PARADIGM pathway analysis of mRNA expression and copy number data
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C10P0XJ9
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNA expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C10P0XJ9
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 75 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 344
PLK2 and PLK4 events 210
Circadian rhythm pathway 153
TCGA08_retinoblastoma 140
S1P3 pathway 139
PLK1 signaling events 137
Osteopontin-mediated events 116
Effects of Botulinum toxin 107
Nongenotropic Androgen signaling 107
Signaling events regulated by Ret tyrosine kinase 105
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 569 . 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 ( 569 ).

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 0.6046 344 17561 51 -0.041 1.9 1000 -1000 -0.043 -1000
PLK2 and PLK4 events 0.3691 210 632 3 0.015 0.066 1000 -1000 -0.02 -1000
Circadian rhythm pathway 0.2689 153 3383 22 -0.095 0.27 1000 -1000 -0.036 -1000
TCGA08_retinoblastoma 0.2460 140 1123 8 -0.077 0.069 1000 -1000 -0.001 -1000
S1P3 pathway 0.2443 139 5838 42 -0.54 0.04 1000 -1000 -0.043 -1000
PLK1 signaling events 0.2408 137 11669 85 -0.12 0.24 1000 -1000 -0.03 -1000
Osteopontin-mediated events 0.2039 116 4435 38 -0.039 0.19 1000 -1000 -0.04 -1000
Effects of Botulinum toxin 0.1880 107 2804 26 -0.12 0.054 1000 -1000 -0.026 -1000
Nongenotropic Androgen signaling 0.1880 107 5575 52 -0.16 0.086 1000 -1000 -0.03 -1000
Signaling events regulated by Ret tyrosine kinase 0.1845 105 8677 82 -0.2 0.029 1000 -1000 -0.057 -1000
Aurora B signaling 0.1582 90 6086 67 -0.063 0.18 1000 -1000 -0.041 -1000
TCGA08_rtk_signaling 0.1547 88 2306 26 -0.032 0.044 1000 -1000 -0.023 -1000
IGF1 pathway 0.1529 87 4999 57 -0.088 0.052 1000 -1000 -0.049 -1000
Endothelins 0.1494 85 8237 96 -0.11 0.09 1000 -1000 -0.044 -1000
Syndecan-1-mediated signaling events 0.1476 84 2856 34 -0.046 0.033 1000 -1000 -0.031 -1000
mTOR signaling pathway 0.1459 83 4448 53 -0.16 0.029 1000 -1000 -0.036 -1000
FoxO family signaling 0.1388 79 5112 64 -0.022 0.36 1000 -1000 -0.031 -1000
Retinoic acid receptors-mediated signaling 0.1388 79 4606 58 -0.39 0.05 1000 -1000 -0.045 -1000
IL2 signaling events mediated by STAT5 0.1388 79 1748 22 -0.36 0.029 1000 -1000 -0.028 -1000
Ras signaling in the CD4+ TCR pathway 0.1318 75 1288 17 0 0.03 1000 -1000 -0.015 -1000
Insulin Pathway 0.1230 70 5182 74 -0.1 0.058 1000 -1000 -0.052 -1000
Ephrin B reverse signaling 0.1213 69 3331 48 -0.17 0.044 1000 -1000 -0.041 -1000
TCGA08_p53 0.1213 69 488 7 -0.007 0.028 1000 -1000 -0.016 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.1178 67 5640 83 -0.13 0.064 1000 -1000 -0.037 -1000
Thromboxane A2 receptor signaling 0.1160 66 6981 105 -0.16 0.044 1000 -1000 -0.045 -1000
Aurora A signaling 0.1125 64 3880 60 -0.003 0.17 1000 -1000 -0.026 -1000
Reelin signaling pathway 0.1090 62 3478 56 -0.073 0.073 1000 -1000 -0.028 -1000
LPA receptor mediated events 0.1090 62 6335 102 -0.057 0.033 1000 -1000 -0.049 -1000
IL2 signaling events mediated by PI3K 0.1072 61 3556 58 -0.17 0.029 1000 -1000 -0.022 -1000
Canonical Wnt signaling pathway 0.1072 61 3143 51 -0.33 0.14 1000 -1000 -0.031 -1000
BARD1 signaling events 0.1019 58 3319 57 -0.045 0.2 1000 -1000 -0.042 -1000
TRAIL signaling pathway 0.1019 58 2826 48 -0.032 0.032 1000 -1000 -0.029 -1000
Integrins in angiogenesis 0.1019 58 4951 84 -0.083 0.055 1000 -1000 -0.055 -1000
Insulin-mediated glucose transport 0.1002 57 1837 32 -0.087 0.036 1000 -1000 -0.024 -1000
Presenilin action in Notch and Wnt signaling 0.0967 55 3394 61 -0.3 0.064 1000 -1000 -0.034 -1000
IL4-mediated signaling events 0.0949 54 4944 91 -0.56 0.3 1000 -1000 -0.083 -1000
PDGFR-alpha signaling pathway 0.0949 54 2408 44 -0.093 0.037 1000 -1000 -0.032 -1000
Nectin adhesion pathway 0.0949 54 3423 63 -0.12 0.047 1000 -1000 -0.04 -1000
Class I PI3K signaling events 0.0949 54 3977 73 -0.032 0.085 1000 -1000 -0.027 -1000
Plasma membrane estrogen receptor signaling 0.0949 54 4684 86 -0.13 0.13 1000 -1000 -0.055 -1000
Signaling events mediated by the Hedgehog family 0.0931 53 2782 52 -0.044 0.049 1000 -1000 -0.036 -1000
IL1-mediated signaling events 0.0931 53 3291 62 -0.07 0.057 1000 -1000 -0.048 -1000
HIF-2-alpha transcription factor network 0.0931 53 2280 43 -0.056 0.19 1000 -1000 -0.037 -1000
Regulation of Telomerase 0.0931 53 5470 102 -0.26 0.065 1000 -1000 -0.046 -1000
Wnt signaling 0.0914 52 368 7 0.007 0.029 1000 -1000 -0.014 -1000
Signaling mediated by p38-gamma and p38-delta 0.0896 51 771 15 -0.083 0.027 1000 -1000 -0.031 -1000
Coregulation of Androgen receptor activity 0.0826 47 3601 76 -0.34 0.043 1000 -1000 -0.027 -1000
amb2 Integrin signaling 0.0826 47 3888 82 -0.056 0.075 1000 -1000 -0.033 -1000
Signaling events mediated by PRL 0.0826 47 1599 34 -0.063 0.051 1000 -1000 -0.032 -1000
IL23-mediated signaling events 0.0808 46 2772 60 -0.01 0.23 1000 -1000 -0.027 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0791 45 2361 52 -0.15 0.096 1000 -1000 -0.029 -1000
p75(NTR)-mediated signaling 0.0738 42 5374 125 -0.071 0.075 1000 -1000 -0.062 -1000
Paxillin-dependent events mediated by a4b1 0.0721 41 1510 36 -0.076 0.063 1000 -1000 -0.04 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0685 39 903 23 -0.014 0.091 1000 -1000 -0.021 -1000
Glucocorticoid receptor regulatory network 0.0685 39 4447 114 -0.3 0.16 1000 -1000 -0.063 -1000
FAS signaling pathway (CD95) 0.0685 39 1859 47 -0.036 0.046 1000 -1000 -0.026 -1000
BMP receptor signaling 0.0650 37 3026 81 -0.054 0.054 1000 -1000 -0.041 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0633 36 1342 37 -0.018 0.066 1000 -1000 -0.036 -1000
Regulation of nuclear SMAD2/3 signaling 0.0615 35 4770 136 -0.1 0.14 1000 -1000 -0.028 -1000
Canonical NF-kappaB pathway 0.0615 35 1381 39 -0.055 0.05 1000 -1000 -0.03 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0615 35 1580 45 -0.085 0.066 1000 -1000 -0.048 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0598 34 1153 33 -0.012 0.076 1000 -1000 -0.031 -1000
PDGFR-beta signaling pathway 0.0598 34 3367 97 -0.073 0.06 1000 -1000 -0.057 -1000
Arf6 signaling events 0.0580 33 2058 62 -0.014 0.067 1000 -1000 -0.016 -1000
IL12-mediated signaling events 0.0562 32 2802 87 -0.36 0.049 1000 -1000 -0.07 -1000
Signaling events mediated by PTP1B 0.0562 32 2459 76 -0.077 0.037 1000 -1000 -0.028 -1000
EPHB forward signaling 0.0562 32 2730 85 -0.07 0.13 1000 -1000 -0.063 -1000
Regulation of p38-alpha and p38-beta 0.0562 32 1750 54 -0.053 0.062 1000 -1000 -0.041 -1000
E-cadherin signaling in the nascent adherens junction 0.0562 32 2475 76 -0.09 0.056 1000 -1000 -0.057 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0562 32 3889 120 -0.16 0.075 1000 -1000 -0.052 -1000
Noncanonical Wnt signaling pathway 0.0545 31 819 26 -0.024 0.042 1000 -1000 -0.036 -1000
Syndecan-3-mediated signaling events 0.0545 31 1113 35 -0.012 0.043 1000 -1000 -0.028 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0527 30 2591 85 -0.067 0.068 1000 -1000 -0.031 -1000
Caspase cascade in apoptosis 0.0510 29 2205 74 -0.057 0.041 1000 -1000 -0.034 -1000
E-cadherin signaling events 0.0510 29 148 5 0.026 0.044 1000 -1000 0.026 -1000
ErbB2/ErbB3 signaling events 0.0492 28 1822 65 -0.037 0.092 1000 -1000 -0.039 -1000
ErbB4 signaling events 0.0492 28 1935 69 -0.032 0.18 1000 -1000 -0.044 -1000
Syndecan-2-mediated signaling events 0.0492 28 1949 69 -0.039 0.041 1000 -1000 -0.029 -1000
Glypican 1 network 0.0492 28 1380 48 -0.043 0.053 1000 -1000 -0.027 -1000
ceramide signaling pathway 0.0492 28 1379 49 -0.052 0.041 1000 -1000 -0.029 -1000
HIF-1-alpha transcription factor network 0.0475 27 2065 76 -0.043 0.34 1000 -1000 -0.075 -1000
BCR signaling pathway 0.0475 27 2752 99 -0.07 0.068 1000 -1000 -0.059 -1000
E-cadherin signaling in keratinocytes 0.0475 27 1192 43 -0.049 0.044 1000 -1000 -0.03 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0457 26 1434 54 -0.059 0.039 1000 -1000 -0.051 -1000
Cellular roles of Anthrax toxin 0.0457 26 1032 39 -0.13 0.029 1000 -1000 -0.023 -1000
IL6-mediated signaling events 0.0457 26 1986 75 -0.27 0.047 1000 -1000 -0.026 -1000
EGFR-dependent Endothelin signaling events 0.0457 26 561 21 -0.056 0.058 1000 -1000 -0.051 -1000
Aurora C signaling 0.0439 25 176 7 -0.001 0.039 1000 -1000 -0.016 -1000
Fc-epsilon receptor I signaling in mast cells 0.0439 25 2513 97 -0.062 0.06 1000 -1000 -0.06 -1000
TCR signaling in naïve CD8+ T cells 0.0439 25 2355 93 -0.094 0.077 1000 -1000 -0.045 -1000
FOXA2 and FOXA3 transcription factor networks 0.0422 24 1128 46 -0.03 0.25 1000 -1000 -0.037 -1000
IFN-gamma pathway 0.0422 24 1654 68 -0.063 0.067 1000 -1000 -0.05 -1000
Ceramide signaling pathway 0.0422 24 1865 76 -0.038 0.065 1000 -1000 -0.026 -1000
Syndecan-4-mediated signaling events 0.0422 24 1650 67 -0.027 0.076 1000 -1000 -0.039 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0422 24 1936 78 -0.18 0.038 1000 -1000 -0.039 -1000
Atypical NF-kappaB pathway 0.0404 23 715 31 -0.038 0.029 1000 -1000 -0.035 -1000
IL27-mediated signaling events 0.0404 23 1184 51 -0.03 0.074 1000 -1000 -0.043 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0404 23 1710 74 -0.13 0.072 1000 -1000 -0.062 -1000
Regulation of Androgen receptor activity 0.0387 22 1600 70 -0.39 0.045 1000 -1000 -0.03 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0369 21 734 34 -0.04 0.081 1000 -1000 -0.032 -1000
Class I PI3K signaling events mediated by Akt 0.0369 21 1483 68 -0.1 0.053 1000 -1000 -0.036 -1000
Signaling events mediated by HDAC Class I 0.0369 21 2206 104 -0.046 0.065 1000 -1000 -0.038 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0351 20 561 28 -0.031 0.04 1000 -1000 -0.019 -1000
JNK signaling in the CD4+ TCR pathway 0.0351 20 349 17 -0.027 0.058 1000 -1000 -0.026 -1000
EPO signaling pathway 0.0351 20 1143 55 -0.076 0.035 1000 -1000 -0.041 -1000
Arf1 pathway 0.0351 20 1115 54 -0.029 0.035 1000 -1000 -0.025 -1000
Signaling events mediated by HDAC Class II 0.0334 19 1449 75 -0.033 0.058 1000 -1000 -0.038 -1000
Hedgehog signaling events mediated by Gli proteins 0.0334 19 1282 65 -0.036 0.054 1000 -1000 -0.045 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0334 19 2496 125 -0.075 0.067 1000 -1000 -0.07 -1000
S1P5 pathway 0.0316 18 312 17 -0.02 0.029 1000 -1000 -0.012 -1000
VEGFR1 specific signals 0.0316 18 1010 56 -0.053 0.052 1000 -1000 -0.046 -1000
p38 MAPK signaling pathway 0.0316 18 820 44 -0.02 0.054 1000 -1000 -0.022 -1000
Arf6 downstream pathway 0.0299 17 763 43 -0.046 0.056 1000 -1000 -0.029 -1000
Signaling events mediated by HDAC Class III 0.0299 17 710 40 -0.051 0.057 1000 -1000 -0.033 -1000
Calcium signaling in the CD4+ TCR pathway 0.0299 17 556 31 -0.07 0.029 1000 -1000 -0.044 -1000
Class IB PI3K non-lipid kinase events 0.0281 16 48 3 -0.028 0.028 1000 -1000 -0.026 -1000
a4b1 and a4b7 Integrin signaling 0.0246 14 70 5 0.027 0.04 1000 -1000 0.026 -1000
Signaling mediated by p38-alpha and p38-beta 0.0246 14 640 44 -0.039 0.046 1000 -1000 -0.037 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0246 14 381 27 -0.039 0.063 1000 -1000 -0.042 -1000
S1P4 pathway 0.0246 14 364 25 -0.029 0.04 1000 -1000 -0.027 -1000
Alternative NF-kappaB pathway 0.0246 14 189 13 0 0.074 1000 -1000 0 -1000
Visual signal transduction: Cones 0.0228 13 528 38 -0.019 0.059 1000 -1000 -0.021 -1000
Ephrin A reverse signaling 0.0228 13 92 7 -0.025 0.034 1000 -1000 -0.02 -1000
S1P1 pathway 0.0193 11 430 36 -0.02 0.029 1000 -1000 -0.036 -1000
Arf6 trafficking events 0.0193 11 816 71 -0.034 0.051 1000 -1000 -0.031 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0193 11 1040 88 -0.045 0.041 1000 -1000 -0.068 -1000
Visual signal transduction: Rods 0.0193 11 597 52 -0.067 0.068 1000 -1000 -0.052 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0158 9 630 68 -0.057 0.046 1000 -1000 -0.067 -1000
Rapid glucocorticoid signaling 0.0123 7 147 20 -0.016 0.037 1000 -1000 -0.015 -1000
Glypican 2 network 0.0105 6 26 4 0.028 0.042 1000 -1000 0.027 -1000
LPA4-mediated signaling events 0.0088 5 71 12 -0.026 0 1000 -1000 -0.016 -1000
Total NA 6061 327125 7203 -11 12 131000 -131000 -4.6 -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 0.39 1.3 474 -10000 0 474
PLK1 0.32 0.38 0.95 112 -10000 0 112
BIRC5 0.35 0.41 1 120 -10000 0 120
HSPA1B 1.2 0.39 1.4 475 -10000 0 475
MAP2K1 0.48 0.17 0.52 498 -10000 0 498
BRCA2 1.4 0.53 1.5 476 -10000 0 476
FOXM1 1.9 0.91 2.3 458 -10000 0 458
XRCC1 1.2 0.42 1.4 476 -10000 0 476
FOXM1B/p19 0.27 0.47 1.1 123 -10000 0 123
Cyclin D1/CDK4 0.67 0.51 1.1 325 -10000 0 325
CDC2 1.5 0.49 1.7 482 -10000 0 482
TGFA 0.74 0.51 1.1 349 -10000 0 349
SKP2 1.4 0.55 1.6 480 -10000 0 480
CCNE1 0.009 0.033 0.13 33 -10000 0 33
CKS1B 1.5 0.58 1.7 481 -10000 0 481
RB1 0.036 0.18 0.8 25 -0.74 2 27
FOXM1C/SP1 0.89 0.44 1.1 416 -10000 0 416
AURKB 0.34 0.4 1 117 -0.74 1 118
CENPF 1.7 0.54 1.8 495 -10000 0 495
CDK4 0.13 0.072 0.18 343 -10000 0 343
MYC 0.58 0.53 1.1 278 -10000 0 278
CHEK2 0.41 0.18 0.48 467 -10000 0 467
ONECUT1 0.76 0.55 1.2 342 -10000 0 342
CDKN2A -0.023 0.11 -10000 0 -0.34 52 52
LAMA4 1.1 0.51 1.4 441 -1.1 3 444
FOXM1B/HNF6 0.76 0.56 1.2 336 -10000 0 336
FOS 1.1 0.54 1.4 425 -10000 0 425
SP1 -0.041 0.086 -10000 0 -0.069 400 400
CDC25B 1.2 0.45 1.4 479 -10000 0 479
response to radiation 0.25 0.074 0.27 497 -10000 0 497
CENPB 1.2 0.44 1.4 476 -10000 0 476
CENPA 1.2 0.4 1.4 477 -10000 0 477
NEK2 1.6 0.57 1.8 483 -10000 0 483
HIST1H2BA 1.2 0.43 1.4 477 -10000 0 477
CCNA2 0.01 0.032 0.12 37 -10000 0 37
EP300 0.027 0.008 -10000 0 -10000 0 0
CCNB1/CDK1 1.4 0.58 1.7 455 -10000 0 455
CCNB2 1.7 0.53 1.8 496 -10000 0 496
CCNB1 1.8 0.65 2 479 -10000 0 479
ETV5 1.4 0.58 1.6 483 -10000 0 483
ESR1 1 0.55 1.3 415 -1 2 417
CCND1 0.78 0.55 1.2 348 -10000 0 348
GSK3A 0.27 0.1 0.31 470 -10000 0 470
Cyclin A-E1/CDK1-2 0.031 0.1 0.36 44 -10000 0 44
CDK2 0.076 0.07 0.14 284 -10000 0 284
G2/M transition of mitotic cell cycle 0.44 0.14 0.47 507 -10000 0 507
FOXM1B/Cbp/p300 0.084 0.25 0.89 28 -10000 0 28
GAS1 1 0.55 1.3 414 -1 1 415
MMP2 1.1 0.56 1.4 430 -1.1 3 433
RB1/FOXM1C 0.57 0.56 1.1 271 -10000 0 271
CREBBP 0.027 0.008 -10000 0 -10000 0 0
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 0.022 0.013 -10000 0 0 135 135
PLK4 0.015 0.015 -10000 0 0 268 268
regulation of centriole replication 0.066 0.11 0.19 229 -9999 0 229
Circadian rhythm pathway

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
chromatin modification 0.003 0.033 0.42 3 -10000 0 3
CLOCK 0.05 0.034 0.088 227 -0.079 3 230
TIMELESS/CRY2 0.19 0.23 0.45 242 -10000 0 242
DEC1/BMAL1 0.058 0.027 -10000 0 -10000 0 0
ATR 0.022 0.013 -10000 0 0 140 140
NR1D1 0.13 0.24 0.42 31 -0.81 13 44
ARNTL 0.051 0.034 0.088 230 -0.079 3 233
TIMELESS 0.27 0.32 0.63 242 -10000 0 242
NPAS2 0.051 0.034 0.088 229 -0.079 3 232
CRY2 0.029 0.003 -10000 0 0 6 6
mol:CO -0.095 0.11 0.13 3 -0.22 245 248
CHEK1 0.002 0.007 -10000 0 0 527 527
mol:HEME 0.095 0.11 0.22 245 -0.13 3 248
PER1 0.027 0.007 -10000 0 0 37 37
BMAL/CLOCK/NPAS2 0.14 0.13 0.29 227 -0.17 3 230
BMAL1/CLOCK 0.13 0.2 0.36 216 -0.66 6 222
S phase of mitotic cell cycle 0.003 0.033 0.42 3 -10000 0 3
TIMELESS/CHEK1/ATR 0.003 0.034 0.42 3 -10000 0 3
mol:NADPH 0.095 0.11 0.22 245 -0.13 3 248
PER1/TIMELESS 0.18 0.23 0.45 229 -10000 0 229
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.028 0.005 -10000 0 0 16 16
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 -0.042 0.033 -10000 0 -0.063 353 353
CDKN2C -0.019 0.049 -10000 0 -0.065 276 276
CDKN2A 0.013 0.023 -10000 0 -0.065 6 6
CCND2 -0.022 0.039 -10000 0 -0.12 39 39
RB1 0.069 0.088 0.17 189 -0.2 7 196
CDK4 -0.015 0.038 -10000 0 -0.14 40 40
CDK6 -0.017 0.037 -10000 0 -0.29 2 2
G1/S progression -0.077 0.092 0.2 7 -0.18 204 211
S1P3 pathway

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
PDGFRB 0.029 0.005 -10000 0 0 15 15
mol:S1P -0.016 0.016 0.072 4 -0.03 283 287
S1P1/S1P/Gi -0.053 0.092 0.26 4 -0.23 49 53
GNAO1 -0.02 0.046 0.12 4 -0.063 285 289
S1P/S1P3/G12/G13 -0.015 0.047 0.16 4 -0.076 1 5
AKT1 -0.043 0.11 0.27 2 -0.5 21 23
AKT3 -0.54 0.5 0.67 3 -0.98 316 319
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.028 0.005 -10000 0 0 15 15
GNAI2 -0.022 0.047 0.12 4 -0.063 314 318
GNAI3 -0.017 0.04 0.099 2 -0.057 265 267
GNAI1 -0.018 0.044 0.1 4 -0.058 296 300
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 -0.018 0.019 0.087 4 -0.034 288 292
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.13 0.15 0.43 4 -0.27 267 271
MAPK3 -0.14 0.14 0.38 4 -0.27 269 273
MAPK1 -0.14 0.14 0.38 4 -0.27 262 266
JAK2 -0.14 0.15 0.34 5 -0.28 234 239
CXCR4 -0.14 0.14 0.36 3 -0.27 264 267
FLT1 -0.025 0.052 0.16 4 -0.072 295 299
RhoA/GDP 0.021 0.007 -10000 0 -0.15 1 1
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
SRC -0.13 0.14 0.38 4 -0.27 244 248
S1P/S1P3/Gi -0.13 0.15 0.43 4 -0.27 267 271
RAC1 0.028 0.006 -10000 0 0 27 27
RhoA/GTP -0.12 0.15 0.36 4 -0.26 265 269
VEGFA -0.022 0.05 0.16 4 -0.07 272 276
S1P/S1P2/Gi -0.074 0.1 0.31 4 -0.25 52 56
VEGFR1 homodimer/VEGFA homodimer -0.029 0.074 0.34 4 -0.11 53 57
RHOA 0.029 0.003 -10000 0 0 6 6
S1P/S1P3/Gq -0.029 0.06 -10000 0 -0.2 48 48
GNAQ 0.028 0.007 -10000 0 0 29 29
GNAZ -0.017 0.043 0.1 4 -0.058 284 288
G12/G13 0.04 0.011 -10000 0 -10000 0 0
GNA14 0.028 0.005 -10000 0 0 19 19
GNA15 0.027 0.008 -10000 0 0 46 46
GNA12 0.028 0.007 -10000 0 0 33 33
GNA13 0.029 0.004 -10000 0 0 13 13
GNA11 0.025 0.01 -10000 0 0 83 83
Rac1/GTP -0.12 0.15 0.36 4 -0.26 266 270
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.12 0.044 0.15 1 -0.13 480 481
BUB1B 0.16 0.069 0.19 460 -0.14 1 461
PLK1 0.069 0.029 0.082 394 -10000 0 394
PLK1S1 0.034 0.017 0.053 179 -10000 0 179
KIF2A 0.047 0.031 0.15 11 -10000 0 11
regulation of mitotic centrosome separation 0.069 0.029 0.082 394 -10000 0 394
GOLGA2 0.028 0.005 -10000 0 0 16 16
Hec1/SPC24 0.005 0.019 -10000 0 -10000 0 0
WEE1 0.081 0.065 0.18 5 -0.28 9 14
cytokinesis 0.22 0.087 0.26 461 -0.16 1 462
PP2A-alpha B56 0.13 0.081 -10000 0 -0.49 6 6
AURKA 0.08 0.036 0.12 125 -10000 0 125
PICH/PLK1 0.11 0.083 0.17 332 -10000 0 332
CENPE 0.063 0.061 0.22 56 -10000 0 56
RhoA/GTP 0.021 0.007 -10000 0 -0.15 1 1
positive regulation of microtubule depolymerization 0.05 0.03 0.15 11 -10000 0 11
PPP2CA 0.029 0.004 -10000 0 0 13 13
FZR1 0.027 0.008 -10000 0 0 45 45
TPX2 0.11 0.031 0.12 470 -10000 0 470
PAK1 0.028 0.011 -10000 0 -0.029 7 7
SPC24 0.02 0.014 -10000 0 0 175 175
FBXW11 0.028 0.005 -10000 0 0 16 16
CLSPN 0.049 0.035 0.14 37 -0.22 3 40
GORASP1 0.029 0.003 -10000 0 0 6 6
metaphase 0.002 0.005 0.012 86 -0.01 1 87
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.034 0.017 0.053 179 -10000 0 179
G2 phase of mitotic cell cycle 0.005 0.003 0.018 20 -10000 0 20
STAG2 0.028 0.006 -10000 0 0 22 22
GRASP65/GM130/RAB1/GTP 0.024 0.041 -10000 0 -0.56 2 2
spindle elongation 0.069 0.029 0.082 394 -10000 0 394
ODF2 0.034 0.007 -10000 0 -0.03 2 2
BUB1 0.002 0.05 -10000 0 -0.61 3 3
TPT1 0.03 0.042 0.1 1 -0.15 25 26
CDC25C 0.083 0.061 0.16 90 -0.23 5 95
CDC25B 0.03 0.02 -10000 0 -0.031 33 33
SGOL1 0.12 0.044 0.14 480 -0.15 1 481
RHOA 0.029 0.003 -10000 0 0 6 6
CCNB1/CDK1 0.008 0.025 -10000 0 -0.14 1 1
CDC14B -0.014 0.003 0.001 20 -10000 0 20
CDC20 0.007 0.012 -10000 0 0 431 431
PLK1/PBIP1 0.04 0.026 0.073 125 -10000 0 125
mitosis 0 0.001 -10000 0 -10000 0 0
FBXO5 0.13 0.078 0.18 360 -0.13 4 364
CDC2 0.007 0.004 0.009 386 -10000 0 386
NDC80 0.003 0.009 -10000 0 0 503 503
metaphase plate congression 0.045 0.042 0.13 1 -0.2 12 13
ERCC6L 0.093 0.078 0.16 325 -0.15 1 326
NLP/gamma Tubulin 0.029 0.026 0.06 104 -0.079 10 114
microtubule cytoskeleton organization 0.03 0.042 0.1 1 -0.15 25 26
G2/M transition DNA damage checkpoint 0.001 0.002 0.014 4 -10000 0 4
PPP1R12A 0.031 0.007 -10000 0 -0.03 3 3
interphase 0.001 0.002 0.014 4 -10000 0 4
PLK1/PRC1-2 0.007 0.022 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.09 0.03 0.14 11 -10000 0 11
RAB1A 0.029 0.004 -10000 0 0 10 10
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.071 0.025 0.08 445 -10000 0 445
mitotic prometaphase 0.003 0.004 0.023 14 -10000 0 14
proteasomal ubiquitin-dependent protein catabolic process 0.065 0.053 -10000 0 -0.29 3 3
microtubule-based process 0.009 0.023 0.098 6 -10000 0 6
Golgi organization 0.069 0.029 0.082 394 -10000 0 394
Cohesin/SA2 0.067 0.026 0.1 109 -10000 0 109
PPP1CB/MYPT1 0.045 0.014 -10000 0 -0.17 1 1
KIF20A 0.005 0.011 -10000 0 0 469 469
APC/C/CDC20 0.013 0.028 0.099 7 -10000 0 7
PPP2R1A 0.028 0.006 -10000 0 0 21 21
chromosome segregation 0.039 0.026 0.072 125 -10000 0 125
PRC1 0.007 0.013 -10000 0 0 424 424
ECT2 0.24 0.069 0.25 520 -10000 0 520
C13orf34 0.062 0.025 0.072 405 -10000 0 405
NUDC 0.045 0.042 0.13 1 -0.2 12 13
regulation of attachment of spindle microtubules to kinetochore 0.16 0.069 0.19 460 -0.14 1 461
spindle assembly 0.048 0.026 0.08 148 -10000 0 148
spindle stabilization 0.034 0.017 0.053 179 -10000 0 179
APC/C/HCDH1 -0.018 0.016 -10000 0 -10000 0 0
MKLP2/PLK1 0.009 0.023 0.099 6 -10000 0 6
CCNB1 0.005 0.012 -10000 0 -10000 0 0
PPP1CB 0.03 0.009 -10000 0 -0.028 8 8
BTRC 0.028 0.005 -10000 0 0 16 16
ROCK2 0.055 0.032 0.16 4 -0.22 3 7
TUBG1 0.031 0.045 0.12 5 -0.16 25 30
G2/M transition of mitotic cell cycle 0.12 0.08 0.17 372 -10000 0 372
MLF1IP -0.013 0.011 0.003 78 -10000 0 78
INCENP 0.034 0.006 -10000 0 -0.031 2 2
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 0.1 0.2 0.37 173 -0.28 2 175
NF kappa B1 p50/RelA/I kappa B alpha 0.11 0.24 0.43 171 -0.33 4 175
alphaV/beta3 Integrin/Osteopontin/Src 0.025 0.058 0.16 60 -0.19 7 67
AP1 0.085 0.28 0.47 158 -0.34 18 176
ILK 0.075 0.17 0.28 177 -0.3 2 179
bone resorption -0.008 0.15 0.25 79 -0.34 3 82
PTK2B 0.024 0.011 -10000 0 0 101 101
PYK2/p130Cas 0.06 0.14 0.27 97 -0.27 3 100
ITGAV 0.009 0.061 0.1 165 -10000 0 165
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.039 0.1 -10000 0 -0.16 217 217
alphaV/beta3 Integrin/Osteopontin 0.022 0.1 0.25 59 -0.16 62 121
MAP3K1 0.075 0.17 0.34 120 -0.3 2 122
JUN 0.026 0.028 0.098 29 -0.034 63 92
MAPK3 0.13 0.25 0.47 177 -0.32 1 178
MAPK1 0.13 0.25 0.48 175 -0.32 1 176
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.008 -10000 0 0 46 46
MAPK8 0.074 0.18 0.36 122 -0.3 2 124
ITGB3 0.012 0.06 0.1 163 -10000 0 163
NFKBIA 0.13 0.25 0.47 177 -0.33 2 179
FOS 0.023 0.026 0.095 24 -0.035 50 74
CD44 0.017 0.015 -10000 0 0 239 239
CHUK 0.027 0.007 -10000 0 0 36 36
PLAU 0.19 0.37 0.72 170 -0.57 2 172
NF kappa B1 p50/RelA 0.12 0.27 0.49 171 -0.32 1 172
BCAR1 0.026 0.009 -10000 0 0 57 57
RELA 0.029 0.003 -10000 0 0 6 6
alphaV beta3 Integrin 0.04 0.11 0.17 155 -0.18 66 221
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.069 0.16 0.31 122 -0.29 2 124
VAV3 0.069 0.16 0.3 142 -0.28 2 144
MAP3K14 0.12 0.22 0.4 178 -0.29 2 180
ROCK2 0.028 0.005 -10000 0 0 18 18
SPP1 -0.005 0.038 0.09 65 -10000 0 65
RAC1 0.028 0.006 -10000 0 0 27 27
Rac1/GTP 0.055 0.15 0.26 135 -0.27 2 137
MMP2 0.018 0.19 0.33 90 -0.35 35 125
Effects of Botulinum toxin

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
STX1A -0.017 0.002 0 7 -10000 0 7
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.041 0.01 -10000 0 -10000 0 0
STXBP1 0.025 0.01 -10000 0 0 76 76
ACh/CHRNA1 -0.043 0.044 -10000 0 -0.073 365 365
RAB3GAP2/RIMS1/UNC13B 0.054 0.018 -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 0.028 0.005 -10000 0 0 20 20
mol:ACh -0.055 0.038 0.077 2 -0.081 362 364
RAB3GAP2 0.028 0.006 -10000 0 0 27 27
STX1A/SNAP25/VAMP2 -0.1 0.095 -10000 0 -0.17 343 343
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.043 0.043 -10000 0 -0.073 365 365
UNC13B 0.029 0.005 -10000 0 0 14 14
CHRNA1 0.027 0.007 -10000 0 0 36 36
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.042 0.044 -10000 0 -0.073 364 364
SNAP25 0.001 0 -10000 0 -10000 0 0
VAMP2 -0.12 0.082 -10000 0 -0.18 389 389
SYT1 0.028 0.007 -10000 0 0 34 34
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 -0.037 0.033 -10000 0 -0.13 57 57
STX1A/SNAP25 fragment 1/VAMP2 -0.1 0.095 -10000 0 -0.17 343 343
Nongenotropic Androgen signaling

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
PTK2 -0.012 0.008 0 163 -10000 0 163
GNB1/GNG2 -0.053 0.09 -10000 0 -0.13 314 314
regulation of S phase of mitotic cell cycle -0.08 0.11 0.13 1 -0.2 224 225
GNAO1 0.024 0.015 -10000 0 -0.011 74 74
HRAS 0.022 0.02 -10000 0 -0.023 87 87
SHBG/T-DHT 0.019 0.004 -10000 0 -10000 0 0
PELP1 0.021 0.021 -10000 0 -0.024 89 89
AKT1 -0.016 0.004 0 27 -10000 0 27
MAP2K1 -0.082 0.098 0.22 23 -0.24 39 62
T-DHT/AR -0.078 0.083 -10000 0 -0.15 319 319
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.003 0.011 26 -0.007 22 48
GNAI2 0.025 0.015 -10000 0 -0.025 43 43
GNAI3 0.022 0.015 -10000 0 -0.005 117 117
GNAI1 0.026 0.013 -10000 0 -0.014 50 50
mol:GDP -0.16 0.14 -10000 0 -0.29 270 270
cell proliferation -0.12 0.18 0.38 25 -0.46 64 89
PIK3CA 0.02 0.014 -10000 0 0 170 170
FOS -0.1 0.26 0.56 26 -0.71 66 92
mol:Ca2+ -0.012 0.023 0.054 16 -0.059 31 47
MAPK3 -0.11 0.14 0.32 24 -0.37 60 84
MAPK1 -0.063 0.15 0.31 26 -0.45 39 65
PIK3R1 0.021 0.013 -10000 0 0 159 159
mol:IP3 0 0.004 0.016 26 -10000 0 26
cAMP biosynthetic process -0.001 0.025 0.27 3 -10000 0 3
GNG2 0.029 0.004 -10000 0 0 12 12
potassium channel inhibitor activity 0 0.004 0.016 26 -10000 0 26
HRAS/GTP -0.049 0.093 0.22 12 -0.13 281 293
actin cytoskeleton reorganization 0.002 0.057 -10000 0 -0.12 77 77
SRC 0.021 0.02 -10000 0 -0.021 92 92
voltage-gated calcium channel activity 0 0.004 0.016 26 -10000 0 26
PI3K 0.001 0.057 -10000 0 -0.13 77 77
apoptosis 0.086 0.18 0.45 68 -0.45 24 92
T-DHT/AR/PELP1 -0.063 0.083 -10000 0 -0.13 315 315
HRAS/GDP -0.15 0.15 0.13 3 -0.3 238 241
CREB1 -0.11 0.15 -10000 0 -0.47 72 72
RAC1-CDC42/GTP 0.008 0.061 -10000 0 -0.12 77 77
AR 0.01 0.017 -10000 0 -0.002 351 351
GNB1 0.028 0.006 -10000 0 0 24 24
RAF1 -0.075 0.091 0.22 14 -0.21 33 47
RAC1-CDC42/GDP -0.15 0.15 -10000 0 -0.31 225 225
T-DHT/AR/PELP1/Src -0.051 0.088 -10000 0 -0.13 283 283
MAP2K2 -0.092 0.1 0.22 19 -0.23 76 95
T-DHT/AR/PELP1/Src/PI3K -0.081 0.11 0.14 1 -0.2 224 225
GNAZ 0.024 0.014 -10000 0 -0.01 72 72
SHBG 0.028 0.006 -10000 0 0 25 25
Gi family/GNB1/GNG2/GDP -0.041 0.1 -10000 0 -0.36 25 25
mol:T-DHT 0 0.001 -10000 0 -10000 0 0
RAC1 0.028 0.006 -10000 0 0 27 27
GNRH1 -0.014 0.007 0 105 -10000 0 105
Gi family/GTP -0.046 0.066 0.16 1 -0.2 36 37
CDC42 0.029 0.004 -10000 0 0 11 11
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.001 0.048 -10000 0 -0.4 5 5
Crk/p130 Cas/Paxillin -0.17 0.097 -10000 0 -0.27 220 220
JUN -0.071 0.091 0.18 3 -0.26 22 25
HRAS 0.028 0.006 -10000 0 0 26 26
RET51/GFRalpha1/GDNF/GRB10 -0.018 0.1 -10000 0 -0.14 222 222
RAP1A 0.029 0.003 -10000 0 0 7 7
FRS2 0.028 0.007 -10000 0 0 30 30
RAP1A/GDP 0.021 0.002 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.018 0.1 -10000 0 -0.14 223 223
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.029 0.003 -10000 0 0 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.007 -10000 0 0 36 36
RET9/GFRalpha1/GDNF/Enigma -0.025 0.089 -10000 0 -0.13 225 225
RHOA 0.029 0.003 -10000 0 0 6 6
RAP1A/GTP -0.019 0.098 -10000 0 -0.14 220 220
GRB7 0.027 0.008 -10000 0 0 40 40
RET51/GFRalpha1/GDNF -0.012 0.097 -10000 0 -0.14 188 188
MAPKKK cascade -0.091 0.076 0.1 1 -0.24 2 3
BCAR1 0.026 0.009 -10000 0 0 57 57
RET9/GFRalpha1/GDNF/IRS1 -0.11 0.097 -10000 0 -0.16 404 404
lamellipodium assembly -0.15 0.097 -10000 0 -0.24 228 228
RET51/GFRalpha1/GDNF/SHC -0.016 0.1 -10000 0 -0.14 216 216
PIK3CA 0.02 0.014 -10000 0 0 170 170
RET9/GFRalpha1/GDNF/SHC -0.024 0.088 -10000 0 -0.13 219 219
RET9/GFRalpha1/GDNF/Shank3 -0.032 0.084 -10000 0 -0.13 224 224
MAPK3 -0.073 0.078 0.28 3 -0.22 9 12
DOK1 0.029 0.004 -10000 0 0 10 10
DOK6 0.027 0.008 -10000 0 0 50 50
PXN 0.029 0.005 -10000 0 0 14 14
neurite development -0.077 0.086 0.24 5 -0.29 20 25
DOK5 0.016 0.015 -10000 0 0 245 245
GFRA1 0.016 0.015 -10000 0 0 257 257
MAPK8 -0.072 0.088 0.18 1 -0.26 22 23
HRAS/GTP -0.038 0.12 -10000 0 -0.18 200 200
tube development -0.035 0.082 0.21 4 -0.13 219 223
MAPK1 -0.067 0.074 0.29 2 -10000 0 2
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.057 0.089 -10000 0 -0.17 206 206
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
SRC 0.028 0.007 -10000 0 0 33 33
PDLIM7 0.028 0.005 -10000 0 0 16 16
RET51/GFRalpha1/GDNF/Dok6 -0.017 0.1 -10000 0 -0.14 213 213
SHC1 0.028 0.006 -10000 0 0 21 21
RET51/GFRalpha1/GDNF/Dok4 -0.019 0.1 -10000 0 -0.14 222 222
RET51/GFRalpha1/GDNF/Dok5 0.008 0.099 -10000 0 -0.15 135 135
PRKCA 0.028 0.006 -10000 0 0 22 22
HRAS/GDP 0.021 0.005 -10000 0 -10000 0 0
CREB1 -0.065 0.11 0.22 1 -0.38 7 8
PIK3R1 0.021 0.013 -10000 0 0 159 159
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.062 0.094 -10000 0 -0.18 216 216
RET51/GFRalpha1/GDNF/Grb7 -0.019 0.1 -10000 0 -0.14 220 220
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.029 0.004 -10000 0 0 11 11
DOK4 0.027 0.007 -10000 0 0 38 38
JNK cascade -0.069 0.091 0.18 5 -0.25 22 27
RET9/GFRalpha1/GDNF/FRS2 -0.024 0.087 -10000 0 -0.13 216 216
SHANK3 0.022 0.012 -10000 0 0 131 131
RASA1 0.027 0.008 -10000 0 0 49 49
NCK1 0.026 0.009 -10000 0 0 64 64
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.052 0.088 -10000 0 -0.28 5 5
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.055 0.091 0.2 1 -0.28 6 7
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.056 0.1 0.2 1 -0.27 22 23
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.052 0.091 -10000 0 -0.3 5 5
PI3K -0.2 0.14 0.33 1 -0.34 218 219
SOS1 0.027 0.007 -10000 0 0 36 36
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.025 0.092 -10000 0 -0.13 219 219
GRB10 0.029 0.004 -10000 0 0 13 13
activation of MAPKK activity -0.05 0.089 0.18 1 -0.28 4 5
RET51/GFRalpha1/GDNF/FRS2 -0.017 0.1 -10000 0 -0.14 213 213
GAB1 0.028 0.006 -10000 0 0 24 24
IRS1 0.011 0.014 -10000 0 0 349 349
IRS2 0.028 0.006 -10000 0 0 25 25
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.059 0.095 -10000 0 -0.27 16 16
RET51/GFRalpha1/GDNF/PKC alpha -0.017 0.1 -10000 0 -0.14 221 221
GRB2 0.028 0.005 -10000 0 0 19 19
PRKACA 0.025 0.01 -10000 0 0 79 79
GDNF 0.027 0.007 -10000 0 0 37 37
RAC1 0.028 0.006 -10000 0 0 27 27
RET51/GFRalpha1/GDNF/IRS1 -0.11 0.11 -10000 0 -0.17 395 395
Rac1/GTP -0.17 0.12 -10000 0 -0.29 218 218
RET9/GFRalpha1/GDNF -0.034 0.083 -10000 0 -0.13 226 226
GFRalpha1/GDNF -0.044 0.099 -10000 0 -0.16 226 226
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.033 0.072 0.2 81 -0.32 1 82
STMN1 0.032 0.093 0.2 126 -10000 0 126
Aurora B/RasGAP/Survivin 0.047 0.039 -10000 0 -0.11 1 1
Chromosomal passenger complex/Cul3 protein complex 0.009 0.096 0.21 48 -0.2 13 61
BIRC5 0.038 0.022 0.061 66 -10000 0 66
DES -0.052 0.14 -10000 0 -0.52 18 18
Aurora C/Aurora B/INCENP 0.054 0.035 -10000 0 -10000 0 0
Aurora B/TACC1 -0.063 0.072 -10000 0 -0.13 310 310
Aurora B/PP2A 0.036 0.023 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.004 0.013 0.12 3 -0.11 3 6
mitotic metaphase/anaphase transition -0.005 0.005 -10000 0 -10000 0 0
NDC80 0.13 0.1 0.21 356 -10000 0 356
Cul3 protein complex -0.011 0.094 -10000 0 -0.15 178 178
KIF2C 0.11 0.095 0.2 297 -10000 0 297
PEBP1 0.042 0.009 0.061 6 -10000 0 6
KIF20A 0.002 0.012 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.034 0.026 -10000 0 -0.15 2 2
SEPT1 0.029 0.004 -10000 0 0 12 12
SMC2 0.016 0.015 -10000 0 0 246 246
SMC4 0.001 0.006 -10000 0 0 534 534
NSUN2/NPM1/Nucleolin 0.001 0.037 -10000 0 -0.41 3 3
PSMA3 0.028 0.005 -10000 0 0 17 17
G2/M transition of mitotic cell cycle 0 0.003 0.02 1 -10000 0 1
H3F3B 0.009 0.018 0.14 1 -0.2 3 4
AURKB 0.028 0.019 0.063 2 -10000 0 2
AURKC 0.028 0.006 -10000 0 0 27 27
CDCA8 0.041 0.021 0.062 107 -10000 0 107
cytokinesis 0.004 0.034 0.24 10 -10000 0 10
Aurora B/Septin1 0.14 0.12 0.26 261 -10000 0 261
AURKA 0.002 0.007 -10000 0 -10000 0 0
INCENP 0.052 0.013 0.065 186 -10000 0 186
KLHL13 0.019 0.014 -10000 0 0 194 194
BUB1 0.002 0.008 -10000 0 -10000 0 0
hSgo1/Aurora B/Survivin 0.008 0.024 -10000 0 -10000 0 0
EVI5 0.04 0.009 0.058 28 -10000 0 28
RhoA/GTP 0.002 0.013 -10000 0 -10000 0 0
SGOL1 0.004 0.01 -10000 0 0 485 485
CENPA 0.017 0.047 0.17 29 -10000 0 29
NCAPG 0.002 0.007 -10000 0 0 523 523
Aurora B/HC8 Proteasome 0.036 0.024 -10000 0 -0.16 1 1
NCAPD2 0.014 0.015 -10000 0 0 296 296
Aurora B/PP1-gamma 0.036 0.023 -10000 0 -10000 0 0
RHOA 0.029 0.003 -10000 0 0 6 6
NCAPH 0.011 0.014 -10000 0 0 347 347
NPM1 0 0.012 -10000 0 -0.29 1 1
RASA1 0.027 0.008 -10000 0 0 49 49
KLHL9 0.027 0.007 -10000 0 0 37 37
mitotic prometaphase 0.013 0.006 0.021 149 -10000 0 149
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.024 -10000 0 -0.16 1 1
PPP1CC 0.028 0.006 -10000 0 0 22 22
Centraspindlin 0.002 0.012 -10000 0 -10000 0 0
RhoA/GDP 0.021 0.007 -10000 0 -0.15 1 1
NSUN2 0 0.012 -10000 0 -0.29 1 1
MYLK -0.005 0.055 0.14 1 -0.2 39 40
KIF23 0.001 0.005 -10000 0 -10000 0 0
VIM 0.011 0.068 0.18 71 -10000 0 71
RACGAP1 0.005 0.013 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0 0.012 -10000 0 -0.29 1 1
Chromosomal passenger complex 0.18 0.12 0.24 392 -10000 0 392
Chromosomal passenger complex/EVI5 0.064 0.057 -10000 0 -10000 0 0
TACC1 0.005 0.011 -10000 0 0 458 458
PPP2R5D 0.028 0.006 -10000 0 0 26 26
CUL3 0.029 0.004 -10000 0 0 9 9
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
TCGA08_rtk_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
PDGFRA 0.024 0.011 -10000 0 0 96 96
HRAS 0.028 0.006 -10000 0 0 26 26
EGFR 0.026 0.009 -10000 0 0 55 55
AKT -0.032 0.12 0.22 26 -0.25 35 61
FOXO3 0.027 0.007 -10000 0 0 38 38
AKT1 0.028 0.006 -10000 0 0 27 27
FOXO1 0.027 0.007 -10000 0 0 39 39
AKT3 0.012 0.014 -10000 0 0 332 332
FOXO4 0.029 0.003 -10000 0 0 7 7
MET 0.025 0.011 -10000 0 0 86 86
PIK3CA 0.02 0.014 -10000 0 0 170 170
PIK3CB 0.025 0.01 -10000 0 0 83 83
NRAS 0.014 0.015 -10000 0 0 300 300
PIK3CG 0.027 0.007 -10000 0 0 36 36
PIK3R3 0.019 0.014 -10000 0 0 205 205
PIK3R2 0.027 0.008 -10000 0 0 49 49
NF1 0.026 0.009 -10000 0 0 60 60
RAS 0.044 0.075 0.17 79 -0.25 5 84
ERBB2 0.027 0.008 -10000 0 0 41 41
proliferation/survival/translation 0.016 0.12 0.32 29 -0.22 12 41
PI3K 0.04 0.096 0.2 76 -0.21 21 97
PIK3R1 0.021 0.013 -10000 0 0 159 159
KRAS 0.024 0.011 -10000 0 0 99 99
FOXO 0.024 0.081 0.22 33 -10000 0 33
AKT2 0.027 0.009 -10000 0 0 52 52
PTEN 0.028 0.007 -10000 0 0 30 30
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.029 0.004 -10000 0 0 10 10
PTK2 0.021 0.013 -10000 0 0 163 163
CRKL -0.079 0.075 0.13 6 -0.2 128 134
GRB2/SOS1/SHC 0.052 0.02 -10000 0 -10000 0 0
HRAS 0.028 0.006 -10000 0 0 26 26
IRS1/Crk -0.08 0.072 0.098 3 -0.2 128 131
IGF-1R heterotetramer/IGF1/PTP1B 0.011 0.099 -10000 0 -0.17 120 120
AKT1 -0.052 0.11 0.15 47 -0.23 74 121
BAD -0.06 0.1 0.16 26 -0.23 74 100
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.079 0.074 0.12 5 -0.2 126 131
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.083 0.073 0.17 3 -0.22 103 106
RAF1 -0.037 0.11 0.27 4 -0.47 3 7
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.048 0.1 0.18 2 -0.2 124 126
YWHAZ 0.025 0.01 -10000 0 0 78 78
IGF-1R heterotetramer/IGF1/IRS1 -0.061 0.094 0.16 2 -0.21 134 136
PIK3CA 0.02 0.014 -10000 0 0 170 170
RPS6KB1 -0.054 0.11 0.15 45 -0.23 71 116
GNB2L1 0.029 0.005 -10000 0 0 15 15
positive regulation of MAPKKK cascade -0.031 0.1 0.26 9 -0.35 3 12
PXN 0.029 0.005 -10000 0 0 14 14
PIK3R1 0.021 0.013 -10000 0 0 159 159
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.039 0.013 -10000 0 -10000 0 0
HRAS/GTP -0.088 0.067 0.048 3 -0.21 115 118
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.036 0.1 -10000 0 -0.15 116 116
IGF-1R heterotetramer 0.005 0.037 0.045 227 -0.089 8 235
IGF-1R heterotetramer/IGF1/IRS/Nck -0.056 0.098 0.17 3 -0.2 134 137
Crk/p130 Cas/Paxillin -0.061 0.1 0.22 2 -0.2 134 136
IGF1R 0.005 0.037 0.045 227 -0.089 8 235
IGF1 -0.008 0.052 0.061 23 -0.089 93 116
IRS2/Crk -0.082 0.071 0.16 2 -0.2 119 121
PI3K -0.053 0.1 -10000 0 -0.19 154 154
apoptosis 0.049 0.1 0.25 22 -0.21 13 35
HRAS/GDP 0.021 0.005 -10000 0 -10000 0 0
PRKCD -0.081 0.11 -10000 0 -0.28 113 113
RAF1/14-3-3 E -0.032 0.11 0.26 4 -0.41 3 7
BAD/14-3-3 -0.051 0.11 0.22 13 -0.26 22 35
PRKCZ -0.054 0.11 0.15 45 -0.23 72 117
Crk/p130 Cas/Paxillin/FAK1 -0.056 0.094 0.14 13 -0.24 47 60
PTPN1 0.027 0.008 -10000 0 0 50 50
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.074 0.12 -10000 0 -0.28 126 126
BCAR1 0.026 0.009 -10000 0 0 57 57
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.026 0.1 0.18 1 -0.15 122 123
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.027 0.007 -10000 0 0 36 36
IRS1/NCK2 -0.082 0.074 0.12 7 -0.2 129 136
GRB10 0.029 0.004 -10000 0 0 13 13
PTPN11 -0.081 0.074 0.13 6 -0.2 131 137
IRS1 -0.056 0.089 0.12 7 -0.21 128 135
IRS2 -0.079 0.074 0.13 6 -0.21 124 130
IGF-1R heterotetramer/IGF1 -0.004 0.12 0.15 3 -0.21 129 132
GRB2 0.028 0.005 -10000 0 0 19 19
PDPK1 -0.048 0.12 0.17 44 -0.23 76 120
YWHAE 0.027 0.008 -10000 0 0 40 40
PRKD1 -0.076 0.11 0.2 4 -0.28 110 114
SHC1 0.028 0.006 -10000 0 0 21 21
Endothelins

