB11A 0.009 0 -10000 0 -10000 0 0
RhoA/GDP -0.003 0.028 -10000 0 -0.23 3 3
NME1 0.016 0.05 0.22 31 -10000 0 31
Rac1/GDP -0.002 0.027 -10000 0 -0.25 2 2
substrate adhesion-dependent cell spreading 0.011 0.03 0.18 13 -0.33 1 14
cortical actin cytoskeleton organization 0.001 0.053 0.29 13 -0.42 1 14
RAC1 0.006 0.016 -10000 0 -0.38 1 1
liver development 0.011 0.03 0.18 13 -0.33 1 14
ARF6/GTP 0.011 0.03 0.18 13 -0.33 1 14
RhoA/GTP 0.009 0.02 -10000 0 -0.25 3 3
mol:GDP 0.004 0.057 0.34 13 -0.33 1 14
ARF6/GTP/RAB11FIP3/RAB11A 0.017 0.023 0.15 13 -0.22 1 14
RHOA 0.005 0.023 -10000 0 -0.38 2 2
PLD1 0.019 0.05 0.18 49 -0.26 1 50
RAB11FIP3 0.006 0 -10000 0 -10000 0 0
tube morphogenesis 0.001 0.053 0.29 13 -0.42 1 14
ruffle organization 0.021 0.047 0.17 17 -0.34 1 18
regulation of epithelial cell migration 0.011 0.03 0.18 13 -0.33 1 14
PLD2 0.008 0.027 0.17 13 -0.26 1 14
PIP5K1A 0.021 0.048 0.17 17 -0.34 1 18
mol:Phosphatidic acid 0.012 0.045 0.16 49 -0.22 1 50
Rac1/GTP 0.001 0.054 0.29 13 -0.43 1 14
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.009 0 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.006 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.028 0.065 0.22 57 -10000 0 57
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.001 0.043 -10000 0 -0.38 7 7
RAC1-CDC42/GTP/PAK family -0.047 0.085 -10000 0 -0.18 156 156
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.011 0.031 0.22 12 -10000 0 12
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.006 0 -10000 0 -10000 0 0
FYN -0.039 0.13 0.22 1 -0.38 67 68
MAP3K12 0.006 0 -10000 0 -10000 0 0
FGR 0.006 0 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.014 0.057 -10000 0 -0.25 4 4
PRKG1 0.007 0.009 0.22 1 -10000 0 1
DUSP8 0.006 0 -10000 0 -10000 0 0
PGK/cGMP/p38 alpha -0.019 0.051 0.12 1 -0.25 4 5
apoptosis -0.014 0.055 -10000 0 -0.24 4 4
RAL/GTP 0.008 0.01 -10000 0 -0.22 1 1
LYN -0.007 0.07 -10000 0 -0.38 19 19
DUSP1 -0.12 0.18 0.22 1 -0.38 179 180
PAK1 0.012 0.041 0.22 18 -0.38 1 19
SRC 0.006 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.014 0.023 -10000 0 -0.2 6 6
TRAF6 0.007 0.013 0.22 2 -10000 0 2
RAC1 0.006 0.016 -10000 0 -0.38 1 1
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 0.006 0 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.008 0.01 -10000 0 -0.22 1 1
MAPK11 -0.023 0.078 0.18 1 -0.25 22 23
BLK 0.007 0.009 0.22 1 -10000 0 1
HCK 0.007 0.009 0.22 1 -10000 0 1
MAP2K3 0.003 0.037 -10000 0 -0.38 5 5
DUSP16 0.008 0.02 0.22 5 -10000 0 5
DUSP10 0.017 0.047 0.22 28 -10000 0 28
TRAF6/MEKK3 0.008 0 -10000 0 -10000 0 0
MAP3K7IP1 0.006 0 -10000 0 -10000 0 0
MAPK14 -0.016 0.06 -10000 0 -0.27 4 4
positive regulation of innate immune response -0.026 0.084 -10000 0 -0.27 22 22
LCK 0.006 0 -10000 0 -10000 0 0
p38alpha-beta/MKP7 -0.022 0.084 0.22 3 -0.26 22 25
p38alpha-beta/MKP5 -0.017 0.085 -10000 0 -0.26 21 21
PGK/cGMP 0.005 0 -10000 0 -10000 0 0
PAK2 0.007 0.013 0.22 2 -10000 0 2
p38alpha-beta/MKP1 -0.069 0.12 -10000 0 -0.33 53 53
CDC42 0.006 0 -10000 0 -10000 0 0
RALB 0.006 0.016 -10000 0 -0.38 1 1
RALA 0.007 0.009 0.22 1 -10000 0 1
PAK3 -0.1 0.18 0.22 3 -0.38 164 167
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.033 0.1 -10000 0 -0.28 83 83
AKT1 -0.042 0.12 0.39 1 -0.41 5 6
PTK2B -0.066 0.13 0.26 6 -0.36 53 59
VEGFR2 homodimer/Frs2 -0.051 0.11 0.27 2 -0.31 7 9
CAV1 -0.062 0.15 0.22 3 -0.38 101 104
CALM1 -0.006 0.068 -10000 0 -0.38 18 18
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.039 0.11 0.28 1 -0.34 7 8
endothelial cell proliferation -0.04 0.1 0.35 1 -0.36 5 6
mol:Ca2+ -0.052 0.1 0.32 1 -0.41 7 8
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.038 0.1 -10000 0 -0.33 9 9
RP11-342D11.1 -0.052 0.1 0.32 1 -0.41 7 8
CDH5 0.006 0 -10000 0 -10000 0 0
VEGFA homodimer 0.022 0.036 -10000 0 -0.21 3 3
SHC1 0.006 0 -10000 0 -10000 0 0
SHC2 -0.013 0.085 -10000 0 -0.38 28 28
HRAS/GDP -0.041 0.088 -10000 0 -0.35 8 8
SH2D2A 0.006 0 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.034 0.1 0.31 1 -0.35 8 9
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.043 0.11 -10000 0 -0.34 7 7
VEGFR1 homodimer 0.006 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.031 0.1 -10000 0 -0.38 8 8
GRB10 -0.053 0.1 0.48 1 -0.41 7 8
PTPN11 0.006 0 -10000 0 -10000 0 0
GRB2 0.006 0.016 -10000 0 -0.38 1 1
PAK1 0.012 0.041 0.22 18 -0.38 1 19
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.034 0.1 -10000 0 -0.32 8 8
HRAS 0.006 0 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.049 0.12 0.28 1 -0.34 45 46
HIF1A 0.004 0.028 -10000 0 -0.38 3 3
FRS2 0.013 0.038 0.22 18 -10000 0 18
oxygen and reactive oxygen species metabolic process -0.038 0.1 -10000 0 -0.33 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.006 0 -10000 0 -10000 0 0
Nck/Pak 0.008 0.012 -10000 0 -0.27 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.067 0.13 -10000 0 -0.38 27 27
mol:GDP -0.041 0.092 -10000 0 -0.37 8 8
mol:NADP -0.037 0.087 0.31 1 -0.33 3 4
eNOS/Hsp90 -0.034 0.085 0.29 1 -0.32 3 4
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
mol:IP3 -0.052 0.1 0.33 1 -0.42 7 8
HIF1A/ARNT 0.008 0.02 -10000 0 -0.27 3 3
SHB 0.006 0 -10000 0 -10000 0 0
VEGFA 0.017 0.05 0.22 30 -10000 0 30
VEGFC -0.008 0.074 -10000 0 -0.38 21 21
FAK1/Vinculin -0.057 0.14 0.31 2 -0.38 47 49
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.005 0.023 -10000 0 -0.38 2 2
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.055 0.15 0.3 6 -0.37 53 59
PTPN6 0.006 0 -10000 0 -10000 0 0
EPAS1 -0.098 0.18 -10000 0 -0.39 152 152
mol:L-citrulline -0.037 0.087 0.31 1 -0.33 3 4
ITGAV 0.017 0.06 0.22 35 -0.38 3 38
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.034 0.1 0.27 1 -0.33 8 9
VEGFR2 homodimer/VEGFA homodimer -0.043 0.12 -10000 0 -0.45 7 7
VEGFR2/3 heterodimer -0.056 0.11 0.27 2 -0.31 7 9
VEGFB 0.001 0.046 -10000 0 -0.38 8 8
MAPK11 -0.054 0.11 0.39 1 -0.43 7 8
VEGFR2 homodimer -0.076 0.12 0.4 2 -0.36 7 9
FLT1 0.006 0 -10000 0 -10000 0 0
NEDD4 0.006 0.018 0.22 3 -10000 0 3
MAPK3 -0.057 0.1 0.3 1 -0.39 7 8
MAPK1 -0.049 0.094 0.3 1 -0.38 7 8
VEGFA145/NRP2 0.008 0.007 -10000 0 -10000 0 0
VEGFR1/2 heterodimer -0.056 0.11 0.27 2 -0.31 7 9
KDR -0.076 0.12 0.4 2 -0.36 7 9
VEGFA165/NRP1/VEGFR2 homodimer -0.032 0.11 0.26 5 -0.41 7 12
SRC 0.006 0 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.054 0.098 0.32 1 -0.39 7 8
PI3K -0.036 0.13 0.42 1 -0.44 5 6
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.032 0.12 0.28 5 -0.34 7 12
FES -0.054 0.1 0.33 1 -0.42 7 8
GAB1 -0.051 0.11 -10000 0 -0.4 9 9
VEGFR2 homodimer/VEGFA homodimer/Src -0.043 0.11 -10000 0 -0.34 7 7
CTNNB1 0.007 0.009 0.22 1 -10000 0 1
SOS1 0.014 0.04 0.22 20 -10000 0 20
ARNT 0.007 0.009 0.22 1 -10000 0 1
