PARADIGM pathway analysis of mRNASeq expression data
Breast Invasive Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1W094X9
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 mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1W094X9
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 58 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
Class IB PI3K non-lipid kinase events 309
Signaling events mediated by Stem cell factor receptor (c-Kit) 297
Signaling mediated by p38-alpha and p38-beta 257
EGFR-dependent Endothelin signaling events 249
Reelin signaling pathway 245
HIF-1-alpha transcription factor network 200
p75(NTR)-mediated signaling 171
FOXM1 transcription factor network 171
Angiopoietin receptor Tie2-mediated signaling 165
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 163
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 1093 . 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 ( 1093 ).

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
Class IB PI3K non-lipid kinase events 0.2827 309 927 3 -0.22 -1000 1000 -1000 -0.026 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.2717 297 23216 78 -0.61 0.19 1000 -1000 -0.06 -1000
Signaling mediated by p38-alpha and p38-beta 0.2351 257 11314 44 -0.4 0 1000 -1000 -0.044 -1000
EGFR-dependent Endothelin signaling events 0.2278 249 5231 21 -0.33 0 1000 -1000 -0.059 -1000
Reelin signaling pathway 0.2242 245 13741 56 -0.47 0 1000 -1000 -0.086 -1000
HIF-1-alpha transcription factor network 0.1830 200 15246 76 -0.75 0.019 1000 -1000 -0.077 -1000
p75(NTR)-mediated signaling 0.1565 171 21392 125 -0.37 0 1000 -1000 -0.093 -1000
FOXM1 transcription factor network 0.1565 171 8757 51 -0.44 0.014 1000 -1000 -0.13 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1510 165 14567 88 -0.38 0.04 1000 -1000 -0.088 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1491 163 11088 68 -0.5 0.15 1000 -1000 -0.089 -1000
FOXA2 and FOXA3 transcription factor networks 0.1436 157 7258 46 -1.2 0.023 1000 -1000 -0.042 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1372 150 8125 54 -0.47 0.022 1000 -1000 -0.085 -1000
Glucocorticoid receptor regulatory network 0.1372 150 17130 114 -0.92 0.34 1000 -1000 -0.072 -1000
Arf6 signaling events 0.1263 138 8595 62 -0.33 0.017 1000 -1000 -0.058 -1000
Wnt signaling 0.1263 138 968 7 -0.17 -0.007 1000 -1000 -0.048 -1000
IL4-mediated signaling events 0.1217 133 12144 91 -0.98 0.51 1000 -1000 -0.14 -1000
Endothelins 0.1217 133 12824 96 -0.37 0.038 1000 -1000 -0.072 -1000
EPHB forward signaling 0.1217 133 11307 85 -0.3 0.16 1000 -1000 -0.08 -1000
Aurora B signaling 0.1208 132 8851 67 -0.31 0.009 1000 -1000 -0.065 -1000
ErbB2/ErbB3 signaling events 0.1171 128 8378 65 -0.38 0.018 1000 -1000 -0.061 -1000
Ephrin B reverse signaling 0.1125 123 5921 48 -0.3 0.17 1000 -1000 -0.064 -1000
IGF1 pathway 0.1116 122 6971 57 -0.18 0.08 1000 -1000 -0.085 -1000
Nongenotropic Androgen signaling 0.1016 111 5778 52 -0.23 0.11 1000 -1000 -0.054 -1000
Signaling events regulated by Ret tyrosine kinase 0.1006 110 9023 82 -0.17 0 1000 -1000 -0.076 -1000
ErbB4 signaling events 0.0997 109 7527 69 -0.41 0.056 1000 -1000 -0.073 -1000
Calcium signaling in the CD4+ TCR pathway 0.0997 109 3404 31 -0.32 0.012 1000 -1000 -0.075 -1000
BMP receptor signaling 0.0988 108 8761 81 -0.54 0.026 1000 -1000 -0.087 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0961 105 12683 120 -0.58 0.24 1000 -1000 -0.061 -1000
Plasma membrane estrogen receptor signaling 0.0924 101 8756 86 -0.19 0.094 1000 -1000 -0.072 -1000
Noncanonical Wnt signaling pathway 0.0915 100 2619 26 -0.17 0 1000 -1000 -0.071 -1000
Glypican 1 network 0.0897 98 4723 48 -0.32 0.032 1000 -1000 -0.041 -1000
IL23-mediated signaling events 0.0887 97 5871 60 -0.46 0.018 1000 -1000 -0.13 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0869 95 8137 85 -0.24 0.011 1000 -1000 -0.07 -1000
Syndecan-1-mediated signaling events 0.0851 93 3175 34 -0.22 0 1000 -1000 -0.066 -1000
Aurora C signaling 0.0842 92 644 7 -0.17 0 1000 -1000 -0.043 -1000
Visual signal transduction: Rods 0.0842 92 4794 52 -0.48 0 1000 -1000 -0.077 -1000
Signaling events mediated by PTP1B 0.0823 90 6843 76 -0.64 0.071 1000 -1000 -0.073 -1000
IL6-mediated signaling events 0.0805 88 6611 75 -0.28 0.05 1000 -1000 -0.075 -1000
amb2 Integrin signaling 0.0787 86 7108 82 -0.48 0 1000 -1000 -0.067 -1000
Integrins in angiogenesis 0.0778 85 7171 84 -0.33 0 1000 -1000 -0.094 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0686 75 2575 34 -0.096 0 1000 -1000 -0.064 -1000
Ephrin A reverse signaling 0.0677 74 522 7 -0.074 0 1000 -1000 -0.029 -1000
S1P1 pathway 0.0668 73 2658 36 -0.33 0.008 1000 -1000 -0.059 -1000
Signaling events mediated by PRL 0.0668 73 2515 34 -0.17 0.021 1000 -1000 -0.051 -1000
Syndecan-3-mediated signaling events 0.0659 72 2530 35 -0.34 0 1000 -1000 -0.062 -1000
PDGFR-alpha signaling pathway 0.0631 69 3037 44 -0.36 0.019 1000 -1000 -0.054 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0631 69 3612 52 -0.19 0.029 1000 -1000 -0.061 -1000
Signaling events mediated by the Hedgehog family 0.0622 68 3574 52 -0.22 0.032 1000 -1000 -0.071 -1000
TCGA08_rtk_signaling 0.0613 67 1760 26 -0.29 0.027 1000 -1000 -0.029 -1000
E-cadherin signaling in keratinocytes 0.0604 66 2850 43 -0.29 0.04 1000 -1000 -0.067 -1000
LPA receptor mediated events 0.0586 64 6564 102 -0.29 0.028 1000 -1000 -0.091 -1000
Ras signaling in the CD4+ TCR pathway 0.0576 63 1077 17 -0.12 -0.001 1000 -1000 -0.05 -1000
PLK1 signaling events 0.0531 58 4956 85 -0.22 0.029 1000 -1000 -0.049 -1000
Nectin adhesion pathway 0.0531 58 3676 63 -0.087 0.001 1000 -1000 -0.064 -1000
Visual signal transduction: Cones 0.0522 57 2198 38 -0.17 0.011 1000 -1000 -0.067 -1000
Fc-epsilon receptor I signaling in mast cells 0.0503 55 5378 97 -0.24 0.028 1000 -1000 -0.085 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0503 55 1815 33 -0.54 0 1000 -1000 -0.055 -1000
Rapid glucocorticoid signaling 0.0503 55 1104 20 -0.19 0.027 1000 -1000 -0.04 -1000
Presenilin action in Notch and Wnt signaling 0.0494 54 3336 61 -0.41 0.014 1000 -1000 -0.077 -1000
Signaling events mediated by HDAC Class III 0.0476 52 2081 40 -0.56 0.022 1000 -1000 -0.044 -1000
FAS signaling pathway (CD95) 0.0476 52 2479 47 -0.47 0.013 1000 -1000 -0.044 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0476 52 3865 74 -0.29 0.072 1000 -1000 -0.084 -1000
IL27-mediated signaling events 0.0467 51 2608 51 -0.29 0.035 1000 -1000 -0.066 -1000
LPA4-mediated signaling events 0.0448 49 589 12 -0.16 0.02 1000 -1000 -0.017 -1000
Effects of Botulinum toxin 0.0430 47 1242 26 -0.099 0.001 1000 -1000 -0.055 -1000
Canonical Wnt signaling pathway 0.0421 46 2362 51 -0.41 0.14 1000 -1000 -0.058 -1000
TCR signaling in naïve CD8+ T cells 0.0384 42 3965 93 -0.16 0.077 1000 -1000 -0.071 -1000
Coregulation of Androgen receptor activity 0.0375 41 3132 76 -0.17 0.034 1000 -1000 -0.049 -1000
Regulation of Androgen receptor activity 0.0375 41 2926 70 -0.25 0.021 1000 -1000 -0.064 -1000
IL12-mediated signaling events 0.0366 40 3504 87 -0.35 0.047 1000 -1000 -0.11 -1000
Insulin Pathway 0.0366 40 3029 74 -0.2 0.033 1000 -1000 -0.078 -1000
Regulation of Telomerase 0.0357 39 3997 102 -0.33 0.026 1000 -1000 -0.083 -1000
Syndecan-4-mediated signaling events 0.0357 39 2660 67 -0.32 0.005 1000 -1000 -0.09 -1000
Regulation of nuclear SMAD2/3 signaling 0.0329 36 4975 136 -0.3 0.052 1000 -1000 -0.06 -1000
Syndecan-2-mediated signaling events 0.0311 34 2390 69 -0.2 0.033 1000 -1000 -0.058 -1000
Regulation of p38-alpha and p38-beta 0.0311 34 1861 54 -0.35 0.029 1000 -1000 -0.066 -1000
TCGA08_retinoblastoma 0.0311 34 274 8 -0.052 0.01 1000 -1000 -0.024 -1000
Osteopontin-mediated events 0.0302 33 1284 38 -0.24 0.022 1000 -1000 -0.089 -1000
IL2 signaling events mediated by STAT5 0.0302 33 737 22 -0.11 0.063 1000 -1000 -0.037 -1000
Thromboxane A2 receptor signaling 0.0293 32 3445 105 -0.29 0.066 1000 -1000 -0.064 -1000
BCR signaling pathway 0.0293 32 3236 99 -0.13 0.042 1000 -1000 -0.079 -1000
Aurora A signaling 0.0265 29 1754 60 -0.21 0.006 1000 -1000 -0.058 -1000
Arf6 trafficking events 0.0256 28 2012 71 -0.44 0.032 1000 -1000 -0.065 -1000
TCGA08_p53 0.0238 26 188 7 -0.025 0.017 1000 -1000 -0.018 -1000
S1P5 pathway 0.0229 25 431 17 -0.045 0.024 1000 -1000 -0.048 -1000
BARD1 signaling events 0.0192 21 1245 57 -0.11 0.024 1000 -1000 -0.068 -1000
Glypican 2 network 0.0192 21 84 4 -0.038 -0.032 1000 -1000 -0.044 -1000
S1P4 pathway 0.0183 20 523 25 -0.045 0.008 1000 -1000 -0.048 -1000
Hedgehog signaling events mediated by Gli proteins 0.0174 19 1247 65 -0.067 0.044 1000 -1000 -0.071 -1000
Class I PI3K signaling events mediated by Akt 0.0174 19 1333 68 -0.25 0.053 1000 -1000 -0.065 -1000
Ceramide signaling pathway 0.0174 19 1495 76 -0.18 0.049 1000 -1000 -0.068 -1000
TRAIL signaling pathway 0.0174 19 947 48 -0.075 0.044 1000 -1000 -0.056 -1000
Retinoic acid receptors-mediated signaling 0.0174 19 1148 58 -0.1 0.037 1000 -1000 -0.069 -1000
Caspase cascade in apoptosis 0.0165 18 1347 74 -0.046 0.045 1000 -1000 -0.052 -1000
Signaling mediated by p38-gamma and p38-delta 0.0165 18 273 15 -0.018 0.022 1000 -1000 -0.046 -1000
Cellular roles of Anthrax toxin 0.0156 17 684 39 -0.14 0.019 1000 -1000 -0.029 -1000
IL2 signaling events mediated by PI3K 0.0156 17 1033 58 -0.044 0.06 1000 -1000 -0.071 -1000
E-cadherin signaling events 0.0156 17 87 5 -0.02 0 1000 -1000 -0.047 -1000
JNK signaling in the CD4+ TCR pathway 0.0146 16 280 17 -0.019 0.043 1000 -1000 -0.058 -1000
IL1-mediated signaling events 0.0137 15 963 62 -0.037 0.031 1000 -1000 -0.079 -1000
S1P3 pathway 0.0119 13 581 42 -0.033 0.021 1000 -1000 -0.053 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0110 12 357 28 -0.045 0.02 1000 -1000 -0.05 -1000
E-cadherin signaling in the nascent adherens junction 0.0110 12 939 76 -0.02 0.05 1000 -1000 -0.075 -1000
mTOR signaling pathway 0.0101 11 619 53 -0.021 0.025 1000 -1000 -0.061 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0101 11 411 37 -0.047 0.034 1000 -1000 -0.067 -1000
p38 MAPK signaling pathway 0.0101 11 516 44 -0.066 0.025 1000 -1000 -0.069 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0091 10 835 83 -0.038 0.053 1000 -1000 -0.078 -1000
Signaling events mediated by HDAC Class II 0.0082 9 704 75 -0.15 0 1000 -1000 -0.061 -1000
a4b1 and a4b7 Integrin signaling 0.0082 9 48 5 -0.009 -0.002 1000 -1000 -0.033 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0082 9 1141 125 -0.17 0.082 1000 -1000 -0.096 -1000
VEGFR1 specific signals 0.0082 9 529 56 -0.17 0.065 1000 -1000 -0.068 -1000
IFN-gamma pathway 0.0073 8 582 68 -0.066 0.075 1000 -1000 -0.08 -1000
HIF-2-alpha transcription factor network 0.0073 8 347 43 -0.17 0.18 1000 -1000 -0.07 -1000
Class I PI3K signaling events 0.0073 8 584 73 -0.044 0.059 1000 -1000 -0.063 -1000
EPO signaling pathway 0.0064 7 397 55 -0.036 0.058 1000 -1000 -0.086 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0064 7 359 45 -0.025 0.072 1000 -1000 -0.083 -1000
PDGFR-beta signaling pathway 0.0064 7 719 97 -0.026 0.05 1000 -1000 -0.08 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0055 6 149 23 -0.029 0.041 1000 -1000 -0.064 -1000
ceramide signaling pathway 0.0046 5 249 49 -0.027 0.054 1000 -1000 -0.046 -1000
FoxO family signaling 0.0046 5 375 64 -0.038 0.09 1000 -1000 -0.072 -1000
Atypical NF-kappaB pathway 0.0046 5 181 31 -0.02 0.03 1000 -1000 -0.066 -1000
Canonical NF-kappaB pathway 0.0037 4 160 39 -0.021 0.077 1000 -1000 -0.071 -1000
Signaling events mediated by HDAC Class I 0.0037 4 495 104 -0.095 0.046 1000 -1000 -0.072 -1000
Paxillin-dependent events mediated by a4b1 0.0037 4 144 36 -0.011 0.022 1000 -1000 -0.067 -1000
Circadian rhythm pathway 0.0027 3 87 22 -0.015 0.042 1000 -1000 -0.064 -1000
Arf6 downstream pathway 0.0027 3 142 43 -0.023 0.023 1000 -1000 -0.036 -1000
Insulin-mediated glucose transport 0.0027 3 101 32 -0.13 0.032 1000 -1000 -0.064 -1000
PLK2 and PLK4 events 0.0000 0 1 3 -0.012 0.013 1000 -1000 -0.028 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 9 27 -0.001 0.029 1000 -1000 -0.059 -1000
Arf1 pathway 0.0000 0 25 54 -0.001 0.025 1000 -1000 -0.037 -1000
Alternative NF-kappaB pathway 0.0000 0 11 13 -0.003 0 1000 -1000 -0.058 -1000
Total NA 8343 488828 7203 -30 -990 131000 -131000 -8.5 -131000
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.22 0.35 0.78 309 -10000 0 309
PI3K Class IB/PDE3B -0.22 0.35 -10000 0 -0.79 309 309
PDE3B -0.22 0.36 -10000 0 -0.79 309 309
Signaling events mediated by Stem cell factor receptor (c-Kit)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.16 0.22 -10000 0 -0.39 499 499
CRKL -0.17 0.23 -10000 0 -0.41 499 499
HRAS -0.16 0.17 -10000 0 -0.45 65 65
mol:PIP3 -0.17 0.21 -10000 0 -0.4 501 501
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0 0 -10000 0 -10000 0 0
GAB1 -0.18 0.24 -10000 0 -0.44 500 500
FOXO3 -0.15 0.21 -10000 0 -0.37 498 498
AKT1 -0.16 0.22 -10000 0 -0.41 499 499
BAD -0.15 0.21 -10000 0 -0.37 498 498
megakaryocyte differentiation -0.18 0.23 -10000 0 -0.43 500 500
GSK3B -0.15 0.21 -10000 0 -0.37 498 498
RAF1 -0.092 0.17 -10000 0 -0.39 44 44
SHC1 0 0 -10000 0 -10000 0 0
STAT3 -0.18 0.24 -10000 0 -0.44 500 500
STAT1 -0.45 0.56 -10000 0 -1 510 510
HRAS/SPRED1 -0.13 0.14 -10000 0 -0.36 65 65
cell proliferation -0.18 0.24 -10000 0 -0.44 501 501
PIK3CA 0 0.009 -10000 0 -0.29 1 1
TEC -0.002 0.041 -10000 0 -0.79 3 3
RPS6KB1 -0.18 0.24 -10000 0 -0.44 502 502
HRAS/SPRED2 -0.13 0.14 -10000 0 -0.39 44 44
LYN/TEC/p62DOK -0.19 0.2 -10000 0 -0.4 500 500
MAPK3 -0.054 0.13 -10000 0 -0.31 22 22
STAP1 -0.2 0.24 -10000 0 -0.45 502 502
GRAP2 -0.014 0.1 -10000 0 -0.72 21 21
JAK2 -0.4 0.44 -10000 0 -0.87 510 510
STAT1 (dimer) -0.44 0.54 -10000 0 -1 510 510
mol:Gleevec 0.006 0.009 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.19 0.2 -10000 0 -0.41 500 500
actin filament polymerization -0.18 0.24 -10000 0 -0.44 500 500
LYN 0 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.27 0.33 -10000 0 -0.62 500 500
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
CBL/CRKL/GRB2 -0.17 0.18 -10000 0 -0.36 498 498
PI3K -0.19 0.21 -10000 0 -0.41 505 505
PTEN -0.001 0.034 -10000 0 -0.79 2 2
SCF/KIT/EPO/EPOR -0.56 0.69 -10000 0 -1.3 498 498
MAPK8 -0.19 0.24 -10000 0 -0.45 501 501
STAT3 (dimer) -0.18 0.23 -10000 0 -0.43 500 500
positive regulation of transcription -0.041 0.11 -10000 0 -0.25 21 21
mol:GDP -0.17 0.18 -10000 0 -0.36 489 489
PIK3C2B -0.18 0.24 -10000 0 -0.44 500 500
CBL/CRKL -0.15 0.22 -10000 0 -0.38 498 498
FER -0.19 0.24 -10000 0 -0.44 505 505
SH2B3 -0.18 0.24 -10000 0 -0.44 500 500
PDPK1 -0.15 0.2 -10000 0 -0.36 501 501
SNAI2 -0.19 0.25 -10000 0 -0.45 502 502
positive regulation of cell proliferation -0.32 0.4 -10000 0 -0.75 510 510
KITLG 0.002 0.067 -10000 0 -0.48 16 16
cell motility -0.32 0.4 -10000 0 -0.75 510 510
PTPN6 0.015 0.021 -10000 0 -0.29 2 2
EPOR -0.096 0.16 -10000 0 -10000 0 0
STAT5A (dimer) -0.26 0.34 -10000 0 -0.62 512 512
SOCS1 -0.005 0.043 -10000 0 -0.32 18 18
cell migration 0.19 0.24 0.44 508 -10000 0 508
SOS1 0 0 -10000 0 -10000 0 0
EPO -0.044 0.11 -10000 0 -0.3 177 177
VAV1 -0.003 0.043 -10000 0 -0.59 5 5
GRB10 -0.18 0.24 -10000 0 -0.44 500 500
PTPN11 0.013 0.013 -10000 0 -10000 0 0
SCF/KIT -0.22 0.23 -10000 0 -0.46 512 512
GO:0007205 0.009 0.013 -10000 0 -10000 0 0
MAP2K1 -0.064 0.14 -10000 0 -0.35 22 22
CBL 0 0 -10000 0 -10000 0 0
KIT -0.61 0.73 -10000 0 -1.4 496 496
MAP2K2 -0.064 0.14 -10000 0 -0.35 22 22
SHC/Grb2/SOS1 -0.19 0.2 -10000 0 -0.4 498 498
STAT5A -0.27 0.35 -10000 0 -0.64 512 512
GRB2 0 0.009 -10000 0 -0.29 1 1
response to radiation -0.18 0.24 -10000 0 -0.44 502 502
SHC/GRAP2 -0.01 0.077 -10000 0 -0.6 18 18
PTPRO -0.18 0.24 -10000 0 -0.44 500 500
SH2B2 -0.19 0.24 -10000 0 -0.44 500 500
DOK1 -0.001 0.018 -10000 0 -0.29 4 4
MATK -0.19 0.25 -10000 0 -0.45 508 508
CREBBP 0.02 0.018 -10000 0 -10000 0 0
BCL2 -0.13 0.3 -10000 0 -1.5 37 37
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.4 0.62 -9999 0 -1.3 370 370
MKNK1 0 0 -9999 0 -10000 0 0
MAPK14 -0.081 0.15 -9999 0 -0.29 369 369
ATF2/c-Jun -0.052 0.15 -9999 0 -0.78 14 14
MAPK11 -0.083 0.16 -9999 0 -0.3 372 372
MITF -0.092 0.2 -9999 0 -0.36 377 377
MAPKAPK5 -0.088 0.19 -9999 0 -0.35 372 372
KRT8 -0.095 0.2 -9999 0 -0.36 373 373
MAPKAPK3 0 0 -9999 0 -10000 0 0
MAPKAPK2 0 0.009 -9999 0 -0.29 1 1
p38alpha-beta/CK2 -0.12 0.23 -9999 0 -0.44 372 372
CEBPB -0.088 0.19 -9999 0 -0.35 372 372
SLC9A1 -0.088 0.19 -9999 0 -0.35 372 372
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.082 0.19 -9999 0 -0.34 374 374
p38alpha-beta/MNK1 -0.12 0.17 -9999 0 -0.35 372 372
JUN -0.051 0.15 -9999 0 -0.77 14 14
PPARGC1A -0.21 0.36 -9999 0 -0.57 452 452
USF1 -0.088 0.19 -9999 0 -0.35 372 372
RAB5/GDP/GDI1 -0.085 0.12 -9999 0 -0.38 16 16
NOS2 -0.092 0.21 -9999 0 -0.82 18 18
DDIT3 -0.088 0.19 -9999 0 -0.35 372 372
RAB5A 0 0 -9999 0 -10000 0 0
HSPB1 -0.074 0.17 -9999 0 -0.43 56 56
p38alpha-beta/HBP1 -0.12 0.17 -9999 0 -0.35 372 372
CREB1 -0.093 0.2 -9999 0 -0.37 372 372
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.069 0.17 -9999 0 -0.49 16 16
RPS6KA4 -0.088 0.19 -9999 0 -0.35 372 372
PLA2G4A -0.13 0.27 -9999 0 -0.72 141 141
GDI1 -0.088 0.19 -9999 0 -0.35 372 372
TP53 -0.11 0.23 -9999 0 -0.44 372 372
RPS6KA5 -0.095 0.2 -9999 0 -0.36 381 381
ESR1 -0.17 0.25 -9999 0 -0.42 506 506
HBP1 0 0 -9999 0 -10000 0 0
MEF2C -0.09 0.2 -9999 0 -0.35 372 372
MEF2A -0.089 0.19 -9999 0 -0.35 372 372
EIF4EBP1 -0.093 0.2 -9999 0 -0.37 372 372
KRT19 -0.1 0.21 -9999 0 -0.37 377 377
ELK4 -0.088 0.19 -9999 0 -0.35 372 372
ATF6 -0.088 0.19 -9999 0 -0.35 372 372
ATF1 -0.093 0.2 -9999 0 -0.37 372 372
p38alpha-beta/MAPKAPK2 -0.12 0.17 -9999 0 -0.35 372 372
p38alpha-beta/MAPKAPK3 -0.12 0.17 -9999 0 -0.52 19 19
EGFR-dependent Endothelin signaling events

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
HRAS -0.003 0.028 -9999 0 -0.29 10 10
EGFR -0.29 0.38 -9999 0 -0.78 410 410
EGF/EGFR -0.28 0.3 -9999 0 -0.53 563 563
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.25 0.26 -9999 0 -0.49 552 552
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.002 0.035 -9999 0 -0.62 3 3
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.15 0.31 -9999 0 -0.78 214 214
EGF/EGFR dimer/SHC -0.29 0.3 -9999 0 -0.57 552 552
mol:GDP -0.24 0.26 -9999 0 -0.48 552 552
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.059 0.21 -9999 0 -0.79 82 82
GRB2/SOS1 0 0.006 -9999 0 -10000 0 0
HRAS/GTP -0.23 0.24 -9999 0 -0.45 552 552
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.23 0.24 -9999 0 -0.45 552 552
FRAP1 -0.24 0.25 -9999 0 -0.46 552 552
EGF/EGFR dimer -0.33 0.35 -9999 0 -0.66 552 552
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0 0.009 -9999 0 -0.29 1 1
ETA receptor/Endothelin-1 -0.046 0.16 -9999 0 -0.6 84 84
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 -0.006 0.034 -9999 0 -10000 0 0
VLDLR -0.025 0.14 -9999 0 -0.79 35 35
CRKL 0 0 -9999 0 -10000 0 0
LRPAP1 0 0 -9999 0 -10000 0 0
FYN -0.001 0.034 -9999 0 -0.79 2 2
ITGA3 -0.004 0.05 -9999 0 -0.57 7 7
RELN/VLDLR/Fyn -0.32 0.27 -9999 0 -0.54 660 660
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.005 0.046 -9999 0 -0.44 12 12
AKT1 -0.18 0.18 -9999 0 -0.36 230 230
MAP2K7 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
DAB1 -0.017 0.069 -9999 0 -0.29 65 65
RELN/LRP8/DAB1 -0.31 0.24 -9999 0 -0.5 652 652
LRPAP1/LRP8 -0.019 0.057 -9999 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.29 0.23 -9999 0 -0.47 652 652
DAB1/alpha3/beta1 Integrin -0.27 0.22 -9999 0 -0.44 663 663
long-term memory -0.35 0.29 -9999 0 -0.53 706 706
DAB1/LIS1 -0.28 0.23 -9999 0 -0.45 660 660
DAB1/CRLK/C3G -0.27 0.22 -9999 0 -0.44 657 657
PIK3CA 0 0.009 -9999 0 -0.29 1 1
DAB1/NCK2 -0.28 0.23 -9999 0 -0.46 660 660
ARHGEF2 0 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.091 0.25 -9999 0 -0.74 135 135
CDK5R1 -0.008 0.049 -9999 0 -0.29 31 31
RELN -0.47 0.39 -9999 0 -0.78 654 654
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
RELN/LRP8/Fyn -0.32 0.26 -9999 0 -0.54 651 651
GRIN2A/RELN/LRP8/DAB1/Fyn -0.33 0.29 -9999 0 -0.53 672 672
MAPK8 -0.006 0.071 -9999 0 -0.79 9 9
RELN/VLDLR/DAB1 -0.31 0.25 -9999 0 -0.5 660 660
ITGB1 0 0 -9999 0 -10000 0 0
MAP1B -0.3 0.25 -9999 0 -0.49 666 666
RELN/LRP8 -0.32 0.26 -9999 0 -0.53 651 651
GRIN2B/RELN/LRP8/DAB1/Fyn -0.31 0.25 -9999 0 -0.49 689 689
PI3K -0.008 0.068 -9999 0 -0.6 14 14
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.003 0.037 -9999 0 -0.6 4 4
RAP1A -0.25 0.2 -9999 0 -0.54 142 142
PAFAH1B1 0 0 -9999 0 -10000 0 0
MAPK8IP1 -0.004 0.046 -9999 0 -0.48 8 8
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.053 0.2 -9999 0 -0.77 75 75
NCK2 0 0 -9999 0 -10000 0 0
neuron differentiation -0.12 0.13 -9999 0 -0.48 13 13
neuron adhesion -0.23 0.19 -9999 0 -0.5 145 145
LRP8 -0.03 0.089 -9999 0 -10000 0 0
GSK3B -0.17 0.18 -9999 0 -0.46 70 70
RELN/VLDLR/DAB1/Fyn -0.29 0.24 -9999 0 -0.47 660 660
MAP3K11 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.21 0.18 -9999 0 -0.35 667 667
CDK5 -0.002 0.023 -9999 0 -0.29 7 7
MAPT -0.045 0.24 -9999 0 -0.73 117 117
neuron migration -0.22 0.23 -9999 0 -0.41 652 652
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.13 0.11 -9999 0 -0.48 13 13
RELN/VLDLR -0.31 0.25 -9999 0 -0.5 660 660
HIF-1-alpha transcription factor network

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
PKM2 -0.41 0.46 -9999 0 -1 273 273
HDAC7 0 0.002 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.32 0.31 -9999 0 -0.8 196 196
SMAD4 -0.001 0.024 -9999 0 -0.78 1 1
ID2 -0.41 0.46 -9999 0 -1 281 281
AP1 -0.18 0.28 -9999 0 -0.61 330 330
ABCG2 -0.43 0.5 -9999 0 -1.1 301 301
HIF1A -0.051 0.064 -9999 0 -10000 0 0
TFF3 -0.48 0.52 -9999 0 -1.1 320 320
GATA2 -0.013 0.13 -9999 0 -0.63 41 41
AKT1 -0.052 0.08 -9999 0 -10000 0 0
response to hypoxia -0.074 0.086 -9999 0 -0.24 43 43
MCL1 -0.41 0.46 -9999 0 -1 281 281
NDRG1 -0.41 0.46 -9999 0 -1 281 281
SERPINE1 -0.41 0.46 -9999 0 -1 271 271
FECH -0.41 0.46 -9999 0 -1 275 275
FURIN -0.41 0.46 -9999 0 -1 297 297
NCOA2 -0.03 0.17 -9999 0 -0.79 54 54
EP300 -0.051 0.12 -9999 0 -0.36 53 53
HMOX1 -0.41 0.46 -9999 0 -1 281 281
BHLHE40 -0.41 0.46 -9999 0 -1 280 280
BHLHE41 -0.41 0.47 -9999 0 -1 274 274
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.049 0.055 -9999 0 -0.6 1 1
ENG -0.025 0.078 -9999 0 -0.54 1 1
JUN 0.003 0.064 -9999 0 -0.79 7 7
RORA -0.41 0.46 -9999 0 -1 276 276
ABCB1 -0.34 0.55 -9999 0 -1.4 215 215
TFRC -0.41 0.46 -9999 0 -1 297 297
CXCR4 -0.41 0.46 -9999 0 -1 264 264
TF -0.64 0.57 -9999 0 -1.1 522 522
CITED2 -0.41 0.46 -9999 0 -1 265 265
HIF1A/ARNT -0.48 0.53 -9999 0 -1.2 301 301
LDHA -0.048 0.047 -9999 0 -10000 0 0
ETS1 -0.41 0.46 -9999 0 -1 297 297
PGK1 -0.41 0.46 -9999 0 -1 273 273
NOS2 -0.41 0.46 -9999 0 -1 298 298
ITGB2 -0.41 0.46 -9999 0 -1 297 297
ALDOA -0.41 0.46 -9999 0 -1 299 299
Cbp/p300/CITED2 -0.42 0.44 -9999 0 -1.1 240 240
FOS -0.23 0.37 -9999 0 -0.79 329 329
HK2 -0.41 0.46 -9999 0 -1 273 273
SP1 0.012 0.023 -9999 0 -10000 0 0
GCK -0.13 0.36 -9999 0 -1.6 56 56
HK1 -0.41 0.46 -9999 0 -1 273 273
NPM1 -0.41 0.46 -9999 0 -1 264 264
EGLN1 -0.41 0.46 -9999 0 -1 297 297
CREB1 0.019 0 -9999 0 -10000 0 0
PGM1 -0.41 0.46 -9999 0 -1 280 280
SMAD3 0 0 -9999 0 -10000 0 0
EDN1 -0.19 0.4 -9999 0 -1.2 119 119
IGFBP1 -0.5 0.52 -9999 0 -1.1 363 363
VEGFA -0.24 0.31 -9999 0 -0.77 102 102
HIF1A/JAB1 -0.028 0.026 -9999 0 -10000 0 0
CP -0.52 0.55 -9999 0 -1.1 385 385
CXCL12 -0.43 0.5 -9999 0 -1.1 308 308
COPS5 0.009 0.006 -9999 0 -10000 0 0
SMAD3/SMAD4 -0.001 0.018 -9999 0 -0.6 1 1
BNIP3 -0.41 0.46 -9999 0 -1 297 297
EGLN3 -0.41 0.46 -9999 0 -1 291 291
CA9 -0.45 0.48 -9999 0 -1.1 297 297
TERT -0.42 0.47 -9999 0 -1 299 299
ENO1 -0.41 0.46 -9999 0 -1 297 297
PFKL -0.41 0.46 -9999 0 -0.99 297 297
NCOA1 0 0.024 -9999 0 -0.79 1 1
ADM -0.44 0.49 -9999 0 -1.1 302 302
ARNT -0.051 0.064 -9999 0 -10000 0 0
HNF4A -0.002 0.046 -9999 0 -0.29 22 22
ADFP -0.41 0.46 -9999 0 -1 301 301
SLC2A1 -0.24 0.32 -9999 0 -0.77 108 108
LEP -0.75 0.52 -9999 0 -1.1 589 589
HIF1A/ARNT/Cbp/p300 -0.33 0.33 -9999 0 -0.8 236 236
EPO -0.23 0.28 -9999 0 -0.85 54 54
CREBBP -0.051 0.12 -9999 0 -0.36 52 52
HIF1A/ARNT/Cbp/p300/HDAC7 -0.31 0.31 -9999 0 -0.82 171 171
PFKFB3 -0.41 0.46 -9999 0 -1 299 299
NT5E -0.41 0.47 -9999 0 -1 297 297
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 -0.001 0.018 -10000 0 -0.6 1 1
Necdin/E2F1 -0.082 0.15 -10000 0 -0.68 43 43
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.14 0.21 -10000 0 -0.45 344 344
NGF (dimer)/p75(NTR)/BEX1 -0.25 0.31 -10000 0 -0.62 423 423
NT-4/5 (dimer)/p75(NTR) -0.37 0.41 -10000 0 -0.75 541 541
IKBKB -0.001 0.013 -10000 0 -0.29 2 2
AKT1 -0.14 0.22 -10000 0 -0.45 348 348
IKBKG 0 0 -10000 0 -10000 0 0
BDNF -0.064 0.21 -10000 0 -0.66 105 105
MGDIs/NGR/p75(NTR)/LINGO1 -0.2 0.24 -10000 0 -0.55 334 334
FURIN 0 0.009 -10000 0 -0.29 1 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.2 0.28 -10000 0 -0.56 378 378
LINGO1 -0.07 0.12 -10000 0 -0.29 261 261
Sortilin/TRAF6/NRIF -0.001 0.024 -10000 0 -0.78 1 1
proBDNF (dimer) -0.064 0.21 -10000 0 -0.66 105 105
NTRK1 -0.011 0.07 -10000 0 -0.37 33 33
RTN4R -0.011 0.056 -10000 0 -0.29 41 41
neuron apoptosis -0.13 0.26 -10000 0 -0.47 378 378
IRAK1 -0.001 0.018 -10000 0 -0.29 4 4
SHC1 -0.15 0.26 -10000 0 -0.52 342 342
ARHGDIA 0 0 -10000 0 -10000 0 0
RhoA/GTP 0 0 -10000 0 -10000 0 0
Gamma Secretase -0.001 0.014 -10000 0 -0.44 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.15 0.23 -10000 0 -0.48 342 342
MAGEH1 -0.001 0.024 -10000 0 -0.79 1 1
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.17 0.26 -10000 0 -0.52 356 356
Mammalian IAPs/DIABLO -0.005 0.044 -10000 0 -0.47 9 9
proNGF (dimer) -0.014 0.097 -10000 0 -0.62 24 24
MAGED1 -0.001 0.018 -10000 0 -0.29 4 4
APP 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.27 0.37 -10000 0 -0.79 371 371
ZNF274 0 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.14 0.21 -10000 0 -0.45 342 342
NGF -0.014 0.098 -10000 0 -0.62 24 24
cell cycle arrest -0.11 0.23 -10000 0 -0.43 342 342
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.1 0.16 -10000 0 -0.33 342 342
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.33 0.36 -10000 0 -0.66 541 541
NCSTN 0 0 -10000 0 -10000 0 0
mol:GTP -0.17 0.25 -10000 0 -0.54 342 342
PSENEN -0.001 0.013 -10000 0 -10000 0 0
mol:ceramide -0.13 0.24 -10000 0 -0.47 342 342
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.082 0.12 -10000 0 -0.48 13 13
p75(NTR)/beta APP -0.18 0.28 -10000 0 -0.6 334 334
BEX1 -0.15 0.27 -10000 0 -0.51 317 317
mol:GDP -0.16 0.26 -10000 0 -0.53 342 342
NGF (dimer) -0.081 0.18 -10000 0 -0.48 172 172
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.18 0.22 -10000 0 -0.5 334 334
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
RAC1/GTP -0.14 0.22 -10000 0 -0.46 342 342
MYD88 0 0 -10000 0 -10000 0 0
CHUK 0 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.17 0.26 -10000 0 -0.54 342 342
RHOB 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.059 0.087 -10000 0 -10000 0 0
NT3 (dimer) -0.13 0.29 -10000 0 -0.75 185 185
TP53 -0.16 0.22 -10000 0 -0.45 378 378
PRDM4 -0.13 0.24 -10000 0 -0.48 342 342
BDNF (dimer) -0.17 0.23 -10000 0 -0.56 226 226
PIK3CA 0 0.009 -10000 0 -0.29 1 1
SORT1 -0.001 0.024 -10000 0 -0.79 1 1
activation of caspase activity -0.14 0.21 -10000 0 -0.44 344 344
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.15 0.23 -10000 0 -0.48 342 342
RHOC 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.15 0.27 -10000 0 -0.49 349 349
DIABLO 0 0 -10000 0 -10000 0 0
SMPD2 -0.13 0.24 -10000 0 -0.48 342 342
APH1B -0.001 0.024 -10000 0 -0.79 1 1
APH1A 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.17 0.25 -10000 0 -0.53 342 342
PSEN1 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.27 0.35 -10000 0 -0.68 434 434
MAPK8 -0.1 0.24 -10000 0 -0.43 334 334
MAPK9 -0.1 0.23 -10000 0 -0.43 334 334
APAF1 0 0 -10000 0 -10000 0 0
NTF3 -0.13 0.29 -10000 0 -0.75 185 185
NTF4 -0.27 0.37 -10000 0 -0.79 371 371
NDN -0.031 0.15 -10000 0 -0.79 43 43
RAC1/GDP 0 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.14 0.2 -10000 0 -0.42 342 342
p75 CTF/Sortilin/TRAF6/NRIF 0 0.014 -10000 0 -0.47 1 1
RhoA-B-C/GTP -0.17 0.25 -10000 0 -0.54 342 342
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.17 0.24 -10000 0 -0.48 378 378
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.18 0.26 -10000 0 -0.51 378 378
PRKACB -0.016 0.077 -10000 0 -0.33 53 53
proBDNF (dimer)/p75 ECD -0.048 0.16 -10000 0 -0.6 79 79
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.077 -10000 0 -0.5 21 21
BIRC2 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.12 0.25 0.24 75 -0.46 343 418
BAD -0.11 0.24 -10000 0 -0.44 337 337
RIPK2 -0.001 0.02 -10000 0 -0.29 5 5
NGFR -0.24 0.36 -10000 0 -0.79 334 334
CYCS -0.14 0.21 -10000 0 -0.44 342 342
ADAM17 0 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.15 0.22 -10000 0 -0.48 342 342
BCL2L11 -0.11 0.24 -10000 0 -0.44 337 337
BDNF (dimer)/p75(NTR) -0.23 0.32 -10000 0 -0.65 378 378
PI3K -0.16 0.23 -10000 0 -0.49 348 348
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.15 0.23 -10000 0 -0.48 342 342
NDNL2 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
PRKCI 0 0.009 -10000 0 -0.29 1 1
NGF (dimer)/p75(NTR) -0.19 0.29 -10000 0 -0.61 342 342
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.15 0.23 -10000 0 -0.48 342 342
TRAF6 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCZ -0.001 0.024 -10000 0 -0.79 1 1
PLG -0.002 0.025 -10000 0 -0.29 8 8
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.18 0.26 -10000 0 -0.51 386 386
SQSTM1 0 0.009 -10000 0 -0.29 1 1
NGFRAP1 -0.002 0.041 -10000 0 -0.79 3 3
CASP3 -0.1 0.22 -10000 0 -0.41 337 337
E2F1 -0.092 0.14 -10000 0 -0.29 345 345
CASP9 0 0 -10000 0 -10000 0 0
IKK complex -0.064 0.11 -10000 0 -0.56 22 22
NGF (dimer)/TRKA -0.018 0.088 -10000 0 -0.6 21 21
MMP7 -0.12 0.28 -10000 0 -0.7 191 191
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.14 0.21 -10000 0 -0.45 342 342
MMP3 -0.12 0.16 -10000 0 -0.31 421 421
APAF-1/Caspase 9 -0.1 0.16 -10000 0 -0.59 20 20
FOXM1 transcription factor network

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
NFATC3 -0.24 0.44 -9999 0 -0.88 222 222
PLK1 -0.087 0.11 -9999 0 -10000 0 0
BIRC5 -0.1 0.1 -9999 0 -10000 0 0
HSPA1B -0.24 0.44 -9999 0 -0.9 203 203
MAP2K1 0.008 0.03 -9999 0 -10000 0 0
BRCA2 -0.24 0.44 -9999 0 -0.94 181 181
FOXM1 -0.29 0.52 -9999 0 -0.98 289 289
XRCC1 -0.24 0.44 -9999 0 -0.89 213 213
FOXM1B/p19 -0.29 0.42 -9999 0 -0.89 271 271
Cyclin D1/CDK4 -0.22 0.41 -9999 0 -0.84 206 206
CDC2 -0.26 0.46 -9999 0 -0.86 289 289
TGFA -0.22 0.42 -9999 0 -0.84 227 227
SKP2 -0.24 0.44 -9999 0 -0.91 195 195
CCNE1 -0.056 0.13 -9999 0 -0.3 223 223
CKS1B -0.24 0.44 -9999 0 -0.9 209 209
RB1 -0.12 0.13 -9999 0 -0.9 1 1
FOXM1C/SP1 -0.3 0.45 -9999 0 -0.91 284 284
AURKB -0.079 0.11 -9999 0 -10000 0 0
CENPF -0.27 0.46 -9999 0 -0.91 247 247
CDK4 0.007 0.022 -9999 0 -0.3 4 4
MYC -0.21 0.41 -9999 0 -0.82 228 228
CHEK2 0.008 0.033 -9999 0 -0.32 2 2
ONECUT1 -0.24 0.43 -9999 0 -0.86 229 229
CDKN2A -0.038 0.11 -9999 0 -0.29 188 188
LAMA4 -0.24 0.44 -9999 0 -0.9 208 208
FOXM1B/HNF6 -0.27 0.49 -9999 0 -1 228 228
FOS -0.44 0.67 -9999 0 -1.3 377 377
SP1 0 0 -9999 0 -10000 0 0
CDC25B -0.24 0.44 -9999 0 -0.9 202 202
response to radiation -0.007 0.03 -9999 0 -10000 0 0
CENPB -0.24 0.44 -9999 0 -0.88 222 222
CENPA -0.27 0.46 -9999 0 -0.95 213 213
NEK2 -0.29 0.45 -9999 0 -0.95 220 220
HIST1H2BA -0.24 0.44 -9999 0 -0.9 209 209
CCNA2 -0.11 0.15 -9999 0 -0.3 427 427
EP300 0 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.28 0.49 -9999 0 -1 226 226
CCNB2 -0.27 0.46 -9999 0 -0.92 237 237
CCNB1 -0.26 0.46 -9999 0 -0.94 226 226
ETV5 -0.24 0.44 -9999 0 -0.9 202 202
ESR1 -0.34 0.58 -9999 0 -1.2 273 273
CCND1 -0.23 0.42 -9999 0 -0.85 219 219
GSK3A 0.014 0.021 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.081 0.14 -9999 0 -0.33 189 189
CDK2 0.006 0.009 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.01 0.036 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.33 0.38 -9999 0 -0.86 298 298
GAS1 -0.28 0.5 -9999 0 -1 223 223
MMP2 -0.24 0.44 -9999 0 -0.91 209 209
RB1/FOXM1C -0.24 0.44 -9999 0 -0.88 238 238
CREBBP 0 0 -9999 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