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
AKT1 0.044 0.21 0.39 135 -0.32 3 138
PTK2B 0.023 0.015 -10000 0 -0.029 17 17
mol:Ca2+ 0.036 0.2 0.56 12 -0.66 8 20
EDN1 0.025 0.14 0.26 131 -0.22 4 135
EDN3 0.026 0.009 -10000 0 0 60 60
EDN2 0.027 0.008 -10000 0 0 46 46
HRAS/GDP 0.016 0.21 0.42 33 -0.42 36 69
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.015 0.16 0.27 80 -0.37 28 108
ADCY4 0.088 0.19 0.32 181 -0.29 2 183
ADCY5 0.086 0.19 0.32 179 -0.29 2 181
ADCY6 0.09 0.2 0.32 184 -0.29 2 186
ADCY7 0.087 0.19 0.32 177 -0.28 3 180
ADCY1 0.089 0.19 0.32 180 -0.29 2 182
ADCY2 0.085 0.19 0.32 170 -0.29 2 172
ADCY3 0.088 0.19 0.3 214 -0.28 3 217
ADCY8 0.001 0.13 0.32 48 -0.27 20 68
ADCY9 0.084 0.2 0.3 206 -0.27 8 214
arachidonic acid secretion -0.1 0.27 0.57 22 -0.57 78 100
ETB receptor/Endothelin-1/Gq/GTP 0.042 0.14 0.25 90 -0.31 28 118
GNAO1 0.027 0.008 -10000 0 0 45 45
HRAS 0.022 0.02 0.052 5 -0.021 87 92
ETA receptor/Endothelin-1/G12/GTP 0.027 0.16 0.39 70 -0.24 9 79
ETA receptor/Endothelin-1/Gs/GTP 0.04 0.16 0.36 72 -0.22 12 84
mol:GTP 0.003 0.015 0.057 33 -10000 0 33
COL3A1 0.041 0.25 0.55 95 -0.42 4 99
EDNRB 0.05 0.11 0.22 174 -0.12 3 177
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 0.012 0.24 0.39 124 -0.38 79 203
CYSLTR1 0.037 0.22 0.41 122 -0.33 3 125
SLC9A1 0.028 0.14 0.26 124 -0.28 7 131
mol:GDP 0.014 0.21 0.43 31 -0.44 36 67
SLC9A3 0.071 0.2 0.43 12 -0.57 18 30
RAF1 0.003 0.24 0.55 28 -0.44 59 87
JUN 0.031 0.21 0.69 11 -0.72 10 21
JAK2 0.038 0.21 0.39 126 -0.32 4 130
mol:IP3 0.021 0.17 0.31 82 -0.38 29 111
ETA receptor/Endothelin-1 -0.054 0.097 0.32 5 -0.37 4 9
PLCB1 0.021 0.023 0.066 7 -0.033 70 77
PLCB2 0.018 0.027 0.076 17 -0.034 102 119
ETA receptor/Endothelin-3 0.015 0.11 0.2 121 -0.22 1 122
FOS -0.057 0.35 0.73 24 -0.83 68 92
Gai/GDP -0.004 0.2 -10000 0 -0.69 37 37
CRK 0.026 0.013 -10000 0 -0.029 19 19
mol:Ca ++ 0.078 0.25 0.41 152 -0.4 24 176
BCAR1 0.021 0.018 -10000 0 -0.029 49 49
PRKCB1 0.038 0.18 0.3 84 -0.37 30 114
GNAQ 0.018 0.032 0.11 13 -0.053 2 15
GNAZ 0.027 0.008 -10000 0 0 47 47
GNAL 0.028 0.005 -10000 0 0 20 20
Gs family/GDP 0.013 0.2 0.4 31 -0.41 35 66
ETA receptor/Endothelin-1/Gq/GTP 0.015 0.17 0.29 81 -0.37 29 110
MAPK14 0.025 0.13 0.29 25 -0.31 24 49
TRPC6 0.035 0.2 0.57 11 -0.69 8 19
GNAI2 0.029 0.003 -10000 0 0 6 6
GNAI3 0.024 0.011 -10000 0 0 98 98
GNAI1 0.028 0.006 -10000 0 0 26 26
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.034 0.14 0.29 34 -0.32 28 62
ETB receptor/Endothelin-2 0.071 0.068 0.17 157 -0.082 6 163
ETB receptor/Endothelin-3 0.07 0.068 0.17 156 -0.083 4 160
ETB receptor/Endothelin-1 -0.007 0.097 0.32 25 -0.22 4 29
MAPK3 -0.05 0.34 0.7 24 -0.77 69 93
MAPK1 -0.053 0.34 0.69 24 -0.76 70 94
Rac1/GDP 0.015 0.2 0.42 29 -0.43 33 62
cAMP biosynthetic process 0.051 0.18 0.29 119 -0.32 13 132
MAPK8 0.029 0.21 0.58 11 -0.7 14 25
SRC 0.026 0.013 -10000 0 -0.029 22 22
ETB receptor/Endothelin-1/Gi/GTP 0.049 0.11 0.2 146 -0.24 10 156
p130Cas/CRK/Src/PYK2 0.008 0.21 0.49 22 -0.52 26 48
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP 0.014 0.2 0.42 28 -0.43 33 61
COL1A2 0.078 0.28 0.66 90 -0.5 5 95
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.012 0.11 0.2 117 -0.22 1 118
mol:DAG 0.021 0.17 0.31 82 -0.38 29 111
MAP2K2 -0.031 0.27 0.61 26 -0.56 71 97
MAP2K1 -0.02 0.28 0.62 26 -0.56 68 94
EDNRA 0.023 0.15 0.27 134 -0.22 12 146
positive regulation of muscle contraction 0.026 0.17 0.32 127 -0.29 2 129
Gq family/GDP -0.027 0.16 0.41 16 -0.41 31 47
HRAS/GTP 0.021 0.21 0.44 33 -0.42 37 70
PRKCH 0.032 0.18 0.35 33 -0.39 28 61
RAC1 0.028 0.006 -10000 0 0 27 27
PRKCA 0.035 0.17 0.35 34 -0.37 27 61
PRKCB 0.038 0.18 0.3 85 -0.36 32 117
PRKCE 0.035 0.18 0.3 83 -0.37 29 112
PRKCD 0.031 0.18 0.35 35 -0.37 32 67
PRKCG 0.035 0.18 0.36 35 -0.37 28 63
regulation of vascular smooth muscle contraction -0.083 0.4 0.72 24 -0.99 69 93
PRKCQ 0.035 0.18 0.35 40 -0.39 28 68
PLA2G4A -0.11 0.29 0.59 21 -0.62 80 101
GNA14 0.018 0.032 0.11 13 -0.053 2 15
GNA15 0.021 0.026 0.095 13 -0.035 56 69
GNA12 0.028 0.007 -10000 0 0 33 33
GNA11 0.019 0.025 0.1 9 -0.036 34 43
Rac1/GTP 0.026 0.16 0.39 69 -0.23 12 81
MMP1 0.032 0.1 0.4 34 -10000 0 34
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.023 0.012 -10000 0 0 112 112
CCL5 0.025 0.01 -10000 0 0 81 81
SDCBP 0.028 0.007 -10000 0 0 34 34
FGFR/FGF2/Syndecan-1 -0.016 0.14 0.23 43 -0.32 53 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 -0.021 0.14 0.23 38 -0.32 51 89
Syndecan-1/Syntenin -0.015 0.14 0.22 56 -0.31 51 107
MAPK3 -0.036 0.14 0.2 40 -0.3 59 99
HGF/MET 0.033 0.033 -10000 0 -0.16 12 12
TGFB1/TGF beta receptor Type II 0.023 0.012 -10000 0 0 112 112
BSG 0.027 0.008 -10000 0 0 51 51
keratinocyte migration -0.021 0.14 0.22 46 -0.31 51 97
Syndecan-1/RANTES -0.022 0.15 0.23 48 -0.32 67 115
Syndecan-1/CD147 -0.006 0.15 0.24 36 -0.31 57 93
Syndecan-1/Syntenin/PIP2 -0.017 0.14 0.21 47 -0.3 51 98
LAMA5 0.026 0.01 -10000 0 0 68 68
positive regulation of cell-cell adhesion -0.017 0.13 0.21 47 -0.3 51 98
MMP7 0.017 0.014 -10000 0 0 236 236
HGF 0.028 0.005 -10000 0 0 16 16
Syndecan-1/CASK -0.036 0.12 0.19 27 -0.3 59 86
Syndecan-1/HGF/MET -0.007 0.15 0.25 34 -0.3 55 89
regulation of cell adhesion -0.046 0.13 0.18 33 -0.3 57 90
HPSE 0.027 0.008 -10000 0 0 42 42
positive regulation of cell migration -0.016 0.14 0.23 43 -0.32 53 96
SDC1 -0.013 0.13 0.22 41 -0.33 43 84
Syndecan-1/Collagen -0.016 0.14 0.23 43 -0.32 53 96
PPIB 0.029 0.004 -10000 0 0 13 13
MET 0.025 0.011 -10000 0 0 86 86
PRKACA 0.025 0.01 -10000 0 0 79 79
MMP9 0.022 0.012 -10000 0 0 130 130
MAPK1 -0.034 0.13 0.2 39 -0.3 56 95
homophilic cell adhesion -0.016 0.14 0.22 57 -0.31 57 114
MMP1 0.022 0.013 -10000 0 0 142 142
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.029 0.004 -10000 0 0 13 13
mol:PIP3 -0.12 0.11 0.14 14 -0.25 222 236
FRAP1 -0.004 0.066 -10000 0 -0.41 8 8
AKT1 -0.1 0.12 0.15 21 -0.22 208 229
INSR 0.025 0.011 -10000 0 0 85 85
Insulin Receptor/Insulin 0.022 0.047 -10000 0 -0.13 43 43
mol:GTP -0.091 0.11 0.16 16 -0.25 51 67
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.05 0.049 -10000 0 -0.19 12 12
TSC2 0.028 0.006 -10000 0 0 23 23
RHEB/GDP -0.085 0.09 0.11 19 -0.19 173 192
TSC1 0.028 0.006 -10000 0 -0.001 22 22
Insulin Receptor/IRS1 -0.15 0.14 -10000 0 -0.27 335 335
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.047 0.059 0.13 2 -0.22 9 11
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.029 0.003 -10000 0 0 8 8
RPS6KB1 -0.036 0.085 0.21 5 -0.29 13 18
MAP3K5 -0.006 0.047 0.19 6 -0.2 25 31
PIK3R1 0.021 0.014 -10000 0 -0.029 4 4
apoptosis -0.006 0.047 0.19 6 -0.2 26 32
mol:LY294002 -0.001 0.001 -10000 0 -0.001 343 343
EIF4B -0.039 0.079 0.2 6 -0.29 9 15
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.025 0.089 0.2 5 -0.28 9 14
eIF4E/eIF4G1/eIF4A1 -0.028 0.044 -10000 0 -0.26 6 6
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.12 0.13 -10000 0 -0.25 245 245
mTOR/RHEB/GTP/Raptor/GBL -0.029 0.056 0.14 8 -0.17 7 15
FKBP1A 0.019 0.021 -10000 0 -0.029 79 79
RHEB/GTP -0.08 0.097 0.15 21 -0.24 36 57
mol:Amino Acids -0.001 0.001 -10000 0 -0.001 343 343
FKBP12/Rapamycin 0.016 0.015 -10000 0 -10000 0 0
PDPK1 -0.12 0.11 0.13 28 -0.24 212 240
EIF4E 0.027 0.007 -10000 0 0 38 38
ASK1/PP5C 0.002 0.14 -10000 0 -0.54 30 30
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.004 0.069 -10000 0 -0.25 38 38
TSC1/TSC2 -0.096 0.12 0.18 15 -0.27 51 66
tumor necrosis factor receptor activity 0.001 0.001 0.001 343 -10000 0 343
RPS6 0.028 0.007 -10000 0 0 32 32
PPP5C 0.028 0.006 -10000 0 0 25 25
EIF4G1 0.024 0.011 -10000 0 0 95 95
IRS1 -0.16 0.13 -10000 0 -0.27 346 346
INS 0.028 0.006 -10000 0 0 22 22
PTEN 0.012 0.026 -10000 0 -0.03 154 154
PDK2 -0.12 0.11 0.13 28 -0.24 215 243
EIF4EBP1 -0.051 0.27 -10000 0 -1 40 40
PIK3CA 0.012 0.021 -10000 0 -0.029 77 77
PPP2R5D -0.005 0.069 0.25 5 -0.36 8 13
peptide biosynthetic process -0.035 0.039 0.17 9 -0.22 1 10
RHEB 0.026 0.01 -10000 0 -0.002 57 57
EIF4A1 0.028 0.006 -10000 0 0 25 25
mol:Rapamycin 0 0.001 0.003 17 -0.003 1 18
EEF2 -0.035 0.039 0.18 9 -0.22 1 10
eIF4E/4E-BP1 -0.036 0.26 -10000 0 -0.96 40 40
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.025 0.083 0.42 1 -10000 0 1
PLK1 0.27 0.4 0.82 98 -0.8 17 115
CDKN1B 0.19 0.3 0.64 80 -0.47 1 81
FOXO3 0.23 0.41 0.6 252 -0.76 26 278
KAT2B 0.061 0.067 0.11 300 -0.075 5 305
FOXO1/SIRT1 0.008 0.086 0.27 5 -0.27 4 9
CAT 0.24 0.38 0.71 78 -0.81 22 100
CTNNB1 0.023 0.017 -10000 0 -0.029 53 53
AKT1 0.074 0.089 0.19 98 -10000 0 98
FOXO1 0.037 0.095 0.34 4 -0.3 3 7
MAPK10 0.013 0.062 0.2 13 -10000 0 13
mol:GTP 0 0.007 0.027 12 -0.021 1 13
FOXO4 0.012 0.16 0.44 31 -0.49 5 36
response to oxidative stress 0.06 0.069 0.16 95 -0.082 2 97
FOXO3A/SIRT1 0.22 0.37 0.65 103 -0.7 31 134
XPO1 0.017 0.023 -10000 0 -0.031 93 93
EP300 0.016 0.027 0.081 1 -10000 0 1
BCL2L11 0.084 0.14 0.77 1 -1 4 5
FOXO1/SKP2 0.022 0.078 0.39 1 -0.28 3 4
mol:GDP 0.06 0.069 0.16 95 -0.082 2 97
RAN 0.015 0.028 -10000 0 -0.033 133 133
GADD45A 0.19 0.29 0.75 66 -0.67 3 69
YWHAQ 0.029 0.005 -10000 0 0 15 15
FOXO1/14-3-3 family 0.002 0.14 0.2 1 -0.47 28 29
MST1 0.078 0.086 0.14 298 -10000 0 298
CSNK1D 0.028 0.006 -10000 0 0 25 25
CSNK1E 0.027 0.008 -10000 0 0 45 45
FOXO4/14-3-3 family 0.005 0.12 0.22 1 -0.52 17 18
YWHAB 0.027 0.008 -10000 0 0 45 45
MAPK8 0.014 0.064 0.2 17 -10000 0 17
MAPK9 0.014 0.063 0.21 13 -10000 0 13
YWHAG 0.029 0.004 -10000 0 0 11 11
YWHAE 0.027 0.008 -10000 0 0 40 40
YWHAZ 0.025 0.01 -10000 0 0 78 78
SIRT1 -0.011 0.054 0.15 32 -0.098 4 36
SOD2 0.039 0.45 0.61 63 -0.74 109 172
RBL2 0.16 0.37 0.68 38 -0.9 21 59
RAL/GDP 0.066 0.069 0.18 59 -10000 0 59
CHUK 0.077 0.085 0.14 293 -10000 0 293
Ran/GTP 0.015 0.024 -10000 0 -10000 0 0
CSNK1G2 0.027 0.008 -10000 0 0 45 45
RAL/GTP 0.064 0.076 0.25 30 -10000 0 30
CSNK1G1 0.029 0.004 -10000 0 0 13 13
FASLG 0.091 0.093 -10000 0 -10000 0 0
SKP2 0.021 0.013 -10000 0 0 157 157
USP7 0.016 0.026 -10000 0 -0.032 120 120
IKBKB 0.075 0.084 0.15 272 -10000 0 272
CCNB1 0.36 0.42 0.71 292 -0.94 9 301
FOXO1-3a-4/beta catenin 0.12 0.29 0.6 64 -10000 0 64
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.077 0.39 1 -0.28 3 4
CSNK1A1 0.029 0.004 -10000 0 0 13 13
SGK1 0.061 0.067 0.11 300 -0.075 5 305
CSNK1G3 0.028 0.006 -10000 0 0 21 21
Ran/GTP/Exportin 1 0.028 0.036 0.14 1 -10000 0 1
ZFAND5 0.011 0.14 0.46 8 -0.64 2 10
SFN 0.027 0.007 -10000 0 0 37 37
CDK2 -0.01 0.025 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.082 0.15 0.29 55 -0.48 14 69
CREBBP -0.022 0.028 -10000 0 -0.08 1 1
FBXO32 0.094 0.61 0.77 132 -0.8 144 276
BCL6 0.17 0.34 0.66 35 -0.88 22 57
RALB 0.014 0.028 -10000 0 -0.034 142 142
RALA 0.014 0.028 -10000 0 -0.033 137 137
YWHAH 0.027 0.008 -10000 0 0 42 42
Retinoic acid receptors-mediated 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
HDAC1 0.027 0.008 -10000 0 0 49 49
HDAC3 0.029 0.003 -10000 0 0 7 7
VDR 0.029 0.003 -10000 0 0 7 7
Cbp/p300/PCAF 0.032 0.026 -10000 0 -0.13 10 10
EP300 0.027 0.008 -10000 0 0 50 50
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.032 0.08 0.17 1 -0.3 24 25
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.028 0.005 -10000 0 0 19 19
AKT1 0.008 0.09 0.21 12 -0.28 5 17
RAR alpha/9cRA/Cyclin H -0.076 0.13 -10000 0 -0.24 199 199
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.034 0.075 -10000 0 -0.26 32 32
CDC2 -0.005 0.007 -10000 0 -0.017 19 19
response to UV -0.009 0.012 -10000 0 -0.025 199 199
RAR alpha/Jnk1 -0.025 0.067 -10000 0 -0.22 20 20
NCOR2 0.028 0.005 -10000 0 0 17 17
VDR/VDR/Vit D3 0.021 0.002 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.2 0.26 -10000 0 -0.52 207 207
NCOA2 0.027 0.008 -10000 0 0 45 45
NCOA3 0.026 0.009 -10000 0 0 60 60
NCOA1 0.029 0.005 -10000 0 0 15 15
VDR/VDR/DNA 0.029 0.003 -10000 0 0 7 7
RARG 0.003 0.033 -10000 0 -0.04 205 205
RAR gamma1/9cRA 0.01 0.032 -10000 0 -10000 0 0
MAPK3 0.001 0.036 -10000 0 -0.046 202 202
MAPK1 0.027 0.008 -10000 0 0 42 42
MAPK8 -0.002 0.04 -10000 0 -0.053 207 207
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.12 0.17 -10000 0 -0.33 192 192
RARA -0.03 0.053 -10000 0 -0.22 12 12
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.032 0.072 -10000 0 -0.26 28 28
PRKCA -0.012 0.053 -10000 0 -0.083 201 201
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.22 0.29 -10000 0 -0.58 213 213
RXRG -0.027 0.061 -10000 0 -0.24 5 5
RXRA -0.08 0.093 -10000 0 -0.28 28 28
RXRB -0.027 0.052 -10000 0 -0.22 3 3
VDR/Vit D3/DNA 0.021 0.002 -10000 0 -10000 0 0
RBP1 0.019 0.014 -10000 0 0 196 196
CRBP1/9-cic-RA -0.028 0.076 -10000 0 -0.15 157 157
RARB -0.003 0.04 -10000 0 -0.055 206 206
PRKCG -0.012 0.052 -10000 0 -0.081 205 205
MNAT1 0.029 0.005 -10000 0 0 14 14
RAR alpha/RXRs -0.11 0.19 -10000 0 -0.38 137 137
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.096 0.15 -10000 0 -0.42 30 30
proteasomal ubiquitin-dependent protein catabolic process -0.042 0.088 -10000 0 -0.3 28 28
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.22 0.29 -10000 0 -0.58 213 213
positive regulation of DNA binding -0.076 0.12 -10000 0 -0.22 200 200
NRIP1 -0.39 0.5 -10000 0 -1 213 213
RXRs/RARs -0.15 0.21 -10000 0 -0.41 204 204
RXRs/RXRs/DNA/9cRA -0.13 0.16 -10000 0 -0.33 195 195
PRKACA 0.025 0.01 -10000 0 0 79 79
CDK7 0.026 0.01 -10000 0 0 70 70
TFIIH 0.05 0.022 -10000 0 -10000 0 0
RAR alpha/9cRA -0.008 0.082 -10000 0 -0.22 18 18
CCNH 0.027 0.008 -10000 0 0 46 46
CREBBP 0.027 0.008 -10000 0 0 41 41
RAR gamma2/9cRA -0.046 0.031 0.094 12 -10000 0 12
IL2 signaling events mediated by STAT5

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
GAB2 0.026 0.009 -10000 0 -10000 0 0
ELF1 -0.024 0.02 -10000 0 -10000 0 0
CCNA2 0.003 0.009 -10000 0 0 492 492
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
JAK3 0.027 0.008 -10000 0 -10000 0 0
PIK3R1 0.021 0.013 -10000 0 -10000 0 0
JAK1 0.029 0.004 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.016 0.1 -10000 0 -0.47 9 9
SHC1 0.028 0.006 -10000 0 -10000 0 0
SP1 -0.21 0.14 -10000 0 -0.29 415 415
IL2RA -0.024 0.046 0.4 6 -10000 0 6
IL2RB 0.027 0.008 -10000 0 -10000 0 0
SOS1 0.027 0.007 -10000 0 -10000 0 0
IL2RG 0.026 0.009 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.31 0.29 0.32 23 -0.48 386 409
PTPN11 0.029 0.003 -10000 0 -10000 0 0
CCND2 -0.36 0.24 0.4 3 -0.52 379 382
LCK 0.028 0.006 -10000 0 -10000 0 0
GRB2 0.028 0.005 -10000 0 -10000 0 0
IL2 0.028 0.007 -10000 0 -10000 0 0
CDK6 0.028 0.007 -10000 0 0 31 31
CCND3 -0.014 0.1 -10000 0 -0.49 4 4
Ras signaling in the CD4+ TCR 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
ERK1-2/ELK1 0.003 0.12 -10000 0 -0.4 16 16
MAP3K8 0.023 0.023 0.06 26 -0.037 62 88
FOS 0.025 0.13 0.46 26 -0.38 11 37
PRKCA 0.022 0.029 0.1 25 -0.04 75 100
PTPN7 0.022 0.039 0.16 25 -0.048 59 84
HRAS 0.022 0.021 0.051 1 -0.023 87 88
PRKCB 0.001 0.016 0.07 26 -0.022 1 27
NRAS 0.012 0.017 -10000 0 -0.002 320 320
RAS family/GTP 0.022 0.043 0.18 23 -10000 0 23
MAPK3 0.026 0.12 0.32 26 -0.42 21 47
MAP2K1 0.03 0.077 0.27 27 -0.28 7 34
ELK1 0.021 0.028 0.071 26 -0.052 61 87
BRAF 0.02 0.049 0.19 24 -0.24 3 27
mol:GTP 0 0.003 0.012 26 -0.005 62 88
MAPK1 0.019 0.12 0.32 26 -0.39 30 56
RAF1 0.021 0.054 0.22 14 -0.35 3 17
KRAS 0.019 0.02 -10000 0 -0.011 149 149
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 -0.073 0.093 -10000 0 -0.14 330 330
TC10/GTP -0.05 0.023 -10000 0 -0.13 31 31
Insulin Receptor/Insulin/IRS1/Shp2 -0.068 0.11 -10000 0 -0.15 325 325
HRAS 0.028 0.006 -10000 0 0 26 26
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 0.028 0.007 -10000 0 0 32 32
FOXO3 -0.035 0.14 -10000 0 -0.6 33 33
AKT1 -0.061 0.11 0.23 13 -0.24 29 42
INSR -0.02 0.027 0.067 15 -10000 0 15
Insulin Receptor/Insulin 0.036 0.064 0.2 24 -0.14 38 62
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.029 0.004 -10000 0 0 13 13
SORBS1 0.027 0.008 -10000 0 0 51 51
CRK 0.027 0.007 -10000 0 0 36 36
PTPN1 -0.037 0.045 -10000 0 -10000 0 0
CAV1 -0.098 0.076 0.16 5 -0.22 83 88
CBL/APS/CAP/Crk-II/C3G 0.047 0.055 -10000 0 -0.13 34 34
Insulin Receptor/Insulin/IRS1/NCK2 -0.067 0.11 -10000 0 -0.15 325 325
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.062 0.092 -10000 0 -0.16 242 242
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.1 0.15 -10000 0 -0.45 67 67
RPS6KB1 -0.068 0.099 0.21 12 -0.23 28 40
PARD6A 0.026 0.009 -10000 0 0 60 60
CBL 0.029 0.004 -10000 0 0 12 12
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.022 0.044 -10000 0 -0.69 2 2
PIK3R1 0.021 0.013 -10000 0 0 159 159
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.08 0.095 0.18 7 -0.24 44 51
HRAS/GTP -0.097 0.058 -10000 0 -0.15 245 245
Insulin Receptor -0.02 0.027 0.067 15 -10000 0 15
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.062 0.11 -10000 0 -0.15 308 308
PRKCI 0.001 0.08 -10000 0 -0.35 20 20
Insulin Receptor/Insulin/GRB14/PDK1 -0.084 0.076 0.055 7 -0.22 55 62
SHC1 0.028 0.006 -10000 0 0 21 21
negative regulation of MAPKKK cascade 0.043 0.048 -10000 0 -0.61 2 2
PI3K -0.058 0.1 -10000 0 -0.16 240 240
NCK2 0.029 0.004 -10000 0 0 10 10
RHOQ 0.028 0.005 -10000 0 0 20 20
mol:H2O2 -0.006 0.006 0.018 4 -10000 0 4
HRAS/GDP 0.021 0.005 -10000 0 -10000 0 0
AKT2 -0.062 0.1 0.23 9 -0.29 5 14
PRKCZ -0.018 0.1 -10000 0 -0.38 32 32
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.087 0.06 0.15 4 -0.2 35 39
F2RL2 0.027 0.008 -10000 0 0 51 51
TRIP10 0.027 0.007 -10000 0 0 35 35
Insulin Receptor/Insulin/Shc 0.036 0.054 -10000 0 -0.12 42 42
TC10/GTP/CIP4/Exocyst 0.036 0.012 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.058 0.071 -10000 0 -0.14 34 34
RAPGEF1 0.028 0.005 -10000 0 0 18 18
RASA1 0.027 0.008 -10000 0 0 49 49
NCK1 0.026 0.009 -10000 0 0 64 64
CBL/APS/CAP/Crk-II 0.038 0.049 -10000 0 -0.13 35 35
TC10/GDP 0.021 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.048 0.065 -10000 0 -0.14 42 42
INPP5D -0.088 0.055 -10000 0 -0.13 277 277
SOS1 0.027 0.007 -10000 0 0 36 36
SGK1 -0.01 0.008 -10000 0 -0.025 47 47
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.029 0.003 -10000 0 0 8 8
IRS1 0.011 0.014 -10000 0 0 349 349
p62DOK/RasGAP 0.043 0.049 -10000 0 -0.62 2 2
INS -0.022 0.029 0.068 19 -10000 0 19
mol:PI-3-4-P2 -0.087 0.054 -10000 0 -0.13 277 277
GRB2 0.028 0.005 -10000 0 0 19 19
EIF4EBP1 -0.07 0.092 0.19 6 -0.22 45 51
PTPRA -0.026 0.023 0.067 2 -10000 0 2
PIK3CA 0.02 0.014 -10000 0 0 170 170
TC10/GTP/CIP4 0.036 0.012 -10000 0 -10000 0 0
PDPK1 0.028 0.005 -10000 0 0 18 18
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.098 0.1 -10000 0 -0.28 58 58
Insulin Receptor/Insulin/IRS1 -0.066 0.095 -10000 0 -0.14 327 327
Insulin Receptor/Insulin/IRS3 0.026 0.06 -10000 0 -0.17 43 43
Par3/Par6 0.046 0.044 -10000 0 -0.13 1 1
Ephrin B reverse 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
EFNB2 0.026 0.009 -10000 0 0 58 58
EPHB2 0 0.032 -10000 0 -10000 0 0
EFNB1 -0.027 0.016 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.001 0.072 0.18 3 -10000 0 3
Ephrin B2/EPHB1-2 0.044 0.039 -10000 0 -0.12 18 18
neuron projection morphogenesis -0.027 0.05 0.068 30 -10000 0 30
Ephrin B1/EPHB1-2/Tiam1 0.001 0.067 0.17 6 -10000 0 6
DNM1 0 0.031 -10000 0 -10000 0 0
cell-cell signaling 0.001 0.005 0.017 4 -10000 0 4
MAP2K4 -0.12 0.21 0.23 1 -0.48 136 137
YES1 -0.16 0.31 -10000 0 -0.7 138 138
Ephrin B1/EPHB1-2/NCK2 0.001 0.066 0.17 5 -10000 0 5
PI3K -0.11 0.22 -10000 0 -0.47 138 138
mol:GDP -0.002 0.066 0.16 8 -10000 0 8
ITGA2B 0.028 0.006 -10000 0 0 22 22
endothelial cell proliferation 0.03 0.034 -10000 0 -0.13 20 20
FYN -0.17 0.32 -10000 0 -0.72 138 138
MAP3K7 -0.12 0.22 0.23 5 -0.51 134 139
FGR -0.16 0.31 -10000 0 -0.69 139 139
TIAM1 0.028 0.005 -10000 0 0 20 20
PIK3R1 0.021 0.013 -10000 0 0 159 159
RGS3 0.028 0.005 -10000 0 0 16 16
cell adhesion -0.13 0.21 0.2 5 -0.47 137 142
LYN -0.16 0.31 -10000 0 -0.7 138 138
Ephrin B1/EPHB1-2/Src Family Kinases -0.15 0.28 -10000 0 -0.64 139 139
Ephrin B1/EPHB1-2 -0.12 0.24 -10000 0 -0.54 133 133
SRC -0.15 0.31 -10000 0 -0.69 138 138
ITGB3 0.024 0.011 -10000 0 0 98 98
EPHB1 -0.004 0.031 -10000 0 -10000 0 0
EPHB4 0.028 0.005 -10000 0 0 18 18
RAC1 0.028 0.006 -10000 0 0 27 27
Ephrin B2/EPHB4 0.03 0.034 -10000 0 -0.13 20 20
alphaIIb/beta3 Integrin 0.016 0.068 -10000 0 -0.16 68 68
BLK -0.17 0.31 -10000 0 -0.7 139 139
HCK -0.15 0.31 -10000 0 -0.69 136 136
regulation of stress fiber formation 0.002 0.065 -10000 0 -0.16 6 6
MAPK8 -0.12 0.2 -10000 0 -0.47 135 135
Ephrin B1/EPHB1-2/RGS3 0.002 0.067 0.17 6 -10000 0 6
endothelial cell migration -0.1 0.18 0.29 3 -0.42 133 136
NCK2 0.029 0.004 -10000 0 0 10 10
PTPN13 0.022 0.016 -10000 0 0 178 178
regulation of focal adhesion formation 0.002 0.065 -10000 0 -0.16 6 6
chemotaxis 0.001 0.066 -10000 0 -0.16 7 7
PIK3CA 0.02 0.014 -10000 0 0 170 170
Rac1/GTP -0.013 0.064 0.14 8 -10000 0 8
angiogenesis -0.12 0.24 -10000 0 -0.54 136 136
LCK -0.15 0.31 -10000 0 -0.69 139 139
TCGA08_p53

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
CDKN2A -0.007 0.008 0 339 -10000 0 339
TP53 0.025 0.076 -10000 0 -0.22 36 36
Senescence 0.023 0.08 -10000 0 -0.22 40 40
Apoptosis 0.023 0.08 -10000 0 -0.22 40 40
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.001 0.042 0.3 10 -10000 0 10
MDM4 0.028 0.006 -10000 0 0 23 23
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.027 0.008 -10000 0 0 50 50
NFATC1 0.056 0.094 0.26 8 -0.35 11 19
NFATC2 -0.015 0.059 0.25 4 -0.23 6 10
NFATC3 -0.001 0.026 -10000 0 -0.31 2 2
YWHAE 0.027 0.008 -10000 0 0 40 40
Calcineurin A alpha-beta B1/CABIN1 -0.008 0.061 0.24 1 -0.26 16 17
Exportin 1/Ran/NUP214 0.05 0.022 -10000 0 -10000 0 0
mol:DAG -0.001 0.003 0.029 4 -10000 0 4
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.004 0.077 0.21 1 -0.26 17 18
BCL2/BAX 0.011 0.07 -10000 0 -0.16 74 74
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.032 0.12 4 -0.15 9 13
CaM/Ca2+ -0.001 0.032 0.12 4 -0.15 9 13
BAX 0.028 0.006 -10000 0 0 21 21
MAPK14 0.005 0.029 0.059 4 -0.029 234 238
BAD 0.029 0.002 -10000 0 0 4 4
CABIN1/MEF2D 0.003 0.065 0.23 1 -0.26 16 17
Calcineurin A alpha-beta B1/BCL2 0.023 0.012 -10000 0 0 123 123
FKBP8 0.025 0.011 -10000 0 0 88 88
activation-induced cell death of T cells -0.003 0.064 0.26 16 -0.23 1 17
KPNB1 0.028 0.005 -10000 0 0 20 20
KPNA2 0.003 0.009 -10000 0 0 494 494
XPO1 0.005 0.027 -10000 0 -0.023 254 254
SFN 0.027 0.007 -10000 0 0 37 37
MAP3K8 0.004 0.03 0.061 4 -0.032 219 223
NFAT4/CK1 alpha -0.047 0.031 0.15 4 -0.19 8 12
MEF2D/NFAT1/Cbp/p300 -0.057 0.12 -10000 0 -0.26 40 40
CABIN1 -0.008 0.062 0.25 1 -0.26 16 17
CALM1 0.003 0.031 0.063 4 -0.034 216 220
RAN 0.006 0.028 -10000 0 -0.028 229 229
MAP3K1 0.027 0.008 -10000 0 0 50 50
CAMK4 0.027 0.007 -10000 0 0 39 39
mol:Ca2+ -0.003 0.007 0.067 4 -10000 0 4
MAPK3 0.028 0.006 -10000 0 0 22 22
YWHAH 0.027 0.008 -10000 0 0 42 42
Calcineurin A alpha-beta B1/AKAP79/PKA 0.035 0.016 -10000 0 -10000 0 0
YWHAB 0.027 0.008 -10000 0 0 45 45
MAPK8 0.004 0.03 0.065 4 -0.033 221 225
MAPK9 0.028 0.005 -10000 0 0 18 18
YWHAG 0.029 0.004 -10000 0 0 11 11
FKBP1A 0.027 0.007 -10000 0 0 39 39
NFAT1-c-4/YWHAQ 0.038 0.11 0.26 6 -0.38 11 17
PRKCH 0.029 0.005 -10000 0 0 15 15
CABIN1/Cbp/p300 0.001 0.05 -10000 0 -0.17 10 10
CASP3 0.005 0.028 0.059 4 -0.032 195 199
PIM1 0.028 0.006 -10000 0 0 28 28
Calcineurin A alpha-beta B1/FKBP12/FK506 0.005 0.018 0.065 4 -10000 0 4
apoptosis 0.01 0.035 0.19 1 -0.15 1 2
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.004 0.057 -10000 0 -0.23 15 15
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.028 0.005 -10000 0 0 19 19
JNK2/NFAT4 -0.002 0.071 -10000 0 -0.19 63 63
BAD/BCL-XL 0.039 0.013 -10000 0 -10000 0 0
PRKCD 0.029 0.005 -10000 0 0 15 15
NUP214 0.006 0.028 -10000 0 -0.027 235 235
PRKCZ 0.004 0.03 0.065 4 -0.033 219 223
PRKCA 0.028 0.006 -10000 0 0 22 22
PRKCG 0.028 0.005 -10000 0 0 20 20
PRKCQ 0.027 0.008 -10000 0 0 46 46
FKBP38/BCL2 -0.002 0.081 -10000 0 -0.17 102 102
EP300 0 0.033 0.071 4 -0.039 217 221
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.027 0.008 -10000 0 0 41 41
NFATc/JNK1 0.062 0.097 0.26 6 -0.33 12 18
CaM/Ca2+/FKBP38 -0.002 0.052 0.13 4 -0.14 43 47
FKBP12/FK506 0.02 0.006 -10000 0 -10000 0 0
CSNK1A1 -0.031 0.02 0.1 4 -0.14 8 12
CaM/Ca2+/CAMK IV 0.007 0.04 0.13 4 -0.14 8 12
NFATc/ERK1 0.064 0.097 0.26 8 -0.34 10 18
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.017 0.073 0.21 1 -0.26 17 18
NR4A1 -0.13 0.13 0.17 3 -0.29 204 207
GSK3B 0.005 0.03 0.065 4 -0.033 215 219
positive T cell selection -0.001 0.026 -10000 0 -0.31 2 2
NFAT1/CK1 alpha -0.025 0.05 0.21 4 -0.19 8 12
RCH1/ KPNB1 0.005 0.014 -10000 0 -10000 0 0
YWHAQ 0.029 0.005 -10000 0 0 15 15
PRKACA 0.004 0.028 0.058 3 -0.022 274 277
AKAP5 0.029 0.005 -10000 0 0 14 14
MEF2D 0.001 0.034 0.071 4 -0.039 223 227
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.025 0.01 -10000 0 0 78 78
NFATc/p38 alpha 0.061 0.095 0.26 4 -0.34 11 15
CREBBP 0.001 0.033 0.071 4 -0.039 216 220
BCL2 0.023 0.012 -10000 0 0 123 123
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.01 0.02 0.1 8 -0.03 13 21
GNB1/GNG2 -0.067 0.065 -10000 0 -0.19 93 93
AKT1 -0.016 0.23 0.48 77 -0.38 8 85
EGF 0.027 0.008 -10000 0 0 41 41
mol:TXA2 0 0.002 0.035 1 -10000 0 1
FGR -0.024 0.066 0.22 10 -10000 0 10
mol:Ca2+ -0.065 0.29 0.56 78 -0.4 4 82
LYN -0.026 0.065 0.22 11 -10000 0 11
RhoA/GTP -0.041 0.11 0.25 59 -0.19 1 60
mol:PGI2 0 0.002 0.029 1 -10000 0 1
SYK -0.059 0.3 0.57 78 -0.4 3 81
GNG2 0.029 0.004 -10000 0 0 12 12
ARRB2 0.028 0.006 -10000 0 0 25 25
TP alpha/Gq family/GDP/G beta5/gamma2 -0.067 0.17 -10000 0 -0.43 81 81
G beta5/gamma2 -0.08 0.086 0.17 1 -0.25 92 93
PRKCH -0.068 0.31 0.58 78 -0.43 43 121
DNM1 0.028 0.005 -10000 0 0 17 17
TXA2/TP beta/beta Arrestin3 0.03 0.035 -10000 0 -0.51 1 1
mol:GTP 0.001 0.011 0.074 8 -10000 0 8
PTGDR 0.023 0.018 0.059 1 -0.024 69 70
G12 family/GTP -0.14 0.13 -10000 0 -0.31 114 114
ADRBK1 0.029 0.003 -10000 0 0 6 6
ADRBK2 0.025 0.01 -10000 0 0 77 77
RhoA/GTP/ROCK1 0.038 0.013 0.16 1 -0.14 1 2
mol:GDP 0.044 0.24 0.47 46 -0.42 75 121
mol:NADP -0.002 0.029 0.068 1 -0.029 286 287
RAB11A 0.029 0.004 -10000 0 0 13 13
PRKG1 -0.003 0.03 0.069 1 -0.029 306 307
mol:IP3 -0.096 0.33 0.59 78 -0.46 59 137
cell morphogenesis 0.038 0.013 0.16 1 -0.13 1 2
PLCB2 -0.16 0.38 0.62 70 -0.62 83 153
mol:cGMP 0 0.002 0.036 1 -10000 0 1
BLK -0.021 0.062 0.22 10 -10000 0 10
mol:PDG2 0 0.002 0.029 1 -10000 0 1
HCK -0.025 0.064 0.22 8 -10000 0 8
RHOA 0.029 0.003 -10000 0 0 6 6
PTGIR 0.023 0.018 0.059 1 -0.019 80 81
PRKCB1 -0.084 0.32 0.59 78 -0.44 58 136
GNAQ 0.028 0.007 -10000 0 0 29 29
mol:L-citrulline -0.002 0.029 0.068 1 -0.029 286 287
TXA2/TXA2-R family -0.11 0.38 0.64 78 -0.59 65 143
LCK -0.023 0.066 0.22 11 -10000 0 11
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.016 0.056 0.16 12 -10000 0 12
TXA2-R family/G12 family/GDP/G beta/gamma -0.017 0.12 -10000 0 -0.44 39 39
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.017 0.054 0.15 10 -10000 0 10
MAPK14 -0.028 0.24 0.48 78 -10000 0 78
TGM2/GTP -0.14 0.36 0.62 70 -0.53 72 142
MAPK11 -0.03 0.24 0.48 78 -10000 0 78
ARHGEF1 -0.031 0.2 0.4 76 -10000 0 76
GNAI2 0.029 0.003 -10000 0 0 6 6
JNK cascade -0.064 0.33 0.61 78 -0.44 18 96
RAB11/GDP 0.012 0.034 -10000 0 -0.099 12 12
ICAM1 -0.028 0.29 0.58 79 -10000 0 79
cAMP biosynthetic process -0.1 0.31 0.55 78 -0.42 54 132
Gq family/GTP/EBP50 -0.052 0.1 0.24 1 -0.21 146 147
actin cytoskeleton reorganization 0.038 0.013 0.16 1 -0.13 1 2
SRC -0.025 0.065 0.22 8 -10000 0 8
GNB5 0.028 0.007 -10000 0 0 34 34
GNB1 0.028 0.006 -10000 0 0 24 24
EGF/EGFR -0.034 0.082 0.22 12 -0.25 15 27
VCAM1 -0.037 0.3 0.6 78 -10000 0 78
TP beta/Gq family/GDP/G beta5/gamma2 -0.067 0.17 -10000 0 -0.43 81 81
platelet activation -0.059 0.28 0.55 78 -10000 0 78
PGI2/IP 0.021 0.012 0.09 1 -0.15 2 3
PRKACA -0.003 0.024 0.17 1 -0.15 2 3
Gq family/GDP/G beta5/gamma2 -0.052 0.14 -10000 0 -0.36 76 76
TXA2/TP beta/beta Arrestin2 0.018 0.054 -10000 0 -0.34 8 8
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.015 0.024 0.22 1 -0.15 3 4
mol:DAG -0.1 0.34 0.61 78 -0.51 60 138
EGFR 0.026 0.009 -10000 0 0 55 55
TXA2/TP alpha -0.16 0.38 0.62 75 -0.58 81 156
Gq family/GTP -0.033 0.077 -10000 0 -0.23 57 57
YES1 -0.025 0.065 0.22 10 -10000 0 10
GNAI2/GTP -0.021 0.064 0.15 18 -0.18 6 24
PGD2/DP 0.022 0.005 0.09 1 -10000 0 1
SLC9A3R1 0.022 0.013 -10000 0 0 139 139
FYN -0.029 0.07 0.22 11 -0.19 6 17
mol:NO -0.002 0.029 0.068 1 -0.029 286 287
GNA15 0.027 0.008 -10000 0 0 46 46
PGK/cGMP 0.037 0.012 0.15 1 -10000 0 1
RhoA/GDP 0.013 0.034 -10000 0 -0.096 13 13
TP alpha/TGM2/GDP/G beta/gamma -0.076 0.065 -10000 0 -0.23 5 5
NOS3 -0.002 0.029 0.068 1 -0.029 286 287
RAC1 0.028 0.006 -10000 0 0 27 27
PRKCA -0.068 0.31 0.58 78 -0.42 50 128
PRKCB -0.068 0.31 0.58 78 -0.42 52 130
PRKCE -0.059 0.32 0.59 78 -0.42 35 113
PRKCD -0.069 0.32 0.59 78 -0.44 50 128
PRKCG -0.087 0.32 0.59 78 -0.46 56 134
muscle contraction -0.11 0.37 0.63 78 -0.55 63 141
PRKCZ -0.057 0.3 0.57 78 -0.41 1 79
ARR3 0.029 0.003 -10000 0 0 5 5
TXA2/TP beta -0.01 0.07 0.22 11 -0.19 3 14
PRKCQ -0.06 0.31 0.58 78 -0.42 46 124
MAPKKK cascade -0.11 0.36 0.61 78 -0.54 66 144
SELE -0.03 0.28 0.56 78 -10000 0 78
TP beta/GNAI2/GDP/G beta/gamma -0.022 0.063 0.22 5 -10000 0 5
ROCK1 0.029 0.005 -10000 0 0 14 14
GNA14 0.028 0.005 -10000 0 0 19 19
chemotaxis -0.11 0.4 0.68 78 -0.62 74 152
GNA12 0.028 0.007 -10000 0 0 33 33
GNA13 0.029 0.004 -10000 0 0 13 13
GNA11 0.025 0.01 -10000 0 0 83 83
Rac1/GTP 0.021 0.01 0.12 2 -10000 0 2
Aurora A 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
Aurora A/GADD45A 0.073 0.052 0.19 2 -10000 0 2
BIRC5 0.023 0.012 -10000 0 0 121 121
NFKBIA 0.065 0.049 0.2 4 -10000 0 4
CPEB1 0.028 0.005 -10000 0 0 19 19
AKT1 0.065 0.051 0.29 3 -10000 0 3
NDEL1 0.028 0.007 -10000 0 0 31 31
Aurora A/BRCA1 0.065 0.046 0.16 1 -10000 0 1
NDEL1/TACC3 0.045 0.053 -10000 0 -10000 0 0
GADD45A 0.027 0.009 -10000 0 0 53 53
GSK3B 0.024 0.016 0.084 3 -10000 0 3
PAK1/Aurora A 0.075 0.051 0.18 2 -10000 0 2
MDM2 0.028 0.006 -10000 0 0 26 26
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.17 0.066 0.19 486 -10000 0 486
TP53 0.053 0.056 0.17 2 -0.31 4 6
DLG7 0.076 0.052 0.11 386 -10000 0 386
AURKAIP1 0.028 0.006 -10000 0 0 27 27
ARHGEF7 0.028 0.006 -10000 0 0 25 25
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.048 0.056 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.064 0.045 0.16 1 -10000 0 1
AURKA 0.093 0.063 0.13 386 -10000 0 386
AURKB 0.025 0.025 -10000 0 -0.16 2 2
CDC25B 0.07 0.049 0.18 3 -10000 0 3
G2/M transition checkpoint 0 0.002 -10000 0 -10000 0 0
mRNA polyadenylation 0.069 0.043 0.16 1 -10000 0 1
Aurora A/CPEB 0.07 0.044 0.16 1 -10000 0 1
Aurora A/TACC1/TRAP/chTOG -0.003 0.054 0.19 4 -10000 0 4
BRCA1 0.026 0.009 -10000 0 0 59 59
centrosome duplication 0.074 0.051 0.18 2 -10000 0 2
regulation of centrosome cycle 0.044 0.051 -10000 0 -10000 0 0
spindle assembly -0.003 0.053 0.18 4 -10000 0 4
TDRD7 0.028 0.006 -10000 0 0 27 27
Aurora A/RasGAP/Survivin 0.075 0.063 0.18 1 -10000 0 1
CENPA 0.038 0.034 -10000 0 -10000 0 0
Aurora A/PP2A 0.078 0.05 0.18 3 -10000 0 3
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.043 0.049 0.17 12 -0.26 2 14
negative regulation of DNA binding 0.052 0.056 0.17 2 -0.31 4 6
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.04 0.012 -10000 0 -10000 0 0
RASA1 0.027 0.008 -10000 0 0 49 49
Ajuba/Aurora A 0 0.002 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.015 0.073 23 -10000 0 23
proteasomal ubiquitin-dependent protein catabolic process 0.093 0.063 0.13 386 -10000 0 386
TACC1 0.005 0.011 -10000 0 0 458 458
TACC3 0.016 0.015 -10000 0 0 259 259
Aurora A/Antizyme1 0.06 0.059 -10000 0 -10000 0 0
Aurora A/RasGAP 0.074 0.051 -10000 0 -10000 0 0
OAZ1 0.019 0.014 -10000 0 0 195 195
RAN 0.029 0.004 -10000 0 0 12 12
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.021 0.017 0.084 3 -10000 0 3
GIT1 0.028 0.007 -10000 0 0 30 30
GIT1/beta-PIX/PAK1 0.051 0.021 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.17 0.066 0.19 486 -10000 0 486
PPP2R5D 0.028 0.006 -10000 0 0 26 26
Aurora A/TPX2 0.005 0.031 0.16 17 -10000 0 17
PAK1 0.027 0.008 -10000 0 0 48 48
CKAP5 0.02 0.014 -10000 0 0 179 179
Reelin signaling pathway

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
CDK5R1/CDK5 0.034 0.018 -10000 0 -10000 0 0
VLDLR 0.026 0.009 -10000 0 0 61 61
CRKL 0.028 0.007 -10000 0 0 31 31
LRPAP1 0.028 0.007 -10000 0 0 33 33
FYN 0.024 0.011 -10000 0 0 99 99
ITGA3 0.026 0.01 -10000 0 0 67 67
RELN/VLDLR/Fyn -0.007 0.093 -10000 0 -0.16 147 147
MAPK8IP1/MKK7/MAP3K11/JNK1 0.073 0.038 -10000 0 -0.14 1 1
AKT1 -0.044 0.09 -10000 0 -0.21 85 85
MAP2K7 0.027 0.007 -10000 0 0 36 36
RAPGEF1 0.028 0.005 -10000 0 0 18 18
DAB1 0.029 0.004 -10000 0 0 12 12
RELN/LRP8/DAB1 0.021 0.068 -10000 0 -0.13 90 90
LRPAP1/LRP8 0.039 0.017 -10000 0 -0.16 2 2
RELN/LRP8/DAB1/Fyn 0.011 0.092 -10000 0 -0.14 141 141
DAB1/alpha3/beta1 Integrin 0.004 0.093 -10000 0 -0.15 124 124
long-term memory 0.011 0.1 -10000 0 -0.15 130 130
DAB1/LIS1 0.031 0.09 -10000 0 -0.15 90 90
DAB1/CRLK/C3G 0.015 0.086 -10000 0 -0.15 91 91
PIK3CA 0.02 0.014 -10000 0 0 170 170
DAB1/NCK2 0.032 0.092 -10000 0 -0.15 93 93
ARHGEF2 0.028 0.006 -10000 0 0 27 27
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.027 0.008 -10000 0 0 49 49
CDK5R1 0.027 0.007 -10000 0 0 36 36
RELN 0.022 0.012 -10000 0 0 130 130
PIK3R1 0.021 0.013 -10000 0 0 159 159
RELN/LRP8/Fyn -0.002 0.091 -10000 0 -0.15 141 141
GRIN2A/RELN/LRP8/DAB1/Fyn 0.017 0.1 -10000 0 -0.15 140 140
MAPK8 0.029 0.004 -10000 0 0 11 11
RELN/VLDLR/DAB1 0.014 0.071 -10000 0 -0.13 98 98
ITGB1 0.028 0.006 -10000 0 0 21 21
MAP1B -0.044 0.068 0.13 31 -0.24 11 42
RELN/LRP8 0.018 0.075 -10000 0 -0.15 88 88
GRIN2B/RELN/LRP8/DAB1/Fyn 0.016 0.1 -10000 0 -0.15 130 130
PI3K -0.001 0.068 -10000 0 -0.16 77 77
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.023 0.058 -10000 0 -0.16 48 48
RAP1A -0.06 0.087 0.35 8 -10000 0 8
PAFAH1B1 0.028 0.007 -10000 0 0 32 32
MAPK8IP1 0.029 0.003 -10000 0 0 7 7
CRLK/C3G 0.04 0.012 -10000 0 -10000 0 0
GRIN2B 0.026 0.009 -10000 0 0 57 57
NCK2 0.029 0.004 -10000 0 0 10 10
neuron differentiation -0.034 0.087 -10000 0 -0.28 30 30
neuron adhesion -0.073 0.096 0.32 12 -10000 0 12
LRP8 0.028 0.005 -10000 0 0 19 19
GSK3B -0.049 0.093 0.16 7 -0.28 31 38
RELN/VLDLR/DAB1/Fyn 0.006 0.093 -10000 0 -0.14 145 145
MAP3K11 0.029 0.003 -10000 0 0 6 6
RELN/VLDLR/DAB1/P13K -0.035 0.099 -10000 0 -0.2 126 126
CDK5 0.025 0.011 -10000 0 0 85 85
MAPT -0.013 0.016 -10000 0 -10000 0 0
neuron migration -0.059 0.11 0.24 7 -0.28 55 62
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.034 0.088 -10000 0 -0.28 30 30
RELN/VLDLR 0.027 0.085 -10000 0 -0.14 93 93
LPA receptor mediated 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
GNB1/GNG2 0.012 0.062 -10000 0 -0.15 60 60
NF kappa B1 p50/RelA/I kappa B alpha -0.048 0.094 0.21 6 -0.26 29 35
AP1 -0.019 0.085 0.21 48 -0.15 58 106
mol:PIP3 -0.056 0.061 0.03 2 -0.15 142 144
AKT1 -0.027 0.1 0.24 13 -0.3 5 18
PTK2B -0.048 0.11 0.19 31 -0.2 146 177
RHOA -0.007 0.059 0.17 27 -0.32 4 31
PIK3CB 0.02 0.019 -10000 0 -0.034 5 5
mol:Ca2+ -0.038 0.061 0.17 7 -0.18 29 36
MAGI3 0.022 0.018 -10000 0 -0.029 56 56
RELA 0.029 0.003 -10000 0 0 6 6
apoptosis -0.004 0.075 0.25 30 -0.15 53 83
HRAS/GDP 0.021 0.005 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.055 0.1 0.16 36 -0.22 101 137
NF kappa B1 p50/RelA -0.05 0.11 0.22 55 -0.21 46 101
endothelial cell migration -0.046 0.099 -10000 0 -0.32 62 62
ADCY4 -0.01 0.095 0.24 32 -0.2 53 85
ADCY5 -0.008 0.093 0.24 32 -0.2 51 83
ADCY6 -0.009 0.093 0.24 32 -0.2 51 83
ADCY7 -0.007 0.093 0.24 32 -0.21 51 83
ADCY1 -0.009 0.093 0.24 32 -0.2 50 82
ADCY2 -0.008 0.092 0.24 32 -0.2 47 79
ADCY3 -0.009 0.094 0.24 32 -0.2 53 85
ADCY8 -0.05 0.097 0.23 9 -0.24 53 62
ADCY9 -0.018 0.1 0.24 32 -0.23 54 86
GSK3B -0.05 0.11 0.17 43 -0.21 133 176
arachidonic acid secretion -0.021 0.092 0.22 32 -0.2 59 91
GNG2 0.016 0.024 -10000 0 -0.034 8 8
TRIP6 0.01 0.031 -10000 0 -0.27 3 3
GNAO1 -0.012 0.089 0.3 31 -0.16 61 92
HRAS 0.028 0.006 -10000 0 0 26 26
NFKBIA -0.047 0.085 0.19 6 -0.26 32 38
GAB1 0.028 0.006 -10000 0 0 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.026 0.14 -10000 0 -0.81 14 14
JUN 0.028 0.007 -10000 0 0 32 32
LPA/LPA2/NHERF2 -0.009 0.053 -10000 0 -0.1 121 121
TIAM1 0.013 0.15 -10000 0 -0.94 14 14
PIK3R1 0.01 0.023 -10000 0 -0.033 13 13
mol:IP3 -0.032 0.059 0.17 7 -0.18 31 38
PLCB3 -0.028 0.056 0.13 35 -0.13 63 98
FOS 0.024 0.012 -10000 0 0 105 105
positive regulation of mitosis -0.021 0.092 0.22 32 -0.2 59 91
LPA/LPA1-2-3 -0.013 0.044 0.044 44 -0.13 62 106
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -10000 0 0
BCAR1 0.026 0.009 -10000 0 0 57 57
stress fiber formation -0.018 0.097 0.23 31 -0.27 27 58
GNAZ -0.011 0.086 0.3 30 -0.16 53 83
EGFR/PI3K-beta/Gab1 -0.057 0.065 0.043 25 -0.15 142 167
positive regulation of dendritic cell cytokine production -0.013 0.044 0.042 43 -0.13 62 105
LPA/LPA2/MAGI-3 0.008 0.028 -10000 0 -0.068 57 57
ARHGEF1 -0.027 0.08 0.24 37 -10000 0 37
GNAI2 -0.013 0.089 0.3 31 -0.16 61 92
GNAI3 -0.011 0.084 0.3 28 -0.16 55 83
GNAI1 -0.012 0.088 0.3 31 -0.16 56 87
LPA/LPA3 -0.008 0.022 0.019 3 -0.07 62 65
LPA/LPA2 -0.008 0.022 0.019 3 -0.069 62 65
LPA/LPA1 -0.022 0.056 -10000 0 -0.18 62 62
HB-EGF/EGFR -0.006 0.078 0.16 78 -0.15 26 104
HBEGF 0.006 0.084 0.2 87 -10000 0 87
mol:DAG -0.032 0.059 0.17 7 -0.18 31 38
cAMP biosynthetic process -0.022 0.094 0.22 32 -0.22 42 74
NFKB1 0.027 0.008 -10000 0 0 46 46
SRC 0.028 0.007 -10000 0 0 33 33
GNB1 0.016 0.024 -10000 0 -0.033 11 11
LYN -0.04 0.083 0.23 7 -0.26 24 31
GNAQ 0.005 0.039 0.13 31 -0.064 60 91
LPAR2 0 0.002 -10000 0 -10000 0 0
LPAR3 0 0.002 -10000 0 -10000 0 0
LPAR1 -0.015 0.034 -10000 0 -0.11 62 62
IL8 0.033 0.24 0.56 67 -0.35 49 116
PTK2 0.005 0.065 0.26 22 -0.13 44 66
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
CASP3 -0.004 0.076 0.25 30 -0.15 53 83
EGFR 0.028 0.01 0.054 4 0 55 59
PLCG1 -0.003 0.044 0.13 27 -0.13 15 42
PLD2 0.008 0.076 0.26 30 -0.13 57 87
G12/G13 0.012 0.062 -10000 0 -0.15 61 61
PI3K-beta -0.057 0.063 -10000 0 -0.24 26 26
cell migration 0 0.059 0.21 1 -0.24 14 15
SLC9A3R2 0.025 0.011 -10000 0 0 92 92
PXN -0.018 0.099 0.23 31 -0.27 27 58
HRAS/GTP -0.022 0.093 0.22 32 -0.2 59 91
RAC1 0.028 0.006 -10000 0 0 27 27
MMP9 0.023 0.013 -10000 0 0 130 130
PRKCE 0.02 0.021 -10000 0 -0.03 78 78
PRKCD -0.044 0.063 0.17 8 -0.19 26 34
Gi(beta/gamma) -0.012 0.092 0.24 29 -0.19 53 82
mol:LPA -0.015 0.034 -10000 0 -0.11 62 62
TRIP6/p130 Cas/FAK1/Paxillin -0.006 0.084 0.24 21 -0.24 15 36
MAPKKK cascade -0.021 0.092 0.22 32 -0.2 59 91
contractile ring contraction involved in cytokinesis -0.005 0.06 0.17 27 -0.31 4 31
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.005 0.039 0.13 31 -0.064 59 90
GNA15 0.005 0.037 0.13 30 -0.064 53 83
GNA12 0.026 0.012 -10000 0 -0.03 15 15
GNA13 0.027 0.011 -10000 0 -0.03 16 16
MAPT -0.057 0.1 0.16 36 -0.22 102 138
GNA11 0.003 0.041 0.13 28 -0.08 52 80
Rac1/GTP 0.027 0.14 -10000 0 -0.86 14 14
MMP2 -0.046 0.099 -10000 0 -0.32 62 62
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.027 0.095 -10000 0 -0.47 4 4
UGCG -0.018 0.12 -10000 0 -0.7 16 16
AKT1/mTOR/p70S6K/Hsp90/TERT -0.079 0.18 -10000 0 -0.48 50 50
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.017 0.12 -10000 0 -0.69 16 16
mol:DAG -0.003 0.12 -10000 0 -0.84 11 11
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.12 0.23 -10000 0 -0.51 108 108
FRAP1 -0.14 0.27 -10000 0 -0.6 106 106
FOXO3 -0.11 0.23 -10000 0 -0.62 64 64
AKT1 -0.11 0.25 0.34 1 -0.62 77 78
GAB2 0.01 0.027 -10000 0 -0.035 138 138
SMPD1 -0.023 0.14 -10000 0 -0.7 20 20
SGMS1 -0.011 0.097 -10000 0 -0.65 11 11
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 -0.032 0.049 0.15 8 -0.14 76 84
CALM1 0.028 0.006 -10000 0 0 26 26
cell proliferation -0.017 0.15 -10000 0 -0.56 17 17
EIF3A 0.029 0.003 -10000 0 0 8 8
PI3K -0.011 0.068 -10000 0 -0.17 77 77
RPS6KB1 -0.016 0.12 -10000 0 -0.92 7 7
mol:sphingomyelin -0.003 0.12 -10000 0 -0.84 11 11
natural killer cell activation -0.002 0.004 -10000 0 -0.018 7 7
JAK3 0.01 0.029 0.16 1 -0.036 138 139
PIK3R1 0.008 0.026 0.17 1 -0.038 87 88
JAK1 0.011 0.03 0.17 1 -0.036 126 127
NFKB1 0.027 0.008 -10000 0 0 46 46
MYC -0.079 0.3 0.44 1 -0.85 62 63
MYB -0.062 0.26 0.54 1 -1 36 37
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.064 0.15 0.35 1 -0.44 39 40
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.004 0.12 -10000 0 -0.86 7 7
mol:PI-3-4-5-P3 -0.063 0.14 0.35 1 -0.44 36 37
Rac1/GDP -0.026 0.066 0.14 48 -0.14 23 71
T cell proliferation -0.064 0.14 0.32 1 -0.42 35 36
SHC1 0.011 0.029 -10000 0 -0.035 150 150
RAC1 0.017 0.023 -10000 0 -0.029 102 102
positive regulation of cyclin-dependent protein kinase activity -0.004 0.019 0.24 1 -10000 0 1
PRKCZ -0.067 0.14 0.33 1 -0.43 36 37
NF kappa B1 p50/RelA -0.11 0.24 -10000 0 -0.53 102 102
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.028 0.1 0.67 1 -0.36 17 18
HSP90AA1 0.028 0.006 -10000 0 0 21 21
RELA 0.029 0.003 -10000 0 0 6 6
IL2RA 0.01 0.028 -10000 0 -0.035 146 146
IL2RB 0.01 0.029 0.17 1 -0.036 142 143
TERT 0.026 0.009 -10000 0 0 61 61
E2F1 -0.014 0.11 0.46 1 -0.41 36 37
SOS1 0.011 0.028 -10000 0 -0.035 144 144
RPS6 0.028 0.007 -10000 0 0 32 32
mol:cAMP 0.002 0.008 -10000 0 -0.084 1 1
PTPN11 0.011 0.03 -10000 0 -0.036 155 155
IL2RG 0.01 0.029 0.16 1 -0.038 117 118
actin cytoskeleton organization -0.064 0.14 0.32 1 -0.42 35 36
GRB2 0.011 0.029 -10000 0 -0.036 152 152
IL2 0.01 0.03 0.16 1 -0.037 143 144
PIK3CA 0.008 0.025 -10000 0 -0.036 93 93
Rac1/GTP -0.007 0.058 -10000 0 -0.13 73 73
LCK 0.01 0.03 0.17 1 -0.038 128 129
BCL2 -0.17 0.3 -10000 0 -0.75 105 105
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.056 0.055 0.12 167 -0.057 1 168
AES 0.042 0.044 0.11 132 -10000 0 132
FBXW11 0.028 0.005 -10000 0 0 16 16
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.036 0.016 -10000 0 -10000 0 0
SMAD4 0.028 0.007 -10000 0 0 34 34
DKK2 0.027 0.008 -10000 0 -0.001 40 40
TLE1 0.052 0.044 0.11 144 -0.062 1 145
MACF1 0.026 0.01 -10000 0 -0.029 7 7
CTNNB1 0.026 0.079 0.3 16 -0.41 1 17
WIF1 0.024 0.016 -10000 0 -0.03 40 40
beta catenin/RanBP3 0.14 0.2 0.41 170 -0.36 1 171
KREMEN2 0.028 0.007 -10000 0 -0.001 25 25
DKK1 0.028 0.006 -10000 0 0 22 22
beta catenin/beta TrCP1 0.047 0.078 0.28 16 -0.39 1 17
FZD1 0.015 0.025 -10000 0 -10000 0 0
AXIN2 -0.08 0.18 0.63 5 -0.68 23 28
AXIN1 0.027 0.012 -10000 0 -10000 0 0
RAN 0.03 0.006 -10000 0 -0.031 2 2
Axin1/APC/GSK3/beta catenin 0.02 0.1 -10000 0 -0.47 19 19
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.043 0.18 0.29 7 -0.56 38 45
Axin1/APC/GSK3 0.014 0.064 0.22 14 -0.32 3 17
Axin1/APC/GSK3/beta catenin/Macf1 0.002 0.079 0.29 7 -0.38 6 13
HNF1A 0.055 0.047 0.12 150 -0.062 2 152
CTBP1 0.052 0.048 0.12 143 -0.062 2 145
MYC 0.009 0.48 0.59 126 -1.1 58 184
RANBP3 0.029 0.008 -10000 0 -0.03 1 1
DKK2/LRP6/Kremen 2 0.048 0.025 -10000 0 -10000 0 0
NKD1 0.02 0.021 -10000 0 -0.03 73 73
TCF4 0.053 0.05 0.12 163 -0.063 2 165
TCF3 0.051 0.046 0.11 159 -0.063 1 160
WNT1/LRP6/FZD1/Axin1 0.063 0.037 0.18 1 -10000 0 1
Ran/GTP 0.024 0.006 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.11 0.28 0.54 117 -0.54 14 131
LEF1 0.049 0.051 0.12 151 -0.063 2 153
DVL1 0.017 0.06 0.18 5 -0.33 6 11
CSNK2A1 0.027 0.008 -10000 0 -0.029 1 1
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.12 0.2 -10000 0 -0.47 96 96
DKK1/LRP6/Kremen 2 0.048 0.025 -10000 0 -10000 0 0
LRP6 0.014 0.024 -10000 0 -10000 0 0
CSNK1A1 0.058 0.055 0.12 175 -0.066 2 177
NLK 0.006 0.032 -10000 0 -0.04 178 178
CCND1 -0.33 0.56 0.64 15 -1.2 155 170
WNT1 0.016 0.025 -10000 0 -10000 0 0
GSK3A 0.015 0.024 -10000 0 -10000 0 0
GSK3B 0.015 0.025 -10000 0 -10000 0 0
FRAT1 0.01 0.027 -10000 0 -0.03 173 173
PPP2R5D 0.03 0.051 0.23 1 -0.3 8 9
APC -0.02 0.081 0.19 55 -10000 0 55
WNT1/LRP6/FZD1 0.017 0.044 0.21 4 -0.22 2 6
CREBBP 0.051 0.047 0.12 142 -0.062 2 144
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.033 0.019 -10000 0 -10000 0 0
ATM 0.028 0.007 -10000 0 0 30 30
UBE2D3 0.027 0.008 -10000 0 0 41 41
PRKDC 0.024 0.011 -10000 0 0 96 96
ATR 0.022 0.013 -10000 0 0 140 140
UBE2L3 0.028 0.007 -10000 0 0 31 31
FANCD2 0.052 0.063 -10000 0 -10000 0 0
protein ubiquitination 0.053 0.064 -10000 0 -10000 0 0
XRCC5 0.027 0.007 -10000 0 0 36 36
XRCC6 0.027 0.008 -10000 0 0 49 49
M/R/N Complex 0.043 0.027 -10000 0 -10000 0 0
MRE11A 0.025 0.01 -10000 0 0 81 81
DNA-PK 0.042 0.027 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.03 0.075 0.21 8 -0.52 4 12
FANCF 0.028 0.005 -10000 0 0 16 16
BRCA1 0.026 0.009 -10000 0 0 59 59
CCNE1 0.003 0.008 -10000 0 0 506 506
CDK2/Cyclin E1 0.003 0.01 -10000 0 -10000 0 0
FANCG 0.028 0.005 -10000 0 0 16 16
BRCA1/BACH1/BARD1 0.033 0.018 -10000 0 -10000 0 0
FANCE 0.028 0.005 -10000 0 0 19 19
FANCC 0.028 0.006 -10000 0 0 24 24
NBN 0.025 0.01 -10000 0 0 82 82
FANCA 0.025 0.01 -10000 0 0 83 83
DNA repair 0.2 0.2 0.37 266 -0.36 2 268
BRCA1/BARD1/ubiquitin 0.033 0.018 -10000 0 -10000 0 0
BARD1/DNA-PK 0.07 0.047 -10000 0 -10000 0 0
FANCL 0.027 0.008 -10000 0 0 44 44
mRNA polyadenylation -0.032 0.019 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.016 0.069 0.18 34 -0.32 4 38
BRCA1/BACH1/BARD1/TopBP1 0.018 0.027 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.047 0.073 -10000 0 -0.14 45 45
BARD1/CSTF1/BRCA1 0.04 0.028 -10000 0 -10000 0 0
BRCA1/BACH1 0.026 0.009 -10000 0 0 59 59
BARD1 0.025 0.011 -10000 0 0 89 89
PCNA 0.022 0.013 -10000 0 0 147 147
BRCA1/BARD1/UbcH5C 0.044 0.026 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.044 0.026 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.06 0.057 -10000 0 -10000 0 0
BARD1/DNA-PK/P53 0.052 0.08 -10000 0 -0.14 51 51
BRCA1/BARD1/Ubiquitin 0.033 0.018 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP -0.023 0.049 0.16 30 -10000 0 30
FA complex 0.029 0.049 0.19 9 -0.21 5 14
BARD1/EWS 0.034 0.018 -10000 0 -10000 0 0
RBBP8 -0.009 0.067 0.19 54 -10000 0 54
TP53 0.024 0.011 -10000 0 0 101 101
TOPBP1 0.01 0.014 -10000 0 0 362 362
G1/S transition of mitotic cell cycle -0.045 0.072 0.14 45 -10000 0 45
BRCA1/BARD1 0.058 0.07 -10000 0 -10000 0 0
CSTF1 0.026 0.009 -10000 0 0 58 58
BARD1/EWS-Fli1 0.018 0.008 -10000 0 -10000 0 0
CDK2 0.017 0.014 -10000 0 0 227 227
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.013 0.015 -10000 0 0 308 308
RAD50 0.029 0.005 -10000 0 0 15 15
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.033 0.018 -10000 0 -10000 0 0
EWSR1 0.027 0.008 -10000 0 0 43 43
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.019 0.014 -10000 0 0 188 188
positive regulation of NF-kappaB transcription factor activity 0.015 0.046 -10000 0 -0.16 29 29
MAP2K4 -0.02 0.076 -10000 0 -0.3 14 14
IKBKB 0.027 0.007 -10000 0 0 39 39
TNFRSF10B 0.024 0.012 -10000 0 0 107 107
TNFRSF10A 0.024 0.012 -10000 0 0 109 109
SMPD1 -0.012 0.04 0.098 30 -0.12 29 59
IKBKG 0.028 0.006 -10000 0 0 25 25
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.024 0.012 -10000 0 0 108 108
TRAIL/TRAILR2 0.015 0.047 -10000 0 -0.16 29 29
TRAIL/TRAILR3 -0.029 0.088 -10000 0 -0.18 138 138
TRAIL/TRAILR1 0.015 0.047 -10000 0 -0.16 29 29
TRAIL/TRAILR4 0.015 0.047 -10000 0 -0.16 29 29
TRAIL/TRAILR1/DAP3/GTP 0.018 0.048 -10000 0 -0.13 29 29
IKK complex -0.003 0.067 -10000 0 -0.27 18 18
RIPK1 0.027 0.007 -10000 0 0 38 38
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.021 0.005 -10000 0 -10000 0 0
MAPK3 -0.009 0.055 0.19 35 -10000 0 35
MAP3K1 -0.02 0.082 0.18 1 -0.3 23 24
TRAILR4 (trimer) 0.024 0.012 -10000 0 0 108 108
TRADD 0.026 0.009 -10000 0 0 65 65
TRAILR1 (trimer) 0.024 0.012 -10000 0 0 109 109
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.018 0.073 -10000 0 -0.21 40 40
CFLAR 0.029 0.004 -10000 0 0 9 9
MAPK1 -0.009 0.054 0.19 35 -10000 0 35
TRAIL/TRAILR1/FADD/TRADD/RIP 0.031 0.07 -10000 0 -0.14 29 29
mol:ceramide -0.012 0.04 0.098 30 -0.12 29 59
FADD 0.028 0.005 -10000 0 0 19 19
MAPK8 -0.032 0.087 0.2 2 -0.3 24 26
TRAF2 0.028 0.006 -10000 0 0 25 25
TRAILR3 (trimer) 0.015 0.015 -10000 0 0 280 280
CHUK 0.027 0.007 -10000 0 0 36 36
TRAIL/TRAILR1/FADD 0.024 0.047 -10000 0 -0.14 26 26
DAP3 0.028 0.006 -10000 0 0 27 27
CASP10 0.011 0.081 0.15 76 -0.19 23 99
JNK cascade 0.015 0.046 -10000 0 -0.16 29 29
TRAIL (trimer) 0.019 0.014 -10000 0 0 188 188
TNFRSF10C 0.015 0.015 -10000 0 0 280 280
TRAIL/TRAILR1/DAP3/GTP/FADD 0.031 0.058 -10000 0 -0.13 26 26
TRAIL/TRAILR2/FADD 0.024 0.047 -10000 0 -0.14 26 26
cell death -0.012 0.04 0.098 30 -0.12 29 59
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.018 0.072 -10000 0 -0.21 40 40
TRAILR2 (trimer) 0.024 0.012 -10000 0 0 107 107
CASP8 -0.005 0.056 -10000 0 -0.47 3 3
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.032 0.07 -10000 0 -0.14 29 29
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.037 0.016 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.024 0.073 -10000 0 -0.15 73 73
PTK2 -0.019 0.13 0.28 18 -0.35 24 42
IGF1R 0.022 0.013 -10000 0 0 138 138
PI4KB 0.027 0.007 -10000 0 0 35 35
MFGE8 0.027 0.008 -10000 0 0 45 45
SRC 0.028 0.007 -10000 0 0 33 33
CDKN1B -0.006 0.06 -10000 0 -0.29 17 17
VEGFA 0.026 0.01 -10000 0 0 70 70
ILK -0.006 0.059 -10000 0 -0.28 17 17
ROCK1 0.029 0.005 -10000 0 0 14 14
AKT1 -0.023 0.053 0.15 3 -0.27 16 19
PTK2B -0.021 0.085 0.21 32 -0.23 2 34
alphaV/beta3 Integrin/JAM-A 0.024 0.074 -10000 0 -0.15 69 69
CBL 0.029 0.004 -10000 0 0 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.028 0.068 -10000 0 -0.15 66 66
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.083 0.12 -10000 0 -0.17 350 350
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.007 0.079 0.18 5 -0.29 15 20
alphaV/beta3 Integrin/Syndecan-1 0.028 0.067 -10000 0 -0.15 64 64
PI4KA 0.028 0.007 -10000 0 0 33 33
IGF-1R heterotetramer/IGF1/IRS1 -0.07 0.12 -10000 0 -0.19 230 230
PI4 Kinase 0.038 0.014 -10000 0 -10000 0 0
PIK3CA 0.02 0.014 -10000 0 0 170 170
alphaV/beta3 Integrin/Osteopontin 0.009 0.064 -10000 0 -0.15 63 63
RPS6KB1 -0.071 0.12 0.28 11 -0.32 15 26
TLN1 0.028 0.005 -10000 0 0 16 16
MAPK3 -0.077 0.16 -10000 0 -0.39 94 94
GPR124 0.025 0.01 -10000 0 0 75 75
MAPK1 -0.073 0.16 -10000 0 -0.39 92 92
PXN 0.029 0.005 -10000 0 0 14 14
PIK3R1 0.021 0.013 -10000 0 0 159 159
alphaV/beta3 Integrin/Tumstatin 0.028 0.069 -10000 0 -0.15 68 68
cell adhesion 0.009 0.082 -10000 0 -0.19 71 71
ANGPTL3 0.029 0.004 -10000 0 0 11 11
VEGFR2 homodimer/VEGFA homodimer/Src 0.048 0.024 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.022 0.013 -10000 0 0 138 138
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
TGFBR2 0.029 0.005 -10000 0 0 15 15
ITGB3 0.024 0.011 -10000 0 0 98 98
IGF1 0.028 0.007 -10000 0 0 32 32
RAC1 0.028 0.006 -10000 0 0 27 27
regulation of cell-matrix adhesion 0.02 0.07 -10000 0 -0.15 74 74
apoptosis 0.028 0.007 -10000 0 0 32 32
CD47 0.027 0.008 -10000 0 0 49 49
alphaV/beta3 Integrin/CD47 0.026 0.066 -10000 0 -0.15 62 62
VCL 0.029 0.004 -10000 0 0 12 12
alphaV/beta3 Integrin/Del1 0.018 0.066 -10000 0 -0.15 65 65
CSF1 0.028 0.006 -10000 0 0 27 27
PIK3C2A -0.004 0.054 -10000 0 -0.27 14 14
PI4 Kinase/Pyk2 -0.065 0.062 0.099 27 -0.24 5 32
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.046 0.075 -10000 0 -0.14 60 60
FAK1/Vinculin -0.01 0.12 0.27 18 -0.3 22 40
alphaV beta3/Integrin/ppsTEM5 0.021 0.071 -10000 0 -0.15 74 74
RHOA 0.029 0.003 -10000 0 0 6 6
VTN 0.028 0.007 -10000 0 0 32 32
BCAR1 0.026 0.009 -10000 0 0 57 57
FGF2 0.027 0.008 -10000 0 0 43 43
F11R -0.03 0.014 0.19 1 -10000 0 1
alphaV/beta3 Integrin/Lactadherin 0.021 0.076 -10000 0 -0.16 79 79
alphaV/beta3 Integrin/TGFBR2 0.026 0.072 -10000 0 -0.16 70 70
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.055 0.055 -10000 0 -0.14 22 22
HSP90AA1 0.028 0.006 -10000 0 0 21 21
alphaV/beta3 Integrin/Talin 0.026 0.063 -10000 0 -0.13 67 67
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.018 0.014 -10000 0 0 213 213
alphaV/beta3 Integrin/Pyk2 -0.041 0.068 0.17 37 -0.23 2 39
SDC1 0.028 0.005 -10000 0 0 17 17
VAV3 -0.038 0.055 0.17 17 -0.23 1 18
PTPN11 0.029 0.003 -10000 0 0 8 8
IRS1 0.011 0.014 -10000 0 0 349 349
FAK1/Paxillin -0.01 0.12 0.27 18 -0.29 23 41
cell migration -0.019 0.11 0.24 20 -0.28 21 41
ITGAV 0.028 0.007 -10000 0 0 32 32
PI3K 0.001 0.095 -10000 0 -0.16 109 109
SPP1 0.017 0.014 -10000 0 0 227 227
KDR 0.028 0.006 -10000 0 0 22 22
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.028 0.007 -10000 0 0 32 32
COL4A3 0.029 0.003 -10000 0 0 8 8
angiogenesis -0.077 0.17 0.31 2 -0.42 91 93
Rac1/GTP -0.042 0.055 0.16 20 -0.22 1 21
EDIL3 0.023 0.012 -10000 0 0 122 122
cell proliferation 0.026 0.071 -10000 0 -0.15 70 70
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.082 0.12 -10000 0 -0.36 48 48
CaM/Ca2+ 0.018 0.022 -10000 0 -0.15 9 9
AKT1 0.028 0.006 -10000 0 0 27 27
AKT2 0.027 0.009 -10000 0 0 52 52
STXBP4 0.028 0.005 -10000 0 0 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.045 0.12 -10000 0 -0.37 42 42
YWHAZ 0.025 0.01 -10000 0 0 78 78
CALM1 0.028 0.006 -10000 0 0 26 26
YWHAQ 0.029 0.005 -10000 0 0 15 15
TBC1D4 -0.03 0.013 0.19 1 -10000 0 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.027 0.008 -10000 0 0 42 42
YWHAB 0.027 0.008 -10000 0 0 45 45
SNARE/Synip -0.087 0.09 -10000 0 -0.15 384 384
YWHAG 0.029 0.004 -10000 0 0 11 11
ASIP 0.027 0.008 -10000 0 0 43 43
PRKCI 0.014 0.015 -10000 0 0 289 289
AS160/CaM/Ca2+ 0.018 0.022 -10000 0 -0.15 9 9
RHOQ 0.028 0.005 -10000 0 0 20 20
GYS1 -0.014 0.012 0.24 1 -10000 0 1
PRKCZ 0.028 0.006 -10000 0 0 23 23
TRIP10 0.027 0.007 -10000 0 0 35 35
TC10/GTP/CIP4/Exocyst 0.036 0.012 -10000 0 -10000 0 0
AS160/14-3-3 -0.008 0.07 0.16 4 -0.32 15 19
VAMP2 0.007 0.013 -10000 0 0 417 417
SLC2A4 -0.051 0.13 -10000 0 -0.41 42 42
STX4 0.029 0.004 -10000 0 0 11 11
GSK3B 0.009 0.004 -10000 0 -10000 0 0
SFN 0.027 0.007 -10000 0 0 37 37
LNPEP 0.027 0.009 -10000 0 0 53 53
YWHAE 0.027 0.008 -10000 0 0 40 40
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.01 0.13 -10000 0 -0.44 41 41
HDAC1 0.038 0.022 0.097 16 -0.071 1 17
AES 0.026 0.016 0.068 11 -0.038 1 12
FBXW11 0.028 0.005 -10000 0 0 16 16
DTX1 0.029 0.004 -10000 0 0 9 9
LRP6/FZD1 0.036 0.016 -10000 0 -10000 0 0
TLE1 0.03 0.013 0.065 10 -0.029 14 24
AP1 -0.008 0.073 0.2 7 -0.2 50 57
NCSTN 0.011 0.027 -10000 0 -0.029 163 163
ADAM10 0.029 0.006 -10000 0 -0.029 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.13 0.22 -10000 0 -0.62 60 60
NICD/RBPSUH 0.004 0.13 -10000 0 -0.44 40 40
WIF1 0.01 0.027 -10000 0 -0.029 173 173
NOTCH1 -0.01 0.12 -10000 0 -0.47 37 37
PSENEN 0.01 0.025 -10000 0 -0.029 144 144
KREMEN2 0.028 0.006 -10000 0 0 24 24
DKK1 0.028 0.006 -10000 0 0 22 22
beta catenin/beta TrCP1 -0.004 0.066 0.22 1 -0.27 2 3
APH1B 0.009 0.026 -10000 0 -0.029 159 159
APH1A 0.011 0.026 -10000 0 -0.029 161 161
AXIN1 -0.011 0.1 -10000 0 -0.43 22 22
CtBP/CBP/TCF1/TLE1/AES 0.013 0.1 0.25 22 -0.28 12 34
PSEN1 0.011 0.027 -10000 0 -0.029 170 170
FOS 0.024 0.011 -10000 0 0 105 105
JUN 0.028 0.007 -10000 0 0 32 32
MAP3K7 0.033 0.011 -10000 0 -0.046 1 1
CTNNB1 -0.012 0.059 0.22 1 -0.28 2 3
MAPK3 0.028 0.006 -10000 0 0 22 22
DKK2/LRP6/Kremen 2 0.047 0.024 -10000 0 -10000 0 0
HNF1A 0.033 0.01 0.069 13 -0.038 1 14
CTBP1 0.031 0.012 0.068 13 -10000 0 13
MYC -0.16 0.36 -10000 0 -1.2 59 59
NKD1 0.029 0.008 -10000 0 -10000 0 0
FZD1 0.01 0.027 -10000 0 -0.029 172 172
NOTCH1 precursor/Deltex homolog 1 0.004 0.13 -10000 0 -0.44 41 41
apoptosis -0.008 0.073 0.2 7 -0.2 50 57
Delta 1/NOTCHprecursor 0.003 0.13 -10000 0 -0.44 41 41
DLL1 0.027 0.008 -10000 0 0 48 48
PPARD -0.02 0.1 -10000 0 -0.99 5 5
Gamma Secretase 0.041 0.077 -10000 0 -0.14 65 65
APC -0.016 0.11 -10000 0 -0.44 27 27
DVL1 -0.005 0.057 -10000 0 -0.25 22 22
CSNK2A1 0.008 0.028 -10000 0 -0.032 170 170
MAP3K7IP1 0.005 0.008 0.018 99 -0.017 1 100
DKK1/LRP6/Kremen 2 0.048 0.024 -10000 0 -10000 0 0
LRP6 0.009 0.026 -10000 0 -0.029 155 155
CSNK1A1 0.008 0.029 -10000 0 -0.032 183 183
NLK 0.018 0.019 -10000 0 -10000 0 0
CCND1 -0.3 0.51 -10000 0 -1.1 147 147
WNT1 0.01 0.027 -10000 0 -0.029 179 179
Axin1/APC/beta catenin -0.024 0.099 -10000 0 -0.43 16 16
DKK2 0.027 0.007 -10000 0 0 39 39
NOTCH1 precursor/DVL1 -0.01 0.13 -10000 0 -0.46 36 36
GSK3B 0.029 0.006 -10000 0 -0.03 1 1
FRAT1 0.031 0.007 -10000 0 -0.036 1 1
NOTCH/Deltex homolog 1 0.013 0.13 -10000 0 -0.44 41 41
PPP2R5D 0.009 0.046 -10000 0 -0.36 6 6
MAPK1 0.027 0.008 -10000 0 0 42 42
WNT1/LRP6/FZD1 0.064 0.033 -10000 0 -10000 0 0
RBPJ 0.028 0.005 -10000 0 0 18 18
CREBBP 0.011 0.024 -10000 0 -0.026 144 144
IL4-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
BCL2L1 0.027 0.58 1.1 16 -1.2 40 56
STAT6 (cleaved dimer) -0.1 0.5 0.66 2 -1.2 55 57
IGHG1 0.091 0.31 0.68 40 -0.97 2 42
IGHG3 -0.005 0.53 0.81 6 -1.1 49 55
AKT1 -0.039 0.37 -10000 0 -0.98 29 29
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.015 0.33 0.57 7 -0.96 28 35
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.08 0.39 0.64 3 -1 39 42
THY1 0.078 0.65 1.2 43 -1.2 41 84
MYB 0.026 0.009 -10000 0 0 62 62
HMGA1 0.028 0.006 -10000 0 0 23 23
IL4/IL4R/JAK1/IL2R gamma/JAK3 0.051 0.42 0.77 32 -0.94 24 56
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP 0.022 0.4 0.64 9 -1.1 27 36
SP1 0.11 0.13 0.3 178 -0.14 6 184
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 -0.018 0.058 -10000 0 -0.15 5 5
STAT6 (dimer)/ETS1 -0.049 0.54 0.73 3 -1.2 52 55
SOCS1 -0.002 0.4 0.62 17 -0.78 46 63
SOCS3 0.029 0.35 0.87 1 -0.88 17 18
FCER2 0.043 0.48 0.99 7 -1.1 18 25
PARP14 0.022 0.013 -10000 0 -10000 0 0
CCL17 0.006 0.57 0.97 6 -1.2 40 46
GRB2 0.028 0.005 -10000 0 0 19 19
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.044 0.31 0.59 13 -0.68 25 38
T cell proliferation -0.056 0.59 -10000 0 -1.3 62 62
IL4R/JAK1 -0.069 0.61 0.82 1 -1.4 65 66
EGR2 0.012 0.58 1.3 5 -1.2 41 46
JAK2 0.042 0.11 0.25 43 -10000 0 43
JAK3 0.002 0.034 0.11 2 -10000 0 2
PIK3R1 0.021 0.013 -10000 0 0 159 159
JAK1 0.023 0.059 0.14 17 -10000 0 17
COL1A2 0.16 0.39 0.73 102 -1.1 8 110
CCL26 0.008 0.57 1 2 -1.2 40 42
IL4R -0.017 0.7 1.1 25 -1.4 64 89
PTPN6 -0.013 0.05 -10000 0 -0.1 13 13
IL13RA2 0.018 0.58 1.1 11 -1.2 42 53
IL13RA1 0.045 0.11 0.25 49 -10000 0 49
IRF4 0.067 0.21 0.73 1 -0.67 6 7
ARG1 0.08 0.27 0.72 6 -0.98 1 7
CBL 0.029 0.38 0.68 13 -0.88 25 38
GTF3A 0.16 0.14 0.31 276 -0.11 1 277
PIK3CA 0.02 0.014 -10000 0 0 170 170
IL13RA1/JAK2 0.073 0.16 0.35 56 -10000 0 56
IRF4/BCL6 0.046 0.18 0.54 1 -0.64 6 7
CD40LG 0.029 0.018 0.33 2 -10000 0 2
MAPK14 0.031 0.38 0.7 8 -0.9 23 31
mitosis -0.032 0.35 0.59 1 -0.9 29 30
STAT6 0.034 0.71 1.4 40 -1.4 45 85
SPI1 0.029 0.011 0.27 1 -10000 0 1
RPS6KB1 -0.036 0.34 0.63 2 -0.88 28 30
STAT6 (dimer) 0.033 0.7 1.4 40 -1.4 44 84
STAT6 (dimer)/PARP14 -0.055 0.54 -10000 0 -1.3 47 47
mast cell activation -0.01 0.028 -10000 0 -0.068 41 41
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.006 0.39 0.63 10 -1 30 40
FRAP1 -0.039 0.37 -10000 0 -0.98 29 29
LTA 0.011 0.57 1 9 -1.2 41 50
FES 0.028 0.005 -10000 0 0 20 20
T-helper 1 cell differentiation -0.046 0.7 1.4 44 -1.4 40 84
CCL11 0.003 0.55 0.97 21 -1.1 49 70
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.019 0.38 0.62 11 -1.1 25 36
IL2RG 0 0.034 0.12 2 -10000 0 2
IL10 0.009 0.57 0.97 7 -1.2 45 52
IRS1 0.011 0.014 -10000 0 0 349 349
IRS2 0.028 0.006 -10000 0 0 25 25
IL4 0.11 0.31 0.78 39 -0.99 7 46
IL5 0.007 0.57 0.97 6 -1.2 44 50
IL4/IL4R/JAK1/IL13RA1/JAK2 0.053 0.58 1.1 39 -1.2 32 71
COL1A1 0.3 0.51 0.99 117 -1.2 9 126
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.087 0.61 -10000 0 -1.4 65 65
IL2R gamma/JAK3 0.028 0.046 0.18 2 -0.16 23 25
TFF3 -0.56 0.62 0.97 5 -1.3 152 157
ALOX15 0.008 0.58 1.1 7 -1.2 46 53
MYBL1 0.024 0.011 -10000 0 0 104 104
T-helper 2 cell differentiation -0.025 0.54 0.87 9 -1.2 48 57
SHC1 0.028 0.006 -10000 0 0 21 21
CEBPB 0.027 0.013 0.27 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 0.02 0.39 0.63 9 -1.1 28 37
mol:PI-3-4-5-P3 -0.038 0.37 -10000 0 -0.98 29 29
PI3K -0.048 0.39 -10000 0 -1.1 30 30
DOK2 0.024 0.012 -10000 0 0 106 106
ETS1 -0.023 0.063 -10000 0 -0.15 16 16
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.046 0.3 0.58 14 -0.66 24 38
ITGB3 -0.062 0.68 1.2 8 -1.3 81 89
PIGR -0.016 0.62 1.2 13 -1.3 53 66
IGHE -0.051 0.12 0.22 12 -0.31 50 62
MAPKKK cascade 0.047 0.3 0.58 14 -0.64 24 38
BCL6 0.024 0.011 -10000 0 -10000 0 0
OPRM1 0.008 0.57 0.97 6 -1.2 43 49
RETNLB 0.015 0.57 1 8 -1.2 43 51
SELP -0.015 0.6 1 8 -1.2 50 58
AICDA 0.005 0.53 1.1 3 -1.1 45 48
PDGFR-alpha signaling pathway