eNOS/Caveolin-1 -0.058 0.11 0.29 1 -0.37 16 17
VEGFR2 homodimer/VEGFA homodimer/Yes -0.04 0.11 -10000 0 -0.34 7 7
PI3K/GAB1 -0.051 0.14 0.39 1 -0.41 26 27
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.017 0.11 0.26 11 -0.32 7 18
PRKACA 0.006 0 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.056 0.11 -10000 0 -0.34 14 14
HSP90AA1 0.006 0 -10000 0 -10000 0 0
CDC42 -0.054 0.1 0.33 1 -0.42 7 8
actin cytoskeleton reorganization -0.043 0.11 -10000 0 -0.34 7 7
PTK2 -0.063 0.15 0.32 2 -0.4 48 50
EDG1 -0.058 0.12 0.32 1 -0.55 13 14
mol:DAG -0.052 0.1 0.33 1 -0.42 7 8
CaM/Ca2+ -0.056 0.095 -10000 0 -0.37 13 13
MAP2K3 -0.052 0.1 0.46 1 -0.39 9 10
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.038 0.11 -10000 0 -0.42 7 7
PLCG1 -0.053 0.1 0.33 1 -0.42 7 8
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.037 0.1 -10000 0 -0.32 7 7
IQGAP1 0.005 0.025 0.22 1 -0.38 2 3
YES1 0.011 0.031 0.22 12 -10000 0 12
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.043 0.11 -10000 0 -0.34 7 7
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.043 0.11 -10000 0 -0.34 7 7
cell migration -0.056 0.14 0.29 2 -0.36 47 49
mol:PI-3-4-5-P3 -0.034 0.12 0.41 1 -0.41 5 6
FYN -0.039 0.13 0.22 1 -0.38 67 68
VEGFB/NRP1 -0.053 0.099 0.22 2 -0.4 11 13
mol:NO -0.037 0.087 0.31 1 -0.33 3 4
PXN -0.002 0.056 -10000 0 -0.38 12 12
HRAS/GTP -0.055 0.078 -10000 0 -0.35 8 8
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.041 0.11 -10000 0 -0.42 7 7
VHL 0.007 0.016 0.22 3 -10000 0 3
ITGB3 -0.045 0.14 0.22 13 -0.38 82 95
NOS3 -0.041 0.094 0.32 1 -0.37 3 4
VEGFR2 homodimer/VEGFA homodimer/Sck -0.053 0.12 -10000 0 -0.36 14 14
RAC1 0.006 0.016 -10000 0 -0.38 1 1
PRKCA -0.05 0.098 0.31 1 -0.38 8 9
PRKCB -0.049 0.095 0.31 1 -0.39 7 8
VCL 0.007 0.016 0.22 3 -10000 0 3
VEGFA165/NRP1 -0.051 0.1 0.32 1 -0.41 7 8
VEGFR1/2 heterodimer/VEGFA homodimer -0.043 0.11 -10000 0 -0.34 7 7
VEGFA165/NRP2 0.008 0.007 -10000 0 -10000 0 0
MAPKKK cascade -0.045 0.093 0.4 1 -0.37 6 7
NRP2 0.017 0.047 0.22 28 -10000 0 28
VEGFC homodimer -0.008 0.074 -10000 0 -0.38 21 21
NCK1 0.024 0.059 0.22 47 -10000 0 47
ROCK1 0.007 0.009 0.22 1 -10000 0 1
FAK1/Paxillin -0.061 0.15 0.31 2 -0.38 51 53
MAP3K13 -0.052 0.1 0.38 2 -0.42 7 9
PDPK1 -0.037 0.11 0.38 1 -0.38 5 6
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0 0.059 -10000 0 -0.25 29 29
E-cadherin/beta catenin 0.001 0.048 -10000 0 -0.27 17 17
CTNNB1 0.007 0.009 0.22 1 -10000 0 1
JUP -0.004 0.063 -10000 0 -0.38 15 15
CDH1 -0.005 0.067 -10000 0 -0.38 17 17
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.003 0.008 -10000 0 -10000 0 0
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A -0.009 0.064 -10000 0 -0.24 38 38
AP2 -0.01 0.071 -10000 0 -0.27 40 40
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.006 0.012 -10000 0 -0.23 1 1
CLTB 0.006 0 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein -0.011 0.056 -10000 0 -0.22 38 38
CD4 0.009 0.039 0.22 12 -0.38 2 14
CLTA 0.006 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.006 -10000 0 -10000 0 0
ARFGAP1 -0.002 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.002 0.039 -10000 0 -10000 0 0
ARF1/GTP -0.011 0.054 -10000 0 -0.21 38 38
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.011 0.047 -10000 0 -0.19 38 38
mol:Choline 0.002 0.038 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 -0.02 0.1 -10000 0 -0.39 38 38
DDEF1 0.001 0.036 -10000 0 -10000 0 0
ARF1/GDP 0.004 0.009 -10000 0 -10000 0 0
AP2M1 0.007 0.016 0.22 3 -10000 0 3
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.016 0.049 -10000 0 -0.2 39 39
Rac/GTP 0.003 0.013 -10000 0 -0.28 1 1
ARF1/GTP/GGA3/ARF-GAP1 -0.005 0.048 -10000 0 -0.18 38 38
ARFIP2 0.004 0.007 -10000 0 -10000 0 0
COPA 0.007 0.013 0.22 2 -10000 0 2
RAC1 0.006 0.016 -10000 0 -0.38 1 1
ARF1/GTP/coatomer protein complex -0.007 0.051 0.14 1 -0.2 35 36
ARF1/GTP/ARHGAP10 -0.011 0.057 -10000 0 -0.22 38 38
GGA3 0.006 0 -10000 0 -10000 0 0
ARF1/GTP/Membrin -0.008 0.05 -10000 0 -0.19 38 38
AP2A1 -0.021 0.1 -10000 0 -0.38 40 40
coatomer protein complex/ARF1/GTP/ARF-GAP1 -0.009 0.047 -10000 0 -0.18 38 38
ARF1/GDP/Membrin -0.007 0.047 -10000 0 -0.18 38 38
Arfaptin 2/Rac/GDP 0.007 0.011 -10000 0 -0.22 1 1
CYTH2 -0.002 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3 -0.008 0.058 -10000 0 -0.22 38 38
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.004 0.011 -10000 0 -0.27 1 1
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 -0.017 0.065 -10000 0 -0.31 7 7
PLD2 0.002 0.038 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE -0.002 0 -10000 0 -10000 0 0
PIP5K1A 0.002 0.039 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 -0.01 0.05 -10000 0 -0.19 38 38
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.002 0.038 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 -0.002 0 -10000 0 -10000 0 0
GOSR2 0.004 0.019 -10000 0 -10000 0 0
USO1 0.003 0.031 -10000 0 -0.39 2 2
GBF1 0 0.043 -10000 0 -0.4 5 5
ARF1/GTP/Arfaptin 2 -0.008 0.058 -10000 0 -0.22 38 38
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.005 0.061 -10000 0 -0.23 40 40
Ephrin A reverse signaling

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
MAPKKK cascade 0.007 0.017 -10000 0 -0.22 3 3
EFNA5 0.006 0.035 0.22 5 -0.38 3 8
FYN -0.027 0.068 0.14 5 -0.21 68 73
neuron projection morphogenesis 0.007 0.017 -10000 0 -0.22 3 3
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.007 0.017 -10000 0 -0.22 3 3
EPHA5 0.006 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.003 0.037 -10000 0 -0.38 5 5
HDAC4 0.006 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.004 0.028 -10000 0 -0.14 1 1
CDKN1A -0.026 0.15 -10000 0 -0.59 35 35
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.006 0 -10000 0 -10000 0 0
FOXO3 -0.001 0.035 0.34 4 -0.18 7 11
FOXO1 0 0.049 -10000 0 -0.38 9 9
FOXO4 -0.003 0.044 -10000 0 -0.3 11 11
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.006 0 -10000 0 -10000 0 0
TAT 0.006 0 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.002 0 -10000 0 -10000 0 0
PPARGC1A 0.008 0.02 0.22 5 -10000 0 5
FHL2 0.007 0.009 0.22 1 -10000 0 1
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.016 0.027 0.13 31 -10000 0 31
HIST2H4A 0.004 0.028 0.14 1 -10000 0 1
SIRT1/FOXO3a 0.011 0.038 0.22 5 -10000 0 5
SIRT1 0.015 0.039 0.18 31 -10000 0 31
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.019 0.025 0.14 1 -10000 0 1
SIRT1/Histone H1b 0.009 0.05 -10000 0 -0.26 11 11
apoptosis -0.019 0.025 -10000 0 -0.14 1 1
SIRT1/PGC1A 0.015 0.026 0.12 31 -10000 0 31
p53/SIRT1 -0.008 0.13 0.35 31 -0.27 72 103
SIRT1/FOXO4 0.008 0.049 -10000 0 -0.26 11 11
FOXO1/FHL2/SIRT1 0.014 0.034 -10000 0 -0.2 6 6
HIST1H1E -0.002 0.047 -10000 0 -0.3 11 11
SIRT1/p300 0.013 0.038 0.15 1 -0.27 5 6