Figure S9.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S9.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.14 0.42 -10000 0 -0.91 248 248
NCK1/PAK1/Dok-R -0.096 0.18 -10000 0 -0.42 248 248
NCK1/Dok-R -0.26 0.48 -10000 0 -1.1 248 248
PIK3CA 0.003 0.011 -10000 0 -0.29 1 1
mol:beta2-estradiol 0.039 0.1 0.24 207 -10000 0 207
RELA 0 0 -10000 0 -10000 0 0
SHC1 0.008 0.006 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.04 0.11 0.25 203 -0.32 11 214
TNIP2 0 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.24 0.44 -10000 0 -1 248 248
FN1 -0.12 0.14 -10000 0 -0.29 431 431
PLD2 -0.21 0.54 -10000 0 -1.2 248 248
PTPN11 0 0 -10000 0 -10000 0 0
GRB14 -0.1 0.22 -10000 0 -0.48 231 231
ELK1 -0.17 0.48 -10000 0 -1 248 248
GRB7 -0.023 0.085 -10000 0 -0.31 79 79
PAK1 -0.007 0.044 -10000 0 -0.29 25 25
Tie2/Ang1/alpha5/beta1 Integrin -0.22 0.5 -10000 0 -1.1 248 248
CDKN1A -0.072 0.28 -10000 0 -0.59 206 206
ITGA5 0 0.009 -10000 0 -0.29 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.26 0.48 -10000 0 -1.1 248 248
CRK 0 0 -10000 0 -10000 0 0
mol:NO -0.077 0.32 -10000 0 -0.66 248 248
PLG -0.22 0.54 -10000 0 -1.2 248 248
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.19 0.38 -10000 0 -0.88 248 248
GRB2 0 0.009 -10000 0 -0.29 1 1
PIK3R1 -0.002 0.09 -10000 0 -0.79 14 14
ANGPT2 -0.12 0.28 -10000 0 -0.72 127 127
BMX -0.38 0.6 -10000 0 -1.4 249 249
ANGPT1 -0.25 0.58 -10000 0 -1.4 218 218
tube development -0.09 0.31 -10000 0 -0.64 248 248
ANGPT4 -0.24 0.36 -10000 0 -0.79 331 331
response to hypoxia -0.011 0.031 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.3 0.55 -10000 0 -1.3 248 248
alpha5/beta1 Integrin 0 0.006 -10000 0 -10000 0 0
FGF2 -0.32 0.39 -10000 0 -0.79 446 446
STAT5A (dimer) -0.11 0.36 -10000 0 -0.77 206 206
mol:L-citrulline -0.077 0.32 -10000 0 -0.66 248 248
AGTR1 -0.2 0.34 -10000 0 -0.7 328 328
MAPK14 -0.2 0.52 -10000 0 -1.1 248 248
Tie2/SHP2 -0.11 0.3 -10000 0 -1.3 58 58
TEK -0.11 0.34 -10000 0 -1.5 58 58
RPS6KB1 -0.13 0.41 -10000 0 -0.87 248 248
Angiotensin II/AT1 -0.15 0.26 -10000 0 -0.61 268 268
Tie2/Ang1/GRB2 -0.28 0.53 -10000 0 -1.2 248 248
MAPK3 -0.18 0.49 -10000 0 -1.1 248 248
MAPK1 -0.18 0.49 -10000 0 -1.1 248 248
Tie2/Ang1/GRB7 -0.27 0.53 -10000 0 -1.2 248 248
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.21 0.54 -10000 0 -1.2 248 248
PI3K -0.17 0.48 -10000 0 -1.1 248 248
FES -0.2 0.51 -10000 0 -1.1 248 248
Crk/Dok-R -0.26 0.48 -10000 0 -1.1 248 248
Tie2/Ang1/ABIN2 -0.28 0.53 -10000 0 -1.2 248 248
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.11 0.38 -10000 0 -0.8 248 248
STAT5A -0.004 0.067 -10000 0 -0.79 8 8
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.13 0.41 -10000 0 -0.87 248 248
Tie2/Ang2 -0.15 0.42 -10000 0 -0.9 226 226
Tie2/Ang1 -0.24 0.59 -10000 0 -1.3 248 248
FOXO1 -0.11 0.38 -10000 0 -0.81 249 249
ELF1 0.013 0.024 -10000 0 -10000 0 0
ELF2 -0.21 0.53 -10000 0 -1.2 248 248
mol:Choline -0.2 0.51 -10000 0 -1.1 248 248
cell migration -0.045 0.11 -10000 0 -0.24 208 208
FYN -0.11 0.35 -10000 0 -0.73 247 247
DOK2 -0.003 0.045 -10000 0 -0.5 7 7
negative regulation of cell cycle -0.061 0.26 -10000 0 -0.54 206 206
ETS1 -0.031 0.12 -10000 0 -0.96 6 6
PXN -0.09 0.34 -10000 0 -0.71 248 248
ITGB1 0 0 -10000 0 -10000 0 0
NOS3 -0.097 0.36 -10000 0 -0.75 248 248
RAC1 0 0 -10000 0 -10000 0 0
TNF -0.042 0.14 -10000 0 -0.5 38 38
MAPKKK cascade -0.2 0.51 -10000 0 -1.1 248 248
RASA1 0 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.23 0.55 -10000 0 -1.2 248 248
NCK1 0 0 -10000 0 -10000 0 0
vasculogenesis -0.063 0.29 -10000 0 -0.58 248 248
mol:Phosphatidic acid -0.2 0.51 -10000 0 -1.1 248 248
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.077 0.32 -10000 0 -0.66 248 248
Rac1/GTP -0.18 0.34 -10000 0 -0.81 248 248
MMP2 -0.21 0.54 -10000 0 -1.2 249 249
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.078 0.16 -10000 0 -0.39 153 153
NFATC2 -0.055 0.27 -10000 0 -0.76 127 127
NFATC3 -0.048 0.12 -10000 0 -0.28 95 95
CD40LG -0.36 0.57 -10000 0 -1.1 343 343
ITCH 0.016 0.095 -10000 0 -10000 0 0
CBLB 0.016 0.095 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.25 0.36 -10000 0 -1.1 123 123
JUNB -0.001 0.013 -10000 0 -0.29 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.034 0.1 -10000 0 -0.33 109 109
T cell anergy -0.024 0.16 -10000 0 -0.48 109 109
TLE4 -0.031 0.26 -10000 0 -0.72 103 103
Jun/NFAT1-c-4/p21SNFT -0.28 0.43 -10000 0 -0.91 308 308
AP-1/NFAT1-c-4 -0.5 0.65 -10000 0 -1.3 344 344
IKZF1 -0.019 0.21 -10000 0 -0.62 89 89
T-helper 2 cell differentiation -0.11 0.3 -10000 0 -0.83 119 119
AP-1/NFAT1 -0.23 0.32 -10000 0 -0.64 375 375
CALM1 -0.018 0.053 -10000 0 -10000 0 0
EGR2 -0.27 0.63 -10000 0 -1.6 170 170
EGR3 -0.36 0.71 -10000 0 -1.5 299 299
NFAT1/FOXP3 -0.12 0.22 -10000 0 -0.56 147 147
EGR1 -0.24 0.37 -10000 0 -0.79 347 347
JUN -0.001 0.066 -10000 0 -0.8 7 7
EGR4 -0.015 0.078 -10000 0 -0.29 80 80
mol:Ca2+ -0.021 0.061 -10000 0 -10000 0 0
GBP3 -0.023 0.22 -10000 0 -0.67 89 89
FOSL1 -0.009 0.061 -10000 0 -0.34 30 30
NFAT1-c-4/MAF/IRF4 -0.3 0.46 -10000 0 -0.94 321 321
DGKA -0.018 0.21 -10000 0 -0.62 85 85
CREM 0 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.38 0.52 -10000 0 -1.1 343 343
CTLA4 -0.089 0.24 -10000 0 -0.61 109 109
NFAT1-c-4 (dimer)/EGR1 -0.42 0.56 -10000 0 -1.2 340 340
NFAT1-c-4 (dimer)/EGR4 -0.28 0.45 -10000 0 -0.9 330 330
FOS -0.24 0.37 -10000 0 -0.8 329 329
IFNG -0.15 0.27 -10000 0 -0.83 112 112
T cell activation -0.17 0.35 -10000 0 -0.78 203 203
MAF -0.001 0.024 -10000 0 -0.79 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.15 0.36 0.66 325 -10000 0 325
TNF -0.3 0.51 -10000 0 -1 328 328
FASLG -0.34 0.67 -10000 0 -1.3 329 329
TBX21 -0.022 0.15 -10000 0 -0.66 55 55
BATF3 -0.002 0.03 -10000 0 -0.39 5 5
PRKCQ -0.023 0.16 -10000 0 -0.68 57 57
PTPN1 -0.019 0.21 -10000 0 -0.64 79 79
NFAT1-c-4/ICER1 -0.28 0.44 -10000 0 -0.9 328 328
GATA3 -0.035 0.15 -10000 0 -0.57 70 70
T-helper 1 cell differentiation -0.15 0.26 -10000 0 -0.81 112 112
IL2RA -0.24 0.34 -10000 0 -0.96 130 130
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.018 0.21 -10000 0 -0.61 91 91
E2F1 -0.078 0.14 -10000 0 -0.28 345 345
PPARG -0.19 0.34 -10000 0 -0.79 268 268
SLC3A2 -0.018 0.21 -10000 0 -0.57 112 112
IRF4 -0.07 0.22 -10000 0 -0.73 106 106
PTGS2 -0.46 0.65 -10000 0 -1.2 417 417
CSF2 -0.35 0.55 -10000 0 -1.1 336 336
JunB/Fra1/NFAT1-c-4 -0.27 0.42 -10000 0 -0.88 314 314
IL4 -0.12 0.32 -10000 0 -0.88 117 117
IL5 -0.35 0.55 -10000 0 -1.1 334 334
IL2 -0.17 0.36 -10000 0 -0.8 199 199
IL3 -0.062 0.065 -10000 0 -10000 0 0
RNF128 -0.045 0.27 -10000 0 -0.85 109 109
NFATC1 -0.15 0.36 -10000 0 -0.67 324 324
CDK4 0.079 0.23 0.6 45 -10000 0 45
PTPRK -0.023 0.23 -10000 0 -0.71 75 75
IL8 -0.35 0.56 -10000 0 -1.1 336 336
POU2F1 0.001 0.01 -10000 0 -0.29 1 1
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.24 0.28 -9999 0 -0.79 109 109
PCK1 -1 0.7 -9999 0 -1.6 667 667
HNF4A -0.25 0.28 -9999 0 -0.87 70 70
KCNJ11 -0.27 0.31 -9999 0 -0.86 134 134
AKT1 -0.14 0.14 -9999 0 -0.39 35 35
response to starvation -0.001 0.008 -9999 0 -10000 0 0
DLK1 -0.49 0.55 -9999 0 -1.2 358 358
NKX2-1 -0.054 0.15 -9999 0 -10000 0 0
ACADM -0.24 0.28 -9999 0 -0.8 115 115
TAT -1.2 0.68 -9999 0 -1.6 775 775
CEBPB 0.006 0.007 -9999 0 -10000 0 0
CEBPA -0.002 0.076 -9999 0 -0.79 10 10
TTR -0.45 0.28 -9999 0 -0.8 292 292
PKLR -0.24 0.28 -9999 0 -0.8 107 107
APOA1 -0.3 0.3 -9999 0 -0.89 98 98
CPT1C -0.24 0.28 -9999 0 -0.8 105 105
ALAS1 -0.14 0.15 -9999 0 -10000 0 0
TFRC -0.45 0.26 -9999 0 -0.7 406 406
FOXF1 -0.003 0.053 -9999 0 -0.52 9 9
NF1 0.017 0.024 -9999 0 -0.78 1 1
HNF1A (dimer) 0.003 0.027 -9999 0 -0.3 8 8
CPT1A -0.24 0.28 -9999 0 -0.79 109 109
HMGCS1 -0.24 0.28 -9999 0 -0.77 124 124
NR3C1 -0.11 0.13 -9999 0 -0.57 36 36
CPT1B -0.24 0.28 -9999 0 -0.8 110 110
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.002 0.007 -9999 0 -10000 0 0
GCK -0.28 0.35 -9999 0 -0.98 137 137
CREB1 -0.059 0.067 -9999 0 -10000 0 0
IGFBP1 -0.44 0.59 -9999 0 -1.5 244 244
PDX1 -0.13 0.15 -9999 0 -10000 0 0
UCP2 -0.24 0.28 -9999 0 -0.78 117 117
ALDOB -0.26 0.3 -9999 0 -0.84 121 121
AFP -0.68 0.6 -9999 0 -1.2 547 547
BDH1 -0.24 0.28 -9999 0 -0.8 109 109
HADH -0.26 0.3 -9999 0 -0.85 106 106
F2 -0.29 0.3 -9999 0 -0.91 83 83
HNF1A 0.003 0.027 -9999 0 -0.3 8 8
G6PC -0.2 0.12 -9999 0 -0.64 8 8
SLC2A2 -0.16 0.17 -9999 0 -10000 0 0
INS 0.023 0.066 -9999 0 -10000 0 0
FOXA1 -0.24 0.28 -9999 0 -0.57 315 315
FOXA3 -0.42 0.23 -9999 0 -0.55 730 730
FOXA2 -0.31 0.34 -9999 0 -0.86 180 180
ABCC8 -0.34 0.43 -9999 0 -1.2 170 170
ALB -0.93 0.64 -9999 0 -1.4 705 705
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0 0 -9999 0 -10000 0 0
VLDLR -0.025 0.14 -9999 0 -0.79 35 35
LRPAP1 0 0 -9999 0 -10000 0 0
NUDC 0 0 -9999 0 -10000 0 0
RELN/LRP8 -0.32 0.26 -9999 0 -0.53 651 651
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0 0.009 -9999 0 -0.29 1 1
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.28 0.25 -9999 0 -0.48 651 651
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.017 0.069 -9999 0 -0.29 65 65
IQGAP1 0 0 -9999 0 -10000 0 0
PLA2G7 -0.015 0.091 -9999 0 -0.43 39 39
CALM1 0 0 -9999 0 -10000 0 0
DYNLT1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.019 0.057 -9999 0 -10000 0 0
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0 0 -9999 0 -10000 0 0
CDK5R1 -0.008 0.049 -9999 0 -0.29 31 31
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.044 0.1 -9999 0 -10000 0 0
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.33 0.27 -9999 0 -0.55 660 660
YWHAE 0 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.23 0.19 -9999 0 -0.45 184 184
MAP1B -0.008 0.054 -9999 0 -0.37 23 23
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.26 0.21 -9999 0 -0.42 651 651
RELN -0.47 0.39 -9999 0 -0.78 654 654
PAFAH/LIS1 -0.009 0.056 -9999 0 -0.52 11 11
LIS1/CLIP170 0 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.18 0.15 -9999 0 -0.4 25 25
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.2 0.18 -9999 0 -0.33 663 663
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.25 0.2 -9999 0 -0.41 651 651
LIS1/IQGAP1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.022 0 -9999 0 -10000 0 0
PAFAH1B3 -0.035 0.095 -9999 0 -0.29 131 131
PAFAH1B2 -0.005 0.063 -9999 0 -0.79 7 7
MAP1B/LIS1/Dynein heavy chain -0.005 0.034 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.22 0.18 -9999 0 -0.43 185 185
LRP8 -0.03 0.089 -9999 0 -10000 0 0
NDEL1/Katanin 60 -0.23 0.19 -9999 0 -0.45 185 185
P39/CDK5 -0.27 0.22 -9999 0 -0.44 651 651
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -9999 0 -10000 0 0
CDK5 -0.26 0.24 -9999 0 -0.45 651 651
PPP2R5D 0 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.28 0.24 -9999 0 -0.46 660 660
RELN/VLDLR -0.31 0.25 -9999 0 -0.5 660 660
CDC42 0 0 -9999 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 0.024 0.079 0.37 1 -10000 0 1
SMARCC2 0.012 0.01 -10000 0 -10000 0 0
SMARCC1 0.012 0.01 -10000 0 -10000 0 0
TBX21 -0.13 0.25 -10000 0 -0.74 100 100
SUMO2 0 0.01 -10000 0 -0.29 1 1
STAT1 (dimer) 0.014 0.04 -10000 0 -0.29 19 19
FKBP4 -0.002 0.026 -10000 0 -0.29 9 9
FKBP5 -0.015 0.1 -10000 0 -0.68 24 24
GR alpha/HSP90/FKBP51/HSP90 0.11 0.14 0.34 60 -0.43 17 77
PRL -0.086 0.12 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.26 0.3 0.55 445 -0.55 31 476
RELA -0.039 0.083 -10000 0 -0.3 1 1
FGG 0.23 0.22 0.5 294 -0.52 2 296
GR beta/TIF2 0.1 0.2 0.35 114 -0.57 56 170
IFNG -0.42 0.35 -10000 0 -0.76 483 483
apoptosis -0.27 0.3 0.59 3 -0.65 303 306
CREB1 -0.009 0.031 -10000 0 -10000 0 0
histone acetylation 0.022 0.14 0.42 34 -0.42 26 60
BGLAP -0.1 0.15 -10000 0 -0.53 17 17
GR/PKAc 0.11 0.12 0.34 53 -0.46 4 57
NF kappa B1 p50/RelA -0.066 0.15 -10000 0 -0.43 31 31
SMARCD1 0.012 0.01 -10000 0 -10000 0 0
MDM2 0.12 0.1 0.25 270 -10000 0 270
GATA3 -0.026 0.16 -10000 0 -0.57 70 70
AKT1 0 0.004 -10000 0 -10000 0 0
CSF2 -0.039 0.11 -10000 0 -0.59 8 8
GSK3B 0 0.004 -10000 0 -10000 0 0
NR1I3 -0.21 0.26 0.56 3 -0.62 176 179
CSN2 0.19 0.18 0.44 135 -0.53 1 136
BRG1/BAF155/BAF170/BAF60A -0.003 0.032 -10000 0 -0.46 5 5
NFATC1 0.001 0.042 -10000 0 -0.79 3 3
POU2F1 0.007 0.013 -10000 0 -0.29 1 1
CDKN1A 0.046 0.072 -10000 0 -1.5 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.007 0.008 -10000 0 -10000 0 0
SFN -0.016 0.099 -10000 0 -0.5 36 36
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.1 0.14 0.34 45 -0.48 9 54
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.36 0.43 0.54 3 -0.88 397 400
JUN -0.31 0.29 -10000 0 -0.6 449 449
IL4 -0.12 0.16 -10000 0 -0.53 34 34
CDK5R1 -0.008 0.05 -10000 0 -0.3 31 31
PRKACA 0 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.41 0.4 -10000 0 -0.73 587 587
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.11 0.13 0.34 48 -0.51 4 52
cortisol/GR alpha (monomer) 0.34 0.32 0.64 483 -0.66 1 484
NCOA2 -0.039 0.17 -10000 0 -0.79 54 54
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.28 0.38 -10000 0 -0.86 329 329
AP-1/NFAT1-c-4 -0.65 0.52 -10000 0 -1 666 666
AFP -0.6 0.7 -10000 0 -1.5 366 366
SUV420H1 0 0 -10000 0 -10000 0 0
IRF1 0.19 0.16 0.47 95 -10000 0 95
TP53 0.032 0.023 -10000 0 -0.5 2 2
PPP5C 0 0 -10000 0 -10000 0 0
KRT17 -0.82 0.8 -10000 0 -1.6 503 503
KRT14 -0.81 0.77 -10000 0 -1.5 566 566
TBP 0.019 0.007 -10000 0 -10000 0 0
CREBBP 0.14 0.14 0.31 178 -10000 0 178
HDAC1 0 0.004 -10000 0 -10000 0 0
HDAC2 0.001 0.004 -10000 0 -10000 0 0
AP-1 -0.66 0.52 -10000 0 -1 667 667
MAPK14 0 0.003 -10000 0 -10000 0 0
MAPK10 -0.12 0.29 -10000 0 -0.79 171 171
MAPK11 -0.002 0.042 -10000 0 -0.8 3 3
KRT5 -0.92 0.81 -10000 0 -1.6 580 580
interleukin-1 receptor activity -0.001 0.003 -10000 0 -10000 0 0
NCOA1 0.014 0.024 -10000 0 -0.78 1 1
STAT1 0.014 0.04 -10000 0 -0.29 19 19
CGA -0.16 0.18 -10000 0 -0.53 77 77
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.2 0.18 0.38 474 -10000 0 474
MAPK3 0 0.003 -10000 0 -10000 0 0
MAPK1 0 0.003 -10000 0 -10000 0 0
ICAM1 -0.18 0.25 -10000 0 -0.57 219 219
NFKB1 -0.039 0.083 -10000 0 -10000 0 0
MAPK8 -0.23 0.22 -10000 0 -0.48 344 344
MAPK9 0 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.29 0.31 0.59 3 -0.69 303 306
BAX 0.048 0.032 -10000 0 -10000 0 0
POMC -0.19 0.32 -10000 0 -1 76 76
EP300 0.14 0.14 0.29 341 -10000 0 341
cortisol/GR alpha (dimer)/p53 0.31 0.26 0.56 450 -0.56 1 451
proteasomal ubiquitin-dependent protein catabolic process 0.085 0.079 0.24 63 -10000 0 63
SGK1 0.22 0.21 -10000 0 -1.2 7 7
IL13 -0.31 0.28 -10000 0 -0.59 421 421
IL6 -0.49 0.62 -10000 0 -1.3 410 410
PRKACG 0 0 -10000 0 -10000 0 0
IL5 -0.27 0.23 -10000 0 -0.71 78 78
IL2 -0.41 0.35 -10000 0 -0.74 493 493
CDK5 -0.002 0.024 -10000 0 -0.3 7 7
PRKACB -0.016 0.077 -10000 0 -0.33 53 53
HSP90AA1 0 0.009 -10000 0 -0.29 1 1
IL8 -0.2 0.3 -10000 0 -0.66 222 222
CDK5R1/CDK5 -0.007 0.036 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.055 0.1 -10000 0 -0.54 7 7
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.28 0.24 0.53 425 -0.49 2 427
SMARCA4 0.012 0.013 -10000 0 -0.29 1 1
chromatin remodeling 0.2 0.16 0.39 299 -0.66 1 300
NF kappa B1 p50/RelA/Cbp 0.06 0.17 0.35 52 -0.49 1 53
JUN (dimer) -0.31 0.29 -10000 0 -0.6 451 451
YWHAH 0 0 -10000 0 -10000 0 0
VIPR1 -0.13 0.25 -10000 0 -0.62 143 143
NR3C1 0.2 0.2 0.46 268 -0.57 6 274
NR4A1 -0.063 0.24 -10000 0 -0.74 115 115
TIF2/SUV420H1 -0.03 0.13 -10000 0 -0.6 54 54
MAPKKK cascade -0.27 0.3 0.59 3 -0.65 303 306
cortisol/GR alpha (dimer)/Src-1 0.3 0.26 0.55 464 -0.57 1 465
PBX1 0.005 0.037 -10000 0 -0.54 4 4
POU1F1 0.003 0.015 -10000 0 -0.29 2 2
SELE -0.22 0.36 -10000 0 -1 119 119
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.2 0.16 0.39 297 -0.66 1 298
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.28 0.24 0.53 425 -0.49 2 427
mol:cortisol 0.19 0.2 0.37 512 -10000 0 512
MMP1 -0.22 0.11 -10000 0 -10000 0 0
Arf6 signaling events

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
CENTA1/KIF3B -0.004 0.043 -9999 0 -0.64 4 4
ARNO/beta Arrestin1-2 -0.12 0.18 -9999 0 -0.42 253 253
EGFR -0.29 0.38 -9999 0 -0.78 410 410
EPHA2 -0.004 0.058 -9999 0 -0.79 6 6
USP6 0 0 -9999 0 -10000 0 0
IQSEC1 0 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.33 0.35 -9999 0 -0.66 552 552
ARRB2 -0.051 0.15 -9999 0 -0.44 148 148
mol:GTP 0.017 0.018 -9999 0 -0.16 4 4
ARRB1 -0.002 0.035 -9999 0 -0.79 2 2
FBXO8 0 0 -9999 0 -10000 0 0
TSHR -0.037 0.16 -9999 0 -0.74 54 54
EGF -0.15 0.31 -9999 0 -0.78 214 214
somatostatin receptor activity 0 0 -9999 0 -0.001 378 378
ARAP2 -0.004 0.058 -9999 0 -0.79 6 6
mol:GDP -0.14 0.18 -9999 0 -0.35 351 351
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 292 292
ITGA2B -0.018 0.078 -9999 0 -0.32 62 62
ARF6 0 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.036 -9999 0 -0.47 6 6
ADAP1 -0.005 0.05 -9999 0 -0.41 13 13
KIF13B -0.001 0.034 -9999 0 -0.79 2 2
HGF/MET -0.14 0.27 -9999 0 -0.64 240 240
PXN 0 0 -9999 0 -10000 0 0
ARF6/GTP -0.13 0.15 -9999 0 -0.31 352 352
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.29 0.3 -9999 0 -0.57 552 552
ADRB2 -0.18 0.33 -9999 0 -0.79 253 253
receptor agonist activity 0 0 -9999 0 0 354 354
actin filament binding 0 0 -9999 0 -0.001 365 365
SRC 0 0.009 -9999 0 -0.29 1 1
ITGB3 -0.028 0.14 -9999 0 -0.79 37 37
GNAQ -0.002 0.041 -9999 0 -0.79 3 3
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 331 331
ARF6/GDP -0.014 0.083 -9999 0 -0.41 18 18
ARF6/GDP/GULP/ACAP1 -0.15 0.2 -9999 0 -0.51 190 190
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.025 0.094 -9999 0 -0.48 40 40
ACAP1 -0.02 0.095 -9999 0 -0.38 57 57
ACAP2 0 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.088 0.22 -9999 0 -0.65 148 148
EFNA1 0 0.009 -9999 0 -0.29 1 1
HGF -0.053 0.2 -9999 0 -0.79 73 73
CYTH3 0.01 0.027 -9999 0 -0.61 2 2
CYTH2 0.006 0.002 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 287 287
endosomal lumen acidification 0 0 -9999 0 -0.001 299 299
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.053 0.2 -9999 0 -0.79 73 73
GNAQ/ARNO 0.004 0.025 -9999 0 -0.45 3 3
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 360 360
MET -0.14 0.3 -9999 0 -0.78 189 189
GNA14 -0.013 0.084 -9999 0 -0.46 30 30
GNA15 -0.003 0.033 -9999 0 -0.36 8 8
GIT1 -0.001 0.02 -9999 0 -0.29 5 5
mol:PI-4-5-P2 0 0 -9999 0 -0.001 347 347
GNA11 -0.003 0.048 -9999 0 -0.79 4 4
LHCGR -0.11 0.27 -9999 0 -0.79 148 148
AGTR1 -0.21 0.34 -9999 0 -0.7 328 328
desensitization of G-protein coupled receptor protein signaling pathway -0.088 0.22 -9999 0 -0.65 148 148
IPCEF1/ARNO -0.23 0.24 -9999 0 -0.46 552 552
alphaIIb/beta3 Integrin -0.033 0.12 -9999 0 -0.62 40 40
Wnt signaling

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
Noncanonical Wnts/FZD -0.16 0.25 -9999 0 -0.44 385 385
FZD6 -0.007 0.075 -9999 0 -0.79 10 10
WNT6 -0.16 0.31 -9999 0 -0.69 255 255
WNT4 -0.021 0.12 -9999 0 -0.55 43 43
FZD3 -0.011 0.092 -9999 0 -0.79 15 15
WNT5A -0.016 0.1 -9999 0 -0.79 18 18
WNT11 -0.17 0.32 -9999 0 -0.76 242 242
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.45 0.46 -10000 0 -1.1 232 232
STAT6 (cleaved dimer) -0.5 0.45 -10000 0 -1 387 387
IGHG1 -0.16 0.16 -10000 0 -0.36 83 83
IGHG3 -0.45 0.44 -10000 0 -0.98 340 340
AKT1 -0.2 0.24 -10000 0 -0.65 92 92
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.15 0.2 -10000 0 -0.61 53 53
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.22 0.24 -10000 0 -0.65 105 105
THY1 -0.45 0.46 -10000 0 -1.1 243 243
MYB -0.017 0.11 -10000 0 -0.79 23 23
HMGA1 -0.014 0.063 -10000 0 -0.29 53 53
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.28 0.29 -10000 0 -0.67 233 233
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.21 0.23 -10000 0 -0.61 78 78
SP1 0.018 0.006 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.024 0.028 -10000 0 -0.76 1 1
STAT6 (dimer)/ETS1 -0.48 0.44 -10000 0 -1 341 341
SOCS1 -0.29 0.31 -10000 0 -0.74 208 208
SOCS3 -0.22 0.26 -10000 0 -0.81 68 68
FCER2 -0.58 0.64 -10000 0 -1.4 373 373
PARP14 0.004 0.018 -10000 0 -10000 0 0
CCL17 -0.46 0.46 -10000 0 -1.1 261 261
GRB2 0 0.009 -10000 0 -0.29 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.16 0.19 -10000 0 -0.6 25 25
T cell proliferation -0.45 0.48 -10000 0 -1.1 261 261
IL4R/JAK1 -0.45 0.46 -10000 0 -1.1 250 250
EGR2 -0.58 0.62 -10000 0 -1.4 336 336
JAK2 -0.008 0.035 -10000 0 -0.81 1 1
JAK3 0.01 0.035 -10000 0 -0.29 14 14
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
JAK1 0.004 0.026 -10000 0 -0.78 1 1
COL1A2 -0.14 0.16 -10000 0 -1.6 3 3
CCL26 -0.46 0.46 -10000 0 -1.1 230 230
IL4R -0.48 0.49 -10000 0 -1.2 251 251
PTPN6 0.022 0.018 -10000 0 -0.28 2 2
IL13RA2 -0.46 0.46 -10000 0 -1.2 219 219
IL13RA1 -0.007 0.025 -10000 0 -10000 0 0
IRF4 -0.22 0.48 -10000 0 -1.5 114 114
ARG1 -0.11 0.12 -10000 0 -10000 0 0
CBL -0.26 0.28 -10000 0 -0.65 204 204
GTF3A 0.013 0.015 -10000 0 -0.29 2 2
PIK3CA 0 0.009 -10000 0 -0.29 1 1
IL13RA1/JAK2 -0.013 0.041 -10000 0 -0.61 1 1
IRF4/BCL6 -0.2 0.42 -10000 0 -1.4 116 116
CD40LG -0.031 0.18 -10000 0 -0.71 67 67
MAPK14 -0.25 0.28 -10000 0 -0.67 177 177
mitosis -0.2 0.23 -10000 0 -0.62 92 92
STAT6 -0.52 0.54 -10000 0 -1.2 315 315
SPI1 0.007 0.024 -10000 0 -0.29 6 6
RPS6KB1 -0.18 0.22 -10000 0 -0.61 77 77
STAT6 (dimer) -0.52 0.54 -10000 0 -1.2 315 315
STAT6 (dimer)/PARP14 -0.5 0.51 -10000 0 -1.1 345 345
mast cell activation 0.012 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.2 0.23 -10000 0 -0.63 80 80
FRAP1 -0.2 0.24 -10000 0 -0.65 92 92
LTA -0.46 0.46 -10000 0 -1.1 240 240
FES -0.002 0.041 -10000 0 -0.79 3 3
T-helper 1 cell differentiation 0.51 0.52 1.2 316 -10000 0 316
CCL11 -0.48 0.44 -10000 0 -1.1 284 284
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.2 0.23 -10000 0 -0.64 80 80
IL2RG -0.004 0.088 -10000 0 -0.36 53 53
IL10 -0.46 0.46 -10000 0 -1.1 236 236
IRS1 -0.032 0.16 -10000 0 -0.79 45 45
IRS2 -0.033 0.16 -10000 0 -0.79 46 46
IL4 -0.11 0.11 -10000 0 -10000 0 0
IL5 -0.46 0.46 -10000 0 -1.2 218 218
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.37 0.36 -10000 0 -0.82 299 299
COL1A1 -0.18 0.17 -10000 0 -1.7 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.46 0.47 -10000 0 -1.2 209 209
IL2R gamma/JAK3 -0.011 0.071 -10000 0 -0.45 20 20
TFF3 -0.56 0.58 -10000 0 -1.4 291 291
ALOX15 -0.53 0.57 -10000 0 -1.4 269 269
MYBL1 -0.042 0.1 -10000 0 -0.29 155 155
T-helper 2 cell differentiation -0.39 0.38 -10000 0 -0.86 312 312
SHC1 0 0 -10000 0 -10000 0 0
CEBPB 0.009 0.009 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.21 0.23 -10000 0 -0.62 98 98
mol:PI-3-4-5-P3 -0.2 0.24 -10000 0 -0.65 92 92
PI3K -0.21 0.25 -10000 0 -0.69 92 92
DOK2 -0.003 0.045 -10000 0 -0.5 7 7
ETS1 0.018 0.058 -10000 0 -0.75 6 6
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.15 0.18 -10000 0 -0.67 15 15
ITGB3 -0.48 0.5 -10000 0 -1.2 227 227
PIGR -0.98 0.75 -10000 0 -1.5 682 682
IGHE 0.045 0.04 -10000 0 -10000 0 0
MAPKKK cascade -0.15 0.18 -10000 0 -0.65 15 15
BCL6 0.001 0.059 -10000 0 -0.78 6 6
OPRM1 -0.46 0.46 -10000 0 -1.1 249 249
RETNLB -0.46 0.46 -10000 0 -1.2 225 225
SELP -0.62 0.68 -10000 0 -1.6 314 314
AICDA -0.44 0.44 -10000 0 -1.1 253 253
Endothelins

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
AKT1 -0.01 0.2 -9999 0 -0.6 89 89
PTK2B 0.006 0.006 -9999 0 -10000 0 0
mol:Ca2+ 0.021 0.2 -9999 0 -0.97 33 33
EDN1 -0.035 0.24 -9999 0 -0.82 83 83
EDN3 -0.37 0.39 -9999 0 -0.78 511 511
EDN2 -0.076 0.14 -9999 0 -0.31 269 269
HRAS/GDP -0.03 0.21 -9999 0 -0.54 103 103
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.003 0.14 -9999 0 -0.48 48 48
ADCY4 -0.14 0.29 -9999 0 -0.55 313 313
ADCY5 -0.27 0.36 -9999 0 -0.6 515 515
ADCY6 -0.13 0.27 -9999 0 -0.52 294 294
ADCY7 -0.13 0.27 -9999 0 -0.52 294 294
ADCY1 -0.15 0.29 -9999 0 -0.56 309 309
ADCY2 -0.17 0.32 -9999 0 -0.59 327 327
ADCY3 -0.13 0.27 -9999 0 -0.52 294 294
ADCY8 -0.14 0.27 -9999 0 -0.53 294 294
ADCY9 -0.13 0.27 -9999 0 -0.52 294 294
arachidonic acid secretion -0.11 0.3 -9999 0 -0.56 230 230
ETB receptor/Endothelin-1/Gq/GTP -0.034 0.18 -9999 0 -0.4 158 158
GNAO1 -0.03 0.13 -9999 0 -0.48 67 67
HRAS 0.003 0.029 -9999 0 -0.29 10 10
ETA receptor/Endothelin-1/G12/GTP 0.038 0.21 -9999 0 -0.56 89 89
ETA receptor/Endothelin-1/Gs/GTP -0.087 0.32 -9999 0 -0.56 294 294
mol:GTP -0.001 0.006 -9999 0 -10000 0 0
COL3A1 -0.019 0.21 -9999 0 -0.6 89 89
EDNRB -0.074 0.24 -9999 0 -0.79 114 114
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.025 0.25 -9999 0 -0.69 107 107
CYSLTR1 -0.021 0.24 -9999 0 -0.67 102 102
SLC9A1 0.002 0.1 -9999 0 -0.3 88 88
mol:GDP -0.038 0.22 -9999 0 -0.57 108 108
SLC9A3 -0.053 0.28 -9999 0 -0.66 162 162
RAF1 -0.085 0.25 -9999 0 -0.54 167 167
JUN 0.027 0.18 -9999 0 -0.85 30 30
JAK2 -0.01 0.2 -9999 0 -0.6 89 89
mol:IP3 -0.03 0.18 -9999 0 -0.53 74 74
ETA receptor/Endothelin-1 0.035 0.25 -9999 0 -0.69 89 89
PLCB1 -0.052 0.21 -9999 0 -0.79 82 82
PLCB2 0.007 0.026 -9999 0 -0.54 2 2
ETA receptor/Endothelin-3 -0.27 0.31 -9999 0 -0.6 510 510
FOS -0.25 0.5 -9999 0 -0.98 336 336
Gai/GDP -0.016 0.16 -9999 0 -0.76 30 30
CRK 0.006 0.006 -9999 0 -10000 0 0
mol:Ca ++ -0.051 0.25 -9999 0 -0.67 116 116
BCAR1 0.005 0.006 -9999 0 -10000 0 0
PRKCB1 -0.032 0.17 -9999 0 -0.48 88 88
GNAQ 0.008 0.043 -9999 0 -0.79 3 3
GNAZ -0.007 0.075 -9999 0 -0.79 10 10
GNAL -0.19 0.33 -9999 0 -0.79 258 258
Gs family/GDP -0.17 0.26 -9999 0 -0.58 258 258
ETA receptor/Endothelin-1/Gq/GTP 0.017 0.13 -9999 0 -0.43 50 50
MAPK14 -0.032 0.17 -9999 0 -0.49 89 89
TRPC6 0.018 0.22 -9999 0 -1.1 33 33
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
GNAI1 -0.045 0.18 -9999 0 -0.79 62 62
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.041 0.18 -9999 0 -0.47 117 117
ETB receptor/Endothelin-2 -0.11 0.21 -9999 0 -0.65 121 121
ETB receptor/Endothelin-3 -0.34 0.34 -9999 0 -0.65 568 568
ETB receptor/Endothelin-1 -0.082 0.27 -9999 0 -0.66 183 183
MAPK3 -0.2 0.41 -9999 0 -0.79 339 339
MAPK1 -0.2 0.41 -9999 0 -0.79 339 339
Rac1/GDP -0.028 0.2 -9999 0 -0.53 102 102
cAMP biosynthetic process -0.18 0.3 -9999 0 -0.6 302 302
MAPK8 0.019 0.2 -9999 0 -0.79 40 40
SRC 0 0.009 -9999 0 -0.29 1 1
ETB receptor/Endothelin-1/Gi/GTP -0.05 0.18 -9999 0 -0.53 89 89
p130Cas/CRK/Src/PYK2 -0.015 0.22 -9999 0 -0.64 74 74
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.028 0.2 -9999 0 -0.53 102 102
COL1A2 -0.056 0.26 -9999 0 -0.7 105 105
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.03 0.12 -9999 0 -0.45 24 24
mol:DAG -0.03 0.18 -9999 0 -0.53 74 74
MAP2K2 -0.13 0.32 -9999 0 -0.57 345 345
MAP2K1 -0.13 0.32 -9999 0 -0.57 345 345
EDNRA 0.025 0.08 -9999 0 -0.49 8 8
positive regulation of muscle contraction -0.011 0.17 -9999 0 -0.52 89 89
Gq family/GDP -0.074 0.16 -9999 0 -0.61 62 62
HRAS/GTP -0.053 0.21 -9999 0 -0.49 136 136
PRKCH -0.024 0.17 -9999 0 -0.56 58 58
RAC1 0 0 -9999 0 -10000 0 0
PRKCA -0.036 0.2 -9999 0 -0.58 87 87
PRKCB -0.035 0.2 -9999 0 -0.57 80 80
PRKCE -0.024 0.17 -9999 0 -0.57 54 54
PRKCD -0.025 0.17 -9999 0 -0.58 54 54
PRKCG -0.034 0.18 -9999 0 -0.52 74 74
regulation of vascular smooth muscle contraction -0.3 0.57 -9999 0 -1.1 336 336
PRKCQ -0.045 0.21 -9999 0 -0.62 91 91
PLA2G4A -0.12 0.33 -9999 0 -0.63 230 230
GNA14 -0.003 0.086 -9999 0 -0.46 30 30
GNA15 0.007 0.035 -9999 0 -0.36 8 8
GNA12 0 0 -9999 0 -10000 0 0
GNA11 0.006 0.049 -9999 0 -0.79 4 4
Rac1/GTP 0.038 0.21 -9999 0 -0.56 89 89
MMP1 -0.12 0.13 -9999 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.052 0.15 -10000 0 -0.52 103 103
cell-cell adhesion 0.16 0.21 0.67 79 -10000 0 79
Ephrin B/EPHB2/RasGAP -0.041 0.13 -10000 0 -0.44 96 96
ITSN1 -0.001 0.034 -10000 0 -0.79 2 2
PIK3CA 0 0.009 -10000 0 -0.29 1 1
SHC1 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.002 0.018 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.2 0.26 -10000 0 -0.52 423 423
HRAS/GDP -0.17 0.22 -10000 0 -0.64 104 104
Ephrin B/EPHB1/GRB7 -0.22 0.28 -10000 0 -0.52 448 448
Endophilin/SYNJ1 -0.038 0.12 -10000 0 -0.41 96 96
KRAS -0.001 0.013 -10000 0 -0.29 2 2
Ephrin B/EPHB1/Src -0.21 0.27 -10000 0 -0.51 446 446
endothelial cell migration -0.006 0.054 -10000 0 -0.47 14 14
GRB2 0 0.009 -10000 0 -0.29 1 1
GRB7 -0.023 0.085 -10000 0 -0.31 79 79
PAK1 -0.047 0.14 -10000 0 -0.46 105 105
HRAS -0.003 0.028 -10000 0 -0.29 10 10
RRAS -0.039 0.12 -10000 0 -0.42 96 96
DNM1 -0.005 0.063 -10000 0 -0.73 8 8
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.2 0.26 -10000 0 -0.48 446 446
lamellipodium assembly -0.16 0.21 -10000 0 -0.67 79 79
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.15 0.19 -10000 0 -0.36 424 424
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
EPHB2 -0.005 0.038 -10000 0 -0.29 19 19
EPHB3 -0.004 0.035 -10000 0 -0.29 16 16
EPHB1 -0.3 0.38 -10000 0 -0.79 424 424
EPHB4 0 0.009 -10000 0 -0.29 1 1
mol:GDP -0.15 0.21 -10000 0 -0.64 97 97
Ephrin B/EPHB2 -0.041 0.13 -10000 0 -0.45 96 96
Ephrin B/EPHB3 -0.041 0.13 -10000 0 -0.45 96 96
JNK cascade -0.17 0.21 -10000 0 -0.43 423 423
Ephrin B/EPHB1 -0.21 0.28 -10000 0 -0.52 446 446
RAP1/GDP -0.13 0.18 -10000 0 -0.55 95 95
EFNB2 -0.001 0.024 -10000 0 -0.79 1 1
EFNB3 -0.069 0.22 -10000 0 -0.79 96 96
EFNB1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.19 0.23 -10000 0 -0.48 424 424
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.17 0.23 -10000 0 -0.67 100 100
Rap1/GTP -0.17 0.22 -10000 0 -0.69 78 78
axon guidance -0.052 0.15 -10000 0 -0.52 103 103
MAPK3 -0.095 0.19 -10000 0 -0.52 75 75
MAPK1 -0.095 0.19 -10000 0 -0.52 75 75
Rac1/GDP -0.14 0.19 -10000 0 -0.58 95 95
actin cytoskeleton reorganization -0.13 0.16 -10000 0 -0.51 85 85
CDC42/GDP -0.14 0.19 -10000 0 -0.57 96 96
PI3K -0.006 0.055 -10000 0 -0.48 14 14
EFNA5 -0.074 0.23 -10000 0 -0.78 104 104
Ephrin B2/EPHB4 -0.001 0.017 -10000 0 -0.52 1 1
Ephrin B/EPHB2/Intersectin/N-WASP -0.03 0.099 -10000 0 -0.34 96 96
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.16 0.21 -10000 0 -0.66 83 83
PTK2 0.04 0.05 -10000 0 -10000 0 0
MAP4K4 -0.17 0.21 -10000 0 -0.43 423 423
SRC 0 0.009 -10000 0 -0.29 1 1
KALRN -0.014 0.11 -10000 0 -0.79 20 20
Intersectin/N-WASP -0.001 0.026 -10000 0 -0.6 2 2
neuron projection morphogenesis -0.13 0.17 -10000 0 -0.54 84 84
MAP2K1 -0.11 0.2 -10000 0 -0.34 424 424
WASL 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.18 0.23 -10000 0 -0.47 423 423
cell migration -0.12 0.22 -10000 0 -0.37 424 424
NRAS -0.001 0.013 -10000 0 -0.29 2 2
SYNJ1 -0.039 0.12 -10000 0 -0.42 96 96
PXN 0 0 -10000 0 -10000 0 0
TF -0.24 0.26 -10000 0 -0.45 624 624
HRAS/GTP -0.18 0.23 -10000 0 -0.44 446 446
Ephrin B1/EPHB1-2 -0.19 0.23 -10000 0 -0.48 423 423
cell adhesion mediated by integrin 0.01 0.13 0.42 96 -10000 0 96
RAC1 0 0 -10000 0 -10000 0 0
mol:GTP -0.19 0.25 -10000 0 -0.47 446 446
RAC1-CDC42/GTP -0.16 0.21 -10000 0 -0.68 80 80
RASA1 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.13 0.18 -10000 0 -0.55 95 95
ruffle organization -0.17 0.22 -10000 0 -0.69 79 79
NCK1 0 0 -10000 0 -10000 0 0
receptor internalization 0.002 0.14 -10000 0 -0.42 98 98
Ephrin B/EPHB2/KALRN -0.049 0.15 -10000 0 -0.49 105 105
ROCK1 0.022 0.024 -10000 0 -0.48 1 1
RAS family/GDP -0.11 0.15 -10000 0 -0.52 75 75
Rac1/GTP -0.18 0.23 -10000 0 -0.73 79 79
Ephrin B/EPHB1/Src/Paxillin -0.15 0.2 -10000 0 -0.37 446 446
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.053 0.067 -9999 0 -10000 0 0
STMN1 -0.11 0.12 -9999 0 -0.37 80 80
Aurora B/RasGAP/Survivin -0.18 0.13 -9999 0 -10000 0 0
Chromosomal passenger complex/Cul3 protein complex -0.16 0.15 -9999 0 -0.33 435 435
BIRC5 -0.21 0.14 -9999 0 -0.3 780 780
DES -0.29 0.34 -9999 0 -0.65 499 499
Aurora C/Aurora B/INCENP -0.069 0.076 -9999 0 -0.62 1 1
Aurora B/TACC1 -0.1 0.13 -9999 0 -0.61 42 42
Aurora B/PP2A -0.098 0.097 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.008 0.017 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition -0.003 0.003 -9999 0 -10000 0 0
NDC80 -0.21 0.18 -9999 0 -0.37 550 550
Cul3 protein complex -0.21 0.25 -9999 0 -0.52 435 435
KIF2C -0.045 0.034 -9999 0 -10000 0 0
PEBP1 0.002 0.005 -9999 0 -10000 0 0
KIF20A -0.22 0.13 -9999 0 -0.3 820 820
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.098 0.097 -9999 0 -10000 0 0
SEPT1 -0.009 0.052 -9999 0 -0.29 35 35
SMC2 0 0 -9999 0 -10000 0 0
SMC4 -0.004 0.034 -9999 0 -0.29 15 15
NSUN2/NPM1/Nucleolin 0.005 0.019 -9999 0 -10000 0 0
PSMA3 0 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.003 0.002 -9999 0 -10000 0 0
H3F3B -0.034 0.046 -9999 0 -10000 0 0
AURKB -0.16 0.15 -9999 0 -0.29 625 625
AURKC -0.005 0.043 -9999 0 -0.32 18 18
CDCA8 -0.099 0.14 -9999 0 -0.3 371 371
cytokinesis -0.11 0.08 -9999 0 -10000 0 0
Aurora B/Septin1 -0.098 0.088 -9999 0 -10000 0 0
AURKA -0.14 0.15 -9999 0 -0.3 506 506
INCENP 0.003 0.005 -9999 0 -10000 0 0
KLHL13 -0.31 0.38 -9999 0 -0.79 434 434
BUB1 -0.2 0.14 -9999 0 -0.3 731 731
hSgo1/Aurora B/Survivin -0.26 0.18 -9999 0 -0.41 538 538
EVI5 0.009 0.004 -9999 0 -10000 0 0
RhoA/GTP -0.1 0.1 -9999 0 -0.35 14 14
SGOL1 -0.18 0.14 -9999 0 -0.29 682 682
CENPA -0.059 0.064 -9999 0 -10000 0 0
NCAPG -0.14 0.15 -9999 0 -10000 0 0
Aurora B/HC8 Proteasome -0.098 0.097 -9999 0 -10000 0 0
NCAPD2 -0.002 0.025 -9999 0 -0.29 8 8
Aurora B/PP1-gamma -0.098 0.097 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
NCAPH -0.11 0.14 -9999 0 -0.29 422 422
NPM1 -0.019 0.025 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
KLHL9 -0.001 0.034 -9999 0 -0.79 2 2
mitotic prometaphase -0.006 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.098 0.096 -9999 0 -10000 0 0
PPP1CC 0 0 -9999 0 -10000 0 0
Centraspindlin -0.12 0.11 -9999 0 -0.37 37 37
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.019 0.025 -9999 0 -10000 0 0
MYLK -0.088 0.15 -9999 0 -0.47 140 140
KIF23 -0.088 0.14 -9999 0 -0.3 334 334
VIM -0.094 0.1 -9999 0 -0.68 2 2
RACGAP1 -0.007 0.058 -9999 0 -0.3 41 41
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.019 0.025 -9999 0 -10000 0 0
Chromosomal passenger complex -0.084 0.079 -9999 0 -10000 0 0
Chromosomal passenger complex/EVI5 -0.16 0.18 -9999 0 -0.37 212 212
TACC1 -0.03 0.15 -9999 0 -0.79 42 42
PPP2R5D 0 0 -9999 0 -10000 0 0
CUL3 0 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 0.013 0.01 -9999 0 -10000 0 0
RAS family/GTP -0.11 0.14 -9999 0 -0.35 70 70
NFATC4 -0.087 0.16 -9999 0 -0.38 31 31
ERBB2IP 0.008 0.008 -9999 0 -10000 0 0
HSP90 (dimer) 0 0.009 -9999 0 -0.29 1 1
mammary gland morphogenesis -0.15 0.18 -9999 0 -0.39 403 403
JUN -0.018 0.08 -9999 0 -0.37 6 6
HRAS -0.003 0.028 -9999 0 -0.29 10 10
DOCK7 -0.12 0.19 -9999 0 -0.36 403 403
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.18 0.22 -9999 0 -0.46 403 403
AKT1 0.008 0.005 -9999 0 -10000 0 0
BAD 0.018 0.006 -9999 0 -10000 0 0
MAPK10 -0.11 0.13 -9999 0 -0.35 174 174
mol:GTP -0.001 0.001 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.16 0.2 -9999 0 -0.42 403 403
RAF1 -0.08 0.16 -9999 0 -0.41 23 23
ErbB2/ErbB3/neuregulin 2 -0.25 0.25 -9999 0 -0.5 528 528
STAT3 0.001 0.003 -9999 0 -10000 0 0
cell migration -0.062 0.13 -9999 0 -0.31 94 94
mol:PI-3-4-5-P3 -0.002 0.003 -9999 0 -10000 0 0
cell proliferation -0.14 0.22 -9999 0 -0.51 176 176
FOS -0.16 0.26 -9999 0 -0.53 333 333
NRAS -0.001 0.013 -9999 0 -0.3 2 2
mol:Ca2+ -0.15 0.18 -9999 0 -0.39 403 403
MAPK3 -0.11 0.19 -9999 0 -0.42 174 174
MAPK1 -0.11 0.19 -9999 0 -0.42 174 174
JAK2 -0.12 0.19 -9999 0 -0.36 404 404
NF2 -0.006 0.009 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.13 0.18 -9999 0 -0.36 403 403
NRG1 -0.29 0.38 -9999 0 -0.78 406 406
GRB2/SOS1 0 0.006 -9999 0 -10000 0 0
MAPK8 -0.11 0.17 -9999 0 -0.32 408 408
MAPK9 -0.069 0.087 -9999 0 -0.23 26 26
ERBB2 -0.017 0.059 -9999 0 -0.63 1 1
ERBB3 0 0.054 -9999 0 -0.79 5 5
SHC1 0.002 0.004 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
apoptosis 0.014 0.017 -9999 0 -10000 0 0
STAT3 (dimer) 0.001 0.003 -9999 0 -10000 0 0
RNF41 0.018 0.014 -9999 0 -10000 0 0
FRAP1 0.008 0.004 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.098 0.12 -9999 0 -0.33 26 26
ErbB2/ErbB2/HSP90 (dimer) -0.013 0.046 -9999 0 -0.54 1 1
CHRNA1 -0.092 0.16 -9999 0 -0.41 58 58
myelination -0.081 0.16 -9999 0 -0.36 31 31
PPP3CB -0.12 0.18 -9999 0 -0.34 403 403
KRAS -0.001 0.012 -9999 0 -0.29 2 2
RAC1-CDC42/GDP -0.11 0.15 -9999 0 -0.39 30 30
NRG2 -0.38 0.39 -9999 0 -0.79 523 523
mol:GDP -0.12 0.18 -9999 0 -0.35 403 403
SOS1 0 0 -9999 0 -10000 0 0
MAP2K2 -0.072 0.15 -9999 0 -0.43 17 17
SRC 0 0.009 -9999 0 -0.29 1 1
mol:cAMP -0.002 0.002 -9999 0 -10000 0 0
PTPN11 -0.14 0.18 -9999 0 -0.36 403 403
MAP2K1 -0.13 0.21 -9999 0 -0.48 173 173
heart morphogenesis -0.15 0.18 -9999 0 -0.39 403 403
RAS family/GDP -0.11 0.14 -9999 0 -0.4 29 29
GRB2 0 0.009 -9999 0 -0.29 1 1
PRKACA -0.01 0.014 -9999 0 -10000 0 0
CHRNE 0.007 0.023 -9999 0 -0.18 6 6
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
activation of caspase activity -0.008 0.005 -9999 0 -10000 0 0
nervous system development -0.15 0.18 -9999 0 -0.39 403 403
CDC42 0 0 -9999 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 -0.001 0.024 -10000 0 -0.79 1 1
EPHB2 -0.003 0.039 -10000 0 -0.29 19 19
EFNB1 0.017 0.05 -10000 0 -0.6 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.16 0.2 -10000 0 -0.41 424 424
Ephrin B2/EPHB1-2 -0.18 0.23 -10000 0 -0.47 424 424
neuron projection morphogenesis -0.15 0.19 -10000 0 -0.39 424 424
Ephrin B1/EPHB1-2/Tiam1 -0.17 0.22 -10000 0 -0.44 424 424
DNM1 -0.005 0.064 -10000 0 -0.73 8 8
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.003 0.13 -10000 0 -0.74 33 33
YES1 -0.025 0.17 -10000 0 -0.98 32 32
Ephrin B1/EPHB1-2/NCK2 -0.17 0.22 -10000 0 -0.44 424 424
PI3K -0.028 0.14 -10000 0 -0.68 45 45
mol:GDP -0.17 0.21 -10000 0 -0.44 424 424
ITGA2B -0.018 0.077 -10000 0 -0.32 62 62
endothelial cell proliferation -0.001 0.016 -10000 0 -0.52 1 1
FYN -0.025 0.16 -10000 0 -0.97 32 32
MAP3K7 -0.022 0.14 -10000 0 -0.79 32 32
FGR -0.027 0.16 -10000 0 -0.98 32 32
TIAM1 -0.001 0.018 -10000 0 -0.29 4 4
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
RGS3 0 0 -10000 0 -10000 0 0
cell adhesion -0.046 0.16 -10000 0 -0.62 72 72
LYN -0.025 0.16 -10000 0 -0.97 32 32
Ephrin B1/EPHB1-2/Src Family Kinases -0.026 0.16 -10000 0 -0.92 32 32
Ephrin B1/EPHB1-2 -0.028 0.14 -10000 0 -0.86 32 32
SRC -0.027 0.16 -10000 0 -0.98 32 32
ITGB3 -0.028 0.14 -10000 0 -0.79 37 37
EPHB1 -0.3 0.38 -10000 0 -0.78 424 424
EPHB4 0 0.009 -10000 0 -0.29 1 1
RAC1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.001 0.017 -10000 0 -0.52 1 1
alphaIIb/beta3 Integrin -0.033 0.12 -10000 0 -0.62 40 40
BLK -0.027 0.17 -10000 0 -0.98 32 32
HCK -0.027 0.16 -10000 0 -0.98 32 32
regulation of stress fiber formation 0.17 0.21 0.44 424 -10000 0 424
MAPK8 0.001 0.14 -10000 0 -0.7 38 38
Ephrin B1/EPHB1-2/RGS3 -0.17 0.22 -10000 0 -0.44 424 424
endothelial cell migration -0.016 0.12 -10000 0 -0.68 33 33
NCK2 0 0 -10000 0 -10000 0 0
PTPN13 -0.017 0.15 -10000 0 -0.9 32 32
regulation of focal adhesion formation 0.17 0.21 0.44 424 -10000 0 424
chemotaxis 0.17 0.21 0.44 424 -10000 0 424
PIK3CA 0 0.009 -10000 0 -0.29 1 1
Rac1/GTP -0.16 0.2 -10000 0 -0.4 424 424
angiogenesis -0.028 0.14 -10000 0 -0.85 32 32
LCK -0.029 0.17 -10000 0 -0.98 32 32
IGF1 pathway

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
NCK2 0 0 -10000 0 -10000 0 0
PTK2 0 0 -10000 0 -10000 0 0
CRKL -0.1 0.23 -10000 0 -0.48 271 271
GRB2/SOS1/SHC 0 0.004 -10000 0 -10000 0 0
HRAS -0.003 0.028 -10000 0 -0.29 10 10
IRS1/Crk -0.12 0.22 -10000 0 -0.48 271 271
IGF-1R heterotetramer/IGF1/PTP1B -0.13 0.23 -10000 0 -0.53 256 256
AKT1 -0.068 0.21 -10000 0 -0.71 54 54
BAD -0.055 0.2 -10000 0 -0.66 52 52
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.1 0.23 -10000 0 -0.48 271 271
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.12 0.23 -10000 0 -0.48 271 271
RAF1 -0.048 0.19 -10000 0 -0.62 49 49
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.11 0.21 -10000 0 -0.45 271 271
YWHAZ -0.001 0.015 -10000 0 -0.29 3 3
IGF-1R heterotetramer/IGF1/IRS1 -0.13 0.24 -10000 0 -0.52 271 271
PIK3CA 0 0.009 -10000 0 -0.29 1 1
RPS6KB1 -0.068 0.21 -10000 0 -0.71 54 54
GNB2L1 0 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.041 0.16 -10000 0 -0.5 52 52
PXN 0 0 -10000 0 -10000 0 0
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
HRAS/GTP -0.1 0.19 -10000 0 -0.41 257 257
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.098 0.19 -10000 0 -0.42 256 256
IGF-1R heterotetramer -0.033 0.13 -10000 0 -0.65 36 36
IGF-1R heterotetramer/IGF1/IRS/Nck -0.12 0.23 -10000 0 -0.48 271 271
Crk/p130 Cas/Paxillin -0.1 0.2 -10000 0 -0.44 256 256
IGF1R -0.033 0.13 -10000 0 -0.66 36 36
IGF1 -0.18 0.34 -10000 0 -0.81 247 247
IRS2/Crk -0.13 0.25 -10000 0 -0.5 274 274
PI3K -0.12 0.22 -10000 0 -0.48 258 258
apoptosis 0.08 0.15 0.54 53 -10000 0 53
HRAS/GDP -0.002 0.019 -10000 0 -10000 0 0
PRKCD -0.094 0.25 -10000 0 -0.53 256 256
RAF1/14-3-3 E -0.033 0.16 -10000 0 -0.52 49 49
BAD/14-3-3 -0.044 0.18 -10000 0 -0.59 53 53
PRKCZ -0.068 0.21 -10000 0 -0.7 55 55
Crk/p130 Cas/Paxillin/FAK1 -0.085 0.16 -10000 0 -0.61 49 49
PTPN1 -0.003 0.029 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.13 0.24 -10000 0 -0.56 256 256
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.11 0.2 -10000 0 -0.46 256 256
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.12 0.22 -10000 0 -0.48 271 271
GRB10 0 0 -10000 0 -10000 0 0
PTPN11 -0.1 0.23 -10000 0 -0.48 271 271
IRS1 -0.12 0.25 -10000 0 -0.52 271 271
IRS2 -0.12 0.27 -10000 0 -0.53 285 285
IGF-1R heterotetramer/IGF1 -0.16 0.28 -10000 0 -0.66 256 256
GRB2 0 0.009 -10000 0 -0.29 1 1
PDPK1 -0.11 0.21 -10000 0 -0.45 258 258
YWHAE 0 0 -10000 0 -10000 0 0
PRKD1 -0.11 0.28 -10000 0 -0.56 269 269
SHC1 0 0 -10000 0 -10000 0 0
Nongenotropic Androgen 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
PTK2 0.011 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.071 0.17 -10000 0 -0.48 159 159
regulation of S phase of mitotic cell cycle -0.044 0.12 -10000 0 -0.34 152 152
GNAO1 -0.03 0.13 -10000 0 -0.48 67 67
HRAS -0.003 0.028 -10000 0 -0.3 10 10
SHBG/T-DHT 0 0 -10000 0 -10000 0 0
PELP1 0 0 -10000 0 -10000 0 0
AKT1 0.011 0.001 -10000 0 -10000 0 0
MAP2K1 -0.045 0.16 -10000 0 -0.42 146 146
T-DHT/AR -0.082 0.21 -10000 0 -0.61 147 147
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.004 -10000 0 -0.007 328 328
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.045 0.18 -10000 0 -0.79 62 62
mol:GDP -0.084 0.21 -10000 0 -0.6 152 152
cell proliferation -0.11 0.24 -10000 0 -0.42 332 332
PIK3CA 0 0.009 -10000 0 -0.29 1 1
FOS -0.23 0.42 -10000 0 -0.86 329 329
mol:Ca2+ -0.017 0.028 -10000 0 -0.076 151 151
MAPK3 -0.076 0.2 -10000 0 -0.45 149 149
MAPK1 -0.047 0.12 -10000 0 -0.3 66 66
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
mol:IP3 -0.001 0.002 -10000 0 -0.005 329 329
cAMP biosynthetic process 0.013 0.025 -10000 0 -10000 0 0
GNG2 -0.011 0.092 -10000 0 -0.79 15 15
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.005 329 329
HRAS/GTP -0.068 0.15 -10000 0 -0.45 146 146
actin cytoskeleton reorganization -0.005 0.047 -10000 0 -0.42 14 14
SRC 0 0.009 -10000 0 -0.29 1 1
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.005 329 329
PI3K -0.007 0.059 -10000 0 -0.52 14 14
apoptosis 0.11 0.23 0.43 331 -10000 0 331
T-DHT/AR/PELP1 -0.071 0.18 -10000 0 -0.53 146 146
HRAS/GDP -0.08 0.2 -10000 0 -0.58 148 148
CREB1 -0.12 0.24 -10000 0 -0.46 331 331
RAC1-CDC42/GTP -0.006 0.048 -10000 0 -0.43 14 14
AR -0.11 0.27 -10000 0 -0.79 147 147
GNB1 0 0 -10000 0 -10000 0 0
RAF1 -0.045 0.16 -10000 0 -0.44 146 146
RAC1-CDC42/GDP -0.075 0.19 -10000 0 -0.55 146 146
T-DHT/AR/PELP1/Src -0.065 0.16 -10000 0 -0.48 146 146
MAP2K2 -0.045 0.16 -10000 0 -0.42 146 146
T-DHT/AR/PELP1/Src/PI3K -0.044 0.12 -10000 0 -0.35 152 152
GNAZ -0.007 0.075 -10000 0 -0.79 10 10
SHBG 0 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.04 0.11 -10000 0 -0.48 40 40
mol:T-DHT -0.001 0.001 0.001 63 -0.003 263 326
RAC1 0 0 -10000 0 -10000 0 0
GNRH1 0.006 0.056 -10000 0 -0.61 9 9
Gi family/GTP -0.051 0.1 -10000 0 -0.3 98 98
CDC42 0 0 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.035 0.049 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.082 0.16 -9999 0 -0.46 98 98
JUN -0.051 0.14 -9999 0 -0.53 27 27
HRAS -0.003 0.028 -9999 0 -0.29 10 10
RET51/GFRalpha1/GDNF/GRB10 -0.15 0.2 -9999 0 -0.52 210 210
RAP1A 0 0 -9999 0 -10000 0 0
FRS2 -0.003 0.029 -9999 0 -0.29 11 11
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.15 0.2 -9999 0 -0.52 210 210
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.1 0.19 -9999 0 -0.48 206 206
RHOA 0 0 -9999 0 -10000 0 0
RAP1A/GTP -0.13 0.18 -9999 0 -0.46 210 210
GRB7 -0.023 0.085 -9999 0 -0.31 79 79
RET51/GFRalpha1/GDNF -0.15 0.2 -9999 0 -0.52 210 210
MAPKKK cascade -0.1 0.16 -9999 0 -0.42 207 207
BCAR1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.12 0.23 -9999 0 -0.56 213 213
lamellipodium assembly -0.083 0.15 -9999 0 -0.36 210 210
RET51/GFRalpha1/GDNF/SHC -0.15 0.2 -9999 0 -0.52 210 210
PIK3CA 0 0.009 -9999 0 -0.29 1 1
RET9/GFRalpha1/GDNF/SHC -0.1 0.19 -9999 0 -0.48 206 206
RET9/GFRalpha1/GDNF/Shank3 -0.1 0.19 -9999 0 -0.48 206 206
MAPK3 -0.12 0.17 -9999 0 -0.44 207 207
DOK1 -0.001 0.018 -9999 0 -0.29 4 4
DOK6 -0.013 0.094 -9999 0 -0.63 22 22
PXN 0 0 -9999 0 -10000 0 0
neurite development -0.11 0.16 -9999 0 -0.53 57 57
DOK5 -0.019 0.12 -9999 0 -0.7 30 30
GFRA1 -0.16 0.3 -9999 0 -0.68 257 257
MAPK8 -0.068 0.14 -9999 0 -0.43 57 57
HRAS/GTP -0.12 0.18 -9999 0 -0.48 207 207
tube development -0.094 0.17 -9999 0 -0.45 201 201
MAPK1 -0.12 0.17 -9999 0 -0.44 207 207
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.065 0.13 -9999 0 -0.33 201 201
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -0.29 1 1
PDLIM7 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.14 0.2 -9999 0 -0.5 216 216
SHC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.15 0.2 -9999 0 -0.52 210 210
RET51/GFRalpha1/GDNF/Dok5 -0.16 0.22 -9999 0 -0.54 226 226
PRKCA -0.021 0.13 -9999 0 -0.76 31 31
HRAS/GDP -0.002 0.019 -9999 0 -10000 0 0
CREB1 -0.073 0.15 -9999 0 -0.38 201 201
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.065 0.13 -9999 0 -0.33 201 201
RET51/GFRalpha1/GDNF/Grb7 -0.16 0.21 -9999 0 -0.54 212 212
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.11 0.16 -9999 0 -0.31 401 401
DOK4 0 0 -9999 0 -10000 0 0
JNK cascade -0.049 0.14 -9999 0 -0.43 48 48
RET9/GFRalpha1/GDNF/FRS2 -0.1 0.19 -9999 0 -0.48 206 206
SHANK3 0 0 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.065 0.13 -9999 0 -0.33 201 201
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.083 0.14 -9999 0 -0.35 207 207
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.082 0.14 -9999 0 -0.35 207 207
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.084 0.14 -9999 0 -0.36 207 207
PI3K -0.13 0.24 -9999 0 -0.58 213 213
SOS1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.094 0.17 -9999 0 -0.45 201 201
GRB10 0 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.078 0.13 -9999 0 -0.33 201 201
RET51/GFRalpha1/GDNF/FRS2 -0.15 0.2 -9999 0 -0.52 210 210
GAB1 0 0 -9999 0 -10000 0 0
IRS1 -0.032 0.16 -9999 0 -0.79 45 45
IRS2 -0.033 0.16 -9999 0 -0.79 46 46
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.084 0.14 -9999 0 -0.36 207 207
RET51/GFRalpha1/GDNF/PKC alpha -0.16 0.21 -9999 0 -0.53 237 237
GRB2 0 0.009 -9999 0 -0.29 1 1
PRKACA 0 0 -9999 0 -10000 0 0
GDNF -0.015 0.065 -9999 0 -0.29 56 56
RAC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.17 0.24 -9999 0 -0.59 221 221
Rac1/GTP -0.1 0.18 -9999 0 -0.44 210 210
RET9/GFRalpha1/GDNF -0.11 0.21 -9999 0 -0.53 206 206
GFRalpha1/GDNF -0.13 0.24 -9999 0 -0.6 206 206
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.027 0.062 -10000 0 -0.48 2 2
epithelial cell differentiation -0.021 0.065 -10000 0 -0.49 9 9
ITCH 0.01 0.021 -10000 0 -10000 0 0
WWP1 0.007 0.068 -10000 0 -10000 0 0
FYN -0.001 0.034 -10000 0 -0.79 2 2
EGFR -0.29 0.38 -10000 0 -0.78 410 410
PRL -0.003 0.032 -10000 0 -10000 0 0
neuron projection morphogenesis -0.1 0.21 -10000 0 -0.46 76 76
PTPRZ1 -0.41 0.39 -10000 0 -0.78 570 570
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.16 0.2 -10000 0 -0.41 401 401
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.19 0.23 -10000 0 -0.49 401 401
ADAM17 0.01 0.021 -10000 0 -10000 0 0
ErbB4/ErbB4 0 0.086 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.055 0.13 -10000 0 -0.5 64 64
NCOR1 -0.001 0.024 -10000 0 -0.79 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.18 0.22 -10000 0 -0.46 401 401
GRIN2B -0.17 0.25 -10000 0 -0.45 451 451
ErbB4/ErbB2/betacellulin -0.05 0.11 -10000 0 -0.47 62 62
STAT1 -0.005 0.038 -10000 0 -0.29 19 19
HBEGF -0.001 0.034 -10000 0 -0.79 2 2
PRLR -0.008 0.071 -10000 0 -0.54 16 16
E4ICDs/ETO2 -0.035 0.09 -10000 0 -0.55 19 19
axon guidance 0.042 0.12 -10000 0 -0.43 3 3
NEDD4 0.01 0.021 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.008 0.058 -10000 0 -0.6 8 8
CBFA2T3 -0.015 0.1 -10000 0 -0.79 19 19
ErbB4/ErbB2/HBEGF -0.026 0.054 -10000 0 -0.48 3 3
MAPK3 -0.15 0.18 -10000 0 -0.47 79 79
STAT1 (dimer) -0.028 0.063 -10000 0 -0.31 7 7
MAPK1 -0.15 0.18 -10000 0 -0.47 79 79
JAK2 -0.001 0.024 -10000 0 -0.79 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.19 0.22 -10000 0 -0.47 401 401
NRG1 -0.21 0.3 -10000 0 -0.61 401 401
NRG3 -0.048 0.18 -10000 0 -0.62 85 85
NRG2 -0.38 0.39 -10000 0 -0.79 523 523
NRG4 -0.005 0.038 -10000 0 -0.29 19 19
heart development 0.042 0.12 -10000 0 -0.43 3 3
neural crest cell migration -0.18 0.22 -10000 0 -0.46 401 401
ERBB2 0.009 0.062 -10000 0 -0.59 1 1
WWOX/E4ICDs -0.026 0.059 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.19 0.21 -10000 0 -0.45 405 405
apoptosis 0.056 0.14 0.55 56 -10000 0 56
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.26 0.24 -10000 0 -0.5 523 523
ErbB4/ErbB2/epiregulin -0.082 0.14 -10000 0 -0.45 126 126
ErbB4/ErbB4/betacellulin/betacellulin -0.053 0.12 -10000 0 -0.5 61 61
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.023 0.067 -10000 0 -0.52 11 11
MDM2 0.008 0.075 -10000 0 -0.31 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.18 0.22 -10000 0 -0.47 401 401
STAT5A 0.043 0.12 -10000 0 -0.44 9 9
ErbB4/EGFR/neuregulin 1 beta -0.34 0.35 -10000 0 -0.65 558 558
DLG4 0 0 -10000 0 -10000 0 0
GRB2/SHC 0 0.006 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.024 0.055 -10000 0 -0.45 1 1
STAT5A (dimer) -0.022 0.07 -10000 0 -0.53 9 9
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.024 0.11 -10000 0 -0.42 6 6
LRIG1 -0.002 0.041 -10000 0 -0.79 3 3
EREG -0.11 0.25 -10000 0 -0.6 203 203
BTC -0.045 0.18 -10000 0 -0.76 64 64
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.042 0.12 -10000 0 -0.43 3 3
ERBB4 -0.032 0.072 -10000 0 -10000 0 0
STAT5B -0.002 0.041 -10000 0 -0.79 3 3
YAP1 -0.01 0.043 -10000 0 -0.64 4 4
GRB2 0 0.009 -10000 0 -0.29 1 1
ErbB4/ErbB2/neuregulin 4 -0.027 0.055 -10000 0 -0.56 1 1
glial cell differentiation 0.024 0.055 0.45 1 -10000 0 1
WWOX -0.001 0.013 -10000 0 -0.29 2 2
cell proliferation -0.12 0.23 -10000 0 -0.5 136 136
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.01 0.038 -9999 0 -0.53 3 3
NFATC2 -0.041 0.16 -9999 0 -0.55 104 104
NFATC3 0.012 0.025 -9999 0 -10000 0 0
CD40LG -0.22 0.36 -9999 0 -0.71 311 311
PTGS2 -0.32 0.46 -9999 0 -0.85 428 428
JUNB -0.001 0.013 -9999 0 -0.29 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.004 0.009 -9999 0 -10000 0 0
CaM/Ca2+ -0.004 0.009 -9999 0 -10000 0 0
CALM1 0 0.003 -9999 0 -10000 0 0
JUN -0.005 0.064 -9999 0 -0.8 7 7
mol:Ca2+ -0.007 0.009 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.005 -9999 0 -0.17 1 1
FOSL1 -0.009 0.061 -9999 0 -0.34 30 30
CREM 0 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.077 0.15 -9999 0 -0.51 87 87
FOS -0.24 0.37 -9999 0 -0.8 329 329
IFNG -0.22 0.35 -9999 0 -0.67 327 327
AP-1/NFAT1-c-4 -0.31 0.38 -9999 0 -0.81 326 326
FASLG -0.21 0.35 -9999 0 -0.68 314 314
NFAT1-c-4/ICER1 -0.06 0.14 -9999 0 -0.46 107 107
IL2RA -0.21 0.35 -9999 0 -0.68 308 308
FKBP12/FK506 0 0.006 -9999 0 -0.2 1 1
CSF2 -0.2 0.34 -9999 0 -0.67 304 304
JunB/Fra1/NFAT1-c-4 -0.057 0.14 -9999 0 -0.45 106 106
IL4 -0.2 0.34 -9999 0 -0.67 302 302
IL2 -0.009 0.024 -9999 0 -10000 0 0
IL3 -0.024 0.026 -9999 0 -10000 0 0
FKBP1A 0 0.009 -9999 0 -0.29 1 1
BATF3 -0.002 0.03 -9999 0 -0.39 5 5
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.001 0.01 -9999 0 -0.29 1 1
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.12 0.21 -9999 0 -0.6 141 141
SMAD6-7/SMURF1 0 0.016 -9999 0 -0.52 1 1
NOG -0.025 0.13 -9999 0 -0.58 47 47
SMAD9 -0.11 0.26 -9999 0 -0.76 124 124
SMAD4 -0.001 0.024 -9999 0 -0.79 1 1
SMAD5 -0.075 0.18 -9999 0 -0.47 141 141
BMP7/USAG1 -0.34 0.34 -9999 0 -0.66 559 559
SMAD5/SKI -0.087 0.16 -9999 0 -0.51 93 93
SMAD1 0.026 0.03 -9999 0 -10000 0 0
BMP2 -0.14 0.3 -9999 0 -0.78 194 194
SMAD1/SMAD1/SMAD4 -0.002 0.014 -9999 0 -10000 0 0
BMPR1A -0.002 0.041 -9999 0 -0.79 3 3
BMPR1B -0.14 0.18 -9999 0 -0.32 468 468
BMPR1A-1B/BAMBI -0.091 0.14 -9999 0 -0.55 68 68
AHSG -0.005 0.038 -9999 0 -0.29 19 19
CER1 -0.001 0.015 -9999 0 -10000 0 0
BMP2-4/CER1 -0.13 0.24 -9999 0 -0.56 242 242
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.1 0.2 -9999 0 -0.51 152 152
BMP2-4 (homodimer) -0.14 0.27 -9999 0 -0.64 242 242
RGMB -0.001 0.024 -9999 0 -0.79 1 1
BMP6/BMPR2/BMPR1A-1B -0.097 0.16 -9999 0 -0.54 109 109
RGMA -0.11 0.27 -9999 0 -0.79 147 147
SMURF1 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.11 0.2 -9999 0 -0.44 207 207
BMP2-4/USAG1 -0.37 0.36 -9999 0 -0.64 621 621
SMAD6/SMURF1/SMAD5 -0.087 0.16 -9999 0 -0.51 94 94
SOSTDC1 -0.38 0.39 -9999 0 -0.78 531 531
BMP7/BMPR2/BMPR1A-1B -0.1 0.17 -9999 0 -0.57 111 111
SKI 0 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.059 0.21 -9999 0 -0.77 84 84
HFE2 -0.003 0.029 -9999 0 -10000 0 0
ZFYVE16 0 0 -9999 0 -10000 0 0
MAP3K7 0 0.009 -9999 0 -0.29 1 1
BMP2-4/CHRD -0.14 0.26 -9999 0 -0.6 246 246
SMAD5/SMAD5/SMAD4 -0.087 0.16 -9999 0 -0.51 95 95
MAPK1 0 0 -9999 0 -10000 0 0
TAK1/TAB family -0.086 0.17 -9999 0 -0.52 107 107
BMP7 (homodimer) -0.075 0.22 -9999 0 -0.64 129 129
NUP214 0 0 -9999 0 -10000 0 0
BMP6/FETUA -0.049 0.16 -9999 0 -0.61 82 82
SMAD1/SKI 0.004 0.018 -9999 0 -10000 0 0
SMAD6 -0.001 0.024 -9999 0 -0.79 1 1
CTDSP2 0 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.13 0.24 -9999 0 -0.56 242 242
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.037 0.12 -9999 0 -0.36 113 113
BMPR2 (homodimer) 0 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.001 0.009 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.091 0.12 -9999 0 -0.62 29 29
CHRDL1 -0.54 0.36 -9999 0 -0.79 750 750
ENDOFIN/SMAD1 0.004 0.018 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.003 0.013 -9999 0 -10000 0 0
SMAD6/SMURF1 0 0 -9999 0 -10000 0 0
BAMBI -0.033 0.14 -9999 0 -0.5 72 72
SMURF2 0 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.47 0.36 -9999 0 -0.66 768 768
BMP2-4/GREM1 -0.14 0.25 -9999 0 -0.57 248 248
SMAD7 0 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.1 0.24 -9999 0 -0.72 123 123
SMAD1/SMAD6 0.004 0.018 -9999 0 -10000 0 0
TAK1/SMAD6 0 0.006 -9999 0 -10000 0 0
BMP7 -0.075 0.22 -9999 0 -0.64 129 129
BMP6 -0.06 0.21 -9999 0 -0.78 84 84
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.099 0.19 -9999 0 -0.59 107 107
PPM1A 0 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.004 0.018 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0 0 -9999 0 -10000 0 0
PPP1CA -0.001 0.018 -9999 0 -0.29 4 4
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0 0 -9999 0 -10000 0 0
PPP1R15A 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.13 0.24 -9999 0 -0.49 249 249
CHRD -0.032 0.13 -9999 0 -0.42 83 83
BMPR2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.13 0.23 -9999 0 -0.54 201 201
BMP4 -0.051 0.19 -9999 0 -0.78 72 72
FST -0.04 0.17 -9999 0 -0.76 57 57
BMP2-4/NOG -0.14 0.26 -9999 0 -0.58 258 258
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.094 0.16 -9999 0 -0.53 111 111
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.1 0.12 -10000 0 -0.32 90 90
NT3 (dimer)/TRKC -0.29 0.36 -10000 0 -0.68 465 465
NT3 (dimer)/TRKB -0.49 0.44 -10000 0 -0.77 696 696
SHC/Grb2/SOS1/GAB1/PI3K -0.004 0.036 -10000 0 -0.32 14 14
RAPGEF1 0 0 -10000 0 -10000 0 0
BDNF -0.064 0.21 -10000 0 -0.66 105 105
PIK3CA 0 0.009 -10000 0 -0.29 1 1
DYNLT1 0 0 -10000 0 -10000 0 0
NTRK1 -0.011 0.07 -10000 0 -0.37 33 33
NTRK2 -0.41 0.39 -10000 0 -0.79 573 573
NTRK3 -0.27 0.37 -10000 0 -0.78 377 377
NT-4/5 (dimer)/TRKB -0.58 0.48 -10000 0 -0.84 746 746
neuron apoptosis 0.24 0.24 0.58 300 -10000 0 300
SHC 2-3/Grb2 -0.26 0.27 -10000 0 -0.66 299 299
SHC1 0 0 -10000 0 -10000 0 0
SHC2 -0.24 0.29 -10000 0 -0.67 283 283
SHC3 -0.24 0.28 -10000 0 -0.58 358 358
STAT3 (dimer) -0.005 0.03 -10000 0 -0.38 4 4
NT3 (dimer)/TRKA -0.24 0.31 -10000 0 -0.6 434 434
RIN/GDP -0.065 0.12 -10000 0 -0.24 205 205
GIPC1 0 0.009 -10000 0 -0.29 1 1
KRAS -0.001 0.013 -10000 0 -0.29 2 2
DNAJA3 -0.14 0.2 -10000 0 -0.43 342 342
RIN/GTP -0.001 0.01 -10000 0 -10000 0 0
CCND1 0.018 0.075 -10000 0 -1 4 4
MAGED1 -0.001 0.018 -10000 0 -0.29 4 4
PTPN11 0 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.27 0.37 -10000 0 -0.79 371 371
SHC/GRB2/SOS1 0 0.004 -10000 0 -10000 0 0
GRB2 0 0.009 -10000 0 -0.29 1 1
NGF (dimer)/TRKA/MATK -0.028 0.11 -10000 0 -0.53 41 41
TRKA/NEDD4-2 -0.008 0.053 -10000 0 -0.6 6 6
ELMO1 0 0 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0 0 -10000 0 -10000 0 0
NGF -0.014 0.098 -10000 0 -0.62 24 24
HRAS -0.003 0.028 -10000 0 -0.29 10 10
DOCK1 0 0 -10000 0 -10000 0 0
GAB2 -0.004 0.042 -10000 0 -0.39 10 10
RIT2 -0.001 0.015 -10000 0 -0.29 3 3
RIT1 0 0 -10000 0 -10000 0 0
FRS2 -0.003 0.029 -10000 0 -0.29 11 11
DNM1 -0.005 0.063 -10000 0 -0.73 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.13 0.2 -10000 0 -0.42 342 342
mol:GDP -0.1 0.18 -10000 0 -0.35 275 275
NGF (dimer) -0.014 0.097 -10000 0 -0.62 24 24
RhoG/GDP 0 0 -10000 0 -10000 0 0
RIT1/GDP -0.061 0.12 -10000 0 -0.24 228 228
TIAM1 -0.001 0.018 -10000 0 -0.29 4 4
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
BDNF (dimer)/TRKB -0.31 0.3 -10000 0 -0.56 598 598
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 -0.001 0.014 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0 0.004 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.13 0.29 -10000 0 -0.75 185 185
RAP1/GDP -0.072 0.084 -10000 0 -0.24 42 42
KIDINS220/CRKL 0 0 -10000 0 -10000 0 0
BDNF (dimer) -0.064 0.21 -10000 0 -0.66 105 105
ubiquitin-dependent protein catabolic process -0.015 0.076 -10000 0 -0.51 22 22
Schwann cell development -0.058 0.044 -10000 0 -10000 0 0
EHD4 0 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 -0.001 0.012 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 -0.001 0.011 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.42 0.38 -10000 0 -0.65 711 711
ABL1 0 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
Rap1/GTP -0.1 0.097 -10000 0 -10000 0 0
STAT3 -0.005 0.03 -10000 0 -0.38 4 4
axon guidance -0.4 0.34 -10000 0 -0.61 711 711
MAPK3 0.006 0.1 -10000 0 -0.5 38 38
MAPK1 0.006 0.1 -10000 0 -0.5 38 38
CDC42/GDP -0.061 0.12 -10000 0 -0.24 230 230
NTF3 -0.13 0.29 -10000 0 -0.75 185 185
NTF4 -0.27 0.37 -10000 0 -0.79 371 371
NGF (dimer)/TRKA/FAIM -0.015 0.075 -10000 0 -0.52 21 21
PI3K -0.008 0.068 -10000 0 -0.6 14 14
FRS3 0 0 -10000 0 -10000 0 0
FAIM 0 0 -10000 0 -10000 0 0
GAB1 0 0 -10000 0 -10000 0 0
RASGRF1 -0.15 0.21 -10000 0 -0.45 345 345
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.24 0.33 -10000 0 -0.59 467 467
RGS19 -0.001 0.013 -10000 0 -0.29 2 2
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.082 -10000 0 -10000 0 0
Rac1/GDP -0.061 0.12 -10000 0 -0.25 120 120
NGF (dimer)/TRKA/GRIT -0.015 0.076 -10000 0 -0.52 21 21
neuron projection morphogenesis -0.1 0.21 -10000 0 -0.62 29 29
NGF (dimer)/TRKA/NEDD4-2 -0.015 0.076 -10000 0 -0.52 22 22
MAP2K1 0 0.003 -10000 0 -10000 0 0
NGFR -0.24 0.36 -10000 0 -0.79 334 334
NGF (dimer)/TRKA/GIPC/GAIP -0.009 0.053 -10000 0 -0.33 27 27
RAS family/GTP/PI3K -0.005 0.038 -10000 0 -0.34 14 14
FRS2 family/SHP2/GRB2/SOS1 -0.001 0.011 -10000 0 -10000 0 0
NRAS -0.001 0.013 -10000 0 -0.29 2 2
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
PRKCI 0 0.009 -10000 0 -0.29 1 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCZ -0.001 0.024 -10000 0 -0.79 1 1
MAPKKK cascade -0.064 0.12 -10000 0 -0.82 21 21
RASA1 0 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.008 0.05 -10000 0 -0.6 5 5
SQSTM1 0 0.009 -10000 0 -0.29 1 1
BDNF (dimer)/TRKB/GIPC -0.28 0.27 -10000 0 -0.51 598 598
NGF (dimer)/TRKA/p62/Atypical PKCs -0.012 0.064 -10000 0 -0.44 22 22
MATK -0.022 0.11 -10000 0 -0.48 49 49
NEDD4L -0.001 0.024 -10000 0 -0.79 1 1
RAS family/GDP -0.065 0.078 -10000 0 -0.23 15 15
NGF (dimer)/TRKA -0.15 0.22 -10000 0 -0.46 342 342
Rac1/GTP -0.12 0.14 -10000 0 -0.34 261 261
FRS2 family/SHP2/CRK family -0.001 0.01 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.095 0.18 -10000 0 -0.46 197 197
ER alpha/Gai/GDP/Gbeta gamma -0.093 0.19 -10000 0 -0.47 189 189
AKT1 -0.1 0.32 -10000 0 -0.83 171 171
PIK3CA 0 0.009 -10000 0 -0.29 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.1 0.32 -10000 0 -0.85 168 168
mol:Ca2+ -0.028 0.15 -10000 0 -0.45 93 93
IGF1R -0.02 0.12 -10000 0 -0.6 36 36
E2/ER alpha (dimer)/Striatin -0.11 0.2 -10000 0 -0.53 183 183
SHC1 0 0 -10000 0 -10000 0 0
apoptosis 0.094 0.3 0.78 171 -10000 0 171
RhoA/GTP -0.069 0.14 -10000 0 -0.39 165 165
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.093 0.2 -10000 0 -0.54 175 175
regulation of stress fiber formation 0.023 0.14 0.36 35 -10000 0 35
E2/ERA-ERB (dimer) -0.11 0.2 -10000 0 -0.54 187 187
KRAS -0.001 0.013 -10000 0 -0.29 2 2
G13/GTP -0.088 0.17 -10000 0 -0.48 165 165
pseudopodium formation -0.023 0.14 -10000 0 -0.36 35 35
E2/ER alpha (dimer)/PELP1 -0.096 0.19 -10000 0 -0.52 165 165
GRB2 0 0.009 -10000 0 -0.29 1 1
GNG2 -0.011 0.092 -10000 0 -0.79 15 15
GNAO1 -0.03 0.13 -10000 0 -0.48 67 67
HRAS -0.003 0.028 -10000 0 -0.29 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.061 0.22 -10000 0 -0.54 179 179
E2/ER beta (dimer) -0.013 0.089 -10000 0 -0.61 24 24
mol:GDP -0.086 0.2 -10000 0 -0.53 187 187
mol:NADP -0.061 0.22 -10000 0 -0.54 179 179
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
mol:IP3 -0.03 0.15 -10000 0 -0.47 93 93
IGF-1R heterotetramer -0.02 0.12 -10000 0 -0.59 36 36
PLCB1 -0.065 0.14 -10000 0 -0.49 92 92
PLCB2 -0.034 0.089 -10000 0 -0.62 15 15
IGF1 -0.18 0.33 -10000 0 -0.79 247 247
mol:L-citrulline -0.061 0.22 -10000 0 -0.54 179 179
RHOA 0 0 -10000 0 -10000 0 0
Gai/GDP -0.04 0.15 -10000 0 -0.85 26 26
JNK cascade -0.013 0.089 -10000 0 -0.61 24 24
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 -0.017 0.12 -10000 0 -0.79 24 24
GNAQ -0.002 0.041 -10000 0 -0.79 3 3
ESR1 -0.15 0.28 -10000 0 -0.58 288 288
Gq family/GDP/Gbeta gamma -0.009 0.078 -10000 0 -0.71 9 9
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.023 0.13 -10000 0 -0.32 165 165
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.093 0.2 -10000 0 -0.54 175 175
GNAZ -0.007 0.075 -10000 0 -0.79 10 10
E2/ER alpha (dimer) -0.11 0.22 -10000 0 -0.61 165 165
STRN -0.015 0.11 -10000 0 -0.79 21 21
GNAL -0.19 0.33 -10000 0 -0.79 258 258
PELP1 0 0 -10000 0 -10000 0 0
MAPK11 0.005 0.084 -10000 0 -0.52 27 27
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.045 0.18 -10000 0 -0.79 62 62
HBEGF -0.071 0.19 -10000 0 -0.45 187 187
cAMP biosynthetic process -0.19 0.25 -10000 0 -0.5 389 389
SRC -0.052 0.2 -10000 0 -0.45 177 177
PI3K -0.008 0.068 -10000 0 -0.6 14 14
GNB1 0 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.079 0.18 -10000 0 -0.46 197 197
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.15 0.23 -10000 0 -0.51 246 246
Gs family/GTP -0.19 0.26 -10000 0 -0.52 389 389
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.002 0.014 -10000 0 -10000 0 0
vasodilation -0.057 0.21 -10000 0 -0.51 179 179
mol:DAG -0.03 0.15 -10000 0 -0.47 93 93
Gs family/GDP/Gbeta gamma -0.16 0.23 -10000 0 -0.44 391 391
MSN -0.027 0.15 -10000 0 -0.39 35 35
Gq family/GTP -0.038 0.094 -10000 0 -0.66 14 14
mol:PI-3-4-5-P3 -0.099 0.31 -10000 0 -0.81 168 168
NRAS -0.001 0.013 -10000 0 -0.29 2 2
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.057 0.21 0.51 179 -10000 0 179
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
RhoA/GDP -0.079 0.19 -10000 0 -0.49 187 187
NOS3 -0.066 0.24 -10000 0 -0.57 179 179
GNA11 -0.003 0.048 -10000 0 -0.79 4 4
MAPKKK cascade -0.069 0.26 -10000 0 -0.63 183 183
E2/ER alpha (dimer)/PELP1/Src -0.098 0.22 -10000 0 -0.56 175 175
ruffle organization -0.023 0.14 -10000 0 -0.36 35 35
ROCK2 -0.074 0.14 -10000 0 -0.37 194 194
GNA14 -0.013 0.084 -10000 0 -0.46 30 30
GNA15 -0.003 0.033 -10000 0 -0.36 8 8
GNA13 0 0 -10000 0 -10000 0 0
MMP9 -0.097 0.2 -10000 0 -0.48 184 184
MMP2 -0.045 0.19 -10000 0 -0.43 184 184
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.075 0.23 -9999 0 -0.79 104 104
GNB1/GNG2 -0.14 0.23 -9999 0 -0.68 116 116
mol:DAG -0.097 0.22 -9999 0 -0.6 116 116
PLCG1 -0.13 0.21 -9999 0 -0.63 116 116
YES1 -0.14 0.23 -9999 0 -0.66 120 120
FZD3 -0.011 0.092 -9999 0 -0.79 15 15
FZD6 -0.007 0.075 -9999 0 -0.79 10 10
G protein -0.13 0.22 -9999 0 -0.64 118 118
MAP3K7 -0.069 0.19 -9999 0 -0.49 113 113
mol:Ca2+ -0.093 0.22 -9999 0 -0.58 116 116
mol:IP3 -0.097 0.22 -9999 0 -0.6 116 116
NLK -0.005 0.01 -9999 0 -10000 0 0
GNB1 0 0 -9999 0 -10000 0 0
CAMK2A -0.083 0.2 -9999 0 -0.54 114 114
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.16 0.25 -9999 0 -0.44 385 385
CSNK1A1 0 0 -9999 0 -10000 0 0
GNAS -0.14 0.23 -9999 0 -0.66 121 121
GO:0007205 -0.094 0.22 -9999 0 -0.59 116 116
WNT6 -0.16 0.31 -9999 0 -0.69 255 255
WNT4 -0.021 0.12 -9999 0 -0.55 43 43
NFAT1/CK1 alpha -0.16 0.23 -9999 0 -0.63 145 145
GNG2 -0.011 0.092 -9999 0 -0.79 15 15
WNT5A -0.016 0.1 -9999 0 -0.79 18 18
WNT11 -0.17 0.32 -9999 0 -0.76 242 242
CDC42 -0.11 0.24 -9999 0 -0.66 105 105
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.22 0.26 -10000 0 -0.52 452 452
fibroblast growth factor receptor signaling pathway -0.22 0.26 -10000 0 -0.52 452 452
LAMA1 -0.088 0.25 -10000 0 -0.77 124 124
PRNP -0.013 0.1 -10000 0 -0.79 18 18
GPC1/SLIT2 -0.07 0.19 -10000 0 -0.6 125 125
SMAD2 0.01 0.1 -10000 0 -0.47 50 50
GPC1/PrPc/Cu2+ -0.01 0.069 -10000 0 -0.52 19 19
GPC1/Laminin alpha1 -0.068 0.19 -10000 0 -0.6 121 121
TDGF1 -0.005 0.063 -10000 0 -0.73 8 8
CRIPTO/GPC1 -0.006 0.053 -10000 0 -0.6 8 8
APP/GPC1 -0.002 0.023 -10000 0 -0.6 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.02 0.051 -10000 0 -0.52 9 9
FLT1 -0.001 0.024 -10000 0 -0.79 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.025 0.11 -10000 0 -0.52 50 50
SERPINC1 -0.018 0.07 -10000 0 -0.29 67 67
FYN 0.02 0.053 -10000 0 -0.52 10 10
FGR 0.02 0.051 -10000 0 -0.52 9 9
positive regulation of MAPKKK cascade 0.032 0.066 -10000 0 -0.52 10 10
SLIT2 -0.089 0.25 -10000 0 -0.79 124 124
GPC1/NRG -0.22 0.29 -10000 0 -0.6 402 402
NRG1 -0.29 0.38 -10000 0 -0.78 406 406
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.003 0.029 -10000 0 -0.52 2 2
LYN 0.021 0.048 -10000 0 -0.51 8 8
mol:Spermine 0.009 0.024 -10000 0 -0.61 1 1
cell growth -0.22 0.26 -10000 0 -0.52 452 452
BMP signaling pathway 0.002 0.032 0.36 7 -10000 0 7
SRC 0.021 0.048 -10000 0 -0.51 8 8
TGFBR1 0 0.009 -10000 0 -0.29 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.26 0.37 -10000 0 -0.75 382 382
GPC1 -0.002 0.032 -10000 0 -0.36 7 7
TGFBR1 (dimer) 0 0.009 -10000 0 -0.29 1 1
VEGFA -0.003 0.031 -10000 0 -0.29 12 12
BLK -0.006 0.082 -10000 0 -0.56 10 10
HCK 0.018 0.052 -10000 0 -0.51 8 8
FGF2 -0.32 0.39 -10000 0 -0.79 446 446
FGFR1 -0.009 0.08 -10000 0 -0.68 14 14
VEGFR1 homodimer -0.001 0.024 -10000 0 -0.79 1 1
TGFBR2 -0.035 0.16 -10000 0 -0.79 49 49
cell death -0.002 0.023 -10000 0 -0.6 1 1
ATIII/GPC1 -0.013 0.05 -10000 0 -0.61 1 1
PLA2G2A/GPC1 -0.2 0.28 -10000 0 -0.6 356 356
LCK 0.008 0.082 -10000 0 -0.53 21 21
neuron differentiation -0.22 0.29 -10000 0 -0.6 402 402
PrPc/Cu2+ -0.01 0.077 -10000 0 -0.61 18 18
APP 0 0 -10000 0 -10000 0 0
TGFBR2 (dimer) -0.035 0.16 -10000 0 -0.79 49 49
IL23-mediated signaling events

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
CCL2 -0.16 0.39 -9999 0 -0.91 130 130
IL23A -0.17 0.39 -9999 0 -1 93 93
NF kappa B1 p50/RelA/I kappa B alpha -0.23 0.32 -9999 0 -0.88 140 140
positive regulation of T cell mediated cytotoxicity -0.18 0.42 -9999 0 -0.85 231 231
ITGA3 -0.16 0.38 -9999 0 -0.97 98 98
IL17F -0.1 0.28 -9999 0 -0.64 100 100
IL12B -0.05 0.12 -9999 0 -0.31 115 115
STAT1 (dimer) -0.21 0.37 -9999 0 -0.84 206 206
CD4 -0.16 0.38 -9999 0 -0.87 128 128
IL23 -0.17 0.38 -9999 0 -0.99 93 93
IL23R -0.012 0.087 -9999 0 -10000 0 0
IL1B -0.17 0.41 -9999 0 -0.97 130 130
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.16 0.38 -9999 0 -0.96 95 95
TYK2 0.012 0.017 -9999 0 -10000 0 0
STAT4 -0.032 0.16 -9999 0 -0.78 45 45
STAT3 0 0 -9999 0 -10000 0 0
IL18RAP -0.021 0.14 -9999 0 -0.73 42 42
IL12RB1 -0.001 0.07 -9999 0 -0.32 43 43
PIK3CA 0 0.009 -9999 0 -0.29 1 1
IL12Rbeta1/TYK2 -0.002 0.052 -9999 0 -0.6 2 2
IL23R/JAK2 -0.009 0.11 -9999 0 -0.63 1 1
positive regulation of chronic inflammatory response -0.18 0.42 -9999 0 -0.85 231 231
natural killer cell activation 0.002 0.008 -9999 0 -10000 0 0
JAK2 0.018 0.034 -9999 0 -0.83 1 1
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
NFKB1 0.005 0.007 -9999 0 -10000 0 0
RELA 0.005 0.007 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.16 0.37 -9999 0 -0.94 94 94
ALOX12B -0.16 0.38 -9999 0 -0.95 94 94
CXCL1 -0.34 0.63 -9999 0 -1.4 278 278
T cell proliferation -0.18 0.42 -9999 0 -0.85 231 231
NFKBIA 0.005 0.007 -9999 0 -10000 0 0
IL17A -0.068 0.24 -9999 0 -0.54 59 59
PI3K -0.24 0.32 -9999 0 -0.82 198 198
IFNG -0.005 0.027 -9999 0 -0.089 23 23
STAT3 (dimer) -0.23 0.31 -9999 0 -0.85 143 143
IL18R1 -0.007 0.11 -9999 0 -0.78 20 20
IL23/IL23R/JAK2/TYK2/SOCS3 -0.081 0.24 -9999 0 -0.57 48 48
IL18/IL18R -0.03 0.12 -9999 0 -0.53 56 56
macrophage activation -0.013 0.016 -9999 0 -0.041 135 135
TNF -0.17 0.4 -9999 0 -1 103 103
STAT3/STAT4 -0.25 0.34 -9999 0 -0.86 200 200
STAT4 (dimer) -0.23 0.39 -9999 0 -0.88 217 217
IL18 0.001 0.047 -9999 0 -0.3 27 27
IL19 -0.17 0.38 -9999 0 -0.92 115 115
STAT5A (dimer) -0.21 0.37 -9999 0 -0.84 215 215
STAT1 -0.005 0.038 -9999 0 -0.29 19 19
SOCS3 -0.004 0.058 -9999 0 -0.79 6 6
CXCL9 -0.18 0.38 -9999 0 -0.97 103 103
MPO -0.2 0.46 -9999 0 -1.1 159 159
positive regulation of humoral immune response -0.18 0.42 -9999 0 -0.85 231 231
IL23/IL23R/JAK2/TYK2 -0.19 0.44 -9999 0 -0.88 231 231
IL6 -0.46 0.7 -9999 0 -1.3 408 408
STAT5A -0.006 0.067 -9999 0 -0.79 8 8
IL2 0.004 0.028 -9999 0 -0.3 8 8
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.008 -9999 0 -10000 0 0
CD3E -0.17 0.41 -9999 0 -0.95 141 141
keratinocyte proliferation -0.18 0.42 -9999 0 -0.85 231 231
NOS2 -0.16 0.38 -9999 0 -0.9 131 131
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.1 0.23 -10000 0 -0.6 188 188
CRKL -0.04 0.16 -10000 0 -0.34 188 188
mol:PIP3 -0.018 0.035 0.77 2 -10000 0 2
AKT1 0.003 0.021 0.48 2 -10000 0 2
PTK2B 0 0 -10000 0 -10000 0 0
RAPGEF1 -0.03 0.15 -10000 0 -0.54 21 21
RANBP10 0 0 -10000 0 -10000 0 0
PIK3CA 0 0.009 -10000 0 -0.29 1 1
HGF/MET/SHIP2 -0.12 0.24 -10000 0 -0.56 240 240
MAP3K5 -0.021 0.15 -10000 0 -0.53 25 25
HGF/MET/CIN85/CBL/ENDOPHILINS -0.11 0.22 -10000 0 -0.51 240 240
AP1 -0.19 0.26 -10000 0 -0.58 330 330
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
apoptosis -0.24 0.37 -10000 0 -0.78 330 330
STAT3 (dimer) -0.039 0.16 -10000 0 -0.62 21 21
GAB1/CRKL/SHP2/PI3K -0.066 0.13 -10000 0 -0.52 35 35
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.032 0.15 -10000 0 -0.54 21 21
PTPN11 0 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0 0 -10000 0 -10000 0 0
PTEN -0.001 0.034 -10000 0 -0.79 2 2
ELK1 -0.044 0.1 -10000 0 -0.27 188 188
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.046 0.092 -10000 0 -0.41 21 21
PAK1 0.008 0.028 0.45 2 -10000 0 2
HGF/MET/RANBP10 -0.12 0.24 -10000 0 -0.56 240 240
HRAS -0.15 0.3 -10000 0 -0.68 240 240
DOCK1 -0.03 0.15 -10000 0 -0.54 21 21
GAB1 -0.05 0.16 -10000 0 -0.35 240 240
CRK -0.04 0.16 -10000 0 -0.34 188 188
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.15 0.3 -10000 0 -0.7 240 240
JUN -0.005 0.063 -10000 0 -0.79 7 7
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.078 0.15 -10000 0 -0.35 240 240
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
cell morphogenesis -0.019 0.18 -10000 0 -0.59 31 31
GRB2/SHC -0.066 0.13 -10000 0 -0.33 188 188
FOS -0.24 0.36 -10000 0 -0.79 329 329
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.044 0.1 -10000 0 -0.27 188 188
HGF/MET/MUC20 -0.12 0.24 -10000 0 -0.56 240 240
cell migration -0.065 0.13 -10000 0 -0.32 188 188
GRB2 0 0.009 -10000 0 -0.29 1 1
CBL 0 0 -10000 0 -10000 0 0
MET/RANBP10 -0.1 0.23 -10000 0 -0.6 188 188
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.077 0.15 -10000 0 -0.35 240 240
MET/MUC20 -0.1 0.23 -10000 0 -0.61 189 189
RAP1B -0.021 0.14 -10000 0 -0.5 21 21
RAP1A -0.021 0.14 -10000 0 -0.5 21 21
HGF/MET/RANBP9 -0.12 0.24 -10000 0 -0.56 240 240
RAF1 -0.1 0.29 -10000 0 -0.7 191 191
STAT3 -0.073 0.14 -10000 0 -0.63 21 21
cell proliferation -0.061 0.23 -10000 0 -0.48 240 240
RPS6KB1 -0.027 0.052 -10000 0 -0.18 21 21
MAPK3 -0.044 0.092 -10000 0 -0.24 188 188
MAPK1 -0.044 0.092 -10000 0 -0.24 188 188
RANBP9 0 0 -10000 0 -10000 0 0
MAPK8 -0.004 0.14 -10000 0 -0.48 33 33
SRC -0.071 0.14 -10000 0 -0.61 21 21
PI3K -0.072 0.14 -10000 0 -0.35 197 197
MET/Glomulin -0.094 0.21 -10000 0 -0.55 188 188
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 -0.086 0.27 -10000 0 -0.64 188 188
MET -0.14 0.3 -10000 0 -0.78 189 189
MAP4K1 -0.03 0.15 -10000 0 -0.51 26 26
PTK2 0 0 -10000 0 -10000 0 0
MAP2K2 -0.086 0.27 -10000 0 -0.64 188 188
BAD 0.011 0.02 0.45 2 -10000 0 2
MAP2K4 -0.011 0.14 -10000 0 -0.47 26 26
SHP2/GRB2/SOS1/GAB1 -0.096 0.19 -10000 0 -0.5 188 188
INPPL1 0 0 -10000 0 -10000 0 0
PXN 0 0 -10000 0 -10000 0 0
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS -0.071 0.14 -10000 0 -0.35 188 188
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.053 0.2 -10000 0 -0.79 73 73
RASA1 0 0 -10000 0 -10000 0 0
NCK1 0 0 -10000 0 -10000 0 0
PTPRJ 0 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.067 0.13 -10000 0 -0.32 188 188
PDPK1 -0.006 0.025 0.56 2 -10000 0 2
HGF/MET/SHIP -0.12 0.24 -10000 0 -0.56 240 240
Syndecan-1-mediated signaling events

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
TGFB1 -0.001 0.015 -9999 0 -0.29 3 3
CCL5 -0.014 0.079 -9999 0 -0.36 44 44
SDCBP 0 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.08 0.11 -9999 0 -0.34 106 106
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.074 0.096 -9999 0 -0.35 46 46
Syndecan-1/Syntenin -0.074 0.096 -9999 0 -0.48 6 6
MAPK3 -0.047 0.095 -9999 0 -0.48 5 5
HGF/MET -0.14 0.27 -9999 0 -0.64 240 240
TGFB1/TGF beta receptor Type II -0.001 0.015 -9999 0 -0.29 3 3
BSG 0 0.009 -9999 0 -0.29 1 1
keratinocyte migration -0.073 0.095 -9999 0 -0.35 46 46
Syndecan-1/RANTES -0.081 0.11 -9999 0 -0.39 50 50
Syndecan-1/CD147 -0.065 0.093 -9999 0 -0.49 6 6
Syndecan-1/Syntenin/PIP2 -0.071 0.093 -9999 0 -0.46 6 6
LAMA5 0 0.009 -9999 0 -0.29 1 1
positive regulation of cell-cell adhesion -0.07 0.091 -9999 0 -0.33 46 46
MMP7 -0.12 0.28 -9999 0 -0.7 191 191
HGF -0.053 0.2 -9999 0 -0.79 73 73
Syndecan-1/CASK -0.076 0.1 -9999 0 -0.33 106 106
Syndecan-1/HGF/MET -0.17 0.24 -9999 0 -0.58 243 243
regulation of cell adhesion -0.038 0.093 -9999 0 -0.48 4 4
HPSE -0.007 0.051 -9999 0 -0.34 21 21
positive regulation of cell migration -0.08 0.11 -9999 0 -0.34 106 106
SDC1 -0.08 0.11 -9999 0 -0.35 106 106
Syndecan-1/Collagen -0.08 0.11 -9999 0 -0.34 106 106
PPIB -0.001 0.015 -9999 0 -0.29 3 3
MET -0.14 0.3 -9999 0 -0.78 189 189
PRKACA 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.15 -9999 0 -0.29 483 483
MAPK1 -0.047 0.095 -9999 0 -0.48 5 5
homophilic cell adhesion -0.079 0.11 -9999 0 -0.34 106 106
MMP1 -0.22 0.13 -9999 0 -0.29 824 824
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.076 0.068 -9999 0 -0.61 1 1
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.02 0.018 -9999 0 -10000 0 0
AURKB -0.17 0.14 -9999 0 -0.29 625 625
AURKC -0.005 0.043 -9999 0 -0.32 18 18
Visual signal transduction: Rods

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
mol:K + 0 0 -9999 0 -10000 0 0
GNAT1/GTP -0.003 0.023 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.01 0.04 -9999 0 -0.31 2 2
PDE6G/GNAT1/GTP -0.008 0.036 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.004 0.034 -9999 0 -10000 0 0
GRK1 -0.003 0.029 -9999 0 -0.29 11 11
CNG Channel -0.14 0.2 -9999 0 -0.43 316 316
mol:Na + -0.13 0.18 -9999 0 -0.41 309 309
mol:ADP -0.003 0.029 -9999 0 -0.29 11 11
RGS9-1/Gbeta5/R9AP -0.061 0.16 -9999 0 -0.53 106 106
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.13 0.19 -9999 0 -0.42 309 309
CNGB1 -0.015 0.064 -9999 0 -0.29 55 55
RDH5 -0.48 0.38 -9999 0 -0.79 660 660
SAG -0.015 0.064 -9999 0 -0.29 55 55
mol:Ca2+ -0.12 0.18 -9999 0 -0.4 186 186
Na + (4 Units) -0.12 0.17 -9999 0 -0.39 186 186
RGS9 -0.08 0.23 -9999 0 -0.73 121 121
GNB1/GNGT1 -0.03 0.068 -9999 0 -10000 0 0
GNAT1/GDP -0.054 0.14 -9999 0 -0.46 106 106
GUCY2D -0.008 0.057 -9999 0 -0.36 24 24
GNGT1 -0.047 0.11 -9999 0 -0.29 175 175
GUCY2F -0.001 0.013 -9999 0 -0.29 2 2
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.018 0.069 -9999 0 -0.45 22 22
mol:11-cis-retinal -0.48 0.38 -9999 0 -0.79 660 660
mol:cGMP -0.011 0.048 -9999 0 -0.45 8 8
GNB1 0 0 -9999 0 -10000 0 0
Rhodopsin -0.37 0.29 -9999 0 -0.6 660 660
SLC24A1 0 0 -9999 0 -10000 0 0
CNGA1 -0.22 0.35 -9999 0 -0.78 310 310
Metarhodopsin II -0.003 0.022 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.012 0.051 -9999 0 -0.48 8 8
RGS9BP -0.019 0.072 -9999 0 -0.29 70 70
Metarhodopsin II/Transducin -0.009 0.021 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.008 0.042 -9999 0 -0.48 5 5
PDE6A/B -0.017 0.089 -9999 0 -0.6 22 22
mol:Pi -0.061 0.16 -9999 0 -0.52 106 106
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.023 0.051 -9999 0 -10000 0 0
PDE6B -0.017 0.11 -9999 0 -0.73 25 25
PDE6A -0.006 0.042 -9999 0 -0.29 23 23
PDE6G -0.012 0.058 -9999 0 -0.29 44 44
RHO -0.004 0.035 -9999 0 -0.29 16 16
PDE6 -0.062 0.14 -9999 0 -0.44 124 124
GUCA1A -0.012 0.059 -9999 0 -0.29 46 46
GC2/GCAP Family -0.008 0.043 -9999 0 -0.48 5 5
GUCA1C 0 0.009 -9999 0 -0.29 1 1
GUCA1B -0.004 0.053 -9999 0 -0.79 5 5
Signaling events mediated by PTP1B

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
PDGFRB -0.003 0.048 -10000 0 -0.79 4 4
Jak2/Leptin Receptor -0.16 0.23 -10000 0 -0.52 299 299
PTP1B/AKT1 -0.07 0.11 -10000 0 -0.34 115 115
FYN -0.001 0.034 -10000 0 -0.79 2 2
p210 bcr-abl/PTP1B -0.071 0.13 -10000 0 -0.38 119 119
EGFR -0.29 0.39 -10000 0 -0.79 410 410
EGF/EGFR -0.29 0.3 -10000 0 -0.56 554 554
CSF1 -0.006 0.071 -10000 0 -0.79 9 9
AKT1 0.001 0.003 -10000 0 -10000 0 0
INSR 0.001 0.01 -10000 0 -0.3 1 1
PTP1B/N-cadherin -0.097 0.12 -10000 0 -0.37 123 123
Insulin Receptor/Insulin -0.049 0.08 -10000 0 -0.4 22 22
HCK -0.004 0.033 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
TYK2 -0.06 0.12 -10000 0 -0.36 117 117
EGF -0.15 0.32 -10000 0 -0.79 214 214
YES1 -0.001 0.024 -10000 0 -0.79 1 1
CAV1 -0.18 0.24 -10000 0 -0.51 294 294
TXN 0 0.018 -10000 0 -0.3 4 4
PTP1B/IRS1/GRB2 -0.087 0.14 -10000 0 -0.4 151 151
cell migration 0.071 0.13 0.38 119 -10000 0 119
STAT3 0 0.001 -10000 0 -10000 0 0
PRLR -0.006 0.072 -10000 0 -0.54 16 16
ITGA2B -0.018 0.078 -10000 0 -0.32 62 62
CSF1R -0.001 0.025 -10000 0 -0.54 2 2
Prolactin Receptor/Prolactin -0.007 0.058 -10000 0 -0.6 8 8
FGR -0.001 0.025 -10000 0 -0.54 2 2
PTP1B/p130 Cas -0.074 0.12 -10000 0 -0.36 117 117
Crk/p130 Cas -0.069 0.11 -10000 0 -0.35 105 105
DOK1 -0.046 0.12 -10000 0 -0.33 99 99
JAK2 -0.042 0.08 -10000 0 -0.32 30 30
Jak2/Leptin Receptor/Leptin -0.36 0.18 -10000 0 -0.49 576 576
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
PTPN1 -0.072 0.13 -10000 0 -0.39 119 119
LYN 0 0 -10000 0 -10000 0 0
CDH2 -0.054 0.12 -10000 0 -0.3 200 200
SRC -0.013 0.047 -10000 0 -10000 0 0
ITGB3 -0.028 0.14 -10000 0 -0.79 37 37
CAT1/PTP1B -0.084 0.17 -10000 0 -0.43 116 116
CAPN1 0.001 0.01 -10000 0 -0.29 1 1
CSK 0 0 -10000 0 -10000 0 0
PI3K -0.044 0.094 -10000 0 -0.55 20 20
mol:H2O2 -0.005 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.32 0.16 -10000 0 -0.43 551 551
negative regulation of transcription -0.041 0.079 -10000 0 -0.32 30 30
FCGR2A -0.001 0.013 -10000 0 -0.29 2 2
FER -0.007 0.08 -10000 0 -0.8 11 11
alphaIIb/beta3 Integrin -0.033 0.12 -10000 0 -0.62 40 40
BLK -0.044 0.11 -10000 0 -0.3 159 159
Insulin Receptor/Insulin/Shc 0 0.005 -10000 0 -10000 0 0
RHOA 0.002 0.004 -10000 0 -10000 0 0
LEPR -0.2 0.35 -10000 0 -0.79 292 292
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0 0.009 -10000 0 -0.29 1 1
mol:NADPH -0.005 0.005 -10000 0 -10000 0 0
TRPV6 -0.03 0.13 -10000 0 -0.44 22 22
PRL -0.004 0.032 -10000 0 -0.33 1 1
SOCS3 0.018 0.11 -10000 0 -1.5 6 6
SPRY2 -0.095 0.26 -10000 0 -0.8 130 130
Insulin Receptor/Insulin/IRS1 -0.022 0.11 -10000 0 -0.53 45 45
CSF1/CSF1R -0.073 0.12 -10000 0 -0.37 108 108
Ras protein signal transduction 0.037 0.036 -10000 0 -0.21 1 1
IRS1 -0.032 0.16 -10000 0 -0.79 45 45
INS 0 0.001 -10000 0 -10000 0 0
LEP -0.64 0.31 -10000 0 -0.79 881 881
STAT5B -0.058 0.11 -10000 0 -0.31 122 122
STAT5A -0.059 0.11 -10000 0 -0.31 125 125
GRB2 0 0.009 -10000 0 -0.29 1 1
PDGFB-D/PDGFRB -0.076 0.12 -10000 0 -0.37 119 119
CSN2 0.018 0.035 -10000 0 -10000 0 0
PIK3CA 0 0.009 -10000 0 -0.29 1 1
LAT -0.014 0.053 -10000 0 -0.57 2 2
YBX1 -0.001 0.014 -10000 0 -10000 0 0
LCK -0.02 0.1 -10000 0 -0.41 53 53
SHC1 0 0 -10000 0 -10000 0 0
NOX4 -0.004 0.05 -10000 0 -0.41 13 13
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.065 0.22 -9999 0 -0.64 55 55
CRP -0.07 0.22 -9999 0 -0.67 46 46
cell cycle arrest -0.084 0.24 -9999 0 -0.71 71 71
TIMP1 -0.063 0.2 -9999 0 -0.56 63 63
IL6ST -0.086 0.26 -9999 0 -0.78 137 137
Rac1/GDP -0.12 0.23 -9999 0 -0.67 91 91
AP1 -0.13 0.23 -9999 0 -0.48 282 282
GAB2 0.005 0.043 -9999 0 -0.39 10 10
TNFSF11 -0.076 0.22 -9999 0 -0.66 49 49
HSP90B1 0.015 0.047 -9999 0 -10000 0 0
GAB1 0.008 0.006 -9999 0 -10000 0 0
MAPK14 -0.13 0.25 -9999 0 -0.72 97 97
AKT1 0.038 0.042 -9999 0 -10000 0 0
FOXO1 0.046 0.061 -9999 0 -0.42 12 12
MAP2K6 -0.15 0.26 -9999 0 -0.66 128 128
mol:GTP 0 0.001 -9999 0 -10000 0 0
MAP2K4 -0.086 0.23 -9999 0 -0.64 88 88
MITF -0.14 0.26 -9999 0 -0.67 113 113
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0 0 -9999 0 -10000 0 0
A2M 0.013 0.13 -9999 0 -1.5 8 8
CEBPB 0.016 0.007 -9999 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.044 0.093 -9999 0 -0.54 6 6
STAT3 -0.091 0.26 -9999 0 -0.77 71 71
STAT1 -0.013 0.021 -9999 0 -10000 0 0
CEBPD -0.067 0.22 -9999 0 -0.64 63 63
PIK3CA 0.012 0.009 -9999 0 -0.29 1 1
PI3K -0.008 0.067 -9999 0 -0.6 14 14
JUN -0.005 0.063 -9999 0 -0.79 7 7
PIAS3/MITF -0.16 0.22 -9999 0 -0.72 85 85
MAPK11 -0.13 0.25 -9999 0 -0.73 97 97
STAT3 (dimer)/FOXO1 -0.036 0.22 -9999 0 -0.59 68 68
GRB2/SOS1/GAB family -0.14 0.2 -9999 0 -0.71 72 72
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.16 0.26 -9999 0 -0.46 283 283
GRB2 0.008 0.011 -9999 0 -0.29 1 1
JAK2 -0.001 0.024 -9999 0 -0.79 1 1
LBP -0.24 0.45 -9999 0 -0.95 286 286
PIK3R1 0.002 0.09 -9999 0 -0.79 14 14
JAK1 0.009 0.025 -9999 0 -0.79 1 1
MYC -0.078 0.26 -9999 0 -0.8 69 69
FGG -0.075 0.22 -9999 0 -0.63 63 63
macrophage differentiation -0.084 0.24 -9999 0 -0.71 71 71
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.23 0.28 -9999 0 -0.5 504 504
JUNB -0.064 0.21 -9999 0 -0.6 64 64
FOS -0.24 0.36 -9999 0 -0.79 329 329
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.15 0.26 -9999 0 -0.47 283 283
STAT1/PIAS1 -0.13 0.23 -9999 0 -0.47 211 211
GRB2/SOS1/GAB family/SHP2/PI3K 0.002 0.037 -9999 0 -0.29 5 5
STAT3 (dimer) -0.087 0.25 -9999 0 -0.74 71 71
PRKCD -0.061 0.22 -9999 0 -0.61 77 77
IL6R -0.022 0.16 -9999 0 -0.79 44 44
SOCS3 -0.12 0.24 -9999 0 -0.74 87 87
gp130 (dimer)/JAK1/JAK1/LMO4 -0.057 0.18 -9999 0 -0.52 140 140
Rac1/GTP -0.15 0.21 -9999 0 -0.67 91 91
HCK -0.004 0.033 -9999 0 -10000 0 0
MAPKKK cascade -0.006 0.084 -9999 0 -1 2 2
bone resorption -0.072 0.21 -9999 0 -0.61 57 57
IRF1 -0.066 0.22 -9999 0 -0.65 51 51
mol:GDP -0.13 0.25 -9999 0 -0.55 159 159
SOS1 0 0.003 -9999 0 -10000 0 0
VAV1 -0.13 0.25 -9999 0 -0.6 136 136
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.16 0.25 -9999 0 -0.8 92 92
PTPN11 -0.013 0.019 -9999 0 -10000 0 0
IL6/IL6RA -0.24 0.31 -9999 0 -0.62 419 419
gp130 (dimer)/TYK2/TYK2/LMO4 -0.06 0.18 -9999 0 -0.51 140 140
gp130 (dimer)/JAK2/JAK2/LMO4 -0.06 0.18 -9999 0 -0.52 140 140
IL6 -0.28 0.38 -9999 0 -0.78 401 401
PIAS3 0 0 -9999 0 -10000 0 0
PTPRE 0.003 0.035 -9999 0 -0.79 2 2
PIAS1 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.18 0.24 -9999 0 -0.4 503 503
LMO4 0.009 0.049 -9999 0 -0.44 10 10
STAT3 (dimer)/PIAS3 -0.15 0.21 -9999 0 -0.78 70 70
MCL1 0.05 0.035 -9999 0 -10000 0 0
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 -0.023 0.062 -9999 0 -0.56 11 11
alphaM/beta2 Integrin/GPIbA -0.024 0.057 -9999 0 -0.52 9 9
alphaM/beta2 Integrin/proMMP-9 -0.083 0.082 -9999 0 -0.39 8 8
PLAUR -0.023 0.079 -9999 0 -0.29 86 86
HMGB1 -0.013 0.017 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.017 0.029 -9999 0 -10000 0 0
AGER -0.015 0.04 -9999 0 -0.66 3 3
RAP1A 0 0 -9999 0 -10000 0 0
SELPLG 0 0 -9999 0 -10000 0 0
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.074 0.096 -9999 0 -0.46 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.15 -9999 0 -0.29 483 483
CYR61 -0.043 0.18 -9999 0 -0.79 59 59
TLN1 0 0 -9999 0 -10000 0 0
Rap1/GTP -0.057 0.11 -9999 0 -0.52 22 22
RHOA 0 0 -9999 0 -10000 0 0
P-selectin oligomer -0.18 0.33 -9999 0 -0.79 257 257
MYH2 -0.07 0.16 -9999 0 -0.41 111 111
MST1R -0.011 0.083 -9999 0 -0.55 21 21
leukocyte activation during inflammatory response -0.29 0.22 -9999 0 -0.46 668 668
APOB -0.48 0.38 -9999 0 -0.79 668 668
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.008 0.079 -9999 0 -0.75 12 12
JAM3 -0.005 0.063 -9999 0 -0.79 7 7
GP1BA -0.012 0.077 -9999 0 -0.4 33 33
alphaM/beta2 Integrin/CTGF -0.025 0.071 -9999 0 -0.57 15 15
alphaM/beta2 Integrin -0.071 0.13 -9999 0 -0.35 107 107
JAM3 homodimer -0.005 0.063 -9999 0 -0.79 7 7
ICAM2 -0.004 0.053 -9999 0 -0.79 5 5
ICAM1 -0.004 0.035 -9999 0 -0.29 16 16
phagocytosis triggered by activation of immune response cell surface activating receptor -0.061 0.14 -9999 0 -0.3 202 202
cell adhesion -0.024 0.057 -9999 0 -0.52 9 9
NFKB1 -0.096 0.21 -9999 0 -0.66 15 15
THY1 -0.002 0.025 -9999 0 -0.29 8 8
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.33 0.26 -9999 0 -0.53 668 668
alphaM/beta2 Integrin/LRP/tPA -0.034 0.11 -9999 0 -0.54 46 46
IL6 -0.3 0.48 -9999 0 -0.93 400 400
ITGB2 -0.017 0.039 -9999 0 -0.3 16 16
elevation of cytosolic calcium ion concentration -0.025 0.049 -9999 0 -0.36 2 2
alphaM/beta2 Integrin/JAM2/JAM3 -0.044 0.13 -9999 0 -0.53 68 68
JAM2 -0.048 0.19 -9999 0 -0.79 66 66
alphaM/beta2 Integrin/ICAM1 -0.022 0.08 -9999 0 -0.53 21 21
alphaM/beta2 Integrin/uPA/Plg -0.019 0.033 -9999 0 -10000 0 0
RhoA/GTP -0.088 0.16 -9999 0 -0.38 199 199
positive regulation of phagocytosis -0.049 0.089 -9999 0 -0.45 19 19
Ron/MSP -0.016 0.098 -9999 0 -0.66 22 22
alphaM/beta2 Integrin/uPAR/uPA -0.025 0.05 -9999 0 -0.36 2 2
alphaM/beta2 Integrin/uPAR -0.029 0.048 -9999 0 -0.34 4 4
PLAU -0.007 0.045 -9999 0 -0.29 27 27
PLAT -0.028 0.14 -9999 0 -0.74 41 41
actin filament polymerization -0.066 0.15 -9999 0 -0.39 112 112
MST1 -0.012 0.089 -9999 0 -0.58 22 22
alphaM/beta2 Integrin/lipoprotein(a) -0.29 0.22 -9999 0 -0.47 668 668
TNF -0.087 0.22 -9999 0 -0.96 17 17
RAP1B 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.021 0.036 -9999 0 -10000 0 0
fibrinolysis -0.019 0.032 -9999 0 -10000 0 0
HCK -0.004 0.033 -9999 0 -10000 0 0
dendritic cell antigen processing and presentation -0.061 0.14 -9999 0 -0.3 202 202
VTN -0.027 0.1 -9999 0 -0.34 88 88
alphaM/beta2 Integrin/CYR61 -0.046 0.13 -9999 0 -0.57 59 59
LPA -0.001 0.02 -9999 0 -0.29 5 5
LRP1 -0.009 0.085 -9999 0 -0.79 13 13
cell migration -0.073 0.084 -9999 0 -0.47 16 16
FN1 -0.12 0.14 -9999 0 -0.29 431 431
alphaM/beta2 Integrin/Thy1 -0.018 0.031 -9999 0 -10000 0 0
MPO -0.051 0.19 -9999 0 -0.77 72 72
KNG1 -0.006 0.041 -9999 0 -10000 0 0
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.065 0.16 -9999 0 -0.4 120 120
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.002 0.025 -9999 0 -0.29 8 8
CTGF -0.012 0.093 -9999 0 -0.7 18 18
alphaM/beta2 Integrin/Hck -0.019 0.035 -9999 0 -0.33 2 2
ITGAM -0.015 0.028 -9999 0 -0.35 2 2
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.13 0.21 -9999 0 -0.5 257 257
HP -0.16 0.31 -9999 0 -0.71 244 244
leukocyte adhesion -0.076 0.13 -9999 0 -0.58 46 46
SELP -0.18 0.33 -9999 0 -0.79 257 257
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.005 0.048 -9999 0 -0.6 6 6
alphaV beta3 Integrin -0.23 0.28 -9999 0 -0.54 459 459
PTK2 -0.089 0.19 -9999 0 -0.68 42 42
IGF1R -0.02 0.12 -9999 0 -0.6 36 36
PI4KB 0 0 -9999 0 -10000 0 0
MFGE8 -0.012 0.091 -9999 0 -0.62 21 21
SRC 0 0.009 -9999 0 -0.29 1 1
CDKN1B -0.088 0.12 -9999 0 -0.88 11 11
VEGFA -0.003 0.031 -9999 0 -0.29 12 12
ILK -0.086 0.12 -9999 0 -0.83 8 8
ROCK1 -0.001 0.024 -9999 0 -0.79 1 1
AKT1 -0.076 0.1 -9999 0 -0.77 8 8
PTK2B -0.019 0.095 -9999 0 -0.49 38 38
alphaV/beta3 Integrin/JAM-A -0.2 0.24 -9999 0 -0.47 463 463
CBL 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.019 0.095 -9999 0 -0.52 37 37
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.14 0.25 -9999 0 -0.54 271 271
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.013 0.062 -9999 0 -0.53 7 7
alphaV/beta3 Integrin/Syndecan-1 -0.028 0.1 -9999 0 -0.53 38 38
PI4KA 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.33 0.35 -9999 0 -0.76 354 354
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.29 1 1
alphaV/beta3 Integrin/Osteopontin -0.056 0.11 -9999 0 -0.54 37 37
RPS6KB1 -0.3 0.32 -9999 0 -0.69 355 355
TLN1 0 0 -9999 0 -10000 0 0
MAPK3 -0.33 0.39 -9999 0 -0.76 459 459
GPR124 -0.009 0.085 -9999 0 -0.79 13 13
MAPK1 -0.33 0.39 -9999 0 -0.76 459 459
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
alphaV/beta3 Integrin/Tumstatin -0.1 0.21 -9999 0 -0.53 214 214
cell adhesion -0.023 0.11 -9999 0 -0.51 47 47
ANGPTL3 -0.001 0.018 -9999 0 -0.29 4 4
VEGFR2 homodimer/VEGFA homodimer/Src -0.005 0.041 -9999 0 -0.52 6 6
IGF-1R heterotetramer -0.02 0.12 -9999 0 -0.59 36 36
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 -0.035 0.16 -9999 0 -0.79 49 49
ITGB3 -0.028 0.14 -9999 0 -0.79 37 37
IGF1 -0.18 0.33 -9999 0 -0.79 247 247
RAC1 0 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.024 0.12 -9999 0 -0.59 43 43
apoptosis 0 0 -9999 0 -10000 0 0
CD47 -0.001 0.024 -9999 0 -0.79 1 1
alphaV/beta3 Integrin/CD47 -0.018 0.095 -9999 0 -0.52 38 38
VCL 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.05 0.18 -9999 0 -0.65 80 80
CSF1 -0.006 0.071 -9999 0 -0.79 9 9
PIK3C2A -0.087 0.12 -9999 0 -0.85 9 9
PI4 Kinase/Pyk2 -0.17 0.21 -9999 0 -0.6 76 76
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.02 0.1 -9999 0 -0.53 38 38
FAK1/Vinculin -0.064 0.16 -9999 0 -0.51 42 42
alphaV beta3/Integrin/ppsTEM5 -0.024 0.12 -9999 0 -0.59 43 43
RHOA 0 0 -9999 0 -10000 0 0
VTN -0.027 0.1 -9999 0 -0.34 88 88
BCAR1 0 0 -9999 0 -10000 0 0
FGF2 -0.32 0.39 -9999 0 -0.79 446 446
F11R -0.23 0.31 -9999 0 -0.6 446 446
alphaV/beta3 Integrin/Lactadherin -0.025 0.12 -9999 0 -0.57 46 46
alphaV/beta3 Integrin/TGFBR2 -0.04 0.16 -9999 0 -0.66 66 66
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.004 0.042 -9999 0 -0.47 9 9
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
alphaV/beta3 Integrin/Talin -0.017 0.086 -9999 0 -0.48 37 37
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.12 0.14 -9999 0 -0.29 431 431
alphaV/beta3 Integrin/Pyk2 -0.019 0.096 -9999 0 -0.5 38 38
SDC1 -0.02 0.076 -9999 0 -0.3 73 73
VAV3 -0.008 0.054 -9999 0 -0.44 16 16
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 -0.032 0.16 -9999 0 -0.79 45 45
FAK1/Paxillin -0.064 0.16 -9999 0 -0.51 42 42
cell migration -0.05 0.14 -9999 0 -0.45 40 40
ITGAV 0 0 -9999 0 -10000 0 0
PI3K -0.19 0.23 -9999 0 -0.67 74 74
SPP1 -0.077 0.13 -9999 0 -0.29 288 288
KDR -0.004 0.058 -9999 0 -0.79 6 6
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0 0 -9999 0 -10000 0 0
COL4A3 -0.13 0.29 -9999 0 -0.78 187 187
angiogenesis -0.3 0.39 -9999 0 -0.74 459 459
Rac1/GTP -0.007 0.049 -9999 0 -0.4 16 16
EDIL3 -0.052 0.19 -9999 0 -0.7 81 81
cell proliferation -0.04 0.16 -9999 0 -0.65 66 66
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.096 0.2 0.63 121 -10000 0 121
KIRREL -0.079 0.25 -10000 0 -0.79 121 121
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.096 0.2 -10000 0 -0.63 121 121
PLCG1 0 0 -10000 0 -10000 0 0
ARRB2 0 0 -10000 0 -10000 0 0
WASL 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.07 0.15 -10000 0 -0.48 121 121
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.043 0.11 -10000 0 -0.36 121 121
FYN -0.065 0.14 -10000 0 -0.46 121 121
mol:Ca2+ -0.069 0.15 -10000 0 -0.47 121 121
mol:DAG -0.069 0.15 -10000 0 -0.48 121 121
NPHS2 -0.008 0.031 -10000 0 -0.29 5 5
mol:IP3 -0.069 0.15 -10000 0 -0.48 121 121
regulation of endocytosis -0.055 0.14 -10000 0 -0.43 121 121
Nephrin/NEPH1/podocin/Cholesterol -0.072 0.15 -10000 0 -0.49 121 121
establishment of cell polarity -0.096 0.2 -10000 0 -0.63 121 121
Nephrin/NEPH1/podocin/NCK1-2 -0.062 0.14 -10000 0 -0.44 121 121
Nephrin/NEPH1/beta Arrestin2 -0.056 0.14 -10000 0 -0.43 121 121
NPHS1 -0.047 0.11 -10000 0 -0.36 17 17
Nephrin/NEPH1/podocin -0.065 0.14 -10000 0 -0.46 121 121
TJP1 -0.001 0.024 -10000 0 -0.79 1 1
NCK1 0 0 -10000 0 -10000 0 0
NCK2 0 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.07 0.15 -10000 0 -0.48 121 121
CD2AP 0 0.009 -10000 0 -0.29 1 1
Nephrin/NEPH1/podocin/GRB2 -0.07 0.15 -10000 0 -0.48 121 121
GRB2 0 0.009 -10000 0 -0.29 1 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.057 0.18 -10000 0 -0.5 130 130
cytoskeleton organization -0.055 0.14 -10000 0 -0.44 121 121
Nephrin/NEPH1 -0.069 0.15 -10000 0 -0.47 121 121
Nephrin/NEPH1/ZO-1 -0.076 0.16 -10000 0 -0.52 121 121
Ephrin A reverse signaling

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
MAPKKK cascade -0.05 0.15 -9999 0 -0.53 103 103
EFNA5 -0.074 0.23 -9999 0 -0.78 104 104
FYN -0.026 0.15 -9999 0 -0.48 104 104
neuron projection morphogenesis -0.05 0.15 -9999 0 -0.53 103 103
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.051 0.16 -9999 0 -0.53 103 103
EPHA5 -0.001 0.02 -9999 0 -0.29 5 5
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.005 0.049 -9999 0 -0.61 6 6
PDGFRB 0.005 0.049 -9999 0 -0.79 4 4
SPHK1 -0.025 0.055 -9999 0 -1.1 2 2
mol:S1P -0.031 0.057 -9999 0 -0.97 2 2
S1P1/S1P/Gi -0.1 0.23 -9999 0 -0.39 380 380
GNAO1 -0.023 0.14 -9999 0 -0.5 67 67
PDGFB-D/PDGFRB/PLCgamma1 -0.12 0.18 -9999 0 -0.59 77 77
PLCG1 -0.091 0.22 -9999 0 -0.56 99 99
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.005 0.049 -9999 0 -0.79 4 4
GNAI2 0.008 0.006 -9999 0 -10000 0 0
GNAI3 0.008 0.006 -9999 0 -10000 0 0
GNAI1 -0.038 0.19 -9999 0 -0.8 62 62
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.005 0.046 -9999 0 -0.54 6 6
S1P1/S1P -0.044 0.075 -9999 0 -0.58 8 8
negative regulation of cAMP metabolic process -0.098 0.22 -9999 0 -0.38 380 380
MAPK3 -0.16 0.31 -9999 0 -0.57 370 370
calcium-dependent phospholipase C activity -0.003 0.004 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR -0.004 0.059 -9999 0 -0.8 6 6
PLCB2 -0.008 0.086 -9999 0 -0.5 9 9
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.038 0.061 -9999 0 -0.48 8 8
receptor internalization -0.043 0.07 -9999 0 -0.53 8 8
PTGS2 -0.33 0.55 -9999 0 -1.1 370 370
Rac1/GTP -0.038 0.061 -9999 0 -0.48 8 8
RHOA 0 0 -9999 0 -10000 0 0
VEGFA -0.003 0.031 -9999 0 -0.29 12 12
negative regulation of T cell proliferation -0.098 0.22 -9999 0 -0.38 380 380
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.001 0.077 -9999 0 -0.79 10 10
MAPK1 -0.16 0.31 -9999 0 -0.57 370 370
S1P1/S1P/PDGFB-D/PDGFRB -0.021 0.11 -9999 0 -0.64 10 10
ABCC1 0 0 -9999 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 -0.06 0.12 -9999 0 -0.29 223 223
mol:Halofuginone 0 0.003 -9999 0 -10000 0 0
ITGA1 -0.008 0.079 -9999 0 -0.79 11 11
CDKN1A -0.057 0.087 -9999 0 -0.84 2 2
PRL-3/alpha Tubulin -0.002 0.018 -9999 0 -10000 0 0
mol:Ca2+ -0.033 0.096 -9999 0 -0.61 15 15
AGT -0.047 0.13 -9999 0 -0.34 151 151
CCNA2 -0.16 0.24 -9999 0 -0.49 347 347
TUBA1B 0 0 -9999 0 -10000 0 0
EGR1 -0.17 0.29 -9999 0 -0.6 347 347
CDK2/Cyclin E1 -0.067 0.09 -9999 0 -0.81 2 2
MAPK3 0.021 0.02 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0.006 -9999 0 -10000 0 0
MAPK1 0.021 0.02 -9999 0 -10000 0 0
PTP4A1 -0.12 0.23 -9999 0 -0.46 347 347
PTP4A3 -0.003 0.028 -9999 0 -0.29 10 10
PTP4A2 0 0.009 -9999 0 -0.29 1 1
ITGB1 0.021 0.02 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -0.29 1 1
RAC1 -0.055 0.081 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.14 0.2 -9999 0 -0.42 347 347
RABGGTA 0 0 -9999 0 -10000 0 0
BCAR1 0.001 0.009 -9999 0 -10000 0 0
RHOC -0.055 0.081 -9999 0 -10000 0 0
RHOA -0.055 0.081 -9999 0 -10000 0 0
cell motility -0.034 0.1 -9999 0 -0.24 1 1
PRL-1/alpha Tubulin -0.13 0.2 -9999 0 -0.42 347 347
PRL-3/alpha1 Integrin -0.008 0.062 -9999 0 -0.6 11 11
ROCK1 -0.034 0.1 -9999 0 -0.24 1 1
RABGGTB 0 0 -9999 0 -10000 0 0
CDK2 0 0 -9999 0 -10000 0 0
mitosis -0.12 0.23 -9999 0 -0.45 347 347
ATF5 -0.001 0.018 -9999 0 -0.29 4 4
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.002 0.026 -9999 0 -0.29 9 9
Syndecan-3/Src/Cortactin -0.18 0.2 -9999 0 -0.4 478 478
Syndecan-3/Neurocan -0.007 0.028 -9999 0 -10000 0 0
POMC -0.024 0.12 -9999 0 -0.79 22 22
EGFR -0.29 0.38 -9999 0 -0.78 410 410
Syndecan-3/EGFR -0.16 0.21 -9999 0 -0.44 405 405
AGRP -0.003 0.028 -9999 0 -0.29 10 10
NCSTN 0 0 -9999 0 -10000 0 0
PSENEN -0.001 0.013 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B -0.001 0.024 -9999 0 -0.79 1 1
APH1A 0 0 -9999 0 -10000 0 0
NCAN -0.019 0.073 -9999 0 -0.29 72 72
long-term memory -0.002 0.02 -9999 0 -0.41 2 2
Syndecan-3/IL8 -0.016 0.066 -9999 0 -0.44 22 22
PSEN1 0 0 -9999 0 -10000 0 0
Src/Cortactin -0.002 0.018 -9999 0 -10000 0 0
FYN -0.001 0.034 -9999 0 -0.79 2 2
limb bud formation 0 0.003 -9999 0 -10000 0 0
MC4R -0.003 0.032 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -0.29 1 1
PTN -0.34 0.39 -9999 0 -0.78 480 480
FGFR/FGF/Syndecan-3 0 0.003 -9999 0 -10000 0 0
neuron projection morphogenesis -0.17 0.19 -9999 0 -0.39 478 478
Syndecan-3/AgRP -0.001 0.011 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.002 0.015 -9999 0 -10000 0 0
Fyn/Cortactin -0.003 0.031 -9999 0 -0.6 2 2
SDC3 0 0.003 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.015 0.065 -9999 0 -0.43 22 22
IL8 -0.033 0.13 -9999 0 -0.42 87 87
Syndecan-3/Fyn/Cortactin -0.002 0.02 -9999 0 -0.42 2 2
Syndecan-3/CASK 0 0.003 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.02 0.094 -9999 0 -0.6 24 24
Gamma Secretase -0.001 0.014 -9999 0 -0.44 1 1
PDGFR-alpha signaling 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
PDGFRA -0.052 0.2 -9999 0 -0.8 74 74
PDGF/PDGFRA/CRKL -0.041 0.15 -9999 0 -0.6 73 73
positive regulation of JUN kinase activity -0.031 0.12 -9999 0 -0.46 73 73
CRKL 0 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.044 0.15 -9999 0 -0.61 73 73
AP1 -0.36 0.54 -9999 0 -1.2 329 329
mol:IP3 -0.035 0.16 -9999 0 -0.63 73 73
PLCG1 -0.035 0.16 -9999 0 -0.63 73 73
PDGF/PDGFRA/alphaV Integrin -0.041 0.15 -9999 0 -0.6 73 73
RAPGEF1 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.035 0.16 -9999 0 -0.63 73 73
CAV3 -0.001 0.015 -9999 0 -0.29 3 3
CAV1 -0.17 0.33 -9999 0 -0.79 241 241
SHC/Grb2/SOS1 -0.031 0.12 -9999 0 -0.46 73 73
PDGF/PDGFRA/Shf -0.041 0.15 -9999 0 -0.61 73 73
FOS -0.32 0.55 -9999 0 -1.1 329 329
JUN -0.024 0.059 -9999 0 -0.67 7 7
oligodendrocyte development -0.04 0.15 -9999 0 -0.6 73 73
GRB2 0 0.009 -9999 0 -0.29 1 1
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
mol:DAG -0.035 0.16 -9999 0 -0.63 73 73
PDGF/PDGFRA -0.052 0.2 -9999 0 -0.8 74 74
actin cytoskeleton reorganization -0.041 0.15 -9999 0 -0.6 74 74
SRF 0.015 0.022 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
PI3K -0.041 0.15 -9999 0 -0.54 83 83
PDGF/PDGFRA/Crk/C3G -0.035 0.13 -9999 0 -0.52 73 73
JAK1 -0.025 0.16 -9999 0 -0.6 74 74
ELK1/SRF -0.027 0.12 -9999 0 -0.47 73 73
SHB -0.001 0.025 -9999 0 -0.54 2 2
SHF -0.001 0.027 -9999 0 -0.46 3 3
CSNK2A1 0.019 0.027 -9999 0 -10000 0 0
GO:0007205 -0.037 0.17 -9999 0 -0.65 73 73
SOS1 0 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.031 0.12 -9999 0 -0.46 73 73
PDGF/PDGFRA/SHB -0.041 0.15 -9999 0 -0.6 74 74
PDGF/PDGFRA/Caveolin-1 -0.17 0.32 -9999 0 -0.7 266 266
ITGAV 0 0 -9999 0 -10000 0 0
ELK1 -0.035 0.16 -9999 0 -0.59 73 73
PIK3CA 0 0.009 -9999 0 -0.29 1 1
PDGF/PDGFRA/Crk -0.041 0.15 -9999 0 -0.6 73 73
JAK-STAT cascade -0.025 0.16 -9999 0 -0.6 74 74
cell proliferation -0.041 0.15 -9999 0 -0.61 73 73
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.017 0.031 -9999 0 -10000 0 0
VDR 0 0 -9999 0 -10000 0 0
FAM120B 0 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.034 0.16 -9999 0 -0.42 19 19
RXRs/LXRs/DNA/Oxysterols -0.014 0.14 -9999 0 -0.49 19 19
MED1 -0.006 0.043 -9999 0 -0.29 24 24
mol:9cRA 0.005 0.008 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.024 0.092 -9999 0 -0.35 72 72
RXRs/NUR77 -0.16 0.24 -9999 0 -0.5 337 337
RXRs/PPAR -0.13 0.23 -9999 0 -0.51 165 165
NCOR2 0 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0 0 -9999 0 -10000 0 0
RARs/VDR/DNA/Vit D3 -0.008 0.054 -9999 0 -0.45 15 15
RARA -0.004 0.035 -9999 0 -0.29 16 16
NCOA1 -0.001 0.024 -9999 0 -0.79 1 1
VDR/VDR/DNA 0 0 -9999 0 -10000 0 0
RARs/RARs/DNA/9cRA -0.008 0.055 -9999 0 -0.46 15 15
RARG 0 0 -9999 0 -10000 0 0
RPS6KB1 0.029 0.052 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.023 0.088 -9999 0 -0.34 72 72
THRA -0.001 0.024 -9999 0 -0.79 1 1
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0 0 -9999 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.12 0.2 -9999 0 -0.46 268 268
NR1H4 -0.003 0.032 -9999 0 -0.29 13 13
RXRs/LXRs/DNA -0.1 0.18 -9999 0 -0.42 268 268
NR1H2 0.016 0.006 -9999 0 -10000 0 0
NR1H3 0.016 0.007 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.11 0.19 -9999 0 -0.44 268 268
NR4A1 -0.071 0.23 -9999 0 -0.79 99 99
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.043 0.13 -9999 0 -0.27 268 268
RXRG -0.18 0.34 -9999 0 -0.78 268 268
RXR alpha/CCPG 0 0 -9999 0 -10000 0 0
RXRA 0.016 0.006 -9999 0 -10000 0 0
RXRB 0.016 0.007 -9999 0 -10000 0 0
THRB -0.044 0.18 -9999 0 -0.79 61 61
PPARG -0.19 0.34 -9999 0 -0.79 268 268
PPARD 0 0 -9999 0 -10000 0 0
TNF -0.014 0.18 -9999 0 -1.2 14 14
mol:Oxysterols 0.005 0.007 -9999 0 -10000 0 0
cholesterol transport -0.014 0.14 -9999 0 -0.48 19 19
PPARA -0.006 0.067 -9999 0 -0.79 8 8
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.011 0.092 -9999 0 -0.79 15 15
RXRs/NUR77/BCL2 -0.12 0.19 -9999 0 -0.37 359 359
SREBF1 -0.005 0.14 -9999 0 -0.68 5 5
RXRs/RXRs/DNA/9cRA -0.12 0.2 -9999 0 -0.46 268 268
ABCA1 -0.008 0.16 -9999 0 -1.1 10 10
RARs/THRs -0.032 0.12 -9999 0 -0.47 72 72
RXRs/FXR -0.11 0.2 -9999 0 -0.47 268 268
BCL2 -0.027 0.14 -9999 0 -0.79 37 37
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.054 0.3 -10000 0 -0.81 131 131
IHH -0.014 0.082 -10000 0 -0.42 9 9
SHH Np/Cholesterol/GAS1 -0.032 0.12 -10000 0 -0.49 66 66
LRPAP1 0 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.032 0.12 0.48 66 -10000 0 66
SMO/beta Arrestin2 -0.076 0.23 -10000 0 -0.84 82 82
SMO -0.036 0.26 -10000 0 -0.89 85 85
AKT1 0.006 0.12 -10000 0 -0.48 23 23
ARRB2 0 0 -10000 0 -10000 0 0
BOC -0.058 0.21 -10000 0 -0.79 81 81
ADRBK1 0 0 -10000 0 -10000 0 0
heart looping -0.035 0.26 -10000 0 -0.84 90 90
STIL -0.039 0.21 -10000 0 -0.7 86 86
DHH N/PTCH2 -0.061 0.19 -10000 0 -0.63 104 104
DHH N/PTCH1 -0.09 0.24 -10000 0 -0.74 116 116
PIK3CA 0 0.009 -10000 0 -0.29 1 1
DHH -0.022 0.13 -10000 0 -0.79 30 30
PTHLH -0.081 0.38 -10000 0 -1.1 131 131
determination of left/right symmetry -0.035 0.26 -10000 0 -0.84 90 90
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
skeletal system development -0.079 0.37 -10000 0 -1 131 131
IHH N/Hhip -0.009 0.051 -10000 0 -0.53 3 3
DHH N/Hhip -0.019 0.1 -10000 0 -0.61 32 32
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.035 0.26 -10000 0 -0.84 90 90
pancreas development -0.003 0.041 -10000 0 -0.4 9 9
HHAT -0.001 0.024 -10000 0 -0.79 1 1
PI3K -0.008 0.068 -10000 0 -0.6 14 14
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.047 0.19 -10000 0 -0.79 65 65
somite specification -0.035 0.26 -10000 0 -0.84 90 90
SHH Np/Cholesterol/PTCH1 -0.071 0.2 -10000 0 -0.71 91 91
SHH Np/Cholesterol/PTCH2 -0.039 0.13 -10000 0 -0.48 82 82
SHH Np/Cholesterol/Megalin -0.14 0.21 -10000 0 -0.48 292 292
SHH 0.01 0.035 -10000 0 -0.61 1 1
catabolic process -0.047 0.26 -10000 0 -0.82 97 97
SMO/Vitamin D3 -0.075 0.22 -10000 0 -0.81 83 83
SHH Np/Cholesterol/Hhip -0.005 0.035 -10000 0 -0.49 3 3
LRP2 -0.22 0.35 -10000 0 -0.74 318 318
receptor-mediated endocytosis -0.15 0.25 -10000 0 -0.82 99 99
SHH Np/Cholesterol/BOC -0.039 0.13 -10000 0 -0.49 82 82
SHH Np/Cholesterol/CDO -0.009 0.059 -10000 0 -0.48 15 15
mesenchymal cell differentiation 0.005 0.035 0.48 3 -10000 0 3
mol:Vitamin D3 -0.03 0.22 -10000 0 -0.71 93 93
IHH N/PTCH2 -0.055 0.18 -10000 0 -0.66 85 85
CDON -0.01 0.089 -10000 0 -0.79 14 14
IHH N/PTCH1 -0.045 0.26 -10000 0 -0.83 97 97
Megalin/LRPAP1 -0.16 0.26 -10000 0 -0.6 291 291
PTCH2 -0.058 0.21 -10000 0 -0.79 81 81
SHH Np/Cholesterol -0.003 0.025 -10000 0 -0.49 1 1
PTCH1 -0.047 0.26 -10000 0 -0.82 97 97
HHIP -0.003 0.041 -10000 0 -0.4 9 9
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.053 0.2 -10000 0 -0.78 74 74
HRAS -0.003 0.028 -10000 0 -0.29 10 10
EGFR -0.29 0.38 -10000 0 -0.78 410 410
AKT 0.013 0.084 -10000 0 -0.57 20 20
FOXO3 -0.002 0.041 -10000 0 -0.79 3 3
AKT1 0 0 -10000 0 -10000 0 0
FOXO1 -0.009 0.082 -10000 0 -0.79 12 12
AKT3 -0.014 0.11 -10000 0 -0.79 20 20
FOXO4 0 0 -10000 0 -10000 0 0
MET -0.14 0.3 -10000 0 -0.78 189 189
PIK3CA 0 0.009 -10000 0 -0.29 1 1
PIK3CB 0 0 -10000 0 -10000 0 0
NRAS -0.001 0.013 -10000 0 -0.29 2 2
PIK3CG -0.013 0.099 -10000 0 -0.69 21 21
PIK3R3 0 0.009 -10000 0 -0.29 1 1
PIK3R2 0 0 -10000 0 -10000 0 0
NF1 -0.001 0.024 -10000 0 -0.79 1 1
RAS -0.095 0.16 0.25 1 -0.26 453 454
ERBB2 -0.024 0.083 -10000 0 -0.3 89 89
proliferation/survival/translation -0.004 0.059 0.28 14 -10000 0 14
PI3K -0.087 0.16 -10000 0 -0.26 420 420
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
KRAS -0.001 0.013 -10000 0 -0.29 2 2
FOXO 0.027 0.029 -10000 0 -0.49 1 1
AKT2 0 0 -10000 0 -10000 0 0
PTEN -0.001 0.034 -10000 0 -0.79 2 2
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.009 0.053 -10000 0 -0.42 14 14
adherens junction organization 0.032 0.061 -10000 0 -0.3 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.14 0.18 -10000 0 -0.37 412 412
FMN1 0.025 0.086 -10000 0 -0.44 21 21
mol:IP3 -0.009 0.05 -10000 0 -0.39 14 14
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.01 0.052 -10000 0 -0.31 29 29
CTNNB1 0.001 0.004 -10000 0 -10000 0 0
AKT1 -0.01 0.051 -10000 0 -0.38 14 14
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.013 0.079 -10000 0 -0.5 28 28
CTNND1 0.011 0.009 -10000 0 -0.29 1 1
mol:PI-4-5-P2 0.033 0.055 -10000 0 -10000 0 0
VASP 0.033 0.056 -10000 0 -10000 0 0
ZYX 0.033 0.056 -10000 0 -10000 0 0
JUB 0.032 0.062 -10000 0 -0.41 4 4
EGFR(dimer) -0.16 0.21 -10000 0 -0.42 406 406
E-cadherin/beta catenin-gamma catenin -0.013 0.081 -10000 0 -0.5 29 29
mol:PI-3-4-5-P3 -0.01 0.055 -10000 0 -0.4 14 14
PIK3CA 0.011 0.009 -10000 0 -0.29 1 1
PI3K -0.011 0.056 -10000 0 -0.41 14 14
FYN 0.04 0.055 -10000 0 -0.34 16 16
mol:Ca2+ -0.009 0.049 -10000 0 -0.38 14 14
JUP 0 0.026 -10000 0 -0.54 2 2
PIK3R1 0.001 0.09 -10000 0 -0.79 14 14
mol:DAG -0.009 0.05 -10000 0 -0.39 14 14
CDH1 -0.02 0.12 -10000 0 -0.79 28 28
RhoA/GDP -0.14 0.18 -10000 0 -0.37 412 412
establishment of polarity of embryonic epithelium 0.033 0.055 -10000 0 -10000 0 0
SRC 0 0.009 -10000 0 -0.29 1 1
RAC1 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
EGFR -0.29 0.38 -10000 0 -0.78 410 410
CASR 0.033 0.056 -10000 0 -0.36 14 14
RhoA/GTP -0.008 0.044 -10000 0 -0.34 14 14
AKT2 -0.01 0.051 -10000 0 -0.38 14 14
actin cable formation 0.032 0.084 -10000 0 -0.42 21 21
apoptosis 0.01 0.052 0.39 14 -10000 0 14
CTNNA1 0.012 0.002 -10000 0 -10000 0 0
mol:GDP -0.15 0.2 -10000 0 -0.4 412 412
PIP5K1A 0.033 0.056 -10000 0 -10000 0 0
PLCG1 -0.009 0.051 -10000 0 -0.4 14 14
Rac1/GTP -0.15 0.19 -10000 0 -0.39 406 406
homophilic cell adhesion 0.001 0.002 -10000 0 -10000 0 0
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.019 0.097 -9999 0 -0.51 37 37
NF kappa B1 p50/RelA/I kappa B alpha -0.043 0.11 -9999 0 -0.46 6 6
AP1 -0.19 0.25 -9999 0 -0.47 423 423
mol:PIP3 -0.2 0.24 -9999 0 -0.7 123 123
AKT1 -0.016 0.078 -9999 0 -0.59 10 10
PTK2B 0.014 0.062 -9999 0 -0.29 26 26
RHOA 0.028 0.028 -9999 0 -10000 0 0
PIK3CB 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.007 0.13 -9999 0 -0.35 128 128
MAGI3 -0.001 0.034 -9999 0 -0.79 2 2
RELA 0 0 -9999 0 -10000 0 0
apoptosis -0.062 0.15 -9999 0 -0.42 147 147
HRAS/GDP -0.002 0.019 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.019 0.14 -9999 0 -0.4 122 122
NF kappa B1 p50/RelA -0.053 0.14 -9999 0 -0.63 10 10
endothelial cell migration 0.007 0.12 -9999 0 -0.63 34 34
ADCY4 -0.004 0.15 -9999 0 -0.63 41 41
ADCY5 -0.071 0.19 -9999 0 -0.59 82 82
ADCY6 0.006 0.13 -9999 0 -0.6 31 31
ADCY7 0.006 0.13 -9999 0 -0.6 31 31
ADCY1 -0.003 0.14 -9999 0 -0.64 37 37
ADCY2 -0.015 0.16 -9999 0 -0.62 49 49
ADCY3 0.006 0.13 -9999 0 -0.6 31 31
ADCY8 0.003 0.13 -9999 0 -0.61 31 31
ADCY9 0.006 0.13 -9999 0 -0.6 31 31
GSK3B 0.021 0.059 -9999 0 -0.35 10 10
arachidonic acid secretion 0.009 0.13 -9999 0 -0.56 34 34
GNG2 -0.011 0.092 -9999 0 -0.79 15 15
TRIP6 -0.001 0.016 -9999 0 -0.51 1 1
GNAO1 -0.006 0.13 -9999 0 -0.52 56 56
HRAS -0.003 0.028 -9999 0 -0.29 10 10
NFKBIA -0.003 0.15 -9999 0 -0.39 128 128
GAB1 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly 0.001 0.004 -9999 0 -10000 0 0
JUN -0.005 0.063 -9999 0 -0.79 7 7
LPA/LPA2/NHERF2 -0.002 0.016 -9999 0 -10000 0 0
TIAM1 0.001 0.004 -9999 0 -10000 0 0
PIK3R1 -0.01 0.088 -9999 0 -0.79 14 14
mol:IP3 -0.007 0.13 -9999 0 -0.35 128 128
PLCB3 0.026 0.016 -9999 0 -10000 0 0
FOS -0.24 0.36 -9999 0 -0.79 329 329
positive regulation of mitosis 0.009 0.13 -9999 0 -0.56 34 34
LPA/LPA1-2-3 -0.073 0.17 -9999 0 -0.49 147 147
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
stress fiber formation 0.002 0.1 -9999 0 -0.38 25 25
GNAZ 0.008 0.1 -9999 0 -0.48 43 43
EGFR/PI3K-beta/Gab1 -0.2 0.26 -9999 0 -0.74 123 123
positive regulation of dendritic cell cytokine production -0.072 0.17 -9999 0 -0.48 147 147
LPA/LPA2/MAGI-3 -0.002 0.025 -9999 0 -0.52 2 2
ARHGEF1 -0.011 0.069 -9999 0 -0.44 24 24
GNAI2 0.013 0.087 -9999 0 -0.46 34 34
GNAI3 0.013 0.087 -9999 0 -0.46 34 34
GNAI1 -0.018 0.16 -9999 0 -0.53 89 89
LPA/LPA3 -0.08 0.2 -9999 0 -0.6 128 128
LPA/LPA2 -0.002 0.016 -9999 0 -10000 0 0
LPA/LPA1 -0.017 0.096 -9999 0 -0.54 34 34
HB-EGF/EGFR -0.26 0.25 -9999 0 -0.57 405 405
HBEGF -0.071 0.11 -9999 0 -0.6 3 3
mol:DAG -0.007 0.13 -9999 0 -0.35 128 128
cAMP biosynthetic process -0.012 0.15 -9999 0 -0.56 55 55
NFKB1 0 0 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -0.29 1 1
GNB1 0 0 -9999 0 -10000 0 0
LYN -0.003 0.15 -9999 0 -0.46 14 14
GNAQ -0.053 0.13 -9999 0 -0.41 131 131
LPAR2 -0.001 0.015 -9999 0 -0.29 2 2
LPAR3 -0.1 0.26 -9999 0 -0.79 128 128
LPAR1 -0.019 0.12 -9999 0 -0.79 24 24
IL8 -0.19 0.23 -9999 0 -0.44 432 432
PTK2 -0.066 0.16 -9999 0 -0.45 147 147
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.062 0.15 -9999 0 -0.42 147 147
EGFR -0.29 0.38 -9999 0 -0.78 410 410
PLCG1 -0.029 0.15 -9999 0 -0.42 128 128
PLD2 -0.066 0.16 -9999 0 -0.45 147 147
G12/G13 -0.013 0.074 -9999 0 -0.48 24 24
PI3K-beta -0.019 0.093 -9999 0 -0.72 10 10
cell migration -0.021 0.053 -9999 0 -0.24 5 5
SLC9A3R2 -0.001 0.02 -9999 0 -0.29 5 5
PXN 0.002 0.1 -9999 0 -0.39 25 25
HRAS/GTP -0.035 0.12 -9999 0 -0.58 34 34
RAC1 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.15 -9999 0 -0.29 483 483
PRKCE 0.01 0.002 -9999 0 -10000 0 0
PRKCD 0.001 0.12 -9999 0 -0.54 2 2
Gi(beta/gamma) -0.037 0.12 -9999 0 -0.58 39 39
mol:LPA -0.002 0.021 -9999 0 -0.22 10 10
TRIP6/p130 Cas/FAK1/Paxillin -0.055 0.14 -9999 0 -0.68 9 9
MAPKKK cascade 0.009 0.13 -9999 0 -0.56 34 34
contractile ring contraction involved in cytokinesis 0.028 0.028 -9999 0 -0.23 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.057 0.14 -9999 0 -0.42 136 136
GNA15 -0.053 0.13 -9999 0 -0.41 129 129
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
MAPT -0.021 0.15 -9999 0 -0.42 122 122
GNA11 -0.053 0.13 -9999 0 -0.41 132 132
Rac1/GTP 0.001 0.005 -9999 0 -10000 0 0
MMP2 0.007 0.12 -9999 0 -0.63 34 34
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.12 0.18 -9999 0 -0.39 330 330
MAP3K8 0.001 0.073 -9999 0 -0.74 10 10
FOS -0.035 0.14 -9999 0 -0.46 41 41
PRKCA -0.013 0.13 -9999 0 -0.76 31 31
PTPN7 -0.009 0.073 -9999 0 -0.3 63 63
HRAS -0.003 0.028 -9999 0 -0.3 10 10
PRKCB -0.011 0.12 -9999 0 -0.55 39 39
NRAS -0.001 0.013 -9999 0 -0.3 2 2
RAS family/GTP -0.002 0.015 -9999 0 -10000 0 0
MAPK3 -0.008 0.073 -9999 0 -0.25 35 35
MAP2K1 -0.013 0.14 -9999 0 -0.57 53 53
ELK1 -0.003 0.01 -9999 0 -0.29 1 1
BRAF -0.033 0.12 -9999 0 -0.57 48 48
mol:GTP -0.002 0.003 -9999 0 -0.006 329 329
MAPK1 -0.008 0.073 -9999 0 -0.25 35 35
RAF1 -0.033 0.12 -9999 0 -0.57 48 48
KRAS -0.001 0.012 -9999 0 -0.29 2 2
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.029 0.031 -9999 0 -10000 0 0
BUB1B -0.041 0.053 -9999 0 -10000 0 0
PLK1 -0.008 0.024 -9999 0 -10000 0 0
PLK1S1 0 0.014 -9999 0 -10000 0 0
KIF2A 0.002 0.021 -9999 0 -10000 0 0
regulation of mitotic centrosome separation -0.008 0.024 -9999 0 -10000 0 0
GOLGA2 0 0 -9999 0 -10000 0 0
Hec1/SPC24 -0.17 0.12 -9999 0 -0.28 534 534
WEE1 -0.002 0.024 -9999 0 -10000 0 0
cytokinesis -0.056 0.058 -9999 0 -0.26 21 21
PP2A-alpha B56 0.027 0.019 -9999 0 -10000 0 0
AURKA 0 0.015 -9999 0 -10000 0 0
PICH/PLK1 -0.072 0.098 -9999 0 -0.34 11 11
CENPE -0.053 0.087 -9999 0 -0.18 179 179
RhoA/GTP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.002 0.021 -9999 0 -10000 0 0
PPP2CA 0 0 -9999 0 -10000 0 0
FZR1 0 0 -9999 0 -10000 0 0
TPX2 -0.006 0.017 -9999 0 -10000 0 0
PAK1 -0.006 0.043 -9999 0 -0.29 25 25
SPC24 -0.18 0.14 -9999 0 -0.29 689 689
FBXW11 0 0 -9999 0 -10000 0 0
CLSPN -0.006 0.019 -9999 0 -10000 0 0
GORASP1 0 0 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NLP -0.005 0.013 -9999 0 -0.052 2 2
G2 phase of mitotic cell cycle -0.001 0.002 -9999 0 -10000 0 0
STAG2 -0.001 0.024 -9999 0 -0.79 1 1
GRASP65/GM130/RAB1/GTP 0.008 0.009 -9999 0 -10000 0 0
spindle elongation -0.008 0.024 -9999 0 -10000 0 0
ODF2 0.002 0.004 -9999 0 -10000 0 0
BUB1 0.021 0.015 -9999 0 -10000 0 0
TPT1 0 0.014 -9999 0 -10000 0 0
CDC25C -0.009 0.017 -9999 0 -10000 0 0
CDC25B 0.005 0.041 -9999 0 -0.29 20 20
SGOL1 -0.029 0.031 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.021 0.044 -9999 0 -10000 0 0
CDC14B -0.01 0.11 -9999 0 -0.62 36 36
CDC20 -0.16 0.15 -9999 0 -0.29 588 588
PLK1/PBIP1 -0.028 0.053 -9999 0 -0.18 4 4
mitosis -0.006 0.007 -9999 0 -0.022 2 2
FBXO5 0 0.023 -9999 0 -10000 0 0
CDC2 -0.001 0.002 -9999 0 -10000 0 0
NDC80 -0.18 0.14 -9999 0 -0.29 662 662
metaphase plate congression -0.002 0.016 -9999 0 -10000 0 0
ERCC6L -0.064 0.089 -9999 0 -0.29 11 11
NLP/gamma Tubulin -0.001 0.014 -9999 0 -10000 0 0
microtubule cytoskeleton organization 0 0.014 -9999 0 -10000 0 0
G2/M transition DNA damage checkpoint -0.001 0.001 -9999 0 -10000 0 0
PPP1R12A 0 0 -9999 0 -10000 0 0
interphase -0.001 0.001 -9999 0 -10000 0 0
PLK1/PRC1-2 -0.14 0.1 -9999 0 -0.29 274 274
GRASP65/GM130/RAB1/GTP/PLK1 -0.002 0.004 -9999 0 -10000 0 0
RAB1A 0 0 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
Aurora A/BORA -0.003 0.024 -9999 0 -10000 0 0
mitotic prometaphase -0.002 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.014 0.051 -9999 0 -0.3 25 25
microtubule-based process -0.12 0.069 -9999 0 -0.18 218 218
Golgi organization -0.008 0.024 -9999 0 -10000 0 0
Cohesin/SA2 -0.01 0.018 -9999 0 -0.45 1 1
PPP1CB/MYPT1 0 0 -9999 0 -10000 0 0
KIF20A -0.22 0.13 -9999 0 -0.29 820 820
APC/C/CDC20 -0.088 0.081 -9999 0 -0.2 7 7
PPP2R1A 0 0 -9999 0 -10000 0 0
chromosome segregation -0.028 0.052 -9999 0 -0.18 4 4
PRC1 -0.074 0.13 -9999 0 -0.29 275 275
ECT2 -0.004 0.039 -9999 0 -0.17 38 38
C13orf34 -0.001 0.022 -9999 0 -10000 0 0
NUDC -0.002 0.016 -9999 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.04 0.052 -9999 0 -10000 0 0
spindle assembly -0.004 0.02 -9999 0 -10000 0 0
spindle stabilization 0 0.014 -9999 0 -10000 0 0
APC/C/HCDH1 -0.017 0.094 -9999 0 -0.53 36 36
MKLP2/PLK1 -0.12 0.069 -9999 0 -0.18 218 218
CCNB1 -0.05 0.12 -9999 0 -0.29 221 221
PPP1CB 0 0 -9999 0 -10000 0 0
BTRC 0 0 -9999 0 -10000 0 0
ROCK2 -0.01 0.089 -9999 0 -0.51 32 32
TUBG1 0 0.014 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.024 0.041 -9999 0 -10000 0 0
MLF1IP -0.025 0.074 -9999 0 -0.2 2 2
INCENP 0.002 0.004 -9999 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.003 0.048 -9999 0 -0.79 4 4
alphaV beta3 Integrin -0.021 0.11 -9999 0 -0.6 37 37
PTK2 -0.066 0.19 -9999 0 -0.57 122 122
positive regulation of JNK cascade -0.038 0.11 -9999 0 -0.34 122 122
CDC42/GDP -0.001 0.16 -9999 0 -0.46 122 122
Rac1/GDP 0.001 0.16 -9999 0 -0.45 122 122
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
CDC42/GTP -0.047 0.13 -9999 0 -0.42 122 122
nectin-3/I-afadin -0.069 0.2 -9999 0 -0.62 122 122
RAPGEF1 -0.01 0.18 -9999 0 -0.52 122 122
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.024 0.21 -9999 0 -0.61 122 122
PDGFB-D/PDGFRB -0.003 0.047 -9999 0 -0.79 4 4
TLN1 0 0.1 -9999 0 -0.54 15 15
Rap1/GTP -0.041 0.11 -9999 0 -0.36 122 122
IQGAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.003 0.035 -9999 0 -0.48 6 6
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.069 0.2 -9999 0 -0.62 122 122
PVR 0 0.009 -9999 0 -0.29 1 1
Necl-5(dimer) 0 0.009 -9999 0 -0.29 1 1
mol:GDP -0.013 0.2 -9999 0 -0.58 122 122
MLLT4 -0.005 0.059 -9999 0 -0.72 7 7
PIK3CA 0 0.009 -9999 0 -0.29 1 1
PI3K -0.058 0.17 -9999 0 -0.5 128 128
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.003 0.045 -9999 0 -0.6 6 6
positive regulation of lamellipodium assembly -0.04 0.11 -9999 0 -0.35 122 122
PVRL1 0 0 -9999 0 -10000 0 0
PVRL3 -0.087 0.25 -9999 0 -0.79 121 121
PVRL2 -0.001 0.015 -9999 0 -0.29 3 3
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
CDH1 -0.02 0.12 -9999 0 -0.79 28 28
CLDN1 -0.036 0.15 -9999 0 -0.58 68 68
JAM-A/CLDN1 -0.074 0.18 -9999 0 -0.51 154 154
SRC -0.078 0.22 -9999 0 -0.69 122 122
ITGB3 -0.028 0.14 -9999 0 -0.79 37 37
nectin-1(dimer)/I-afadin/I-afadin -0.003 0.045 -9999 0 -0.6 6 6
FARP2 -0.018 0.2 -9999 0 -0.57 122 122
RAC1 0 0 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.06 0.17 -9999 0 -0.54 122 122
nectin-1/I-afadin -0.003 0.045 -9999 0 -0.6 6 6
nectin-2/I-afadin -0.004 0.046 -9999 0 -0.6 6 6
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.06 0.17 -9999 0 -0.54 122 122
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.038 0.11 -9999 0 -0.34 122 122
alphaV/beta3 Integrin/Talin -0.04 0.13 -9999 0 -0.61 42 42
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.004 0.046 -9999 0 -0.6 6 6
nectin-2(dimer)/I-afadin/I-afadin -0.004 0.046 -9999 0 -0.6 6 6
PIP5K1C -0.033 0.1 -9999 0 -0.29 126 126
VAV2 -0.02 0.2 -9999 0 -0.58 122 122
RAP1/GDP -0.048 0.13 -9999 0 -0.42 122 122
ITGAV 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.06 0.17 -9999 0 -0.54 122 122
nectin-3(dimer)/I-afadin/I-afadin -0.069 0.2 -9999 0 -0.62 122 122
Rac1/GTP -0.049 0.14 -9999 0 -0.44 122 122
PTPRM -0.037 0.12 -9999 0 -0.32 126 126
E-cadherin/beta catenin/alpha catenin -0.013 0.074 -9999 0 -0.43 33 33
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
Visual signal transduction: Cones

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin -0.007 0.054 -9999 0 -0.45 15 15
RGS9BP -0.019 0.072 -9999 0 -0.29 70 70
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.003 0.029 -9999 0 -0.29 11 11
mol:Na + -0.02 0.053 -9999 0 -10000 0 0
mol:ADP 0.007 0.028 -9999 0 -10000 0 0
GNAT2 -0.001 0.018 -9999 0 -0.29 4 4
RGS9-1/Gbeta5/R9AP -0.061 0.16 -9999 0 -0.53 106 106
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.015 -9999 0 -10000 0 0
GRK7 -0.002 0.026 -9999 0 -0.29 9 9
CNGB3 -0.01 0.054 -9999 0 -0.29 39 39
Cone Metarhodopsin II/X-Arrestin -0.001 0.017 -9999 0 -10000 0 0
mol:Ca2+ -0.092 0.088 -9999 0 -0.28 39 39
Cone PDE6 -0.053 0.14 -9999 0 -0.46 106 106
Cone Metarhodopsin II -0.003 0.019 -9999 0 -10000 0 0
Na + (4 Units) -0.097 0.082 -9999 0 -10000 0 0
GNAT2/GDP -0.052 0.14 -9999 0 -0.45 106 106
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.011 0.016 -9999 0 -10000 0 0
Cone Transducin -0.008 0.057 -9999 0 -0.48 15 15
SLC24A2 -0.17 0.14 -9999 0 -0.29 649 649
GNB3/GNGT2 -0.009 0.071 -9999 0 -0.6 15 15
GNB3 -0.011 0.088 -9999 0 -0.63 19 19
GNAT2/GTP -0.001 0.012 -9999 0 -10000 0 0
CNGA3 -0.028 0.086 -9999 0 -0.29 103 103
ARR3 -0.002 0.025 -9999 0 -0.29 8 8
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.02 0.053 -9999 0 -10000 0 0
mol:Pi -0.061 0.16 -9999 0 -0.52 106 106
Cone CNG Channel -0.016 0.04 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.17 0.14 -9999 0 -0.29 649 649
RGS9 -0.08 0.23 -9999 0 -0.73 121 121
PDE6C 0 0.009 -9999 0 -10000 0 0
GNGT2 -0.001 0.034 -9999 0 -0.79 2 2
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.002 0.022 -9999 0 -0.29 6 6
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A -0.001 0.034 -9999 0 -0.79 2 2
LAT2 -0.063 0.14 -9999 0 -0.53 51 51
AP1 -0.15 0.21 -9999 0 -0.57 154 154
mol:PIP3 -0.027 0.2 -9999 0 -0.5 99 99
IKBKB 0.002 0.12 -9999 0 -0.32 54 54
AKT1 -0.082 0.17 -9999 0 -0.68 44 44
IKBKG 0.002 0.12 -9999 0 -0.32 54 54
MS4A2 -0.069 0.22 -9999 0 -0.79 94 94
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.3 1 1
MAP3K1 0.005 0.13 -9999 0 -0.45 43 43
mol:Ca2+ -0.013 0.15 -9999 0 -0.36 99 99
LYN 0.011 0.004 -9999 0 -10000 0 0
CBLB -0.062 0.14 -9999 0 -0.57 42 42
SHC1 0 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.062 0.16 -9999 0 -0.48 142 142
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0 0 -9999 0 -10000 0 0
PLD2 -0.096 0.2 -9999 0 -0.48 217 217
PTPN13 -0.031 0.17 -9999 0 -0.6 49 49
PTPN11 0.01 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.006 0.15 -9999 0 -0.41 45 45
SYK 0.011 0.01 -9999 0 -0.29 1 1
GRB2 0 0.009 -9999 0 -0.29 1 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.086 0.18 -9999 0 -0.51 99 99
LAT -0.064 0.14 -9999 0 -0.58 43 43
PAK2 -0.004 0.14 -9999 0 -0.51 42 42
NFATC2 -0.1 0.24 -9999 0 -0.69 130 130
HRAS -0.014 0.15 -9999 0 -0.55 45 45
GAB2 -0.004 0.042 -9999 0 -0.39 10 10
PLA2G1B 0.028 0.018 -9999 0 -10000 0 0
Fc epsilon R1 -0.12 0.25 -9999 0 -0.6 217 217
Antigen/IgE/Fc epsilon R1 -0.11 0.23 -9999 0 -0.55 217 217
mol:GDP -0.02 0.16 -9999 0 -0.56 45 45
JUN -0.005 0.063 -9999 0 -0.79 7 7
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
FOS -0.24 0.36 -9999 0 -0.79 329 329
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.067 0.15 -9999 0 -0.46 95 95
CHUK 0.002 0.12 -9999 0 -0.32 54 54
KLRG1 -0.062 0.14 -9999 0 -0.55 43 43
VAV1 -0.064 0.14 -9999 0 -0.58 45 45
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.062 0.14 -9999 0 -0.57 42 42
negative regulation of mast cell degranulation -0.056 0.12 -9999 0 -0.51 43 43
BTK -0.061 0.14 -9999 0 -0.57 42 42
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.086 0.2 -9999 0 -0.47 166 166
GAB2/PI3K/SHP2 -0.091 0.19 -9999 0 -0.74 47 47
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.069 0.16 -9999 0 -0.68 42 42
RAF1 0.015 0.022 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.1 0.22 -9999 0 -0.54 173 173
FCER1G 0.003 0.012 -9999 0 -10000 0 0
FCER1A -0.11 0.29 -9999 0 -0.8 161 161
Antigen/IgE/Fc epsilon R1/Fyn -0.1 0.22 -9999 0 -0.51 217 217
MAPK3 0.026 0.019 -9999 0 -10000 0 0
MAPK1 0.026 0.019 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 0.009 0.081 -9999 0 -0.68 10 10
DUSP1 -0.1 0.26 -9999 0 -0.79 142 142
NF-kappa-B/RelA -0.027 0.054 -9999 0 -0.23 6 6
actin cytoskeleton reorganization -0.027 0.15 -9999 0 -0.56 41 41
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.059 0.14 -9999 0 -0.55 46 46
FER -0.066 0.15 -9999 0 -0.58 50 50
RELA 0 0 -9999 0 -10000 0 0
ITK -0.035 0.11 -9999 0 -0.6 39 39
SOS1 0 0 -9999 0 -10000 0 0
PLCG1 -0.017 0.16 -9999 0 -0.58 44 44
cytokine secretion -0.019 0.04 -9999 0 -10000 0 0
SPHK1 -0.065 0.14 -9999 0 -0.58 46 46
PTK2 -0.029 0.16 -9999 0 -0.59 41 41
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.089 0.19 -9999 0 -0.54 99 99
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.022 0.2 -9999 0 -0.58 56 56
MAP2K2 0.023 0.019 -9999 0 -10000 0 0
MAP2K1 0.023 0.019 -9999 0 -10000 0 0
MAP2K7 0 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.057 0.13 -9999 0 -0.51 43 43
MAP2K4 0.017 0.033 -9999 0 -1 1 1
Fc epsilon R1/FcgammaRIIB -0.11 0.23 -9999 0 -0.55 219 219
mol:Choline -0.094 0.2 -9999 0 -0.47 217 217
SHC/Grb2/SOS1 -0.056 0.13 -9999 0 -0.54 41 41
FYN -0.001 0.034 -9999 0 -0.79 2 2
DOK1 -0.001 0.018 -9999 0 -0.29 4 4
PXN -0.019 0.15 -9999 0 -0.54 40 40
HCLS1 -0.062 0.14 -9999 0 -0.57 42 42
PRKCB -0.015 0.16 -9999 0 -0.38 105 105
FCGR2B -0.004 0.054 -9999 0 -0.7 6 6
IGHE 0 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.057 0.13 -9999 0 -0.52 43 43
LCP2 0 0.009 -9999 0 -0.29 1 1
PLA2G4A -0.11 0.21 -9999 0 -0.55 166 166
RASA1 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.094 0.2 -9999 0 -0.47 217 217
IKK complex 0.019 0.093 -9999 0 -0.23 51 51
WIPF1 0 0 -9999 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.54 0.36 -9999 0 -0.79 751 751
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 -0.007 0.045 -9999 0 -0.29 27 27
TCEB1 -0.001 0.015 -9999 0 -0.29 3 3
HIF1A/p53 -0.001 0.005 -9999 0 -10000 0 0
HIF1A -0.002 0.008 -9999 0 -10000 0 0
COPS5 0 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.003 0.018 -9999 0 -10000 0 0
FIH (dimer) 0 0 -9999 0 -10000 0 0
CDKN2A -0.05 0.11 -9999 0 -0.29 188 188
ARNT/IPAS -0.41 0.28 -9999 0 -0.6 751 751
HIF1AN 0 0 -9999 0 -10000 0 0
GNB2L1 0 0 -9999 0 -10000 0 0
HIF1A/ARNT -0.001 0.005 -9999 0 -10000 0 0
CUL2 0 0 -9999 0 -10000 0 0
OS9 -0.001 0.013 -9999 0 -0.29 2 2
RACK1/Elongin B/Elongin C -0.004 0.024 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.001 0.006 -9999 0 -10000 0 0
PHD1-3/OS9 -0.011 0.039 -9999 0 -0.47 2 2
HIF1A/RACK1/Elongin B/Elongin C -0.003 0.016 -9999 0 -10000 0 0
VHL 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
HIF1A/JAB1 -0.001 0.005 -9999 0 -10000 0 0
EGLN3 -0.023 0.081 -9999 0 -0.3 83 83
EGLN2 -0.002 0.022 -9999 0 -0.29 6 6
EGLN1 -0.001 0.024 -9999 0 -0.79 1 1
TP53 0 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.001 0.005 -9999 0 -10000 0 0
ARNT 0 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.019 0.04 -9999 0 -10000 0 0
Rapid glucocorticoid 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
Gs family/GDP/Gbeta gamma -0.11 0.2 -10000 0 -0.47 262 262
MAPK9 0.008 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.001 0.022 -10000 0 -0.2 13 13
GNB1/GNG2 -0.007 0.061 -10000 0 -0.52 15 15
GNB1 0 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.008 0 -10000 0 -10000 0 0
Gs family/GTP -0.12 0.21 -10000 0 -0.49 258 258
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.027 0.048 0.11 258 -10000 0 258
GNAL -0.19 0.33 -10000 0 -0.79 258 258
GNG2 -0.011 0.092 -10000 0 -0.79 15 15
CRH -0.003 0.032 -10000 0 -0.29 13 13
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.005 0.041 -10000 0 -0.44 9 9
MAPK11 0.007 0.024 -10000 0 -0.44 3 3
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.005 0.056 -10000 0 -0.67 5 5
HDAC1 0.002 0.008 -10000 0 -10000 0 0
AES 0.001 0.004 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
DTX1 -0.07 0.22 -10000 0 -0.79 97 97
LRP6/FZD1 0 0.006 -10000 0 -10000 0 0
TLE1 -0.005 0.067 -10000 0 -0.79 8 8
AP1 -0.11 0.17 -10000 0 -0.36 332 332
NCSTN 0 0 -10000 0 -10000 0 0
ADAM10 -0.003 0.048 -10000 0 -0.79 4 4
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.008 0.044 -10000 0 -0.34 1 1
NICD/RBPSUH -0.003 0.042 -10000 0 -0.7 4 4
WIF1 -0.41 0.39 -10000 0 -0.78 581 581
NOTCH1 -0.003 0.045 -10000 0 -0.74 4 4
PSENEN -0.001 0.013 -10000 0 -10000 0 0
KREMEN2 -0.14 0.15 -10000 0 -0.29 527 527
DKK1 -0.08 0.19 -10000 0 -0.42 206 206
beta catenin/beta TrCP1 -0.002 0.029 -10000 0 -10000 0 0
APH1B -0.001 0.024 -10000 0 -0.79 1 1
APH1A 0 0 -10000 0 -10000 0 0
AXIN1 0.003 0.015 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.003 0.039 -10000 0 -0.33 8 8
PSEN1 0 0 -10000 0 -10000 0 0
FOS -0.24 0.36 -10000 0 -0.79 329 329
JUN -0.005 0.063 -10000 0 -0.79 7 7
MAP3K7 0.001 0.01 -10000 0 -0.3 1 1
CTNNB1 -0.002 0.034 0.23 2 -10000 0 2
MAPK3 0 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.085 0.12 -10000 0 -0.61 33 33
HNF1A -0.001 0.025 -10000 0 -0.29 8 8
CTBP1 0.001 0.004 -10000 0 -10000 0 0
MYC -0.032 0.22 -10000 0 -1.5 24 24
NKD1 -0.009 0.069 -10000 0 -0.42 24 24
FZD1 0 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.041 0.13 -10000 0 -0.44 101 101
apoptosis -0.11 0.17 -10000 0 -0.36 332 332
Delta 1/NOTCHprecursor -0.005 0.055 -10000 0 -0.53 11 11
DLL1 -0.005 0.063 -10000 0 -0.79 7 7
PPARD -0.001 0.013 -10000 0 -10000 0 0
Gamma Secretase -0.001 0.014 -10000 0 -0.44 1 1
APC 0.003 0.015 -10000 0 -10000 0 0
DVL1 -0.037 0.035 -10000 0 -10000 0 0
CSNK2A1 0.011 0.003 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.12 0.14 -10000 0 -0.57 55 55
LRP6 0 0.009 -10000 0 -0.29 1 1
CSNK1A1 0.011 0.003 -10000 0 -10000 0 0
NLK 0.002 0.01 -10000 0 -10000 0 0
CCND1 -0.012 0.094 -10000 0 -1.5 4 4
WNT1 -0.001 0.013 -10000 0 -0.29 2 2
Axin1/APC/beta catenin 0.011 0.037 -10000 0 -10000 0 0
DKK2 -0.024 0.14 -10000 0 -0.76 35 35
NOTCH1 precursor/DVL1 -0.018 0.041 -10000 0 -0.64 4 4
GSK3B 0.001 0.003 -10000 0 -10000 0 0
FRAT1 0.001 0.004 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.041 0.13 -10000 0 -0.67 5 5
PPP2R5D -0.015 0.037 0.35 6 -10000 0 6
MAPK1 0 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.24 0.23 -10000 0 -0.47 566 566
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.014 0.004 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0 0 -10000 0 -10000 0 0
HDAC4 -0.001 0.024 -10000 0 -0.79 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.011 0.076 0.6 1 -10000 0 1
CDKN1A -0.002 0.04 -10000 0 -0.94 2 2
KAT2B -0.001 0.024 -10000 0 -0.79 1 1
BAX -0.001 0.018 -10000 0 -0.29 4 4
FOXO3 -0.001 0.017 -10000 0 -0.33 3 3
FOXO1 -0.009 0.082 -10000 0 -0.79 12 12
FOXO4 0.022 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0 0 -10000 0 -10000 0 0
TAT -0.56 0.35 -10000 0 -0.77 788 788
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.01 0.029 -10000 0 -0.6 1 1
PPARGC1A -0.17 0.32 -10000 0 -0.76 241 241
FHL2 -0.004 0.054 -10000 0 -0.7 6 6
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0.007 -10000 0 -10000 0 0
HIST2H4A -0.011 0.076 -10000 0 -0.6 1 1
SIRT1/FOXO3a 0 0.014 -10000 0 -0.25 3 3
SIRT1 0 0.009 0.21 2 -10000 0 2
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0.017 -10000 0 -0.52 1 1
SIRT1/Histone H1b -0.003 0.012 -10000 0 -10000 0 0
apoptosis 0 0.011 -10000 0 -10000 0 0
SIRT1/PGC1A -0.11 0.21 -10000 0 -0.52 230 230
p53/SIRT1 0.001 0.019 0.43 2 -10000 0 2
SIRT1/FOXO4 0 0.007 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.007 0.059 -10000 0 -0.48 17 17
HIST1H1E 0.015 0.022 -10000 0 -10000 0 0
SIRT1/p300 0 0.007 -10000 0 -10000 0 0
muscle cell differentiation 0.002 0.023 0.51 1 -10000 0 1
TP53 0 0.009 0.21 2 -10000 0 2
KU70/SIRT1/BAX 0 0.011 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
MEF2D 0 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.42 0.27 -10000 0 -0.6 760 760
ACSS2 0.02 0.019 -10000 0 -0.6 1 1
SIRT1/PCAF/MYOD -0.002 0.023 -10000 0 -0.52 1 1
FAS signaling pathway (CD95)

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
SPTAN1 0.011 0.052 0.28 37 -10000 0 37
RFC1 0.011 0.052 0.28 38 -10000 0 38
PRKDC 0.01 0.053 0.28 37 -10000 0 37
RIPK1 0 0.001 -10000 0 -10000 0 0
CASP7 -0.023 0.037 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 -0.017 0.067 0.25 17 -0.38 18 35
MAP2K4 -0.058 0.16 -10000 0 -0.5 22 22
mol:ceramide -0.032 0.12 -10000 0 -0.55 22 22
GSN 0.004 0.076 0.28 37 -0.49 14 51
FASLG/FAS/FADD/FAF1/Caspase 8 -0.031 0.074 0.23 14 -0.46 18 32
FAS 0.003 0.06 -10000 0 -0.8 6 6
BID 0.001 0.015 0.32 2 -10000 0 2
MAP3K1 -0.021 0.094 -10000 0 -0.3 11 11
MAP3K7 0.006 0.011 -10000 0 -0.29 1 1
RB1 0.01 0.052 0.28 36 -0.29 1 37
CFLAR -0.001 0.023 -10000 0 -0.76 1 1
HGF/MET -0.14 0.26 -10000 0 -0.58 256 256
ARHGDIB 0.01 0.053 0.28 39 -10000 0 39
FADD 0.003 0.037 -10000 0 -0.31 15 15
actin filament polymerization -0.004 0.076 0.49 14 -0.28 37 51
NFKB1 -0.076 0.1 -10000 0 -0.33 1 1
MAPK8 -0.12 0.24 -10000 0 -0.43 403 403
DFFA 0.011 0.052 0.28 37 -10000 0 37
DNA fragmentation during apoptosis 0.01 0.052 0.28 37 -10000 0 37
FAS/FADD/MET -0.096 0.21 -10000 0 -0.55 190 190
CFLAR/RIP1 -0.001 0.017 -10000 0 -0.56 1 1
FAIM3 -0.002 0.056 -10000 0 -0.33 27 27
FAF1 0.008 0.006 -10000 0 -10000 0 0
PARP1 0.01 0.052 0.28 39 -10000 0 39
DFFB 0.011 0.052 0.28 37 -10000 0 37
CHUK -0.066 0.088 -10000 0 -10000 0 0
FASLG -0.015 0.11 -10000 0 -0.42 58 58
FAS/FADD -0.006 0.053 -10000 0 -0.64 6 6
HGF -0.053 0.2 -10000 0 -0.79 73 73
LMNA 0.01 0.047 0.26 37 -10000 0 37
CASP6 0.01 0.052 0.28 39 -10000 0 39
CASP10 0.005 0.049 -10000 0 -0.8 4 4
CASP3 0.013 0.063 0.34 39 -10000 0 39
PTPN13 -0.023 0.13 -10000 0 -0.79 32 32
CASP8 0.003 0.023 0.45 2 -10000 0 2
IL6 -0.47 0.67 -10000 0 -1.4 400 400
MET -0.14 0.3 -10000 0 -0.78 189 189
ICAD/CAD 0.01 0.048 0.26 37 -10000 0 37
FASLG/FAS/FADD/FAF1/Caspase 10 -0.033 0.12 -10000 0 -0.56 22 22
activation of caspase activity by cytochrome c 0.001 0.015 0.32 2 -10000 0 2
PAK2 0.01 0.052 0.28 37 -10000 0 37
BCL2 -0.022 0.14 -10000 0 -0.79 37 37
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.009 0.052 -10000 0 -0.32 29 29
epithelial cell differentiation -0.011 0.069 -10000 0 -0.44 28 28
CYFIP2 -0.01 0.065 -10000 0 -0.36 31 31
ENAH 0.058 0.057 -10000 0 -10000 0 0
EGFR -0.29 0.38 -10000 0 -0.78 410 410
EPHA2 -0.004 0.058 -10000 0 -0.79 6 6
MYO6 -0.011 0.067 -10000 0 -0.42 29 29
CTNNB1 0 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.005 0.038 -10000 0 -0.52 4 4
AQP5 -0.23 0.29 -10000 0 -0.58 428 428
CTNND1 0 0.009 -10000 0 -0.29 1 1
mol:PI-4-5-P2 -0.011 0.065 -10000 0 -0.41 28 28
regulation of calcium-dependent cell-cell adhesion -0.032 0.11 -10000 0 -0.41 85 85
EGF -0.15 0.31 -10000 0 -0.78 214 214
NCKAP1 0 0 -10000 0 -10000 0 0
AQP3 -0.037 0.14 -10000 0 -0.52 80 80
cortical microtubule organization -0.011 0.069 -10000 0 -0.44 28 28
GO:0000145 0.027 0.068 -10000 0 -0.39 28 28
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.011 0.07 -10000 0 -0.44 28 28
MLLT4 -0.005 0.059 -10000 0 -0.72 7 7
ARF6/GDP -0.011 0.059 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.036 -10000 0 -0.47 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.037 0.071 -10000 0 -0.38 28 28
PVRL2 -0.001 0.015 -10000 0 -0.29 3 3
ZYX -0.011 0.066 -10000 0 -0.42 28 28
ARF6/GTP -0.003 0.033 -10000 0 -0.43 6 6
CDH1 -0.02 0.12 -10000 0 -0.79 28 28
EGFR/EGFR/EGF/EGF -0.24 0.26 -10000 0 -0.46 562 562
RhoA/GDP -0.011 0.065 -10000 0 -0.41 28 28
actin cytoskeleton organization 0.033 0.07 -10000 0 -0.39 29 29
IGF-1R heterotetramer -0.02 0.12 -10000 0 -0.59 36 36
GIT1 -0.001 0.02 -10000 0 -0.29 5 5
IGF1R -0.02 0.12 -10000 0 -0.6 36 36
IGF1 -0.18 0.33 -10000 0 -0.79 247 247
DIAPH1 -0.002 0.043 -10000 0 -0.69 4 4
Wnt receptor signaling pathway 0.011 0.069 0.44 28 -10000 0 28
RHOA 0 0 -10000 0 -10000 0 0
RhoA/GTP -0.011 0.06 -10000 0 -10000 0 0
CTNNA1 0 0 -10000 0 -10000 0 0
VCL 0.033 0.072 -10000 0 -0.4 29 29
EFNA1 0 0.009 -10000 0 -0.29 1 1
LPP 0.031 0.078 -10000 0 -0.39 36 36
Ephrin A1/EPHA2 -0.012 0.069 -10000 0 -0.4 34 34
SEC6/SEC8 -0.012 0.065 -10000 0 -0.74 1 1
MGAT3 -0.033 0.11 -10000 0 -0.42 85 85
HGF/MET -0.11 0.2 -10000 0 -0.44 262 262
HGF -0.053 0.2 -10000 0 -0.79 73 73
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.009 0.052 -10000 0 -0.32 29 29
actin cable formation 0.072 0.055 -10000 0 -0.32 1 1
KIAA1543 0.032 0.087 -10000 0 -0.46 29 29
KIFC3 -0.011 0.068 -10000 0 -0.42 30 30
NCK1 0 0 -10000 0 -10000 0 0
EXOC3 0 0 -10000 0 -10000 0 0
ACTN1 -0.011 0.067 -10000 0 -0.42 29 29
NCK1/GIT1 -0.001 0.013 -10000 0 -10000 0 0
mol:GDP -0.011 0.069 -10000 0 -0.44 28 28
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.011 0.066 -10000 0 -0.42 28 28
PIP5K1C -0.011 0.066 -10000 0 -0.42 28 28
LIMA1 -0.001 0.024 -10000 0 -0.79 1 1
ABI1 0 0 -10000 0 -10000 0 0
ROCK1 -0.01 0.053 -10000 0 -10000 0 0
adherens junction assembly 0.048 0.083 -10000 0 -0.62 7 7
IGF-1R heterotetramer/IGF1 -0.11 0.19 -10000 0 -0.43 279 279
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.004 0.046 -10000 0 -0.6 6 6
MET -0.14 0.3 -10000 0 -0.78 189 189
PLEKHA7 -0.012 0.076 -10000 0 -0.46 28 28
mol:GTP -0.003 0.035 -10000 0 -0.46 6 6
establishment of epithelial cell apical/basal polarity -0.011 0.061 -10000 0 -0.7 1 1
cortical actin cytoskeleton stabilization -0.009 0.052 -10000 0 -0.32 29 29
regulation of cell-cell adhesion 0.033 0.07 -10000 0 -0.39 29 29
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.009 0.052 -10000 0 -0.32 29 29
IL27-mediated signaling events

Figure S63.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S63.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.001 0.017 -10000 0 -0.29 3 3
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.035 0.13 0.41 52 -10000 0 52
IL27/IL27R/JAK1 -0.074 0.19 -10000 0 -0.6 73 73
TBX21 -0.043 0.21 -10000 0 -0.58 91 91
IL12B -0.055 0.12 -10000 0 -0.29 229 229
IL12A -0.027 0.14 -10000 0 -0.61 58 58
IL6ST -0.091 0.27 -10000 0 -0.8 137 137
IL27RA/JAK1 -0.008 0.073 -10000 0 -1.1 4 4
IL27 -0.025 0.095 -10000 0 -0.29 121 121
TYK2 0.01 0.006 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.12 0.18 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.035 0.13 0.41 52 -10000 0 52
T cell proliferation during immune response 0.035 0.13 0.41 52 -10000 0 52
MAPKKK cascade -0.035 0.13 -10000 0 -0.41 52 52
STAT3 0 0 -10000 0 -10000 0 0
STAT2 0 0 -10000 0 -10000 0 0
STAT1 -0.004 0.039 -10000 0 -0.3 19 19
IL12RB1 -0.004 0.067 -10000 0 -0.32 43 43
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.059 0.23 -10000 0 -0.61 103 103
IL27/IL27R/JAK2/TYK2 -0.035 0.13 -10000 0 -0.41 52 52
positive regulation of T cell mediated cytotoxicity -0.035 0.13 -10000 0 -0.41 52 52
STAT1 (dimer) -0.092 0.22 0.46 22 -0.71 65 87
JAK2 0.005 0.025 -10000 0 -0.79 1 1
JAK1 0 0.024 -10000 0 -0.79 1 1
STAT2 (dimer) -0.044 0.11 -10000 0 -0.44 27 27
T cell proliferation -0.18 0.25 -10000 0 -0.46 421 421
IL12/IL12R/TYK2/JAK2 0.012 0.069 -10000 0 -10000 0 0
IL17A -0.12 0.18 -10000 0 -10000 0 0
mast cell activation 0.035 0.13 0.41 52 -10000 0 52
IFNG -0.001 0.025 -10000 0 -0.074 18 18
T cell differentiation -0.004 0.006 -10000 0 -0.019 33 33
STAT3 (dimer) -0.044 0.11 -10000 0 -0.44 26 26
STAT5A (dimer) -0.048 0.12 -10000 0 -0.46 33 33
STAT4 (dimer) -0.062 0.15 -10000 0 -0.49 67 67
STAT4 -0.032 0.16 -10000 0 -0.78 45 45
T cell activation -0.009 0.009 0.13 3 -10000 0 3
IL27R/JAK2/TYK2 -0.062 0.17 -10000 0 -0.55 52 52
GATA3 -0.039 0.28 -10000 0 -1.4 40 40
IL18 0.006 0.032 -10000 0 -10000 0 0
positive regulation of mast cell cytokine production -0.044 0.11 -10000 0 -0.43 27 27
IL27/EBI3 -0.026 0.083 -10000 0 -0.52 14 14
IL27RA -0.001 0.078 -10000 0 -1.4 3 3
IL6 -0.29 0.38 -10000 0 -0.79 401 401
STAT5A -0.006 0.067 -10000 0 -0.79 8 8
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.004 0.03 0.48 3 -10000 0 3
IL1B 0.002 0.073 -10000 0 -0.52 19 19
EBI3 -0.004 0.076 -10000 0 -0.49 21 21
TNF -0.001 0.074 -10000 0 -0.61 13 13
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0 0.1 -9999 0 -0.53 41 41
ADCY5 -0.16 0.26 -9999 0 -0.53 354 354
ADCY6 0.02 0 -9999 0 -10000 0 0
ADCY7 0.02 0 -9999 0 -10000 0 0
ADCY1 -0.008 0.097 -9999 0 -0.53 29 29
ADCY2 -0.032 0.15 -9999 0 -0.53 90 90
ADCY3 0.02 0.005 -9999 0 -10000 0 0
ADCY8 0.01 0.028 -9999 0 -10000 0 0
PRKCE 0.011 0 -9999 0 -10000 0 0
ADCY9 0.02 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.032 0.1 -9999 0 -0.31 75 75
Effects of Botulinum toxin

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
STX1A 0.003 0.041 -9999 0 -0.2 43 43
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.046 0.13 -9999 0 -0.6 46 46
STXBP1 -0.006 0.067 -9999 0 -0.79 8 8
ACh/CHRNA1 -0.062 0.082 -9999 0 -0.25 16 16
RAB3GAP2/RIMS1/UNC13B -0.038 0.11 -9999 0 -0.52 46 46
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.066 0.18 -9999 0 -0.43 170 170
mol:ACh 0.001 0.031 -9999 0 -0.11 62 62
RAB3GAP2 0 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.038 0.093 -9999 0 -0.39 54 54
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.062 0.082 -9999 0 -0.25 16 16
UNC13B 0 0 -9999 0 -10000 0 0
CHRNA1 -0.099 0.14 -9999 0 -0.29 371 371
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.059 0.12 -9999 0 -0.47 60 60
SNAP25 -0.009 0.068 -9999 0 -0.37 35 35
VAMP2 0 0 -9999 0 -10000 0 0
SYT1 -0.087 0.18 -9999 0 -0.38 253 253
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.01 0.053 -9999 0 -0.52 8 8
STX1A/SNAP25 fragment 1/VAMP2 -0.038 0.093 -9999 0 -0.39 54 54
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.004 0.018 -10000 0 -10000 0 0
AES 0.004 0.015 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0 0.006 -10000 0 -10000 0 0
SMAD4 -0.001 0.024 -10000 0 -0.79 1 1
DKK2 -0.024 0.14 -10000 0 -0.76 35 35
TLE1 -0.002 0.069 -10000 0 -0.79 8 8
MACF1 0.006 0.006 -10000 0 -10000 0 0
CTNNB1 0.1 0.087 -10000 0 -10000 0 0
WIF1 -0.41 0.39 -10000 0 -0.77 581 581
beta catenin/RanBP3 0.014 0.078 0.37 46 -10000 0 46
KREMEN2 -0.14 0.15 -10000 0 -0.29 527 527
DKK1 -0.08 0.19 -10000 0 -0.42 206 206
beta catenin/beta TrCP1 0.1 0.083 -10000 0 -10000 0 0
FZD1 0 0.002 -10000 0 -10000 0 0
AXIN2 -0.014 0.21 -10000 0 -1.5 20 20
AXIN1 0.007 0.006 -10000 0 -10000 0 0
RAN 0.001 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.007 0.024 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.092 0.078 0.3 1 -0.49 6 7
Axin1/APC/GSK3 0.001 0.014 0.24 1 -10000 0 1
Axin1/APC/GSK3/beta catenin/Macf1 0.077 0.033 -10000 0 -10000 0 0
HNF1A 0.002 0.029 -10000 0 -0.29 7 7
CTBP1 0.004 0.016 -10000 0 -10000 0 0
MYC -0.018 0.23 -10000 0 -1.5 25 25
RANBP3 0.001 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.085 0.12 -10000 0 -0.6 33 33
NKD1 -0.009 0.069 -10000 0 -0.42 24 24
TCF4 -0.005 0.083 -10000 0 -0.78 12 12
TCF3 0.004 0.017 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0 0.006 -10000 0 -10000 0 0
Ran/GTP 0 0.001 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.014 0.099 0.45 45 -0.42 1 46
LEF1 -0.036 0.1 -10000 0 -0.3 140 140
DVL1 0.071 0.065 -10000 0 -10000 0 0
CSNK2A1 0 0.002 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.098 0.089 -10000 0 -0.54 6 6
DKK1/LRP6/Kremen 2 -0.12 0.14 -10000 0 -0.57 55 55
LRP6 0.002 0.01 -10000 0 -0.29 1 1
CSNK1A1 0.004 0.018 -10000 0 -10000 0 0
NLK 0.011 0.014 -10000 0 -0.3 2 2
CCND1 0.002 0.11 -10000 0 -1.6 4 4
WNT1 0.005 0.014 -10000 0 -0.29 2 2
GSK3A 0.009 0.006 -10000 0 -10000 0 0
GSK3B 0 0.001 -10000 0 -10000 0 0
FRAT1 0 0 -10000 0 -10000 0 0
PPP2R5D 0.044 0.045 0.34 7 -10000 0 7
APC 0.001 0.009 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.14 0.13 0.27 566 -10000 0 566
CREBBP 0.004 0.016 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.035 0.12 -10000 0 -0.59 40 40
FYN 0.017 0.18 -10000 0 -0.7 47 47
LAT/GRAP2/SLP76 -0.028 0.14 -10000 0 -0.65 42 42
IKBKB -0.001 0.013 -10000 0 -0.29 2 2
AKT1 0.031 0.12 -10000 0 -0.46 44 44
B2M 0.012 0.004 -10000 0 -10000 0 0
IKBKG -0.008 0.026 -10000 0 -0.14 14 14
MAP3K8 -0.007 0.072 -10000 0 -0.74 10 10
mol:Ca2+ -0.024 0.047 -10000 0 -0.12 212 212
integrin-mediated signaling pathway -0.002 0.028 -10000 0 -0.52 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.022 0.17 -10000 0 -0.7 45 45
TRPV6 -0.16 0.32 -10000 0 -0.77 225 225
CD28 0.002 0.074 -10000 0 -0.52 18 18
SHC1 0.012 0.18 -10000 0 -0.75 44 44
receptor internalization -0.001 0.2 -10000 0 -0.76 53 53
PRF1 0 0.22 -10000 0 -1.2 30 30
KRAS -0.001 0.013 -10000 0 -0.29 2 2
GRB2 0 0.009 -10000 0 -0.29 1 1
COT/AKT1 0.032 0.1 -10000 0 -0.37 47 47
LAT 0.01 0.18 -10000 0 -0.73 48 48
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D -0.023 0.14 -10000 0 -0.48 78 78
CD3E -0.016 0.13 -10000 0 -0.49 61 61
CD3G -0.031 0.16 -10000 0 -0.56 82 82
RASGRP2 0.004 0.041 -10000 0 -0.18 45 45
RASGRP1 0.036 0.12 -10000 0 -0.47 44 44
HLA-A 0.009 0.031 -10000 0 -0.29 11 11
RASSF5 -0.002 0.042 -10000 0 -0.66 4 4
RAP1A/GTP/RAPL -0.002 0.028 -10000 0 -0.52 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.033 0.043 -10000 0 -0.12 39 39
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.014 0.047 -10000 0 -0.23 33 33
PRKCA -0.013 0.084 -10000 0 -0.3 62 62
GRAP2 -0.013 0.1 -10000 0 -0.72 21 21
mol:IP3 0.019 0.15 0.27 182 -0.45 41 223
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.005 0.2 -10000 0 -0.9 40 40
ORAI1 0.077 0.15 0.38 211 -10000 0 211
CSK 0.009 0.18 -10000 0 -0.74 46 46
B7 family/CD28 -0.026 0.18 -10000 0 -0.7 51 51
CHUK 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.001 0.21 -10000 0 -0.75 61 61
PTPN6 0.008 0.18 -10000 0 -0.76 45 45
VAV1 0.011 0.18 -10000 0 -0.75 46 46
Monovalent TCR/CD3 -0.023 0.2 -10000 0 -0.65 72 72
CBL 0 0 -10000 0 -10000 0 0
LCK 0.011 0.19 -10000 0 -0.77 46 46
PAG1 0.009 0.18 -10000 0 -0.75 46 46
RAP1A 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.001 0.21 -10000 0 -0.76 58 58
CD80 -0.068 0.13 -10000 0 -0.29 285 285
CD86 0.008 0.023 -10000 0 -0.3 6 6
PDK1/CARD11/BCL10/MALT1 -0.017 0.057 -10000 0 -0.28 35 35
HRAS -0.003 0.028 -10000 0 -0.29 10 10
GO:0035030 0 0.15 -10000 0 -0.57 51 51
CD8A 0 0.073 -10000 0 -0.8 5 5
CD8B -0.021 0.15 -10000 0 -0.55 66 66
PTPRC -0.001 0.071 -10000 0 -0.48 19 19
PDK1/PKC theta 0.034 0.15 -10000 0 -0.6 45 45
CSK/PAG1 0.014 0.18 -10000 0 -0.75 42 42
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I -0.002 0.018 -10000 0 -10000 0 0
GRAP2/SLP76 -0.034 0.17 -10000 0 -0.75 45 45
STIM1 0.04 0.078 -10000 0 -10000 0 0
RAS family/GTP 0.041 0.054 -10000 0 -0.17 32 32
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.005 0.22 -10000 0 -0.84 53 53
mol:DAG -0.007 0.1 -10000 0 -0.41 42 42
RAP1A/GDP 0.016 0.018 -10000 0 -10000 0 0
PLCG1 0.001 0.003 -10000 0 -10000 0 0
CD247 -0.008 0.12 -10000 0 -0.58 37 37
cytotoxic T cell degranulation 0.003 0.21 -10000 0 -1 33 33
RAP1A/GTP -0.003 0.013 -10000 0 -0.071 5 5
mol:PI-3-4-5-P3 0.027 0.14 -10000 0 -0.56 45 45
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.012 0.17 0.29 170 -0.6 42 212
NRAS -0.001 0.013 -10000 0 -0.29 2 2
ZAP70 -0.031 0.12 -10000 0 -0.42 81 81
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.025 0.14 -10000 0 -0.62 42 42
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
CD8 heterodimer -0.031 0.13 -10000 0 -0.56 53 53
CARD11 -0.007 0.052 -10000 0 -0.34 23 23
PRKCB -0.012 0.084 -10000 0 -0.32 53 53
PRKCE -0.006 0.068 -10000 0 -0.29 36 36
PRKCQ 0.025 0.17 -10000 0 -0.69 47 47
LCP2 0 0.009 -10000 0 -0.29 1 1
BCL10 0 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.032 0.1 -10000 0 -0.39 44 44
IKK complex 0.041 0.044 -10000 0 -0.12 30 30
RAS family/GDP -0.002 0.006 -10000 0 -10000 0 0
MAP3K14 0.036 0.08 -10000 0 -0.29 39 39
PDPK1 0.034 0.11 -10000 0 -0.44 41 41
TCR/CD3/MHC I/CD8/Fyn -0.004 0.23 -10000 0 -0.92 50 50
Coregulation of Androgen receptor activity

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
NRIP1 -0.002 0.032 -10000 0 -0.79 1 1
SVIL -0.004 0.056 -10000 0 -0.79 5 5
ZNF318 0.022 0.057 -10000 0 -10000 0 0
JMJD2C -0.003 0.041 -10000 0 -0.12 106 106
T-DHT/AR/Ubc9 -0.081 0.18 -10000 0 -0.54 147 147
CARM1 0 0 -10000 0 -10000 0 0
PRDX1 0.003 0.012 -10000 0 -0.29 1 1
PELP1 0.005 0.012 -10000 0 -10000 0 0
CTNNB1 0.001 0.015 -10000 0 -10000 0 0
AKT1 0.007 0.018 -10000 0 -10000 0 0
PTK2B 0.001 0.013 -10000 0 -10000 0 0
MED1 0.002 0.047 -10000 0 -0.29 20 20
MAK 0.011 0.1 0.26 1 -0.55 20 21
response to oxidative stress 0.001 0.004 -10000 0 -10000 0 0
HIP1 -0.005 0.061 -10000 0 -0.79 6 6
GSN -0.012 0.091 -10000 0 -0.79 14 14
NCOA2 -0.039 0.17 -10000 0 -0.79 54 54
NCOA6 -0.001 0.02 -10000 0 -0.29 1 1
DNA-PK 0.022 0.058 0.22 2 -10000 0 2
NCOA4 0 0 -10000 0 -10000 0 0
PIAS3 0.001 0.015 -10000 0 -10000 0 0
cell proliferation -0.008 0.11 -10000 0 -0.87 11 11
XRCC5 0.006 0.015 -10000 0 -10000 0 0
UBE3A -0.005 0.03 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.094 0.21 -10000 0 -0.57 162 162
FHL2 -0.018 0.12 -10000 0 -1.2 5 5
RANBP9 0 0.018 -10000 0 -10000 0 0
JMJD1A -0.011 0.056 -10000 0 -0.14 152 152
CDK6 -0.009 0.093 -10000 0 -0.73 17 17
TGFB1I1 -0.003 0.046 -10000 0 -0.79 3 3
T-DHT/AR/CyclinD1 -0.094 0.19 -10000 0 -0.52 163 163
XRCC6 0.006 0.015 -10000 0 -10000 0 0
T-DHT/AR -0.067 0.21 -10000 0 -0.53 164 164
CTDSP1 0.004 0.005 -10000 0 -10000 0 0
CTDSP2 0.015 0.038 -10000 0 -10000 0 0
BRCA1 -0.002 0.034 -10000 0 -0.49 3 3
TCF4 0.003 0.088 -10000 0 -0.78 12 12
CDKN2A -0.042 0.11 -10000 0 -0.29 167 167
SRF 0.024 0.019 -10000 0 -10000 0 0
NKX3-1 -0.082 0.19 -10000 0 -0.83 41 41
KLK3 -0.17 0.5 -10000 0 -1.5 127 127
TMF1 0.004 0.005 -10000 0 -10000 0 0
HNRNPA1 0.008 0.021 -10000 0 -10000 0 0
AOF2 -0.008 0.023 -10000 0 -0.072 127 127
APPL1 0.034 0.032 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.074 0.19 -10000 0 -0.54 146 146
AR -0.1 0.27 -10000 0 -0.79 147 147
UBA3 0.004 0.005 -10000 0 -10000 0 0
PATZ1 0.008 0.021 -10000 0 -10000 0 0
PAWR 0.003 0.025 -10000 0 -0.79 1 1
PRKDC 0.005 0.024 -10000 0 -0.29 4 4
PA2G4 0.011 0.027 -10000 0 -10000 0 0
UBE2I 0 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.069 0.17 -10000 0 -0.5 146 146
RPS6KA3 -0.008 0.074 -10000 0 -0.79 9 9
T-DHT/AR/ARA70 -0.085 0.18 -10000 0 -0.54 147 147
LATS2 0.009 0.023 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.064 0.18 0.19 1 -0.49 147 148
Cyclin D3/CDK11 p58 0 0.006 -10000 0 -10000 0 0
VAV3 -0.01 0.075 -10000 0 -0.43 26 26
KLK2 -0.12 0.32 -10000 0 -1.2 79 79
CASP8 0.004 0.011 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.099 0.2 -10000 0 -0.54 181 181
TMPRSS2 -0.17 0.39 -10000 0 -1.2 137 137
CCND1 -0.016 0.074 -10000 0 -0.34 46 46
PIAS1 -0.005 0.03 -10000 0 -10000 0 0
mol:T-DHT -0.008 0.033 -10000 0 -0.078 182 182
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.011 0.049 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.085 0.2 -10000 0 -0.54 161 161
CMTM2 0.003 0.013 -10000 0 -10000 0 0
SNURF -0.021 0.13 -10000 0 -0.79 29 29
ZMIZ1 0.004 0.03 -10000 0 -0.36 1 1
CCND3 0.002 0.01 -10000 0 -0.29 1 1
TGIF1 0.008 0.021 -10000 0 -10000 0 0
FKBP4 -0.003 0.033 -10000 0 -0.3 9 9
Regulation of Androgen receptor activity

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
HDAC1 0.021 0.003 -9999 0 -10000 0 0
SMARCC1 0.005 0.019 -9999 0 -10000 0 0
REL -0.006 0.09 -9999 0 -0.79 14 14
HDAC7 0.008 0.13 -9999 0 -0.58 19 19
JUN 0 0.063 -9999 0 -0.79 7 7
EP300 0 0 -9999 0 -10000 0 0
KAT2B -0.001 0.024 -9999 0 -0.79 1 1
KAT5 0.002 0.005 -9999 0 -10000 0 0
MAPK14 0.006 0.095 -9999 0 -0.61 25 25
FOXO1 -0.009 0.082 -9999 0 -0.79 12 12
T-DHT/AR -0.004 0.14 -9999 0 -0.52 35 35
MAP2K6 -0.01 0.12 -9999 0 -0.78 26 26
BRM/BAF57 -0.001 0.01 -9999 0 -10000 0 0
MAP2K4 0.008 0.025 -9999 0 -0.79 1 1
SMARCA2 0.004 0.006 -9999 0 -10000 0 0
PDE9A -0.088 0.29 -9999 0 -1.2 64 64
NCOA2 -0.032 0.17 -9999 0 -0.79 54 54
CEBPA -0.005 0.075 -9999 0 -0.79 10 10
EHMT2 0.005 0.006 -9999 0 -10000 0 0
cell proliferation 0.014 0.15 -9999 0 -0.49 26 26
NR0B1 -0.01 0.053 -9999 0 -0.29 37 37
EGR1 -0.25 0.37 -9999 0 -0.79 347 347
RXRs/9cRA -0.12 0.21 -9999 0 -0.48 268 268
AR/RACK1/Src -0.005 0.11 -9999 0 -0.5 28 28
AR/GR -0.054 0.13 -9999 0 -0.45 58 58
GNB2L1 0.002 0.004 -9999 0 -10000 0 0
PKN1 0 0.009 -9999 0 -0.29 1 1
RCHY1 0 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.003 -9999 0 -10000 0 0
MAPK8 0.015 0.061 -9999 0 -0.61 10 10
T-DHT/AR/TIF2/CARM1 -0.018 0.16 -9999 0 -0.51 78 78
SRC 0.021 0.094 -9999 0 -0.46 34 34
NR3C1 -0.012 0.095 -9999 0 -0.79 16 16
KLK3 -0.2 0.41 -9999 0 -1.1 164 164
APPBP2 0.008 0.017 -9999 0 -0.29 3 3
TRIM24 0.005 0.006 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.028 0.099 -9999 0 -0.51 34 34
TMPRSS2 -0.16 0.41 -9999 0 -1.2 138 138
RXRG -0.19 0.34 -9999 0 -0.79 268 268
mol:9cRA -0.001 0.002 -9999 0 -10000 0 0
RXRA 0 0 -9999 0 -10000 0 0
RXRB 0 0 -9999 0 -10000 0 0
CARM1 0.008 0.006 -9999 0 -10000 0 0
NR2C2 -0.008 0.079 -9999 0 -0.79 11 11
KLK2 -0.043 0.24 -9999 0 -0.73 103 103
AR -0.028 0.14 -9999 0 -0.34 172 172
SENP1 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
MDM2 0.004 0.024 -9999 0 -0.29 5 5
SRY 0.003 0.01 -9999 0 -10000 0 0
GATA2 -0.024 0.13 -9999 0 -0.63 41 41
MYST2 0.002 0.01 -9999 0 -0.29 1 1
HOXB13 -0.14 0.15 -9999 0 -0.3 501 501
T-DHT/AR/RACK1/Src -0.013 0.1 -9999 0 -0.51 28 28
positive regulation of transcription -0.024 0.13 -9999 0 -0.63 41 41
DNAJA1 0.009 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.013 -9999 0 -10000 0 0
NCOA1 0.012 0.026 -9999 0 -0.82 1 1
SPDEF -0.057 0.2 -9999 0 -0.61 110 110
T-DHT/AR/TIF2 0.011 0.1 -9999 0 -0.45 27 27
T-DHT/AR/Hsp90 -0.035 0.095 -9999 0 -0.51 34 34
GSK3B 0.008 0.006 -9999 0 -10000 0 0
NR2C1 0.003 0.006 -9999 0 -10000 0 0
mol:T-DHT 0.014 0.099 -9999 0 -0.5 34 34
SIRT1 0 0 -9999 0 -10000 0 0
ZMIZ2 0.005 0.013 -9999 0 -10000 0 0
POU2F1 0.021 0.026 -9999 0 -0.42 1 1
T-DHT/AR/DAX-1 -0.036 0.099 -9999 0 -0.52 34 34
CREBBP 0 0 -9999 0 -10000 0 0
SMARCE1 0.004 0.017 -9999 0 -0.3 3 3
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.004 0.13 -10000 0 -0.4 54 54
TBX21 -0.013 0.34 -10000 0 -1.3 57 57
B2M 0.011 0.005 -10000 0 -10000 0 0
TYK2 0.017 0.015 -10000 0 -10000 0 0
IL12RB1 0.004 0.072 -10000 0 -0.33 43 43
GADD45B 0.031 0.22 -10000 0 -0.81 34 34
IL12RB2 -0.056 0.19 -10000 0 -0.49 133 133
GADD45G 0.021 0.22 -10000 0 -0.81 36 36
natural killer cell activation 0.007 0.018 -10000 0 -10000 0 0
RELB -0.003 0.028 -10000 0 -0.29 10 10
RELA 0 0 -10000 0 -10000 0 0
IL18 0.007 0.048 -10000 0 -0.29 18 18
IL2RA -0.031 0.12 -10000 0 -0.38 87 87
IFNG -0.04 0.1 -10000 0 -0.29 150 150
STAT3 (dimer) 0.024 0.22 -10000 0 -0.66 55 55
HLA-DRB5 -0.017 0.096 -10000 0 -0.33 84 84
FASLG 0.002 0.29 -10000 0 -1.1 49 49
NF kappa B2 p52/RelB -0.079 0.2 -10000 0 -0.8 54 54
CD4 0.008 0.006 -10000 0 -10000 0 0
SOCS1 -0.005 0.043 -10000 0 -0.32 18 18
EntrezGene:6955 -0.006 0.014 -10000 0 -10000 0 0
CD3D -0.026 0.14 -10000 0 -0.49 78 78
CD3E -0.019 0.13 -10000 0 -0.5 61 61
CD3G -0.035 0.17 -10000 0 -0.57 82 82
IL12Rbeta2/JAK2 -0.026 0.15 -10000 0 -0.61 50 50
CCL3 0.012 0.26 -10000 0 -0.97 41 41
CCL4 0.014 0.25 -10000 0 -0.95 38 38
HLA-A 0.008 0.032 -10000 0 -0.3 11 11
IL18/IL18R 0.02 0.14 -10000 0 -0.54 55 55
NOS2 0.018 0.25 -10000 0 -0.9 44 44
IL12/IL12R/TYK2/JAK2/SPHK2 -0.003 0.13 -10000 0 -0.4 53 53
IL1R1 -0.001 0.31 -10000 0 -1.2 49 49
IL4 -0.004 0.018 -10000 0 -10000 0 0
JAK2 0.016 0.029 -10000 0 -0.82 1 1
EntrezGene:6957 -0.005 0.013 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.032 0.25 -10000 0 -0.99 50 50
RAB7A 0.045 0.19 -10000 0 -0.74 25 25
lysosomal transport 0.047 0.19 -10000 0 -0.7 25 25
FOS -0.35 0.66 -10000 0 -1.3 342 342
STAT4 (dimer) 0.02 0.26 -10000 0 -0.86 56 56
STAT5A (dimer) -0.086 0.22 -10000 0 -0.76 66 66
GZMA 0.002 0.28 -10000 0 -1.1 40 40
GZMB -0.012 0.31 -10000 0 -1.1 52 52
HLX -0.001 0.015 -10000 0 -0.29 3 3
LCK 0.003 0.29 -10000 0 -0.86 67 67
TCR/CD3/MHC II/CD4 -0.065 0.19 -10000 0 -0.52 94 94
IL2/IL2R -0.03 0.1 -10000 0 -0.48 41 41
MAPK14 0.035 0.22 -10000 0 -0.77 43 43
CCR5 0.025 0.22 -10000 0 -0.87 32 32
IL1B 0.005 0.098 -10000 0 -0.69 19 19
STAT6 0.025 0.087 -10000 0 -0.24 14 14
STAT4 -0.032 0.16 -10000 0 -0.78 45 45
STAT3 0 0 -10000 0 -10000 0 0
STAT1 -0.005 0.038 -10000 0 -0.29 19 19
NFKB1 0 0 -10000 0 -10000 0 0
NFKB2 0 0.009 -10000 0 -0.29 1 1
IL12B -0.047 0.12 -10000 0 -0.3 131 131
CD8A 0 0.074 -10000 0 -0.79 5 5
CD8B -0.022 0.14 -10000 0 -0.54 66 66
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.003 0.13 0.4 54 -10000 0 54
IL2RB -0.012 0.064 -10000 0 -0.32 42 42
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.24 -10000 0 -0.78 56 56
IL2RG -0.017 0.085 -10000 0 -0.36 53 53
IL12 -0.052 0.16 -10000 0 -0.59 65 65
STAT5A -0.006 0.067 -10000 0 -0.79 8 8
CD247 -0.011 0.12 -10000 0 -0.58 37 37
IL2 -0.002 0.025 -10000 0 -0.29 8 8
SPHK2 0 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.031 0.19 -10000 0 -0.73 67 67
IL12/IL12R/TYK2/JAK2 0.007 0.29 -10000 0 -0.83 72 72
MAP2K3 0.03 0.22 -10000 0 -0.79 41 41
RIPK2 -0.001 0.02 -10000 0 -0.29 5 5
MAP2K6 0.026 0.23 -10000 0 -0.77 47 47
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.008 0.026 -10000 0 -0.79 1 1
IL18RAP -0.014 0.15 -10000 0 -0.73 42 42
IL12Rbeta1/TYK2 0.014 0.056 -10000 0 -0.63 2 2
EOMES -0.024 0.18 -10000 0 -1.5 17 17
STAT1 (dimer) 0.027 0.22 -10000 0 -0.7 44 44
T cell proliferation 0.031 0.2 -10000 0 -0.62 56 56
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0 0.11 -10000 0 -0.79 20 20
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.062 0.17 -10000 0 -0.74 46 46
ATF2 0.041 0.21 -10000 0 -0.74 40 40
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.13 0.22 -9999 0 -0.46 301 301
TC10/GTP -0.11 0.18 -9999 0 -0.4 285 285
Insulin Receptor/Insulin/IRS1/Shp2 -0.02 0.097 -9999 0 -0.49 45 45
HRAS -0.003 0.028 -9999 0 -0.29 10 10
APS homodimer -0.013 0.06 -9999 0 -0.29 49 49
GRB14 -0.1 0.22 -9999 0 -0.48 231 231
FOXO3 -0.015 0.07 -9999 0 -0.7 10 10
AKT1 -0.058 0.12 -9999 0 -0.51 11 11
INSR 0.012 0.009 -9999 0 -0.29 1 1
Insulin Receptor/Insulin -0.003 0.026 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0 0 -9999 0 -10000 0 0
SORBS1 -0.2 0.35 -9999 0 -0.79 285 285
CRK 0 0 -9999 0 -10000 0 0
PTPN1 0.033 0.03 -9999 0 -10000 0 0
CAV1 -0.099 0.24 -9999 0 -0.5 259 259
CBL/APS/CAP/Crk-II/C3G -0.12 0.2 -9999 0 -0.45 285 285
Insulin Receptor/Insulin/IRS1/NCK2 -0.02 0.097 -9999 0 -0.49 45 45
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.023 0.096 -9999 0 -0.42 59 59
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.012 0.055 -9999 0 -10000 0 0
RPS6KB1 -0.009 0.13 -9999 0 -0.46 11 11
PARD6A -0.002 0.023 -9999 0 -0.29 7 7
CBL 0 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.002 -9999 0 -10000 0 0
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.05 0.11 -9999 0 -0.48 11 11
HRAS/GTP -0.016 0.073 -9999 0 -0.47 2 2
Insulin Receptor 0.012 0.009 -9999 0 -0.29 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.019 0.09 -9999 0 -0.45 45 45
PRKCI -0.013 0.032 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.063 0.14 -9999 0 -0.4 143 143
SHC1 0 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0.002 -9999 0 -10000 0 0
PI3K -0.023 0.097 -9999 0 -0.43 59 59
NCK2 0 0 -9999 0 -10000 0 0
RHOQ 0 0 -9999 0 -10000 0 0
mol:H2O2 0 0.003 -9999 0 -10000 0 0
HRAS/GDP -0.002 0.019 -9999 0 -10000 0 0
AKT2 -0.058 0.12 -9999 0 -0.51 11 11
PRKCZ -0.014 0.036 -9999 0 -0.6 1 1
SH2B2 -0.013 0.061 -9999 0 -0.29 49 49
SHC/SHIP -0.017 0.085 -9999 0 -0.42 45 45
F2RL2 -0.06 0.15 -9999 0 -0.36 185 185
TRIP10 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0 0.004 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0 0.004 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.13 0.21 -9999 0 -0.48 285 285
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0 0.003 -9999 0 -10000 0 0
INPP5D 0.007 0.096 -9999 0 -0.46 45 45
SOS1 0 0 -9999 0 -10000 0 0
SGK1 -0.01 0.08 -9999 0 -1 7 7
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 -0.032 0.16 -9999 0 -0.79 45 45
p62DOK/RasGAP 0 0.003 -9999 0 -10000 0 0
INS 0.003 0.004 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.007 0.095 -9999 0 -0.45 45 45
GRB2 0 0.009 -9999 0 -0.29 1 1
EIF4EBP1 -0.014 0.14 -9999 0 -0.46 26 26
PTPRA 0.012 0.002 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.29 1 1
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.013 0.064 -9999 0 -0.32 45 45
Insulin Receptor/Insulin/IRS1 -0.021 0.098 -9999 0 -0.5 45 45
Insulin Receptor/Insulin/IRS3 -0.001 0.007 -9999 0 -10000 0 0
Par3/Par6 -0.027 0.075 -9999 0 -0.45 24 24
Regulation of Telomerase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Telomerase catalytic core complex -0.055 0.12 -9999 0 -0.57 6 6
RAD9A 0 0.009 -9999 0 -0.29 1 1
AP1 -0.18 0.28 -9999 0 -0.61 330 330
IFNAR2 0.01 0.025 -9999 0 -0.79 1 1
AKT1 -0.036 0.11 -9999 0 -0.28 165 165
ER alpha/Oestrogen -0.11 0.22 -9999 0 -0.61 166 166
NFX1/SIN3/HDAC complex 0.026 0.025 -9999 0 -10000 0 0
EGF -0.15 0.31 -9999 0 -0.78 214 214
SMG5 0 0 -9999 0 -10000 0 0
SMG6 0 0 -9999 0 -10000 0 0
SP3/HDAC2 0 0 -9999 0 -10000 0 0
TERT/c-Abl -0.067 0.089 -9999 0 -0.58 4 4
SAP18 0.006 0.006 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.14 0.15 -9999 0 -0.29 561 561
WRN 0 0 -9999 0 -10000 0 0
SP1 0.011 0.006 -9999 0 -10000 0 0
SP3 0.009 0.005 -9999 0 -10000 0 0
TERF2IP 0 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.052 0.078 -9999 0 -0.55 3 3
Mad/Max 0 0.006 -9999 0 -10000 0 0
TERT -0.056 0.12 -9999 0 -0.61 5 5
CCND1 -0.048 0.13 -9999 0 -1.3 4 4
MAX 0.009 0.005 -9999 0 -10000 0 0
RBBP7 0.004 0.026 -9999 0 -0.29 8 8
RBBP4 0.005 0.025 -9999 0 -0.79 1 1
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0 0 -9999 0 -10000 0 0
SIN3A 0.006 0.006 -9999 0 -10000 0 0
Telomerase/911 0.012 0.024 -9999 0 -10000 0 0
CDKN1B 0.009 0.074 -9999 0 -0.86 3 3
RAD1 0 0 -9999 0 -10000 0 0
XRCC5 0 0 -9999 0 -10000 0 0
XRCC6 0 0 -9999 0 -10000 0 0
SAP30 0.005 0.019 -9999 0 -0.29 4 4
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.009 0.005 -9999 0 -10000 0 0
JUN 0.002 0.064 -9999 0 -0.79 7 7
E6 0 0.001 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0 0 -9999 0 -10000 0 0
FOS -0.23 0.37 -9999 0 -0.79 329 329
IFN-gamma/IRF1 -0.025 0.063 -9999 0 -0.36 5 5
PARP2 0 0 -9999 0 -10000 0 0
BLM -0.03 0.089 -9999 0 -0.29 113 113
Telomerase -0.006 0.028 -9999 0 -10000 0 0
IRF1 0.011 0.02 -9999 0 -0.28 3 3
ESR1 -0.15 0.29 -9999 0 -0.58 288 288
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0.007 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0 0.007 -9999 0 -10000 0 0
HDAC1 0.006 0.006 -9999 0 -10000 0 0
HDAC2 0.011 0.005 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.021 0.011 -9999 0 -10000 0 0
ABL1 0 0 -9999 0 -10000 0 0
MXD1 0.009 0.01 -9999 0 -0.29 1 1
MRE11A 0 0 -9999 0 -10000 0 0
HUS1 0 0 -9999 0 -10000 0 0
RPS6KB1 -0.001 0.015 -9999 0 -0.29 3 3
TERT/NF kappa B1/14-3-3 -0.065 0.1 -9999 0 -0.67 3 3
NR2F2 0.001 0.042 -9999 0 -0.79 3 3
MAPK3 0.014 0.019 -9999 0 -10000 0 0
MAPK1 0.014 0.019 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.001 0.016 -9999 0 -0.29 3 3
NFKB1 0 0 -9999 0 -10000 0 0
HNRNPC 0 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0 0 -9999 0 -10000 0 0
EGFR -0.29 0.38 -9999 0 -0.78 410 410
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.33 0.35 -9999 0 -0.66 552 552
MYC -0.008 0.12 -9999 0 -0.79 24 24
IL2 0.004 0.026 -9999 0 -0.29 8 8
KU 0 0 -9999 0 -10000 0 0
RAD50 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
TGFB1 0.001 0.016 -9999 0 -0.29 3 3
TRF2/BLM -0.017 0.051 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.063 0.087 -9999 0 -0.58 4 4
SP1/HDAC2 0 0 -9999 0 -10000 0 0
PINX1 0 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.052 0.078 -9999 0 -0.55 3 3
Smad3/Myc -0.012 0.076 -9999 0 -0.52 24 24
911 complex 0 0.004 -9999 0 -10000 0 0
IFNG -0.03 0.1 -9999 0 -0.28 150 150
Telomerase/PinX1 -0.052 0.078 -9999 0 -0.55 3 3
Telomerase/AKT1/mTOR/p70S6K 0.003 0.055 -9999 0 -10000 0 0
SIN3B 0.006 0.006 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.052 0.078 -9999 0 -0.52 4 4
response to DNA damage stimulus 0.003 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN 0 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.052 0.078 -9999 0 -0.55 3 3
E2F1 -0.085 0.14 -9999 0 -0.29 345 345
ZNFX1 0.006 0.006 -9999 0 -10000 0 0
PIF1 -0.061 0.12 -9999 0 -0.29 227 227
NCL 0 0 -9999 0 -10000 0 0
DKC1 -0.001 0.013 -9999 0 -0.29 2 2
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Syndecan-4-mediated signaling events

Figure S73.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S73.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.002 0.036 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.024 0.037 -9999 0 -0.63 1 1
positive regulation of JNK cascade -0.05 0.1 -9999 0 -0.51 2 2
Syndecan-4/ADAM12 -0.032 0.055 -9999 0 -0.63 1 1
CCL5 -0.014 0.079 -9999 0 -0.36 44 44
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0 0 -9999 0 -10000 0 0
ITGA5 0 0.009 -9999 0 -0.29 1 1
SDCBP 0 0 -9999 0 -10000 0 0
PLG -0.001 0.026 -9999 0 -0.29 8 8
ADAM12 -0.019 0.077 -9999 0 -0.31 68 68
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 -0.001 0.02 -9999 0 -0.29 5 5
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.054 0.044 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.07 0.13 -9999 0 -0.59 5 5
Syndecan-4/CXCL12/CXCR4 -0.053 0.11 -9999 0 -0.6 1 1
Syndecan-4/Laminin alpha3 -0.13 0.19 -9999 0 -0.5 120 120
MDK -0.012 0.057 -9999 0 -0.29 43 43
Syndecan-4/FZD7 -0.033 0.068 -9999 0 -0.56 2 2
Syndecan-4/Midkine -0.028 0.042 -9999 0 -0.63 1 1
FZD7 -0.017 0.11 -9999 0 -0.79 23 23
Syndecan-4/FGFR1/FGF -0.19 0.2 -9999 0 -0.67 15 15
THBS1 -0.004 0.053 -9999 0 -0.79 5 5
integrin-mediated signaling pathway -0.034 0.072 -9999 0 -0.7 2 2
positive regulation of MAPKKK cascade -0.05 0.1 -9999 0 -0.51 2 2
Syndecan-4/TACI -0.036 0.066 -9999 0 -0.52 5 5
CXCR4 -0.007 0.045 -9999 0 -0.29 26 26
cell adhesion -0.02 0.061 -9999 0 -0.34 29 29
Syndecan-4/Dynamin -0.024 0.036 -9999 0 -0.63 1 1
Syndecan-4/TSP1 -0.026 0.046 -9999 0 -0.63 1 1
Syndecan-4/GIPC -0.024 0.036 -9999 0 -0.63 1 1
Syndecan-4/RANTES -0.03 0.052 -9999 0 -0.57 2 2
ITGB1 0 0 -9999 0 -10000 0 0
LAMA1 -0.088 0.25 -9999 0 -0.77 124 124
LAMA3 -0.2 0.34 -9999 0 -0.79 276 276
RAC1 0 0 -9999 0 -10000 0 0
PRKCA 0.004 0.13 -9999 0 -0.72 31 31
Syndecan-4/alpha-Actinin -0.024 0.038 -9999 0 -0.63 1 1
TFPI -0.041 0.18 -9999 0 -0.79 57 57
F2 0 0.034 -9999 0 -0.29 14 14
alpha5/beta1 Integrin 0 0.006 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.16 0.23 -9999 0 -0.58 113 113
ACTN1 -0.001 0.024 -9999 0 -0.79 1 1
TNC -0.022 0.12 -9999 0 -0.64 37 37
Syndecan-4/CXCL12 -0.056 0.11 -9999 0 -0.5 7 7
FGF6 -0.001 0.034 -9999 0 -0.79 2 2
RHOA 0 0 -9999 0 -10000 0 0
CXCL12 -0.061 0.21 -9999 0 -0.79 85 85
TNFRSF13B -0.028 0.11 -9999 0 -0.39 78 78
FGF2 -0.32 0.39 -9999 0 -0.79 446 446
FGFR1 -0.009 0.08 -9999 0 -0.68 14 14
Syndecan-4/PI-4-5-P2 -0.018 0.048 -9999 0 -0.64 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.11 0.15 -9999 0 -0.3 431 431
cell migration -0.024 0.019 -9999 0 -10000 0 0
PRKCD 0.005 0.014 -9999 0 -0.29 1 1
vasculogenesis -0.025 0.044 -9999 0 -0.6 1 1
SDC4 -0.018 0.051 -9999 0 -0.68 1 1
Syndecan-4/Tenascin C -0.035 0.075 -9999 0 -0.74 2 2
Syndecan-4/PI-4-5-P2/PKC alpha -0.043 0.035 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.024 0.036 -9999 0 -0.63 1 1
MMP9 -0.12 0.15 -9999 0 -0.29 483 483
Rac1/GTP -0.028 0.057 -9999 0 -0.34 29 29
cytoskeleton organization -0.024 0.036 -9999 0 -0.6 1 1
GIPC1 0 0.009 -9999 0 -0.29 1 1
Syndecan-4/TFPI -0.046 0.098 -9999 0 -0.52 8 8
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.002 0.01 -10000 0 -10000 0 0
HSPA8 0.001 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.099 0.2 0.25 1 -0.56 165 166
AKT1 0.014 0.006 -10000 0 -10000 0 0
GSC -0.036 0.3 -10000 0 -1.5 42 42
NKX2-5 -0.045 0.1 -10000 0 -0.29 171 171
muscle cell differentiation 0.007 0.051 0.76 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.006 0.04 -10000 0 -0.45 2 2
SMAD4 0.014 0.041 -10000 0 -0.82 1 1
CBFB 0 0 -10000 0 -10000 0 0
SAP18 0.001 0.002 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.19 0.25 -10000 0 -0.51 406 406
SMAD3/SMAD4/VDR 0.005 0.03 -10000 0 -0.43 2 2
MYC -0.017 0.12 -10000 0 -0.79 24 24
CDKN2B 0.029 0.13 -10000 0 -1.5 7 7
AP1 -0.12 0.2 -10000 0 -0.41 329 329
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.002 0.02 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.001 0.041 -10000 0 -0.32 4 4
SP3 0 0 -10000 0 -10000 0 0
CREB1 0 0 -10000 0 -10000 0 0
FOXH1 -0.044 0.12 -10000 0 -0.29 204 204
SMAD3/SMAD4/GR -0.01 0.073 -10000 0 -0.56 17 17
GATA3 -0.037 0.15 -10000 0 -0.57 70 70
SKI/SIN3/HDAC complex/NCoR1 0.002 0.014 -10000 0 -10000 0 0
MEF2C/TIF2 -0.055 0.13 -10000 0 -0.54 57 57
endothelial cell migration -0.008 0.06 1.5 1 -10000 0 1
MAX 0.001 0.005 -10000 0 -10000 0 0
RBBP7 -0.002 0.025 -10000 0 -0.29 8 8
RBBP4 0 0.024 -10000 0 -0.79 1 1
RUNX2 -0.005 0.036 -10000 0 -0.29 17 17
RUNX3 -0.006 0.066 -10000 0 -0.79 7 7
RUNX1 -0.001 0.024 -10000 0 -0.79 1 1
CTBP1 0 0 -10000 0 -10000 0 0
NR3C1 -0.011 0.095 -10000 0 -0.79 16 16
VDR 0 0 -10000 0 -10000 0 0
CDKN1A 0.05 0.078 -10000 0 -1.5 2 2
KAT2B 0 0.024 -10000 0 -0.79 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.03 0.072 -10000 0 -0.46 6 6
DCP1A 0 0 -10000 0 -10000 0 0
SKI 0.001 0.002 -10000 0 -10000 0 0
SERPINE1 0.007 0.061 -10000 0 -1.5 1 1
SMAD3/SMAD4/ATF2 -0.003 0.04 -10000 0 -0.56 4 4
SMAD3/SMAD4/ATF3 -0.078 0.19 -10000 0 -0.55 154 154
SAP30 -0.001 0.018 -10000 0 -0.29 4 4
Cbp/p300/PIAS3 0.005 0.023 -10000 0 -10000 0 0
JUN -0.074 0.22 -10000 0 -0.4 323 323
SMAD3/SMAD4/IRF7 -0.02 0.068 -10000 0 -0.36 18 18
TFE3 0.017 0.006 -10000 0 -10000 0 0
COL1A2 0.027 0.1 -10000 0 -1.2 3 3
mesenchymal cell differentiation 0.004 0.034 0.54 1 -10000 0 1
DLX1 -0.053 0.13 -10000 0 -0.32 184 184
TCF3 0 0.009 -10000 0 -10000 0 0
FOS -0.22 0.37 -10000 0 -0.78 329 329
SMAD3/SMAD4/Max -0.002 0.029 -10000 0 -0.54 1 1
Cbp/p300/SNIP1 0 0.002 -10000 0 -10000 0 0
ZBTB17 0 0.006 -10000 0 -10000 0 0
LAMC1 0.042 0.047 -10000 0 -0.62 2 2
TGIF2/HDAC complex/SMAD3/SMAD4 -0.001 0.028 -10000 0 -0.54 1 1
IRF7 -0.031 0.092 -10000 0 -0.31 104 104
ESR1 -0.15 0.28 -10000 0 -0.58 287 287
HNF4A -0.006 0.041 -10000 0 -0.29 22 22
MEF2C 0 0.097 -10000 0 -0.62 5 5
SMAD2-3/SMAD4 -0.003 0.033 -10000 0 -0.53 1 1
Cbp/p300/Src-1 0.003 0.022 -10000 0 -0.52 1 1
IGHV3OR16-13 -0.001 0.01 -10000 0 -10000 0 0
TGIF2/HDAC complex 0 0 -10000 0 -10000 0 0
CREBBP 0.002 0.007 -10000 0 -10000 0 0
SKIL -0.003 0.029 -10000 0 -0.29 11 11
HDAC1 0.001 0.002 -10000 0 -10000 0 0
HDAC2 0.001 0.002 -10000 0 -10000 0 0
SNIP1 0.001 0.003 -10000 0 -10000 0 0
GCN5L2 0.001 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.001 0.029 -10000 0 -0.53 1 1
MSG1/HSC70 -0.22 0.29 -10000 0 -0.6 406 406
SMAD2 0.015 0.02 -10000 0 -10000 0 0
SMAD3 0.015 0.029 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.034 0.038 -10000 0 -0.35 2 2
SMAD2/SMAD2/SMAD4 0.026 0.039 -10000 0 -1.1 1 1
NCOR1 0 0.024 -10000 0 -0.79 1 1
NCOA2 -0.039 0.17 -10000 0 -0.79 54 54
NCOA1 -0.001 0.024 -10000 0 -0.79 1 1
MYOD/E2A -0.003 0.022 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.028 0.051 -10000 0 -0.41 2 2
IFNB1 0.011 0.093 -10000 0 -0.42 18 18
SMAD3/SMAD4/MEF2C -0.027 0.078 -10000 0 -0.76 3 3
CITED1 -0.3 0.38 -10000 0 -0.77 421 421
SMAD2-3/SMAD4/ARC105 -0.001 0.028 -10000 0 -0.47 1 1
RBL1 -0.003 0.043 -10000 0 -0.59 5 5
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.047 0.062 -10000 0 -0.49 7 7
RUNX1-3/PEBPB2 -0.004 0.049 -10000 0 -0.58 7 7
SMAD7 -0.067 0.14 -10000 0 -0.58 8 8
MYC/MIZ-1 -0.012 0.09 -10000 0 -0.61 24 24
SMAD3/SMAD4 0.017 0.06 0.29 22 -0.43 2 24
IL10 0.018 0.12 -10000 0 -0.5 42 42
PIASy/HDAC complex 0.011 0.004 -10000 0 -10000 0 0
PIAS3 0.001 0.005 -10000 0 -10000 0 0
CDK2 0.002 0.008 -10000 0 -10000 0 0
IL5 0.014 0.11 -10000 0 -0.5 40 40
CDK4 0.001 0.02 -10000 0 -0.29 4 4
PIAS4 0.011 0.004 -10000 0 -10000 0 0
ATF3 -0.11 0.27 -10000 0 -0.78 154 154
SMAD3/SMAD4/SP1 0 0.032 -10000 0 -0.52 2 2
FOXG1 -0.023 0.077 -10000 0 -0.29 80 80
FOXO3 0.025 0.034 -10000 0 -0.6 3 3
FOXO1 0.02 0.066 -10000 0 -0.6 12 12
FOXO4 0.026 0.008 -10000 0 -10000 0 0
heart looping 0 0.096 -10000 0 -0.61 5 5
CEBPB 0.012 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.029 0.078 -10000 0 -0.55 10 10
MYOD1 -0.004 0.033 -10000 0 -0.29 14 14
SMAD3/SMAD4/HNF4 -0.006 0.037 -10000 0 -0.68 1 1
SMAD3/SMAD4/GATA3 -0.024 0.11 -10000 0 -0.56 40 40
SnoN/SIN3/HDAC complex/NCoR1 -0.003 0.029 -10000 0 -0.29 11 11
SMAD3/SMAD4/RUNX1-3/PEBPB2 0 0.051 -10000 0 -0.52 8 8
SMAD3/SMAD4/SP1-3 0.003 0.029 -10000 0 -0.45 2 2
MED15 0 0 -10000 0 -10000 0 0
SP1 0.019 0.015 -10000 0 -10000 0 0
SIN3B 0.001 0.002 -10000 0 -10000 0 0
SIN3A 0.001 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.014 0.091 -10000 0 -0.4 13 13
ITGB5 0.052 0.046 -10000 0 -0.41 1 1
TGIF/SIN3/HDAC complex/CtBP 0.002 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.074 0.19 -10000 0 -0.55 147 147
AR -0.1 0.27 -10000 0 -0.78 147 147
negative regulation of cell growth -0.025 0.072 -10000 0 -0.48 2 2
SMAD3/SMAD4/MYOD -0.006 0.034 -10000 0 -0.54 1 1
E2F5 -0.005 0.039 -10000 0 -0.29 20 20
E2F4 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.002 0.057 -10000 0 -0.44 2 2
SMAD2-3/SMAD4/FOXO1-3a-4 0.002 0.046 -10000 0 -0.32 9 9
TFDP1 -0.001 0.018 -10000 0 -0.29 4 4
SMAD3/SMAD4/AP1 -0.12 0.2 -10000 0 -0.43 192 192
SMAD3/SMAD4/RUNX2 -0.004 0.034 -10000 0 -0.54 1 1
TGIF2 0 0 -10000 0 -10000 0 0
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 -0.002 0.041 -10000 0 -0.79 3 3
Syndecan-2-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
Syndecan-2/Fibronectin -0.06 0.077 -9999 0 -0.42 7 7
EPHB2 -0.005 0.038 -9999 0 -0.29 19 19
Syndecan-2/TACI -0.018 0.075 -9999 0 -0.52 19 19
LAMA1 -0.088 0.25 -9999 0 -0.77 124 124
Syndecan-2/alpha2 ITGB1 -0.12 0.21 -9999 0 -0.46 293 293
HRAS -0.003 0.028 -9999 0 -0.29 10 10
Syndecan-2/CASK -0.003 0.033 -9999 0 -0.52 4 4
ITGA5 0 0.009 -9999 0 -0.29 1 1
BAX 0.033 0.061 -9999 0 -0.72 3 3
EPB41 0 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.002 0.03 -9999 0 -0.47 4 4
LAMA3 -0.2 0.34 -9999 0 -0.79 276 276
EZR -0.001 0.015 -9999 0 -0.29 3 3
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.1 0.27 -9999 0 -0.79 146 146
Syndecan-2/MMP2 -0.008 0.07 -9999 0 -0.63 12 12
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.016 0.096 -9999 0 -0.6 29 29
dendrite morphogenesis -0.005 0.037 -9999 0 -0.51 4 4
Syndecan-2/GM-CSF -0.006 0.039 -9999 0 -0.52 4 4
determination of left/right symmetry 0.017 0.039 -9999 0 -0.6 4 4
Syndecan-2/PKC delta -0.003 0.033 -9999 0 -0.52 4 4
GNB2L1 0 0 -9999 0 -10000 0 0
MAPK3 0.022 0.039 -9999 0 -0.47 4 4
MAPK1 0.022 0.039 -9999 0 -0.47 4 4
Syndecan-2/RACK1 -0.003 0.032 -9999 0 -0.48 4 4
NF1 -0.001 0.024 -9999 0 -0.79 1 1
FGFR/FGF/Syndecan-2 0.017 0.039 -9999 0 -0.6 4 4
ITGA2 -0.021 0.13 -9999 0 -0.79 29 29
MAPK8 0.027 0.065 -9999 0 -0.57 12 12
Syndecan-2/alpha2/beta1 Integrin -0.062 0.18 -9999 0 -0.5 133 133
Syndecan-2/Kininogen -0.005 0.039 -9999 0 -0.52 4 4
ITGB1 0 0 -9999 0 -10000 0 0
SRC -0.003 0.029 -9999 0 -0.45 4 4
Syndecan-2/CASK/Protein 4.1 -0.002 0.03 -9999 0 -0.48 4 4
extracellular matrix organization -0.003 0.033 -9999 0 -0.51 4 4
actin cytoskeleton reorganization -0.06 0.077 -9999 0 -0.42 7 7
Syndecan-2/Caveolin-2/Ras -0.066 0.17 -9999 0 -0.48 146 146
Syndecan-2/Laminin alpha3 -0.13 0.23 -9999 0 -0.52 280 280
Syndecan-2/RasGAP -0.003 0.03 -9999 0 -0.45 4 4
alpha5/beta1 Integrin 0 0.006 -9999 0 -10000 0 0
PRKCD 0 0.009 -9999 0 -0.29 1 1
Syndecan-2 dimer -0.005 0.037 -9999 0 -0.52 4 4
GO:0007205 0 0.002 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.003 0.028 -9999 0 -0.43 4 4
RHOA 0 0 -9999 0 -10000 0 0
SDCBP 0 0 -9999 0 -10000 0 0
TNFRSF13B -0.028 0.11 -9999 0 -0.39 78 78
RASA1 0 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.016 0.096 -9999 0 -0.6 29 29
Syndecan-2/Synbindin -0.002 0.032 -9999 0 -0.52 4 4
TGFB1 -0.001 0.015 -9999 0 -0.29 3 3
CASP3 0.03 0.032 -9999 0 -0.46 4 4
FN1 -0.12 0.14 -9999 0 -0.29 431 431
Syndecan-2/IL8 -0.022 0.085 -9999 0 -0.52 26 26
SDC2 0.017 0.04 -9999 0 -0.6 4 4
KNG1 -0.006 0.041 -9999 0 -10000 0 0
Syndecan-2/Neurofibromin -0.003 0.036 -9999 0 -0.52 5 5
TRAPPC4 0 0 -9999 0 -10000 0 0
CSF2 -0.007 0.045 -9999 0 -0.29 26 26
Syndecan-2/TGFB1 -0.003 0.033 -9999 0 -0.52 4 4
Syndecan-2/Syntenin/PI-4-5-P2 -0.002 0.03 -9999 0 -0.48 4 4
Syndecan-2/Ezrin -0.002 0.03 -9999 0 -0.47 4 4
PRKACA 0.029 0.035 -9999 0 -0.47 5 5
angiogenesis -0.021 0.085 -9999 0 -0.52 26 26
MMP2 -0.008 0.079 -9999 0 -0.75 12 12
IL8 -0.033 0.13 -9999 0 -0.42 87 87
calcineurin-NFAT signaling pathway -0.018 0.075 -9999 0 -0.52 19 19
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.018 0.12 -9999 0 -0.77 26 26
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 -0.001 0.024 -9999 0 -0.79 1 1
RAC1-CDC42/GTP/PAK family -0.12 0.14 -9999 0 -0.27 487 487
response to UV 0 0 -9999 0 -10000 0 0
YES1 -0.001 0.024 -9999 0 -0.79 1 1
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0 0 -9999 0 -10000 0 0
FYN -0.001 0.034 -9999 0 -0.79 2 2
MAP3K12 0 0 -9999 0 -10000 0 0
FGR -0.001 0.025 -9999 0 -0.54 2 2
p38 alpha/TAB1 -0.007 0.033 -9999 0 -0.32 4 4
PRKG1 -0.053 0.2 -9999 0 -0.79 74 74
DUSP8 -0.002 0.042 -9999 0 -0.66 4 4
PGK/cGMP/p38 alpha -0.032 0.1 -9999 0 -0.39 77 77
apoptosis -0.006 0.032 -9999 0 -0.3 4 4
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0 0 -9999 0 -10000 0 0
DUSP1 -0.1 0.26 -9999 0 -0.79 142 142
PAK1 -0.007 0.044 -9999 0 -0.29 25 25
SRC 0 0.009 -9999 0 -0.29 1 1
RAC1/OSM/MEKK3/MKK3 0 0.006 -9999 0 -10000 0 0
TRAF6 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 -0.001 0.013 -9999 0 -0.29 2 2
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.018 0.068 -9999 0 -0.34 21 21
BLK -0.044 0.11 -9999 0 -0.3 159 159
HCK -0.004 0.033 -9999 0 -10000 0 0
MAP2K3 0 0.009 -9999 0 -0.29 1 1
DUSP16 0 0 -9999 0 -10000 0 0
DUSP10 -0.001 0.015 -9999 0 -0.29 3 3
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.029 0.048 -9999 0 -0.34 4 4
positive regulation of innate immune response 0.024 0.074 -9999 0 -0.36 21 21
LCK -0.02 0.1 -9999 0 -0.41 53 53
p38alpha-beta/MKP7 -0.012 0.054 -9999 0 -0.38 8 8
p38alpha-beta/MKP5 -0.012 0.054 -9999 0 -0.34 20 20
PGK/cGMP -0.041 0.15 -9999 0 -0.61 74 74
PAK2 0 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.058 0.13 -9999 0 -0.37 158 158
CDC42 0 0 -9999 0 -10000 0 0
RALB 0 0 -9999 0 -10000 0 0
RALA 0 0 -9999 0 -10000 0 0
PAK3 -0.35 0.39 -9999 0 -0.79 487 487
TCGA08_retinoblastoma

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
CDKN2B -0.003 0.063 -10000 0 -0.66 9 9
CDKN2C 0.006 0.037 -10000 0 -0.78 2 2
CDKN2A -0.052 0.12 -10000 0 -0.31 188 188
CCND2 0.006 0.033 0.24 8 -0.16 12 20
RB1 -0.007 0.032 0.19 4 -0.25 8 12
CDK4 0.01 0.03 0.25 9 -10000 0 9
CDK6 0.006 0.039 0.27 8 -0.21 14 22
G1/S progression -0.006 0.036 0.25 8 -0.18 4 12
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.037 0.084 -9999 0 -0.43 37 37
NF kappa B1 p50/RelA/I kappa B alpha -0.023 0.069 -9999 0 -0.46 6 6
alphaV/beta3 Integrin/Osteopontin/Src -0.046 0.076 -9999 0 -10000 0 0
AP1 -0.14 0.21 -9999 0 -0.79 38 38
ILK -0.006 0.11 -9999 0 -0.46 37 37
bone resorption -0.038 0.11 -9999 0 -0.67 22 22
PTK2B 0 0 -9999 0 -10000 0 0
PYK2/p130Cas 0.004 0.089 -9999 0 -0.48 10 10
ITGAV 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.018 0.1 -9999 0 -0.6 32 32
alphaV/beta3 Integrin/Osteopontin -0.05 0.1 -9999 0 -0.52 37 37
MAP3K1 -0.007 0.11 -9999 0 -0.48 37 37
JUN -0.005 0.063 -9999 0 -0.79 7 7
MAPK3 0.009 0.1 -9999 0 -0.43 37 37
MAPK1 0.009 0.1 -9999 0 -0.43 37 37
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 0.002 0.13 -9999 0 -0.53 39 39
ITGB3 -0.027 0.14 -9999 0 -0.78 37 37
NFKBIA 0.022 0.1 -9999 0 -0.48 10 10
FOS -0.24 0.36 -9999 0 -0.79 329 329
CD44 -0.001 0.015 -9999 0 -0.29 3 3
CHUK 0 0 -9999 0 -10000 0 0
PLAU 0.021 0.1 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.022 0.065 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.021 0.11 -9999 0 -0.59 37 37
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.008 0.11 -9999 0 -0.47 37 37
VAV3 -0.002 0.11 -9999 0 -0.44 44 44
MAP3K14 -0.004 0.11 -9999 0 -0.47 37 37
ROCK2 -0.023 0.13 -9999 0 -0.79 32 32
SPP1 -0.075 0.12 -9999 0 -0.28 288 288
RAC1 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.036 0.083 -9999 0 -0.45 16 16
MMP2 -0.074 0.21 -9999 0 -0.68 38 38
IL2 signaling events mediated by STAT5

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
GAB2 0.008 0.043 -9999 0 -0.39 10 10
ELF1 -0.012 0.051 -9999 0 -0.38 16 16
CCNA2 -0.11 0.14 -9999 0 -0.29 427 427
PIK3CA 0.012 0.009 -9999 0 -0.29 1 1
JAK3 0.008 0.034 -9999 0 -0.29 14 14
PIK3R1 0.001 0.09 -9999 0 -0.79 14 14
JAK1 0.011 0.024 -9999 0 -0.79 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.057 0.08 -9999 0 -0.58 9 9
SHC1 0.012 0.001 -9999 0 -10000 0 0
SP1 -0.005 0.041 -9999 0 -0.38 13 13
IL2RA 0.001 0.13 -9999 0 -1 16 16
IL2RB -0.001 0.066 -9999 0 -0.32 42 42
SOS1 0.012 0.001 -9999 0 -10000 0 0
IL2RG -0.006 0.087 -9999 0 -0.36 53 53
G1/S transition of mitotic cell cycle 0.004 0.13 -9999 0 -0.8 24 24
PTPN11 0.012 0.001 -9999 0 -10000 0 0
CCND2 0.017 0.11 -9999 0 -1 13 13
LCK -0.009 0.1 -9999 0 -0.41 53 53
GRB2 0.011 0.009 -9999 0 -0.29 1 1
IL2 0.004 0.026 -9999 0 -0.29 8 8
CDK6 -0.011 0.092 -9999 0 -0.73 17 17
CCND3 0.063 0.071 -9999 0 -0.57 5 5
Thromboxane A2 receptor signaling

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
TGM2 0.005 0.035 -10000 0 -0.29 15 15
GNB1/GNG2 -0.015 0.048 -10000 0 -0.19 68 68
AKT1 0.05 0.072 -10000 0 -0.21 32 32
EGF -0.15 0.31 -10000 0 -0.78 214 214
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.01 0.053 -10000 0 -0.45 5 5
mol:Ca2+ 0.047 0.1 -10000 0 -0.3 64 64
LYN -0.01 0.05 -10000 0 -0.51 2 2
RhoA/GTP -0.008 0.03 -10000 0 -0.14 7 7
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.052 0.11 -10000 0 -0.35 64 64
GNG2 -0.011 0.092 -10000 0 -0.79 15 15
ARRB2 0 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.028 0.063 -10000 0 -0.55 9 9
G beta5/gamma2 -0.019 0.065 -10000 0 -0.28 40 40
PRKCH 0.048 0.11 -10000 0 -0.35 64 64
DNM1 -0.005 0.063 -10000 0 -0.73 8 8
TXA2/TP beta/beta Arrestin3 -0.004 0.026 -10000 0 -0.3 7 7
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.031 0.15 -10000 0 -0.71 47 47
G12 family/GTP -0.021 0.073 -10000 0 -0.31 64 64
ADRBK1 0 0 -10000 0 -10000 0 0
ADRBK2 -0.004 0.053 -10000 0 -0.79 5 5
RhoA/GTP/ROCK1 0 0.016 -10000 0 -0.52 1 1
mol:GDP -0.036 0.081 0.36 23 -10000 0 23
mol:NADP 0 0 -10000 0 -10000 0 0
RAB11A -0.001 0.013 -10000 0 -0.29 2 2
PRKG1 -0.053 0.2 -10000 0 -0.79 74 74
mol:IP3 0.047 0.12 -10000 0 -0.38 64 64
cell morphogenesis 0 0.016 -10000 0 -0.52 1 1
PLCB2 0.044 0.15 -10000 0 -0.52 64 64
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.008 0.062 -10000 0 -0.41 8 8
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.011 0.051 -10000 0 -0.51 2 2
RHOA 0 0 -10000 0 -10000 0 0
PTGIR -0.002 0.026 -10000 0 -0.29 9 9
PRKCB1 0.045 0.12 -10000 0 -0.38 64 64
GNAQ -0.002 0.041 -10000 0 -0.79 3 3
mol:L-citrulline 0 0 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.047 0.16 -10000 0 -0.54 64 64
LCK -0.015 0.071 -10000 0 -0.46 16 16
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.012 0.056 -10000 0 -0.35 1 1
TXA2-R family/G12 family/GDP/G beta/gamma 0.024 0.037 -10000 0 -0.29 9 9
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.011 0.055 -10000 0 -0.34 1 1
MAPK14 0.051 0.079 -10000 0 -0.23 64 64
TGM2/GTP 0.047 0.13 -10000 0 -0.43 64 64
MAPK11 0.051 0.082 -10000 0 -0.24 64 64
ARHGEF1 0.039 0.061 -10000 0 -0.18 37 37
GNAI2 0 0 -10000 0 -10000 0 0
JNK cascade 0.049 0.12 -10000 0 -0.4 64 64
RAB11/GDP -0.001 0.012 -10000 0 -0.29 2 2
ICAM1 0.046 0.093 -10000 0 -0.28 64 64
cAMP biosynthetic process 0.043 0.12 -10000 0 -0.36 64 64
Gq family/GTP/EBP50 0.017 0.04 -10000 0 -0.32 5 5
actin cytoskeleton reorganization 0 0.016 -10000 0 -0.52 1 1
SRC -0.01 0.05 -10000 0 -0.41 4 4
GNB5 0 0 -10000 0 -10000 0 0
GNB1 0 0 -10000 0 -10000 0 0
EGF/EGFR -0.028 0.1 -10000 0 -0.32 34 34
VCAM1 0.044 0.1 -10000 0 -0.32 64 64
TP beta/Gq family/GDP/G beta5/gamma2 0.028 0.063 -10000 0 -0.55 9 9
platelet activation 0.066 0.1 -10000 0 -0.31 64 64
PGI2/IP -0.002 0.018 -10000 0 -10000 0 0
PRKACA -0.014 0.07 -10000 0 -0.37 40 40
Gq family/GDP/G beta5/gamma2 0.026 0.065 -10000 0 -0.55 9 9
TXA2/TP beta/beta Arrestin2 -0.005 0.052 -10000 0 -0.65 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.01 0.07 -10000 0 -0.34 40 40
mol:DAG 0.046 0.13 -10000 0 -0.42 64 64
EGFR -0.29 0.38 -10000 0 -0.78 410 410
TXA2/TP alpha 0.048 0.15 -10000 0 -0.5 64 64
Gq family/GTP -0.004 0.036 -10000 0 -0.27 18 18
YES1 -0.01 0.051 -10000 0 -0.42 4 4
GNAI2/GTP -0.012 0.058 -10000 0 -0.46 5 5
PGD2/DP -0.024 0.12 -10000 0 -0.55 47 47
SLC9A3R1 -0.026 0.083 -10000 0 -0.29 97 97
FYN -0.011 0.054 -10000 0 -0.43 6 6
mol:NO 0 0 -10000 0 -10000 0 0
GNA15 -0.003 0.033 -10000 0 -0.36 8 8
PGK/cGMP -0.036 0.13 -10000 0 -0.52 74 74
RhoA/GDP 0 0 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.017 0.082 -10000 0 -0.56 15 15
NOS3 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCA 0.041 0.13 -10000 0 -0.38 72 72
PRKCB 0.043 0.12 -10000 0 -0.37 72 72
PRKCE 0.05 0.11 -10000 0 -0.35 64 64
PRKCD 0.048 0.12 -10000 0 -0.38 64 64
PRKCG 0.044 0.12 -10000 0 -0.39 64 64
muscle contraction 0.05 0.15 -10000 0 -0.5 64 64
PRKCZ 0.052 0.11 -10000 0 -0.35 64 64
ARR3 -0.002 0.025 -10000 0 -0.29 8 8
TXA2/TP beta -0.013 0.065 -10000 0 -0.49 6 6
PRKCQ 0.037 0.14 -10000 0 -0.39 77 77
MAPKKK cascade 0.044 0.14 -10000 0 -0.48 64 64
SELE 0.038 0.12 -10000 0 -0.42 64 64
TP beta/GNAI2/GDP/G beta/gamma -0.016 0.082 -10000 0 -0.56 15 15
ROCK1 -0.001 0.024 -10000 0 -0.79 1 1
GNA14 -0.013 0.084 -10000 0 -0.46 30 30
chemotaxis 0.046 0.18 -10000 0 -0.62 64 64
GNA12 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
GNA11 -0.003 0.048 -10000 0 -0.79 4 4
Rac1/GTP 0 0 -10000 0 -10000 0 0
BCR signaling pathway

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
JUN 0.004 0.11 -10000 0 -0.44 36 36
IKBKB 0.015 0.053 -10000 0 -0.26 3 3
AKT1 0.002 0.082 0.24 2 -0.27 25 27
IKBKG 0.018 0.055 -10000 0 -0.28 3 3
CALM1 -0.011 0.092 -10000 0 -0.45 30 30
PIK3CA 0 0.009 -10000 0 -0.29 1 1
MAP3K1 -0.01 0.15 -10000 0 -0.66 32 32
MAP3K7 0 0.009 -10000 0 -0.29 1 1
mol:Ca2+ -0.019 0.097 -10000 0 -0.48 30 30
DOK1 -0.001 0.018 -10000 0 -0.29 4 4
AP-1 -0.041 0.11 -10000 0 -0.26 78 78
LYN 0 0.001 -10000 0 -10000 0 0
BLNK 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
BCR complex -0.079 0.21 -10000 0 -0.62 119 119
CD22 -0.061 0.18 -10000 0 -0.54 100 100
CAMK2G -0.002 0.086 -10000 0 -0.42 29 29
CSNK2A1 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.047 0.13 -10000 0 -0.76 16 16
GO:0007205 -0.02 0.098 -10000 0 -0.49 30 30
SYK 0 0.009 -10000 0 -0.29 1 1
ELK1 -0.011 0.093 -10000 0 -0.46 30 30
NFATC1 -0.018 0.13 -10000 0 -0.56 34 34
B-cell antigen/BCR complex -0.079 0.21 -10000 0 -0.62 119 119
PAG1/CSK -0.001 0.013 -10000 0 -10000 0 0
NFKBIB 0.015 0.02 -10000 0 -10000 0 0
HRAS -0.009 0.1 -10000 0 -0.47 31 31
NFKBIA 0.015 0.02 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.019 0.016 -10000 0 -10000 0 0
RasGAP/Csk -0.058 0.16 -10000 0 -0.51 100 100
mol:GDP -0.02 0.09 -10000 0 -0.46 30 30
PTEN -0.001 0.034 -10000 0 -0.79 2 2
CD79B -0.027 0.13 -10000 0 -0.58 52 52
NF-kappa-B/RelA/I kappa B alpha 0.019 0.016 -10000 0 -10000 0 0
GRB2 0 0.009 -10000 0 -0.29 1 1
PI3K/BCAP/CD19 -0.029 0.16 -10000 0 -0.47 101 101
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
mol:IP3 -0.029 0.096 -10000 0 -0.5 30 30
CSK 0 0 -10000 0 -10000 0 0
FOS -0.13 0.22 -10000 0 -0.44 349 349
CHUK 0.018 0.055 -10000 0 -0.28 3 3
IBTK 0 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.023 0.077 -10000 0 -0.48 18 18
PTPN6 -0.057 0.16 -10000 0 -0.72 41 41
RELA 0 0 -10000 0 -10000 0 0
BCL2A1 0.015 0.02 -10000 0 -0.12 1 1
VAV2 -0.071 0.16 -10000 0 -0.6 62 62
ubiquitin-dependent protein catabolic process 0.019 0.019 -10000 0 -10000 0 0
BTK -0.004 0.005 -10000 0 -10000 0 0
CD19 -0.081 0.17 -10000 0 -0.53 97 97
MAP4K1 -0.015 0.07 -10000 0 -0.31 53 53
CD72 -0.009 0.054 -10000 0 -0.31 32 32
PAG1 -0.001 0.02 -10000 0 -0.29 5 5
MAPK14 0.002 0.13 -10000 0 -0.54 31 31
SH3BP5 -0.001 0.024 -10000 0 -0.79 1 1
PIK3AP1 -0.01 0.1 0.27 1 -0.53 30 31
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.041 0.13 -10000 0 -0.47 85 85
RAF1 0 0.096 -10000 0 -0.44 30 30
RasGAP/p62DOK/SHIP -0.055 0.15 -10000 0 -0.49 100 100
CD79A -0.083 0.22 -10000 0 -0.53 171 171
re-entry into mitotic cell cycle -0.04 0.11 -10000 0 -0.26 75 75
RASA1 0 0 -10000 0 -10000 0 0
MAPK3 0.016 0.082 -10000 0 -0.42 17 17
MAPK1 0.016 0.082 -10000 0 -0.42 17 17
CD72/SHP1 -0.055 0.15 -10000 0 -0.68 41 41
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.001 0.13 -10000 0 -0.53 37 37
actin cytoskeleton organization -0.027 0.15 -10000 0 -0.64 33 33
NF-kappa-B/RelA 0.042 0.033 -10000 0 -10000 0 0
Calcineurin -0.02 0.07 -10000 0 -0.44 17 17
PI3K -0.06 0.13 -10000 0 -0.53 44 44
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.031 0.11 0.27 1 -0.57 30 31
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.048 0.17 -10000 0 -0.83 35 35
DAPP1 -0.05 0.19 -10000 0 -0.98 34 34
cytokine secretion -0.015 0.12 -10000 0 -0.52 34 34
mol:DAG -0.029 0.096 -10000 0 -0.5 30 30
PLCG2 -0.002 0.035 -10000 0 -0.62 3 3
MAP2K1 0.008 0.089 -10000 0 -0.48 17 17
B-cell antigen/BCR complex/FcgammaRIIB -0.07 0.19 -10000 0 -0.6 100 100
mol:PI-3-4-5-P3 -0.044 0.093 0.34 2 -0.36 44 46
ETS1 0.004 0.089 -10000 0 -0.48 21 21
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.056 0.16 -10000 0 -0.51 97 97
B-cell antigen/BCR complex/LYN -0.057 0.18 -10000 0 -0.57 97 97
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0.001 0.003 -10000 0 -10000 0 0
RAC1 -0.03 0.16 -10000 0 -0.71 33 33
B-cell antigen/BCR complex/LYN/SYK -0.057 0.17 -10000 0 -0.55 98 98
CARD11 -0.014 0.1 -10000 0 -0.48 30 30
FCGR2B -0.004 0.054 -10000 0 -0.7 6 6
PPP3CA -0.001 0.013 -10000 0 -0.29 2 2
BCL10 0 0 -10000 0 -10000 0 0
IKK complex 0.017 0.027 -10000 0 -10000 0 0
PTPRC -0.008 0.07 -10000 0 -0.48 19 19
PDPK1 -0.029 0.063 0.22 2 -0.26 25 27
PPP3CB 0 0 -10000 0 -10000 0 0
PPP3CC 0 0 -10000 0 -10000 0 0
POU2F2 0.019 0.014 -10000 0 -0.14 1 1
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A -0.026 0.031 -9999 0 -10000 0 0
BIRC5 -0.21 0.13 -9999 0 -0.29 780 780
NFKBIA -0.024 0.034 -9999 0 -10000 0 0
CPEB1 -0.15 0.31 -9999 0 -0.78 204 204
AKT1 -0.024 0.034 -9999 0 -10000 0 0
NDEL1 0 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.024 0.033 -9999 0 -0.55 1 1
NDEL1/TACC3 -0.041 0.061 -9999 0 -10000 0 0
GADD45A 0 0 -9999 0 -10000 0 0
GSK3B 0.003 0.004 -9999 0 -10000 0 0
PAK1/Aurora A -0.03 0.04 -9999 0 -10000 0 0
MDM2 -0.001 0.02 -9999 0 -0.29 5 5
JUB -0.003 0.048 -9999 0 -0.79 4 4
TPX2 -0.11 0.1 -9999 0 -10000 0 0
TP53 -0.011 0.017 -9999 0 -10000 0 0
DLG7 -0.03 0.037 -9999 0 -10000 0 0
AURKAIP1 -0.003 0.031 -9999 0 -0.29 12 12
ARHGEF7 0 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.043 0.065 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.024 0.033 -9999 0 -0.54 1 1
AURKA -0.037 0.046 -9999 0 -10000 0 0
AURKB -0.009 0.011 -9999 0 -10000 0 0
CDC25B -0.018 0.026 -9999 0 -10000 0 0
G2/M transition checkpoint -0.025 0.04 -9999 0 -0.49 4 4
mRNA polyadenylation -0.11 0.19 -9999 0 -0.52 203 203
Aurora A/CPEB -0.11 0.2 -9999 0 -0.52 203 203
Aurora A/TACC1/TRAP/chTOG -0.032 0.089 -9999 0 -0.47 42 42
BRCA1 -0.001 0.027 -9999 0 -0.46 3 3
centrosome duplication -0.03 0.039 -9999 0 -10000 0 0
regulation of centrosome cycle -0.04 0.061 -9999 0 -10000 0 0
spindle assembly -0.032 0.088 -9999 0 -0.46 42 42
TDRD7 0 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.1 0.072 -9999 0 -0.61 1 1
CENPA -0.006 0.012 -9999 0 -10000 0 0
Aurora A/PP2A -0.026 0.031 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.006 0.029 -9999 0 -10000 0 0
negative regulation of DNA binding -0.009 0.02 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX -0.001 0.013 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.025 0.04 -9999 0 -0.49 4 4
mitotic prometaphase -0.013 0.011 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.037 0.046 -9999 0 -10000 0 0
TACC1 -0.03 0.15 -9999 0 -0.79 42 42
TACC3 -0.046 0.11 -9999 0 -0.29 173 173
Aurora A/Antizyme1 -0.022 0.025 -9999 0 -10000 0 0
Aurora A/RasGAP -0.026 0.031 -9999 0 -10000 0 0
OAZ1 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.003 0.004 -9999 0 -10000 0 0
GIT1 -0.001 0.02 -9999 0 -0.29 5 5
GIT1/beta-PIX/PAK1 -0.004 0.023 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.11 0.1 -9999 0 -10000 0 0
PPP2R5D 0 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.11 0.09 -9999 0 -10000 0 0
PAK1 -0.007 0.044 -9999 0 -0.29 25 25
CKAP5 0 0 -9999 0 -10000 0 0
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.44 0.39 -10000 0 -0.79 610 610
CLTC 0.027 0.018 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.024 0.02 -10000 0 -10000 0 0
Dynamin 2/GTP -0.007 0.028 -10000 0 -10000 0 0
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.025 0.019 -10000 0 -10000 0 0
CPE 0.006 0.081 -10000 0 -0.53 25 25
CTNNB1 0 0 -10000 0 -10000 0 0
membrane fusion -0.002 0.019 -10000 0 -10000 0 0
CTNND1 0.025 0.032 -10000 0 -10000 0 0
DNM2 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.029 0.014 -10000 0 -10000 0 0
TSHR -0.007 0.11 -10000 0 -0.53 49 49
INS 0.011 0.005 -10000 0 -10000 0 0
BIN1 -0.007 0.072 -10000 0 -0.79 9 9
mol:Choline -0.002 0.019 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.009 0.038 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.007 0.028 -10000 0 -10000 0 0
JUP 0.025 0.017 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.004 0.045 -10000 0 -0.48 10 10
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.018 0.049 -10000 0 -0.37 1 1
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0 0.009 -10000 0 -0.29 1 1
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 -0.005 0.037 -10000 0 -0.29 18 18
substrate adhesion-dependent cell spreading 0 0.001 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.008 0.032 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.018 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0.005 -10000 0 -10000 0 0
ACAP1 -0.001 0.019 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.02 0.015 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.032 0.022 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0 0 -10000 0 -10000 0 0
exocyst 0 0.001 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.025 0.031 -10000 0 -10000 0 0
NME1 0.009 0.038 -10000 0 -10000 0 0
clathrin coat assembly 0.027 0.018 -10000 0 -10000 0 0
IL2RA 0.017 0.045 -10000 0 -0.37 7 7
VAMP3 0.018 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.22 0.2 -10000 0 -0.39 610 610
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 -0.003 0.032 -10000 0 -0.34 10 10
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0 0 -10000 0 -10000 0 0
PIP5K1C 0.03 0.014 -10000 0 -10000 0 0
SDC1 0.021 0.024 -10000 0 -0.35 1 1
ARF6/GDP -0.008 0.034 -10000 0 -10000 0 0
EXOC7 0 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.008 0.033 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.002 0.019 -10000 0 -10000 0 0
endocytosis 0.004 0.045 0.47 10 -10000 0 10
SCAMP2 0 0 -10000 0 -10000 0 0
ADRB2 -0.071 0.19 -10000 0 -0.42 253 253
EXOC3 0 0 -10000 0 -10000 0 0
ASAP2 -0.001 0.024 -10000 0 -0.79 1 1
Dynamin 2/GDP -0.007 0.028 -10000 0 -10000 0 0
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 -0.13 0.22 -10000 0 -0.42 397 397
RALA 0 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.007 0.028 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.025 0.079 -9999 0 -0.2 188 188
TP53 -0.008 0.02 -9999 0 -10000 0 0
Senescence -0.008 0.02 -9999 0 -10000 0 0
Apoptosis -0.008 0.02 -9999 0 -10000 0 0
Activated_Oncogenes 0 0 -9999 0 -10000 0 0
MDM2 0.017 0.041 -9999 0 -10000 0 0
MDM4 0 0 -9999 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.024 0.077 0.32 36 -10000 0 36
GNAI2 0 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.005 0.035 -10000 0 -0.52 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.03 0.13 -10000 0 -0.48 67 67
RhoA/GTP -0.025 0.078 -10000 0 -0.32 36 36
negative regulation of cAMP metabolic process -0.028 0.087 -10000 0 -0.3 96 96
GNAZ -0.007 0.075 -10000 0 -0.79 10 10
GNAI3 0 0 -10000 0 -10000 0 0
GNA12 0 0 -10000 0 -10000 0 0
S1PR5 -0.008 0.058 -10000 0 -0.35 25 25
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.028 0.088 -10000 0 -0.3 96 96
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
GNAI1 -0.045 0.18 -10000 0 -0.79 62 62
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 -0.011 0.079 -10000 0 -0.6 19 19
ATM 0 0 -10000 0 -10000 0 0
UBE2D3 0 0 -10000 0 -10000 0 0
PRKDC -0.001 0.018 -10000 0 -0.29 4 4
ATR 0 0 -10000 0 -10000 0 0
UBE2L3 0 0 -10000 0 -10000 0 0
FANCD2 0.024 0.01 -10000 0 -10000 0 0
protein ubiquitination -0.029 0.073 -10000 0 -0.47 20 20
XRCC5 0 0 -10000 0 -10000 0 0
XRCC6 0 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0 0 -10000 0 -10000 0 0
DNA-PK -0.001 0.009 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.001 0.011 -10000 0 -10000 0 0
FANCF 0 0.009 -10000 0 -0.29 1 1
BRCA1 -0.001 0.027 -10000 0 -0.46 3 3
CCNE1 -0.06 0.12 -10000 0 -0.29 223 223
CDK2/Cyclin E1 -0.038 0.075 -10000 0 -10000 0 0
FANCG 0 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.011 0.081 -10000 0 -0.6 20 20
FANCE 0 0 -10000 0 -10000 0 0
FANCC 0 0 -10000 0 -10000 0 0
NBN 0 0 -10000 0 -10000 0 0
FANCA -0.051 0.11 -10000 0 -0.29 192 192
DNA repair 0.008 0.094 -10000 0 -0.47 6 6
BRCA1/BARD1/ubiquitin -0.011 0.081 -10000 0 -0.6 20 20
BARD1/DNA-PK -0.009 0.062 -10000 0 -0.47 19 19
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.011 0.079 0.6 19 -10000 0 19
BRCA1/BARD1/CTIP/M/R/N Complex -0.006 0.041 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 -0.01 0.07 -10000 0 -0.52 20 20
BRCA1/BARD1/P53 -0.009 0.063 -10000 0 -0.47 20 20
BARD1/CSTF1/BRCA1 -0.01 0.07 -10000 0 -0.52 20 20
BRCA1/BACH1 -0.001 0.027 -10000 0 -0.46 3 3
BARD1 -0.014 0.1 -10000 0 -0.76 20 20
PCNA -0.001 0.015 -10000 0 -0.29 3 3
BRCA1/BARD1/UbcH5C -0.01 0.07 -10000 0 -0.52 20 20
BRCA1/BARD1/UbcH7 -0.01 0.07 -10000 0 -0.52 20 20
BRCA1/BARD1/RAD51/PCNA -0.053 0.086 -10000 0 -0.51 20 20
BARD1/DNA-PK/P53 -0.008 0.057 -10000 0 -0.44 19 19
BRCA1/BARD1/Ubiquitin -0.011 0.081 -10000 0 -0.6 20 20
BRCA1/BARD1/CTIP -0.009 0.063 -10000 0 -0.47 20 20
FA complex -0.005 0.011 -10000 0 -10000 0 0
BARD1/EWS -0.011 0.079 -10000 0 -0.6 19 19
RBBP8 0.022 0.006 -10000 0 -10000 0 0
TP53 0 0 -10000 0 -10000 0 0
TOPBP1 0 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.009 0.063 0.46 20 -10000 0 20
BRCA1/BARD1 -0.029 0.074 -10000 0 -0.48 20 20
CSTF1 0 0.009 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.011 0.08 -10000 0 -0.61 19 19
CDK2 0 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.11 0.14 -10000 0 -0.29 396 396
RAD50 0 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.011 0.081 -10000 0 -0.6 20 20
EWSR1 0 0 -10000 0 -10000 0 0
Glypican 2 network

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
MDK -0.012 0.057 -9999 0 -0.29 43 43
GPC2 -0.038 0.1 -9999 0 -0.79 3 3
GPC2/Midkine -0.032 0.081 -9999 0 -0.4 19 19
neuron projection morphogenesis -0.032 0.081 -9999 0 -0.4 19 19
S1P4 pathway

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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.03 0.13 -9999 0 -0.48 67 67
CDC42/GTP -0.026 0.077 -9999 0 -0.31 40 40
PLCG1 0.008 0.092 -9999 0 -0.32 40 40
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.025 0.076 -9999 0 -0.3 40 40
S1PR5 -0.008 0.058 -9999 0 -0.35 25 25
S1PR4 -0.014 0.079 -9999 0 -0.36 44 44
MAPK3 0.008 0.092 -9999 0 -0.5 4 4
MAPK1 0.008 0.092 -9999 0 -0.32 40 40
S1P/S1P5/Gi -0.028 0.088 -9999 0 -0.3 96 96
GNAI1 -0.045 0.18 -9999 0 -0.79 62 62
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.005 0.035 -9999 0 -0.52 3 3
RHOA -0.006 0.038 -9999 0 -0.44 6 6
S1P/S1P4/Gi -0.029 0.087 -9999 0 -0.34 40 40
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.007 0.075 -9999 0 -0.79 10 10
S1P/S1P4/G12/G13 -0.007 0.042 -9999 0 -0.48 6 6
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.001 0.004 -9999 0 -10000 0 0
HDAC2 0.001 0.004 -9999 0 -10000 0 0
GNB1/GNG2 -0.011 0.081 -9999 0 -0.56 22 22
forebrain development -0.024 0.2 -9999 0 -0.51 136 136
GNAO1 -0.021 0.13 -9999 0 -0.48 67 67
SMO/beta Arrestin2 -0.005 0.055 -9999 0 -0.6 9 9
SMO 0.004 0.073 -9999 0 -0.79 9 9
ARRB2 0.011 0.004 -9999 0 -10000 0 0
GLI3/SPOP 0.044 0.037 -9999 0 -10000 0 0
mol:GTP 0 0.003 -9999 0 -10000 0 0
GSK3B 0 0 -9999 0 -10000 0 0
GNAI2 0.01 0.004 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0.007 -9999 0 -10000 0 0
GNAI1 -0.035 0.18 -9999 0 -0.79 62 62
XPO1 0.012 0.004 -9999 0 -10000 0 0
GLI1/Su(fu) -0.054 0.16 -9999 0 -0.67 37 37
SAP30 0 0.018 -9999 0 -0.29 4 4
mol:GDP 0.004 0.073 -9999 0 -0.79 9 9
MIM/GLI2A 0.002 0.028 -9999 0 -0.3 9 9
IFT88 0 0 -9999 0 -10000 0 0
GNAI3 0.01 0.004 -9999 0 -10000 0 0
GLI2 0.04 0.037 -9999 0 -10000 0 0
GLI3 0.04 0.039 -9999 0 -0.3 10 10
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
SAP18 0.001 0.004 -9999 0 -10000 0 0
embryonic digit morphogenesis 0 0 -9999 0 -10000 0 0
GNG2 -0.011 0.092 -9999 0 -0.79 15 15
Gi family/GTP -0.002 0.1 -9999 0 -0.36 50 50
SIN3B 0.001 0.004 -9999 0 -10000 0 0
SIN3A 0.001 0.004 -9999 0 -10000 0 0
GLI3/Su(fu) -0.002 0.025 -9999 0 -0.44 1 1
GLI2/Su(fu) 0.008 0.048 -9999 0 -0.39 7 7
FOXA2 -0.012 0.031 -9999 0 -10000 0 0
neural tube patterning -0.024 0.2 -9999 0 -0.51 136 136
SPOP 0 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 -0.002 0.026 -9999 0 -0.45 1 1
GNB1 0 0 -9999 0 -10000 0 0
CSNK1G2 0 0 -9999 0 -10000 0 0
CSNK1G3 0 0 -9999 0 -10000 0 0
MTSS1 0.002 0.028 -9999 0 -0.3 9 9
embryonic limb morphogenesis -0.024 0.2 -9999 0 -0.51 136 136
SUFU 0.004 0.032 -9999 0 -0.5 1 1
LGALS3 -0.012 0.095 -9999 0 -0.79 16 16
catabolic process -0.004 0.027 -9999 0 -10000 0 0
GLI3A/CBP -0.008 0.097 -9999 0 -0.38 70 70
KIF3A 0 0 -9999 0 -10000 0 0
GLI1 -0.026 0.21 -9999 0 -0.52 136 136
RAB23 0 0 -9999 0 -10000 0 0
CSNK1A1 0 0 -9999 0 -10000 0 0
IFT172 -0.001 0.024 -9999 0 -0.79 1 1
RBBP7 -0.001 0.025 -9999 0 -0.29 8 8
Su(fu)/Galectin3 -0.009 0.067 -9999 0 -0.51 17 17
GNAZ 0.003 0.076 -9999 0 -0.79 10 10
RBBP4 0.001 0.024 -9999 0 -0.79 1 1
CSNK1G1 0 0 -9999 0 -10000 0 0
PIAS1 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GLI2/SPOP -0.004 0.027 -9999 0 -10000 0 0
STK36 0.011 0.024 -9999 0 -0.79 1 1
Gi family/GNB1/GNG2/GDP -0.031 0.1 -9999 0 -0.57 18 18
PTCH1 -0.067 0.34 -9999 0 -1.1 95 95
MIM/GLI1 -0.018 0.19 -9999 0 -0.57 74 74
CREBBP -0.008 0.097 -9999 0 -0.38 70 70
Su(fu)/SIN3/HDAC complex 0.008 0.023 -9999 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.022 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0.007 -10000 0 -10000 0 0
CDKN1B 0.036 0.024 -10000 0 -0.42 3 3
CDKN1A 0.036 0.02 -10000 0 -0.42 2 2
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC -0.001 0.018 -10000 0 -0.29 4 4
FOXO3 0.036 0.024 -10000 0 -0.42 3 3
AKT1 0 0.001 -10000 0 -10000 0 0
BAD 0 0.009 -10000 0 -0.29 1 1
AKT3 0.008 0.061 -10000 0 -0.44 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.037 0.003 -10000 0 -10000 0 0
AKT1/ASK1 -0.001 0.025 -10000 0 -0.41 4 4
BAD/YWHAZ -0.001 0.009 -10000 0 -10000 0 0
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0 0 -10000 0 -10000 0 0
JNK cascade 0.001 0.024 0.39 4 -10000 0 4
TSC1 0.037 0.003 -10000 0 -10000 0 0
YWHAZ -0.001 0.015 -10000 0 -0.29 3 3
AKT1/RAF1 0 0.001 -10000 0 -10000 0 0
EP300 0 0 -10000 0 -10000 0 0
mol:GDP 0 0.001 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.037 0.003 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
TBC1D4 0.022 0.04 -10000 0 -0.51 6 6
MAP3K5 -0.003 0.048 -10000 0 -0.79 4 4
MAPKAP1 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.04 0.022 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
AKT1S1 0.037 0.003 -10000 0 -10000 0 0
CASP9 0.037 0.003 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 -0.001 0.021 -10000 0 -0.39 3 3
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0 0.006 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
SRC 0 0.009 -10000 0 -0.29 1 1
AKT2/p21CIP1 -0.001 0.017 -10000 0 -0.4 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.018 0.001 -10000 0 -10000 0 0
CHUK 0.037 0.003 -10000 0 -10000 0 0
BAD/BCL-XL 0 0.003 -10000 0 -10000 0 0
mTORC2 0 0 -10000 0 -10000 0 0
AKT2 0.017 0 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.053 0.03 -10000 0 -10000 0 0
PDPK1 0 0 -10000 0 -10000 0 0
MDM2 0.036 0.01 -10000 0 -10000 0 0
MAPKKK cascade 0 0.001 -10000 0 -10000 0 0
MDM2/Cbp/p300 0 0.005 -10000 0 -10000 0 0
TSC1/TSC2 0.044 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0.005 -10000 0 -10000 0 0
glucose import -0.25 0.25 -10000 0 -0.47 612 612
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.031 0.002 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.25 0.25 -10000 0 -0.47 612 612
GSK3A 0.037 0.003 -10000 0 -10000 0 0
FOXO1 0.032 0.048 -10000 0 -0.42 12 12
GSK3B 0.037 0.003 -10000 0 -10000 0 0
SFN -0.016 0.099 -10000 0 -0.5 36 36
G1/S transition of mitotic cell cycle 0.044 0.003 -10000 0 -10000 0 0
p27Kip1/14-3-3 family 0.042 0.032 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
KPNA1 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0.009 -10000 0 -0.29 1 1
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0 0 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
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 0.022 0.02 -10000 0 -0.6 1 1
MAP4K4 0.041 0.044 -10000 0 -0.68 1 1
BAG4 -0.006 0.055 -10000 0 -0.43 14 14
PKC zeta/ceramide -0.023 0.047 0.18 1 -0.57 1 2
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.077 -10000 0 -0.5 21 21
BAX -0.008 0.021 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
AKT1 0.024 0.009 -10000 0 -10000 0 0
BAD -0.021 0.045 0.2 1 -0.25 1 2
SMPD1 0.026 0.032 -10000 0 -0.24 13 13
RB1 -0.022 0.047 0.2 1 -0.47 1 2
FADD/Caspase 8 0.049 0.046 -10000 0 -0.64 1 1
MAP2K4 -0.014 0.046 -10000 0 -0.44 2 2
NSMAF 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.014 0.045 -10000 0 -0.45 1 1
EGF -0.15 0.31 -10000 0 -0.78 214 214
mol:ceramide -0.033 0.047 0.21 1 -10000 0 1
MADD 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.021 0.023 -10000 0 -0.6 1 1
ASAH1 -0.001 0.015 -10000 0 -0.29 3 3
negative regulation of cell cycle -0.022 0.046 0.2 1 -0.46 1 2
cell proliferation -0.094 0.16 -10000 0 -0.38 247 247
BID 0.024 0.033 -10000 0 -0.39 1 1
MAP3K1 -0.022 0.047 0.2 1 -0.47 1 2
EIF2A -0.005 0.04 -10000 0 -10000 0 0
TRADD 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
MAPK3 -0.001 0.043 -10000 0 -0.41 1 1
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.001 0.043 -10000 0 -0.41 1 1
Cathepsin D/ceramide -0.027 0.049 0.18 1 -0.25 2 3
FADD 0.04 0.048 -10000 0 -0.47 3 3
KSR1 -0.022 0.048 0.2 1 -0.32 3 4
MAPK8 -0.012 0.054 0.2 1 -0.34 11 12
PRKRA -0.021 0.045 0.2 1 -10000 0 1
PDGFA -0.001 0.025 -10000 0 -0.54 2 2
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
IGF1 -0.18 0.33 -10000 0 -0.79 247 247
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.032 0.047 0.21 1 -10000 0 1
CTSD -0.01 0.053 -10000 0 -0.29 37 37
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.1 0.17 -10000 0 -0.41 247 247
PRKCD 0 0.009 -10000 0 -0.29 1 1
PRKCZ -0.001 0.024 -10000 0 -0.79 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.021 0.023 -10000 0 -0.6 1 1
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR -0.001 0.024 -10000 0 -0.79 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.006 0.04 -10000 0 -0.72 1 1
TNFR1A/BAG4/TNF-alpha -0.013 0.069 -10000 0 -0.52 17 17
mol:Sphingosine-1-phosphate 0.022 0.02 -10000 0 -0.6 1 1
MAP2K1 -0.005 0.043 -10000 0 -0.42 1 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
CYCS -0.007 0.043 0.18 25 -10000 0 25
TNFRSF1A 0 0 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.004 0.04 -10000 0 -0.6 4 4
EIF2AK2 -0.013 0.042 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.009 0.06 -10000 0 -0.52 13 13
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.002 0.02 -10000 0 -0.32 1 1
MAP2K2 -0.005 0.043 -10000 0 -0.42 1 1
SMPD3 0.026 0.039 -10000 0 -0.27 16 16
TNF -0.016 0.095 -10000 0 -0.46 38 38
PKC zeta/PAR4 -0.001 0.026 -10000 0 -0.6 2 2
mol:PHOSPHOCHOLINE 0.044 0.11 0.27 213 -10000 0 213
NF kappa B1/RelA/I kappa B alpha -0.001 0.019 -10000 0 -0.43 2 2
AIFM1 -0.007 0.043 0.18 25 -10000 0 25
BCL2 -0.027 0.14 -10000 0 -0.79 37 37
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.007 0.072 -10000 0 -0.74 10 10
positive regulation of NF-kappaB transcription factor activity -0.062 0.18 -10000 0 -0.6 113 113
MAP2K4 0.042 0.038 -10000 0 -0.42 1 1
IKBKB -0.001 0.013 -10000 0 -0.29 2 2
TNFRSF10B 0 0 -10000 0 -10000 0 0
TNFRSF10A -0.005 0.063 -10000 0 -0.79 7 7
SMPD1 -0.002 0.026 -10000 0 -0.28 9 9
IKBKG 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.075 0.23 -10000 0 -0.79 104 104
TRAIL/TRAILR2 -0.005 0.054 -10000 0 -0.6 9 9
TRAIL/TRAILR3 -0.008 0.068 -10000 0 -0.64 11 11
TRAIL/TRAILR1 -0.009 0.072 -10000 0 -0.6 16 16
TRAIL/TRAILR4 -0.062 0.18 -10000 0 -0.6 113 113
TRAIL/TRAILR1/DAP3/GTP -0.007 0.057 -10000 0 -0.48 16 16
IKK complex -0.003 0.019 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0.006 -10000 0 -0.2 1 1
MAPK3 0.017 0.056 -10000 0 -0.6 9 9
MAP3K1 -0.004 0.032 -10000 0 -0.32 10 10
TRAILR4 (trimer) -0.075 0.23 -10000 0 -0.79 104 104
TRADD 0 0 -10000 0 -10000 0 0
TRAILR1 (trimer) -0.005 0.063 -10000 0 -0.79 7 7
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.005 0.039 -10000 0 -0.32 16 16
CFLAR -0.001 0.024 -10000 0 -0.79 1 1
MAPK1 0.017 0.056 -10000 0 -0.6 9 9
TRAIL/TRAILR1/FADD/TRADD/RIP -0.008 0.055 -10000 0 -0.44 16 16
mol:ceramide -0.002 0.025 -10000 0 -0.28 9 9
FADD -0.004 0.034 -10000 0 -0.29 15 15
MAPK8 0.044 0.057 -10000 0 -0.43 10 10
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
TRAILR3 (trimer) -0.004 0.048 -10000 0 -0.43 11 11
CHUK 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.01 0.065 -10000 0 -0.52 16 16
DAP3 0 0.009 -10000 0 -0.29 1 1
CASP10 0.021 0.11 0.31 98 -0.49 13 111
JNK cascade -0.062 0.18 -10000 0 -0.6 113 113
TRAIL (trimer) -0.007 0.072 -10000 0 -0.74 10 10
TNFRSF10C -0.004 0.048 -10000 0 -0.43 11 11
TRAIL/TRAILR1/DAP3/GTP/FADD -0.008 0.056 -10000 0 -0.45 16 16
TRAIL/TRAILR2/FADD -0.006 0.05 -10000 0 -0.52 9 9
cell death -0.002 0.025 -10000 0 -0.28 9 9
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.003 0.029 -10000 0 -0.32 9 9
TRAILR2 (trimer) 0 0 -10000 0 -10000 0 0
CASP8 0.001 0.016 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.005 0.041 -10000 0 -0.44 9 9
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0 0 -10000 0 -10000 0 0
HDAC3 0 0 -10000 0 -10000 0 0
VDR 0 0 -10000 0 -10000 0 0
Cbp/p300/PCAF 0 0.016 -10000 0 -0.52 1 1
EP300 0 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.037 0.043 -10000 0 -0.34 6 6
KAT2B -0.001 0.024 -10000 0 -0.79 1 1
MAPK14 0 0 -10000 0 -10000 0 0
AKT1 0.019 0.054 0.24 4 -0.36 14 18
RAR alpha/9cRA/Cyclin H -0.012 0.067 -10000 0 -0.39 29 29
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.033 0.052 -10000 0 -0.41 8 8
CDC2 0.001 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.013 0.074 -10000 0 -0.66 10 10
NCOR2 0 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0 0 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA 0.006 0.13 -10000 0 -0.58 35 35
NCOA2 -0.039 0.17 -10000 0 -0.79 54 54
NCOA3 0 0.009 -10000 0 -0.29 1 1
NCOA1 -0.001 0.024 -10000 0 -0.79 1 1
VDR/VDR/DNA 0 0 -10000 0 -10000 0 0
RARG 0.012 0.001 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0.011 0.002 -10000 0 -10000 0 0
MAPK1 0 0 -10000 0 -10000 0 0
MAPK8 0.006 0.072 -10000 0 -0.79 9 9
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.042 0.11 -10000 0 -0.63 29 29
RARA 0.014 0.066 -10000 0 -0.32 36 36
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.019 0.09 -10000 0 -0.42 21 21
PRKCA -0.007 0.13 -10000 0 -0.75 31 31
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.006 0.14 -10000 0 -0.6 36 36
RXRG -0.1 0.21 -10000 0 -0.44 290 290
RXRA 0.021 0.067 -10000 0 -0.33 36 36
RXRB 0.01 0.076 -10000 0 -0.43 29 29
VDR/Vit D3/DNA 0 0 -10000 0 -10000 0 0
RBP1 -0.026 0.097 -10000 0 -0.33 86 86
CRBP1/9-cic-RA -0.018 0.07 -10000 0 -0.23 86 86
RARB 0.002 0.093 -10000 0 -0.79 15 15
PRKCG -0.003 0.062 -10000 0 -0.29 49 49
MNAT1 0 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.009 0.13 -10000 0 -0.62 33 33
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.012 0.11 -10000 0 -0.51 34 34
proteasomal ubiquitin-dependent protein catabolic process 0.035 0.062 -10000 0 -0.48 7 7
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.006 0.14 -10000 0 -0.6 36 36
positive regulation of DNA binding -0.011 0.063 -10000 0 -0.37 29 29
NRIP1 -0.004 0.13 -10000 0 -0.64 24 24
RXRs/RARs -0.013 0.13 -10000 0 -0.6 36 36
RXRs/RXRs/DNA/9cRA -0.046 0.12 -10000 0 -0.65 30 30
PRKACA 0 0 -10000 0 -10000 0 0
CDK7 0 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.007 0.038 -10000 0 -0.53 2 2
CCNH 0 0 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.005 0.094 -10000 0 -0.44 38 38
ACTA1 -0.018 0.13 0.27 1 -0.64 36 37
NUMA1 0.005 0.094 0.23 1 -0.44 38 39
SPTAN1 -0.005 0.12 -10000 0 -0.61 35 35
LIMK1 -0.005 0.12 -10000 0 -0.61 35 35
BIRC3 -0.01 0.077 -10000 0 -0.5 21 21
BIRC2 0 0 -10000 0 -10000 0 0
BAX -0.001 0.018 -10000 0 -0.29 4 4
CASP10 -0.015 0.14 -10000 0 -0.65 39 39
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0.005 0.094 0.23 1 -0.44 38 39
DIABLO 0 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.004 0.12 -10000 0 -0.6 35 35
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
GSN -0.011 0.14 -10000 0 -0.61 45 45
MADD 0 0 -10000 0 -10000 0 0
TFAP2A 0.014 0.083 -10000 0 -0.67 15 15
BID 0.005 0.062 -10000 0 -0.29 38 38
MAP3K1 0.004 0.042 -10000 0 -0.28 8 8
TRADD 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.005 0.12 -10000 0 -0.61 35 35
CASP9 0.002 0.004 -10000 0 -10000 0 0
DNA repair -0.002 0.031 0.18 7 -0.22 4 11
neuron apoptosis 0.022 0.013 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.003 0.12 -10000 0 -0.58 35 35
APAF1 0.001 0.003 -10000 0 -10000 0 0
CASP6 0.023 0.057 -10000 0 -0.35 10 10
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
ICAD/CAD 0.003 0.12 -10000 0 -0.58 35 35
CASP7 -0.007 0.037 0.36 9 -10000 0 9
KRT18 0.015 0.024 -10000 0 -0.59 1 1
apoptosis 0.009 0.11 0.3 1 -0.51 35 36
DFFA -0.005 0.12 -10000 0 -0.61 35 35
DFFB -0.005 0.12 -10000 0 -0.61 35 35
PARP1 0.002 0.031 0.22 4 -0.18 7 11
actin filament polymerization -0.002 0.12 0.55 39 -10000 0 39
TNF -0.016 0.095 -10000 0 -0.46 38 38
CYCS 0.007 0.05 -10000 0 -0.21 38 38
SATB1 0.016 0.099 -10000 0 -0.46 34 34
SLK -0.005 0.12 -10000 0 -0.61 35 35
p15 BID/BAX -0.014 0.049 -10000 0 -0.35 8 8
CASP2 0.044 0.039 -10000 0 -0.45 1 1
JNK cascade -0.004 0.042 0.27 8 -10000 0 8
CASP3 -0.014 0.13 0.28 1 -0.64 36 37
LMNB2 0.041 0.036 -10000 0 -0.33 3 3
RIPK1 0 0 -10000 0 -10000 0 0
CASP4 -0.001 0.024 -10000 0 -0.79 1 1
Mammalian IAPs/DIABLO -0.005 0.044 -10000 0 -0.47 9 9
negative regulation of DNA binding 0.014 0.082 -10000 0 -0.66 15 15
stress fiber formation -0.004 0.12 -10000 0 -0.6 35 35
GZMB -0.029 0.15 -10000 0 -0.64 47 47
CASP1 0.014 0.033 -10000 0 -0.44 6 6
LMNB1 0.044 0.037 -10000 0 -0.38 2 2
APP 0.022 0.013 -10000 0 -10000 0 0
TNFRSF1A 0 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.011 0 -10000 0 -10000 0 0
VIM 0.003 0.1 0.3 1 -0.5 35 36
LMNA 0.04 0.036 -10000 0 -0.38 2 2
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.005 0.034 -10000 0 -0.48 1 1
LRDD -0.002 0.022 -10000 0 -0.29 6 6
SREBF1 -0.007 0.13 -10000 0 -0.61 35 35
APAF-1/Caspase 9 -0.004 0.02 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.005 0.092 0.23 1 -0.43 38 39
CFL2 0.001 0.12 -10000 0 -0.56 39 39
GAS2 -0.046 0.18 -10000 0 -0.52 126 126
positive regulation of apoptosis 0.045 0.036 -10000 0 -0.37 2 2
PRF1 -0.017 0.11 -10000 0 -0.79 20 20
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.03 0.007 -9999 0 -10000 0 0
SNTA1 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.017 0.046 -9999 0 -10000 0 0
MAPK12 0.017 0.082 -9999 0 -0.46 30 30
CCND1 0.015 0.043 -9999 0 -0.22 29 29
p38 gamma/SNTA1 -0.012 0.071 -9999 0 -0.42 30 30
MAP2K3 0 0.009 -9999 0 -0.29 1 1
PKN1 0 0.009 -9999 0 -0.29 1 1
G2/M transition checkpoint 0.017 0.082 -9999 0 -0.45 30 30
MAP2K6 0.01 0.084 -9999 0 -0.49 30 30
MAPT -0.018 0.13 -9999 0 -0.4 117 117
MAPK13 0.022 0.009 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.014 0.031 -9999 0 -0.44 5 5
Cellular roles of Anthrax toxin

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
ANTXR1 -0.003 0.048 -10000 0 -0.69 5 5
ANTXR2 -0.009 0.082 -10000 0 -0.79 12 12
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.012 -10000 0 -0.1 14 14
monocyte activation 0.004 0.073 -10000 0 -0.46 26 26
MAP2K2 -0.001 0.005 -10000 0 -10000 0 0
MAP2K1 -0.001 0.01 -10000 0 -10000 0 0
MAP2K7 -0.001 0.01 -10000 0 -10000 0 0
MAP2K6 -0.012 0.071 -10000 0 -0.47 25 25
CYAA 0.009 0.062 -10000 0 -0.52 14 14
MAP2K4 -0.002 0.017 -10000 0 -0.46 1 1
IL1B 0.007 0.064 -10000 0 -0.34 31 31
Channel -0.007 0.064 -10000 0 -0.55 14 14
NLRP1 -0.008 0.059 -10000 0 -0.49 16 16
CALM1 0 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.002 0.014 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.012 0.1 14 -10000 0 14
MAPK3 -0.001 0.01 -10000 0 -10000 0 0
MAPK1 -0.001 0.01 -10000 0 -10000 0 0
PGR -0.14 0.21 -10000 0 -0.47 313 313
PA/Cellular Receptors -0.008 0.069 -10000 0 -0.59 14 14
apoptosis -0.001 0.012 -10000 0 -0.1 14 14
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.007 0.06 -10000 0 -0.51 14 14
macrophage activation 0.019 0.011 -10000 0 -10000 0 0
TNF -0.016 0.095 -10000 0 -0.46 38 38
VCAM1 -0.011 0.071 -10000 0 -0.46 26 26
platelet activation -0.002 0.014 -10000 0 -10000 0 0
MAPKKK cascade -0.013 0.022 0.17 4 -10000 0 4
IL18 0.01 0.037 -10000 0 -0.22 16 16
negative regulation of macrophage activation -0.001 0.012 -10000 0 -0.1 14 14
LEF -0.001 0.012 -10000 0 -0.1 14 14
CASP1 -0.005 0.031 -10000 0 -0.23 17 17
mol:cAMP -0.002 0.014 -10000 0 -10000 0 0
necrosis -0.001 0.012 -10000 0 -0.1 14 14
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.007 0.061 -10000 0 -0.52 14 14
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.045 0.065 -10000 0 -0.57 2 2
UGCG -0.011 0.095 -10000 0 -0.79 15 15
AKT1/mTOR/p70S6K/Hsp90/TERT 0.054 0.091 -10000 0 -0.39 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.013 0.097 -10000 0 -0.78 15 15
mol:DAG 0 0.002 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.026 0.09 -10000 0 -0.37 55 55
FRAP1 0.052 0.13 -10000 0 -0.41 67 67
FOXO3 0.06 0.11 -10000 0 -0.41 37 37
AKT1 0.055 0.11 -10000 0 -0.45 34 34
GAB2 0.008 0.043 -10000 0 -0.39 10 10
SMPD1 -0.002 0.014 -10000 0 -10000 0 0
SGMS1 -0.002 0.014 -10000 0 -10000 0 0
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 0.015 0.062 -10000 0 -0.52 14 14
CALM1 0 0 -10000 0 -10000 0 0
cell proliferation 0.032 0.089 -10000 0 -0.35 39 39
EIF3A 0 0 -10000 0 -10000 0 0
PI3K -0.008 0.068 -10000 0 -0.6 14 14
RPS6KB1 0.021 0.034 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.002 -10000 0 -10000 0 0
natural killer cell activation 0 0.002 -10000 0 -0.012 10 10
JAK3 0.01 0.034 -10000 0 -0.29 14 14
PIK3R1 0.003 0.09 -10000 0 -0.79 14 14
JAK1 0.013 0.024 -10000 0 -0.78 1 1
NFKB1 0 0 -10000 0 -10000 0 0
MYC 0.046 0.18 -10000 0 -0.92 30 30
MYB 0.006 0.19 -10000 0 -1.3 23 23
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.052 0.094 -10000 0 -0.56 11 11
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.004 0.023 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.052 0.092 -10000 0 -0.54 11 11
Rac1/GDP -0.006 0.053 -10000 0 -0.47 14 14
T cell proliferation 0.058 0.087 -10000 0 -0.5 11 11
SHC1 0.011 0.003 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.01 -10000 0 -0.066 23 23
PRKCZ 0.058 0.09 -10000 0 -0.53 11 11
NF kappa B1 p50/RelA -0.025 0.088 -10000 0 -0.49 15 15
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.039 0.07 -10000 0 -0.52 6 6
HSP90AA1 0 0.009 -10000 0 -0.29 1 1
RELA 0 0 -10000 0 -10000 0 0
IL2RA -0.02 0.12 -10000 0 -0.38 87 87
IL2RB 0.001 0.066 -10000 0 -0.31 42 42
TERT -0.044 0.1 -10000 0 -0.29 165 165
E2F1 0.02 0.068 -10000 0 -0.44 23 23
SOS1 0.011 0.003 -10000 0 -10000 0 0
RPS6 0 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.005 0.03 23 -10000 0 23
PTPN11 0.011 0.003 -10000 0 -10000 0 0
IL2RG -0.004 0.087 -10000 0 -0.36 53 53
actin cytoskeleton organization 0.058 0.087 -10000 0 -0.5 11 11
GRB2 0.011 0.01 -10000 0 -0.29 1 1
IL2 0.006 0.026 -10000 0 -0.29 8 8
PIK3CA 0.013 0.01 -10000 0 -0.29 1 1
Rac1/GTP 0.025 0.055 -10000 0 -0.45 14 14
LCK -0.007 0.1 -10000 0 -0.41 53 53
BCL2 0.039 0.2 -10000 0 -0.86 43 43
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.014 0.083 -9999 0 -0.52 29 29
E-cadherin/beta catenin -0.015 0.095 -9999 0 -0.6 28 28
CTNNB1 0 0 -9999 0 -10000 0 0
JUP -0.001 0.025 -9999 0 -0.54 2 2
CDH1 -0.02 0.12 -9999 0 -0.79 28 28
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.017 0.082 -9999 0 -0.51 23 23
MAP4K1 -0.015 0.07 -9999 0 -0.31 53 53
MAP3K8 -0.007 0.072 -9999 0 -0.74 10 10
PRKCB -0.019 0.11 -9999 0 -0.55 39 39
DBNL 0 0 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
MAP3K1 0.036 0.053 -9999 0 -0.47 4 4
JUN 0.016 0.12 -9999 0 -0.6 35 35
MAP3K7 0.036 0.052 -9999 0 -0.48 3 3
GRAP2 -0.014 0.1 -9999 0 -0.72 21 21
CRK 0 0 -9999 0 -10000 0 0
MAP2K4 0.043 0.056 -9999 0 -0.46 5 5
LAT -0.005 0.048 -9999 0 -0.35 17 17
LCP2 0 0.009 -9999 0 -0.29 1 1
MAPK8 0.012 0.12 -9999 0 -0.68 28 28
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.008 0.048 -9999 0 -0.35 18 18
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.016 0.077 -9999 0 -0.48 23 23
IL1-mediated signaling events

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
UBC13/UEV1A 0 0.008 -10000 0 -10000 0 0
PRKCZ -0.001 0.024 -10000 0 -0.79 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.007 0.042 -10000 0 -0.44 5 5
IRAK/TOLLIP -0.001 0.01 -10000 0 -10000 0 0
IKBKB -0.001 0.013 -10000 0 -0.29 2 2
IKBKG 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.031 0.12 -10000 0 -0.58 43 43
IL1A -0.005 0.039 -10000 0 -0.29 20 20
IL1B 0.011 0.092 -10000 0 -0.69 17 17
IRAK/TRAF6/p62/Atypical PKCs -0.001 0.014 -10000 0 -0.39 1 1
IL1R2 -0.037 0.15 -10000 0 -0.57 71 71
IL1R1 -0.017 0.12 -10000 0 -0.79 24 24
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.002 0.063 0.23 33 -0.32 19 52
TOLLIP 0 0.009 -10000 0 -0.29 1 1
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0 0.004 -10000 0 -10000 0 0
JUN 0.031 0.08 -10000 0 -0.37 40 40
MAP3K7 0 0.009 -10000 0 -0.29 1 1
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.023 0.11 -10000 0 -0.49 51 51
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.013 0.075 -10000 0 -0.49 25 25
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.012 0.07 -10000 0 -0.45 25 25
IL1 beta fragment/IL1R1/IL1RAP -0.02 0.11 -10000 0 -0.53 40 40
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 0.027 0.075 -10000 0 -0.39 34 34
IRAK1 0.021 0.013 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.021 0.097 -10000 0 -0.6 26 26
IRAK4 0 0 -10000 0 -10000 0 0
PRKCI 0 0.009 -10000 0 -0.29 1 1
TRAF6 0 0 -10000 0 -10000 0 0
PI3K -0.008 0.068 -10000 0 -0.6 14 14
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.012 0.063 -10000 0 -0.35 26 26
CHUK 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.02 0.11 -10000 0 -0.53 40 40
IL1 beta/IL1R2 -0.033 0.13 -10000 0 -0.55 56 56
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.001 0.008 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.021 0.099 -10000 0 -0.84 7 7
IRAK3 -0.031 0.15 -10000 0 -0.78 44 44
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.018 0.097 -10000 0 -0.48 40 40
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.008 0.051 -10000 0 -0.33 25 25
IL1 alpha/IL1R1/IL1RAP -0.015 0.083 -10000 0 -0.54 25 25
RELA 0 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0 0.009 -10000 0 -0.29 1 1
MYD88 0 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 -0.001 0.008 -10000 0 -10000 0 0
IL1RAP -0.001 0.034 -10000 0 -0.79 2 2
UBE2N 0 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.015 0.078 -10000 0 -0.81 4 4
CASP1 -0.004 0.053 -10000 0 -0.79 5 5
IL1RN/IL1R2 -0.035 0.12 -10000 0 -0.57 47 47
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.019 0.1 -10000 0 -0.5 40 40
TMEM189-UBE2V1 -0.001 0.013 -10000 0 -0.29 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.009 0.057 -10000 0 -0.38 24 24
PIK3CA 0 0.009 -10000 0 -0.29 1 1
IL1RN -0.012 0.064 -10000 0 -0.32 41 41
TRAF6/TAK1/TAB1/TAB2 0 0.006 -10000 0 -10000 0 0
MAP2K6 -0.01 0.062 -10000 0 -0.41 25 25
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.003 0.048 -9999 0 -0.79 4 4
mol:S1P 0.001 0.004 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.03 0.095 -9999 0 -0.33 95 95
GNAO1 -0.018 0.13 -9999 0 -0.48 67 67
S1P/S1P3/G12/G13 -0.001 0.013 -9999 0 -10000 0 0
AKT1 -0.011 0.051 -9999 0 -0.68 4 4
AKT3 0.012 0.2 -9999 0 -1.4 20 20
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.003 0.047 -9999 0 -0.79 4 4
GNAI2 0.013 0.003 -9999 0 -10000 0 0
GNAI3 0.012 0.002 -9999 0 -10000 0 0
GNAI1 -0.033 0.19 -9999 0 -0.79 62 62
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.01 0.029 -9999 0 -0.3 10 10
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.009 0.11 -9999 0 -0.39 40 40
MAPK3 0.017 0.1 -9999 0 -0.51 14 14
MAPK1 0.017 0.1 -9999 0 -0.51 14 14
JAK2 0.019 0.1 -9999 0 -0.45 20 20
CXCR4 0.014 0.1 -9999 0 -0.48 19 19
FLT1 0.013 0.025 -9999 0 -0.8 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.017 0.1 -9999 0 -0.51 14 14
S1P/S1P3/Gi 0.009 0.11 -9999 0 -0.39 40 40
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.026 0.084 -9999 0 -0.49 14 14
VEGFA 0.01 0.032 -9999 0 -0.3 12 12
S1P/S1P2/Gi 0.008 0.1 -9999 0 -0.37 39 39
VEGFR1 homodimer/VEGFA homodimer 0.021 0.03 -9999 0 -0.62 1 1
RHOA 0 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.007 0.043 -9999 0 -0.34 18 18
GNAQ -0.002 0.041 -9999 0 -0.79 3 3
GNAZ 0.005 0.076 -9999 0 -0.79 10 10
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.013 0.084 -9999 0 -0.46 30 30
GNA15 -0.003 0.033 -9999 0 -0.36 8 8
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 -0.003 0.048 -9999 0 -0.79 4 4
Rac1/GTP -0.026 0.084 -9999 0 -0.49 14 14
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 0 -9999 0 -10000 0 0
SPHK1 -0.007 0.052 -9999 0 -0.34 23 23
GNAI2 0 0 -9999 0 -10000 0 0
mol:S1P 0.02 0.019 -9999 0 -0.36 2 2
GNAO1 -0.03 0.13 -9999 0 -0.48 67 67
mol:Sphinganine-1-P 0.017 0.039 -9999 0 -0.6 2 2
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.001 0.011 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 -0.003 0.028 -9999 0 -0.29 10 10
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.001 0.014 -9999 0 -0.31 2 2
S1PR5 -0.008 0.058 -9999 0 -0.35 25 25
S1PR4 -0.014 0.079 -9999 0 -0.36 44 44
GNAI1 -0.045 0.18 -9999 0 -0.79 62 62
S1P/S1P5/G12 -0.005 0.032 -9999 0 -0.38 5 5
S1P/S1P3/Gq -0.005 0.038 -9999 0 -0.29 18 18
S1P/S1P4/Gi -0.028 0.084 -9999 0 -0.33 42 42
GNAQ -0.002 0.041 -9999 0 -0.79 3 3
GNAZ -0.007 0.075 -9999 0 -0.79 10 10
GNA14 -0.013 0.084 -9999 0 -0.46 30 30
GNA15 -0.003 0.033 -9999 0 -0.36 8 8
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 -0.003 0.048 -9999 0 -0.79 4 4
ABCC1 0 0 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.016 0.092 -9999 0 -0.58 28 28
KLHL20 -0.008 0.031 -9999 0 -0.24 3 3
CYFIP2 -0.01 0.065 -9999 0 -0.36 31 31
Rac1/GDP 0.05 0.065 -9999 0 -0.34 28 28
ENAH -0.015 0.091 -9999 0 -0.57 28 28
AP1M1 0 0 -9999 0 -10000 0 0
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
CDC42/GTP -0.008 0.045 -9999 0 -0.49 1 1
ABI1/Sra1/Nap1 -0.006 0.023 -9999 0 -0.19 4 4
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.016 0.078 -9999 0 -0.47 30 30
RAPGEF1 0.04 0.085 -9999 0 -0.48 28 28
CTNND1 0 0.009 -9999 0 -0.29 1 1
regulation of calcium-dependent cell-cell adhesion -0.016 0.095 -9999 0 -0.6 28 28
CRK 0.032 0.092 -9999 0 -0.53 28 28
E-cadherin/gamma catenin/alpha catenin -0.014 0.083 -9999 0 -0.52 29 29
alphaE/beta7 Integrin -0.006 0.04 -9999 0 -0.6 2 2
IQGAP1 0 0 -9999 0 -10000 0 0
NCKAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.003 0.035 -9999 0 -0.48 6 6
DLG1 -0.015 0.091 -9999 0 -0.57 28 28
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.008 0.039 -9999 0 -0.31 2 2
MLLT4 -0.005 0.059 -9999 0 -0.72 7 7
ARF6/GTP/NME1/Tiam1 -0.007 0.029 -9999 0 -10000 0 0
PI3K -0.01 0.051 -9999 0 -0.42 2 2
ARF6 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.016 0.097 -9999 0 -0.6 29 29
TIAM1 -0.001 0.018 -9999 0 -0.29 4 4
E-cadherin(dimer)/Ca2+ -0.011 0.07 -9999 0 -0.44 28 28
AKT1 -0.006 0.028 -9999 0 -0.24 1 1
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
CDH1 -0.02 0.12 -9999 0 -0.79 28 28
RhoA/GDP 0.05 0.065 -9999 0 -0.43 2 2
actin cytoskeleton organization -0.006 0.023 -9999 0 -0.17 3 3
CDC42/GDP 0.05 0.065 -9999 0 -0.34 28 28
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.009 0.054 -9999 0 -0.33 29 29
ITGB7 -0.009 0.058 -9999 0 -0.32 32 32
RAC1 0 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.012 0.074 -9999 0 -0.47 28 28
E-cadherin/Ca2+/beta catenin/alpha catenin -0.012 0.071 -9999 0 -0.45 28 28
mol:GDP 0.047 0.075 -9999 0 -0.41 28 28
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP -0.001 0.025 -9999 0 -0.54 2 2
p120 catenin/RhoA/GDP -0.009 0.056 -9999 0 -0.54 1 1
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.007 0.029 -9999 0 -0.22 7 7
NME1 -0.015 0.065 -9999 0 -0.29 56 56
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.015 0.092 -9999 0 -0.57 29 29
regulation of cell-cell adhesion -0.007 0.04 -9999 0 -0.42 1 1
WASF2 -0.003 0.012 -9999 0 -10000 0 0
Rap1/GTP -0.009 0.053 -9999 0 -0.58 1 1
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.015 0.074 -9999 0 -0.44 31 31
CCND1 -0.009 0.035 -9999 0 -0.27 7 7
VAV2 0.036 0.089 -9999 0 -0.51 28 28
RAP1/GDP -0.009 0.053 -9999 0 -0.56 1 1
adherens junction assembly -0.015 0.088 -9999 0 -0.55 29 29
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0 0 -9999 0 -10000 0 0
PIP5K1C 0 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.014 0.07 -9999 0 -0.41 31 31
E-cadherin/beta catenin -0.012 0.077 -9999 0 -0.49 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.015 0.091 -9999 0 -0.57 28 28
PIK3CA 0 0.009 -9999 0 -0.29 1 1
Rac1/GTP -0.01 0.051 -9999 0 -0.35 6 6
E-cadherin/beta catenin/alpha catenin -0.013 0.082 -9999 0 -0.52 28 28
ITGAE 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.016 0.097 -9999 0 -0.61 28 28
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0 0 -10000 0 -10000 0 0
mol:PIP3 -0.019 0.082 0.33 1 -0.36 58 59
FRAP1 0.01 0.023 -10000 0 -10000 0 0
AKT1 -0.017 0.071 0.24 1 -0.31 58 59
INSR 0 0.009 -10000 0 -0.29 1 1
Insulin Receptor/Insulin 0 0.005 -10000 0 -10000 0 0
mol:GTP -0.013 0.055 -10000 0 -0.33 15 15
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.004 0.018 -10000 0 -10000 0 0
TSC2 0 0.002 -10000 0 -10000 0 0
RHEB/GDP -0.011 0.048 -10000 0 -0.34 1 1
TSC1 0 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.017 0.082 -10000 0 -0.42 45 45
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.005 0.021 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.018 0.045 -10000 0 -0.25 15 15
MAP3K5 0.009 0.027 -10000 0 -0.44 4 4
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
apoptosis 0.009 0.027 -10000 0 -0.44 4 4
mol:LY294002 0 0 -10000 0 -0.002 45 45
EIF4B 0.024 0.041 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.007 0.03 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 -0.001 0.008 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.021 0.087 -10000 0 -0.38 59 59
mTOR/RHEB/GTP/Raptor/GBL 0.025 0.033 0.18 1 -10000 0 1
FKBP1A 0 0.009 -10000 0 -0.29 1 1
RHEB/GTP -0.011 0.047 -10000 0 -0.34 1 1
mol:Amino Acids 0 0 -10000 0 -0.002 45 45
FKBP12/Rapamycin 0 0.006 -10000 0 -0.2 1 1
PDPK1 -0.017 0.074 0.26 1 -0.33 58 59
EIF4E 0 0 -10000 0 -10000 0 0
ASK1/PP5C -0.004 0.039 -10000 0 -0.62 4 4
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.016 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.014 0.059 -10000 0 -0.35 15 15
tumor necrosis factor receptor activity 0 0 0.002 45 -10000 0 45
RPS6 0 0 -10000 0 -10000 0 0
PPP5C 0 0 -10000 0 -10000 0 0
EIF4G1 0 0 -10000 0 -10000 0 0
IRS1 -0.011 0.09 -10000 0 -0.45 45 45
INS 0 0 -10000 0 -10000 0 0
PTEN -0.001 0.034 -10000 0 -0.79 2 2
PDK2 -0.019 0.079 0.26 1 -0.34 61 62
EIF4EBP1 0.013 0.01 -10000 0 -10000 0 0
PIK3CA 0 0.009 -10000 0 -0.29 1 1
PPP2R5D 0.017 0.021 -10000 0 -10000 0 0
peptide biosynthetic process 0.016 0.005 -10000 0 -10000 0 0
RHEB 0 0 -10000 0 -10000 0 0
EIF4A1 0 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.003 2 -0.003 14 16
EEF2 0.016 0.005 -10000 0 -10000 0 0
eIF4E/4E-BP1 0 0 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.004 0.024 -9999 0 -0.4 2 2
CRKL 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0 0 -9999 0 -10000 0 0
ITGA4 -0.003 0.028 -9999 0 -0.29 10 10
alpha4/beta7 Integrin/MAdCAM1 -0.01 0.043 -9999 0 -0.45 3 3
EPO -0.047 0.11 -9999 0 -0.29 177 177
alpha4/beta7 Integrin -0.008 0.046 -9999 0 -0.44 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.002 0.018 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.03 0.069 -9999 0 -10000 0 0
lamellipodium assembly -0.004 0.046 -9999 0 -0.4 14 14
PIK3CA 0 0.009 -9999 0 -0.29 1 1
PI3K -0.008 0.068 -9999 0 -0.6 14 14
ARF6 0 0 -9999 0 -10000 0 0
JAK2 -0.01 0.025 -9999 0 -0.5 1 1
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
MADCAM1 -0.012 0.057 -9999 0 -0.29 43 43
cell adhesion -0.01 0.043 -9999 0 -0.45 3 3
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0 0 -9999 0 -10000 0 0
SRC 0.025 0.057 -9999 0 -0.47 13 13
ITGB7 -0.009 0.058 -9999 0 -0.32 32 32
RAC1 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.008 0.058 -9999 0 -0.52 13 13
p130Cas/Crk/Dock1 -0.006 0.042 -9999 0 -0.38 13 13
VCAM1 -0.011 0.088 -9999 0 -0.63 19 19
RHOA 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.002 0.014 -9999 0 -10000 0 0
BCAR1 0.034 0.054 -9999 0 -0.43 13 13
EPOR 0 0.009 -9999 0 -0.29 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
GIT1 -0.001 0.02 -9999 0 -0.29 5 5
Rac1/GTP -0.005 0.047 -9999 0 -0.41 14 14
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 -0.002 0.028 -10000 0 -0.46 4 4
TRAF2/ASK1 -0.002 0.033 -10000 0 -0.52 4 4
ATM 0 0 -10000 0 -10000 0 0
MAP2K3 0.025 0.045 -10000 0 -0.44 2 2
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.025 0.064 -10000 0 -0.43 6 6
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.038 0.098 -10000 0 -0.29 141 141
TXN 0.008 0.006 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
GADD45A 0 0 -10000 0 -10000 0 0
GADD45B 0 0 -10000 0 -10000 0 0
MAP3K1 -0.001 0.024 -10000 0 -0.79 1 1
MAP3K6 -0.001 0.024 -10000 0 -0.79 1 1
MAP3K7 0 0.009 -10000 0 -0.29 1 1
MAP3K4 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.003 0.04 -10000 0 -0.6 5 5
TAK1/TAB family 0.001 0.011 0.21 3 -10000 0 3
RAC1/OSM/MEKK3 0 0.005 -10000 0 -10000 0 0
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
RAC1/OSM/MEKK3/MKK3 -0.006 0.023 -10000 0 -0.4 1 1
TRAF6 0.008 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.066 0.2 -10000 0 -0.59 123 123
CCM2 -0.001 0.013 -10000 0 -0.29 2 2
CaM/Ca2+/CAMKIIB -0.042 0.13 -10000 0 -0.52 74 74
MAPK11 -0.002 0.041 -10000 0 -0.79 3 3
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.04 0.12 -10000 0 -0.48 77 77
OSM/MEKK3 0 0.008 -10000 0 -10000 0 0
TAOK1 -0.006 0.099 -10000 0 -0.44 55 55
TAOK2 0.017 0 -10000 0 -10000 0 0
TAOK3 0.017 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 -0.003 0.048 -10000 0 -0.79 4 4
MAP3K10 0 0.009 -10000 0 -0.29 1 1
MAP3K3 0 0 -10000 0 -10000 0 0
TRX/ASK1 -0.002 0.031 -10000 0 -0.52 4 4
GADD45/MTK1/MTK1 -0.014 0.037 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0 0 -10000 0 -10000 0 0
NFATC1 0.049 0.029 -10000 0 -0.39 1 1
NFATC2 0.015 0.064 -10000 0 -0.31 11 11
NFATC3 0 0.015 -10000 0 -0.51 1 1
YWHAE 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.012 0.094 -10000 0 -0.39 38 38
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.019 0.075 -10000 0 -0.49 17 17
BCL2/BAX -0.021 0.11 -10000 0 -0.61 37 37
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.003 -10000 0 -10000 0 0
CaM/Ca2+ -0.001 0.003 -10000 0 -10000 0 0
BAX -0.001 0.018 -10000 0 -0.29 4 4
MAPK14 0.01 0.003 -10000 0 -10000 0 0
BAD 0 0.009 -10000 0 -0.29 1 1
CABIN1/MEF2D -0.02 0.08 -10000 0 -0.52 17 17
Calcineurin A alpha-beta B1/BCL2 -0.027 0.14 -10000 0 -0.79 37 37
FKBP8 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.019 0.079 0.51 17 -10000 0 17
KPNB1 0 0 -10000 0 -10000 0 0
KPNA2 -0.029 0.087 -10000 0 -0.29 108 108
XPO1 0 0 -10000 0 -10000 0 0
SFN -0.016 0.099 -10000 0 -0.5 36 36
MAP3K8 0.004 0.073 -10000 0 -0.74 10 10
NFAT4/CK1 alpha -0.001 0.016 -10000 0 -0.43 1 1
MEF2D/NFAT1/Cbp/p300 -0.038 0.093 -10000 0 -0.46 3 3
CABIN1 0.012 0.095 -10000 0 -0.39 38 38
CALM1 0.001 0.003 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
MAP3K1 -0.001 0.024 -10000 0 -0.79 1 1
CAMK4 -0.011 0.059 -10000 0 -0.79 1 1
mol:Ca2+ -0.001 0.006 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.01 0.044 -10000 0 -0.6 1 1
YWHAB 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.072 -10000 0 -0.79 9 9
MAPK9 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0 0.009 -10000 0 -0.29 1 1
NFAT1-c-4/YWHAQ -0.002 0.021 -10000 0 -0.4 1 1
PRKCH -0.001 0.024 -10000 0 -0.79 1 1
CABIN1/Cbp/p300 -0.001 0.003 -10000 0 -10000 0 0
CASP3 0.01 0.003 -10000 0 -10000 0 0
PIM1 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.005 -10000 0 -10000 0 0
apoptosis -0.007 0.035 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.003 0.024 -10000 0 -10000 0 0
PRKCB -0.019 0.11 -10000 0 -0.55 39 39
PRKCE 0 0 -10000 0 -10000 0 0
JNK2/NFAT4 0 0.014 -10000 0 -0.46 1 1
BAD/BCL-XL 0 0.006 -10000 0 -10000 0 0
PRKCD 0 0.009 -10000 0 -0.29 1 1
NUP214 0 0 -10000 0 -10000 0 0
PRKCZ 0.01 0.024 -10000 0 -0.79 1 1
PRKCA -0.021 0.13 -10000 0 -0.76 31 31
PRKCG -0.013 0.061 -10000 0 -0.29 49 49
PRKCQ -0.036 0.16 -10000 0 -0.68 57 57
FKBP38/BCL2 -0.02 0.11 -10000 0 -0.6 37 37
EP300 0 0.001 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
NFATc/JNK1 0.047 0.049 -10000 0 -0.37 10 10
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0.006 -10000 0 -0.2 1 1
CSNK1A1 0.018 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.006 0.032 -10000 0 -0.52 1 1
NFATc/ERK1 0.053 0.027 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.019 0.075 -10000 0 -0.48 17 17
NR4A1 -0.014 0.22 -10000 0 -0.7 99 99
GSK3B 0.011 0.003 -10000 0 -10000 0 0
positive T cell selection 0 0.015 -10000 0 -0.5 1 1
NFAT1/CK1 alpha -0.016 0.039 -10000 0 -0.29 3 3
RCH1/ KPNB1 -0.018 0.056 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
PRKACA 0.01 0.003 -10000 0 -10000 0 0
AKAP5 -0.015 0.067 -10000 0 -0.3 54 54
MEF2D 0 0.001 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ -0.001 0.015 -10000 0 -0.29 3 3
NFATc/p38 alpha 0.051 0.031 -10000 0 -0.36 1 1
CREBBP 0 0.001 -10000 0 -10000 0 0
BCL2 -0.027 0.14 -10000 0 -0.79 37 37
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 -0.006 0.054 -10000 0 -0.47 15 15
HDAC3 0 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.012 -10000 0 -0.39 1 1
GATA1/HDAC4 -0.004 0.03 -10000 0 -0.6 1 1
GATA1/HDAC5 -0.003 0.024 -10000 0 -10000 0 0
GATA2/HDAC5 -0.018 0.097 -10000 0 -0.6 28 28
HDAC5/BCL6/BCoR -0.004 0.044 -10000 0 -0.52 8 8
HDAC9 -0.01 0.081 -10000 0 -0.52 22 22
Glucocorticoid receptor/Hsp90/HDAC6 -0.008 0.062 -10000 0 -0.52 16 16
HDAC4/ANKRA2 -0.001 0.018 -10000 0 -0.6 1 1
HDAC5/YWHAB 0 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0 0.001 -10000 0 -10000 0 0
GATA2 -0.024 0.13 -10000 0 -0.63 41 41
HDAC4/RFXANK -0.002 0.023 -10000 0 -0.6 1 1
BCOR -0.001 0.034 -10000 0 -0.79 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 -0.001 0.013 -10000 0 -0.29 2 2
HDAC5 0 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.008 0.07 -10000 0 -0.6 15 15
Histones -0.003 0.026 -10000 0 -10000 0 0
ADRBK1 0 0 -10000 0 -10000 0 0
HDAC4 -0.001 0.024 -10000 0 -0.79 1 1
XPO1 0 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 0 0 -10000 0 -10000 0 0
HDAC4/Ubc9 -0.001 0.018 -10000 0 -0.6 1 1
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -10000 0 -10000 0 0
TUBA1B 0 0 -10000 0 -10000 0 0
HDAC6 0 0 -10000 0 -10000 0 0
HDAC5/RFXANK -0.001 0.014 -10000 0 -10000 0 0
CAMK4 -0.011 0.059 -10000 0 -0.79 1 1
Tubulin/HDAC6 -0.001 0.017 -10000 0 -0.52 1 1
SUMO1 0 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
GATA1 -0.005 0.037 -10000 0 -0.29 18 18
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
NR3C1 -0.012 0.095 -10000 0 -0.79 16 16
SUMO1/HDAC4 0 0.013 -10000 0 -0.43 1 1
SRF 0 0 -10000 0 -10000 0 0
HDAC4/YWHAB -0.001 0.018 -10000 0 -0.6 1 1
Tubulin -0.001 0.02 -10000 0 -0.6 1 1
HDAC4/14-3-3 E -0.001 0.018 -10000 0 -0.6 1 1
GNB1 0 0 -10000 0 -10000 0 0
RANGAP1 0 0.009 -10000 0 -0.29 1 1
BCL6/BCoR -0.004 0.051 -10000 0 -0.6 8 8
HDAC4/HDAC3/SMRT (N-CoR2) 0 0.016 -10000 0 -0.52 1 1
HDAC4/SRF -0.006 0.034 -10000 0 -0.52 2 2
HDAC4/ER alpha -0.11 0.21 -10000 0 -0.6 166 166
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.003 0.025 -10000 0 -10000 0 0
cell motility -0.001 0.017 -10000 0 -0.51 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0 0 -10000 0 -10000 0 0
BCL6 -0.004 0.058 -10000 0 -0.79 6 6
HDAC4/CaMK II delta B -0.001 0.024 -10000 0 -0.79 1 1
Hsp90/HDAC6 0 0.006 -10000 0 -10000 0 0
ESR1 -0.15 0.28 -10000 0 -0.58 288 288
HDAC6/HDAC11 -0.001 0.011 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -10000 0 -10000 0 0
NPC 0 0 -10000 0 -10000 0 0
MEF2C -0.001 0.034 -10000 0 -0.79 2 2
RAN 0 0 -10000 0 -10000 0 0
HDAC4/MEF2C -0.001 0.023 -10000 0 -0.44 3 3
GNG2 -0.011 0.092 -10000 0 -0.79 15 15
NCOR2 0 0 -10000 0 -10000 0 0
TUBB2A -0.001 0.027 -10000 0 -0.46 3 3
HDAC11 -0.001 0.018 -10000 0 -0.29 4 4
HSP90AA1 0 0.009 -10000 0 -0.29 1 1
RANBP2 0 0 -10000 0 -10000 0 0
ANKRA2 0 0 -10000 0 -10000 0 0
RFXANK -0.002 0.022 -10000 0 -0.29 6 6
nuclear import 0 0.013 0.43 1 -10000 0 1
a4b1 and a4b7 Integrin signaling

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
ITGB1 0 0 -9999 0 -10000 0 0
ITGB7 -0.009 0.058 -9999 0 -0.32 32 32
ITGA4 -0.003 0.028 -9999 0 -0.29 10 10
alpha4/beta7 Integrin -0.008 0.046 -9999 0 -0.44 6 6
alpha4/beta1 Integrin -0.002 0.018 -9999 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.021 0.11 -9999 0 -0.6 37 37
AKT1 0.079 0.073 -9999 0 -0.68 7 7
PTK2B 0.035 0.12 -9999 0 -1 8 8
VEGFR2 homodimer/Frs2 -0.009 0.083 -9999 0 -0.81 10 10
CAV1 -0.17 0.33 -9999 0 -0.79 241 241
CALM1 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.009 0.077 -9999 0 -0.74 10 10
endothelial cell proliferation 0.082 0.087 -9999 0 -0.69 7 7
mol:Ca2+ 0.05 0.074 -9999 0 -0.84 6 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.007 0.073 -9999 0 -0.9 6 6
RP11-342D11.1 0.042 0.074 -9999 0 -0.85 6 6
CDH5 -0.007 0.075 -9999 0 -0.79 10 10
VEGFA homodimer -0.001 0.012 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
SHC2 -0.02 0.12 -9999 0 -0.77 28 28
HRAS/GDP -0.006 0.06 -9999 0 -0.75 6 6
SH2D2A -0.035 0.1 -9999 0 -0.3 125 125
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.003 0.055 -9999 0 -0.67 6 6
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.021 0.087 -9999 0 -0.7 13 13
VEGFR1 homodimer -0.001 0.024 -9999 0 -0.79 1 1
SHC/GRB2/SOS1 -0.005 0.066 -9999 0 -0.82 6 6
GRB10 0.05 0.074 -9999 0 -0.84 6 6
PTPN11 0 0 -9999 0 -10000 0 0
GRB2 0 0.009 -9999 0 -0.29 1 1
PAK1 -0.007 0.044 -9999 0 -0.29 25 25
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.009 0.095 -9999 0 -1 8 8
HRAS -0.003 0.028 -9999 0 -0.29 10 10
VEGF/Rho/ROCK1/Integrin Complex -0.011 0.065 -9999 0 -0.59 8 8
HIF1A 0 0 -9999 0 -10000 0 0
FRS2 -0.003 0.029 -9999 0 -0.29 11 11
oxygen and reactive oxygen species metabolic process -0.007 0.071 -9999 0 -0.88 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.002 0.041 -9999 0 -0.79 3 3
Nck/Pak -0.004 0.028 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.009 0.084 -9999 0 -0.77 11 11
mol:GDP -0.005 0.062 -9999 0 -0.78 6 6
mol:NADP 0.073 0.053 -9999 0 -0.55 6 6
eNOS/Hsp90 0.074 0.049 -9999 0 -0.51 6 6
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
mol:IP3 0.05 0.076 -9999 0 -0.86 6 6
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB -0.001 0.025 -9999 0 -0.54 2 2
VEGFA -0.003 0.03 -9999 0 -10000 0 0
VEGFC 0 0 -9999 0 -10000 0 0
FAK1/Vinculin 0.056 0.1 -9999 0 -0.96 7 7
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.022 0.12 -9999 0 -1.1 8 8
PTPN6 -0.001 0.013 -9999 0 -0.29 2 2
EPAS1 -0.006 0.071 -9999 0 -0.69 10 10
mol:L-citrulline 0.073 0.053 -9999 0 -0.55 6 6
ITGAV 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.29 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.008 0.073 -9999 0 -0.9 6 6
VEGFR2 homodimer/VEGFA homodimer -0.008 0.076 -9999 0 -0.94 6 6
VEGFR2/3 heterodimer -0.009 0.092 -9999 0 -0.86 11 11
VEGFB 0 0 -9999 0 -10000 0 0
MAPK11 0.054 0.08 -9999 0 -0.9 6 6
VEGFR2 homodimer 0.027 0.094 -9999 0 -0.9 10 10
FLT1 -0.001 0.024 -9999 0 -0.79 1 1
NEDD4 0 0 -9999 0 -10000 0 0
MAPK3 0.05 0.084 -9999 0 -0.83 7 7
MAPK1 0.05 0.084 -9999 0 -0.83 7 7
VEGFA145/NRP2 -0.004 0.039 -9999 0 -0.65 3 3
VEGFR1/2 heterodimer -0.008 0.087 -9999 0 -0.85 10 10
KDR 0.027 0.094 -9999 0 -0.91 10 10
VEGFA165/NRP1/VEGFR2 homodimer -0.006 0.082 -9999 0 -0.93 7 7
SRC 0 0.009 -9999 0 -0.29 1 1
platelet activating factor biosynthetic process 0.052 0.085 -9999 0 -0.86 7 7
PI3K -0.009 0.079 -9999 0 -0.9 7 7
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.008 0.077 -9999 0 -0.74 10 10
FES 0.049 0.081 -9999 0 -0.88 6 6
GAB1 -0.006 0.071 -9999 0 -0.9 6 6
VEGFR2 homodimer/VEGFA homodimer/Src -0.008 0.077 -9999 0 -0.74 10 10
CTNNB1 0 0 -9999 0 -10000 0 0
SOS1 0 0 -9999 0 -10000 0 0
ARNT 0 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.01 0.17 -9999 0 -0.7 9 9
VEGFR2 homodimer/VEGFA homodimer/Yes -0.008 0.078 -9999 0 -0.88 7 7
PI3K/GAB1 0.078 0.081 -9999 0 -0.72 7 7
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.003 0.071 -9999 0 -0.87 6 6
PRKACA 0 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.008 0.086 -9999 0 -0.8 11 11
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
CDC42 0.05 0.077 -9999 0 -0.88 6 6
actin cytoskeleton reorganization -0.021 0.086 -9999 0 -0.69 13 13
PTK2 0.051 0.11 -9999 0 -1.1 7 7
EDG1 0.042 0.074 -9999 0 -0.85 6 6
mol:DAG 0.05 0.076 -9999 0 -0.86 6 6
CaM/Ca2+ -0.006 0.063 -9999 0 -0.79 6 6
MAP2K3 0.055 0.079 -9999 0 -0.83 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.005 0.072 -9999 0 -0.9 6 6
PLCG1 0.05 0.077 -9999 0 -0.88 6 6
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.008 0.074 -9999 0 -0.9 6 6
IQGAP1 0 0 -9999 0 -10000 0 0
YES1 -0.001 0.024 -9999 0 -0.79 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.008 0.077 -9999 0 -0.74 10 10
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.008 0.077 -9999 0 -0.74 10 10
cell migration 0.078 0.091 -9999 0 -0.79 7 7
mol:PI-3-4-5-P3 -0.008 0.07 -9999 0 -0.79 7 7
FYN -0.001 0.034 -9999 0 -0.79 2 2
VEGFB/NRP1 -0.007 0.064 -9999 0 -0.8 6 6
mol:NO 0.073 0.053 -9999 0 -0.55 6 6
PXN 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.006 0.06 -9999 0 -0.75 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.005 0.073 -9999 0 -0.9 6 6
VHL 0 0 -9999 0 -10000 0 0
ITGB3 -0.028 0.14 -9999 0 -0.79 37 37
NOS3 0.075 0.059 -9999 0 -0.63 6 6
VEGFR2 homodimer/VEGFA homodimer/Sck -0.019 0.1 -9999 0 -0.54 37 37
RAC1 0 0 -9999 0 -10000 0 0
PRKCA 0.045 0.11 -9999 0 -0.99 6 6
PRKCB 0.046 0.1 -9999 0 -0.86 8 8
VCL 0 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.007 0.069 -9999 0 -0.86 6 6
VEGFR1/2 heterodimer/VEGFA homodimer -0.008 0.082 -9999 0 -0.79 10 10
VEGFA165/NRP2 -0.004 0.039 -9999 0 -0.65 3 3
MAPKKK cascade -0.004 0.06 -9999 0 -0.75 6 6
NRP2 -0.002 0.042 -9999 0 -0.66 4 4
VEGFC homodimer 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
ROCK1 -0.001 0.024 -9999 0 -0.79 1 1
FAK1/Paxillin 0.056 0.1 -9999 0 -0.96 7 7
MAP3K13 0.048 0.083 -9999 0 -0.88 6 6
PDPK1 0.073 0.07 -9999 0 -0.67 7 7
VEGFR1 specific signals

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer -0.001 0.027 -9999 0 -0.89 1 1
VEGFR1 homodimer/NRP1 -0.001 0.027 -9999 0 -0.9 1 1
mol:DAG 0.038 0.032 -9999 0 -0.64 2 2
VEGFR1 homodimer/NRP1/VEGFR 121 -0.002 0.028 -9999 0 -0.84 1 1
CaM/Ca2+ -0.002 0.027 -9999 0 -0.6 2 2
HIF1A 0 0.011 -9999 0 -0.38 1 1
GAB1 0 0 -9999 0 -10000 0 0
AKT1 -0.006 0.052 -9999 0 -0.71 1 1
PLCG1 0.038 0.032 -9999 0 -0.64 2 2
NOS3 0.061 0.033 -9999 0 -0.7 1 1
CBL 0 0 -9999 0 -10000 0 0
mol:NO 0.06 0.032 -9999 0 -0.53 2 2
FLT1 0.029 0.031 -9999 0 -1 1 1
PGF -0.002 0.031 -9999 0 -0.38 6 6
VEGFR1 homodimer/NRP2/VEGFR121 -0.003 0.046 -9999 0 -0.78 3 3
CALM1 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.29 1 1
eNOS/Hsp90 0.065 0.031 -9999 0 -0.64 1 1
endothelial cell proliferation 0.036 0.089 -9999 0 -0.56 8 8
mol:Ca2+ 0.038 0.031 -9999 0 -0.63 2 2
MAPK3 0.039 0.082 -9999 0 -0.43 30 30
MAPK1 0.039 0.082 -9999 0 -0.43 30 30
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
PLGF homodimer -0.002 0.031 -9999 0 -0.38 6 6
PRKACA 0 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.17 0.33 -9999 0 -0.79 241 241
VEGFA homodimer -0.003 0.03 -9999 0 -0.29 12 12
VEGFR1 homodimer/VEGFA homodimer -0.002 0.031 -9999 0 -0.89 1 1
platelet activating factor biosynthetic process 0.046 0.079 -9999 0 -1.1 1 1
PI3K -0.007 0.056 -9999 0 -0.45 16 16
PRKCA 0.032 0.086 -9999 0 -0.46 30 30
PRKCB 0.034 0.077 -9999 0 -0.47 21 21
VEGFR1 homodimer/PLGF homodimer -0.002 0.032 -9999 0 -0.7 2 2
VEGFA -0.003 0.031 -9999 0 -0.29 12 12
VEGFB 0 0 -9999 0 -10000 0 0
mol:IP3 0.038 0.032 -9999 0 -0.64 2 2
RASA1 0.039 0.026 -9999 0 -0.83 1 1
NRP2 -0.002 0.042 -9999 0 -0.66 4 4
VEGFR1 homodimer 0.029 0.031 -9999 0 -1 1 1
VEGFB homodimer 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.03 0.18 -9999 0 -0.58 9 9
PTPN11 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.007 0.055 -9999 0 -0.45 16 16
mol:L-citrulline 0.06 0.032 -9999 0 -0.53 2 2
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.002 0.027 -9999 0 -0.79 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.002 0.028 -9999 0 -0.83 1 1
CD2AP 0 0.009 -9999 0 -0.29 1 1
PI3K/GAB1 -0.007 0.053 -9999 0 -0.43 15 15
PDPK1 -0.007 0.052 -9999 0 -0.42 16 16
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.002 0.028 -9999 0 -0.83 1 1
mol:NADP 0.06 0.032 -9999 0 -0.53 2 2
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
ubiquitin-dependent protein catabolic process -0.002 0.026 -9999 0 -0.78 1 1
VEGFR1 homodimer/NRP2 -0.002 0.046 -9999 0 -0.78 3 3
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.01 0.035 -9999 0 -0.41 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.007 0.028 -9999 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0 0.022 -9999 0 -0.52 2 2
antigen processing and presentation of peptide antigen via MHC class I -0.006 0.039 -9999 0 -0.33 2 2
CaM/Ca2+ 0.009 0.031 -9999 0 -0.38 2 2
RAP1A 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.011 0.036 -9999 0 -0.38 2 2
AKT1 -0.011 0.047 -9999 0 -0.45 2 2
MAP2K1 0.04 0.044 -9999 0 -0.39 1 1
MAP3K11 0.03 0.043 -9999 0 -0.38 2 2
IFNGR1 0.012 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.023 0.093 -9999 0 -0.41 23 23
Rap1/GTP -0.004 0.015 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.013 0.036 -9999 0 -0.43 2 2
CEBPB 0.075 0.039 -9999 0 -10000 0 0
STAT3 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.007 0.055 -9999 0 -1.2 1 1
STAT1 -0.011 0.036 -9999 0 -0.38 2 2
CALM1 0 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.03 0.1 -9999 0 -0.28 150 150
PIK3CA 0 0.009 -9999 0 -0.29 1 1
STAT1 (dimer)/PIAS1 -0.01 0.032 -9999 0 -0.36 2 2
CEBPB/PTGES2/Cbp/p300 -0.001 0.012 -9999 0 -10000 0 0
mol:Ca2+ 0.008 0.034 -9999 0 -0.41 2 2
MAPK3 0.054 0.04 -9999 0 -10000 0 0
STAT1 (dimer) -0.006 0.054 -9999 0 -0.48 2 2
MAPK1 0.054 0.04 -9999 0 -10000 0 0
JAK2 0.011 0.024 -9999 0 -0.79 1 1
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
JAK1 0.011 0.024 -9999 0 -0.78 1 1
CAMK2D -0.002 0.041 -9999 0 -0.79 3 3
DAPK1 0.07 0.033 -9999 0 -10000 0 0
SMAD7 0.05 0.038 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.007 0.022 -9999 0 -10000 0 0
PI3K 0.002 0.055 -9999 0 -0.4 15 15
IFNG -0.03 0.1 -9999 0 -0.28 150 150
apoptosis 0.053 0.029 -9999 0 -10000 0 0
CAMK2G 0 0 -9999 0 -10000 0 0
STAT3 (dimer) 0 0 -9999 0 -10000 0 0
CAMK2A -0.01 0.053 -9999 0 -0.29 37 37
CAMK2B -0.066 0.2 -9999 0 -0.59 123 123
FRAP1 0.037 0.058 -9999 0 -0.42 2 2
PRKCD -0.011 0.047 -9999 0 -0.45 2 2
RAP1B 0 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.006 0.039 -9999 0 -0.33 2 2
PTPN2 0 0 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
IRF1 0.064 0.047 -9999 0 -10000 0 0
STAT1 (dimer)/PIASy -0.01 0.033 -9999 0 -0.37 1 1
SOCS1 0 0.049 -9999 0 -1.5 1 1
mol:GDP -0.007 0.021 -9999 0 -10000 0 0
CASP1 0.049 0.045 -9999 0 -0.35 5 5
PTGES2 0 0.009 -9999 0 -0.29 1 1
IRF9 0.058 0.019 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.012 0.05 -9999 0 -0.39 15 15
RAP1/GDP -0.004 0.015 -9999 0 -10000 0 0
CBL 0.029 0.043 -9999 0 -0.38 2 2
MAP3K1 0.031 0.045 -9999 0 -0.39 3 3
PIAS1 0 0 -9999 0 -10000 0 0
PIAS4 0 0.002 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.006 0.039 -9999 0 -0.33 2 2
PTPN11 0.021 0.044 -9999 0 -0.41 2 2
CREBBP 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 0 0.017 -10000 0 -10000 0 0
oxygen homeostasis 0.012 0.012 -10000 0 -10000 0 0
TCEB2 -0.007 0.045 -10000 0 -0.29 27 27
TCEB1 -0.001 0.015 -10000 0 -0.29 3 3
VHL/Elongin B/Elongin C/HIF2A -0.007 0.039 -10000 0 -0.4 3 3
EPO 0.14 0.15 -10000 0 -0.65 3 3
FIH (dimer) 0.023 0.012 -10000 0 -10000 0 0
APEX1 0.022 0.014 -10000 0 -0.31 1 1
SERPINE1 0.16 0.15 -10000 0 -0.66 5 5
FLT1 -0.004 0.085 -10000 0 -1.1 6 6
ADORA2A 0.14 0.16 -10000 0 -0.64 5 5
germ cell development 0.16 0.15 -10000 0 -0.65 5 5
SLC11A2 0.16 0.15 -10000 0 -0.68 4 4
BHLHE40 0.16 0.16 -10000 0 -0.8 5 5
HIF1AN 0.023 0.012 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.013 0.07 -10000 0 -0.42 5 5
ETS1 0.022 0.061 -10000 0 -0.8 6 6
CITED2 0.001 0.011 -10000 0 -10000 0 0
KDR -0.008 0.12 -10000 0 -1.3 9 9
PGK1 0.16 0.15 -10000 0 -0.68 4 4
SIRT1 0 0 -10000 0 -10000 0 0
response to hypoxia -0.001 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.18 0.16 -10000 0 -0.77 5 5
EPAS1 0.091 0.083 -10000 0 -0.41 5 5
SP1 0.019 0.002 -10000 0 -10000 0 0
ABCG2 0.12 0.25 -10000 0 -0.69 80 80
EFNA1 0.16 0.15 -10000 0 -0.68 4 4
FXN 0.15 0.15 -10000 0 -0.66 4 4
POU5F1 0.16 0.15 -10000 0 -0.68 5 5
neuron apoptosis -0.17 0.16 0.74 5 -10000 0 5
EP300 0 0 -10000 0 -10000 0 0
EGLN3 -0.001 0.085 -10000 0 -0.29 83 83
EGLN2 0.021 0.026 -10000 0 -0.28 6 6
EGLN1 0.022 0.027 -10000 0 -0.8 1 1
VHL/Elongin B/Elongin C -0.004 0.024 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.023 0.01 -10000 0 -10000 0 0
SLC2A1 0.15 0.16 -10000 0 -0.64 6 6
TWIST1 0.13 0.21 -10000 0 -0.68 46 46
ELK1 0.019 0.009 -10000 0 -0.29 1 1
HIF2A/ARNT/Cbp/p300 0.008 0.063 -10000 0 -0.6 1 1
VEGFA 0.16 0.15 -10000 0 -0.71 4 4
CREBBP 0 0 -10000 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.002 0.028 0.3 2 -0.44 2 4
DAPP1 0.036 0.052 -10000 0 -0.58 4 4
Src family/SYK family/BLNK-LAT/BTK-ITK 0.046 0.078 -10000 0 -0.56 10 10
mol:DAG 0.052 0.05 0.21 1 -0.27 7 8
HRAS 0.009 0.029 -10000 0 -0.29 10 10
RAP1A 0 0 -10000 0 -10000 0 0
ARF5/GDP 0.038 0.032 -10000 0 -0.3 2 2
PLCG2 -0.002 0.035 -10000 0 -0.62 3 3
PLCG1 0 0 -10000 0 -10000 0 0
ARF5 0 0.009 -10000 0 -0.29 1 1
mol:GTP -0.001 0.022 0.26 2 -0.38 2 4
ARF1/GTP -0.001 0.023 0.28 2 -0.37 2 4
RHOA 0 0 -10000 0 -10000 0 0
YES1 -0.001 0.024 -10000 0 -0.79 1 1
RAP1A/GTP -0.001 0.022 0.25 2 -0.38 2 4
ADAP1 -0.003 0.032 0.26 2 -0.39 5 7
ARAP3 -0.001 0.022 0.26 2 -0.39 2 4
INPPL1 0 0 -10000 0 -10000 0 0
PREX1 -0.01 0.057 -10000 0 -0.31 36 36
ARHGEF6 -0.011 0.092 -10000 0 -0.79 15 15
ARHGEF7 0 0 -10000 0 -10000 0 0
ARF1 0 0 -10000 0 -10000 0 0
NRAS 0.011 0.013 -10000 0 -0.29 2 2
FYN -0.001 0.034 -10000 0 -0.79 2 2
ARF6 0 0 -10000 0 -10000 0 0
FGR -0.001 0.025 -10000 0 -0.54 2 2
mol:Ca2+ 0.039 0.029 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.001 0.018 -10000 0 -0.29 4 4
ZAP70 -0.031 0.12 -10000 0 -0.42 81 81
mol:IP3 0.047 0.038 -10000 0 -0.22 1 1
LYN 0 0 -10000 0 -10000 0 0
ARF1/GDP 0.038 0.032 -10000 0 -0.3 2 2
RhoA/GDP -0.002 0.022 0.27 2 -10000 0 2
PDK1/Src/Hsp90 0 0.006 -10000 0 -10000 0 0
BLNK 0 0 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.061 0.035 -10000 0 -10000 0 0
SRC 0 0.009 -10000 0 -0.29 1 1
PLEKHA2 0.03 0.007 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PTEN -0.001 0.033 -10000 0 -0.76 2 2
HSP90AA1 0 0.009 -10000 0 -0.29 1 1
ARF6/GTP -0.001 0.021 0.3 2 -10000 0 2
RhoA/GTP -0.001 0.021 0.25 2 -0.36 2 4
Src family/SYK family/BLNK-LAT -0.011 0.056 -10000 0 -0.53 6 6
BLK -0.044 0.11 -10000 0 -0.3 159 159
PDPK1 0 0 -10000 0 -10000 0 0
CYTH1 -0.001 0.021 0.26 2 -0.36 2 4
HCK -0.004 0.033 -10000 0 -10000 0 0
CYTH3 -0.002 0.028 0.26 2 -0.41 4 6
CYTH2 -0.001 0.021 0.26 2 -0.36 2 4
KRAS 0.011 0.013 -10000 0 -0.29 2 2
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.005 0.055 -10000 0 -0.55 10 10
SGK1 -0.004 0.057 0.23 2 -0.7 7 9
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.034 0.033 -10000 0 -0.28 4 4
SOS1 0 0 -10000 0 -10000 0 0
SYK 0 0.009 -10000 0 -0.29 1 1
ARF6/GDP -0.002 0.023 0.28 2 -10000 0 2
mol:PI-3-4-5-P3 -0.001 0.024 0.36 2 -0.38 2 4
ARAP3/RAP1A/GTP -0.001 0.022 0.25 2 -0.38 2 4
VAV1 -0.003 0.043 -10000 0 -0.59 5 5
mol:PI-3-4-P2 0.022 0 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I -0.002 0.019 -10000 0 -0.39 2 2
PLEKHA1 0.03 0.017 -10000 0 -0.52 1 1
Rac1/GDP 0.038 0.032 -10000 0 -0.3 2 2
LAT -0.005 0.048 -10000 0 -0.35 17 17
Rac1/GTP -0.006 0.045 -10000 0 -0.37 15 15
ITK -0.019 0.083 0.26 1 -0.43 38 39
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.059 0.065 0.24 1 -0.39 7 8
LCK -0.02 0.1 -10000 0 -0.41 53 53
BTK -0.001 0.021 0.26 2 -0.36 2 4
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.058 0.076 -9999 0 -0.51 1 1
CRKL 0.028 0.05 -9999 0 -0.48 1 1
mol:DAG -0.007 0.026 -9999 0 -0.39 1 1
HRAS -0.006 0.022 -9999 0 -0.39 1 1
MAPK8 0.01 0.07 -9999 0 -0.5 9 9
RAP1A 0.028 0.05 -9999 0 -0.48 1 1
GAB1 0.028 0.05 -9999 0 -0.48 1 1
MAPK14 0.015 0.052 -9999 0 -10000 0 0
EPO -0.036 0.11 -9999 0 -0.28 177 177
PLCG1 -0.007 0.026 -9999 0 -0.4 1 1
EPOR/TRPC2/IP3 Receptors 0.012 0.01 -9999 0 -0.28 1 1
RAPGEF1 0 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.024 0.065 -9999 0 -0.62 6 6
GAB1/SHC/GRB2/SOS1 -0.008 0.022 -9999 0 -0.41 1 1
EPO/EPOR (dimer) -0.027 0.067 -9999 0 -10000 0 0
IRS2 0.009 0.11 -9999 0 -0.46 47 47
STAT1 0.049 0.056 -9999 0 -0.5 1 1
STAT5B -0.004 0.043 -9999 0 -0.43 4 4
cell proliferation 0.02 0.065 -9999 0 -0.46 9 9
GAB1/SHIP/PIK3R1/SHP2/SHC -0.011 0.044 -9999 0 -0.42 4 4
TEC 0.027 0.056 -9999 0 -0.48 4 4
SOCS3 -0.004 0.058 -9999 0 -0.79 6 6
STAT1 (dimer) 0.048 0.056 -9999 0 -0.49 1 1
JAK2 0.011 0.025 -9999 0 -0.8 1 1
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
EPO/EPOR (dimer)/JAK2 0.054 0.04 -9999 0 -0.51 1 1
EPO/EPOR -0.027 0.067 -9999 0 -10000 0 0
LYN 0.013 0.002 -9999 0 -10000 0 0
TEC/VAV2 0.034 0.055 -9999 0 -0.46 4 4
elevation of cytosolic calcium ion concentration 0.012 0.01 -9999 0 -0.28 1 1
SHC1 0 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.017 0.05 -9999 0 -10000 0 0
mol:IP3 -0.007 0.026 -9999 0 -0.39 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.03 0.096 -9999 0 -0.49 23 23
SH2B3 0.012 0.004 -9999 0 -10000 0 0
NFKB1 0.015 0.052 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 -0.01 0.031 -9999 0 -0.32 7 7
PTPN6 0.021 0.052 -9999 0 -0.51 1 1
TEC/VAV2/GRB2 -0.01 0.034 -9999 0 -0.46 3 3
EPOR 0.012 0.01 -9999 0 -0.28 1 1
INPP5D 0 0 -9999 0 -10000 0 0
mol:GDP -0.008 0.022 -9999 0 -0.42 1 1
SOS1 0 0 -9999 0 -10000 0 0
PLCG2 -0.002 0.035 -9999 0 -0.62 3 3
CRKL/CBL/C3G -0.009 0.025 -9999 0 -0.44 1 1
VAV2 0.028 0.05 -9999 0 -0.48 1 1
CBL 0.028 0.05 -9999 0 -0.48 1 1
SHC/Grb2/SOS1 0.005 0.028 -9999 0 -0.44 1 1
STAT5A -0.006 0.055 -9999 0 -0.47 9 9
GRB2 0 0.009 -9999 0 -0.29 1 1
STAT5 (dimer) 0.058 0.085 -9999 0 -0.56 5 5
LYN/PLCgamma2 -0.001 0.026 -9999 0 -0.6 2 2
PTPN11 0 0 -9999 0 -10000 0 0
BTK 0.028 0.051 -9999 0 -0.48 1 1
BCL2 0.036 0.19 -9999 0 -0.98 37 37
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 -0.006 0.055 -9999 0 -0.43 14 14
Caspase 8 (4 units) -0.01 0.052 -9999 0 -0.85 2 2
NEF -0.006 0.028 -9999 0 -10000 0 0
NFKBIA -0.001 0.011 -9999 0 -10000 0 0
BIRC3 0.035 0.081 -9999 0 -0.79 9 9
CYCS 0.04 0.06 -9999 0 -0.93 1 1
RIPK1 0 0 -9999 0 -10000 0 0
CD247 -0.025 0.12 -9999 0 -0.61 37 37
MAP2K7 0.042 0.049 -9999 0 -0.8 1 1
protein ubiquitination 0.066 0.034 -9999 0 -10000 0 0
CRADD 0 0 -9999 0 -10000 0 0
DAXX 0 0 -9999 0 -10000 0 0
FAS -0.004 0.058 -9999 0 -0.79 6 6
BID 0.033 0.063 -9999 0 -1 1 1
NF-kappa-B/RelA/I kappa B alpha -0.004 0.033 -9999 0 -10000 0 0
TRADD 0 0 -9999 0 -10000 0 0
MAP3K5 -0.003 0.048 -9999 0 -0.79 4 4
CFLAR -0.001 0.024 -9999 0 -0.79 1 1
FADD -0.004 0.034 -9999 0 -0.29 15 15
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.004 0.033 -9999 0 -10000 0 0
MAPK8 0.045 0.064 -9999 0 -0.48 10 10
APAF1 0 0 -9999 0 -10000 0 0
TRAF1 -0.001 0.015 -9999 0 -0.29 3 3
TRAF2 -0.001 0.018 -9999 0 -0.29 4 4
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.012 0.058 -9999 0 -0.33 24 24
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.002 0.03 -9999 0 -0.37 2 2
CHUK 0.068 0.035 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.005 0.049 -9999 0 -0.5 9 9
TCRz/NEF -0.025 0.11 -9999 0 -0.51 41 41
TNF -0.016 0.095 -9999 0 -0.46 38 38
FASLG -0.007 0.15 -9999 0 -0.66 41 41
NFKB1 -0.001 0.011 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.013 0.069 -9999 0 -0.52 17 17
CASP6 -0.005 0.037 -9999 0 -0.68 2 2
CASP7 0.072 0.077 -9999 0 -0.62 9 9
RELA -0.001 0.011 -9999 0 -10000 0 0
CASP2 0 0 -9999 0 -10000 0 0
CASP3 0.072 0.077 -9999 0 -0.6 10 10
TNFRSF1A 0 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.004 0.04 -9999 0 -0.6 4 4
CASP8 0 0 -9999 0 -10000 0 0
CASP9 0 0 -9999 0 -10000 0 0
MAP3K14 0.063 0.038 -9999 0 -0.36 1 1
APAF-1/Caspase 9 -0.01 0.053 -9999 0 -0.5 9 9
BCL2 0.036 0.1 -9999 0 -0.42 44 44
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate -0.004 0.045 -9999 0 -0.56 6 6
PDGFB-D/PDGFRB/SLAP -0.004 0.041 -9999 0 -0.6 4 4
PDGFB-D/PDGFRB/APS/CBL -0.008 0.043 -9999 0 -0.51 4 4
AKT1 -0.012 0.052 -9999 0 -0.49 4 4
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.035 0.052 -9999 0 -0.58 6 6
PIK3CA 0 0.009 -9999 0 -0.29 1 1
FGR -0.003 0.038 -9999 0 -0.53 5 5
mol:Ca2+ 0.033 0.048 -9999 0 -0.68 4 4
MYC 0.039 0.14 -9999 0 -0.8 28 28
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.003 0.028 -9999 0 -0.42 4 4
LRP1/PDGFRB/PDGFB -0.008 0.07 -9999 0 -0.58 15 15
GRB10 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
GO:0007205 0.033 0.048 -9999 0 -0.69 4 4
PTEN -0.001 0.034 -9999 0 -0.79 2 2
GRB2 0 0.009 -9999 0 -0.29 1 1
GRB7 -0.023 0.085 -9999 0 -0.31 79 79
PDGFB-D/PDGFRB/SHP2 -0.002 0.036 -9999 0 -0.6 4 4
PDGFB-D/PDGFRB/GRB10 -0.002 0.036 -9999 0 -0.6 4 4
cell cycle arrest -0.004 0.04 -9999 0 -0.6 4 4
HRAS -0.003 0.028 -9999 0 -0.29 10 10
HIF1A 0.05 0.061 -9999 0 -0.43 4 4
GAB1 0.035 0.055 -9999 0 -0.67 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.04 0.053 -9999 0 -0.61 4 4
PDGFB-D/PDGFRB -0.003 0.035 -9999 0 -0.52 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.002 0.036 -9999 0 -0.6 4 4
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.005 0.049 -9999 0 -0.57 6 6
positive regulation of MAPKKK cascade -0.002 0.036 -9999 0 -0.6 4 4
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
mol:IP3 0.033 0.049 -9999 0 -0.7 4 4
E5 0 0.001 -9999 0 -10000 0 0
CSK 0 0.003 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.017 0.067 -9999 0 -0.6 7 7
SHB -0.001 0.025 -9999 0 -0.54 2 2
BLK -0.002 0.049 -9999 0 -0.58 7 7
PTPN2 0.002 0.004 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.002 0.036 -9999 0 -0.6 4 4
BCAR1 0 0 -9999 0 -10000 0 0
VAV2 0.04 0.062 -9999 0 -0.61 5 5
CBL 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.002 0.036 -9999 0 -0.6 4 4
LCK -0.01 0.08 -9999 0 -0.63 16 16
PDGFRB 0.009 0.049 -9999 0 -0.79 4 4
ACP1 0 0 -9999 0 -10000 0 0
HCK -0.002 0.033 -9999 0 -0.5 4 4
ABL1 0.034 0.049 -9999 0 -0.63 4 4
PDGFB-D/PDGFRB/CBL 0.034 0.06 -9999 0 -0.79 4 4
PTPN1 -0.001 0.03 -9999 0 -0.3 1 1
SNX15 0 0 -9999 0 -10000 0 0
STAT3 0 0 -9999 0 -10000 0 0
STAT1 -0.005 0.038 -9999 0 -0.29 19 19
cell proliferation 0.041 0.12 -9999 0 -0.69 28 28
SLA -0.003 0.029 -9999 0 -0.29 11 11
actin cytoskeleton reorganization -0.002 0.028 -9999 0 -0.4 1 1
SRC -0.002 0.033 -9999 0 -0.5 4 4
PI3K -0.014 0.059 -9999 0 -0.56 4 4
PDGFB-D/PDGFRB/GRB7/SHC -0.013 0.054 -9999 0 -0.52 7 7
SH2B2 -0.013 0.061 -9999 0 -0.29 49 49
PLCgamma1/SPHK1 0.036 0.054 -9999 0 -0.61 6 6
LYN -0.002 0.033 -9999 0 -0.5 4 4
LRP1 -0.009 0.085 -9999 0 -0.79 13 13
SOS1 0 0 -9999 0 -10000 0 0
STAT5B -0.002 0.041 -9999 0 -0.79 3 3
STAT5A -0.006 0.067 -9999 0 -0.79 8 8
NCK1-2/p130 Cas -0.002 0.026 -9999 0 -0.41 4 4
SPHK1 0.004 0.054 -9999 0 -0.33 23 23
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.033 0.049 -9999 0 -0.7 4 4
PLCG1 0.033 0.05 -9999 0 -0.72 4 4
NHERF/PDGFRB -0.015 0.052 -9999 0 -0.51 4 4
YES1 -0.003 0.038 -9999 0 -0.52 5 5
cell migration -0.015 0.052 -9999 0 -0.51 4 4
SHC/Grb2/SOS1 -0.002 0.026 -9999 0 -0.41 4 4
SLC9A3R2 -0.001 0.02 -9999 0 -0.29 5 5
SLC9A3R1 -0.026 0.083 -9999 0 -0.29 97 97
NHERF1-2/PDGFRB/PTEN -0.014 0.049 -9999 0 -0.47 6 6
FYN -0.003 0.06 -9999 0 -0.89 4 4
DOK1 0.029 0.035 -9999 0 -0.47 4 4
HRAS/GTP -0.002 0.019 -9999 0 -0.2 10 10
PDGFB 0 0 -9999 0 -10000 0 0
RAC1 0.046 0.082 -9999 0 -0.44 28 28
PRKCD 0.03 0.035 -9999 0 -0.47 4 4
FER 0.025 0.061 -9999 0 -0.48 15 15
MAPKKK cascade -0.002 0.027 -9999 0 -0.4 4 4
RASA1 0.03 0.035 -9999 0 -0.47 4 4
NCK1 0 0 -9999 0 -10000 0 0
NCK2 0 0 -9999 0 -10000 0 0
p62DOK/Csk -0.002 0.029 -9999 0 -0.43 4 4
PDGFB-D/PDGFRB/SHB -0.003 0.041 -9999 0 -0.6 5 5
chemotaxis 0.034 0.048 -9999 0 -0.6 4 4
STAT1-3-5/STAT1-3-5 -0.008 0.054 -9999 0 -0.46 13 13
Bovine Papilomavirus E5/PDGFRB -0.002 0.037 -9999 0 -0.61 4 4
PTPRJ 0 0 -9999 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 -0.001 0.024 -9999 0 -0.79 1 1
SMAD2 0.014 0.004 -9999 0 -10000 0 0
SMAD3 0.041 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.004 0.015 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0 0.016 -9999 0 -0.52 1 1
SMAD2/SMAD2/SMAD4 -0.009 0.031 -9999 0 -0.52 1 1
PPM1A 0 0 -9999 0 -10000 0 0
CALM1 0 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0 0.015 -9999 0 -0.47 1 1
MAP3K1 -0.001 0.024 -9999 0 -0.79 1 1
TRAP-1/SMAD4 -0.01 0.076 -9999 0 -0.6 18 18
MAPK3 0 0 -9999 0 -10000 0 0
MAPK1 0 0 -9999 0 -10000 0 0
NUP214 0 0 -9999 0 -10000 0 0
CTDSP1 0 0 -9999 0 -10000 0 0
CTDSP2 0 0 -9999 0 -10000 0 0
CTDSPL 0 0 -9999 0 -10000 0 0
KPNB1 0 0 -9999 0 -10000 0 0
TGFBRAP1 -0.012 0.097 -9999 0 -0.79 17 17
UBE2I 0 0 -9999 0 -10000 0 0
NUP153 0 0.009 -9999 0 -0.29 1 1
KPNA2 -0.029 0.087 -9999 0 -0.29 108 108
PIAS4 0 0 -9999 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.046 0.045 -10000 0 -0.55 1 1
BAG4 -0.006 0.055 -10000 0 -0.43 14 14
BAD 0.032 0.017 -10000 0 -10000 0 0
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.077 -10000 0 -0.5 21 21
BAX 0.032 0.018 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.015 0.012 -10000 0 -0.1 2 2
IKBKB 0.052 0.043 -10000 0 -0.51 1 1
MAP2K2 0.044 0.024 -10000 0 -0.46 1 1
MAP2K1 0.044 0.024 -10000 0 -0.46 1 1
SMPD1 0.021 0.012 -10000 0 -0.11 1 1
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.051 0.048 -10000 0 -0.45 3 3
MAP2K4 0.038 0.025 -10000 0 -0.38 2 2
protein ubiquitination 0.054 0.044 -10000 0 -0.52 1 1
EnzymeConsortium:2.7.1.37 0.049 0.026 -10000 0 -0.48 1 1
response to UV 0 0 -10000 0 -0.003 1 1
RAF1 0.039 0.024 -10000 0 -0.49 1 1
CRADD 0.011 0.002 -10000 0 -10000 0 0
mol:ceramide 0.025 0.017 -10000 0 -0.14 2 2
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0.011 0.002 -10000 0 -10000 0 0
MAP3K1 0.032 0.021 -10000 0 -0.4 1 1
TRADD 0.011 0.002 -10000 0 -10000 0 0
RELA/p50 0 0 -10000 0 -10000 0 0
MAPK3 0.047 0.023 -10000 0 -0.45 1 1
MAPK1 0.047 0.023 -10000 0 -0.45 1 1
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.044 0.049 -10000 0 -0.47 3 3
KSR1 0.032 0.024 -10000 0 -0.52 1 1
MAPK8 0.041 0.047 -10000 0 -0.41 10 10
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
response to radiation 0 0 -10000 0 -0.002 1 1
CHUK 0.052 0.043 -10000 0 -0.51 1 1
TNF R/SODD -0.004 0.04 -10000 0 -0.6 4 4
TNF -0.005 0.097 -10000 0 -0.46 38 38
CYCS 0.037 0.025 0.15 32 -10000 0 32
IKBKG 0.052 0.043 -10000 0 -0.51 1 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.039 0.047 -10000 0 -0.35 9 9
RELA 0 0 -10000 0 -10000 0 0
RIPK1 0 0.001 -10000 0 -10000 0 0
AIFM1 0.037 0.025 0.15 32 -10000 0 32
TNF/TNF R/SODD -0.013 0.069 -10000 0 -0.52 17 17
TNFRSF1A 0 0.001 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -0.002 1 1
CASP8 0.028 0.012 -10000 0 -10000 0 0
NSMAF 0.046 0.045 -10000 0 -0.54 1 1
response to hydrogen peroxide 0 0 -10000 0 -0.003 1 1
BCL2 -0.027 0.14 -10000 0 -0.79 37 37
FoxO family signaling

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
G6PC 0.029 0.039 -9999 0 -10000 0 0
PLK1 0.004 0.12 -9999 0 -0.82 2 2
CDKN1B 0.079 0.072 -9999 0 -0.54 3 3
FOXO3 0.039 0.11 -9999 0 -0.56 12 12
KAT2B 0.008 0.028 -9999 0 -0.83 1 1
FOXO1/SIRT1 0.007 0.039 -9999 0 -0.32 12 12
CAT 0.041 0.13 -9999 0 -1.1 7 7
CTNNB1 0 0 -9999 0 -10000 0 0
AKT1 0.015 0.011 -9999 0 -10000 0 0
FOXO1 0.031 0.042 -9999 0 -0.36 12 12
MAPK10 -0.038 0.18 -9999 0 -0.44 171 171
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.063 0.089 -9999 0 -0.41 1 1
response to oxidative stress 0.005 0.012 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.016 0.069 -9999 0 -0.52 8 8
XPO1 0.012 0.001 -9999 0 -10000 0 0
EP300 0.01 0.005 -9999 0 -10000 0 0
BCL2L11 0.028 0.02 -9999 0 -10000 0 0
FOXO1/SKP2 -0.004 0.033 -9999 0 -0.32 12 12
mol:GDP 0.005 0.012 -9999 0 -10000 0 0
RAN 0.013 0.001 -9999 0 -10000 0 0
GADD45A 0.068 0.064 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.069 0.027 -9999 0 -10000 0 0
MST1 -0.003 0.092 -9999 0 -0.59 22 22
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.049 0.045 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
MAPK8 0.033 0.044 -9999 0 -0.44 9 9
MAPK9 0.036 0.006 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
YWHAZ -0.001 0.015 -9999 0 -0.29 3 3
SIRT1 0.004 0.009 -9999 0 -10000 0 0
SOD2 0.09 0.079 -9999 0 -0.45 1 1
RBL2 0.06 0.083 -9999 0 -0.56 1 1
RAL/GDP 0.012 0.016 -9999 0 -10000 0 0
CHUK 0.009 0.013 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
CSNK1G2 0 0 -9999 0 -10000 0 0
RAL/GTP 0.031 0.01 -9999 0 -10000 0 0
CSNK1G1 0 0 -9999 0 -10000 0 0
FASLG 0.002 0.18 -9999 0 -1.5 15 15
SKP2 0 0 -9999 0 -10000 0 0
USP7 0.013 0.001 -9999 0 -10000 0 0
IKBKB 0.008 0.018 -9999 0 -0.28 2 2
CCNB1 0.032 0.12 -9999 0 -0.62 7 7
FOXO1-3a-4/beta catenin -0.009 0.043 -9999 0 -0.41 7 7
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.033 -9999 0 -0.32 12 12
CSNK1A1 0 0 -9999 0 -10000 0 0
SGK1 0.004 0.065 -9999 0 -0.79 7 7
CSNK1G3 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
ZFAND5 0.068 0.079 -9999 0 -10000 0 0
SFN -0.016 0.099 -9999 0 -0.5 36 36
CDK2 0.004 0.006 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.044 0.048 -9999 0 -10000 0 0
CREBBP 0.004 0.006 -9999 0 -10000 0 0
FBXO32 0.042 0.12 -9999 0 -1.1 5 5
BCL6 0.054 0.13 -9999 0 -1.2 7 7
RALB 0 0 -9999 0 -10000 0 0
RALA 0 0 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
Atypical 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
BCL3/RelA -0.001 0.01 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.007 0.058 -9999 0 -0.52 14 14
NF kappa B1 p50/RelA/I kappa B alpha -0.003 0.024 -9999 0 -10000 0 0
NFKBIA 0.024 0.034 -9999 0 -0.27 13 13
MAPK14 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0 0.006 -9999 0 -10000 0 0
ARRB2 0.017 0 -9999 0 -10000 0 0
REL -0.01 0.089 -9999 0 -0.79 14 14
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.001 0.01 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0 0.006 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.29 1 1
NF kappa B1 p50 dimer 0 0.008 -9999 0 -10000 0 0
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
NFKB1 0.022 0.009 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.03 0.033 -9999 0 -0.26 13 13
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.003 0.023 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -0.29 1 1
PI3K -0.008 0.068 -9999 0 -0.6 14 14
NF kappa B1 p50/RelA -0.004 0.029 -9999 0 -0.26 13 13
IKBKB -0.001 0.013 -9999 0 -0.29 2 2
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
SYK 0 0.009 -9999 0 -0.29 1 1
I kappa B alpha/PIK3R1 -0.009 0.056 -9999 0 -0.44 14 14
cell death -0.003 0.022 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel -0.007 0.058 -9999 0 -0.52 14 14
LCK -0.02 0.1 -9999 0 -0.41 53 53
BCL3 -0.001 0.015 -9999 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.077 0.036 -9999 0 -10000 0 0
ERC1 0 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.007 0.04 -9999 0 -0.48 2 2
NFKBIA 0.047 0 -9999 0 -10000 0 0
BIRC2 0 0 -9999 0 -10000 0 0
IKBKB -0.001 0.013 -9999 0 -0.29 2 2
RIPK2 -0.001 0.02 -9999 0 -0.29 5 5
IKBKG 0 0.008 -9999 0 -10000 0 0
IKK complex/A20 -0.003 0.043 -9999 0 -10000 0 0
NEMO/A20/RIP2 -0.001 0.02 -9999 0 -0.29 5 5
XPO1 0 0 -9999 0 -10000 0 0
NEMO/ATM 0 0.007 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0 0.007 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 -0.01 0.056 -9999 0 -0.31 35 35
NFKB1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
MALT1 0 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.011 0.07 -9999 0 -0.6 13 13
TRAF6 0 0 -9999 0 -10000 0 0
PRKCA -0.021 0.13 -9999 0 -0.76 31 31
CHUK 0 0 -9999 0 -10000 0 0
UBE2D3 0 0 -9999 0 -10000 0 0
TNF -0.016 0.095 -9999 0 -0.46 38 38
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.047 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
TNFRSF1A 0 0 -9999 0 -10000 0 0
IKK complex 0 0.008 -9999 0 -10000 0 0
CYLD 0 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.009 0.06 -9999 0 -0.37 29 29
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.004 0.053 -9999 0 -0.48 13 13
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.005 0.044 -9999 0 -0.4 13 13
SUMO1 0 0 -9999 0 -10000 0 0
ZFPM1 -0.002 0.026 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0 0.001 -9999 0 -10000 0 0
FKBP3 0 0 -9999 0 -10000 0 0
Histones -0.003 0.022 -9999 0 -10000 0 0
YY1/LSF -0.001 0.017 -9999 0 -0.4 2 2
SMG5 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.005 0.039 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 -0.004 0.026 -9999 0 -10000 0 0
SAP18 0 0 -9999 0 -10000 0 0
RELA -0.004 0.034 -9999 0 -0.31 13 13
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0 0.009 -9999 0 -0.29 1 1
HDAC3/TR2 -0.004 0.026 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0 0.006 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.004 0.03 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.024 0.13 -9999 0 -0.63 41 41
GATA1 -0.005 0.037 -9999 0 -0.29 18 18
Mad/Max 0 0.006 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0 0.007 -9999 0 -10000 0 0
RBBP7 -0.002 0.025 -9999 0 -0.29 8 8
NPC 0 0 -9999 0 -10000 0 0
RBBP4 -0.001 0.024 -9999 0 -0.79 1 1
MAX 0 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
NFKBIA -0.004 0.03 -9999 0 -10000 0 0
KAT2B -0.001 0.024 -9999 0 -0.79 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0.008 -9999 0 -10000 0 0
SIN3 complex 0 0.007 -9999 0 -10000 0 0
SMURF1 0 0 -9999 0 -10000 0 0
CHD3 0 0 -9999 0 -10000 0 0
SAP30 -0.001 0.018 -9999 0 -0.29 4 4
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 -0.001 0.024 -9999 0 -0.79 1 1
YY1/HDAC3 -0.003 0.024 -9999 0 -10000 0 0
YY1/HDAC2 0 0.009 -9999 0 -0.29 1 1
YY1/HDAC1 0 0.009 -9999 0 -0.29 1 1
NuRD/MBD2 Complex (MeCP1) 0 0.006 -9999 0 -10000 0 0
PPARG -0.095 0.17 -9999 0 -0.37 277 277
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
TNFRSF1A 0 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) -0.004 0.026 -9999 0 -10000 0 0
MBD3L2 -0.001 0.013 -9999 0 -0.29 2 2
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0 0.007 -9999 0 -10000 0 0
HDAC1 0 0 -9999 0 -10000 0 0
HDAC3 -0.004 0.03 -9999 0 -10000 0 0
HDAC2 0 0 -9999 0 -10000 0 0
YY1 0.029 0.011 -9999 0 -0.35 1 1
HDAC8 0 0 -9999 0 -10000 0 0
SMAD7 0 0 -9999 0 -10000 0 0
NCOR2 0 0 -9999 0 -10000 0 0
MXD1 0 0.009 -9999 0 -0.29 1 1
STAT3 0.025 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.001 0.016 -9999 0 -0.46 1 1
YY1/SAP30/HDAC1 -0.001 0.01 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.025 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.03 -9999 0 -10000 0 0
histone deacetylation 0.046 0.008 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.003 0.023 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GATAD2B 0 0 -9999 0 -10000 0 0
GATAD2A 0 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.017 0.079 -9999 0 -0.47 28 28
GATA1/HDAC1 -0.003 0.024 -9999 0 -10000 0 0
GATA1/HDAC3 -0.006 0.031 -9999 0 -10000 0 0
CHD4 0 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.011 0.07 -9999 0 -0.6 13 13
SIN3/HDAC complex/Mad/Max 0 0.006 -9999 0 -10000 0 0
NuRD Complex 0 0.007 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.003 0.021 -9999 0 -10000 0 0
SIN3B 0 0 -9999 0 -10000 0 0
MTA2 0 0 -9999 0 -10000 0 0
SIN3A 0 0 -9999 0 -10000 0 0
XPO1 0 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0 0.001 -9999 0 -10000 0 0
HDAC complex -0.001 0.017 -9999 0 -0.47 1 1
GATA1/Fog1 -0.005 0.029 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.016 0.095 -9999 0 -0.46 38 38
negative regulation of cell growth 0.046 0.009 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0 0.006 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.006 0.046 -9999 0 -0.42 13 13
SIN3/HDAC complex/NCoR1 0 0.01 -9999 0 -10000 0 0
TFCP2 -0.001 0.024 -9999 0 -0.79 1 1
NR2C1 0 0 -9999 0 -10000 0 0
MBD3 0 0.009 -9999 0 -0.29 1 1
MBD2 0 0 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0.003 -9999 0 -10000 0 0
DOCK1 0 0 -9999 0 -10000 0 0
ITGA4 -0.003 0.028 -9999 0 -0.29 10 10
RAC1 0 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.008 0.046 -9999 0 -0.44 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.001 0.014 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin -0.005 0.032 -9999 0 -0.47 2 2
lamellipodium assembly -0.005 0.052 -9999 0 -0.46 14 14
PIK3CA 0 0.009 -9999 0 -0.29 1 1
PI3K -0.008 0.068 -9999 0 -0.6 14 14
ARF6 0 0 -9999 0 -10000 0 0
TLN1 0 0 -9999 0 -10000 0 0
PXN 0.022 0 -9999 0 -10000 0 0
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
ARF6/GTP -0.001 0.01 -9999 0 -10000 0 0
cell adhesion -0.001 0.01 -9999 0 -10000 0 0
CRKL/CBL 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.001 0.011 -9999 0 -10000 0 0
ITGB1 0 0 -9999 0 -10000 0 0
ITGB7 -0.009 0.058 -9999 0 -0.32 32 32
ARF6/GDP 0 0.003 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.007 0.049 -9999 0 -0.44 13 13
p130Cas/Crk/Dock1 0 0 -9999 0 -10000 0 0
VCAM1 -0.011 0.088 -9999 0 -0.63 19 19
alpha4/beta1 Integrin/Paxillin/Talin -0.001 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.001 0.012 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
mol:GDP 0.001 0.012 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GIT1 -0.001 0.02 -9999 0 -0.29 5 5
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.001 0.01 -9999 0 -10000 0 0
Rac1/GTP -0.006 0.058 -9999 0 -0.51 14 14
Circadian rhythm 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
chromatin modification -0.003 0.019 -9999 0 -10000 0 0
CLOCK 0.006 0.083 -9999 0 -0.78 12 12
TIMELESS/CRY2 -0.001 0.01 -9999 0 -10000 0 0
DEC1/BMAL1 -0.001 0.014 -9999 0 -10000 0 0
ATR 0 0 -9999 0 -10000 0 0
NR1D1 0.041 0.017 -9999 0 -10000 0 0
ARNTL 0.014 0.002 -9999 0 -10000 0 0
TIMELESS 0.04 0.019 -9999 0 -10000 0 0
NPAS2 0.009 0.061 -9999 0 -0.78 6 6
CRY2 0 0 -9999 0 -10000 0 0
mol:CO -0.014 0.003 -9999 0 -10000 0 0
CHEK1 -0.006 0.043 -9999 0 -0.29 24 24
mol:HEME 0.014 0.003 -9999 0 -10000 0 0
PER1 -0.015 0.11 -9999 0 -0.79 21 21
BMAL/CLOCK/NPAS2 0.03 0.07 -9999 0 -0.51 18 18
BMAL1/CLOCK 0.042 0.053 -9999 0 -10000 0 0
S phase of mitotic cell cycle -0.003 0.019 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR -0.003 0.019 -9999 0 -10000 0 0
mol:NADPH 0.014 0.003 -9999 0 -10000 0 0
PER1/TIMELESS -0.01 0.062 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.002 0.022 -9999 0 -0.29 6 6
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.027 0.047 -10000 0 -10000 0 0
regulation of axonogenesis -0.023 0.034 0.31 10 -10000 0 10
myoblast fusion 0.008 0.026 -10000 0 -10000 0 0
mol:GTP -0.005 0.016 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.009 0.031 -10000 0 -10000 0 0
ARF1/GTP -0.003 0.008 -10000 0 -10000 0 0
mol:GM1 0.006 0.015 -10000 0 -10000 0 0
mol:Choline 0.02 0.052 -10000 0 -0.51 10 10
lamellipodium assembly -0.004 0.031 -10000 0 -10000 0 0
MAPK3 0.02 0.026 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.009 0.031 -10000 0 -10000 0 0
ARF1 0 0 -10000 0 -10000 0 0
ARF6/GDP -0.008 0.026 -10000 0 -10000 0 0
ARF1/GDP -0.004 0.024 -10000 0 -10000 0 0
ARF6 0.007 0.008 -10000 0 -10000 0 0
RAB11A -0.001 0.013 -10000 0 -0.29 2 2
TIAM1 0.011 0.019 -10000 0 -0.29 4 4
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.02 0.026 -10000 0 -10000 0 0
actin filament bundle formation 0.006 0.021 -10000 0 -10000 0 0
KALRN -0.011 0.065 -10000 0 -0.47 20 20
RAB11FIP3/RAB11A 0 0.008 -10000 0 -10000 0 0
RhoA/GDP -0.006 0.021 -10000 0 -10000 0 0
NME1 -0.004 0.067 -10000 0 -0.29 56 56
Rac1/GDP -0.006 0.021 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.005 0.016 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.004 0.031 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
liver development -0.005 0.016 -10000 0 -10000 0 0
ARF6/GTP -0.005 0.016 -10000 0 -10000 0 0
RhoA/GTP -0.003 0.008 -10000 0 -10000 0 0
mol:GDP -0.006 0.029 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A -0.001 0.007 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
PLD1 0.011 0.058 -10000 0 -0.57 10 10
RAB11FIP3 0 0 -10000 0 -10000 0 0
tube morphogenesis -0.004 0.031 -10000 0 -10000 0 0
ruffle organization 0.023 0.034 -10000 0 -0.31 10 10
regulation of epithelial cell migration -0.005 0.016 -10000 0 -10000 0 0
PLD2 0.016 0.014 -10000 0 -10000 0 0
PIP5K1A -0.004 0.03 -10000 0 -0.31 10 10
mol:Phosphatidic acid 0.02 0.052 -10000 0 -0.51 10 10
Rac1/GTP -0.004 0.031 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.13 0.12 -9999 0 -0.52 9 9
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
AKT2 0 0 -9999 0 -10000 0 0
STXBP4 -0.001 0.013 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose -0.12 0.15 -9999 0 -0.34 13 13
YWHAZ -0.001 0.015 -9999 0 -0.29 3 3
CALM1 0 0 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
TBC1D4 0.019 0.046 -9999 0 -0.6 6 6
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
SNARE/Synip 0 0.006 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
ASIP -0.003 0.029 -9999 0 -0.29 11 11
PRKCI 0 0.009 -9999 0 -0.29 1 1
AS160/CaM/Ca2+ 0 0 -9999 0 -10000 0 0
RHOQ 0 0 -9999 0 -10000 0 0
GYS1 0.032 0 -9999 0 -10000 0 0
PRKCZ -0.001 0.024 -9999 0 -0.79 1 1
TRIP10 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
AS160/14-3-3 -0.004 0.031 -9999 0 -10000 0 0
VAMP2 0 0 -9999 0 -10000 0 0
SLC2A4 -0.13 0.16 -9999 0 -0.38 13 13
STX4 0 0 -9999 0 -10000 0 0
GSK3B 0.025 0 -9999 0 -10000 0 0
SFN -0.016 0.099 -9999 0 -0.5 36 36
LNPEP -0.006 0.067 -9999 0 -0.79 8 8
YWHAE 0 0 -9999 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0 0.009 -9999 0 -0.29 1 1
PLK4 -0.012 0.059 -9999 0 -10000 0 0
regulation of centriole replication 0.013 0.042 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.011 -9999 0 -0.36 1 1
MDM2/SUMO1 -0.001 0.007 -9999 0 -10000 0 0
HDAC4 -0.001 0.024 -9999 0 -0.79 1 1
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
SUMO1 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0 0.002 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.029 0.001 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0 0.013 -9999 0 -0.43 1 1
SUMO1/HDAC1 0 0.001 -9999 0 -10000 0 0
RANGAP1 0 0.009 -9999 0 -0.29 1 1
MDM2/SUMO1/SUMO1 -0.001 0.008 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0 0.001 -9999 0 -10000 0 0
Ran/GTP 0 0.001 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 -0.001 0.02 -9999 0 -0.29 5 5
UBE2I 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
PIAS2 0 0 -9999 0 -10000 0 0
PIAS1 0 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex -0.001 0.008 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.02 0 -9999 0 -10000 0 0
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB -0.001 0.018 -9999 0 -0.29 4 4
coatomer protein complex/ARF1/GTP/ER cargo protein 0 0.003 -9999 0 -10000 0 0
CD4 0 0 -9999 0 -10000 0 0
CLTA 0 0 -9999 0 -10000 0 0
mol:GTP 0.002 0 -9999 0 -10000 0 0
ARFGAP1 0.01 0.017 -9999 0 -0.2 7 7
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.001 0.008 -9999 0 -10000 0 0
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP -0.001 0.009 -9999 0 -10000 0 0
AP2M1 0 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0 -9999 0 -10000 0 0
Rac/GTP 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 -0.001 0.01 -9999 0 -10000 0 0
ARFIP2 0 0 -9999 0 -10000 0 0
COPA 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.025 0.002 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -10000 0 0
AP2A1 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0 0.004 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0 0.001 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.01 0.017 -9999 0 -0.2 7 7
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.01 0.017 -9999 0 -0.2 7 7
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0 0 -9999 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0 0 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
CHUK 0 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.001 0.01 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAP3K14 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB -0.002 0.018 -9999 0 -10000 0 0
RELB -0.003 0.028 -9999 0 -0.29 10 10
NFKB2 0 0.009 -9999 0 -0.29 1 1
NF kappa B2 p52/RelB -0.002 0.015 -9999 0 -10000 0 0
regulation of B cell activation -0.002 0.015 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 1093 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.Z7.A8R6 TCGA.Z7.A8R5 TCGA.XX.A89A TCGA.XX.A899
109_MAP3K5 -0.27 0.054 0.054 0.054
47_PPARGC1A -0.79 0 0 0
105_BMP4 0 0 0 0
105_BMP6 0 0 0 0
105_BMP7 0 0 0 0
105_BMP2 -0.79 0 0 0
131_RELN/VLDLR -0.47 -0.47 0 0
30_TGFB1/TGF beta receptor Type II 0.013 0 0.013 0.012
84_STAT5B -0.1 -0.073 0.032 0.046
84_STAT5A -0.1 -0.073 0.032 0.046
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BRCA-TP/14525124/BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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