Figure S37.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S37.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.016 0.037 0.1 24 -10000 0 24
PDGF/PDGFRA/CRKL 0.009 0.07 -10000 0 -0.16 65 65
positive regulation of JUN kinase activity 0.034 0.075 -10000 0 -0.14 61 61
CRKL 0.028 0.007 -10000 0 0 31 31
PDGF/PDGFRA/Caveolin-3 0.009 0.071 -10000 0 -0.16 65 65
AP1 -0.093 0.25 0.59 19 -0.69 62 81
mol:IP3 -0.022 0.06 0.18 30 -0.22 7 37
PLCG1 -0.022 0.06 0.18 30 -0.22 7 37
PDGF/PDGFRA/alphaV Integrin 0.008 0.071 -10000 0 -0.17 66 66
RAPGEF1 0.028 0.005 -10000 0 0 18 18
CRK 0.027 0.007 -10000 0 0 36 36
mol:Ca2+ -0.022 0.06 0.18 30 -0.22 7 37
CAV3 0.029 0.004 -10000 0 0 10 10
CAV1 0.024 0.012 -10000 0 0 108 108
SHC/Grb2/SOS1 0.037 0.077 -10000 0 -0.14 61 61
PDGF/PDGFRA/Shf 0.009 0.07 -10000 0 -0.16 65 65
FOS -0.085 0.26 0.64 25 -0.7 59 84
JUN -0.026 0.058 0.18 32 -0.22 1 33
oligodendrocyte development 0.008 0.071 -10000 0 -0.16 66 66
GRB2 0.028 0.005 -10000 0 0 19 19
PIK3R1 0.021 0.013 -10000 0 0 159 159
mol:DAG -0.022 0.06 0.18 30 -0.22 7 37
PDGF/PDGFRA -0.016 0.037 0.1 24 -10000 0 24
actin cytoskeleton reorganization 0.01 0.071 -10000 0 -0.16 65 65
SRF -0.026 0.021 -10000 0 -10000 0 0
SHC1 0.028 0.006 -10000 0 0 21 21
PI3K -0.012 0.085 -10000 0 -0.16 109 109
PDGF/PDGFRA/Crk/C3G 0.02 0.071 -10000 0 -0.14 64 64
JAK1 -0.026 0.041 0.18 9 -0.18 9 18
ELK1/SRF -0.049 0.062 0.13 30 -0.21 5 35
SHB 0.029 0.003 -10000 0 0 8 8
SHF 0.028 0.007 -10000 0 0 32 32
CSNK2A1 0.023 0.036 -10000 0 -0.086 28 28
GO:0007205 -0.035 0.081 0.19 31 -0.21 56 87
SOS1 0.027 0.007 -10000 0 0 36 36
Ras protein signal transduction 0.034 0.075 -10000 0 -0.14 61 61
PDGF/PDGFRA/SHB 0.01 0.071 -10000 0 -0.16 65 65
PDGF/PDGFRA/Caveolin-1 -0.016 0.099 -10000 0 -0.19 125 125
ITGAV 0.028 0.007 -10000 0 0 32 32
ELK1 -0.039 0.085 0.22 30 -0.2 50 80
PIK3CA 0.02 0.014 -10000 0 0 170 170
PDGF/PDGFRA/Crk 0.008 0.07 -10000 0 -0.16 65 65
JAK-STAT cascade -0.026 0.041 0.18 9 -0.18 9 18
cell proliferation 0.009 0.07 -10000 0 -0.16 65 65
Nectin adhesion pathway

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
PDGFRB 0.029 0.005 -10000 0 0 15 15
alphaV beta3 Integrin 0.013 0.069 -10000 0 -0.17 68 68
PTK2 -0.037 0.11 -10000 0 -0.34 42 42
positive regulation of JNK cascade -0.015 0.11 -10000 0 -0.3 48 48
CDC42/GDP -0.017 0.15 -10000 0 -0.4 54 54
Rac1/GDP -0.02 0.15 -10000 0 -0.4 55 55
RAP1B 0.028 0.006 -10000 0 0 22 22
RAP1A 0.029 0.003 -10000 0 0 7 7
CTNNB1 0.029 0.003 -10000 0 0 8 8
CDC42/GTP -0.016 0.14 -10000 0 -0.37 47 47
nectin-3/I-afadin 0.025 0.043 -10000 0 -0.16 23 23
RAPGEF1 -0.04 0.14 0.26 1 -0.41 54 55
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.042 0.15 -10000 0 -0.45 55 55
PDGFB-D/PDGFRB 0.028 0.005 -10000 0 0 15 15
TLN1 -0.094 0.12 -10000 0 -0.25 185 185
Rap1/GTP -0.029 0.11 -10000 0 -0.31 55 55
IQGAP1 0.028 0.006 -10000 0 0 24 24
Rap1/GTP/I-afadin 0.04 0.042 -10000 0 -0.13 21 21
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.025 0.043 -10000 0 -0.16 23 23
PVR 0.028 0.007 -10000 0 0 33 33
Necl-5(dimer) 0.028 0.007 -10000 0 0 33 33
mol:GDP -0.038 0.17 -10000 0 -0.48 55 55
MLLT4 0.026 0.01 -10000 0 0 70 70
PIK3CA 0.02 0.014 -10000 0 0 170 170
PI3K 0.026 0.091 -10000 0 -0.15 79 79
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.031 0.041 -10000 0 -0.16 21 21
positive regulation of lamellipodium assembly -0.016 0.12 -10000 0 -0.32 55 55
PVRL1 0.029 0.005 -10000 0 0 15 15
PVRL3 0.024 0.011 -10000 0 0 93 93
PVRL2 0.028 0.007 -10000 0 0 33 33
PIK3R1 0.021 0.013 -10000 0 0 159 159
CDH1 0.026 0.01 -10000 0 0 72 72
CLDN1 0.017 0.014 -10000 0 0 234 234
JAM-A/CLDN1 0.005 0.094 -10000 0 -0.14 136 136
SRC -0.039 0.16 -10000 0 -0.48 55 55
ITGB3 0.024 0.011 -10000 0 0 98 98
nectin-1(dimer)/I-afadin/I-afadin 0.031 0.041 -10000 0 -0.16 21 21
FARP2 -0.032 0.17 -10000 0 -0.49 48 48
RAC1 0.028 0.006 -10000 0 0 27 27
CTNNA1 0.029 0.004 -10000 0 0 11 11
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.036 0.045 -10000 0 -0.14 22 22
nectin-1/I-afadin 0.031 0.041 -10000 0 -0.16 21 21
nectin-2/I-afadin 0.03 0.042 -10000 0 -0.16 22 22
RAC1/GTP/IQGAP1/filamentous actin 0.036 0.015 -10000 0 -0.13 2 2
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.037 0.046 -10000 0 -0.15 23 23
CDC42/GTP/IQGAP1/filamentous actin 0.037 0.014 -10000 0 -0.13 2 2
F11R 0.029 0.005 -10000 0 0 14 14
positive regulation of filopodium formation -0.015 0.11 -10000 0 -0.3 48 48
alphaV/beta3 Integrin/Talin -0.12 0.12 0.2 5 -0.26 196 201
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.03 0.042 -10000 0 -0.16 22 22
nectin-2(dimer)/I-afadin/I-afadin 0.03 0.042 -10000 0 -0.16 22 22
PIP5K1C -0.092 0.12 -10000 0 -0.26 185 185
VAV2 -0.035 0.18 -10000 0 -0.5 50 50
RAP1/GDP -0.015 0.14 -10000 0 -0.37 54 54
ITGAV 0.028 0.007 -10000 0 0 32 32
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.036 0.046 -10000 0 -0.14 23 23
nectin-3(dimer)/I-afadin/I-afadin 0.025 0.043 -10000 0 -0.16 23 23
Rac1/GTP -0.019 0.14 -10000 0 -0.38 54 54
PTPRM -0.1 0.13 0.098 24 -0.27 203 227
E-cadherin/beta catenin/alpha catenin 0.047 0.071 -10000 0 -0.15 25 25
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.029 0.004 -10000 0 0 11 11
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.061 0.1 0.21 88 -10000 0 88
DAPP1 -0.029 0.098 0.2 7 -0.31 23 30
Src family/SYK family/BLNK-LAT/BTK-ITK -0.004 0.12 -10000 0 -0.42 17 17
mol:DAG 0.023 0.089 0.2 57 -0.21 7 64
HRAS 0.013 0.035 0.052 77 -10000 0 77
RAP1A 0.014 0.036 0.048 118 -10000 0 118
ARF5/GDP 0.052 0.065 0.19 3 -0.26 8 11
PLCG2 0.026 0.009 -10000 0 0 62 62
PLCG1 0.028 0.007 -10000 0 0 33 33
ARF5 0.028 0.006 -10000 0 0 24 24
mol:GTP 0.059 0.097 0.21 93 -10000 0 93
ARF1/GTP 0.056 0.089 0.25 54 -10000 0 54
RHOA 0.029 0.003 -10000 0 0 6 6
YES1 0.027 0.008 -10000 0 0 41 41
RAP1A/GTP 0.072 0.11 0.16 311 -10000 0 311
ADAP1 0.054 0.092 0.2 91 -10000 0 91
ARAP3 0.059 0.096 0.21 93 -10000 0 93
INPPL1 0.028 0.006 -10000 0 0 21 21
PREX1 0.027 0.008 -10000 0 0 48 48
ARHGEF6 0.028 0.005 -10000 0 0 18 18
ARHGEF7 0.028 0.006 -10000 0 0 25 25
ARF1 0.026 0.009 -10000 0 0 54 54
NRAS -0.008 0.022 0.041 41 -10000 0 41
FYN 0.024 0.011 -10000 0 0 99 99
ARF6 0.029 0.004 -10000 0 0 11 11
FGR 0.029 0.005 -10000 0 0 14 14
mol:Ca2+ 0.008 0.053 0.14 35 -10000 0 35
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.028 0.005 -10000 0 0 20 20
ZAP70 0.029 0.004 -10000 0 0 10 10
mol:IP3 0.006 0.065 0.17 32 -0.16 3 35
LYN 0.027 0.008 -10000 0 0 50 50
ARF1/GDP 0.048 0.066 0.19 3 -0.25 9 12
RhoA/GDP 0.085 0.1 0.22 126 -10000 0 126
PDK1/Src/Hsp90 0.053 0.019 -10000 0 -10000 0 0
BLNK 0.028 0.007 -10000 0 0 30 30
actin cytoskeleton reorganization 0.07 0.096 0.24 67 -0.26 2 69
SRC 0.028 0.007 -10000 0 0 33 33
PLEKHA2 -0.023 0.009 -10000 0 -10000 0 0
RAC1 0.028 0.006 -10000 0 0 27 27
PTEN -0.011 0.035 -10000 0 -0.04 322 322
HSP90AA1 0.028 0.006 -10000 0 0 21 21
ARF6/GTP 0.063 0.1 0.21 91 -10000 0 91
RhoA/GTP 0.063 0.1 0.23 79 -10000 0 79
Src family/SYK family/BLNK-LAT -0.032 0.089 -10000 0 -0.3 25 25
BLK 0.024 0.011 -10000 0 0 101 101
PDPK1 0.028 0.005 -10000 0 0 18 18
CYTH1 0.054 0.092 0.2 91 -10000 0 91
HCK 0.027 0.008 -10000 0 0 47 47
CYTH3 0.054 0.092 0.2 91 -10000 0 91
CYTH2 0.054 0.092 0.2 91 -10000 0 91
KRAS 0.006 0.033 0.049 30 -10000 0 30
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.034 0.058 0.17 47 -0.19 1 48
SGK1 0.045 0.063 0.18 48 -0.18 6 54
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.041 0.064 0.18 7 -0.26 8 15
SOS1 0.027 0.007 -10000 0 0 36 36
SYK 0.028 0.006 -10000 0 0 24 24
ARF6/GDP 0.07 0.098 0.22 86 -10000 0 86
mol:PI-3-4-5-P3 0.061 0.098 0.2 90 -10000 0 90
ARAP3/RAP1A/GTP 0.072 0.11 0.16 311 -10000 0 311
VAV1 0.027 0.008 -10000 0 0 40 40
mol:PI-3-4-P2 -0.016 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I -0.014 0.035 0.2 9 -10000 0 9
PLEKHA1 -0.023 0.023 0.18 7 -10000 0 7
Rac1/GDP 0.053 0.065 0.2 2 -0.25 8 10
LAT 0.029 0.003 -10000 0 0 8 8
Rac1/GTP 0.016 0.055 0.19 1 -0.28 8 9
ITK 0.048 0.093 0.21 71 -10000 0 71
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.019 0.11 0.22 52 -0.27 9 61
LCK 0.028 0.006 -10000 0 0 25 25
BTK 0.048 0.094 0.21 75 -10000 0 75
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.033 0.07 -10000 0 -0.13 71 71
ER alpha/Gai/GDP/Gbeta gamma -0.038 0.14 -10000 0 -0.44 28 28
AKT1 -0.13 0.27 -10000 0 -0.67 102 102
PIK3CA 0.02 0.014 -10000 0 0 170 170
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.12 0.28 -10000 0 -0.68 102 102
mol:Ca2+ -0.043 0.078 -10000 0 -0.32 20 20
IGF1R 0.022 0.013 -10000 0 0 138 138
E2/ER alpha (dimer)/Striatin 0.015 0.057 -10000 0 -0.13 68 68
SHC1 0.028 0.006 -10000 0 0 21 21
apoptosis 0.13 0.26 0.64 102 -10000 0 102
RhoA/GTP -0.025 0.035 -10000 0 -0.14 23 23
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.022 0.15 0.24 2 -0.33 72 74
regulation of stress fiber formation -0.031 0.1 -10000 0 -0.24 60 60
E2/ERA-ERB (dimer) 0.014 0.058 -10000 0 -0.13 72 72
KRAS 0.024 0.011 -10000 0 0 99 99
G13/GTP 0.013 0.053 -10000 0 -0.12 72 72
pseudopodium formation 0.031 0.1 0.24 60 -10000 0 60
E2/ER alpha (dimer)/PELP1 0.014 0.058 -10000 0 -0.13 72 72
GRB2 0.028 0.005 -10000 0 0 19 19
GNG2 0.029 0.004 -10000 0 0 12 12
GNAO1 0.027 0.008 -10000 0 0 45 45
HRAS 0.028 0.006 -10000 0 0 26 26
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.067 0.17 -10000 0 -0.4 93 93
E2/ER beta (dimer) 0.021 0.003 -10000 0 -10000 0 0
mol:GDP -0.035 0.069 -10000 0 -0.25 36 36
mol:NADP -0.067 0.17 -10000 0 -0.4 93 93
PIK3R1 0.021 0.013 -10000 0 0 159 159
mol:IP3 -0.047 0.074 -10000 0 -0.34 18 18
IGF-1R heterotetramer 0.022 0.013 -10000 0 0 138 138
PLCB1 -0.035 0.072 -10000 0 -0.36 15 15
PLCB2 -0.038 0.071 -10000 0 -0.36 17 17
IGF1 0.028 0.007 -10000 0 0 32 32
mol:L-citrulline -0.067 0.17 -10000 0 -0.4 93 93
RHOA 0.029 0.003 -10000 0 0 6 6
Gai/GDP -0.006 0.17 -10000 0 -0.6 34 34
JNK cascade 0.021 0.003 -10000 0 -10000 0 0
BCAR1 0.026 0.009 -10000 0 0 57 57
ESR2 0.029 0.005 -10000 0 0 14 14
GNAQ 0.028 0.007 -10000 0 0 29 29
ESR1 0.024 0.012 -10000 0 0 106 106
Gq family/GDP/Gbeta gamma -0.071 0.22 -10000 0 -0.66 59 59
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.001 0.11 -10000 0 -0.7 7 7
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.02 0.15 0.24 2 -0.33 69 71
GNAZ 0.027 0.008 -10000 0 0 47 47
E2/ER alpha (dimer) -0.002 0.057 -10000 0 -0.15 72 72
STRN 0.028 0.005 -10000 0 0 16 16
GNAL 0.028 0.005 -10000 0 0 20 20
PELP1 0.028 0.006 -10000 0 0 25 25
MAPK11 -0.02 0.012 -10000 0 -10000 0 0
GNAI2 0.029 0.003 -10000 0 0 6 6
GNAI3 0.024 0.011 -10000 0 0 98 98
GNAI1 0.028 0.006 -10000 0 0 26 26
HBEGF -0.02 0.15 0.29 15 -0.43 24 39
cAMP biosynthetic process 0.01 0.05 -10000 0 -0.11 71 71
SRC -0.039 0.14 -10000 0 -0.43 27 27
PI3K -0.001 0.068 -10000 0 -0.16 77 77
GNB1 0.028 0.006 -10000 0 0 24 24
G13/GDP/Gbeta gamma 0.017 0.09 -10000 0 -0.24 35 35
SOS1 0.027 0.007 -10000 0 0 36 36
IGF-1R heterotetramer/IGF1 -0.069 0.11 -10000 0 -0.3 74 74
Gs family/GTP 0.017 0.054 -10000 0 -0.12 71 71
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.02 0.028 -10000 0 -10000 0 0
vasodilation -0.064 0.16 -10000 0 -0.38 93 93
mol:DAG -0.047 0.074 -10000 0 -0.34 18 18
Gs family/GDP/Gbeta gamma -0.029 0.081 -10000 0 -0.24 35 35
MSN 0.03 0.1 0.24 57 -0.21 2 59
Gq family/GTP -0.017 0.082 -10000 0 -0.37 18 18
mol:PI-3-4-5-P3 -0.11 0.27 -10000 0 -0.66 102 102
NRAS 0.014 0.015 -10000 0 0 300 300
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.064 0.16 0.38 93 -10000 0 93
GRB2/SOS1 0.039 0.013 -10000 0 -10000 0 0
RhoA/GDP -0.018 0.087 -10000 0 -0.25 35 35
NOS3 -0.071 0.18 -10000 0 -0.42 93 93
GNA11 0.025 0.01 -10000 0 0 83 83
MAPKKK cascade -0.063 0.2 -10000 0 -0.47 99 99
E2/ER alpha (dimer)/PELP1/Src -0.024 0.15 0.26 2 -0.33 71 73
ruffle organization 0.031 0.1 0.24 60 -10000 0 60
ROCK2 0.047 0.11 0.27 58 -10000 0 58
GNA14 0.028 0.005 -10000 0 0 19 19
GNA15 0.027 0.008 -10000 0 0 46 46
GNA13 0.029 0.004 -10000 0 0 13 13
MMP9 -0.015 0.15 0.29 27 -0.43 24 51
MMP2 -0.044 0.14 0.25 7 -0.41 32 39
Signaling events mediated by the Hedgehog family

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
TGFB2 0.03 0.21 0.5 81 -0.45 15 96
IHH -0.005 0.078 0.16 91 -10000 0 91
SHH Np/Cholesterol/GAS1 -0.044 0.037 0.14 1 -0.13 76 77
LRPAP1 0.028 0.007 -10000 0 0 33 33
dorsoventral neural tube patterning 0.044 0.037 0.13 76 -0.14 1 77
SMO/beta Arrestin2 0.025 0.13 0.3 85 -0.39 9 94
SMO 0.028 0.13 0.31 84 -0.4 9 93
AKT1 -0.025 0.15 0.33 2 -0.45 18 20
ARRB2 0.028 0.006 -10000 0 0 25 25
BOC 0.025 0.01 -10000 0 0 80 80
ADRBK1 0.029 0.003 -10000 0 0 6 6
heart looping 0.028 0.13 0.31 84 -0.39 9 93
STIL 0.001 0.065 0.27 20 -10000 0 20
DHH N/PTCH2 0.042 0.009 -10000 0 -10000 0 0
DHH N/PTCH1 0.006 0.13 0.31 79 -0.29 8 87
PIK3CA 0.02 0.014 -10000 0 0 170 170
DHH 0.029 0.002 -10000 0 0 4 4
PTHLH 0.032 0.19 0.5 71 -0.42 21 92
determination of left/right symmetry 0.028 0.13 0.31 84 -0.39 9 93
PIK3R1 0.021 0.013 -10000 0 0 159 159
skeletal system development 0.033 0.19 0.49 71 -0.41 21 92
IHH N/Hhip 0.048 0.042 0.18 3 -0.088 8 11
DHH N/Hhip 0.041 0.01 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.028 0.13 0.31 84 -0.39 9 93
pancreas development 0.028 0.006 -10000 0 0 26 26
HHAT 0.028 0.005 -10000 0 0 19 19
PI3K -0.001 0.068 -10000 0 -0.16 77 77
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.024 0.011 -10000 0 0 95 95
somite specification 0.028 0.13 0.31 84 -0.39 9 93
SHH Np/Cholesterol/PTCH1 -0.003 0.12 0.27 75 -0.27 8 83
SHH Np/Cholesterol/PTCH2 -0.032 0.016 0.14 1 -0.13 5 6
SHH Np/Cholesterol/Megalin -0.025 0.019 -10000 0 -0.13 4 4
SHH -0.03 0.014 0.19 1 -10000 0 1
catabolic process 0.023 0.16 0.38 84 -0.32 8 92
SMO/Vitamin D3 0.004 0.12 0.26 76 -0.36 9 85
SHH Np/Cholesterol/Hhip -0.031 0.017 0.14 1 -0.13 5 6
LRP2 0.022 0.013 -10000 0 0 140 140
receptor-mediated endocytosis 0.026 0.13 0.28 75 -0.4 8 83
SHH Np/Cholesterol/BOC -0.04 0.033 0.14 1 -0.13 55 56
SHH Np/Cholesterol/CDO -0.032 0.018 0.14 1 -0.13 7 8
mesenchymal cell differentiation 0.031 0.016 0.13 5 -0.14 1 6
mol:Vitamin D3 0.004 0.12 0.26 75 -0.27 8 83
IHH N/PTCH2 0.049 0.042 0.18 4 -0.088 7 11
CDON 0.028 0.007 -10000 0 0 32 32
IHH N/PTCH1 -0.034 0.054 -10000 0 -0.28 24 24
Megalin/LRPAP1 0.03 0.023 -10000 0 -0.16 2 2
PTCH2 0.028 0.005 -10000 0 0 20 20
SHH Np/Cholesterol -0.022 0.014 0.16 1 -0.12 5 6
PTCH1 0.023 0.16 0.38 84 -0.32 8 92
HHIP 0.028 0.006 -10000 0 0 26 26
IL1-mediated signaling events

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
UBC13/UEV1A 0.021 0.008 -10000 0 -0.15 1 1
PRKCZ 0.028 0.006 -10000 0 0 23 23
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.026 0.009 -10000 0 0 65 65
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.009 0.048 -10000 0 -0.26 4 4
IRAK/TOLLIP -0.031 0.016 0.17 2 -10000 0 2
IKBKB 0.027 0.007 -10000 0 0 39 39
IKBKG 0.028 0.006 -10000 0 0 25 25
IL1 alpha/IL1R2 0.038 0.024 -10000 0 -0.16 6 6
IL1A 0.028 0.006 -10000 0 0 22 22
IL1B -0.009 0.064 0.19 49 -10000 0 49
IRAK/TRAF6/p62/Atypical PKCs 0.057 0.052 -10000 0 -0.14 1 1
IL1R2 0.028 0.007 -10000 0 0 30 30
IL1R1 0.017 0.014 -10000 0 0 226 226
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.054 0.11 0.18 8 -0.29 38 46
TOLLIP 0.028 0.006 -10000 0 0 24 24
TICAM2 0.028 0.007 -10000 0 0 30 30
MAP3K3 0.029 0.004 -10000 0 0 13 13
TAK1/TAB1/TAB2 0.019 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.009 0.065 0.22 1 -0.29 6 7
JUN -0.024 0.061 0.22 7 -10000 0 7
MAP3K7 0.028 0.007 -10000 0 0 30 30
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.015 0.11 0.29 2 -0.17 137 139
IL1 alpha/IL1R1/IL1RAP/MYD88 0.011 0.094 -10000 0 -0.14 132 132
PIK3R1 0.021 0.013 -10000 0 0 159 159
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.018 0.096 -10000 0 -0.14 117 117
IL1 beta fragment/IL1R1/IL1RAP -0.045 0.079 0.16 29 -0.23 20 49
NFKB1 0.027 0.008 -10000 0 0 46 46
MAPK8 -0.035 0.033 0.15 11 -10000 0 11
IRAK1 -0.025 0.008 -10000 0 -0.13 1 1
IL1RN/IL1R1 -0.037 0.099 -10000 0 -0.16 210 210
IRAK4 0.026 0.009 -10000 0 0 54 54
PRKCI 0.014 0.015 -10000 0 0 289 289
TRAF6 0.029 0.004 -10000 0 0 12 12
PI3K -0.001 0.068 -10000 0 -0.16 77 77
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.027 0.1 0.19 14 -0.25 28 42
CHUK 0.027 0.007 -10000 0 0 36 36
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.045 0.079 0.16 29 -0.23 20 49
IL1 beta/IL1R2 -0.031 0.07 0.19 38 -10000 0 38
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.036 0.017 0.14 3 -10000 0 3
NF kappa B1 p50/RelA -0.054 0.093 0.12 20 -0.25 40 60
IRAK3 0.027 0.008 -10000 0 0 41 41
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.004 0.1 0.29 2 -0.16 121 123
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.02 0.091 0.2 7 -0.25 8 15
IL1 alpha/IL1R1/IL1RAP -0.011 0.08 -10000 0 -0.15 132 132
RELA 0.029 0.003 -10000 0 0 6 6
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.028 0.005 -10000 0 0 20 20
MYD88 0.029 0.003 -10000 0 0 6 6
IRAK/TRAF6/MEKK3 -0.039 0.019 0.17 3 -10000 0 3
IL1RAP 0.02 0.014 -10000 0 0 181 181
UBE2N 0.029 0.004 -10000 0 0 13 13
IRAK/TRAF6 -0.052 0.075 0.097 1 -0.23 16 17
CASP1 0.025 0.011 -10000 0 0 88 88
IL1RN/IL1R2 0.037 0.024 -10000 0 -0.16 6 6
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0 0.1 0.29 3 -0.16 136 139
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.07 0.14 -10000 0 -0.28 114 114
PIK3CA 0.02 0.014 -10000 0 0 170 170
IL1RN 0.028 0.007 -10000 0 0 31 31
TRAF6/TAK1/TAB1/TAB2 0.038 0.018 -10000 0 -0.12 1 1
MAP2K6 -0.028 0.034 0.17 11 -10000 0 11
HIF-2-alpha transcription factor network

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
MMP14 0.001 0.099 0.65 5 -0.72 6 11
oxygen homeostasis 0.044 0.072 0.19 86 -10000 0 86
TCEB2 0.028 0.005 -10000 0 0 18 18
TCEB1 0.027 0.007 -10000 0 0 36 36
VHL/Elongin B/Elongin C/HIF2A 0.11 0.25 0.54 90 -10000 0 90
EPO 0.14 0.34 0.83 65 -10000 0 65
FIH (dimer) 0.045 0.093 0.21 88 -10000 0 88
APEX1 0.025 0.072 0.17 67 -10000 0 67
SERPINE1 0.09 0.32 0.89 40 -10000 0 40
FLT1 -0.021 0.13 -10000 0 -0.65 20 20
ADORA2A 0.19 0.39 0.87 89 -10000 0 89
germ cell development 0.16 0.38 0.89 76 -10000 0 76
SLC11A2 0.14 0.37 0.9 62 -10000 0 62
BHLHE40 0.14 0.36 0.88 65 -10000 0 65
HIF1AN 0.045 0.093 0.21 88 -10000 0 88
HIF2A/ARNT/SIRT1 0.04 0.2 0.45 31 -10000 0 31
ETS1 -0.023 0.023 0.26 2 -10000 0 2
CITED2 -0.046 0.19 -10000 0 -0.75 36 36
KDR -0.012 0.098 -10000 0 -0.62 13 13
PGK1 0.015 0.26 0.91 22 -10000 0 22
SIRT1 0.017 0.024 -10000 0 -0.03 116 116
response to hypoxia -0.001 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.058 0.27 0.63 24 -10000 0 24
EPAS1 0.15 0.34 0.82 84 -10000 0 84
SP1 0.037 0.051 0.3 18 -0.16 2 20
ABCG2 0.14 0.37 0.88 69 -0.62 1 70
EFNA1 0.13 0.36 0.89 62 -10000 0 62
FXN 0.19 0.38 0.86 86 -10000 0 86
POU5F1 0.15 0.37 0.89 69 -10000 0 69
neuron apoptosis -0.056 0.27 -10000 0 -0.62 23 23
EP300 0.027 0.008 -10000 0 0 50 50
EGLN3 0.042 0.092 0.22 83 -10000 0 83
EGLN2 0.044 0.093 0.22 81 -10000 0 81
EGLN1 0.044 0.091 0.21 85 -10000 0 85
VHL/Elongin B/Elongin C 0.053 0.018 -10000 0 -10000 0 0
VHL 0.029 0.004 -10000 0 0 9 9
ARNT 0.026 0.073 0.17 65 -10000 0 65
SLC2A1 0.18 0.38 0.9 78 -10000 0 78
TWIST1 0.19 0.38 0.86 87 -10000 0 87
ELK1 0.02 0.035 -10000 0 -0.14 24 24
HIF2A/ARNT/Cbp/p300 0.086 0.27 0.61 61 -10000 0 61
VEGFA 0.12 0.35 0.87 57 -10000 0 57
CREBBP 0.027 0.008 -10000 0 0 41 41
Regulation of Telomerase

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
Telomerase catalytic core complex -0.12 0.2 0.62 1 -0.64 14 15
RAD9A 0.029 0.003 -10000 0 0 7 7
AP1 -0.004 0.069 -10000 0 -0.17 61 61
IFNAR2 0.01 0.032 0.098 1 -0.043 145 146
AKT1 -0.02 0.05 -10000 0 -0.17 20 20
ER alpha/Oestrogen -0.012 0.057 -10000 0 -0.15 72 72
NFX1/SIN3/HDAC complex -0.013 0.075 0.19 3 -0.31 18 21
EGF 0.012 0.028 -10000 0 -0.037 128 128
SMG5 0.028 0.006 -10000 0 0 24 24
SMG6 0.028 0.006 -10000 0 0 28 28
SP3/HDAC2 0.016 0.043 0.16 1 -10000 0 1
TERT/c-Abl -0.1 0.2 0.55 1 -0.58 18 19
SAP18 0.013 0.026 -10000 0 -0.031 139 139
MRN complex 0.043 0.027 -10000 0 -10000 0 0
WT1 0.01 0.03 0.11 1 -0.043 125 126
WRN 0.023 0.012 -10000 0 0 122 122
SP1 0.008 0.036 0.14 1 -0.051 146 147
SP3 0.011 0.029 0.065 1 -0.038 143 144
TERF2IP 0.026 0.009 -10000 0 0 60 60
Telomerase/Nucleolin -0.11 0.19 -10000 0 -0.52 30 30
Mad/Max 0.018 0.04 -10000 0 -10000 0 0
TERT -0.12 0.2 -10000 0 -0.65 14 14
CCND1 -0.26 0.43 0.8 1 -0.96 147 148
MAX 0.011 0.029 -10000 0 -0.038 145 145
RBBP7 0.013 0.027 -10000 0 -0.032 143 143
RBBP4 0.013 0.026 -10000 0 -0.031 131 131
TERF2 -0.031 0.018 0.076 7 -10000 0 7
PTGES3 0.024 0.011 -10000 0 0 99 99
SIN3A 0.013 0.026 -10000 0 -0.031 143 143
Telomerase/911 -0.009 0.085 0.22 1 -0.32 6 7
CDKN1B -0.029 0.062 0.2 28 -0.37 2 30
RAD1 0.027 0.008 -10000 0 0 47 47
XRCC5 0.027 0.007 -10000 0 0 36 36
XRCC6 0.027 0.008 -10000 0 0 49 49
SAP30 0.012 0.026 -10000 0 -0.032 135 135
TRF2/PARP2 -0.03 0.022 0.083 6 -10000 0 6
UBE3A 0.012 0.028 -10000 0 -0.037 131 131
JUN 0.011 0.029 -10000 0 -0.037 138 138
E6 -0.002 0.004 0.03 1 -0.016 1 2
HPV-16 E6/E6AP 0.008 0.022 0.095 1 -10000 0 1
FOS 0.009 0.027 -10000 0 -0.038 120 120
IFN-gamma/IRF1 0.014 0.049 -10000 0 -0.19 9 9
PARP2 0.026 0.01 -10000 0 0 71 71
BLM 0.018 0.014 -10000 0 0 212 212
Telomerase -0.013 0.083 -10000 0 -0.37 10 10
IRF1 -0.031 0.025 0.17 6 -0.14 2 8
ESR1 0.01 0.026 -10000 0 -0.034 123 123
KU/TER 0.037 0.015 -10000 0 -10000 0 0
ATM/TRF2 0.035 0.02 -10000 0 -0.082 7 7
ubiquitin-dependent protein catabolic process -0.014 0.076 0.18 5 -0.3 18 23
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.014 0.077 0.18 5 -0.3 18 23
HDAC1 0.013 0.026 -10000 0 -0.031 131 131
HDAC2 0.008 0.034 0.12 1 -0.05 136 137
ATM 0.02 0.025 0.24 2 -10000 0 2
SMAD3 -0.025 0.015 -10000 0 -0.2 1 1
ABL1 0.028 0.006 -10000 0 0 21 21
MXD1 0.012 0.029 -10000 0 -0.038 143 143
MRE11A 0.025 0.01 -10000 0 0 81 81
HUS1 0.028 0.005 -10000 0 0 17 17
RPS6KB1 0.028 0.006 -10000 0 0 22 22
TERT/NF kappa B1/14-3-3 -0.1 0.21 -10000 0 -0.62 20 20
NR2F2 0.032 0.012 -10000 0 -0.089 1 1
MAPK3 -0.035 0.016 -10000 0 -0.18 2 2
MAPK1 -0.033 0.014 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.024 0.012 -10000 0 -10000 0 0
NFKB1 0.027 0.008 -10000 0 0 46 46
HNRNPC 0.028 0.006 -10000 0 0 27 27
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.02 0.025 0.24 2 -10000 0 2
NBN 0.025 0.01 -10000 0 0 82 82
EGFR 0.012 0.027 -10000 0 -0.038 118 118
mol:Oestrogen -0.002 0.003 0.021 1 -10000 0 1
EGF/EGFR 0.007 0.062 -10000 0 -0.17 43 43
MYC 0.008 0.023 0.079 1 -0.037 79 80
IL2 0.008 0.035 0.12 1 -0.052 135 136
KU 0.037 0.015 -10000 0 -10000 0 0
RAD50 0.029 0.005 -10000 0 0 15 15
HSP90AA1 0.028 0.006 -10000 0 0 21 21
TGFB1 0.024 0.012 -10000 0 -10000 0 0
TRF2/BLM -0.022 0.022 0.083 3 -10000 0 3
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.1 0.21 0.55 1 -0.59 19 20
SP1/HDAC2 0.013 0.048 0.24 1 -10000 0 1
PINX1 0.024 0.012 -10000 0 0 110 110
Telomerase/EST1A -0.11 0.19 -10000 0 -0.51 33 33
Smad3/Myc -0.042 0.057 -10000 0 -0.16 85 85
911 complex 0.052 0.019 -10000 0 -10000 0 0
IFNG -0.03 0.028 0.18 7 -0.16 3 10
Telomerase/PinX1 -0.11 0.18 -10000 0 -0.52 29 29
Telomerase/AKT1/mTOR/p70S6K -0.064 0.14 -10000 0 -0.39 50 50
SIN3B 0.012 0.026 -10000 0 -0.032 130 130
YWHAE 0.027 0.008 -10000 0 0 40 40
Telomerase/EST1B -0.11 0.19 -10000 0 -0.52 27 27
response to DNA damage stimulus 0.008 0.02 0.084 14 -0.1 7 21
MRN complex/TRF2/Rap1 0.065 0.048 -10000 0 -10000 0 0
TRF2/WRN -0.028 0.022 0.083 4 -10000 0 4
Telomerase/hnRNP C1/C2 -0.11 0.19 -10000 0 -0.52 30 30
E2F1 0.009 0.031 -10000 0 -0.043 138 138
ZNFX1 0.012 0.026 -10000 0 -0.031 135 135
PIF1 0.029 0.004 -10000 0 0 13 13
NCL 0.029 0.003 -10000 0 0 7 7
DKC1 0.024 0.012 -10000 0 0 107 107
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Wnt 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
Noncanonical Wnts/FZD 0.007 0.064 0.2 3 -0.22 10 13
FZD6 0.024 0.011 -10000 0 0 104 104
WNT6 0.029 0.003 -10000 0 0 7 7
WNT4 0.029 0.004 -10000 0 0 11 11
FZD3 0.022 0.013 -10000 0 0 141 141
WNT5A 0.028 0.005 -10000 0 0 17 17
WNT11 0.025 0.01 -10000 0 0 75 75
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.035 0.018 0.17 2 -10000 0 2
SNTA1 0.027 0.008 -10000 0 0 41 41
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.015 0.089 0.17 136 -10000 0 136
MAPK12 -0.002 0.059 0.16 56 -0.18 11 67
CCND1 -0.083 0.16 -10000 0 -0.36 134 134
p38 gamma/SNTA1 0.002 0.081 0.17 75 -0.19 14 89
MAP2K3 0.027 0.008 -10000 0 0 43 43
PKN1 0.025 0.01 -10000 0 0 80 80
G2/M transition checkpoint -0.002 0.059 0.16 56 -0.18 11 67
MAP2K6 0.007 0.073 0.19 66 -0.19 12 78
MAPT -0.008 0.059 0.19 5 -0.27 13 18
MAPK13 -0.03 0.017 0.19 2 -10000 0 2
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0 0.034 -10000 0 -0.21 14 14
Coregulation of Androgen receptor activity