muscle cell differentiation -0.003 0.028 -10000 0 -0.12 31 31
TP53 -0.034 0.14 0.18 33 -0.39 72 105
KU70/SIRT1/BAX 0.019 0.025 0.14 1 -10000 0 1
CREBBP 0.001 0.046 -10000 0 -0.38 8 8
MEF2D 0.006 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.016 0.027 0.15 1 -10000 0 1
ACSS2 0.002 0.031 -10000 0 -0.27 1 1
SIRT1/PCAF/MYOD 0.003 0.028 0.12 31 -10000 0 31
EPO signaling pathway

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
BCL2L1 0.001 0.13 0.51 2 -0.51 2 4
CRKL -0.018 0.041 0.22 2 -10000 0 2
mol:DAG -0.021 0.072 0.28 2 -0.3 13 15
HRAS -0.017 0.044 0.22 2 -0.26 1 3
MAPK8 -0.015 0.039 0.2 1 -0.22 15 16
RAP1A -0.018 0.041 0.22 2 -10000 0 2
GAB1 -0.019 0.044 0.22 2 -0.21 4 6
MAPK14 -0.016 0.042 0.36 1 -0.22 17 18
EPO 0.003 0.011 -10000 0 -10000 0 0
PLCG1 -0.021 0.073 0.29 2 -0.3 13 15
EPOR/TRPC2/IP3 Receptors 0.004 0.019 0.21 3 -10000 0 3
RAPGEF1 0.006 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.005 0.035 0.21 1 -0.24 9 10
GAB1/SHC/GRB2/SOS1 -0.003 0.046 -10000 0 -0.27 1 1
EPO/EPOR (dimer) 0.005 0.018 0.23 1 -10000 0 1
IRS2 -0.018 0.041 0.22 2 -10000 0 2
STAT1 0.037 0.11 0.41 2 -0.42 5 7
STAT5B -0.034 0.098 0.35 2 -0.43 8 10
cell proliferation -0.015 0.037 0.32 1 -0.2 15 16
GAB1/SHIP/PIK3R1/SHP2/SHC -0.039 0.061 -10000 0 -0.26 11 11
TEC 0 0.061 0.3 2 -10000 0 2
SOCS3 0.001 0.051 0.22 2 -0.38 9 11
STAT1 (dimer) 0.037 0.11 0.41 2 -0.42 5 7
JAK2 0.001 0.036 0.2 2 -0.39 4 6
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
EPO/EPOR (dimer)/JAK2 0.002 0.054 0.35 3 -10000 0 3
EPO/EPOR 0.005 0.018 0.23 1 -10000 0 1
LYN -0.01 0.07 -10000 0 -0.38 19 19
TEC/VAV2 -0.003 0.06 0.3 2 -10000 0 2
elevation of cytosolic calcium ion concentration 0.004 0.019 0.21 3 -10000 0 3
SHC1 0.006 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.001 0.051 0.27 2 -0.24 18 20
mol:IP3 -0.021 0.072 0.28 2 -0.3 13 15
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.036 0.066 0.24 1 -0.28 10 11
SH2B3 0.003 0.01 -10000 0 -10000 0 0
NFKB1 -0.02 0.058 0.2 1 -0.29 21 22
EPO/EPOR (dimer)/JAK2/SOCS3 -0.001 0.03 -10000 0 -0.2 12 12
PTPN6 -0.017 0.043 0.23 2 -0.18 4 6
TEC/VAV2/GRB2 0.008 0.059 0.4 1 -10000 0 1
EPOR 0.004 0.019 0.21 3 -10000 0 3
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.003 0.047 -10000 0 -0.27 1 1
SOS1 0.014 0.04 0.22 20 -10000 0 20
PLCG2 0.006 0 -10000 0 -10000 0 0
CRKL/CBL/C3G -0.005 0.044 0.27 1 -10000 0 1
VAV2 -0.019 0.043 0.22 2 -10000 0 2
CBL -0.018 0.041 0.22 2 -10000 0 2
SHC/Grb2/SOS1 -0.004 0.041 0.16 1 -10000 0 1
STAT5A -0.033 0.099 0.35 2 -0.43 10 12
GRB2 0.006 0.016 -10000 0 -0.38 1 1
STAT5 (dimer) -0.047 0.14 0.48 2 -0.37 77 79
LYN/PLCgamma2 -0.003 0.05 -10000 0 -0.27 19 19
PTPN11 0.006 0 -10000 0 -10000 0 0
BTK -0.012 0.051 0.23 3 -10000 0 3
BCL2 -0.06 0.28 0.51 2 -0.76 73 75
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.11 0.22 0.67 2 -10000 0 2
PCK1 0.14 0.22 0.58 40 -0.86 4 44
HNF4A 0.14 0.25 0.75 6 -10000 0 6
KCNJ11 0.12 0.23 0.65 1 -10000 0 1
AKT1 0.089 0.14 0.4 5 -10000 0 5
response to starvation 0.017 0.029 -10000 0 -10000 0 0
DLK1 0.13 0.25 0.79 14 -10000 0 14
NKX2-1 0.08 0.15 -10000 0 -10000 0 0
ACADM 0.11 0.22 0.64 4 -10000 0 4
TAT 0.11 0.16 0.53 2 -10000 0 2
CEBPB 0.005 0.035 0.22 1 -0.38 4 5
CEBPA 0.007 0.007 -10000 0 -10000 0 0
TTR 0.099 0.13 0.91 2 -10000 0 2
PKLR 0.11 0.22 0.64 1 -10000 0 1
APOA1 0.18 0.31 0.79 38 -10000 0 38
CPT1C 0.12 0.22 0.7 10 -10000 0 10
ALAS1 0.076 0.16 0.88 2 -10000 0 2
TFRC 0.19 0.28 0.78 50 -10000 0 50
FOXF1 0.006 0 -10000 0 -10000 0 0
NF1 -0.008 0.081 0.2 4 -0.38 24 28
HNF1A (dimer) 0.007 0.025 -10000 0 -0.33 3 3
CPT1A 0.11 0.22 0.64 1 -0.81 1 2
HMGCS1 0.13 0.24 0.7 14 -10000 0 14
NR3C1 -0.001 0.059 -10000 0 -0.38 13 13
CPT1B 0.11 0.22 0.59 3 -10000 0 3
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.007 0.01 -10000 0 -0.23 1 1
GCK 0.11 0.22 0.59 3 -10000 0 3
CREB1 0.032 0.071 0.19 52 -0.31 5 57
IGFBP1 0.082 0.14 -10000 0 -10000 0 0
PDX1 0.082 0.16 -10000 0 -1.1 1 1
UCP2 0.023 0.36 0.64 1 -0.81 52 53
ALDOB 0.12 0.23 0.65 1 -10000 0 1
AFP 0.033 0.052 0.45 1 -10000 0 1
BDH1 0.11 0.22 0.69 2 -0.81 1 3
HADH 0.079 0.3 0.65 1 -0.83 25 26
F2 0.15 0.26 0.78 3 -10000 0 3
HNF1A 0.007 0.025 -10000 0 -0.33 3 3
G6PC 0.037 0.065 -10000 0 -10000 0 0
SLC2A2 0.095 0.17 -10000 0 -10000 0 0
INS 0.003 0.016 -10000 0 -0.19 2 2
FOXA1 0.009 0.032 0.48 1 -0.39 2 3
FOXA3 0.081 0.11 0.37 23 -10000 0 23
FOXA2 0.17 0.3 0.84 13 -10000 0 13
ABCC8 0.12 0.23 0.65 1 -10000 0 1
ALB 0.033 0.053 0.44 2 -10000 0 2
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.005 0.04 0.17 22 -10000 0 22
GNAI2 0.006 0 -10000 0 -10000 0 0
S1P/S1P5/G12 0.004 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.006 0.036 0.22 6 -0.38 3 9
RhoA/GTP 0.005 0.041 -10000 0 -0.17 22 22
negative regulation of cAMP metabolic process 0.003 0.044 0.18 1 -0.19 20 21
GNAZ 0.002 0.04 -10000 0 -0.38 6 6
GNAI3 0.017 0.047 0.22 29 -10000 0 29
GNA12 0.006 0 -10000 0 -10000 0 0
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.003 0.044 0.18 1 -0.19 20 21
RhoA/GDP 0.004 0.016 -10000 0 -0.27 2 2
RHOA 0.005 0.023 -10000 0 -0.38 2 2
GNAI1 0 0.063 0.22 7 -0.38 13 20
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.003 0.032 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.002 0.016 -10000 0 -10000 0 0
mol:DAG -0.004 0.021 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.013 0.034 -10000 0 -10000 0 0
CaM/Ca2+ 0 0.04 -10000 0 -10000 0 0
HIF1A 0.007 0.029 -10000 0 -0.39 3 3
GAB1 0.004 0.033 -10000 0 -0.38 4 4
AKT1 -0.001 0.089 -10000 0 -0.37 1 1
PLCG1 -0.004 0.021 -10000 0 -10000 0 0
NOS3 -0.002 0.052 -10000 0 -10000 0 0
CBL 0.006 0 -10000 0 -10000 0 0
mol:NO -0.002 0.051 -10000 0 -10000 0 0
FLT1 0.003 0.02 -10000 0 -10000 0 0
PGF 0.006 0 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2/VEGFR121 0.024 0.046 0.28 3 -10000 0 3
CALM1 -0.006 0.068 -10000 0 -0.38 18 18
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
eNOS/Hsp90 0.001 0.051 -10000 0 -10000 0 0
endothelial cell proliferation -0.004 0.03 0.26 1 -10000 0 1
mol:Ca2+ -0.004 0.021 -10000 0 -10000 0 0
MAPK3 -0.022 0.06 0.25 1 -0.36 1 2
MAPK1 -0.006 0.031 0.25 1 -10000 0 1
PIK3R1 -0.038 0.12 -10000 0 -0.38 64 64
PLGF homodimer 0.006 0 -10000 0 -10000 0 0
PRKACA 0.006 0 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.062 0.15 0.22 3 -0.38 101 104
VEGFA homodimer 0.018 0.048 0.22 30 -10000 0 30
VEGFR1 homodimer/VEGFA homodimer 0.015 0.038 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.022 0.059 0.24 1 -0.35 1 2
PI3K 0.02 0.091 -10000 0 -0.37 1 1
PRKCA -0.005 0.031 0.27 1 -10000 0 1
PRKCB -0.004 0.019 -10000 0 -10000 0 0
VEGFR1 homodimer/PLGF homodimer 0.007 0.017 -10000 0 -10000 0 0
VEGFA 0.018 0.048 0.22 30 -10000 0 30
