PARADIGM pathway analysis of mRNA expression and copy number data
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1QZ292M
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNA expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1QZ292M
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 80 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 337
PLK2 and PLK4 events 211
Circadian rhythm pathway 154
S1P3 pathway 147
TCGA08_retinoblastoma 131
PLK1 signaling events 122
Osteopontin-mediated events 113
Signaling events regulated by Ret tyrosine kinase 113
Effects of Botulinum toxin 107
Nongenotropic Androgen signaling 95
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 0.5923 337 17203 51 -0.022 1.7 1000 -1000 -0.047 -1000
PLK2 and PLK4 events 0.3708 211 633 3 0.015 0.065 1000 -1000 -0.022 -1000
Circadian rhythm pathway 0.2707 154 3402 22 -0.093 0.27 1000 -1000 -0.025 -1000
S1P3 pathway 0.2583 147 6192 42 -0.54 0.041 1000 -1000 -0.02 -1000
TCGA08_retinoblastoma 0.2302 131 1049 8 -0.071 0.063 1000 -1000 -0.001 -1000
PLK1 signaling events 0.2144 122 10411 85 -0.12 0.23 1000 -1000 -0.022 -1000
Osteopontin-mediated events 0.1986 113 4328 38 -0.039 0.19 1000 -1000 -0.038 -1000
Signaling events regulated by Ret tyrosine kinase 0.1986 113 9266 82 -0.2 0.029 1000 -1000 -0.052 -1000
Effects of Botulinum toxin 0.1880 107 2797 26 -0.12 0.055 1000 -1000 -0.024 -1000
Nongenotropic Androgen signaling 0.1670 95 4942 52 -0.16 0.085 1000 -1000 -0.031 -1000
Endothelins 0.1652 94 9051 96 -0.11 0.089 1000 -1000 -0.044 -1000
TCGA08_rtk_signaling 0.1582 90 2341 26 -0.031 0.043 1000 -1000 -0.022 -1000
Aurora B signaling 0.1564 89 5987 67 -0.064 0.16 1000 -1000 -0.028 -1000
mTOR signaling pathway 0.1459 83 4435 53 -0.16 0.029 1000 -1000 -0.051 -1000
Syndecan-1-mediated signaling events 0.1441 82 2813 34 -0.046 0.033 1000 -1000 -0.033 -1000
IGF1 pathway 0.1406 80 4609 57 -0.088 0.053 1000 -1000 -0.047 -1000
Retinoic acid receptors-mediated signaling 0.1388 79 4589 58 -0.39 0.051 1000 -1000 -0.039 -1000
IL2 signaling events mediated by STAT5 0.1388 79 1755 22 -0.36 0.03 1000 -1000 -0.029 -1000
Insulin Pathway 0.1248 71 5298 74 -0.1 0.058 1000 -1000 -0.053 -1000
Ephrin B reverse signaling 0.1230 70 3371 48 -0.18 0.06 1000 -1000 -0.042 -1000
TCGA08_p53 0.1230 70 491 7 -0.007 0.029 1000 -1000 -0.015 -1000
Thromboxane A2 receptor signaling 0.1195 68 7166 105 -0.16 0.046 1000 -1000 -0.044 -1000
FoxO family signaling 0.1195 68 4356 64 -0.02 0.35 1000 -1000 -0.024 -1000
Canonical Wnt signaling pathway 0.1160 66 3396 51 -0.33 0.14 1000 -1000 -0.043 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.1142 65 5413 83 -0.13 0.063 1000 -1000 -0.031 -1000
LPA receptor mediated events 0.1125 64 6533 102 -0.058 0.03 1000 -1000 -0.047 -1000
Reelin signaling pathway 0.1090 62 3483 56 -0.068 0.075 1000 -1000 -0.028 -1000
Integrins in angiogenesis 0.1037 59 4977 84 -0.082 0.056 1000 -1000 -0.056 -1000
BARD1 signaling events 0.1019 58 3343 57 -0.033 0.2 1000 -1000 -0.038 -1000
HIF-1-alpha transcription factor network 0.1002 57 4386 76 -0.047 0.34 1000 -1000 -0.09 -1000
Insulin-mediated glucose transport 0.1002 57 1843 32 -0.086 0.037 1000 -1000 -0.024 -1000
TRAIL signaling pathway 0.1002 57 2773 48 -0.029 0.032 1000 -1000 -0.028 -1000
IL23-mediated signaling events 0.1002 57 3447 60 -0.01 0.22 1000 -1000 -0.049 -1000
PDGFR-alpha signaling pathway 0.0967 55 2438 44 -0.094 0.037 1000 -1000 -0.034 -1000
Nectin adhesion pathway 0.0967 55 3526 63 -0.12 0.049 1000 -1000 -0.033 -1000
IL2 signaling events mediated by PI3K 0.0967 55 3222 58 -0.16 0.029 1000 -1000 -0.035 -1000
Regulation of Telomerase 0.0967 55 5700 102 -0.26 0.066 1000 -1000 -0.037 -1000
Plasma membrane estrogen receptor signaling 0.0967 55 4756 86 -0.14 0.13 1000 -1000 -0.051 -1000
Aurora A signaling 0.0949 54 3248 60 -0.004 0.16 1000 -1000 -0.025 -1000
IL4-mediated signaling events 0.0949 54 4998 91 -0.57 0.29 1000 -1000 -0.083 -1000
IL1-mediated signaling events 0.0931 53 3318 62 -0.068 0.058 1000 -1000 -0.058 -1000
HIF-2-alpha transcription factor network 0.0914 52 2265 43 -0.055 0.19 1000 -1000 -0.043 -1000
Wnt signaling 0.0914 52 365 7 0.007 0.029 1000 -1000 -0.013 -1000
Signaling events mediated by the Hedgehog family 0.0896 51 2662 52 -0.045 0.05 1000 -1000 -0.043 -1000
Coregulation of Androgen receptor activity 0.0879 50 3842 76 -0.33 0.043 1000 -1000 -0.029 -1000
Ras signaling in the CD4+ TCR pathway 0.0879 50 860 17 0 0.029 1000 -1000 -0.017 -1000
Class I PI3K signaling events 0.0861 49 3613 73 -0.031 0.083 1000 -1000 -0.028 -1000
amb2 Integrin signaling 0.0844 48 3952 82 -0.056 0.075 1000 -1000 -0.034 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0826 47 2445 52 -0.15 0.098 1000 -1000 -0.022 -1000
Signaling mediated by p38-gamma and p38-delta 0.0826 47 715 15 -0.082 0.028 1000 -1000 -0.026 -1000
Signaling events mediated by PRL 0.0808 46 1597 34 -0.063 0.051 1000 -1000 -0.037 -1000
Presenilin action in Notch and Wnt signaling 0.0738 42 2567 61 -0.3 0.063 1000 -1000 -0.039 -1000
p75(NTR)-mediated signaling 0.0738 42 5356 125 -0.071 0.076 1000 -1000 -0.062 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0685 39 907 23 -0.013 0.088 1000 -1000 -0.02 -1000
Glucocorticoid receptor regulatory network 0.0668 38 4379 114 -0.3 0.16 1000 -1000 -0.062 -1000
Paxillin-dependent events mediated by a4b1 0.0668 38 1390 36 -0.074 0.064 1000 -1000 -0.039 -1000
Regulation of nuclear SMAD2/3 signaling 0.0650 37 5081 136 -0.098 0.13 1000 -1000 -0.032 -1000
BMP receptor signaling 0.0650 37 3042 81 -0.053 0.054 1000 -1000 -0.046 -1000
Canonical NF-kappaB pathway 0.0633 36 1432 39 -0.054 0.051 1000 -1000 -0.03 -1000
FAS signaling pathway (CD95) 0.0633 36 1693 47 -0.036 0.046 1000 -1000 -0.024 -1000
E-cadherin signaling in keratinocytes 0.0633 36 1579 43 -0.047 0.045 1000 -1000 -0.027 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0598 34 1288 37 -0.019 0.067 1000 -1000 -0.035 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0598 34 1135 33 -0.011 0.077 1000 -1000 -0.036 -1000
PDGFR-beta signaling pathway 0.0598 34 3331 97 -0.071 0.06 1000 -1000 -0.058 -1000
IL12-mediated signaling events 0.0580 33 2892 87 -0.36 0.05 1000 -1000 -0.059 -1000
Regulation of p38-alpha and p38-beta 0.0580 33 1812 54 -0.053 0.064 1000 -1000 -0.037 -1000
Syndecan-2-mediated signaling events 0.0562 32 2267 69 -0.039 0.041 1000 -1000 -0.031 -1000
Arf6 signaling events 0.0562 32 1995 62 -0.013 0.068 1000 -1000 -0.012 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0562 32 1456 45 -0.085 0.068 1000 -1000 -0.042 -1000
EPHB forward signaling 0.0562 32 2779 85 -0.068 0.13 1000 -1000 -0.06 -1000
E-cadherin signaling in the nascent adherens junction 0.0562 32 2467 76 -0.088 0.058 1000 -1000 -0.054 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0562 32 3908 120 -0.15 0.077 1000 -1000 -0.052 -1000
Noncanonical Wnt signaling pathway 0.0545 31 816 26 -0.025 0.042 1000 -1000 -0.034 -1000
Signaling events mediated by PTP1B 0.0545 31 2413 76 -0.077 0.037 1000 -1000 -0.028 -1000
Syndecan-3-mediated signaling events 0.0545 31 1111 35 -0.011 0.044 1000 -1000 -0.028 -1000
Caspase cascade in apoptosis 0.0527 30 2285 74 -0.056 0.042 1000 -1000 -0.027 -1000
ErbB4 signaling events 0.0527 30 2133 69 -0.03 0.18 1000 -1000 -0.04 -1000
ceramide signaling pathway 0.0527 30 1488 49 -0.051 0.042 1000 -1000 -0.026 -1000
ErbB2/ErbB3 signaling events 0.0510 29 1934 65 -0.037 0.089 1000 -1000 -0.051 -1000
BCR signaling pathway 0.0510 29 2924 99 -0.069 0.069 1000 -1000 -0.058 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0492 28 2435 85 -0.066 0.068 1000 -1000 -0.044 -1000
FOXA2 and FOXA3 transcription factor networks 0.0492 28 1294 46 0 0.25 1000 -1000 -0.045 -1000
Glypican 1 network 0.0492 28 1387 48 -0.043 0.054 1000 -1000 -0.028 -1000
E-cadherin signaling events 0.0492 28 142 5 0.026 0.045 1000 -1000 0.027 -1000
IL27-mediated signaling events 0.0475 27 1381 51 -0.03 0.07 1000 -1000 -0.041 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0457 26 1447 54 -0.059 0.04 1000 -1000 -0.045 -1000
Cellular roles of Anthrax toxin 0.0457 26 1029 39 -0.13 0.03 1000 -1000 -0.023 -1000
EGFR-dependent Endothelin signaling events 0.0457 26 562 21 -0.056 0.059 1000 -1000 -0.049 -1000
Aurora C signaling 0.0439 25 175 7 -0.001 0.04 1000 -1000 -0.017 -1000
Fc-epsilon receptor I signaling in mast cells 0.0439 25 2446 97 -0.069 0.06 1000 -1000 -0.06 -1000
Ceramide signaling pathway 0.0439 25 1957 76 -0.038 0.065 1000 -1000 -0.024 -1000
IL6-mediated signaling events 0.0439 25 1916 75 -0.27 0.044 1000 -1000 -0.031 -1000
Syndecan-4-mediated signaling events 0.0439 25 1701 67 -0.024 0.074 1000 -1000 -0.038 -1000
EPO signaling pathway 0.0422 24 1326 55 -0.072 0.036 1000 -1000 -0.042 -1000
Atypical NF-kappaB pathway 0.0422 24 749 31 -0.038 0.029 1000 -1000 -0.035 -1000
TCR signaling in naïve CD8+ T cells 0.0422 24 2278 93 -0.093 0.077 1000 -1000 -0.045 -1000
IFN-gamma pathway 0.0404 23 1629 68 -0.061 0.068 1000 -1000 -0.049 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0404 23 1735 74 -0.13 0.073 1000 -1000 -0.062 -1000
Regulation of Androgen receptor activity 0.0404 23 1640 70 -0.4 0.047 1000 -1000 -0.041 -1000
Class I PI3K signaling events mediated by Akt 0.0387 22 1500 68 -0.1 0.054 1000 -1000 -0.036 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0387 22 1793 78 -0.18 0.039 1000 -1000 -0.041 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0351 20 572 28 -0.031 0.041 1000 -1000 -0.019 -1000
JNK signaling in the CD4+ TCR pathway 0.0351 20 344 17 -0.025 0.06 1000 -1000 -0.027 -1000
Signaling events mediated by HDAC Class I 0.0351 20 2141 104 -0.047 0.065 1000 -1000 -0.036 -1000
Calcium signaling in the CD4+ TCR pathway 0.0351 20 632 31 -0.071 0.029 1000 -1000 -0.046 -1000
Arf1 pathway 0.0351 20 1113 54 -0.029 0.035 1000 -1000 -0.025 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0334 19 653 34 -0.041 0.082 1000 -1000 -0.028 -1000
Signaling events mediated by HDAC Class II 0.0334 19 1465 75 -0.033 0.059 1000 -1000 -0.036 -1000
Hedgehog signaling events mediated by Gli proteins 0.0334 19 1272 65 -0.036 0.055 1000 -1000 -0.045 -1000
Arf6 downstream pathway 0.0334 19 825 43 -0.047 0.057 1000 -1000 -0.03 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0334 19 2454 125 -0.074 0.068 1000 -1000 -0.067 -1000
S1P5 pathway 0.0316 18 318 17 -0.02 0.029 1000 -1000 -0.009 -1000
Signaling mediated by p38-alpha and p38-beta 0.0316 18 795 44 -0.037 0.047 1000 -1000 -0.033 -1000
VEGFR1 specific signals 0.0316 18 1015 56 -0.052 0.053 1000 -1000 -0.041 -1000
Class IB PI3K non-lipid kinase events 0.0316 18 54 3 -0.029 0.029 1000 -1000 -0.026 -1000
p38 MAPK signaling pathway 0.0316 18 821 44 -0.021 0.055 1000 -1000 -0.019 -1000
Signaling events mediated by HDAC Class III 0.0299 17 701 40 -0.055 0.059 1000 -1000 -0.037 -1000
Visual signal transduction: Cones 0.0246 14 532 38 -0.019 0.06 1000 -1000 -0.023 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0246 14 387 27 -0.038 0.064 1000 -1000 -0.04 -1000
S1P4 pathway 0.0246 14 373 25 -0.028 0.041 1000 -1000 -0.022 -1000
Alternative NF-kappaB pathway 0.0246 14 187 13 0 0.075 1000 -1000 0 -1000
Ephrin A reverse signaling 0.0228 13 95 7 -0.025 0.035 1000 -1000 -0.017 -1000
a4b1 and a4b7 Integrin signaling 0.0228 13 69 5 0.028 0.04 1000 -1000 0.027 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0228 13 1188 88 -0.044 0.041 1000 -1000 -0.059 -1000
S1P1 pathway 0.0193 11 400 36 -0.02 0.029 1000 -1000 -0.041 -1000
Arf6 trafficking events 0.0193 11 851 71 -0.034 0.051 1000 -1000 -0.028 -1000
Visual signal transduction: Rods 0.0193 11 602 52 -0.067 0.068 1000 -1000 -0.053 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0141 8 591 68 -0.057 0.052 1000 -1000 -0.072 -1000
Rapid glucocorticoid signaling 0.0123 7 145 20 -0.016 0.038 1000 -1000 -0.015 -1000
LPA4-mediated signaling events 0.0105 6 78 12 -0.025 0.002 1000 -1000 -0.018 -1000
Glypican 2 network 0.0105 6 26 4 0.029 0.042 1000 -1000 0.027 -1000
Total NA 6049 328682 7203 -11 11 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 0.4 1.3 468 -10000 0 468
PLK1 0.32 0.38 0.92 119 -10000 0 119
BIRC5 0.35 0.4 0.85 172 -10000 0 172
HSPA1B 1.2 0.4 1.3 475 -10000 0 475
MAP2K1 0.46 0.17 0.51 496 -10000 0 496
BRCA2 1.3 0.53 1.5 470 -10000 0 470
FOXM1 1.7 0.89 2.1 456 -10000 0 456
XRCC1 1.2 0.43 1.3 468 -10000 0 468
FOXM1B/p19 0.27 0.46 1.1 124 -10000 0 124
Cyclin D1/CDK4 0.66 0.5 1.1 327 -10000 0 327
CDC2 1.5 0.5 1.6 482 -10000 0 482
TGFA 0.72 0.51 1.1 348 -10000 0 348
SKP2 1.3 0.55 1.5 475 -10000 0 475
CCNE1 0.009 0.032 0.13 32 -10000 0 32
CKS1B 1.2 0.4 1.3 475 -10000 0 475
RB1 0.033 0.17 0.79 23 -0.74 2 25
FOXM1C/SP1 0.88 0.44 1.1 419 -10000 0 419
AURKB 0.34 0.4 0.99 116 -0.75 1 117
CENPF 1.6 0.55 1.8 489 -10000 0 489
CDK4 0.13 0.072 0.18 340 -10000 0 340
MYC 0.6 0.53 1.1 296 -10000 0 296
CHEK2 0.39 0.18 0.46 463 -10000 0 463
ONECUT1 0.75 0.55 1.2 342 -10000 0 342
CDKN2A -0.022 0.11 -10000 0 -0.34 52 52
LAMA4 1.1 0.51 1.3 440 -1.1 3 443
FOXM1B/HNF6 0.75 0.55 1.2 336 -10000 0 336
FOS 1.1 0.54 1.3 422 -10000 0 422
SP1 -0.002 0.093 -10000 0 -0.18 91 91
CDC25B 1.2 0.45 1.4 470 -10000 0 470
response to radiation 0.24 0.076 0.26 491 -10000 0 491
CENPB 1.2 0.45 1.3 472 -10000 0 472
CENPA 1.2 0.42 1.3 470 -10000 0 470
NEK2 1.6 0.57 1.8 476 -10000 0 476
HIST1H2BA 1.2 0.44 1.3 470 -10000 0 470
CCNA2 0.009 0.03 0.11 37 -10000 0 37
EP300 0.027 0.009 -10000 0 -10000 0 0
CCNB1/CDK1 1.3 0.59 1.6 448 -10000 0 448
CCNB2 1.6 0.54 1.8 491 -10000 0 491
CCNB1 1.7 0.66 1.9 473 -10000 0 473
ETV5 1.3 0.56 1.5 476 -10000 0 476
ESR1 1 0.56 1.3 410 -1 2 412
CCND1 0.77 0.54 1.2 348 -10000 0 348
GSK3A 0.26 0.1 0.3 466 -10000 0 466
Cyclin A-E1/CDK1-2 0.029 0.095 0.35 44 -10000 0 44
CDK2 0.074 0.068 0.14 281 -10000 0 281
G2/M transition of mitotic cell cycle 0.42 0.15 0.46 507 -10000 0 507
FOXM1B/Cbp/p300 0.1 0.28 0.88 43 -10000 0 43
GAS1 1 0.54 1.3 408 -1.1 1 409
MMP2 1.1 0.56 1.3 429 -1.1 4 433
RB1/FOXM1C 0.54 0.55 1.1 264 -10000 0 264
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 0.023 0.013 -10000 0 0 135 135
PLK4 0.015 0.015 -10000 0 0 269 269
regulation of centriole replication 0.065 0.1 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 0.41 3 -10000 0 3
CLOCK 0.05 0.034 0.087 227 -0.043 13 240
TIMELESS/CRY2 0.2 0.21 0.44 242 -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 21 -0.82 13 34
ARNTL 0.051 0.033 0.087 230 -0.043 13 243
TIMELESS 0.27 0.31 0.62 242 -10000 0 242
NPAS2 0.051 0.034 0.087 229 -0.043 13 242
CRY2 0.029 0.003 -10000 0 0 6 6
mol:CO -0.093 0.11 0.13 3 -0.21 245 248
CHEK1 0.002 0.007 -10000 0 0 527 527
mol:HEME 0.093 0.11 0.21 245 -0.13 3 248
PER1 0.028 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 0.35 215 -0.66 6 221
S phase of mitotic cell cycle 0.003 0.033 0.41 3 -10000 0 3
TIMELESS/CHEK1/ATR 0.003 0.033 0.42 3 -10000 0 3
mol:NADPH 0.093 0.11 0.21 245 -0.13 3 248
PER1/TIMELESS 0.19 0.21 0.44 229 -10000 0 229
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.029 0.005 -10000 0 0 16 16
S1P3 pathway

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
PDGFRB 0.029 0.005 -10000 0 0 16 16
mol:S1P -0.016 0.016 0.07 4 -0.03 296 300
S1P1/S1P/Gi -0.053 0.092 0.26 4 -0.23 52 56
GNAO1 -0.019 0.046 0.12 4 -0.063 285 289
S1P/S1P3/G12/G13 -0.015 0.047 0.16 4 -0.06 55 59
AKT1 -0.043 0.11 0.27 2 -0.5 21 23
AKT3 -0.54 0.5 0.66 3 -0.98 316 319
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.029 0.005 -10000 0 0 16 16
GNAI2 -0.022 0.047 0.12 4 -0.063 314 318
GNAI3 -0.017 0.04 0.098 2 -0.058 265 267
GNAI1 -0.018 0.044 0.1 4 -0.058 295 299
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 -0.018 0.019 0.084 4 -0.034 309 313
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.13 0.15 0.42 4 -0.27 271 275
MAPK3 -0.14 0.14 0.37 4 -0.27 267 271
MAPK1 -0.14 0.14 0.37 4 -0.27 263 267
JAK2 -0.14 0.15 0.33 5 -0.28 243 248
CXCR4 -0.14 0.14 0.35 3 -0.27 264 267
FLT1 -0.025 0.052 0.16 4 -0.072 295 299
RhoA/GDP 0.022 0.008 -10000 0 -0.15 1 1
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
SRC -0.13 0.14 0.37 4 -0.27 243 247
S1P/S1P3/Gi -0.13 0.15 0.42 4 -0.27 271 275
RAC1 0.028 0.006 -10000 0 0 26 26
RhoA/GTP -0.12 0.15 0.35 4 -0.26 269 273
VEGFA -0.022 0.05 0.16 4 -0.07 273 277
S1P/S1P2/Gi -0.075 0.1 0.3 4 -0.22 90 94
VEGFR1 homodimer/VEGFA homodimer -0.029 0.074 0.33 4 -0.1 258 262
RHOA 0.029 0.003 -10000 0 0 7 7
S1P/S1P3/Gq -0.028 0.059 -10000 0 -0.2 47 47
GNAQ 0.028 0.007 -10000 0 0 28 28
GNAZ -0.017 0.043 0.1 4 -0.058 280 284
G12/G13 0.041 0.012 -10000 0 -10000 0 0
GNA14 0.029 0.005 -10000 0 0 18 18
GNA15 0.027 0.008 -10000 0 0 46 46
GNA12 0.028 0.007 -10000 0 0 34 34
GNA13 0.029 0.005 -10000 0 0 13 13
GNA11 0.025 0.011 -10000 0 0 83 83
Rac1/GTP -0.12 0.15 0.35 4 -0.26 271 275
TCGA08_retinoblastoma

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
CDKN2B -0.042 0.033 -10000 0 -0.063 348 348
CDKN2C -0.019 0.048 -10000 0 -0.064 276 276
CDKN2A 0.013 0.023 -10000 0 -0.065 6 6
CCND2 -0.022 0.039 -10000 0 -0.26 2 2
RB1 0.063 0.085 0.17 174 -0.2 7 181
CDK4 -0.015 0.037 -10000 0 -0.14 39 39
CDK6 -0.017 0.036 -10000 0 -0.28 2 2
G1/S progression -0.071 0.089 0.2 7 -0.17 188 195
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 0.14 1 -0.13 479 480
BUB1B 0.16 0.068 0.18 459 -0.14 1 460
PLK1 0.068 0.029 0.1 158 -10000 0 158
PLK1S1 0.034 0.017 0.055 157 -10000 0 157
KIF2A 0.047 0.031 0.14 15 -10000 0 15
regulation of mitotic centrosome separation 0.068 0.029 0.1 158 -10000 0 158
GOLGA2 0.029 0.005 -10000 0 0 15 15
Hec1/SPC24 0.005 0.019 -10000 0 -10000 0 0
WEE1 0.08 0.065 0.17 8 -0.27 10 18
cytokinesis 0.22 0.085 0.26 461 -10000 0 461
PP2A-alpha B56 0.13 0.08 -10000 0 -0.49 6 6
AURKA 0.078 0.035 0.11 127 -10000 0 127
PICH/PLK1 0.11 0.082 0.17 331 -10000 0 331
CENPE 0.062 0.061 0.22 56 -10000 0 56
RhoA/GTP 0.022 0.008 -10000 0 -0.15 1 1
positive regulation of microtubule depolymerization 0.049 0.03 0.14 15 -10000 0 15
PPP2CA 0.029 0.005 -10000 0 0 13 13
FZR1 0.027 0.008 -10000 0 0 45 45
TPX2 0.11 0.033 0.12 405 -10000 0 405
PAK1 0.029 0.009 -10000 0 -0.03 1 1
SPC24 0.02 0.014 -10000 0 0 176 176
FBXW11 0.029 0.005 -10000 0 0 16 16
CLSPN 0.048 0.035 0.14 34 -0.22 3 37
GORASP1 0.03 0.003 -10000 0 0 5 5
metaphase 0.002 0.005 0.012 85 -0.01 1 86
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.034 0.017 0.055 157 -10000 0 157
G2 phase of mitotic cell cycle 0.005 0.003 0.018 18 -10000 0 18
STAG2 0.028 0.006 -10000 0 0 27 27
GRASP65/GM130/RAB1/GTP 0.026 0.033 -10000 0 -0.42 2 2
spindle elongation 0.068 0.029 0.1 158 -10000 0 158
ODF2 0.035 0.007 -10000 0 -0.03 2 2
BUB1 0.001 0.049 -10000 0 -0.61 3 3
TPT1 0.03 0.042 0.099 2 -0.15 25 27
CDC25C 0.081 0.059 0.16 87 -0.23 5 92
CDC25B 0.03 0.02 -10000 0 -0.03 42 42
SGOL1 0.12 0.044 0.13 479 -0.14 1 480
RHOA 0.029 0.003 -10000 0 0 7 7
CCNB1/CDK1 0.008 0.025 -10000 0 -0.14 1 1
CDC14B -0.014 0.003 0.001 19 -10000 0 19
CDC20 0.007 0.012 -10000 0 0 431 431
PLK1/PBIP1 0.04 0.026 0.073 121 -10000 0 121
mitosis 0 0.001 -10000 0 -10000 0 0
FBXO5 0.12 0.077 0.18 360 -0.13 5 365
CDC2 0.007 0.004 0.009 379 -10000 0 379
NDC80 0.003 0.009 -10000 0 0 503 503
metaphase plate congression 0.045 0.042 -10000 0 -0.2 12 12
ERCC6L 0.092 0.077 0.15 325 -0.15 1 326
NLP/gamma Tubulin 0.029 0.025 0.069 39 -0.081 10 49
microtubule cytoskeleton organization 0.03 0.042 0.099 2 -0.14 25 27
G2/M transition DNA damage checkpoint 0.001 0.002 0.014 4 -10000 0 4
PPP1R12A 0.031 0.006 -10000 0 -0.034 1 1
interphase 0.001 0.002 0.014 4 -10000 0 4
PLK1/PRC1-2 0.007 0.023 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.091 0.029 0.14 10 -10000 0 10
RAB1A 0.029 0.004 -10000 0 0 11 11
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.07 0.025 0.079 445 -10000 0 445
mitotic prometaphase 0.003 0.004 0.022 14 -10000 0 14
proteasomal ubiquitin-dependent protein catabolic process 0.064 0.053 -10000 0 -0.29 3 3
microtubule-based process 0.009 0.023 0.1 5 -10000 0 5
Golgi organization 0.068 0.029 0.1 158 -10000 0 158
Cohesin/SA2 0.067 0.027 0.1 99 -10000 0 99
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 0.027 0.098 7 -10000 0 7
PPP2R1A 0.029 0.005 -10000 0 0 19 19
chromosome segregation 0.039 0.025 0.072 121 -10000 0 121
PRC1 0.007 0.013 -10000 0 0 424 424
ECT2 0.23 0.068 0.25 520 -10000 0 520
C13orf34 0.061 0.024 0.071 395 -10000 0 395
NUDC 0.045 0.042 -10000 0 -0.2 12 12
regulation of attachment of spindle microtubules to kinetochore 0.16 0.067 0.18 459 -0.14 1 460
spindle assembly 0.047 0.025 0.08 142 -10000 0 142
spindle stabilization 0.034 0.017 0.054 157 -10000 0 157
APC/C/HCDH1 -0.015 0.019 -10000 0 -10000 0 0
MKLP2/PLK1 0.009 0.023 0.1 5 -10000 0 5
CCNB1 0.005 0.012 -10000 0 -0.026 1 1
PPP1CB 0.03 0.009 -10000 0 -0.028 7 7
BTRC 0.029 0.005 -10000 0 0 18 18
ROCK2 0.055 0.032 -10000 0 -0.22 3 3
TUBG1 0.031 0.045 0.11 6 -0.16 25 31
G2/M transition of mitotic cell cycle 0.11 0.079 0.17 372 -10000 0 372
MLF1IP -0.014 0.006 0.013 1 -10000 0 1
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 0.36 173 -0.28 2 175
NF kappa B1 p50/RelA/I kappa B alpha 0.1 0.24 0.43 171 -0.33 4 175
alphaV/beta3 Integrin/Osteopontin/Src 0.026 0.057 0.15 59 -0.19 7 66
AP1 0.083 0.28 0.46 158 -0.34 16 174
ILK 0.073 0.17 0.32 133 -0.3 2 135
bone resorption -0.009 0.15 0.25 80 -0.34 3 83
PTK2B 0.024 0.011 -10000 0 0 100 100
PYK2/p130Cas 0.062 0.13 0.26 93 -0.27 3 96
ITGAV 0.009 0.06 0.098 165 -10000 0 165
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.039 0.1 -10000 0 -0.16 216 216
alphaV/beta3 Integrin/Osteopontin 0.022 0.1 0.25 59 -0.16 62 121
MAP3K1 0.073 0.17 0.33 120 -0.3 2 122
JUN 0.027 0.027 0.096 29 -0.035 58 87
MAPK3 0.13 0.25 0.46 177 -0.32 1 178
MAPK1 0.13 0.25 0.46 175 -0.32 1 176
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.008 -10000 0 0 45 45
MAPK8 0.072 0.18 0.35 122 -0.3 2 124
ITGB3 0.012 0.059 0.099 163 -10000 0 163
NFKBIA 0.13 0.25 0.46 177 -0.33 2 179
FOS 0.024 0.026 0.093 24 -0.035 46 70
CD44 0.017 0.015 -10000 0 0 239 239
CHUK 0.028 0.007 -10000 0 0 35 35
PLAU 0.19 0.36 0.71 170 -0.57 2 172
NF kappa B1 p50/RelA 0.12 0.26 0.48 171 -0.32 1 172
BCAR1 0.027 0.009 -10000 0 0 56 56
RELA 0.029 0.003 -10000 0 0 7 7
alphaV beta3 Integrin 0.04 0.11 0.18 113 -0.18 66 179
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.068 0.16 0.3 121 -0.29 2 123
VAV3 0.068 0.16 0.29 142 -0.28 2 144
MAP3K14 0.11 0.22 0.39 178 -0.29 2 180
ROCK2 0.029 0.005 -10000 0 0 19 19
SPP1 -0.004 0.038 0.089 65 -10000 0 65
RAC1 0.028 0.006 -10000 0 0 26 26
Rac1/GTP 0.054 0.14 0.26 134 -0.27 2 136
MMP2 0.017 0.19 0.33 90 -0.35 35 125
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0 0.053 -10000 0 -0.4 7 7
Crk/p130 Cas/Paxillin -0.17 0.097 -10000 0 -0.26 229 229
JUN -0.071 0.09 0.18 3 -0.26 23 26
HRAS 0.028 0.006 -10000 0 0 27 27
RET51/GFRalpha1/GDNF/GRB10 -0.018 0.1 -10000 0 -0.14 222 222
RAP1A 0.029 0.004 -10000 0 0 8 8
FRS2 0.028 0.007 -10000 0 0 30 30
RAP1A/GDP 0.022 0.003 -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 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.028 0.007 -10000 0 0 36 36
RET9/GFRalpha1/GDNF/Enigma -0.025 0.089 -10000 0 -0.13 226 226
RHOA 0.029 0.003 -10000 0 0 7 7
RAP1A/GTP -0.018 0.098 -10000 0 -0.14 219 219
GRB7 0.028 0.008 -10000 0 0 40 40
RET51/GFRalpha1/GDNF -0.011 0.097 -10000 0 -0.14 187 187
MAPKKK cascade -0.09 0.076 0.1 1 -0.19 124 125
BCAR1 0.027 0.009 -10000 0 0 56 56
RET9/GFRalpha1/GDNF/IRS1 -0.11 0.097 -10000 0 -0.16 405 405
lamellipodium assembly -0.15 0.097 -10000 0 -0.24 235 235
RET51/GFRalpha1/GDNF/SHC -0.016 0.1 -10000 0 -0.14 217 217
PIK3CA 0.021 0.014 -10000 0 0 174 174
RET9/GFRalpha1/GDNF/SHC -0.024 0.088 -10000 0 -0.13 221 221
RET9/GFRalpha1/GDNF/Shank3 -0.031 0.085 -10000 0 -0.13 225 225
MAPK3 -0.072 0.078 0.28 3 -0.22 9 12
DOK1 0.029 0.004 -10000 0 0 10 10
DOK6 0.027 0.009 -10000 0 0 55 55
PXN 0.029 0.005 -10000 0 0 14 14
neurite development -0.077 0.086 0.24 5 -0.29 20 25
DOK5 0.017 0.015 -10000 0 0 245 245
GFRA1 0.016 0.015 -10000 0 0 258 258
MAPK8 -0.068 0.092 0.18 1 -0.26 23 24
HRAS/GTP -0.036 0.12 -10000 0 -0.18 199 199
tube development -0.035 0.083 0.21 4 -0.13 220 224
MAPK1 -0.067 0.074 0.29 2 -10000 0 2
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.057 0.089 -10000 0 -0.17 207 207
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
SRC 0.028 0.007 -10000 0 0 33 33
PDLIM7 0.029 0.005 -10000 0 0 16 16
RET51/GFRalpha1/GDNF/Dok6 -0.017 0.11 -10000 0 -0.14 213 213
SHC1 0.029 0.006 -10000 0 0 20 20
RET51/GFRalpha1/GDNF/Dok4 -0.018 0.1 -10000 0 -0.14 222 222
RET51/GFRalpha1/GDNF/Dok5 0.008 0.099 -10000 0 -0.15 136 136
PRKCA 0.028 0.006 -10000 0 0 25 25
HRAS/GDP 0.021 0.005 -10000 0 -10000 0 0
CREB1 -0.062 0.11 0.21 1 -0.36 7 8
PIK3R1 0.021 0.013 -10000 0 0 159 159
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.063 0.094 -10000 0 -0.18 218 218
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 0.028 0.007 -10000 0 0 37 37
JNK cascade -0.069 0.091 0.18 5 -0.25 23 28
RET9/GFRalpha1/GDNF/FRS2 -0.024 0.087 -10000 0 -0.13 217 217
SHANK3 0.023 0.013 -10000 0 0 127 127
RASA1 0.027 0.009 -10000 0 0 51 51
NCK1 0.026 0.009 -10000 0 0 63 63
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.052 0.088 -10000 0 -0.17 200 200
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.054 0.091 0.19 1 -0.17 203 204
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.056 0.1 0.19 1 -0.26 23 24
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.052 0.091 -10000 0 -0.28 5 5
PI3K -0.2 0.14 0.32 1 -0.34 233 234
SOS1 0.028 0.007 -10000 0 0 34 34
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.025 0.092 -10000 0 -0.13 220 220
GRB10 0.029 0.005 -10000 0 0 13 13
activation of MAPKK activity -0.05 0.089 -10000 0 -0.28 4 4
RET51/GFRalpha1/GDNF/FRS2 -0.016 0.1 -10000 0 -0.14 213 213
GAB1 0.028 0.006 -10000 0 0 25 25
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 17 17
RET51/GFRalpha1/GDNF/PKC alpha -0.017 0.1 -10000 0 -0.14 220 220
GRB2 0.029 0.005 -10000 0 0 19 19
PRKACA 0.026 0.01 -10000 0 0 78 78
GDNF 0.028 0.007 -10000 0 0 36 36
RAC1 0.028 0.006 -10000 0 0 26 26
RET51/GFRalpha1/GDNF/IRS1 -0.11 0.11 -10000 0 -0.17 401 401
Rac1/GTP -0.17 0.12 -10000 0 -0.28 234 234
RET9/GFRalpha1/GDNF -0.034 0.083 -10000 0 -0.13 227 227
GFRalpha1/GDNF -0.045 0.1 -10000 0 -0.16 227 227
Effects of Botulinum toxin

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
STX1A -0.017 0.002 0 7 -10000 0 7
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.042 0.01 -10000 0 -10000 0 0
STXBP1 0.026 0.01 -10000 0 0 75 75
ACh/CHRNA1 -0.043 0.044 -10000 0 -0.073 364 364
RAB3GAP2/RIMS1/UNC13B 0.055 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 0.029 0.006 -10000 0 0 20 20
mol:ACh -0.055 0.038 0.088 1 -0.081 363 364
RAB3GAP2 0.028 0.007 -10000 0 0 28 28
STX1A/SNAP25/VAMP2 -0.1 0.096 -10000 0 -0.17 340 340
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.042 0.044 -10000 0 -0.073 364 364
UNC13B 0.029 0.005 -10000 0 0 14 14
CHRNA1 0.028 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 35 35
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 0.096 -10000 0 -0.17 340 340
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.012 0.008 0 162 -10000 0 162
GNB1/GNG2 -0.052 0.09 -10000 0 -0.13 311 311
regulation of S phase of mitotic cell cycle -0.078 0.11 -10000 0 -0.2 220 220
GNAO1 0.027 0.009 -10000 0 -0.002 47 47
HRAS 0.022 0.021 -10000 0 -0.033 61 61
SHBG/T-DHT 0.019 0.004 -10000 0 -10000 0 0
PELP1 0.022 0.021 -10000 0 -0.033 64 64
AKT1 -0.016 0.004 0 26 -10000 0 26
MAP2K1 -0.082 0.098 0.23 16 -0.24 36 52
T-DHT/AR -0.077 0.083 -10000 0 -0.15 316 316
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.003 0.01 26 -0.007 20 46
GNAI2 0.029 0.006 -10000 0 -0.012 10 10
GNAI3 0.025 0.012 -10000 0 0 99 99
GNAI1 0.028 0.007 -10000 0 -0.002 29 29
mol:GDP -0.16 0.14 -10000 0 -0.29 268 268
cell proliferation -0.12 0.18 0.38 24 -0.46 64 88
PIK3CA 0.021 0.014 -10000 0 0 174 174
FOS -0.1 0.26 0.55 26 -0.71 66 92
mol:Ca2+ -0.012 0.022 0.054 16 -0.058 33 49
MAPK3 -0.11 0.14 0.31 24 -0.37 59 83
MAPK1 -0.062 0.15 0.3 26 -0.5 32 58
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 0.005 -10000 0 0 14 14
potassium channel inhibitor activity 0 0.004 0.016 26 -10000 0 26
HRAS/GTP -0.048 0.093 0.21 12 -0.13 278 290
actin cytoskeleton reorganization 0.003 0.057 -10000 0 -0.12 77 77
SRC 0.022 0.02 -10000 0 -0.033 59 59
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 0.085 0.18 0.44 69 -0.44 24 93
T-DHT/AR/PELP1 -0.062 0.083 -10000 0 -0.13 312 312
HRAS/GDP -0.15 0.15 0.13 1 -0.31 225 226
CREB1 -0.11 0.15 0.24 1 -0.46 77 78
RAC1-CDC42/GTP 0.009 0.062 -10000 0 -0.12 77 77
AR 0.01 0.017 -10000 0 -0.034 23 23
GNB1 0.029 0.006 -10000 0 0 23 23
RAF1 -0.075 0.091 0.21 15 -0.21 29 44
RAC1-CDC42/GDP -0.15 0.15 -10000 0 -0.31 220 220
T-DHT/AR/PELP1/Src -0.05 0.089 -10000 0 -0.13 281 281
MAP2K2 -0.092 0.1 0.24 11 -0.26 38 49
T-DHT/AR/PELP1/Src/PI3K -0.079 0.11 -10000 0 -0.2 220 220
GNAZ 0.027 0.009 -10000 0 -0.001 53 53
SHBG 0.028 0.006 -10000 0 0 26 26
Gi family/GNB1/GNG2/GDP -0.04 0.1 -10000 0 -0.37 24 24
mol:T-DHT 0 0.001 -10000 0 -10000 0 0
RAC1 0.028 0.006 -10000 0 0 26 26
GNRH1 -0.014 0.007 0 103 -10000 0 103
Gi family/GTP -0.046 0.066 0.16 1 -0.2 38 39
CDC42 0.029 0.005 -10000 0 0 13 13
Endothelins

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
AKT1 0.043 0.21 0.38 135 -0.32 3 138
PTK2B 0.024 0.013 -10000 0 -0.03 5 5
mol:Ca2+ 0.037 0.19 0.54 13 -0.64 9 22
EDN1 0.025 0.14 0.26 132 -0.22 4 136
EDN3 0.027 0.009 -10000 0 0 58 58
EDN2 0.027 0.008 -10000 0 0 46 46
HRAS/GDP 0.017 0.21 0.41 34 -0.42 36 70
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.023 0.16 0.27 80 -0.36 30 110
ADCY4 0.088 0.19 0.3 215 -0.28 3 218
ADCY5 0.086 0.19 0.3 210 -0.29 2 212
ADCY6 0.089 0.19 0.3 218 -0.28 3 221
ADCY7 0.086 0.19 0.3 211 -0.29 2 213
ADCY1 0.088 0.19 0.3 215 -0.29 2 217
ADCY2 0.086 0.19 0.3 204 -0.29 2 206
ADCY3 0.088 0.19 0.3 215 -0.28 3 218
ADCY8 0.001 0.13 0.3 60 -0.27 21 81
ADCY9 0.083 0.19 0.3 205 -0.27 9 214
arachidonic acid secretion -0.099 0.27 0.54 24 -0.57 79 103
ETB receptor/Endothelin-1/Gq/GTP 0.042 0.14 0.24 91 -0.31 28 119
GNAO1 0.027 0.008 -10000 0 0 44 44
HRAS 0.023 0.02 0.053 2 -0.021 87 89
ETA receptor/Endothelin-1/G12/GTP 0.027 0.16 0.38 74 -0.2 67 141
ETA receptor/Endothelin-1/Gs/GTP 0.04 0.16 0.36 74 -0.19 68 142
mol:GTP 0.002 0.015 0.054 34 -10000 0 34
COL3A1 0.04 0.24 0.54 95 -0.42 4 99
EDNRB 0.05 0.11 0.21 174 -0.12 3 177
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 0.012 0.24 0.39 125 -0.38 80 205
CYSLTR1 0.036 0.21 0.4 122 -0.32 4 126
SLC9A1 0.028 0.14 0.26 125 -0.28 7 132
mol:GDP 0.015 0.21 0.42 32 -0.44 36 68
SLC9A3 0.072 0.2 0.43 11 -0.59 16 27
RAF1 0.004 0.23 0.5 33 -0.44 58 91
JUN 0.033 0.21 0.67 11 -0.72 10 21
JAK2 0.038 0.2 0.39 127 -0.32 4 131
mol:IP3 0.02 0.17 0.3 83 -0.38 30 113
ETA receptor/Endothelin-1 -0.054 0.097 0.3 6 -0.31 9 15
PLCB1 0.022 0.022 0.062 14 -0.034 59 73
PLCB2 0.021 0.025 0.074 18 -0.035 76 94
ETA receptor/Endothelin-3 0.024 0.11 0.2 117 -0.16 9 126
FOS -0.056 0.35 0.69 26 -0.83 68 94
Gai/GDP -0.006 0.19 -10000 0 -0.67 38 38
CRK 0.028 0.009 -10000 0 -0.03 5 5
mol:Ca ++ 0.075 0.24 0.4 151 -0.4 23 174
BCAR1 0.023 0.016 -10000 0 -0.029 34 34
PRKCB1 0.036 0.17 0.29 86 -0.37 31 117
GNAQ 0.021 0.03 0.11 13 -0.038 60 73
GNAZ 0.027 0.009 -10000 0 0 51 51
GNAL 0.029 0.006 -10000 0 0 21 21
Gs family/GDP 0.015 0.2 0.38 34 -0.4 37 71
ETA receptor/Endothelin-1/Gq/GTP 0.014 0.16 0.29 82 -0.36 30 112
MAPK14 0.025 0.13 0.27 30 -0.3 25 55
TRPC6 0.036 0.2 0.55 12 -0.67 9 21
GNAI2 0.029 0.003 -10000 0 0 6 6
GNAI3 0.025 0.011 -10000 0 0 98 98
GNAI1 0.028 0.006 -10000 0 0 27 27
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.034 0.14 0.23 85 -0.32 29 114
ETB receptor/Endothelin-2 0.071 0.067 0.17 157 -0.082 6 163
ETB receptor/Endothelin-3 0.07 0.067 0.17 156 -0.081 5 161
ETB receptor/Endothelin-1 -0.009 0.089 0.31 18 -0.21 5 23
MAPK3 -0.05 0.33 0.66 26 -0.77 69 95
MAPK1 -0.052 0.33 0.66 26 -0.76 70 96
Rac1/GDP 0.016 0.2 0.4 32 -0.42 35 67
cAMP biosynthetic process 0.051 0.18 0.28 129 -0.31 15 144
MAPK8 0.03 0.21 0.51 16 -0.65 16 32
SRC 0.028 0.009 -10000 0 -0.03 5 5
ETB receptor/Endothelin-1/Gi/GTP 0.048 0.11 0.2 145 -0.23 11 156
p130Cas/CRK/Src/PYK2 0.009 0.21 0.47 24 -0.5 29 53
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP 0.015 0.2 0.4 31 -0.42 35 66
COL1A2 0.071 0.27 0.64 86 -0.5 5 91
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.021 0.11 0.2 113 -0.16 9 122
mol:DAG 0.02 0.17 0.3 83 -0.38 30 113
MAP2K2 -0.031 0.27 0.59 27 -0.56 72 99
MAP2K1 -0.019 0.27 0.59 28 -0.56 69 97
EDNRA 0.022 0.15 0.26 134 -0.22 12 146
positive regulation of muscle contraction 0.026 0.17 0.31 128 -0.28 3 131
Gq family/GDP -0.026 0.16 0.38 21 -0.4 34 55
HRAS/GTP 0.022 0.21 0.43 35 -0.43 36 71
PRKCH 0.03 0.17 0.28 83 -0.39 28 111
RAC1 0.028 0.006 -10000 0 0 26 26
PRKCA 0.034 0.17 0.34 34 -0.37 26 60
PRKCB 0.036 0.17 0.29 86 -0.36 32 118
PRKCE 0.033 0.18 0.29 86 -0.37 31 117
PRKCD 0.03 0.17 0.34 36 -0.37 31 67
PRKCG 0.033 0.17 0.29 88 -0.36 30 118
regulation of vascular smooth muscle contraction -0.082 0.4 0.71 24 -1 68 92
PRKCQ 0.034 0.18 0.29 87 -0.38 28 115
PLA2G4A -0.11 0.29 0.56 23 -0.6 88 111
GNA14 0.021 0.03 0.1 15 -0.035 96 111
GNA15 0.023 0.025 0.091 14 -0.035 64 78
GNA12 0.028 0.007 -10000 0 0 34 34
GNA11 0.021 0.024 0.094 11 -0.034 56 67
Rac1/GTP 0.026 0.16 0.38 73 -0.2 68 141
MMP1 0.03 0.1 0.39 33 -10000 0 33
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 0.025 0.011 -10000 0 0 95 95
HRAS 0.028 0.006 -10000 0 0 27 27
EGFR 0.027 0.009 -10000 0 0 55 55
AKT -0.031 0.12 0.22 29 -0.24 45 74
FOXO3 0.028 0.008 -10000 0 0 40 40
AKT1 0.028 0.006 -10000 0 0 26 26
FOXO1 0.028 0.008 -10000 0 0 40 40
AKT3 0.012 0.015 -10000 0 0 332 332
FOXO4 0.029 0.003 -10000 0 0 7 7
MET 0.025 0.011 -10000 0 0 88 88
PIK3CA 0.021 0.014 -10000 0 0 174 174
PIK3CB 0.025 0.011 -10000 0 0 83 83
NRAS 0.014 0.015 -10000 0 0 300 300
PIK3CG 0.028 0.007 -10000 0 0 36 36
PIK3R3 0.019 0.014 -10000 0 0 205 205
PIK3R2 0.027 0.009 -10000 0 0 50 50
NF1 0.026 0.01 -10000 0 0 70 70
RAS 0.043 0.074 0.18 53 -0.25 5 58
ERBB2 0.028 0.008 -10000 0 0 40 40
proliferation/survival/translation 0.016 0.12 0.26 51 -0.21 14 65
PI3K 0.04 0.095 0.2 73 -0.21 21 94
PIK3R1 0.021 0.013 -10000 0 0 159 159
KRAS 0.025 0.011 -10000 0 0 97 97
FOXO 0.024 0.082 0.22 36 -10000 0 36
AKT2 0.027 0.009 -10000 0 0 53 53
PTEN 0.028 0.007 -10000 0 0 37 37
Aurora B signaling