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
NRIP1 0.018 0.014 -10000 0 -10000 0 0
SVIL 0.028 0.007 -10000 0 -10000 0 0
ZNF318 0.028 0.006 -10000 0 -10000 0 0
JMJD2C -0.001 0 -10000 0 -10000 0 0
T-DHT/AR/Ubc9 -0.1 0.077 -10000 0 -0.16 318 318
CARM1 0.026 0.009 -10000 0 -10000 0 0
PRDX1 0.029 0.005 -10000 0 -10000 0 0
PELP1 0.028 0.006 -10000 0 -10000 0 0
CTNNB1 0.029 0.003 -10000 0 -10000 0 0
AKT1 0.028 0.006 -10000 0 -10000 0 0
PTK2B 0.024 0.011 -10000 0 -10000 0 0
MED1 0.028 0.007 -10000 0 -10000 0 0
MAK 0.022 0.013 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
HIP1 0.029 0.004 -10000 0 -10000 0 0
GSN 0.025 0.011 -10000 0 -10000 0 0
NCOA2 0.027 0.008 -10000 0 -10000 0 0
NCOA6 0.027 0.007 -10000 0 -10000 0 0
DNA-PK 0.043 0.027 -10000 0 -10000 0 0
NCOA4 0.029 0.003 -10000 0 -10000 0 0
PIAS3 0.028 0.005 -10000 0 -10000 0 0
cell proliferation -0.14 0.23 -10000 0 -0.59 116 116
XRCC5 0.027 0.007 -10000 0 -10000 0 0
UBE3A 0.027 0.007 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.1 0.077 -10000 0 -0.16 320 320
FHL2 -0.062 0.072 0.53 2 -0.4 11 13
RANBP9 0.027 0.007 -10000 0 -10000 0 0
JMJD1A -0.051 0.057 -10000 0 -0.12 130 130
CDK6 0.028 0.007 -10000 0 -10000 0 0
TGFB1I1 0.027 0.008 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.13 0.092 -10000 0 -0.18 366 366
XRCC6 0.027 0.008 -10000 0 -10000 0 0
T-DHT/AR -0.13 0.094 -10000 0 -0.24 110 110
CTDSP1 0.029 0.004 -10000 0 -10000 0 0
CTDSP2 0.029 0.005 -10000 0 -10000 0 0
BRCA1 0.026 0.009 -10000 0 -10000 0 0
TCF4 0.027 0.008 -10000 0 -10000 0 0
CDKN2A 0.012 0.014 -10000 0 -10000 0 0
SRF 0.029 0.018 0.3 2 -10000 0 2
NKX3-1 -0.17 0.14 -10000 0 -0.44 73 73
KLK3 -0.025 0.065 -10000 0 -10000 0 0
TMF1 0.029 0.004 -10000 0 -10000 0 0
HNRNPA1 0.029 0.004 -10000 0 -10000 0 0
AOF2 0 0 -10000 0 -10000 0 0
APPL1 -0.031 0.008 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.1 0.078 -10000 0 -0.16 316 316
AR -0.028 0.043 -10000 0 -0.29 6 6
UBA3 0 0 -10000 0 -10000 0 0
PATZ1 0.027 0.008 -10000 0 -10000 0 0
PAWR 0.029 0.004 -10000 0 -10000 0 0
PRKDC 0.024 0.011 -10000 0 -10000 0 0
PA2G4 0.028 0.006 -10000 0 -10000 0 0
UBE2I 0.028 0.006 -10000 0 0 23 23
T-DHT/AR/Cyclin D3/CDK11 p58 -0.089 0.071 -10000 0 -0.14 307 307
RPS6KA3 0.028 0.006 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.1 0.078 -10000 0 -0.16 320 320
LATS2 0.028 0.007 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.091 0.071 -10000 0 -0.14 317 317
Cyclin D3/CDK11 p58 0.021 0.005 -10000 0 -10000 0 0
VAV3 0.026 0.01 -10000 0 -10000 0 0
KLK2 -0.072 0.053 -10000 0 -0.39 8 8
CASP8 0.029 0.003 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.085 0.082 -10000 0 -0.15 267 267
TMPRSS2 -0.34 0.32 -10000 0 -0.7 241 241
CCND1 0.021 0.013 -10000 0 -10000 0 0
PIAS1 0.028 0.005 -10000 0 -10000 0 0
mol:T-DHT -0.022 0.021 -10000 0 -0.072 5 5
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.027 0.008 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.1 0.079 -10000 0 -0.16 307 307
CMTM2 0.026 0.009 -10000 0 -10000 0 0
SNURF 0.027 0.007 -10000 0 0 36 36
ZMIZ1 -0.048 0.024 -10000 0 -10000 0 0
CCND3 0.028 0.006 -10000 0 -10000 0 0
TGIF1 0.028 0.006 -10000 0 -10000 0 0
FKBP4 0.026 0.01 -10000 0 -10000 0 0
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 0.023 0.07 0.18 8 -0.15 62 70
alphaM/beta2 Integrin/GPIbA 0.05 0.037 0.18 11 -0.15 3 14
alphaM/beta2 Integrin/proMMP-9 0.04 0.037 0.18 7 -0.15 2 9
PLAUR 0.027 0.008 -10000 0 0 44 44
HMGB1 -0.026 0.02 0.1 11 -0.086 1 12
alphaM/beta2 Integrin/Talin 0.051 0.037 0.18 11 -0.15 4 15
AGER -0.027 0.02 0.1 11 -10000 0 11
RAP1A 0.029 0.003 -10000 0 0 7 7
SELPLG 0.028 0.005 -10000 0 0 18 18
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.064 0.063 0.36 10 -0.2 8 18
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.022 0.012 -10000 0 0 130 130
CYR61 0.027 0.008 -10000 0 0 41 41
TLN1 0.028 0.005 -10000 0 0 16 16
Rap1/GTP -0.019 0.12 0.19 18 -0.28 38 56
RHOA 0.029 0.003 -10000 0 0 6 6
P-selectin oligomer 0.027 0.007 -10000 0 0 36 36
MYH2 -0.037 0.13 0.22 18 -0.33 32 50
MST1R 0.029 0.004 -10000 0 0 12 12
leukocyte activation during inflammatory response 0.048 0.042 0.16 1 -0.13 3 4
APOB 0.029 0.005 -10000 0 0 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.022 0.013 -10000 0 0 134 134
JAM3 0.027 0.007 -10000 0 0 38 38
GP1BA 0.028 0.006 -10000 0 0 24 24
alphaM/beta2 Integrin/CTGF 0.009 0.088 0.18 10 -0.15 118 128
alphaM/beta2 Integrin -0.026 0.11 0.18 40 -0.3 33 73
JAM3 homodimer 0.027 0.007 -10000 0 0 38 38
ICAM2 0.028 0.005 -10000 0 0 17 17
ICAM1 0.023 0.012 -10000 0 0 122 122
phagocytosis triggered by activation of immune response cell surface activating receptor -0.027 0.11 0.18 27 -0.29 38 65
cell adhesion 0.049 0.037 0.17 11 -0.15 3 14
NFKB1 -0.044 0.087 0.42 11 -0.33 8 19
THY1 0.02 0.014 -10000 0 0 183 183
RhoA/GDP 0.021 0.007 -10000 0 -0.15 1 1
Lipoprotein(a) 0.036 0.012 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.021 0.092 -10000 0 -0.15 110 110
IL6 -0.056 0.078 0.42 1 -0.53 9 10
ITGB2 -0.026 0.02 0.1 11 -10000 0 11
elevation of cytosolic calcium ion concentration 0.072 0.052 -10000 0 -0.14 2 2
alphaM/beta2 Integrin/JAM2/JAM3 0.004 0.099 -10000 0 -0.14 156 156
JAM2 0.019 0.014 -10000 0 0 194 194
alphaM/beta2 Integrin/ICAM1 0.071 0.055 -10000 0 -0.14 6 6
alphaM/beta2 Integrin/uPA/Plg 0.069 0.063 -10000 0 -0.15 11 11
RhoA/GTP -0.04 0.14 0.2 46 -0.33 40 86
positive regulation of phagocytosis -0.023 0.1 0.2 9 -0.31 16 25
Ron/MSP 0.042 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA 0.075 0.053 -10000 0 -0.14 2 2
alphaM/beta2 Integrin/uPAR 0.047 0.034 0.18 5 -0.15 2 7
PLAU 0.02 0.014 -10000 0 0 183 183
PLAT 0.021 0.013 -10000 0 0 151 151
actin filament polymerization -0.038 0.13 0.22 22 -0.32 33 55
MST1 0.029 0.003 -10000 0 0 7 7
alphaM/beta2 Integrin/lipoprotein(a) 0.054 0.045 -10000 0 -0.13 3 3
TNF -0.051 0.077 0.41 10 -10000 0 10
RAP1B 0.028 0.006 -10000 0 0 22 22
alphaM/beta2 Integrin/uPA 0.032 0.037 0.18 2 -0.15 3 5
fibrinolysis 0.066 0.061 -10000 0 -0.15 11 11
HCK 0.027 0.008 -10000 0 0 47 47
dendritic cell antigen processing and presentation -0.027 0.11 0.18 27 -0.29 38 65
VTN 0.028 0.007 -10000 0 0 32 32
alphaM/beta2 Integrin/CYR61 0.044 0.047 0.18 8 -0.15 18 26
LPA 0.027 0.008 -10000 0 0 45 45
LRP1 0.028 0.005 -10000 0 0 20 20
cell migration -0.01 0.09 0.17 97 -10000 0 97
FN1 0.018 0.014 -10000 0 0 213 213
alphaM/beta2 Integrin/Thy1 0.034 0.037 0.17 4 -0.15 2 6
MPO 0.029 0.005 -10000 0 0 14 14
KNG1 0.025 0.011 -10000 0 0 90 90
RAP1/GDP 0.038 0.009 -10000 0 -10000 0 0
ROCK1 -0.041 0.14 0.22 20 -0.32 39 59
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.026 0.009 -10000 0 0 57 57
CTGF 0.022 0.013 -10000 0 0 148 148
alphaM/beta2 Integrin/Hck 0.049 0.035 0.18 10 -0.15 2 12
ITGAM -0.027 0.02 0.1 11 -0.086 1 12
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.055 0.062 -10000 0 -0.16 31 31
HP 0.01 0.014 -10000 0 0 366 366
leukocyte adhesion -0.03 0.1 0.29 4 -0.29 1 5
SELP 0.027 0.007 -10000 0 0 36 36
Signaling events mediated by PRL

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
CCNE1 0.003 0.008 -10000 0 0 506 506
mol:Halofuginone -0.003 0.012 -10000 0 -0.16 3 3
ITGA1 0.023 0.012 -10000 0 0 128 128
CDKN1A -0.021 0.088 -10000 0 -0.4 23 23
PRL-3/alpha Tubulin 0.029 0.029 -10000 0 -0.16 7 7
mol:Ca2+ -0.019 0.035 0.26 7 -10000 0 7
AGT 0.026 0.009 -10000 0 0 58 58
CCNA2 0.051 0.088 0.3 2 -0.62 3 5
TUBA1B 0.029 0.002 -10000 0 0 4 4
EGR1 -0.014 0.028 -10000 0 -0.36 3 3
CDK2/Cyclin E1 -0.007 0.042 -10000 0 -0.3 4 4
MAPK3 -0.022 0.02 0.19 2 -10000 0 2
PRL-2 /Rab GGTase beta 0.022 0.022 -10000 0 -10000 0 0
MAPK1 -0.021 0.021 0.19 2 -10000 0 2
PTP4A1 -0.063 0.067 -10000 0 -0.65 3 3
PTP4A3 0.021 0.013 -10000 0 0 162 162
PTP4A2 0.028 0.006 -10000 0 0 25 25
ITGB1 -0.021 0.024 0.19 4 -10000 0 4
SRC 0.028 0.007 -10000 0 0 33 33
RAC1 -0.018 0.08 -10000 0 -0.4 19 19
Rab GGTase beta/Rab GGTase alpha 0.023 0.022 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.059 0.084 0.34 3 -0.62 3 6
RABGGTA 0.028 0.006 -10000 0 0 22 22
BCAR1 -0.019 0.035 0.26 7 -10000 0 7
RHOC -0.011 0.064 -10000 0 -0.44 9 9
RHOA -0.014 0.072 -10000 0 -0.43 13 13
cell motility -0.008 0.077 0.28 3 -0.4 11 14
PRL-1/alpha Tubulin -0.06 0.084 0.34 3 -0.62 3 6
PRL-3/alpha1 Integrin 0.022 0.029 -10000 0 -0.16 6 6
ROCK1 -0.011 0.074 0.27 2 -0.4 11 13
RABGGTB 0.016 0.015 -10000 0 0 257 257
CDK2 0.017 0.014 -10000 0 0 227 227
mitosis -0.063 0.066 -10000 0 -0.64 3 3
ATF5 0.028 0.005 -10000 0 0 18 18
IL23-mediated signaling events

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
CCL2 0.18 0.51 1.3 51 -1.2 17 68
IL23A 0.18 0.42 1.1 42 -10000 0 42
NF kappa B1 p50/RelA/I kappa B alpha 0.12 0.33 0.74 39 -0.81 8 47
positive regulation of T cell mediated cytotoxicity 0.21 0.52 1.3 61 -1 1 62
ITGA3 0.11 0.49 1.1 29 -1.1 35 64
IL17F 0.12 0.32 0.74 56 -0.66 1 57
IL12B 0.069 0.14 0.36 75 -10000 0 75
STAT1 (dimer) 0.004 0.25 0.92 10 -0.83 6 16
CD4 0.2 0.44 1.2 35 -1.1 2 37
IL23 0.15 0.38 0.94 42 -0.84 1 43
IL23R 0.14 0.27 0.94 29 -0.79 4 33
IL1B 0.19 0.44 1.2 43 -0.89 1 44
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.17 0.42 1 44 -0.94 1 45
TYK2 0.038 0.096 0.24 74 -10000 0 74
STAT4 0.028 0.005 -10000 0 0 16 16
STAT3 0.004 0.028 -10000 0 -10000 0 0
IL18RAP 0.004 0.037 0.091 25 -10000 0 25
IL12RB1 0.038 0.097 0.24 74 -10000 0 74
PIK3CA 0.005 0.024 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.071 0.093 0.26 73 -10000 0 73
IL23R/JAK2 0.15 0.26 0.72 60 -0.77 3 63
positive regulation of chronic inflammatory response 0.21 0.52 1.3 61 -1 1 62
natural killer cell activation -0.01 0.022 -10000 0 -0.066 47 47
JAK2 0.068 0.14 0.36 75 -10000 0 75
PIK3R1 0.004 0.025 -10000 0 -10000 0 0
NFKB1 0.025 0.027 0.096 1 -10000 0 1
RELA 0.023 0.029 0.096 1 -10000 0 1
positive regulation of dendritic cell antigen processing and presentation 0.15 0.38 0.94 43 -10000 0 43
ALOX12B 0.17 0.41 1 44 -0.94 1 45
CXCL1 0.18 0.46 1.1 46 -1.2 8 54
T cell proliferation 0.21 0.52 1.3 61 -1 1 62
NFKBIA 0.023 0.028 0.096 1 -10000 0 1
IL17A 0.11 0.29 0.69 54 -10000 0 54
PI3K 0.043 0.3 0.81 24 -0.85 6 30
IFNG 0.04 0.093 0.34 36 -10000 0 36
STAT3 (dimer) 0.046 0.3 0.81 19 -0.84 7 26
IL18R1 0.004 0.037 0.091 25 -10000 0 25
IL23/IL23R/JAK2/TYK2/SOCS3 0.16 0.35 0.88 61 -0.71 4 65
IL18/IL18R 0.032 0.077 0.32 24 -10000 0 24
macrophage activation 0.003 0.021 0.06 27 -10000 0 27
TNF 0.18 0.42 1.1 43 -0.89 1 44
STAT3/STAT4 0.12 0.34 0.79 25 -0.83 8 33
STAT4 (dimer) 0.16 0.38 0.92 40 -0.84 7 47
IL18 0.008 0.03 0.088 16 -10000 0 16
IL19 0.17 0.42 1.1 43 -0.94 1 44
STAT5A (dimer) 0.16 0.39 0.91 44 -0.83 8 52
STAT1 0.013 0.015 -10000 0 0 315 315
SOCS3 0.028 0.005 -10000 0 0 20 20
CXCL9 0.23 0.5 1.2 74 -0.94 1 75
MPO 0.17 0.41 1 42 -0.94 1 43
positive regulation of humoral immune response 0.21 0.52 1.3 61 -1 1 62
IL23/IL23R/JAK2/TYK2 0.21 0.52 1.3 61 -0.99 2 63
IL6 0.16 0.43 1.1 35 -1.1 9 44
STAT5A 0.028 0.007 -10000 0 0 33 33
IL2 0.005 0.061 0.23 25 -0.12 1 26
positive regulation of tyrosine phosphorylation of STAT protein -0.01 0.022 -10000 0 -0.066 47 47
CD3E 0.17 0.43 1.1 44 -1 3 47
keratinocyte proliferation 0.21 0.52 1.3 61 -1 1 62
NOS2 0.18 0.42 1 61 -0.87 2 63
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.15 0.34 0.67 1 -0.96 82 83
VDR 0.029 0.003 -10000 0 0 7 7
FAM120B 0.027 0.008 -10000 0 0 47 47
RXRs/LXRs/DNA/9cRA 0.013 0.11 0.4 34 -0.33 1 35
RXRs/LXRs/DNA/Oxysterols 0.021 0.13 0.5 34 -0.42 2 36
MED1 0.028 0.007 -10000 0 0 34 34
mol:9cRA 0.009 0.027 0.1 39 -10000 0 39
RARs/THRs/DNA/Src-1 -0.028 0.09 -10000 0 -0.23 25 25
RXRs/NUR77 0.007 0.12 0.3 22 -0.21 6 28
RXRs/PPAR 0.003 0.076 0.23 5 -0.24 11 16
NCOR2 0.028 0.005 -10000 0 0 17 17
VDR/VDR/Vit D3 0.021 0.002 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.065 0.03 -10000 0 -10000 0 0
RARA 0.028 0.007 -10000 0 0 32 32
NCOA1 0.029 0.005 -10000 0 0 15 15
VDR/VDR/DNA 0.029 0.003 -10000 0 0 7 7
RARs/RARs/DNA/9cRA 0.05 0.028 -10000 0 -10000 0 0
RARG 0.028 0.005 -10000 0 0 17 17
RPS6KB1 -0.075 0.17 0.52 11 -0.43 84 95
RARs/THRs/DNA/SMRT -0.031 0.093 -10000 0 -0.24 29 29
THRA 0.021 0.013 -10000 0 0 158 158
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.021 0.002 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.095 0.12 0.32 105 -10000 0 105
NR1H4 0.029 0.004 -10000 0 0 13 13
RXRs/LXRs/DNA 0.096 0.11 0.44 34 -0.24 2 36
NR1H2 0.026 0.035 0.13 37 -0.079 1 38
NR1H3 0.033 0.032 0.13 39 -0.073 4 43
RXRs/VDR/DNA/Vit D3 0.082 0.075 0.28 40 -10000 0 40
NR4A1 0.017 0.014 -10000 0 0 234 234
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.009 0.069 0.19 38 -0.23 6 44
RXRG -0.006 0.046 0.13 41 -10000 0 41
RXR alpha/CCPG 0.04 0.039 -10000 0 -0.16 12 12
RXRA -0.006 0.047 0.12 44 -10000 0 44
RXRB -0.007 0.047 0.13 42 -10000 0 42
THRB 0.028 0.007 -10000 0 0 32 32
PPARG 0.029 0.004 -10000 0 0 13 13
PPARD 0.028 0.005 -10000 0 0 17 17
TNF 0.014 0.13 0.45 34 -0.43 1 35
mol:Oxysterols 0.006 0.025 0.097 39 -10000 0 39
cholesterol transport 0.021 0.13 0.5 34 -0.42 2 36
PPARA 0.024 0.011 -10000 0 0 98 98
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.028 0.006 -10000 0 0 21 21
RXRs/NUR77/BCL2 -0.077 0.11 0.16 1 -0.2 205 206
SREBF1 0.009 0.13 0.44 31 -0.77 4 35
RXRs/RXRs/DNA/9cRA 0.094 0.12 0.31 105 -10000 0 105
ABCA1 0.024 0.16 0.62 34 -0.43 1 35
RARs/THRs 0.033 0.096 -10000 0 -0.14 114 114
RXRs/FXR 0.089 0.081 0.3 40 -10000 0 40
BCL2 0.023 0.012 -10000 0 0 123 123
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.042 0.008 -10000 0 -10000 0 0
Necdin/E2F1 -0.06 0.099 -10000 0 -0.16 263 263
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.06 0.032 -10000 0 -0.13 3 3
NGF (dimer)/p75(NTR)/BEX1 -0.019 0.08 -10000 0 -0.13 180 180
NT-4/5 (dimer)/p75(NTR) 0.021 0.004 -10000 0 -10000 0 0
IKBKB 0.027 0.007 -10000 0 0 39 39
AKT1 0.005 0.1 0.16 136 -10000 0 136
IKBKG 0.028 0.006 -10000 0 0 25 25
BDNF 0.029 0.004 -10000 0 0 13 13
MGDIs/NGR/p75(NTR)/LINGO1 0.054 0.018 -10000 0 -10000 0 0
FURIN 0.028 0.006 -10000 0 0 27 27
proBDNF (dimer)/p75(NTR)/Sortilin 0.056 0.014 -10000 0 -10000 0 0
LINGO1 0.028 0.006 -10000 0 0 23 23
Sortilin/TRAF6/NRIF -0.071 0.043 -10000 0 -0.23 1 1
proBDNF (dimer) 0.029 0.004 -10000 0 0 13 13
NTRK1 0.029 0.005 -10000 0 0 15 15
RTN4R 0.028 0.007 -10000 0 0 32 32
neuron apoptosis -0.035 0.13 0.3 3 -0.55 18 21
IRAK1 0.028 0.007 -10000 0 0 31 31
SHC1 -0.025 0.01 0.17 1 -10000 0 1
ARHGDIA 0.024 0.011 -10000 0 0 96 96
RhoA/GTP 0.021 0.007 -10000 0 -0.15 1 1
Gamma Secretase 0.043 0.077 -10000 0 -0.14 65 65
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.047 0.036 -10000 0 -0.13 17 17
MAGEH1 0.028 0.006 -10000 0 0 27 27
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.041 0.09 -10000 0 -0.13 274 274
Mammalian IAPs/DIABLO 0.012 0.051 -10000 0 -0.13 46 46
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.028 0.006 -10000 0 0 21 21
APP 0.028 0.006 -10000 0 0 28 28
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.028 0.007 -10000 0 0 34 34
RhoA/GDP/RHOGDI 0.013 0.053 0.16 2 -0.12 72 74
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.001 0.055 0.23 10 -10000 0 10
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.029 0.05 -10000 0 -0.21 1 1
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.038 0.009 -10000 0 -10000 0 0
NCSTN 0.028 0.005 -10000 0 0 19 19
mol:GTP 0.037 0.01 -10000 0 -10000 0 0
PSENEN 0.025 0.01 -10000 0 0 75 75
mol:ceramide -0.027 0.035 0.18 14 -10000 0 14
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.036 0.065 0.18 45 -0.23 5 50
p75(NTR)/beta APP 0.038 0.025 -10000 0 -0.16 7 7
BEX1 0.018 0.014 -10000 0 0 210 210
mol:GDP -0.013 0.002 -10000 0 -10000 0 0
NGF (dimer) -0.02 0.087 -10000 0 -0.13 200 200
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.038 0.075 -10000 0 -0.14 72 72
PIK3R1 0.021 0.013 -10000 0 0 159 159
RAC1/GTP 0.031 0.012 -10000 0 -10000 0 0
MYD88 0.029 0.003 -10000 0 0 6 6
CHUK 0.027 0.007 -10000 0 0 36 36
NGF (dimer)/p75(NTR)/PKA 0.037 0.01 -10000 0 -10000 0 0
RHOB 0.028 0.006 -10000 0 0 23 23
RHOA 0.029 0.003 -10000 0 0 6 6
MAGE-G1/E2F1 0.037 0.017 -10000 0 -0.16 1 1
NT3 (dimer) 0.023 0.012 -10000 0 0 115 115
TP53 -0.058 0.057 0.31 3 -10000 0 3
PRDM4 -0.03 0.032 0.18 12 -10000 0 12
BDNF (dimer) -0.007 0.1 -10000 0 -0.14 193 193
PIK3CA 0.02 0.014 -10000 0 0 170 170
SORT1 0.029 0.004 -10000 0 0 11 11
activation of caspase activity 0.053 0.03 -10000 0 -0.13 3 3
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.052 0.018 -10000 0 -10000 0 0
RHOC 0.029 0.003 -10000 0 0 7 7
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.045 0.062 0.24 7 -0.24 7 14
DIABLO 0.019 0.014 -10000 0 0 191 191
SMPD2 -0.028 0.035 0.18 14 -10000 0 14
APH1B 0.026 0.01 -10000 0 0 68 68
APH1A 0.028 0.007 -10000 0 0 31 31
proNGF (dimer)/p75(NTR)/Sortilin 0.038 0.008 -10000 0 -10000 0 0
PSEN1 0.029 0.005 -10000 0 0 14 14
APAF-1/Pro-Caspase 9 0.041 0.011 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.033 0.018 -10000 0 -10000 0 0
MAPK8 -0.04 0.058 0.24 7 -0.24 6 13
MAPK9 -0.042 0.056 0.23 6 -0.24 5 11
APAF1 0.028 0.006 -10000 0 0 27 27
NTF3 0.023 0.012 -10000 0 0 115 115
NTF4 0 0 -10000 0 -10000 0 0
NDN 0.013 0.015 -10000 0 0 316 316
RAC1/GDP 0.021 0.005 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.056 0.033 -10000 0 -0.13 8 8
p75 CTF/Sortilin/TRAF6/NRIF 0.074 0.041 -10000 0 -10000 0 0
RhoA-B-C/GTP 0.036 0.01 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.075 0.038 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.07 0.025 -10000 0 -10000 0 0
PRKACB 0.028 0.006 -10000 0 0 21 21
proBDNF (dimer)/p75 ECD 0.034 0.018 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.023 0.012 -10000 0 0 122 122
BIRC2 0.021 0.013 -10000 0 0 159 159
neuron projection morphogenesis -0.036 0.064 0.18 12 -0.21 9 21
BAD -0.046 0.062 0.22 6 -0.28 6 12
RIPK2 0.019 0.014 -10000 0 0 200 200
NGFR 0.028 0.005 -10000 0 0 17 17
CYCS -0.031 0.049 0.18 27 -10000 0 27
ADAM17 0.024 0.012 -10000 0 0 106 106
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.033 0.029 -10000 0 -10000 0 0
BCL2L11 -0.046 0.062 0.22 6 -0.28 7 13
BDNF (dimer)/p75(NTR) 0.041 0.009 -10000 0 -10000 0 0
PI3K 0.008 0.062 -10000 0 -0.13 76 76
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.048 0.025 -10000 0 -0.13 1 1
NDNL2 0.027 0.007 -10000 0 0 38 38
YWHAE 0.027 0.008 -10000 0 0 40 40
PRKCI 0.014 0.015 -10000 0 0 289 289
NGF (dimer)/p75(NTR) 0.021 0.004 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.05 0.023 -10000 0 -0.13 3 3
TRAF6 0.029 0.004 -10000 0 0 12 12
RAC1 0.028 0.006 -10000 0 0 27 27
PRKCZ 0.028 0.006 -10000 0 0 23 23
PLG 0.026 0.009 -10000 0 0 57 57
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.019 0.023 0.14 7 -10000 0 7
SQSTM1 0.028 0.005 -10000 0 0 20 20
NGFRAP1 0.029 0.002 -10000 0 0 3 3
CASP3 -0.047 0.067 0.22 6 -0.3 13 19
E2F1 0.027 0.008 -10000 0 0 42 42
CASP9 0.029 0.004 -10000 0 0 13 13
IKK complex 0.064 0.062 -10000 0 -0.24 3 3
NGF (dimer)/TRKA 0.021 0.004 -10000 0 -10000 0 0
MMP7 0.017 0.014 -10000 0 0 236 236
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.06 0.03 -10000 0 -10000 0 0
MMP3 0.027 0.007 -10000 0 0 36 36
APAF-1/Caspase 9 -0.042 0.048 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.028 0.007 -10000 0 0 31 31
Rac1/GDP 0.021 0.028 -10000 0 -0.034 87 87
DOCK1 0.028 0.005 -10000 0 0 18 18
ITGA4 0.027 0.008 -10000 0 0 40 40
RAC1 0.028 0.006 -10000 0 0 27 27
alpha4/beta7 Integrin 0.04 0.015 -10000 0 -0.16 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.007 -10000 0 0 36 36
alpha4/beta1 Integrin 0.046 0.025 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin -0.038 0.022 -10000 0 -10000 0 0
lamellipodium assembly -0.067 0.15 -10000 0 -0.34 101 101
PIK3CA 0.02 0.014 -10000 0 0 170 170
PI3K -0.001 0.068 -10000 0 -0.16 77 77
ARF6 0.029 0.004 -10000 0 0 11 11
TLN1 0.028 0.005 -10000 0 0 16 16
PXN -0.028 0.013 -10000 0 -10000 0 0
PIK3R1 0.021 0.013 -10000 0 0 159 159
ARF6/GTP -0.025 0.07 0.13 90 -10000 0 90
cell adhesion 0.06 0.048 -10000 0 -0.16 5 5
CRKL/CBL 0.041 0.011 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.037 0.022 -10000 0 -10000 0 0
ITGB1 0.028 0.006 -10000 0 0 21 21
ITGB7 0.029 0.003 -10000 0 0 8 8
ARF6/GDP 0.022 0.028 -10000 0 -0.034 92 92
alpha4/beta1 Integrin/Paxillin/VCAM1 0.047 0.078 -10000 0 -0.14 58 58
p130Cas/Crk/Dock1 0.049 0.025 -10000 0 -0.15 2 2
VCAM1 0.021 0.013 -10000 0 0 161 161
alpha4/beta1 Integrin/Paxillin/Talin 0.063 0.05 -10000 0 -0.16 5 5
alpha4/beta1 Integrin/Paxillin/GIT1 0.061 0.05 -10000 0 -0.14 5 5
BCAR1 0.026 0.009 -10000 0 0 57 57
mol:GDP -0.059 0.049 0.14 5 -10000 0 5
CBL 0.029 0.004 -10000 0 0 12 12
PRKACA 0.025 0.01 -10000 0 0 79 79
GIT1 0.028 0.007 -10000 0 0 30 30
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.063 0.05 -10000 0 -0.16 5 5
Rac1/GTP -0.076 0.16 -10000 0 -0.38 101 101
Regulation of cytoplasmic and nuclear SMAD2/3 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
SMAD4 0.028 0.007 -10000 0 0 34 34
SMAD2 -0.002 0.045 0.18 1 -0.23 2 3
SMAD3 -0.014 0.048 -10000 0 -0.23 7 7
SMAD3/SMAD4 0.061 0.085 -10000 0 -0.5 9 9
SMAD4/Ubc9/PIASy 0.051 0.021 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.091 0.058 -10000 0 -0.23 1 1
PPM1A 0.029 0.004 -10000 0 0 13 13
CALM1 0.028 0.006 -10000 0 0 26 26
SMAD2/SMAD4 0.013 0.045 -10000 0 -0.19 5 5
MAP3K1 0.027 0.008 -10000 0 0 50 50
TRAP-1/SMAD4 0.04 0.011 -10000 0 -10000 0 0
MAPK3 0.028 0.006 -10000 0 0 22 22
MAPK1 0.027 0.008 -10000 0 0 42 42
NUP214 0.028 0.005 -10000 0 0 18 18
CTDSP1 0.029 0.004 -10000 0 0 12 12
CTDSP2 0.028 0.005 -10000 0 0 18 18
CTDSPL 0.029 0.003 -10000 0 0 6 6
KPNB1 0.028 0.005 -10000 0 0 20 20
TGFBRAP1 0.029 0.004 -10000 0 0 9 9
UBE2I 0.028 0.006 -10000 0 0 23 23
NUP153 0.027 0.008 -10000 0 0 45 45
KPNA2 0.003 0.009 -10000 0 0 494 494
PIAS4 0.027 0.008 -10000 0 0 46 46
Glucocorticoid receptor regulatory network

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
PCK2 -0.059 0.078 -10000 0 -0.43 9 9
SMARCC2 0.028 0.006 -10000 0 0 21 21
SMARCC1 0.029 0.003 -10000 0 0 7 7
TBX21 0.04 0.08 0.32 5 -10000 0 5
SUMO2 0.005 0.032 -10000 0 -0.038 185 185
STAT1 (dimer) 0.017 0.052 0.31 13 -0.18 7 20
FKBP4 0.026 0.01 -10000 0 0 69 69
FKBP5 0.026 0.009 -10000 0 0 59 59
GR alpha/HSP90/FKBP51/HSP90 -0.04 0.094 -10000 0 -0.24 16 16
PRL 0.043 0.063 0.71 1 -10000 0 1
cortisol/GR alpha (dimer)/TIF2 -0.095 0.15 -10000 0 -0.42 28 28
RELA 0.008 0.095 0.18 112 -0.18 14 126
FGG -0.13 0.12 -10000 0 -0.42 29 29
GR beta/TIF2 -0.078 0.063 -10000 0 -0.28 3 3
IFNG 0.11 0.17 0.55 42 -10000 0 42
apoptosis -0.18 0.21 0.48 2 -0.56 49 51
CREB1 0.027 0.013 -10000 0 -10000 0 0
histone acetylation 0.042 0.066 -10000 0 -10000 0 0
BGLAP 0.056 0.068 0.66 1 -10000 0 1
GR/PKAc -0.017 0.09 -10000 0 -0.21 2 2
NF kappa B1 p50/RelA 0.079 0.13 0.33 96 -0.3 14 110
SMARCD1 0.029 0.002 -10000 0 0 4 4
MDM2 -0.036 0.041 -10000 0 -0.17 3 3
GATA3 -0.027 0.007 -10000 0 -10000 0 0
AKT1 0.029 0.007 -10000 0 -10000 0 0
CSF2 0.013 0.043 -10000 0 -10000 0 0
GSK3B 0.005 0.032 -10000 0 -0.037 183 183
NR1I3 -0.16 0.18 -10000 0 -0.63 11 11
CSN2 -0.12 0.11 -10000 0 -0.39 28 28
BRG1/BAF155/BAF170/BAF60A 0.063 0.032 -10000 0 -0.14 2 2
NFATC1 0.025 0.012 -10000 0 -10000 0 0
POU2F1 0.029 0.008 0.2 1 -10000 0 1
CDKN1A -0.06 0.22 -10000 0 -1.2 16 16
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.006 0.039 2 -10000 0 2
SFN 0.027 0.007 -10000 0 0 37 37
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.024 0.1 -10000 0 -0.23 12 12
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.3 0.34 0.58 2 -0.72 208 210
JUN 0.089 0.17 0.5 42 -10000 0 42
IL4 0.051 0.058 -10000 0 -10000 0 0
CDK5R1 0.005 0.03 -10000 0 -0.035 193 193
PRKACA 0.025 0.01 -10000 0 0 79 79
cortisol/GR alpha (monomer)/AP-1 -0.073 0.076 -10000 0 -0.27 13 13
GR alpha/HSP90/FKBP51/HSP90/PP5C -0.029 0.1 -10000 0 -0.23 12 12
cortisol/GR alpha (monomer) -0.15 0.14 -10000 0 -0.48 27 27
NCOA2 0.027 0.008 -10000 0 0 45 45
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.036 0.094 0.18 122 -0.3 1 123
AP-1/NFAT1-c-4 0.098 0.21 0.61 33 -10000 0 33
AFP 0.059 0.12 0.47 4 -10000 0 4
SUV420H1 0.029 0.003 -10000 0 0 7 7
IRF1 -0.002 0.15 0.52 10 -0.72 9 19
TP53 -0.038 0.084 -10000 0 -0.52 16 16
PPP5C 0.028 0.006 -10000 0 0 25 25
KRT17 0.098 0.19 0.67 26 -10000 0 26
KRT14 0.067 0.12 0.66 14 -10000 0 14
TBP 0.025 0.015 0.19 1 -10000 0 1
CREBBP 0.022 0.038 -10000 0 -0.22 13 13
HDAC1 0.027 0.008 -10000 0 -10000 0 0
HDAC2 0.027 0.007 -10000 0 -10000 0 0
AP-1 0.098 0.21 0.61 33 -10000 0 33
MAPK14 0.005 0.032 -10000 0 -0.038 184 184
MAPK10 0.005 0.032 -10000 0 -0.039 176 176
MAPK11 0.004 0.029 -10000 0 -0.038 150 150
KRT5 0.16 0.26 0.65 103 -10000 0 103
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
NCOA1 0.02 0.02 -10000 0 -10000 0 0
STAT1 0.017 0.052 0.31 13 -0.18 7 20
CGA 0.055 0.06 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.066 0.1 -10000 0 -0.43 16 16
MAPK3 0.005 0.032 -10000 0 -0.038 182 182
MAPK1 0.004 0.032 -10000 0 -0.038 180 180
ICAM1 0.1 0.23 0.63 64 -0.72 7 71
NFKB1 0.009 0.094 0.18 112 -0.19 6 118
MAPK8 0.076 0.14 0.41 36 -10000 0 36
MAPK9 0.005 0.032 -10000 0 -0.038 185 185
cortisol/GR alpha (dimer) -0.19 0.22 0.49 2 -0.59 51 53
BAX -0.04 0.11 -10000 0 -10000 0 0
POMC 0.004 0.12 0.64 1 -10000 0 1
EP300 0.022 0.037 -10000 0 -0.22 12 12
cortisol/GR alpha (dimer)/p53 -0.13 0.16 -10000 0 -0.46 31 31
proteasomal ubiquitin-dependent protein catabolic process -0.035 0.052 0.22 13 -0.19 1 14
SGK1 -0.033 0.087 -10000 0 -0.29 35 35
IL13 0.077 0.13 0.5 8 -10000 0 8
IL6 0.065 0.18 0.52 24 -0.83 9 33
PRKACG 0.028 0.005 -10000 0 0 19 19
IL5 0.065 0.12 0.46 6 -10000 0 6
IL2 0.085 0.16 0.48 29 -10000 0 29
CDK5 0.007 0.028 -10000 0 -0.034 161 161
PRKACB 0.028 0.006 -10000 0 0 21 21
HSP90AA1 0.028 0.006 -10000 0 0 21 21
IL8 0.1 0.2 0.64 57 -10000 0 57
CDK5R1/CDK5 0.011 0.038 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.09 0.12 0.41 22 -0.24 12 34
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.067 0.15 -10000 0 -0.4 25 25
SMARCA4 0.026 0.009 -10000 0 0 60 60
chromatin remodeling -0.073 0.083 -10000 0 -0.32 7 7
NF kappa B1 p50/RelA/Cbp 0.077 0.13 0.42 18 -0.27 12 30
JUN (dimer) 0.088 0.17 0.5 42 -10000 0 42
YWHAH 0.027 0.008 -10000 0 0 42 42
VIPR1 0.04 0.082 0.4 4 -10000 0 4
NR3C1 -0.1 0.085 -10000 0 -0.36 4 4
NR4A1 0.017 0.014 -10000 0 -10000 0 0
TIF2/SUV420H1 0.04 0.012 -10000 0 -10000 0 0
MAPKKK cascade -0.18 0.21 0.48 2 -0.56 49 51
cortisol/GR alpha (dimer)/Src-1 -0.098 0.16 -10000 0 -0.42 28 28
PBX1 0.028 0.009 0.2 1 -10000 0 1
POU1F1 0.029 0.008 0.2 1 -10000 0 1
SELE 0.075 0.12 0.41 22 -10000 0 22
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.073 0.083 -10000 0 -0.33 7 7
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.067 0.15 -10000 0 -0.4 25 25
mol:cortisol -0.078 0.076 -10000 0 -0.26 9 9
MMP1 0.14 0.25 0.63 110 -0.51 5 115
FAS signaling pathway (CD95)

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
SPTAN1 -0.005 0.066 0.3 2 -0.2 27 29
RFC1 -0.002 0.067 0.24 6 -0.2 25 31
PRKDC 0.024 0.1 0.22 79 -0.2 26 105
RIPK1 0.026 0.016 -10000 0 -0.081 9 9
CASP7 0.009 0.065 -10000 0 -0.54 6 6
FASLG/FAS/FADD/FAF1 0.023 0.07 0.2 2 -10000 0 2
MAP2K4 0.002 0.093 0.36 10 -0.37 6 16
mol:ceramide 0.009 0.063 0.31 9 -0.26 3 12
GSN -0.013 0.067 0.22 3 -0.2 24 27
FASLG/FAS/FADD/FAF1/Caspase 8 0.005 0.072 0.19 14 -0.23 2 16
FAS 0.027 0.013 0.078 9 -0.048 7 16
BID -0.036 0.015 0.18 1 -10000 0 1
MAP3K1 0.018 0.08 0.29 10 -0.32 7 17
MAP3K7 0.027 0.011 -10000 0 -0.009 39 39
RB1 0.001 0.07 0.22 17 -0.2 23 40
CFLAR 0.027 0.014 -10000 0 -0.081 9 9
HGF/MET 0.006 0.081 -10000 0 -0.15 105 105
ARHGDIB 0.006 0.084 0.22 32 -0.2 23 55
FADD 0.028 0.013 0.078 10 -0.049 8 18
actin filament polymerization 0.015 0.072 0.22 28 -0.22 4 32
NFKB1 -0.022 0.18 0.39 9 -0.6 42 51
MAPK8 -0.007 0.1 0.41 11 -0.42 12 23
DFFA -0.005 0.069 0.32 3 -0.2 30 33
DNA fragmentation during apoptosis -0.004 0.067 0.22 6 -0.2 29 35
FAS/FADD/MET 0.038 0.05 -10000 0 -0.16 24 24
CFLAR/RIP1 0.038 0.023 -10000 0 -0.12 9 9
FAIM3 0.028 0.01 -10000 0 -0.038 10 10
FAF1 0.028 0.015 0.098 10 -0.055 9 19
PARP1 0.01 0.086 0.22 40 -0.2 27 67
DFFB -0.004 0.066 0.22 4 -0.2 28 32
CHUK -0.029 0.16 0.32 9 -0.56 43 52
FASLG 0.028 0.015 0.098 10 -0.055 9 19
FAS/FADD 0.034 0.04 0.12 1 -0.16 17 18
HGF 0.028 0.005 -10000 0 0 16 16
LMNA 0.038 0.1 0.27 45 -0.2 10 55
CASP6 0.046 0.11 0.21 126 -0.2 11 137
CASP10 0.028 0.013 0.078 10 -0.05 9 19
CASP3 0.005 0.076 0.15 69 -0.22 31 100
PTPN13 0.02 0.014 -10000 0 0 170 170
CASP8 -0.033 0.009 -10000 0 -10000 0 0
IL6 -0.033 0.22 0.67 9 -0.73 28 37
MET 0.025 0.011 -10000 0 0 86 86
ICAD/CAD -0.013 0.065 0.27 6 -0.2 27 33
FASLG/FAS/FADD/FAF1/Caspase 10 0.009 0.064 0.31 9 -0.26 3 12
activation of caspase activity by cytochrome c -0.036 0.015 0.18 1 -10000 0 1
PAK2 0.024 0.1 0.25 64 -0.2 21 85
BCL2 0.022 0.014 -10000 0 -0.002 131 131
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.037 0.091 -10000 0 -0.15 73 73
SMAD6-7/SMURF1 0.054 0.018 -10000 0 -10000 0 0
NOG 0.028 0.005 -10000 0 0 18 18
SMAD9 -0.019 0.13 -10000 0 -0.48 41 41
SMAD4 0.028 0.007 -10000 0 0 34 34
SMAD5 -0.025 0.082 0.2 2 -0.35 16 18
BMP7/USAG1 0.014 0.052 -10000 0 -0.17 36 36
SMAD5/SKI -0.014 0.091 0.2 2 -0.34 19 21
SMAD1 -0.023 0.089 -10000 0 -0.39 19 19
BMP2 0.027 0.007 -10000 0 0 36 36
SMAD1/SMAD1/SMAD4 -0.054 0.079 -10000 0 -0.35 19 19
BMPR1A 0.028 0.006 -10000 0 0 21 21
BMPR1B 0.025 0.011 -10000 0 0 90 90
BMPR1A-1B/BAMBI 0.03 0.059 -10000 0 -0.15 49 49
AHSG 0.025 0.011 -10000 0 0 91 91
CER1 0.027 0.008 -10000 0 0 40 40
BMP2-4/CER1 0.05 0.022 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.035 0.1 -10000 0 -0.33 31 31
BMP2-4 (homodimer) 0.039 0.013 -10000 0 -10000 0 0
RGMB 0.027 0.007 -10000 0 0 36 36
BMP6/BMPR2/BMPR1A-1B 0.043 0.066 -10000 0 -0.14 46 46
RGMA 0.028 0.007 -10000 0 0 32 32
SMURF1 0.028 0.005 -10000 0 0 19 19
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.019 0.07 -10000 0 -0.26 21 21
BMP2-4/USAG1 0.04 0.03 -10000 0 -0.15 2 2
SMAD6/SMURF1/SMAD5 -0.014 0.091 0.2 1 -0.33 21 22
SOSTDC1 0.022 0.013 -10000 0 0 137 137
BMP7/BMPR2/BMPR1A-1B 0.03 0.084 -10000 0 -0.15 76 76
SKI 0.028 0.006 -10000 0 0 23 23
BMP6 (homodimer) 0.027 0.008 -10000 0 0 45 45
HFE2 0.028 0.005 -10000 0 0 16 16
ZFYVE16 0.026 0.009 -10000 0 0 57 57
MAP3K7 0.028 0.007 -10000 0 0 30 30
BMP2-4/CHRD 0.045 0.026 -10000 0 -10000 0 0
SMAD5/SMAD5/SMAD4 -0.014 0.092 0.2 2 -0.33 21 23
MAPK1 0.027 0.008 -10000 0 0 42 42
TAK1/TAB family -0.003 0.08 -10000 0 -0.26 20 20
BMP7 (homodimer) 0.022 0.013 -10000 0 0 135 135
NUP214 0.028 0.005 -10000 0 0 18 18
BMP6/FETUA 0.034 0.018 -10000 0 -10000 0 0
SMAD1/SKI -0.009 0.09 -10000 0 -0.39 17 17
SMAD6 0.029 0.005 -10000 0 0 15 15
CTDSP2 0.028 0.005 -10000 0 0 18 18
BMP2-4/FETUA 0.045 0.025 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.026 0.009 -10000 0 0 60 60
BMPR2 (homodimer) 0.029 0.003 -10000 0 0 7 7
GADD34/PP1CA 0.036 0.057 -10000 0 -0.14 44 44
BMPR1A-1B (homodimer) 0.02 0.061 -10000 0 -0.16 53 53
CHRDL1 0.016 0.015 -10000 0 0 262 262
ENDOFIN/SMAD1 -0.008 0.091 -10000 0 -0.41 16 16
SMAD6-7/SMURF1/SMAD1 0.012 0.099 -10000 0 -0.37 19 19
SMAD6/SMURF1 0.028 0.005 -10000 0 0 19 19
BAMBI 0.026 0.009 -10000 0 0 61 61
SMURF2 0.029 0.005 -10000 0 0 14 14
BMP2-4/CHRDL1 -0.033 0.098 -10000 0 -0.15 234 234
BMP2-4/GREM1 0.048 0.024 -10000 0 -10000 0 0
SMAD7 0.028 0.006 -10000 0 0 28 28
SMAD8A/SMAD8A/SMAD4 -0.011 0.14 -10000 0 -0.46 45 45
SMAD1/SMAD6 -0.009 0.09 -10000 0 -0.37 19 19
TAK1/SMAD6 0.04 0.012 -10000 0 -10000 0 0
BMP7 0.022 0.013 -10000 0 0 135 135
BMP6 0.027 0.008 -10000 0 0 45 45
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.019 0.076 -10000 0 -0.29 20 20
PPM1A 0.029 0.004 -10000 0 0 13 13
SMAD1/SMURF2 -0.009 0.092 -10000 0 -0.38 19 19
SMAD7/SMURF1 0.04 0.012 -10000 0 -10000 0 0
CTDSPL 0.029 0.003 -10000 0 0 6 6
PPP1CA 0.029 0.003 -10000 0 0 7 7
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 0.029 0.004 -10000 0 0 12 12
PPP1R15A 0.026 0.01 -10000 0 0 68 68
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.017 0.084 0.16 1 -0.3 24 25
CHRD 0.024 0.011 -10000 0 0 94 94
BMPR2 0.029 0.003 -10000 0 0 7 7
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.019 0.074 0.18 1 -0.27 18 19
BMP4 0.028 0.006 -10000 0 0 22 22
FST 0.025 0.011 -10000 0 0 91 91
BMP2-4/NOG 0.052 0.021 -10000 0 -0.15 1 1
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.037 0.088 -10000 0 -0.15 74 74
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.009 0.036 0.16 20 -0.17 1 21
CRKL 0.028 0.007 -10000 0 0 31 31
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
DOCK1 0.028 0.005 -10000 0 0 18 18
ITGA4 0.027 0.008 -10000 0 0 40 40
alpha4/beta7 Integrin/MAdCAM1 0.065 0.04 -10000 0 -0.14 1 1
EPO 0.028 0.005 -10000 0 0 18 18
alpha4/beta7 Integrin 0.04 0.015 -10000 0 -0.16 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.007 -10000 0 0 36 36
alpha4/beta1 Integrin 0.039 0.013 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.038 0.015 -10000 0 -10000 0 0
lamellipodium assembly -0.01 0.11 -10000 0 -0.36 20 20
PIK3CA 0.02 0.014 -10000 0 0 170 170
PI3K -0.001 0.068 -10000 0 -0.16 77 77
ARF6 0.029 0.004 -10000 0 0 11 11
JAK2 -0.009 0.031 -10000 0 -0.24 1 1
PXN 0.029 0.005 -10000 0 0 14 14
PIK3R1 0.021 0.013 -10000 0 0 159 159
MADCAM1 0.027 0.008 -10000 0 0 51 51
cell adhesion 0.063 0.039 -10000 0 -0.14 1 1
CRKL/CBL 0.041 0.011 -10000 0 -10000 0 0
ITGB1 0.028 0.006 -10000 0 0 21 21
SRC -0.008 0.1 0.17 115 -10000 0 115
ITGB7 0.029 0.003 -10000 0 0 8 8
RAC1 0.028 0.006 -10000 0 0 27 27
alpha4/beta1 Integrin/VCAM1 0.021 0.067 -10000 0 -0.15 68 68
p130Cas/Crk/Dock1 -0.018 0.11 0.17 110 -10000 0 110
VCAM1 0.021 0.013 -10000 0 0 161 161
RHOA 0.029 0.003 -10000 0 0 6 6
alpha4/beta1 Integrin/Paxillin/GIT1 0.066 0.04 -10000 0 -0.14 6 6
BCAR1 -0.011 0.093 0.24 28 -10000 0 28
EPOR 0.026 0.009 -10000 0 0 60 60
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.029 0.004 -10000 0 0 12 12
GIT1 0.028 0.007 -10000 0 0 30 30
Rac1/GTP -0.011 0.12 -10000 0 -0.38 20 20
Regulation of 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
EP300 0.032 0.019 0.079 56 -10000 0 56
HSPA8 0.019 0.024 -10000 0 -0.042 68 68
SMAD3/SMAD4/ER alpha -0.051 0.087 0.25 10 -0.29 2 12
AKT1 0.026 0.013 -10000 0 -0.039 16 16
GSC -0.001 0.059 -10000 0 -10000 0 0
NKX2-5 -0.031 0.009 0.039 1 -10000 0 1
muscle cell differentiation -0.026 0.11 0.35 6 -0.3 2 8
SMAD2-3/SMAD4/SP1 0.026 0.14 0.37 9 -10000 0 9
SMAD4 -0.007 0.079 0.21 12 -10000 0 12
CBFB 0.026 0.009 -10000 0 0 61 61
SAP18 0.02 0.021 -10000 0 -0.032 67 67
Cbp/p300/MSG1 0.057 0.044 -10000 0 -0.14 8 8
SMAD3/SMAD4/VDR 0.062 0.1 0.31 8 -10000 0 8
MYC 0.017 0.015 -10000 0 -10000 0 0
CDKN2B -0.057 0.12 -10000 0 -0.61 6 6
AP1 -0.025 0.089 0.26 2 -10000 0 2
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.02 0.11 0.21 7 -0.38 25 32
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.022 0.073 -10000 0 -0.34 11 11
SP3 -0.023 0.037 0.17 20 -10000 0 20
CREB1 0.029 0.003 -10000 0 0 8 8
FOXH1 -0.023 0.016 -10000 0 -10000 0 0
SMAD3/SMAD4/GR -0.031 0.1 0.25 15 -0.26 1 16
GATA3 -0.033 0.009 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 -0.012 0.09 0.18 4 -0.34 24 28
MEF2C/TIF2 -0.006 0.11 0.25 10 -0.29 12 22
endothelial cell migration -0.1 0.21 0.62 2 -0.65 68 70
MAX 0.008 0.056 -10000 0 -0.14 68 68
RBBP7 0.021 0.02 -10000 0 -0.032 65 65
RBBP4 0.02 0.02 -10000 0 -0.032 66 66
RUNX2 0.028 0.007 -10000 0 0 29 29
RUNX3 0.029 0.004 -10000 0 0 13 13
RUNX1 0.029 0.004 -10000 0 0 9 9
CTBP1 0.027 0.008 -10000 0 0 42 42
NR3C1 0.008 0.056 -10000 0 -0.14 68 68
VDR 0.029 0.003 -10000 0 0 7 7
CDKN1A 0.005 0.22 -10000 0 -0.98 20 20
KAT2B 0.002 0.005 0.018 13 -10000 0 13
SMAD2/SMAD2/SMAD4/FOXH1 -0.002 0.066 -10000 0 -10000 0 0
DCP1A 0.029 0.004 -10000 0 0 11 11
SKI 0.021 0.02 -10000 0 -0.032 66 66
SERPINE1 0.099 0.21 0.66 68 -0.63 2 70
SMAD3/SMAD4/ATF2 -0.012 0.09 0.25 19 -10000 0 19
SMAD3/SMAD4/ATF3 -0.013 0.089 0.25 18 -0.26 1 19
SAP30 0.02 0.021 -10000 0 -0.032 67 67
Cbp/p300/PIAS3 0.062 0.054 0.18 64 -0.15 7 71
JUN -0.023 0.09 0.27 6 -10000 0 6
SMAD3/SMAD4/IRF7 -0.013 0.095 0.25 22 -10000 0 22
TFE3 0 0.067 0.13 101 -10000 0 101
COL1A2 0.14 0.25 0.52 156 -0.6 7 163
mesenchymal cell differentiation 0.011 0.09 -10000 0 -0.25 20 20
DLX1 0.029 0.004 -10000 0 0 13 13
TCF3 0.027 0.008 -10000 0 0 50 50
FOS -0.008 0.041 0.16 7 -10000 0 7
SMAD3/SMAD4/Max -0.03 0.098 0.25 15 -0.26 1 16
Cbp/p300/SNIP1 0.05 0.038 -10000 0 -0.14 10 10
ZBTB17 0.029 0.005 -10000 0 -10000 0 0
LAMC1 -0.014 0.081 0.29 7 -10000 0 7
TGIF2/HDAC complex/SMAD3/SMAD4 -0.011 0.09 0.25 20 -10000 0 20
IRF7 -0.03 0.007 -10000 0 -10000 0 0
ESR1 -0.032 0.026 0.11 5 -0.07 82 87
HNF4A 0.027 0.007 -10000 0 0 39 39
MEF2C 0.005 0.11 0.25 13 -0.29 12 25
SMAD2-3/SMAD4 -0.015 0.092 0.27 9 -10000 0 9
Cbp/p300/Src-1 0.055 0.044 -10000 0 -0.14 12 12
IGHV3OR16-13 -0.007 0.033 -10000 0 -0.42 3 3
TGIF2/HDAC complex 0.027 0.007 -10000 0 0 37 37
CREBBP 0.031 0.014 0.071 4 -10000 0 4
SKIL 0.01 0.014 -10000 0 0 361 361
HDAC1 0.02 0.021 -10000 0 -0.032 65 65
HDAC2 0.02 0.021 -10000 0 -0.032 66 66
SNIP1 0.02 0.022 -10000 0 -0.038 64 64
GCN5L2 0.005 0.013 0.038 68 -10000 0 68
SMAD3/SMAD4/TFE3 0 0.1 0.27 13 -10000 0 13
MSG1/HSC70 0.03 0.03 -10000 0 -10000 0 0
SMAD2 -0.031 0.01 -10000 0 -10000 0 0
SMAD3 -0.006 0.078 0.2 17 -10000 0 17
SMAD3/E2F4-5/DP1/p107/SMAD4 0.009 0.077 0.24 14 -0.25 2 16
SMAD2/SMAD2/SMAD4 -0.006 0.061 0.18 2 -0.2 21 23
NCOR1 0.02 0.02 -10000 0 -0.032 65 65
NCOA2 0.027 0.008 -10000 0 0 45 45
NCOA1 0.029 0.005 -10000 0 0 15 15
MYOD/E2A 0.039 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.091 0.13 0.38 7 -10000 0 7
IFNB1 -0.022 0.082 0.23 12 -10000 0 12
SMAD3/SMAD4/MEF2C 0.008 0.13 0.33 11 -0.31 10 21
CITED1 0.024 0.016 -10000 0 -0.029 41 41
SMAD2-3/SMAD4/ARC105 0.038 0.096 0.32 1 -10000 0 1
RBL1 0.026 0.01 -10000 0 0 68 68
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.019 0.077 -10000 0 -0.46 4 4
RUNX1-3/PEBPB2 0.052 0.02 -10000 0 -10000 0 0
SMAD7 0.016 0.16 0.47 17 -0.42 1 18
MYC/MIZ-1 0.012 0.056 -10000 0 -0.16 45 45
SMAD3/SMAD4 0.053 0.13 0.35 55 -0.44 3 58
IL10 -0.017 0.092 0.24 16 -10000 0 16
PIASy/HDAC complex 0.016 0.031 -10000 0 -0.067 64 64
PIAS3 0.031 0.008 -10000 0 -10000 0 0
CDK2 0.02 0.018 -10000 0 -10000 0 0
IL5 -0.015 0.094 0.28 8 -10000 0 8
CDK4 0.033 0.014 0.073 29 -10000 0 29
PIAS4 0.016 0.031 -10000 0 -0.067 64 64
ATF3 0.028 0.006 -10000 0 0 24 24
SMAD3/SMAD4/SP1 0.018 0.13 0.36 6 -10000 0 6
FOXG1 0.029 0.007 -10000 0 -10000 0 0
FOXO3 -0.031 0.011 -10000 0 -10000 0 0
FOXO1 -0.031 0.013 -10000 0 -0.18 1 1
FOXO4 -0.032 0.008 -10000 0 -10000 0 0
heart looping 0.005 0.11 0.25 13 -0.29 12 25
CEBPB 0.026 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.011 0.091 0.25 20 -10000 0 20
MYOD1 0.029 0.003 -10000 0 0 8 8
SMAD3/SMAD4/HNF4 -0.011 0.089 0.25 20 -10000 0 20
SMAD3/SMAD4/GATA3 -0.012 0.097 0.26 21 -10000 0 21
SnoN/SIN3/HDAC complex/NCoR1 0.01 0.014 -10000 0 0 361 361
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.058 0.094 0.31 3 -10000 0 3
SMAD3/SMAD4/SP1-3 0.066 0.13 0.35 15 -10000 0 15
MED15 0.028 0.007 -10000 0 0 31 31
SP1 0.022 0.088 0.14 188 -0.17 3 191
SIN3B 0.019 0.021 -10000 0 -0.032 65 65
SIN3A 0.021 0.02 -10000 0 -0.032 68 68
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.032 0.073 -10000 0 -0.21 5 5
ITGB5 0.004 0.12 0.3 21 -10000 0 21
TGIF/SIN3/HDAC complex/CtBP -0.007 0.082 0.19 3 -0.29 26 29
SMAD3/SMAD4/AR -0.087 0.099 0.25 9 -0.27 6 15
AR 0.012 0.014 -10000 0 0 328 328
negative regulation of cell growth 0.006 0.093 0.26 10 -0.3 14 24
SMAD3/SMAD4/MYOD -0.012 0.091 0.25 20 -10000 0 20
E2F5 0.025 0.01 -10000 0 0 81 81
E2F4 0.026 0.009 -10000 0 0 60 60
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.041 0.073 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 -0.018 0.063 -10000 0 -0.33 3 3
TFDP1 0.027 0.007 -10000 0 0 37 37
SMAD3/SMAD4/AP1 -0.02 0.094 0.26 1 -10000 0 1
SMAD3/SMAD4/RUNX2 -0.011 0.09 0.25 20 -10000 0 20
TGIF2 0.027 0.007 -10000 0 0 37 37
TGIF1 0.028 0.006 -10000 0 0 26 26
ATF2 0.029 0.005 -10000 0 0 15 15
Canonical NF-kappaB pathway

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
FBXW11 -0.031 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.017 0.12 0.24 9 -0.36 16 25
ERC1 0.026 0.009 -10000 0 0 65 65
RIP2/NOD2 0.026 0.021 -10000 0 -10000 0 0
NFKBIA -0.055 0.043 -10000 0 -0.32 12 12
BIRC2 0.021 0.013 -10000 0 0 159 159
IKBKB 0.027 0.007 -10000 0 0 39 39
RIPK2 0.019 0.014 -10000 0 0 200 200
IKBKG 0.026 0.1 -10000 0 -0.43 18 18
IKK complex/A20 0.046 0.13 -10000 0 -0.39 27 27
NEMO/A20/RIP2 0.019 0.014 -10000 0 0 200 200
XPO1 0.027 0.008 -10000 0 0 51 51
NEMO/ATM 0.035 0.13 0.24 9 -0.4 30 39
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.029 0.004 -10000 0 0 12 12
Exportin 1/RanGTP 0.035 0.012 -10000 0 -10000 0 0
IKK complex/ELKS 0.035 0.12 -10000 0 -0.37 28 28
BCL10/MALT1/TRAF6 0.05 0.022 -10000 0 -10000 0 0
NOD2 0.027 0.007 -10000 0 0 39 39
NFKB1 -0.029 0.012 -10000 0 -10000 0 0
RELA -0.032 0.009 -10000 0 -10000 0 0
MALT1 0.025 0.01 -10000 0 0 76 76
cIAP1/UbcH5C 0.029 0.021 -10000 0 -10000 0 0
ATM 0.028 0.007 -10000 0 0 30 30
TNF/TNFR1A 0.032 0.037 -10000 0 -0.16 16 16
TRAF6 0.029 0.004 -10000 0 0 12 12
PRKCA 0.028 0.006 -10000 0 0 22 22
CHUK 0.027 0.007 -10000 0 0 36 36
UBE2D3 0.027 0.008 -10000 0 0 41 41
TNF 0.028 0.005 -10000 0 0 16 16
NF kappa B1 p50/RelA 0.043 0.052 -10000 0 -0.2 17 17
BCL10 0.029 0.004 -10000 0 0 10 10
proteasomal ubiquitin-dependent protein catabolic process -0.055 0.043 -10000 0 -0.32 12 12
beta TrCP1/SCF ubiquitin ligase complex -0.031 0.01 -10000 0 -10000 0 0
TNFRSF1A 0.025 0.01 -10000 0 0 77 77
IKK complex 0.045 0.13 0.24 9 -0.4 28 37
CYLD 0.027 0.007 -10000 0 0 38 38
IKK complex/PKC alpha 0.05 0.13 -10000 0 -0.4 27 27
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.026 0.009 -10000 0 0 62 62
Caspase 8 (4 units) 0.026 0.06 -10000 0 -0.26 2 2
NEF -0.004 0.001 -10000 0 -10000 0 0
NFKBIA -0.031 0.039 0.17 15 -0.089 59 74
BIRC3 -0.083 0.1 0.16 8 -0.31 80 88
CYCS -0.024 0.043 0.17 6 -0.25 2 8
RIPK1 0.027 0.007 -10000 0 0 38 38
CD247 -0.031 0.005 -10000 0 -10000 0 0
MAP2K7 -0.022 0.15 -10000 0 -0.62 25 25
protein ubiquitination -0.034 0.097 0.23 5 -0.3 29 34
CRADD 0.029 0.004 -10000 0 0 13 13
DAXX 0.028 0.005 -10000 0 0 17 17
FAS 0.027 0.008 -10000 0 0 42 42
BID -0.02 0.039 0.15 6 -0.25 2 8
NF-kappa-B/RelA/I kappa B alpha 0.011 0.097 -10000 0 -0.21 84 84
TRADD 0.026 0.009 -10000 0 0 65 65
MAP3K5 0.028 0.007 -10000 0 0 32 32
CFLAR 0.029 0.004 -10000 0 0 9 9
FADD 0.028 0.005 -10000 0 0 19 19
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.01 0.097 -10000 0 -0.21 84 84
MAPK8 -0.028 0.14 -10000 0 -0.58 24 24
APAF1 0.028 0.006 -10000 0 0 27 27
TRAF1 0.028 0.005 -10000 0 0 17 17
TRAF2 0.028 0.006 -10000 0 0 25 25
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.008 0.037 0.16 6 -0.26 1 7
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.035 0.11 0.22 1 -0.36 33 34
CHUK -0.037 0.1 0.24 5 -0.32 33 38
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.066 0.053 -10000 0 -0.14 15 15
TCRz/NEF 0.023 0.006 -10000 0 -10000 0 0
TNF 0.028 0.005 -10000 0 0 16 16
FASLG -0.029 0.005 -10000 0 -10000 0 0
NFKB1 -0.03 0.039 0.17 15 -0.089 60 75
TNFR1A/BAG4/TNF-alpha 0.041 0.04 -10000 0 -0.14 15 15
CASP6 0.006 0.15 -10000 0 -0.51 36 36
CASP7 -0.075 0.16 0.38 16 -0.41 79 95
RELA -0.033 0.04 0.17 16 -0.089 60 76
CASP2 0.027 0.008 -10000 0 0 45 45
CASP3 -0.085 0.17 0.38 16 -0.42 85 101
TNFRSF1A 0.025 0.01 -10000 0 0 77 77
TNFR1A/BAG4 0.029 0.036 -10000 0 -0.16 15 15
CASP8 0.029 0.003 -10000 0 0 7 7
CASP9 0.029 0.004 -10000 0 0 13 13
MAP3K14 -0.038 0.1 0.2 1 -0.34 33 34
APAF-1/Caspase 9 -0.082 0.086 0.16 1 -0.27 59 60
BCL2 -0.044 0.12 -10000 0 -0.54 24 24
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.028 0.006 -10000 0 0 26 26
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.028 0.005 -10000 0 0 18 18
TCEB1 0.027 0.007 -10000 0 0 36 36
HIF1A/p53 -0.012 0.065 0.24 1 -0.31 16 17
HIF1A -0.007 0.056 -10000 0 -0.33 13 13
COPS5 0.025 0.01 -10000 0 0 77 77
VHL/Elongin B/Elongin C/RBX1/CUL2 0.076 0.053 -10000 0 -10000 0 0
FIH (dimer) 0.028 0.005 -10000 0 0 19 19
CDKN2A 0.011 0.014 -10000 0 0 339 339
ARNT/IPAS 0.039 0.014 -10000 0 -10000 0 0
HIF1AN 0.028 0.005 -10000 0 0 19 19
GNB2L1 0.029 0.005 -10000 0 0 15 15
HIF1A/ARNT -0.011 0.065 0.24 1 -0.33 13 14
CUL2 0.023 0.012 -10000 0 0 114 114
OS9 0.028 0.005 -10000 0 0 17 17
RACK1/Elongin B/Elongin C 0.053 0.019 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.01 0.066 0.24 1 -0.33 13 14
PHD1-3/OS9 0.061 0.047 -10000 0 -0.14 11 11
HIF1A/RACK1/Elongin B/Elongin C 0.032 0.071 0.25 1 -0.32 14 15
VHL 0.029 0.004 -10000 0 0 9 9
HSP90AA1 0.028 0.006 -10000 0 0 21 21
HIF1A/JAB1 -0.011 0.064 0.24 1 -0.33 13 14
EGLN3 0.026 0.01 -10000 0 0 70 70
EGLN2 0.027 0.008 -10000 0 0 40 40
EGLN1 0.028 0.007 -10000 0 0 33 33
TP53 0.024 0.011 -10000 0 0 101 101
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.021 0.07 -10000 0 -0.62 5 5
ARNT 0.027 0.007 -10000 0 0 37 37
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.027 0.008 -10000 0 0 50 50
HIF1A/p19ARF -0.007 0.05 0.24 1 -0.32 8 9
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.002 0.087 0.24 9 -0.33 11 20
PDGFB-D/PDGFRB/SLAP 0.023 0.032 -10000 0 -0.16 5 5
PDGFB-D/PDGFRB/APS/CBL 0.034 0.021 -10000 0 -0.13 5 5
AKT1 -0.04 0.11 0.27 22 -0.25 5 27
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.006 0.089 0.27 5 -0.35 12 17
PIK3CA 0.02 0.014 -10000 0 0 170 170
FGR -0.002 0.08 0.32 1 -0.37 11 12
mol:Ca2+ -0.001 0.083 0.27 3 -0.37 12 15
MYC -0.026 0.24 0.4 4 -0.67 59 63
SHC1 0.028 0.006 -10000 0 0 21 21
HRAS/GDP -0.035 0.056 0.16 41 -10000 0 41
LRP1/PDGFRB/PDGFB 0.047 0.038 -10000 0 -0.15 13 13
GRB10 0.029 0.004 -10000 0 0 13 13
PTPN11 0.029 0.003 -10000 0 0 8 8
GO:0007205 -0.001 0.084 0.27 3 -0.37 12 15
PTEN 0.028 0.007 -10000 0 0 30 30
GRB2 0.028 0.005 -10000 0 0 19 19
GRB7 0.027 0.008 -10000 0 0 40 40
PDGFB-D/PDGFRB/SHP2 0.033 0.031 -10000 0 -0.16 5 5
PDGFB-D/PDGFRB/GRB10 0.033 0.031 -10000 0 -0.16 5 5
cell cycle arrest 0.022 0.032 -10000 0 -0.16 5 5
HRAS 0.028 0.006 -10000 0 0 26 26
HIF1A -0.045 0.1 0.24 22 -0.23 5 27
GAB1 -0.01 0.099 0.3 3 -0.35 18 21
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.01 0.1 0.29 10 -0.34 15 25
PDGFB-D/PDGFRB 0.04 0.044 -10000 0 -0.14 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.031 0.031 -10000 0 -0.16 5 5
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.026 0.1 0.26 6 -0.32 21 27
positive regulation of MAPKKK cascade 0.033 0.031 -10000 0 -0.16 5 5
PIK3R1 0.021 0.013 -10000 0 0 159 159
mol:IP3 -0.001 0.084 0.27 3 -0.38 12 15
E5 -0.001 0.001 -10000 0 -10000 0 0
CSK 0.02 0.023 -10000 0 -0.047 2 2
PDGFB-D/PDGFRB/GRB7 0.03 0.035 -10000 0 -0.16 8 8
SHB 0.029 0.003 -10000 0 0 8 8
BLK -0.058 0.16 0.32 1 -0.39 91 92
PTPN2 0.013 0.028 -10000 0 -0.051 1 1
PDGFB-D/PDGFRB/SNX15 0.033 0.031 -10000 0 -0.16 5 5
BCAR1 0.026 0.009 -10000 0 0 57 57
VAV2 -0.022 0.12 0.3 4 -0.37 34 38
CBL 0.029 0.004 -10000 0 0 12 12
PDGFB-D/PDGFRB/DEP1 0.033 0.031 -10000 0 -0.16 5 5
LCK 0 0.073 0.32 1 -0.36 8 9
PDGFRB 0.009 0.03 -10000 0 -10000 0 0
ACP1 0.026 0.009 -10000 0 0 58 58
HCK 0.002 0.053 0.32 1 -10000 0 1
ABL1 -0.01 0.088 0.32 2 -0.29 17 19
PDGFB-D/PDGFRB/CBL -0.009 0.1 0.33 1 -0.4 18 19
PTPN1 0.011 0.028 -10000 0 -0.051 1 1
SNX15 0.029 0.003 -10000 0 0 5 5
STAT3 0.027 0.007 -10000 0 0 36 36
STAT1 0.013 0.015 -10000 0 0 315 315
cell proliferation -0.019 0.22 0.38 5 -0.6 59 64
SLA 0.02 0.014 -10000 0 0 171 171
actin cytoskeleton reorganization -0.022 0.1 0.33 15 -10000 0 15
SRC 0 0.064 0.32 1 -0.88 1 2
PI3K -0.073 0.068 -10000 0 -0.21 41 41
PDGFB-D/PDGFRB/GRB7/SHC 0.048 0.033 -10000 0 -0.15 8 8
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.006 0.09 0.28 5 -0.36 12 17
LYN -0.009 0.088 0.31 1 -0.49 11 12
LRP1 0.028 0.005 -10000 0 0 20 20
SOS1 0.027 0.007 -10000 0 0 36 36
STAT5B 0.028 0.007 -10000 0 0 32 32
STAT5A 0.028 0.007 -10000 0 0 33 33
NCK1-2/p130 Cas 0.053 0.068 -10000 0 -0.15 6 6
SPHK1 0.015 0.026 -10000 0 -10000 0 0
EDG1 -0.001 0.003 0.019 1 -10000 0 1
mol:DAG -0.001 0.084 0.27 3 -0.38 12 15
PLCG1 -0.001 0.086 0.27 3 -0.38 12 15
NHERF/PDGFRB -0.013 0.1 -10000 0 -0.16 170 170
YES1 -0.001 0.083 0.31 1 -0.52 7 8
cell migration -0.014 0.1 -10000 0 -0.16 170 170
SHC/Grb2/SOS1 0.059 0.06 -10000 0 -0.15 4 4
SLC9A3R2 0.024 0.011 -10000 0 0 92 92
SLC9A3R1 0.022 0.013 -10000 0 0 139 139
NHERF1-2/PDGFRB/PTEN -0.005 0.11 -10000 0 -0.16 170 170
FYN -0.067 0.17 -10000 0 -0.43 88 88
DOK1 -0.028 0.06 0.16 50 -10000 0 50
HRAS/GTP 0.021 0.005 -10000 0 -10000 0 0
PDGFB 0.027 0.008 -10000 0 0 46 46
RAC1 -0.059 0.2 0.41 1 -0.53 64 65
PRKCD -0.029 0.061 0.16 49 -10000 0 49
FER -0.028 0.06 0.16 46 -10000 0 46
MAPKKK cascade -0.025 0.083 0.32 10 -10000 0 10
RASA1 -0.028 0.057 0.16 43 -10000 0 43
NCK1 0.026 0.009 -10000 0 0 64 64
NCK2 0.029 0.004 -10000 0 0 10 10
p62DOK/Csk -0.031 0.065 0.16 52 -10000 0 52
PDGFB-D/PDGFRB/SHB 0.034 0.031 -10000 0 -0.16 5 5
chemotaxis -0.01 0.087 0.32 2 -0.29 17 19
STAT1-3-5/STAT1-3-5 0.06 0.065 -10000 0 -0.16 10 10
Bovine Papilomavirus E5/PDGFRB 0.013 0.023 -10000 0 -0.15 5 5
PTPRJ 0.029 0.003 -10000 0 0 8 8
Arf6 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
CENTA1/KIF3B 0.01 0.03 -10000 0 -0.12 26 26
ARNO/beta Arrestin1-2 0.025 0.029 -10000 0 -0.1 6 6
EGFR 0.026 0.009 -10000 0 0 55 55
EPHA2 0.028 0.005 -10000 0 0 16 16
USP6 0.028 0.006 -10000 0 0 25 25
IQSEC1 0.029 0.003 -10000 0 0 8 8
EGFR/EGFR/EGF/EGF 0.024 0.055 -10000 0 -0.16 43 43
ARRB2 0.006 0.002 -10000 0 -10000 0 0
mol:GTP 0.001 0.02 0.11 4 -0.07 8 12
ARRB1 0.027 0.007 -10000 0 0 36 36
FBXO8 0.027 0.008 -10000 0 0 43 43
TSHR 0.028 0.007 -10000 0 0 32 32
EGF 0.027 0.008 -10000 0 0 41 41
somatostatin receptor activity 0 0 0 4 -0.001 28 32
ARAP2 0 0 0 7 0 25 32
mol:GDP -0.009 0.072 0.14 2 -0.25 23 25
mol:PI-3-4-5-P3 0 0 0 6 -0.001 28 34
ITGA2B 0.028 0.006 -10000 0 0 22 22
ARF6 0.029 0.004 -10000 0 0 11 11
Ephrin A1/EPHA2/NCK1/GIT1 0.067 0.04 -10000 0 -10000 0 0
ADAP1 0 0 0 1 0 12 13
KIF13B 0.023 0.012 -10000 0 0 113 113
HGF/MET 0.033 0.033 -10000 0 -0.16 12 12
PXN 0.029 0.005 -10000 0 0 14 14
ARF6/GTP -0.014 0.077 0.16 4 -0.25 28 32
EGFR/EGFR/EGF/EGF/ARFGEP100 0.039 0.055 -10000 0 -0.15 41 41
ADRB2 0.029 0.004 -10000 0 0 11 11
receptor agonist activity 0 0 0 7 0 24 31
actin filament binding 0 0 0 4 0 29 33
SRC 0.028 0.007 -10000 0 0 33 33
ITGB3 0.024 0.011 -10000 0 0 98 98
GNAQ 0.028 0.007 -10000 0 -0.002 31 31
EFA6/PI-4-5-P2 0 0 0.001 11 -0.001 16 27
ARF6/GDP -0.003 0.072 0.16 9 -0.28 20 29
ARF6/GDP/GULP/ACAP1 -0.005 0.09 -10000 0 -0.26 28 28
alphaIIb/beta3 Integrin/paxillin/GIT1 0.041 0.077 -10000 0 -0.14 72 72
ACAP1 0 0 0 3 -10000 0 3
ACAP2 0 0 0 5 0 25 30
LHCGR/beta Arrestin2 0.021 0.019 -10000 0 -10000 0 0
EFNA1 0.027 0.008 -10000 0 0 46 46
HGF 0.028 0.005 -10000 0 0 16 16
CYTH3 0 0 0.001 8 -0.001 25 33
CYTH2 0 0.001 0.002 3 -0.004 28 31
NCK1 0.026 0.009 -10000 0 0 64 64
fibronectin binding 0 0 0 6 0 18 24
endosomal lumen acidification 0 0 0 9 0 16 25
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.024 0.011 -10000 0 0 92 92
GNAQ/ARNO 0.018 0.007 -10000 0 -0.004 39 39
mol:Phosphatidic acid 0 0 0 5 0 25 30
PIP3-E 0 0 0 5 0 22 27
MET 0.025 0.011 -10000 0 0 86 86
GNA14 0.028 0.005 -10000 0 0 19 19
GNA15 0.027 0.008 -10000 0 0 46 46
GIT1 0.028 0.007 -10000 0 0 30 30
mol:PI-4-5-P2 0 0 0.001 7 -0.001 21 28
GNA11 0.025 0.01 -10000 0 0 83 83
LHCGR 0.028 0.008 -10000 0 -0.006 26 26
AGTR1 0.027 0.009 -10000 0 0 52 52
desensitization of G-protein coupled receptor protein signaling pathway 0.021 0.019 -10000 0 -10000 0 0
IPCEF1/ARNO 0.021 0.037 -10000 0 -0.1 43 43
alphaIIb/beta3 Integrin 0.016 0.068 -10000 0 -0.16 68 68
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.016 0.11 0.36 14 -0.3 10 24
TBX21 -0.11 0.27 0.78 9 -0.8 3 12
B2M 0.027 0.007 -10000 0 -10000 0 0
TYK2 -0.012 0.051 0.18 9 -10000 0 9
IL12RB1 -0.014 0.051 0.18 10 -10000 0 10
GADD45B -0.079 0.26 0.75 10 -0.73 13 23
IL12RB2 -0.015 0.055 0.18 13 -10000 0 13
GADD45G -0.074 0.26 0.72 7 -0.94 12 19
natural killer cell activation -0.006 0.034 0.15 13 -10000 0 13
RELB 0.028 0.006 -10000 0 0 27 27
RELA 0.029 0.003 -10000 0 0 6 6
IL18 -0.012 0.027 0.11 2 -10000 0 2
IL2RA 0.027 0.008 -10000 0 0 43 43
IFNG 0.027 0.008 -10000 0 0 46 46
STAT3 (dimer) -0.1 0.25 0.62 12 -0.64 28 40
HLA-DRB5 0.017 0.026 0.082 16 -0.046 50 66
FASLG -0.1 0.27 0.78 10 -0.79 3 13
NF kappa B2 p52/RelB -0.099 0.26 0.52 14 -0.59 31 45
CD4 0.02 0.027 0.082 20 -0.046 55 75
SOCS1 0.028 0.007 -10000 0 0 32 32
EntrezGene:6955 0 0.015 0.059 26 -0.032 12 38
CD3D 0.02 0.027 0.092 18 -0.053 48 66
CD3E 0.022 0.027 0.082 20 -0.046 61 81
CD3G 0.021 0.028 0.089 22 -0.051 55 77
IL12Rbeta2/JAK2 0.005 0.078 0.28 10 -0.18 1 11
CCL3 -0.1 0.29 0.86 17 -0.8 3 20
CCL4 -0.1 0.27 0.76 11 -0.6 24 35
HLA-A 0.028 0.005 -10000 0 -10000 0 0
IL18/IL18R 0.015 0.068 0.43 4 -10000 0 4
NOS2 -0.082 0.25 0.74 12 -0.6 8 20
IL12/IL12R/TYK2/JAK2/SPHK2 -0.015 0.11 0.36 14 -0.3 5 19
IL1R1 -0.36 0.53 0.74 6 -1 207 213
IL4 0.026 0.051 -10000 0 -0.18 12 12
JAK2 -0.013 0.052 0.18 10 -10000 0 10
EntrezGene:6957 0 0.012 0.052 22 -0.032 5 27
TCR/CD3/MHC I/CD8 -0.012 0.08 0.24 2 -0.34 12 14
RAB7A -0.062 0.23 0.7 6 -0.68 5 11
lysosomal transport -0.059 0.23 0.7 6 -0.66 4 10
FOS -0.14 0.43 0.74 21 -1.1 73 94
STAT4 (dimer) -0.057 0.26 0.67 15 -0.66 8 23
STAT5A (dimer) -0.11 0.25 0.52 12 -0.59 29 41
GZMA -0.11 0.28 0.77 12 -0.82 5 17
GZMB -0.1 0.28 0.82 14 -0.75 4 18
HLX 0.028 0.006 -10000 0 0 22 22
LCK -0.12 0.27 0.73 9 -0.63 25 34
TCR/CD3/MHC II/CD4 -0.024 0.16 0.34 23 -0.38 51 74
IL2/IL2R 0.049 0.061 -10000 0 -0.14 28 28
MAPK14 -0.074 0.26 0.72 10 -0.76 10 20
CCR5 -0.057 0.23 0.72 7 -0.68 2 9
IL1B -0.017 0.049 0.18 9 -10000 0 9
STAT6 -0.026 0.14 0.49 8 -0.7 8 16
STAT4 0.028 0.005 -10000 0 0 16 16
STAT3 0.027 0.007 -10000 0 0 36 36
STAT1 0.013 0.015 -10000 0 0 315 315
NFKB1 0.027 0.008 -10000 0 0 46 46
NFKB2 0.029 0.005 -10000 0 0 14 14
IL12B -0.016 0.055 0.18 13 -10000 0 13
CD8A 0.029 0.003 -10000 0 -10000 0 0
CD8B 0.029 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.016 0.11 0.29 10 -0.36 14 24
IL2RB 0.027 0.008 -10000 0 0 51 51
proteasomal ubiquitin-dependent protein catabolic process -0.052 0.25 0.66 15 -0.64 6 21
IL2RG 0.026 0.009 -10000 0 0 65 65
IL12 0.007 0.076 0.29 10 -0.17 1 11
STAT5A 0.028 0.007 -10000 0 0 33 33
CD247 0.023 0.027 0.083 22 -0.047 60 82
IL2 0.028 0.007 -10000 0 0 33 33
SPHK2 0.028 0.005 -10000 0 0 20 20
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.013 0.051 0.18 11 -10000 0 11
IL12/IL12R/TYK2/JAK2 -0.12 0.28 0.87 8 -0.67 21 29
MAP2K3 -0.085 0.27 0.71 10 -0.75 18 28
RIPK2 0.019 0.014 -10000 0 0 200 200
MAP2K6 -0.068 0.25 0.73 9 -0.74 10 19
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.019 0.027 0.093 22 -0.055 34 56
IL18RAP -0.011 0.033 0.11 4 -10000 0 4
IL12Rbeta1/TYK2 0.005 0.066 0.23 8 -10000 0 8
EOMES 0.006 0.079 -10000 0 -0.49 7 7
STAT1 (dimer) -0.051 0.22 0.64 11 -0.6 7 18
T cell proliferation -0.039 0.22 0.63 12 -0.55 6 18
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.011 0.033 0.11 4 -10000 0 4
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.085 0.17 -10000 0 -0.54 9 9
ATF2 -0.074 0.25 0.68 10 -0.72 10 20
Signaling events mediated by PTP1B

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
PDGFRB 0.029 0.005 -10000 0 0 15 15
Jak2/Leptin Receptor 0.009 0.11 -10000 0 -0.38 25 25
PTP1B/AKT1 0.001 0.088 -10000 0 -0.34 6 6
FYN 0.024 0.011 -10000 0 0 99 99
p210 bcr-abl/PTP1B -0.007 0.089 0.21 1 -0.34 7 8
EGFR 0.018 0.025 -10000 0 -10000 0 0
EGF/EGFR 0.006 0.099 -10000 0 -0.31 14 14
CSF1 0.028 0.006 -10000 0 0 27 27
AKT1 0.012 0.027 -10000 0 -10000 0 0
INSR 0.015 0.023 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.005 0.091 -10000 0 -0.32 12 12
Insulin Receptor/Insulin 0.004 0.097 -10000 0 -0.32 7 7
HCK 0.027 0.008 -10000 0 0 47 47
CRK 0.027 0.007 -10000 0 0 36 36
TYK2 0 0.1 0.25 22 -0.33 7 29
EGF 0.017 0.027 -10000 0 -10000 0 0
YES1 0.027 0.008 -10000 0 0 41 41
CAV1 -0.031 0.1 0.22 2 -0.34 24 26
TXN 0.014 0.026 -10000 0 -0.059 1 1
PTP1B/IRS1/GRB2 -0.059 0.1 -10000 0 -0.31 25 25
cell migration 0.007 0.089 0.34 7 -0.21 1 8
STAT3 0.015 0.024 -10000 0 -10000 0 0
PRLR 0.017 0.023 0.15 1 -10000 0 1
ITGA2B 0.008 0.028 -10000 0 -0.045 1 1
CSF1R 0.028 0.005 -10000 0 0 16 16
Prolactin Receptor/Prolactin 0.037 0.019 0.29 1 -10000 0 1
FGR 0.029 0.005 -10000 0 0 14 14
PTP1B/p130 Cas 0.002 0.092 -10000 0 -0.33 7 7
Crk/p130 Cas 0.006 0.1 -10000 0 -0.33 7 7
DOK1 -0.016 0.086 0.28 1 -0.34 9 10
JAK2 -0.003 0.11 -10000 0 -0.37 31 31
Jak2/Leptin Receptor/Leptin -0.003 0.12 0.27 2 -0.35 12 14
PIK3R1 0.021 0.013 -10000 0 0 159 159
PTPN1 -0.008 0.089 0.21 1 -0.34 7 8
LYN 0.027 0.008 -10000 0 0 50 50
CDH2 0.019 0.014 -10000 0 0 188 188
SRC 0.009 0.092 -10000 0 -0.47 15 15
ITGB3 0.011 0.025 -10000 0 -0.045 1 1
CAT1/PTP1B -0.019 0.12 0.25 10 -0.39 17 27
CAPN1 0 0.03 -10000 0 -10000 0 0
CSK 0.028 0.006 -10000 0 0 21 21
PI3K -0.013 0.096 -10000 0 -0.33 7 7
mol:H2O2 0 0.003 0.019 2 -0.037 1 3
STAT3 (dimer) -0.017 0.11 0.32 2 -0.32 12 14
negative regulation of transcription -0.002 0.11 -10000 0 -0.37 31 31
FCGR2A 0.028 0.006 -10000 0 0 28 28
FER 0.014 0.026 -10000 0 -0.059 1 1
alphaIIb/beta3 Integrin 0.015 0.069 -10000 0 -0.17 68 68
BLK 0.024 0.011 -10000 0 0 101 101
Insulin Receptor/Insulin/Shc 0.034 0.058 -10000 0 -0.15 42 42
RHOA 0 0.03 -10000 0 -10000 0 0
LEPR 0.025 0.016 -10000 0 -0.031 36 36
BCAR1 0.026 0.009 -10000 0 0 57 57
p210 bcr-abl/Grb2 0.028 0.005 -10000 0 0 19 19
mol:NADPH -0.001 0.002 -10000 0 -0.031 1 1
TRPV6 -0.031 0.13 0.27 2 -0.39 30 32
PRL 0.018 0.023 0.15 1 -10000 0 1
SOCS3 0.002 0.14 0.66 2 -1.1 8 10
SPRY2 -0.011 0.023 -10000 0 -0.065 1 1
Insulin Receptor/Insulin/IRS1 -0.077 0.1 -10000 0 -0.16 337 337
CSF1/CSF1R 0.005 0.1 -10000 0 -0.32 9 9
Ras protein signal transduction -0.009 0.087 0.55 12 -10000 0 12
IRS1 0.011 0.014 -10000 0 0 349 349
INS 0.013 0.027 -10000 0 -10000 0 0
LEP 0.013 0.026 -10000 0 -10000 0 0
STAT5B -0.008 0.11 -10000 0 -0.37 23 23
STAT5A -0.008 0.11 -10000 0 -0.36 23 23
GRB2 0.028 0.005 -10000 0 0 19 19
PDGFB-D/PDGFRB 0 0.094 -10000 0 -0.34 7 7
CSN2 0.007 0.077 0.63 1 -10000 0 1
PIK3CA 0.02 0.014 -10000 0 0 170 170
LAT 0.012 0.087 -10000 0 -0.47 14 14
YBX1 -0.001 0.033 -10000 0 -10000 0 0
LCK 0.028 0.006 -10000 0 0 25 25
SHC1 0.028 0.006 -10000 0 0 21 21
NOX4 -0.002 0.024 -10000 0 -10000 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 0.035 0.017 -10000 0 -0.13 3 3
cell-cell adhesion 0.063 0.031 -10000 0 -10000 0 0
Ephrin B/EPHB2/RasGAP 0.059 0.065 -10000 0 -0.14 26 26
ITSN1 0.029 0.003 -10000 0 0 8 8
PIK3CA 0.02 0.014 -10000 0 0 170 170
SHC1 0.028 0.006 -10000 0 0 21 21
Ephrin B1/EPHB3 0.031 0.017 -10000 0 -0.13 1 1
Ephrin B1/EPHB1 0.036 0.013 -10000 0 -0.13 1 1
HRAS/GDP -0.07 0.069 0.12 4 -0.22 38 42
Ephrin B/EPHB1/GRB7 0.061 0.061 -10000 0 -0.14 23 23
Endophilin/SYNJ1 -0.039 0.055 0.18 18 -10000 0 18
KRAS 0.024 0.011 -10000 0 0 99 99
Ephrin B/EPHB1/Src 0.062 0.059 -10000 0 -0.14 21 21
endothelial cell migration 0.007 0.068 -10000 0 -0.14 82 82
GRB2 0.028 0.005 -10000 0 0 19 19
GRB7 0.027 0.008 -10000 0 0 40 40
PAK1 -0.039 0.065 0.3 3 -10000 0 3
HRAS 0.028 0.006 -10000 0 0 26 26
RRAS -0.036 0.057 0.18 18 -0.22 3 21
DNM1 0.028 0.005 -10000 0 0 17 17
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.029 0.065 0.16 37 -10000 0 37
lamellipodium assembly -0.063 0.031 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.004 0.049 -10000 0 -0.24 5 5
PIK3R1 0.021 0.013 -10000 0 0 159 159
EPHB2 0.028 0.006 -10000 0 0 21 21
EPHB3 0.024 0.012 -10000 0 0 107 107
EPHB1 0.027 0.007 -10000 0 0 36 36
EPHB4 0.028 0.005 -10000 0 0 18 18
mol:GDP -0.048 0.079 0.23 4 -0.23 27 31
Ephrin B/EPHB2 0.053 0.05 -10000 0 -0.13 23 23
Ephrin B/EPHB3 0.044 0.051 -10000 0 -0.13 21 21
JNK cascade -0.013 0.098 0.33 27 -10000 0 27
Ephrin B/EPHB1 0.052 0.049 -10000 0 -0.13 21 21
RAP1/GDP -0.059 0.088 0.23 7 -0.27 10 17
EFNB2 0.026 0.009 -10000 0 0 58 58
EFNB3 0.028 0.007 -10000 0 0 30 30
EFNB1 0.029 0.003 -10000 0 0 8 8
Ephrin B2/EPHB1-2 0.041 0.039 -10000 0 -0.13 18 18
RAP1B 0.028 0.006 -10000 0 0 22 22
RAP1A 0.029 0.003 -10000 0 0 7 7
CDC42/GTP -0.049 0.064 0.14 32 -10000 0 32
Rap1/GTP -0.068 0.039 0.066 12 -10000 0 12
axon guidance 0.034 0.017 -10000 0 -0.13 3 3
MAPK3 -0.026 0.05 0.16 1 -0.25 5 6
MAPK1 -0.02 0.047 0.16 6 -0.22 1 7
Rac1/GDP -0.055 0.086 0.24 6 -0.24 25 31
actin cytoskeleton reorganization -0.035 0.049 -10000 0 -0.18 9 9
CDC42/GDP -0.057 0.086 0.23 7 -0.24 25 32
PI3K 0.022 0.078 -10000 0 -0.14 82 82
EFNA5 0.027 0.008 -10000 0 0 42 42
Ephrin B2/EPHB4 0.03 0.034 -10000 0 -0.13 20 20
Ephrin B/EPHB2/Intersectin/N-WASP 0.001 0.055 -10000 0 -0.19 28 28
CDC42 0.029 0.004 -10000 0 0 11 11
RAS family/GTP -0.028 0.041 0.056 7 -10000 0 7
PTK2 0.13 0.26 0.56 149 -10000 0 149
MAP4K4 -0.013 0.099 0.33 27 -10000 0 27
SRC 0.028 0.007 -10000 0 0 33 33
KALRN 0.028 0.006 -10000 0 0 23 23
Intersectin/N-WASP 0.041 0.009 -10000 0 -10000 0 0
neuron projection morphogenesis -0.045 0.083 0.22 26 -10000 0 26
MAP2K1 -0.017 0.047 0.16 5 -0.22 3 8
WASL 0.028 0.006 -10000 0 0 21 21
Ephrin B1/EPHB1-2/NCK1 0.073 0.033 -10000 0 -0.14 1 1
cell migration -0.022 0.073 0.24 5 -0.28 5 10
NRAS 0.014 0.015 -10000 0 0 300 300
SYNJ1 -0.039 0.056 0.18 18 -10000 0 18
PXN 0.029 0.005 -10000 0 0 14 14
TF -0.044 0.053 0.16 17 -10000 0 17
HRAS/GTP -0.052 0.053 0.12 41 -10000 0 41
Ephrin B1/EPHB1-2 0.049 0.021 -10000 0 -0.13 1 1
cell adhesion mediated by integrin 0.019 0.062 0.16 2 -0.19 22 24
RAC1 0.028 0.006 -10000 0 0 27 27
mol:GTP -0.043 0.058 0.14 45 -10000 0 45
RAC1-CDC42/GTP -0.062 0.04 -10000 0 -10000 0 0
RASA1 0.027 0.008 -10000 0 0 49 49
RAC1-CDC42/GDP -0.06 0.087 0.23 7 -0.24 24 31
ruffle organization -0.049 0.078 0.27 9 -10000 0 9
NCK1 0.026 0.009 -10000 0 0 64 64
receptor internalization -0.046 0.053 0.16 18 -0.22 1 19
Ephrin B/EPHB2/KALRN 0.064 0.06 -10000 0 -0.14 23 23
ROCK1 0.006 0.082 0.17 107 -10000 0 107
RAS family/GDP -0.038 0.05 -10000 0 -0.19 12 12
Rac1/GTP -0.066 0.033 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/Paxillin -0.001 0.053 -10000 0 -0.21 2 2
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.036 0.011 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.027 0.007 -10000 0 0 38 38
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.025 0.011 -10000 0 0 89 89
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.027 0.008 -10000 0 0 50 50
RAC1-CDC42/GTP/PAK family -0.032 0.066 -10000 0 -0.15 114 114
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.027 0.008 -10000 0 0 41 41
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.029 0.004 -10000 0 0 13 13
FYN 0.024 0.011 -10000 0 0 99 99
MAP3K12 0.029 0.003 -10000 0 0 5 5
FGR 0.029 0.005 -10000 0 0 14 14
p38 alpha/TAB1 -0.048 0.093 -10000 0 -0.32 41 41
PRKG1 0.029 0.003 -10000 0 0 5 5
DUSP8 0.028 0.006 -10000 0 0 24 24
PGK/cGMP/p38 alpha -0.027 0.11 0.18 1 -0.36 30 31
apoptosis -0.046 0.089 -10000 0 -0.3 41 41
RAL/GTP 0.038 0.008 -10000 0 -10000 0 0
LYN 0.027 0.008 -10000 0 0 50 50
DUSP1 0.023 0.012 -10000 0 0 124 124
PAK1 0.027 0.008 -10000 0 0 48 48
SRC 0.028 0.007 -10000 0 0 33 33
RAC1/OSM/MEKK3/MKK3 0.062 0.036 -10000 0 -10000 0 0
TRAF6 0.029 0.004 -10000 0 0 12 12
RAC1 0.028 0.006 -10000 0 0 27 27
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 0.029 0.005 -10000 0 0 14 14
RAC1-CDC42/GTP 0.037 0.01 -10000 0 -10000 0 0
MAPK11 -0.05 0.12 0.2 2 -0.35 39 41
BLK 0.024 0.011 -10000 0 0 101 101
HCK 0.027 0.008 -10000 0 0 47 47
MAP2K3 0.027 0.008 -10000 0 0 43 43
DUSP16 0.026 0.009 -10000 0 0 57 57
DUSP10 0.027 0.007 -10000 0 0 36 36
TRAF6/MEKK3 0.036 0.01 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.032 0.11 0.18 4 -0.4 30 34
positive regulation of innate immune response -0.051 0.13 0.23 2 -0.41 37 39
LCK 0.028 0.006 -10000 0 0 25 25
p38alpha-beta/MKP7 -0.045 0.13 0.21 1 -0.4 35 36
p38alpha-beta/MKP5 -0.043 0.13 0.27 1 -0.4 35 36
PGK/cGMP 0.022 0.002 -10000 0 -10000 0 0
PAK2 0.024 0.011 -10000 0 0 93 93
p38alpha-beta/MKP1 -0.053 0.14 0.24 2 -0.4 42 44
CDC42 0.029 0.004 -10000 0 0 11 11
RALB 0.029 0.004 -10000 0 0 10 10
RALA 0.029 0.005 -10000 0 0 15 15
PAK3 0.02 0.013 -10000 0 0 169 169
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.048 0.1 -10000 0 -0.32 64 64
KLHL20 -0.059 0.078 0.48 1 -0.27 17 18
CYFIP2 0.028 0.006 -10000 0 0 24 24
Rac1/GDP -0.046 0.079 0.24 5 -0.25 20 25
ENAH -0.049 0.1 -10000 0 -0.32 66 66
AP1M1 0.026 0.009 -10000 0 0 66 66
RAP1B 0.028 0.006 -10000 0 0 22 22
RAP1A 0.029 0.003 -10000 0 0 7 7
CTNNB1 0.028 0.007 -10000 0 -0.013 15 15
CDC42/GTP -0.059 0.05 0.12 22 -0.23 2 24
ABI1/Sra1/Nap1 -0.053 0.045 -10000 0 -0.17 34 34
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.055 0.048 -10000 0 -0.14 9 9
RAPGEF1 -0.047 0.1 0.25 3 -0.31 56 59
CTNND1 0.029 0.004 -10000 0 -0.005 6 6
regulation of calcium-dependent cell-cell adhesion -0.025 0.12 -10000 0 -0.32 68 68
CRK -0.047 0.1 -10000 0 -0.32 61 61
E-cadherin/gamma catenin/alpha catenin 0.043 0.044 -10000 0 -0.16 20 20
alphaE/beta7 Integrin 0.04 0.014 -10000 0 -0.16 1 1
IQGAP1 0.028 0.006 -10000 0 0 24 24
NCKAP1 0.028 0.005 -10000 0 0 17 17
Rap1/GTP/I-afadin 0.04 0.042 -10000 0 -0.13 21 21
DLG1 -0.034 0.1 0.19 1 -0.32 54 55
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.044 0.042 -10000 0 -0.16 8 8
MLLT4 0.026 0.01 -10000 0 0 70 70
ARF6/GTP/NME1/Tiam1 0.048 0.024 -10000 0 -0.13 1 1
PI3K -0.054 0.054 -10000 0 -0.21 7 7
ARF6 0.029 0.004 -10000 0 0 11 11
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.03 0.042 -10000 0 -0.18 19 19
TIAM1 0.028 0.006 -10000 0 -0.001 21 21
E-cadherin(dimer)/Ca2+ 0.051 0.043 -10000 0 -0.13 9 9
AKT1 -0.013 0.069 0.14 53 -10000 0 53
PIK3R1 0.021 0.013 -10000 0 0 159 159
CDH1 0.025 0.011 -10000 0 -0.003 79 79
RhoA/GDP -0.046 0.079 0.24 4 -0.25 19 23
actin cytoskeleton organization -0.044 0.058 0.41 1 -0.21 9 10
CDC42/GDP -0.045 0.08 0.24 5 -0.25 19 24
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.015 0.058 -10000 0 -0.19 36 36
ITGB7 0.029 0.003 -10000 0 0 8 8
RAC1 0.028 0.007 -10000 0 -0.001 28 28
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.056 0.046 -10000 0 -0.14 9 9
E-cadherin/Ca2+/beta catenin/alpha catenin 0.039 0.033 -10000 0 -0.12 9 9
mol:GDP -0.044 0.085 0.24 5 -0.28 21 26
CDC42/GTP/IQGAP1 0.037 0.014 -10000 0 -0.13 2 2
JUP 0.027 0.008 -10000 0 0 41 41
p120 catenin/RhoA/GDP -0.048 0.082 0.24 4 -0.26 18 22
RAC1/GTP/IQGAP1 0.036 0.015 -10000 0 -0.13 2 2
PIP5K1C/AP1M1 0.036 0.016 -10000 0 -10000 0 0
RHOA 0.029 0.003 -10000 0 0 6 6
CDC42 0.029 0.004 -10000 0 0 11 11
CTNNA1 0.029 0.005 -10000 0 -0.002 12 12
positive regulation of S phase of mitotic cell cycle -0.045 0.057 0.12 1 -0.13 141 142
NME1 0.027 0.008 -10000 0 0 42 42
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.05 0.11 -10000 0 -0.32 68 68
regulation of cell-cell adhesion -0.054 0.041 0.083 21 -0.21 2 23
WASF2 -0.031 0.035 0.09 4 -0.1 38 42
Rap1/GTP -0.055 0.058 0.25 2 -0.25 2 4
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.056 0.063 -10000 0 -0.15 20 20
CCND1 -0.055 0.069 0.13 1 -0.16 143 144
VAV2 -0.041 0.16 -10000 0 -0.65 24 24
RAP1/GDP -0.046 0.066 0.25 3 -0.25 3 6
adherens junction assembly -0.048 0.1 -10000 0 -0.32 68 68
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.029 0.005 -10000 0 0 14 14
PIP5K1C 0.027 0.008 -10000 0 0 43 43
regulation of heterotypic cell-cell adhesion -0.06 0.03 0.17 4 -0.23 2 6
E-cadherin/beta catenin -0.022 0.046 -10000 0 -0.18 40 40
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.047 0.1 -10000 0 -0.33 62 62
PIK3CA 0.02 0.014 -10000 0 0 170 170
Rac1/GTP -0.09 0.11 0.57 1 -0.39 37 38
E-cadherin/beta catenin/alpha catenin 0.048 0.032 -10000 0 -0.15 9 9
ITGAE 0.028 0.007 -10000 0 0 30 30
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.025 0.12 -10000 0 -0.33 68 68
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.028 0.007 -10000 0 0 31 31
RAS family/GTP/Tiam1 0.035 0.05 -10000 0 -0.24 2 2
NT3 (dimer)/TRKC 0.033 0.018 -10000 0 -10000 0 0
NT3 (dimer)/TRKB 0.045 0.026 -10000 0 -10000 0 0
SHC/Grb2/SOS1/GAB1/PI3K -0.013 0.081 0.2 5 -0.24 8 13
RAPGEF1 0.028 0.005 -10000 0 0 18 18
BDNF 0.029 0.004 -10000 0 0 13 13
PIK3CA 0.02 0.014 -10000 0 0 170 170
DYNLT1 0.025 0.01 -10000 0 0 82 82
NTRK1 0.029 0.005 -10000 0 0 15 15
NTRK2 0.028 0.005 -10000 0 0 20 20
NTRK3 0.028 0.005 -10000 0 0 19 19
NT-4/5 (dimer)/TRKB 0.037 0.009 -10000 0 -10000 0 0
neuron apoptosis 0.019 0.11 0.29 44 -10000 0 44
SHC 2-3/Grb2 -0.021 0.12 -10000 0 -0.31 44 44
SHC1 0.028 0.006 -10000 0 0 21 21
SHC2 -0.042 0.15 -10000 0 -0.39 76 76
SHC3 0.001 0.09 -10000 0 -0.41 16 16
STAT3 (dimer) -0.052 0.14 -10000 0 -0.28 142 142
NT3 (dimer)/TRKA 0.045 0.026 -10000 0 -10000 0 0
RIN/GDP 0.042 0.079 0.22 22 -0.26 10 32
GIPC1 0.025 0.01 -10000 0 0 81 81
KRAS 0.024 0.011 -10000 0 0 99 99
DNAJA3 -0.013 0.056 0.18 2 -0.25 2 4
RIN/GTP 0.021 0.005 -10000 0 -10000 0 0
CCND1 -0.16 0.21 -10000 0 -0.52 141 141
MAGED1 0.028 0.006 -10000 0 0 21 21
PTPN11 0.029 0.003 -10000 0 0 8 8
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.052 0.02 -10000 0 -10000 0 0
GRB2 0.028 0.005 -10000 0 0 19 19
NGF (dimer)/TRKA/MATK 0.036 0.012 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.038 0.016 -10000 0 -0.16 1 1
ELMO1 0.028 0.007 -10000 0 0 31 31
RhoG/GTP/ELMO1/DOCK1 0.036 0.013 -10000 0 -0.13 1 1
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.028 0.006 -10000 0 0 26 26
DOCK1 0.028 0.005 -10000 0 0 18 18
GAB2 0.026 0.009 -10000 0 0 63 63
RIT2 0.028 0.006 -10000 0 0 28 28
RIT1 0.026 0.009 -10000 0 0 65 65
FRS2 0.028 0.007 -10000 0 0 30 30
DNM1 0.028 0.005 -10000 0 0 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.007 -10000 0 0 36 36
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.009 0.064 0.22 1 -0.18 11 12
mol:GDP 0.041 0.1 0.28 18 -0.4 10 28
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.021 0.005 -10000 0 -10000 0 0
RIT1/GDP 0.034 0.072 0.21 15 -0.24 10 25
TIAM1 0.028 0.005 -10000 0 0 20 20
PIK3R1 0.021 0.013 -10000 0 0 159 159
BDNF (dimer)/TRKB 0.053 0.019 -10000 0 -10000 0 0
KIDINS220/CRKL/C3G 0.04 0.012 -10000 0 -10000 0 0
SHC/RasGAP 0.038 0.02 -10000 0 -0.16 3 3
FRS2 family/SHP2 0.053 0.018 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.066 0.035 -10000 0 -0.14 2 2
RIT1/GTP 0.019 0.007 -10000 0 -10000 0 0
NT3 (dimer) 0.023 0.012 -10000 0 0 115 115
RAP1/GDP 0.031 0.063 0.16 14 -0.23 10 24
KIDINS220/CRKL 0.028 0.007 -10000 0 0 31 31
BDNF (dimer) 0.029 0.004 -10000 0 0 13 13
ubiquitin-dependent protein catabolic process 0.035 0.014 -10000 0 -0.13 1 1
Schwann cell development -0.01 0.013 -10000 0 -0.055 3 3
EHD4 0.027 0.007 -10000 0 0 39 39
FRS2 family/GRB2/SOS1 0.066 0.032 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.002 0.059 -10000 0 -0.25 16 16
RAP1B 0.028 0.006 -10000 0 0 22 22
RAP1A 0.029 0.003 -10000 0 0 7 7
CDC42/GTP -0.028 0.076 0.14 93 -10000 0 93
ABL1 0.028 0.006 -10000 0 0 21 21
SH2B family/GRB2/SOS1 0.039 0.013 -10000 0 -10000 0 0
Rap1/GTP 0.002 0.074 -10000 0 -0.27 17 17
STAT3 -0.052 0.14 -10000 0 -0.28 142 142
axon guidance -0.04 0.051 0.1 54 -10000 0 54
MAPK3 -0.028 0.034 0.18 15 -10000 0 15
MAPK1 -0.027 0.033 0.18 13 -10000 0 13
CDC42/GDP 0.043 0.08 0.21 27 -0.26 10 37
NTF3 0.023 0.012 -10000 0 0 115 115
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.036 0.015 -10000 0 -0.13 2 2
PI3K -0.001 0.068 -10000 0 -0.16 77 77
FRS3 0.028 0.006 -10000 0 0 27 27
FAIM 0.027 0.008 -10000 0 0 40 40
GAB1 0.028 0.006 -10000 0 0 24 24
RASGRF1 -0.014 0.057 0.18 2 -0.21 2 4
SOS1 0.027 0.007 -10000 0 0 36 36
MCF2L -0.012 0.062 0.16 58 -10000 0 58
RGS19 0.026 0.009 -10000 0 0 62 62
CDC42 0.029 0.004 -10000 0 0 11 11
RAS family/GTP 0.043 0.077 0.26 5 -0.36 5 10
Rac1/GDP 0.041 0.079 0.22 22 -0.26 10 32
NGF (dimer)/TRKA/GRIT 0.019 0.003 -10000 0 -10000 0 0
neuron projection morphogenesis -0.1 0.23 -10000 0 -0.86 36 36
NGF (dimer)/TRKA/NEDD4-2 0.035 0.014 -10000 0 -0.13 1 1
MAP2K1 -0.028 0.07 0.17 44 -10000 0 44
NGFR 0.028 0.005 -10000 0 0 17 17
NGF (dimer)/TRKA/GIPC/GAIP -0.008 0.052 -10000 0 -0.18 38 38
RAS family/GTP/PI3K 0.013 0.067 -10000 0 -0.18 32 32
FRS2 family/SHP2/GRB2/SOS1 0.075 0.037 -10000 0 -10000 0 0
NRAS 0.014 0.015 -10000 0 0 300 300
GRB2/SOS1 0.039 0.013 -10000 0 -10000 0 0
PRKCI 0.014 0.015 -10000 0 0 289 289
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.028 0.006 -10000 0 0 27 27
PRKCZ 0.028 0.006 -10000 0 0 23 23
MAPKKK cascade 0.014 0.041 -10000 0 -0.36 2 2
RASA1 0.027 0.008 -10000 0 0 49 49
TRKA/c-Abl 0.04 0.018 -10000 0 -0.16 3 3
SQSTM1 0.028 0.005 -10000 0 0 20 20
BDNF (dimer)/TRKB/GIPC 0.044 0.059 -10000 0 -0.14 32 32
NGF (dimer)/TRKA/p62/Atypical PKCs 0.064 0.05 -10000 0 -10000 0 0
MATK 0.027 0.008 -10000 0 0 44 44
NEDD4L 0.027 0.008 -10000 0 0 48 48
RAS family/GDP -0.012 0.032 -10000 0 -0.19 10 10
NGF (dimer)/TRKA -0.007 0.054 0.15 1 -0.18 10 11
Rac1/GTP -0.011 0.043 -10000 0 -0.19 6 6
FRS2 family/SHP2/CRK family 0.068 0.044 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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
NFATC2 0.025 0.01 -10000 0 0 77 77
GNB1/GNG2 0.042 0.08 0.2 4 -0.22 9 13
mol:DAG -0.009 0.076 0.18 23 -0.25 2 25
PLCG1 -0.009 0.077 0.18 23 -0.26 2 25
YES1 -0.008 0.066 0.2 16 -0.22 9 25
FZD3 0.022 0.013 -10000 0 0 141 141
FZD6 0.024 0.011 -10000 0 0 104 104
G protein 0.016 0.1 0.21 61 -0.26 2 63
MAP3K7 -0.024 0.068 0.23 7 -0.24 2 9
mol:Ca2+ -0.009 0.074 0.17 23 -0.25 2 25
mol:IP3 -0.009 0.076 0.18 23 -0.25 2 25
NLK -0.019 0.16 -10000 0 -0.79 23 23
GNB1 0.028 0.006 -10000 0 0 24 24
CAMK2A -0.017 0.072 0.21 12 -0.24 2 14
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD 0.007 0.064 0.2 3 -0.22 10 13
CSNK1A1 0.029 0.004 -10000 0 0 13 13
GNAS -0.012 0.058 0.18 4 -0.22 10 14
GO:0007205 -0.006 0.072 0.2 14 -0.25 2 16
WNT6 0.029 0.003 -10000 0 0 7 7
WNT4 0.029 0.004 -10000 0 0 11 11
NFAT1/CK1 alpha -0.007 0.092 0.23 21 -0.27 2 23
GNG2 0.029 0.004 -10000 0 0 12 12
WNT5A 0.028 0.005 -10000 0 0 17 17
WNT11 0.025 0.01 -10000 0 0 75 75
CDC42 -0.005 0.068 0.19 22 -0.23 3 25
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.028 0.006 -10000 0 0 21 21
Syndecan-3/Src/Cortactin 0.028 0.092 -10000 0 -0.41 15 15
Syndecan-3/Neurocan 0.008 0.083 -10000 0 -0.45 16 16
POMC 0.029 0.004 -10000 0 0 13 13
EGFR 0.026 0.009 -10000 0 0 55 55
Syndecan-3/EGFR 0.008 0.087 -10000 0 -0.47 16 16
AGRP 0.026 0.009 -10000 0 0 57 57
NCSTN 0.028 0.005 -10000 0 0 19 19
PSENEN 0.025 0.01 -10000 0 0 75 75
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.026 0.01 -10000 0 0 68 68
APH1A 0.028 0.007 -10000 0 0 31 31
NCAN 0.027 0.008 -10000 0 0 50 50
long-term memory 0.007 0.094 -10000 0 -0.44 16 16
Syndecan-3/IL8 0.007 0.084 -10000 0 -0.45 16 16
PSEN1 0.029 0.005 -10000 0 0 14 14
Src/Cortactin 0.039 0.013 -10000 0 -10000 0 0
FYN 0.024 0.011 -10000 0 0 99 99
limb bud formation -0.012 0.079 -10000 0 -0.46 16 16
MC4R 0 0 -10000 0 -10000 0 0
SRC 0.028 0.007 -10000 0 0 33 33
PTN 0.023 0.012 -10000 0 0 127 127
FGFR/FGF/Syndecan-3 -0.012 0.08 -10000 0 -0.47 16 16
neuron projection morphogenesis -0.005 0.11 0.26 6 -0.43 13 19
Syndecan-3/AgRP 0.01 0.083 -10000 0 -0.44 16 16
Syndecan-3/AgRP/MC4R 0.009 0.081 -10000 0 -0.43 16 16
Fyn/Cortactin 0.015 0.066 -10000 0 -0.16 65 65
SDC3 -0.012 0.08 -10000 0 -0.47 16 16
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.007 0.083 -10000 0 -0.44 16 16
IL8 0.024 0.011 -10000 0 0 95 95
Syndecan-3/Fyn/Cortactin 0.008 0.096 -10000 0 -0.45 16 16
Syndecan-3/CASK -0.012 0.076 -10000 0 -0.45 16 16
alpha-MSH/MC4R 0.021 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.043 0.077 -10000 0 -0.14 65 65
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.031 0.032 -10000 0 -0.16 11 11
CRKL -0.007 0.11 0.23 1 -0.45 22 23
mol:PIP3 0.015 0.063 -10000 0 -0.79 3 3
AKT1 -0.003 0.066 -10000 0 -0.71 3 3
PTK2B 0.024 0.011 -10000 0 0 101 101
RAPGEF1 -0.015 0.1 -10000 0 -0.44 20 20
RANBP10 0.026 0.009 -10000 0 0 59 59
PIK3CA 0.02 0.014 -10000 0 0 170 170
HGF/MET/SHIP2 0.045 0.035 -10000 0 -0.15 11 11
MAP3K5 -0.008 0.11 0.25 1 -0.45 21 22
HGF/MET/CIN85/CBL/ENDOPHILINS 0.068 0.047 -10000 0 -0.14 12 12
AP1 -0.021 0.071 0.12 56 -0.16 47 103
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.028 0.006 -10000 0 0 21 21
apoptosis -0.067 0.27 -10000 0 -0.71 80 80
STAT3 (dimer) -0.001 0.078 0.17 16 -0.25 19 35
GAB1/CRKL/SHP2/PI3K -0.009 0.11 -10000 0 -0.44 20 20
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.009 0.11 0.28 3 -0.44 20 23
PTPN11 0.029 0.003 -10000 0 0 8 8
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.028 0.007 -10000 0 0 33 33
PTEN 0.028 0.007 -10000 0 0 30 30
ELK1 0.033 0.15 0.36 62 -0.26 1 63
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.006 0.049 0.15 6 -0.2 9 15
PAK1 0.004 0.083 0.38 1 -0.68 3 4
HGF/MET/RANBP10 0.041 0.038 -10000 0 -0.15 12 12
HRAS 0.004 0.1 -10000 0 -0.47 22 22
DOCK1 -0.013 0.1 0.34 2 -0.44 21 23
GAB1 0.002 0.11 0.24 1 -0.46 22 23
CRK -0.003 0.11 0.28 3 -0.46 20 23
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.095 -10000 0 -0.39 25 25
JUN 0.028 0.007 -10000 0 0 32 32
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.001 0.033 0.092 3 -0.18 14 17
PIK3R1 0.021 0.013 -10000 0 0 159 159
cell morphogenesis 0 0.13 0.26 24 -0.37 16 40
GRB2/SHC 0.039 0.052 0.19 4 -0.18 13 17
FOS 0.024 0.011 -10000 0 0 105 105
GLMN 0.002 0.001 -10000 0 -10000 0 0
cell motility 0.032 0.15 0.36 62 -0.26 1 63
HGF/MET/MUC20 0.03 0.028 -10000 0 -0.13 12 12
cell migration 0.039 0.051 0.18 4 -0.18 13 17
GRB2 0.028 0.005 -10000 0 0 19 19
CBL 0.029 0.004 -10000 0 0 12 12
MET/RANBP10 0.029 0.034 -10000 0 -0.16 12 12
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.005 0.06 0.2 1 -0.27 8 9
MET/MUC20 0.015 0.025 -10000 0 -0.15 12 12
RAP1B -0.018 0.099 0.25 1 -0.43 19 20
RAP1A -0.023 0.097 0.36 1 -0.43 20 21
HGF/MET/RANBP9 0.044 0.036 -10000 0 -0.15 11 11
RAF1 -0.003 0.1 -10000 0 -0.45 22 22
STAT3 -0.003 0.077 0.17 11 -0.26 19 30
cell proliferation -0.007 0.095 0.27 10 -0.34 15 25
RPS6KB1 0.019 0.046 -10000 0 -0.24 7 7
MAPK3 0.025 0.16 0.63 29 -10000 0 29
MAPK1 0.04 0.19 0.66 40 -10000 0 40
RANBP9 0.027 0.007 -10000 0 0 39 39
MAPK8 -0.011 0.1 0.25 1 -0.43 18 19
SRC -0.021 0.054 0.18 1 -0.26 8 9
PI3K 0.007 0.066 0.21 1 -0.18 19 20
MET/Glomulin 0.027 0.034 0.097 70 -0.072 21 91
SOS1 0.027 0.007 -10000 0 0 36 36
MAP2K1 -0.011 0.094 -10000 0 -0.42 22 22
MET 0.025 0.011 -10000 0 0 86 86
MAP4K1 -0.001 0.11 0.27 1 -0.48 21 22
PTK2 0.021 0.013 -10000 0 0 163 163
MAP2K2 -0.021 0.097 0.27 1 -0.44 22 23
BAD -0.012 0.064 -10000 0 -0.68 3 3
MAP2K4 -0.015 0.099 -10000 0 -0.42 21 21
SHP2/GRB2/SOS1/GAB1 0.015 0.1 -10000 0 -0.38 25 25
INPPL1 0.028 0.006 -10000 0 0 21 21
PXN 0.029 0.005 -10000 0 0 14 14
SH3KBP1 0.028 0.005 -10000 0 0 18 18
HGS -0.01 0.042 0.092 47 -0.18 14 61
PLCgamma1/PKC 0.02 0.005 -10000 0 -10000 0 0
HGF 0.028 0.005 -10000 0 0 16 16
RASA1 0.027 0.008 -10000 0 0 49 49
NCK1 0.026 0.009 -10000 0 0 64 64
PTPRJ 0.029 0.003 -10000 0 0 8 8
NCK/PLCgamma1 0.038 0.05 0.2 3 -0.18 14 17
PDPK1 0.003 0.062 -10000 0 -0.74 3 3
HGF/MET/SHIP 0.03 0.028 -10000 0 -0.13 12 12
Caspase cascade in apoptosis

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
TOP1 0.009 0.11 0.28 4 -0.38 21 25
ACTA1 -0.006 0.081 0.22 11 -0.25 9 20
NUMA1 0.011 0.11 0.28 4 -0.37 23 27
SPTAN1 -0.007 0.078 0.24 7 -0.25 7 14
LIMK1 -0.005 0.081 0.24 11 -0.24 8 19
BIRC3 0.023 0.013 -10000 0 -0.001 125 125
BIRC2 0.02 0.014 -10000 0 -0.03 7 7
BAX 0.028 0.006 -10000 0 0 21 21
CASP10 -0.029 0.052 0.17 29 -0.15 5 34
CRMA 0 0 -10000 0 -0.001 1 1
XIAP 0 0 0.001 5 -0.001 40 45
PTK2 -0.002 0.11 0.28 4 -0.37 29 33
DIABLO 0.018 0.016 -10000 0 -0.002 206 206
apoptotic nuclear changes -0.007 0.078 0.24 7 -0.24 7 14
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.029 0.004 -10000 0 0 13 13
GSN -0.017 0.084 0.27 6 -0.25 12 18
MADD 0.029 0.003 -10000 0 0 8 8
TFAP2A 0.025 0.12 -10000 0 -0.8 9 9
BID -0.015 0.043 0.11 27 -0.14 41 68
MAP3K1 -0.02 0.12 -10000 0 -0.39 48 48
TRADD 0.026 0.009 -10000 0 0 65 65
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.041 0.011 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.005 0.1 0.25 38 -0.24 10 48
CASP9 0.026 0.013 -10000 0 -0.029 28 28
DNA repair -0.024 0.062 0.23 4 -0.18 18 22
neuron apoptosis -0.007 0.15 -10000 0 -0.71 22 22
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.002 0.098 0.26 6 -0.33 21 27
APAF1 0.024 0.015 -10000 0 -0.029 36 36
CASP6 -0.02 0.24 -10000 0 -0.89 36 36
TRAF2 0.028 0.006 -10000 0 0 25 25
ICAD/CAD -0.013 0.078 0.26 7 -0.25 7 14
CASP7 0.028 0.096 0.21 25 -0.26 18 43
KRT18 0.015 0.068 -10000 0 -0.66 3 3
apoptosis -0.015 0.14 0.29 10 -0.44 31 41
DFFA -0.005 0.078 0.26 6 -0.25 7 13
DFFB -0.005 0.079 0.23 8 -0.25 7 15
PARP1 0.024 0.062 0.18 18 -0.23 4 22
actin filament polymerization 0.013 0.079 0.24 7 -0.26 9 16
TNF 0.028 0.005 -10000 0 0 16 16
CYCS -0.009 0.053 0.17 5 -0.22 15 20
SATB1 -0.057 0.22 -10000 0 -0.87 36 36
SLK -0.007 0.079 0.26 7 -0.25 7 14
p15 BID/BAX -0.021 0.049 0.19 2 -0.2 4 6
CASP2 -0.029 0.086 0.18 15 -0.27 37 52
JNK cascade 0.02 0.12 0.38 48 -10000 0 48
CASP3 0.004 0.083 0.29 5 -0.25 8 13
LMNB2 -0.028 0.18 0.24 14 -0.49 56 70
RIPK1 0.027 0.007 -10000 0 0 38 38
CASP4 0.027 0.007 -10000 0 0 36 36
Mammalian IAPs/DIABLO 0.012 0.051 -10000 0 -0.13 46 46
negative regulation of DNA binding 0.026 0.12 -10000 0 -0.78 9 9
stress fiber formation -0.006 0.078 0.26 7 -0.24 7 14
GZMB -0.021 0.047 0.19 25 -10000 0 25
CASP1 -0.02 0.085 -10000 0 -0.26 55 55
LMNB1 0.012 0.14 0.25 16 -0.42 34 50
APP -0.007 0.16 -10000 0 -0.72 22 22
TNFRSF1A 0.025 0.01 -10000 0 0 77 77
response to stress 0 0 0.001 12 -0.001 8 20
CASP8 -0.017 0.002 0 7 -10000 0 7
VIM -0.006 0.14 0.28 12 -0.44 33 45
LMNA -0.004 0.12 0.25 11 -0.41 32 43
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.023 0.088 -10000 0 -0.27 41 41
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.007 0.077 0.26 5 -0.25 7 12
APAF-1/Caspase 9 -0.032 0.17 -10000 0 -0.54 15 15
nuclear fragmentation during apoptosis 0.011 0.1 0.28 4 -0.36 23 27
CFL2 -0.014 0.08 0.27 9 -0.24 7 16
GAS2 -0.003 0.085 0.28 13 -0.25 7 20
positive regulation of apoptosis -0.002 0.15 0.25 18 -0.45 40 58
PRF1 0.026 0.013 -10000 0 -0.029 23 23
E-cadherin 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
E-cadherin/beta catenin-gamma catenin 0.044 0.043 -9999 0 -0.16 19 19
E-cadherin/beta catenin 0.035 0.028 -9999 0 -0.16 8 8
CTNNB1 0.029 0.003 -9999 0 0 8 8
JUP 0.027 0.008 -9999 0 0 41 41
CDH1 0.026 0.01 -9999 0 0 72 72
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.021 0.026 0.18 8 -10000 0 8
RAS family/GTP 0.029 0.11 0.37 33 -0.26 1 34
NFATC4 -0.024 0.087 0.25 26 -10000 0 26
ERBB2IP 0.012 0.028 -10000 0 -0.052 3 3
HSP90 (dimer) 0.028 0.006 -10000 0 0 21 21
mammary gland morphogenesis -0.021 0.1 0.3 26 -10000 0 26
JUN 0.032 0.14 0.43 45 -10000 0 45
HRAS 0.023 0.02 0.064 4 -0.031 59 63
DOCK7 -0.023 0.089 0.26 19 -10000 0 19
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.016 0.077 0.18 28 -10000 0 28
AKT1 -0.015 0.009 0.013 33 -10000 0 33
BAD -0.025 0.007 -10000 0 -10000 0 0
MAPK10 -0.017 0.075 0.22 19 -10000 0 19
mol:GTP 0.001 0.004 0.018 18 -10000 0 18
ErbB2/ErbB3/neuregulin 1 beta -0.021 0.11 0.32 26 -10000 0 26
RAF1 0.092 0.17 0.41 77 -10000 0 77
ErbB2/ErbB3/neuregulin 2 -0.02 0.064 0.16 34 -10000 0 34
STAT3 -0.025 0.22 -10000 0 -0.87 36 36
cell migration -0.015 0.076 0.24 19 -10000 0 19
mol:PI-3-4-5-P3 -0.001 0.002 0.013 2 -10000 0 2
cell proliferation 0.067 0.25 0.68 48 -0.61 5 53
FOS 0.045 0.27 0.67 53 -0.42 53 106
NRAS 0.012 0.017 0.056 2 -0.031 21 23
mol:Ca2+ -0.021 0.1 0.3 26 -10000 0 26
MAPK3 0.071 0.23 0.66 42 -0.54 4 46
MAPK1 0.065 0.23 0.64 44 -0.61 6 50
JAK2 -0.025 0.087 0.26 18 -10000 0 18
NF2 -0.001 0.064 -10000 0 -0.64 5 5
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.001 0.06 0.18 10 -0.19 26 36
NRG1 -0.007 0.029 0.072 7 -10000 0 7
GRB2/SOS1 0.04 0.014 -10000 0 -10000 0 0
MAPK8 -0.019 0.1 0.34 10 -0.24 16 26
MAPK9 -0.017 0.076 0.2 27 -10000 0 27
ERBB2 -0.027 0.02 0.26 1 -10000 0 1
ERBB3 -0.007 0.03 0.072 7 -10000 0 7
SHC1 0.023 0.019 0.063 6 -0.03 56 62
RAC1 0.028 0.006 -10000 0 0 27 27
apoptosis 0.017 0.01 -10000 0 -10000 0 0
STAT3 (dimer) -0.024 0.22 -10000 0 -0.85 36 36
RNF41 -0.028 0.026 0.15 9 -10000 0 9
FRAP1 -0.012 0.005 0.003 43 -10000 0 43
RAC1-CDC42/GTP -0.037 0.058 0.17 2 -10000 0 2
ErbB2/ErbB2/HSP90 (dimer) -0.031 0.025 0.2 1 -0.15 2 3
CHRNA1 0.077 0.22 0.66 45 -0.43 1 46
myelination -0.018 0.098 0.27 31 -10000 0 31
PPP3CB -0.024 0.086 0.25 20 -10000 0 20
KRAS 0.02 0.02 0.06 5 -0.031 47 52
RAC1-CDC42/GDP 0.018 0.082 0.22 2 -0.19 24 26
NRG2 0.029 0.003 -10000 0 0 7 7
mol:GDP -0.001 0.06 0.18 10 -0.19 26 36
SOS1 0.022 0.019 0.061 2 -0.03 57 59
MAP2K2 0.062 0.17 0.46 51 -10000 0 51
SRC 0.028 0.007 -10000 0 0 33 33
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.027 0.086 0.24 18 -10000 0 18
MAP2K1 0.085 0.22 0.63 45 -0.6 5 50
heart morphogenesis -0.021 0.1 0.3 26 -10000 0 26
RAS family/GDP 0.047 0.09 0.31 20 -0.23 3 23
GRB2 0.023 0.019 0.059 3 -0.03 60 63
PRKACA 0.005 0.065 -10000 0 -0.67 5 5
CHRNE 0.011 0.057 0.18 35 -10000 0 35
HSP90AA1 0.028 0.006 -10000 0 0 21 21
activation of caspase activity 0.015 0.009 -10000 0 -0.013 33 33
nervous system development -0.021 0.1 0.3 26 -10000 0 26
CDC42 0.029 0.004 -10000 0 0 11 11
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF 0.006 0.078 0.38 3 -0.63 1 4
epithelial cell differentiation -0.022 0.066 0.24 1 -0.63 1 2
ITCH -0.008 0.04 0.12 6 -0.12 1 7
WWP1 -0.005 0.092 0.74 3 -1.1 1 4
FYN 0.024 0.011 -10000 0 0 99 99
EGFR 0.026 0.009 -10000 0 0 55 55
PRL 0.027 0.007 -10000 0 0 39 39
neuron projection morphogenesis -0.032 0.081 0.31 6 -0.51 1 7
PTPRZ1 0.028 0.006 -10000 0 0 26 26
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.027 0.084 0.32 2 -0.54 1 3
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.02 0.051 0.36 2 -0.57 1 3
ADAM17 -0.005 0.037 0.084 18 -0.12 1 19
ErbB4/ErbB4 -0.007 0.08 0.76 2 -0.68 1 3
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.029 0.093 0.41 1 -0.4 4 5
NCOR1 0.027 0.008 -10000 0 0 40 40
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.024 0.075 0.29 1 -0.56 1 2
GRIN2B -0.029 0.073 0.26 3 -0.54 1 4
ErbB4/ErbB2/betacellulin -0.009 0.073 0.35 3 -0.56 1 4
STAT1 0.013 0.015 -10000 0 0 315 315
HBEGF 0.029 0.004 -10000 0 0 11 11
PRLR 0.027 0.008 -10000 0 0 51 51
E4ICDs/ETO2 0.003 0.075 0.36 2 -0.63 1 3
axon guidance -0.001 0.061 0.42 2 -0.69 1 3
NEDD4 -0.01 0.04 0.087 15 -0.12 1 16
Prolactin receptor/Prolactin receptor/Prolactin 0.037 0.016 -10000 0 -10000 0 0
CBFA2T3 0.026 0.009 -10000 0 0 62 62
ErbB4/ErbB2/HBEGF -0.009 0.075 0.35 3 -0.56 1 4
MAPK3 -0.022 0.087 0.31 8 -0.52 1 9
STAT1 (dimer) -0.001 0.05 -10000 0 -0.47 1 1
MAPK1 -0.02 0.083 0.31 7 -0.52 1 8
JAK2 0.027 0.008 -10000 0 0 47 47
ErbB4/ErbB2/neuregulin 1 beta -0.026 0.05 0.31 2 -0.56 1 3
NRG1 0.005 0.073 0.18 78 -10000 0 78
NRG3 0.007 0.013 -10000 0 0 421 421
NRG2 0.029 0.003 -10000 0 0 7 7
NRG4 0.027 0.008 -10000 0 0 45 45
heart development -0.001 0.061 0.42 2 -0.69 1 3
neural crest cell migration -0.026 0.05 0.31 2 -0.55 1 3
ERBB2 0.007 0.078 0.18 88 -10000 0 88
WWOX/E4ICDs 0.003 0.074 0.36 2 -0.63 1 3
SHC1 0.028 0.006 -10000 0 0 21 21
ErbB4/EGFR/neuregulin 4 0.003 0.089 0.35 3 -0.61 1 4
apoptosis 0.18 0.17 0.38 89 -0.43 1 90
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.006 0.079 0.38 3 -0.63 1 4
ErbB4/ErbB2/epiregulin -0.008 0.074 0.35 3 -0.56 1 4
ErbB4/ErbB4/betacellulin/betacellulin 0.004 0.077 0.38 3 -0.63 1 4
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.029 0.088 0.38 1 -0.58 1 2
MDM2 -0.014 0.075 0.36 4 -0.63 1 5
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.008 0.064 0.32 2 -0.51 1 3
STAT5A -0.007 0.062 0.38 3 -0.68 1 4
ErbB4/EGFR/neuregulin 1 beta -0.019 0.074 0.32 2 -0.56 1 3
DLG4 0.028 0.006 -10000 0 0 22 22
GRB2/SHC 0.041 0.011 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.002 0.068 0.26 1 -0.6 1 2
STAT5A (dimer) 0.012 0.079 0.35 1 -0.69 1 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.013 0.071 0.38 3 -0.68 1 4
LRIG1 0.028 0.007 -10000 0 0 32 32
EREG 0.027 0.008 -10000 0 0 40 40
BTC 0.027 0.008 -10000 0 0 47 47
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.001 0.06 0.42 2 -0.7 1 3
ERBB4 -0.007 0.08 0.76 2 -0.69 1 3
STAT5B 0.028 0.007 -10000 0 0 32 32
YAP1 0.013 0.05 -10000 0 -0.48 4 4
GRB2 0.028 0.005 -10000 0 0 19 19
ErbB4/ErbB2/neuregulin 4 -0.01 0.077 0.35 3 -0.56 1 4
glial cell differentiation -0.002 0.068 0.59 1 -0.26 1 2
WWOX 0.026 0.009 -10000 0 0 64 64
cell proliferation -0.01 0.078 0.32 3 -0.57 1 4
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.02 0.03 0.16 2 -0.24 1 3
EPHB2 0.028 0.006 -10000 0 0 21 21
Syndecan-2/TACI -0.025 0.024 0.16 3 -10000 0 3
LAMA1 0.024 0.012 -10000 0 0 110 110
Syndecan-2/alpha2 ITGB1 0.023 0.064 0.17 4 -0.14 57 61
HRAS 0.028 0.006 -10000 0 0 26 26
Syndecan-2/CASK -0.015 0.017 -10000 0 -0.12 13 13
ITGA5 0.028 0.005 -10000 0 0 19 19
BAX -0.027 0.027 -10000 0 -10000 0 0
EPB41 0.027 0.007 -10000 0 0 36 36
positive regulation of cell-cell adhesion -0.023 0.018 -10000 0 -0.12 14 14
LAMA3 0.025 0.01 -10000 0 0 74 74
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.027 0.008 -10000 0 0 44 44
Syndecan-2/MMP2 -0.033 0.045 0.16 4 -0.24 6 10
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.033 0.037 -10000 0 -0.16 17 17
dendrite morphogenesis -0.025 0.025 0.16 4 -10000 0 4
Syndecan-2/GM-CSF -0.025 0.024 0.16 4 -10000 0 4
determination of left/right symmetry -0.015 0.006 -10000 0 -10000 0 0
Syndecan-2/PKC delta -0.026 0.025 0.16 4 -10000 0 4
GNB2L1 0.029 0.005 -10000 0 0 15 15
MAPK3 -0.014 0.068 0.18 57 -0.22 3 60
MAPK1 -0.013 0.066 0.18 56 -10000 0 56
Syndecan-2/RACK1 0.027 0.032 0.15 4 -0.12 13 17
NF1 0.026 0.009 -10000 0 0 60 60
FGFR/FGF/Syndecan-2 -0.015 0.006 -10000 0 -10000 0 0
ITGA2 0.026 0.009 -10000 0 0 60 60
MAPK8 -0.022 0.024 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.027 0.048 0.17 2 -0.14 26 28
Syndecan-2/Kininogen -0.022 0.025 0.16 3 -10000 0 3
ITGB1 0.028 0.006 -10000 0 0 21 21
SRC -0.018 0.069 0.17 60 -10000 0 60
Syndecan-2/CASK/Protein 4.1 -0.022 0.017 -10000 0 -0.12 11 11
extracellular matrix organization -0.038 0.047 0.16 4 -0.24 5 9
actin cytoskeleton reorganization -0.02 0.03 0.16 2 -0.24 1 3
Syndecan-2/Caveolin-2/Ras 0.025 0.041 0.16 4 -0.14 26 30
Syndecan-2/Laminin alpha3 -0.031 0.037 0.16 4 -0.24 1 5
Syndecan-2/RasGAP 0.033 0.041 0.16 4 -0.13 15 19
alpha5/beta1 Integrin 0.041 0.011 -10000 0 -10000 0 0
PRKCD 0.029 0.005 -10000 0 0 15 15
Syndecan-2 dimer -0.025 0.025 0.16 4 -10000 0 4
GO:0007205 -0.001 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.039 0.032 0.15 6 -10000 0 6
RHOA 0.029 0.003 -10000 0 0 6 6
SDCBP 0.028 0.007 -10000 0 0 34 34
TNFRSF13B 0.027 0.007 -10000 0 0 37 37
RASA1 0.027 0.008 -10000 0 0 49 49
alpha2/beta1 Integrin 0.033 0.037 -10000 0 -0.16 17 17
Syndecan-2/Synbindin -0.024 0.024 0.16 3 -10000 0 3
TGFB1 0.023 0.012 -10000 0 0 112 112
CASP3 -0.014 0.064 0.18 52 -10000 0 52
FN1 0.018 0.014 -10000 0 0 213 213
Syndecan-2/IL8 -0.021 0.026 0.16 4 -10000 0 4
SDC2 -0.016 0.006 -10000 0 -10000 0 0
KNG1 0.025 0.011 -10000 0 0 90 90
Syndecan-2/Neurofibromin -0.025 0.026 0.16 2 -10000 0 2
TRAPPC4 0.027 0.008 -10000 0 0 49 49
CSF2 0.028 0.005 -10000 0 0 18 18
Syndecan-2/TGFB1 -0.038 0.047 0.16 4 -0.24 5 9
Syndecan-2/Syntenin/PI-4-5-P2 -0.023 0.018 -10000 0 -0.12 14 14
Syndecan-2/Ezrin -0.024 0.017 -10000 0 -0.12 14 14
PRKACA -0.013 0.061 0.18 45 -10000 0 45
angiogenesis -0.021 0.025 0.16 4 -10000 0 4
MMP2 0.022 0.013 -10000 0 0 134 134
IL8 0.024 0.011 -10000 0 0 95 95
calcineurin-NFAT signaling pathway -0.025 0.024 0.16 3 -10000 0 3
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.04 0.048 -10000 0 -0.15 26 26
fibroblast growth factor receptor signaling pathway 0.039 0.047 -10000 0 -0.15 26 26
LAMA1 0.024 0.012 -10000 0 0 110 110
PRNP 0.027 0.008 -10000 0 0 44 44
GPC1/SLIT2 0.021 0.058 -10000 0 -0.16 48 48
SMAD2 -0.042 0.028 0.17 7 -10000 0 7
GPC1/PrPc/Cu2+ 0.033 0.024 -10000 0 -0.13 9 9
GPC1/Laminin alpha1 0.034 0.018 -10000 0 -10000 0 0
TDGF1 0.029 0.003 -10000 0 0 6 6
CRIPTO/GPC1 0.042 0.008 -10000 0 -10000 0 0
APP/GPC1 0.038 0.025 -10000 0 -0.16 7 7
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.036 0.013 -10000 0 -10000 0 0
FLT1 0.028 0.006 -10000 0 0 28 28
GPC1/TGFB/TGFBR1/TGFBR2 0.053 0.027 -10000 0 -0.14 7 7
SERPINC1 0.029 0.005 -10000 0 0 14 14
FYN -0.032 0.016 -10000 0 -10000 0 0
FGR -0.038 0.009 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.027 0.075 0.24 6 -0.27 12 18
SLIT2 0.025 0.011 -10000 0 0 89 89
GPC1/NRG 0.036 0.016 -10000 0 -10000 0 0
NRG1 0.025 0.01 -10000 0 0 80 80
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.049 0.023 -10000 0 -10000 0 0
LYN -0.035 0.013 -10000 0 -10000 0 0
mol:Spermine -0.017 0.003 -10000 0 -10000 0 0
cell growth 0.039 0.047 -10000 0 -0.15 26 26
BMP signaling pathway -0.028 0.005 0 17 -10000 0 17
SRC -0.036 0.012 -10000 0 -10000 0 0
TGFBR1 0.028 0.005 -10000 0 0 17 17
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.016 0.015 -10000 0 0 248 248
GPC1 0.028 0.005 -10000 0 0 17 17
TGFBR1 (dimer) 0.028 0.005 -10000 0 0 17 17
VEGFA 0.026 0.01 -10000 0 0 70 70
BLK -0.032 0.016 -10000 0 -10000 0 0
HCK -0.035 0.013 -10000 0 -10000 0 0
FGF2 0.027 0.008 -10000 0 0 43 43
FGFR1 0.025 0.01 -10000 0 0 77 77
VEGFR1 homodimer 0.028 0.006 -10000 0 0 28 28
TGFBR2 0.029 0.005 -10000 0 0 15 15
cell death 0.038 0.025 -10000 0 -0.16 7 7
ATIII/GPC1 0.041 0.01 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.043 0.1 -10000 0 -0.16 227 227
LCK -0.037 0.011 -10000 0 -10000 0 0
neuron differentiation 0.036 0.016 -10000 0 -10000 0 0
PrPc/Cu2+ 0.018 0.022 -10000 0 -0.15 9 9
APP 0.028 0.006 -10000 0 0 28 28
TGFBR2 (dimer) 0.028 0.005 -10000 0 0 15 15
ceramide 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
MAP4K4 -0.05 0.13 0.24 2 -0.39 43 45
BAG4 0.026 0.009 -10000 0 0 62 62
BAD -0.029 0.044 0.18 1 -0.16 25 26
NFKBIA 0.028 0.006 -10000 0 0 27 27
BIRC3 0.023 0.012 -10000 0 -0.029 2 2
BAX -0.027 0.046 0.17 4 -0.16 24 28
EnzymeConsortium:3.1.4.12 -0.012 0.03 0.068 1 -0.09 41 42
IKBKB -0.049 0.13 0.26 5 -0.41 35 40
MAP2K2 -0.047 0.051 0.16 4 -0.2 13 17
MAP2K1 -0.04 0.046 0.14 5 -0.19 8 13
SMPD1 -0.017 0.037 -10000 0 -0.13 28 28
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.044 0.13 0.22 5 -0.42 33 38
MAP2K4 -0.034 0.041 -10000 0 -0.18 14 14
protein ubiquitination -0.051 0.12 0.27 2 -0.4 37 39
EnzymeConsortium:2.7.1.37 -0.051 0.049 0.16 1 -0.2 10 11
response to UV 0 0 -10000 0 -0.002 4 4
RAF1 -0.035 0.046 0.15 6 -0.18 13 19
CRADD 0.02 0.02 -10000 0 -0.029 77 77
mol:ceramide -0.021 0.045 -10000 0 -0.15 34 34
I-kappa-B-alpha/RELA/p50/ubiquitin 0.034 0.027 -10000 0 -0.13 13 13
MADD 0.02 0.021 -10000 0 -0.029 81 81
MAP3K1 -0.028 0.043 -10000 0 -0.16 25 25
TRADD 0.019 0.02 -10000 0 -0.029 66 66
RELA/p50 0.029 0.003 -10000 0 0 6 6
MAPK3 -0.046 0.052 0.17 1 -0.21 14 15
MAPK1 -0.049 0.056 0.17 1 -0.22 22 23
p50/RELA/I-kappa-B-alpha 0.037 0.032 -10000 0 -0.16 13 13
FADD -0.048 0.13 0.23 5 -0.39 43 48
KSR1 -0.028 0.046 0.15 4 -0.16 23 27
MAPK8 -0.042 0.041 0.19 2 -0.19 6 8
TRAF2 0.027 0.011 -10000 0 -0.029 15 15
response to radiation 0 0 -10000 0 -10000 0 0
CHUK -0.052 0.12 0.23 2 -0.41 34 36
TNF R/SODD 0.029 0.036 -10000 0 -0.16 15 15
TNF 0.02 0.02 -10000 0 -0.029 78 78
CYCS -0.015 0.054 0.14 5 -0.17 12 17
IKBKG -0.052 0.12 0.23 7 -0.4 33 40
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.04 0.13 -10000 0 -0.4 43 43
RELA 0.029 0.003 -10000 0 0 6 6
RIPK1 0.026 0.011 -10000 0 -0.029 13 13
AIFM1 -0.011 0.055 0.14 11 -0.17 10 21
TNF/TNF R/SODD 0.041 0.039 -10000 0 -0.14 15 15
TNFRSF1A 0.024 0.013 -10000 0 -0.029 13 13
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.017 0.057 -10000 0 -0.62 3 3
NSMAF -0.044 0.13 0.23 7 -0.39 39 46
response to hydrogen peroxide 0 0 -10000 0 -0.002 4 4
BCL2 0.023 0.012 -10000 0 0 123 123
HIF-1-alpha transcription factor network

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
PKM2 0.33 0.46 0.91 3 -0.92 3 6
HDAC7 -0.004 0.005 -10000 0 -0.078 1 1
HIF1A/ARNT/Cbp/p300/Src-1 0.023 0.29 0.73 38 -0.72 3 41
SMAD4 -0.028 0.008 -10000 0 -10000 0 0
ID2 0.33 0.46 -10000 0 -0.92 3 3
AP1 0.02 0.072 0.24 11 -0.17 60 71
ABCG2 0.28 0.46 0.89 12 -0.92 3 15
HIF1A 0.12 0.15 0.34 57 -10000 0 57
TFF3 0.029 0.37 -10000 0 -1 3 3
GATA2 0.031 0.029 0.21 12 -0.067 1 13
AKT1 0.15 0.18 0.41 92 -10000 0 92
response to hypoxia 0.082 0.16 0.34 117 -10000 0 117
MCL1 0.31 0.46 -10000 0 -0.92 3 3
NDRG1 0.2 0.42 0.91 2 -1 2 4
SERPINE1 0.24 0.44 0.91 3 -0.92 3 6
FECH 0.32 0.46 -10000 0 -0.92 3 3
FURIN 0.32 0.46 0.91 3 -0.92 3 6
NCOA2 0.027 0.008 -10000 0 -10000 0 0
EP300 0.23 0.3 0.71 100 -0.4 2 102
HMOX1 0.31 0.46 0.9 6 -0.92 3 9
BHLHE40 0.099 0.39 0.81 75 -0.91 3 78
BHLHE41 0.099 0.39 0.81 75 -0.91 3 78
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.14 0.19 0.41 81 -10000 0 81
ENG 0.12 0.18 0.47 2 -10000 0 2
JUN 0.03 0.017 0.13 11 -0.047 1 12
RORA 0.33 0.46 -10000 0 -0.92 3 3
ABCB1 -0.009 0.065 0.64 1 -10000 0 1
TFRC 0.12 0.39 0.9 3 -0.92 3 6
CXCR4 0.33 0.46 -10000 0 -0.92 3 3
TF 0.32 0.45 0.91 3 -0.92 3 6
CITED2 0.31 0.46 0.91 3 -0.98 3 6
HIF1A/ARNT -0.043 0.26 0.84 12 -1 3 15
LDHA 0.016 0.14 0.64 21 -0.71 3 24
ETS1 0.31 0.46 -10000 0 -0.92 3 3
PGK1 0.13 0.39 -10000 0 -0.92 3 3
NOS2 0.099 0.39 0.81 75 -0.91 3 78
ITGB2 0.32 0.46 0.91 3 -0.92 3 6
ALDOA 0.33 0.46 -10000 0 -0.92 3 3
Cbp/p300/CITED2 0.23 0.45 0.9 72 -0.98 3 75
FOS 0.026 0.021 0.14 13 -0.029 1 14
HK2 0.34 0.46 0.91 3 -0.92 3 6
SP1 -0.03 0.022 0.22 4 -10000 0 4
GCK 0.29 0.34 0.88 69 -10000 0 69
HK1 0.33 0.46 0.91 3 -0.92 3 6
NPM1 0.33 0.46 -10000 0 -0.92 3 3
EGLN1 0.32 0.45 0.9 4 -0.92 3 7
CREB1 0.083 0.1 0.27 126 -10000 0 126
PGM1 0.28 0.45 0.91 3 -0.92 3 6
SMAD3 -0.03 0.005 -10000 0 -10000 0 0
EDN1 0.19 0.26 0.8 33 -1.1 1 34
IGFBP1 0.33 0.46 0.89 13 -0.92 3 16
VEGFA 0.26 0.4 0.84 79 -0.67 1 80
HIF1A/JAB1 0.07 0.1 0.27 12 -10000 0 12
CP 0.061 0.35 0.96 1 -1 3 4
CXCL12 0.28 0.46 0.9 9 -0.95 3 12
COPS5 0.019 0.019 -10000 0 -0.029 56 56
SMAD3/SMAD4 0.037 0.017 -10000 0 -0.13 2 2
BNIP3 0.29 0.45 0.91 2 -0.92 3 5
EGLN3 0.28 0.45 0.91 1 -0.95 3 4
CA9 0.26 0.44 -10000 0 -0.92 3 3
TERT 0.28 0.45 0.9 3 -0.92 3 6
ENO1 0.33 0.46 0.91 3 -0.92 3 6
PFKL 0.32 0.46 -10000 0 -0.92 3 3
NCOA1 0.019 0.022 -10000 0 -0.029 92 92
ADM 0.26 0.44 0.96 1 -0.92 3 4
ARNT 0.12 0.15 0.34 61 -10000 0 61
HNF4A 0.027 0.007 -10000 0 -10000 0 0
ADFP 0.099 0.39 0.81 75 -0.91 3 78
SLC2A1 0.25 0.4 0.83 76 -0.67 1 77
LEP 0.32 0.45 -10000 0 -0.92 3 3
HIF1A/ARNT/Cbp/p300 0.013 0.29 0.76 34 -0.73 3 37
EPO 0.26 0.36 0.79 47 -0.71 2 49
CREBBP 0.24 0.29 0.72 99 -10000 0 99
HIF1A/ARNT/Cbp/p300/HDAC7 -0.005 0.25 0.68 31 -0.7 4 35
PFKFB3 0.3 0.46 0.91 3 -0.97 3 6
NT5E 0.24 0.45 0.91 2 -1 3 5
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.031 0.11 0.22 3 -0.38 27 30
IKBKB 0.006 0.079 0.26 7 -0.31 7 14
AKT1 -0.001 0.099 0.27 34 -0.23 4 38
IKBKG 0.004 0.064 0.25 2 -0.27 6 8
CALM1 -0.01 0.063 0.18 3 -0.27 11 14
PIK3CA 0.02 0.014 -10000 0 0 170 170
MAP3K1 -0.027 0.14 0.26 3 -0.47 32 35
MAP3K7 0.028 0.007 -10000 0 0 30 30
mol:Ca2+ -0.004 0.069 0.2 1 -0.27 15 16
DOK1 0.029 0.004 -10000 0 0 10 10
AP-1 -0.022 0.073 0.22 4 -0.22 21 25
LYN 0.027 0.009 -10000 0 -0.001 51 51
BLNK 0.028 0.007 -10000 0 0 30 30
SHC1 0.028 0.006 -10000 0 0 21 21
BCR complex 0.04 0.012 -10000 0 -10000 0 0
CD22 -0.038 0.08 0.23 2 -0.3 22 24
CAMK2G -0.019 0.068 -10000 0 -0.27 12 12
CSNK2A1 0.027 0.008 -10000 0 0 41 41
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.063 0.037 -10000 0 -0.23 2 2
GO:0007205 -0.004 0.07 0.2 1 -0.28 14 15
SYK 0.028 0.006 -10000 0 -0.001 25 25
ELK1 -0.008 0.076 0.21 14 -0.27 14 28
NFATC1 -0.029 0.091 0.21 8 -0.34 19 27
B-cell antigen/BCR complex 0.04 0.012 -10000 0 -10000 0 0
PAG1/CSK 0.039 0.013 -10000 0 -10000 0 0
NFKBIB 0.009 0.048 0.14 2 -0.13 24 26
HRAS -0.016 0.069 0.2 1 -0.29 13 14
NFKBIA 0.01 0.046 0.14 2 -0.13 20 22
NF-kappa-B/RelA/I kappa B beta 0.013 0.042 0.14 2 -0.11 11 13
RasGAP/Csk 0.068 0.052 -10000 0 -0.14 4 4
mol:GDP -0.004 0.069 0.19 1 -0.27 14 15
PTEN 0.028 0.007 -10000 0 0 30 30
CD79B 0.028 0.006 -10000 0 -0.004 15 15
NF-kappa-B/RelA/I kappa B alpha 0.013 0.042 0.14 2 -0.11 8 10
GRB2 0.028 0.005 -10000 0 0 19 19
PI3K/BCAP/CD19 -0.07 0.15 0.3 1 -0.42 33 34
PIK3R1 0.021 0.013 -10000 0 0 159 159
mol:IP3 -0.004 0.07 0.2 1 -0.27 15 16
CSK 0.028 0.006 -10000 0 0 21 21
FOS -0.016 0.083 0.23 7 -0.27 17 24
CHUK 0.001 0.081 0.23 3 -0.3 19 22
IBTK 0.028 0.007 -10000 0 0 30 30
CARD11/BCL10/MALT1/TAK1 0.01 0.082 0.21 1 -0.28 8 9
PTPN6 -0.037 0.083 0.2 3 -0.3 21 24
RELA 0.029 0.003 -10000 0 0 6 6
BCL2A1 0.007 0.031 0.1 4 -0.097 5 9
VAV2 -0.019 0.096 0.25 3 -0.34 25 28
ubiquitin-dependent protein catabolic process 0.009 0.047 0.14 2 -0.12 46 48
BTK 0.018 0.044 -10000 0 -0.98 1 1
CD19 -0.015 0.078 0.23 2 -0.3 18 20
MAP4K1 0.026 0.01 -10000 0 0 70 70
CD72 0.029 0.005 -10000 0 0 14 14
PAG1 0.027 0.008 -10000 0 0 42 42
MAPK14 -0.026 0.13 0.26 7 -0.4 32 39
SH3BP5 0.029 0.004 -10000 0 0 12 12
PIK3AP1 -0.008 0.07 0.25 3 -0.29 11 14
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.002 0.088 -10000 0 -0.32 28 28
RAF1 -0.024 0.067 0.24 2 -0.28 13 15
RasGAP/p62DOK/SHIP 0.056 0.046 -10000 0 -0.14 6 6
CD79A 0.027 0.007 -10000 0 0 37 37
re-entry into mitotic cell cycle -0.022 0.072 0.22 4 -0.22 20 24
RASA1 0.027 0.008 -10000 0 0 49 49
MAPK3 -0.038 0.061 0.25 3 -0.26 12 15
MAPK1 -0.032 0.065 0.25 4 -0.26 12 16
CD72/SHP1 -0.022 0.11 0.26 26 -0.3 20 46
NFKB1 0.027 0.008 -10000 0 0 46 46
MAPK8 -0.029 0.12 0.24 4 -0.41 30 34
actin cytoskeleton organization -0.022 0.094 0.26 7 -0.32 25 32
NF-kappa-B/RelA 0.021 0.087 0.26 2 -0.25 11 13
Calcineurin 0.008 0.082 -10000 0 -0.26 12 12
PI3K -0.054 0.08 -10000 0 -0.29 18 18
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.001 0.064 0.22 1 -0.26 16 17
SOS1 0.027 0.007 -10000 0 0 36 36
Bam32/HPK1 -0.019 0.21 -10000 0 -0.68 41 41
DAPP1 -0.035 0.23 -10000 0 -0.77 41 41
cytokine secretion -0.027 0.086 0.21 8 -0.32 19 27
mol:DAG -0.004 0.07 0.2 1 -0.27 15 16
PLCG2 0.026 0.009 -10000 0 0 62 62
MAP2K1 -0.03 0.065 0.25 2 -0.28 13 15
B-cell antigen/BCR complex/FcgammaRIIB 0.05 0.023 -10000 0 -0.15 1 1
mol:PI-3-4-5-P3 -0.012 0.11 0.25 34 -0.27 6 40
ETS1 -0.021 0.072 0.21 4 -0.27 10 14
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.061 0.061 -10000 0 -0.15 25 25
B-cell antigen/BCR complex/LYN 0.005 0.081 0.21 1 -0.31 19 20
MALT1 0.025 0.01 -10000 0 0 76 76
TRAF6 0.028 0.006 -10000 0 -0.029 4 4
RAC1 -0.024 0.093 0.24 5 -0.33 23 28
B-cell antigen/BCR complex/LYN/SYK -0.006 0.12 0.32 5 -0.3 13 18
CARD11 -0.013 0.069 0.19 2 -0.28 13 15
FCGR2B 0.027 0.008 -10000 0 0 47 47
PPP3CA 0.027 0.008 -10000 0 0 44 44
BCL10 0.029 0.004 -10000 0 0 10 10
IKK complex 0.011 0.045 0.16 17 -0.13 2 19
PTPRC 0.024 0.011 -10000 0 0 103 103
PDPK1 -0.008 0.094 0.23 40 -0.19 6 46
PPP3CB 0.029 0.004 -10000 0 0 12 12
PPP3CC 0.024 0.011 -10000 0 0 103 103
POU2F2 0.006 0.03 0.15 3 -0.12 2 5
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.027 0.094 0.18 1 -0.28 22 23
adherens junction organization -0.03 0.097 -10000 0 -0.36 26 26
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.029 0.1 0.22 6 -0.26 9 15
FMN1 -0.032 0.091 -10000 0 -0.32 30 30
mol:IP3 -0.031 0.07 0.12 44 -0.21 20 64
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.022 0.097 0.15 1 -0.28 44 45
CTNNB1 0 0.031 0.054 1 -10000 0 1
AKT1 -0.035 0.076 0.19 2 -0.23 29 31
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.021 0.1 -10000 0 -0.32 28 28
CTNND1 -0.008 0.031 0.044 8 -10000 0 8
mol:PI-4-5-P2 -0.028 0.089 0.2 3 -0.29 32 35
VASP -0.032 0.091 -10000 0 -0.31 32 32
ZYX -0.039 0.095 -10000 0 -0.31 39 39
JUB -0.023 0.092 0.14 1 -0.27 44 45
EGFR(dimer) -0.013 0.1 -10000 0 -0.3 37 37
E-cadherin/beta catenin-gamma catenin 0.044 0.041 -10000 0 -0.14 19 19
mol:PI-3-4-5-P3 -0.018 0.08 0.2 1 -0.23 33 34
PIK3CA -0.017 0.02 -10000 0 -10000 0 0
PI3K -0.018 0.081 0.21 1 -0.23 33 34
FYN -0.049 0.12 0.16 3 -0.28 80 83
mol:Ca2+ -0.031 0.069 0.12 44 -0.21 20 64
JUP -0.002 0.03 0.048 1 -10000 0 1
PIK3R1 -0.003 0.027 -10000 0 -10000 0 0
mol:DAG -0.031 0.07 0.12 44 -0.21 20 64
CDH1 -0.004 0.029 -10000 0 -10000 0 0
RhoA/GDP -0.028 0.1 0.22 6 -0.27 9 15
establishment of polarity of embryonic epithelium -0.031 0.089 -10000 0 -0.31 31 31
SRC 0.028 0.007 -10000 0 0 33 33
RAC1 0.028 0.006 -10000 0 0 27 27
RHOA 0.029 0.003 -10000 0 0 6 6
EGFR 0.026 0.009 -10000 0 0 55 55
CASR -0.025 0.083 0.18 2 -0.23 12 14
RhoA/GTP -0.022 0.086 0.18 2 -0.23 11 13
AKT2 -0.036 0.078 0.19 2 -0.23 31 33
actin cable formation -0.038 0.089 0.22 2 -0.35 21 23
apoptosis 0.021 0.095 0.26 24 -0.2 5 29
CTNNA1 -0.009 0.031 0.044 8 -10000 0 8
mol:GDP -0.031 0.089 0.18 2 -0.24 16 18
PIP5K1A -0.029 0.091 0.21 3 -0.3 32 35
PLCG1 -0.032 0.071 0.12 44 -0.21 20 64
Rac1/GTP -0.012 0.11 -10000 0 -0.31 30 30
homophilic cell adhesion 0 0.005 -10000 0 -10000 0 0
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 0.028 0.005 -10000 0 0 20 20
VLDLR 0.026 0.009 -10000 0 0 61 61
LRPAP1 0.028 0.007 -10000 0 0 33 33
NUDC 0.028 0.005 -10000 0 0 17 17
RELN/LRP8 0.018 0.075 -10000 0 -0.15 88 88
CaM/Ca2+ 0.018 0.022 -10000 0 -0.15 9 9
KATNA1 0.028 0.007 -10000 0 0 33 33
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.042 0.071 0.16 47 -0.23 1 48
IQGAP1/CaM 0.037 0.03 -10000 0 -0.16 11 11
DAB1 0.029 0.004 -10000 0 0 12 12
IQGAP1 0.028 0.006 -10000 0 0 24 24
PLA2G7 0.025 0.01 -10000 0 0 83 83
CALM1 0.028 0.006 -10000 0 0 26 26
DYNLT1 0.025 0.01 -10000 0 0 82 82
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.039 0.017 -10000 0 -0.16 2 2
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.029 0.003 -10000 0 0 7 7
CDK5R1 0.027 0.007 -10000 0 0 36 36
LIS1/Poliovirus Protein 3A -0.023 0.009 -10000 0 -10000 0 0
CDK5R2 0.029 0.003 -10000 0 0 7 7
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.014 0.077 -10000 0 -0.15 98 98
YWHAE 0.027 0.008 -10000 0 0 40 40
NDEL1/14-3-3 E -0.034 0.1 0.29 16 -0.25 1 17
MAP1B -0.012 0.052 0.13 1 -0.19 43 44
RAC1 -0.014 0.04 -10000 0 -0.26 14 14
p35/CDK5 -0.037 0.085 0.21 21 -0.22 1 22
RELN 0.022 0.012 -10000 0 0 130 130
PAFAH/LIS1 -0.031 0.017 -10000 0 -10000 0 0
LIS1/CLIP170 -0.036 0.012 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.059 0.086 0.18 9 -0.25 2 11
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.024 0.09 0.2 1 -0.26 26 27
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.029 0.086 0.25 14 -0.21 4 18
LIS1/IQGAP1 -0.036 0.014 -10000 0 -0.15 2 2
RHOA -0.009 0.019 -10000 0 -0.29 2 2
PAFAH1B1 -0.03 0.011 -10000 0 -10000 0 0
PAFAH1B3 0.027 0.008 -10000 0 0 47 47
PAFAH1B2 0.028 0.005 -10000 0 0 18 18
MAP1B/LIS1/Dynein heavy chain -0.041 0.043 -10000 0 -0.22 4 4
NDEL1/Katanin 60/Dynein heavy chain -0.039 0.1 0.27 16 -0.25 1 17
LRP8 0.028 0.005 -10000 0 0 19 19
NDEL1/Katanin 60 -0.035 0.098 0.27 15 -0.25 1 16
P39/CDK5 -0.038 0.086 0.2 23 -0.22 1 24
LIS1/NudC/Dynein intermediate chain/microtubule organizing center -0.035 0.013 -10000 0 -10000 0 0
CDK5 -0.036 0.077 0.18 16 -0.23 1 17
PPP2R5D 0.028 0.006 -10000 0 0 26 26
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.03 0.009 -10000 0 -10000 0 0
CSNK2A1 0.027 0.008 -10000 0 0 41 41
RELN/VLDLR/DAB1/LIS1 0.02 0.079 -10000 0 -0.14 85 85
RELN/VLDLR 0.027 0.085 -10000 0 -0.14 93 93
CDC42 -0.009 0.02 -10000 0 -0.26 3 3
Cellular roles of Anthrax toxin

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
ANTXR1 0.028 0.006 -10000 0 0 25 25
ANTXR2 0.027 0.008 -10000 0 0 41 41
negative regulation of myeloid dendritic cell antigen processing and presentation -0.007 0.007 -10000 0 -0.036 24 24
monocyte activation -0.022 0.14 0.19 1 -0.35 76 77
MAP2K2 -0.13 0.27 -10000 0 -0.63 123 123
MAP2K1 -0.016 0.01 0.15 1 -10000 0 1
MAP2K7 -0.016 0.007 -10000 0 -0.062 2 2
MAP2K6 0.005 0.057 0.15 70 -0.062 2 72
CYAA -0.025 0.02 -10000 0 -0.12 24 24
MAP2K4 -0.015 0.008 -10000 0 -10000 0 0
IL1B -0.01 0.052 0.15 42 -0.12 2 44
Channel 0.027 0.035 -10000 0 -0.12 24 24
NLRP1 -0.016 0.009 0.12 1 -0.062 2 3
CALM1 0.028 0.006 -10000 0 0 26 26
negative regulation of phagocytosis -0.009 0.079 -10000 0 -0.44 18 18
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.007 0.007 0.036 24 -10000 0 24
MAPK3 -0.016 0.007 -10000 0 -0.062 2 2
MAPK1 -0.015 0.007 -10000 0 -0.062 2 2
PGR -0.006 0.027 -10000 0 -0.13 23 23
PA/Cellular Receptors 0.029 0.038 -10000 0 -0.14 24 24
apoptosis -0.007 0.007 -10000 0 -0.036 24 24
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.026 0.035 -10000 0 -0.12 24 24
macrophage activation -0.025 0.015 -10000 0 -0.11 11 11
TNF 0.028 0.005 -10000 0 0 16 16
VCAM1 -0.023 0.14 -10000 0 -0.36 76 76
platelet activation -0.009 0.079 -10000 0 -0.44 18 18
MAPKKK cascade 0.017 0.035 0.095 5 -0.1 10 15
IL18 0.008 0.07 0.14 104 -0.12 2 106
negative regulation of macrophage activation -0.007 0.007 -10000 0 -0.036 24 24
LEF -0.007 0.007 -10000 0 -0.037 24 24
CASP1 -0.014 0.023 0.044 5 -0.087 44 49
mol:cAMP -0.009 0.08 -10000 0 -0.44 18 18
necrosis -0.007 0.007 -10000 0 -0.036 24 24
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.027 0.033 -10000 0 -0.12 24 24
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.2 0.31 0.78 1 -0.84 63 64
CRP -0.2 0.31 -10000 0 -0.85 65 65
cell cycle arrest -0.24 0.37 -10000 0 -1 73 73
TIMP1 -0.2 0.31 -10000 0 -0.82 71 71
IL6ST 0.002 0.037 0.16 1 -0.1 1 2
Rac1/GDP -0.065 0.11 0.49 1 -0.41 6 7
AP1 0 0.13 0.42 4 -0.52 17 21
GAB2 0.025 0.016 0.099 1 -0.031 23 24
TNFSF11 -0.21 0.3 -10000 0 -0.85 65 65
HSP90B1 -0.025 0.13 -10000 0 -0.79 12 12
GAB1 0.026 0.014 0.093 1 -0.031 25 26
MAPK14 -0.023 0.088 0.55 2 -0.5 2 4
AKT1 -0.014 0.088 0.59 1 -0.42 4 5
FOXO1 -0.023 0.084 0.54 1 -0.51 2 3
MAP2K6 -0.025 0.092 0.74 1 -0.34 4 5
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
MAP2K4 -0.1 0.15 0.6 1 -0.49 12 13
MITF -0.054 0.092 0.49 1 -0.37 7 8
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.026 0.009 -10000 0 0 62 62
A2M -0.059 0.28 0.66 3 -1.2 31 34
CEBPB 0.027 0.01 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.003 0.1 -10000 0 -0.43 15 15
STAT3 -0.26 0.41 -10000 0 -1.1 74 74
STAT1 0.047 0.059 -10000 0 -10000 0 0
CEBPD -0.24 0.38 -10000 0 -0.98 91 91
PIK3CA 0.018 0.016 -10000 0 -0.029 18 18
PI3K -0.001 0.068 -10000 0 -0.16 77 77
JUN 0.025 0.014 -10000 0 -0.03 24 24
PIAS3/MITF -0.055 0.095 0.45 1 -0.36 6 7
MAPK11 -0.019 0.077 0.36 1 -0.49 2 3
STAT3 (dimer)/FOXO1 -0.2 0.28 -10000 0 -0.77 62 62
GRB2/SOS1/GAB family 0.016 0.1 -10000 0 -0.28 5 5
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.017 0.07 0.31 2 -0.27 8 10
GRB2 0.027 0.014 0.093 1 -0.031 24 25
JAK2 0.027 0.008 -10000 0 0 47 47
LBP -0.14 0.24 0.68 1 -0.71 21 22
PIK3R1 0.019 0.016 0.093 1 -0.029 19 20
JAK1 0.005 0.035 0.15 1 -0.093 2 3
MYC -0.18 0.38 0.75 1 -0.93 82 83
FGG -0.21 0.3 -10000 0 -0.85 64 64
macrophage differentiation -0.24 0.37 -10000 0 -1 73 73
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.014 0.093 0.36 1 -0.2 4 5
JUNB -0.27 0.41 -10000 0 -0.94 139 139
FOS 0.021 0.016 -10000 0 -0.03 25 25
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.043 0.1 0.57 1 -0.38 8 9
STAT1/PIAS1 -0.032 0.13 0.4 2 -0.39 8 10
GRB2/SOS1/GAB family/SHP2/PI3K -0.003 0.087 0.48 1 -0.4 7 8
STAT3 (dimer) -0.26 0.4 -10000 0 -1.1 74 74
PRKCD -0.14 0.2 0.67 1 -0.57 43 44
IL6R 0.005 0.035 0.15 1 -0.069 2 3
SOCS3 -0.009 0.1 0.64 2 -0.85 2 4
gp130 (dimer)/JAK1/JAK1/LMO4 0.009 0.071 0.36 1 -0.18 6 7
Rac1/GTP -0.077 0.13 0.52 1 -0.43 10 11
HCK 0.026 0.01 -10000 0 -0.033 6 6
MAPKKK cascade -0.002 0.12 0.44 1 -0.54 17 18
bone resorption -0.2 0.29 -10000 0 -0.79 65 65
IRF1 -0.21 0.32 0.74 2 -0.87 65 67
mol:GDP -0.056 0.098 -10000 0 -0.4 7 7
SOS1 0.026 0.015 -10000 0 -0.031 23 23
VAV1 -0.058 0.098 -10000 0 -0.4 7 7
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.008 0.07 0.69 1 -0.45 3 4
PTPN11 0.005 0.08 -10000 0 -0.78 5 5
IL6/IL6RA 0.007 0.053 0.26 1 -0.18 9 10
gp130 (dimer)/TYK2/TYK2/LMO4 0.011 0.06 0.23 1 -0.15 10 11
gp130 (dimer)/JAK2/JAK2/LMO4 0.011 0.061 0.23 1 -0.16 10 11
IL6 0.003 0.037 0.16 1 -0.1 1 2
PIAS3 0.028 0.005 -10000 0 0 17 17
PTPRE 0.032 0.027 -10000 0 -0.17 1 1
PIAS1 0.029 0.005 -10000 0 0 14 14
RAC1 0.007 0.029 -10000 0 -0.037 5 5
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.02 0.072 0.32 1 -0.29 9 10
LMO4 0.002 0.038 0.16 1 -0.1 1 2
STAT3 (dimer)/PIAS3 -0.24 0.36 -10000 0 -1 73 73
MCL1 -0.011 0.098 0.71 1 -0.59 1 2
EGFR-dependent Endothelin signaling events

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

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

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 0.028 0.006 -10000 0 0 26 26
EGFR 0.026 0.009 -10000 0 0 55 55
EGF/EGFR 0.032 0.053 -10000 0 -0.12 41 41
EGF/EGFR dimer/SHC/GRB2/SOS1 0.058 0.067 -10000 0 -0.14 36 36
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.028 0.006 -10000 0 0 27 27
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.027 0.008 -10000 0 0 41 41
EGF/EGFR dimer/SHC 0.037 0.055 -10000 0 -0.15 41 41
mol:GDP 0.051 0.064 -10000 0 -0.14 36 36
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.027 0.008 -10000 0 0 49 49
GRB2/SOS1 0.039 0.013 -10000 0 -10000 0 0
HRAS/GTP -0.056 0.03 -10000 0 -0.14 34 34
SHC1 0.028 0.006 -10000 0 0 21 21
HRAS/GDP 0.046 0.065 -10000 0 -0.14 36 36
FRAP1 -0.046 0.039 0.1 19 -10000 0 19
EGF/EGFR dimer 0.024 0.055 -10000 0 -0.16 43 43
SOS1 0.027 0.007 -10000 0 0 36 36
GRB2 0.028 0.005 -10000 0 0 19 19
ETA receptor/Endothelin-1 0.038 0.017 -10000 0 -0.16 1 1
Aurora C signaling

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
INCENP 0.029 0.003 -9999 0 0 6 6
Aurora C/Aurora B/INCENP 0.039 0.029 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.001 0.043 -9999 0 -0.37 7 7
AURKB 0.022 0.013 -9999 0 0 136 136
AURKC 0.028 0.006 -9999 0 0 27 27
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.027 0.008 -10000 0 0 45 45
LAT2 -0.009 0.075 0.14 4 -0.27 24 28
AP1 0.025 0.1 -10000 0 -0.37 13 13
mol:PIP3 -0.019 0.091 0.25 9 -0.31 18 27
IKBKB -0.011 0.071 0.21 17 -0.19 16 33
AKT1 -0.008 0.13 0.25 51 -0.25 8 59
IKBKG -0.013 0.065 0.19 15 -0.19 14 29
MS4A2 -0.012 0.031 0.06 7 -10000 0 7
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.007 0.024 -10000 0 -10000 0 0
MAP3K1 0.015 0.11 0.24 41 -0.31 14 55
mol:Ca2+ -0.013 0.076 0.22 10 -0.25 17 27
LYN -0.011 0.03 0.064 1 -10000 0 1
CBLB -0.008 0.074 0.15 4 -0.26 22 26
SHC1 0.028 0.006 -10000 0 -0.001 22 22
RasGAP/p62DOK 0.012 0.074 -10000 0 -0.13 108 108
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.031 0.087 0.25 17 -0.2 4 21
PTPN13 -0.022 0.11 -10000 0 -0.5 8 8
PTPN11 -0.009 0.034 0.062 6 -10000 0 6
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.013 0.1 0.26 17 -0.32 4 21
SYK -0.008 0.031 0.064 1 -10000 0 1
GRB2 0.023 0.017 -10000 0 -0.03 50 50
LAT/PLCgamma1/GRB2/SLP76/GADs -0.026 0.076 0.16 1 -0.29 21 22
LAT -0.008 0.073 0.14 4 -0.26 23 27
PAK2 0.022 0.12 0.23 64 -0.33 15 79
NFATC2 -0.02 0.072 -10000 0 -0.39 20 20
HRAS 0.003 0.095 0.24 7 -0.34 17 24
GAB2 0.026 0.009 -10000 0 0 63 63
PLA2G1B -0.004 0.066 -10000 0 -0.91 2 2
Fc epsilon R1 0.038 0.046 -10000 0 -0.12 30 30
Antigen/IgE/Fc epsilon R1 0.036 0.041 -10000 0 -0.12 23 23
mol:GDP 0.01 0.092 0.2 3 -0.35 17 20
JUN 0.028 0.007 -10000 0 0 32 32
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.018 0.017 -10000 0 -10000 0 0
FOS 0.024 0.011 -10000 0 0 105 105
Antigen/IgE/Fc epsilon R1/LYN/SYK 0.003 0.077 -10000 0 -0.27 24 24
CHUK -0.013 0.064 0.18 14 -0.19 16 30
KLRG1 -0.012 0.062 0.14 1 -0.27 14 15
VAV1 -0.007 0.074 0.14 5 -0.27 20 25
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.008 0.075 0.15 3 -0.27 23 26
negative regulation of mast cell degranulation -0.02 0.05 -10000 0 -0.26 13 13
BTK 0.012 0.088 0.21 1 -0.36 14 15
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.001 0.068 0.19 24 -0.19 12 36
GAB2/PI3K/SHP2 -0.06 0.063 -10000 0 -0.18 71 71
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.001 0.058 -10000 0 -0.23 13 13
RAF1 0.02 0.063 -10000 0 -0.96 2 2
Fc epsilon R1/FcgammaRIIB/SHIP 0.056 0.049 -10000 0 -0.12 28 28
FCER1G -0.017 0.024 0.064 1 -10000 0 1
FCER1A -0.01 0.031 -10000 0 -10000 0 0
Antigen/IgE/Fc epsilon R1/Fyn 0.034 0.077 -10000 0 -0.14 77 77
MAPK3 -0.004 0.067 -10000 0 -0.89 2 2
MAPK1 -0.007 0.072 -10000 0 -0.95 2 2
NFKB1 0.027 0.008 -10000 0 0 46 46
MAPK8 -0.003 0.16 -10000 0 -0.52 29 29
DUSP1 0.023 0.012 -10000 0 0 124 124
NF-kappa-B/RelA -0.013 0.053 0.14 16 -0.15 10 26
actin cytoskeleton reorganization -0.006 0.1 -10000 0 -0.55 5 5
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.031 0.091 -10000 0 -0.36 17 17
FER -0.006 0.073 0.14 3 -0.27 22 25
RELA 0.029 0.003 -10000 0 0 6 6
ITK 0.002 0.042 0.12 6 -0.23 11 17
SOS1 0.027 0.007 -10000 0 0 36 36
PLCG1 0.006 0.095 0.28 6 -0.34 14 20
cytokine secretion -0.013 0.034 0.07 9 -0.1 17 26
SPHK1 -0.007 0.073 0.14 4 -0.27 21 25
PTK2 -0.007 0.1 -10000 0 -0.57 5 5
NTAL/PLCgamma1/GRB2/SLP76/GADs 0 0.084 -10000 0 -0.3 24 24
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.021 0.095 0.23 8 -0.3 23 31
MAP2K2 -0.009 0.067 -10000 0 -0.91 2 2
MAP2K1 0.006 0.061 -10000 0 -0.91 2 2
MAP2K7 0.027 0.007 -10000 0 0 36 36
KLRG1/SHP2 -0.007 0.072 0.18 38 -0.25 13 51
MAP2K4 -0.062 0.29 -10000 0 -0.87 63 63
Fc epsilon R1/FcgammaRIIB 0.06 0.053 -10000 0 -0.12 28 28
mol:Choline -0.03 0.086 0.25 17 -0.2 4 21
SHC/Grb2/SOS1 0.05 0.083 -10000 0 -0.26 17 17
FYN 0.024 0.011 -10000 0 0 99 99
DOK1 0.029 0.004 -10000 0 0 10 10
PXN -0.016 0.099 -10000 0 -0.54 5 5
HCLS1 -0.008 0.076 0.15 7 -0.28 22 29
PRKCB -0.015 0.075 0.2 10 -0.24 21 31
FCGR2B 0.027 0.008 -10000 0 0 47 47
IGHE 0 0.006 0.021 8 -10000 0 8
KLRG1/SHIP -0.02 0.052 0.13 1 -0.26 13 14
LCP2 0.024 0.016 -10000 0 -0.03 35 35
PLA2G4A -0.046 0.089 0.15 5 -0.3 28 33
RASA1 0.027 0.008 -10000 0 0 49 49
mol:Phosphatidic acid -0.03 0.086 0.25 17 -0.2 4 21
IKK complex -0.01 0.066 0.19 21 -0.17 2 23
WIPF1 0.029 0.004 -10000 0 0 13 13
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.012 0.11 0.29 15 -0.33 16 31
FYN -0.023 0.13 0.29 17 -0.37 25 42
LAT/GRAP2/SLP76 -0.02 0.1 0.28 10 -0.33 17 27
IKBKB 0.027 0.007 -10000 0 0 39 39
AKT1 -0.022 0.098 0.28 9 -0.3 27 36
B2M 0.021 0.021 0.11 1 -0.051 6 7
IKBKG -0.02 0.039 0.12 10 -0.12 6 16
MAP3K8 0.029 0.005 -10000 0 0 15 15
mol:Ca2+ -0.026 0.013 0.08 1 -0.06 1 2
integrin-mediated signaling pathway 0.038 0.007 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.027 0.12 0.31 9 -0.4 26 35
TRPV6 0.077 0.34 1.3 38 -10000 0 38
CD28 0.019 0.023 -10000 0 -10000 0 0
SHC1 -0.013 0.11 0.28 15 -0.36 18 33
receptor internalization -0.012 0.096 0.26 9 -0.36 19 28
PRF1 -0.024 0.19 0.8 1 -0.93 19 20
KRAS 0.024 0.011 -10000 0 0 99 99
GRB2 0.028 0.005 -10000 0 0 19 19
COT/AKT1 -0.018 0.089 0.25 11 -0.26 24 35
LAT -0.017 0.1 0.31 9 -0.36 17 26
EntrezGene:6955 -0.001 0.004 0.07 1 -0.022 8 9
CD3D 0.023 0.017 0.11 1 -0.05 6 7
CD3E -0.005 0.03 -10000 0 -10000 0 0
CD3G 0.016 0.024 -10000 0 -0.05 12 12
RASGRP2 -0.003 0.016 -10000 0 -0.14 2 2
RASGRP1 -0.053 0.13 0.27 7 -0.3 72 79
HLA-A -0.005 0.03 0.11 1 -10000 0 1
RASSF5 0.029 0.004 -10000 0 0 12 12
RAP1A/GTP/RAPL 0.038 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.003 0.05 0.16 10 -0.12 10 20
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.035 0.045 -10000 0 -0.17 24 24
PRKCA -0.026 0.064 0.2 11 -0.21 10 21
GRAP2 0.027 0.008 -10000 0 -0.001 48 48
mol:IP3 -0.031 0.076 -10000 0 -0.27 16 16
EntrezGene:6957 0 0.005 0.076 1 -0.021 13 14
TCR/CD3/MHC I/CD8 -0.014 0.089 0.32 4 -0.34 21 25
ORAI1 -0.094 0.29 -10000 0 -1.1 38 38
CSK -0.015 0.1 0.32 8 -0.37 16 24
B7 family/CD28 0.013 0.11 0.39 3 -0.4 16 19
CHUK 0.027 0.007 -10000 0 0 36 36
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.015 0.1 0.25 10 -0.38 18 28
PTPN6 -0.011 0.11 0.28 14 -0.35 18 32
VAV1 -0.015 0.1 0.29 10 -0.36 18 28
Monovalent TCR/CD3 -0.013 0.062 0.38 1 -0.18 49 50
CBL 0.029 0.004 -10000 0 0 12 12
LCK -0.01 0.12 0.29 15 -0.36 21 36
PAG1 -0.011 0.1 0.29 11 -0.38 15 26
RAP1A 0.029 0.003 -10000 0 0 7 7
TCR/CD3/MHC I/CD8/LCK -0.015 0.1 0.26 10 -0.38 19 29
CD80 0.018 0.023 -10000 0 -10000 0 0
CD86 0.017 0.023 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1 -0.03 0.059 0.096 4 -0.2 22 26
HRAS 0.028 0.006 -10000 0 0 26 26
GO:0035030 -0.029 0.089 0.26 6 -0.33 19 25
CD8A 0.021 0.022 0.11 1 -0.051 4 5
CD8B -0.004 0.031 0.11 1 -10000 0 1
PTPRC 0.017 0.02 -10000 0 -10000 0 0
PDK1/PKC theta -0.031 0.11 0.3 10 -0.36 22 32
CSK/PAG1 -0.016 0.1 0.28 13 -0.37 15 28
SOS1 0.027 0.007 -10000 0 0 36 36
peptide-MHC class I 0.035 0.03 0.18 1 -0.14 8 9
GRAP2/SLP76 0.012 0.11 0.31 8 -0.36 19 27
STIM1 -0.038 0.071 -10000 0 -10000 0 0
RAS family/GTP 0.023 0.07 0.18 29 -0.18 7 36
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.013 0.099 0.26 9 -0.38 19 28
mol:DAG -0.04 0.058 -10000 0 -0.23 21 21
RAP1A/GDP -0.002 0.026 0.081 9 -0.07 1 10
PLCG1 0.027 0.007 -10000 0 -0.001 34 34
CD247 0.017 0.025 0.1 1 -0.051 8 9
cytotoxic T cell degranulation -0.022 0.18 0.79 1 -0.88 19 20
RAP1A/GTP -0.004 0.008 -10000 0 -0.057 2 2
mol:PI-3-4-5-P3 -0.022 0.11 0.28 11 -0.34 26 37
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.033 0.096 0.21 3 -0.33 16 19
NRAS 0.014 0.015 -10000 0 0 300 300
ZAP70 0.028 0.009 -10000 0 -0.029 12 12
GRB2/SOS1 0.039 0.013 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.029 0.096 0.27 8 -0.33 17 25
MALT1 0.025 0.01 -10000 0 0 76 76
TRAF6 0.029 0.004 -10000 0 0 12 12
CD8 heterodimer 0.039 0.022 0.18 1 -10000 0 1
CARD11 0.027 0.007 -10000 0 0 35 35
PRKCB -0.034 0.039 -10000 0 -0.17 21 21
PRKCE -0.026 0.063 0.2 11 -0.21 9 20
PRKCQ -0.028 0.12 0.3 9 -0.38 23 32
LCP2 0.027 0.007 -10000 0 -0.001 34 34
BCL10 0.029 0.004 -10000 0 0 10 10
regulation of survival gene product expression -0.019 0.089 0.26 10 -0.26 25 35
IKK complex -0.004 0.041 0.15 18 -0.12 1 19
RAS family/GDP -0.004 0.009 -10000 0 -0.037 10 10
MAP3K14 -0.022 0.07 0.23 8 -0.22 16 24
PDPK1 -0.025 0.095 0.29 8 -0.29 25 33
TCR/CD3/MHC I/CD8/Fyn -0.016 0.11 0.48 1 -0.42 21 22
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.12 0.25 0.61 15 -0.77 1 16
PCK1 0.17 0.24 0.62 68 -10000 0 68
HNF4A 0.15 0.3 0.74 46 -0.77 1 47
KCNJ11 0.12 0.27 0.63 1 -0.82 1 2
AKT1 0.096 0.19 0.4 41 -10000 0 41
response to starvation 0 0.01 0.17 2 -10000 0 2
DLK1 0.14 0.29 0.82 19 -0.82 1 20
NKX2-1 0.11 0.18 0.7 3 -10000 0 3
ACADM 0.12 0.25 0.6 17 -0.77 1 18
TAT 0.12 0.19 0.51 18 -10000 0 18
CEBPB 0.027 0.013 0.19 2 -10000 0 2
CEBPA 0.027 0.013 0.18 2 -10000 0 2
TTR 0.14 0.18 0.7 11 -10000 0 11
PKLR 0.13 0.26 0.66 22 -0.77 1 23
APOA1 0.2 0.37 0.92 56 -1 1 57
CPT1C 0.12 0.26 0.69 21 -0.77 1 22
ALAS1 0.089 0.18 0.91 2 -0.63 1 3
TFRC 0.25 0.36 0.76 141 -10000 0 141
FOXF1 0.026 0.009 -10000 0 -10000 0 0
NF1 0.027 0.02 0.24 4 -10000 0 4
HNF1A (dimer) -0.03 0.01 -10000 0 -0.25 1 1
CPT1A 0.12 0.25 0.6 18 -0.85 2 20
HMGCS1 0.14 0.29 0.69 48 -0.77 1 49
NR3C1 -0.028 0.006 -10000 0 -10000 0 0
CPT1B 0.1 0.24 0.59 14 -0.77 1 15
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.028 0.012 -10000 0 -0.25 1 1
GCK 0.12 0.25 0.6 16 -0.77 1 17
CREB1 0.036 0.094 0.23 98 -10000 0 98
IGFBP1 0.099 0.16 0.52 4 -10000 0 4
PDX1 0.092 0.18 -10000 0 -0.98 1 1
UCP2 0.039 0.37 0.63 19 -0.76 56 75
ALDOB 0.13 0.27 0.63 1 -0.82 1 2
AFP 0.041 0.064 0.42 2 -10000 0 2
BDH1 0.15 0.28 0.71 39 -0.79 1 40
HADH 0.11 0.28 0.63 1 -0.95 4 5
F2 0.17 0.31 0.8 23 -0.96 1 24
HNF1A -0.03 0.01 -10000 0 -0.25 1 1
G6PC 0.05 0.083 -10000 0 -10000 0 0
SLC2A2 0.12 0.2 0.59 7 -10000 0 7
INS 0.027 0.023 -10000 0 -0.24 4 4
FOXA1 -0.028 0.026 0.35 2 -10000 0 2
FOXA3 0.098 0.16 0.29 207 -10000 0 207
FOXA2 0.19 0.36 0.82 47 -0.83 2 49
ABCC8 0.12 0.27 0.63 1 -0.82 1 2
ALB 0.042 0.066 0.52 2 -10000 0 2
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.056 0.065 0.36 9 -0.15 8 17
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.028 0.007 -10000 0 0 31 31
STAT1 (dimer)/Cbp/p300 0.009 0.087 0.22 1 -10000 0 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.049 0.046 0.2 9 -0.16 8 17
antigen processing and presentation of peptide antigen via MHC class I -0.028 0.068 0.13 3 -0.23 27 30
CaM/Ca2+ 0.051 0.067 0.32 8 -0.17 2 10
RAP1A 0.029 0.003 -10000 0 0 7 7
STAT1 (dimer)/SHP2 -0.016 0.05 0.22 3 -10000 0 3
AKT1 -0.001 0.12 0.28 31 -0.23 6 37
MAP2K1 -0.032 0.078 0.3 16 -10000 0 16
MAP3K11 -0.026 0.083 0.33 16 -10000 0 16
IFNGR1 -0.019 0.031 0.078 15 -10000 0 15
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.009 0.093 0.21 1 -0.31 28 29
Rap1/GTP -0.063 0.043 -10000 0 -0.19 1 1
CRKL/C3G 0.04 0.012 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.067 0.062 0.26 8 -0.15 8 16
CEBPB -0.036 0.15 0.4 7 -0.6 20 27
STAT3 0.027 0.007 -10000 0 0 36 36
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.019 0.19 -10000 0 -0.84 22 22
STAT1 -0.018 0.047 0.38 2 -10000 0 2
CALM1 0.027 0.009 -10000 0 -0.006 33 33
IFN-gamma (dimer) -0.024 0.025 0.07 7 -10000 0 7
PIK3CA 0.02 0.014 -10000 0 0 172 172
STAT1 (dimer)/PIAS1 -0.02 0.051 0.37 2 -10000 0 2
CEBPB/PTGES2/Cbp/p300 -0.053 0.094 -10000 0 -0.4 18 18
mol:Ca2+ 0.051 0.061 0.33 8 -0.15 8 16
MAPK3 -0.039 0.16 0.45 3 -0.68 25 28
STAT1 (dimer) -0.03 0.1 0.43 4 -0.36 13 17
MAPK1 -0.053 0.19 0.44 4 -0.71 36 40
JAK2 -0.02 0.03 0.076 14 -10000 0 14
PIK3R1 0.02 0.014 -10000 0 -0.001 165 165
JAK1 -0.02 0.031 0.079 14 -10000 0 14
CAMK2D 0.026 0.011 -10000 0 -0.005 53 53
DAPK1 -0.023 0.11 0.42 5 -0.41 15 20
SMAD7 0.024 0.11 0.36 31 -10000 0 31
CBL/CRKL/C3G -0.036 0.09 0.33 15 -10000 0 15
PI3K 0.018 0.083 0.25 6 -0.23 7 13
IFNG -0.024 0.025 0.07 7 -10000 0 7
apoptosis 0.004 0.097 0.42 6 -0.41 2 8
CAMK2G 0.028 0.008 -10000 0 -0.01 20 20
STAT3 (dimer) 0.027 0.007 -10000 0 0 36 36
CAMK2A 0.028 0.008 -10000 0 -0.013 18 18
CAMK2B 0.028 0.007 -10000 0 -0.008 18 18
FRAP1 -0.005 0.1 0.26 33 -0.22 6 39
PRKCD -0.001 0.12 0.29 30 -0.24 3 33
RAP1B 0.028 0.006 -10000 0 0 22 22
negative regulation of cell growth -0.028 0.068 0.13 3 -0.23 27 30
PTPN2 0.027 0.011 -10000 0 -0.012 39 39
EP300 0.025 0.016 0.072 13 -0.034 22 35
IRF1 0.001 0.094 0.19 21 -0.32 12 33
STAT1 (dimer)/PIASy -0.017 0.053 0.23 6 -10000 0 6
SOCS1 -0.032 0.22 -10000 0 -1.1 22 22
mol:GDP -0.036 0.085 0.31 15 -10000 0 15
CASP1 0.001 0.081 0.22 11 -0.2 25 36
PTGES2 0.028 0.005 -10000 0 0 17 17
IRF9 -0.022 0.063 0.29 12 -0.19 4 16
mol:PI-3-4-5-P3 -0.036 0.063 0.14 9 -0.22 7 16
RAP1/GDP -0.057 0.059 0.17 5 -10000 0 5
CBL -0.025 0.083 0.33 16 -10000 0 16
MAP3K1 -0.024 0.081 0.33 16 -10000 0 16
PIAS1 0.029 0.005 -10000 0 0 14 14
PIAS4 0.027 0.008 -10000 0 0 46 46
antigen processing and presentation of peptide antigen via MHC class II -0.028 0.068 0.13 3 -0.23 27 30
PTPN11 -0.018 0.084 0.35 15 -0.19 1 16
CREBBP 0.026 0.016 0.071 14 -0.034 22 36
RAPGEF1 0.028 0.005 -10000 0 0 18 18
Ceramide signaling 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 -0.03 0.011 -10000 0 -10000 0 0
MAP4K4 -0.036 0.087 0.18 1 -0.3 34 35
BAG4 0.026 0.009 -10000 0 0 62 62
PKC zeta/ceramide 0.029 0.031 -10000 0 -0.18 9 9
NFKBIA 0.028 0.006 -10000 0 0 27 27
BIRC3 0.023 0.012 -10000 0 0 122 122
BAX 0.007 0.058 -10000 0 -0.33 15 15
RIPK1 0.027 0.007 -10000 0 0 38 38
AKT1 -0.009 0.11 0.68 15 -10000 0 15
BAD 0.001 0.031 0.22 2 -0.18 10 12
SMPD1 -0.01 0.064 0.18 6 -0.21 26 32
RB1 0.006 0.043 0.18 19 -0.18 10 29
FADD/Caspase 8 -0.035 0.097 0.22 7 -0.32 35 42
MAP2K4 -0.009 0.027 -10000 0 -0.19 9 9
NSMAF 0.028 0.007 -10000 0 0 33 33
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.006 0.037 0.19 10 -0.19 9 19
EGF 0.027 0.008 -10000 0 0 41 41
mol:ceramide 0.012 0.03 -10000 0 -0.19 10 10
MADD 0.029 0.003 -10000 0 0 8 8
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.026 0.014 -10000 0 -10000 0 0
ASAH1 0.024 0.011 -10000 0 0 95 95
negative regulation of cell cycle 0.006 0.043 0.18 19 -0.18 10 29
cell proliferation -0.034 0.054 0.18 6 -0.22 8 14
BID -0.038 0.18 -10000 0 -0.64 41 41
MAP3K1 0 0.028 -10000 0 -0.18 10 10
EIF2A 0.065 0.099 0.22 82 -0.2 2 84
TRADD 0.026 0.009 -10000 0 0 65 65
CRADD 0.029 0.004 -10000 0 0 13 13
MAPK3 -0.023 0.048 0.18 6 -0.23 7 13
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.025 0.05 0.19 4 -0.23 6 10
Cathepsin D/ceramide 0.029 0.032 -10000 0 -0.18 10 10
FADD -0.036 0.088 0.18 4 -0.29 35 39
KSR1 0.002 0.035 0.22 5 -0.18 10 15
MAPK8 0 0.041 -10000 0 -10000 0 0
PRKRA 0.006 0.044 0.21 15 -0.18 10 25
PDGFA 0.027 0.008 -10000 0 0 46 46
TRAF2 0.028 0.006 -10000 0 0 25 25
IGF1 0.028 0.007 -10000 0 0 32 32
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process 0.012 0.03 0.13 1 -0.18 10 11
CTSD 0.028 0.006 -10000 0 0 28 28
regulation of nitric oxide biosynthetic process 0.037 0.025 -10000 0 -0.16 7 7
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.035 0.058 0.2 6 -0.24 8 14
PRKCD 0.029 0.005 -10000 0 0 15 15
PRKCZ 0.028 0.006 -10000 0 0 23 23
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.026 0.014 -10000 0 -10000 0 0
RelA/NF kappa B1 0.038 0.026 -10000 0 -0.16 7 7
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.029 0.004 -10000 0 0 13 13
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.021 0.092 -10000 0 -0.28 39 39
TNFR1A/BAG4/TNF-alpha 0.041 0.04 -10000 0 -0.14 15 15
mol:Sphingosine-1-phosphate -0.03 0.011 -10000 0 -10000 0 0
MAP2K1 -0.014 0.038 0.17 11 -0.19 7 18
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.029 0.003 -10000 0 0 6 6
CYCS 0.024 0.057 0.18 5 -0.17 8 13
TNFRSF1A 0.025 0.01 -10000 0 0 77 77
NFKB1 0.027 0.008 -10000 0 0 46 46
TNFR1A/BAG4 0.029 0.036 -10000 0 -0.16 15 15
EIF2AK2 0.06 0.089 0.19 79 -0.19 4 83
TNF-alpha/TNFR1A/FAN 0.044 0.037 -10000 0 -0.15 13 13
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.018 0.11 -10000 0 -0.41 32 32
MAP2K2 -0.026 0.046 0.18 8 -0.21 8 16
SMPD3 -0.027 0.11 0.18 4 -0.32 58 62
TNF 0.028 0.005 -10000 0 0 16 16
PKC zeta/PAR4 0.041 0.01 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.011 0.037 0.14 2 -0.15 8 10
NF kappa B1/RelA/I kappa B alpha 0.064 0.057 -10000 0 -0.15 17 17
AIFM1 0.03 0.062 0.2 15 -0.17 7 22
BCL2 0.023 0.012 -10000 0 0 123 123
Syndecan-4-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
PTK2 0.076 0.11 0.24 51 -0.39 11 62
Syndecan-4/Syndesmos 0.072 0.1 0.33 3 -0.45 1 4
positive regulation of JNK cascade 0.061 0.11 0.32 3 -0.42 1 4
Syndecan-4/ADAM12 0.039 0.086 0.29 1 -0.45 1 2
CCL5 0.025 0.01 -10000 0 0 81 81
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
DNM2 0.026 0.009 -10000 0 0 56 56
ITGA5 0.028 0.005 -10000 0 0 19 19
SDCBP 0.028 0.007 -10000 0 0 34 34
PLG -0.009 0.039 -10000 0 -0.085 25 25
ADAM12 0.022 0.013 -10000 0 0 140 140
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.028 0.006 -10000 0 0 26 26
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.019 0.034 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.062 0.096 0.38 1 -0.45 1 2
Syndecan-4/CXCL12/CXCR4 0.065 0.12 0.33 3 -0.44 1 4
Syndecan-4/Laminin alpha3 0.064 0.099 0.33 3 -0.45 1 4
MDK 0.029 0.003 -10000 0 0 7 7
Syndecan-4/FZD7 0.07 0.1 0.33 3 -0.45 1 4
Syndecan-4/Midkine 0.073 0.1 0.33 3 -0.45 1 4
FZD7 0.028 0.006 -10000 0 0 26 26
Syndecan-4/FGFR1/FGF 0.066 0.1 0.34 2 -0.43 1 3
THBS1 0.024 0.011 -10000 0 0 95 95
integrin-mediated signaling pathway 0.041 0.083 0.28 2 -0.43 1 3
positive regulation of MAPKKK cascade 0.061 0.11 0.32 3 -0.42 1 4
Syndecan-4/TACI 0.073 0.099 0.33 3 -0.45 1 4
CXCR4 0.028 0.005 -10000 0 0 17 17
cell adhesion 0.02 0.065 0.18 9 -0.19 12 21
Syndecan-4/Dynamin 0.07 0.098 0.33 3 -0.45 1 4
Syndecan-4/TSP1 0.063 0.1 0.33 3 -0.45 1 4
Syndecan-4/GIPC 0.065 0.097 0.33 3 -0.45 1 4
Syndecan-4/RANTES 0.067 0.1 0.33 3 -0.45 1 4
ITGB1 0.028 0.006 -10000 0 0 21 21
LAMA1 0.024 0.012 -10000 0 0 110 110
LAMA3 0.025 0.01 -10000 0 0 74 74
RAC1 0.028 0.006 -10000 0 0 27 27
PRKCA -0.027 0.09 0.6 9 -10000 0 9
Syndecan-4/alpha-Actinin 0.073 0.1 0.33 3 -0.45 1 4
TFPI 0.027 0.008 -10000 0 0 51 51
F2 0.018 0.032 0.078 1 -0.049 2 3
alpha5/beta1 Integrin 0.041 0.011 -10000 0 -10000 0 0
positive regulation of cell adhesion 0.038 0.094 0.32 7 -0.44 1 8
ACTN1 0.028 0.006 -10000 0 0 21 21
TNC 0.02 0.013 -10000 0 0 168 168
Syndecan-4/CXCL12 0.065 0.11 0.33 3 -0.45 1 4
FGF6 0.026 0.009 -10000 0 0 59 59
RHOA 0.029 0.003 -10000 0 0 6 6
CXCL12 0.025 0.011 -10000 0 0 91 91
TNFRSF13B 0.027 0.007 -10000 0 0 37 37
FGF2 0.027 0.008 -10000 0 0 43 43
FGFR1 0.025 0.01 -10000 0 0 77 77
Syndecan-4/PI-4-5-P2 0.04 0.087 -10000 0 -0.44 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.009 0.026 -10000 0 -0.071 8 8
cell migration -0.014 0.014 -10000 0 -10000 0 0
PRKCD -0.007 0.04 -10000 0 -0.074 33 33
vasculogenesis 0.062 0.1 0.3 5 -0.44 1 6
SDC4 0.05 0.093 0.34 2 -0.46 1 3
Syndecan-4/Tenascin C 0.041 0.084 0.29 1 -0.45 1 2
Syndecan-4/PI-4-5-P2/PKC alpha -0.018 0.025 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.07 0.099 0.33 3 -0.45 1 4
MMP9 0.007 0.027 -10000 0 -0.053 2 2
Rac1/GTP 0.012 0.062 0.18 9 -0.2 12 21
cytoskeleton organization 0.071 0.098 0.3 5 -0.43 1 6
GIPC1 0.025 0.01 -10000 0 0 81 81
Syndecan-4/TFPI 0.066 0.1 0.35 2 -0.45 1 3
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.008 0.12 0.37 19 -0.32 1 20
CRKL -0.019 0.12 0.39 13 -0.32 2 15
HRAS -0.018 0.12 0.38 11 -0.36 6 17
mol:PIP3 0.008 0.13 0.4 16 -0.43 2 18
SPRED1 0.027 0.008 -10000 0 0 40 40
SPRED2 0.029 0.004 -10000 0 0 9 9
GAB1 -0.01 0.12 0.42 15 -0.41 2 17
FOXO3 -0.012 0.13 0.39 16 -0.42 10 26
AKT1 -0.005 0.14 0.4 16 -0.45 10 26
BAD -0.012 0.13 0.38 16 -0.42 10 26
megakaryocyte differentiation -0.006 0.12 0.45 15 -0.41 2 17
GSK3B -0.007 0.14 0.39 18 -0.43 9 27
RAF1 -0.02 0.11 0.34 14 -0.32 4 18
SHC1 0.028 0.006 -10000 0 0 21 21
STAT3 -0.011 0.12 0.42 13 -0.41 2 15
STAT1 -0.012 0.23 0.59 15 -0.61 24 39
HRAS/SPRED1 -0.012 0.11 0.34 12 -0.32 4 16
cell proliferation -0.01 0.12 0.44 15 -0.41 2 17
PIK3CA 0.01 0.022 -10000 0 -0.029 102 102
TEC 0.026 0.009 -10000 0 0 55 55
RPS6KB1 0.001 0.14 0.43 16 -0.4 4 20
HRAS/SPRED2 -0.011 0.11 0.34 12 -0.32 4 16
LYN/TEC/p62DOK 0.013 0.13 0.4 10 -0.35 5 15
MAPK3 -0.027 0.091 0.31 8 -0.29 7 15
STAP1 -0.008 0.12 0.42 15 -0.41 2 17
GRAP2 0.027 0.008 -10000 0 0 47 47
JAK2 -0.02 0.22 0.57 15 -0.68 11 26
STAT1 (dimer) -0.01 0.23 0.59 16 -0.6 22 38
mol:Gleevec 0.001 0.009 -10000 0 -0.035 18 18
GRB2/SOCS1/VAV1 0.014 0.14 0.41 13 -0.35 4 17
actin filament polymerization -0.001 0.12 0.43 15 -0.4 2 17
LYN 0.027 0.008 -10000 0 0 50 50
STAP1/STAT5A (dimer) -0.03 0.18 0.47 14 -0.51 17 31
PIK3R1 0.016 0.019 -10000 0 -0.029 46 46
CBL/CRKL/GRB2 -0.016 0.13 0.36 16 -0.32 1 17
PI3K -0.016 0.12 0.41 9 -0.38 5 14
PTEN 0.022 0.018 -10000 0 -0.03 54 54
SCF/KIT/EPO/EPOR 0.006 0.23 0.62 10 -0.67 6 16
MAPK8 -0.009 0.13 0.45 15 -0.41 2 17
STAT3 (dimer) -0.011 0.12 0.42 13 -0.41 2 15
positive regulation of transcription -0.021 0.08 0.26 13 -0.25 4 17
mol:GDP -0.017 0.12 0.36 10 -0.35 4 14
PIK3C2B -0.01 0.13 0.45 15 -0.41 2 17
CBL/CRKL -0.017 0.12 0.37 16 -0.32 1 17
FER -0.01 0.12 0.42 14 -0.41 2 16
SH2B3 -0.009 0.12 0.42 15 -0.32 2 17
PDPK1 0.001 0.12 0.39 17 -0.39 2 19
SNAI2 -0.01 0.12 0.42 14 -0.38 3 17
positive regulation of cell proliferation -0.017 0.2 0.54 15 -0.55 15 30
KITLG 0.018 0.041 0.12 16 -10000 0 16
cell motility -0.017 0.2 0.54 15 -0.55 15 30
PTPN6 -0.001 0.035 -10000 0 -0.076 15 15
EPOR -0.029 0.2 0.99 1 -0.69 23 24
STAT5A (dimer) -0.02 0.18 0.5 15 -0.52 16 31
SOCS1 0.028 0.007 -10000 0 0 32 32
cell migration 0.011 0.12 0.41 2 -0.43 13 15
SOS1 0.027 0.007 -10000 0 0 36 36
EPO 0.021 0.031 0.09 9 -0.043 68 77
VAV1 0.027 0.008 -10000 0 0 40 40
GRB10 -0.009 0.12 0.42 15 -0.41 2 17
PTPN11 0 0.034 -10000 0 -0.065 17 17
SCF/KIT 0.002 0.13 0.47 15 -0.42 2 17
GO:0007205 0 0.012 -10000 0 -0.046 18 18
MAP2K1 -0.02 0.094 0.3 15 -0.27 2 17
CBL 0.029 0.004 -10000 0 0 12 12
KIT -0.011 0.21 0.69 17 -0.7 13 30
MAP2K2 -0.027 0.091 0.29 13 -0.3 2 15
SHC/Grb2/SOS1 0.019 0.13 0.41 12 -0.41 2 14
STAT5A -0.019 0.19 0.5 15 -0.53 17 32
GRB2 0.028 0.005 -10000 0 0 19 19
response to radiation -0.007 0.13 0.42 16 -0.37 3 19
SHC/GRAP2 0.038 0.014 -10000 0 -10000 0 0
PTPRO -0.007 0.12 0.45 15 -0.41 2 17
SH2B2 -0.001 0.12 0.43 15 -0.4 2 17
DOK1 0.029 0.004 -10000 0 0 10 10
MATK -0.01 0.12 0.43 13 -0.41 2 15
CREBBP 0 0.084 0.36 16 -10000 0 16
BCL2 -0.18 0.45 0.95 1 -1 106 107
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.039 0.021 -10000 0 -0.2 3 3
FBXW11 0.028 0.005 -10000 0 0 16 16
NF kappa B1 p50/c-Rel -0.037 0.016 0.16 1 -0.15 4 5
NF kappa B1 p50/RelA/I kappa B alpha -0.028 0.053 0.23 1 -0.23 8 9
NFKBIA -0.005 0.04 -10000 0 -10000 0 0
MAPK14 0.028 0.005 -10000 0 0 19 19
NF kappa B1 p105/p50 -0.037 0.017 0.16 1 -0.15 5 6
ARRB2 0.006 0.002 -10000 0 -10000 0 0
REL 0.029 0.004 -10000 0 0 12 12
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.036 0.019 0.16 1 -0.15 7 8
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA -0.038 0.017 0.16 1 -0.15 6 7
PIK3CA 0.02 0.014 -10000 0 0 170 170
NF kappa B1 p50 dimer -0.032 0.016 -10000 0 -0.16 5 5
PIK3R1 0.021 0.013 -10000 0 0 159 159
NFKB1 -0.029 0.015 0.19 1 -10000 0 1
RELA 0.029 0.003 -10000 0 0 6 6
positive regulation of anti-apoptosis -0.006 0.041 -10000 0 -0.21 3 3
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.032 0.054 -10000 0 -0.25 7 7
SRC 0.028 0.007 -10000 0 0 33 33
PI3K -0.001 0.068 -10000 0 -0.16 77 77
NF kappa B1 p50/RelA -0.006 0.041 -10000 0 -0.21 3 3
IKBKB 0.027 0.007 -10000 0 0 39 39
beta TrCP1/SCF ubiquitin ligase complex 0.028 0.005 -10000 0 0 16 16
SYK 0.028 0.006 -10000 0 0 24 24
I kappa B alpha/PIK3R1 0.006 0.053 -10000 0 -0.22 14 14
cell death -0.031 0.052 -10000 0 -0.24 7 7
NF kappa B1 p105/c-Rel -0.037 0.016 0.16 1 -0.15 4 5
LCK 0.028 0.006 -10000 0 0 25 25
BCL3 0.027 0.007 -10000 0 0 36 36
IL27-mediated signaling events

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
TGFB1 0.023 0.012 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response -0.002 0.14 0.84 3 -0.39 25 28
IL27/IL27R/JAK1 0.056 0.13 0.56 6 -0.94 3 9
TBX21 0.046 0.14 0.43 31 -0.56 3 34
IL12B 0.031 0.014 0.091 26 -10000 0 26
IL12A -0.012 0.015 0.046 23 -10000 0 23
IL6ST -0.011 0.035 0.095 29 -10000 0 29
IL27RA/JAK1 0.011 0.11 0.39 1 -1 3 4
IL27 -0.012 0.036 0.095 30 -10000 0 30
TYK2 -0.012 0.041 0.15 26 -10000 0 26
T-helper cell lineage commitment -0.03 0.092 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.002 0.14 0.84 3 -0.39 25 28
T cell proliferation during immune response -0.002 0.14 0.84 3 -0.39 25 28
MAPKKK cascade 0.002 0.14 0.39 25 -0.84 3 28
STAT3 0.027 0.007 -10000 0 0 36 36
STAT2 0.025 0.01 -10000 0 0 75 75
STAT1 -0.011 0.016 0.062 3 -10000 0 3
IL12RB1 0.028 0.011 0.059 26 0 48 74
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.042 0.14 0.44 25 -0.56 3 28
IL27/IL27R/JAK2/TYK2 0.002 0.14 0.4 25 -0.86 3 28
positive regulation of T cell mediated cytotoxicity 0.002 0.14 0.39 25 -0.84 3 28
STAT1 (dimer) 0.074 0.13 0.55 2 -0.78 3 5
JAK2 -0.009 0.038 0.12 24 -10000 0 24
JAK1 -0.024 0.018 0.065 6 -10000 0 6
STAT2 (dimer) 0.01 0.13 0.44 3 -0.73 3 6
T cell proliferation -0.014 0.13 0.46 6 -0.82 3 9
IL12/IL12R/TYK2/JAK2 0.017 0.19 0.48 22 -0.72 25 47
IL17A -0.03 0.09 -10000 0 -10000 0 0
mast cell activation -0.002 0.14 0.84 3 -0.39 25 28
IFNG 0.016 0.064 0.28 27 -10000 0 27
T cell differentiation -0.001 0.006 0.027 19 -0.022 3 22
STAT3 (dimer) 0.016 0.14 0.41 4 -0.72 4 8
STAT5A (dimer) 0.017 0.14 0.42 5 -0.82 3 8
STAT4 (dimer) 0.017 0.14 0.42 5 -0.78 3 8
STAT4 0.028 0.005 -10000 0 0 16 16
T cell activation -0.001 0.012 0.11 1 -0.25 1 2
IL27R/JAK2/TYK2 0.047 0.12 0.53 4 -0.95 3 7
GATA3 0.007 0.12 0.62 18 -10000 0 18
IL18 -0.012 0.008 0.002 137 -10000 0 137
positive regulation of mast cell cytokine production 0.016 0.14 0.4 4 -0.7 4 8
IL27/EBI3 0.045 0.032 0.17 23 -10000 0 23
IL27RA 0.019 0.12 0.57 1 -1.1 3 4
IL6 0.026 0.01 -10000 0 -10000 0 0
STAT5A 0.028 0.007 -10000 0 0 33 33
monocyte differentiation 0.001 0.004 0.018 26 -10000 0 26
IL2 -0.009 0.045 0.45 3 -10000 0 3
IL1B -0.014 0.008 0.005 76 -10000 0 76
EBI3 -0.012 0.034 0.095 27 -10000 0 27
TNF -0.015 0.007 0.009 41 -10000 0 41
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.011 0.058 -10000 0 -0.2 28 28
epithelial cell differentiation 0.047 0.041 -10000 0 -0.13 9 9
CYFIP2 0.028 0.006 -10000 0 0 24 24
ENAH -0.05 0.063 0.21 8 -10000 0 8
EGFR 0.026 0.009 -10000 0 0 55 55
EPHA2 0.028 0.005 -10000 0 0 16 16
MYO6 -0.047 0.026 0.16 4 -0.22 1 5
CTNNB1 0.029 0.003 -10000 0 0 8 8
ABI1/Sra1/Nap1 0.052 0.03 -10000 0 -0.15 9 9
AQP5 -0.012 0.049 -10000 0 -0.32 4 4
CTNND1 0.029 0.003 -10000 0 0 5 5
mol:PI-4-5-P2 -0.045 0.027 0.16 4 -10000 0 4
regulation of calcium-dependent cell-cell adhesion -0.045 0.027 0.16 4 -10000 0 4
EGF 0.027 0.008 -10000 0 0 41 41
NCKAP1 0.028 0.005 -10000 0 0 17 17
AQP3 -0.13 0.17 -10000 0 -0.39 153 153
cortical microtubule organization 0.047 0.041 -10000 0 -0.13 9 9
GO:0000145 -0.043 0.025 0.14 4 -10000 0 4
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.052 0.043 -10000 0 -0.13 9 9
MLLT4 0.026 0.01 -10000 0 0 70 70
ARF6/GDP -0.065 0.034 -10000 0 -10000 0 0
ARF6 0.029 0.004 -10000 0 0 11 11
Ephrin A1/EPHA2/NCK1/GIT1 0.067 0.04 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.051 0.066 -10000 0 -0.23 59 59
PVRL2 0.028 0.007 -10000 0 0 33 33
ZYX -0.042 0.026 0.15 1 -0.22 1 2
ARF6/GTP 0.072 0.044 -10000 0 -10000 0 0
CDH1 0.026 0.01 -10000 0 0 72 72
EGFR/EGFR/EGF/EGF -0.062 0.032 0.094 7 -0.22 2 9
RhoA/GDP 0.047 0.044 -10000 0 -0.13 10 10
actin cytoskeleton organization -0.051 0.027 0.14 3 -0.22 1 4
IGF-1R heterotetramer 0.022 0.013 -10000 0 0 138 138
GIT1 0.028 0.007 -10000 0 0 30 30
IGF1R 0.022 0.013 -10000 0 0 138 138
IGF1 0.028 0.007 -10000 0 0 32 32
DIAPH1 0.028 0.13 -10000 0 -0.54 25 25
Wnt receptor signaling pathway -0.047 0.041 0.13 9 -10000 0 9
RHOA 0.029 0.003 -10000 0 0 6 6
RhoA/GTP -0.065 0.034 -10000 0 -10000 0 0
CTNNA1 0.029 0.004 -10000 0 0 11 11
VCL -0.052 0.027 0.14 3 -0.23 1 4
EFNA1 0.027 0.008 -10000 0 0 46 46
LPP -0.048 0.034 0.14 4 -0.3 1 5
Ephrin A1/EPHA2 -0.05 0.033 0.094 21 -10000 0 21
SEC6/SEC8 -0.064 0.034 -10000 0 -0.23 1 1
MGAT3 -0.045 0.027 0.16 4 -10000 0 4
HGF/MET -0.044 0.048 0.094 49 -10000 0 49
HGF 0.028 0.005 -10000 0 0 16 16
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.011 0.058 -10000 0 -0.2 28 28
actin cable formation -0.031 0.087 0.28 12 -0.27 10 22
KIAA1543 -0.047 0.022 0.14 4 -10000 0 4
KIFC3 -0.047 0.024 0.16 2 -10000 0 2
NCK1 0.026 0.009 -10000 0 0 64 64
EXOC3 0.026 0.009 -10000 0 0 60 60
ACTN1 -0.048 0.026 0.16 4 -0.22 1 5
NCK1/GIT1 0.036 0.016 -10000 0 -10000 0 0
mol:GDP 0.047 0.041 -10000 0 -0.13 9 9
EXOC4 0.028 0.007 -10000 0 0 34 34
STX4 -0.049 0.024 0.16 4 -10000 0 4
PIP5K1C -0.046 0.027 0.16 4 -10000 0 4
LIMA1 0.028 0.005 -10000 0 0 19 19
ABI1 0.029 0.005 -10000 0 0 14 14
ROCK1 -0.046 0.077 0.24 13 -10000 0 13
adherens junction assembly -0.065 0.1 0.22 1 -0.54 17 18
IGF-1R heterotetramer/IGF1 -0.075 0.042 0.094 3 -0.22 3 6
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.03 0.042 -10000 0 -0.16 22 22
MET 0.025 0.011 -10000 0 0 86 86
PLEKHA7 -0.049 0.024 0.16 4 -10000 0 4
mol:GTP 0.065 0.039 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity -0.044 0.09 0.28 15 -10000 0 15
cortical actin cytoskeleton stabilization -0.011 0.058 -10000 0 -0.2 28 28
regulation of cell-cell adhesion -0.051 0.027 0.14 3 -0.22 1 4
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.011 0.058 -10000 0 -0.2 28 28
Regulation of Androgen receptor activity

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
HDAC1 -0.017 0.056 0.19 36 -10000 0 36
SMARCC1 -0.013 0.034 0.62 1 -10000 0 1
REL 0.029 0.004 -10000 0 -10000 0 0
HDAC7 -0.13 0.11 0.29 2 -0.31 32 34
JUN 0.028 0.007 -10000 0 -10000 0 0
EP300 0.027 0.008 -10000 0 -10000 0 0
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.015 0.079 0.18 74 -10000 0 74
FOXO1 0.027 0.007 -10000 0 -10000 0 0
T-DHT/AR -0.13 0.12 0.34 1 -0.34 15 16
MAP2K6 -0.031 0.018 -10000 0 -10000 0 0
BRM/BAF57 -0.003 0.081 -10000 0 -0.16 111 111
MAP2K4 -0.027 0.024 -10000 0 -10000 0 0
SMARCA2 0.021 0.013 -10000 0 -10000 0 0
PDE9A -0.15 0.28 -10000 0 -0.9 59 59
NCOA2 0.027 0.008 -10000 0 -10000 0 0
CEBPA 0.027 0.009 -10000 0 -10000 0 0
EHMT2 0.029 0.005 -10000 0 -10000 0 0
cell proliferation -0.14 0.14 -10000 0 -0.36 42 42
NR0B1 0.027 0.007 -10000 0 0 38 38
EGR1 0.018 0.014 -10000 0 -10000 0 0
RXRs/9cRA 0.045 0.034 -10000 0 -0.13 13 13
AR/RACK1/Src -0.075 0.096 0.3 3 -0.28 2 5
AR/GR -0.12 0.1 0.18 2 -0.21 264 266
GNB2L1 0.029 0.005 -10000 0 -10000 0 0
PKN1 0.025 0.01 -10000 0 0 80 80
RCHY1 0.027 0.008 -10000 0 0 47 47
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.041 0.027 0.18 4 -0.19 1 5
T-DHT/AR/TIF2/CARM1 -0.074 0.09 0.37 1 -0.29 2 3
SRC -0.052 0.066 0.24 1 -10000 0 1
NR3C1 0.029 0.005 -10000 0 0 15 15
KLK3 -0.048 0.078 -10000 0 -10000 0 0
APPBP2 -0.029 0.023 -10000 0 -10000 0 0
TRIM24 0.027 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.081 0.068 0.12 1 -0.2 19 20
TMPRSS2 -0.39 0.45 -10000 0 -0.89 244 244
RXRG 0.028 0.007 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.028 0.007 -10000 0 -10000 0 0
RXRB 0.028 0.005 -10000 0 -10000 0 0
CARM1 0.026 0.009 -10000 0 -10000 0 0
NR2C2 0.029 0.003 -10000 0 -10000 0 0
KLK2 -0.061 0.079 0.32 1 -0.35 2 3
AR -0.11 0.11 0.17 1 -0.22 253 254
SENP1 0.028 0.007 -10000 0 -10000 0 0
HSP90AA1 0.028 0.006 -10000 0 0 21 21
MDM2 0.028 0.006 -10000 0 -10000 0 0
SRY 0 0 -10000 0 -10000 0 0
GATA2 0.028 0.006 -10000 0 0 28 28
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 0.028 0.006 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.075 0.1 0.28 7 -0.29 2 9
positive regulation of transcription 0.028 0.006 -10000 0 0 28 28
DNAJA1 -0.029 0.024 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.057 0.3 4 -0.22 18 22
NCOA1 0.031 0.018 0.23 1 -10000 0 1
SPDEF 0.027 0.008 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.058 0.083 0.25 2 -0.28 26 28
T-DHT/AR/Hsp90 -0.079 0.088 0.26 4 -0.26 4 8
GSK3B -0.007 0.031 -10000 0 -10000 0 0
NR2C1 0.029 0.005 -10000 0 -10000 0 0
mol:T-DHT -0.045 0.071 0.21 2 -0.2 1 3
SIRT1 0.029 0.003 -10000 0 0 6 6
ZMIZ2 0.029 0.004 -10000 0 -10000 0 0
POU2F1 -0.065 0.064 -10000 0 -0.19 30 30
T-DHT/AR/DAX-1 -0.076 0.089 0.27 5 -0.24 3 8
CREBBP 0.027 0.008 -10000 0 0 41 41
SMARCE1 0.028 0.007 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.04 0.022 0.2 1 -10000 0 1
KIRREL -0.022 0.03 0.048 81 -10000 0 81
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.04 0.022 -10000 0 -0.2 1 1
PLCG1 0.028 0.007 -10000 0 0 33 33
ARRB2 0.028 0.006 -10000 0 0 25 25
WASL 0.028 0.006 -10000 0 0 21 21
Nephrin/NEPH1/podocin/CD2AP 0.064 0.039 0.2 1 -10000 0 1
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.014 0.034 0.16 1 -0.19 1 2
FYN -0.004 0.064 0.14 76 -0.22 1 77
mol:Ca2+ 0.06 0.038 -10000 0 -0.17 1 1
mol:DAG 0.062 0.039 -10000 0 -0.17 1 1
NPHS2 -0.02 0.033 0.049 97 -10000 0 97
mol:IP3 0.062 0.039 -10000 0 -0.17 1 1
regulation of endocytosis 0.031 0.052 -10000 0 -0.21 1 1
Nephrin/NEPH1/podocin/Cholesterol 0.051 0.03 0.15 3 -0.16 1 4
establishment of cell polarity 0.04 0.022 -10000 0 -0.2 1 1
Nephrin/NEPH1/podocin/NCK1-2 0.081 0.047 -10000 0 -0.16 1 1
Nephrin/NEPH1/beta Arrestin2 0.033 0.054 -10000 0 -0.21 1 1
NPHS1 -0.023 0.027 0.05 54 -10000 0 54
Nephrin/NEPH1/podocin 0.03 0.049 0.19 4 -0.087 62 66
TJP1 0.027 0.007 -10000 0 0 38 38
NCK1 0.026 0.009 -10000 0 0 64 64
NCK2 0.029 0.004 -10000 0 0 10 10
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.063 0.04 -10000 0 -0.17 1 1
CD2AP 0.028 0.007 -10000 0 0 31 31
Nephrin/NEPH1/podocin/GRB2 0.064 0.039 0.2 1 -0.17 1 2
GRB2 0.028 0.005 -10000 0 0 19 19
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.012 0.072 0.15 83 -0.15 1 84
cytoskeleton organization -0.017 0.048 0.2 12 -0.2 1 13
Nephrin/NEPH1 0.034 0.018 -10000 0 -0.13 1 1
Nephrin/NEPH1/ZO-1 0.048 0.03 -10000 0 -0.16 1 1
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.027 0.014 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ -0.032 0.022 -10000 0 -10000 0 0
CDKN1B 0.019 0.075 0.25 12 -0.32 9 21
CDKN1A 0.009 0.065 0.28 3 -0.31 9 12
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.024 0.011 -10000 0 0 96 96
FOXO3 0.007 0.055 -10000 0 -0.34 6 6
AKT1 0.014 0.057 -10000 0 -0.34 9 9
BAD 0.029 0.002 -10000 0 0 4 4
AKT3 -0.1 0.11 -10000 0 -0.21 281 281
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.008 0.06 -10000 0 -0.31 10 10
AKT1/ASK1 0.034 0.063 0.21 2 -0.3 12 14
BAD/YWHAZ 0.044 0.026 -10000 0 -10000 0 0
RICTOR 0.027 0.008 -10000 0 0 40 40
RAF1 0.029 0.003 -10000 0 0 7 7
JNK cascade -0.032 0.061 0.29 12 -0.2 2 14
TSC1 0.008 0.051 -10000 0 -0.3 7 7
YWHAZ 0.025 0.01 -10000 0 0 78 78
AKT1/RAF1 0.037 0.066 0.22 2 -0.31 12 14
EP300 0.027 0.008 -10000 0 0 50 50
mol:GDP 0.015 0.057 -10000 0 -0.34 9 9
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.005 0.056 -10000 0 -0.31 10 10
YWHAQ 0.029 0.005 -10000 0 0 15 15
TBC1D4 -0.014 0.011 0.19 1 -10000 0 1
MAP3K5 0.028 0.007 -10000 0 0 32 32
MAPKAP1 0.028 0.005 -10000 0 0 18 18
negative regulation of cell cycle -0.018 0.064 0.29 8 -0.17 4 12
YWHAH 0.027 0.008 -10000 0 0 42 42
AKT1S1 0.006 0.06 -10000 0 -0.34 9 9
CASP9 0.007 0.056 0.18 1 -0.31 9 10
YWHAB 0.027 0.008 -10000 0 0 45 45
p27Kip1/KPNA1 0.021 0.089 0.26 20 -0.32 9 29
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.053 0.019 -10000 0 -10000 0 0
YWHAE 0.027 0.008 -10000 0 0 40 40
SRC 0.028 0.007 -10000 0 0 33 33
AKT2/p21CIP1 0.002 0.061 0.2 11 -0.32 8 19
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.014 0.032 -10000 0 -0.28 3 3
CHUK 0.012 0.064 0.24 9 -0.31 9 18
BAD/BCL-XL -0.006 0.061 -10000 0 -0.34 8 8
mTORC2 0.033 0.013 -10000 0 -10000 0 0
AKT2 0.006 0.002 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.016 0.083 0.25 2 -0.38 9 11
PDPK1 0.028 0.005 -10000 0 0 18 18
MDM2 0.011 0.069 0.26 4 -0.34 9 13
MAPKKK cascade -0.036 0.065 0.3 12 -0.22 2 14
MDM2/Cbp/p300 0.039 0.075 0.32 5 -0.33 10 15
TSC1/TSC2 -0.004 0.063 0.27 5 -0.32 10 15
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.072 0.3 5 -0.31 10 15
glucose import -0.021 0.035 0.19 11 -10000 0 11
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.013 0.046 0.21 4 -0.2 9 13
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.018 0.031 0.19 11 -10000 0 11
GSK3A 0.009 0.059 0.23 8 -0.3 8 16
FOXO1 0.006 0.051 -10000 0 -0.3 7 7
GSK3B 0.009 0.064 0.2 11 -0.32 10 21
SFN 0.027 0.007 -10000 0 0 37 37
G1/S transition of mitotic cell cycle 0.008 0.077 0.28 16 -0.33 8 24
p27Kip1/14-3-3 family 0.019 0.044 0.23 1 -0.39 1 2
PRKACA 0.025 0.01 -10000 0 0 79 79
KPNA1 0.028 0.005 -10000 0 0 18 18
HSP90AA1 0.028 0.006 -10000 0 0 21 21
YWHAG 0.029 0.004 -10000 0 0 11 11
RHEB 0.026 0.009 -10000 0 0 54 54
CREBBP 0.027 0.008 -10000 0 0 41 41
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.028 0.084 -10000 0 -0.25 25 25
Ran/GTP/Exportin 1/HDAC1 -0.032 0.014 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.003 0.089 0.2 1 -0.31 27 28
SUMO1 0.029 0.003 -10000 0 0 7 7
ZFPM1 0.026 0.009 -10000 0 0 62 62
NPC/RanGAP1/SUMO1/Ubc9 -0.006 0.034 -10000 0 -0.27 3 3
FKBP3 0.028 0.006 -10000 0 0 23 23
Histones 0.055 0.061 -10000 0 -0.22 12 12
YY1/LSF 0 0.064 -10000 0 -0.23 21 21
SMG5 0.028 0.006 -10000 0 0 24 24
RAN 0.029 0.004 -10000 0 0 12 12
I kappa B alpha/HDAC3 -0.022 0.041 0.11 1 -0.2 22 23
I kappa B alpha/HDAC1 0.018 0.064 -10000 0 -0.22 25 25
SAP18 0.028 0.007 -10000 0 0 31 31
RELA -0.006 0.078 0.25 1 -0.38 9 10
HDAC1/Smad7 0.05 0.022 -10000 0 -10000 0 0
RANGAP1 0.027 0.008 -10000 0 0 47 47
HDAC3/TR2 0.026 0.051 -10000 0 -0.21 13 13
NuRD/MBD3 Complex 0.004 0.066 0.24 1 -0.26 15 16
NF kappa B1 p50/RelA 0.002 0.09 0.22 1 -0.32 22 23
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.028 0.006 -10000 0 0 28 28
GATA1 0.028 0.007 -10000 0 0 31 31
Mad/Max 0.042 0.009 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.008 0.085 0.24 1 -0.35 18 19
RBBP7 0.028 0.005 -10000 0 0 19 19
NPC 0.017 0.002 -10000 0 -10000 0 0
RBBP4 0.027 0.007 -10000 0 0 38 38
MAX 0.028 0.005 -10000 0 0 16 16
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.028 0.005 -10000 0 0 16 16
NFKBIA 0 0.049 -10000 0 -0.31 11 11
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.002 0.068 0.18 4 -0.26 18 22
SIN3 complex 0.053 0.042 -10000 0 -10000 0 0
SMURF1 0.028 0.005 -10000 0 0 19 19
CHD3 0.028 0.007 -10000 0 0 34 34
SAP30 0.027 0.008 -10000 0 0 46 46
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.027 0.008 -10000 0 0 40 40
YY1/HDAC3 -0.011 0.061 -10000 0 -0.27 16 16
YY1/HDAC2 0.002 0.063 -10000 0 -0.23 22 22
YY1/HDAC1 0.002 0.062 -10000 0 -0.16 64 64
NuRD/MBD2 Complex (MeCP1) 0.006 0.065 0.24 1 -0.28 11 12
PPARG -0.001 0.078 0.28 1 -0.32 11 12
HDAC8/hEST1B 0.047 0.024 -10000 0 -10000 0 0
UBE2I 0.028 0.006 -10000 0 0 23 23
beta TrCP1/SCF ubiquitin ligase complex 0.028 0.005 -10000 0 0 16 16
TNFRSF1A 0.025 0.01 -10000 0 0 77 77
HDAC3/SMRT (N-CoR2) 0.026 0.051 -10000 0 -0.21 13 13
MBD3L2 0.027 0.007 -10000 0 0 37 37
ubiquitin-dependent protein catabolic process 0.05 0.021 -10000 0 -10000 0 0
CREBBP 0.027 0.008 -10000 0 0 41 41
NuRD/MBD3/MBD3L2 Complex -0.002 0.086 0.25 1 -0.33 20 21
HDAC1 0.027 0.008 -10000 0 0 49 49
HDAC3 0.005 0.029 -10000 0 -0.32 2 2
HDAC2 0.027 0.007 -10000 0 0 38 38
YY1 0 0.025 -10000 0 -0.19 9 9
HDAC8 0.028 0.006 -10000 0 0 26 26
SMAD7 0.028 0.006 -10000 0 0 28 28
NCOR2 0.028 0.005 -10000 0 0 17 17
MXD1 0.029 0.004 -10000 0 0 10 10
STAT3 0.003 0.04 -10000 0 -0.23 15 15
NFKB1 0.027 0.008 -10000 0 0 46 46
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.029 0.004 -10000 0 0 10 10
YY1/LSF/HDAC1 0.013 0.066 -10000 0 -0.22 20 20
YY1/SAP30/HDAC1 0.013 0.066 -10000 0 -0.22 20 20
EP300 0.027 0.008 -10000 0 0 50 50
STAT3 (dimer non-phopshorylated) 0.003 0.04 -10000 0 -0.23 15 15
proteasomal ubiquitin-dependent protein catabolic process 0.001 0.049 -10000 0 -0.31 11 11
histone deacetylation 0.006 0.064 0.24 1 -0.28 11 12
STAT3 (dimer non-phopshorylated)/HDAC3 -0.001 0.067 -10000 0 -0.28 13 13
nuclear export -0.046 0.024 -10000 0 -10000 0 0
PRKACA 0.025 0.01 -10000 0 0 79 79
GATAD2B 0.028 0.006 -10000 0 0 23 23
GATAD2A 0.027 0.008 -10000 0 0 44 44
GATA2/HDAC3 0.025 0.051 -10000 0 -0.21 13 13
GATA1/HDAC1 0.038 0.015 -10000 0 -10000 0 0
GATA1/HDAC3 0.025 0.05 -10000 0 -0.21 13 13
CHD4 0.026 0.009 -10000 0 0 58 58
TNF-alpha/TNFR1A 0.032 0.037 -10000 0 -0.16 16 16
SIN3/HDAC complex/Mad/Max -0.001 0.075 0.19 5 -0.26 23 28
NuRD Complex -0.005 0.084 0.25 1 -0.34 16 17
positive regulation of chromatin silencing 0.052 0.059 -10000 0 -0.21 12 12
SIN3B 0.026 0.009 -10000 0 0 62 62
MTA2 0.029 0.003 -10000 0 0 6 6
SIN3A 0.028 0.005 -10000 0 0 18 18
XPO1 0.027 0.008 -10000 0 0 51 51
SUMO1/HDAC1 0.022 0.051 -10000 0 -0.22 10 10
HDAC complex 0.065 0.039 -10000 0 -0.14 2 2
GATA1/Fog1 0.037 0.016 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.049 0.023 -10000 0 -10000 0 0
TNF 0.028 0.005 -10000 0 0 16 16
negative regulation of cell growth -0.001 0.075 0.19 5 -0.26 23 28
NuRD/MBD2/PRMT5 Complex 0.006 0.065 0.24 1 -0.28 11 12
Ran/GTP/Exportin 1 0.021 0.051 -10000 0 -0.22 11 11
NF kappa B/RelA/I kappa B alpha -0.017 0.075 -10000 0 -0.29 29 29
SIN3/HDAC complex/NCoR1 -0.008 0.083 0.17 4 -0.33 22 26
TFCP2 0.027 0.008 -10000 0 0 42 42
NR2C1 0.029 0.005 -10000 0 0 14 14
MBD3 0.027 0.008 -10000 0 0 51 51
MBD2 0.027 0.007 -10000 0 0 36 36
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.028 0.005 -10000 0 0 20 20
SPHK1 0.028 0.005 -10000 0 0 18 18
GNAI2 0.029 0.003 -10000 0 0 6 6
mol:S1P 0.004 0.009 0.13 3 -10000 0 3
GNAO1 0.027 0.008 -10000 0 0 45 45
mol:Sphinganine-1-P -0.031 0.012 0.19 1 -10000 0 1
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.033 0.038 0.17 1 -0.26 3 4
GNAI3 0.024 0.011 -10000 0 0 98 98
G12/G13 0.04 0.011 -10000 0 -10000 0 0
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P -0.003 0.029 -10000 0 -0.28 3 3
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 0.028 0.006 -10000 0 0 26 26
S1P/S1P5/G12 0.018 0.035 0.16 1 -0.26 3 4
S1P/S1P3/Gq -0.009 0.084 -10000 0 -0.32 26 26
S1P/S1P4/Gi 0.009 0.062 0.18 2 -0.22 18 20
GNAQ 0.028 0.007 -10000 0 0 29 29
GNAZ 0.027 0.008 -10000 0 0 47 47
GNA14 0.028 0.005 -10000 0 0 19 19
GNA15 0.027 0.008 -10000 0 0 46 46
GNA12 0.028 0.007 -10000 0 0 33 33
GNA13 0.029 0.004 -10000 0 0 13 13
GNA11 0.025 0.01 -10000 0 0 83 83
ABCC1 0.028 0.005 -10000 0 0 17 17
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.051 0.048 -10000 0 -0.14 12 12
MAP4K1 0.026 0.01 -10000 0 0 70 70
MAP3K8 0.029 0.005 -10000 0 0 15 15
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0.029 0.004 -10000 0 0 12 12
CRKL 0.028 0.007 -10000 0 0 31 31
MAP3K1 -0.016 0.05 -10000 0 -0.27 9 9
JUN -0.002 0.064 0.24 1 -0.57 4 5
MAP3K7 -0.015 0.049 0.15 3 -0.23 10 13
GRAP2 0.027 0.008 -10000 0 0 47 47
CRK 0.027 0.007 -10000 0 0 36 36
MAP2K4 -0.027 0.084 0.26 1 -0.32 27 28
LAT 0.029 0.003 -10000 0 0 8 8
LCP2 0.028 0.007 -10000 0 0 33 33
MAPK8 0.004 0.056 -10000 0 -0.59 4 4
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.005 0.06 -10000 0 -0.28 14 14
LAT/GRAP2/SLP76/HPK1/HIP-55 0.058 0.055 -10000 0 -0.14 12 12
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.007 0.13 0.59 1 -0.45 2 3
CRKL -0.026 0.091 0.26 12 -0.21 6 18
mol:DAG -0.034 0.075 0.36 2 -0.28 7 9
HRAS -0.033 0.1 0.26 25 -10000 0 25
MAPK8 -0.019 0.076 0.17 32 -10000 0 32
RAP1A -0.025 0.094 0.26 14 -0.21 4 18
GAB1 -0.025 0.094 0.26 14 -10000 0 14
MAPK14 -0.019 0.076 0.16 63 -10000 0 63
EPO -0.02 0.034 0.076 6 -10000 0 6
PLCG1 -0.034 0.076 0.36 2 -0.29 7 9
EPOR/TRPC2/IP3 Receptors -0.023 0.029 0.076 2 -10000 0 2
RAPGEF1 0.028 0.005 -10000 0 0 18 18
EPO/EPOR (dimer)/SOCS3 0.035 0.049 0.18 2 -0.16 2 4
GAB1/SHC/GRB2/SOS1 -0.037 0.098 0.25 12 -10000 0 12
EPO/EPOR (dimer) 0.024 0.042 0.16 1 -10000 0 1
IRS2 -0.025 0.093 0.26 14 -0.21 3 17
STAT1 -0.025 0.076 0.48 2 -0.34 3 5
STAT5B -0.045 0.095 0.44 2 -0.32 6 8
cell proliferation -0.025 0.079 0.17 37 -10000 0 37
GAB1/SHIP/PIK3R1/SHP2/SHC -0.065 0.078 0.17 1 -0.23 18 19
TEC -0.022 0.091 0.26 13 -0.21 4 17
SOCS3 0.028 0.005 -10000 0 0 20 20
STAT1 (dimer) -0.024 0.076 0.48 2 -0.34 3 5
JAK2 -0.019 0.032 0.068 8 -10000 0 8
PIK3R1 0.021 0.013 -10000 0 0 159 159
EPO/EPOR (dimer)/JAK2 0.035 0.092 0.48 2 -0.21 6 8
EPO/EPOR 0.024 0.042 0.16 1 -10000 0 1
LYN 0.015 0.028 0.09 2 -0.047 83 85
TEC/VAV2 -0.032 0.089 0.27 9 -10000 0 9
elevation of cytosolic calcium ion concentration -0.023 0.029 0.076 2 -10000 0 2
SHC1 0.028 0.006 -10000 0 0 21 21
EPO/EPOR (dimer)/LYN 0.028 0.059 0.3 2 -0.16 9 11
mol:IP3 -0.034 0.075 0.36 2 -0.28 7 9
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.049 0.089 0.25 7 -0.23 13 20
SH2B3 -0.018 0.035 0.065 13 -10000 0 13
NFKB1 -0.019 0.074 0.17 30 -0.24 2 32
EPO/EPOR (dimer)/JAK2/SOCS3 0.008 0.029 0.2 1 -0.18 3 4
PTPN6 -0.033 0.077 0.28 6 -0.21 6 12
TEC/VAV2/GRB2 -0.031 0.098 0.27 10 -10000 0 10
EPOR -0.023 0.029 0.076 2 -10000 0 2
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.038 0.098 0.25 12 -10000 0 12
SOS1 0.027 0.007 -10000 0 0 36 36
PLCG2 0.026 0.009 -10000 0 0 62 62
CRKL/CBL/C3G -0.04 0.094 0.25 9 -10000 0 9
VAV2 -0.026 0.092 0.26 13 -0.21 5 18
CBL -0.025 0.094 0.26 14 -10000 0 14
SHC/Grb2/SOS1 -0.051 0.066 0.27 2 -0.22 4 6
STAT5A -0.046 0.097 0.44 2 -0.33 10 12
GRB2 0.028 0.005 -10000 0 0 19 19
STAT5 (dimer) -0.076 0.14 0.57 2 -0.38 63 65
LYN/PLCgamma2 0.021 0.042 -10000 0 -0.16 12 12
PTPN11 0.029 0.003 -10000 0 0 8 8
BTK -0.024 0.094 0.26 14 -0.21 3 17
BCL2 -0.071 0.26 0.5 1 -0.64 84 85
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.005 0.043 0.13 52 -0.15 1 53
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A -0.001 0.054 0.12 4 -0.2 30 34
AP2 0.026 0.044 -10000 0 -0.16 25 25
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.032 0.023 -10000 0 -10000 0 0
CLTB 0.029 0.004 -10000 0 0 13 13
coatomer protein complex/ARF1/GTP/ER cargo protein -0.013 0.039 0.12 1 -0.18 23 24
CD4 0.026 0.01 -10000 0 0 71 71
CLTA 0.029 0.004 -10000 0 0 12 12
mol:GTP -0.004 0.004 0.012 4 -0.022 25 29
ARFGAP1 -0.015 0.005 0 62 -10000 0 62
mol:PI-4-5-P2 -0.005 0.023 0.093 7 -0.15 1 8
ARF1/GTP -0.025 0.03 -10000 0 -0.15 26 26
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.016 0.031 -10000 0 -0.16 21 21
mol:Choline -0.005 0.023 0.092 7 -0.15 1 8
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 -0.02 0.023 0.044 17 -10000 0 17
DDEF1 -0.003 0.023 0.093 7 -0.16 1 8
ARF1/GDP -0.002 0.013 -10000 0 -0.099 4 4
AP2M1 0.024 0.011 -10000 0 0 97 97
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.024 0.025 -10000 0 -0.12 24 24
Rac/GTP 0.019 0.011 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.024 0.035 -10000 0 -0.12 24 24
ARFIP2 -0.029 0.011 0.026 12 -10000 0 12
COPA 0.028 0.005 -10000 0 0 20 20
RAC1 0.028 0.006 -10000 0 0 27 27
ARF1/GTP/coatomer protein complex -0.001 0.04 -10000 0 -0.16 23 23
ARF1/GTP/ARHGAP10 0.012 0.031 -10000 0 -0.13 25 25
GGA3 0.028 0.005 -10000 0 0 18 18
ARF1/GTP/Membrin 0.007 0.051 -10000 0 -0.16 40 40
AP2A1 0.027 0.008 -10000 0 0 48 48
coatomer protein complex/ARF1/GTP/ARF-GAP1 -0.01 0.035 -10000 0 -0.18 5 5
ARF1/GDP/Membrin 0.013 0.056 -10000 0 -0.26 16 16
Arfaptin 2/Rac/GDP 0.034 0.019 -10000 0 -10000 0 0
CYTH2 -0.004 0.004 0.012 4 -0.022 25 29
ARF1/GTP/GGA3 0.028 0.039 -10000 0 -0.14 25 25
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.021 0.005 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP -0.005 0.044 -10000 0 -0.22 7 7
PLD2 -0.005 0.023 0.092 7 -0.15 1 8
ARF-GAP1/v-SNARE -0.015 0.005 0 62 -10000 0 62
PIP5K1A -0.005 0.024 0.093 7 -0.15 1 8
ARF1/GTP/Membrin/GBF1/p115 0.004 0.037 -10000 0 -0.13 32 32
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.005 0.023 0.092 7 -0.15 1 8
KDEL Receptor/Ligand/ARF-GAP1 -0.015 0.005 0 62 -10000 0 62
GOSR2 0.001 0.051 -10000 0 -0.35 11 11
USO1 0.001 0.053 -10000 0 -0.35 12 12
GBF1 0.001 0.052 -10000 0 -0.34 12 12
ARF1/GTP/Arfaptin 2 0.027 0.041 -10000 0 -0.15 25 25
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.035 0.044 -10000 0 -0.15 20 20
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.064 0.037 -10000 0 -0.14 5 5
HDAC3 0.029 0.003 -10000 0 0 7 7
Ran/GTP/Exportin 1/HDAC4 -0.033 0.012 -10000 0 -10000 0 0
GATA1/HDAC4 0.04 0.012 -10000 0 -10000 0 0
GATA1/HDAC5 0.038 0.021 -10000 0 -0.16 4 4
GATA2/HDAC5 0.037 0.028 -10000 0 -0.16 9 9
HDAC5/BCL6/BCoR 0.041 0.04 -10000 0 -0.15 15 15
HDAC9 0.027 0.008 -10000 0 0 51 51
Glucocorticoid receptor/Hsp90/HDAC6 0.051 0.03 -10000 0 -0.15 8 8
HDAC4/ANKRA2 0.039 0.014 -10000 0 -10000 0 0
HDAC5/YWHAB 0.037 0.022 -10000 0 -0.16 4 4
NPC/RanGAP1/SUMO1/Ubc9 -0.006 0.034 -10000 0 -0.27 3 3
GATA2 0.028 0.006 -10000 0 0 28 28
HDAC4/RFXANK 0.038 0.014 -10000 0 -10000 0 0
BCOR 0.029 0.005 -10000 0 0 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.022 0.012 -10000 0 0 131 131
HDAC5 0.028 0.006 -10000 0 0 28 28
GNB1/GNG2 0.041 0.013 -10000 0 -0.16 1 1
Histones -0.02 0.069 -10000 0 -0.23 27 27
ADRBK1 0.029 0.003 -10000 0 0 6 6
HDAC4 0.028 0.005 -10000 0 0 16 16
XPO1 0.027 0.008 -10000 0 0 51 51
HDAC5/ANKRA2 0.037 0.022 -10000 0 -0.16 4 4
HDAC4/Ubc9 0.041 0.011 -10000 0 -10000 0 0
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.038 0.023 -10000 0 -0.16 5 5
TUBA1B 0.029 0.002 -10000 0 0 4 4
HDAC6 0.028 0.007 -10000 0 0 31 31
HDAC5/RFXANK 0.036 0.023 -10000 0 -0.16 4 4
CAMK4 0.027 0.007 -10000 0 0 39 39
Tubulin/HDAC6 0.052 0.02 -10000 0 -10000 0 0
SUMO1 0.029 0.003 -10000 0 0 7 7
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.027 0.008 -10000 0 0 45 45
GATA1 0.028 0.007 -10000 0 0 31 31
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.027 0.008 -10000 0 0 40 40
NR3C1 0.029 0.005 -10000 0 0 15 15
SUMO1/HDAC4 0.023 0.054 -10000 0 -0.22 12 12
SRF 0.028 0.007 -10000 0 0 30 30
HDAC4/YWHAB 0.039 0.013 -10000 0 -10000 0 0
Tubulin 0.04 0.012 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.039 0.015 -10000 0 -0.16 1 1
GNB1 0.028 0.006 -10000 0 0 24 24
RANGAP1 0.027 0.008 -10000 0 0 47 47
BCL6/BCoR 0.031 0.033 -10000 0 -0.16 12 12
HDAC4/HDAC3/SMRT (N-CoR2) 0.053 0.029 -10000 0 -0.15 9 9
HDAC4/SRF 0.051 0.023 -10000 0 -0.15 2 2
HDAC4/ER alpha 0.014 0.069 -10000 0 -0.16 71 71
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.02 0.069 -10000 0 -0.23 27 27
cell motility 0.051 0.02 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.028 0.006 -10000 0 0 23 23
HDAC7/HDAC3 0.021 0.002 -10000 0 -10000 0 0
BCL6 0.024 0.011 -10000 0 0 100 100
HDAC4/CaMK II delta B 0.028 0.005 -10000 0 0 16 16
Hsp90/HDAC6 0.04 0.012 -10000 0 -10000 0 0
ESR1 0.024 0.012 -10000 0 0 106 106
HDAC6/HDAC11 0.041 0.011 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.021 0.051 -10000 0 -0.22 11 11
NPC 0.017 0.002 -10000 0 -10000 0 0
MEF2C 0.026 0.009 -10000 0 0 65 65
RAN 0.029 0.004 -10000 0 0 12 12
HDAC4/MEF2C 0.058 0.064 -10000 0 -0.14 29 29
GNG2 0.029 0.004 -10000 0 0 12 12
NCOR2 0.028 0.005 -10000 0 0 17 17
TUBB2A 0.027 0.008 -10000 0 0 41 41
HDAC11 0.029 0.003 -10000 0 0 7 7
HSP90AA1 0.028 0.006 -10000 0 0 21 21
RANBP2 0.029 0.004 -10000 0 0 10 10
ANKRA2 0.027 0.009 -10000 0 0 53 53
RFXANK 0.027 0.009 -10000 0 0 53 53
nuclear import -0.016 0.038 0.19 5 -10000 0 5
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.027 0.008 -10000 0 -10000 0 0
HDAC2 0.028 0.007 -10000 0 -10000 0 0
GNB1/GNG2 0.052 0.023 -10000 0 -0.16 1 1
forebrain development -0.004 0.083 -10000 0 -0.44 6 6
GNAO1 0.022 0.018 -10000 0 -0.035 40 40
SMO/beta Arrestin2 0.033 0.025 -10000 0 -10000 0 0
SMO 0.022 0.019 -10000 0 -0.038 47 47
ARRB2 0.023 0.017 -10000 0 -0.034 39 39
GLI3/SPOP 0.017 0.089 0.22 5 -0.33 16 21
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
GSK3B 0.028 0.005 -10000 0 0 19 19
GNAI2 0.024 0.017 -10000 0 -0.035 42 42
SIN3/HDAC complex 0.054 0.042 -10000 0 -10000 0 0
GNAI1 0.023 0.017 -10000 0 -0.034 41 41
XPO1 0.006 0.028 -10000 0 -0.044 36 36
GLI1/Su(fu) -0.001 0.086 -10000 0 -0.52 5 5
SAP30 0.027 0.008 -10000 0 -10000 0 0
mol:GDP 0.022 0.019 -10000 0 -0.038 47 47
MIM/GLI2A 0.013 0.036 -10000 0 -0.13 29 29
IFT88 0.027 0.008 -10000 0 0 44 44
GNAI3 0.021 0.017 -10000 0 -0.034 29 29
GLI2 -0.009 0.076 0.22 1 -0.3 21 22
GLI3 0.003 0.086 0.22 6 -0.33 16 22
CSNK1D 0.028 0.006 -10000 0 0 25 25
CSNK1E 0.027 0.008 -10000 0 0 45 45
SAP18 0.028 0.007 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.027 0.008 -10000 0 0 44 44
GNG2 0.029 0.004 -10000 0 0 12 12
Gi family/GTP 0.009 0.052 -10000 0 -0.21 9 9
SIN3B 0.026 0.009 -10000 0 -10000 0 0
SIN3A 0.029 0.005 -10000 0 -10000 0 0
GLI3/Su(fu) -0.001 0.096 0.22 3 -0.37 18 21
GLI2/Su(fu) -0.009 0.088 0.19 1 -0.35 23 24
FOXA2 -0.036 0.21 -10000 0 -0.78 37 37
neural tube patterning -0.004 0.083 -10000 0 -0.44 6 6
SPOP 0.029 0.005 -10000 0 0 15 15
Su(fu)/PIAS1 0.018 0.043 -10000 0 -0.19 15 15
GNB1 0.028 0.006 -10000 0 0 24 24
CSNK1G2 0.027 0.008 -10000 0 0 45 45
CSNK1G3 0.028 0.006 -10000 0 0 21 21
MTSS1 0.013 0.036 -10000 0 -0.13 29 29
embryonic limb morphogenesis -0.004 0.083 -10000 0 -0.44 6 6
SUFU 0.006 0.016 -10000 0 -10000 0 0
LGALS3 0.026 0.009 -10000 0 0 56 56
catabolic process 0.005 0.11 0.25 1 -0.43 18 19
GLI3A/CBP -0.031 0.01 -10000 0 -10000 0 0
KIF3A 0.028 0.005 -10000 0 0 17 17
GLI1 -0.005 0.084 -10000 0 -0.45 6 6
RAB23 0.028 0.005 -10000 0 0 18 18
CSNK1A1 0.029 0.004 -10000 0 0 13 13
IFT172 0.028 0.005 -10000 0 0 17 17
RBBP7 0.029 0.005 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.016 0.044 -10000 0 -0.18 16 16
GNAZ 0.022 0.017 -10000 0 -0.035 38 38
RBBP4 0.027 0.007 -10000 0 -10000 0 0
CSNK1G1 0.029 0.004 -10000 0 0 13 13
PIAS1 0.029 0.005 -10000 0 0 14 14
PRKACA 0.025 0.01 -10000 0 0 79 79
GLI2/SPOP 0.005 0.085 0.21 1 -0.33 20 21
STK36 0.007 0.029 -10000 0 -0.044 42 42
Gi family/GNB1/GNG2/GDP 0.003 0.064 -10000 0 -0.3 7 7
PTCH1 -0.017 0.13 -10000 0 -0.96 8 8
MIM/GLI1 -0.007 0.11 -10000 0 -0.54 4 4
CREBBP -0.031 0.01 -10000 0 -10000 0 0
Su(fu)/SIN3/HDAC complex -0.002 0.099 0.18 6 -0.4 20 26
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.013 0.069 -10000 0 -0.17 68 68
AKT1 -0.049 0.11 0.27 2 -0.39 7 9
PTK2B -0.043 0.1 0.31 14 -0.31 2 16
VEGFR2 homodimer/Frs2 -0.06 0.048 -10000 0 -10000 0 0
CAV1 0.024 0.012 -10000 0 0 108 108
CALM1 0.028 0.006 -10000 0 0 26 26
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.059 0.05 0.28 1 -10000 0 1
endothelial cell proliferation -0.028 0.1 0.29 8 -0.38 4 12
mol:Ca2+ -0.046 0.082 0.33 5 -10000 0 5
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.01 0.09 0.28 1 -0.24 1 2
RP11-342D11.1 -0.047 0.069 0.33 2 -10000 0 2
CDH5 0.026 0.009 -10000 0 0 59 59
VEGFA homodimer 0.067 0.036 -10000 0 -0.14 1 1
SHC1 0.028 0.006 -10000 0 0 21 21
SHC2 0.025 0.01 -10000 0 0 80 80
HRAS/GDP -0.068 0.065 0.098 9 -10000 0 9
SH2D2A 0.029 0.005 -10000 0 0 15 15
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.023 0.086 0.26 2 -0.45 4 6
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.061 0.05 0.28 1 -10000 0 1
VEGFR1 homodimer 0.028 0.006 -10000 0 0 28 28
SHC/GRB2/SOS1 0.02 0.096 0.26 1 -10000 0 1
GRB10 -0.049 0.083 0.33 5 -10000 0 5
PTPN11 0.029 0.003 -10000 0 0 8 8
GRB2 0.028 0.005 -10000 0 0 19 19
PAK1 0.027 0.008 -10000 0 0 48 48
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.012 0.096 0.28 1 -0.24 1 2
HRAS 0.028 0.006 -10000 0 0 26 26
VEGF/Rho/ROCK1/Integrin Complex -0.027 0.093 0.29 1 -0.27 37 38
HIF1A 0.028 0.005 -10000 0 0 17 17
FRS2 0.028 0.007 -10000 0 0 30 30
oxygen and reactive oxygen species metabolic process -0.055 0.07 0.16 15 -10000 0 15
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.028 0.005 -10000 0 0 16 16
Nck/Pak 0.035 0.017 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.07 0.06 0.28 1 -0.24 16 17
mol:GDP -0.062 0.07 0.14 10 -10000 0 10
mol:NADP -0.019 0.088 0.27 10 -0.43 4 14
eNOS/Hsp90 -0.02 0.089 0.27 9 -0.42 4 13
PIK3R1 0.021 0.013 -10000 0 0 159 159
mol:IP3 -0.047 0.082 0.33 5 -10000 0 5
HIF1A/ARNT 0.039 0.015 -10000 0 -0.16 1 1
SHB 0.029 0.003 -10000 0 0 8 8
VEGFA -0.026 0.01 -10000 0 -10000 0 0
VEGFC 0.023 0.012 -10000 0 0 112 112
FAK1/Vinculin -0.038 0.13 0.29 13 -0.38 10 23
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.029 0.003 -10000 0 0 6 6
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.002 0.1 0.28 1 -0.24 29 30
PTPN6 0.026 0.009 -10000 0 0 58 58
EPAS1 -0.025 0.015 -10000 0 -10000 0 0
mol:L-citrulline -0.019 0.088 0.27 10 -0.43 4 14
ITGAV 0.028 0.007 -10000 0 0 32 32
PIK3CA 0.02 0.014 -10000 0 0 170 170
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.014 0.087 0.28 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer -0.062 0.052 0.2 3 -10000 0 3
VEGFR2/3 heterodimer -0.063 0.049 -10000 0 -10000 0 0
VEGFB 0.028 0.006 -10000 0 0 24 24
MAPK11 -0.044 0.092 0.34 8 -0.33 1 9
VEGFR2 homodimer -0.061 0.064 0.4 2 -10000 0 2
FLT1 0.028 0.006 -10000 0 0 28 28
NEDD4 -0.029 0.006 -10000 0 -10000 0 0
MAPK3 -0.04 0.091 0.32 12 -10000 0 12
MAPK1 -0.038 0.091 0.32 12 -10000 0 12
VEGFA145/NRP2 0.035 0.017 -10000 0 -10000 0 0
VEGFR1/2 heterodimer -0.063 0.049 -10000 0 -10000 0 0
KDR -0.061 0.064 0.4 2 -10000 0 2
VEGFA165/NRP1/VEGFR2 homodimer -0.049 0.072 0.26 1 -10000 0 1
SRC 0.028 0.007 -10000 0 0 33 33
platelet activating factor biosynthetic process -0.039 0.094 0.32 13 -10000 0 13
PI3K -0.046 0.088 0.23 3 -10000 0 3
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.056 0.052 0.28 1 -10000 0 1
FES -0.049 0.084 0.33 5 -10000 0 5
GAB1 -0.048 0.093 0.24 9 -0.34 4 13
VEGFR2 homodimer/VEGFA homodimer/Src -0.057 0.049 0.28 1 -10000 0 1
CTNNB1 0.029 0.003 -10000 0 0 8 8
SOS1 0.027 0.007 -10000 0 0 36 36
ARNT 0.027 0.007 -10000 0 0 37 37
eNOS/Caveolin-1 -0.025 0.093 0.27 8 -0.4 5 13
VEGFR2 homodimer/VEGFA homodimer/Yes -0.057 0.05 0.28 1 -10000 0 1
PI3K/GAB1 -0.059 0.14 0.29 1 -0.37 23 24
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.023 0.09 0.28 1 -10000 0 1
PRKACA 0.025 0.01 -10000 0 0 79 79
VEGFR2/3 heterodimer/VEGFC homodimer -0.074 0.059 0.28 1 -0.24 16 17
HSP90AA1 0.028 0.006 -10000 0 0 21 21
CDC42 -0.05 0.085 0.33 5 -10000 0 5
actin cytoskeleton reorganization -0.061 0.05 0.27 1 -10000 0 1
PTK2 -0.045 0.11 0.31 6 -0.38 11 17
EDG1 -0.047 0.069 0.33 2 -10000 0 2
mol:DAG -0.047 0.082 0.33 5 -10000 0 5
CaM/Ca2+ -0.05 0.081 0.3 4 -10000 0 4
MAP2K3 -0.043 0.079 0.3 6 -10000 0 6
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.061 0.063 0.16 19 -10000 0 19
PLCG1 -0.047 0.083 0.33 5 -10000 0 5
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.014 0.087 0.28 1 -10000 0 1
IQGAP1 0.028 0.006 -10000 0 0 24 24
YES1 0.027 0.008 -10000 0 0 41 41
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.061 0.05 0.28 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.054 0.049 0.28 1 -10000 0 1
cell migration -0.046 0.12 0.28 10 -0.36 11 21
mol:PI-3-4-5-P3 -0.044 0.085 0.23 3 -10000 0 3
FYN 0.024 0.011 -10000 0 0 99 99
VEGFB/NRP1 -0.05 0.082 0.3 5 -10000 0 5
mol:NO -0.019 0.088 0.27 10 -0.43 4 14
PXN 0.029 0.005 -10000 0 0 14 14
HRAS/GTP -0.075 0.05 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.065 0.054 0.26 1 -10000 0 1
VHL 0.029 0.004 -10000 0 0 9 9
ITGB3 0.024 0.011 -10000 0 0 98 98
NOS3 -0.021 0.094 0.28 8 -0.49 4 12
VEGFR2 homodimer/VEGFA homodimer/Sck -0.064 0.056 0.28 1 -0.24 5 6
RAC1 0.028 0.006 -10000 0 0 27 27
PRKCA -0.048 0.086 0.31 9 -10000 0 9
PRKCB -0.042 0.082 0.32 9 -10000 0 9
VCL 0.029 0.004 -10000 0 0 12 12
VEGFA165/NRP1 -0.053 0.058 0.27 1 -10000 0 1
VEGFR1/2 heterodimer/VEGFA homodimer -0.061 0.051 0.28 1 -10000 0 1
VEGFA165/NRP2 0.035 0.017 -10000 0 -10000 0 0
MAPKKK cascade -0.069 0.077 0.27 4 -10000 0 4
NRP2 0.028 0.007 -10000 0 0 34 34
VEGFC homodimer 0.023 0.012 -10000 0 0 112 112
NCK1 0.026 0.009 -10000 0 0 64 64
ROCK1 0.029 0.005 -10000 0 0 14 14
FAK1/Paxillin -0.039 0.13 0.3 11 -0.37 12 23
MAP3K13 -0.042 0.078 0.33 4 -10000 0 4
PDPK1 -0.046 0.081 0.21 2 -10000 0 2
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.02 0.056 0.19 9 -0.16 1 10
GNAI2 0.029 0.003 -10000 0 0 6 6
S1P/S1P5/G12 0.019 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.027 0.008 -10000 0 0 45 45
RhoA/GTP 0.021 0.058 0.17 1 -0.19 9 10
negative regulation of cAMP metabolic process 0.011 0.052 0.18 1 -0.18 14 15
GNAZ 0.027 0.008 -10000 0 0 47 47
GNAI3 0.024 0.011 -10000 0 0 98 98
GNA12 0.028 0.007 -10000 0 0 33 33
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.011 0.052 0.18 1 -0.19 14 15
RhoA/GDP 0.021 0.007 -10000 0 -0.15 1 1
RHOA 0.029 0.003 -10000 0 0 6 6
GNAI1 0.028 0.006 -10000 0 0 26 26
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.042 0.022 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 -0.024 0.008 -10000 0 -10000 0 0
mol:DAG -0.041 0.021 0.17 3 -10000 0 3
VEGFR1 homodimer/NRP1/VEGFR 121 -0.03 0.013 -10000 0 -10000 0 0
CaM/Ca2+ -0.049 0.025 0.17 3 -10000 0 3
HIF1A 0.031 0.006 -10000 0 -10000 0 0
GAB1 0.028 0.006 -10000 0 0 24 24
AKT1 -0.03 0.088 0.29 1 -10000 0 1
PLCG1 -0.041 0.021 0.17 3 -10000 0 3
NOS3 -0.019 0.055 -10000 0 -0.3 2 2
CBL 0.029 0.004 -10000 0 0 12 12
mol:NO -0.011 0.066 0.4 2 -0.29 1 3
FLT1 -0.03 0.008 -10000 0 -10000 0 0
PGF 0.028 0.005 -10000 0 0 18 18
VEGFR1 homodimer/NRP2/VEGFR121 -0.037 0.019 -10000 0 -10000 0 0
CALM1 0.028 0.006 -10000 0 0 26 26
PIK3CA 0.02 0.014 -10000 0 0 170 170
eNOS/Hsp90 -0.009 0.074 0.32 1 -0.29 2 3
endothelial cell proliferation -0.022 0.047 0.33 1 -0.31 1 2
mol:Ca2+ -0.041 0.021 0.17 3 -10000 0 3
MAPK3 -0.053 0.035 0.32 1 -10000 0 1
MAPK1 -0.048 0.036 0.32 1 -10000 0 1
PIK3R1 0.021 0.013 -10000 0 0 159 159
PLGF homodimer 0.028 0.005 -10000 0 0 18 18
PRKACA 0.025 0.01 -10000 0 0 79 79
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.024 0.012 -10000 0 0 108 108
VEGFA homodimer 0.026 0.01 -10000 0 0 70 70
VEGFR1 homodimer/VEGFA homodimer -0.034 0.014 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.053 0.048 0.3 1 -10000 0 1
PI3K 0.016 0.074 -10000 0 -10000 0 0
PRKCA -0.045 0.028 -10000 0 -10000 0 0
PRKCB -0.037 0.019 0.16 3 -10000 0 3
VEGFR1 homodimer/PLGF homodimer -0.038 0.01 -10000 0 -10000 0 0
VEGFA 0.026 0.01 -10000 0 0 70 70
VEGFB 0.028 0.006 -10000 0 0 24 24
mol:IP3 -0.041 0.021 0.17 3 -10000 0 3
RASA1 -0.044 0.03 0.17 4 -10000 0 4
NRP2 0.028 0.007 -10000 0 0 34 34
VEGFR1 homodimer -0.03 0.008 -10000 0 -10000 0 0
VEGFB homodimer 0.028 0.006 -10000 0 0 24 24
NCK1 0.026 0.009 -10000 0 0 64 64
eNOS/Caveolin-1 -0.013 0.081 0.39 2 -0.32 5 7
PTPN11 0.029 0.003 -10000 0 0 8 8
mol:PI-3-4-5-P3 0.015 0.073 -10000 0 -10000 0 0
mol:L-citrulline -0.011 0.066 0.4 2 -0.29 1 3
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.052 0.037 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.035 0.02 -10000 0 -10000 0 0
CD2AP 0.028 0.007 -10000 0 0 31 31
PI3K/GAB1 0.02 0.081 -10000 0 -10000 0 0
PDPK1 -0.02 0.089 0.32 1 -10000 0 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.039 0.017 -10000 0 -10000 0 0
mol:NADP -0.011 0.066 0.4 2 -0.29 1 3
HSP90AA1 0.028 0.006 -10000 0 0 21 21
ubiquitin-dependent protein catabolic process 0.05 0.036 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 -0.036 0.012 -10000 0 -10000 0 0
p38 MAPK signaling 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
TRAF6/ASK1 0.018 0.014 -9999 0 -0.1 7 7
TRAF2/ASK1 0.036 0.013 -9999 0 -0.13 1 1
ATM 0.028 0.007 -9999 0 0 30 30
MAP2K3 -0.02 0.098 -9999 0 -0.31 38 38
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.014 0.088 -9999 0 -0.37 17 17
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0.028 0.006 -9999 0 0 23 23
TXN -0.003 0.036 -9999 0 -0.21 17 17
CALM1 0.028 0.006 -9999 0 0 26 26
GADD45A 0.027 0.009 -9999 0 0 53 53
GADD45B 0.027 0.008 -9999 0 0 49 49
MAP3K1 0.027 0.008 -9999 0 0 50 50
MAP3K6 0.028 0.005 -9999 0 0 16 16
MAP3K7 0.028 0.007 -9999 0 0 30 30
MAP3K4 0.027 0.008 -9999 0 0 48 48
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 0.04 0.014 -9999 0 -0.16 1 1
TAK1/TAB family 0.016 0.028 -9999 0 -0.14 2 2
RAC1/OSM/MEKK3 0.051 0.02 -9999 0 -10000 0 0
TRAF2 0.028 0.006 -9999 0 0 25 25
RAC1/OSM/MEKK3/MKK3 0.003 0.095 -9999 0 -0.27 37 37
TRAF6 0.003 0 -9999 0 -10000 0 0
RAC1 0.028 0.006 -9999 0 0 27 27
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B 0.029 0.004 -9999 0 0 13 13
CCM2 0.029 0.005 -9999 0 0 14 14
CaM/Ca2+/CAMKIIB 0.035 0.022 -9999 0 -0.13 8 8
MAPK11 0.022 0.012 -9999 0 0 131 131
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.047 0.032 -9999 0 -0.13 9 9
OSM/MEKK3 0.042 0.009 -9999 0 -10000 0 0
TAOK1 0.006 0.002 -9999 0 -10000 0 0
TAOK2 0.006 0.002 -9999 0 -10000 0 0
TAOK3 0.006 0.002 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.028 0.005 -9999 0 0 19 19
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0.028 0.007 -9999 0 0 32 32
MAP3K10 0.026 0.009 -9999 0 0 54 54
MAP3K3 0.029 0.004 -9999 0 0 13 13
TRX/ASK1 0.015 0.039 -9999 0 -0.17 23 23
GADD45/MTK1/MTK1 0.054 0.047 -9999 0 -0.13 7 7
Arf6 downstream pathway