VEGFB 0.001 0.046 -10000 0 -0.38 8 8
mol:IP3 -0.004 0.021 -10000 0 -10000 0 0
RASA1 -0.009 0.031 -10000 0 -10000 0 0
NRP2 0.017 0.047 0.22 28 -10000 0 28
VEGFR1 homodimer 0.003 0.02 -10000 0 -10000 0 0
VEGFB homodimer 0.001 0.046 -10000 0 -0.38 8 8
NCK1 0.024 0.059 0.22 47 -10000 0 47
eNOS/Caveolin-1 -0.024 0.086 -10000 0 -0.37 5 5
PTPN11 0.006 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.019 0.089 -10000 0 -0.37 1 1
mol:L-citrulline -0.002 0.051 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.021 0.037 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.029 0.053 0.28 5 -10000 0 5
CD2AP 0.007 0.031 0.22 5 -0.38 2 7
PI3K/GAB1 0.02 0.088 -10000 0 -0.36 1 1
PDPK1 0.002 0.082 -10000 0 -0.35 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.018 0.034 -10000 0 -10000 0 0
mol:NADP -0.002 0.051 -10000 0 -10000 0 0
HSP90AA1 0.006 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.02 0.036 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.014 0.037 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.012 0.11 0.79 2 -0.85 1 3
NCK1/PAK1/Dok-R -0.019 0.046 -10000 0 -0.41 1 1
NCK1/Dok-R 0.018 0.062 -10000 0 -0.87 1 1
PIK3CA 0.056 0.091 0.22 131 -10000 0 131
mol:beta2-estradiol -0.002 0.018 -10000 0 -0.16 7 7
RELA 0.005 0.023 -10000 0 -0.38 2 2
SHC1 0.006 0.004 -10000 0 -10000 0 0
Rac/GDP 0.004 0.011 -10000 0 -0.27 1 1
F2 0.003 0.028 0.23 1 -0.29 2 3
TNIP2 0.007 0.009 0.22 1 -10000 0 1
NF kappa B/RelA 0.005 0.053 -10000 0 -0.82 1 1
FN1 0.074 0.12 0.22 201 -0.38 13 214
PLD2 0.001 0.06 0.72 1 -0.89 1 2
PTPN11 0.006 0 -10000 0 -10000 0 0
GRB14 0.015 0.042 0.22 22 -10000 0 22
ELK1 -0.009 0.063 0.64 1 -0.84 1 2
GRB7 0.006 0.035 0.22 5 -0.38 3 8
PAK1 0.012 0.041 0.22 18 -0.38 1 19
Tie2/Ang1/alpha5/beta1 Integrin 0.05 0.09 -10000 0 -0.85 1 1
CDKN1A -0.042 0.2 0.57 6 -0.76 36 42
ITGA5 0.008 0.018 0.22 4 -10000 0 4
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.007 0.053 -10000 0 -0.87 1 1
CRK 0.006 0 -10000 0 -10000 0 0
mol:NO -0.01 0.098 0.57 4 -0.64 1 5
PLG -0.002 0.064 0.72 1 -0.89 1 2
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.001 0.094 0.7 2 -0.8 1 3
GRB2 0.006 0.016 -10000 0 -0.38 1 1
PIK3R1 -0.038 0.12 -10000 0 -0.39 64 64
ANGPT2 0 0.082 0.58 8 -10000 0 8
BMX 0.001 0.06 0.72 1 -0.89 1 2
ANGPT1 0.007 0.051 0.56 2 -10000 0 2
tube development -0.034 0.13 0.56 7 -0.66 1 8
ANGPT4 0.006 0.01 0.22 1 -10000 0 1
response to hypoxia 0 0.007 0.11 1 -10000 0 1
Tie2/Ang1/GRB14 0.011 0.064 0.65 1 -0.91 1 2
alpha5/beta1 Integrin 0.009 0.001 -10000 0 -10000 0 0
FGF2 0.006 0.005 -10000 0 -10000 0 0
STAT5A (dimer) -0.029 0.16 0.79 2 -0.58 36 38
mol:L-citrulline -0.01 0.098 0.57 4 -0.64 1 5
AGTR1 0.006 0.008 -10000 0 -10000 0 0
MAPK14 0 0.077 0.86 1 -1 1 2
Tie2/SHP2 0.001 0.054 -10000 0 -0.96 1 1
TEK 0 0.068 0.73 1 -1 1 2
RPS6KB1 -0.006 0.1 0.74 2 -0.82 1 3
Angiotensin II/AT1 0.006 0.018 0.15 8 -10000 0 8
Tie2/Ang1/GRB2 0.005 0.059 0.65 1 -0.91 1 2
MAPK3 -0.016 0.075 0.66 1 -0.84 1 2
MAPK1 -0.001 0.057 0.66 1 -0.84 1 2
Tie2/Ang1/GRB7 0.005 0.052 -10000 0 -0.91 1 1
NFKB1 -0.001 0.054 -10000 0 -0.38 11 11
MAPK8 0.002 0.061 0.72 1 -0.89 1 2
PI3K -0.008 0.11 0.78 2 -0.96 1 3
FES -0.002 0.077 0.86 1 -1 1 2
Crk/Dok-R 0.008 0.051 -10000 0 -0.87 1 1
Tie2/Ang1/ABIN2 0.006 0.059 0.65 1 -0.91 1 2
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.011 0.11 0.78 2 -0.76 1 3
STAT5A -0.001 0.049 -10000 0 -0.38 9 9
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.003 0.11 0.74 2 -0.82 1 3
Tie2/Ang2 -0.021 0.13 0.86 2 -0.87 1 3
Tie2/Ang1 0.003 0.065 0.82 1 -0.94 1 2
FOXO1 -0.017 0.12 0.8 2 -0.77 1 3
ELF1 0.002 0.044 0.21 1 -0.38 7 8
ELF2 0.003 0.062 0.79 1 -0.9 1 2
mol:Choline 0.001 0.059 0.71 1 -0.87 1 2
cell migration -0.011 0.029 -10000 0 -0.23 1 1
FYN -0.037 0.14 0.57 7 -0.75 1 8
DOK2 0.007 0.009 0.22 1 -10000 0 1
negative regulation of cell cycle -0.036 0.18 0.56 6 -0.68 36 42
ETS1 0.009 0.03 0.22 4 -0.4 1 5
PXN 0 0.1 0.71 2 -0.68 1 3
ITGB1 0.007 0.016 0.22 3 -10000 0 3
NOS3 -0.011 0.1 0.75 2 -0.72 1 3
RAC1 0.006 0.016 -10000 0 -0.38 1 1
TNF 0.009 0.021 0.21 2 -10000 0 2
MAPKKK cascade 0.001 0.059 0.71 1 -0.87 1 2
RASA1 0.004 0.028 -10000 0 -0.38 3 3
Tie2/Ang1/Shc 0.007 0.061 0.69 1 -0.91 1 2
NCK1 0.024 0.059 0.22 47 -10000 0 47
vasculogenesis -0.008 0.093 0.49 7 -0.57 1 8
mol:Phosphatidic acid 0.001 0.059 0.71 1 -0.87 1 2
mol:Angiotensin II 0.001 0.008 -10000 0 -10000 0 0
mol:NADP -0.01 0.098 0.57 4 -0.64 1 5
Rac1/GTP -0.013 0.079 -10000 0 -0.76 1 1
MMP2 -0.027 0.098 0.72 1 -0.89 1 2
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.007 0.016 0.22 3 -10000 0 3
ITGB7 0.003 0.038 0.22 1 -0.38 5 6
ITGA4 0.017 0.047 0.22 29 -10000 0 29
alpha4/beta7 Integrin 0.007 0.024 -10000 0 -0.27 4 4
alpha4/beta1 Integrin 0.009 0.002 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.004 0.008 0.2 1 -10000 0 1
BAD/BCL-XL/YWHAZ 0.01 0.005 -10000 0 -10000 0 0
CDKN1B 0.026 0.051 0.25 1 -10000 0 1
CDKN1A 0.015 0.061 -10000 0 -10000 0 0
FRAP1 0.006 0 -10000 0 -10000 0 0
PRKDC 0.048 0.085 0.22 110 -10000 0 110
FOXO3 0.023 0.053 -10000 0 -10000 0 0
AKT1 0.028 0.05 -10000 0 -10000 0 0
BAD 0.006 0 -10000 0 -10000 0 0
AKT3 -0.16 0.14 0.15 4 -0.27 337 341
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.025 0.048 -10000 0 -10000 0 0
AKT1/ASK1 0.026 0.047 -10000 0 -10000 0 0
BAD/YWHAZ 0.013 0 -10000 0 -10000 0 0
RICTOR 0.009 0.024 0.22 7 -10000 0 7
RAF1 0.006 0 -10000 0 -10000 0 0
JNK cascade -0.004 0.018 -10000 0 -10000 0 0
TSC1 0.025 0.048 -10000 0 -10000 0 0
YWHAZ 0.006 0 -10000 0 -10000 0 0
AKT1/RAF1 0.03 0.045 -10000 0 -10000 0 0
EP300 0.003 0.037 -10000 0 -0.38 5 5
mol:GDP 0.027 0.05 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.025 0.048 -10000 0 -10000 0 0
YWHAQ 0.006 0 -10000 0 -10000 0 0
TBC1D4 0.001 0.017 0.16 2 -10000 0 2
MAP3K5 0.002 0.044 0.22 1 -0.38 7 8
MAPKAP1 0.006 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.014 0.033 0.2 3 -10000 0 3
YWHAH 0.005 0.03 0.22 1 -0.38 3 4
AKT1S1 0.025 0.048 -10000 0 -10000 0 0
CASP9 0.025 0.048 -10000 0 -10000 0 0
YWHAB 0.007 0.009 0.22 1 -10000 0 1
p27Kip1/KPNA1 0.028 0.048 0.23 1 -10000 0 1
GBL 0.006 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.013 0 -10000 0 -10000 0 0
YWHAE 0.006 0.016 -10000 0 -0.38 1 1
SRC 0.006 0 -10000 0 -10000 0 0
AKT2/p21CIP1 0.013 0.059 0.19 4 -10000 0 4
KIAA1303 0.006 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.022 0.028 -10000 0 -10000 0 0
CHUK 0.028 0.052 0.25 4 -10000 0 4
BAD/BCL-XL 0.029 0.043 -10000 0 -10000 0 0
mTORC2 0.018 0.014 -10000 0 -10000 0 0
AKT2 0.004 0.017 0.15 7 -10000 0 7
FOXO1-3a-4/14-3-3 family 0.022 0.045 -10000 0 -10000 0 0
PDPK1 0.006 0 -10000 0 -10000 0 0
MDM2 0.026 0.049 -10000 0 -10000 0 0