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
Condensin I complex 0.033 0.071 0.19 81 -0.32 1 82
STMN1 0.031 0.091 0.2 124 -10000 0 124
Aurora B/RasGAP/Survivin 0.048 0.039 -10000 0 -0.12 1 1
Chromosomal passenger complex/Cul3 protein complex 0.009 0.095 0.21 48 -0.2 15 63
BIRC5 0.038 0.022 0.062 65 -10000 0 65
DES -0.053 0.14 -10000 0 -0.46 45 45
Aurora C/Aurora B/INCENP 0.055 0.035 -10000 0 -10000 0 0
Aurora B/TACC1 -0.064 0.072 -10000 0 -0.13 311 311
Aurora B/PP2A 0.037 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 0.093 0.19 299 -10000 0 299
PEBP1 0.043 0.009 -10000 0 -0.032 1 1
KIF20A 0.002 0.012 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.035 0.025 -10000 0 -0.15 1 1
SEPT1 0.029 0.004 -10000 0 0 11 11
SMC2 0.017 0.015 -10000 0 0 246 246
SMC4 0.001 0.006 -10000 0 0 534 534
NSUN2/NPM1/Nucleolin 0.001 0.039 -10000 0 -0.39 4 4
PSMA3 0.029 0.005 -10000 0 0 17 17
G2/M transition of mitotic cell cycle 0 0.002 0.02 1 -10000 0 1
H3F3B 0.009 0.017 -10000 0 -0.2 3 3
AURKB 0.028 0.019 -10000 0 -10000 0 0
AURKC 0.028 0.006 -10000 0 0 26 26
CDCA8 0.042 0.021 0.064 82 -10000 0 82
cytokinesis 0.003 0.033 0.24 9 -10000 0 9
Aurora B/Septin1 0.14 0.12 0.26 262 -10000 0 262
AURKA 0.002 0.007 -10000 0 -10000 0 0
INCENP 0.052 0.013 0.068 140 -10000 0 140
KLHL13 0.019 0.014 -10000 0 0 195 195
BUB1 0.002 0.008 -10000 0 -10000 0 0
hSgo1/Aurora B/Survivin 0.009 0.024 -10000 0 -10000 0 0
EVI5 0.04 0.008 -10000 0 -10000 0 0
RhoA/GTP 0.002 0.014 -10000 0 -10000 0 0
SGOL1 0.004 0.01 -10000 0 0 485 485
CENPA 0.017 0.047 0.17 30 -10000 0 30
NCAPG 0.002 0.007 -10000 0 0 523 523
Aurora B/HC8 Proteasome 0.037 0.025 -10000 0 -0.16 1 1
NCAPD2 0.014 0.015 -10000 0 0 296 296
Aurora B/PP1-gamma 0.037 0.023 -10000 0 -10000 0 0
RHOA 0.029 0.003 -10000 0 0 7 7
NCAPH 0.011 0.014 -10000 0 0 347 347
NPM1 0 0.012 -10000 0 -0.29 1 1
RASA1 0.027 0.009 -10000 0 0 51 51
KLHL9 0.028 0.007 -10000 0 0 36 36
mitotic prometaphase 0.013 0.006 0.02 147 -10000 0 147
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.025 -10000 0 -0.16 1 1
PPP1CC 0.029 0.006 -10000 0 0 21 21
Centraspindlin 0.002 0.013 -10000 0 -10000 0 0
RhoA/GDP 0.022 0.008 -10000 0 -0.15 1 1
NSUN2 0 0.012 -10000 0 -0.29 1 1
MYLK -0.004 0.053 -10000 0 -0.2 37 37
KIF23 0.001 0.005 -10000 0 -10000 0 0
VIM 0.01 0.066 0.18 69 -10000 0 69
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 0.16 0.11 0.23 378 -10000 0 378
Chromosomal passenger complex/EVI5 0.066 0.058 -10000 0 -10000 0 0
TACC1 0.005 0.011 -10000 0 0 458 458
PPP2R5D 0.029 0.006 -10000 0 0 24 24
CUL3 0.029 0.004 -10000 0 0 10 10
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.029 0.005 -10000 0 0 13 13
mol:PIP3 -0.12 0.11 0.13 15 -0.25 223 238
FRAP1 -0.002 0.066 -10000 0 -0.41 8 8
AKT1 -0.098 0.12 0.15 23 -0.22 204 227
INSR 0.025 0.011 -10000 0 0 90 90
Insulin Receptor/Insulin 0.022 0.047 -10000 0 -0.13 43 43
mol:GTP -0.088 0.11 0.16 22 -0.25 53 75
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.048 0.05 -10000 0 -0.19 13 13
TSC2 0.029 0.006 -10000 0 0 22 22
RHEB/GDP -0.083 0.09 0.11 19 -0.19 169 188
TSC1 0.029 0.006 -10000 0 0 23 23
Insulin Receptor/IRS1 -0.15 0.14 -10000 0 -0.27 334 334
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.046 0.06 0.14 1 -0.23 9 10
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.029 0.004 -10000 0 0 9 9
RPS6KB1 -0.035 0.087 0.21 4 -0.3 13 17
MAP3K5 -0.006 0.046 0.19 5 -0.2 25 30
PIK3R1 0.021 0.014 -10000 0 -0.03 1 1
apoptosis -0.006 0.047 0.19 5 -0.2 26 31
mol:LY294002 -0.001 0.001 0.001 1 -0.001 344 345
EIF4B -0.038 0.08 0.2 6 -0.28 13 19
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.023 0.09 0.2 4 -0.27 13 17
eIF4E/eIF4G1/eIF4A1 -0.026 0.045 -10000 0 -0.26 6 6
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.12 0.13 -10000 0 -0.25 244 244
mTOR/RHEB/GTP/Raptor/GBL -0.028 0.058 0.14 9 -0.17 8 17
FKBP1A 0.021 0.02 -10000 0 -0.029 70 70
RHEB/GTP -0.078 0.098 0.15 20 -0.25 37 57
mol:Amino Acids -0.001 0.001 0.001 1 -0.001 344 345
FKBP12/Rapamycin 0.016 0.015 -10000 0 -10000 0 0
PDPK1 -0.11 0.11 0.13 29 -0.24 206 235
EIF4E 0.028 0.007 -10000 0 0 36 36
ASK1/PP5C 0.003 0.14 -10000 0 -0.54 30 30
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.003 0.068 -10000 0 -0.25 37 37
TSC1/TSC2 -0.094 0.12 0.17 22 -0.27 53 75
tumor necrosis factor receptor activity 0.001 0.001 0.001 344 -0.001 1 345
RPS6 0.028 0.007 -10000 0 0 32 32
PPP5C 0.028 0.006 -10000 0 0 26 26
EIF4G1 0.025 0.011 -10000 0 0 92 92
IRS1 -0.16 0.13 -10000 0 -0.27 346 346
INS 0.029 0.006 -10000 0 0 23 23
PTEN 0.013 0.026 -10000 0 -0.03 143 143
PDK2 -0.11 0.11 0.13 29 -0.24 209 238
EIF4EBP1 -0.047 0.27 -10000 0 -1 38 38
PIK3CA 0.013 0.021 -10000 0 -0.029 68 68
PPP2R5D -0.004 0.068 0.24 4 -0.36 8 12
peptide biosynthetic process -0.034 0.042 0.18 12 -0.22 1 13
RHEB 0.027 0.009 -10000 0 0 54 54
EIF4A1 0.028 0.006 -10000 0 0 25 25
mol:Rapamycin 0 0.001 0.003 22 -0.003 2 24
EEF2 -0.034 0.042 0.18 12 -0.22 1 13
eIF4E/4E-BP1 -0.031 0.26 -10000 0 -0.97 38 38
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 0.024 0.012 -10000 0 0 111 111
CCL5 0.025 0.011 -10000 0 0 81 81
SDCBP 0.028 0.007 -10000 0 0 33 33
FGFR/FGF2/Syndecan-1 -0.017 0.14 0.23 43 -0.32 54 97
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 -0.015 0.14 0.23 34 -0.31 52 86
Syndecan-1/Syntenin -0.009 0.14 0.24 43 -0.31 53 96
MAPK3 -0.036 0.14 0.2 40 -0.3 60 100
HGF/MET 0.033 0.033 -10000 0 -0.16 12 12
TGFB1/TGF beta receptor Type II 0.024 0.012 -10000 0 0 111 111
BSG 0.027 0.009 -10000 0 0 51 51
keratinocyte migration -0.014 0.14 0.23 34 -0.31 52 86
Syndecan-1/RANTES -0.015 0.15 0.24 42 -0.31 71 113
Syndecan-1/CD147 -0.006 0.15 0.24 36 -0.3 58 94
Syndecan-1/Syntenin/PIP2 -0.011 0.14 0.22 42 -0.3 53 95
LAMA5 0.026 0.01 -10000 0 0 66 66
positive regulation of cell-cell adhesion -0.011 0.13 0.22 37 -0.29 53 90
MMP7 0.017 0.015 -10000 0 0 234 234
HGF 0.029 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 -0.008 0.15 0.25 34 -0.3 54 88
regulation of cell adhesion -0.046 0.13 0.18 33 -0.3 56 89
HPSE 0.028 0.008 -10000 0 0 41 41
positive regulation of cell migration -0.017 0.14 0.23 43 -0.32 54 97
SDC1 -0.014 0.13 0.22 41 -0.33 44 85
Syndecan-1/Collagen -0.017 0.14 0.23 43 -0.32 54 97
PPIB 0.029 0.005 -10000 0 0 13 13
MET 0.025 0.011 -10000 0 0 88 88
PRKACA 0.026 0.01 -10000 0 0 78 78
MMP9 0.023 0.013 -10000 0 0 129 129
MAPK1 -0.034 0.13 0.2 39 -0.3 56 95
homophilic cell adhesion -0.017 0.14 0.22 56 -0.31 58 114
MMP1 0.022 0.013 -10000 0 0 141 141
IGF1 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
NCK2 0.029 0.004 -10000 0 0 10 10
PTK2 0.021 0.014 -10000 0 0 162 162
CRKL -0.077 0.075 0.13 6 -0.21 119 125
GRB2/SOS1/SHC 0.053 0.02 -10000 0 -10000 0 0
HRAS 0.028 0.006 -10000 0 0 27 27
IRS1/Crk -0.08 0.072 0.097 3 -0.2 128 131
IGF-1R heterotetramer/IGF1/PTP1B 0.011 0.099 -10000 0 -0.17 120 120
AKT1 -0.051 0.11 0.14 62 -0.23 74 136
BAD -0.059 0.1 0.16 22 -0.23 74 96
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.079 0.074 0.12 5 -0.21 122 127
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.083 0.073 0.17 3 -0.22 102 105
RAF1 -0.036 0.11 0.27 3 -0.47 3 6
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.048 0.1 -10000 0 -0.2 124 124
YWHAZ 0.026 0.01 -10000 0 0 77 77
IGF-1R heterotetramer/IGF1/IRS1 -0.061 0.095 0.16 2 -0.21 134 136
PIK3CA 0.021 0.014 -10000 0 0 174 174
RPS6KB1 -0.052 0.11 0.15 45 -0.23 72 117
GNB2L1 0.029 0.005 -10000 0 0 14 14
positive regulation of MAPKKK cascade -0.03 0.1 0.26 10 -0.35 3 13
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 0.04 0.013 -10000 0 -10000 0 0
HRAS/GTP -0.088 0.067 -10000 0 -0.21 114 114
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.036 0.11 -10000 0 -0.15 115 115
IGF-1R heterotetramer 0.005 0.037 0.073 8 -0.089 8 16
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 -0.2 132 134
IGF1R 0.005 0.037 0.073 8 -0.089 8 16
IGF1 -0.008 0.052 0.061 23 -0.089 92 115
IRS2/Crk -0.082 0.071 0.16 2 -0.21 118 120
PI3K -0.053 0.1 -10000 0 -0.19 152 152
apoptosis 0.048 0.1 0.22 62 -0.2 15 77
HRAS/GDP 0.021 0.005 -10000 0 -10000 0 0
PRKCD -0.08 0.11 -10000 0 -0.28 113 113
RAF1/14-3-3 E -0.031 0.11 0.25 5 -0.41 3 8
BAD/14-3-3 -0.05 0.11 0.21 15 -0.23 62 77
PRKCZ -0.053 0.11 0.15 44 -0.23 74 118
Crk/p130 Cas/Paxillin/FAK1 -0.056 0.095 0.14 13 -0.24 47 60
PTPN1 0.027 0.009 -10000 0 0 50 50
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.075 0.12 -10000 0 -0.28 125 125
BCAR1 0.027 0.009 -10000 0 0 56 56
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.027 0.1 0.18 1 -0.15 121 122
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.028 0.007 -10000 0 0 34 34
IRS1/NCK2 -0.081 0.074 0.12 7 -0.2 128 135
GRB10 0.029 0.005 -10000 0 0 13 13
PTPN11 -0.081 0.074 0.13 6 -0.2 127 133
IRS1 -0.056 0.089 0.12 7 -0.21 127 134
IRS2 -0.079 0.074 0.13 6 -0.2 127 133
IGF-1R heterotetramer/IGF1 -0.003 0.12 0.15 3 -0.21 128 131
GRB2 0.029 0.005 -10000 0 0 19 19
PDPK1 -0.047 0.12 0.19 28 -0.23 76 104
YWHAE 0.028 0.008 -10000 0 0 41 41
PRKD1 -0.076 0.11 0.2 4 -0.28 110 114
SHC1 0.029 0.006 -10000 0 0 20 20
Retinoic acid receptors-mediated 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
HDAC1 0.027 0.009 -10000 0 0 51 51
HDAC3 0.029 0.003 -10000 0 0 7 7
VDR 0.029 0.004 -10000 0 0 8 8
Cbp/p300/PCAF 0.032 0.024 -10000 0 -0.13 8 8
EP300 0.027 0.009 -10000 0 0 54 54
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.031 0.08 0.17 1 -0.29 27 28
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.029 0.005 -10000 0 0 19 19
AKT1 0.008 0.09 0.21 12 -0.24 8 20
RAR alpha/9cRA/Cyclin H -0.075 0.13 -10000 0 -0.24 174 174
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.034 0.072 -10000 0 -0.25 33 33
CDC2 -0.005 0.007 -10000 0 -0.019 12 12
response to UV -0.009 0.012 -10000 0 -0.025 206 206
RAR alpha/Jnk1 -0.024 0.068 -10000 0 -0.23 20 20
NCOR2 0.029 0.006 -10000 0 0 20 20
VDR/VDR/Vit D3 0.022 0.003 -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 47 47
NCOA3 0.026 0.01 -10000 0 0 64 64
NCOA1 0.029 0.005 -10000 0 0 14 14
VDR/VDR/DNA 0.029 0.004 -10000 0 0 8 8
RARG 0.003 0.033 -10000 0 -0.04 205 205
RAR gamma1/9cRA 0.01 0.033 -10000 0 -10000 0 0
MAPK3 0.001 0.036 -10000 0 -0.046 203 203
MAPK1 0.028 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 0.18 -10000 0 -0.34 189 189
RARA -0.029 0.053 -10000 0 -0.21 11 11
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.032 0.071 -10000 0 -0.25 35 35
PRKCA -0.012 0.053 -10000 0 -0.083 200 200
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.22 0.29 -10000 0 -0.58 213 213
RXRG -0.026 0.061 -10000 0 -0.23 6 6
RXRA -0.079 0.094 0.23 1 -0.31 20 21
RXRB -0.026 0.052 -10000 0 -0.22 3 3
VDR/Vit D3/DNA 0.022 0.003 -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 -0.15 158 158
RARB -0.003 0.04 -10000 0 -0.055 205 205
PRKCG -0.012 0.053 -10000 0 -0.081 205 205
MNAT1 0.029 0.005 -10000 0 0 15 15
RAR alpha/RXRs -0.11 0.2 0.26 1 -0.38 136 137
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.095 0.15 -10000 0 -0.42 33 33
proteasomal ubiquitin-dependent protein catabolic process -0.042 0.087 -10000 0 -0.32 25 25
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.22 0.29 -10000 0 -0.59 213 213
positive regulation of DNA binding -0.074 0.12 -10000 0 -0.22 199 199
NRIP1 -0.39 0.51 -10000 0 -1 213 213
RXRs/RARs -0.15 0.22 -10000 0 -0.41 205 205
RXRs/RXRs/DNA/9cRA -0.13 0.16 -10000 0 -0.34 193 193
PRKACA 0.026 0.01 -10000 0 0 78 78
CDK7 0.026 0.01 -10000 0 0 70 70
TFIIH 0.051 0.022 -10000 0 -10000 0 0
RAR alpha/9cRA -0.009 0.081 -10000 0 -0.23 18 18
CCNH 0.027 0.008 -10000 0 0 47 47
CREBBP 0.027 0.008 -10000 0 0 44 44
RAR gamma2/9cRA 0.006 0.055 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.026 0.009 -10000 0 -10000 0 0
ELF1 0.03 0.009 -10000 0 -10000 0 0
CCNA2 0.003 0.01 -10000 0 0 492 492
PIK3CA 0.02 0.014 -10000 0 -10000 0 0
JAK3 0.027 0.009 -10000 0 -10000 0 0
PIK3R1 0.021 0.013 -10000 0 -10000 0 0
JAK1 0.029 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.014 0.1 -10000 0 -0.44 10 10
SHC1 0.029 0.006 -10000 0 -10000 0 0
SP1 -0.21 0.14 -10000 0 -0.29 416 416
IL2RA -0.024 0.045 0.4 6 -10000 0 6
IL2RB 0.027 0.009 -10000 0 -10000 0 0
SOS1 0.028 0.007 -10000 0 -10000 0 0
IL2RG 0.026 0.01 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.31 0.29 0.32 25 -0.48 386 411
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 0.029 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 32 32
CCND3 -0.012 0.1 0.32 2 -0.49 4 6
Insulin Pathway

Figure S19.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S19.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.073 0.093 -10000 0 -0.14 329 329
TC10/GTP -0.05 0.024 -10000 0 -0.13 32 32
Insulin Receptor/Insulin/IRS1/Shp2 -0.067 0.11 -10000 0 -0.15 324 324
HRAS 0.028 0.006 -10000 0 0 27 27
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 0.028 0.007 -10000 0 0 32 32
FOXO3 -0.035 0.15 -10000 0 -0.6 34 34
AKT1 -0.059 0.11 0.23 14 -0.24 28 42
INSR -0.02 0.027 0.057 38 -10000 0 38
Insulin Receptor/Insulin 0.036 0.065 0.2 23 -0.14 38 61
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.029 0.005 -10000 0 0 13 13
SORBS1 0.027 0.009 -10000 0 0 54 54
CRK 0.028 0.007 -10000 0 0 36 36
PTPN1 -0.036 0.046 -10000 0 -10000 0 0
CAV1 -0.097 0.078 0.16 7 -0.22 81 88
CBL/APS/CAP/Crk-II/C3G 0.047 0.056 -10000 0 -0.13 35 35
Insulin Receptor/Insulin/IRS1/NCK2 -0.067 0.11 -10000 0 -0.15 324 324
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.061 0.092 -10000 0 -0.16 239 239
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.1 0.15 -10000 0 -0.44 70 70
RPS6KB1 -0.067 0.1 0.21 13 -0.22 43 56
PARD6A 0.027 0.009 -10000 0 0 58 58
CBL 0.029 0.004 -10000 0 0 12 12
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.023 0.045 -10000 0 -0.7 2 2
PIK3R1 0.021 0.013 -10000 0 0 159 159
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.079 0.096 0.18 9 -0.24 43 52
HRAS/GTP -0.096 0.058 -10000 0 -0.15 241 241
Insulin Receptor -0.02 0.027 0.057 38 -10000 0 38
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.062 0.11 -10000 0 -0.15 308 308
PRKCI 0.002 0.078 -10000 0 -0.34 20 20
Insulin Receptor/Insulin/GRB14/PDK1 -0.083 0.076 0.055 7 -0.22 54 61
SHC1 0.029 0.006 -10000 0 0 20 20
negative regulation of MAPKKK cascade 0.044 0.048 -10000 0 -0.62 2 2
PI3K -0.057 0.099 -10000 0 -0.16 239 239
NCK2 0.029 0.004 -10000 0 0 10 10
RHOQ 0.029 0.005 -10000 0 0 19 19
mol:H2O2 -0.006 0.006 0.016 6 -10000 0 6
HRAS/GDP 0.021 0.005 -10000 0 -10000 0 0
AKT2 -0.059 0.11 0.24 10 -0.24 29 39
PRKCZ -0.016 0.1 -10000 0 -0.37 33 33
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.086 0.062 0.15 6 -0.2 35 41
F2RL2 0.027 0.009 -10000 0 0 51 51
TRIP10 0.028 0.007 -10000 0 0 34 34
Insulin Receptor/Insulin/Shc 0.036 0.054 -10000 0 -0.12 42 42
TC10/GTP/CIP4/Exocyst 0.037 0.012 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.058 0.071 -10000 0 -0.14 34 34
RAPGEF1 0.029 0.006 -10000 0 0 21 21
RASA1 0.027 0.009 -10000 0 0 51 51
NCK1 0.026 0.009 -10000 0 0 63 63
CBL/APS/CAP/Crk-II 0.038 0.05 -10000 0 -0.13 36 36
TC10/GDP 0.021 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.048 0.066 -10000 0 -0.14 42 42
INPP5D -0.088 0.055 -10000 0 -0.13 288 288
SOS1 0.028 0.007 -10000 0 0 34 34
SGK1 -0.01 0.008 -10000 0 -0.025 46 46
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.029 0.003 -10000 0 0 7 7
IRS1 0.011 0.014 -10000 0 0 349 349
p62DOK/RasGAP 0.044 0.049 -10000 0 -0.62 2 2
INS -0.022 0.03 0.068 20 -10000 0 20
mol:PI-3-4-P2 -0.087 0.055 -10000 0 -0.13 288 288
GRB2 0.029 0.005 -10000 0 0 19 19
EIF4EBP1 -0.069 0.093 0.2 7 -0.22 45 52
PTPRA -0.025 0.024 0.067 3 -10000 0 3
PIK3CA 0.021 0.014 -10000 0 0 174 174
TC10/GTP/CIP4 0.037 0.012 -10000 0 -10000 0 0
PDPK1 0.029 0.005 -10000 0 0 18 18
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.099 0.1 -10000 0 -0.28 60 60
Insulin Receptor/Insulin/IRS1 -0.066 0.096 -10000 0 -0.14 326 326
Insulin Receptor/Insulin/IRS3 0.027 0.06 -10000 0 -0.17 43 43
Par3/Par6 0.047 0.044 -10000 0 -0.13 1 1
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.027 0.009 -10000 0 0 57 57
EPHB2 0 0.033 -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 0.06 0.041 -10000 0 -0.14 2 2
Ephrin B2/EPHB1-2 0.045 0.039 -10000 0 -0.12 18 18
neuron projection morphogenesis -0.024 0.052 0.068 42 -10000 0 42
Ephrin B1/EPHB1-2/Tiam1 0.002 0.067 0.18 5 -10000 0 5
DNM1 0.001 0.031 -10000 0 -10000 0 0
cell-cell signaling 0.001 0.005 0.018 3 -10000 0 3
MAP2K4 -0.12 0.21 0.21 3 -0.48 138 141
YES1 -0.16 0.32 -10000 0 -0.7 139 139
Ephrin B1/EPHB1-2/NCK2 0.002 0.067 0.18 4 -10000 0 4
PI3K -0.11 0.22 -10000 0 -0.47 139 139
mol:GDP 0 0.066 0.17 6 -10000 0 6
ITGA2B 0.029 0.006 -10000 0 0 22 22
endothelial cell proliferation 0.031 0.034 -10000 0 -0.13 20 20
FYN -0.18 0.32 -10000 0 -0.72 140 140
MAP3K7 -0.12 0.22 0.23 5 -0.51 135 140
FGR -0.16 0.31 -10000 0 -0.69 140 140
TIAM1 0.029 0.006 -10000 0 0 23 23
PIK3R1 0.021 0.013 -10000 0 0 159 159
RGS3 0.029 0.005 -10000 0 0 18 18
cell adhesion -0.13 0.21 0.19 5 -0.47 137 142
LYN -0.16 0.32 -10000 0 -0.7 139 139
Ephrin B1/EPHB1-2/Src Family Kinases -0.15 0.29 -10000 0 -0.64 140 140
Ephrin B1/EPHB1-2 -0.12 0.24 -10000 0 -0.54 135 135
SRC -0.16 0.31 -10000 0 -0.69 140 140
ITGB3 0.025 0.011 -10000 0 0 99 99
EPHB1 -0.003 0.031 -10000 0 -10000 0 0
EPHB4 0.029 0.005 -10000 0 0 19 19
RAC1 0.028 0.006 -10000 0 0 26 26
Ephrin B2/EPHB4 0.031 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 -0.7 140 140
HCK -0.16 0.31 -10000 0 -0.7 138 138
regulation of stress fiber formation -0.001 0.065 -10000 0 -0.17 5 5
MAPK8 -0.13 0.2 -10000 0 -0.47 139 139
Ephrin B1/EPHB1-2/RGS3 0.004 0.067 0.17 6 -10000 0 6
endothelial cell migration -0.1 0.18 0.29 3 -0.42 135 138
NCK2 0.029 0.004 -10000 0 0 10 10
PTPN13 0.023 0.016 -10000 0 0 181 181
regulation of focal adhesion formation -0.001 0.065 -10000 0 -0.17 5 5
chemotaxis -0.002 0.066 -10000 0 -0.17 6 6
PIK3CA 0.021 0.014 -10000 0 0 174 174
Rac1/GTP -0.007 0.066 0.15 5 -10000 0 5
angiogenesis -0.13 0.24 -10000 0 -0.54 138 138
LCK -0.16 0.31 -10000 0 -0.69 140 140
TCGA08_p53

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2A -0.007 0.008 0 339 -10000 0 339
TP53 0.024 0.075 -10000 0 -0.22 36 36
Senescence 0.022 0.082 -10000 0 -0.23 41 41
Apoptosis 0.022 0.082 -10000 0 -0.23 41 41
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.001 0.042 0.3 10 -10000 0 10
MDM4 0.029 0.006 -10000 0 0 24 24
Thromboxane A2 receptor 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
TGM2 0.01 0.02 0.097 8 -0.03 14 22
GNB1/GNG2 -0.067 0.065 -10000 0 -0.19 93 93
AKT1 -0.019 0.23 0.46 77 -0.38 8 85
EGF 0.028 0.008 -10000 0 0 41 41
mol:TXA2 0 0.002 0.032 1 -10000 0 1
FGR -0.025 0.065 0.23 7 -10000 0 7
mol:Ca2+ -0.068 0.29 0.55 78 -0.36 41 119
LYN -0.027 0.064 0.24 7 -10000 0 7
RhoA/GTP -0.042 0.11 0.24 58 -0.19 1 59
mol:PGI2 0 0.002 0.027 1 -10000 0 1
SYK -0.062 0.3 0.56 78 -0.38 47 125
GNG2 0.029 0.005 -10000 0 0 14 14
ARRB2 0.028 0.006 -10000 0 0 25 25
TP alpha/Gq family/GDP/G beta5/gamma2 -0.064 0.17 -10000 0 -0.42 80 80
G beta5/gamma2 -0.08 0.086 0.17 1 -0.25 92 93
PRKCH -0.075 0.31 0.56 78 -0.42 60 138
DNM1 0.029 0.005 -10000 0 0 16 16
TXA2/TP beta/beta Arrestin3 0.03 0.035 -10000 0 -0.51 1 1
mol:GTP 0.001 0.011 0.069 8 -10000 0 8
PTGDR 0.029 0.005 0.058 1 0 12 13
G12 family/GTP -0.14 0.13 -10000 0 -0.32 102 102
ADRBK1 0.03 0.003 -10000 0 0 6 6
ADRBK2 0.026 0.01 -10000 0 0 76 76
RhoA/GTP/ROCK1 0.038 0.013 0.16 1 -0.14 1 2
mol:GDP 0.046 0.23 0.46 47 -0.41 75 122
mol:NADP 0 0.029 0.066 1 -0.029 264 265
RAB11A 0.029 0.005 -10000 0 0 13 13
PRKG1 0.001 0.03 0.066 1 -0.029 267 268
mol:IP3 -0.098 0.32 0.58 78 -0.44 79 157
cell morphogenesis 0.038 0.013 0.16 1 -0.14 1 2
PLCB2 -0.16 0.37 0.61 71 -0.62 86 157
mol:cGMP 0 0.002 0.033 1 -10000 0 1
BLK -0.021 0.061 0.23 8 -10000 0 8
mol:PDG2 0 0.002 0.027 1 -10000 0 1
HCK -0.025 0.063 0.24 6 -10000 0 6
RHOA 0.029 0.003 -10000 0 0 7 7
PTGIR 0.029 0.007 0.058 1 0 26 27
PRKCB1 -0.087 0.32 0.58 78 -0.44 60 138
GNAQ 0.028 0.007 -10000 0 0 28 28
mol:L-citrulline 0 0.029 0.066 1 -0.029 264 265
TXA2/TXA2-R family -0.11 0.38 0.63 78 -0.57 78 156
LCK -0.024 0.065 0.23 8 -10000 0 8
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.016 0.056 0.18 7 -10000 0 7
TXA2-R family/G12 family/GDP/G beta/gamma -0.017 0.12 -10000 0 -0.44 40 40
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.017 0.054 0.16 6 -10000 0 6
MAPK14 -0.03 0.24 0.47 78 -10000 0 78
TGM2/GTP -0.15 0.35 0.61 69 -0.52 76 145
MAPK11 -0.033 0.24 0.47 78 -10000 0 78
ARHGEF1 -0.033 0.19 0.38 76 -10000 0 76
GNAI2 0.029 0.003 -10000 0 0 6 6
JNK cascade -0.067 0.32 0.6 78 -0.43 59 137
RAB11/GDP 0.017 0.032 -10000 0 -0.064 31 31
ICAM1 -0.03 0.28 0.57 79 -0.37 5 84
cAMP biosynthetic process -0.11 0.31 0.53 78 -0.41 74 152
Gq family/GTP/EBP50 -0.051 0.1 0.24 2 -0.2 146 148
actin cytoskeleton reorganization 0.038 0.013 0.16 1 -0.14 1 2
SRC -0.025 0.064 0.24 6 -10000 0 6
GNB5 0.028 0.007 -10000 0 0 33 33
GNB1 0.029 0.006 -10000 0 0 23 23
EGF/EGFR -0.034 0.081 0.23 9 -0.26 14 23
VCAM1 -0.039 0.29 0.59 78 -0.36 59 137
TP beta/Gq family/GDP/G beta5/gamma2 -0.064 0.17 -10000 0 -0.42 80 80
platelet activation -0.062 0.28 0.53 78 -0.36 1 79
PGI2/IP 0.021 0.012 0.086 1 -0.15 2 3
PRKACA -0.002 0.024 0.16 1 -0.15 2 3
Gq family/GDP/G beta5/gamma2 -0.051 0.14 -10000 0 -0.36 75 75
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 0.2 1 -0.15 3 4
mol:DAG -0.1 0.34 0.6 78 -0.5 66 144
EGFR 0.027 0.009 -10000 0 0 55 55
TXA2/TP alpha -0.16 0.37 0.6 78 -0.57 83 161
Gq family/GTP -0.032 0.076 -10000 0 -0.23 54 54
YES1 -0.025 0.064 0.26 5 -10000 0 5
GNAI2/GTP -0.021 0.063 0.15 17 -0.18 6 23
PGD2/DP 0.022 0.005 0.086 1 -10000 0 1
SLC9A3R1 0.022 0.013 -10000 0 0 140 140
FYN -0.029 0.069 0.23 8 -0.2 1 9
mol:NO 0 0.029 0.066 1 -0.029 264 265
GNA15 0.027 0.008 -10000 0 0 46 46
PGK/cGMP 0.037 0.013 0.15 1 -10000 0 1
RhoA/GDP 0.017 0.032 -10000 0 -0.051 72 72
TP alpha/TGM2/GDP/G beta/gamma -0.075 0.065 -10000 0 -0.23 6 6
NOS3 0 0.029 0.066 1 -0.029 264 265
RAC1 0.028 0.006 -10000 0 0 26 26
PRKCA -0.074 0.31 0.57 78 -0.42 58 136
PRKCB -0.071 0.3 0.57 78 -0.41 60 138
PRKCE -0.061 0.31 0.58 78 -0.42 55 133
PRKCD -0.074 0.31 0.58 78 -0.43 60 138
PRKCG -0.09 0.32 0.58 78 -0.46 58 136
muscle contraction -0.11 0.36 0.61 78 -0.54 72 150
PRKCZ -0.061 0.3 0.56 78 -0.38 47 125
ARR3 0.03 0.003 -10000 0 0 5 5
TXA2/TP beta -0.01 0.069 0.21 11 -0.19 3 14
PRKCQ -0.064 0.31 0.56 78 -0.42 54 132
MAPKKK cascade -0.11 0.35 0.59 78 -0.52 80 158
SELE -0.033 0.27 0.54 78 -10000 0 78
TP beta/GNAI2/GDP/G beta/gamma 0.006 0.066 0.22 5 -10000 0 5
ROCK1 0.029 0.005 -10000 0 0 17 17
GNA14 0.029 0.005 -10000 0 0 18 18
chemotaxis -0.11 0.39 0.66 78 -0.62 74 152
GNA12 0.028 0.007 -10000 0 0 34 34
GNA13 0.029 0.005 -10000 0 0 13 13
GNA11 0.025 0.011 -10000 0 0 83 83
Rac1/GTP 0.021 0.009 0.15 1 -10000 0 1
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.025 0.083 -10000 0 -10000 0 0
PLK1 0.26 0.4 0.87 75 -0.85 13 88
CDKN1B 0.18 0.3 0.65 70 -0.47 1 71
FOXO3 0.22 0.4 0.77 87 -0.79 23 110
KAT2B 0.058 0.066 0.11 304 -0.076 3 307
FOXO1/SIRT1 0.01 0.086 0.29 5 -0.28 3 8
CAT 0.23 0.37 0.79 48 -0.9 16 64
CTNNB1 0.026 0.014 -10000 0 -0.023 37 37
AKT1 0.075 0.085 0.2 84 -0.11 1 85
FOXO1 0.036 0.095 0.38 4 -0.29 3 7
MAPK10 0.013 0.061 0.2 12 -10000 0 12
mol:GTP 0 0.007 0.024 31 -0.02 2 33
FOXO4 0.011 0.16 0.43 31 -0.49 5 36
response to oxidative stress 0.058 0.067 0.16 94 -0.083 2 96
FOXO3A/SIRT1 0.22 0.36 0.65 98 -0.69 31 129
XPO1 0.018 0.023 -10000 0 -0.031 86 86
EP300 0.016 0.027 -10000 0 -10000 0 0
BCL2L11 0.079 0.14 0.75 1 -0.93 5 6
FOXO1/SKP2 0.022 0.077 0.33 2 -0.28 3 5
mol:GDP 0.058 0.067 0.16 94 -0.082 2 96
RAN 0.018 0.026 -10000 0 -0.033 111 111
GADD45A 0.19 0.29 0.72 71 -0.71 2 73
YWHAQ 0.029 0.005 -10000 0 0 15 15
FOXO1/14-3-3 family 0.002 0.14 -10000 0 -0.47 28 28
MST1 0.08 0.081 0.14 276 -0.1 4 280
CSNK1D 0.029 0.006 -10000 0 0 23 23
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 44 44
MAPK8 0.013 0.064 0.2 17 -10000 0 17
MAPK9 0.013 0.062 0.2 13 -10000 0 13
YWHAG 0.029 0.004 -10000 0 0 11 11
YWHAE 0.028 0.008 -10000 0 0 41 41
YWHAZ 0.026 0.01 -10000 0 0 77 77
SIRT1 -0.01 0.053 0.13 42 -0.096 4 46
SOD2 0.034 0.45 0.61 55 -0.75 105 160
RBL2 0.15 0.36 0.66 39 -0.82 29 68
RAL/GDP 0.064 0.068 0.18 59 -10000 0 59
CHUK 0.079 0.08 0.18 112 -0.11 2 114
Ran/GTP 0.015 0.024 -10000 0 -10000 0 0
CSNK1G2 0.027 0.008 -10000 0 0 46 46
RAL/GTP 0.063 0.075 0.25 30 -10000 0 30
CSNK1G1 0.029 0.005 -10000 0 0 13 13
FASLG 0.087 0.092 -10000 0 -10000 0 0
SKP2 0.021 0.013 -10000 0 0 156 156
USP7 0.018 0.025 -10000 0 -0.033 100 100
IKBKB 0.076 0.08 0.18 102 -0.1 1 103
CCNB1 0.35 0.42 0.7 287 -0.95 8 295
FOXO1-3a-4/beta catenin 0.12 0.29 0.6 63 -10000 0 63
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.077 0.32 2 -0.28 3 5
CSNK1A1 0.029 0.005 -10000 0 0 13 13
SGK1 0.058 0.066 0.11 304 -0.076 3 307
CSNK1G3 0.029 0.006 -10000 0 0 22 22
Ran/GTP/Exportin 1 0.029 0.035 0.14 1 -10000 0 1
ZFAND5 0.01 0.14 0.45 8 -0.64 2 10
SFN 0.028 0.007 -10000 0 0 37 37
CDK2 -0.008 0.025 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.079 0.15 0.3 48 -0.48 14 62
CREBBP -0.02 0.029 -10000 0 -0.074 3 3
FBXO32 0.079 0.61 0.78 116 -0.81 142 258
BCL6 0.17 0.34 0.67 30 -0.9 21 51
RALB 0.017 0.027 -10000 0 -0.035 111 111
RALA 0.018 0.026 -10000 0 -0.034 109 109
YWHAH 0.028 0.008 -10000 0 0 42 42
Canonical Wnt signaling pathway

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
HDAC1 0.056 0.055 0.13 145 -0.057 1 146
AES 0.043 0.044 0.11 119 -10000 0 119
FBXW11 0.029 0.005 -10000 0 0 16 16
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.037 0.017 -10000 0 -10000 0 0
SMAD4 0.028 0.007 -10000 0 0 37 37
DKK2 0.028 0.008 -10000 0 0 40 40
TLE1 0.053 0.045 0.12 129 -0.062 1 130
MACF1 0.027 0.009 -10000 0 -10000 0 0
CTNNB1 0.026 0.078 0.28 19 -0.41 1 20
WIF1 0.026 0.015 -10000 0 -0.03 32 32
beta catenin/RanBP3 0.14 0.2 0.41 169 -0.35 1 170
KREMEN2 0.029 0.007 -10000 0 -0.001 24 24
DKK1 0.029 0.006 -10000 0 0 21 21
beta catenin/beta TrCP1 0.048 0.077 0.26 22 -0.39 1 23
FZD1 0.018 0.023 -10000 0 -0.03 101 101
AXIN2 -0.08 0.18 0.62 5 -0.67 24 29
AXIN1 0.028 0.009 -10000 0 -0.029 6 6
RAN 0.03 0.006 -10000 0 -0.031 2 2
Axin1/APC/GSK3/beta catenin 0.022 0.1 -10000 0 -0.47 18 18
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.043 0.18 0.29 7 -0.6 34 41
Axin1/APC/GSK3 0.014 0.064 0.22 13 -0.32 3 16
Axin1/APC/GSK3/beta catenin/Macf1 0.003 0.08 0.28 8 -0.36 7 15
HNF1A 0.056 0.047 0.12 141 -0.062 2 143
CTBP1 0.053 0.049 0.12 133 -0.062 2 135
MYC 0.004 0.48 0.6 115 -1.1 57 172
RANBP3 0.029 0.008 -10000 0 -0.03 1 1
DKK2/LRP6/Kremen 2 0.049 0.025 -10000 0 -10000 0 0
NKD1 0.022 0.018 -10000 0 -0.03 53 53
TCF4 0.054 0.05 0.12 152 -0.063 2 154
TCF3 0.051 0.047 0.12 128 -0.062 1 129
WNT1/LRP6/FZD1/Axin1 0.063 0.037 -10000 0 -10000 0 0
Ran/GTP 0.024 0.006 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.11 0.28 0.55 113 -0.56 12 125
LEF1 0.05 0.051 0.12 139 -0.063 2 141
DVL1 0.021 0.058 0.2 3 -0.3 5 8
CSNK2A1 0.028 0.008 -10000 0 0 42 42
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.13 0.2 -10000 0 -0.49 86 86
DKK1/LRP6/Kremen 2 0.049 0.024 -10000 0 -10000 0 0
LRP6 0.017 0.022 -10000 0 -0.029 83 83
CSNK1A1 0.058 0.055 0.13 164 -0.065 2 166
NLK 0.006 0.032 -10000 0 -0.04 178 178
CCND1 -0.33 0.56 0.66 12 -1.2 155 167
WNT1 0.019 0.023 -10000 0 -0.03 97 97
GSK3A 0.018 0.023 -10000 0 -0.03 94 94
GSK3B 0.018 0.024 -10000 0 -0.03 103 103
FRAT1 0.017 0.024 -10000 0 -0.03 110 110
PPP2R5D 0.03 0.05 0.23 1 -0.3 7 8
APC -0.019 0.082 0.19 61 -10000 0 61
WNT1/LRP6/FZD1 0.017 0.044 0.2 5 -0.2 3 8
CREBBP 0.051 0.047 0.12 124 -0.062 2 126
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.027 0.008 -10000 0 0 49 49
NFATC1 0.056 0.094 0.27 6 -0.33 13 19
NFATC2 -0.015 0.058 0.24 4 -0.23 6 10
NFATC3 0 0.024 -10000 0 -0.31 1 1
YWHAE 0.028 0.008 -10000 0 0 41 41
Calcineurin A alpha-beta B1/CABIN1 -0.007 0.062 0.2 2 -0.25 18 20
Exportin 1/Ran/NUP214 0.05 0.022 -10000 0 -10000 0 0
mol:DAG -0.001 0.003 0.028 4 -10000 0 4
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.003 0.078 0.21 1 -0.25 19 20
BCL2/BAX 0.011 0.071 -10000 0 -0.16 76 76
CaM/Ca2+/Calcineurin A alpha-beta B1 0 0.032 0.12 4 -0.15 9 13
CaM/Ca2+ 0 0.032 0.12 4 -0.15 9 13
BAX 0.029 0.005 -10000 0 0 19 19
MAPK14 0.005 0.03 0.059 4 -0.031 215 219
BAD 0.03 0.003 -10000 0 0 5 5
CABIN1/MEF2D 0.006 0.066 0.23 1 -0.25 18 19
Calcineurin A alpha-beta B1/BCL2 0.023 0.012 -10000 0 0 123 123
FKBP8 0.025 0.011 -10000 0 0 90 90
activation-induced cell death of T cells -0.006 0.065 0.24 18 -0.23 1 19
KPNB1 0.029 0.006 -10000 0 0 20 20
KPNA2 0.003 0.009 -10000 0 0 494 494
XPO1 0.007 0.027 -10000 0 -0.029 187 187
SFN 0.028 0.007 -10000 0 0 37 37
MAP3K8 0.005 0.03 0.06 4 -0.032 218 222
NFAT4/CK1 alpha -0.046 0.031 0.15 4 -0.19 8 12
MEF2D/NFAT1/Cbp/p300 -0.056 0.12 -10000 0 -0.26 40 40
CABIN1 -0.008 0.063 0.2 2 -0.25 18 20
CALM1 0.004 0.031 0.063 4 -0.034 215 219
RAN 0.008 0.028 -10000 0 -0.029 203 203
MAP3K1 0.027 0.009 -10000 0 0 52 52
CAMK4 0.028 0.008 -10000 0 0 40 40
mol:Ca2+ -0.003 0.007 0.066 4 -10000 0 4
MAPK3 0.029 0.006 -10000 0 0 22 22
YWHAH 0.028 0.008 -10000 0 0 42 42
Calcineurin A alpha-beta B1/AKAP79/PKA 0.036 0.016 -10000 0 -10000 0 0
YWHAB 0.027 0.008 -10000 0 0 44 44
MAPK8 0.005 0.031 0.065 4 -0.033 221 225
MAPK9 0.029 0.005 -10000 0 0 17 17
YWHAG 0.029 0.004 -10000 0 0 11 11
FKBP1A 0.028 0.008 -10000 0 0 38 38
NFAT1-c-4/YWHAQ 0.038 0.11 0.27 5 -0.37 12 17
PRKCH 0.029 0.005 -10000 0 0 17 17
CABIN1/Cbp/p300 0.002 0.049 -10000 0 -0.17 8 8
CASP3 0.005 0.029 0.059 4 -0.032 195 199
PIM1 0.028 0.007 -10000 0 0 28 28
Calcineurin A alpha-beta B1/FKBP12/FK506 0.005 0.018 0.064 4 -10000 0 4
apoptosis 0.01 0.036 0.19 1 -0.15 1 2
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.005 0.057 -10000 0 -0.23 16 16
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.029 0.006 -10000 0 0 23 23
JNK2/NFAT4 0 0.07 -10000 0 -0.18 62 62
BAD/BCL-XL 0.04 0.013 -10000 0 -10000 0 0
PRKCD 0.029 0.005 -10000 0 0 15 15
NUP214 0.007 0.028 -10000 0 -0.029 204 204
PRKCZ 0.004 0.03 0.065 4 -0.033 219 223
PRKCA 0.028 0.006 -10000 0 0 25 25
PRKCG 0.029 0.005 -10000 0 0 19 19
PRKCQ 0.027 0.008 -10000 0 0 46 46
FKBP38/BCL2 -0.002 0.082 -10000 0 -0.17 102 102
EP300 0.002 0.033 0.07 4 -0.039 206 210
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.028 0.008 -10000 0 0 42 42
NFATc/JNK1 0.062 0.097 0.27 5 -0.33 13 18
CaM/Ca2+/FKBP38 -0.002 0.052 0.13 4 -0.14 43 47
FKBP12/FK506 0.021 0.006 -10000 0 -10000 0 0
CSNK1A1 -0.031 0.019 0.1 4 -0.14 8 12
CaM/Ca2+/CAMK IV 0.007 0.04 0.13 4 -0.14 8 12
NFATc/ERK1 0.063 0.098 0.27 6 -0.32 13 19
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.018 0.074 0.22 1 -0.25 17 18
NR4A1 -0.13 0.13 0.18 4 -0.29 202 206
GSK3B 0.005 0.03 0.065 4 -0.033 216 220
positive T cell selection 0 0.023 -10000 0 -0.3 1 1
NFAT1/CK1 alpha -0.025 0.049 0.2 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 -0.031 195 198
AKAP5 0.029 0.005 -10000 0 0 14 14
MEF2D 0.002 0.034 0.07 4 -0.039 220 224
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.026 0.01 -10000 0 0 77 77
NFATc/p38 alpha 0.061 0.095 0.27 3 -0.34 11 14
CREBBP 0.002 0.033 0.07 4 -0.039 208 212
BCL2 0.023 0.012 -10000 0 0 123 123
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.012 0.062 -10000 0 -0.15 61 61
NF kappa B1 p50/RelA/I kappa B alpha -0.046 0.094 0.22 5 -0.27 25 30
AP1 -0.017 0.084 0.2 48 -0.14 62 110
mol:PIP3 -0.056 0.061 0.028 8 -0.15 142 150
AKT1 -0.029 0.1 0.23 17 -0.28 8 25
PTK2B -0.047 0.11 0.19 31 -0.2 142 173
RHOA -0.007 0.06 0.17 27 -0.31 5 32
PIK3CB 0.021 0.019 -10000 0 -0.03 46 46
mol:Ca2+ -0.037 0.061 0.17 7 -0.18 27 34
MAGI3 0.025 0.015 -10000 0 -0.03 31 31
RELA 0.03 0.003 -10000 0 0 7 7
apoptosis -0.005 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 11 -0.22 94 105
NF kappa B1 p50/RelA -0.05 0.1 0.22 54 -0.22 37 91
endothelial cell migration -0.045 0.099 -10000 0 -0.32 62 62
ADCY4 -0.01 0.094 0.24 32 -0.2 54 86
ADCY5 -0.008 0.092 0.24 32 -0.2 51 83
ADCY6 -0.008 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 0.091 0.24 32 -0.2 47 79
ADCY3 -0.009 0.093 0.24 32 -0.2 53 85
ADCY8 -0.05 0.097 0.23 9 -0.19 135 144
ADCY9 -0.018 0.1 0.24 32 -0.23 55 87
GSK3B -0.05 0.11 0.17 41 -0.22 102 143
arachidonic acid secretion -0.021 0.092 0.22 31 -0.2 59 90
GNG2 0.02 0.022 -10000 0 -0.03 85 85
TRIP6 0.01 0.031 -10000 0 -0.27 3 3
GNAO1 -0.012 0.088 0.29 31 -0.16 61 92
HRAS 0.028 0.006 -10000 0 0 27 27
NFKBIA -0.045 0.083 0.21 4 -0.25 31 35
GAB1 0.028 0.006 -10000 0 0 25 25
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.023 0.15 -10000 0 -0.81 16 16
JUN 0.028 0.007 -10000 0 0 32 32
LPA/LPA2/NHERF2 -0.008 0.053 -10000 0 -0.1 120 120
TIAM1 0.009 0.16 -10000 0 -0.94 16 16
PIK3R1 0.013 0.022 -10000 0 -0.03 76 76
mol:IP3 -0.032 0.059 0.16 8 -0.18 26 34
PLCB3 -0.028 0.056 0.13 35 -0.13 60 95
FOS 0.025 0.012 -10000 0 0 104 104
positive regulation of mitosis -0.021 0.092 0.22 31 -0.2 59 90
LPA/LPA1-2-3 -0.013 0.044 0.042 45 -0.13 62 107
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -10000 0 0
BCAR1 0.027 0.009 -10000 0 0 56 56
stress fiber formation -0.017 0.097 0.22 31 -0.27 28 59
GNAZ -0.011 0.085 0.29 30 -0.16 53 83
EGFR/PI3K-beta/Gab1 -0.057 0.064 0.043 24 -0.15 141 165
positive regulation of dendritic cell cytokine production -0.013 0.044 0.041 44 -0.13 62 106
LPA/LPA2/MAGI-3 0.008 0.028 -10000 0 -0.068 57 57
ARHGEF1 -0.027 0.08 0.23 37 -0.16 4 41
GNAI2 -0.013 0.088 0.29 31 -0.16 61 92
GNAI3 -0.011 0.084 0.29 28 -0.16 55 83
GNAI1 -0.012 0.087 0.29 31 -0.16 56 87
LPA/LPA3 -0.008 0.022 0.018 3 -0.07 62 65
LPA/LPA2 -0.008 0.022 0.018 3 -0.069 62 65
LPA/LPA1 -0.022 0.057 -10000 0 -0.18 62 62
HB-EGF/EGFR -0.007 0.077 0.16 78 -0.15 29 107
HBEGF 0.005 0.081 0.19 86 -10000 0 86
mol:DAG -0.032 0.059 0.16 8 -0.18 26 34
cAMP biosynthetic process -0.022 0.093 0.22 32 -0.22 41 73
NFKB1 0.028 0.008 -10000 0 0 45 45
SRC 0.028 0.007 -10000 0 0 33 33
GNB1 0.02 0.022 -10000 0 -0.03 82 82
LYN -0.039 0.083 0.22 7 -0.25 28 35
GNAQ 0.005 0.038 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 0.03 0.23 0.6 56 -0.36 41 97
PTK2 0.006 0.066 0.26 23 -0.13 44 67
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
CASP3 -0.005 0.075 0.25 30 -0.15 53 83
EGFR 0.028 0.01 0.055 3 0 55 58
PLCG1 -0.003 0.044 0.13 27 -0.1 41 68
PLD2 0.008 0.075 0.26 30 -0.13 57 87
G12/G13 0.013 0.062 -10000 0 -0.15 60 60
PI3K-beta -0.058 0.065 -10000 0 -0.24 29 29
cell migration 0 0.061 0.21 1 -0.24 16 17
SLC9A3R2 0.025 0.011 -10000 0 0 91 91
PXN -0.018 0.098 0.23 31 -0.27 28 59
HRAS/GTP -0.022 0.093 0.22 31 -0.2 59 90
RAC1 0.028 0.006 -10000 0 0 26 26
MMP9 0.023 0.013 -10000 0 0 129 129
PRKCE 0.023 0.019 -10000 0 -0.03 58 58
PRKCD -0.043 0.063 0.17 8 -0.19 23 31
Gi(beta/gamma) -0.012 0.092 0.24 29 -0.2 52 81
mol:LPA -0.015 0.034 -10000 0 -0.11 62 62
TRIP6/p130 Cas/FAK1/Paxillin -0.004 0.085 0.23 22 -0.22 22 44
MAPKKK cascade -0.021 0.092 0.22 31 -0.2 59 90
contractile ring contraction involved in cytokinesis -0.006 0.061 0.17 28 -0.31 5 33
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.005 0.038 0.13 31 -0.064 59 90
GNA15 0.005 0.037 0.13 30 -0.064 53 83
GNA12 0.027 0.011 -10000 0 -0.03 12 12
GNA13 0.028 0.01 -10000 0 -0.03 13 13
MAPT -0.056 0.1 0.16 11 -0.23 95 106
GNA11 0.003 0.041 0.13 28 -0.08 52 80
Rac1/GTP 0.023 0.15 -10000 0 -0.86 16 16
MMP2 -0.046 0.099 -10000 0 -0.32 62 62
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 0.035 0.018 -10000 0 -10000 0 0
VLDLR 0.027 0.009 -10000 0 0 60 60
CRKL 0.027 0.008 -10000 0 0 46 46
LRPAP1 0.028 0.007 -10000 0 0 33 33
FYN 0.024 0.011 -10000 0 0 100 100
ITGA3 0.026 0.01 -10000 0 0 68 68
RELN/VLDLR/Fyn -0.006 0.093 -10000 0 -0.16 147 147
MAPK8IP1/MKK7/MAP3K11/JNK1 0.075 0.038 -10000 0 -10000 0 0
AKT1 -0.043 0.09 -10000 0 -0.21 83 83
MAP2K7 0.028 0.008 -10000 0 0 38 38
RAPGEF1 0.029 0.006 -10000 0 0 21 21
DAB1 0.029 0.006 -10000 0 0 20 20
RELN/LRP8/DAB1 0.021 0.068 -10000 0 -0.13 89 89
LRPAP1/LRP8 0.04 0.018 -10000 0 -0.16 2 2
RELN/LRP8/DAB1/Fyn 0.012 0.092 -10000 0 -0.14 139 139
DAB1/alpha3/beta1 Integrin 0.004 0.093 -10000 0 -0.16 120 120
long-term memory 0.012 0.1 -10000 0 -0.15 127 127
DAB1/LIS1 0.031 0.09 -10000 0 -0.15 91 91
DAB1/CRLK/C3G 0.014 0.085 -10000 0 -0.15 88 88
PIK3CA 0.021 0.014 -10000 0 0 174 174
DAB1/NCK2 0.032 0.092 -10000 0 -0.15 93 93
ARHGEF2 0.028 0.006 -10000 0 0 26 26
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.027 0.009 -10000 0 0 50 50
CDK5R1 0.028 0.007 -10000 0 0 36 36
RELN 0.023 0.013 -10000 0 0 132 132
PIK3R1 0.021 0.013 -10000 0 0 159 159
RELN/LRP8/Fyn -0.002 0.092 -10000 0 -0.15 141 141
GRIN2A/RELN/LRP8/DAB1/Fyn 0.017 0.1 -10000 0 -0.15 138 138
MAPK8 0.029 0.004 -10000 0 0 10 10
RELN/VLDLR/DAB1 0.015 0.071 -10000 0 -0.13 97 97
ITGB1 0.029 0.006 -10000 0 0 20 20
MAP1B -0.042 0.071 0.16 18 -0.24 10 28
RELN/LRP8 0.019 0.075 -10000 0 -0.15 89 89
GRIN2B/RELN/LRP8/DAB1/Fyn 0.017 0.1 -10000 0 -0.15 127 127
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 -0.053 0.093 0.34 10 -10000 0 10
PAFAH1B1 0.028 0.007 -10000 0 0 31 31
MAPK8IP1 0.029 0.003 -10000 0 0 7 7
CRLK/C3G 0.039 0.014 -10000 0 -10000 0 0
GRIN2B 0.027 0.009 -10000 0 0 59 59
NCK2 0.029 0.004 -10000 0 0 10 10
neuron differentiation -0.034 0.089 -10000 0 -0.27 33 33
neuron adhesion -0.068 0.1 0.33 13 -10000 0 13
LRP8 0.029 0.006 -10000 0 0 20 20
GSK3B -0.048 0.093 0.16 6 -0.28 31 37
RELN/VLDLR/DAB1/Fyn 0.007 0.093 -10000 0 -0.14 142 142
MAP3K11 0.029 0.003 -10000 0 0 7 7
RELN/VLDLR/DAB1/P13K -0.033 0.099 -10000 0 -0.2 122 122
CDK5 0.025 0.011 -10000 0 0 85 85
MAPT -0.011 0.037 0.78 1 -10000 0 1
neuron migration -0.058 0.11 0.25 7 -0.28 55 62
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.034 0.089 -10000 0 -0.28 33 33
RELN/VLDLR 0.028 0.085 -10000 0 -0.14 94 94
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.038 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 -0.34 27 45
IGF1R 0.022 0.013 -10000 0 0 141 141
PI4KB 0.028 0.007 -10000 0 0 34 34
MFGE8 0.027 0.008 -10000 0 0 45 45
SRC 0.028 0.007 -10000 0 0 33 33
CDKN1B -0.005 0.058 -10000 0 -0.29 16 16
VEGFA 0.026 0.01 -10000 0 0 69 69
ILK -0.005 0.059 -10000 0 -0.28 17 17
ROCK1 0.029 0.005 -10000 0 0 17 17
AKT1 -0.023 0.053 -10000 0 -0.27 16 16
PTK2B -0.021 0.085 0.21 32 -0.23 2 34
alphaV/beta3 Integrin/JAM-A 0.025 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 0.029 0.068 -10000 0 -0.15 66 66
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.082 0.12 -10000 0 -0.17 349 349
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.005 0.079 0.18 5 -0.28 16 21
alphaV/beta3 Integrin/Syndecan-1 0.029 0.067 -10000 0 -0.15 64 64
PI4KA 0.027 0.008 -10000 0 0 47 47
IGF-1R heterotetramer/IGF1/IRS1 -0.069 0.12 -10000 0 -0.19 228 228
PI4 Kinase 0.038 0.015 -10000 0 -10000 0 0
PIK3CA 0.021 0.014 -10000 0 0 174 174
alphaV/beta3 Integrin/Osteopontin 0.009 0.065 -10000 0 -0.15 63 63
RPS6KB1 -0.071 0.12 0.28 11 -0.32 15 26
TLN1 0.029 0.005 -10000 0 0 15 15
MAPK3 -0.075 0.16 -10000 0 -0.39 93 93
GPR124 0.026 0.01 -10000 0 0 72 72
MAPK1 -0.071 0.15 -10000 0 -0.39 90 90
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 0.049 0.024 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.022 0.013 -10000 0 0 141 141
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
TGFBR2 0.029 0.005 -10000 0 0 14 14
ITGB3 0.025 0.011 -10000 0 0 99 99
IGF1 0.028 0.007 -10000 0 0 32 32
RAC1 0.028 0.006 -10000 0 0 26 26
regulation of cell-matrix adhesion 0.021 0.071 -10000 0 -0.15 74 74
apoptosis 0.028 0.007 -10000 0 0 32 32
CD47 0.027 0.009 -10000 0 0 51 51
alphaV/beta3 Integrin/CD47 0.026 0.067 -10000 0 -0.15 62 62
VCL 0.029 0.005 -10000 0 0 13 13
alphaV/beta3 Integrin/Del1 0.019 0.067 -10000 0 -0.15 65 65
CSF1 0.028 0.006 -10000 0 0 27 27
PIK3C2A -0.003 0.053 -10000 0 -0.27 13 13
PI4 Kinase/Pyk2 -0.063 0.062 0.1 26 -0.24 5 31
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.046 0.075 -10000 0 -0.14 60 60
FAK1/Vinculin -0.009 0.12 0.26 20 -0.29 24 44
alphaV beta3/Integrin/ppsTEM5 0.022 0.071 -10000 0 -0.15 74 74
RHOA 0.029 0.003 -10000 0 0 7 7
VTN 0.028 0.007 -10000 0 0 32 32
BCAR1 0.027 0.009 -10000 0 0 56 56
FGF2 0.028 0.008 -10000 0 0 42 42
F11R -0.03 0.014 0.19 1 -10000 0 1
alphaV/beta3 Integrin/Lactadherin 0.021 0.077 -10000 0 -0.16 79 79
alphaV/beta3 Integrin/TGFBR2 0.027 0.072 -10000 0 -0.16 70 70
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.056 0.055 -10000 0 -0.14 22 22
HSP90AA1 0.029 0.006 -10000 0 0 21 21
alphaV/beta3 Integrin/Talin 0.027 0.064 -10000 0 -0.13 67 67
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.018 0.015 -10000 0 0 214 214
alphaV/beta3 Integrin/Pyk2 -0.04 0.068 0.17 37 -0.23 2 39
SDC1 0.029 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 7 7
IRS1 0.011 0.014 -10000 0 0 349 349
FAK1/Paxillin -0.009 0.12 0.27 19 -0.29 25 44
cell migration -0.018 0.11 0.24 20 -0.27 25 45
ITGAV 0.028 0.007 -10000 0 0 32 32
PI3K 0.001 0.094 -10000 0 -0.16 109 109
SPP1 0.018 0.015 -10000 0 0 226 226
KDR 0.029 0.006 -10000 0 0 21 21
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 0.004 -10000 0 0 8 8
angiogenesis -0.075 0.17 0.28 3 -0.42 91 94
Rac1/GTP -0.042 0.055 0.16 20 -0.22 1 21
EDIL3 0.023 0.012 -10000 0 0 124 124
cell proliferation 0.026 0.072 -10000 0 -0.15 70 70
BARD1 signaling events

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
BARD1/CSTF1 0.033 0.019 -10000 0 -10000 0 0
ATM 0.028 0.007 -10000 0 0 33 33
UBE2D3 0.028 0.008 -10000 0 0 42 42
PRKDC 0.025 0.011 -10000 0 0 98 98
ATR 0.022 0.013 -10000 0 0 140 140
UBE2L3 0.027 0.008 -10000 0 0 46 46
FANCD2 0.051 0.062 -10000 0 -10000 0 0
protein ubiquitination 0.051 0.062 -10000 0 -10000 0 0
XRCC5 0.028 0.007 -10000 0 0 36 36
XRCC6 0.027 0.008 -10000 0 0 49 49
M/R/N Complex 0.044 0.027 -10000 0 -10000 0 0
MRE11A 0.025 0.011 -10000 0 0 81 81
DNA-PK 0.043 0.028 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.031 0.074 0.22 2 -0.52 4 6
FANCF 0.029 0.005 -10000 0 0 16 16
BRCA1 0.026 0.01 -10000 0 0 65 65
CCNE1 0.003 0.009 -10000 0 0 506 506
CDK2/Cyclin E1 0.003 0.01 -10000 0 -10000 0 0
FANCG 0.029 0.005 -10000 0 0 14 14
BRCA1/BACH1/BARD1 0.033 0.019 -10000 0 -10000 0 0
FANCE 0.029 0.005 -10000 0 0 18 18
FANCC 0.028 0.006 -10000 0 0 25 25
NBN 0.025 0.011 -10000 0 0 81 81
FANCA 0.025 0.011 -10000 0 0 82 82
DNA repair 0.2 0.2 0.37 265 -0.36 2 267
BRCA1/BARD1/ubiquitin 0.033 0.019 -10000 0 -10000 0 0
BARD1/DNA-PK 0.069 0.047 -10000 0 -10000 0 0
FANCL 0.027 0.008 -10000 0 0 45 45
mRNA polyadenylation -0.033 0.019 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.016 0.07 0.18 36 -0.32 4 40
BRCA1/BACH1/BARD1/TopBP1 0.018 0.028 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.046 0.072 -10000 0 -0.14 45 45
BARD1/CSTF1/BRCA1 0.041 0.028 -10000 0 -10000 0 0
BRCA1/BACH1 0.026 0.01 -10000 0 0 65 65
BARD1 0.025 0.011 -10000 0 0 90 90
PCNA 0.022 0.013 -10000 0 0 146 146
BRCA1/BARD1/UbcH5C 0.044 0.027 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.043 0.028 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.059 0.056 -10000 0 -10000 0 0
BARD1/DNA-PK/P53 0.052 0.079 -10000 0 -0.14 49 49
BRCA1/BARD1/Ubiquitin 0.033 0.019 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP -0.022 0.048 0.16 29 -10000 0 29
FA complex 0.029 0.049 0.19 10 -0.21 5 15
BARD1/EWS 0.034 0.019 -10000 0 -10000 0 0
RBBP8 -0.009 0.065 0.19 53 -10000 0 53
TP53 0.024 0.012 -10000 0 0 102 102
TOPBP1 0.01 0.014 -10000 0 0 362 362
G1/S transition of mitotic cell cycle -0.025 0.062 0.14 45 -10000 0 45
BRCA1/BARD1 0.056 0.068 -10000 0 -10000 0 0
CSTF1 0.027 0.009 -10000 0 0 57 57
BARD1/EWS-Fli1 0.019 0.008 -10000 0 -10000 0 0
CDK2 0.018 0.015 -10000 0 0 226 226
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 0.019 -10000 0 -10000 0 0
EWSR1 0.027 0.008 -10000 0 0 46 46
HIF-1-alpha transcription factor network