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
PLAUR 0.001 0.093 0.6 12 -10000 0 12
regulation of axonogenesis 0.002 0.05 0.28 6 -0.21 12 18
myoblast fusion -0.021 0.061 0.33 1 -0.35 13 14
mol:GTP 0.027 0.038 0.23 12 -0.18 7 19
regulation of calcium-dependent cell-cell adhesion -0.046 0.053 0.15 1 -0.31 13 14
ARF1/GTP 0.032 0.048 0.21 10 -0.14 30 40
mol:GM1 0.01 0.034 0.2 13 -0.13 7 20
mol:Choline -0.011 0.041 0.16 25 -10000 0 25
lamellipodium assembly 0.005 0.068 0.35 12 -0.38 6 18
MAPK3 -0.005 0.063 0.39 13 -10000 0 13
ARF6/GTP/NME1/Tiam1 0.047 0.054 0.31 13 -0.15 1 14
ARF1 0.026 0.009 -10000 0 0 54 54
ARF6/GDP 0.021 0.061 0.35 13 -0.33 1 14
ARF1/GDP 0.019 0.058 0.31 11 -0.23 7 18
ARF6 0.043 0.022 0.17 13 -10000 0 13
RAB11A 0.029 0.004 -10000 0 0 13 13
TIAM1 -0.021 0.023 0.064 13 -10000 0 13
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 -0.004 0.063 0.39 13 -10000 0 13
actin filament bundle formation -0.025 0.059 0.23 7 -0.3 12 19
KALRN 0.002 0.022 0.14 3 -0.28 1 4
RAB11FIP3/RAB11A 0.041 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.025 0.06 0.3 12 -0.23 7 19
NME1 -0.02 0.023 0.064 13 -10000 0 13
Rac1/GDP 0.024 0.059 0.3 12 -0.23 7 19
substrate adhesion-dependent cell spreading 0.027 0.038 0.23 12 -0.18 7 19
cortical actin cytoskeleton organization 0.005 0.069 0.35 12 -0.38 6 18
RAC1 0.028 0.006 -10000 0 0 27 27
liver development 0.027 0.038 0.23 12 -0.18 7 19
ARF6/GTP 0.027 0.038 0.23 12 -0.18 7 19
RhoA/GTP 0.042 0.035 0.21 12 -0.14 8 20
mol:GDP 0.007 0.065 0.4 12 -0.22 6 18
ARF6/GTP/RAB11FIP3/RAB11A 0.056 0.036 0.21 13 -0.13 7 20
RHOA 0.029 0.003 -10000 0 0 6 6
PLD1 -0.007 0.034 0.21 10 -0.15 6 16
RAB11FIP3 0.028 0.006 -10000 0 0 27 27
tube morphogenesis 0.005 0.068 0.35 12 -0.38 6 18
ruffle organization -0.002 0.05 0.21 12 -0.28 6 18
regulation of epithelial cell migration 0.027 0.038 0.23 12 -0.18 7 19
PLD2 -0.008 0.038 0.21 13 -0.14 6 19
PIP5K1A -0.002 0.05 0.21 12 -0.28 6 18
mol:Phosphatidic acid -0.011 0.041 0.16 25 -10000 0 25
Rac1/GTP 0.005 0.069 0.35 12 -0.38 6 18
Signaling events mediated by HDAC Class III

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
EP300 0.027 0.008 -10000 0 0 50 50
HDAC4 0.028 0.005 -10000 0 0 16 16
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.015 0.023 -10000 0 -0.12 16 16
CDKN1A -0.015 0.084 0.37 2 -0.49 13 15
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.028 0.006 -10000 0 0 21 21
FOXO3 0.004 0.013 0.26 1 -10000 0 1
FOXO1 0.027 0.007 -10000 0 0 39 39
FOXO4 0 0.026 -10000 0 -0.19 10 10
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.027 0.008 -10000 0 0 49 49
TAT 0.026 0.009 -10000 0 0 59 59
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.017 0.002 -10000 0 -10000 0 0
PPARGC1A 0.028 0.006 -10000 0 0 25 25
FHL2 0.029 0.004 -10000 0 0 11 11
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.042 0.022 0.15 13 -10000 0 13
HIST2H4A -0.015 0.024 0.12 16 -10000 0 16
SIRT1/FOXO3a 0.031 0.039 0.22 3 -10000 0 3
SIRT1 -0.025 0.035 0.18 16 -10000 0 16
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.057 0.024 0.16 12 -10000 0 12
SIRT1/Histone H1b 0.007 0.068 0.17 2 -0.22 21 23
apoptosis -0.051 0.033 -10000 0 -0.16 12 12
SIRT1/PGC1A 0.04 0.018 0.14 14 -10000 0 14
p53/SIRT1 0.022 0.088 0.34 13 -0.17 74 87
SIRT1/FOXO4 0.005 0.065 -10000 0 -0.22 20 20
FOXO1/FHL2/SIRT1 0.05 0.032 0.15 10 -0.13 4 14
HIST1H1E 0.001 0.03 0.13 7 -0.19 10 17
SIRT1/p300 0.042 0.023 0.15 13 -0.17 1 14
muscle cell differentiation 0.024 0.025 -10000 0 -0.12 15 15
TP53 -0.02 0.035 0.18 14 -10000 0 14
KU70/SIRT1/BAX 0.052 0.033 0.16 12 -10000 0 12
CREBBP 0.027 0.008 -10000 0 0 41 41
MEF2D 0.029 0.005 -10000 0 0 15 15
HIV-1 Tat/SIRT1 0.041 0.021 0.15 10 -10000 0 10
ACSS2 -0.029 0.026 0.12 15 -10000 0 15
SIRT1/PCAF/MYOD -0.024 0.025 0.12 15 -10000 0 15
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.022 0.049 0.23 8 -10000 0 8
NFATC2 -0.019 0.05 0.23 8 -10000 0 8
NFATC3 -0.021 0.051 0.22 9 -10000 0 9
CD40LG -0.048 0.16 0.63 9 -10000 0 9
PTGS2 -0.058 0.15 0.51 20 -10000 0 20
JUNB 0.019 0.014 -10000 0 0 188 188
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.017 0.031 0.1 8 -0.16 6 14
CaM/Ca2+ -0.017 0.031 0.1 8 -0.16 6 14
CALM1 -0.024 0.027 0.095 9 -10000 0 9
JUN -0.023 0.028 0.093 10 -10000 0 10
mol:Ca2+ -0.003 0.007 0.038 12 -0.027 1 13
Calcineurin A alpha-beta B1/FKBP12/FK506 0.019 0.011 0.09 2 -10000 0 2
FOSL1 0.029 0.003 -10000 0 0 5 5
CREM 0.028 0.009 -10000 0 -0.03 9 9
Jun/NFAT1-c-4/p21SNFT -0.045 0.11 0.35 27 -10000 0 27
FOS -0.021 0.025 0.098 4 -10000 0 4
IFNG -0.068 0.12 0.46 9 -10000 0 9
AP-1/NFAT1-c-4 -0.07 0.13 0.5 17 -10000 0 17
FASLG -0.051 0.16 0.63 9 -10000 0 9
NFAT1-c-4/ICER1 -0.038 0.1 0.3 30 -10000 0 30
IL2RA -0.052 0.15 0.47 23 -10000 0 23
FKBP12/FK506 0.02 0.006 -10000 0 -10000 0 0
CSF2 -0.049 0.16 0.63 9 -10000 0 9
JunB/Fra1/NFAT1-c-4 -0.059 0.098 0.3 19 -10000 0 19
IL4 -0.05 0.16 0.63 9 -10000 0 9
IL2 -0.035 0.21 -10000 0 -0.93 29 29
IL3 0 0.11 -10000 0 -0.66 14 14
FKBP1A 0.027 0.007 -10000 0 0 39 39
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.028 0.004 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.028 0.005 0 16 -9999 0 16
PI3K Class IB/PDE3B 0.028 0.005 -9999 0 0 16 16
PDE3B 0.028 0.005 -9999 0 0 16 16
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.028 0.006 -9999 0 0 21 21
ITGB7 0.029 0.003 -9999 0 0 8 8
ITGA4 0.027 0.008 -9999 0 0 40 40
alpha4/beta7 Integrin 0.04 0.015 -9999 0 -0.16 1 1
alpha4/beta1 Integrin 0.039 0.013 -9999 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.001 0.096 0.53 9 -0.85 3 12
MKNK1 0.029 0.004 -10000 0 0 13 13
MAPK14 -0.01 0.059 0.2 24 -0.3 3 27
ATF2/c-Jun -0.039 0.055 0.14 8 -0.25 7 15
MAPK11 -0.018 0.052 0.2 19 -0.3 3 22
MITF -0.001 0.048 0.25 9 -0.34 3 12
MAPKAPK5 -0.001 0.049 0.25 9 -0.34 3 12
KRT8 -0.001 0.05 0.25 9 -0.3 4 13
MAPKAPK3 0.029 0.003 -10000 0 0 5 5
MAPKAPK2 0.029 0.004 -10000 0 0 12 12
p38alpha-beta/CK2 -0.022 0.066 0.27 18 -0.42 3 21
CEBPB 0 0.046 0.25 9 -0.25 3 12
SLC9A1 -0.001 0.048 0.25 9 -0.34 3 12
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.001 0.073 0.35 18 -0.33 3 21
p38alpha-beta/MNK1 0.045 0.054 0.28 9 -0.35 3 12
JUN -0.038 0.055 -10000 0 -0.25 7 7
PPARGC1A 0 0.049 0.25 8 -0.34 3 11
USF1 0 0.051 0.26 10 -0.34 3 13
RAB5/GDP/GDI1 -0.005 0.071 -10000 0 -0.21 8 8
NOS2 0 0.048 0.22 18 -0.33 3 21
DDIT3 0.011 0.065 0.29 9 -0.34 3 12
RAB5A 0.029 0.003 -10000 0 0 7 7
HSPB1 -0.012 0.043 0.26 3 -0.29 3 6
p38alpha-beta/HBP1 0.043 0.054 0.28 8 -0.35 3 11
CREB1 -0.027 0.099 0.25 9 -0.35 3 12
RAB5/GDP 0.021 0.002 -10000 0 -10000 0 0
EIF4E -0.035 0.054 0.18 16 -0.32 3 19
RPS6KA4 -0.001 0.049 0.25 9 -0.34 3 12
PLA2G4A -0.018 0.046 0.18 6 -0.38 3 9
GDI1 -0.001 0.051 0.26 10 -0.34 3 13
TP53 -0.022 0.061 0.26 9 -0.46 3 12
RPS6KA5 -0.001 0.048 0.25 9 -0.34 3 12
ESR1 -0.025 0.08 0.25 7 -0.22 59 66
HBP1 0.027 0.007 -10000 0 0 36 36
MEF2C -0.006 0.058 0.25 8 -0.26 13 21
MEF2A -0.002 0.047 0.25 8 -0.34 3 11
EIF4EBP1 -0.024 0.094 0.25 9 -0.36 3 12
KRT19 -0.008 0.062 0.25 9 -0.24 19 28
ELK4 -0.001 0.049 0.26 9 -0.34 3 12
ATF6 -0.001 0.05 0.26 10 -0.34 3 13
ATF1 -0.028 0.099 0.25 9 -0.35 3 12
p38alpha-beta/MAPKAPK2 0.045 0.053 0.28 8 -0.35 3 11
p38alpha-beta/MAPKAPK3 0.046 0.054 0.28 9 -0.35 3 12
Sumoylation by RanBP2 regulates transcriptional repression

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 0.027 0.008 -10000 0 0 49 49
Ran/GTP/Exportin 1/HDAC4 -0.039 0.02 -10000 0 -0.15 2 2
MDM2/SUMO1 0.023 0.053 -10000 0 -0.22 12 12
HDAC4 0.028 0.005 -10000 0 0 16 16
Ran/GTP/Exportin 1/HDAC1 -0.037 0.021 -10000 0 -0.15 2 2
SUMO1 0.029 0.003 -10000 0 0 7 7
NPC/RanGAP1/SUMO1 0.003 0.018 -10000 0 -0.2 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 -0.009 0.049 0.15 32 -0.26 3 35
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.029 0.004 -10000 0 0 12 12
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.029 0.004 -10000 0 0 10 10
SUMO1/HDAC4 0.023 0.054 -10000 0 -0.22 12 12
SUMO1/HDAC1 0.022 0.051 -10000 0 -0.22 10 10
RANGAP1 0.027 0.008 -10000 0 0 47 47
MDM2/SUMO1/SUMO1 0.063 0.034 -10000 0 -0.14 1 1
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 -0.006 0.034 -10000 0 -0.27 3 3
Ran/GTP 0.009 0.048 -10000 0 -0.22 12 12
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.028 0.006 -10000 0 0 26 26
UBE2I 0.028 0.006 -10000 0 0 23 23
Ran/GTP/Exportin 1 -0.014 0.063 0.16 40 -0.22 11 51
NPC 0.017 0.002 -10000 0 -10000 0 0
PIAS2 0.028 0.007 -10000 0 0 33 33
PIAS1 0.029 0.005 -10000 0 0 14 14
EntrezGene:9972 0 0 -10000 0 -10000 0 0
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 0.027 0.008 -10000 0 0 45 45
CDC42/GTP 0.02 0.058 0.17 1 -0.19 10 11
PLCG1 -0.01 0.052 0.16 1 -0.2 10 11
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.029 0.003 -10000 0 0 6 6
GNAI3 0.024 0.011 -10000 0 0 98 98
G12/G13 0.04 0.011 -10000 0 -10000 0 0
cell migration 0.019 0.057 0.16 1 -0.19 10 11
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.011 0.052 0.16 1 -0.2 8 9
MAPK1 -0.007 0.046 0.16 1 -0.21 4 5
S1P/S1P5/Gi 0.011 0.052 0.18 1 -0.19 14 15
GNAI1 0.028 0.006 -10000 0 0 26 26
CDC42/GDP 0.021 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.019 0.005 -10000 0 -10000 0 0
RHOA -0.029 0.029 0.2 8 -10000 0 8
S1P/S1P4/Gi 0.011 0.052 0.18 1 -0.19 14 15
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.027 0.008 -10000 0 0 47 47
S1P/S1P4/G12/G13 0.034 0.014 -10000 0 -10000 0 0
GNA12 0.028 0.007 -10000 0 0 33 33
GNA13 0.029 0.004 -10000 0 0 13 13
CDC42 0.029 0.004 -10000 0 0 11 11
Alternative NF-kappaB 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
IKK alpha homodimer 0.039 0.013 -9999 0 -10000 0 0
FBXW11 0.028 0.005 -9999 0 0 16 16
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.028 0.005 -9999 0 0 16 16
CHUK 0.027 0.007 -9999 0 0 36 36
NF kappa B2 p100/RelB 0.074 0.043 -9999 0 -0.14 2 2
NFKB1 0.027 0.008 -9999 0 0 46 46
MAP3K14 0.028 0.005 -9999 0 0 20 20
NF kappa B1 p50/RelB 0.036 0.027 -9999 0 -0.16 8 8
RELB 0.028 0.006 -9999 0 0 27 27
NFKB2 0.029 0.005 -9999 0 0 14 14
NF kappa B2 p52/RelB 0.037 0.014 -9999 0 -0.13 2 2
regulation of B cell activation 0.036 0.014 -9999 0 -0.13 2 2
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.045 0.02 -10000 0 -10000 0 0
RGS9BP 0.026 0.009 -10000 0 0 57 57
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.036 0.012 -10000 0 -10000 0 0
mol:ADP -0.016 0.004 -10000 0 -10000 0 0
GNAT2 0.029 0.003 -10000 0 0 5 5
RGS9-1/Gbeta5/R9AP 0.048 0.03 -10000 0 -0.15 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.036 0.012 -10000 0 -10000 0 0
GRK7 0.027 0.008 -10000 0 0 40 40
CNGB3 0.027 0.008 -10000 0 0 46 46
Cone Metarhodopsin II/X-Arrestin 0.022 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.019 0.053 0.18 38 -10000 0 38
Cone PDE6 0.059 0.05 -10000 0 -0.14 5 5
Cone Metarhodopsin II 0.017 0.005 -10000 0 -10000 0 0
Na + (4 Units) 0.046 0.024 -10000 0 -10000 0 0
GNAT2/GDP 0.054 0.037 -10000 0 -0.13 6 6
GNB5 0.028 0.007 -10000 0 0 34 34
mol:GMP (4 units) -0.016 0.06 0.18 49 -10000 0 49
Cone Transducin 0.048 0.022 -10000 0 -10000 0 0
SLC24A2 0.028 0.007 -10000 0 0 31 31
GNB3/GNGT2 0.038 0.015 -10000 0 -10000 0 0
GNB3 0.026 0.009 -10000 0 0 58 58
GNAT2/GTP 0.022 0.002 -10000 0 -10000 0 0
CNGA3 0.029 0.003 -10000 0 0 8 8
ARR3 0.029 0.003 -10000 0 0 5 5
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.036 0.012 -10000 0 -10000 0 0
mol:Pi 0.047 0.03 -10000 0 -0.15 6 6
Cone CNG Channel 0.055 0.035 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.028 0.007 -10000 0 0 31 31
RGS9 0.029 0.005 -10000 0 0 14 14
PDE6C 0.028 0.005 -10000 0 0 17 17
GNGT2 0.028 0.005 -10000 0 0 17 17
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.026 0.009 -10000 0 0 55 55
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.034 0.018 -10000 0 -0.13 3 3
EFNA5 0.027 0.008 -10000 0 0 42 42
FYN -0.025 0.032 0.17 11 -0.22 1 12
neuron projection morphogenesis 0.034 0.018 -10000 0 -0.13 3 3
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.034 0.018 -10000 0 -0.13 3 3
EPHA5 0.028 0.007 -10000 0 0 29 29
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.038 0.019 -10000 0 -10000 0 0
PDGFRB 0.023 0.02 0.071 1 -10000 0 1
SPHK1 0.005 0.078 -10000 0 -0.67 7 7
mol:S1P 0.001 0.075 0.22 9 -0.58 7 16
S1P1/S1P/Gi 0.002 0.098 0.48 12 -0.33 7 19
GNAO1 0.019 0.024 0.087 11 -0.045 3 14
PDGFB-D/PDGFRB/PLCgamma1 0.005 0.11 0.44 13 -0.37 3 16
PLCG1 -0.004 0.097 0.45 12 -0.33 5 17
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.023 0.02 0.071 1 -10000 0 1
GNAI2 0.02 0.024 0.087 11 -0.045 3 14
GNAI3 -0.008 0.027 0.078 10 -10000 0 10
GNAI1 -0.004 0.03 0.078 11 -10000 0 11
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.01 0.049 0.14 50 -10000 0 50
S1P1/S1P -0.01 0.067 0.27 12 -0.39 7 19
negative regulation of cAMP metabolic process 0.002 0.097 0.48 12 -0.32 7 19
MAPK3 -0.002 0.11 0.56 11 -0.47 4 15
calcium-dependent phospholipase C activity 0 0.005 0.031 11 -10000 0 11
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.021 0.007 -10000 0 -0.15 1 1
KDR 0.028 0.01 0.064 2 -0.033 8 10
PLCB2 0.001 0.083 0.27 17 -0.36 7 24
RAC1 0.028 0.006 -10000 0 0 27 27
RhoA/GTP -0.02 0.046 -10000 0 -0.35 7 7
receptor internalization -0.01 0.063 0.25 12 -0.37 7 19
PTGS2 0.002 0.13 0.66 11 -0.89 3 14
Rac1/GTP -0.02 0.046 -10000 0 -0.35 7 7
RHOA 0.029 0.003 -10000 0 0 6 6
VEGFA 0.025 0.013 0.067 1 -0.034 7 8
negative regulation of T cell proliferation 0.002 0.097 0.48 12 -0.32 7 19
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.005 0.029 0.076 10 -10000 0 10
MAPK1 0.001 0.1 0.55 10 -0.48 4 14
S1P1/S1P/PDGFB-D/PDGFRB 0.003 0.089 0.32 17 -0.34 7 24
ABCC1 0.022 0.02 -10000 0 -10000 0 0
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 0.028 0.006 -10000 0 0 25 25
CLTC 0.011 0.066 0.2 1 -0.42 8 9
calcium ion-dependent exocytosis 0 0.031 0.16 1 -0.2 7 8
Dynamin 2/GTP -0.024 0.036 0.14 23 -10000 0 23
EXOC4 0.028 0.007 -10000 0 0 34 34
CD59 -0.001 0.044 0.19 1 -0.37 6 7
CPE -0.023 0.01 -10000 0 -10000 0 0
CTNNB1 0.029 0.003 -10000 0 0 8 8
membrane fusion -0.002 0.028 -10000 0 -0.18 7 7
CTNND1 -0.028 0.046 0.15 30 -10000 0 30
DNM2 0.026 0.009 -10000 0 0 56 56
mol:PI-4-5-P2 0.001 0.05 -10000 0 -0.24 11 11
TSHR -0.025 0.007 -10000 0 -10000 0 0
INS -0.003 0.097 -10000 0 -0.48 21 21
BIN1 0.029 0.004 -10000 0 0 12 12
mol:Choline -0.002 0.028 -10000 0 -0.18 7 7
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP -0.024 0.008 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.029 0.004 -10000 0 0 11 11
mol:Ca2+ -0.024 0.036 0.14 23 -10000 0 23
JUP -0.004 0.049 -10000 0 -0.4 6 6
ASAP2/amphiphysin II 0.035 0.014 -10000 0 -0.12 2 2
ARF6/GTP 0.021 0.003 -10000 0 -10000 0 0
CDH1 -0.006 0.054 -10000 0 -0.46 6 6
clathrin-independent pinocytosis 0.021 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.028 0.006 -10000 0 0 24 24
positive regulation of endocytosis 0.021 0.003 -10000 0 -10000 0 0
EXOC2 0.027 0.008 -10000 0 0 48 48
substrate adhesion-dependent cell spreading 0.007 0.052 0.18 1 -0.26 8 9
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.028 0.005 -10000 0 0 16 16
regulation of calcium-dependent cell-cell adhesion -0.026 0.064 0.34 7 -0.21 1 8
positive regulation of phagocytosis -0.025 0.006 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.037 0.009 -10000 0 -10000 0 0
ACAP1 0.001 0.026 -10000 0 -0.18 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.001 0.047 0.19 1 -0.35 7 8
clathrin heavy chain/ACAP1 -0.002 0.061 0.2 5 -0.32 10 15
JIP4/KLC1 0.051 0.02 -10000 0 -10000 0 0
EXOC1 0.028 0.006 -10000 0 0 26 26
exocyst 0.007 0.052 0.19 1 -0.26 8 9
RALA/GTP 0.021 0.004 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.038 0.008 -10000 0 -10000 0 0
receptor recycling 0.021 0.003 -10000 0 -10000 0 0
CTNNA1 -0.028 0.046 0.15 30 -10000 0 30
NME1 -0.024 0.008 -10000 0 -10000 0 0
clathrin coat assembly 0.01 0.07 0.2 1 -0.39 11 12
IL2RA 0.002 0.052 -10000 0 -0.38 7 7
VAMP3 -0.025 0.006 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.027 0.065 -10000 0 -0.32 10 10
EXOC6 0.027 0.007 -10000 0 0 36 36
PLD1 0.002 0.01 -10000 0 -10000 0 0
PLD2 0.003 0.01 -10000 0 -10000 0 0
EXOC5 0.029 0.004 -10000 0 0 13 13
PIP5K1C -0.004 0.04 -10000 0 -0.26 6 6
SDC1 -0.001 0.046 -10000 0 -0.35 7 7
ARF6/GDP -0.017 0.039 0.16 26 -10000 0 26
EXOC7 0.028 0.005 -10000 0 0 16 16
E-cadherin/beta catenin 0.028 0.066 0.22 1 -0.34 7 8
mol:Phosphatidic acid -0.002 0.028 -10000 0 -0.18 7 7
endocytosis -0.034 0.013 0.12 2 -10000 0 2
SCAMP2 0.028 0.005 -10000 0 0 19 19
ADRB2 0.002 0.069 0.22 4 -0.38 10 14
EXOC3 0.026 0.009 -10000 0 0 60 60
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP -0.028 0.018 0.17 2 -10000 0 2
KLC1 0.028 0.006 -10000 0 0 22 22
AVPR2 0.007 0.077 0.22 12 -0.41 9 21
RALA 0.029 0.005 -10000 0 0 15 15
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.023 0.065 -10000 0 -0.34 7 7
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.037 0.12 0.74 4 -10000 0 4
NCK1/PAK1/Dok-R -0.044 0.055 -10000 0 -0.32 2 2
NCK1/Dok-R 0.014 0.07 0.71 1 -10000 0 1
PIK3CA 0.019 0.015 -10000 0 -0.029 10 10
mol:beta2-estradiol 0 0.021 -10000 0 -0.18 7 7
RELA 0.029 0.003 -10000 0 0 6 6
SHC1 0.025 0.016 0.074 1 -10000 0 1
Rac/GDP 0.021 0.005 -10000 0 -10000 0 0
F2 0.012 0.045 -10000 0 -0.23 11 11
TNIP2 0.028 0.007 -10000 0 0 34 34
NF kappa B/RelA 0.029 0.078 0.68 1 -10000 0 1
FN1 0.018 0.014 -10000 0 0 213 213
PLD2 -0.011 0.06 0.82 1 -10000 0 1
PTPN11 0.029 0.003 -10000 0 0 8 8
GRB14 0.028 0.007 -10000 0 0 32 32
ELK1 -0.017 0.065 0.72 1 -10000 0 1
GRB7 0.027 0.008 -10000 0 0 40 40
PAK1 0.027 0.008 -10000 0 0 48 48
Tie2/Ang1/alpha5/beta1 Integrin 0.034 0.072 -10000 0 -10000 0 0
CDKN1A -0.04 0.16 0.73 5 -0.72 16 21
ITGA5 0.028 0.005 -10000 0 0 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.016 0.071 0.71 1 -10000 0 1
CRK 0.027 0.007 -10000 0 0 36 36
mol:NO -0.03 0.12 0.64 5 -10000 0 5
PLG -0.012 0.058 0.82 1 -10000 0 1
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.026 0.1 0.81 2 -10000 0 2
GRB2 0.028 0.005 -10000 0 0 19 19
PIK3R1 0.018 0.018 0.075 1 -10000 0 1
ANGPT2 -0.026 0.14 0.74 6 -0.67 2 8
BMX -0.012 0.061 0.82 1 -10000 0 1
ANGPT1 0.001 0.063 0.53 6 -10000 0 6
tube development -0.042 0.12 0.7 6 -10000 0 6
ANGPT4 0.021 0.02 0.081 6 -10000 0 6
response to hypoxia -0.002 0.009 0.084 3 -10000 0 3
Tie2/Ang1/GRB14 -0.004 0.067 0.75 1 -10000 0 1
alpha5/beta1 Integrin 0.041 0.011 -10000 0 -10000 0 0
FGF2 0.024 0.016 -10000 0 -0.079 5 5
STAT5A (dimer) -0.04 0.15 0.74 5 -0.67 4 9
mol:L-citrulline -0.03 0.12 0.64 5 -10000 0 5
AGTR1 0.026 0.016 0.12 5 -0.033 16 21
MAPK14 0 0.092 0.79 2 -0.76 1 3
Tie2/SHP2 0.005 0.089 -10000 0 -10000 0 0
TEK -0.001 0.089 0.87 1 -10000 0 1
RPS6KB1 -0.039 0.12 0.75 3 -10000 0 3
Angiotensin II/AT1 0.02 0.021 0.21 5 -10000 0 5
Tie2/Ang1/GRB2 -0.002 0.068 0.75 1 -10000 0 1
MAPK3 -0.02 0.061 0.73 1 -10000 0 1
MAPK1 -0.014 0.063 0.73 1 -10000 0 1
Tie2/Ang1/GRB7 -0.003 0.056 -10000 0 -10000 0 0
NFKB1 0.027 0.008 -10000 0 0 46 46
MAPK8 -0.011 0.062 0.82 1 -10000 0 1
PI3K -0.035 0.12 0.9 2 -10000 0 2
FES -0.003 0.1 0.8 2 -0.71 3 5
Crk/Dok-R 0.017 0.071 0.71 1 -10000 0 1
Tie2/Ang1/ABIN2 -0.002 0.067 0.75 1 -10000 0 1
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.034 0.12 0.73 4 -10000 0 4
STAT5A 0.026 0.012 -10000 0 -0.033 15 15
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.001 0.14 0.75 3 -10000 0 3
Tie2/Ang2 -0.035 0.13 0.76 5 -10000 0 5
Tie2/Ang1 0.002 0.064 0.96 1 -10000 0 1
FOXO1 -0.036 0.12 0.75 4 -10000 0 4
ELF1 -0.011 0.032 0.26 1 -10000 0 1
ELF2 -0.002 0.061 0.92 1 -10000 0 1
mol:Choline -0.01 0.062 0.81 1 -10000 0 1
cell migration -0.024 0.036 -10000 0 -0.18 1 1
FYN -0.045 0.13 0.71 6 -10000 0 6
DOK2 0.024 0.012 -10000 0 0 106 106
negative regulation of cell cycle -0.036 0.15 0.72 5 -0.64 16 21
ETS1 -0.009 0.034 0.2 5 -10000 0 5
PXN 0 0.14 0.65 4 -10000 0 4
ITGB1 0.028 0.006 -10000 0 0 21 21
NOS3 -0.034 0.12 0.7 4 -10000 0 4
RAC1 0.028 0.006 -10000 0 0 27 27
TNF -0.008 0.038 0.22 7 -10000 0 7
MAPKKK cascade -0.01 0.062 0.81 1 -10000 0 1
RASA1 0.027 0.008 -10000 0 0 49 49
Tie2/Ang1/Shc 0.002 0.072 0.8 1 -10000 0 1
NCK1 0.026 0.009 -10000 0 0 64 64
vasculogenesis -0.027 0.11 0.6 6 -10000 0 6
mol:Phosphatidic acid -0.01 0.062 0.81 1 -10000 0 1
mol:Angiotensin II 0.001 0.009 0.088 6 -10000 0 6
mol:NADP -0.03 0.12 0.64 5 -10000 0 5
Rac1/GTP -0.032 0.11 0.56 2 -10000 0 2
MMP2 -0.007 0.073 0.82 1 -10000 0 1
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 + 0.028 0.005 -10000 0 0 15 15
GNAT1/GTP 0.021 0.003 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.038 0.009 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.038 0.009 -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 0.029 0.003 -10000 0 0 8 8
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel -0.056 0.02 0.094 2 -10000 0 2
mol:Na + -0.061 0.029 0.12 6 -10000 0 6
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.048 0.03 -10000 0 -0.15 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.049 0.05 -10000 0 -0.15 8 8
CNGB1 0.027 0.008 -10000 0 0 40 40
RDH5 0.028 0.007 -10000 0 0 30 30
SAG 0.029 0.004 -10000 0 0 10 10
mol:Ca2+ -0.048 0.087 0.31 22 -10000 0 22
Na + (4 Units) -0.067 0.026 0.076 2 -10000 0 2
RGS9 0.029 0.005 -10000 0 0 14 14
GNB1/GNGT1 0.04 0.014 -10000 0 -0.16 1 1
GNAT1/GDP 0.053 0.037 -10000 0 -0.13 6 6
GUCY2D 0.028 0.006 -10000 0 0 27 27
GNGT1 0.028 0.006 -10000 0 0 21 21
GUCY2F 0.029 0.002 -10000 0 0 2 2
GNB5 0.028 0.007 -10000 0 0 34 34
mol:GMP (4 units) -0.038 0.016 0.14 1 -10000 0 1
mol:11-cis-retinal 0.028 0.007 -10000 0 0 30 30
mol:cGMP 0.047 0.028 -10000 0 -10000 0 0
GNB1 0.028 0.006 -10000 0 0 24 24
Rhodopsin 0.04 0.012 -10000 0 -10000 0 0
SLC24A1 0.029 0.005 -10000 0 0 15 15
CNGA1 0.028 0.006 -10000 0 0 26 26
Metarhodopsin II 0.018 0.003 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.064 0.031 -10000 0 -10000 0 0
RGS9BP 0.026 0.009 -10000 0 0 57 57
Metarhodopsin II/Transducin 0.005 0.026 -10000 0 -0.18 2 2
GCAP Family/Ca ++ 0.051 0.017 -10000 0 -10000 0 0
PDE6A/B 0.039 0.013 -10000 0 -10000 0 0
mol:Pi 0.047 0.03 -10000 0 -0.15 6 6
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.051 0.021 -10000 0 -0.13 1 1
PDE6B 0.027 0.008 -10000 0 0 43 43
PDE6A 0.029 0.004 -10000 0 0 13 13
PDE6G 0.028 0.006 -10000 0 0 21 21
RHO 0.028 0.005 -10000 0 0 19 19
PDE6 0.061 0.051 -10000 0 -0.14 6 6
GUCA1A 0.028 0.006 -10000 0 0 27 27
GC2/GCAP Family 0.068 0.024 -10000 0 -10000 0 0
GUCA1C 0.028 0.006 -10000 0 0 26 26
GUCA1B 0.028 0.006 -10000 0 0 26 26
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.027 0.035 0.22 10 -10000 0 10
NFATC2 -0.024 0.18 0.42 11 -0.52 5 16
NFATC3 -0.003 0.074 0.36 3 -0.25 2 5
CD40LG -0.005 0.22 0.73 10 -0.73 1 11
ITCH -0.032 0.047 0.3 9 -10000 0 9
CBLB -0.032 0.049 0.3 10 -10000 0 10
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.01 0.18 0.64 13 -0.54 4 17
JUNB 0.019 0.014 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.035 0.019 -10000 0 -0.17 9 9
T cell anergy -0.01 0.081 0.5 10 -10000 0 10
TLE4 -0.046 0.16 0.32 1 -0.53 38 39
Jun/NFAT1-c-4/p21SNFT -0.012 0.16 0.56 4 -0.69 1 5
AP-1/NFAT1-c-4 -0.027 0.21 0.66 5 -0.8 1 6
IKZF1 -0.025 0.12 0.32 1 -0.38 4 5
T-helper 2 cell differentiation 0.002 0.15 -10000 0 -0.63 3 3
AP-1/NFAT1 -0.02 0.15 0.35 16 -0.36 8 24
CALM1 -0.032 0.039 0.2 15 -10000 0 15
EGR2 0.002 0.15 0.88 4 -0.73 1 5
EGR3 -0.007 0.15 0.77 4 -0.68 2 6
NFAT1/FOXP3 -0.014 0.14 0.41 10 -0.39 4 14
EGR1 -0.017 0.017 0.15 1 -10000 0 1
JUN -0.013 0.052 0.15 21 -10000 0 21
EGR4 -0.017 0.025 0.15 1 -10000 0 1
mol:Ca2+ -0.011 0.003 -10000 0 -10000 0 0
GBP3 -0.03 0.17 0.44 21 -0.54 25 46
FOSL1 0.029 0.003 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 0.046 0.15 0.57 2 -0.69 1 3
DGKA -0.023 0.12 0.4 8 -0.38 3 11
CREM 0.029 0.005 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.005 0.16 0.5 5 -0.71 1 6
CTLA4 -0.026 0.11 0.42 10 -0.34 4 14
NFAT1-c-4 (dimer)/EGR1 -0.054 0.16 0.53 4 -0.8 1 5
NFAT1-c-4 (dimer)/EGR4 -0.01 0.16 0.52 5 -0.71 1 6
FOS -0.012 0.048 0.12 47 -10000 0 47
IFNG 0.004 0.18 0.57 26 -0.62 8 34
T cell activation 0 0.16 0.65 5 -10000 0 5
MAF 0.026 0.009 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.005 0.13 0.99 1 -0.69 6 7
TNF -0.057 0.15 0.6 4 -0.75 1 5
FASLG -0.004 0.17 0.85 2 -0.83 1 3
TBX21 0.04 0.054 0.28 26 -10000 0 26
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.027 0.008 -10000 0 -10000 0 0
PTPN1 -0.027 0.12 -10000 0 -0.4 3 3
NFAT1-c-4/ICER1 -0.005 0.16 0.49 6 -0.71 1 7
GATA3 0.027 0.007 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.014 0.18 0.57 27 -0.61 8 35
IL2RA -0.019 0.16 0.63 6 -0.54 4 10
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.019 0.12 0.43 8 -0.38 4 12
E2F1 0.028 0.015 0.18 4 -10000 0 4
PPARG 0.029 0.004 -10000 0 -10000 0 0
SLC3A2 -0.025 0.12 0.42 2 -0.38 4 6
IRF4 0.027 0.008 -10000 0 -10000 0 0
PTGS2 -0.017 0.2 0.62 8 -0.73 1 9
CSF2 -0.006 0.22 0.73 10 -0.73 1 11
JunB/Fra1/NFAT1-c-4 0.014 0.16 0.57 2 -0.77 1 3
IL4 0 0.15 -10000 0 -0.66 3 3
IL5 -0.007 0.22 0.7 12 -0.73 1 13
IL2 0 0.16 0.65 5 -10000 0 5
IL3 -0.008 0.083 -10000 0 -0.53 11 11
RNF128 -0.034 0.048 0.32 9 -10000 0 9
NFATC1 0.006 0.13 0.69 6 -1 1 7
CDK4 0.004 0.14 0.8 3 -0.72 3 6
PTPRK -0.027 0.13 0.38 5 -0.45 9 14
IL8 -0.051 0.15 0.6 1 -0.73 1 2
POU2F1 0.029 0.004 -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 0.046 0.022 -9999 0 -0.12 1 1
MAPK9 0.003 0.009 -9999 0 -0.21 1 1
adrenocorticotropin secretion -0.016 0.005 0 44 -10000 0 44
GNB1/GNG2 0.037 0.012 -9999 0 -0.13 1 1
GNB1 0.028 0.006 -9999 0 0 24 24
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
MAPK14 0.003 0.001 -9999 0 -10000 0 0
Gs family/GTP 0.018 0.004 -9999 0 -10000 0 0
EntrezGene:2778 0 0 -9999 0 -10000 0 0
vasopressin secretion 0 0 -9999 0 -10000 0 0
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
glutamate secretion 0.004 0 -9999 0 -10000 0 0
GNAL 0.028 0.005 -9999 0 0 20 20
GNG2 0.029 0.004 -9999 0 0 12 12
CRH 0.027 0.008 -9999 0 0 44 44
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.003 0 -9999 0 -10000 0 0
MAPK11 0.003 0.001 -9999 0 -10000 0 0
Glypican 2 network

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
MDK 0.029 0.003 -9999 0 0 7 7
GPC2 0.028 0.005 -9999 0 0 19 19
GPC2/Midkine 0.042 0.009 -9999 0 -9999 0 0
neuron projection morphogenesis 0.042 0.009 -9999 0 -9999 0 0
LPA4-mediated signaling events

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
ADCY4 -0.024 0.011 0.18 1 -10000 0 1
ADCY5 -0.024 0.014 0.18 2 -10000 0 2
ADCY6 -0.026 0.005 -10000 0 -10000 0 0
ADCY7 -0.024 0.008 -10000 0 -10000 0 0
ADCY1 -0.025 0.006 -10000 0 -10000 0 0
ADCY2 -0.024 0.009 -10000 0 -10000 0 0
ADCY3 -0.025 0.01 0.18 1 -10000 0 1
ADCY8 -0.008 0.02 0.18 4 -10000 0 4
PRKCE -0.016 0.003 0 19 -10000 0 19
ADCY9 -0.023 0.009 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0 0.09 0.2 43 -0.24 1 44
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 557 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.61.2614 TCGA.61.2613 TCGA.61.2612 TCGA.61.2113
109_MAP3K5 0.06 -0.002 0.011 -0.026
47_PPARGC1A 0.029 0.029 0.029 0.029
105_BMP4 0.029 0.029 0.029 0.029
105_BMP6 0.029 0.029 0.029 0.029
105_BMP7 0 0.029 0.029 0.029
105_BMP2 0 0.029 0.029 0.029
131_RELN/VLDLR 0.075 0.075 0.075 0.075
30_TGFB1/TGF beta receptor Type II 0.029 0.029 0 0.029
84_STAT5B 0.037 -0.026 -0.026 0.067
84_STAT5A 0.037 -0.026 -0.026 0.067
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/5952850/GDAC_MergeDataFiles_3126555/OV-TP.exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/OV-TP/6154705/Gistic2_Analysis_6154868/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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)
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