MAPKKK cascade -0.029 0.045 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.026 0.054 -10000 0 -0.33 2 2
TSC1/TSC2 0.023 0.046 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.052 -10000 0 -0.32 2 2
glucose import 0 0.015 0.14 2 -10000 0 2
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.027 0.038 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0 0.015 0.14 2 -10000 0 2
GSK3A 0.023 0.051 -10000 0 -10000 0 0
FOXO1 0.022 0.053 -10000 0 -10000 0 0
GSK3B 0.025 0.048 -10000 0 -10000 0 0
SFN 0.013 0.039 0.22 19 -10000 0 19
G1/S transition of mitotic cell cycle 0.021 0.049 -10000 0 -10000 0 0
p27Kip1/14-3-3 family 0.011 0.036 -10000 0 -0.31 4 4
PRKACA 0.006 0 -10000 0 -10000 0 0
KPNA1 0.007 0.013 0.22 2 -10000 0 2
HSP90AA1 0.006 0 -10000 0 -10000 0 0
YWHAG 0.004 0.033 -10000 0 -0.38 4 4
RHEB 0.017 0.047 0.22 28 -10000 0 28
CREBBP 0.001 0.046 -10000 0 -0.38 8 8
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA -0.003 0.074 -10000 0 -0.31 27 27
Ran/GTP/Exportin 1/HDAC1 -0.004 0.001 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.015 0.089 -10000 0 -0.36 27 27
SUMO1 0.006 0 -10000 0 -10000 0 0
ZFPM1 0.006 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.003 0.005 -10000 0 -10000 0 0
FKBP3 0.01 0.027 0.22 9 -10000 0 9
Histones 0.027 0.058 0.26 8 -10000 0 8
YY1/LSF 0.015 0.062 0.16 53 -0.25 13 66
SMG5 0.007 0.016 0.22 3 -10000 0 3
RAN 0.006 0 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.011 0.066 -10000 0 -0.25 36 36
I kappa B alpha/HDAC1 -0.001 0.07 -10000 0 -0.4 10 10
SAP18 0.006 0.016 -10000 0 -0.38 1 1
RELA -0.01 0.061 -10000 0 -0.28 13 13
HDAC1/Smad7 0.012 0.003 -10000 0 -10000 0 0
RANGAP1 0.006 0 -10000 0 -10000 0 0
HDAC3/TR2 0.005 0.035 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.011 0.042 0.26 1 -10000 0 1
NF kappa B1 p50/RelA -0.01 0.068 -10000 0 -0.39 10 10
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.004 0.034 0.22 1 -0.38 4 5
GATA1 0.006 0 -10000 0 -10000 0 0
Mad/Max 0.009 0 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.013 0.042 0.25 1 -10000 0 1
RBBP7 0.006 0.019 0.22 1 -0.38 1 2
NPC 0.004 0 -10000 0 -10000 0 0
RBBP4 0.015 0.042 0.22 22 -10000 0 22
MAX 0.006 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.006 0 -10000 0 -10000 0 0
NFKBIA -0.012 0.074 -10000 0 -0.39 16 16
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.014 0.039 0.19 14 -10000 0 14
SIN3 complex 0.016 0.011 -10000 0 -0.2 1 1
SMURF1 0.006 0 -10000 0 -10000 0 0
CHD3 0.001 0.046 -10000 0 -0.38 8 8
SAP30 0.006 0 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.002 0.04 -10000 0 -0.38 6 6
YY1/HDAC3 -0.005 0.044 -10000 0 -0.38 3 3
YY1/HDAC2 0.005 0.046 0.16 13 -0.25 12 25
YY1/HDAC1 0.009 0.051 0.16 27 -0.26 10 37
NuRD/MBD2 Complex (MeCP1) 0.011 0.042 0.26 1 -10000 0 1
PPARG -0.011 0.067 -10000 0 -0.28 30 30
HDAC8/hEST1B 0.012 0.004 -10000 0 -10000 0 0
UBE2I 0.006 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.006 0 -10000 0 -10000 0 0
TNFRSF1A -0.011 0.08 -10000 0 -0.38 25 25
HDAC3/SMRT (N-CoR2) -0.002 0.041 -10000 0 -0.22 8 8
MBD3L2 0.006 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.012 0.003 -10000 0 -10000 0 0
CREBBP 0.001 0.046 -10000 0 -0.38 8 8
NuRD/MBD3/MBD3L2 Complex 0.013 0.044 0.27 1 -10000 0 1
HDAC1 0.017 0.047 0.22 28 -10000 0 28
HDAC3 -0.003 0.034 -10000 0 -10000 0 0
HDAC2 0.011 0.036 0.22 13 -0.38 1 14
YY1 -0.003 0.044 -10000 0 -0.3 11 11
HDAC8 0.023 0.058 0.22 44 -10000 0 44
SMAD7 0.006 0 -10000 0 -10000 0 0
NCOR2 0 0.049 -10000 0 -0.38 9 9
MXD1 0.006 0 -10000 0 -10000 0 0
STAT3 -0.008 0.066 -10000 0 -0.31 22 22
NFKB1 -0.001 0.054 -10000 0 -0.38 11 11
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.007 0.013 0.22 2 -10000 0 2
YY1/LSF/HDAC1 0.024 0.066 0.29 6 -0.23 13 19
YY1/SAP30/HDAC1 0.012 0.047 -10000 0 -0.24 10 10
EP300 0.003 0.037 -10000 0 -0.38 5 5
STAT3 (dimer non-phopshorylated) -0.008 0.066 -10000 0 -0.31 22 22
proteasomal ubiquitin-dependent protein catabolic process -0.012 0.073 -10000 0 -0.39 16 16
histone deacetylation 0.011 0.041 0.21 2 -10000 0 2
STAT3 (dimer non-phopshorylated)/HDAC3 -0.009 0.06 -10000 0 -0.42 5 5
nuclear export -0.012 0.003 -10000 0 -10000 0 0
PRKACA 0.006 0 -10000 0 -10000 0 0
GATAD2B 0.006 0.016 -10000 0 -0.38 1 1
GATAD2A 0.006 0.016 -10000 0 -0.38 1 1
GATA2/HDAC3 0 0.036 -10000 0 -0.2 4 4
GATA1/HDAC1 0.009 0.002 -10000 0 -10000 0 0
GATA1/HDAC3 0.001 0.032 -10000 0 -10000 0 0
CHD4 0.007 0.016 0.22 3 -10000 0 3
TNF-alpha/TNFR1A -0.003 0.057 -10000 0 -0.27 25 25
SIN3/HDAC complex/Mad/Max 0.014 0.035 0.17 14 -10000 0 14
NuRD Complex 0.013 0.044 0.27 1 -10000 0 1
positive regulation of chromatin silencing 0.026 0.056 0.25 8 -10000 0 8
SIN3B 0.007 0.009 0.22 1 -10000 0 1
MTA2 0.006 0 -10000 0 -10000 0 0
SIN3A 0.006 0 -10000 0 -10000 0 0
XPO1 0.026 0.062 0.22 52 -10000 0 52
SUMO1/HDAC1 0.016 0.029 0.2 1 -10000 0 1
HDAC complex 0.023 0.034 -10000 0 -0.2 2 2
GATA1/Fog1 0.009 0 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.011 0.011 -10000 0 -0.23 1 1
TNF 0.007 0.009 0.22 1 -10000 0 1
negative regulation of cell growth 0.014 0.035 0.17 14 -10000 0 14
NuRD/MBD2/PRMT5 Complex 0.011 0.042 0.26 1 -10000 0 1
Ran/GTP/Exportin 1 0.021 0.035 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.016 0.08 -10000 0 -0.34 27 27
SIN3/HDAC complex/NCoR1 0.012 0.041 0.19 14 -10000 0 14
TFCP2 0.025 0.07 0.22 54 -0.38 3 57
NR2C1 0.012 0.033 0.22 14 -10000 0 14
MBD3 0.006 0 -10000 0 -10000 0 0
MBD2 0.006 0 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.003 0.024 0.32 1 -0.13 3 4
KIRREL 0.009 0.043 0.2 22 -0.42 1 23
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.003 0.024 0.13 3 -0.32 1 4
PLCG1 0.009 0.022 0.22 6 -10000 0 6
ARRB2 0.006 0 -10000 0 -10000 0 0
WASL 0.006 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.012 0.033 -10000 0 -0.22 1 1
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.014 0.038 0.2 1 -0.24 1 2
FYN -0.016 0.054 0.21 1 -0.15 64 65
mol:Ca2+ 0.008 0.025 0.12 4 -0.25 1 5
mol:DAG 0.012 0.032 -10000 0 -0.25 1 1
NPHS2 0.003 0.014 -10000 0 -10000 0 0
mol:IP3 0.012 0.032 -10000 0 -0.25 1 1
regulation of endocytosis 0 0.055 0.21 1 -0.34 1 2
Nephrin/NEPH1/podocin/Cholesterol 0.005 0.023 0.12 3 -0.25 1 4
establishment of cell polarity 0.003 0.024 0.13 3 -0.32 1 4
Nephrin/NEPH1/podocin/NCK1-2 0.026 0.046 -10000 0 -0.23 1 1
Nephrin/NEPH1/beta Arrestin2 0 0.056 0.22 1 -0.34 1 2
NPHS1 0.003 0.02 0.2 3 -10000 0 3
Nephrin/NEPH1/podocin -0.002 0.058 0.23 1 -0.15 64 65
TJP1 0.006 0.021 0.22 2 -0.38 1 3
NCK1 0.024 0.059 0.22 47 -10000 0 47
NCK2 0.006 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.013 0.033 -10000 0 -0.25 1 1
CD2AP 0.007 0.031 0.22 5 -0.38 2 7
Nephrin/NEPH1/podocin/GRB2 0.012 0.035 -10000 0 -0.26 2 2