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
PKM2 0.093 0.38 0.78 82 -0.9 3 85
HDAC7 -0.004 0.004 -10000 0 -0.078 1 1
HIF1A/ARNT/Cbp/p300/Src-1 0.022 0.28 0.69 51 -0.7 4 55
SMAD4 -0.02 0.021 -10000 0 -10000 0 0
ID2 0.33 0.45 0.87 46 -0.91 3 49
AP1 0.02 0.072 0.24 11 -0.17 60 71
ABCG2 0.28 0.45 0.86 60 -0.91 3 63
HIF1A 0.12 0.15 0.33 97 -10000 0 97
TFF3 0.03 0.37 0.87 32 -0.93 4 36
GATA2 0.032 0.028 0.2 13 -0.067 1 14
AKT1 0.15 0.17 0.39 112 -10000 0 112
response to hypoxia 0.081 0.15 0.3 151 -10000 0 151
MCL1 0.31 0.45 0.86 68 -0.91 3 71
NDRG1 0.2 0.42 0.86 41 -1 2 43
SERPINE1 0.24 0.43 0.86 44 -0.91 3 47
FECH 0.32 0.45 0.86 66 -0.91 3 69
FURIN 0.33 0.45 0.86 66 -0.91 3 69
NCOA2 0.027 0.008 -10000 0 -10000 0 0
EP300 0.23 0.29 0.64 132 -0.39 2 134
HMOX1 0.31 0.45 0.85 79 -0.91 3 82
BHLHE40 0.093 0.38 0.78 82 -0.9 3 85
BHLHE41 0.093 0.38 0.78 82 -0.9 3 85
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.14 0.19 0.41 83 -10000 0 83
ENG 0.12 0.18 0.47 2 -10000 0 2
JUN 0.03 0.016 0.13 11 -0.047 1 12
RORA 0.33 0.45 0.86 69 -0.91 3 72
ABCB1 -0.008 0.064 0.63 1 -10000 0 1
TFRC 0.12 0.38 0.86 28 -0.91 3 31
CXCR4 0.33 0.45 0.86 67 -0.91 3 70
TF 0.32 0.45 0.86 70 -0.91 3 73
CITED2 0.31 0.45 0.86 65 -0.97 3 68
HIF1A/ARNT -0.047 0.25 0.79 13 -0.86 6 19
LDHA 0.017 0.14 0.63 21 -0.67 3 24
ETS1 0.31 0.45 0.86 66 -0.91 3 69
PGK1 0.13 0.38 0.87 12 -0.91 3 15
NOS2 0.093 0.38 0.78 82 -0.9 3 85
ITGB2 0.32 0.45 0.86 60 -0.91 3 63
ALDOA 0.34 0.45 0.86 58 -0.91 3 61
Cbp/p300/CITED2 0.23 0.44 0.84 100 -0.92 4 104
FOS 0.027 0.021 0.14 13 -10000 0 13
HK2 0.34 0.45 0.85 87 -0.91 3 90
SP1 -0.03 0.022 0.22 4 -10000 0 4
GCK 0.29 0.34 0.83 93 -10000 0 93
HK1 0.34 0.45 0.86 73 -0.91 3 76
NPM1 0.33 0.45 0.85 90 -0.91 3 93
EGLN1 0.32 0.45 0.86 55 -0.91 3 58
CREB1 0.082 0.099 0.26 126 -10000 0 126
PGM1 0.28 0.44 0.86 52 -0.91 3 55
SMAD3 -0.021 0.021 -10000 0 -10000 0 0
EDN1 0.19 0.26 0.7 47 -1.1 1 48
IGFBP1 0.33 0.45 0.86 67 -0.91 3 70
VEGFA 0.26 0.4 0.84 80 -0.67 1 81
HIF1A/JAB1 0.07 0.1 0.25 31 -10000 0 31
CP 0.06 0.35 0.87 19 -0.99 3 22
CXCL12 0.28 0.45 0.87 37 -0.94 3 40
COPS5 0.025 0.012 -10000 0 -0.03 6 6
SMAD3/SMAD4 0.038 0.017 -10000 0 -0.11 3 3
BNIP3 0.3 0.44 0.86 54 -0.91 3 57
EGLN3 0.28 0.44 0.85 66 -0.94 3 69
CA9 0.26 0.44 0.86 43 -0.91 3 46
TERT 0.29 0.44 0.86 54 -0.91 3 57
ENO1 0.33 0.45 0.86 72 -0.91 3 75
PFKL 0.33 0.45 0.86 64 -0.91 3 67
NCOA1 0.026 0.013 -10000 0 -0.03 23 23
ADM 0.26 0.44 0.86 39 -0.91 3 42
ARNT 0.12 0.15 0.32 105 -10000 0 105
HNF4A 0.028 0.008 -10000 0 -10000 0 0
ADFP 0.093 0.38 0.78 82 -0.9 3 85
SLC2A1 0.25 0.39 0.82 80 -0.67 1 81
LEP 0.32 0.45 0.86 71 -0.91 3 74
HIF1A/ARNT/Cbp/p300 0.001 0.26 0.71 35 -0.71 4 39
EPO 0.26 0.36 0.76 74 -0.7 2 76
CREBBP 0.24 0.29 0.64 141 -10000 0 141
HIF1A/ARNT/Cbp/p300/HDAC7 -0.008 0.24 0.67 29 -0.69 4 33
PFKFB3 0.3 0.45 0.86 65 -0.91 4 69
NT5E 0.24 0.44 0.85 64 -0.99 3 67
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.082 0.12 -10000 0 -0.35 52 52
CaM/Ca2+ 0.019 0.022 -10000 0 -0.15 9 9
AKT1 0.028 0.006 -10000 0 0 26 26
AKT2 0.027 0.009 -10000 0 0 53 53
STXBP4 0.029 0.006 -10000 0 0 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.045 0.12 0.22 1 -0.35 48 49
YWHAZ 0.026 0.01 -10000 0 0 77 77
CALM1 0.028 0.006 -10000 0 0 25 25
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 0.028 0.008 -10000 0 0 42 42
YWHAB 0.027 0.008 -10000 0 0 44 44
SNARE/Synip -0.086 0.09 -10000 0 -0.15 382 382
YWHAG 0.029 0.004 -10000 0 0 11 11
ASIP 0.028 0.008 -10000 0 0 43 43
PRKCI 0.014 0.015 -10000 0 0 287 287
AS160/CaM/Ca2+ 0.019 0.022 -10000 0 -0.15 9 9
RHOQ 0.029 0.005 -10000 0 0 19 19
GYS1 -0.015 0.006 -10000 0 -10000 0 0
PRKCZ 0.029 0.006 -10000 0 0 22 22
TRIP10 0.028 0.007 -10000 0 0 34 34
TC10/GTP/CIP4/Exocyst 0.037 0.012 -10000 0 -10000 0 0
AS160/14-3-3 -0.008 0.069 -10000 0 -0.32 15 15
VAMP2 0.007 0.013 -10000 0 0 417 417
SLC2A4 -0.051 0.13 0.22 1 -0.39 48 49
STX4 0.029 0.004 -10000 0 0 10 10
GSK3B 0.009 0.004 -10000 0 -10000 0 0
SFN 0.028 0.007 -10000 0 0 37 37
LNPEP 0.027 0.009 -10000 0 0 54 54
YWHAE 0.028 0.008 -10000 0 0 41 41
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 0.02 0.014 -10000 0 0 185 185
positive regulation of NF-kappaB transcription factor activity 0.015 0.047 -10000 0 -0.16 29 29
MAP2K4 -0.019 0.075 -10000 0 -0.3 14 14
IKBKB 0.028 0.008 -10000 0 0 39 39
TNFRSF10B 0.024 0.012 -10000 0 0 106 106
TNFRSF10A 0.024 0.012 -10000 0 0 108 108
SMPD1 -0.012 0.04 0.097 31 -0.12 29 60
IKBKG 0.028 0.007 -10000 0 0 33 33
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.024 0.012 -10000 0 0 106 106
TRAIL/TRAILR2 0.015 0.047 -10000 0 -0.16 29 29
TRAIL/TRAILR3 -0.029 0.089 -10000 0 -0.18 140 140
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 0.019 0.048 -10000 0 -0.13 29 29
IKK complex -0.003 0.068 -10000 0 -0.26 20 20
RIPK1 0.028 0.008 -10000 0 0 41 41
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 0.054 0.19 36 -10000 0 36
MAP3K1 -0.019 0.082 0.18 1 -0.29 24 25
TRAILR4 (trimer) 0.024 0.012 -10000 0 0 106 106
TRADD 0.026 0.009 -10000 0 0 63 63
TRAILR1 (trimer) 0.024 0.012 -10000 0 0 108 108
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.018 0.073 -10000 0 -0.26 17 17
CFLAR 0.029 0.004 -10000 0 0 9 9
MAPK1 -0.009 0.054 0.19 36 -10000 0 36
TRAIL/TRAILR1/FADD/TRADD/RIP 0.032 0.071 -10000 0 -0.14 30 30
mol:ceramide -0.012 0.04 0.097 31 -0.12 29 60
FADD 0.029 0.005 -10000 0 0 18 18
MAPK8 -0.029 0.086 0.2 2 -0.3 22 24
TRAF2 0.029 0.006 -10000 0 0 24 24
TRAILR3 (trimer) 0.015 0.015 -10000 0 0 278 278
CHUK 0.028 0.007 -10000 0 0 35 35
TRAIL/TRAILR1/FADD 0.025 0.048 -10000 0 -0.15 26 26
DAP3 0.028 0.006 -10000 0 0 25 25
CASP10 0.011 0.081 0.15 73 -0.19 23 96
JNK cascade 0.015 0.047 -10000 0 -0.16 29 29
TRAIL (trimer) 0.02 0.014 -10000 0 0 185 185
TNFRSF10C 0.015 0.015 -10000 0 0 278 278
TRAIL/TRAILR1/DAP3/GTP/FADD 0.032 0.058 -10000 0 -0.13 26 26
TRAIL/TRAILR2/FADD 0.025 0.048 -10000 0 -0.15 26 26
cell death -0.012 0.04 0.097 31 -0.12 29 60
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.018 0.073 -10000 0 -0.26 17 17
TRAILR2 (trimer) 0.024 0.012 -10000 0 0 106 106
CASP8 -0.004 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 0.071 -10000 0 -0.14 30 30
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 0.18 0.5 1.2 61 -1.2 17 78
IL23A 0.18 0.41 1.1 43 -10000 0 43
NF kappa B1 p50/RelA/I kappa B alpha 0.12 0.33 0.73 40 -0.81 8 48
positive regulation of T cell mediated cytotoxicity 0.21 0.51 1.3 63 -0.96 2 65
ITGA3 0.11 0.49 0.98 43 -1.1 35 78
IL17F 0.12 0.32 0.72 61 -0.64 2 63
IL12B 0.068 0.14 0.35 75 -10000 0 75
STAT1 (dimer) 0.006 0.25 0.87 14 -0.82 7 21
CD4 0.19 0.43 1 63 -1.1 2 65
IL23 0.15 0.37 0.93 43 -0.84 1 44
IL23R 0.14 0.26 0.82 43 -0.8 3 46
IL1B 0.18 0.43 1.1 57 -0.89 1 58
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.17 0.41 0.97 62 -0.94 1 63
TYK2 0.038 0.095 0.23 74 -10000 0 74
STAT4 0.029 0.005 -10000 0 0 16 16
STAT3 0.014 0.025 -10000 0 -0.03 127 127
IL18RAP 0.009 0.036 0.09 25 -0.055 9 34
IL12RB1 0.038 0.095 0.23 74 -10000 0 74
PIK3CA 0.013 0.021 -10000 0 -0.03 67 67
IL12Rbeta1/TYK2 0.072 0.091 0.26 74 -10000 0 74
IL23R/JAK2 0.15 0.25 0.71 60 -0.8 2 62
positive regulation of chronic inflammatory response 0.21 0.51 1.3 63 -0.96 2 65
natural killer cell activation -0.01 0.021 -10000 0 -0.06 61 61
JAK2 0.067 0.14 0.35 76 -10000 0 76
PIK3R1 0.011 0.023 -10000 0 -0.03 93 93
NFKB1 0.026 0.026 0.096 1 -10000 0 1
RELA 0.025 0.027 0.096 1 -10000 0 1
positive regulation of dendritic cell antigen processing and presentation 0.15 0.37 0.92 43 -0.81 1 44
ALOX12B 0.17 0.41 0.97 61 -0.94 1 62
CXCL1 0.18 0.46 1 64 -1.2 8 72
T cell proliferation 0.21 0.51 1.3 63 -0.96 2 65
NFKBIA 0.026 0.027 0.096 1 -10000 0 1
IL17A 0.11 0.29 0.67 59 -10000 0 59
PI3K 0.042 0.29 0.78 28 -0.82 8 36
IFNG 0.039 0.091 0.33 36 -10000 0 36
STAT3 (dimer) 0.04 0.29 0.77 27 -0.82 8 35
IL18R1 0.009 0.036 0.09 25 -0.057 4 29
IL23/IL23R/JAK2/TYK2/SOCS3 0.16 0.35 0.86 62 -0.7 5 67
IL18/IL18R 0.033 0.076 0.31 24 -10000 0 24
macrophage activation 0.003 0.02 0.058 27 -10000 0 27
TNF 0.18 0.42 1 62 -0.89 1 63
STAT3/STAT4 0.14 0.35 0.78 49 -0.83 8 57
STAT4 (dimer) 0.16 0.38 0.86 59 -0.83 8 67
IL18 0.009 0.03 0.087 16 -10000 0 16
IL19 0.17 0.41 0.98 62 -0.94 1 63
STAT5A (dimer) 0.16 0.38 0.86 61 -0.83 8 69
STAT1 0.013 0.015 -10000 0 0 315 315
SOCS3 0.029 0.006 -10000 0 0 20 20
CXCL9 0.22 0.49 1.1 78 -0.94 1 79
MPO 0.17 0.41 0.97 61 -0.94 1 62
positive regulation of humoral immune response 0.21 0.51 1.3 63 -0.96 2 65
IL23/IL23R/JAK2/TYK2 0.21 0.51 1.3 64 -0.92 4 68
IL6 0.16 0.42 1 45 -1.1 9 54
STAT5A 0.028 0.007 -10000 0 0 33 33
IL2 0.005 0.06 0.22 25 -0.096 6 31
positive regulation of tyrosine phosphorylation of STAT protein -0.01 0.021 -10000 0 -0.06 61 61
CD3E 0.17 0.43 1 62 -1 3 65
keratinocyte proliferation 0.21 0.51 1.3 63 -0.96 2 65
NOS2 0.18 0.41 0.98 61 -0.81 4 65
PDGFR-alpha signaling pathway

Figure S34.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S34.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.016 0.037 0.1 24 -10000 0 24
PDGF/PDGFRA/CRKL 0.009 0.07 -10000 0 -0.16 64 64
positive regulation of JUN kinase activity 0.032 0.074 -10000 0 -0.14 61 61
CRKL 0.027 0.008 -10000 0 0 46 46
PDGF/PDGFRA/Caveolin-3 0.01 0.071 -10000 0 -0.16 65 65
AP1 -0.094 0.25 0.58 19 -0.7 61 80
mol:IP3 -0.023 0.059 0.18 30 -0.22 7 37
PLCG1 -0.023 0.059 0.18 30 -0.22 7 37
PDGF/PDGFRA/alphaV Integrin 0.009 0.072 -10000 0 -0.17 66 66
RAPGEF1 0.029 0.006 -10000 0 0 21 21
CRK 0.028 0.007 -10000 0 0 36 36
mol:Ca2+ -0.023 0.059 0.18 30 -0.22 7 37
CAV3 0.029 0.004 -10000 0 0 11 11
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 0.071 -10000 0 -0.16 65 65
FOS -0.087 0.26 0.64 23 -0.7 59 82
JUN -0.026 0.057 0.17 32 -0.22 1 33
oligodendrocyte development 0.008 0.071 -10000 0 -0.16 66 66
GRB2 0.029 0.005 -10000 0 0 19 19
PIK3R1 0.021 0.013 -10000 0 0 159 159
mol:DAG -0.023 0.059 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 0.029 0.006 -10000 0 0 20 20
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 0.14 14 -0.18 9 23
ELK1/SRF -0.049 0.062 0.13 31 -0.22 4 35
SHB 0.029 0.004 -10000 0 0 10 10
SHF 0.028 0.007 -10000 0 0 32 32
CSNK2A1 0.024 0.036 -10000 0 -0.085 27 27
GO:0007205 -0.035 0.08 0.18 31 -0.21 55 86
SOS1 0.028 0.007 -10000 0 0 34 34
Ras protein signal transduction 0.032 0.074 -10000 0 -0.14 61 61
PDGF/PDGFRA/SHB 0.01 0.071 -10000 0 -0.16 65 65
PDGF/PDGFRA/Caveolin-1 -0.015 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 32 -0.19 52 84
PIK3CA 0.021 0.014 -10000 0 0 174 174
PDGF/PDGFRA/Crk 0.009 0.07 -10000 0 -0.16 65 65
JAK-STAT cascade -0.026 0.041 0.14 14 -0.18 9 23
cell proliferation 0.009 0.07 -10000 0 -0.16 65 65
Nectin adhesion pathway

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
PDGFRB 0.029 0.005 -10000 0 0 16 16
alphaV beta3 Integrin 0.014 0.069 -10000 0 -0.17 68 68
PTK2 -0.037 0.11 -10000 0 -0.34 43 43
positive regulation of JNK cascade -0.014 0.11 -10000 0 -0.29 60 60
CDC42/GDP -0.017 0.15 -10000 0 -0.4 60 60
Rac1/GDP -0.019 0.15 -10000 0 -0.39 61 61
RAP1B 0.029 0.006 -10000 0 0 23 23
RAP1A 0.029 0.004 -10000 0 0 8 8
CTNNB1 0.029 0.004 -10000 0 0 8 8
CDC42/GTP -0.016 0.14 -10000 0 -0.36 59 59
nectin-3/I-afadin 0.026 0.043 -10000 0 -0.16 23 23
RAPGEF1 -0.04 0.14 0.25 2 -0.4 57 59
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.039 0.15 0.27 1 -0.45 58 59
PDGFB-D/PDGFRB 0.029 0.005 -10000 0 0 16 16
TLN1 -0.094 0.12 -10000 0 -0.25 185 185
Rap1/GTP -0.029 0.11 -10000 0 -0.31 58 58
IQGAP1 0.029 0.006 -10000 0 0 24 24
Rap1/GTP/I-afadin 0.04 0.043 -10000 0 -0.13 21 21
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.026 0.043 -10000 0 -0.16 23 23
PVR 0.028 0.007 -10000 0 0 31 31
Necl-5(dimer) 0.028 0.007 -10000 0 0 31 31
mol:GDP -0.037 0.17 -10000 0 -0.47 61 61
MLLT4 0.026 0.01 -10000 0 0 72 72
PIK3CA 0.021 0.014 -10000 0 0 174 174
PI3K 0.027 0.091 -10000 0 -0.15 77 77
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 60 60
PVRL1 0.029 0.005 -10000 0 0 16 16
PVRL3 0.025 0.011 -10000 0 0 91 91
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 69 69
CLDN1 0.017 0.015 -10000 0 0 233 233
JAM-A/CLDN1 0.005 0.094 -10000 0 -0.14 136 136
SRC -0.039 0.16 -10000 0 -0.48 58 58
ITGB3 0.025 0.011 -10000 0 0 99 99
nectin-1(dimer)/I-afadin/I-afadin 0.031 0.041 -10000 0 -0.16 21 21
FARP2 -0.032 0.18 -10000 0 -0.48 52 52
RAC1 0.028 0.006 -10000 0 0 26 26
CTNNA1 0.029 0.005 -10000 0 0 13 13
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.037 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 -0.014 0.11 -10000 0 -0.29 60 60
alphaV/beta3 Integrin/Talin -0.12 0.12 0.2 4 -0.26 197 201
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 -0.26 186 186
VAV2 -0.035 0.18 -10000 0 -0.51 54 54
RAP1/GDP -0.013 0.14 -10000 0 -0.37 60 60
ITGAV 0.028 0.007 -10000 0 0 32 32
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.037 0.046 -10000 0 -0.14 23 23
nectin-3(dimer)/I-afadin/I-afadin 0.026 0.043 -10000 0 -0.16 23 23
Rac1/GTP -0.019 0.15 -10000 0 -0.38 59 59
PTPRM -0.1 0.13 0.097 24 -0.27 210 234
E-cadherin/beta catenin/alpha catenin 0.049 0.07 -10000 0 -0.15 24 24
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.029 0.005 -10000 0 0 13 13
IL2 signaling events mediated by PI3K

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 -0.026 0.097 -10000 0 -0.48 3 3
UGCG -0.018 0.12 -10000 0 -0.7 16 16
AKT1/mTOR/p70S6K/Hsp90/TERT -0.077 0.18 -10000 0 -0.48 48 48
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 0.13 -10000 0 -0.86 11 11
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.11 0.23 -10000 0 -0.52 101 101
FRAP1 -0.14 0.27 -10000 0 -0.61 102 102
FOXO3 -0.11 0.23 -10000 0 -0.63 61 61
AKT1 -0.11 0.25 0.33 1 -0.67 66 67
GAB2 0.01 0.028 -10000 0 -0.035 139 139
SMPD1 -0.022 0.14 -10000 0 -0.7 20 20
SGMS1 -0.01 0.096 -10000 0 -0.67 10 10
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 -0.034 0.044 -10000 0 -0.14 77 77
CALM1 0.028 0.006 -10000 0 0 25 25
cell proliferation -0.017 0.15 -10000 0 -0.56 17 17
EIF3A 0.029 0.004 -10000 0 0 9 9
PI3K -0.011 0.068 -10000 0 -0.17 77 77
RPS6KB1 -0.015 0.12 -10000 0 -0.92 7 7
mol:sphingomyelin -0.003 0.13 -10000 0 -0.86 11 11
natural killer cell activation -0.002 0.004 -10000 0 -0.018 6 6
JAK3 0.011 0.029 0.16 1 -0.038 99 100
PIK3R1 0.009 0.026 0.16 1 -0.04 49 50
JAK1 0.012 0.03 0.16 1 -0.038 75 76
NFKB1 0.027 0.008 -10000 0 0 45 45
MYC -0.079 0.3 0.43 1 -0.85 62 63
MYB -0.062 0.26 0.53 1 -1 36 37
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.062 0.15 0.35 1 -0.44 38 39
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.005 0.12 -10000 0 -0.86 7 7
mol:PI-3-4-5-P3 -0.061 0.14 0.35 1 -0.44 36 37
Rac1/GDP -0.025 0.067 0.14 51 -0.14 23 74
T cell proliferation -0.062 0.14 0.3 2 -0.42 36 38
SHC1 0.011 0.029 -10000 0 -0.035 151 151
RAC1 0.019 0.022 -10000 0 -0.03 85 85
positive regulation of cyclin-dependent protein kinase activity -0.004 0.018 0.23 1 -10000 0 1
PRKCZ -0.066 0.14 0.32 1 -0.43 38 39
NF kappa B1 p50/RelA -0.11 0.24 -10000 0 -0.53 101 101
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.026 0.1 0.65 1 -0.36 17 18
HSP90AA1 0.029 0.006 -10000 0 0 21 21
RELA 0.029 0.003 -10000 0 0 7 7
IL2RA 0.011 0.028 -10000 0 -0.035 146 146
IL2RB 0.01 0.029 0.16 1 -0.038 83 84
TERT 0.027 0.009 -10000 0 0 59 59
E2F1 -0.013 0.11 0.45 1 -0.41 36 37
SOS1 0.011 0.029 -10000 0 -0.035 145 145
RPS6 0.028 0.007 -10000 0 0 32 32
mol:cAMP 0.002 0.008 -10000 0 -0.081 1 1
PTPN11 0.011 0.03 -10000 0 -0.036 155 155
IL2RG 0.01 0.029 0.16 1 -0.039 99 100
actin cytoskeleton organization -0.062 0.14 0.3 2 -0.42 36 38
GRB2 0.011 0.029 -10000 0 -0.036 152 152
IL2 0.011 0.03 0.16 1 -0.038 123 124
PIK3CA 0.008 0.025 -10000 0 -0.039 44 44
Rac1/GTP -0.007 0.059 -10000 0 -0.13 73 73
LCK 0.011 0.03 0.16 1 -0.038 114 115
BCL2 -0.16 0.3 -10000 0 -0.75 105 105
Regulation of Telomerase

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
Telomerase catalytic core complex -0.12 0.2 0.6 1 -0.56 30 31
RAD9A 0.029 0.003 -10000 0 0 7 7
AP1 -0.003 0.069 -10000 0 -0.17 61 61
IFNAR2 0.01 0.032 0.096 1 -0.043 145 146
AKT1 -0.02 0.05 -10000 0 -0.17 20 20
ER alpha/Oestrogen -0.012 0.056 0.069 1 -0.15 71 72
NFX1/SIN3/HDAC complex -0.012 0.075 0.19 3 -0.3 18 21
EGF 0.012 0.028 -10000 0 -0.037 128 128
SMG5 0.029 0.006 -10000 0 0 23 23
SMG6 0.028 0.007 -10000 0 0 30 30
SP3/HDAC2 0.017 0.043 0.16 1 -10000 0 1
TERT/c-Abl -0.1 0.2 0.54 1 -0.51 41 42
SAP18 0.013 0.026 -10000 0 -0.031 139 139
MRN complex 0.044 0.027 -10000 0 -10000 0 0
WT1 0.011 0.03 0.1 1 -0.043 125 126
WRN 0.023 0.012 -10000 0 0 120 120
SP1 0.008 0.036 0.13 1 -0.051 147 148
SP3 0.012 0.029 0.065 1 -0.038 142 143
TERF2IP 0.027 0.009 -10000 0 0 58 58
Telomerase/Nucleolin -0.11 0.19 -10000 0 -0.47 59 59
Mad/Max 0.019 0.04 -10000 0 -10000 0 0
TERT -0.12 0.2 -10000 0 -0.57 30 30
CCND1 -0.26 0.43 0.78 1 -0.96 147 148
MAX 0.011 0.03 -10000 0 -0.038 145 145
RBBP7 0.013 0.027 -10000 0 -0.032 143 143
RBBP4 0.014 0.026 -10000 0 -0.031 130 130
TERF2 -0.031 0.018 0.077 8 -10000 0 8
PTGES3 0.024 0.011 -10000 0 0 100 100
SIN3A 0.013 0.026 -10000 0 -0.031 141 141
Telomerase/911 -0.01 0.092 0.22 1 -0.39 7 8
CDKN1B -0.028 0.062 0.2 28 -0.27 4 32
RAD1 0.027 0.008 -10000 0 0 46 46
XRCC5 0.028 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 0.084 7 -10000 0 7
UBE3A 0.012 0.028 0.06 1 -0.037 128 129
JUN 0.011 0.029 -10000 0 -0.037 138 138
E6 -0.002 0.004 0.03 1 -10000 0 1
HPV-16 E6/E6AP 0.008 0.022 0.093 1 -10000 0 1
FOS 0.01 0.027 -10000 0 -0.038 121 121
IFN-gamma/IRF1 0.015 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 0 213 213
Telomerase -0.014 0.085 -10000 0 -0.31 18 18
IRF1 -0.031 0.024 0.17 6 -0.14 2 8
ESR1 0.01 0.026 -10000 0 -0.034 123 123
KU/TER 0.038 0.016 -10000 0 -10000 0 0
ATM/TRF2 0.036 0.021 -10000 0 -0.081 8 8
ubiquitin-dependent protein catabolic process -0.014 0.077 0.2 2 -0.3 18 20
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.014 0.078 0.18 1 -0.31 18 19
HDAC1 0.013 0.026 -10000 0 -0.031 129 129
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 0.029 0.006 -10000 0 0 22 22
MXD1 0.012 0.029 -10000 0 -0.038 143 143
MRE11A 0.025 0.011 -10000 0 0 81 81
HUS1 0.029 0.005 -10000 0 0 17 17
RPS6KB1 0.029 0.006 -10000 0 0 22 22
TERT/NF kappa B1/14-3-3 -0.1 0.21 -10000 0 -0.55 34 34
NR2F2 0.032 0.012 -10000 0 -0.088 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 0.025 0.012 -10000 0 -10000 0 0
NFKB1 0.027 0.008 -10000 0 0 45 45
HNRNPC 0.028 0.006 -10000 0 0 27 27
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.019 0.025 0.24 2 -10000 0 2
NBN 0.025 0.011 -10000 0 0 81 81
EGFR 0.013 0.027 -10000 0 -0.038 118 118
mol:Oestrogen -0.001 0.003 0.021 1 -10000 0 1
EGF/EGFR 0.007 0.063 -10000 0 -0.17 44 44
MYC 0.008 0.023 0.078 1 -0.037 81 82
IL2 0.008 0.035 0.11 1 -0.052 135 136
KU 0.038 0.016 -10000 0 -10000 0 0
RAD50 0.029 0.005 -10000 0 0 15 15
HSP90AA1 0.029 0.006 -10000 0 0 21 21
TGFB1 0.025 0.012 -10000 0 -10000 0 0
TRF2/BLM -0.021 0.022 0.084 3 -10000 0 3
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.1 0.21 0.54 1 -0.53 34 35
SP1/HDAC2 0.014 0.048 0.23 1 -10000 0 1
PINX1 0.024 0.012 -10000 0 0 108 108
Telomerase/EST1A -0.11 0.19 -10000 0 -0.47 57 57
Smad3/Myc -0.042 0.058 -10000 0 -0.16 86 86
911 complex 0.053 0.02 -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 -0.47 53 53
Telomerase/AKT1/mTOR/p70S6K -0.064 0.14 -10000 0 -0.39 53 53
SIN3B 0.012 0.026 -10000 0 -0.032 130 130
YWHAE 0.028 0.008 -10000 0 0 41 41
Telomerase/EST1B -0.11 0.19 -10000 0 -0.46 58 58
response to DNA damage stimulus 0.008 0.021 0.085 15 -0.1 8 23
MRN complex/TRF2/Rap1 0.066 0.047 -10000 0 -10000 0 0
TRF2/WRN -0.028 0.022 0.084 5 -10000 0 5
Telomerase/hnRNP C1/C2 -0.11 0.19 -10000 0 -0.47 56 56
E2F1 0.01 0.031 -10000 0 -0.043 137 137
ZNFX1 0.012 0.026 -10000 0 -0.031 136 136
PIF1 0.029 0.005 -10000 0 0 13 13
NCL 0.029 0.004 -10000 0 0 8 8
DKC1 0.024 0.012 -10000 0 0 112 112
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.033 0.071 -10000 0 -0.13 70 70
ER alpha/Gai/GDP/Gbeta gamma -0.039 0.14 -10000 0 -0.43 31 31
AKT1 -0.14 0.28 -10000 0 -0.67 107 107
PIK3CA 0.021 0.014 -10000 0 0 174 174
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.12 0.28 -10000 0 -0.68 107 107
mol:Ca2+ -0.041 0.078 -10000 0 -0.32 18 18
IGF1R 0.022 0.013 -10000 0 0 141 141
E2/ER alpha (dimer)/Striatin 0.015 0.056 -10000 0 -0.13 67 67
SHC1 0.029 0.006 -10000 0 0 20 20
apoptosis 0.13 0.26 0.64 107 -10000 0 107
RhoA/GTP -0.025 0.035 -10000 0 -0.14 22 22
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.024 0.15 0.24 2 -0.33 75 77
regulation of stress fiber formation -0.031 0.1 0.2 2 -0.24 58 60
E2/ERA-ERB (dimer) 0.014 0.058 -10000 0 -0.13 71 71
KRAS 0.025 0.011 -10000 0 0 97 97
G13/GTP 0.014 0.053 -10000 0 -0.12 71 71
pseudopodium formation 0.031 0.1 0.24 58 -0.2 2 60
E2/ER alpha (dimer)/PELP1 0.014 0.058 -10000 0 -0.13 71 71
GRB2 0.029 0.005 -10000 0 0 19 19
GNG2 0.029 0.005 -10000 0 0 14 14
GNAO1 0.027 0.008 -10000 0 0 44 44
HRAS 0.028 0.006 -10000 0 0 27 27
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.07 0.17 -10000 0 -0.4 96 96
E2/ER beta (dimer) 0.021 0.004 -10000 0 -10000 0 0
mol:GDP -0.035 0.068 -10000 0 -0.25 36 36
mol:NADP -0.07 0.17 -10000 0 -0.4 96 96
PIK3R1 0.021 0.013 -10000 0 0 159 159
mol:IP3 -0.045 0.072 -10000 0 -0.33 17 17
IGF-1R heterotetramer 0.022 0.013 -10000 0 0 141 141
PLCB1 -0.033 0.07 -10000 0 -0.36 14 14
PLCB2 -0.037 0.069 -10000 0 -0.35 16 16
IGF1 0.028 0.007 -10000 0 0 32 32
mol:L-citrulline -0.07 0.17 -10000 0 -0.4 96 96
RHOA 0.029 0.003 -10000 0 0 7 7
Gai/GDP -0.005 0.16 -10000 0 -0.57 38 38
JNK cascade 0.021 0.004 -10000 0 -10000 0 0
BCAR1 0.027 0.009 -10000 0 0 56 56
ESR2 0.029 0.005 -10000 0 0 16 16
GNAQ 0.028 0.007 -10000 0 0 28 28
ESR1 0.024 0.012 -10000 0 0 114 114
Gq family/GDP/Gbeta gamma -0.071 0.22 -10000 0 -0.7 53 53
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.001 0.11 -10000 0 -0.73 7 7
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.022 0.15 0.24 2 -0.33 73 75
GNAZ 0.027 0.009 -10000 0 0 51 51
E2/ER alpha (dimer) -0.001 0.057 -10000 0 -0.15 71 71
STRN 0.029 0.005 -10000 0 0 14 14
GNAL 0.029 0.006 -10000 0 0 21 21
PELP1 0.028 0.006 -10000 0 0 26 26
MAPK11 -0.02 0.011 -10000 0 -10000 0 0
GNAI2 0.029 0.003 -10000 0 0 6 6
GNAI3 0.025 0.011 -10000 0 0 98 98
GNAI1 0.028 0.006 -10000 0 0 27 27
HBEGF -0.021 0.15 0.29 13 -0.4 32 45
cAMP biosynthetic process 0.01 0.05 -10000 0 -0.11 70 70
SRC -0.04 0.14 -10000 0 -0.42 30 30
PI3K -0.001 0.068 -10000 0 -0.16 77 77
GNB1 0.029 0.006 -10000 0 0 23 23
G13/GDP/Gbeta gamma 0.016 0.091 -10000 0 -0.24 36 36
SOS1 0.028 0.007 -10000 0 0 34 34
IGF-1R heterotetramer/IGF1 -0.07 0.11 -10000 0 -0.3 76 76
Gs family/GTP 0.016 0.054 -10000 0 -0.12 70 70
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.02 0.029 -10000 0 -10000 0 0
vasodilation -0.067 0.16 -10000 0 -0.38 97 97
mol:DAG -0.045 0.072 -10000 0 -0.33 17 17
Gs family/GDP/Gbeta gamma -0.028 0.081 -10000 0 -0.24 36 36
MSN 0.03 0.1 0.24 57 -0.21 2 59
Gq family/GTP -0.015 0.08 -10000 0 -0.36 17 17
mol:PI-3-4-5-P3 -0.12 0.27 -10000 0 -0.66 107 107
NRAS 0.014 0.015 -10000 0 0 300 300
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.067 0.16 0.38 97 -10000 0 97
GRB2/SOS1 0.04 0.013 -10000 0 -10000 0 0
RhoA/GDP -0.018 0.087 -10000 0 -0.25 35 35
NOS3 -0.073 0.18 -10000 0 -0.42 96 96
GNA11 0.025 0.011 -10000 0 0 83 83
MAPKKK cascade -0.067 0.2 -10000 0 -0.48 103 103
E2/ER alpha (dimer)/PELP1/Src -0.026 0.15 0.26 2 -0.33 76 78
ruffle organization 0.031 0.1 0.24 58 -0.2 2 60
ROCK2 0.047 0.11 0.27 58 -10000 0 58
GNA14 0.029 0.005 -10000 0 0 18 18
GNA15 0.027 0.008 -10000 0 0 46 46
GNA13 0.029 0.005 -10000 0 0 13 13
MMP9 -0.016 0.15 0.3 22 -0.41 28 50
MMP2 -0.045 0.14 0.28 4 -0.4 35 39
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.073 0.05 0.19 1 -10000 0 1
BIRC5 0.023 0.012 -10000 0 0 121 121
NFKBIA 0.064 0.047 0.2 3 -10000 0 3
CPEB1 0.029 0.006 -10000 0 0 20 20
AKT1 0.064 0.05 0.34 2 -10000 0 2
NDEL1 0.028 0.007 -10000 0 0 31 31
Aurora A/BRCA1 0.064 0.045 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 52 52
GSK3B 0.024 0.015 0.083 2 -10000 0 2
PAK1/Aurora A 0.074 0.05 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 0.16 0.065 0.19 486 -10000 0 486
TP53 0.052 0.055 0.17 1 -0.31 4 5
DLG7 0.075 0.05 0.11 390 -10000 0 390
AURKAIP1 0.028 0.006 -10000 0 0 26 26
ARHGEF7 0.029 0.006 -10000 0 0 24 24
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 0.063 0.045 0.16 1 -10000 0 1
AURKA 0.091 0.061 0.14 77 -10000 0 77
AURKB 0.025 0.025 -10000 0 -0.16 2 2
CDC25B 0.068 0.048 0.18 2 -10000 0 2
G2/M transition checkpoint 0 0.002 -10000 0 -10000 0 0
mRNA polyadenylation 0.068 0.042 0.16 1 -10000 0 1
Aurora A/CPEB 0.069 0.043 0.16 1 -10000 0 1
Aurora A/TACC1/TRAP/chTOG -0.003 0.054 -10000 0 -10000 0 0
BRCA1 0.026 0.01 -10000 0 0 65 65
centrosome duplication 0.074 0.05 0.18 2 -10000 0 2
regulation of centrosome cycle 0.044 0.051 -10000 0 -10000 0 0
spindle assembly -0.004 0.053 -10000 0 -10000 0 0
TDRD7 0.028 0.006 -10000 0 0 26 26
Aurora A/RasGAP/Survivin 0.074 0.063 -10000 0 -10000 0 0
CENPA 0.038 0.034 -10000 0 -10000 0 0
Aurora A/PP2A 0.078 0.048 0.18 2 -10000 0 2
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.043 0.048 0.18 10 -0.26 2 12
negative regulation of DNA binding 0.052 0.055 0.16 1 -0.31 4 5
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.041 0.012 -10000 0 -10000 0 0
RASA1 0.027 0.009 -10000 0 0 51 51
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 0.091 0.061 0.14 77 -10000 0 77
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 0.073 0.05 -10000 0 -10000 0 0
OAZ1 0.019 0.014 -10000 0 0 196 196
RAN 0.029 0.004 -10000 0 0 12 12
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.021 0.017 0.083 2 -10000 0 2
GIT1 0.028 0.007 -10000 0 0 30 30
GIT1/beta-PIX/PAK1 0.052 0.022 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.16 0.065 0.19 486 -10000 0 486
PPP2R5D 0.029 0.006 -10000 0 0 24 24
Aurora A/TPX2 0.004 0.027 0.15 16 -10000 0 16
PAK1 0.027 0.008 -10000 0 0 47 47
CKAP5 0.02 0.014 -10000 0 0 179 179
IL4-mediated signaling events

Figure S40.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S40.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.02 0.58 1.1 16 -1.2 41 57
STAT6 (cleaved dimer) -0.097 0.5 0.65 3 -1.2 61 64
IGHG1 0.086 0.31 0.67 41 -0.82 3 44
IGHG3 -0.011 0.53 0.81 6 -1.1 50 56
AKT1 -0.042 0.37 -10000 0 -0.98 29 29
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.013 0.33 0.57 8 -0.98 27 35
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.084 0.39 0.64 3 -1 40 43
THY1 0.069 0.64 1.2 43 -1.2 42 85
MYB 0.027 0.009 -10000 0 0 62 62
HMGA1 0.029 0.006 -10000 0 0 21 21
IL4/IL4R/JAK1/IL2R gamma/JAK3 0.046 0.42 0.76 29 -0.95 23 52
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP 0.018 0.4 0.64 11 -1.1 27 38
SP1 0.11 0.13 0.29 178 -0.14 6 184
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 -0.017 0.058 -10000 0 -0.14 7 7
STAT6 (dimer)/ETS1 -0.053 0.54 -10000 0 -1.2 52 52
SOCS1 -0.006 0.39 0.64 10 -0.78 46 56
SOCS3 0.026 0.35 0.86 1 -0.88 17 18
FCER2 0.038 0.48 0.98 7 -1 21 28
PARP14 0.022 0.013 -10000 0 -10000 0 0
CCL17 0.001 0.56 0.96 6 -1.2 44 50
GRB2 0.029 0.005 -10000 0 0 19 19
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.041 0.31 0.59 13 -0.68 25 38
T cell proliferation -0.061 0.58 -10000 0 -1.3 63 63
IL4R/JAK1 -0.074 0.61 -10000 0 -1.4 65 65
EGR2 0.006 0.57 1.2 6 -1.2 43 49
JAK2 0.041 0.1 0.25 43 -10000 0 43
JAK3 0.002 0.034 0.11 3 -10000 0 3
PIK3R1 0.021 0.013 -10000 0 0 159 159
JAK1 0.023 0.059 0.15 10 -10000 0 10
COL1A2 0.16 0.38 0.72 100 -1.1 8 108
CCL26 0.002 0.57 0.96 7 -1.2 42 49
IL4R -0.025 0.7 1.1 26 -1.4 65 91
PTPN6 -0.012 0.05 -10000 0 -0.1 12 12
IL13RA2 0.011 0.57 1.1 11 -1.2 48 59
IL13RA1 0.044 0.11 0.25 47 -10000 0 47
IRF4 0.065 0.2 0.72 1 -0.79 3 4
ARG1 0.076 0.26 0.69 9 -0.8 2 11
CBL 0.024 0.38 0.68 12 -0.88 25 37
GTF3A 0.16 0.14 0.3 277 -0.11 1 278
PIK3CA 0.021 0.014 -10000 0 0 174 174
IL13RA1/JAK2 0.071 0.15 0.36 46 -10000 0 46
IRF4/BCL6 0.046 0.18 -10000 0 -0.76 3 3
CD40LG 0.03 0.018 0.32 2 -10000 0 2
MAPK14 0.027 0.38 0.69 10 -0.9 23 33
mitosis -0.035 0.35 -10000 0 -0.9 29 29
STAT6 0.027 0.7 1.3 40 -1.4 49 89
SPI1 0.029 0.011 0.26 1 -10000 0 1
RPS6KB1 -0.038 0.34 0.68 1 -0.88 28 29
STAT6 (dimer) 0.025 0.7 1.3 40 -1.4 49 89
STAT6 (dimer)/PARP14 -0.058 0.54 -10000 0 -1.2 50 50
mast cell activation -0.009 0.027 -10000 0 -0.069 31 31
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.008 0.39 0.64 6 -1.1 28 34
FRAP1 -0.042 0.37 -10000 0 -0.98 29 29
LTA 0.004 0.57 0.98 9 -1.2 41 50
FES 0.029 0.006 -10000 0 0 20 20
T-helper 1 cell differentiation -0.037 0.69 1.3 48 -1.3 40 88
CCL11 -0.002 0.55 0.98 19 -1.1 49 68
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.016 0.38 0.63 7 -1.1 26 33
IL2RG 0 0.034 0.11 3 -10000 0 3
IL10 0.003 0.57 0.96 7 -1.2 43 50
IRS1 0.011 0.014 -10000 0 0 349 349
IRS2 0.028 0.006 -10000 0 0 25 25
IL4 0.1 0.31 0.78 37 -1.1 6 43
IL5 0.001 0.57 0.96 6 -1.2 45 51
IL4/IL4R/JAK1/IL13RA1/JAK2 0.047 0.57 1.1 39 -1.2 32 71
COL1A1 0.29 0.5 0.92 142 -1.1 11 153
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.092 0.61 -10000 0 -1.4 65 65
IL2R gamma/JAK3 0.028 0.046 0.17 2 -0.15 24 26
TFF3 -0.57 0.62 0.97 4 -1.3 156 160
ALOX15 0.002 0.57 1 7 -1.2 46 53
MYBL1 0.024 0.012 -10000 0 0 102 102
T-helper 2 cell differentiation -0.028 0.54 0.86 9 -1.2 50 59
SHC1 0.029 0.006 -10000 0 0 20 20
CEBPB 0.027 0.013 0.26 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 0.017 0.39 0.62 11 -1.1 28 39
mol:PI-3-4-5-P3 -0.042 0.37 -10000 0 -0.98 29 29
PI3K -0.051 0.39 -10000 0 -1.1 29 29
DOK2 0.024 0.012 -10000 0 0 104 104
ETS1 -0.022 0.063 -10000 0 -0.14 29 29
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.043 0.3 0.57 14 -0.64 26 40
ITGB3 -0.068 0.68 1.2 8 -1.4 81 89
PIGR -0.022 0.62 1.2 12 -1.3 55 67
IGHE -0.05 0.12 0.21 13 -0.3 50 63
MAPKKK cascade 0.044 0.3 0.57 14 -0.63 26 40
BCL6 0.025 0.011 -10000 0 -10000 0 0
OPRM1 0.001 0.57 0.96 6 -1.2 48 54
RETNLB 0.009 0.57 1 8 -1.2 45 53
SELP -0.022 0.59 1 8 -1.2 51 59
AICDA 0.001 0.53 1 3 -1.1 45 48
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.022 0.003 -10000 0 -10000 0 0
PRKCZ 0.029 0.006 -10000 0 0 22 22
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.026 0.01 -10000 0 0 67 67
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.01 0.045 -10000 0 -0.25 2 2
IRAK/TOLLIP -0.031 0.016 0.17 2 -10000 0 2
IKBKB 0.028 0.008 -10000 0 0 39 39
IKBKG 0.028 0.007 -10000 0 0 33 33
IL1 alpha/IL1R2 0.039 0.024 -10000 0 -0.16 6 6
IL1A 0.029 0.006 -10000 0 0 22 22
IL1B -0.009 0.063 0.19 49 -10000 0 49
IRAK/TRAF6/p62/Atypical PKCs 0.058 0.05 0.19 2 -10000 0 2
IL1R2 0.028 0.007 -10000 0 0 30 30
IL1R1 0.018 0.015 -10000 0 0 227 227
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.053 0.11 0.17 11 -0.29 37 48
TOLLIP 0.029 0.006 -10000 0 0 24 24
TICAM2 0.028 0.007 -10000 0 0 30 30
MAP3K3 0.029 0.005 -10000 0 0 13 13
TAK1/TAB1/TAB2 0.019 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0.009 0.063 0.23 1 -0.29 5 6
JUN -0.024 0.061 0.17 16 -10000 0 16
MAP3K7 0.028 0.007 -10000 0 0 30 30
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.014 0.11 0.28 2 -0.17 133 135
IL1 alpha/IL1R1/IL1RAP/MYD88 0.012 0.094 -10000 0 -0.14 129 129
PIK3R1 0.021 0.013 -10000 0 0 159 159
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.019 0.095 -10000 0 -0.14 114 114
IL1 beta fragment/IL1R1/IL1RAP -0.044 0.079 0.16 29 -0.23 20 49
NFKB1 0.027 0.008 -10000 0 0 45 45
MAPK8 -0.034 0.033 0.15 11 -10000 0 11
IRAK1 -0.025 0.007 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.037 0.099 -10000 0 -0.16 208 208
IRAK4 0.027 0.009 -10000 0 0 54 54
PRKCI 0.014 0.015 -10000 0 0 287 287
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 0.099 0.19 14 -0.25 23 37
CHUK 0.028 0.007 -10000 0 0 35 35
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.044 0.079 0.16 29 -0.23 20 49
IL1 beta/IL1R2 -0.03 0.07 0.19 38 -10000 0 38
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.035 0.017 0.14 3 -10000 0 3
NF kappa B1 p50/RelA -0.053 0.092 0.12 19 -0.25 38 57
IRAK3 0.028 0.008 -10000 0 0 41 41
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.005 0.1 0.28 2 -0.16 119 121
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.019 0.089 0.19 7 -0.24 8 15
IL1 alpha/IL1R1/IL1RAP -0.009 0.08 -10000 0 -0.15 129 129
RELA 0.029 0.003 -10000 0 0 7 7
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.029 0.005 -10000 0 0 19 19
MYD88 0.03 0.003 -10000 0 0 5 5
IRAK/TRAF6/MEKK3 0.038 0.021 0.18 2 -10000 0 2
IL1RAP 0.02 0.014 -10000 0 0 182 182
UBE2N 0.029 0.005 -10000 0 0 13 13
IRAK/TRAF6 -0.051 0.074 0.085 25 -0.23 15 40
CASP1 0.025 0.011 -10000 0 0 89 89
IL1RN/IL1R2 0.038 0.025 -10000 0 -0.16 6 6
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.001 0.1 0.28 3 -0.16 134 137
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.068 0.14 -10000 0 -0.27 129 129
PIK3CA 0.021 0.014 -10000 0 0 174 174
IL1RN 0.028 0.007 -10000 0 0 31 31
TRAF6/TAK1/TAB1/TAB2 0.039 0.017 -10000 0 -10000 0 0
MAP2K6 -0.028 0.033 0.17 11 -10000 0 11
HIF-2-alpha transcription factor network

Figure S42.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S42.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 0.002 0.098 0.63 5 -0.72 6 11
oxygen homeostasis 0.043 0.071 0.18 87 -10000 0 87
TCEB2 0.029 0.005 -10000 0 0 17 17
TCEB1 0.028 0.007 -10000 0 0 34 34
VHL/Elongin B/Elongin C/HIF2A 0.11 0.25 0.54 91 -0.35 1 92
EPO 0.14 0.33 0.82 64 -10000 0 64
FIH (dimer) 0.044 0.092 0.21 89 -10000 0 89
APEX1 0.025 0.071 0.17 67 -10000 0 67
SERPINE1 0.09 0.32 0.88 40 -10000 0 40
FLT1 -0.02 0.12 -10000 0 -0.63 21 21
ADORA2A 0.19 0.38 0.86 89 -10000 0 89
germ cell development 0.16 0.37 0.86 78 -10000 0 78
SLC11A2 0.14 0.36 0.89 62 -10000 0 62
BHLHE40 0.14 0.35 0.86 64 -10000 0 64
HIF1AN 0.044 0.091 0.21 89 -10000 0 89
HIF2A/ARNT/SIRT1 0.04 0.2 0.44 31 -10000 0 31
ETS1 0.029 0.016 0.25 2 -10000 0 2
CITED2 -0.045 0.19 -10000 0 -0.77 34 34
KDR -0.011 0.096 -10000 0 -0.62 12 12
PGK1 0.012 0.25 0.87 21 -10000 0 21
SIRT1 0.02 0.022 -10000 0 -0.03 88 88
response to hypoxia -0.001 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.057 0.27 0.62 24 -10000 0 24
EPAS1 0.15 0.34 0.8 86 -10000 0 86
SP1 0.038 0.049 0.3 18 -0.16 2 20
ABCG2 0.14 0.37 0.88 66 -0.62 1 67
EFNA1 0.13 0.35 0.87 61 -10000 0 61
FXN 0.19 0.38 0.85 90 -10000 0 90
POU5F1 0.15 0.37 0.88 69 -10000 0 69
neuron apoptosis -0.055 0.26 -10000 0 -0.61 23 23
EP300 0.027 0.009 -10000 0 0 54 54
EGLN3 0.041 0.09 0.21 84 -10000 0 84
EGLN2 0.043 0.092 0.22 81 -10000 0 81
EGLN1 0.043 0.09 0.21 86 -10000 0 86
VHL/Elongin B/Elongin C 0.054 0.019 -10000 0 -10000 0 0
VHL 0.029 0.004 -10000 0 0 10 10
ARNT 0.025 0.071 0.17 64 -10000 0 64
SLC2A1 0.17 0.38 0.89 78 -10000 0 78
TWIST1 0.18 0.38 0.85 85 -10000 0 85
ELK1 0.021 0.035 -10000 0 -0.14 24 24
HIF2A/ARNT/Cbp/p300 0.088 0.27 0.59 70 -10000 0 70
VEGFA 0.12 0.34 0.87 53 -10000 0 53
CREBBP 0.027 0.008 -10000 0 0 44 44
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD 0.007 0.064 0.19 3 -0.22 10 13
FZD6 0.024 0.012 -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 0 140 140
WNT5A 0.029 0.005 -10000 0 0 17 17
WNT11 0.026 0.01 -10000 0 0 73 73
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.031 0.11 0.49 12 -0.45 15 27
IHH -0.005 0.077 0.16 88 -10000 0 88
SHH Np/Cholesterol/GAS1 -0.045 0.037 0.14 1 -0.13 77 78
LRPAP1 0.028 0.007 -10000 0 0 33 33
dorsoventral neural tube patterning 0.044 0.037 0.13 77 -0.14 1 78
SMO/beta Arrestin2 0.026 0.13 0.29 84 -0.39 9 93
SMO 0.028 0.13 0.3 84 -0.4 9 93
AKT1 -0.024 0.15 0.32 2 -0.45 18 20
ARRB2 0.028 0.006 -10000 0 0 25 25
BOC 0.026 0.01 -10000 0 0 80 80
ADRBK1 0.029 0.003 -10000 0 0 6 6
heart looping 0.028 0.13 0.3 84 -0.39 9 93
STIL 0.001 0.064 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 -0.28 10 89
PIK3CA 0.021 0.014 -10000 0 0 174 174
DHH 0.03 0.003 -10000 0 0 4 4
PTHLH 0.032 0.19 0.49 71 -0.44 1 72
determination of left/right symmetry 0.028 0.13 0.3 84 -0.39 9 93
PIK3R1 0.021 0.013 -10000 0 0 159 159
skeletal system development 0.032 0.19 0.48 71 -0.44 1 72
IHH N/Hhip 0.049 0.041 0.18 3 -10000 0 3
DHH N/Hhip 0.042 0.01 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.028 0.13 0.3 84 -0.39 9 93
pancreas development 0.028 0.006 -10000 0 0 26 26
HHAT 0.029 0.006 -10000 0 0 20 20
PI3K -0.001 0.068 -10000 0 -0.16 77 77
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.025 0.011 -10000 0 0 94 94
somite specification 0.028 0.13 0.3 84 -0.39 9 93
SHH Np/Cholesterol/PTCH1 -0.003 0.11 0.26 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 0.022 0.16 0.37 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 0.016 0.14 1 -0.13 5 6
LRP2 0.022 0.013 -10000 0 0 140 140
receptor-mediated endocytosis 0.026 0.12 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 0.05 0.041 0.18 4 -10000 0 4
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 0.031 0.023 -10000 0 -0.16 2 2
PTCH2 0.029 0.006 -10000 0 0 20 20
SHH Np/Cholesterol -0.022 0.014 0.16 1 -0.12 5 6
PTCH1 0.022 0.16 0.37 84 -0.32 8 92
HHIP 0.028 0.006 -10000 0 0 26 26
Coregulation of Androgen receptor activity

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
NRIP1 0.018 0.015 -10000 0 -10000 0 0
SVIL 0.028 0.007 -10000 0 -10000 0 0
ZNF318 0.029 0.006 -10000 0 -10000 0 0
JMJD2C -0.001 0 -10000 0 -10000 0 0
T-DHT/AR/Ubc9 -0.1 0.078 -10000 0 -0.16 314 314
CARM1 0.027 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 0.004 -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 0.028 0.008 -10000 0 -10000 0 0
DNA-PK 0.043 0.028 -10000 0 -10000 0 0
NCOA4 0.029 0.003 -10000 0 -10000 0 0
PIAS3 0.028 0.007 -10000 0 -10000 0 0
cell proliferation -0.14 0.23 -10000 0 -0.59 116 116
XRCC5 0.028 0.007 -10000 0 -10000 0 0
UBE3A 0.028 0.008 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.1 0.077 -10000 0 -0.16 317 317
FHL2 -0.06 0.072 0.52 2 -0.43 6 8
RANBP9 0.028 0.008 -10000 0 -10000 0 0
JMJD1A -0.05 0.057 -10000 0 -0.12 235 235
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 -0.12 0.094 -10000 0 -0.24 116 116
CTDSP1 0.029 0.004 -10000 0 -10000 0 0
CTDSP2 0.029 0.005 -10000 0 -10000 0 0
BRCA1 0.026 0.01 -10000 0 -10000 0 0
TCF4 0.028 0.008 -10000 0 -10000 0 0
CDKN2A 0.012 0.015 -10000 0 -10000 0 0
SRF 0.03 0.017 0.3 2 -10000 0 2
NKX3-1 -0.12 0.087 -10000 0 -0.22 237 237
KLK3 -0.024 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 -0.16 313 313
AR -0.027 0.043 -10000 0 -0.29 6 6
UBA3 0 0 -10000 0 -10000 0 0
PATZ1 0.028 0.008 -10000 0 -10000 0 0
PAWR 0.029 0.005 -10000 0 -10000 0 0
PRKDC 0.025 0.011 -10000 0 -10000 0 0
PA2G4 0.029 0.006 -10000 0 -10000 0 0
UBE2I 0.029 0.006 -10000 0 0 23 23
T-DHT/AR/Cyclin D3/CDK11 p58 -0.087 0.071 -10000 0 -0.14 304 304
RPS6KA3 0.028 0.006 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.1 0.078 -10000 0 -0.16 316 316
LATS2 0.028 0.007 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.089 0.07 -10000 0 -0.14 314 314
Cyclin D3/CDK11 p58 0.021 0.005 -10000 0 -10000 0 0
VAV3 0.026 0.01 -10000 0 -10000 0 0
KLK2 -0.071 0.053 -10000 0 -0.38 8 8
CASP8 0.029 0.004 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.082 0.082 -10000 0 -0.15 261 261
TMPRSS2 -0.33 0.32 -10000 0 -0.69 242 242
CCND1 0.021 0.014 -10000 0 -10000 0 0
PIAS1 0.029 0.005 -10000 0 -10000 0 0
mol:T-DHT -0.021 0.022 -10000 0 -0.07 5 5
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.027 0.008 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.098 0.08 -10000 0 -0.16 303 303
CMTM2 0.027 0.009 -10000 0 -10000 0 0
SNURF 0.028 0.007 -10000 0 0 36 36
ZMIZ1 -0.047 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
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.004 0.12 -10000 0 -0.4 16 16
MAP3K8 0.023 0.023 0.06 26 -0.037 62 88
FOS 0.026 0.13 0.44 26 -0.38 11 37
PRKCA 0.023 0.027 0.098 23 -0.042 60 83
PTPN7 0.023 0.038 0.15 25 -0.043 84 109
HRAS 0.022 0.021 -10000 0 -0.033 61 61
PRKCB 0.001 0.015 0.068 26 -0.022 1 27
NRAS 0.012 0.017 -10000 0 -0.032 20 20
RAS family/GTP 0.023 0.043 0.17 23 -10000 0 23
MAPK3 0.027 0.11 0.32 25 -0.42 20 45
MAP2K1 0.029 0.076 0.26 26 -0.28 7 33
ELK1 0.022 0.028 0.069 25 -0.052 61 86
BRAF 0.02 0.046 0.18 22 -0.24 3 25
mol:GTP 0 0.003 0.012 26 -0.005 62 88
MAPK1 0.019 0.12 0.32 25 -0.4 29 54
RAF1 0.021 0.051 0.21 12 -0.35 3 15
KRAS 0.019 0.02 -10000 0 -0.033 50 50
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.06 0.1 0.26 52 -10000 0 52
DAPP1 -0.029 0.099 0.2 6 -0.3 26 32
Src family/SYK family/BLNK-LAT/BTK-ITK -0.003 0.12 0.22 4 -0.42 17 21
mol:DAG 0.025 0.091 0.2 60 -0.2 8 68
HRAS 0.014 0.035 0.052 82 -10000 0 82
RAP1A 0.015 0.036 0.048 123 -10000 0 123
ARF5/GDP 0.053 0.065 0.19 4 -0.25 7 11
PLCG2 0.027 0.009 -10000 0 0 62 62
PLCG1 0.028 0.007 -10000 0 0 32 32
ARF5 0.029 0.006 -10000 0 0 23 23
mol:GTP 0.058 0.096 0.22 77 -10000 0 77
ARF1/GTP 0.054 0.087 0.25 51 -10000 0 51
RHOA 0.029 0.003 -10000 0 0 7 7
YES1 0.028 0.008 -10000 0 0 43 43
RAP1A/GTP 0.069 0.1 0.22 86 -10000 0 86
ADAP1 0.053 0.091 0.2 90 -10000 0 90
ARAP3 0.057 0.095 0.22 77 -10000 0 77
INPPL1 0.029 0.006 -10000 0 0 20 20
PREX1 0.027 0.008 -10000 0 0 45 45
ARHGEF6 0.029 0.005 -10000 0 0 17 17
ARHGEF7 0.029 0.006 -10000 0 0 24 24
ARF1 0.027 0.009 -10000 0 0 54 54
NRAS -0.007 0.022 0.041 45 -10000 0 45
FYN 0.024 0.011 -10000 0 0 100 100
ARF6 0.029 0.004 -10000 0 0 11 11
FGR 0.029 0.005 -10000 0 0 14 14
mol:Ca2+ 0.011 0.057 0.15 36 -10000 0 36
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.029 0.006 -10000 0 0 23 23
ZAP70 0.029 0.004 -10000 0 0 9 9
mol:IP3 0.009 0.07 0.18 34 -0.16 2 36
LYN 0.027 0.008 -10000 0 0 49 49
ARF1/GDP 0.049 0.066 0.19 2 -0.25 7 9
RhoA/GDP 0.083 0.1 0.21 129 -10000 0 129
PDK1/Src/Hsp90 0.054 0.019 -10000 0 -10000 0 0
BLNK 0.028 0.007 -10000 0 0 29 29
actin cytoskeleton reorganization 0.071 0.095 0.24 70 -0.3 1 71
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 26 26
PTEN -0.01 0.035 -10000 0 -0.039 318 318
HSP90AA1 0.029 0.006 -10000 0 0 21 21
ARF6/GTP 0.062 0.1 0.21 89 -10000 0 89
RhoA/GTP 0.06 0.1 0.26 53 -10000 0 53
Src family/SYK family/BLNK-LAT -0.031 0.089 -10000 0 -0.29 28 28
BLK 0.025 0.011 -10000 0 0 98 98
PDPK1 0.029 0.005 -10000 0 0 18 18
CYTH1 0.053 0.091 0.2 90 -10000 0 90
HCK 0.027 0.008 -10000 0 0 46 46
CYTH3 0.053 0.091 0.2 90 -10000 0 90
CYTH2 0.053 0.091 0.2 90 -10000 0 90
KRAS 0.007 0.033 0.04 254 -10000 0 254
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.034 0.057 0.17 46 -10000 0 46
SGK1 0.045 0.063 0.18 48 -0.19 3 51
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.042 0.063 0.18 5 -0.25 7 12
SOS1 0.028 0.007 -10000 0 0 34 34
SYK 0.029 0.006 -10000 0 0 23 23
ARF6/GDP 0.068 0.097 0.22 82 -10000 0 82
mol:PI-3-4-5-P3 0.06 0.097 0.2 89 -10000 0 89
ARAP3/RAP1A/GTP 0.069 0.1 0.23 86 -10000 0 86
VAV1 0.028 0.008 -10000 0 0 41 41
mol:PI-3-4-P2 -0.016 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I -0.012 0.039 0.2 13 -10000 0 13
PLEKHA1 -0.023 0.023 0.17 7 -10000 0 7
Rac1/GDP 0.053 0.064 0.19 3 -0.25 7 10
LAT 0.029 0.004 -10000 0 0 8 8
Rac1/GTP 0.016 0.056 0.19 1 -0.29 8 9
ITK 0.046 0.092 0.24 50 -10000 0 50
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.022 0.11 0.23 50 -0.27 11 61
LCK 0.028 0.006 -10000 0 0 26 26
BTK 0.047 0.093 0.24 53 -10000 0 53
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 0.025 0.07 0.17 8 -0.15 62 70
alphaM/beta2 Integrin/GPIbA 0.052 0.035 0.17 11 -0.15 3 14
alphaM/beta2 Integrin/proMMP-9 0.042 0.036 0.17 7 -0.1 8 15
PLAUR 0.027 0.008 -10000 0 0 44 44
HMGB1 0.018 0.027 0.1 11 -0.086 1 12
alphaM/beta2 Integrin/Talin 0.053 0.035 0.17 11 -0.15 4 15
AGER 0.018 0.028 0.1 11 -0.086 1 12
RAP1A 0.029 0.004 -10000 0 0 8 8
SELPLG 0.029 0.005 -10000 0 0 17 17
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.066 0.063 0.36 10 -0.2 8 18
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.023 0.013 -10000 0 0 129 129
CYR61 0.028 0.008 -10000 0 0 41 41
TLN1 0.029 0.005 -10000 0 0 15 15
Rap1/GTP -0.019 0.12 0.19 20 -0.27 40 60
RHOA 0.029 0.003 -10000 0 0 7 7
P-selectin oligomer 0.028 0.007 -10000 0 0 35 35
MYH2 -0.037 0.13 0.19 39 -0.33 32 71
MST1R 0.029 0.004 -10000 0 0 11 11
leukocyte activation during inflammatory response 0.049 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 0.023 0.013 -10000 0 0 134 134
JAM3 0.028 0.007 -10000 0 0 36 36
GP1BA 0.029 0.006 -10000 0 0 24 24
alphaM/beta2 Integrin/CTGF 0.01 0.088 0.17 10 -0.15 118 128
alphaM/beta2 Integrin -0.026 0.11 0.17 40 -0.29 33 73
JAM3 homodimer 0.028 0.007 -10000 0 0 36 36
ICAM2 0.029 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 0.17 40 -0.29 36 76
cell adhesion 0.051 0.035 0.17 11 -0.15 3 14
NFKB1 -0.044 0.085 0.42 11 -0.33 8 19
THY1 0.02 0.014 -10000 0 0 183 183
RhoA/GDP 0.022 0.008 -10000 0 -0.15 1 1
Lipoprotein(a) 0.036 0.012 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.022 0.093 -10000 0 -0.15 110 110
IL6 -0.056 0.077 0.41 1 -0.54 9 10
ITGB2 0.018 0.027 0.1 11 -10000 0 11
elevation of cytosolic calcium ion concentration 0.04 0.045 -10000 0 -0.14 2 2
alphaM/beta2 Integrin/JAM2/JAM3 0.005 0.1 -10000 0 -0.14 157 157
JAM2 0.019 0.014 -10000 0 0 193 193
alphaM/beta2 Integrin/ICAM1 0.072 0.055 -10000 0 -0.14 6 6
alphaM/beta2 Integrin/uPA/Plg 0.069 0.061 -10000 0 -0.15 11 11
RhoA/GTP -0.041 0.13 0.19 44 -0.33 40 84
positive regulation of phagocytosis -0.022 0.1 0.2 9 -0.3 17 26
Ron/MSP 0.043 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA 0.075 0.052 -10000 0 -0.14 2 2
alphaM/beta2 Integrin/uPAR 0.05 0.032 0.17 5 -0.15 2 7
PLAU 0.02 0.014 -10000 0 0 182 182
PLAT 0.022 0.013 -10000 0 0 148 148
actin filament polymerization -0.038 0.13 0.21 22 -0.32 34 56
MST1 0.029 0.003 -10000 0 0 6 6
alphaM/beta2 Integrin/lipoprotein(a) 0.056 0.045 -10000 0 -0.13 3 3
TNF -0.051 0.076 0.4 10 -10000 0 10
RAP1B 0.029 0.006 -10000 0 0 23 23
alphaM/beta2 Integrin/uPA 0.034 0.036 0.18 2 -0.15 3 5
fibrinolysis 0.034 0.052 0.18 1 -0.15 11 12
HCK 0.027 0.008 -10000 0 0 46 46
dendritic cell antigen processing and presentation -0.027 0.11 0.17 40 -0.29 36 76
VTN 0.028 0.007 -10000 0 0 32 32
alphaM/beta2 Integrin/CYR61 0.046 0.046 0.17 8 -0.15 18 26
LPA 0.027 0.008 -10000 0 0 45 45
LRP1 0.029 0.006 -10000 0 0 22 22
cell migration -0.01 0.089 0.17 98 -10000 0 98
FN1 0.018 0.015 -10000 0 0 214 214
alphaM/beta2 Integrin/Thy1 0.035 0.036 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 89 89
RAP1/GDP 0.038 0.009 -10000 0 -10000 0 0
ROCK1 -0.04 0.14 0.19 41 -0.32 39 80
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.027 0.009 -10000 0 0 57 57
CTGF 0.022 0.013 -10000 0 0 148 148
alphaM/beta2 Integrin/Hck 0.051 0.034 0.17 10 -0.15 2 12
ITGAM 0.017 0.028 0.1 11 -0.086 1 12
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.057 0.062 -10000 0 -0.16 31 31
HP 0.01 0.014 -10000 0 0 364 364
leukocyte adhesion -0.03 0.1 0.29 4 -0.29 1 5
SELP 0.028 0.007 -10000 0 0 35 35
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.15 0.35 0.67 1 -0.96 83 84
VDR 0.029 0.004 -10000 0 0 8 8
FAM120B 0.027 0.008 -10000 0 0 47 47
RXRs/LXRs/DNA/9cRA 0.028 0.11 0.4 35 -0.33 1 36
RXRs/LXRs/DNA/Oxysterols 0.021 0.13 0.49 35 -0.42 2 37
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 -0.027 0.09 -10000 0 -0.18 133 133
RXRs/NUR77 0.007 0.12 0.3 22 -0.21 6 28
RXRs/PPAR 0.003 0.074 0.22 3 -0.24 10 13
NCOR2 0.029 0.006 -10000 0 0 20 20
VDR/VDR/Vit D3 0.022 0.003 -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 14 14
VDR/VDR/DNA 0.029 0.004 -10000 0 0 8 8
RARs/RARs/DNA/9cRA 0.05 0.028 -10000 0 -10000 0 0
RARG 0.029 0.005 -10000 0 0 17 17
RPS6KB1 -0.074 0.17 0.52 11 -0.42 84 95
RARs/THRs/DNA/SMRT -0.029 0.093 -10000 0 -0.18 136 136
THRA 0.021 0.013 -10000 0 0 157 157
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.022 0.003 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.096 0.12 0.39 42 -10000 0 42
NR1H4 0.029 0.005 -10000 0 0 14 14
RXRs/LXRs/DNA 0.098 0.11 0.44 35 -0.26 1 36
NR1H2 0.033 0.028 0.13 37 -0.074 2 39
NR1H3 0.036 0.028 0.13 39 -0.073 4 43
RXRs/VDR/DNA/Vit D3 0.084 0.074 0.28 40 -10000 0 40
NR4A1 0.017 0.015 -10000 0 0 234 234
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.017 0.067 0.19 38 -0.23 6 44
RXRG 0.029 0.035 0.13 37 -10000 0 37
RXR alpha/CCPG 0.041 0.039 -10000 0 -0.16 12 12
RXRA 0.029 0.036 0.13 39 -10000 0 39
RXRB 0.033 0.035 0.13 38 -10000 0 38
THRB 0.028 0.007 -10000 0 0 32 32
PPARG 0.029 0.005 -10000 0 0 13 13
PPARD 0.029 0.005 -10000 0 0 17 17
TNF 0.015 0.12 0.44 35 -0.43 1 36
mol:Oxysterols 0.006 0.025 0.094 39 -10000 0 39
cholesterol transport 0.021 0.13 0.48 35 -0.42 2 37
PPARA 0.025 0.011 -10000 0 0 96 96
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.029 0.006 -10000 0 0 23 23
RXRs/NUR77/BCL2 -0.076 0.11 0.16 1 -0.2 206 207
SREBF1 0.01 0.13 0.43 32 -0.77 4 36
RXRs/RXRs/DNA/9cRA 0.095 0.11 0.39 42 -10000 0 42
ABCA1 0.025 0.16 0.61 35 -10000 0 35
RARs/THRs 0.034 0.096 -10000 0 -0.14 113 113
RXRs/FXR 0.091 0.08 0.3 40 -10000 0 40
BCL2 0.023 0.012 -10000 0 0 123 123
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.035 0.018 0.16 2 -10000 0 2
SNTA1 0.028 0.008 -10000 0 0 40 40
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.015 0.088 0.17 137 -10000 0 137
MAPK12 0.001 0.053 0.15 57 -0.18 1 58
CCND1 -0.082 0.16 -10000 0 -0.36 136 136
p38 gamma/SNTA1 0.006 0.073 0.17 75 -0.18 1 76
MAP2K3 0.028 0.008 -10000 0 0 43 43
PKN1 0.026 0.01 -10000 0 0 78 78
G2/M transition checkpoint 0.001 0.053 0.15 57 -0.18 1 58
MAP2K6 0.012 0.067 0.19 68 -0.19 1 69
MAPT -0.004 0.049 0.19 5 -0.22 10 15
MAPK13 -0.03 0.017 0.19 2 -10000 0 2
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.003 0.009 -10000 0 -0.21 1 1
Signaling events mediated by PRL

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
CCNE1 0.003 0.009 -10000 0 0 506 506
mol:Halofuginone -0.003 0.012 -10000 0 -0.16 3 3
ITGA1 0.023 0.013 -10000 0 0 132 132
CDKN1A -0.02 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 0.036 0.26 7 -10000 0 7
AGT 0.027 0.009 -10000 0 0 58 58
CCNA2 0.051 0.088 0.3 2 -0.62 3 5
TUBA1B 0.03 0.003 -10000 0 0 4 4
EGR1 -0.014 0.028 -10000 0 -0.37 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 0.023 0.022 -10000 0 -10000 0 0
MAPK1 -0.021 0.02 0.19 2 -10000 0 2
PTP4A1 -0.063 0.067 -10000 0 -0.65 3 3
PTP4A3 0.021 0.014 -10000 0 0 162 162
PTP4A2 0.028 0.006 -10000 0 0 25 25
ITGB1 -0.022 0.024 0.19 4 -10000 0 4
SRC 0.028 0.007 -10000 0 0 33 33
RAC1 -0.017 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 0.085 0.34 3 -0.62 3 6
RABGGTA 0.029 0.006 -10000 0 0 21 21
BCAR1 -0.019 0.036 0.26 7 -10000 0 7
RHOC -0.01 0.065 -10000 0 -0.45 9 9
RHOA -0.014 0.074 -10000 0 -0.43 14 14
cell motility -0.008 0.078 0.28 3 -0.42 10 13
PRL-1/alpha Tubulin -0.059 0.085 0.34 3 -0.62 3 6
PRL-3/alpha1 Integrin 0.022 0.029 -10000 0 -0.16 6 6
ROCK1 -0.009 0.076 0.27 2 -0.42 10 12
RABGGTB 0.016 0.015 -10000 0 0 256 256
CDK2 0.018 0.015 -10000 0 0 226 226
mitosis -0.063 0.067 -10000 0 -0.64 3 3
ATF5 0.029 0.005 -10000 0 0 16 16
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) 0.011 0.13 -10000 0 -0.44 41 41
HDAC1 0.038 0.022 0.097 16 -0.07 1 17
AES 0.027 0.016 0.069 10 -0.038 1 11
FBXW11 0.029 0.005 -10000 0 0 16 16
DTX1 0.029 0.004 -10000 0 0 8 8
LRP6/FZD1 0.037 0.016 -10000 0 -10000 0 0
TLE1 0.03 0.013 0.067 7 -0.03 11 18
AP1 -0.008 0.073 0.2 7 -0.2 56 63
NCSTN 0.023 0.018 -10000 0 -0.022 76 76
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 -0.7 47 47
NICD/RBPSUH 0.005 0.13 -10000 0 -0.44 40 40
WIF1 0.021 0.02 -10000 0 -0.029 69 69
NOTCH1 -0.009 0.12 -10000 0 -0.47 37 37
PSENEN 0.021 0.018 -10000 0 -0.011 119 119
KREMEN2 0.029 0.006 -10000 0 0 23 23
DKK1 0.029 0.006 -10000 0 0 21 21
beta catenin/beta TrCP1 -0.003 0.066 -10000 0 -0.28 2 2
APH1B 0.019 0.02 -10000 0 -0.014 131 131
APH1A 0.022 0.019 -10000 0 -0.019 86 86
AXIN1 -0.011 0.099 -10000 0 -0.44 20 20
CtBP/CBP/TCF1/TLE1/AES 0.013 0.1 0.25 22 -0.28 12 34
PSEN1 0.022 0.02 -10000 0 -0.025 82 82
FOS 0.024 0.012 -10000 0 0 104 104
JUN 0.028 0.007 -10000 0 0 32 32
MAP3K7 0.033 0.012 -10000 0 -0.045 1 1
CTNNB1 -0.012 0.058 -10000 0 -0.29 2 2
MAPK3 0.029 0.006 -10000 0 0 22 22
DKK2/LRP6/Kremen 2 0.048 0.024 -10000 0 -10000 0 0
HNF1A 0.034 0.01 0.07 12 -0.038 1 13
CTBP1 0.032 0.012 0.069 11 -10000 0 11
MYC -0.16 0.36 -10000 0 -1.2 59 59
NKD1 0.029 0.008 -10000 0 -10000 0 0
FZD1 0.021 0.02 -10000 0 -0.029 70 70
NOTCH1 precursor/Deltex homolog 1 0.005 0.13 -10000 0 -0.44 41 41
apoptosis -0.008 0.072 0.2 7 -0.2 56 63
Delta 1/NOTCHprecursor 0.004 0.13 -10000 0 -0.44 40 40
DLL1 0.027 0.008 -10000 0 0 47 47
PPARD -0.019 0.099 -10000 0 -1 4 4
Gamma Secretase 0.042 0.078 -10000 0 -0.14 65 65
APC -0.018 0.12 -10000 0 -0.44 30 30
DVL1 -0.005 0.057 -10000 0 -0.25 22 22
CSNK2A1 0.009 0.028 -10000 0 -0.032 170 170
MAP3K7IP1 0.005 0.008 0.022 27 -10000 0 27
DKK1/LRP6/Kremen 2 0.048 0.024 -10000 0 -10000 0 0
LRP6 0.02 0.019 -10000 0 -0.029 50 50
CSNK1A1 0.009 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 -1.2 147 147
WNT1 0.022 0.02 -10000 0 -0.029 75 75
Axin1/APC/beta catenin -0.024 0.099 -10000 0 -0.43 15 15
DKK2 0.028 0.008 -10000 0 0 40 40
NOTCH1 precursor/DVL1 -0.009 0.13 -10000 0 -0.46 36 36
GSK3B 0.03 0.006 -10000 0 -0.03 1 1
FRAT1 0.031 0.007 -10000 0 -0.036 1 1
NOTCH/Deltex homolog 1 0.014 0.13 -10000 0 -0.44 41 41
PPP2R5D 0.012 0.045 -10000 0 -0.37 5 5
MAPK1 0.028 0.008 -10000 0 0 42 42
WNT1/LRP6/FZD1 0.063 0.033 -10000 0 -10000 0 0
RBPJ 0.029 0.005 -10000 0 0 18 18
CREBBP 0.012 0.024 -10000 0 -0.026 128 128
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.043 0.009 -10000 0 -10000 0 0
Necdin/E2F1 -0.059 0.099 -10000 0 -0.16 263 263
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.061 0.032 -10000 0 -0.13 2 2
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 0.028 0.008 -10000 0 0 39 39
AKT1 0.006 0.1 0.17 137 -10000 0 137
IKBKG 0.028 0.007 -10000 0 0 33 33
BDNF 0.029 0.005 -10000 0 0 13 13
MGDIs/NGR/p75(NTR)/LINGO1 0.053 0.02 -10000 0 -10000 0 0
FURIN 0.028 0.006 -10000 0 0 27 27
proBDNF (dimer)/p75(NTR)/Sortilin 0.057 0.015 -10000 0 -10000 0 0
LINGO1 0.029 0.006 -10000 0 0 24 24
Sortilin/TRAF6/NRIF -0.071 0.042 -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 13 13
RTN4R 0.027 0.008 -10000 0 0 47 47
neuron apoptosis -0.034 0.13 0.29 3 -0.44 30 33
IRAK1 0.028 0.007 -10000 0 0 31 31
SHC1 -0.025 0.01 0.17 1 -10000 0 1
ARHGDIA 0.025 0.011 -10000 0 0 95 95
RhoA/GTP 0.022 0.008 -10000 0 -0.15 1 1
Gamma Secretase 0.044 0.078 -10000 0 -0.14 65 65
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.048 0.036 -10000 0 -0.13 17 17
MAGEH1 0.028 0.006 -10000 0 0 26 26
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.041 0.09 -10000 0 -0.13 275 275
Mammalian IAPs/DIABLO 0.012 0.051 -10000 0 -0.13 46 46
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.029 0.006 -10000 0 0 21 21
APP 0.028 0.006 -10000 0 0 27 27
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.028 0.007 -10000 0 0 32 32
RhoA/GDP/RHOGDI 0.013 0.054 0.16 2 -0.12 73 75
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 0.049 -10000 0 -0.21 1 1
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.038 0.009 -10000 0 -10000 0 0
NCSTN 0.029 0.005 -10000 0 0 19 19
mol:GTP 0.037 0.01 -10000 0 -10000 0 0
PSENEN 0.026 0.01 -10000 0 0 74 74
mol:ceramide -0.027 0.035 0.18 14 -10000 0 14
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.021 0.049 -10000 0 -0.23 5 5
p75(NTR)/beta APP 0.039 0.025 -10000 0 -0.16 7 7
BEX1 0.019 0.014 -10000 0 0 210 210
mol:GDP -0.013 0.002 -10000 0 -10000 0 0
NGF (dimer) -0.019 0.087 -10000 0 -0.13 200 200
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.037 0.076 -10000 0 -0.14 72 72
PIK3R1 0.021 0.013 -10000 0 0 159 159
RAC1/GTP 0.032 0.012 -10000 0 -10000 0 0
MYD88 0.03 0.003 -10000 0 0 5 5
CHUK 0.028 0.007 -10000 0 0 35 35
NGF (dimer)/p75(NTR)/PKA 0.038 0.01 -10000 0 -10000 0 0
RHOB 0.029 0.006 -10000 0 0 22 22
RHOA 0.029 0.003 -10000 0 0 7 7
MAGE-G1/E2F1 0.038 0.017 -10000 0 -0.16 1 1
NT3 (dimer) 0.024 0.012 -10000 0 0 116 116
TP53 -0.058 0.057 0.31 3 -10000 0 3
PRDM4 -0.03 0.032 0.18 12 -10000 0 12
BDNF (dimer) -0.006 0.1 -10000 0 -0.14 192 192
PIK3CA 0.021 0.014 -10000 0 0 174 174
SORT1 0.029 0.004 -10000 0 0 11 11
activation of caspase activity 0.054 0.03 -10000 0 -0.13 2 2
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.053 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 0.061 0.24 7 -0.24 7 14
DIABLO 0.02 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 69 69
APH1A 0.028 0.007 -10000 0 0 30 30
proNGF (dimer)/p75(NTR)/Sortilin 0.038 0.009 -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) 0.034 0.019 -10000 0 -10000 0 0
MAPK8 -0.04 0.057 0.24 7 -0.24 6 13
MAPK9 -0.041 0.056 0.23 6 -0.24 5 11
APAF1 0.028 0.007 -10000 0 0 28 28
NTF3 0.024 0.012 -10000 0 0 116 116
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 0.057 0.034 -10000 0 -0.13 8 8
p75 CTF/Sortilin/TRAF6/NRIF 0.075 0.04 -10000 0 -10000 0 0
RhoA-B-C/GTP 0.037 0.01 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.076 0.038 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.071 0.025 -10000 0 -10000 0 0
PRKACB 0.029 0.006 -10000 0 0 21 21
proBDNF (dimer)/p75 ECD 0.035 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 0 121 121
BIRC2 0.021 0.013 -10000 0 0 159 159
neuron projection morphogenesis -0.036 0.063 0.18 11 -0.21 9 20
BAD -0.045 0.061 0.22 6 -0.28 6 12
RIPK2 0.019 0.014 -10000 0 0 199 199
NGFR 0.029 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 0 107 107
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.034 0.03 -10000 0 -10000 0 0
BCL2L11 -0.045 0.062 0.22 6 -0.28 7 13
BDNF (dimer)/p75(NTR) 0.042 0.01 -10000 0 -10000 0 0
PI3K 0.008 0.062 -10000 0 -0.13 76 76
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.049 0.026 -10000 0 -0.13 1 1
NDNL2 0.028 0.008 -10000 0 0 41 41
YWHAE 0.028 0.008 -10000 0 0 41 41
PRKCI 0.014 0.015 -10000 0 0 287 287
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 0.051 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 26 26
PRKCZ 0.029 0.006 -10000 0 0 22 22
PLG 0.027 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 0.029 0.005 -10000 0 0 19 19
NGFRAP1 0.03 0.002 -10000 0 0 3 3
CASP3 -0.046 0.067 0.22 6 -0.3 13 19
E2F1 0.028 0.008 -10000 0 0 42 42
CASP9 0.029 0.005 -10000 0 0 13 13
IKK complex 0.064 0.063 -10000 0 -0.24 3 3
NGF (dimer)/TRKA 0.022 0.003 -10000 0 -10000 0 0
MMP7 0.017 0.015 -10000 0 0 234 234
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.062 0.029 -10000 0 -10000 0 0
MMP3 0.028 0.007 -10000 0 0 35 35
APAF-1/Caspase 9 -0.042 0.048 -10000 0 -10000 0 0
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 37 37
SMAD2 -0.001 0.046 0.18 1 -0.23 2 3
SMAD3 -0.013 0.048 -10000 0 -0.23 6 6
SMAD3/SMAD4 0.059 0.085 -10000 0 -0.48 10 10
SMAD4/Ubc9/PIASy 0.051 0.022 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.088 0.058 -10000 0 -0.22 1 1
PPM1A 0.029 0.005 -10000 0 0 14 14
CALM1 0.028 0.006 -10000 0 0 25 25
SMAD2/SMAD4 0.013 0.046 -10000 0 -0.22 2 2
MAP3K1 0.027 0.009 -10000 0 0 52 52
TRAP-1/SMAD4 0.041 0.012 -10000 0 -10000 0 0
MAPK3 0.029 0.006 -10000 0 0 22 22
MAPK1 0.028 0.008 -10000 0 0 42 42
NUP214 0.029 0.005 -10000 0 0 18 18
CTDSP1 0.029 0.004 -10000 0 0 12 12
CTDSP2 0.029 0.005 -10000 0 0 19 19
CTDSPL 0.029 0.003 -10000 0 0 6 6
KPNB1 0.029 0.006 -10000 0 0 20 20
TGFBRAP1 0.029 0.004 -10000 0 0 10 10
UBE2I 0.029 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 -0.058 0.077 -10000 0 -0.42 9 9
SMARCC2 0.029 0.006 -10000 0 0 22 22
SMARCC1 0.029 0.004 -10000 0 0 8 8
TBX21 0.04 0.079 0.32 5 -10000 0 5
SUMO2 0.006 0.032 -10000 0 -0.037 192 192
STAT1 (dimer) 0.017 0.05 0.29 13 -0.18 7 20
FKBP4 0.026 0.01 -10000 0 0 68 68
FKBP5 0.027 0.009 -10000 0 0 59 59
GR alpha/HSP90/FKBP51/HSP90 -0.039 0.094 -10000 0 -0.24 16 16
PRL 0.044 0.062 0.69 1 -10000 0 1
cortisol/GR alpha (dimer)/TIF2 -0.095 0.15 -10000 0 -0.42 26 26
RELA 0.008 0.094 0.18 112 -0.19 6 118
FGG -0.13 0.12 -10000 0 -0.42 22 22
GR beta/TIF2 -0.077 0.062 -10000 0 -0.27 3 3
IFNG 0.11 0.17 0.53 45 -10000 0 45
apoptosis -0.18 0.21 0.47 2 -0.6 31 33
CREB1 0.03 0.004 -10000 0 -10000 0 0
histone acetylation 0.042 0.065 0.29 1 -10000 0 1
BGLAP 0.056 0.067 0.65 1 -10000 0 1
GR/PKAc -0.016 0.09 -10000 0 -0.21 2 2
NF kappa B1 p50/RelA 0.08 0.13 0.32 97 -0.3 14 111
SMARCD1 0.03 0.002 -10000 0 0 3 3
MDM2 -0.036 0.04 -10000 0 -0.17 3 3
GATA3 0.028 0.007 -10000 0 -10000 0 0
AKT1 0.029 0.006 -10000 0 -10000 0 0
CSF2 0.012 0.042 -10000 0 -10000 0 0
GSK3B 0.006 0.032 -10000 0 -0.037 187 187
NR1I3 -0.16 0.18 -10000 0 -0.63 10 10
CSN2 -0.12 0.11 -10000 0 -0.38 25 25
BRG1/BAF155/BAF170/BAF60A 0.064 0.032 -10000 0 -0.14 1 1
NFATC1 0.027 0.009 -10000 0 -10000 0 0
POU2F1 0.029 0.008 0.2 1 -10000 0 1
CDKN1A -0.059 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 0.037 2 -10000 0 2
SFN 0.028 0.007 -10000 0 0 37 37
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.023 0.1 -10000 0 -0.23 13 13
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.3 0.34 0.57 2 -0.72 208 210
JUN 0.088 0.17 0.5 42 -10000 0 42
IL4 0.051 0.057 -10000 0 -10000 0 0
CDK5R1 0.006 0.03 -10000 0 -0.035 189 189
PRKACA 0.026 0.01 -10000 0 0 78 78
cortisol/GR alpha (monomer)/AP-1 -0.073 0.076 -10000 0 -0.26 15 15
GR alpha/HSP90/FKBP51/HSP90/PP5C -0.028 0.1 -10000 0 -0.23 15 15
cortisol/GR alpha (monomer) -0.15 0.14 -10000 0 -0.48 23 23
NCOA2 0.027 0.008 -10000 0 0 47 47
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.035 0.092 0.18 114 -0.3 1 115
AP-1/NFAT1-c-4 0.097 0.2 0.6 33 -10000 0 33
AFP 0.059 0.12 0.56 3 -10000 0 3
SUV420H1 0.029 0.003 -10000 0 0 7 7
IRF1 -0.006 0.15 0.52 8 -0.72 9 17
TP53 0.007 0.092 -10000 0 -0.52 16 16
PPP5C 0.028 0.006 -10000 0 0 26 26
KRT17 0.098 0.18 0.67 25 -10000 0 25
KRT14 0.066 0.12 0.65 14 -10000 0 14
TBP 0.028 0.011 0.19 1 -10000 0 1
CREBBP 0.022 0.038 -10000 0 -0.22 13 13
HDAC1 0.027 0.009 -10000 0 -10000 0 0
HDAC2 0.028 0.008 -10000 0 -10000 0 0
AP-1 0.097 0.2 0.6 33 -10000 0 33
MAPK14 0.005 0.032 -10000 0 -0.038 187 187
MAPK10 0.005 0.032 -10000 0 -0.038 179 179
MAPK11 0.004 0.029 -10000 0 -0.038 157 157
KRT5 0.16 0.25 0.64 103 -10000 0 103
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
NCOA1 0.024 0.017 -10000 0 -10000 0 0
STAT1 0.017 0.05 0.29 13 -0.18 7 20
CGA 0.055 0.059 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.065 0.1 -10000 0 -0.4 21 21
MAPK3 0.005 0.032 -10000 0 -0.038 184 184
MAPK1 0.005 0.032 -10000 0 -0.038 182 182
ICAM1 0.1 0.22 0.62 65 -0.73 7 72
NFKB1 0.009 0.093 0.18 112 -0.18 14 126
MAPK8 0.076 0.14 0.42 33 -10000 0 33
MAPK9 0.005 0.033 -10000 0 -0.038 189 189
cortisol/GR alpha (dimer) -0.18 0.22 0.48 2 -0.64 31 33
BAX -0.039 0.11 -10000 0 -10000 0 0
POMC 0.003 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 27 27
proteasomal ubiquitin-dependent protein catabolic process -0.035 0.052 0.22 13 -0.2 1 14
SGK1 -0.034 0.088 -10000 0 -0.29 33 33
IL13 0.078 0.12 0.5 8 -10000 0 8
IL6 0.064 0.18 0.51 24 -0.83 9 33
PRKACG 0.029 0.005 -10000 0 0 18 18
IL5 0.064 0.12 0.48 2 -10000 0 2
IL2 0.086 0.16 0.48 29 -0.46 2 31
CDK5 0.007 0.028 -10000 0 -0.034 157 157
PRKACB 0.029 0.006 -10000 0 0 21 21
HSP90AA1 0.029 0.006 -10000 0 0 21 21
IL8 0.1 0.2 0.62 57 -10000 0 57
CDK5R1/CDK5 0.012 0.038 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.092 0.12 0.4 22 -0.24 12 34
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.065 0.15 -10000 0 -0.4 24 24
SMARCA4 0.027 0.009 -10000 0 0 61 61
chromatin remodeling -0.072 0.081 -10000 0 -0.31 7 7
NF kappa B1 p50/RelA/Cbp 0.077 0.13 0.42 19 -0.26 12 31
JUN (dimer) 0.088 0.17 0.5 42 -10000 0 42
YWHAH 0.028 0.008 -10000 0 0 42 42
VIPR1 0.04 0.082 0.4 4 -10000 0 4
NR3C1 -0.1 0.083 -10000 0 -0.38 3 3
NR4A1 0.017 0.015 -10000 0 -10000 0 0
TIF2/SUV420H1 0.04 0.013 -10000 0 -10000 0 0
MAPKKK cascade -0.18 0.21 0.47 2 -0.6 31 33
cortisol/GR alpha (dimer)/Src-1 -0.098 0.15 -10000 0 -0.42 26 26
PBX1 0.028 0.01 0.2 1 -10000 0 1
POU1F1 0.029 0.008 0.2 1 -10000 0 1
SELE 0.075 0.12 0.41 18 -10000 0 18
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.072 0.081 -10000 0 -0.31 7 7
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.065 0.15 -10000 0 -0.4 24 24
mol:cortisol -0.078 0.074 -10000 0 -0.28 3 3
MMP1 0.14 0.25 0.62 110 -0.51 5 115
Paxillin-dependent events mediated by a4b1

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
CRKL 0.027 0.008 -10000 0 0 46 46
Rac1/GDP 0.022 0.028 -10000 0 -0.037 1 1
DOCK1 0.029 0.005 -10000 0 0 18 18
ITGA4 0.028 0.008 -10000 0 0 40 40
RAC1 0.028 0.006 -10000 0 0 26 26
alpha4/beta7 Integrin 0.04 0.015 -10000 0 -0.16 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.028 0.007 -10000 0 0 36 36
alpha4/beta1 Integrin 0.047 0.025 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin -0.038 0.022 -10000 0 -0.14 6 6
lamellipodium assembly -0.066 0.15 -10000 0 -0.34 100 100
PIK3CA 0.021 0.014 -10000 0 0 174 174
PI3K -0.001 0.068 -10000 0 -0.16 77 77
ARF6 0.029 0.004 -10000 0 0 11 11
TLN1 0.029 0.005 -10000 0 0 15 15
PXN -0.028 0.012 -10000 0 -10000 0 0
PIK3R1 0.021 0.013 -10000 0 0 159 159
ARF6/GTP -0.025 0.07 0.14 62 -10000 0 62
cell adhesion 0.061 0.048 -10000 0 -0.16 5 5
CRKL/CBL 0.04 0.013 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.037 0.022 -10000 0 -0.14 5 5
ITGB1 0.029 0.006 -10000 0 0 20 20
ITGB7 0.029 0.004 -10000 0 0 8 8
ARF6/GDP 0.022 0.028 -10000 0 -0.034 64 64
alpha4/beta1 Integrin/Paxillin/VCAM1 0.047 0.078 -10000 0 -0.14 58 58
p130Cas/Crk/Dock1 0.05 0.025 -10000 0 -0.15 2 2
VCAM1 0.021 0.013 -10000 0 0 160 160
alpha4/beta1 Integrin/Paxillin/Talin 0.064 0.049 -10000 0 -0.16 5 5
alpha4/beta1 Integrin/Paxillin/GIT1 0.062 0.05 -10000 0 -0.14 5 5
BCAR1 0.027 0.009 -10000 0 0 56 56
mol:GDP -0.059 0.048 0.14 5 -10000 0 5
CBL 0.029 0.004 -10000 0 0 12 12
PRKACA 0.026 0.01 -10000 0 0 78 78
GIT1 0.028 0.007 -10000 0 0 30 30
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.064 0.049 -10000 0 -0.16 5 5
Rac1/GTP -0.074 0.17 -10000 0 -0.38 100 100
Regulation of nuclear SMAD2/3 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
EP300 0.033 0.019 0.078 58 -10000 0 58
HSPA8 0.02 0.024 -10000 0 -0.041 68 68
SMAD3/SMAD4/ER alpha -0.049 0.087 0.24 11 -0.29 2 13
AKT1 0.026 0.013 -10000 0 -0.038 16 16
GSC 0 0.059 -10000 0 -10000 0 0
NKX2-5 -0.004 0.007 -10000 0 -0.041 20 20
muscle cell differentiation -0.028 0.11 0.33 8 -0.29 4 12
SMAD2-3/SMAD4/SP1 0.063 0.13 0.37 10 -10000 0 10
SMAD4 -0.007 0.079 0.2 19 -10000 0 19
CBFB 0.027 0.009 -10000 0 0 60 60
SAP18 0.021 0.021 -10000 0 -0.032 67 67
Cbp/p300/MSG1 0.057 0.043 -10000 0 -0.14 7 7
SMAD3/SMAD4/VDR 0.062 0.1 0.3 10 -10000 0 10
MYC 0.018 0.015 -10000 0 -10000 0 0
CDKN2B -0.057 0.12 -10000 0 -0.6 6 6
AP1 -0.024 0.089 0.24 4 -10000 0 4
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.02 0.11 0.21 8 -0.39 23 31
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.021 0.074 -10000 0 -0.32 14 14
SP3 -0.023 0.037 0.17 20 -10000 0 20
CREB1 0.029 0.004 -10000 0 0 8 8
FOXH1 -0.023 0.016 -10000 0 -10000 0 0
SMAD3/SMAD4/GR -0.03 0.099 0.23 22 -0.26 1 23
GATA3 -0.033 0.008 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 -0.011 0.092 0.18 4 -0.37 21 25
MEF2C/TIF2 0.003 0.11 0.19 49 -0.28 12 61
endothelial cell migration -0.098 0.21 0.56 3 -0.64 68 71
MAX 0.009 0.055 -10000 0 -0.14 68 68
RBBP7 0.022 0.02 -10000 0 -0.032 65 65
RBBP4 0.02 0.021 -10000 0 -0.032 66 66
RUNX2 0.028 0.007 -10000 0 0 29 29
RUNX3 0.029 0.005 -10000 0 0 13 13
RUNX1 0.029 0.005 -10000 0 0 16 16
CTBP1 0.028 0.008 -10000 0 0 43 43
NR3C1 0.009 0.055 -10000 0 -0.14 68 68
VDR 0.029 0.004 -10000 0 0 8 8
CDKN1A 0.005 0.22 0.44 1 -0.99 20 21
KAT2B 0.002 0.005 0.018 8 -10000 0 8
SMAD2/SMAD2/SMAD4/FOXH1 0.02 0.063 -10000 0 -10000 0 0
DCP1A 0.029 0.005 -10000 0 0 14 14
SKI 0.021 0.02 -10000 0 -0.032 66 66
SERPINE1 0.098 0.21 0.64 68 -0.57 3 71
SMAD3/SMAD4/ATF2 -0.011 0.09 0.23 30 -10000 0 30
SMAD3/SMAD4/ATF3 -0.012 0.089 0.23 29 -0.26 1 30
SAP30 0.02 0.021 -10000 0 -0.032 66 66
Cbp/p300/PIAS3 0.06 0.054 0.18 63 -0.15 6 69
JUN -0.023 0.09 0.26 7 -10000 0 7
SMAD3/SMAD4/IRF7 -0.013 0.094 0.24 32 -10000 0 32
TFE3 0 0.067 0.14 96 -10000 0 96
COL1A2 0.13 0.25 0.51 156 -0.6 7 163
mesenchymal cell differentiation 0.01 0.089 -10000 0 -0.23 30 30
DLX1 0.029 0.005 -10000 0 0 13 13
TCF3 0.027 0.009 -10000 0 0 51 51
FOS -0.008 0.041 0.16 7 -10000 0 7
SMAD3/SMAD4/Max -0.029 0.097 0.23 24 -0.26 1 25
Cbp/p300/SNIP1 0.05 0.037 -10000 0 -0.14 8 8
ZBTB17 0.029 0.005 -10000 0 -10000 0 0
LAMC1 -0.014 0.081 0.28 8 -10000 0 8
TGIF2/HDAC complex/SMAD3/SMAD4 -0.01 0.089 0.23 31 -10000 0 31
IRF7 -0.03 0.007 -10000 0 -10000 0 0
ESR1 -0.03 0.027 0.058 14 -0.078 11 25
HNF4A 0.028 0.008 -10000 0 0 39 39
MEF2C 0.012 0.11 0.2 46 -0.28 12 58
SMAD2-3/SMAD4 -0.014 0.092 0.25 19 -10000 0 19
Cbp/p300/Src-1 0.056 0.043 -10000 0 -0.14 10 10
IGHV3OR16-13 -0.006 0.033 -10000 0 -0.42 3 3
TGIF2/HDAC complex 0.028 0.007 -10000 0 0 37 37
CREBBP 0.031 0.014 0.069 8 -10000 0 8
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 0.012 0.038 68 -10000 0 68
SMAD3/SMAD4/TFE3 0.001 0.1 0.26 22 -10000 0 22
MSG1/HSC70 0.03 0.03 -10000 0 -10000 0 0
SMAD2 -0.031 0.011 -10000 0 -10000 0 0
SMAD3 -0.006 0.078 0.2 19 -10000 0 19
SMAD3/E2F4-5/DP1/p107/SMAD4 0.01 0.076 0.23 15 -0.24 4 19
SMAD2/SMAD2/SMAD4 -0.005 0.062 0.17 3 -0.19 24 27
NCOR1 0.021 0.021 -10000 0 -0.032 65 65
NCOA2 0.027 0.008 -10000 0 0 47 47
NCOA1 0.029 0.005 -10000 0 0 14 14
MYOD/E2A 0.04 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.092 0.13 0.36 16 -10000 0 16
IFNB1 -0.021 0.082 0.23 12 -10000 0 12
SMAD3/SMAD4/MEF2C 0.02 0.13 0.28 21 -0.3 11 32
CITED1 0.025 0.014 -10000 0 -0.029 32 32
SMAD2-3/SMAD4/ARC105 0.042 0.093 0.29 2 -10000 0 2
RBL1 0.026 0.01 -10000 0 0 73 73
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.019 0.077 -10000 0 -0.4 6 6
RUNX1-3/PEBPB2 0.052 0.021 -10000 0 -10000 0 0
SMAD7 0.016 0.16 0.41 29 -0.39 4 33
MYC/MIZ-1 0.012 0.056 -10000 0 -0.16 45 45
SMAD3/SMAD4 0.052 0.13 0.34 57 -0.44 3 60
IL10 -0.016 0.093 0.28 7 -10000 0 7
PIASy/HDAC complex 0.016 0.031 -10000 0 -0.067 64 64
PIAS3 0.03 0.009 -10000 0 -10000 0 0
CDK2 0.02 0.018 0.071 1 -10000 0 1
IL5 -0.014 0.094 0.29 8 -10000 0 8
CDK4 0.033 0.014 0.072 29 -10000 0 29
PIAS4 0.016 0.031 -10000 0 -0.066 64 64
ATF3 0.029 0.006 -10000 0 0 24 24
SMAD3/SMAD4/SP1 0.018 0.13 0.26 29 -0.29 3 32
FOXG1 0.029 0.007 -10000 0 -10000 0 0
FOXO3 -0.031 0.011 -10000 0 -10000 0 0
FOXO1 -0.031 0.012 -10000 0 -0.18 1 1
FOXO4 -0.032 0.008 -10000 0 -10000 0 0
heart looping 0.012 0.1 0.19 46 -0.28 12 58
CEBPB 0.027 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.011 0.091 0.23 31 -10000 0 31
MYOD1 0.029 0.004 -10000 0 0 8 8
SMAD3/SMAD4/HNF4 -0.01 0.089 0.23 31 -10000 0 31
SMAD3/SMAD4/GATA3 -0.011 0.096 0.24 35 -10000 0 35
SnoN/SIN3/HDAC complex/NCoR1 0.01 0.014 -10000 0 0 361 361
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.058 0.093 0.3 4 -10000 0 4
SMAD3/SMAD4/SP1-3 0.072 0.13 0.34 16 -0.26 4 20
MED15 0.027 0.008 -10000 0 0 46 46
SP1 0.022 0.087 0.14 188 -0.17 3 191
SIN3B 0.019 0.021 -10000 0 -0.032 65 65
SIN3A 0.021 0.021 -10000 0 -0.032 68 68
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.022 0.063 -10000 0 -0.2 6 6
ITGB5 0.004 0.12 0.3 22 -10000 0 22
TGIF/SIN3/HDAC complex/CtBP -0.005 0.082 0.24 1 -0.34 18 19
SMAD3/SMAD4/AR -0.085 0.099 0.23 13 -0.27 7 20
AR 0.012 0.015 -10000 0 0 328 328
negative regulation of cell growth 0.007 0.093 0.25 13 -0.3 15 28
SMAD3/SMAD4/MYOD -0.011 0.091 0.23 30 -10000 0 30
E2F5 0.026 0.01 -10000 0 0 79 79
E2F4 0.027 0.009 -10000 0 0 58 58
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.043 0.072 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 -0.016 0.063 -10000 0 -0.32 4 4
TFDP1 0.028 0.007 -10000 0 0 37 37
SMAD3/SMAD4/AP1 0.011 0.096 0.26 1 -0.25 1 2
SMAD3/SMAD4/RUNX2 -0.01 0.09 0.23 30 -10000 0 30
TGIF2 0.028 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
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.037 0.09 -10000 0 -0.15 72 72
SMAD6-7/SMURF1 0.054 0.019 -10000 0 -10000 0 0
NOG 0.029 0.005 -10000 0 0 18 18
SMAD9 -0.019 0.14 -10000 0 -0.48 42 42
SMAD4 0.028 0.007 -10000 0 0 37 37
SMAD5 -0.023 0.084 0.2 3 -0.34 18 21
BMP7/USAG1 0.014 0.052 -10000 0 -0.17 36 36
SMAD5/SKI -0.012 0.093 0.2 2 -0.33 21 23
SMAD1 -0.022 0.09 -10000 0 -0.42 16 16
BMP2 0.028 0.007 -10000 0 0 35 35
SMAD1/SMAD1/SMAD4 -0.053 0.079 -10000 0 -0.37 16 16
BMPR1A 0.029 0.006 -10000 0 0 21 21
BMPR1B 0.025 0.011 -10000 0 0 92 92
BMPR1A-1B/BAMBI 0.031 0.059 -10000 0 -0.15 48 48
AHSG 0.025 0.011 -10000 0 0 88 88
CER1 0.028 0.008 -10000 0 0 39 39
BMP2-4/CER1 0.052 0.022 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.035 0.1 -10000 0 -0.32 35 35
BMP2-4 (homodimer) 0.04 0.013 -10000 0 -10000 0 0
RGMB 0.028 0.007 -10000 0 0 36 36
BMP6/BMPR2/BMPR1A-1B 0.043 0.066 -10000 0 -0.14 45 45
RGMA 0.028 0.007 -10000 0 0 31 31
SMURF1 0.029 0.006 -10000 0 0 20 20
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.019 0.07 -10000 0 -0.26 21 21
BMP2-4/USAG1 0.041 0.03 -10000 0 -0.15 2 2
SMAD6/SMURF1/SMAD5 -0.012 0.092 0.2 2 -0.33 21 23
SOSTDC1 0.023 0.013 -10000 0 0 136 136
BMP7/BMPR2/BMPR1A-1B 0.031 0.084 -10000 0 -0.15 75 75
SKI 0.029 0.006 -10000 0 0 22 22
BMP6 (homodimer) 0.027 0.008 -10000 0 0 46 46
HFE2 0.028 0.007 -10000 0 0 33 33
ZFYVE16 0.027 0.009 -10000 0 0 57 57
MAP3K7 0.028 0.007 -10000 0 0 30 30
BMP2-4/CHRD 0.046 0.026 -10000 0 -10000 0 0
SMAD5/SMAD5/SMAD4 -0.011 0.093 0.2 3 -0.32 22 25
MAPK1 0.028 0.008 -10000 0 0 42 42
TAK1/TAB family 0 0.081 -10000 0 -0.26 19 19
BMP7 (homodimer) 0.023 0.013 -10000 0 0 133 133
NUP214 0.029 0.005 -10000 0 0 18 18
BMP6/FETUA 0.035 0.018 -10000 0 -10000 0 0
SMAD1/SKI -0.008 0.093 -10000 0 -0.41 16 16
SMAD6 0.029 0.005 -10000 0 0 17 17
CTDSP2 0.029 0.005 -10000 0 0 19 19
BMP2-4/FETUA 0.046 0.026 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.027 0.009 -10000 0 0 60 60
BMPR2 (homodimer) 0.029 0.004 -10000 0 0 8 8
GADD34/PP1CA 0.037 0.057 -10000 0 -0.14 44 44
BMPR1A-1B (homodimer) 0.02 0.06 -10000 0 -0.16 52 52
CHRDL1 0.016 0.015 -10000 0 0 262 262
ENDOFIN/SMAD1 -0.007 0.091 -10000 0 -0.42 15 15
SMAD6-7/SMURF1/SMAD1 0.013 0.1 -10000 0 -0.39 16 16
SMAD6/SMURF1 0.029 0.006 -10000 0 0 20 20
BAMBI 0.027 0.009 -10000 0 0 61 61
SMURF2 0.029 0.005 -10000 0 0 14 14
BMP2-4/CHRDL1 -0.033 0.099 -10000 0 -0.15 235 235
BMP2-4/GREM1 0.049 0.024 -10000 0 -10000 0 0
SMAD7 0.028 0.007 -10000 0 0 28 28
SMAD8A/SMAD8A/SMAD4 -0.01 0.14 -10000 0 -0.46 46 46
SMAD1/SMAD6 -0.008 0.091 -10000 0 -0.4 16 16
TAK1/SMAD6 0.041 0.012 -10000 0 -10000 0 0
BMP7 0.023 0.013 -10000 0 0 133 133
BMP6 0.027 0.008 -10000 0 0 46 46
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.017 0.077 0.16 1 -0.3 19 20
PPM1A 0.029 0.005 -10000 0 0 14 14
SMAD1/SMURF2 -0.008 0.093 -10000 0 -0.41 16 16
SMAD7/SMURF1 0.041 0.012 -10000 0 -10000 0 0
CTDSPL 0.029 0.003 -10000 0 0 6 6
PPP1CA 0.029 0.004 -10000 0 0 8 8
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 66 66
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.015 0.084 0.15 2 -0.28 29 31
CHRD 0.025 0.011 -10000 0 0 91 91
BMPR2 0.029 0.004 -10000 0 0 8 8
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.016 0.075 0.18 1 -0.26 21 22
BMP4 0.029 0.006 -10000 0 0 22 22
FST 0.025 0.011 -10000 0 0 91 91
BMP2-4/NOG 0.053 0.022 -10000 0 -0.15 1 1
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.039 0.088 -10000 0 -0.15 73 73
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.019 0.12 0.23 16 -0.33 21 37
ERC1 0.026 0.01 -10000 0 0 67 67
RIP2/NOD2 0.027 0.022 -10000 0 -10000 0 0
NFKBIA -0.054 0.043 -10000 0 -0.32 12 12
BIRC2 0.021 0.013 -10000 0 0 159 159
IKBKB 0.028 0.008 -10000 0 0 39 39
RIPK2 0.019 0.014 -10000 0 0 199 199
IKBKG 0.026 0.1 -10000 0 -0.39 20 20
IKK complex/A20 0.047 0.13 0.24 9 -0.39 27 36
NEMO/A20/RIP2 0.019 0.014 -10000 0 0 199 199
XPO1 0.027 0.009 -10000 0 0 52 52
NEMO/ATM 0.036 0.13 0.23 11 -0.37 33 44
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 0.036 0.013 -10000 0 -10000 0 0
IKK complex/ELKS 0.036 0.12 -10000 0 -0.35 31 31
BCL10/MALT1/TRAF6 0.051 0.023 -10000 0 -10000 0 0
NOD2 0.028 0.007 -10000 0 0 37 37
NFKB1 -0.029 0.012 -10000 0 -10000 0 0
RELA -0.032 0.009 -10000 0 -10000 0 0
MALT1 0.026 0.01 -10000 0 0 76 76
cIAP1/UbcH5C 0.03 0.021 -10000 0 -10000 0 0
ATM 0.028 0.007 -10000 0 0 33 33
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 25 25
CHUK 0.028 0.007 -10000 0 0 35 35
UBE2D3 0.028 0.008 -10000 0 0 42 42
TNF 0.029 0.005 -10000 0 0 16 16
NF kappa B1 p50/RelA 0.045 0.052 -10000 0 -0.2 16 16
BCL10 0.029 0.004 -10000 0 0 10 10
proteasomal ubiquitin-dependent protein catabolic process -0.054 0.043 -10000 0 -0.32 12 12
beta TrCP1/SCF ubiquitin ligase complex -0.031 0.01 -10000 0 -10000 0 0
TNFRSF1A 0.026 0.01 -10000 0 0 78 78
IKK complex 0.045 0.13 0.24 10 -0.37 33 43
CYLD 0.028 0.007 -10000 0 0 36 36
IKK complex/PKC alpha 0.051 0.13 0.24 10 -0.38 28 38
FAS signaling pathway (CD95)

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
SPTAN1 -0.004 0.065 0.3 2 -0.2 25 27
RFC1 -0.002 0.066 0.24 6 -0.2 23 29
PRKDC 0.024 0.1 0.22 78 -0.2 24 102
RIPK1 0.026 0.016 -10000 0 -0.079 9 9
CASP7 0.01 0.064 -10000 0 -0.54 6 6
FASLG/FAS/FADD/FAF1 0.024 0.07 0.2 2 -0.17 11 13
MAP2K4 0.003 0.091 0.35 10 -0.31 11 21
mol:ceramide 0.011 0.062 0.31 9 -0.26 3 12
GSN -0.012 0.066 0.22 3 -0.2 22 25
FASLG/FAS/FADD/FAF1/Caspase 8 0.006 0.071 0.19 14 -0.23 2 16
FAS 0.027 0.013 0.077 9 -0.047 7 16
BID -0.036 0.015 0.18 1 -10000 0 1
MAP3K1 0.019 0.079 0.28 11 -0.33 6 17
MAP3K7 0.027 0.011 -10000 0 -0.037 9 9
RB1 0.002 0.068 0.21 18 -0.2 20 38
CFLAR 0.028 0.014 -10000 0 -0.079 9 9
HGF/MET 0.007 0.081 -10000 0 -0.15 104 104
ARHGDIB 0.006 0.083 0.22 32 -0.2 21 53
FADD 0.029 0.012 0.077 10 -0.048 8 18
actin filament polymerization 0.014 0.071 0.22 27 -0.22 4 31
NFKB1 -0.021 0.18 0.38 9 -0.6 41 50
MAPK8 -0.007 0.1 0.4 11 -0.42 13 24
DFFA -0.004 0.068 0.32 3 -0.2 28 31
DNA fragmentation during apoptosis -0.004 0.067 0.22 6 -0.2 28 34
FAS/FADD/MET 0.039 0.051 -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 -0.037 10 10
FAF1 0.029 0.015 0.096 10 -0.054 9 19
PARP1 0.01 0.085 0.22 40 -0.2 25 65
DFFB -0.004 0.065 0.22 4 -0.2 27 31
CHUK -0.028 0.16 0.31 9 -0.56 42 51
FASLG 0.029 0.015 0.096 10 -0.054 9 19
FAS/FADD 0.035 0.04 0.12 1 -0.16 17 18
HGF 0.029 0.005 -10000 0 0 16 16
LMNA 0.038 0.1 0.27 44 -0.2 9 53
CASP6 0.046 0.1 0.21 126 -0.2 10 136
CASP10 0.029 0.013 0.077 10 -0.049 9 19
CASP3 0.006 0.075 0.15 69 -0.22 29 98
PTPN13 0.021 0.014 -10000 0 0 171 171
CASP8 -0.033 0.008 -10000 0 -10000 0 0
IL6 -0.032 0.22 0.65 9 -0.74 27 36
MET 0.025 0.011 -10000 0 0 88 88
ICAD/CAD -0.013 0.065 0.27 6 -0.2 27 33
FASLG/FAS/FADD/FAF1/Caspase 10 0.011 0.063 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 62 -0.2 19 81
BCL2 0.022 0.014 -10000 0 -0.033 8 8
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.026 0.095 0.18 2 -0.27 24 26
adherens junction organization -0.029 0.095 -10000 0 -0.3 40 40
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.026 0.1 0.2 9 -0.24 17 26
FMN1 -0.029 0.089 -10000 0 -0.28 38 38
mol:IP3 -0.03 0.07 0.12 46 -0.21 19 65
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.02 0.095 0.15 1 -0.28 41 42
CTNNB1 0.024 0.021 -10000 0 -0.031 64 64
AKT1 -0.034 0.076 0.19 2 -0.22 29 31
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.018 0.098 -10000 0 -0.3 35 35
CTNND1 -0.005 0.032 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.026 0.089 0.22 4 -0.27 40 44
VASP -0.03 0.089 -10000 0 -0.28 40 40
ZYX -0.037 0.093 -10000 0 -0.29 45 45
JUB -0.021 0.09 0.14 1 -0.27 41 42
EGFR(dimer) -0.011 0.1 -10000 0 -0.27 46 46
E-cadherin/beta catenin-gamma catenin 0.045 0.04 -10000 0 -0.14 18 18
mol:PI-3-4-5-P3 -0.017 0.079 0.2 1 -0.23 32 33
PIK3CA 0.007 0.025 -10000 0 -0.036 74 74
PI3K -0.017 0.08 0.2 1 -0.23 32 33
FYN -0.047 0.12 0.16 3 -0.29 72 75
mol:Ca2+ -0.029 0.069 0.12 46 -0.21 19 65
JUP 0.022 0.021 -10000 0 -0.031 65 65
PIK3R1 0.021 0.017 -10000 0 -10000 0 0
mol:DAG -0.03 0.07 0.12 46 -0.21 19 65
CDH1 0.02 0.021 -10000 0 -0.031 65 65
RhoA/GDP -0.026 0.1 0.2 9 -0.24 15 24
establishment of polarity of embryonic epithelium -0.029 0.088 -10000 0 -0.28 40 40
SRC 0.028 0.007 -10000 0 0 33 33
RAC1 0.028 0.006 -10000 0 0 26 26
RHOA 0.029 0.003 -10000 0 0 7 7
EGFR 0.027 0.009 -10000 0 0 55 55
CASR -0.023 0.082 0.18 3 -0.21 17 20
RhoA/GTP -0.02 0.086 0.19 3 -0.22 12 15
AKT2 -0.035 0.077 0.19 2 -0.22 31 33
actin cable formation -0.037 0.086 0.17 5 -0.31 26 31
apoptosis 0.019 0.096 0.25 30 -0.2 6 36
CTNNA1 -0.005 0.032 -10000 0 -10000 0 0
mol:GDP -0.029 0.09 0.2 4 -0.22 26 30
PIP5K1A -0.027 0.09 0.2 3 -0.28 40 43
PLCG1 -0.03 0.071 0.12 46 -0.22 19 65
Rac1/GTP -0.009 0.1 -10000 0 -0.27 44 44
homophilic cell adhesion 0 0.005 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.009 0.035 0.16 20 -0.17 1 21
CRKL 0.027 0.008 -10000 0 0 46 46
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
DOCK1 0.029 0.005 -10000 0 0 18 18
ITGA4 0.028 0.008 -10000 0 0 40 40
alpha4/beta7 Integrin/MAdCAM1 0.066 0.039 -10000 0 -0.14 1 1
EPO 0.029 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 0.028 0.007 -10000 0 0 36 36
alpha4/beta1 Integrin 0.04 0.013 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.038 0.015 -10000 0 -10000 0 0
lamellipodium assembly -0.009 0.11 -10000 0 -0.41 15 15
PIK3CA 0.021 0.014 -10000 0 0 174 174
PI3K -0.001 0.068 -10000 0 -0.16 77 77
ARF6 0.029 0.004 -10000 0 0 11 11
JAK2 -0.008 0.031 0.11 26 -0.24 1 27
PXN 0.029 0.005 -10000 0 0 14 14
PIK3R1 0.021 0.013 -10000 0 0 159 159
MADCAM1 0.027 0.009 -10000 0 0 51 51
cell adhesion 0.058 0.038 -10000 0 -0.14 1 1
CRKL/CBL 0.04 0.013 -10000 0 -10000 0 0
ITGB1 0.029 0.006 -10000 0 0 20 20
SRC -0.009 0.1 0.17 114 -10000 0 114
ITGB7 0.029 0.004 -10000 0 0 8 8
RAC1 0.028 0.006 -10000 0 0 26 26
alpha4/beta1 Integrin/VCAM1 0.021 0.067 -10000 0 -0.15 68 68
p130Cas/Crk/Dock1 -0.019 0.11 0.24 26 -10000 0 26
VCAM1 0.021 0.013 -10000 0 0 160 160
RHOA 0.029 0.003 -10000 0 0 7 7
alpha4/beta1 Integrin/Paxillin/GIT1 0.067 0.039 -10000 0 -0.14 6 6
BCAR1 -0.012 0.093 0.24 26 -10000 0 26
EPOR 0.027 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 -0.01 0.12 -10000 0 -0.43 15 15
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.028 0.006 -10000 0 0 26 26
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.029 0.005 -10000 0 0 17 17
TCEB1 0.028 0.007 -10000 0 0 34 34
HIF1A/p53 -0.011 0.063 0.24 1 -0.31 15 16
HIF1A -0.004 0.046 -10000 0 -0.31 9 9
COPS5 0.026 0.01 -10000 0 0 75 75
VHL/Elongin B/Elongin C/RBX1/CUL2 0.077 0.052 -10000 0 -10000 0 0
FIH (dimer) 0.029 0.005 -10000 0 0 18 18
CDKN2A 0.012 0.015 -10000 0 0 339 339
ARNT/IPAS 0.04 0.014 -10000 0 -10000 0 0
HIF1AN 0.029 0.005 -10000 0 0 18 18
GNB2L1 0.029 0.005 -10000 0 0 14 14
HIF1A/ARNT -0.01 0.064 0.24 1 -0.33 12 13
CUL2 0.024 0.012 -10000 0 0 114 114
OS9 0.029 0.005 -10000 0 0 17 17
RACK1/Elongin B/Elongin C 0.054 0.019 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.009 0.064 0.24 1 -0.33 12 13
PHD1-3/OS9 0.061 0.047 -10000 0 -0.14 11 11
HIF1A/RACK1/Elongin B/Elongin C 0.034 0.07 0.25 1 -0.32 12 13
VHL 0.029 0.004 -10000 0 0 10 10
HSP90AA1 0.029 0.006 -10000 0 0 21 21
HIF1A/JAB1 -0.01 0.062 0.24 1 -0.33 12 13
EGLN3 0.026 0.01 -10000 0 0 71 71
EGLN2 0.028 0.008 -10000 0 0 39 39
EGLN1 0.028 0.007 -10000 0 0 33 33
TP53 0.024 0.012 -10000 0 0 102 102
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.016 0.07 -10000 0 -0.6 6 6
ARNT 0.028 0.007 -10000 0 0 36 36
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.027 0.008 -10000 0 0 48 48
HIF1A/p19ARF -0.007 0.049 0.24 1 -0.32 8 9
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.004 0.088 0.24 9 -0.34 10 19
PDGFB-D/PDGFRB/SLAP 0.023 0.032 -10000 0 -0.16 5 5
PDGFB-D/PDGFRB/APS/CBL 0.035 0.021 -10000 0 -0.13 5 5
AKT1 -0.038 0.11 0.27 22 -0.25 4 26
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.008 0.089 0.29 4 -0.35 11 15
PIK3CA 0.021 0.014 -10000 0 0 174 174
FGR 0 0.08 0.32 1 -0.37 11 12
mol:Ca2+ 0.001 0.083 0.27 3 -0.37 11 14
MYC -0.026 0.24 0.46 2 -0.68 59 61
SHC1 0.029 0.006 -10000 0 0 20 20
HRAS/GDP -0.035 0.056 0.16 41 -10000 0 41
LRP1/PDGFRB/PDGFB 0.048 0.037 -10000 0 -0.14 13 13
GRB10 0.029 0.005 -10000 0 0 13 13
PTPN11 0.029 0.003 -10000 0 0 7 7
GO:0007205 0 0.084 0.3 2 -0.38 11 13
PTEN 0.028 0.007 -10000 0 0 37 37
GRB2 0.029 0.005 -10000 0 0 19 19
GRB7 0.028 0.008 -10000 0 0 40 40
PDGFB-D/PDGFRB/SHP2 0.034 0.031 -10000 0 -0.16 5 5
PDGFB-D/PDGFRB/GRB10 0.034 0.031 -10000 0 -0.16 5 5
cell cycle arrest 0.023 0.032 -10000 0 -0.16 5 5
HRAS 0.028 0.006 -10000 0 0 27 27
HIF1A -0.043 0.1 0.24 22 -0.24 4 26
GAB1 -0.008 0.1 0.32 2 -0.37 16 18
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.008 0.11 0.29 10 -0.36 12 22
PDGFB-D/PDGFRB 0.04 0.044 -10000 0 -0.15 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.032 0.031 -10000 0 -0.16 5 5
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.024 0.1 0.25 7 -0.33 19 26
positive regulation of MAPKKK cascade 0.034 0.031 -10000 0 -0.16 5 5
PIK3R1 0.021 0.013 -10000 0 0 159 159
mol:IP3 0 0.085 0.3 2 -0.38 11 13
E5 -0.001 0.001 -10000 0 -10000 0 0
CSK 0.02 0.023 -10000 0 -0.045 3 3
PDGFB-D/PDGFRB/GRB7 0.031 0.035 -10000 0 -0.16 8 8
SHB 0.029 0.004 -10000 0 0 10 10
BLK -0.056 0.16 0.32 1 -0.4 88 89
PTPN2 0.015 0.027 -10000 0 -0.051 1 1
PDGFB-D/PDGFRB/SNX15 0.034 0.031 -10000 0 -0.16 5 5
BCAR1 0.027 0.009 -10000 0 0 56 56
VAV2 -0.021 0.13 0.32 3 -0.4 27 30
CBL 0.029 0.004 -10000 0 0 12 12
PDGFB-D/PDGFRB/DEP1 0.034 0.031 -10000 0 -0.16 5 5
LCK 0.001 0.076 0.32 1 -0.39 8 9
PDGFRB 0.015 0.028 -10000 0 -0.053 1 1
ACP1 0.027 0.009 -10000 0 0 57 57
HCK 0.002 0.052 0.32 1 -10000 0 1
ABL1 -0.009 0.089 0.32 2 -0.3 17 19
PDGFB-D/PDGFRB/CBL -0.008 0.1 0.33 1 -0.44 14 15
PTPN1 0.013 0.027 -10000 0 -0.051 1 1
SNX15 0.029 0.003 -10000 0 0 7 7
STAT3 0.028 0.008 -10000 0 0 38 38
STAT1 0.013 0.015 -10000 0 0 315 315
cell proliferation -0.019 0.22 0.42 3 -0.6 59 62
SLA 0.021 0.014 -10000 0 0 169 169
actin cytoskeleton reorganization -0.023 0.1 0.27 26 -10000 0 26
SRC 0.001 0.064 0.32 1 -0.88 1 2
PI3K -0.071 0.067 -10000 0 -0.22 35 35
PDGFB-D/PDGFRB/GRB7/SHC 0.05 0.032 -10000 0 -0.15 8 8
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.008 0.091 0.29 4 -0.36 11 15
LYN -0.005 0.091 0.31 1 -0.46 13 14
LRP1 0.029 0.006 -10000 0 0 22 22
SOS1 0.028 0.007 -10000 0 0 34 34
STAT5B 0.028 0.007 -10000 0 0 33 33
STAT5A 0.028 0.007 -10000 0 0 33 33
NCK1-2/p130 Cas 0.054 0.068 -10000 0 -0.15 6 6
SPHK1 0.021 0.022 -10000 0 -0.039 1 1
EDG1 -0.001 0.003 0.019 1 -10000 0 1
mol:DAG 0 0.085 0.3 2 -0.38 11 13
PLCG1 0 0.086 0.3 2 -0.39 11 13
NHERF/PDGFRB -0.012 0.1 -10000 0 -0.16 168 168
YES1 -0.002 0.087 0.31 1 -0.47 10 11
cell migration -0.012 0.1 -10000 0 -0.16 168 168
SHC/Grb2/SOS1 0.06 0.061 -10000 0 -0.15 3 3
SLC9A3R2 0.025 0.011 -10000 0 0 91 91
SLC9A3R1 0.022 0.013 -10000 0 0 140 140
NHERF1-2/PDGFRB/PTEN -0.004 0.11 -10000 0 -0.16 167 167
FYN -0.064 0.17 -10000 0 -0.43 89 89
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 45 45
RAC1 -0.058 0.2 0.41 1 -0.55 58 59
PRKCD -0.028 0.061 0.16 49 -10000 0 49
FER -0.028 0.06 0.16 47 -10000 0 47
MAPKKK cascade -0.025 0.082 0.32 10 -10000 0 10
RASA1 -0.027 0.057 0.16 43 -10000 0 43
NCK1 0.026 0.009 -10000 0 0 63 63
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 -0.009 0.088 0.32 2 -0.29 17 19
STAT1-3-5/STAT1-3-5 0.06 0.064 -10000 0 -0.16 3 3
Bovine Papilomavirus E5/PDGFRB 0.014 0.023 -10000 0 -0.15 5 5
PTPRJ 0.029 0.004 -10000 0 0 10 10
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 -0.015 0.11 0.35 14 -0.29 10 24
TBX21 -0.11 0.27 0.77 9 -0.76 7 16
B2M 0.028 0.007 -10000 0 -10000 0 0
TYK2 -0.011 0.05 0.18 9 -10000 0 9
IL12RB1 -0.013 0.051 0.18 9 -10000 0 9
GADD45B -0.08 0.26 0.74 10 -0.68 23 33
IL12RB2 -0.002 0.057 0.19 11 -10000 0 11
GADD45G -0.074 0.26 0.71 7 -0.97 11 18
natural killer cell activation -0.006 0.034 0.14 13 -10000 0 13
RELB 0.028 0.006 -10000 0 0 27 27
RELA 0.029 0.003 -10000 0 0 7 7
IL18 0.001 0.03 0.11 2 -10000 0 2
IL2RA 0.028 0.008 -10000 0 0 42 42
IFNG 0.027 0.008 -10000 0 0 46 46
STAT3 (dimer) -0.1 0.25 0.62 11 -0.64 29 40
HLA-DRB5 0 0.013 0.048 26 -0.022 48 74
FASLG -0.1 0.27 0.76 10 -0.77 6 16
NF kappa B2 p52/RelB -0.099 0.26 0.56 8 -0.6 33 41
CD4 0.02 0.027 0.079 23 -0.048 55 78
SOCS1 0.028 0.007 -10000 0 0 31 31
EntrezGene:6955 0 0.015 0.058 26 -0.031 11 37
CD3D 0.021 0.027 0.089 18 -0.053 48 66
CD3E 0.022 0.027 0.081 19 -0.048 61 80
CD3G 0.021 0.029 0.089 22 -0.052 55 77
IL12Rbeta2/JAK2 0.005 0.077 0.28 10 -0.18 1 11
CCL3 -0.1 0.29 0.84 17 -0.82 5 22
CCL4 -0.1 0.27 0.74 11 -0.61 27 38
HLA-A 0 0 -10000 0 -10000 0 0
IL18/IL18R 0.015 0.067 0.42 4 -10000 0 4
NOS2 -0.082 0.25 0.72 12 -0.6 11 23
IL12/IL12R/TYK2/JAK2/SPHK2 -0.013 0.11 0.35 14 -0.29 5 19
IL1R1 -0.36 0.53 0.72 7 -1 211 218
IL4 0.027 0.05 -10000 0 -0.19 10 10
JAK2 -0.013 0.052 0.18 9 -10000 0 9
EntrezGene:6957 0 0.013 0.049 25 -0.031 5 30
TCR/CD3/MHC I/CD8 -0.014 0.078 -10000 0 -0.34 12 12
RAB7A -0.063 0.23 0.69 6 -0.67 6 12
lysosomal transport -0.059 0.23 0.68 6 -0.65 5 11
FOS -0.13 0.42 0.71 22 -1.1 72 94
STAT4 (dimer) -0.058 0.26 0.69 12 -0.63 15 27
STAT5A (dimer) -0.11 0.25 0.57 6 -0.6 31 37
GZMA -0.11 0.28 0.76 12 -0.8 8 20
GZMB -0.1 0.28 0.81 14 -0.76 7 21
HLX 0.029 0.006 -10000 0 0 22 22
LCK -0.12 0.27 0.71 9 -0.65 27 36
TCR/CD3/MHC II/CD4 -0.009 0.1 0.29 24 -0.24 46 70
IL2/IL2R 0.05 0.061 -10000 0 -0.14 28 28
MAPK14 -0.074 0.26 0.71 9 -0.71 16 25
CCR5 -0.057 0.22 0.71 7 -0.65 4 11
IL1B -0.016 0.049 0.19 7 -10000 0 7
STAT6 -0.027 0.14 0.46 9 -0.67 9 18
STAT4 0.029 0.005 -10000 0 0 16 16
STAT3 0.028 0.008 -10000 0 0 38 38
STAT1 0.013 0.015 -10000 0 0 315 315
NFKB1 0.027 0.008 -10000 0 0 45 45
NFKB2 0.029 0.005 -10000 0 0 14 14
IL12B -0.002 0.057 0.19 11 -10000 0 11
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 0.015 0.11 0.3 9 -0.35 14 23
IL2RB 0.027 0.009 -10000 0 0 50 50
proteasomal ubiquitin-dependent protein catabolic process -0.052 0.25 0.65 15 -0.6 12 27
IL2RG 0.026 0.01 -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 0.082 21 -0.048 60 81
IL2 0.028 0.007 -10000 0 0 32 32
SPHK2 0.029 0.005 -10000 0 0 19 19
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.012 0.051 0.18 10 -10000 0 10
IL12/IL12R/TYK2/JAK2 -0.12 0.28 0.85 8 -0.68 27 35
MAP2K3 -0.085 0.27 0.71 9 -0.74 19 28
RIPK2 0.019 0.014 -10000 0 0 199 199
MAP2K6 -0.069 0.25 0.71 9 -0.7 14 23
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0 0.015 0.058 26 -0.024 62 88
IL18RAP 0.003 0.035 0.11 3 -10000 0 3
IL12Rbeta1/TYK2 0.006 0.066 0.23 8 -10000 0 8
EOMES 0.007 0.073 -10000 0 -0.45 7 7
STAT1 (dimer) -0.054 0.22 0.63 9 -0.59 12 21
T cell proliferation -0.04 0.22 0.63 11 -0.55 8 19
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.003 0.035 0.11 3 -10000 0 3
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 11 11
ATF2 -0.074 0.25 0.68 9 -0.67 16 25
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.037 0.012 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.028 0.008 -10000 0 0 41 41
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 0.009 -10000 0 0 54 54
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 0.028 0.008 -10000 0 0 43 43
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 0.005 -10000 0 0 13 13
FYN 0.024 0.011 -10000 0 0 100 100
MAP3K12 0.03 0.003 -10000 0 0 5 5
FGR 0.029 0.005 -10000 0 0 14 14
p38 alpha/TAB1 -0.048 0.095 -10000 0 -0.3 47 47
PRKG1 0.029 0.004 -10000 0 0 9 9
DUSP8 0.029 0.006 -10000 0 0 24 24
PGK/cGMP/p38 alpha -0.026 0.11 0.16 3 -0.33 39 42
apoptosis -0.046 0.091 -10000 0 -0.29 47 47
RAL/GTP 0.039 0.008 -10000 0 -10000 0 0
LYN 0.027 0.008 -10000 0 0 49 49
DUSP1 0.023 0.012 -10000 0 0 124 124
PAK1 0.027 0.008 -10000 0 0 47 47
SRC 0.028 0.007 -10000 0 0 33 33
RAC1/OSM/MEKK3/MKK3 0.064 0.035 -10000 0 -10000 0 0
TRAF6 0.029 0.004 -10000 0 0 12 12
RAC1 0.028 0.006 -10000 0 0 26 26
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 0.038 0.01 -10000 0 -10000 0 0
MAPK11 -0.049 0.12 0.2 2 -0.34 43 45
BLK 0.025 0.011 -10000 0 0 98 98
HCK 0.027 0.008 -10000 0 0 46 46
MAP2K3 0.028 0.008 -10000 0 0 43 43
DUSP16 0.027 0.009 -10000 0 0 57 57
DUSP10 0.028 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 0.12 0.18 4 -0.36 39 43
positive regulation of innate immune response -0.05 0.13 0.23 2 -0.4 40 42
LCK 0.028 0.006 -10000 0 0 26 26
p38alpha-beta/MKP7 -0.044 0.13 0.21 1 -0.4 38 39
p38alpha-beta/MKP5 -0.043 0.13 0.27 1 -0.39 40 41
PGK/cGMP 0.022 0.003 -10000 0 -10000 0 0
PAK2 0.025 0.011 -10000 0 0 91 91
p38alpha-beta/MKP1 -0.053 0.14 0.24 2 -0.38 49 51
CDC42 0.029 0.005 -10000 0 0 13 13
RALB 0.029 0.004 -10000 0 0 10 10
RALA 0.029 0.005 -10000 0 0 15 15
PAK3 0.021 0.014 -10000 0 0 169 169
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.02 0.03 0.16 2 -0.24 1 3
EPHB2 0.029 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 0 113 113
Syndecan-2/alpha2 ITGB1 0.034 0.072 -10000 0 -0.14 57 57
HRAS 0.028 0.006 -10000 0 0 27 27
Syndecan-2/CASK -0.015 0.017 -10000 0 -0.12 13 13
ITGA5 0.029 0.006 -10000 0 0 20 20
BAX -0.027 0.027 -10000 0 -10000 0 0
EPB41 0.028 0.008 -10000 0 0 38 38
positive regulation of cell-cell adhesion -0.023 0.018 -10000 0 -0.12 14 14
LAMA3 0.026 0.01 -10000 0 0 78 78
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 45 45
Syndecan-2/MMP2 -0.033 0.045 0.16 4 -0.14 60 64
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.033 0.038 -10000 0 -0.16 17 17
dendrite morphogenesis -0.025 0.024 0.15 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 -0.14 15 19
GNB2L1 0.029 0.005 -10000 0 0 14 14
MAPK3 -0.015 0.067 0.18 55 -0.22 3 58
MAPK1 -0.013 0.065 0.18 54 -10000 0 54
Syndecan-2/RACK1 0.027 0.032 0.15 4 -0.12 13 17
NF1 0.026 0.01 -10000 0 0 70 70
FGFR/FGF/Syndecan-2 -0.015 0.006 -10000 0 -10000 0 0
ITGA2 0.027 0.009 -10000 0 0 62 62
MAPK8 -0.022 0.024 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.039 0.059 -10000 0 -0.14 26 26
Syndecan-2/Kininogen -0.022 0.025 0.16 3 -0.14 13 16
ITGB1 0.029 0.006 -10000 0 0 20 20
SRC -0.018 0.067 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 -0.039 0.047 0.15 4 -0.14 81 85
actin cytoskeleton reorganization -0.02 0.03 0.15 2 -0.24 1 3
Syndecan-2/Caveolin-2/Ras 0.026 0.041 0.16 4 -0.14 26 30
Syndecan-2/Laminin alpha3 -0.031 0.037 0.16 4 -0.14 45 49
Syndecan-2/RasGAP 0.034 0.041 0.16 4 -0.13 14 18
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 -0.038 0.033 0.15 7 -10000 0 7
RHOA 0.029 0.003 -10000 0 0 7 7
SDCBP 0.028 0.007 -10000 0 0 33 33
TNFRSF13B 0.028 0.007 -10000 0 0 36 36
RASA1 0.027 0.009 -10000 0 0 51 51
alpha2/beta1 Integrin 0.033 0.038 -10000 0 -0.16 17 17
Syndecan-2/Synbindin -0.024 0.023 0.16 3 -0.14 12 15
TGFB1 0.024 0.012 -10000 0 0 111 111
CASP3 -0.015 0.063 0.18 49 -10000 0 49
FN1 0.018 0.015 -10000 0 0 214 214
Syndecan-2/IL8 -0.021 0.025 0.16 4 -0.14 11 15
SDC2 -0.015 0.006 -10000 0 -10000 0 0
KNG1 0.025 0.011 -10000 0 0 89 89
Syndecan-2/Neurofibromin -0.024 0.024 0.16 2 -0.14 1 3
TRAPPC4 0.027 0.008 -10000 0 0 49 49
CSF2 0.029 0.005 -10000 0 0 18 18
Syndecan-2/TGFB1 -0.039 0.047 0.16 4 -0.14 81 85
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 0.059 0.18 42 -10000 0 42
angiogenesis -0.021 0.025 0.15 4 -0.14 11 15
MMP2 0.023 0.013 -10000 0 0 134 134
IL8 0.025 0.011 -10000 0 0 94 94
calcineurin-NFAT signaling pathway -0.025 0.023 0.15 3 -10000 0 3
Arf6 signaling events

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
CENTA1/KIF3B 0.01 0.03 -10000 0 -0.12 26 26
ARNO/beta Arrestin1-2 0.027 0.028 -10000 0 -0.1 6 6
EGFR 0.027 0.009 -10000 0 0 55 55
EPHA2 0.029 0.005 -10000 0 0 16 16
USP6 0.028 0.006 -10000 0 0 25 25
IQSEC1 0.029 0.004 -10000 0 0 9 9
EGFR/EGFR/EGF/EGF 0.024 0.056 -10000 0 -0.16 43 43
ARRB2 0.007 0.002 -10000 0 -10000 0 0
mol:GTP 0.001 0.02 0.11 4 -0.07 10 14
ARRB1 0.028 0.007 -10000 0 0 35 35
FBXO8 0.028 0.008 -10000 0 0 42 42
TSHR 0.028 0.007 -10000 0 0 33 33
EGF 0.028 0.008 -10000 0 0 41 41
somatostatin receptor activity 0 0 0 4 -0.001 26 30
ARAP2 0 0 0 7 0 23 30
mol:GDP -0.008 0.071 0.14 1 -0.24 24 25
mol:PI-3-4-5-P3 0 0 0 5 -0.001 26 31
ITGA2B 0.029 0.006 -10000 0 0 22 22
ARF6 0.029 0.004 -10000 0 0 11 11
Ephrin A1/EPHA2/NCK1/GIT1 0.068 0.039 -10000 0 -10000 0 0
ADAP1 0 0 0 2 0 13 15
KIF13B 0.024 0.012 -10000 0 0 112 112
HGF/MET 0.033 0.033 -10000 0 -0.16 12 12
PXN 0.029 0.005 -10000 0 0 14 14
ARF6/GTP -0.013 0.077 0.17 4 -0.26 26 30
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 22 29
actin filament binding 0 0 0 4 0 27 31
SRC 0.028 0.007 -10000 0 0 33 33
ITGB3 0.025 0.011 -10000 0 0 99 99
GNAQ 0.028 0.007 -10000 0 0 28 28
EFA6/PI-4-5-P2 0 0 0.001 9 -0.001 15 24
ARF6/GDP -0.002 0.071 0.17 8 -0.27 21 29
ARF6/GDP/GULP/ACAP1 -0.004 0.089 -10000 0 -0.25 30 30
alphaIIb/beta3 Integrin/paxillin/GIT1 0.042 0.077 -10000 0 -0.14 72 72
ACAP1 0 0 0 4 -10000 0 4
ACAP2 0 0 0 4 0 23 27
LHCGR/beta Arrestin2 0.021 0.019 -10000 0 -10000 0 0
EFNA1 0.027 0.008 -10000 0 0 45 45
HGF 0.029 0.005 -10000 0 0 16 16
CYTH3 0 0 0.001 8 -0.001 23 31
CYTH2 0 0.001 0.003 2 -0.004 26 28
NCK1 0.026 0.009 -10000 0 0 63 63
fibronectin binding 0 0 0 6 0 18 24
endosomal lumen acidification 0 0 0 5 0 13 18
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.025 0.011 -10000 0 0 93 93
GNAQ/ARNO 0.019 0.006 -10000 0 -0.015 7 7
mol:Phosphatidic acid 0 0 0 4 0 23 27
PIP3-E 0 0 0 3 0 25 28
MET 0.025 0.011 -10000 0 0 88 88
GNA14 0.029 0.005 -10000 0 0 18 18
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 8 -0.001 21 29
GNA11 0.025 0.011 -10000 0 0 83 83
LHCGR 0.029 0.006 -10000 0 0 21 21
AGTR1 0.027 0.009 -10000 0 0 51 51
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 -0.095 46 46
alphaIIb/beta3 Integrin 0.016 0.068 -10000 0 -0.16 68 68
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.027 0.009 -10000 0 0 61 61
Caspase 8 (4 units) 0.027 0.058 -10000 0 -0.18 21 21
NEF -0.004 0.001 -10000 0 -10000 0 0
NFKBIA -0.031 0.039 0.17 15 -10000 0 15
BIRC3 -0.083 0.1 0.16 8 -0.31 81 89
CYCS -0.023 0.043 0.17 6 -0.25 2 8
RIPK1 0.028 0.008 -10000 0 0 41 41
CD247 -0.031 0.004 -10000 0 -10000 0 0
MAP2K7 -0.02 0.15 -10000 0 -0.62 24 24
protein ubiquitination -0.033 0.097 0.23 5 -0.3 32 37
CRADD 0.029 0.005 -10000 0 0 13 13
DAXX 0.029 0.005 -10000 0 0 16 16
FAS 0.028 0.008 -10000 0 0 40 40
BID -0.019 0.039 0.15 6 -0.25 2 8
NF-kappa-B/RelA/I kappa B alpha 0.012 0.097 -10000 0 -0.2 85 85
TRADD 0.026 0.009 -10000 0 0 63 63
MAP3K5 0.028 0.007 -10000 0 0 31 31
CFLAR 0.029 0.004 -10000 0 0 9 9
FADD 0.029 0.005 -10000 0 0 18 18
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.011 0.098 -10000 0 -0.21 85 85
MAPK8 -0.027 0.13 -10000 0 -0.58 24 24
APAF1 0.028 0.007 -10000 0 0 28 28
TRAF1 0.029 0.005 -10000 0 0 17 17
TRAF2 0.029 0.006 -10000 0 0 24 24
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.008 0.037 0.17 6 -0.17 13 19
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.034 0.11 0.2 12 -0.36 35 47
CHUK -0.036 0.1 0.24 5 -0.32 32 37
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.068 0.053 -10000 0 -0.14 15 15
TCRz/NEF 0.023 0.007 -10000 0 -10000 0 0
TNF 0.029 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 -0.11 1 16
TNFR1A/BAG4/TNF-alpha 0.042 0.04 -10000 0 -0.14 15 15
CASP6 0.007 0.15 -10000 0 -0.52 35 35
CASP7 -0.074 0.16 0.38 15 -0.4 83 98
RELA -0.033 0.04 0.17 16 -0.11 1 17
CASP2 0.027 0.008 -10000 0 0 45 45
CASP3 -0.085 0.17 0.38 15 -0.42 87 102
TNFRSF1A 0.026 0.01 -10000 0 0 78 78
TNFR1A/BAG4 0.03 0.037 -10000 0 -0.16 15 15
CASP8 0.029 0.004 -10000 0 0 8 8
CASP9 0.029 0.005 -10000 0 0 13 13
MAP3K14 -0.037 0.1 0.23 2 -0.35 32 34
APAF-1/Caspase 9 -0.082 0.086 0.16 1 -0.26 63 64
BCL2 -0.042 0.12 -10000 0 -0.52 25 25
EPHB forward 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
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 0.06 0.065 -10000 0 -0.14 25 25
ITSN1 0.029 0.005 -10000 0 0 13 13
PIK3CA 0.021 0.014 -10000 0 0 174 174
SHC1 0.029 0.006 -10000 0 0 20 20
Ephrin B1/EPHB3 0.032 0.017 -10000 0 -0.13 1 1
Ephrin B1/EPHB1 0.037 0.013 -10000 0 -0.13 1 1
HRAS/GDP -0.068 0.069 0.12 4 -0.2 86 90
Ephrin B/EPHB1/GRB7 0.063 0.061 -10000 0 -0.14 23 23
Endophilin/SYNJ1 -0.039 0.055 0.18 18 -10000 0 18
KRAS 0.025 0.011 -10000 0 0 97 97
Ephrin B/EPHB1/Src 0.063 0.059 -10000 0 -0.14 21 21
endothelial cell migration 0.007 0.068 -10000 0 -0.14 82 82
GRB2 0.029 0.005 -10000 0 0 19 19
GRB7 0.028 0.008 -10000 0 0 40 40
PAK1 -0.038 0.067 0.3 3 -10000 0 3
HRAS 0.028 0.006 -10000 0 0 27 27
RRAS -0.036 0.057 0.18 18 -0.22 3 21
DNM1 0.029 0.005 -10000 0 0 16 16
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.03 0.064 0.16 33 -10000 0 33
lamellipodium assembly -0.063 0.031 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.005 0.049 -10000 0 -0.23 5 5
PIK3R1 0.021 0.013 -10000 0 0 159 159
EPHB2 0.029 0.006 -10000 0 0 21 21
EPHB3 0.024 0.012 -10000 0 0 103 103
EPHB1 0.028 0.007 -10000 0 0 34 34
EPHB4 0.029 0.005 -10000 0 0 19 19
mol:GDP -0.045 0.078 0.23 4 -0.24 22 26
Ephrin B/EPHB2 0.054 0.05 -10000 0 -0.13 23 23
Ephrin B/EPHB3 0.045 0.051 -10000 0 -0.13 21 21
JNK cascade -0.014 0.096 0.27 37 -10000 0 37
Ephrin B/EPHB1 0.054 0.049 -10000 0 -0.13 21 21
RAP1/GDP -0.059 0.086 0.23 7 -0.24 24 31
EFNB2 0.027 0.009 -10000 0 0 57 57
EFNB3 0.028 0.007 -10000 0 0 30 30
EFNB1 0.029 0.004 -10000 0 0 8 8
Ephrin B2/EPHB1-2 0.042 0.039 -10000 0 -0.13 18 18
RAP1B 0.029 0.006 -10000 0 0 23 23
RAP1A 0.029 0.004 -10000 0 0 8 8
CDC42/GTP -0.05 0.062 0.14 29 -10000 0 29
Rap1/GTP -0.068 0.039 0.066 12 -10000 0 12
axon guidance 0.035 0.017 -10000 0 -0.13 3 3
MAPK3 -0.025 0.051 0.16 2 -0.24 5 7
MAPK1 -0.019 0.047 0.16 6 -0.22 1 7
Rac1/GDP -0.053 0.086 0.23 7 -0.24 25 32
actin cytoskeleton reorganization -0.035 0.049 -10000 0 -0.18 9 9
CDC42/GDP -0.055 0.086 0.23 7 -0.24 25 32
PI3K 0.022 0.078 -10000 0 -0.14 82 82
EFNA5 0.028 0.008 -10000 0 0 43 43
Ephrin B2/EPHB4 0.03 0.034 -10000 0 -0.13 20 20
Ephrin B/EPHB2/Intersectin/N-WASP 0.002 0.055 -10000 0 -0.19 28 28
CDC42 0.029 0.005 -10000 0 0 13 13
RAS family/GTP -0.028 0.041 0.057 7 -10000 0 7
PTK2 0.13 0.26 0.56 149 -10000 0 149
MAP4K4 -0.014 0.096 0.27 37 -10000 0 37
SRC 0.028 0.007 -10000 0 0 33 33
KALRN 0.028 0.007 -10000 0 0 28 28
Intersectin/N-WASP 0.042 0.01 -10000 0 -10000 0 0
neuron projection morphogenesis -0.043 0.085 0.24 24 -10000 0 24
MAP2K1 -0.016 0.047 0.16 5 -0.21 3 8
WASL 0.029 0.006 -10000 0 0 21 21
Ephrin B1/EPHB1-2/NCK1 0.074 0.032 -10000 0 -0.14 1 1
cell migration -0.021 0.072 0.25 4 -0.28 6 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 0.052 0.16 17 -10000 0 17
HRAS/GTP -0.051 0.053 0.12 32 -10000 0 32
Ephrin B1/EPHB1-2 0.051 0.021 -10000 0 -0.13 1 1
cell adhesion mediated by integrin 0.019 0.062 0.16 3 -0.22 16 19
RAC1 0.028 0.006 -10000 0 0 26 26
mol:GTP -0.043 0.058 0.15 34 -10000 0 34
RAC1-CDC42/GTP -0.062 0.04 -10000 0 -10000 0 0
RASA1 0.027 0.009 -10000 0 0 51 51
RAC1-CDC42/GDP -0.059 0.088 0.23 8 -0.24 24 32
ruffle organization -0.049 0.077 0.27 9 -10000 0 9
NCK1 0.026 0.009 -10000 0 0 63 63
receptor internalization -0.046 0.053 0.16 18 -0.22 1 19
Ephrin B/EPHB2/KALRN 0.065 0.059 -10000 0 -0.14 22 22
ROCK1 0.005 0.081 0.17 104 -10000 0 104
RAS family/GDP -0.038 0.05 -10000 0 -0.19 10 10
Rac1/GTP -0.065 0.032 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/Paxillin 0 0.053 -10000 0 -0.21 2 2
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.045 0.1 -10000 0 -0.32 62 62
KLHL20 -0.057 0.078 0.47 1 -0.28 16 17
CYFIP2 0.029 0.006 -10000 0 0 24 24
Rac1/GDP -0.044 0.079 0.23 6 -0.26 14 20
ENAH -0.046 0.1 -10000 0 -0.32 63 63
AP1M1 0.026 0.01 -10000 0 0 65 65
RAP1B 0.029 0.006 -10000 0 0 23 23
RAP1A 0.029 0.004 -10000 0 0 8 8
CTNNB1 0.029 0.004 -10000 0 0 8 8
CDC42/GTP -0.057 0.051 0.12 25 -0.23 2 27
ABI1/Sra1/Nap1 -0.052 0.045 -10000 0 -0.17 34 34
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.057 0.047 -10000 0 -0.14 8 8
RAPGEF1 -0.045 0.098 0.24 4 -0.31 53 57
CTNND1 0.029 0.003 -10000 0 0 5 5
regulation of calcium-dependent cell-cell adhesion -0.022 0.11 -10000 0 -0.32 66 66
CRK -0.045 0.1 -10000 0 -0.32 58 58
E-cadherin/gamma catenin/alpha catenin 0.044 0.043 -10000 0 -0.16 18 18
alphaE/beta7 Integrin 0.041 0.014 -10000 0 -0.16 1 1
IQGAP1 0.029 0.006 -10000 0 0 24 24
NCKAP1 0.029 0.005 -10000 0 0 17 17
Rap1/GTP/I-afadin 0.04 0.043 -10000 0 -0.13 21 21
DLG1 -0.031 0.1 0.19 1 -0.32 52 53
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.043 0.042 -10000 0 -0.15 15 15
MLLT4 0.026 0.01 -10000 0 0 72 72
ARF6/GTP/NME1/Tiam1 0.048 0.024 -10000 0 -0.13 1 1
PI3K -0.053 0.054 -10000 0 -0.2 8 8
ARF6 0.029 0.004 -10000 0 0 11 11
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.031 0.041 -10000 0 -0.18 18 18
TIAM1 0.028 0.006 -10000 0 -0.001 24 24
E-cadherin(dimer)/Ca2+ 0.053 0.042 -10000 0 -0.13 7 7
AKT1 -0.012 0.069 0.14 53 -10000 0 53
PIK3R1 0.021 0.013 -10000 0 0 159 159
CDH1 0.026 0.01 -10000 0 0 70 70
RhoA/GDP -0.043 0.08 0.23 6 -0.25 17 23
actin cytoskeleton organization -0.043 0.059 0.4 1 -0.22 7 8
CDC42/GDP -0.042 0.08 0.23 6 -0.25 19 25
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.013 0.057 -10000 0 -0.19 33 33
ITGB7 0.029 0.004 -10000 0 0 8 8
RAC1 0.028 0.007 -10000 0 -0.001 27 27
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.058 0.045 -10000 0 -0.14 7 7
E-cadherin/Ca2+/beta catenin/alpha catenin 0.04 0.032 -10000 0 -0.12 7 7
mol:GDP -0.042 0.085 0.23 6 -0.28 20 26
CDC42/GTP/IQGAP1 0.037 0.014 -10000 0 -0.13 2 2
JUP 0.028 0.008 -10000 0 0 40 40
p120 catenin/RhoA/GDP -0.045 0.083 0.24 6 -0.26 15 21
RAC1/GTP/IQGAP1 0.036 0.015 -10000 0 -0.13 2 2
PIP5K1C/AP1M1 0.037 0.017 -10000 0 -10000 0 0
RHOA 0.029 0.003 -10000 0 0 7 7
CDC42 0.029 0.005 -10000 0 0 13 13
CTNNA1 0.029 0.004 -10000 0 0 13 13
positive regulation of S phase of mitotic cell cycle -0.044 0.057 0.092 3 -0.13 144 147
NME1 0.028 0.008 -10000 0 0 42 42
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.047 0.1 -10000 0 -0.32 66 66
regulation of cell-cell adhesion -0.053 0.041 0.083 24 -0.21 2 26
WASF2 -0.03 0.035 0.096 5 -0.1 40 45
Rap1/GTP -0.053 0.058 0.15 23 -0.25 2 25
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.058 0.063 -10000 0 -0.15 18 18
CCND1 -0.054 0.07 0.11 3 -0.16 144 147
VAV2 -0.038 0.16 -10000 0 -0.66 24 24
RAP1/GDP -0.044 0.067 0.24 4 -0.24 4 8
adherens junction assembly -0.045 0.1 -10000 0 -0.31 66 66
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 44 44
regulation of heterotypic cell-cell adhesion -0.06 0.03 0.17 4 -0.23 2 6
E-cadherin/beta catenin -0.009 0.048 -10000 0 -0.18 37 37
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.044 0.1 -10000 0 -0.32 60 60
PIK3CA 0.021 0.014 -10000 0 0 174 174
Rac1/GTP -0.088 0.11 0.55 1 -0.39 35 36
E-cadherin/beta catenin/alpha catenin 0.049 0.03 -10000 0 -0.15 7 7
ITGAE 0.028 0.007 -10000 0 0 30 30
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.022 0.12 -10000 0 -0.33 66 66
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.027 0.008 -10000 0 0 46 46
RAS family/GTP/Tiam1 0.034 0.049 -10000 0 -0.24 2 2
NT3 (dimer)/TRKC 0.034 0.019 -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 0.19 5 -0.24 8 13
RAPGEF1 0.029 0.006 -10000 0 0 21 21
BDNF 0.029 0.005 -10000 0 0 13 13
PIK3CA 0.021 0.014 -10000 0 0 174 174
DYNLT1 0.025 0.011 -10000 0 0 82 82
NTRK1 0.029 0.005 -10000 0 0 13 13
NTRK2 0.029 0.006 -10000 0 0 20 20
NTRK3 0.029 0.006 -10000 0 0 21 21
NT-4/5 (dimer)/TRKB 0.038 0.01 -10000 0 -10000 0 0
neuron apoptosis 0.018 0.11 0.29 43 -10000 0 43
SHC 2-3/Grb2 -0.019 0.12 -10000 0 -0.31 43 43
SHC1 0.029 0.006 -10000 0 0 20 20
SHC2 -0.04 0.15 -10000 0 -0.39 74 74
SHC3 0.002 0.089 -10000 0 -0.41 16 16
STAT3 (dimer) -0.05 0.14 -10000 0 -0.28 141 141
NT3 (dimer)/TRKA 0.045 0.026 -10000 0 -10000 0 0
RIN/GDP 0.042 0.078 0.21 22 -0.26 10 32
GIPC1 0.026 0.01 -10000 0 0 80 80
KRAS 0.025 0.011 -10000 0 0 97 97
DNAJA3 -0.013 0.057 0.18 2 -0.25 2 4
RIN/GTP 0.021 0.005 -10000 0 -10000 0 0
CCND1 -0.15 0.21 -10000 0 -0.52 140 140
MAGED1 0.029 0.006 -10000 0 0 21 21
PTPN11 0.029 0.003 -10000 0 0 7 7
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.053 0.02 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 0 19 19
NGF (dimer)/TRKA/MATK 0.036 0.012 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.039 0.016 -10000 0 -0.16 1 1
ELMO1 0.028 0.007 -10000 0 0 33 33
RhoG/GTP/ELMO1/DOCK1 0.037 0.014 -10000 0 -0.13 1 1
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.028 0.006 -10000 0 0 27 27
DOCK1 0.029 0.005 -10000 0 0 18 18
GAB2 0.027 0.009 -10000 0 0 62 62
RIT2 0.028 0.007 -10000 0 0 30 30
RIT1 0.026 0.009 -10000 0 0 63 63
FRS2 0.028 0.007 -10000 0 0 30 30
DNM1 0.029 0.005 -10000 0 0 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.028 0.007 -10000 0 0 36 36
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.01 0.065 0.22 1 -0.18 11 12
mol:GDP 0.042 0.1 0.26 18 -0.39 10 28
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.021 0.005 -10000 0 -10000 0 0
RIT1/GDP 0.036 0.073 0.22 14 -0.25 9 23
TIAM1 0.029 0.006 -10000 0 0 23 23
PIK3R1 0.021 0.013 -10000 0 0 159 159
BDNF (dimer)/TRKB 0.054 0.019 -10000 0 -10000 0 0
KIDINS220/CRKL/C3G 0.039 0.014 -10000 0 -10000 0 0
SHC/RasGAP 0.038 0.019 -10000 0 -0.16 2 2
FRS2 family/SHP2 0.055 0.018 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.067 0.035 -10000 0 -0.14 2 2
RIT1/GTP 0.02 0.007 -10000 0 -10000 0 0
NT3 (dimer) 0.024 0.012 -10000 0 0 116 116
RAP1/GDP 0.032 0.063 0.17 14 -0.23 10 24
KIDINS220/CRKL 0.027 0.008 -10000 0 0 46 46
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 -0.056 2 2
EHD4 0.028 0.008 -10000 0 0 40 40
FRS2 family/GRB2/SOS1 0.068 0.032 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.002 0.059 -10000 0 -0.25 17 17
RAP1B 0.029 0.006 -10000 0 0 23 23
RAP1A 0.029 0.004 -10000 0 0 8 8
CDC42/GTP -0.027 0.076 0.14 93 -10000 0 93
ABL1 0.029 0.006 -10000 0 0 22 22
SH2B family/GRB2/SOS1 0.04 0.013 -10000 0 -10000 0 0
Rap1/GTP 0 0.076 -10000 0 -0.26 24 24
STAT3 -0.05 0.14 -10000 0 -0.28 141 141
axon guidance -0.04 0.051 0.1 53 -10000 0 53
MAPK3 -0.028 0.032 0.18 13 -10000 0 13
MAPK1 -0.028 0.03 0.18 11 -10000 0 11
CDC42/GDP 0.044 0.078 0.22 21 -0.26 10 31
NTF3 0.024 0.012 -10000 0 0 116 116
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 0.029 0.006 -10000 0 0 24 24
FAIM 0.028 0.008 -10000 0 0 40 40
GAB1 0.028 0.006 -10000 0 0 25 25
RASGRF1 -0.013 0.057 0.18 2 -0.17 8 10
SOS1 0.028 0.007 -10000 0 0 34 34
MCF2L -0.013 0.061 0.16 58 -10000 0 58
RGS19 0.027 0.009 -10000 0 0 60 60
CDC42 0.029 0.005 -10000 0 0 13 13
RAS family/GTP 0.043 0.075 0.28 2 -0.37 4 6
Rac1/GDP 0.042 0.078 0.22 19 -0.26 10 29
NGF (dimer)/TRKA/GRIT 0.02 0.003 -10000 0 -10000 0 0
neuron projection morphogenesis -0.1 0.24 -10000 0 -0.87 38 38
NGF (dimer)/TRKA/NEDD4-2 0.036 0.014 -10000 0 -0.13 1 1
MAP2K1 -0.029 0.068 0.17 42 -10000 0 42
NGFR 0.029 0.005 -10000 0 0 17 17
NGF (dimer)/TRKA/GIPC/GAIP -0.007 0.052 -10000 0 -0.18 38 38
RAS family/GTP/PI3K 0.012 0.066 -10000 0 -0.18 32 32
FRS2 family/SHP2/GRB2/SOS1 0.077 0.036 -10000 0 -10000 0 0
NRAS 0.014 0.015 -10000 0 0 300 300
GRB2/SOS1 0.04 0.013 -10000 0 -10000 0 0
PRKCI 0.014 0.015 -10000 0 0 287 287
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.028 0.006 -10000 0 0 26 26
PRKCZ 0.029 0.006 -10000 0 0 22 22
MAPKKK cascade 0.015 0.04 -10000 0 -0.36 2 2
RASA1 0.027 0.009 -10000 0 0 51 51
TRKA/c-Abl 0.041 0.018 -10000 0 -0.16 3 3
SQSTM1 0.029 0.005 -10000 0 0 19 19
BDNF (dimer)/TRKB/GIPC 0.045 0.06 -10000 0 -0.14 32 32
NGF (dimer)/TRKA/p62/Atypical PKCs 0.064 0.048 -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 -0.006 0.054 0.15 1 -0.18 10 11
Rac1/GTP -0.012 0.042 -10000 0 -0.2 5 5
FRS2 family/SHP2/CRK family 0.068 0.045 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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
NFATC2 0.026 0.01 -10000 0 0 75 75
GNB1/GNG2 0.042 0.081 -10000 0 -0.22 10 10
mol:DAG -0.01 0.075 0.17 22 -0.22 8 30
PLCG1 -0.01 0.076 0.17 22 -0.22 8 30
YES1 -0.002 0.068 0.2 15 -0.22 8 23
FZD3 0.022 0.013 -10000 0 0 140 140
FZD6 0.024 0.012 -10000 0 0 104 104
G protein 0.016 0.1 0.21 60 -0.26 2 62
MAP3K7 -0.025 0.066 0.23 6 -0.24 2 8
mol:Ca2+ -0.009 0.073 0.17 22 -0.21 8 30
mol:IP3 -0.01 0.075 0.17 22 -0.22 8 30
NLK -0.02 0.17 -10000 0 -0.8 24 24
GNB1 0.029 0.006 -10000 0 0 23 23
CAMK2A -0.017 0.071 0.21 10 -0.24 2 12
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD 0.007 0.064 0.19 3 -0.22 10 13
CSNK1A1 0.029 0.005 -10000 0 0 13 13
GNAS -0.007 0.062 0.18 3 -0.22 10 13
GO:0007205 -0.007 0.071 0.2 12 -0.23 5 17
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 0.24 19 -0.27 2 21
GNG2 0.029 0.005 -10000 0 0 14 14
WNT5A 0.029 0.005 -10000 0 0 17 17
WNT11 0.026 0.01 -10000 0 0 73 73
CDC42 -0.005 0.067 0.21 13 -0.23 3 16
Signaling events mediated by PTP1B

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
PDGFRB 0.029 0.005 -10000 0 0 16 16
Jak2/Leptin Receptor 0.01 0.11 -10000 0 -0.38 25 25
PTP1B/AKT1 0.001 0.088 -10000 0 -0.3 7 7
FYN 0.024 0.011 -10000 0 0 100 100
p210 bcr-abl/PTP1B -0.008 0.088 -10000 0 -0.31 7 7
EGFR 0.019 0.025 -10000 0 -0.046 1 1
EGF/EGFR 0.006 0.099 -10000 0 -0.3 14 14
CSF1 0.028 0.006 -10000 0 0 27 27
AKT1 0.015 0.026 -10000 0 -10000 0 0
INSR 0.018 0.022 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.004 0.09 -10000 0 -0.31 12 12
Insulin Receptor/Insulin 0.004 0.097 -10000 0 -0.3 7 7
HCK 0.027 0.008 -10000 0 0 46 46
CRK 0.028 0.007 -10000 0 0 36 36
TYK2 0 0.1 0.26 20 -0.31 7 27
EGF 0.018 0.026 -10000 0 -10000 0 0
YES1 0.028 0.008 -10000 0 0 43 43
CAV1 -0.031 0.1 0.22 1 -0.33 23 24
TXN 0.015 0.025 -10000 0 -0.058 1 1
PTP1B/IRS1/GRB2 -0.059 0.1 -10000 0 -0.3 24 24
cell migration 0.008 0.088 0.31 7 -10000 0 7
STAT3 0.02 0.021 -10000 0 -10000 0 0
PRLR 0.025 0.014 0.15 1 -10000 0 1
ITGA2B 0.012 0.027 -10000 0 -0.045 1 1
CSF1R 0.029 0.005 -10000 0 0 16 16
Prolactin Receptor/Prolactin 0.037 0.019 0.28 1 -10000 0 1
FGR 0.029 0.005 -10000 0 0 14 14
PTP1B/p130 Cas 0.001 0.091 -10000 0 -0.3 8 8
Crk/p130 Cas 0.006 0.099 -10000 0 -0.31 7 7
DOK1 -0.016 0.086 0.28 1 -0.34 8 9
JAK2 -0.002 0.11 -10000 0 -0.37 30 30
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 0.088 -10000 0 -0.32 7 7
LYN 0.027 0.008 -10000 0 0 49 49
CDH2 0.02 0.014 -10000 0 0 187 187
SRC 0.009 0.091 -10000 0 -0.46 16 16
ITGB3 0.015 0.023 -10000 0 -0.045 1 1
CAT1/PTP1B -0.02 0.12 0.26 6 -0.4 15 21
CAPN1 0.013 0.027 -10000 0 -0.049 1 1
CSK 0.029 0.006 -10000 0 0 22 22
PI3K -0.012 0.096 -10000 0 -0.32 7 7
mol:H2O2 0 0.003 0.019 2 -0.036 1 3
STAT3 (dimer) -0.003 0.11 0.31 2 -0.33 11 13
negative regulation of transcription -0.001 0.1 -10000 0 -0.37 30 30
FCGR2A 0.028 0.007 -10000 0 0 28 28
FER 0.015 0.025 -10000 0 -0.058 1 1
alphaIIb/beta3 Integrin 0.015 0.069 -10000 0 -0.17 68 68
BLK 0.025 0.011 -10000 0 0 98 98
Insulin Receptor/Insulin/Shc 0.035 0.058 -10000 0 -0.15 42 42
RHOA 0.013 0.027 -10000 0 -0.049 1 1
LEPR 0.029 0.006 -10000 0 -0.043 2 2
BCAR1 0.027 0.009 -10000 0 0 56 56
p210 bcr-abl/Grb2 0.029 0.005 -10000 0 0 19 19
mol:NADPH -0.001 0.002 -10000 0 -0.03 1 1
TRPV6 -0.032 0.13 0.27 2 -0.39 32 34
PRL 0.026 0.014 0.15 1 -10000 0 1
SOCS3 0.002 0.14 0.65 2 -1.1 8 10
SPRY2 0 0.026 -10000 0 -0.064 1 1
Insulin Receptor/Insulin/IRS1 -0.077 0.1 -10000 0 -0.16 336 336
CSF1/CSF1R 0.005 0.1 -10000 0 -0.3 8 8
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 0.015 0.026 -10000 0 -10000 0 0
LEP 0.017 0.024 -10000 0 -10000 0 0
STAT5B -0.008 0.11 -10000 0 -0.37 22 22
STAT5A -0.008 0.11 -10000 0 -0.36 22 22
GRB2 0.029 0.005 -10000 0 0 19 19
PDGFB-D/PDGFRB 0 0.093 -10000 0 -0.32 7 7
CSN2 0.008 0.074 0.62 1 -10000 0 1
PIK3CA 0.021 0.014 -10000 0 0 174 174
LAT 0.012 0.087 -10000 0 -0.47 14 14
YBX1 0.007 0.033 -10000 0 -10000 0 0
LCK 0.028 0.006 -10000 0 0 26 26
SHC1 0.029 0.006 -10000 0 0 20 20
NOX4 0.008 0.023 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.029 0.006 -10000 0 0 20 20
Syndecan-3/Src/Cortactin 0.02 0.09 -10000 0 -0.44 14 14
Syndecan-3/Neurocan 0.009 0.081 -10000 0 -0.45 15 15
POMC 0.029 0.004 -10000 0 0 11 11
EGFR 0.027 0.009 -10000 0 0 55 55
Syndecan-3/EGFR 0.009 0.085 -10000 0 -0.47 15 15
AGRP 0.027 0.009 -10000 0 0 55 55
NCSTN 0.029 0.005 -10000 0 0 19 19
PSENEN 0.026 0.01 -10000 0 0 74 74
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.026 0.01 -10000 0 0 69 69
APH1A 0.028 0.007 -10000 0 0 30 30
NCAN 0.027 0.009 -10000 0 0 52 52
long-term memory 0.008 0.093 -10000 0 -0.45 15 15
Syndecan-3/IL8 0.008 0.082 -10000 0 -0.45 15 15
PSEN1 0.029 0.005 -10000 0 0 14 14
Src/Cortactin 0.04 0.013 -10000 0 -10000 0 0
FYN 0.024 0.011 -10000 0 0 100 100
limb bud formation -0.011 0.077 -10000 0 -0.46 15 15
MC4R 0 0 -10000 0 -10000 0 0
SRC 0.028 0.007 -10000 0 0 33 33
PTN 0.023 0.013 -10000 0 0 129 129
FGFR/FGF/Syndecan-3 -0.011 0.078 -10000 0 -0.47 15 15
neuron projection morphogenesis -0.003 0.11 0.21 18 -0.42 14 32
Syndecan-3/AgRP 0.011 0.081 -10000 0 -0.45 15 15
Syndecan-3/AgRP/MC4R 0.01 0.079 -10000 0 -0.43 15 15
Fyn/Cortactin 0.016 0.067 -10000 0 -0.16 65 65
SDC3 -0.011 0.078 -10000 0 -0.47 15 15
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.008 0.081 -10000 0 -0.44 15 15
IL8 0.025 0.011 -10000 0 0 94 94
Syndecan-3/Fyn/Cortactin 0.009 0.096 -10000 0 -0.46 15 15
Syndecan-3/CASK -0.011 0.074 -10000 0 -0.45 15 15
alpha-MSH/MC4R 0.022 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.044 0.078 -10000 0 -0.14 65 65
Caspase cascade in apoptosis

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
TOP1 0.011 0.1 0.28 4 -0.35 24 28
ACTA1 -0.005 0.08 0.22 12 -0.23 10 22
NUMA1 0.012 0.1 0.28 4 -0.36 23 27
SPTAN1 -0.006 0.077 0.24 7 -0.24 7 14
LIMK1 -0.004 0.08 0.24 11 -0.24 7 18
BIRC3 0.023 0.012 -10000 0 0 121 121
BIRC2 0.021 0.015 -10000 0 -0.03 7 7
BAX 0.029 0.005 -10000 0 0 19 19
CASP10 -0.029 0.052 0.17 29 -0.15 2 31
CRMA 0 0 -10000 0 -0.001 1 1
XIAP 0 0 0.001 5 -0.001 41 46
PTK2 -0.002 0.12 0.26 5 -0.38 30 35
DIABLO 0.019 0.015 -10000 0 -0.001 199 199
apoptotic nuclear changes -0.006 0.077 0.24 7 -0.23 7 14
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.029 0.005 -10000 0 0 13 13
GSN -0.016 0.083 0.24 8 -0.24 14 22
MADD 0.029 0.004 -10000 0 0 8 8
TFAP2A 0.024 0.13 -10000 0 -0.81 10 10
BID -0.015 0.043 0.11 27 -0.14 41 68
MAP3K1 -0.021 0.12 -10000 0 -0.39 50 50
TRADD 0.026 0.009 -10000 0 0 63 63
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.042 0.011 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.005 0.098 0.24 43 -0.23 9 52
CASP9 0.029 0.008 -10000 0 -0.03 8 8
DNA repair -0.025 0.061 0.25 3 -0.18 19 22
neuron apoptosis -0.005 0.15 -10000 0 -0.71 21 21
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.003 0.097 0.25 6 -0.32 22 28
APAF1 0.026 0.013 -10000 0 -0.012 48 48
CASP6 -0.019 0.24 -10000 0 -0.9 35 35
TRAF2 0.029 0.006 -10000 0 0 24 24
ICAD/CAD -0.013 0.077 0.24 9 -0.24 6 15
CASP7 0.029 0.096 0.2 68 -0.26 18 86
KRT18 0.015 0.068 -10000 0 -0.67 3 3
apoptosis -0.015 0.13 0.29 9 -0.42 32 41
DFFA -0.005 0.077 0.25 7 -0.23 7 14
DFFB -0.004 0.078 0.22 9 -0.23 8 17
PARP1 0.025 0.061 0.18 18 -0.25 3 21
actin filament polymerization 0.012 0.078 0.23 6 -0.26 9 15
TNF 0.029 0.005 -10000 0 0 16 16
CYCS -0.009 0.052 0.18 4 -0.22 14 18
SATB1 -0.056 0.22 -10000 0 -0.87 35 35
SLK -0.006 0.077 0.26 7 -0.23 7 14
p15 BID/BAX -0.021 0.048 0.19 2 -0.19 4 6
CASP2 -0.027 0.086 0.18 16 -0.27 35 51
JNK cascade 0.021 0.12 0.38 50 -10000 0 50
CASP3 0.005 0.082 0.22 11 -0.23 8 19
LMNB2 -0.028 0.18 0.24 14 -0.48 59 73
RIPK1 0.028 0.008 -10000 0 0 41 41
CASP4 0.028 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 0.025 0.13 -10000 0 -0.79 10 10
stress fiber formation -0.005 0.077 0.26 7 -0.24 6 13
GZMB -0.021 0.047 0.19 25 -10000 0 25
CASP1 -0.02 0.085 -10000 0 -0.26 55 55
LMNB1 0.01 0.14 0.23 23 -0.42 39 62
APP -0.006 0.15 -10000 0 -0.72 21 21
TNFRSF1A 0.026 0.01 -10000 0 0 78 78
response to stress 0 0 0.001 11 -0.001 8 19
CASP8 -0.017 0.002 0 8 -10000 0 8
VIM -0.005 0.14 0.26 14 -0.43 33 47
LMNA -0.003 0.13 0.24 14 -0.4 35 49
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.022 0.088 -10000 0 -0.27 40 40
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.006 0.076 0.26 5 -0.23 8 13
APAF-1/Caspase 9 -0.032 0.16 -10000 0 -0.55 14 14
nuclear fragmentation during apoptosis 0.012 0.1 0.28 4 -0.36 23 27
CFL2 -0.013 0.078 0.27 9 -0.24 6 15
GAS2 -0.002 0.084 0.27 14 -0.23 7 21
positive regulation of apoptosis -0.003 0.16 0.23 23 -0.45 43 66
PRF1 0.028 0.009 -10000 0 -0.009 31 31
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 0.079 0.38 3 -0.63 1 4
epithelial cell differentiation -0.021 0.066 0.24 1 -0.63 1 2
ITCH -0.007 0.04 0.12 6 -0.12 1 7
WWP1 -0.006 0.091 0.73 3 -1.1 1 4
FYN 0.024 0.011 -10000 0 0 100 100
EGFR 0.027 0.009 -10000 0 0 55 55
PRL 0.028 0.008 -10000 0 0 38 38
neuron projection morphogenesis -0.03 0.083 0.3 7 -0.51 1 8
PTPRZ1 0.028 0.006 -10000 0 0 27 27
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.026 0.085 0.32 2 -0.54 1 3
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.019 0.05 0.35 2 -0.58 1 3
ADAM17 -0.005 0.038 0.11 6 -0.12 1 7
ErbB4/ErbB4 -0.008 0.079 0.75 2 -0.69 1 3
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.028 0.092 0.41 1 -0.37 5 6
NCOR1 0.028 0.008 -10000 0 0 39 39
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.023 0.075 0.29 1 -0.56 1 2
GRIN2B -0.026 0.076 0.26 4 -0.54 1 5
ErbB4/ErbB2/betacellulin -0.009 0.071 0.31 2 -0.56 1 3
STAT1 0.013 0.015 -10000 0 0 315 315
HBEGF 0.029 0.004 -10000 0 0 11 11
PRLR 0.027 0.009 -10000 0 0 51 51
E4ICDs/ETO2 0.003 0.075 0.35 2 -0.63 1 3
axon guidance -0.001 0.06 0.41 2 -0.7 1 3
NEDD4 -0.009 0.04 0.16 3 -0.12 1 4
Prolactin receptor/Prolactin receptor/Prolactin 0.038 0.016 -10000 0 -10000 0 0
CBFA2T3 0.026 0.009 -10000 0 0 63 63
ErbB4/ErbB2/HBEGF -0.009 0.073 0.31 2 -0.56 1 3
MAPK3 -0.02 0.089 0.3 10 -0.52 1 11
STAT1 (dimer) -0.001 0.05 -10000 0 -0.48 1 1
MAPK1 -0.018 0.086 0.33 7 -0.52 1 8
JAK2 0.027 0.008 -10000 0 0 49 49
ErbB4/ErbB2/neuregulin 1 beta -0.025 0.05 0.31 2 -0.56 1 3
NRG1 0.006 0.072 0.18 79 -10000 0 79
NRG3 0.007 0.013 -10000 0 0 422 422
NRG2 0.029 0.004 -10000 0 0 8 8
NRG4 0.027 0.008 -10000 0 0 45 45
heart development -0.001 0.06 0.41 2 -0.7 1 3
neural crest cell migration -0.025 0.051 0.31 2 -0.55 1 3
ERBB2 0.007 0.077 0.18 88 -10000 0 88
WWOX/E4ICDs 0.003 0.073 0.35 2 -0.63 1 3
SHC1 0.029 0.006 -10000 0 0 20 20
ErbB4/EGFR/neuregulin 4 0.003 0.089 0.35 3 -0.61 1 4
apoptosis 0.18 0.17 0.32 282 -0.43 1 283
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.006 0.079 0.38 3 -0.63 1 4
ErbB4/ErbB2/epiregulin -0.008 0.071 0.31 2 -0.56 1 3
ErbB4/ErbB4/betacellulin/betacellulin 0.005 0.077 0.38 3 -0.63 1 4
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.03 0.088 0.38 1 -0.58 1 2
MDM2 -0.015 0.074 0.35 4 -0.63 1 5
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.007 0.063 0.31 2 -0.51 1 3
STAT5A -0.008 0.062 0.38 3 -0.68 1 4
ErbB4/EGFR/neuregulin 1 beta -0.018 0.073 0.31 2 -0.56 1 3
DLG4 0.029 0.006 -10000 0 0 22 22
GRB2/SHC 0.041 0.011 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.002 0.069 0.26 1 -0.6 1 2
STAT5A (dimer) 0.011 0.079 0.35 1 -0.69 1 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.014 0.072 0.37 3 -0.68 1 4
LRIG1 0.028 0.007 -10000 0 0 33 33
EREG 0.028 0.008 -10000 0 0 39 39
BTC 0.027 0.008 -10000 0 0 46 46
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.001 0.06 0.41 2 -0.7 1 3
ERBB4 -0.008 0.08 0.75 2 -0.69 1 3
STAT5B 0.028 0.007 -10000 0 0 33 33
YAP1 0.016 0.047 -10000 0 -0.49 3 3
GRB2 0.029 0.005 -10000 0 0 19 19
ErbB4/ErbB2/neuregulin 4 -0.011 0.074 0.31 2 -0.56 1 3
glial cell differentiation -0.002 0.068 0.59 1 -0.26 1 2
WWOX 0.025 0.011 -10000 0 0 86 86
cell proliferation -0.009 0.08 0.32 5 -0.57 1 6
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.049 0.13 0.22 4 -0.4 42 46
BAG4 0.027 0.009 -10000 0 0 61 61
BAD -0.028 0.045 0.19 2 -0.16 25 27
NFKBIA 0.028 0.006 -10000 0 0 27 27
BIRC3 0.023 0.013 -10000 0 0 123 123
BAX -0.028 0.045 0.18 2 -0.16 24 26
EnzymeConsortium:3.1.4.12 -0.012 0.03 0.069 1 -0.09 41 42
IKBKB -0.047 0.13 0.26 5 -0.39 41 46
MAP2K2 -0.047 0.051 0.22 1 -0.2 14 15
MAP2K1 -0.039 0.048 0.15 3 -0.2 9 12
SMPD1 -0.017 0.037 -10000 0 -0.13 32 32
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.044 0.13 0.23 4 -0.39 41 45
MAP2K4 -0.033 0.041 -10000 0 -0.17 17 17
protein ubiquitination -0.049 0.13 0.27 2 -0.39 41 43
EnzymeConsortium:2.7.1.37 -0.05 0.05 0.16 2 -0.21 11 13
response to UV 0 0 0.002 1 -0.002 3 4
RAF1 -0.034 0.047 0.15 7 -0.19 13 20
CRADD 0.028 0.009 -10000 0 -0.029 10 10
mol:ceramide -0.02 0.045 0.089 1 -0.15 34 35
I-kappa-B-alpha/RELA/p50/ubiquitin 0.035 0.026 -10000 0 -0.13 12 12
MADD 0.028 0.009 -10000 0 -0.017 20 20
MAP3K1 -0.027 0.043 -10000 0 -0.16 25 25
TRADD 0.025 0.011 -10000 0 -0.003 70 70
RELA/p50 0.029 0.003 -10000 0 0 7 7
MAPK3 -0.045 0.053 0.17 2 -0.22 13 15
MAPK1 -0.048 0.057 0.17 1 -0.22 21 22
p50/RELA/I-kappa-B-alpha 0.038 0.031 -10000 0 -0.16 12 12
FADD -0.048 0.13 0.23 4 -0.4 42 46
KSR1 -0.028 0.046 0.15 4 -0.17 22 26
MAPK8 -0.041 0.04 0.21 1 -0.19 7 8
TRAF2 0.028 0.007 -10000 0 -0.002 26 26
response to radiation 0 0 -10000 0 -10000 0 0
CHUK -0.051 0.13 0.2 5 -0.38 42 47
TNF R/SODD 0.03 0.037 -10000 0 -0.16 15 15
TNF 0.027 0.01 -10000 0 -0.012 28 28
CYCS -0.014 0.054 0.13 4 -0.16 16 20
IKBKG -0.049 0.12 0.23 8 -0.37 42 50
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.04 0.14 -10000 0 -0.4 45 45
RELA 0.029 0.003 -10000 0 0 7 7
RIPK1 0.028 0.008 -10000 0 0 41 41
AIFM1 -0.011 0.055 0.12 11 -0.16 13 24
TNF/TNF R/SODD 0.042 0.04 -10000 0 -0.14 15 15
TNFRSF1A 0.026 0.01 -10000 0 0 78 78
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.017 0.067 -10000 0 -0.66 4 4
NSMAF -0.043 0.13 0.21 15 -0.4 39 54
response to hydrogen peroxide 0 0 0.002 1 -0.002 3 4
BCL2 0.023 0.012 -10000 0 0 123 123
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.021 0.026 0.17 8 -10000 0 8
RAS family/GTP 0.027 0.1 0.36 30 -0.23 3 33
NFATC4 -0.025 0.09 0.24 29 -10000 0 29
ERBB2IP 0.012 0.028 -10000 0 -0.048 8 8
HSP90 (dimer) 0.029 0.006 -10000 0 0 21 21
mammary gland morphogenesis -0.024 0.098 0.29 25 -10000 0 25
JUN 0.03 0.14 0.42 45 -10000 0 45
HRAS 0.023 0.02 0.063 4 -0.031 59 63
DOCK7 -0.026 0.085 0.25 18 -10000 0 18
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.018 0.075 0.18 32 -10000 0 32
AKT1 -0.015 0.009 0.013 39 -10000 0 39
BAD -0.025 0.007 -10000 0 -10000 0 0
MAPK10 -0.017 0.077 0.18 38 -10000 0 38
mol:GTP 0.001 0.004 0.018 18 -10000 0 18
ErbB2/ErbB3/neuregulin 1 beta -0.024 0.1 0.31 25 -10000 0 25
RAF1 0.089 0.16 0.38 85 -10000 0 85
ErbB2/ErbB3/neuregulin 2 -0.021 0.063 0.16 30 -0.15 1 31
STAT3 -0.029 0.23 -10000 0 -0.88 38 38
cell migration -0.014 0.078 0.22 29 -0.17 1 30
mol:PI-3-4-5-P3 -0.001 0.002 0.017 2 -10000 0 2
cell proliferation 0.064 0.25 0.67 48 -0.6 5 53
FOS 0.042 0.26 0.65 54 -0.42 59 113
NRAS 0.012 0.017 -10000 0 -0.031 21 21
mol:Ca2+ -0.024 0.098 0.29 25 -10000 0 25
MAPK3 0.069 0.22 0.63 43 -0.54 4 47
MAPK1 0.063 0.23 0.61 47 -0.54 9 56
JAK2 -0.028 0.084 0.25 17 -10000 0 17
NF2 -0.001 0.064 -10000 0 -0.64 5 5
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.001 0.059 0.18 9 -0.19 24 33
NRG1 0.019 0.023 0.073 6 -0.033 6 12
GRB2/SOS1 0.041 0.014 -10000 0 -10000 0 0
MAPK8 -0.023 0.1 0.31 12 -0.23 20 32
MAPK9 -0.016 0.078 0.19 36 -10000 0 36
ERBB2 -0.028 0.02 0.26 1 -10000 0 1
ERBB3 0.018 0.025 0.073 6 -0.033 9 15
SHC1 0.024 0.019 0.062 6 -0.03 56 62
RAC1 0.028 0.006 -10000 0 0 26 26
apoptosis 0.017 0.009 -10000 0 -10000 0 0
STAT3 (dimer) -0.027 0.23 -10000 0 -0.86 38 38
RNF41 -0.028 0.026 0.15 9 -10000 0 9
FRAP1 -0.012 0.005 0.003 42 -10000 0 42
RAC1-CDC42/GTP -0.037 0.057 0.16 2 -0.16 15 17
ErbB2/ErbB2/HSP90 (dimer) -0.031 0.025 0.2 1 -0.15 2 3
CHRNA1 0.075 0.21 0.61 51 -0.43 1 52
myelination -0.018 0.1 0.25 39 -10000 0 39
PPP3CB -0.027 0.083 0.24 18 -10000 0 18
KRAS 0.02 0.02 0.061 3 -0.031 47 50
RAC1-CDC42/GDP 0.017 0.083 0.2 1 -0.19 26 27
NRG2 0.029 0.004 -10000 0 0 8 8
mol:GDP -0.001 0.058 0.18 9 -0.19 24 33
SOS1 0.023 0.019 0.059 2 -0.03 51 53
MAP2K2 0.057 0.16 0.41 63 -10000 0 63
SRC 0.028 0.007 -10000 0 0 33 33
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.03 0.083 0.24 15 -10000 0 15
MAP2K1 0.081 0.22 0.61 45 -0.55 7 52
heart morphogenesis -0.024 0.098 0.29 25 -10000 0 25
RAS family/GDP 0.044 0.087 0.31 17 -0.23 3 20
GRB2 0.024 0.019 0.058 3 -0.03 54 57
PRKACA 0.005 0.065 -10000 0 -0.67 5 5
CHRNE 0.01 0.055 0.18 35 -10000 0 35
HSP90AA1 0.029 0.006 -10000 0 0 21 21
activation of caspase activity 0.015 0.009 -10000 0 -0.013 39 39
nervous system development -0.024 0.098 0.29 25 -10000 0 25
CDC42 0.029 0.005 -10000 0 0 13 13
BCR 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
JUN -0.03 0.11 0.22 3 -0.37 27 30
IKBKB 0.007 0.078 0.26 7 -0.3 7 14
AKT1 0 0.099 0.26 37 -0.25 4 41
IKBKG 0.003 0.066 0.25 2 -0.26 8 10
CALM1 -0.01 0.063 0.18 3 -0.25 14 17
PIK3CA 0.021 0.014 -10000 0 0 174 174
MAP3K1 -0.026 0.14 0.26 3 -0.47 33 36
MAP3K7 0.028 0.007 -10000 0 0 30 30
mol:Ca2+ -0.004 0.069 0.2 1 -0.26 17 18
DOK1 0.029 0.004 -10000 0 0 10 10
AP-1 -0.021 0.073 0.22 4 -0.21 21 25
LYN 0.027 0.008 -10000 0 0 49 49
BLNK 0.028 0.007 -10000 0 0 29 29
SHC1 0.029 0.006 -10000 0 0 20 20
BCR complex 0.04 0.012 -10000 0 -10000 0 0
CD22 -0.037 0.08 0.23 2 -0.3 22 24
CAMK2G -0.02 0.068 -10000 0 -0.26 13 13
CSNK2A1 0.028 0.008 -10000 0 0 42 42
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.064 0.036 -10000 0 -0.23 2 2
GO:0007205 -0.005 0.07 0.2 1 -0.26 17 18
SYK 0.029 0.006 -10000 0 0 23 23
ELK1 -0.008 0.076 0.21 17 -0.26 17 34
NFATC1 -0.029 0.091 0.21 8 -0.32 22 30
B-cell antigen/BCR complex 0.04 0.012 -10000 0 -10000 0 0
PAG1/CSK 0.04 0.013 -10000 0 -10000 0 0
NFKBIB 0.01 0.048 0.14 2 -0.13 16 18
HRAS -0.016 0.069 0.19 2 -0.28 14 16
NFKBIA 0.01 0.047 0.13 3 -0.12 43 46
NF-kappa-B/RelA/I kappa B beta 0.014 0.042 0.12 6 -0.1 23 29
RasGAP/Csk 0.069 0.052 -10000 0 -0.14 3 3
mol:GDP -0.005 0.069 0.2 1 -0.25 17 18
PTEN 0.028 0.007 -10000 0 0 37 37
CD79B 0.029 0.005 -10000 0 0 13 13
NF-kappa-B/RelA/I kappa B alpha 0.014 0.042 0.12 6 -0.1 33 39
GRB2 0.029 0.005 -10000 0 0 19 19
PI3K/BCAP/CD19 -0.069 0.15 0.3 1 -0.41 37 38
PIK3R1 0.021 0.013 -10000 0 0 159 159
mol:IP3 -0.004 0.07 0.2 1 -0.26 16 17
CSK 0.029 0.006 -10000 0 0 22 22
FOS -0.017 0.083 0.23 8 -0.27 18 26
CHUK 0.001 0.081 0.22 4 -0.29 22 26
IBTK 0.028 0.007 -10000 0 0 30 30
CARD11/BCL10/MALT1/TAK1 0.011 0.082 0.21 1 -0.26 13 14
PTPN6 -0.036 0.084 0.2 3 -0.3 21 24
RELA 0.029 0.003 -10000 0 0 7 7
BCL2A1 0.007 0.031 0.1 4 -0.083 14 18
VAV2 -0.019 0.096 0.25 3 -0.34 26 29
ubiquitin-dependent protein catabolic process 0.01 0.048 0.13 3 -0.12 48 51
BTK 0.018 0.044 -10000 0 -0.99 1 1
CD19 -0.015 0.078 0.23 2 -0.3 18 20
MAP4K1 0.026 0.01 -10000 0 0 67 67
CD72 0.029 0.005 -10000 0 0 13 13
PAG1 0.028 0.008 -10000 0 0 40 40
MAPK14 -0.025 0.13 0.26 7 -0.4 32 39
SH3BP5 0.029 0.005 -10000 0 0 13 13
PIK3AP1 -0.009 0.071 0.25 3 -0.26 18 21
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.001 0.088 -10000 0 -0.32 29 29
RAF1 -0.024 0.066 0.2 3 -0.28 13 16
RasGAP/p62DOK/SHIP 0.057 0.045 -10000 0 -0.14 5 5
CD79A 0.028 0.007 -10000 0 0 35 35
re-entry into mitotic cell cycle -0.021 0.072 0.22 4 -0.22 19 23
RASA1 0.027 0.009 -10000 0 0 51 51
MAPK3 -0.037 0.062 0.24 3 -0.26 12 15
MAPK1 -0.032 0.065 0.24 4 -0.26 12 16
CD72/SHP1 -0.022 0.11 0.26 24 -0.3 21 45
NFKB1 0.027 0.008 -10000 0 0 45 45
MAPK8 -0.028 0.12 0.24 3 -0.42 30 33
actin cytoskeleton organization -0.022 0.094 0.26 7 -0.33 20 27
NF-kappa-B/RelA 0.023 0.087 0.25 3 -0.22 34 37
Calcineurin 0.008 0.082 -10000 0 -0.26 13 13
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 0.028 0.007 -10000 0 0 34 34
Bam32/HPK1 -0.017 0.21 -10000 0 -0.67 42 42
DAPP1 -0.034 0.23 -10000 0 -0.77 41 41
cytokine secretion -0.027 0.086 0.21 8 -0.31 20 28
mol:DAG -0.004 0.07 0.2 1 -0.26 16 17
PLCG2 0.026 0.009 -10000 0 0 62 62
MAP2K1 -0.029 0.065 0.23 2 -0.27 13 15
B-cell antigen/BCR complex/FcgammaRIIB 0.051 0.024 -10000 0 -0.15 1 1
mol:PI-3-4-5-P3 -0.011 0.1 0.24 37 -0.26 7 44
ETS1 -0.021 0.071 0.22 2 -0.26 12 14
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.062 0.062 -10000 0 -0.15 26 26
B-cell antigen/BCR complex/LYN 0.006 0.081 -10000 0 -0.31 19 19
MALT1 0.026 0.01 -10000 0 0 76 76
TRAF6 0.029 0.004 -10000 0 0 12 12
RAC1 -0.023 0.093 0.24 5 -0.34 21 26
B-cell antigen/BCR complex/LYN/SYK -0.002 0.12 0.32 5 -0.28 15 20
CARD11 -0.013 0.07 0.19 5 -0.26 16 21
FCGR2B 0.027 0.008 -10000 0 0 47 47
PPP3CA 0.028 0.008 -10000 0 0 43 43
BCL10 0.029 0.004 -10000 0 0 10 10
IKK complex 0.012 0.045 0.15 21 -0.12 5 26
PTPRC 0.024 0.012 -10000 0 0 102 102
PDPK1 -0.007 0.093 0.22 43 -0.18 7 50
PPP3CB 0.029 0.004 -10000 0 0 12 12
PPP3CC 0.024 0.012 -10000 0 0 102 102
POU2F2 0.007 0.03 0.15 3 -0.1 4 7
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.032 0.033 -10000 0 -0.16 11 11
CRKL -0.004 0.11 0.27 5 -0.44 23 28
mol:PIP3 0.013 0.07 -10000 0 -0.78 4 4
AKT1 -0.005 0.071 -10000 0 -0.7 4 4
PTK2B 0.024 0.011 -10000 0 0 100 100
RAPGEF1 -0.011 0.11 0.28 4 -0.44 21 25
RANBP10 0.027 0.009 -10000 0 0 59 59
PIK3CA 0.021 0.014 -10000 0 0 174 174
HGF/MET/SHIP2 0.046 0.036 -10000 0 -0.15 11 11
MAP3K5 -0.005 0.11 0.24 5 -0.44 22 27
HGF/MET/CIN85/CBL/ENDOPHILINS 0.068 0.047 -10000 0 -0.14 12 12
AP1 -0.022 0.071 0.14 32 -0.16 46 78
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.029 0.006 -10000 0 0 20 20
apoptosis -0.066 0.27 -10000 0 -0.71 80 80
STAT3 (dimer) -0.003 0.078 0.17 10 -0.27 18 28
GAB1/CRKL/SHP2/PI3K -0.007 0.12 0.28 2 -0.44 21 23
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.009 0.11 0.28 3 -0.44 21 24
PTPN11 0.029 0.003 -10000 0 0 7 7
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.028 0.007 -10000 0 0 32 32
PTEN 0.028 0.007 -10000 0 0 37 37
ELK1 0.032 0.15 0.41 48 -0.26 1 49
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.006 0.048 0.15 5 -0.19 7 12
PAK1 0.001 0.087 0.38 1 -0.68 4 5
HGF/MET/RANBP10 0.042 0.038 -10000 0 -0.15 12 12
HRAS 0.004 0.1 -10000 0 -0.46 22 22
DOCK1 -0.01 0.11 0.3 5 -0.43 22 27
GAB1 0.002 0.11 0.24 1 -0.46 23 24
CRK -0.004 0.11 0.28 3 -0.45 22 25
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.094 -10000 0 -0.42 17 17
JUN 0.028 0.007 -10000 0 0 32 32
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0 0.032 -10000 0 -0.18 13 13
PIK3R1 0.021 0.013 -10000 0 0 159 159
cell morphogenesis 0.004 0.13 0.29 20 -0.37 16 36
GRB2/SHC 0.04 0.052 0.19 3 -0.18 12 15
FOS 0.024 0.012 -10000 0 0 104 104
GLMN 0.002 0.001 -10000 0 -10000 0 0
cell motility 0.032 0.15 0.41 48 -0.26 1 49
HGF/MET/MUC20 0.03 0.028 -10000 0 -0.13 12 12
cell migration 0.039 0.051 0.19 3 -0.18 12 15
GRB2 0.029 0.005 -10000 0 0 19 19
CBL 0.029 0.004 -10000 0 0 12 12
MET/RANBP10 0.03 0.034 -10000 0 -0.16 12 12
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.005 0.06 0.19 1 -0.27 8 9
MET/MUC20 0.015 0.026 -10000 0 -0.15 12 12
RAP1B -0.014 0.11 0.27 6 -0.43 20 26
RAP1A -0.019 0.1 0.28 5 -0.42 21 26
HGF/MET/RANBP9 0.044 0.036 -10000 0 -0.15 11 11
RAF1 -0.002 0.1 0.32 1 -0.45 21 22
STAT3 -0.003 0.076 0.17 10 -0.26 17 27
cell proliferation -0.007 0.094 0.27 9 -0.35 13 22
RPS6KB1 0.019 0.045 -10000 0 -0.24 7 7
MAPK3 0.025 0.16 0.64 28 -10000 0 28
MAPK1 0.041 0.19 0.66 41 -10000 0 41
RANBP9 0.028 0.008 -10000 0 0 40 40
MAPK8 -0.007 0.1 0.3 1 -0.42 18 19
SRC -0.01 0.064 0.18 1 -0.27 8 9
PI3K 0.007 0.066 0.2 1 -0.18 17 18
MET/Glomulin 0.027 0.033 -10000 0 -0.071 21 21
SOS1 0.028 0.007 -10000 0 0 34 34
MAP2K1 -0.009 0.095 0.3 1 -0.42 21 22
MET 0.025 0.011 -10000 0 0 88 88
MAP4K1 0.002 0.12 0.26 4 -0.47 22 26
PTK2 0.021 0.014 -10000 0 0 162 162
MAP2K2 -0.02 0.097 0.28 2 -0.45 19 21
BAD -0.013 0.069 -10000 0 -0.68 4 4
MAP2K4 -0.012 0.1 0.24 2 -0.41 22 24
SHP2/GRB2/SOS1/GAB1 0.015 0.11 -10000 0 -0.4 23 23
INPPL1 0.029 0.006 -10000 0 0 20 20
PXN 0.029 0.005 -10000 0 0 14 14
SH3KBP1 0.029 0.005 -10000 0 0 19 19
HGS -0.009 0.042 0.17 1 -0.18 13 14
PLCgamma1/PKC 0.021 0.005 -10000 0 -10000 0 0
HGF 0.029 0.005 -10000 0 0 16 16
RASA1 0.027 0.009 -10000 0 0 51 51
NCK1 0.026 0.009 -10000 0 0 63 63
PTPRJ 0.029 0.004 -10000 0 0 10 10
NCK/PLCgamma1 0.038 0.049 0.19 3 -0.18 12 15
PDPK1 0.001 0.068 -10000 0 -0.73 4 4
HGF/MET/SHIP 0.03 0.028 -10000 0 -0.13 12 12
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.12 0.25 0.59 19 -0.77 1 20
PCK1 0.17 0.24 0.56 102 -10000 0 102
HNF4A 0.15 0.3 0.72 50 -0.77 1 51
KCNJ11 0.12 0.26 0.6 9 -0.73 2 11
AKT1 0.096 0.19 0.39 55 -0.39 2 57
response to starvation 0 0.01 0.17 2 -10000 0 2
DLK1 0.14 0.29 0.76 24 -0.82 1 25
NKX2-1 0.11 0.18 0.47 33 -10000 0 33
ACADM 0.12 0.25 0.59 23 -0.77 1 24
TAT 0.12 0.19 0.51 17 -10000 0 17
CEBPB 0.028 0.013 0.19 2 -10000 0 2
CEBPA 0.027 0.012 0.18 2 -10000 0 2
TTR 0.13 0.18 0.7 10 -10000 0 10
PKLR 0.12 0.26 0.64 25 -0.77 1 26
APOA1 0.2 0.36 0.91 54 -1 1 55
CPT1C 0.12 0.26 0.64 25 -0.68 2 27
ALAS1 0.085 0.18 0.78 3 -0.63 1 4
TFRC 0.25 0.35 0.75 142 -10000 0 142
FOXF1 0.026 0.009 -10000 0 -10000 0 0
NF1 0.027 0.02 0.23 4 -10000 0 4
HNF1A (dimer) 0.022 0.023 -10000 0 -0.25 1 1
CPT1A 0.12 0.25 0.59 20 -0.77 3 23
HMGCS1 0.14 0.28 0.67 52 -0.77 1 53
NR3C1 0.029 0.005 -10000 0 -10000 0 0
CPT1B 0.1 0.24 0.58 17 -0.77 1 18
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.029 0.012 -10000 0 -0.25 1 1
GCK 0.12 0.25 0.58 20 -0.77 1 21
CREB1 0.064 0.077 0.23 98 -10000 0 98
IGFBP1 0.098 0.16 0.5 5 -10000 0 5
PDX1 0.092 0.17 -10000 0 -0.99 1 1
UCP2 0.036 0.37 0.61 23 -0.76 56 79
ALDOB 0.12 0.26 0.6 7 -0.82 1 8
AFP 0.041 0.063 0.56 1 -10000 0 1
BDH1 0.15 0.28 0.69 41 -0.79 1 42
HADH 0.11 0.27 0.6 7 -0.89 5 12
F2 0.17 0.3 0.77 27 -0.96 1 28
HNF1A 0.022 0.023 -10000 0 -0.25 1 1
G6PC 0.05 0.082 -10000 0 -10000 0 0
SLC2A2 0.12 0.2 0.59 6 -10000 0 6
INS 0.028 0.023 -10000 0 -0.23 4 4
FOXA1 0.017 0.034 0.34 2 -10000 0 2
FOXA3 0.097 0.16 0.28 208 -10000 0 208
FOXA2 0.19 0.36 0.8 50 -0.77 4 54
ABCC8 0.12 0.26 0.6 9 -0.7 3 12
ALB 0.041 0.065 0.51 2 -10000 0 2
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.041 0.048 -10000 0 -0.15 26 26
fibroblast growth factor receptor signaling pathway 0.04 0.048 -10000 0 -0.15 26 26
LAMA1 0.024 0.012 -10000 0 0 113 113
PRNP 0.028 0.008 -10000 0 0 43 43
GPC1/SLIT2 0.022 0.059 -10000 0 -0.16 48 48
SMAD2 -0.042 0.026 0.17 6 -10000 0 6
GPC1/PrPc/Cu2+ 0.034 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 0.043 0.008 -10000 0 -10000 0 0
APP/GPC1 0.039 0.025 -10000 0 -0.16 7 7
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.035 0.013 -10000 0 -10000 0 0
FLT1 0.028 0.007 -10000 0 0 28 28
GPC1/TGFB/TGFBR1/TGFBR2 0.054 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 0.074 0.24 5 -0.26 12 17
SLIT2 0.025 0.011 -10000 0 0 90 90
GPC1/NRG 0.036 0.018 -10000 0 -10000 0 0
NRG1 0.025 0.011 -10000 0 0 96 96
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.05 0.023 -10000 0 -10000 0 0
LYN -0.035 0.013 -10000 0 -10000 0 0
mol:Spermine -0.016 0.003 -10000 0 -10000 0 0
cell growth 0.04 0.048 -10000 0 -0.15 26 26
BMP signaling pathway -0.029 0.005 0 17 -10000 0 17
SRC -0.036 0.012 -10000 0 -10000 0 0
TGFBR1 0.029 0.005 -10000 0 0 16 16
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.017 0.015 -10000 0 0 248 248
GPC1 0.029 0.005 -10000 0 0 17 17
TGFBR1 (dimer) 0.029 0.005 -10000 0 0 16 16
VEGFA 0.026 0.01 -10000 0 0 69 69
BLK -0.032 0.016 -10000 0 -10000 0 0
HCK -0.035 0.013 -10000 0 -10000 0 0
FGF2 0.028 0.008 -10000 0 0 42 42
FGFR1 0.026 0.01 -10000 0 0 74 74
VEGFR1 homodimer 0.028 0.007 -10000 0 0 28 28
TGFBR2 0.029 0.005 -10000 0 0 14 14
cell death 0.039 0.025 -10000 0 -0.16 7 7
ATIII/GPC1 0.042 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 0.035 0.018 -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 27 27
TGFBR2 (dimer) 0.029 0.005 -10000 0 0 14 14
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.045 0.043 -9999 0 -0.16 18 18
E-cadherin/beta catenin 0.036 0.027 -9999 0 -0.16 7 7
CTNNB1 0.029 0.004 -9999 0 0 8 8
JUP 0.028 0.008 -9999 0 0 40 40
CDH1 0.026 0.01 -9999 0 0 69 69
IL27-mediated signaling events

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
TGFB1 0.024 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 0.13 0.57 7 -0.38 25 32
IL27/IL27R/JAK1 0.058 0.13 0.52 8 -0.94 3 11
TBX21 0.046 0.14 0.42 32 -0.57 3 35
IL12B 0.032 0.014 0.09 26 -10000 0 26
IL12A -0.012 0.015 0.045 23 -10000 0 23
IL6ST -0.01 0.035 0.094 29 -10000 0 29
IL27RA/JAK1 0.012 0.11 0.38 2 -1 3 5
IL27 -0.01 0.036 0.093 30 -10000 0 30
TYK2 -0.011 0.041 0.15 26 -10000 0 26
T-helper cell lineage commitment -0.03 0.091 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.002 0.13 0.57 7 -0.38 25 32
T cell proliferation during immune response -0.002 0.13 0.57 7 -0.38 25 32
MAPKKK cascade 0.002 0.13 0.38 25 -0.57 7 32
STAT3 0.028 0.008 -10000 0 0 38 38
STAT2 0.026 0.01 -10000 0 0 74 74
STAT1 0.007 0.018 0.077 1 -10000 0 1
IL12RB1 0.029 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 0.4 35 -0.57 3 38
IL27/IL27R/JAK2/TYK2 0.002 0.14 0.39 25 -0.58 7 32
positive regulation of T cell mediated cytotoxicity 0.002 0.13 0.38 25 -0.57 7 32
STAT1 (dimer) 0.07 0.12 0.54 2 -0.78 3 5
JAK2 -0.008 0.038 0.12 23 -10000 0 23
JAK1 -0.005 0.029 0.076 2 -10000 0 2
STAT2 (dimer) 0.011 0.13 0.36 17 -0.52 7 24
T cell proliferation -0.011 0.13 0.35 26 -0.6 6 32
IL12/IL12R/TYK2/JAK2 0.017 0.19 0.47 22 -0.72 25 47
IL17A -0.029 0.09 -10000 0 -10000 0 0
mast cell activation -0.002 0.13 0.57 7 -0.38 25 32
IFNG 0.016 0.063 0.27 27 -0.11 3 30
T cell differentiation -0.001 0.006 0.027 18 -0.023 3 21
STAT3 (dimer) 0.016 0.14 0.35 23 -0.54 8 31
STAT5A (dimer) 0.017 0.14 0.35 25 -0.56 7 32
STAT4 (dimer) 0.018 0.14 0.35 24 -0.52 8 32
STAT4 0.029 0.005 -10000 0 0 16 16
T cell activation -0.001 0.012 0.11 1 -0.24 1 2
IL27R/JAK2/TYK2 0.046 0.12 0.41 23 -0.96 3 26
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 0.34 23 -0.53 8 31
IL27/EBI3 0.046 0.031 0.16 24 -10000 0 24
IL27RA 0.019 0.12 0.42 5 -1.1 3 8
IL6 0.027 0.009 -10000 0 -10000 0 0
STAT5A 0.028 0.007 -10000 0 0 33 33
monocyte differentiation 0.001 0.004 0.017 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 0.093 27 -10000 0 27
TNF -0.015 0.007 0.009 41 -10000 0 41
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.029 0.006 -10000 0 0 21 21
VLDLR 0.027 0.009 -10000 0 0 60 60
LRPAP1 0.028 0.007 -10000 0 0 33 33
NUDC 0.029 0.005 -10000 0 0 17 17
RELN/LRP8 0.019 0.075 -10000 0 -0.15 89 89
CaM/Ca2+ 0.019 0.022 -10000 0 -0.15 9 9
KATNA1 0.028 0.007 -10000 0 0 35 35
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.041 0.073 0.16 48 -0.23 1 49
IQGAP1/CaM 0.037 0.031 -10000 0 -0.16 11 11
DAB1 0.029 0.006 -10000 0 0 20 20
IQGAP1 0.029 0.006 -10000 0 0 24 24
PLA2G7 0.025 0.011 -10000 0 0 82 82
CALM1 0.028 0.006 -10000 0 0 25 25
DYNLT1 0.025 0.011 -10000 0 0 82 82
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.04 0.018 -10000 0 -0.16 2 2
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.029 0.004 -10000 0 0 10 10
CDK5R1 0.028 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 0.015 0.077 -10000 0 -0.15 97 97
YWHAE 0.028 0.008 -10000 0 0 41 41
NDEL1/14-3-3 E -0.033 0.1 0.28 18 -0.24 1 19
MAP1B -0.012 0.052 0.13 1 -0.19 43 44
RAC1 -0.013 0.039 -10000 0 -0.26 13 13
p35/CDK5 -0.037 0.085 0.21 21 -0.22 1 22
RELN 0.023 0.013 -10000 0 0 132 132
PAFAH/LIS1 -0.031 0.016 -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 0.091 0.2 1 -0.28 20 21
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.029 0.086 0.27 12 -0.21 2 14
LIS1/IQGAP1 -0.035 0.014 -10000 0 -0.15 2 2
RHOA -0.009 0.022 -10000 0 -0.28 3 3
PAFAH1B1 -0.029 0.011 -10000 0 -10000 0 0
PAFAH1B3 0.027 0.008 -10000 0 0 45 45
PAFAH1B2 0.029 0.005 -10000 0 0 19 19
MAP1B/LIS1/Dynein heavy chain -0.041 0.043 -10000 0 -0.22 5 5
NDEL1/Katanin 60/Dynein heavy chain -0.038 0.1 0.27 17 -0.25 1 18
LRP8 0.029 0.006 -10000 0 0 20 20
NDEL1/Katanin 60 -0.034 0.098 0.26 17 -0.24 1 18
P39/CDK5 -0.037 0.087 0.2 24 -0.22 1 25
LIS1/NudC/Dynein intermediate chain/microtubule organizing center -0.035 0.013 -10000 0 -10000 0 0
CDK5 -0.036 0.077 0.18 17 -0.23 1 18
PPP2R5D 0.029 0.006 -10000 0 0 24 24
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.029 0.009 -10000 0 -10000 0 0
CSNK2A1 0.028 0.008 -10000 0 0 42 42
RELN/VLDLR/DAB1/LIS1 0.021 0.08 -10000 0 -0.14 85 85
RELN/VLDLR 0.028 0.085 -10000 0 -0.14 94 94
CDC42 -0.009 0.02 -10000 0 -0.26 3 3
Cellular roles of Anthrax toxin

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
ANTXR1 0.028 0.006 -10000 0 0 25 25
ANTXR2 0.028 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 -10000 0 -0.36 75 75
MAP2K2 -0.13 0.27 -10000 0 -0.63 124 124
MAP2K1 -0.016 0.01 0.15 1 -10000 0 1
MAP2K7 -0.015 0.007 -10000 0 -0.062 2 2
MAP2K6 0.005 0.056 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 -0.062 2 2
IL1B -0.01 0.052 0.15 43 -0.12 2 45
Channel 0.028 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 25 25
negative regulation of phagocytosis -0.008 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 -10000 0 0
PGR -0.006 0.027 -10000 0 -0.13 23 23
PA/Cellular Receptors 0.03 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) 0.027 0.035 -10000 0 -0.12 24 24
macrophage activation -0.025 0.015 -10000 0 -0.11 11 11
TNF 0.029 0.005 -10000 0 0 16 16
VCAM1 -0.023 0.14 -10000 0 -0.36 75 75
platelet activation -0.008 0.079 -10000 0 -0.44 18 18
MAPKKK cascade 0.016 0.035 0.099 4 -0.1 10 14
IL18 0.008 0.069 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 0.043 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) 0.028 0.033 -10000 0 -0.12 24 24
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.028 0.006 -10000 0 0 27 27
EGFR 0.027 0.009 -10000 0 0 55 55
EGF/EGFR 0.033 0.053 -10000 0 -0.12 41 41
EGF/EGFR dimer/SHC/GRB2/SOS1 0.059 0.068 -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 0.028 0.008 -10000 0 0 41 41
EGF/EGFR dimer/SHC 0.038 0.055 -10000 0 -0.15 41 41
mol:GDP 0.053 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 48 48
GRB2/SOS1 0.04 0.013 -10000 0 -10000 0 0
HRAS/GTP -0.056 0.03 -10000 0 -0.14 36 36
SHC1 0.029 0.006 -10000 0 0 20 20
HRAS/GDP 0.048 0.066 -10000 0 -0.14 36 36
FRAP1 -0.046 0.039 0.1 21 -10000 0 21
EGF/EGFR dimer 0.024 0.056 -10000 0 -0.16 43 43
SOS1 0.028 0.007 -10000 0 0 34 34
GRB2 0.029 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 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
INCENP 0.029 0.003 -9999 0 0 6 6
Aurora C/Aurora B/INCENP 0.04 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 0.023 0.013 -9999 0 0 136 136
AURKC 0.028 0.006 -9999 0 0 26 26
Fc-epsilon receptor I signaling in mast 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
PPAP2A 0.027 0.008 -10000 0 0 45 45
LAT2 -0.009 0.073 0.15 2 -0.26 23 25
AP1 0.026 0.1 -10000 0 -0.38 10 10
mol:PIP3 -0.018 0.09 0.24 9 -0.31 19 28
IKBKB -0.01 0.07 0.21 19 -0.19 15 34
AKT1 -0.007 0.13 0.26 48 -0.25 8 56
IKBKG -0.011 0.066 0.2 16 -0.19 15 31
MS4A2 -0.01 0.032 0.061 7 -10000 0 7
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.008 0.024 -10000 0 -0.033 1 1
MAP3K1 0.015 0.11 0.24 34 -0.32 12 46
mol:Ca2+ -0.013 0.075 0.21 10 -0.24 18 28
LYN -0.01 0.03 0.064 1 -10000 0 1
CBLB -0.008 0.072 0.15 3 -0.26 21 24
SHC1 0.029 0.006 -10000 0 0 20 20
RasGAP/p62DOK 0.013 0.074 -10000 0 -0.13 107 107
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.031 0.086 0.24 18 -0.2 4 22
PTPN13 -0.022 0.11 -10000 0 -0.52 9 9
PTPN11 -0.008 0.034 0.065 4 -10000 0 4
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.013 0.1 0.27 14 -0.33 4 18
SYK -0.008 0.032 0.064 1 -10000 0 1
GRB2 0.025 0.016 -10000 0 -0.03 40 40
LAT/PLCgamma1/GRB2/SLP76/GADs -0.024 0.076 0.16 1 -0.29 22 23
LAT -0.008 0.071 0.15 2 -0.26 22 24
PAK2 0.022 0.12 0.23 59 -0.34 13 72
NFATC2 -0.02 0.072 -10000 0 -0.39 20 20
HRAS 0.004 0.094 0.24 7 -0.35 15 22
GAB2 0.027 0.009 -10000 0 0 62 62
PLA2G1B -0.003 0.067 -10000 0 -0.91 2 2
Fc epsilon R1 0.039 0.046 -10000 0 -0.12 30 30
Antigen/IgE/Fc epsilon R1 0.037 0.041 -10000 0 -0.11 25 25
mol:GDP 0.011 0.091 0.2 4 -0.35 15 19
JUN 0.028 0.007 -10000 0 0 32 32
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.02 0.017 -10000 0 -10000 0 0
FOS 0.024 0.012 -10000 0 0 104 104
Antigen/IgE/Fc epsilon R1/LYN/SYK 0.004 0.075 -10000 0 -0.26 23 23
CHUK -0.012 0.063 0.17 14 -0.19 17 31
KLRG1 -0.012 0.06 -10000 0 -0.25 15 15
VAV1 -0.007 0.072 0.15 3 -0.27 19 22
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.008 0.073 0.15 2 -0.26 23 25
negative regulation of mast cell degranulation -0.019 0.049 -10000 0 -0.25 13 13
BTK 0.012 0.086 -10000 0 -0.36 13 13
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.001 0.067 0.18 24 -0.19 12 36
GAB2/PI3K/SHP2 -0.059 0.063 -10000 0 -0.18 71 71
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.001 0.058 -10000 0 -0.21 16 16
RAF1 0.02 0.064 -10000 0 -0.97 2 2
Fc epsilon R1/FcgammaRIIB/SHIP 0.056 0.049 -10000 0 -0.12 23 23
FCER1G -0.016 0.025 0.065 1 -10000 0 1
FCER1A -0.009 0.031 -10000 0 -10000 0 0
Antigen/IgE/Fc epsilon R1/Fyn 0.034 0.077 -10000 0 -0.13 77 77
MAPK3 -0.003 0.068 -10000 0 -0.89 2 2
MAPK1 -0.006 0.073 -10000 0 -0.96 2 2
NFKB1 0.027 0.008 -10000 0 0 45 45
MAPK8 -0.005 0.16 -10000 0 -0.55 24 24
DUSP1 0.023 0.012 -10000 0 0 124 124
NF-kappa-B/RelA -0.012 0.053 0.14 17 -0.15 8 25
actin cytoskeleton reorganization -0.006 0.1 -10000 0 -0.58 6 6
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.03 0.09 0.2 2 -0.36 16 18
FER -0.006 0.07 0.14 1 -0.27 20 21
RELA 0.029 0.003 -10000 0 0 7 7
ITK 0.003 0.039 0.12 6 -0.22 10 16
SOS1 0.028 0.007 -10000 0 0 34 34
PLCG1 0.007 0.095 0.27 7 -0.34 14 21
cytokine secretion -0.012 0.034 0.073 9 -0.1 14 23
SPHK1 -0.007 0.071 0.15 3 -0.26 20 23
PTK2 -0.007 0.11 -10000 0 -0.6 6 6
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.003 0.083 -10000 0 -0.3 24 24
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.021 0.094 0.22 8 -0.3 22 30
MAP2K2 -0.009 0.067 -10000 0 -0.91 2 2
MAP2K1 0.006 0.062 -10000 0 -0.91 2 2
MAP2K7 0.028 0.008 -10000 0 0 38 38
KLRG1/SHP2 -0.005 0.071 0.18 37 -0.25 12 49
MAP2K4 -0.069 0.3 -10000 0 -0.87 67 67
Fc epsilon R1/FcgammaRIIB 0.06 0.052 -10000 0 -0.13 24 24
mol:Choline -0.03 0.086 0.24 18 -0.2 4 22
SHC/Grb2/SOS1 0.051 0.083 -10000 0 -0.26 18 18
FYN 0.024 0.011 -10000 0 0 100 100
DOK1 0.029 0.004 -10000 0 0 10 10
PXN -0.016 0.1 -10000 0 -0.56 6 6
HCLS1 -0.008 0.074 0.16 6 -0.27 21 27
PRKCB -0.015 0.075 0.19 12 -0.24 20 32
FCGR2B 0.027 0.008 -10000 0 0 47 47
IGHE 0 0.006 0.021 8 -10000 0 8
KLRG1/SHIP -0.02 0.05 -10000 0 -0.26 13 13
LCP2 0.025 0.015 -10000 0 -0.03 28 28
PLA2G4A -0.046 0.086 0.15 4 -0.3 27 31
RASA1 0.027 0.009 -10000 0 0 51 51
mol:Phosphatidic acid -0.03 0.086 0.24 18 -0.2 4 22
IKK complex -0.008 0.067 0.2 23 -0.17 2 25
WIPF1 0.029 0.005 -10000 0 0 13 13
Ceramide signaling pathway

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
SPHK2 -0.03 0.011 -10000 0 -10000 0 0
MAP4K4 -0.034 0.088 0.19 2 -0.29 34 36
BAG4 0.027 0.009 -10000 0 0 61 61
PKC zeta/ceramide 0.029 0.029 -10000 0 -0.18 8 8
NFKBIA 0.028 0.006 -10000 0 0 27 27
BIRC3 0.023 0.012 -10000 0 0 121 121
BAX 0.008 0.058 -10000 0 -0.33 15 15
RIPK1 0.028 0.008 -10000 0 0 41 41
AKT1 -0.011 0.11 0.68 14 -10000 0 14
BAD 0.002 0.031 0.21 3 -0.18 9 12
SMPD1 -0.01 0.064 0.18 6 -0.21 28 34
RB1 0.007 0.041 0.18 20 -0.18 8 28
FADD/Caspase 8 -0.033 0.096 0.21 6 -0.32 33 39
MAP2K4 -0.009 0.026 -10000 0 -0.19 8 8
NSMAF 0.028 0.007 -10000 0 0 32 32
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.005 0.038 0.19 11 -0.19 8 19
EGF 0.028 0.008 -10000 0 0 41 41
mol:ceramide 0.012 0.028 0.13 1 -0.19 9 10
MADD 0.029 0.004 -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 0.025 0.011 -10000 0 0 93 93
negative regulation of cell cycle 0.007 0.041 0.18 20 -0.18 8 28
cell proliferation -0.032 0.054 0.19 4 -0.23 5 9
BID -0.038 0.18 -10000 0 -0.63 42 42
MAP3K1 0 0.026 -10000 0 -0.18 9 9
EIF2A 0.065 0.099 0.22 81 -0.2 2 83
TRADD 0.026 0.009 -10000 0 0 63 63
CRADD 0.029 0.005 -10000 0 0 13 13
MAPK3 -0.021 0.047 0.19 4 -0.23 5 9
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.025 0.048 0.19 4 -0.22 4 8
Cathepsin D/ceramide 0.029 0.031 -10000 0 -0.18 9 9
FADD -0.035 0.089 0.19 4 -0.29 35 39
KSR1 0.003 0.034 0.22 5 -0.18 9 14
MAPK8 0.001 0.04 -10000 0 -10000 0 0
PRKRA 0.007 0.044 0.21 16 -0.18 9 25
PDGFA 0.027 0.008 -10000 0 0 45 45
TRAF2 0.029 0.006 -10000 0 0 24 24
IGF1 0.028 0.007 -10000 0 0 32 32
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process 0.012 0.028 0.13 1 -0.18 9 10
CTSD 0.028 0.007 -10000 0 0 28 28
regulation of nitric oxide biosynthetic process 0.038 0.024 -10000 0 -0.16 6 6
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.034 0.058 0.2 4 -0.24 5 9
PRKCD 0.029 0.005 -10000 0 0 15 15
PRKCZ 0.029 0.006 -10000 0 0 22 22
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 0.024 -10000 0 -0.16 6 6
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.029 0.005 -10000 0 0 15 15
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.02 0.092 -10000 0 -0.28 39 39
TNFR1A/BAG4/TNF-alpha 0.042 0.04 -10000 0 -0.14 15 15
mol:Sphingosine-1-phosphate -0.03 0.011 -10000 0 -10000 0 0
MAP2K1 -0.013 0.039 0.18 5 -0.19 6 11
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.029 0.003 -10000 0 0 7 7
CYCS 0.025 0.058 0.18 5 -0.17 8 13
TNFRSF1A 0.026 0.01 -10000 0 0 78 78
NFKB1 0.027 0.008 -10000 0 0 45 45
TNFR1A/BAG4 0.03 0.037 -10000 0 -0.16 15 15
EIF2AK2 0.059 0.087 0.16 213 -0.18 4 217
TNF-alpha/TNFR1A/FAN 0.045 0.038 -10000 0 -0.15 13 13
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.016 0.11 -10000 0 -0.41 32 32
MAP2K2 -0.025 0.044 0.19 5 -0.19 6 11
SMPD3 -0.026 0.11 0.18 4 -0.32 54 58
TNF 0.029 0.005 -10000 0 0 16 16
PKC zeta/PAR4 0.042 0.011 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.011 0.036 0.13 3 -0.14 13 16
NF kappa B1/RelA/I kappa B alpha 0.065 0.058 -10000 0 -0.15 16 16
AIFM1 0.03 0.062 0.2 15 -0.17 7 22
BCL2 0.023 0.012 -10000 0 0 123 123
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.19 0.31 0.77 1 -0.85 61 62
CRP -0.2 0.31 -10000 0 -0.85 65 65
cell cycle arrest -0.24 0.37 -10000 0 -1 70 70
TIMP1 -0.2 0.31 -10000 0 -0.81 74 74
IL6ST 0.004 0.037 0.16 1 -0.09 2 3
Rac1/GDP -0.064 0.11 0.48 1 -0.41 6 7
AP1 0.003 0.13 0.41 4 -0.52 15 19
GAB2 0.025 0.016 0.097 1 -0.031 24 25
TNFSF11 -0.21 0.3 -10000 0 -0.88 54 54
HSP90B1 -0.022 0.13 -10000 0 -0.79 11 11
GAB1 0.027 0.013 0.091 1 -0.031 20 21
MAPK14 -0.024 0.088 0.54 2 -0.44 3 5
AKT1 -0.014 0.086 0.58 1 -0.53 2 3
FOXO1 -0.021 0.082 0.53 1 -0.51 2 3
MAP2K6 -0.024 0.092 0.73 1 -0.34 4 5
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
MAP2K4 -0.099 0.15 0.59 1 -0.5 11 12
MITF -0.053 0.093 0.48 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 63 63
A2M -0.059 0.28 0.65 3 -1.2 31 34
CEBPB 0.027 0.01 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.005 0.1 -10000 0 -0.43 15 15
STAT3 -0.26 0.41 -10000 0 -1.1 73 73
STAT1 0.044 0.056 -10000 0 -10000 0 0
CEBPD -0.24 0.38 -10000 0 -0.98 91 91
PIK3CA 0.019 0.015 -10000 0 -0.029 10 10
PI3K -0.001 0.068 -10000 0 -0.16 77 77
JUN 0.026 0.014 -10000 0 -0.03 24 24
PIAS3/MITF -0.053 0.094 0.44 1 -0.35 5 6
MAPK11 -0.019 0.076 0.35 1 -0.44 3 4
STAT3 (dimer)/FOXO1 -0.2 0.28 -10000 0 -0.77 63 63
GRB2/SOS1/GAB family 0.017 0.1 -10000 0 -0.28 5 5
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.017 0.071 0.38 1 -0.27 7 8
GRB2 0.027 0.013 0.091 1 -0.031 20 21
JAK2 0.027 0.008 -10000 0 0 49 49
LBP -0.13 0.24 0.67 1 -0.72 19 20
PIK3R1 0.021 0.015 0.091 1 -0.029 8 9
JAK1 0.005 0.035 0.14 1 -0.093 2 3
MYC -0.18 0.38 0.74 1 -0.96 74 75
FGG -0.2 0.3 -10000 0 -0.89 51 51
macrophage differentiation -0.24 0.37 -10000 0 -1 70 70
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.015 0.093 0.35 1 -0.2 5 6
JUNB -0.27 0.42 -10000 0 -0.94 139 139
FOS 0.022 0.016 -10000 0 -0.03 25 25
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.038 0.1 0.56 1 -0.4 6 7
STAT1/PIAS1 -0.032 0.13 0.4 1 -0.39 7 8
GRB2/SOS1/GAB family/SHP2/PI3K -0.002 0.085 0.47 1 -0.41 6 7
STAT3 (dimer) -0.26 0.4 -10000 0 -1.1 73 73
PRKCD -0.14 0.2 0.66 1 -0.58 40 41
IL6R 0.005 0.035 0.14 1 -0.069 2 3
SOCS3 -0.009 0.1 0.63 2 -0.86 2 4
gp130 (dimer)/JAK1/JAK1/LMO4 0.01 0.071 0.35 1 -0.18 7 8
Rac1/GTP -0.076 0.13 0.51 1 -0.42 10 11
HCK 0.027 0.01 -10000 0 -0.035 4 4
MAPKKK cascade 0.001 0.12 0.43 1 -0.55 15 16
bone resorption -0.2 0.29 -10000 0 -0.82 52 52
IRF1 -0.21 0.32 0.73 2 -0.87 66 68
mol:GDP -0.056 0.098 -10000 0 -0.39 8 8
SOS1 0.026 0.015 -10000 0 -0.031 23 23
VAV1 -0.057 0.098 -10000 0 -0.39 8 8
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.008 0.071 0.68 1 -0.45 3 4
PTPN11 0.007 0.07 -10000 0 -0.76 4 4
IL6/IL6RA 0.008 0.053 0.25 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 0.012 0.061 0.23 1 -0.15 11 12
IL6 0.005 0.037 0.16 1 -0.1 1 2
PIAS3 0.028 0.007 -10000 0 0 33 33
PTPRE 0.033 0.026 -10000 0 -0.17 1 1
PIAS1 0.029 0.005 -10000 0 0 14 14
RAC1 0.007 0.029 -10000 0 -0.036 7 7
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.019 0.071 0.32 1 -0.28 10 11
LMO4 0.004 0.038 0.16 1 -0.09 2 3
STAT3 (dimer)/PIAS3 -0.24 0.36 -10000 0 -1 73 73
MCL1 -0.01 0.096 0.7 1 -0.59 1 2
Syndecan-4-mediated signaling events

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
PTK2 0.074 0.12 0.24 49 -0.42 12 61
Syndecan-4/Syndesmos 0.072 0.099 0.31 5 -0.44 1 6
positive regulation of JNK cascade 0.061 0.11 0.3 5 -0.42 1 6
Syndecan-4/ADAM12 0.039 0.085 0.28 2 -0.45 1 3
CCL5 0.025 0.011 -10000 0 0 81 81
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
DNM2 0.026 0.009 -10000 0 0 63 63
ITGA5 0.029 0.006 -10000 0 0 20 20
SDCBP 0.028 0.007 -10000 0 0 33 33
PLG -0.009 0.039 -10000 0 -0.081 29 29
ADAM12 0.022 0.013 -10000 0 0 142 142
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.028 0.006 -10000 0 0 25 25
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 0.061 0.095 0.31 3 -0.45 1 4
Syndecan-4/CXCL12/CXCR4 0.065 0.12 0.31 5 -0.44 1 6
Syndecan-4/Laminin alpha3 0.064 0.098 0.31 5 -0.44 1 6
MDK 0.029 0.003 -10000 0 0 7 7
Syndecan-4/FZD7 0.07 0.099 0.31 4 -0.45 1 5
Syndecan-4/Midkine 0.074 0.099 0.31 5 -0.44 1 6
FZD7 0.028 0.006 -10000 0 0 26 26
Syndecan-4/FGFR1/FGF 0.067 0.1 0.32 3 -0.43 1 4
THBS1 0.025 0.011 -10000 0 0 96 96
integrin-mediated signaling pathway 0.041 0.082 0.28 2 -0.43 1 3
positive regulation of MAPKKK cascade 0.061 0.11 0.3 5 -0.42 1 6
Syndecan-4/TACI 0.073 0.098 0.31 5 -0.44 1 6
CXCR4 0.029 0.005 -10000 0 0 17 17
cell adhesion 0.013 0.061 0.19 10 -0.19 12 22
Syndecan-4/Dynamin 0.068 0.097 0.31 4 -0.45 1 5
Syndecan-4/TSP1 0.063 0.1 0.31 5 -0.45 1 6
Syndecan-4/GIPC 0.065 0.096 0.31 5 -0.45 1 6
Syndecan-4/RANTES 0.067 0.1 0.31 5 -0.44 1 6
ITGB1 0.029 0.006 -10000 0 0 20 20
LAMA1 0.024 0.012 -10000 0 0 113 113
LAMA3 0.026 0.01 -10000 0 0 78 78
RAC1 0.028 0.006 -10000 0 0 26 26
PRKCA -0.024 0.1 0.64 11 -10000 0 11
Syndecan-4/alpha-Actinin 0.073 0.099 0.31 5 -0.44 1 6
TFPI 0.027 0.009 -10000 0 0 51 51
F2 0.018 0.032 0.079 1 -0.049 2 3
alpha5/beta1 Integrin 0.041 0.011 -10000 0 -10000 0 0
positive regulation of cell adhesion 0.035 0.09 0.24 10 -0.44 1 11
ACTN1 0.028 0.006 -10000 0 0 25 25
TNC 0.021 0.014 -10000 0 0 168 168
Syndecan-4/CXCL12 0.065 0.11 0.31 5 -0.45 1 6
FGF6 0.027 0.009 -10000 0 0 59 59
RHOA 0.029 0.003 -10000 0 0 7 7
CXCL12 0.025 0.011 -10000 0 0 91 91
TNFRSF13B 0.028 0.007 -10000 0 0 36 36
FGF2 0.028 0.008 -10000 0 0 42 42
FGFR1 0.026 0.01 -10000 0 0 74 74
Syndecan-4/PI-4-5-P2 0.04 0.086 -10000 0 -0.44 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.009 0.026 -10000 0 -0.069 10 10
cell migration -0.013 0.014 -10000 0 -10000 0 0
PRKCD -0.007 0.04 -10000 0 -0.079 26 26
vasculogenesis 0.062 0.1 0.3 5 -0.43 1 6
SDC4 0.049 0.091 0.39 1 -0.46 1 2
Syndecan-4/Tenascin C 0.042 0.084 0.28 2 -0.44 1 3
Syndecan-4/PI-4-5-P2/PKC alpha -0.017 0.025 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.071 0.099 0.31 5 -0.45 1 6
MMP9 0.007 0.027 -10000 0 -0.053 2 2
Rac1/GTP -0.007 0.043 0.18 10 -0.19 12 22
cytoskeleton organization 0.071 0.097 0.3 5 -0.43 1 6
GIPC1 0.026 0.01 -10000 0 0 80 80
Syndecan-4/TFPI 0.066 0.1 0.32 3 -0.45 1 4
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.008 0.13 0.58 1 -0.45 2 3
CRKL -0.024 0.091 0.26 12 -0.21 4 16
mol:DAG -0.032 0.075 0.35 2 -0.28 7 9
HRAS -0.033 0.1 0.25 26 -10000 0 26
MAPK8 -0.018 0.078 0.16 78 -0.17 1 79
RAP1A -0.024 0.094 0.26 15 -0.21 4 19
GAB1 -0.023 0.094 0.26 15 -0.21 3 18
MAPK14 -0.018 0.078 0.16 78 -10000 0 78
EPO -0.02 0.034 0.073 8 -10000 0 8
PLCG1 -0.033 0.076 0.35 2 -0.28 7 9
EPOR/TRPC2/IP3 Receptors -0.022 0.03 0.071 3 -10000 0 3
RAPGEF1 0.029 0.006 -10000 0 0 21 21
EPO/EPOR (dimer)/SOCS3 0.036 0.049 0.19 1 -0.16 2 3
GAB1/SHC/GRB2/SOS1 -0.036 0.099 0.25 12 -10000 0 12
EPO/EPOR (dimer) 0.025 0.042 0.16 1 -10000 0 1
IRS2 -0.023 0.093 0.26 15 -0.21 5 20
STAT1 -0.024 0.076 0.47 2 -0.34 3 5
STAT5B -0.041 0.097 0.43 2 -0.32 7 9
cell proliferation -0.025 0.079 0.17 36 -10000 0 36
GAB1/SHIP/PIK3R1/SHP2/SHC -0.064 0.079 0.12 25 -0.23 18 43
TEC -0.021 0.091 0.25 14 -0.21 4 18
SOCS3 0.029 0.006 -10000 0 0 20 20
STAT1 (dimer) -0.024 0.076 0.47 2 -0.34 3 5
JAK2 -0.018 0.033 0.067 9 -10000 0 9
PIK3R1 0.021 0.013 -10000 0 0 159 159
EPO/EPOR (dimer)/JAK2 0.036 0.092 0.47 2 -0.21 6 8
EPO/EPOR 0.025 0.042 0.16 1 -10000 0 1
LYN 0.016 0.028 0.088 2 -0.047 82 84
TEC/VAV2 -0.031 0.089 0.27 9 -10000 0 9
elevation of cytosolic calcium ion concentration -0.022 0.029 0.071 3 -10000 0 3
SHC1 0.029 0.006 -10000 0 0 20 20
EPO/EPOR (dimer)/LYN 0.029 0.06 0.3 2 -0.15 11 13
mol:IP3 -0.032 0.075 0.35 2 -0.28 7 9
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.048 0.089 0.24 8 -0.23 13 21
SH2B3 -0.018 0.035 0.065 14 -10000 0 14
NFKB1 -0.018 0.076 0.16 71 -0.24 2 73
EPO/EPOR (dimer)/JAK2/SOCS3 0.009 0.029 0.2 1 -0.18 3 4
PTPN6 -0.031 0.078 0.28 6 -0.2 6 12
TEC/VAV2/GRB2 -0.029 0.099 0.26 11 -10000 0 11
EPOR -0.022 0.03 0.071 3 -10000 0 3
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.036 0.099 0.25 12 -10000 0 12
SOS1 0.028 0.007 -10000 0 0 34 34
PLCG2 0.027 0.009 -10000 0 0 62 62
CRKL/CBL/C3G -0.037 0.094 0.19 39 -10000 0 39
VAV2 -0.025 0.093 0.26 14 -0.21 6 20
CBL -0.024 0.094 0.26 15 -0.21 3 18
SHC/Grb2/SOS1 -0.051 0.066 0.26 2 -0.21 4 6
STAT5A -0.042 0.099 0.43 2 -0.32 11 13
GRB2 0.029 0.005 -10000 0 0 19 19
STAT5 (dimer) -0.072 0.14 0.56 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 7 7
BTK -0.023 0.094 0.26 15 -0.21 5 20
BCL2 -0.071 0.26 0.49 1 -0.64 84 85
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.04 0.018 -10000 0 -0.15 3 3
FBXW11 0.029 0.005 -10000 0 0 16 16
NF kappa B1 p50/c-Rel -0.037 0.017 0.16 1 -0.15 5 6
NF kappa B1 p50/RelA/I kappa B alpha -0.027 0.053 0.2 2 -0.23 8 10
NFKBIA -0.004 0.04 -10000 0 -0.15 13 13
MAPK14 0.029 0.005 -10000 0 0 19 19
NF kappa B1 p105/p50 -0.037 0.018 0.16 1 -0.15 6 7
ARRB2 0.007 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 -0.037 0.02 0.16 1 -0.15 8 9
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 0.021 0.014 -10000 0 0 174 174
NF kappa B1 p50 dimer -0.032 0.017 -10000 0 -0.16 6 6
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 7 7
positive regulation of anti-apoptosis -0.005 0.041 -10000 0 -0.21 3 3
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.03 0.054 0.14 1 -0.25 7 8
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 -0.005 0.041 -10000 0 -0.21 3 3
IKBKB 0.028 0.008 -10000 0 0 39 39
beta TrCP1/SCF ubiquitin ligase complex 0.029 0.005 -10000 0 0 16 16
SYK 0.029 0.006 -10000 0 0 23 23
I kappa B alpha/PIK3R1 0.007 0.053 0.18 1 -0.19 23 24
cell death -0.029 0.053 0.14 1 -0.24 7 8
NF kappa B1 p105/c-Rel -0.037 0.017 0.16 1 -0.15 5 6
LCK 0.028 0.006 -10000 0 0 26 26
BCL3 0.028 0.007 -10000 0 0 34 34
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.014 0.1 0.29 14 -0.33 15 29
FYN -0.026 0.12 0.29 16 -0.38 23 39
LAT/GRAP2/SLP76 -0.022 0.099 0.28 9 -0.33 16 25
IKBKB 0.028 0.008 -10000 0 0 39 39
AKT1 -0.023 0.096 0.3 7 -0.31 25 32
B2M 0.022 0.021 0.11 1 -0.05 11 12
IKBKG -0.02 0.039 0.12 10 -0.12 6 16
MAP3K8 0.029 0.005 -10000 0 0 14 14
mol:Ca2+ -0.026 0.014 0.08 2 -0.059 2 4
integrin-mediated signaling pathway 0.038 0.007 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.03 0.12 0.33 7 -0.41 25 32
TRPV6 0.077 0.33 1.3 38 -10000 0 38
CD28 0.021 0.022 -10000 0 -10000 0 0
SHC1 -0.015 0.1 0.28 15 -0.36 17 32
receptor internalization -0.012 0.095 0.29 6 -0.37 18 24
PRF1 -0.025 0.19 0.78 1 -0.93 19 20
KRAS 0.025 0.011 -10000 0 0 97 97
GRB2 0.029 0.005 -10000 0 0 19 19
COT/AKT1 -0.02 0.087 0.26 9 -0.26 22 31
LAT -0.018 0.099 0.3 9 -0.36 17 26
EntrezGene:6955 -0.001 0.004 0.068 1 -0.022 8 9
CD3D 0.023 0.017 0.11 1 -0.05 7 8
CD3E 0.019 0.024 -10000 0 -0.05 10 10
CD3G 0.019 0.022 -10000 0 -0.05 12 12
RASGRP2 -0.003 0.015 -10000 0 -0.14 2 2
RASGRP1 -0.054 0.13 0.27 7 -0.32 64 71
HLA-A -0.001 0.005 0.075 1 -0.023 7 8
RASSF5 0.029 0.004 -10000 0 0 12 12
RAP1A/GTP/RAPL 0.039 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.004 0.049 0.17 8 -0.12 7 15
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.037 0.044 -10000 0 -0.17 24 24
PRKCA -0.026 0.064 0.2 12 -0.21 9 21
GRAP2 0.027 0.008 -10000 0 0 46 46
mol:IP3 -0.032 0.075 -10000 0 -0.27 15 15
EntrezGene:6957 0 0.005 0.074 1 -0.023 6 7
TCR/CD3/MHC I/CD8 -0.016 0.083 0.51 1 -0.34 20 21
ORAI1 -0.093 0.29 -10000 0 -1.1 38 38
CSK -0.016 0.099 0.32 8 -0.37 15 23
B7 family/CD28 0.015 0.11 0.39 3 -0.4 15 18
CHUK 0.028 0.007 -10000 0 0 35 35
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.017 0.1 0.31 4 -0.38 18 22
PTPN6 -0.02 0.096 0.3 8 -0.35 18 26
VAV1 -0.015 0.1 0.29 10 -0.36 17 27
Monovalent TCR/CD3 -0.005 0.062 0.38 1 -0.18 50 51
CBL 0.029 0.004 -10000 0 0 12 12
LCK -0.013 0.11 0.3 12 -0.36 19 31
PAG1 -0.013 0.1 0.29 11 -0.37 15 26
RAP1A 0.029 0.004 -10000 0 0 8 8
TCR/CD3/MHC I/CD8/LCK -0.016 0.099 0.27 7 -0.37 19 26
CD80 0.019 0.022 -10000 0 -10000 0 0
CD86 0.019 0.022 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1 -0.031 0.059 0.098 3 -0.2 23 26
HRAS 0.028 0.006 -10000 0 0 27 27
GO:0035030 -0.029 0.088 0.28 5 -0.34 16 21
CD8A 0.022 0.021 0.11 1 -0.049 10 11
CD8B 0.019 0.025 0.11 1 -0.051 11 12
PTPRC 0.018 0.02 -10000 0 -0.032 9 9
PDK1/PKC theta -0.033 0.11 0.3 8 -0.37 21 29
CSK/PAG1 -0.018 0.1 0.28 12 -0.37 14 26
SOS1 0.028 0.007 -10000 0 0 34 34
peptide-MHC class I 0.015 0.023 0.15 1 -0.16 5 6
GRAP2/SLP76 -0.013 0.11 0.31 8 -0.36 18 26
STIM1 -0.038 0.071 -10000 0 -10000 0 0
RAS family/GTP 0.021 0.068 0.18 24 -0.18 6 30
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.013 0.098 0.29 6 -0.38 19 25
mol:DAG -0.042 0.055 -10000 0 -0.23 20 20
RAP1A/GDP -0.002 0.025 0.083 8 -0.07 1 9
PLCG1 0.028 0.007 -10000 0 0 32 32
CD247 0.02 0.023 0.1 1 -0.048 13 14
cytotoxic T cell degranulation -0.023 0.18 0.78 1 -0.89 19 20
RAP1A/GTP -0.004 0.008 -10000 0 -0.057 2 2
mol:PI-3-4-5-P3 -0.024 0.11 0.32 7 -0.35 25 32
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.034 0.094 0.22 2 -0.33 15 17
NRAS 0.014 0.015 -10000 0 0 300 300
ZAP70 0.029 0.005 -10000 0 -0.03 1 1
GRB2/SOS1 0.04 0.013 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.03 0.095 0.26 8 -0.33 16 24
MALT1 0.026 0.01 -10000 0 0 76 76
TRAF6 0.029 0.004 -10000 0 0 12 12
CD8 heterodimer 0.04 0.022 0.18 1 -10000 0 1
CARD11 0.028 0.007 -10000 0 0 35 35
PRKCB -0.034 0.039 -10000 0 -0.17 20 20
PRKCE -0.027 0.063 0.2 12 -0.22 7 19
PRKCQ -0.03 0.12 0.31 7 -0.39 22 29
LCP2 0.028 0.007 -10000 0 0 33 33
BCL10 0.029 0.004 -10000 0 0 10 10
regulation of survival gene product expression -0.02 0.087 0.26 9 -0.27 23 32
IKK complex -0.004 0.04 0.15 17 -0.11 1 18
RAS family/GDP -0.004 0.009 -10000 0 -0.038 9 9
MAP3K14 -0.023 0.069 0.21 9 -0.22 16 25
PDPK1 -0.026 0.093 0.3 7 -0.3 24 31
TCR/CD3/MHC I/CD8/Fyn -0.019 0.11 0.46 1 -0.42 21 22
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.056 0.065 0.35 9 -0.15 8 17
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.027 0.008 -10000 0 0 46 46
STAT1 (dimer)/Cbp/p300 0.008 0.086 0.27 2 -10000 0 2
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.05 0.046 0.2 9 -0.16 8 17
antigen processing and presentation of peptide antigen via MHC class I -0.027 0.067 0.13 3 -0.23 26 29
CaM/Ca2+ 0.052 0.067 0.31 8 -0.15 7 15
RAP1A 0.029 0.004 -10000 0 0 8 8
STAT1 (dimer)/SHP2 -0.016 0.049 0.32 2 -10000 0 2
AKT1 0.001 0.12 0.29 33 -0.23 6 39
MAP2K1 -0.031 0.078 0.3 17 -10000 0 17
MAP3K11 -0.025 0.083 0.32 17 -10000 0 17
IFNGR1 -0.018 0.031 0.077 16 -10000 0 16
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.01 0.093 -10000 0 -0.28 43 43
Rap1/GTP -0.061 0.043 -10000 0 -0.19 1 1
CRKL/C3G 0.039 0.014 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.068 0.062 0.26 8 -0.15 8 16
CEBPB -0.034 0.14 0.38 8 -0.59 19 27
STAT3 0.028 0.008 -10000 0 0 38 38
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.021 0.19 -10000 0 -0.87 21 21
STAT1 -0.018 0.049 0.35 3 -10000 0 3
CALM1 0.028 0.007 -10000 0 -0.001 26 26
IFN-gamma (dimer) -0.023 0.025 0.069 7 -10000 0 7
PIK3CA 0.021 0.014 -10000 0 0 174 174
STAT1 (dimer)/PIAS1 -0.019 0.052 0.35 3 -10000 0 3
CEBPB/PTGES2/Cbp/p300 -0.052 0.093 -10000 0 -0.4 18 18
mol:Ca2+ 0.052 0.061 0.33 8 -0.15 8 16
MAPK3 -0.036 0.16 0.44 3 -0.68 24 27
STAT1 (dimer) -0.028 0.1 0.49 4 -0.36 13 17
MAPK1 -0.052 0.19 0.44 4 -0.71 36 40
JAK2 -0.02 0.03 0.076 14 -10000 0 14
PIK3R1 0.021 0.014 -10000 0 0 161 161
JAK1 -0.02 0.031 0.078 15 -10000 0 15
CAMK2D 0.027 0.009 -10000 0 -0.001 47 47
DAPK1 -0.022 0.1 0.41 5 -0.41 14 19
SMAD7 0.024 0.11 0.35 34 -10000 0 34
CBL/CRKL/C3G -0.034 0.09 0.32 16 -10000 0 16
PI3K 0.018 0.083 0.25 5 -0.19 14 19
IFNG -0.023 0.025 0.069 7 -10000 0 7
apoptosis 0.004 0.096 0.45 5 -0.41 2 7
CAMK2G 0.029 0.005 -10000 0 -0.002 13 13
STAT3 (dimer) 0.028 0.008 -10000 0 0 38 38
CAMK2A 0.029 0.006 -10000 0 -0.005 13 13
CAMK2B 0.029 0.005 -10000 0 -0.002 14 14
FRAP1 -0.003 0.11 0.26 35 -0.22 6 41
PRKCD 0 0.12 0.29 33 -0.23 6 39
RAP1B 0.029 0.006 -10000 0 0 23 23
negative regulation of cell growth -0.027 0.067 0.13 3 -0.23 26 29
PTPN2 0.028 0.008 -10000 0 -0.004 27 27
EP300 0.026 0.016 0.071 13 -0.035 18 31
IRF1 0.001 0.095 0.2 23 -0.32 11 34
STAT1 (dimer)/PIASy -0.016 0.054 0.24 7 -10000 0 7
SOCS1 -0.03 0.22 -10000 0 -1.1 21 21
mol:GDP -0.034 0.085 0.3 16 -10000 0 16
CASP1 0.001 0.081 0.23 10 -0.2 25 35
PTGES2 0.029 0.005 -10000 0 0 16 16
IRF9 -0.022 0.063 0.28 13 -0.18 8 21
mol:PI-3-4-5-P3 -0.04 0.056 0.13 8 -0.22 7 15
RAP1/GDP -0.055 0.061 0.18 7 -10000 0 7
CBL -0.025 0.083 0.32 17 -10000 0 17
MAP3K1 -0.022 0.082 0.32 17 -10000 0 17
PIAS1 0.029 0.005 -10000 0 0 14 14
PIAS4 0.028 0.008 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.027 0.067 0.13 3 -0.23 26 29
PTPN11 -0.018 0.085 0.35 16 -0.19 1 17
CREBBP 0.026 0.016 0.071 14 -0.035 19 33
RAPGEF1 0.029 0.006 -10000 0 0 21 21
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 -0.01 0.057 -10000 0 -0.2 26 26
epithelial cell differentiation 0.048 0.039 -10000 0 -0.13 7 7
CYFIP2 0.029 0.006 -10000 0 0 24 24
ENAH -0.049 0.061 0.21 6 -10000 0 6
EGFR 0.027 0.009 -10000 0 0 55 55
EPHA2 0.029 0.005 -10000 0 0 16 16
MYO6 -0.046 0.027 0.16 5 -0.22 1 6
CTNNB1 0.029 0.004 -10000 0 0 8 8
ABI1/Sra1/Nap1 0.053 0.03 -10000 0 -0.15 9 9
AQP5 -0.011 0.049 -10000 0 -0.32 4 4
CTNND1 0.03 0.003 -10000 0 0 5 5
mol:PI-4-5-P2 -0.044 0.028 0.16 5 -10000 0 5
regulation of calcium-dependent cell-cell adhesion -0.044 0.028 0.16 5 -10000 0 5
EGF 0.028 0.008 -10000 0 0 41 41
NCKAP1 0.029 0.005 -10000 0 0 17 17
AQP3 -0.13 0.17 -10000 0 -0.39 154 154
cortical microtubule organization 0.048 0.039 -10000 0 -0.13 7 7
GO:0000145 -0.042 0.025 0.14 5 -10000 0 5
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.054 0.042 -10000 0 -0.13 7 7
MLLT4 0.026 0.01 -10000 0 0 72 72
ARF6/GDP -0.064 0.034 -10000 0 -10000 0 0
ARF6 0.029 0.004 -10000 0 0 11 11
Ephrin A1/EPHA2/NCK1/GIT1 0.068 0.039 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.049 0.066 -10000 0 -0.23 51 51
PVRL2 0.028 0.007 -10000 0 0 33 33
ZYX -0.041 0.027 0.16 2 -0.22 1 3
ARF6/GTP 0.073 0.043 -10000 0 -10000 0 0
CDH1 0.026 0.01 -10000 0 0 69 69
EGFR/EGFR/EGF/EGF -0.062 0.031 0.092 6 -0.14 40 46
RhoA/GDP 0.048 0.043 -10000 0 -0.13 8 8
actin cytoskeleton organization -0.05 0.028 0.13 5 -0.22 1 6
IGF-1R heterotetramer 0.022 0.013 -10000 0 0 141 141
GIT1 0.028 0.007 -10000 0 0 30 30
IGF1R 0.022 0.013 -10000 0 0 141 141
IGF1 0.028 0.007 -10000 0 0 32 32
DIAPH1 0.029 0.13 -10000 0 -0.54 23 23
Wnt receptor signaling pathway -0.048 0.039 0.13 7 -10000 0 7
RHOA 0.029 0.003 -10000 0 0 7 7
RhoA/GTP -0.064 0.034 -10000 0 -10000 0 0
CTNNA1 0.029 0.005 -10000 0 0 13 13
VCL -0.051 0.028 0.14 5 -0.23 1 6
EFNA1 0.027 0.008 -10000 0 0 45 45
LPP -0.046 0.035 0.14 5 -0.3 1 6
Ephrin A1/EPHA2 -0.05 0.032 0.092 20 -10000 0 20
SEC6/SEC8 -0.063 0.034 -10000 0 -0.23 1 1
MGAT3 -0.044 0.028 0.16 5 -10000 0 5
HGF/MET -0.044 0.047 0.092 48 -10000 0 48
HGF 0.029 0.005 -10000 0 0 16 16
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.01 0.058 -10000 0 -0.2 26 26
actin cable formation -0.029 0.087 0.28 12 -0.27 11 23
KIAA1543 -0.046 0.023 0.14 5 -10000 0 5
KIFC3 -0.046 0.025 0.16 3 -10000 0 3
NCK1 0.026 0.009 -10000 0 0 63 63
EXOC3 0.027 0.009 -10000 0 0 58 58
ACTN1 -0.047 0.027 0.16 5 -0.22 1 6
NCK1/GIT1 0.037 0.016 -10000 0 -10000 0 0
mol:GDP 0.048 0.039 -10000 0 -0.13 7 7
EXOC4 0.028 0.007 -10000 0 0 37 37
STX4 -0.048 0.025 0.16 5 -10000 0 5
PIP5K1C -0.045 0.028 0.16 5 -10000 0 5
LIMA1 0.029 0.006 -10000 0 0 20 20
ABI1 0.029 0.005 -10000 0 0 14 14
ROCK1 -0.045 0.075 0.24 11 -10000 0 11
adherens junction assembly -0.064 0.1 0.22 1 -0.62 13 14
IGF-1R heterotetramer/IGF1 -0.074 0.042 0.092 3 -0.22 2 5
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 88 88
PLEKHA7 -0.048 0.025 0.16 5 -10000 0 5
mol:GTP 0.054 0.037 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity -0.043 0.089 0.28 13 -10000 0 13
cortical actin cytoskeleton stabilization -0.01 0.057 -10000 0 -0.2 26 26
regulation of cell-cell adhesion -0.05 0.028 0.13 5 -0.22 1 6
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.01 0.058 -10000 0 -0.2 26 26
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 0.055 0.19 36 -10000 0 36
SMARCC1 -0.012 0.033 0.6 1 -10000 0 1
REL 0.029 0.004 -10000 0 -10000 0 0
HDAC7 -0.13 0.1 0.29 2 -0.3 35 37
JUN 0.028 0.007 -10000 0 -10000 0 0
EP300 0.027 0.009 -10000 0 -10000 0 0
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.016 0.078 0.18 73 -10000 0 73
FOXO1 0.028 0.008 -10000 0 -10000 0 0
T-DHT/AR -0.13 0.12 0.32 2 -0.32 29 31
MAP2K6 -0.031 0.018 -10000 0 -10000 0 0
BRM/BAF57 -0.002 0.082 -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 58 58
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 0.28 1 -0.37 40 41
NR0B1 0.028 0.008 -10000 0 0 38 38
EGR1 0.019 0.014 -10000 0 -10000 0 0
RXRs/9cRA 0.047 0.034 -10000 0 -0.13 13 13
AR/RACK1/Src -0.075 0.096 0.26 7 -0.28 2 9
AR/GR -0.12 0.1 0.18 3 -0.21 260 263
GNB2L1 0.029 0.005 -10000 0 -10000 0 0
PKN1 0.026 0.01 -10000 0 0 78 78
RCHY1 0.027 0.008 -10000 0 0 46 46
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.041 0.026 0.17 4 -10000 0 4
T-DHT/AR/TIF2/CARM1 -0.073 0.09 0.28 3 -0.29 2 5
SRC -0.051 0.065 0.23 1 -10000 0 1
NR3C1 0.029 0.005 -10000 0 0 15 15
KLK3 -0.047 0.078 -10000 0 -10000 0 0
APPBP2 -0.029 0.024 -10000 0 -10000 0 0
TRIM24 0.028 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.08 0.067 0.12 1 -0.2 19 20
TMPRSS2 -0.4 0.45 -10000 0 -0.9 244 244
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 0.029 0.005 -10000 0 -10000 0 0
CARM1 0.027 0.009 -10000 0 -10000 0 0
NR2C2 0.029 0.004 -10000 0 -10000 0 0
KLK2 -0.061 0.079 0.28 2 -0.33 5 7
AR -0.11 0.11 0.17 1 -0.22 252 253
SENP1 0.028 0.007 -10000 0 -10000 0 0
HSP90AA1 0.029 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 26 26
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 0.029 0.006 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.075 0.1 0.26 9 -0.29 2 11
positive regulation of transcription 0.028 0.006 -10000 0 0 26 26
DNAJA1 -0.028 0.025 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.007 0.056 0.3 4 -0.22 17 21
NCOA1 0.032 0.018 0.22 1 -10000 0 1
SPDEF 0.027 0.008 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.058 0.084 0.28 1 -0.27 35 36
T-DHT/AR/Hsp90 -0.079 0.088 0.25 5 -0.26 4 9
GSK3B 0 0.032 -10000 0 -0.038 13 13
NR2C1 0.029 0.005 -10000 0 -10000 0 0
mol:T-DHT -0.045 0.068 0.14 3 -10000 0 3
SIRT1 0.029 0.003 -10000 0 0 6 6
ZMIZ2 0.029 0.004 -10000 0 -10000 0 0
POU2F1 -0.044 0.081 -10000 0 -0.15 75 75
T-DHT/AR/DAX-1 -0.076 0.089 0.26 6 -0.25 2 8
CREBBP 0.027 0.008 -10000 0 -10000 0 0
SMARCE1 0.028 0.007 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.027 0.014 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ -0.032 0.022 -10000 0 -10000 0 0
CDKN1B 0.018 0.076 0.27 9 -0.33 8 17
CDKN1A 0.008 0.066 0.28 3 -0.32 9 12
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.025 0.011 -10000 0 0 98 98
FOXO3 0.007 0.055 -10000 0 -0.3 9 9
AKT1 0.014 0.059 -10000 0 -0.33 11 11
BAD 0.03 0.003 -10000 0 0 5 5
AKT3 -0.1 0.11 -10000 0 -0.21 279 279
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.007 0.062 -10000 0 -0.32 10 10
AKT1/ASK1 0.033 0.065 0.21 1 -0.3 14 15
BAD/YWHAZ 0.045 0.027 -10000 0 -10000 0 0
RICTOR 0.028 0.008 -10000 0 0 39 39
RAF1 0.029 0.004 -10000 0 0 8 8
JNK cascade -0.032 0.063 0.29 14 -0.2 1 15
TSC1 0.007 0.053 -10000 0 -0.29 9 9
YWHAZ 0.026 0.01 -10000 0 0 77 77
AKT1/RAF1 0.036 0.068 0.22 1 -0.3 14 15
EP300 0.027 0.009 -10000 0 0 54 54
mol:GDP 0.014 0.059 -10000 0 -0.33 11 11
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.005 0.059 -10000 0 -0.32 10 10
YWHAQ 0.029 0.005 -10000 0 0 15 15
TBC1D4 -0.014 0.01 0.19 1 -10000 0 1
MAP3K5 0.028 0.007 -10000 0 0 31 31
MAPKAP1 0.029 0.005 -10000 0 0 17 17
negative regulation of cell cycle -0.018 0.064 0.29 8 -0.17 4 12
YWHAH 0.028 0.008 -10000 0 0 42 42
AKT1S1 0.005 0.061 -10000 0 -0.32 11 11
CASP9 0.007 0.058 -10000 0 -0.32 9 9
YWHAB 0.027 0.008 -10000 0 0 44 44
p27Kip1/KPNA1 0.021 0.088 0.27 16 -0.32 9 25
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.054 0.019 -10000 0 -10000 0 0
YWHAE 0.028 0.008 -10000 0 0 41 41
SRC 0.028 0.007 -10000 0 0 33 33
AKT2/p21CIP1 0.002 0.062 0.2 11 -0.3 10 21
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.014 0.033 -10000 0 -0.28 3 3
CHUK 0.011 0.066 0.24 9 -0.32 9 18
BAD/BCL-XL -0.005 0.062 -10000 0 -0.33 9 9
mTORC2 0.034 0.013 -10000 0 -10000 0 0
AKT2 0.006 0.002 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.015 0.084 0.24 2 -0.39 9 11
PDPK1 0.029 0.005 -10000 0 0 18 18
MDM2 0.011 0.071 0.26 5 -0.31 13 18
MAPKKK cascade -0.035 0.067 0.3 14 -0.22 1 15
MDM2/Cbp/p300 0.039 0.075 0.29 6 -0.3 14 20
TSC1/TSC2 -0.004 0.064 0.27 5 -0.32 12 17
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.072 0.28 6 -0.29 14 20
glucose import -0.02 0.035 0.19 11 -10000 0 11
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.012 0.046 0.19 4 -0.19 11 15
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.018 0.031 0.19 11 -10000 0 11
GSK3A 0.008 0.061 0.28 4 -0.3 10 14
FOXO1 0.006 0.052 -10000 0 -0.32 6 6
GSK3B 0.008 0.062 -10000 0 -0.32 11 11
SFN 0.028 0.007 -10000 0 0 37 37
G1/S transition of mitotic cell cycle 0.007 0.077 0.3 14 -0.32 9 23
p27Kip1/14-3-3 family 0.019 0.044 0.23 1 -0.39 1 2
PRKACA 0.026 0.01 -10000 0 0 78 78
KPNA1 0.029 0.005 -10000 0 0 17 17
HSP90AA1 0.029 0.006 -10000 0 0 21 21
YWHAG 0.029 0.004 -10000 0 0 11 11
RHEB 0.027 0.009 -10000 0 0 54 54
CREBBP 0.027 0.008 -10000 0 0 44 44
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.006 0.12 0.38 19 -0.32 1 20
CRKL -0.018 0.12 0.39 12 -0.32 2 14
HRAS -0.017 0.12 0.38 11 -0.37 5 16
mol:PIP3 0.009 0.13 0.4 16 -0.42 3 19
SPRED1 0.028 0.008 -10000 0 0 42 42
SPRED2 0.029 0.004 -10000 0 0 9 9
GAB1 -0.009 0.12 0.42 15 -0.38 3 18
FOXO3 -0.011 0.13 0.39 16 -0.42 10 26
AKT1 -0.004 0.14 0.4 16 -0.45 10 26
BAD -0.011 0.13 0.38 16 -0.42 10 26
megakaryocyte differentiation -0.006 0.12 0.44 15 -0.41 2 17
GSK3B -0.007 0.13 0.39 17 -0.43 9 26
RAF1 -0.018 0.11 0.32 15 -0.32 4 19
SHC1 0.029 0.006 -10000 0 0 20 20
STAT3 -0.01 0.12 0.42 13 -0.41 2 15
STAT1 -0.011 0.23 0.58 15 -0.67 12 27
HRAS/SPRED1 -0.01 0.11 0.33 12 -0.32 4 16
cell proliferation -0.01 0.12 0.44 15 -0.37 3 18
PIK3CA 0.017 0.018 -10000 0 -0.029 34 34
TEC 0.027 0.009 -10000 0 0 54 54
RPS6KB1 0.002 0.14 0.42 16 -0.41 4 20
HRAS/SPRED2 -0.01 0.11 0.34 12 -0.32 4 16
LYN/TEC/p62DOK 0.014 0.13 0.39 10 -0.38 3 13
MAPK3 -0.026 0.091 0.27 14 -0.29 7 21
STAP1 -0.008 0.12 0.42 15 -0.41 2 17
GRAP2 0.027 0.008 -10000 0 0 46 46
JAK2 -0.02 0.22 0.56 15 -0.65 12 27
STAT1 (dimer) -0.01 0.23 0.58 16 -0.66 12 28
mol:Gleevec 0.001 0.009 -10000 0 -0.034 18 18
GRB2/SOCS1/VAV1 0.015 0.14 0.4 13 -0.41 2 15
actin filament polymerization -0.001 0.12 0.42 15 -0.36 3 18
LYN 0.027 0.008 -10000 0 0 49 49
STAP1/STAT5A (dimer) -0.03 0.18 0.46 14 -0.51 17 31
PIK3R1 0.021 0.014 -10000 0 -0.029 4 4
CBL/CRKL/GRB2 -0.011 0.13 0.35 17 -0.32 1 18
PI3K -0.015 0.12 0.41 9 -0.38 6 15
PTEN 0.026 0.014 -10000 0 -0.03 22 22
SCF/KIT/EPO/EPOR 0.006 0.23 0.63 9 -0.67 6 15
MAPK8 -0.009 0.13 0.44 15 -0.38 3 18
STAT3 (dimer) -0.011 0.12 0.42 13 -0.41 2 15
positive regulation of transcription -0.02 0.08 0.26 14 -0.24 5 19
mol:GDP -0.014 0.12 0.36 10 -0.35 4 14
PIK3C2B -0.01 0.13 0.44 15 -0.38 3 18
CBL/CRKL -0.013 0.13 0.36 17 -0.32 1 18
FER -0.01 0.12 0.41 14 -0.38 3 17
SH2B3 -0.009 0.12 0.42 15 -0.33 2 17
PDPK1 0.002 0.12 0.38 17 -0.39 3 20
SNAI2 -0.01 0.12 0.42 14 -0.33 7 21
positive regulation of cell proliferation -0.017 0.2 0.53 15 -0.55 15 30
KITLG 0.021 0.039 0.12 16 -0.059 1 17
cell motility -0.017 0.2 0.53 15 -0.55 15 30
PTPN6 -0.001 0.036 -10000 0 -0.075 15 15
EPOR -0.03 0.2 0.97 1 -0.72 20 21
STAT5A (dimer) -0.02 0.18 0.49 15 -0.51 17 32
SOCS1 0.028 0.007 -10000 0 0 31 31
cell migration 0.011 0.12 0.41 2 -0.42 13 15
SOS1 0.028 0.007 -10000 0 0 34 34
EPO 0.021 0.032 0.089 9 -0.043 69 78
VAV1 0.028 0.008 -10000 0 0 41 41
GRB10 -0.009 0.12 0.42 15 -0.41 2 17
PTPN11 0 0.035 -10000 0 -0.064 17 17
SCF/KIT 0.002 0.13 0.46 15 -0.39 3 18
GO:0007205 0 0.012 -10000 0 -0.044 18 18
MAP2K1 -0.02 0.093 0.29 16 -0.26 3 19
CBL 0.029 0.004 -10000 0 0 12 12
KIT -0.011 0.21 0.67 17 -0.7 13 30
MAP2K2 -0.027 0.09 0.28 14 -0.3 2 16
SHC/Grb2/SOS1 0.02 0.14 0.4 12 -0.36 4 16
STAT5A -0.02 0.18 0.5 15 -0.51 19 34
GRB2 0.029 0.005 -10000 0 0 19 19
response to radiation -0.008 0.13 0.42 15 -0.34 5 20
SHC/GRAP2 0.039 0.014 -10000 0 -10000 0 0
PTPRO -0.008 0.12 0.44 15 -0.41 2 17
SH2B2 -0.001 0.12 0.42 15 -0.37 3 18
DOK1 0.029 0.004 -10000 0 0 10 10
MATK -0.01 0.12 0.42 13 -0.38 3 16
CREBBP 0.002 0.083 0.35 16 -10000 0 16
BCL2 -0.18 0.46 0.93 1 -1.1 103 104
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.029 0.005 -10000 0 0 19 19
SPHK1 0.029 0.005 -10000 0 0 17 17
GNAI2 0.029 0.003 -10000 0 0 6 6
mol:S1P 0.005 0.01 0.13 4 -10000 0 4
GNAO1 0.027 0.008 -10000 0 0 44 44
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 0.043 -10000 0 -0.26 6 6
GNAI3 0.025 0.011 -10000 0 0 98 98
G12/G13 0.041 0.012 -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 -0.004 0.035 -10000 0 -0.28 6 6
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 0.028 0.006 -10000 0 0 27 27
S1P/S1P5/G12 0.017 0.04 -10000 0 -0.26 6 6
S1P/S1P3/Gq -0.008 0.082 -10000 0 -0.33 22 22
S1P/S1P4/Gi 0.008 0.065 0.17 1 -0.23 18 19
GNAQ 0.028 0.007 -10000 0 0 28 28
GNAZ 0.027 0.009 -10000 0 0 51 51
GNA14 0.029 0.005 -10000 0 0 18 18
GNA15 0.027 0.008 -10000 0 0 46 46
GNA12 0.028 0.007 -10000 0 0 34 34
GNA13 0.029 0.005 -10000 0 0 13 13
GNA11 0.025 0.011 -10000 0 0 83 83
ABCC1 0.029 0.006 -10000 0 0 24 24
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.053 0.048 -10000 0 -0.14 12 12
MAP4K1 0.026 0.01 -10000 0 0 67 67
MAP3K8 0.029 0.005 -10000 0 0 14 14
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0.029 0.004 -10000 0 0 12 12
CRKL 0.027 0.008 -10000 0 0 46 46
MAP3K1 -0.015 0.048 -10000 0 -0.29 7 7
JUN -0.001 0.064 0.23 1 -0.57 4 5
MAP3K7 -0.013 0.044 0.15 3 -0.21 7 10
GRAP2 0.027 0.008 -10000 0 0 46 46
CRK 0.028 0.007 -10000 0 0 36 36
MAP2K4 -0.025 0.083 0.18 1 -0.36 19 20
LAT 0.029 0.004 -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 0.006 0.058 -10000 0 -0.29 12 12
LAT/GRAP2/SLP76/HPK1/HIP-55 0.06 0.055 -10000 0 -0.14 12 12
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.028 0.085 -10000 0 -0.25 26 26
Ran/GTP/Exportin 1/HDAC1 -0.031 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 26 27
SUMO1 0.029 0.003 -10000 0 0 7 7
ZFPM1 0.026 0.01 -10000 0 0 66 66
NPC/RanGAP1/SUMO1/Ubc9 -0.004 0.033 -10000 0 -0.27 3 3
FKBP3 0.029 0.006 -10000 0 0 23 23
Histones 0.055 0.061 -10000 0 -0.24 7 7
YY1/LSF 0 0.064 -10000 0 -0.22 20 20
SMG5 0.029 0.006 -10000 0 0 23 23
RAN 0.029 0.004 -10000 0 0 12 12
I kappa B alpha/HDAC3 -0.022 0.042 -10000 0 -0.32 5 5
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 -0.007 0.08 0.26 1 -0.38 10 11
HDAC1/Smad7 0.051 0.022 -10000 0 -10000 0 0
RANGAP1 0.027 0.008 -10000 0 0 46 46
HDAC3/TR2 0.028 0.051 -10000 0 -0.21 13 13
NuRD/MBD3 Complex 0.004 0.066 0.24 1 -0.25 16 17
NF kappa B1 p50/RelA 0.002 0.092 0.22 1 -0.32 22 23
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.028 0.006 -10000 0 0 26 26
GATA1 0.028 0.007 -10000 0 0 30 30
Mad/Max 0.042 0.01 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.008 0.087 0.24 1 -0.34 19 20
RBBP7 0.029 0.005 -10000 0 0 19 19
NPC 0.017 0.002 -10000 0 -10000 0 0
RBBP4 0.028 0.008 -10000 0 0 39 39
MAX 0.029 0.005 -10000 0 0 17 17
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.029 0.005 -10000 0 0 16 16
NFKBIA 0.001 0.05 -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 -0.001 0.068 0.18 4 -0.26 18 22
SIN3 complex 0.054 0.042 -10000 0 -10000 0 0
SMURF1 0.029 0.006 -10000 0 0 20 20
CHD3 0.028 0.007 -10000 0 0 35 35
SAP30 0.027 0.008 -10000 0 0 46 46
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.028 0.008 -10000 0 0 39 39
YY1/HDAC3 -0.01 0.061 -10000 0 -0.27 15 15
YY1/HDAC2 0.002 0.063 -10000 0 -0.23 21 21
YY1/HDAC1 0.001 0.062 -10000 0 -0.22 19 19
NuRD/MBD2 Complex (MeCP1) 0.006 0.066 0.24 1 -0.27 13 14
PPARG 0 0.078 0.28 1 -0.32 11 12
HDAC8/hEST1B 0.048 0.025 -10000 0 -10000 0 0
UBE2I 0.029 0.006 -10000 0 0 23 23
beta TrCP1/SCF ubiquitin ligase complex 0.029 0.005 -10000 0 0 16 16
TNFRSF1A 0.026 0.01 -10000 0 0 78 78
HDAC3/SMRT (N-CoR2) 0.027 0.051 -10000 0 -0.21 13 13
MBD3L2 0.028 0.008 -10000 0 0 43 43
ubiquitin-dependent protein catabolic process 0.05 0.022 -10000 0 -10000 0 0
CREBBP 0.027 0.008 -10000 0 0 44 44
NuRD/MBD3/MBD3L2 Complex -0.001 0.087 0.25 1 -0.32 21 22
HDAC1 0.027 0.009 -10000 0 0 51 51
HDAC3 0.006 0.029 -10000 0 -0.32 2 2
HDAC2 0.028 0.008 -10000 0 0 38 38
YY1 0.001 0.023 -10000 0 -0.19 8 8
HDAC8 0.028 0.007 -10000 0 0 28 28
SMAD7 0.028 0.007 -10000 0 0 28 28
NCOR2 0.029 0.006 -10000 0 0 20 20
MXD1 0.029 0.004 -10000 0 0 10 10
STAT3 0.004 0.038 -10000 0 -0.23 13 13
NFKB1 0.027 0.008 -10000 0 0 45 45
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.029 0.004 -10000 0 0 10 10
YY1/LSF/HDAC1 0.012 0.067 -10000 0 -0.21 19 19
YY1/SAP30/HDAC1 0.013 0.066 -10000 0 -0.21 19 19
EP300 0.027 0.009 -10000 0 0 54 54
STAT3 (dimer non-phopshorylated) 0.004 0.038 -10000 0 -0.23 13 13
proteasomal ubiquitin-dependent protein catabolic process 0.001 0.049 -10000 0 -0.31 11 11
histone deacetylation 0.006 0.065 0.24 1 -0.26 13 14
STAT3 (dimer non-phopshorylated)/HDAC3 0 0.066 -10000 0 -0.28 11 11
nuclear export -0.047 0.024 -10000 0 -10000 0 0
PRKACA 0.026 0.01 -10000 0 0 78 78
GATAD2B 0.028 0.006 -10000 0 0 25 25
GATAD2A 0.027 0.008 -10000 0 0 48 48
GATA2/HDAC3 0.026 0.051 -10000 0 -0.21 13 13
GATA1/HDAC1 0.038 0.015 -10000 0 -10000 0 0
GATA1/HDAC3 0.026 0.05 -10000 0 -0.21 13 13
CHD4 0.027 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 0.075 0.19 5 -0.3 15 20
NuRD Complex -0.004 0.084 0.25 1 -0.34 17 18
positive regulation of chromatin silencing 0.046 0.058 -10000 0 -0.24 7 7
SIN3B 0.027 0.009 -10000 0 0 61 61
MTA2 0.029 0.003 -10000 0 0 6 6
SIN3A 0.029 0.005 -10000 0 0 19 19
XPO1 0.027 0.009 -10000 0 0 52 52
SUMO1/HDAC1 0.024 0.05 -10000 0 -0.22 10 10
HDAC complex 0.065 0.039 -10000 0 -0.14 2 2
GATA1/Fog1 0.037 0.017 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.05 0.023 -10000 0 -10000 0 0
TNF 0.029 0.005 -10000 0 0 16 16
negative regulation of cell growth 0 0.074 0.19 5 -0.3 15 20
NuRD/MBD2/PRMT5 Complex 0.006 0.066 0.24 1 -0.27 13 14
Ran/GTP/Exportin 1 0.023 0.051 -10000 0 -0.22 11 11
NF kappa B/RelA/I kappa B alpha -0.017 0.075 -10000 0 -0.3 27 27
SIN3/HDAC complex/NCoR1 -0.007 0.082 0.17 4 -0.33 21 25
TFCP2 0.028 0.008 -10000 0 0 42 42
NR2C1 0.029 0.005 -10000 0 0 14 14
MBD3 0.027 0.009 -10000 0 0 51 51
MBD2 0.028 0.007 -10000 0 0 36 36
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.022 0.049 0.22 8 -10000 0 8
NFATC2 -0.02 0.05 0.22 8 -10000 0 8
NFATC3 -0.021 0.05 0.22 9 -10000 0 9
CD40LG -0.049 0.16 0.48 30 -10000 0 30
PTGS2 -0.059 0.15 0.5 20 -10000 0 20
JUNB 0.02 0.014 -10000 0 0 188 188
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.017 0.031 0.087 35 -0.16 6 41
CaM/Ca2+ -0.017 0.031 0.086 35 -0.16 6 41
CALM1 -0.024 0.027 0.094 9 -10000 0 9
JUN -0.023 0.028 0.092 10 -10000 0 10
mol:Ca2+ -0.004 0.007 0.038 10 -0.027 1 11
Calcineurin A alpha-beta B1/FKBP12/FK506 0.019 0.01 0.089 2 -10000 0 2
FOSL1 0.029 0.003 -10000 0 0 7 7
CREM 0.028 0.007 -10000 0 -0.03 5 5
Jun/NFAT1-c-4/p21SNFT -0.045 0.1 0.34 27 -10000 0 27
FOS -0.021 0.025 0.091 5 -10000 0 5
IFNG -0.068 0.12 0.55 2 -10000 0 2
AP-1/NFAT1-c-4 -0.071 0.13 0.49 17 -10000 0 17
FASLG -0.052 0.16 0.62 9 -10000 0 9
NFAT1-c-4/ICER1 -0.038 0.098 0.29 30 -10000 0 30
IL2RA -0.053 0.15 0.56 7 -10000 0 7
FKBP12/FK506 0.021 0.006 -10000 0 -10000 0 0
CSF2 -0.05 0.16 0.5 24 -10000 0 24
JunB/Fra1/NFAT1-c-4 -0.06 0.097 0.3 19 -10000 0 19
IL4 -0.05 0.16 0.51 22 -10000 0 22
IL2 -0.034 0.21 -10000 0 -0.92 29 29
IL3 0.001 0.11 -10000 0 -0.66 14 14
FKBP1A 0.028 0.008 -10000 0 0 38 38
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.029 0.004 -10000 0 -10000 0 0
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 0.004 0.041 0.14 48 -10000 0 48
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A -0.001 0.055 0.12 2 -0.2 30 32
AP2 0.027 0.045 -10000 0 -0.16 25 25
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.033 0.022 -10000 0 -10000 0 0
CLTB 0.029 0.005 -10000 0 0 13 13
coatomer protein complex/ARF1/GTP/ER cargo protein -0.001 0.041 0.12 1 -0.18 23 24
CD4 0.026 0.01 -10000 0 0 71 71
CLTA 0.029 0.005 -10000 0 0 14 14
mol:GTP -0.004 0.004 0.012 4 -0.022 25 29
ARFGAP1 -0.015 0.005 0 59 -10000 0 59
mol:PI-4-5-P2 -0.004 0.024 0.091 8 -0.15 1 9
ARF1/GTP -0.025 0.03 0.035 5 -0.15 26 31
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.015 0.031 0.094 1 -0.16 21 22
mol:Choline -0.005 0.023 0.09 8 -0.15 1 9
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 -0.019 0.024 0.048 1 -10000 0 1
DDEF1 -0.003 0.023 0.091 8 -0.16 1 9
ARF1/GDP -0.002 0.013 -10000 0 -0.097 5 5
AP2M1 0.025 0.011 -10000 0 0 94 94
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 0.012 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.025 0.035 -10000 0 -0.12 24 24
ARFIP2 -0.029 0.011 0.027 11 -10000 0 11
COPA 0.029 0.006 -10000 0 0 20 20
RAC1 0.028 0.006 -10000 0 0 26 26
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 0.029 0.005 -10000 0 0 19 19
ARF1/GTP/Membrin 0.007 0.051 -10000 0 -0.16 40 40
AP2A1 0.027 0.008 -10000 0 0 47 47
coatomer protein complex/ARF1/GTP/ARF-GAP1 -0.01 0.035 -10000 0 -0.16 26 26
ARF1/GDP/Membrin 0.013 0.056 -10000 0 -0.26 16 16
Arfaptin 2/Rac/GDP 0.034 0.02 -10000 0 -10000 0 0
CYTH2 -0.004 0.004 0.012 4 -0.022 25 29
ARF1/GTP/GGA3 0.029 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 0.045 -10000 0 -0.22 7 7
PLD2 -0.005 0.023 0.09 8 -0.15 1 9
ARF-GAP1/v-SNARE -0.015 0.005 0 59 -10000 0 59
PIP5K1A -0.004 0.024 0.091 8 -0.15 1 9
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 0.09 8 -0.15 1 9
KDEL Receptor/Ligand/ARF-GAP1 -0.015 0.005 0 59 -10000 0 59
GOSR2 0.002 0.051 -10000 0 -0.35 11 11
USO1 0.002 0.052 -10000 0 -0.35 11 11
GBF1 0.001 0.052 -10000 0 -0.34 12 12
ARF1/GTP/Arfaptin 2 0.028 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
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.041 0.022 0.2 1 -10000 0 1
KIRREL -0.021 0.03 0.048 81 -10000 0 81
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.041 0.022 -10000 0 -0.2 1 1
PLCG1 0.028 0.007 -10000 0 0 32 32
ARRB2 0.028 0.006 -10000 0 0 25 25
WASL 0.029 0.006 -10000 0 0 21 21
Nephrin/NEPH1/podocin/CD2AP 0.066 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 0.033 0.16 1 -0.19 1 2
FYN -0.004 0.064 0.14 75 -0.22 1 76
mol:Ca2+ 0.062 0.039 -10000 0 -0.17 1 1
mol:DAG 0.063 0.039 -10000 0 -0.17 1 1
NPHS2 -0.02 0.033 0.05 98 -10000 0 98
mol:IP3 0.063 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 0.052 0.031 0.15 3 -0.16 1 4
establishment of cell polarity 0.041 0.022 -10000 0 -0.2 1 1
Nephrin/NEPH1/podocin/NCK1-2 0.082 0.047 -10000 0 -0.16 1 1
Nephrin/NEPH1/beta Arrestin2 0.034 0.054 -10000 0 -0.21 1 1
NPHS1 -0.023 0.027 0.052 40 -10000 0 40
Nephrin/NEPH1/podocin 0.031 0.049 0.19 4 -0.22 1 5
TJP1 0.028 0.008 -10000 0 0 41 41
NCK1 0.026 0.009 -10000 0 0 63 63
NCK2 0.029 0.004 -10000 0 0 10 10
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.065 0.04 -10000 0 -0.17 1 1
CD2AP 0.028 0.007 -10000 0 0 29 29
Nephrin/NEPH1/podocin/GRB2 0.065 0.039 0.2 1 -0.17 1 2
GRB2 0.029 0.005 -10000 0 0 19 19
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.013 0.072 0.15 80 -10000 0 80
cytoskeleton organization -0.017 0.047 0.19 11 -0.2 1 12
Nephrin/NEPH1 0.034 0.018 -10000 0 -0.13 1 1
Nephrin/NEPH1/ZO-1 0.049 0.03 -10000 0 -0.16 1 1
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.065 0.038 -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 0.039 0.022 -10000 0 -0.16 4 4
GATA2/HDAC5 0.037 0.028 -10000 0 -0.16 9 9
HDAC5/BCL6/BCoR 0.042 0.04 -10000 0 -0.15 15 15
HDAC9 0.027 0.009 -10000 0 0 59 59
Glucocorticoid receptor/Hsp90/HDAC6 0.052 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 -0.004 0.033 -10000 0 -0.27 3 3
GATA2 0.028 0.006 -10000 0 0 26 26
HDAC4/RFXANK 0.039 0.015 -10000 0 -10000 0 0
BCOR 0.029 0.005 -10000 0 0 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.023 0.013 -10000 0 0 127 127
HDAC5 0.028 0.007 -10000 0 0 28 28
GNB1/GNG2 0.041 0.014 -10000 0 -0.16 1 1
Histones -0.018 0.068 -10000 0 -0.23 27 27
ADRBK1 0.029 0.003 -10000 0 0 6 6
HDAC4 0.029 0.005 -10000 0 0 19 19
XPO1 0.027 0.009 -10000 0 0 52 52
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 0.03 0.003 -10000 0 0 4 4
HDAC6 0.028 0.007 -10000 0 0 31 31
HDAC5/RFXANK 0.037 0.023 -10000 0 -0.16 4 4
CAMK4 0.028 0.008 -10000 0 0 40 40
Tubulin/HDAC6 0.052 0.021 -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 44 44
GATA1 0.028 0.007 -10000 0 0 30 30
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.028 0.008 -10000 0 0 41 41
NR3C1 0.029 0.005 -10000 0 0 15 15
SUMO1/HDAC4 0.024 0.053 0.16 1 -0.22 12 13
SRF 0.028 0.007 -10000 0 0 28 28
HDAC4/YWHAB 0.04 0.014 -10000 0 -10000 0 0
Tubulin 0.041 0.012 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.04 0.016 -10000 0 -0.16 1 1
GNB1 0.029 0.006 -10000 0 0 23 23
RANGAP1 0.027 0.008 -10000 0 0 46 46
BCL6/BCoR 0.032 0.034 -10000 0 -0.16 12 12
HDAC4/HDAC3/SMRT (N-CoR2) 0.053 0.03 -10000 0 -0.15 9 9
HDAC4/SRF 0.052 0.024 -10000 0 -0.15 2 2
HDAC4/ER alpha 0.014 0.068 -10000 0 -0.16 70 70
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.018 0.068 -10000 0 -0.23 27 27
cell motility 0.052 0.02 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.029 0.006 -10000 0 0 23 23
HDAC7/HDAC3 0.022 0.002 -10000 0 -10000 0 0
BCL6 0.025 0.011 -10000 0 0 97 97
HDAC4/CaMK II delta B 0.029 0.005 -10000 0 0 19 19
Hsp90/HDAC6 0.04 0.013 -10000 0 -10000 0 0
ESR1 0.024 0.012 -10000 0 0 114 114
HDAC6/HDAC11 0.041 0.011 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.023 0.051 -10000 0 -0.22 11 11
NPC 0.017 0.002 -10000 0 -10000 0 0
MEF2C 0.026 0.01 -10000 0 0 65 65
RAN 0.029 0.004 -10000 0 0 12 12
HDAC4/MEF2C 0.059 0.064 -10000 0 -0.14 29 29
GNG2 0.029 0.005 -10000 0 0 14 14
NCOR2 0.029 0.006 -10000 0 0 20 20
TUBB2A 0.028 0.008 -10000 0 0 41 41
HDAC11 0.029 0.003 -10000 0 0 7 7
HSP90AA1 0.029 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 0.039 0.19 5 -10000 0 5
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.027 0.009 -10000 0 -10000 0 0
HDAC2 0.028 0.008 -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 0.023 0.018 -10000 0 -0.035 40 40
SMO/beta Arrestin2 0.034 0.025 -10000 0 -10000 0 0
SMO 0.023 0.019 -10000 0 -0.039 43 43
ARRB2 0.024 0.017 -10000 0 -0.034 39 39
GLI3/SPOP 0.018 0.088 0.22 5 -0.33 15 20
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
GSK3B 0.029 0.005 -10000 0 0 17 17
GNAI2 0.024 0.017 -10000 0 -0.035 42 42
SIN3/HDAC complex 0.055 0.042 -10000 0 -10000 0 0
GNAI1 0.024 0.017 -10000 0 -0.034 41 41
XPO1 0.021 0.02 -10000 0 -0.044 37 37
GLI1/Su(fu) 0 0.087 -10000 0 -0.51 5 5
SAP30 0.028 0.008 -10000 0 -10000 0 0
mol:GDP 0.023 0.019 -10000 0 -0.039 43 43
MIM/GLI2A 0.013 0.036 -10000 0 -0.13 29 29
IFT88 0.027 0.008 -10000 0 0 45 45
GNAI3 0.021 0.017 -10000 0 -0.034 29 29
GLI2 -0.008 0.076 0.22 1 -0.3 21 22
GLI3 0.004 0.085 0.22 6 -0.33 15 21
CSNK1D 0.029 0.006 -10000 0 0 23 23
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 45 45
GNG2 0.029 0.005 -10000 0 0 14 14
Gi family/GTP 0.009 0.052 -10000 0 -0.21 9 9
SIN3B 0.027 0.009 -10000 0 -10000 0 0
SIN3A 0.029 0.005 -10000 0 -10000 0 0
GLI3/Su(fu) 0 0.095 0.22 3 -0.37 18 21
GLI2/Su(fu) -0.009 0.088 0.2 1 -0.35 23 24
FOXA2 -0.036 0.21 -10000 0 -0.79 36 36
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 0.019 0.045 -10000 0 -0.19 16 16
GNB1 0.029 0.006 -10000 0 0 23 23
CSNK1G2 0.027 0.008 -10000 0 0 46 46
CSNK1G3 0.029 0.006 -10000 0 0 22 22
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 0.027 0.009 -10000 0 0 57 57
catabolic process 0.007 0.11 0.25 1 -0.42 18 19
GLI3A/CBP 0.017 0.028 -10000 0 -10000 0 0
KIF3A 0.029 0.005 -10000 0 0 17 17
GLI1 -0.004 0.084 -10000 0 -0.45 6 6
RAB23 0.029 0.005 -10000 0 0 17 17
CSNK1A1 0.029 0.005 -10000 0 0 13 13
IFT172 0.029 0.005 -10000 0 0 17 17
RBBP7 0.029 0.005 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.016 0.045 -10000 0 -0.19 17 17
GNAZ 0.023 0.018 -10000 0 -0.034 38 38
RBBP4 0.028 0.008 -10000 0 -10000 0 0
CSNK1G1 0.029 0.005 -10000 0 0 13 13
PIAS1 0.029 0.005 -10000 0 0 14 14
PRKACA 0.026 0.01 -10000 0 0 78 78
GLI2/SPOP 0.006 0.085 0.21 1 -0.32 21 22
STK36 0.023 0.02 -10000 0 -0.044 42 42
Gi family/GNB1/GNG2/GDP 0.002 0.064 -10000 0 -0.3 7 7
PTCH1 -0.016 0.13 -10000 0 -0.96 8 8
MIM/GLI1 -0.006 0.11 -10000 0 -0.51 5 5
CREBBP 0.018 0.028 -10000 0 -10000 0 0
Su(fu)/SIN3/HDAC complex -0.001 0.099 0.22 2 -0.4 20 22
Arf6 downstream 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
PLAUR 0.001 0.091 0.59 12 -10000 0 12
regulation of axonogenesis 0.002 0.049 0.27 6 -0.2 13 19
myoblast fusion -0.021 0.06 0.33 1 -0.35 12 13
mol:GTP 0.027 0.038 0.22 12 -0.18 7 19
regulation of calcium-dependent cell-cell adhesion -0.047 0.053 0.15 1 -0.31 13 14
ARF1/GTP 0.033 0.049 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 24 -0.14 5 29
lamellipodium assembly 0.005 0.068 0.34 12 -0.38 6 18
MAPK3 -0.005 0.062 0.38 13 -10000 0 13
ARF6/GTP/NME1/Tiam1 0.048 0.054 0.31 13 -0.15 1 14
ARF1 0.027 0.009 -10000 0 0 54 54
ARF6/GDP 0.021 0.06 0.35 12 -0.33 1 13
ARF1/GDP 0.019 0.059 0.31 11 -0.23 7 18
ARF6 0.044 0.022 0.17 13 -10000 0 13
RAB11A 0.029 0.005 -10000 0 0 13 13
TIAM1 0.02 0.024 0.079 1 -0.04 43 44
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 -0.004 0.062 0.38 13 -10000 0 13
actin filament bundle formation -0.025 0.059 0.23 7 -0.3 12 19
KALRN 0.002 0.023 0.14 3 -0.28 1 4
RAB11FIP3/RAB11A 0.042 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.026 0.06 0.3 12 -0.23 7 19
NME1 0.022 0.022 0.079 1 -0.039 37 38
Rac1/GDP 0.025 0.06 0.3 12 -0.23 7 19
substrate adhesion-dependent cell spreading 0.027 0.038 0.22 12 -0.18 7 19
cortical actin cytoskeleton organization 0.005 0.068 0.34 12 -0.38 6 18
RAC1 0.028 0.006 -10000 0 0 26 26
liver development 0.027 0.038 0.22 12 -0.18 7 19
ARF6/GTP 0.027 0.038 0.22 12 -0.18 7 19
RhoA/GTP 0.042 0.035 0.21 12 -0.14 8 20
mol:GDP 0.007 0.064 0.4 12 -0.22 6 18
ARF6/GTP/RAB11FIP3/RAB11A 0.057 0.036 0.21 12 -0.13 7 19
RHOA 0.029 0.003 -10000 0 0 7 7
PLD1 -0.007 0.034 0.21 10 -0.14 6 16
RAB11FIP3 0.028 0.006 -10000 0 0 25 25
tube morphogenesis 0.005 0.068 0.34 12 -0.38 6 18
ruffle organization -0.002 0.049 0.2 13 -0.27 6 19
regulation of epithelial cell migration 0.027 0.038 0.22 12 -0.18 7 19
PLD2 -0.007 0.038 0.21 13 -0.14 6 19
PIP5K1A -0.002 0.049 0.2 13 -0.28 6 19
mol:Phosphatidic acid -0.011 0.041 0.16 24 -0.14 5 29
Rac1/GTP 0.005 0.069 0.34 12 -0.38 6 18
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.014 0.069 -10000 0 -0.17 68 68
AKT1 -0.048 0.11 0.27 2 -0.38 9 11
PTK2B -0.043 0.1 0.3 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 25 25
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.059 0.05 0.27 1 -10000 0 1
endothelial cell proliferation -0.027 0.1 0.3 7 -0.38 4 11
mol:Ca2+ -0.047 0.081 0.32 5 -10000 0 5
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.011 0.09 0.28 1 -0.24 1 2
RP11-342D11.1 -0.046 0.069 0.32 2 -10000 0 2
CDH5 0.027 0.009 -10000 0 0 57 57
VEGFA homodimer 0.068 0.035 -10000 0 -10000 0 0
SHC1 0.029 0.006 -10000 0 0 20 20
SHC2 0.026 0.01 -10000 0 0 80 80
HRAS/GDP -0.068 0.065 -10000 0 -10000 0 0
SH2D2A 0.029 0.005 -10000 0 0 13 13
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.022 0.085 0.26 2 -0.47 3 5
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.061 0.05 0.27 1 -10000 0 1
VEGFR1 homodimer 0.028 0.007 -10000 0 0 28 28
SHC/GRB2/SOS1 0.021 0.096 0.25 1 -10000 0 1
GRB10 -0.049 0.082 0.32 5 -10000 0 5
PTPN11 0.029 0.003 -10000 0 0 7 7
GRB2 0.029 0.005 -10000 0 0 19 19
PAK1 0.027 0.008 -10000 0 0 47 47
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.014 0.097 0.28 1 -0.24 1 2
HRAS 0.028 0.006 -10000 0 0 27 27
VEGF/Rho/ROCK1/Integrin Complex -0.026 0.093 0.29 1 -0.27 37 38
HIF1A 0.029 0.005 -10000 0 0 17 17
FRS2 0.028 0.007 -10000 0 0 30 30
oxygen and reactive oxygen species metabolic process 0.01 0.088 0.27 1 -0.23 1 2
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.029 0.005 -10000 0 0 15 15
Nck/Pak 0.036 0.018 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.07 0.06 0.27 1 -0.24 16 17
mol:GDP -0.061 0.07 0.14 11 -10000 0 11
mol:NADP -0.018 0.087 0.28 7 -0.45 3 10
eNOS/Hsp90 -0.018 0.089 0.28 8 -0.43 3 11
PIK3R1 0.021 0.013 -10000 0 0 159 159
mol:IP3 -0.047 0.082 0.32 5 -10000 0 5
HIF1A/ARNT 0.04 0.013 -10000 0 -10000 0 0
SHB 0.029 0.004 -10000 0 0 10 10
VEGFA -0.026 0.01 -10000 0 -10000 0 0
VEGFC 0.024 0.012 -10000 0 0 111 111
FAK1/Vinculin -0.037 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 7 7
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.001 0.1 0.28 1 -0.24 29 30
PTPN6 0.027 0.009 -10000 0 0 58 58
EPAS1 -0.025 0.015 -10000 0 -10000 0 0
mol:L-citrulline -0.018 0.087 0.28 7 -0.45 3 10
ITGAV 0.028 0.007 -10000 0 0 32 32
PIK3CA 0.021 0.014 -10000 0 0 174 174
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.015 0.087 0.28 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer -0.061 0.055 0.17 7 -10000 0 7
VEGFR2/3 heterodimer -0.063 0.049 -10000 0 -10000 0 0
VEGFB 0.029 0.006 -10000 0 0 24 24
MAPK11 -0.042 0.091 0.35 7 -0.33 1 8
VEGFR2 homodimer -0.061 0.064 0.39 2 -10000 0 2
FLT1 0.028 0.007 -10000 0 0 28 28
NEDD4 -0.029 0.006 -10000 0 -10000 0 0
MAPK3 -0.04 0.091 0.32 11 -10000 0 11
MAPK1 -0.038 0.091 0.33 11 -10000 0 11
VEGFA145/NRP2 0.036 0.017 -10000 0 -10000 0 0
VEGFR1/2 heterodimer -0.062 0.049 -10000 0 -10000 0 0
KDR -0.061 0.064 0.39 2 -10000 0 2
VEGFA165/NRP1/VEGFR2 homodimer -0.057 0.06 0.26 1 -10000 0 1
SRC 0.028 0.007 -10000 0 0 33 33
platelet activating factor biosynthetic process -0.039 0.093 0.32 12 -10000 0 12
PI3K -0.045 0.087 0.23 3 -10000 0 3
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.056 0.051 0.27 1 -10000 0 1
FES -0.049 0.084 0.33 5 -10000 0 5
GAB1 -0.048 0.093 0.25 8 -0.34 5 13
VEGFR2 homodimer/VEGFA homodimer/Src -0.057 0.049 0.27 1 -10000 0 1
CTNNB1 0.029 0.004 -10000 0 0 8 8
SOS1 0.028 0.007 -10000 0 0 34 34
ARNT 0.028 0.007 -10000 0 0 36 36
eNOS/Caveolin-1 -0.024 0.092 0.27 7 -0.45 3 10
VEGFR2 homodimer/VEGFA homodimer/Yes -0.057 0.05 0.27 1 -10000 0 1
PI3K/GAB1 -0.058 0.14 0.29 1 -0.36 28 29
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.025 0.09 0.28 1 -10000 0 1
PRKACA 0.026 0.01 -10000 0 0 78 78
VEGFR2/3 heterodimer/VEGFC homodimer -0.074 0.059 0.27 1 -0.24 16 17
HSP90AA1 0.029 0.006 -10000 0 0 21 21
CDC42 -0.049 0.085 0.33 5 -10000 0 5
actin cytoskeleton reorganization -0.061 0.05 0.27 1 -10000 0 1
PTK2 -0.044 0.11 0.31 6 -0.38 11 17
EDG1 -0.046 0.069 0.32 2 -10000 0 2
mol:DAG -0.047 0.082 0.32 5 -10000 0 5
CaM/Ca2+ -0.05 0.081 0.3 4 -10000 0 4
MAP2K3 -0.043 0.078 0.31 5 -10000 0 5
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.061 0.063 0.17 19 -10000 0 19
PLCG1 -0.047 0.082 0.33 5 -10000 0 5
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.015 0.087 0.28 1 -10000 0 1
IQGAP1 0.029 0.006 -10000 0 0 24 24
YES1 0.028 0.008 -10000 0 0 43 43
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.061 0.05 0.27 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.054 0.049 0.27 1 -10000 0 1
cell migration -0.046 0.12 0.29 7 -0.37 10 17
mol:PI-3-4-5-P3 -0.043 0.084 0.23 3 -10000 0 3
FYN 0.024 0.011 -10000 0 0 100 100
VEGFB/NRP1 -0.05 0.082 0.3 5 -10000 0 5
mol:NO -0.018 0.087 0.28 7 -0.45 3 10
PXN 0.029 0.005 -10000 0 0 14 14
HRAS/GTP -0.074 0.05 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.064 0.054 0.16 5 -10000 0 5
VHL 0.029 0.004 -10000 0 0 10 10
ITGB3 0.025 0.011 -10000 0 0 99 99
NOS3 -0.02 0.093 0.29 4 -0.51 3 7
VEGFR2 homodimer/VEGFA homodimer/Sck -0.064 0.055 0.27 1 -0.24 5 6
RAC1 0.028 0.006 -10000 0 0 26 26
PRKCA -0.048 0.086 0.31 9 -10000 0 9
PRKCB -0.042 0.082 0.31 9 -10000 0 9
VCL 0.029 0.005 -10000 0 0 13 13
VEGFA165/NRP1 -0.053 0.059 0.26 1 -10000 0 1
VEGFR1/2 heterodimer/VEGFA homodimer -0.061 0.05 0.27 1 -10000 0 1
VEGFA165/NRP2 0.036 0.017 -10000 0 -10000 0 0
MAPKKK cascade -0.068 0.078 0.26 5 -10000 0 5
NRP2 0.028 0.007 -10000 0 0 34 34
VEGFC homodimer 0.024 0.012 -10000 0 0 111 111
NCK1 0.026 0.009 -10000 0 0 63 63
ROCK1 0.029 0.005 -10000 0 0 17 17
FAK1/Paxillin -0.038 0.13 0.31 10 -0.38 11 21
MAP3K13 -0.042 0.078 0.32 4 -10000 0 4
PDPK1 -0.044 0.08 0.21 2 -10000 0 2
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.02 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 44 44
RhoA/GTP 0.021 0.058 0.16 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 0.009 -10000 0 0 51 51
GNAI3 0.025 0.011 -10000 0 0 98 98
GNA12 0.028 0.007 -10000 0 0 34 34
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 0.022 0.008 -10000 0 -0.15 1 1
RHOA 0.029 0.003 -10000 0 0 7 7
GNAI1 0.028 0.006 -10000 0 0 27 27
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.001 0.095 0.52 9 -0.86 3 12
MKNK1 0.029 0.005 -10000 0 0 13 13
MAPK14 -0.01 0.058 0.2 24 -0.3 3 27
ATF2/c-Jun -0.037 0.054 0.13 8 -0.25 7 15
MAPK11 -0.018 0.051 0.2 19 -0.3 3 22
MITF -0.001 0.048 0.24 9 -0.34 3 12
MAPKAPK5 -0.001 0.048 0.24 9 -0.34 3 12
KRT8 -0.001 0.05 0.22 18 -0.31 4 22
MAPKAPK3 0.03 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 0.22 18 -0.25 3 21
SLC9A1 -0.001 0.048 0.22 18 -0.34 3 21
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.001 0.072 0.34 19 -0.33 3 22
p38alpha-beta/MNK1 0.046 0.054 0.25 18 -0.35 3 21
JUN -0.036 0.055 -10000 0 -0.25 7 7
PPARGC1A 0 0.049 0.22 17 -0.34 3 20
USF1 0 0.05 0.25 10 -0.34 3 13
RAB5/GDP/GDI1 -0.003 0.07 -10000 0 -0.2 10 10
NOS2 0 0.047 0.21 18 -0.34 3 21
DDIT3 0.011 0.064 0.24 18 -0.34 3 21
RAB5A 0.029 0.003 -10000 0 0 7 7
HSPB1 -0.011 0.043 0.26 3 -0.29 3 6
p38alpha-beta/HBP1 0.044 0.054 0.25 17 -0.35 3 20
CREB1 -0.025 0.097 0.25 9 -0.35 3 12
RAB5/GDP 0.022 0.002 -10000 0 -10000 0 0
EIF4E -0.036 0.053 0.18 15 -0.32 3 18
RPS6KA4 -0.001 0.048 0.22 18 -0.34 3 21
PLA2G4A -0.018 0.046 0.17 6 -0.38 3 9
GDI1 -0.001 0.051 0.22 18 -0.29 5 23
TP53 -0.022 0.062 0.26 10 -0.46 3 13
RPS6KA5 -0.001 0.048 0.24 9 -0.34 3 12
ESR1 -0.024 0.079 0.21 15 -0.22 61 76
HBP1 0.028 0.007 -10000 0 0 36 36
MEF2C -0.006 0.057 0.22 16 -0.26 13 29
MEF2A -0.002 0.047 0.22 17 -0.34 3 20
EIF4EBP1 -0.021 0.093 0.25 9 -0.36 3 12
KRT19 -0.008 0.061 0.22 18 -0.24 20 38
ELK4 -0.001 0.048 0.22 17 -0.34 3 20
ATF6 -0.001 0.049 0.22 18 -0.34 3 21
ATF1 -0.025 0.098 0.25 9 -0.35 3 12
p38alpha-beta/MAPKAPK2 0.046 0.053 0.25 16 -0.35 3 19
p38alpha-beta/MAPKAPK3 0.047 0.054 0.25 18 -0.35 3 21
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.042 0.021 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 -0.024 0.007 -10000 0 -10000 0 0
mol:DAG -0.04 0.021 0.17 3 -10000 0 3
VEGFR1 homodimer/NRP1/VEGFR 121 -0.029 0.012 -10000 0 -10000 0 0
CaM/Ca2+ -0.049 0.025 0.17 3 -10000 0 3
HIF1A 0.032 0.006 -10000 0 -10000 0 0
GAB1 0.028 0.006 -10000 0 0 25 25
AKT1 -0.029 0.088 0.2 1 -10000 0 1
PLCG1 -0.041 0.021 0.17 3 -10000 0 3
NOS3 -0.015 0.059 0.44 1 -0.29 2 3
CBL 0.029 0.004 -10000 0 0 12 12
mol:NO -0.01 0.066 0.4 2 -0.28 2 4
FLT1 -0.03 0.008 -10000 0 -10000 0 0
PGF 0.029 0.005 -10000 0 0 17 17
VEGFR1 homodimer/NRP2/VEGFR121 -0.037 0.018 -10000 0 -10000 0 0
CALM1 0.028 0.006 -10000 0 0 25 25
PIK3CA 0.021 0.014 -10000 0 0 174 174
eNOS/Hsp90 -0.007 0.073 -10000 0 -0.28 3 3
endothelial cell proliferation -0.021 0.046 0.33 1 -0.3 1 2
mol:Ca2+ -0.04 0.021 0.17 3 -10000 0 3
MAPK3 -0.052 0.035 0.32 1 -10000 0 1
MAPK1 -0.047 0.036 0.32 1 -10000 0 1
PIK3R1 0.021 0.013 -10000 0 0 159 159
PLGF homodimer 0.029 0.005 -10000 0 0 17 17
PRKACA 0.026 0.01 -10000 0 0 78 78
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 69 69
VEGFR1 homodimer/VEGFA homodimer -0.033 0.014 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.052 0.048 0.3 1 -0.23 1 2
PI3K 0.017 0.074 -10000 0 -10000 0 0
PRKCA -0.045 0.028 0.15 3 -10000 0 3
PRKCB -0.037 0.019 0.16 3 -10000 0 3
VEGFR1 homodimer/PLGF homodimer -0.037 0.009 -10000 0 -10000 0 0
VEGFA 0.026 0.01 -10000 0 0 69 69
VEGFB 0.029 0.006 -10000 0 0 24 24
mol:IP3 -0.04 0.021 0.17 3 -10000 0 3
RASA1 -0.043 0.029 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 63 63
eNOS/Caveolin-1 -0.011 0.081 0.4 2 -0.31 6 8
PTPN11 0.029 0.003 -10000 0 0 7 7
mol:PI-3-4-5-P3 0.016 0.072 -10000 0 -10000 0 0
mol:L-citrulline -0.01 0.066 0.4 2 -0.28 2 4
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.053 0.036 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.035 0.019 -10000 0 -10000 0 0
CD2AP 0.028 0.007 -10000 0 0 29 29
PI3K/GAB1 0.02 0.081 -10000 0 -10000 0 0
PDPK1 -0.019 0.09 0.32 1 -10000 0 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.039 0.016 -10000 0 -10000 0 0
mol:NADP -0.01 0.066 0.4 2 -0.28 2 4
HSP90AA1 0.029 0.006 -10000 0 0 21 21
ubiquitin-dependent protein catabolic process 0.051 0.035 -10000 0 -0.14 1 1
VEGFR1 homodimer/NRP2 -0.036 0.011 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.029 0.005 0 18 -9999 0 18
PI3K Class IB/PDE3B 0.029 0.005 -9999 0 0 18 18
PDE3B 0.029 0.005 -9999 0 0 18 18
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.019 0.014 -9999 0 -0.1 7 7
TRAF2/ASK1 0.037 0.013 -9999 0 -0.13 1 1
ATM 0.028 0.007 -9999 0 0 33 33
MAP2K3 -0.021 0.1 -9999 0 -0.32 39 39
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.015 0.089 -9999 0 -0.36 19 19
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0.029 0.006 -9999 0 0 22 22
TXN -0.003 0.036 -9999 0 -0.21 17 17
CALM1 0.028 0.006 -9999 0 0 25 25
GADD45A 0.027 0.009 -9999 0 0 52 52
GADD45B 0.027 0.008 -9999 0 0 49 49
MAP3K1 0.027 0.009 -9999 0 0 52 52
MAP3K6 0.029 0.005 -9999 0 0 17 17
MAP3K7 0.028 0.007 -9999 0 0 30 30
MAP3K4 0.027 0.008 -9999 0 0 49 49
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 0.041 0.015 -9999 0 -0.16 1 1
TAK1/TAB family 0.015 0.027 -9999 0 -0.14 2 2
RAC1/OSM/MEKK3 0.052 0.02 -9999 0 -10000 0 0
TRAF2 0.029 0.006 -9999 0 0 24 24
RAC1/OSM/MEKK3/MKK3 0.003 0.097 -9999 0 -0.27 38 38
TRAF6 0.004 0.001 -9999 0 -10000 0 0
RAC1 0.028 0.006 -9999 0 0 26 26
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B 0.029 0.005 -9999 0 0 13 13
CCM2 0.029 0.005 -9999 0 0 14 14
CaM/Ca2+/CAMKIIB 0.036 0.022 -9999 0 -0.13 8 8
MAPK11 0.023 0.013 -9999 0 0 127 127
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.048 0.032 -9999 0 -0.13 9 9
OSM/MEKK3 0.042 0.009 -9999 0 -10000 0 0
TAOK1 0.007 0.002 -9999 0 -10000 0 0
TAOK2 0.007 0.002 -9999 0 -10000 0 0
TAOK3 0.007 0.002 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.029 0.005 -9999 0 0 19 19
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0.028 0.007 -9999 0 0 31 31
MAP3K10 0.027 0.009 -9999 0 0 54 54
MAP3K3 0.029 0.005 -9999 0 0 13 13
TRX/ASK1 0.016 0.039 -9999 0 -0.17 23 23
GADD45/MTK1/MTK1 0.055 0.047 -9999 0 -0.13 7 7
Signaling events mediated by HDAC Class III

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
EP300 0.027 0.009 -10000 0 0 54 54
HDAC4 0.029 0.005 -10000 0 0 19 19
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.015 0.024 -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 0.029 0.005 -10000 0 0 19 19
FOXO3 0.004 0.007 -10000 0 -10000 0 0
FOXO1 0.028 0.008 -10000 0 0 40 40
FOXO4 0.001 0.023 -10000 0 -0.19 8 8
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.027 0.008 -10000 0 0 49 49
TAT 0.027 0.009 -10000 0 0 56 56
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 12 12
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.043 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 0.24 2 -10000 0 2
SIRT1 -0.025 0.035 0.18 16 -10000 0 16
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.059 0.022 0.16 12 -10000 0 12
SIRT1/Histone H1b 0.007 0.069 0.18 1 -0.22 19 20
apoptosis -0.055 0.026 -10000 0 -0.16 12 12
SIRT1/PGC1A 0.041 0.019 0.14 14 -10000 0 14
p53/SIRT1 0.023 0.088 0.34 13 -0.17 73 86
SIRT1/FOXO4 0.005 0.066 -10000 0 -0.22 18 18
FOXO1/FHL2/SIRT1 0.051 0.032 0.15 10 -0.13 4 14
HIST1H1E 0.002 0.027 0.13 7 -0.19 8 15
SIRT1/p300 0.042 0.022 0.15 13 -10000 0 13
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 0.056 0.026 0.16 12 -10000 0 12
CREBBP 0.027 0.008 -10000 0 0 44 44
MEF2D 0.029 0.005 -10000 0 0 14 14
HIV-1 Tat/SIRT1 0.041 0.021 0.15 10 -10000 0 10
ACSS2 -0.029 0.026 0.12 13 -10000 0 13
SIRT1/PCAF/MYOD -0.024 0.025 0.12 15 -10000 0 15
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.045 0.02 -10000 0 -10000 0 0
RGS9BP 0.027 0.009 -10000 0 0 56 56
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 6 6
RGS9-1/Gbeta5/R9AP 0.049 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 0.028 0.008 -10000 0 0 39 39
CNGB3 0.027 0.008 -10000 0 0 48 48
Cone Metarhodopsin II/X-Arrestin 0.022 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.019 0.052 0.18 36 -10000 0 36
Cone PDE6 0.06 0.05 -10000 0 -0.14 5 5
Cone Metarhodopsin II 0.018 0.005 -10000 0 -10000 0 0
Na + (4 Units) 0.047 0.024 -10000 0 -10000 0 0
GNAT2/GDP 0.055 0.037 -10000 0 -0.13 6 6
GNB5 0.028 0.007 -10000 0 0 33 33
mol:GMP (4 units) -0.015 0.06 0.18 49 -10000 0 49
Cone Transducin 0.049 0.022 -10000 0 -10000 0 0
SLC24A2 0.028 0.007 -10000 0 0 35 35
GNB3/GNGT2 0.038 0.015 -10000 0 -10000 0 0
GNB3 0.027 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 7 7
ARR3 0.03 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 0.048 0.03 -10000 0 -0.15 6 6
Cone CNG Channel 0.056 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 35 35
RGS9 0.029 0.005 -10000 0 0 15 15
PDE6C 0.029 0.005 -10000 0 0 16 16
GNGT2 0.029 0.005 -10000 0 0 17 17
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.027 0.009 -10000 0 0 54 54
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 0.009 -10000 0 0 51 51
Ran/GTP/Exportin 1/HDAC4 -0.038 0.02 -10000 0 -0.15 2 2
MDM2/SUMO1 0.024 0.052 0.16 1 -0.22 12 13
HDAC4 0.029 0.005 -10000 0 0 19 19
Ran/GTP/Exportin 1/HDAC1 -0.036 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 -0.008 0.048 0.15 31 -0.26 3 34
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 0.024 0.053 0.16 1 -0.22 12 13
SUMO1/HDAC1 0.024 0.05 -10000 0 -0.22 10 10
RANGAP1 0.027 0.008 -10000 0 0 46 46
MDM2/SUMO1/SUMO1 0.064 0.035 -10000 0 -0.14 1 1
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 -0.004 0.033 -10000 0 -0.27 3 3
Ran/GTP 0.01 0.047 0.14 1 -0.22 12 13
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.028 0.006 -10000 0 0 26 26
UBE2I 0.029 0.006 -10000 0 0 23 23
Ran/GTP/Exportin 1 -0.013 0.062 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 44 44
CDC42/GTP 0.02 0.058 0.16 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 0.025 0.011 -10000 0 0 98 98
G12/G13 0.041 0.012 -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 9 10
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 27 27
CDC42/GDP 0.022 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.019 0.005 -10000 0 -10000 0 0
RHOA -0.028 0.03 0.2 9 -10000 0 9
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 0.009 -10000 0 0 51 51
S1P/S1P4/G12/G13 0.034 0.014 -10000 0 -10000 0 0
GNA12 0.028 0.007 -10000 0 0 34 34
GNA13 0.029 0.005 -10000 0 0 13 13
CDC42 0.029 0.005 -10000 0 0 13 13
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 0.04 0.013 -9999 0 -10000 0 0
FBXW11 0.029 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 0.029 0.005 -9999 0 0 16 16
CHUK 0.028 0.007 -9999 0 0 35 35
NF kappa B2 p100/RelB 0.075 0.044 -9999 0 -0.14 2 2
NFKB1 0.027 0.008 -9999 0 0 45 45
MAP3K14 0.029 0.006 -9999 0 0 20 20
NF kappa B1 p50/RelB 0.037 0.028 -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 0.037 0.014 -9999 0 -0.13 2 2
Ephrin A reverse signaling

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
MAPKKK cascade 0.034 0.018 -10000 0 -0.13 3 3
EFNA5 0.028 0.008 -10000 0 0 43 43
FYN -0.025 0.033 0.17 12 -0.22 1 13
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 0.035 0.018 -10000 0 -0.13 3 3
EPHA5 0.028 0.007 -10000 0 0 30 30
a4b1 and a4b7 Integrin 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
ITGB1 0.029 0.006 -9999 0 0 20 20
ITGB7 0.029 0.004 -9999 0 0 8 8
ITGA4 0.028 0.008 -9999 0 0 40 40
alpha4/beta7 Integrin 0.04 0.015 -9999 0 -0.16 1 1
alpha4/beta1 Integrin 0.04 0.013 -9999 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.037 0.12 0.64 6 -0.54 2 8
NCK1/PAK1/Dok-R -0.043 0.055 -10000 0 -0.32 2 2
NCK1/Dok-R 0.017 0.069 0.7 1 -10000 0 1
PIK3CA 0.02 0.015 -10000 0 -0.029 9 9
mol:beta2-estradiol 0 0.02 -10000 0 -0.18 7 7
RELA 0.029 0.003 -10000 0 0 7 7
SHC1 0.027 0.014 0.073 1 -0.03 24 25
Rac/GDP 0.021 0.005 -10000 0 -10000 0 0
F2 0.013 0.044 -10000 0 -0.23 11 11
TNIP2 0.028 0.007 -10000 0 0 34 34
NF kappa B/RelA 0.037 0.075 0.68 1 -10000 0 1
FN1 0.018 0.015 -10000 0 0 214 214
PLD2 -0.011 0.06 0.8 1 -10000 0 1
PTPN11 0.029 0.003 -10000 0 0 7 7
GRB14 0.028 0.007 -10000 0 0 32 32
ELK1 -0.015 0.065 0.71 1 -10000 0 1
GRB7 0.028 0.008 -10000 0 0 40 40
PAK1 0.027 0.008 -10000 0 0 47 47
Tie2/Ang1/alpha5/beta1 Integrin 0.019 0.062 -10000 0 -10000 0 0
CDKN1A -0.039 0.16 0.72 5 -0.72 16 21
ITGA5 0.029 0.006 -10000 0 0 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.018 0.071 0.7 1 -10000 0 1
CRK 0.028 0.007 -10000 0 0 36 36
mol:NO -0.03 0.12 0.6 6 -0.44 2 8
PLG -0.011 0.056 0.8 1 -10000 0 1
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.024 0.1 0.57 6 -0.49 1 7
GRB2 0.029 0.005 -10000 0 0 19 19
PIK3R1 0.019 0.017 0.074 1 -0.03 22 23
ANGPT2 -0.025 0.14 0.73 6 -0.67 2 8
BMX -0.011 0.06 0.8 1 -10000 0 1
ANGPT1 0.001 0.062 0.52 6 -10000 0 6
tube development -0.042 0.12 0.68 6 -0.48 1 7
ANGPT4 0.024 0.017 0.08 6 -0.03 37 43
response to hypoxia -0.002 0.008 0.082 3 -10000 0 3
Tie2/Ang1/GRB14 -0.002 0.067 0.74 1 -10000 0 1
alpha5/beta1 Integrin 0.041 0.011 -10000 0 -10000 0 0
FGF2 0.026 0.014 -10000 0 -0.07 6 6
STAT5A (dimer) -0.039 0.15 0.73 5 -0.6 15 20
mol:L-citrulline -0.03 0.12 0.6 6 -0.44 2 8
AGTR1 0.026 0.016 0.11 5 -0.033 16 21
MAPK14 0.002 0.089 0.78 2 -0.76 1 3
Tie2/SHP2 0.006 0.089 -10000 0 -0.36 3 3
TEK 0 0.089 0.86 1 -10000 0 1
RPS6KB1 -0.038 0.12 0.68 4 -0.54 2 6
Angiotensin II/AT1 0.02 0.02 0.21 5 -10000 0 5
Tie2/Ang1/GRB2 0 0.068 0.74 1 -10000 0 1
MAPK3 -0.019 0.061 0.72 1 -10000 0 1
MAPK1 -0.014 0.063 0.72 1 -10000 0 1
Tie2/Ang1/GRB7 -0.001 0.056 -10000 0 -10000 0 0
NFKB1 0.027 0.008 -10000 0 0 45 45
MAPK8 -0.01 0.062 0.8 1 -10000 0 1
PI3K -0.034 0.12 0.76 3 -0.59 2 5
FES -0.002 0.1 0.78 2 -0.65 5 7
Crk/Dok-R 0.019 0.071 0.7 1 -10000 0 1
Tie2/Ang1/ABIN2 -0.001 0.067 0.74 1 -10000 0 1
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.034 0.12 0.64 6 -0.5 2 8
STAT5A 0.026 0.012 -10000 0 -0.033 15 15
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0 0.14 0.68 4 -0.53 3 7
Tie2/Ang2 -0.035 0.13 0.74 5 -0.59 1 6
Tie2/Ang1 0.003 0.063 0.95 1 -10000 0 1
FOXO1 -0.035 0.12 0.66 6 -10000 0 6
ELF1 -0.008 0.033 0.26 1 -10000 0 1
ELF2 -0.001 0.06 0.9 1 -10000 0 1
mol:Choline -0.009 0.062 0.8 1 -10000 0 1
cell migration -0.024 0.035 -10000 0 -0.17 2 2
FYN -0.044 0.13 0.7 6 -0.53 1 7
DOK2 0.024 0.012 -10000 0 0 104 104
negative regulation of cell cycle -0.035 0.15 0.71 5 -0.64 16 21
ETS1 -0.008 0.034 0.2 5 -10000 0 5
PXN 0.001 0.14 0.59 5 -0.48 2 7
ITGB1 0.029 0.006 -10000 0 0 20 20
NOS3 -0.033 0.12 0.61 6 -0.48 3 9
RAC1 0.028 0.006 -10000 0 0 26 26
TNF -0.006 0.038 0.22 7 -10000 0 7
MAPKKK cascade -0.009 0.062 0.8 1 -10000 0 1
RASA1 0.027 0.009 -10000 0 0 51 51
Tie2/Ang1/Shc 0.007 0.071 0.79 1 -10000 0 1
NCK1 0.026 0.009 -10000 0 0 63 63
vasculogenesis -0.027 0.11 0.59 6 -0.41 1 7
mol:Phosphatidic acid -0.009 0.062 0.8 1 -10000 0 1
mol:Angiotensin II 0.001 0.009 0.085 6 -10000 0 6
mol:NADP -0.03 0.12 0.6 6 -0.44 2 8
Rac1/GTP -0.031 0.11 0.48 4 -0.5 3 7
MMP2 -0.006 0.073 0.8 1 -10000 0 1
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.038 0.019 -10000 0 -10000 0 0
PDGFRB 0.024 0.019 0.07 1 -10000 0 1
SPHK1 0.005 0.078 -10000 0 -0.68 7 7
mol:S1P 0.003 0.076 -10000 0 -0.58 7 7
S1P1/S1P/Gi 0.002 0.096 0.47 12 -0.33 7 19
GNAO1 0.021 0.023 0.086 11 -0.045 3 14
PDGFB-D/PDGFRB/PLCgamma1 0.006 0.1 0.43 13 -0.35 4 17
PLCG1 -0.003 0.094 0.44 12 -0.33 6 18
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.024 0.019 0.07 1 -10000 0 1
GNAI2 0.022 0.024 0.086 11 -0.045 3 14
GNAI3 0.022 0.018 0.076 10 -0.037 6 16
GNAI1 0.026 0.017 0.076 11 -0.037 7 18
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.02 0.024 0.11 13 -10000 0 13
S1P1/S1P -0.009 0.067 0.28 10 -0.39 7 17
negative regulation of cAMP metabolic process 0.002 0.095 0.46 12 -0.32 7 19
MAPK3 -0.002 0.11 0.55 11 -0.44 5 16
calcium-dependent phospholipase C activity 0 0.005 0.03 11 -10000 0 11
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.022 0.008 -10000 0 -0.15 1 1
KDR 0.029 0.009 0.062 3 -0.037 4 7
PLCB2 0.002 0.083 0.27 16 -0.36 7 23
RAC1 0.028 0.006 -10000 0 0 26 26
RhoA/GTP -0.019 0.045 -10000 0 -0.35 7 7
receptor internalization -0.009 0.063 0.26 10 -0.37 7 17
PTGS2 0.003 0.13 0.64 11 -0.9 3 14
Rac1/GTP -0.019 0.046 -10000 0 -0.35 7 7
RHOA 0.029 0.003 -10000 0 0 7 7
VEGFA 0.026 0.012 0.062 2 -0.037 4 6
negative regulation of T cell proliferation 0.002 0.095 0.46 12 -0.32 7 19
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.025 0.017 0.074 10 -0.037 7 17
MAPK1 0.001 0.1 0.53 10 -0.45 5 15
S1P1/S1P/PDGFB-D/PDGFRB 0.004 0.089 0.32 17 -0.34 7 24
ABCC1 0.023 0.019 -10000 0 -0.041 2 2
Arf6 trafficking events

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
SLC2A4 0.028 0.006 -10000 0 0 25 25
CLTC 0.012 0.066 0.19 3 -0.38 10 13
calcium ion-dependent exocytosis 0 0.031 0.16 1 -0.2 7 8
Dynamin 2/GTP -0.023 0.036 0.14 23 -10000 0 23
EXOC4 0.028 0.007 -10000 0 0 37 37
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 0.004 -10000 0 0 8 8
membrane fusion -0.002 0.028 -10000 0 -0.18 7 7
CTNND1 -0.028 0.045 0.15 29 -10000 0 29
DNM2 0.026 0.009 -10000 0 0 63 63
mol:PI-4-5-P2 0.001 0.051 0.21 1 -0.23 13 14
TSHR -0.025 0.007 -10000 0 -10000 0 0
INS -0.003 0.099 -10000 0 -0.48 22 22
BIN1 0.029 0.005 -10000 0 0 13 13
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+ -0.023 0.036 0.14 23 -10000 0 23
JUP -0.003 0.049 -10000 0 -0.4 6 6
ASAP2/amphiphysin II 0.036 0.014 -10000 0 -0.12 2 2
ARF6/GTP 0.022 0.003 -10000 0 -10000 0 0
CDH1 -0.005 0.054 -10000 0 -0.46 6 6
clathrin-independent pinocytosis 0.022 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.029 0.006 -10000 0 0 22 22
positive regulation of endocytosis 0.022 0.003 -10000 0 -10000 0 0
EXOC2 0.027 0.008 -10000 0 0 48 48
substrate adhesion-dependent cell spreading 0.008 0.049 0.18 1 -0.24 8 9
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.029 0.005 -10000 0 0 19 19
regulation of calcium-dependent cell-cell adhesion -0.026 0.063 0.33 7 -10000 0 7
positive regulation of phagocytosis -0.025 0.006 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.038 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 -0.001 0.061 0.2 5 -0.32 10 15
JIP4/KLC1 0.051 0.021 -10000 0 -10000 0 0
EXOC1 0.028 0.006 -10000 0 0 25 25
exocyst 0.008 0.049 0.18 1 -0.24 8 9
RALA/GTP 0.021 0.004 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.038 0.009 -10000 0 -10000 0 0
receptor recycling 0.022 0.003 -10000 0 -10000 0 0
CTNNA1 -0.028 0.045 0.15 29 -10000 0 29
NME1 -0.024 0.008 -10000 0 -10000 0 0
clathrin coat assembly 0.01 0.07 0.19 3 -0.36 13 16
IL2RA 0.002 0.051 -10000 0 -0.38 7 7
VAMP3 -0.025 0.006 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.028 0.065 0.18 2 -0.32 10 12
EXOC6 0.028 0.007 -10000 0 0 34 34
PLD1 0.002 0.01 -10000 0 -0.12 1 1
PLD2 0.003 0.01 -10000 0 -10000 0 0
EXOC5 0.029 0.005 -10000 0 0 13 13
PIP5K1C -0.004 0.041 -10000 0 -0.23 8 8
SDC1 0 0.046 -10000 0 -0.35 7 7
ARF6/GDP -0.017 0.038 0.15 26 -10000 0 26
EXOC7 0.029 0.005 -10000 0 0 17 17
E-cadherin/beta catenin 0.028 0.065 -10000 0 -0.34 7 7
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 0.029 0.006 -10000 0 0 20 20
ADRB2 0.002 0.069 0.23 4 -0.36 12 16
EXOC3 0.027 0.009 -10000 0 0 58 58
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP -0.028 0.018 0.17 2 -10000 0 2
KLC1 0.029 0.006 -10000 0 0 22 22
AVPR2 0.008 0.077 0.21 20 -0.36 12 32
RALA 0.029 0.005 -10000 0 0 15 15
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.022 0.064 -10000 0 -0.34 7 7
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 + 0.029 0.005 -10000 0 0 15 15
GNAT1/GTP 0.022 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 0.004 -10000 0 0 8 8
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel 0.043 0.041 -10000 0 -0.14 7 7
mol:Na + -0.06 0.03 0.12 7 -10000 0 7
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.049 0.03 -10000 0 -0.15 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.05 0.051 -10000 0 -0.15 7 7
CNGB1 0.028 0.008 -10000 0 0 38 38
RDH5 0.028 0.007 -10000 0 0 30 30
SAG 0.029 0.004 -10000 0 0 10 10
mol:Ca2+ -0.048 0.086 0.31 21 -10000 0 21
Na + (4 Units) -0.067 0.026 0.074 2 -10000 0 2
RGS9 0.029 0.005 -10000 0 0 15 15
GNB1/GNGT1 0.041 0.014 -10000 0 -0.16 1 1
GNAT1/GDP 0.054 0.037 -10000 0 -0.13 6 6
GUCY2D 0.028 0.007 -10000 0 0 28 28
GNGT1 0.029 0.006 -10000 0 0 22 22
GUCY2F 0.029 0.004 -10000 0 0 12 12
GNB5 0.028 0.007 -10000 0 0 33 33
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 0.03 -10000 0 -10000 0 0
GNB1 0.029 0.006 -10000 0 0 23 23
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 25 25
Metarhodopsin II 0.019 0.003 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.065 0.031 -10000 0 -10000 0 0
RGS9BP 0.027 0.009 -10000 0 0 56 56
Metarhodopsin II/Transducin 0.006 0.026 -10000 0 -0.18 2 2
GCAP Family/Ca ++ 0.052 0.017 -10000 0 -10000 0 0
PDE6A/B 0.04 0.013 -10000 0 -10000 0 0
mol:Pi 0.048 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 0.028 0.008 -10000 0 0 43 43
PDE6A 0.029 0.005 -10000 0 0 14 14
PDE6G 0.029 0.005 -10000 0 0 19 19
RHO 0.029 0.005 -10000 0 0 18 18
PDE6 0.063 0.052 -10000 0 -0.14 6 6
GUCA1A 0.028 0.006 -10000 0 0 25 25
GC2/GCAP Family 0.068 0.027 -10000 0 -10000 0 0
GUCA1C 0.028 0.006 -10000 0 0 26 26
GUCA1B 0.029 0.006 -10000 0 0 24 24
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 0.17 0.42 11 -0.54 4 15
NFATC3 -0.002 0.073 0.36 3 -0.26 1 4
CD40LG -0.005 0.22 0.67 14 -0.73 1 15
ITCH -0.031 0.046 0.3 9 -10000 0 9
CBLB -0.032 0.048 0.3 10 -10000 0 10
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.01 0.18 0.62 12 -0.56 1 13
JUNB 0.02 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 0.08 0.48 11 -10000 0 11
TLE4 -0.045 0.16 -10000 0 -0.53 38 38
Jun/NFAT1-c-4/p21SNFT -0.011 0.16 0.55 4 -0.69 1 5
AP-1/NFAT1-c-4 -0.025 0.21 0.51 42 -0.8 1 43
IKZF1 -0.024 0.12 -10000 0 -0.4 3 3
T-helper 2 cell differentiation 0.003 0.15 -10000 0 -0.63 3 3
AP-1/NFAT1 -0.014 0.15 0.38 9 -0.37 7 16
CALM1 -0.032 0.038 0.19 15 -10000 0 15
EGR2 0.003 0.15 0.96 3 -0.72 1 4
EGR3 -0.005 0.15 0.81 3 -0.68 2 5
NFAT1/FOXP3 0.031 0.13 0.44 8 -0.39 4 12
EGR1 0.003 0.024 0.15 1 -10000 0 1
JUN -0.013 0.051 0.15 18 -10000 0 18
EGR4 0.008 0.029 0.15 1 -10000 0 1
mol:Ca2+ -0.011 0.003 -10000 0 -10000 0 0
GBP3 -0.03 0.17 0.43 21 -0.54 25 46
FOSL1 0.029 0.003 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 0.052 0.15 0.57 2 -0.69 1 3
DGKA -0.021 0.12 0.4 8 -0.38 3 11
CREM 0.029 0.005 -10000 0 -10000 0 0
NFAT1-c-4/PPARG 0.043 0.15 0.49 5 -0.71 1 6
CTLA4 -0.021 0.12 0.46 8 -0.34 3 11
NFAT1-c-4 (dimer)/EGR1 -0.022 0.16 0.58 2 -0.79 1 3
NFAT1-c-4 (dimer)/EGR4 0.041 0.15 0.58 2 -0.71 1 3
FOS -0.012 0.047 0.15 14 -10000 0 14
IFNG 0.004 0.17 0.56 24 -0.62 8 32
T cell activation 0 0.16 0.64 5 -10000 0 5
MAF 0.027 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 -0.006 0.13 0.99 1 -0.81 3 4
TNF -0.057 0.14 0.54 3 -0.75 1 4
FASLG -0.002 0.17 0.84 2 -0.82 1 3
TBX21 0.04 0.052 0.27 26 -10000 0 26
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.027 0.008 -10000 0 -10000 0 0
PTPN1 -0.026 0.12 -10000 0 -0.4 3 3
NFAT1-c-4/ICER1 0.042 0.15 0.49 5 -0.71 1 6
GATA3 0.028 0.007 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.016 0.18 0.56 27 -0.61 8 35
IL2RA -0.017 0.16 0.62 6 -0.53 4 10
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.018 0.12 0.42 8 -0.4 3 11
E2F1 0.029 0.015 0.18 4 -10000 0 4
PPARG 0.029 0.005 -10000 0 -10000 0 0
SLC3A2 -0.024 0.12 0.41 2 -0.4 3 5
IRF4 0.027 0.008 -10000 0 -10000 0 0
PTGS2 -0.017 0.2 0.62 7 -0.73 1 8
CSF2 -0.006 0.22 0.72 10 -0.73 1 11
JunB/Fra1/NFAT1-c-4 0.017 0.16 0.57 2 -0.76 1 3
IL4 0.001 0.15 -10000 0 -0.65 3 3
IL5 -0.007 0.22 0.72 10 -0.73 1 11
IL2 0 0.16 0.64 5 -10000 0 5
IL3 -0.007 0.083 -10000 0 -0.52 12 12
RNF128 -0.033 0.048 0.32 9 -10000 0 9
NFATC1 0.007 0.13 0.81 3 -0.99 1 4
CDK4 0.004 0.14 0.79 3 -0.78 2 5
PTPRK -0.026 0.13 0.4 4 -0.47 8 12
IL8 -0.051 0.14 0.56 2 -0.73 1 3
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 0.004 0 42 -10000 0 42
GNB1/GNG2 0.038 0.012 -9999 0 -0.13 1 1
GNB1 0.029 0.006 -9999 0 0 23 23
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 0.001 -9999 0 -10000 0 0
GNAL 0.029 0.006 -9999 0 0 21 21
GNG2 0.029 0.005 -9999 0 0 14 14
CRH 0.028 0.008 -9999 0 0 42 42
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.004 0 -9999 0 -10000 0 0
MAPK11 0.003 0.002 -9999 0 -10000 0 0
LPA4-mediated signaling events

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
ADCY4 -0.024 0.011 0.17 1 -10000 0 1
ADCY5 -0.024 0.014 0.17 2 -10000 0 2
ADCY6 -0.025 0.006 -10000 0 -10000 0 0
ADCY7 -0.024 0.008 -10000 0 -10000 0 0
ADCY1 -0.025 0.007 -10000 0 -10000 0 0
ADCY2 -0.023 0.009 -10000 0 -10000 0 0
ADCY3 -0.025 0.006 -10000 0 -10000 0 0
ADCY8 -0.008 0.02 0.17 4 -10000 0 4
PRKCE -0.016 0.003 0 23 -10000 0 23
ADCY9 -0.023 0.01 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.002 0.091 0.2 47 -0.2 1 48
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.029 0.003 -9999 0 0 7 7
GPC2 0.029 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
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 0.061 -0.0012 0.012 -0.025
47_PPARGC1A 0.03 0.03 0.03 0.03
105_BMP4 0.03 0.03 0.03 0.03
105_BMP6 0.03 0.03 0.03 0.03
105_BMP7 0 0.03 0.03 0.03
105_BMP2 0 0.03 0.03 0.03
131_RELN/VLDLR 0.077 0.077 0.077 0.077
30_TGFB1/TGF beta receptor Type II 0.03 0.03 0 0.03
84_STAT5B 0.036 -0.027 -0.027 0.066
84_STAT5A 0.036 -0.027 -0.027 0.066
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/14520414/GDAC_MergeDataFiles_12185952/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/15085754/GDAC_Gistic2Report_15092701/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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