GRB2 0.006 0.016 -10000 0 -0.38 1 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.004 0.03 0.18 2 -0.23 1 3
cytoskeleton organization 0.005 0.039 0.22 1 -0.24 2 3
Nephrin/NEPH1 0.004 0.017 0.11 3 -0.22 1 4
Nephrin/NEPH1/ZO-1 0.007 0.023 0.12 3 -0.26 2 5
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.017 0.047 0.22 28 -10000 0 28
HDAC2 0.011 0.036 0.22 13 -0.38 1 14
GNB1/GNG2 0.009 0.023 -10000 0 -0.23 5 5
forebrain development -0.005 0.082 -10000 0 -0.44 8 8
GNAO1 0.005 0.036 0.22 6 -0.38 3 9
SMO/beta Arrestin2 0.008 0.007 -10000 0 -10000 0 0
SMO 0.005 0.006 -10000 0 -10000 0 0
ARRB2 0.005 0.004 -10000 0 -10000 0 0
GLI3/SPOP 0.006 0.044 -10000 0 -0.39 1 1
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
GSK3B 0.006 0 -10000 0 -10000 0 0
GNAI2 0.005 0.005 -10000 0 -10000 0 0
SIN3/HDAC complex 0.017 0.011 -10000 0 -0.2 1 1
GNAI1 -0.001 0.064 0.22 7 -0.38 13 20
XPO1 0.024 0.062 0.22 52 -10000 0 52
GLI1/Su(fu) -0.007 0.075 -10000 0 -0.43 7 7
SAP30 0.006 0.001 -10000 0 -10000 0 0
mol:GDP 0.005 0.006 -10000 0 -10000 0 0
MIM/GLI2A 0.003 0.034 0.22 6 -10000 0 6
IFT88 -0.001 0.054 -10000 0 -0.38 11 11
GNAI3 0.016 0.048 0.22 29 -10000 0 29
GLI2 0.004 0.003 -10000 0 -10000 0 0
GLI3 0.002 0.046 -10000 0 -0.26 9 9
CSNK1D 0.006 0 -10000 0 -10000 0 0
CSNK1E 0.006 0 -10000 0 -10000 0 0
SAP18 0.006 0.016 -10000 0 -0.38 1 1
embryonic digit morphogenesis -0.001 0.054 -10000 0 -0.38 11 11
GNG2 0.004 0.034 0.22 1 -0.38 4 5
Gi family/GTP 0 0.045 0.19 1 -0.21 4 5
SIN3B 0.007 0.009 0.22 1 -10000 0 1
SIN3A 0.006 0.001 -10000 0 -10000 0 0
GLI3/Su(fu) 0.005 0.042 -10000 0 -0.36 1 1
GLI2/Su(fu) 0.006 0.01 -10000 0 -10000 0 0
FOXA2 -0.05 0.23 -10000 0 -0.96 33 33
neural tube patterning -0.005 0.082 -10000 0 -0.44 8 8
SPOP 0.006 0 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.007 0.013 -10000 0 -10000 0 0
GNB1 0.006 0.016 -10000 0 -0.38 1 1
CSNK1G2 0.006 0 -10000 0 -10000 0 0
CSNK1G3 0.006 0 -10000 0 -10000 0 0
MTSS1 0.003 0.034 0.22 6 -10000 0 6
embryonic limb morphogenesis -0.005 0.082 -10000 0 -0.44 8 8
SUFU 0.003 0.013 -10000 0 -10000 0 0
LGALS3 -0.04 0.13 -10000 0 -0.38 68 68
catabolic process 0.009 0.037 -10000 0 -0.3 1 1
GLI3A/CBP 0.001 0.047 -10000 0 -0.39 8 8
KIF3A 0.008 0.02 0.22 5 -10000 0 5
GLI1 -0.005 0.083 -10000 0 -0.45 8 8
RAB23 0.006 0 -10000 0 -10000 0 0
CSNK1A1 0.007 0.009 0.22 1 -10000 0 1
IFT172 0.005 0.023 -10000 0 -0.38 2 2
RBBP7 0.006 0.019 0.22 1 -0.38 1 2
Su(fu)/Galectin3 -0.018 0.068 -10000 0 -0.22 7 7
GNAZ 0.001 0.04 -10000 0 -0.39 6 6
RBBP4 0.015 0.042 0.22 22 -10000 0 22
CSNK1G1 0.006 0 -10000 0 -10000 0 0
PIAS1 0.007 0.009 0.22 1 -10000 0 1
PRKACA 0.006 0 -10000 0 -10000 0 0
GLI2/SPOP 0.008 0.003 -10000 0 -10000 0 0
STK36 0.006 0.017 0.22 3 -10000 0 3
Gi family/GNB1/GNG2/GDP 0.001 0.047 0.27 1 -0.22 2 3
PTCH1 -0.015 0.15 -10000 0 -1 10 10
MIM/GLI1 -0.013 0.12 -10000 0 -0.44 31 31
CREBBP 0.001 0.047 -10000 0 -0.39 8 8
Su(fu)/SIN3/HDAC complex 0.016 0.037 0.23 2 -10000 0 2
S1P4 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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.006 0.036 0.22 6 -0.38 3 9
CDC42/GTP 0.006 0.039 -10000 0 -0.19 3 3
PLCG1 0.003 0.044 0.17 1 -0.18 20 21
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.006 0 -10000 0 -10000 0 0
GNAI3 0.017 0.047 0.22 29 -10000 0 29
G12/G13 0.009 0.012 -10000 0 -0.27 1 1
cell migration 0.006 0.039 -10000 0 -0.18 3 3
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.014 0.067 0.17 1 -0.19 48 49
MAPK1 0.001 0.043 0.17 1 -0.19 4 5
S1P/S1P5/Gi 0.003 0.044 0.18 1 -0.19 20 21
GNAI1 0 0.063 0.22 7 -0.38 13 20
CDC42/GDP 0.005 0 -10000 0 -10000 0 0
S1P/S1P5/G12 0.004 0 -10000 0 -10000 0 0
RHOA -0.005 0.014 -10000 0 -0.19 3 3
S1P/S1P4/Gi 0.003 0.044 0.18 1 -0.19 20 21
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.002 0.04 -10000 0 -0.38 6 6
S1P/S1P4/G12/G13 0.008 0.009 -10000 0 -0.2 1 1
GNA12 0.006 0 -10000 0 -10000 0 0
GNA13 0.006 0.016 -10000 0 -0.38 1 1
CDC42 0.006 0 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.003 0.025 0.14 1 -0.19 9 10
TRAF2/ASK1 0.006 0.026 -10000 0 -0.22 7 7
ATM 0.014 0.04 0.22 20 -10000 0 20
MAP2K3 0.002 0.043 -10000 0 -0.32 4 4
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.012 0.045 0.18 1 -0.22 10 11
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.007 0.024 0.22 4 -0.38 1 5
TXN -0.014 0.062 -10000 0 -0.27 31 31
CALM1 -0.006 0.068 -10000 0 -0.38 18 18
GADD45A 0.024 0.059 0.22 46 -10000 0 46
GADD45B 0.008 0.02 0.22 5 -10000 0 5
MAP3K1 0.004 0.033 -10000 0 -0.38 4 4
MAP3K6 0.006 0 -10000 0 -10000 0 0
MAP3K7 0.01 0.028 0.22 10 -10000 0 10
MAP3K4 0.006 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.006 0.031 -10000 0 -0.27 7 7
TAK1/TAB family 0.004 0.025 -10000 0 -0.33 2 2
RAC1/OSM/MEKK3 0.012 0.009 -10000 0 -0.2 1 1
TRAF2 0.006 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.003 0.033 -10000 0 -0.27 5 5
TRAF6 0.002 0.02 0.15 3 -0.27 2 5
RAC1 0.006 0.016 -10000 0 -0.38 1 1
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.006 0 -10000 0 -10000 0 0
CCM2 0.006 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.001 0.041 -10000 0 -0.22 18 18
MAPK11 0.006 0 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.003 0.045 0.14 1 -0.2 25 26
OSM/MEKK3 0.009 0 -10000 0 -10000 0 0
TAOK1 0.008 0.031 0.15 22 -0.27 1 23
TAOK2 0.008 0.028 0.15 20 -10000 0 20
TAOK3 0.008 0.028 0.15 20 -10000 0 20
MAP3K7IP1 0.006 0 -10000 0 -10000 0 0
MAPK14 0.007 0.009 0.22 1 -10000 0 1
MAP3K7IP2 0.005 0.025 0.22 1 -0.38 2 3
MAP3K5 0.002 0.044 0.22 1 -0.38 7 8
MAP3K10 0.006 0 -10000 0 -10000 0 0
MAP3K3 0.006 0 -10000 0 -10000 0 0
TRX/ASK1 -0.01 0.062 0.16 1 -0.24 36 37
GADD45/MTK1/MTK1 0.024 0.033 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.013 0.03 -10000 0 -0.2 10 10
HDAC3 0.006 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.004 0.001 -10000 0 -10000 0 0
GATA1/HDAC4 0.009 0 -10000 0 -10000 0 0
GATA1/HDAC5 0.007 0.026 -10000 0 -0.27 5 5
GATA2/HDAC5 0.005 0.035 -10000 0 -0.27 9 9
HDAC5/BCL6/BCoR 0.004 0.044 -10000 0 -0.23 20 20
HDAC9 0.015 0.042 0.22 22 -10000 0 22
Glucocorticoid receptor/Hsp90/HDAC6 0.007 0.036 -10000 0 -0.23 13 13
HDAC4/ANKRA2 0.009 0.012 -10000 0 -0.27 1 1
HDAC5/YWHAB 0.007 0.026 -10000 0 -0.27 5 5
NPC/RanGAP1/SUMO1/Ubc9 0.003 0.005 -10000 0 -10000 0 0
GATA2 0.004 0.034 0.22 1 -0.38 4 5
HDAC4/RFXANK 0.009 0.001 -10000 0 -10000 0 0
BCOR 0.007 0.009 0.22 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.006 0 -10000 0 -10000 0 0
HDAC5 0.003 0.037 -10000 0 -0.38 5 5
GNB1/GNG2 0.007 0.026 -10000 0 -0.27 5 5
Histones 0.007 0.027 0.18 1 -0.21 4 5
ADRBK1 0.006 0 -10000 0 -10000 0 0
HDAC4 0.006 0 -10000 0 -10000 0 0
XPO1 0.026 0.062 0.22 52 -10000 0 52
HDAC5/ANKRA2 0.006 0.029 -10000 0 -0.27 6 6
HDAC4/Ubc9 0.009 0 -10000 0 -10000 0 0
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.006 0.029 -10000 0 -0.27 6 6
TUBA1B 0.006 0 -10000 0 -10000 0 0
HDAC6 0.008 0.02 0.22 5 -10000 0 5
HDAC5/RFXANK 0.007 0.026 -10000 0 -0.27 5 5
CAMK4 0.01 0.027 0.22 9 -10000 0 9
Tubulin/HDAC6 0.013 0.001 -10000 0 -10000 0 0
SUMO1 0.006 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.007 0.009 0.22 1 -10000 0 1
GATA1 0.006 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.006 0.016 -10000 0 -0.38 1 1
NR3C1 -0.003 0.058 -10000 0 -0.38 13 13
SUMO1/HDAC4 0.01 0.001 -10000 0 -10000 0 0
SRF 0.002 0.04 -10000 0 -0.38 6 6
HDAC4/YWHAB 0.009 0 -10000 0 -10000 0 0
Tubulin 0.009 0 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.009 0.012 -10000 0 -0.27 1 1
GNB1 0.006 0.016 -10000 0 -0.38 1 1
RANGAP1 0.006 0 -10000 0 -10000 0 0
BCL6/BCoR 0.002 0.045 -10000 0 -0.27 15 15
HDAC4/HDAC3/SMRT (N-CoR2) 0.009 0.03 -10000 0 -0.23 9 9
HDAC4/SRF 0.01 0.024 -10000 0 -0.23 6 6
HDAC4/ER alpha -0.021 0.086 -10000 0 -0.27 61 61
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.007 0.027 0.18 1 -0.2 4 5
cell motility 0.013 0.001 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.006 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0.005 0 -10000 0 -10000 0 0
BCL6 -0.004 0.063 -10000 0 -0.38 15 15
HDAC4/CaMK II delta B 0.006 0 -10000 0 -10000 0 0
Hsp90/HDAC6 0.009 0.001 -10000 0 -10000 0 0
ESR1 -0.036 0.12 -10000 0 -0.38 61 61
HDAC6/HDAC11 0.009 0.001 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.021 0.035 -10000 0 -10000 0 0
NPC 0.004 0 -10000 0 -10000 0 0
MEF2C -0.005 0.067 -10000 0 -0.38 17 17
RAN 0.006 0 -10000 0 -10000 0 0
HDAC4/MEF2C 0.009 0.044 -10000 0 -0.19 26 26
GNG2 0.004 0.034 0.22 1 -0.38 4 5
NCOR2 0 0.049 -10000 0 -0.38 9 9
TUBB2A 0.006 0 -10000 0 -10000 0 0
HDAC11 0.006 0 -10000 0 -10000 0 0
HSP90AA1 0.006 0 -10000 0 -10000 0 0
RANBP2 0.007 0.013 0.22 2 -10000 0 2
ANKRA2 0.006 0.019 0.22 1 -0.38 1 2
RFXANK 0.008 0.018 0.22 4 -10000 0 4
nuclear import -0.005 0.026 0.24 6 -10000 0 6
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.006 0.046 -10000 0 -0.2 26 26
MAP4K1 0.007 0.013 0.22 2 -10000 0 2
MAP3K8 0.006 0 -10000 0 -10000 0 0
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0.006 0 -10000 0 -10000 0 0
CRKL 0.006 0 -10000 0 -10000 0 0
MAP3K1 -0.008 0.044 -10000 0 -10000 0 0
JUN 0.002 0.025 0.16 1 -0.18 3 4
MAP3K7 -0.005 0.045 -10000 0 -10000 0 0
GRAP2 0.006 0 -10000 0 -10000 0 0
CRK 0.006 0 -10000 0 -10000 0 0
MAP2K4 -0.009 0.046 -10000 0 -10000 0 0
LAT 0.006 0 -10000 0 -10000 0 0
LCP2 -0.013 0.085 -10000 0 -0.38 28 28
MAPK8 0.002 0.016 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.005 0.044 -10000 0 -0.21 26 26
LAT/GRAP2/SLP76/HPK1/HIP-55 0.009 0.044 -10000 0 -0.19 26 26
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.009 0.022 -10000 0 -0.22 6 6
PI3K Class IB/PDE3B 0.009 0.022 0.22 6 -10000 0 6
PDE3B 0.009 0.022 0.22 6 -10000 0 6
Arf6 trafficking events

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
SLC2A4 0.006 0 -10000 0 -10000 0 0
CLTC 0.01 0.033 -10000 0 -0.52 1 1
calcium ion-dependent exocytosis 0.006 0.023 -10000 0 -0.22 2 2
Dynamin 2/GTP 0.005 0.01 0.14 1 -0.2 1 2
EXOC4 0.009 0.024 0.22 7 -10000 0 7
CD59 0.007 0.029 -10000 0 -0.47 1 1
CPE -0.009 0.062 0.16 23 -0.23 32 55
CTNNB1 0.007 0.009 0.22 1 -10000 0 1
membrane fusion 0.006 0.023 -10000 0 -0.22 2 2
CTNND1 0.002 0.031 -10000 0 -0.19 1 1
DNM2 0.007 0.009 0.22 1 -10000 0 1
mol:PI-4-5-P2 0.007 0.023 -10000 0 -0.36 1 1
TSHR 0.002 0.03 0.16 18 -0.22 1 19
INS 0.006 0.008 -10000 0 -10000 0 0
BIN1 0.005 0.023 -10000 0 -0.38 2 2
mol:Choline 0.006 0.023 -10000 0 -0.22 2 2
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.005 0.038 0.16 31 -0.22 1 32
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.006 0.016 -10000 0 -0.38 1 1
mol:Ca2+ 0.005 0.01 0.14 1 -0.2 1 2
JUP 0.003 0.039 -10000 0 -0.47 1 1
ASAP2/amphiphysin II 0.007 0.015 -10000 0 -0.2 3 3
ARF6/GTP 0.004 0.011 -10000 0 -0.27 1 1
CDH1 0.003 0.039 -10000 0 -0.47 1 1
clathrin-independent pinocytosis 0.004 0.011 -10000 0 -0.27 1 1
MAPK8IP3 0.006 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0.004 0.011 -10000 0 -0.27 1 1
EXOC2 0.01 0.03 0.22 11 -10000 0 11
substrate adhesion-dependent cell spreading 0.01 0.022 0.2 1 -10000 0 1
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.007 0.009 0.22 1 -10000 0 1
regulation of calcium-dependent cell-cell adhesion -0.004 0.029 0.44 1 -10000 0 1
positive regulation of phagocytosis -0.004 0.009 -10000 0 -0.22 1 1
ARF6/GTP/JIP3 0.008 0.01 -10000 0 -0.22 1 1
ACAP1 0.006 0.02 -10000 0 -0.2 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.008 0.028 -10000 0 -0.47 1 1
clathrin heavy chain/ACAP1 0.01 0.031 -10000 0 -0.44 1 1
JIP4/KLC1 0.013 0.014 0.14 4 -0.2 1 5
EXOC1 0.008 0.02 0.22 5 -10000 0 5
exocyst 0.01 0.023 0.2 1 -10000 0 1
RALA/GTP 0.005 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.008 0.01 -10000 0 -0.22 1 1
receptor recycling 0.004 0.011 -10000 0 -0.27 1 1
CTNNA1 0.001 0.033 0.13 1 -0.19 3 4
NME1 0.005 0.038 0.16 31 -0.22 1 32
clathrin coat assembly 0.01 0.033 -10000 0 -0.51 1 1
IL2RA 0.008 0.029 -10000 0 -0.47 1 1
VAMP3 -0.004 0.009 -10000 0 -0.22 1 1
GLUT4/clathrin heavy chain/ACAP1 0.01 0.026 -10000 0 -0.42 1 1
EXOC6 0.007 0.013 0.22 2 -10000 0 2
PLD1 0.009 0.029 -10000 0 -0.24 1 1
PLD2 0.002 0.012 -10000 0 -0.19 2 2
EXOC5 0.007 0.009 0.22 1 -10000 0 1
PIP5K1C 0.007 0.023 -10000 0 -0.36 1 1
SDC1 0.008 0.029 -10000 0 -0.47 1 1
ARF6/GDP 0.012 0.033 0.14 31 -0.22 1 32
EXOC7 0.006 0 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.011 0.039 -10000 0 -0.45 1 1
mol:Phosphatidic acid 0.006 0.023 -10000 0 -0.22 2 2
endocytosis -0.007 0.015 0.2 3 -10000 0 3
SCAMP2 0.006 0.016 -10000 0 -0.38 1 1
ADRB2 0.009 0.032 -10000 0 -0.49 1 1
EXOC3 0.007 0.009 0.22 1 -10000 0 1
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.014 0.032 0.14 32 -0.2 1 33
KLC1 0.007 0.016 0.22 3 -10000 0 3
AVPR2 0.009 0.032 -10000 0 -0.49 1 1
RALA 0.007 0.009 0.22 1 -10000 0 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.008 0.038 -10000 0 -0.43 1 1
Alternative 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
IKK alpha homodimer 0.009 0.001 -10000 0 -10000 0 0
FBXW11 0.006 0 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.006 0 -10000 0 -10000 0 0
CHUK 0.011 0.031 0.22 12 -10000 0 12
NF kappa B2 p100/RelB 0.02 0.023 -10000 0 -0.19 3 3
NFKB1 -0.001 0.054 -10000 0 -0.38 11 11
MAP3K14 0.006 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelB 0.003 0.043 -10000 0 -0.27 14 14
RELB 0.004 0.028 -10000 0 -0.38 3 3
NFKB2 0.006 0 -10000 0 -10000 0 0
NF kappa B2 p52/RelB 0.007 0.017 -10000 0 -0.22 3 3
regulation of B cell activation 0.007 0.017 -10000 0 -0.22 3 3
Visual signal transduction: Rods

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
mol:K + 0.006 0 -10000 0 -10000 0 0
GNAT1/GTP 0.005 0 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.009 0 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.009 0.001 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.006 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel 0.007 0.031 -10000 0 -0.18 15 15
mol:Na + 0.008 0.03 -10000 0 -0.18 15 15
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.01 0.026 -10000 0 -0.23 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.011 0.032 -10000 0 -0.18 15 15
CNGB1 0.006 0 -10000 0 -10000 0 0
RDH5 0.01 0.03 0.22 11 -10000 0 11
SAG 0.006 0 -10000 0 -10000 0 0
mol:Ca2+ -0.013 0.027 -10000 0 -10000 0 0
Na + (4 Units) 0.006 0.029 -10000 0 -0.17 15 15
RGS9 0.007 0.009 0.22 1 -10000 0 1
GNB1/GNGT1 0.009 0.012 -10000 0 -0.27 1 1
GNAT1/GDP 0.013 0.023 -10000 0 -0.19 7 7
GUCY2D 0.006 0 -10000 0 -10000 0 0
GNGT1 0.01 0.027 0.22 9 -10000 0 9
GUCY2F 0.006 0 -10000 0 -10000 0 0
GNB5 0.001 0.043 -10000 0 -0.38 7 7
mol:GMP (4 units) 0.006 0.011 -10000 0 -10000 0 0
mol:11-cis-retinal 0.01 0.03 0.22 11 -10000 0 11
mol:cGMP 0.014 0.008 -10000 0 -10000 0 0
GNB1 0.006 0.016 -10000 0 -0.38 1 1
Rhodopsin 0.009 0.001 -10000 0 -10000 0 0
SLC24A1 0.006 0 -10000 0 -10000 0 0
CNGA1 -0.004 0.063 -10000 0 -0.38 15 15
Metarhodopsin II 0.004 0 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.017 0.008 -10000 0 -10000 0 0
RGS9BP 0.006 0 -10000 0 -10000 0 0
Metarhodopsin II/Transducin 0.005 0.016 -10000 0 -0.21 1 1
GCAP Family/Ca ++ 0.013 0.008 -10000 0 -10000 0 0
PDE6A/B 0.009 0.001 -10000 0 -10000 0 0
mol:Pi 0.01 0.026 -10000 0 -0.23 7 7
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.014 0.018 -10000 0 -0.2 1 1
PDE6B 0.007 0.009 0.22 1 -10000 0 1
PDE6A 0.007 0.009 0.22 1 -10000 0 1
PDE6G 0.007 0.013 0.22 2 -10000 0 2
RHO 0.006 0 -10000 0 -10000 0 0
PDE6 0.017 0.024 -10000 0 -0.18 7 7
GUCA1A 0.006 0 -10000 0 -10000 0 0
GC2/GCAP Family 0.017 0.008 -10000 0 -10000 0 0
GUCA1C 0.007 0.013 0.22 2 -10000 0 2
GUCA1B 0.006 0 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.017 0.047 0.22 28 -10000 0 28
Ran/GTP/Exportin 1/HDAC4 -0.004 0.001 -10000 0 -10000 0 0
MDM2/SUMO1 0.01 0.014 -10000 0 -0.18 1 1
HDAC4 0.006 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.004 0.001 -10000 0 -10000 0 0
SUMO1 0.006 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.002 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.013 0.038 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.006 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.007 0.013 0.22 2 -10000 0 2
SUMO1/HDAC4 0.01 0.001 -10000 0 -10000 0 0
SUMO1/HDAC1 0.016 0.029 0.2 1 -10000 0 1
RANGAP1 0.006 0 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.02 0.024 -10000 0 -0.2 1 1
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.003 0.005 -10000 0 -10000 0 0
Ran/GTP 0.006 0.005 -10000 0 -10000 0 0
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.007 0.024 0.22 4 -0.38 1 5
UBE2I 0.006 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.015 0.033 -10000 0 -10000 0 0
NPC 0.004 0 -10000 0 -10000 0 0
PIAS2 0.011 0.031 0.22 12 -10000 0 12
PIAS1 0.007 0.009 0.22 1 -10000 0 1
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.01 0.02 0.13 1 -0.19 5 6
MAPK9 0.001 0.013 0.15 1 -0.27 1 2
adrenocorticotropin secretion -0.002 0.008 0.2 1 -10000 0 1
GNB1/GNG2 0.006 0.022 -10000 0 -0.22 5 5
GNB1 0.006 0.016 -10000 0 -0.38 1 1
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 0.002 0.006 0.15 1 -10000 0 1
Gs family/GTP 0.004 0 -10000 0 -10000 0 0
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 0 -10000 0 -10000 0 0
GNAL 0.006 0 -10000 0 -10000 0 0
GNG2 0.004 0.034 0.22 1 -0.38 4 5
CRH 0.007 0.009 0.22 1 -10000 0 1
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.003 0.014 0.15 5 -10000 0 5
MAPK11 0.001 0 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.011 0 -10000 0 -10000 0 0
RGS9BP 0.006 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.008 0 -10000 0 -10000 0 0
mol:ADP -0.002 0 -10000 0 -10000 0 0
GNAT2 0.006 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.01 0.026 -10000 0 -0.23 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.009 0 -10000 0 -10000 0 0
GRK7 0.006 0 -10000 0 -10000 0 0
CNGB3 0.006 0 -10000 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.005 0 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0 -10000 0 -10000 0 0
Cone PDE6 0.016 0.024 -10000 0 -0.19 7 7
Cone Metarhodopsin II 0.004 0 -10000 0 -10000 0 0
Na + (4 Units) 0.012 0 -10000 0 -10000 0 0
GNAT2/GDP 0.013 0.023 -10000 0 -0.19 7 7
GNB5 0.001 0.043 -10000 0 -0.38 7 7
mol:GMP (4 units) -0.004 0 -10000 0 -10000 0 0
Cone Transducin 0.012 0 -10000 0 -10000 0 0
SLC24A2 0.006 0 -10000 0 -10000 0 0
GNB3/GNGT2 0.009 0 -10000 0 -10000 0 0
GNB3 0.006 0 -10000 0 -10000 0 0
GNAT2/GTP 0.005 0 -10000 0 -10000 0 0
CNGA3 0.006 0 -10000 0 -10000 0 0
ARR3 0.006 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.009 0 -10000 0 -10000 0 0
mol:Pi 0.01 0.026 -10000 0 -0.23 7 7
Cone CNG Channel 0.015 0 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.006 0 -10000 0 -10000 0 0
RGS9 0.007 0.009 0.22 1 -10000 0 1
PDE6C 0.006 0 -10000 0 -10000 0 0
GNGT2 0.006 0 -10000 0 -10000 0 0
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.006 0 -10000 0 -10000 0 0
Glypican 2 network

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
MDK 0.007 0.013 0.22 2 -9999 0 2
GPC2 0.006 0 -10000 0 -9999 0 0
GPC2/Midkine 0.009 0.001 -10000 0 -9999 0 0
neuron projection morphogenesis 0.009 0.001 -10000 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 570 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.61.2614 TCGA.61.2613 TCGA.61.2612 TCGA.61.2113
109_MAP3K5 0.0039 0.0039 0.0039 0.0039
47_PPARGC1A 0.0063 0.0063 0.0063 0.0063
105_BMP4 0.0063 0.0063 0.0063 0.0063
105_BMP6 0.0063 0.0063 0.0063 0.0063
105_BMP7 0.22 0.0063 0.0063 0.0063
105_BMP2 0.0063 0.0063 0.0063 0.0063
131_RELN/VLDLR 0.016 0.016 0.016 0.14
30_TGFB1/TGF beta receptor Type II 0.0062 0.0062 0.0062 0.0062
84_STAT5B -0.048 -0.048 -0.048 0.068
84_STAT5A -0.048 -0.048 -0.048 0.068
Methods & Data
Input

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

  • mRNA Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/OV-TP/4393852/GDAC_MergeDataFiles_4397232/OV-TP.exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data.data.txt

  • Copy Number File Used = Copy number data was not used in this analysis.

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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)
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle