PARADIGM pathway analysis of mRNASeq expression data
Breast Invasive Carcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1MC8X9P
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1MC8X9P
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 50 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 268
Signaling events mediated by Stem cell factor receptor (c-Kit) 261
EGFR-dependent Endothelin signaling events 227
Reelin signaling pathway 218
Signaling mediated by p38-alpha and p38-beta 194
HIF-1-alpha transcription factor network 160
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 156
FOXA2 and FOXA3 transcription factor networks 155
p75(NTR)-mediated signaling 142
Glucocorticoid receptor regulatory network 140
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 988 . 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 ( 988 ).

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 0.2713 268 804 3 -0.22 -1000 1000 -1000 -0.024 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.2642 261 20425 78 -0.62 0.19 1000 -1000 -0.078 -1000
EGFR-dependent Endothelin signaling events 0.2298 227 4772 21 -0.35 0 1000 -1000 -0.065 -1000
Reelin signaling pathway 0.2206 218 12250 56 -0.49 0 1000 -1000 -0.091 -1000
Signaling mediated by p38-alpha and p38-beta 0.1964 194 8550 44 -0.4 0 1000 -1000 -0.052 -1000
HIF-1-alpha transcription factor network 0.1619 160 12178 76 -0.76 0.018 1000 -1000 -0.09 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1579 156 10664 68 -0.52 0.17 1000 -1000 -0.086 -1000
FOXA2 and FOXA3 transcription factor networks 0.1569 155 7156 46 -1.2 0.025 1000 -1000 -0.025 -1000
p75(NTR)-mediated signaling 0.1437 142 17855 125 -0.39 0 1000 -1000 -0.1 -1000
Glucocorticoid receptor regulatory network 0.1417 140 15996 114 -0.94 0.35 1000 -1000 -0.063 -1000
FOXM1 transcription factor network 0.1377 136 6971 51 -0.43 0.014 1000 -1000 -0.12 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1356 134 11834 88 -0.36 0.037 1000 -1000 -0.1 -1000
IL4-mediated signaling events 0.1336 132 12056 91 -1 0.52 1000 -1000 -0.12 -1000
Wnt signaling 0.1265 125 880 7 -0.18 -0.007 1000 -1000 -0.042 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1255 124 6710 54 -0.49 0.022 1000 -1000 -0.092 -1000
Arf6 signaling events 0.1235 122 7598 62 -0.35 0.017 1000 -1000 -0.059 -1000
Endothelins 0.1215 120 11603 96 -0.38 0.034 1000 -1000 -0.069 -1000
Ephrin B reverse signaling 0.1184 117 5638 48 -0.34 0.19 1000 -1000 -0.068 -1000
EPHB forward signaling 0.1184 117 9981 85 -0.34 0.18 1000 -1000 -0.08 -1000
IGF1 pathway 0.1083 107 6102 57 -0.18 0.08 1000 -1000 -0.083 -1000
Noncanonical Wnt signaling pathway 0.1022 101 2626 26 -0.18 0 1000 -1000 -0.067 -1000
Signaling events regulated by Ret tyrosine kinase 0.1012 100 8257 82 -0.17 0 1000 -1000 -0.071 -1000
Calcium signaling in the CD4+ TCR pathway 0.1012 100 3110 31 -0.32 0.011 1000 -1000 -0.065 -1000
Nongenotropic Androgen signaling 0.0972 96 5003 52 -0.23 0.11 1000 -1000 -0.057 -1000
ErbB2/ErbB3 signaling events 0.0941 93 6062 65 -0.4 0.018 1000 -1000 -0.067 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0941 93 7961 85 -0.24 0.011 1000 -1000 -0.066 -1000
ErbB4 signaling events 0.0931 92 6386 69 -0.42 0.06 1000 -1000 -0.087 -1000
Aurora B signaling 0.0911 90 6093 67 -0.32 0.012 1000 -1000 -0.071 -1000
Glypican 1 network 0.0891 88 4234 48 -0.32 0.03 1000 -1000 -0.048 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0891 88 10643 120 -0.6 0.24 1000 -1000 -0.08 -1000
BMP receptor signaling 0.0870 86 7031 81 -0.55 0.026 1000 -1000 -0.086 -1000
Visual signal transduction: Rods 0.0870 86 4487 52 -0.48 0 1000 -1000 -0.073 -1000
Plasma membrane estrogen receptor signaling 0.0850 84 7259 86 -0.2 0.091 1000 -1000 -0.074 -1000
IL6-mediated signaling events 0.0820 81 6137 75 -0.29 0.052 1000 -1000 -0.068 -1000
Integrins in angiogenesis 0.0810 80 6737 84 -0.33 0 1000 -1000 -0.08 -1000
Signaling events mediated by PTP1B 0.0789 78 5933 76 -0.65 0.073 1000 -1000 -0.071 -1000
amb2 Integrin signaling 0.0779 77 6359 82 -0.51 0 1000 -1000 -0.073 -1000
IL23-mediated signaling events 0.0759 75 4521 60 -0.46 0.018 1000 -1000 -0.13 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0729 72 3751 52 -0.19 0.03 1000 -1000 -0.064 -1000
Ephrin A reverse signaling 0.0688 68 477 7 -0.078 0 1000 -1000 -0.039 -1000
LPA receptor mediated events 0.0668 66 6778 102 -0.3 0.028 1000 -1000 -0.076 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0658 65 2214 34 -0.089 0 1000 -1000 -0.049 -1000
S1P1 pathway 0.0658 65 2364 36 -0.33 0.008 1000 -1000 -0.064 -1000
Syndecan-3-mediated signaling events 0.0638 63 2222 35 -0.35 0 1000 -1000 -0.063 -1000
Signaling events mediated by the Hedgehog family 0.0617 61 3217 52 -0.22 0.03 1000 -1000 -0.07 -1000
PDGFR-alpha signaling pathway 0.0617 61 2688 44 -0.37 0.019 1000 -1000 -0.054 -1000
Syndecan-1-mediated signaling events 0.0587 58 2000 34 -0.21 0 1000 -1000 -0.062 -1000
Fc-epsilon receptor I signaling in mast cells 0.0587 58 5692 97 -0.24 0.027 1000 -1000 -0.086 -1000
E-cadherin signaling in keratinocytes 0.0587 58 2517 43 -0.3 0.041 1000 -1000 -0.066 -1000
TCGA08_rtk_signaling 0.0506 50 1322 26 -0.3 0.026 1000 -1000 -0.029 -1000
Visual signal transduction: Cones 0.0486 48 1839 38 -0.17 0.007 1000 -1000 -0.067 -1000
Nectin adhesion pathway 0.0486 48 3070 63 -0.085 0.002 1000 -1000 -0.067 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0486 48 3591 74 -0.3 0.07 1000 -1000 -0.079 -1000
Rapid glucocorticoid signaling 0.0486 48 976 20 -0.19 0.027 1000 -1000 -0.046 -1000
Ras signaling in the CD4+ TCR pathway 0.0486 48 827 17 -0.12 -0.001 1000 -1000 -0.062 -1000
FAS signaling pathway (CD95) 0.0476 47 2216 47 -0.47 0.013 1000 -1000 -0.047 -1000
Glypican 2 network 0.0476 47 189 4 -0.034 -0.029 1000 -1000 -0.029 -1000
Signaling events mediated by HDAC Class III 0.0466 46 1876 40 -0.57 0.019 1000 -1000 -0.034 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0466 46 1535 33 -0.55 0 1000 -1000 -0.064 -1000
LPA4-mediated signaling events 0.0445 44 529 12 -0.16 0.019 1000 -1000 -0.022 -1000
Signaling events mediated by PRL 0.0445 44 1517 34 -0.18 0.02 1000 -1000 -0.067 -1000
Presenilin action in Notch and Wnt signaling 0.0405 40 2489 61 -0.42 0.014 1000 -1000 -0.058 -1000
Syndecan-4-mediated signaling events 0.0385 38 2547 67 -0.32 0.005 1000 -1000 -0.079 -1000
Regulation of Androgen receptor activity 0.0364 36 2529 70 -0.26 0.022 1000 -1000 -0.061 -1000
IL12-mediated signaling events 0.0354 35 3096 87 -0.36 0.05 1000 -1000 -0.11 -1000
TCR signaling in naïve CD8+ T cells 0.0354 35 3335 93 -0.16 0.078 1000 -1000 -0.071 -1000
Coregulation of Androgen receptor activity 0.0344 34 2647 76 -0.19 0.035 1000 -1000 -0.048 -1000
BCR signaling pathway 0.0344 34 3383 99 -0.14 0.042 1000 -1000 -0.074 -1000
Insulin Pathway 0.0344 34 2578 74 -0.2 0.033 1000 -1000 -0.08 -1000
Osteopontin-mediated events 0.0324 32 1220 38 -0.24 0.025 1000 -1000 -0.083 -1000
IL27-mediated signaling events 0.0324 32 1665 51 -0.29 0.028 1000 -1000 -0.082 -1000
PLK1 signaling events 0.0314 31 2635 85 -0.21 0.033 1000 -1000 -0.056 -1000
Syndecan-2-mediated signaling events 0.0304 30 2095 69 -0.2 0.035 1000 -1000 -0.056 -1000
TCGA08_retinoblastoma 0.0304 30 244 8 -0.049 0.009 1000 -1000 -0.022 -1000
Regulation of nuclear SMAD2/3 signaling 0.0294 29 4072 136 -0.31 0.051 1000 -1000 -0.071 -1000
Canonical Wnt signaling pathway 0.0294 29 1489 51 -0.42 0.14 1000 -1000 -0.053 -1000
Thromboxane A2 receptor signaling 0.0273 27 2925 105 -0.3 0.066 1000 -1000 -0.075 -1000
Regulation of p38-alpha and p38-beta 0.0273 27 1470 54 -0.37 0.027 1000 -1000 -0.072 -1000
Regulation of Telomerase 0.0273 27 2786 102 -0.35 0.021 1000 -1000 -0.084 -1000
IL2 signaling events mediated by STAT5 0.0263 26 572 22 -0.12 0.064 1000 -1000 -0.038 -1000
Arf6 trafficking events 0.0263 26 1846 71 -0.45 0.032 1000 -1000 -0.066 -1000
TCGA08_p53 0.0233 23 167 7 -0.023 0.015 1000 -1000 -0.03 -1000
S1P5 pathway 0.0213 21 365 17 -0.042 0.023 1000 -1000 -0.049 -1000
Hedgehog signaling events mediated by Gli proteins 0.0182 18 1229 65 -0.069 0.04 1000 -1000 -0.074 -1000
S1P4 pathway 0.0182 18 471 25 -0.042 0 1000 -1000 -0.048 -1000
Class I PI3K signaling events mediated by Akt 0.0172 17 1199 68 -0.26 0.053 1000 -1000 -0.059 -1000
Ceramide signaling pathway 0.0172 17 1303 76 -0.18 0.048 1000 -1000 -0.064 -1000
TRAIL signaling pathway 0.0172 17 853 48 -0.076 0.045 1000 -1000 -0.061 -1000
E-cadherin signaling events 0.0172 17 89 5 -0.024 0 1000 -1000 -0.042 -1000
Effects of Botulinum toxin 0.0162 16 441 26 -0.094 0.001 1000 -1000 -0.057 -1000
Caspase cascade in apoptosis 0.0152 15 1119 74 -0.05 0.045 1000 -1000 -0.052 -1000
Cellular roles of Anthrax toxin 0.0152 15 586 39 -0.14 0.019 1000 -1000 -0.028 -1000
Retinoic acid receptors-mediated signaling 0.0152 15 885 58 -0.11 0.037 1000 -1000 -0.065 -1000
Aurora A signaling 0.0142 14 868 60 -0.2 0.007 1000 -1000 -0.059 -1000
PLK2 and PLK4 events 0.0132 13 40 3 -0.011 0.014 1000 -1000 -0.02 -1000
Signaling mediated by p38-gamma and p38-delta 0.0132 13 208 15 -0.017 0.022 1000 -1000 -0.053 -1000
E-cadherin signaling in the nascent adherens junction 0.0132 13 988 76 -0.024 0.048 1000 -1000 -0.073 -1000
S1P3 pathway 0.0132 13 555 42 -0.03 0.021 1000 -1000 -0.051 -1000
IL1-mediated signaling events 0.0121 12 746 62 -0.037 0.031 1000 -1000 -0.089 -1000
BARD1 signaling events 0.0111 11 640 57 -0.11 0.023 1000 -1000 -0.065 -1000
JNK signaling in the CD4+ TCR pathway 0.0111 11 188 17 -0.02 0.043 1000 -1000 -0.057 -1000
IL2 signaling events mediated by PI3K 0.0111 11 675 58 -0.038 0.061 1000 -1000 -0.077 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0101 10 287 28 -0.042 0.017 1000 -1000 -0.053 -1000
mTOR signaling pathway 0.0101 10 535 53 -0.019 0.026 1000 -1000 -0.056 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0091 9 757 83 -0.066 0.05 1000 -1000 -0.064 -1000
p38 MAPK signaling pathway 0.0091 9 406 44 -0.073 0.027 1000 -1000 -0.055 -1000
Signaling events mediated by HDAC Class II 0.0081 8 632 75 -0.15 0 1000 -1000 -0.056 -1000
a4b1 and a4b7 Integrin signaling 0.0081 8 40 5 -0.008 -0.002 1000 -1000 -0.034 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0081 8 329 37 -0.046 0.033 1000 -1000 -0.071 -1000
VEGFR1 specific signals 0.0071 7 433 56 -0.17 0.061 1000 -1000 -0.071 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0061 6 795 125 -0.17 0.083 1000 -1000 -0.098 -1000
PDGFR-beta signaling pathway 0.0061 6 627 97 -0.023 0.052 1000 -1000 -0.08 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0051 5 130 23 -0.029 0.041 1000 -1000 -0.061 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0051 5 268 45 -0.027 0.073 1000 -1000 -0.085 -1000
ceramide signaling pathway 0.0040 4 197 49 -0.029 0.052 1000 -1000 -0.042 -1000
HIF-2-alpha transcription factor network 0.0040 4 207 43 -0.16 0.18 1000 -1000 -0.068 -1000
Signaling events mediated by HDAC Class I 0.0040 4 444 104 -0.093 0.045 1000 -1000 -0.064 -1000
FoxO family signaling 0.0040 4 308 64 -0.04 0.093 1000 -1000 -0.071 -1000
Class I PI3K signaling events 0.0040 4 305 73 -0.04 0.059 1000 -1000 -0.069 -1000
Canonical NF-kappaB pathway 0.0030 3 131 39 -0.02 0.076 1000 -1000 -0.062 -1000
Circadian rhythm pathway 0.0030 3 70 22 -0.016 0.042 1000 -1000 -0.06 -1000
EPO signaling pathway 0.0030 3 200 55 -0.035 0.056 1000 -1000 -0.085 -1000
Insulin-mediated glucose transport 0.0030 3 101 32 -0.13 0.031 1000 -1000 -0.055 -1000
Atypical NF-kappaB pathway 0.0030 3 104 31 -0.02 0.03 1000 -1000 -0.064 -1000
Arf6 downstream pathway 0.0020 2 112 43 -0.011 0.021 1000 -1000 -0.043 -1000
IFN-gamma pathway 0.0020 2 183 68 -0.073 0.075 1000 -1000 -0.086 -1000
Paxillin-dependent events mediated by a4b1 0.0020 2 98 36 -0.011 0.022 1000 -1000 -0.069 -1000
Aurora C signaling 0.0000 0 2 7 -0.16 0 1000 -1000 -0.045 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 7 27 -0.001 0.028 1000 -1000 -0.049 -1000
Arf1 pathway 0.0000 0 5 54 -0.001 0.025 1000 -1000 -0.044 -1000
Alternative NF-kappaB pathway 0.0000 0 1 13 -0.003 0 1000 -1000 -0.061 -1000
Total NA 7086 419221 7203 -31 -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 0.36 0.8 268 -10000 0 268
PI3K Class IB/PDE3B -0.22 0.36 -10000 0 -0.8 268 268
PDE3B -0.22 0.36 -10000 0 -0.81 268 268
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 -0.39 452 452
CRKL -0.17 0.23 -10000 0 -0.41 451 451
HRAS -0.16 0.17 -10000 0 -0.53 33 33
mol:PIP3 -0.17 0.21 -10000 0 -0.4 453 453
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0 0 -10000 0 -10000 0 0
GAB1 -0.18 0.24 -10000 0 -0.44 453 453
FOXO3 -0.15 0.21 -10000 0 -0.37 451 451
AKT1 -0.17 0.22 -10000 0 -0.41 452 452
BAD -0.15 0.21 -10000 0 -0.37 451 451
megakaryocyte differentiation -0.18 0.24 -10000 0 -0.43 454 454
GSK3B -0.15 0.21 -10000 0 -0.37 451 451
RAF1 -0.093 0.17 -10000 0 -0.44 25 25
SHC1 0 0 -10000 0 -10000 0 0
STAT3 -0.18 0.24 -10000 0 -0.44 453 453
STAT1 -0.46 0.56 -10000 0 -1 462 462
HRAS/SPRED1 -0.13 0.14 -10000 0 -0.44 26 26
cell proliferation -0.18 0.24 -10000 0 -0.44 453 453
PIK3CA 0 0.009 -10000 0 -0.28 1 1
TEC -0.002 0.044 -10000 0 -0.81 3 3
RPS6KB1 -0.18 0.24 -10000 0 -0.44 453 453
HRAS/SPRED2 -0.13 0.14 -10000 0 -0.44 25 25
LYN/TEC/p62DOK -0.19 0.2 -10000 0 -0.4 453 453
MAPK3 -0.055 0.13 -10000 0 -0.32 19 19
STAP1 -0.2 0.24 -10000 0 -0.45 455 455
GRAP2 -0.015 0.11 -10000 0 -0.81 17 17
JAK2 -0.4 0.44 -10000 0 -0.88 455 455
STAT1 (dimer) -0.44 0.55 -10000 0 -1 462 462
mol:Gleevec 0.006 0.009 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.19 0.2 -10000 0 -0.41 452 452
actin filament polymerization -0.18 0.24 -10000 0 -0.44 453 453
LYN 0 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.27 0.34 -10000 0 -0.63 453 453
PIK3R1 -0.006 0.068 -10000 0 -0.81 7 7
CBL/CRKL/GRB2 -0.17 0.18 -10000 0 -0.37 451 451
PI3K -0.19 0.21 -10000 0 -0.41 456 456
PTEN -0.002 0.036 -10000 0 -0.81 2 2
SCF/KIT/EPO/EPOR -0.6 0.67 -10000 0 -1.3 451 451
MAPK8 -0.19 0.24 -10000 0 -0.44 453 453
STAT3 (dimer) -0.18 0.23 -10000 0 -0.43 453 453
positive regulation of transcription -0.042 0.11 -10000 0 -0.26 19 19
mol:GDP -0.17 0.18 -10000 0 -0.52 40 40
PIK3C2B -0.18 0.24 -10000 0 -0.44 453 453
CBL/CRKL -0.18 0.19 -10000 0 -0.38 451 451
FER -0.19 0.24 -10000 0 -0.45 459 459
SH2B3 -0.18 0.24 -10000 0 -0.44 453 453
PDPK1 -0.15 0.2 -10000 0 -0.36 452 452
SNAI2 -0.19 0.25 -10000 0 -0.45 455 455
positive regulation of cell proliferation -0.32 0.41 -10000 0 -0.75 462 462
KITLG 0.001 0.071 -10000 0 -0.48 16 16
cell motility -0.32 0.41 -10000 0 -0.75 462 462
PTPN6 0.015 0.021 -10000 0 -0.29 1 1
EPOR -0.098 0.16 -10000 0 -10000 0 0
STAT5A (dimer) -0.26 0.34 -10000 0 -0.62 463 463
SOCS1 -0.005 0.042 -10000 0 -0.81 1 1
cell migration 0.19 0.24 0.44 461 -10000 0 461
SOS1 0 0 -10000 0 -10000 0 0
EPO -0.043 0.11 -10000 0 -0.3 100 100
VAV1 -0.001 0.029 -10000 0 -0.46 3 3
GRB10 -0.18 0.24 -10000 0 -0.44 453 453
PTPN11 0.013 0.013 -10000 0 -10000 0 0
SCF/KIT -0.22 0.24 -10000 0 -0.47 454 454
GO:0007205 0.009 0.013 -10000 0 -10000 0 0
MAP2K1 -0.064 0.14 -10000 0 -0.36 19 19
CBL 0 0 -10000 0 -10000 0 0
KIT -0.62 0.73 -10000 0 -1.4 449 449
MAP2K2 -0.064 0.14 -10000 0 -0.36 19 19
SHC/Grb2/SOS1 -0.19 0.2 -10000 0 -0.4 451 451
STAT5A -0.27 0.35 -10000 0 -0.64 457 457
GRB2 0 0.009 -10000 0 -0.28 1 1
response to radiation -0.18 0.24 -10000 0 -0.44 455 455
SHC/GRAP2 -0.011 0.081 -10000 0 -0.62 17 17
PTPRO -0.18 0.24 -10000 0 -0.44 454 454
SH2B2 -0.19 0.24 -10000 0 -0.44 453 453
DOK1 -0.001 0.013 -10000 0 -0.28 2 2
MATK -0.2 0.25 -10000 0 -0.45 461 461
CREBBP 0.019 0.018 -10000 0 -10000 0 0
BCL2 -0.14 0.31 -10000 0 -1.5 35 35
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS -0.001 0.02 -9999 0 -10000 0 0
EGFR -0.3 0.39 -9999 0 -0.8 369 369
EGF/EGFR -0.29 0.32 -9999 0 -0.56 513 513
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.26 0.28 -9999 0 -0.51 504 504
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.001 0.026 -9999 0 -0.81 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.17 0.33 -9999 0 -0.8 206 206
EGF/EGFR dimer/SHC -0.3 0.32 -9999 0 -0.59 504 504
mol:GDP -0.26 0.27 -9999 0 -0.5 504 504
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.062 0.22 -9999 0 -0.8 77 77
GRB2/SOS1 0 0.006 -9999 0 -10000 0 0
HRAS/GTP -0.24 0.25 -9999 0 -0.46 504 504
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.24 0.26 -9999 0 -0.47 504 504
FRAP1 -0.25 0.26 -9999 0 -0.48 504 504
EGF/EGFR dimer -0.35 0.36 -9999 0 -0.68 504 504
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0 0.009 -9999 0 -0.28 1 1
ETA receptor/Endothelin-1 -0.048 0.17 -9999 0 -0.62 77 77
Reelin signaling pathway

Figure S4.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S4.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 -0.007 0.033 -9999 0 -10000 0 0
VLDLR -0.025 0.14 -9999 0 -0.81 30 30
CRKL 0 0 -9999 0 -10000 0 0
LRPAP1 0 0 -9999 0 -10000 0 0
FYN -0.002 0.036 -9999 0 -0.81 2 2
ITGA3 -0.004 0.053 -9999 0 -0.81 4 4
RELN/VLDLR/Fyn -0.34 0.28 -9999 0 -0.55 606 606
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.004 0.041 -9999 0 -0.45 8 8
AKT1 -0.2 0.17 -9999 0 -0.33 610 610
MAP2K7 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
DAB1 -0.017 0.067 -9999 0 -0.28 60 60
RELN/LRP8/DAB1 -0.32 0.25 -9999 0 -0.52 599 599
LRPAP1/LRP8 -0.019 0.055 -9999 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.3 0.24 -9999 0 -0.49 599 599
DAB1/alpha3/beta1 Integrin -0.28 0.23 -9999 0 -0.51 247 247
long-term memory -0.36 0.3 -9999 0 -0.55 649 649
DAB1/LIS1 -0.29 0.23 -9999 0 -0.46 606 606
DAB1/CRLK/C3G -0.28 0.23 -9999 0 -0.51 246 246
PIK3CA 0 0.009 -9999 0 -0.28 1 1
DAB1/NCK2 -0.29 0.24 -9999 0 -0.47 606 606
ARHGEF2 0 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.092 0.25 -9999 0 -0.76 121 121
CDK5R1 -0.009 0.049 -9999 0 -10000 0 0
RELN -0.49 0.39 -9999 0 -0.8 601 601
PIK3R1 -0.006 0.068 -9999 0 -0.81 7 7
RELN/LRP8/Fyn -0.34 0.27 -9999 0 -0.55 598 598
GRIN2A/RELN/LRP8/DAB1/Fyn -0.35 0.3 -9999 0 -0.55 615 615
MAPK8 -0.004 0.057 -9999 0 -0.81 5 5
RELN/VLDLR/DAB1 -0.32 0.26 -9999 0 -0.52 606 606
ITGB1 0 0 -9999 0 -10000 0 0
MAP1B -0.31 0.26 -9999 0 -0.5 608 608
RELN/LRP8 -0.34 0.27 -9999 0 -0.55 598 598
GRIN2B/RELN/LRP8/DAB1/Fyn -0.33 0.26 -9999 0 -0.51 633 633
PI3K -0.005 0.052 -9999 0 -0.62 7 7
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.003 0.04 -9999 0 -0.62 4 4
RAP1A -0.26 0.21 -9999 0 -0.54 136 136
PAFAH1B1 0 0 -9999 0 -10000 0 0
MAPK8IP1 -0.004 0.049 -9999 0 -0.46 9 9
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.06 0.21 -9999 0 -0.79 75 75
NCK2 0 0 -9999 0 -10000 0 0
neuron differentiation -0.13 0.11 -9999 0 -0.45 10 10
neuron adhesion -0.24 0.2 -9999 0 -0.51 138 138
LRP8 -0.031 0.087 -9999 0 -10000 0 0
GSK3B -0.17 0.17 -9999 0 -0.44 64 64
RELN/VLDLR/DAB1/Fyn -0.3 0.25 -9999 0 -0.49 606 606
MAP3K11 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.22 0.18 -9999 0 -0.35 610 610
CDK5 -0.002 0.022 -9999 0 -0.28 6 6
MAPT -0.043 0.24 -9999 0 -0.73 105 105
neuron migration -0.23 0.24 -9999 0 -0.42 599 599
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.14 0.11 -9999 0 -0.46 10 10
RELN/VLDLR -0.32 0.26 -9999 0 -0.52 606 606
Signaling mediated by p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.4 0.62 -9999 0 -1.3 330 330
MKNK1 0 0 -9999 0 -10000 0 0
MAPK14 -0.081 0.15 -9999 0 -0.4 15 15
ATF2/c-Jun -0.054 0.16 -9999 0 -0.84 16 16
MAPK11 -0.084 0.16 -9999 0 -0.49 18 18
MITF -0.093 0.2 -9999 0 -0.36 337 337
MAPKAPK5 -0.089 0.19 -9999 0 -0.35 333 333
KRT8 -0.094 0.19 -9999 0 -0.36 334 334
MAPKAPK3 0 0 -9999 0 -10000 0 0
MAPKAPK2 0 0.009 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.12 0.24 -9999 0 -0.45 333 333
CEBPB -0.089 0.19 -9999 0 -0.35 333 333
SLC9A1 -0.089 0.19 -9999 0 -0.35 333 333
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.082 0.19 -9999 0 -0.34 333 333
p38alpha-beta/MNK1 -0.12 0.17 -9999 0 -0.55 18 18
JUN -0.053 0.16 -9999 0 -0.83 16 16
PPARGC1A -0.21 0.36 -9999 0 -0.57 412 412
USF1 -0.089 0.19 -9999 0 -0.35 333 333
RAB5/GDP/GDI1 -0.085 0.12 -9999 0 -0.38 18 18
NOS2 -0.093 0.22 -9999 0 -1.1 11 11
DDIT3 -0.089 0.19 -9999 0 -0.35 333 333
RAB5A 0 0 -9999 0 -10000 0 0
HSPB1 -0.072 0.16 -9999 0 -0.43 44 44
p38alpha-beta/HBP1 -0.12 0.17 -9999 0 -0.55 18 18
CREB1 -0.093 0.2 -9999 0 -0.37 333 333
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.07 0.17 -9999 0 -0.52 14 14
RPS6KA4 -0.089 0.19 -9999 0 -0.35 333 333
PLA2G4A -0.13 0.27 -9999 0 -0.74 120 120
GDI1 -0.089 0.19 -9999 0 -0.35 333 333
TP53 -0.11 0.24 -9999 0 -0.44 333 333
RPS6KA5 -0.094 0.2 -9999 0 -0.36 341 341
ESR1 -0.17 0.25 -9999 0 -0.42 454 454
HBP1 0 0 -9999 0 -10000 0 0
MEF2C -0.09 0.2 -9999 0 -0.36 333 333
MEF2A -0.089 0.19 -9999 0 -0.36 333 333
EIF4EBP1 -0.093 0.2 -9999 0 -0.37 333 333
KRT19 -0.1 0.21 -9999 0 -0.38 336 336
ELK4 -0.089 0.19 -9999 0 -0.35 333 333
ATF6 -0.089 0.19 -9999 0 -0.35 333 333
ATF1 -0.093 0.2 -9999 0 -0.37 333 333
p38alpha-beta/MAPKAPK2 -0.12 0.17 -9999 0 -0.55 19 19
p38alpha-beta/MAPKAPK3 -0.12 0.17 -9999 0 -0.55 18 18
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 -1 231 231
HDAC7 0 0.001 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.32 0.31 -9999 0 -0.81 175 175
SMAD4 -0.001 0.026 -9999 0 -0.8 1 1
ID2 -0.41 0.46 -9999 0 -1.1 202 202
AP1 -0.19 0.29 -9999 0 -0.63 299 299
ABCG2 -0.44 0.5 -9999 0 -1.1 219 219
HIF1A -0.052 0.062 -9999 0 -10000 0 0
TFF3 -0.48 0.52 -9999 0 -1.1 278 278
GATA2 -0.015 0.14 -9999 0 -0.66 38 38
AKT1 -0.053 0.08 -9999 0 -10000 0 0
response to hypoxia -0.075 0.086 -9999 0 -0.24 44 44
MCL1 -0.41 0.46 -9999 0 -1.1 219 219
NDRG1 -0.41 0.46 -9999 0 -1.1 205 205
SERPINE1 -0.41 0.46 -9999 0 -1 228 228
FECH -0.41 0.46 -9999 0 -1 222 222
FURIN -0.41 0.46 -9999 0 -1.1 212 212
NCOA2 -0.017 0.14 -9999 0 -0.81 31 31
EP300 -0.053 0.12 -9999 0 -0.35 54 54
HMOX1 -0.41 0.46 -9999 0 -1.1 204 204
BHLHE40 -0.41 0.46 -9999 0 -1.1 205 205
BHLHE41 -0.42 0.47 -9999 0 -1.1 204 204
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.05 0.055 -9999 0 -0.62 1 1
ENG -0.036 0.061 -9999 0 -0.56 1 1
JUN -0.007 0.077 -9999 0 -0.81 9 9
RORA -0.41 0.46 -9999 0 -1.1 205 205
ABCB1 -0.34 0.55 -9999 0 -1.4 191 191
TFRC -0.41 0.46 -9999 0 -1.1 218 218
CXCR4 -0.41 0.46 -9999 0 -1.1 209 209
TF -0.65 0.58 -9999 0 -1.2 470 470
CITED2 -0.41 0.46 -9999 0 -1.1 200 200
HIF1A/ARNT -0.5 0.52 -9999 0 -1.2 269 269
LDHA -0.049 0.047 -9999 0 -10000 0 0
ETS1 -0.41 0.46 -9999 0 -1.1 219 219
PGK1 -0.41 0.46 -9999 0 -1 227 227
NOS2 -0.41 0.46 -9999 0 -1.1 220 220
ITGB2 -0.41 0.46 -9999 0 -1.1 218 218
ALDOA -0.41 0.46 -9999 0 -1.1 211 211
Cbp/p300/CITED2 -0.43 0.44 -9999 0 -1.1 215 215
FOS -0.24 0.37 -9999 0 -0.81 298 298
HK2 -0.41 0.46 -9999 0 -1 238 238
SP1 0.012 0.023 -9999 0 -10000 0 0
GCK -0.14 0.38 -9999 0 -1.6 55 55
HK1 -0.41 0.46 -9999 0 -1.1 204 204
NPM1 -0.41 0.46 -9999 0 -1.1 206 206
EGLN1 -0.41 0.46 -9999 0 -1.1 202 202
CREB1 0.018 0 -9999 0 -10000 0 0
PGM1 -0.41 0.46 -9999 0 -1 222 222
SMAD3 0 0 -9999 0 -10000 0 0
EDN1 -0.2 0.41 -9999 0 -1.1 128 128
IGFBP1 -0.51 0.53 -9999 0 -1.2 299 299
VEGFA -0.24 0.31 -9999 0 -0.77 100 100
HIF1A/JAB1 -0.028 0.026 -9999 0 -10000 0 0
CP -0.52 0.55 -9999 0 -1.2 328 328
CXCL12 -0.44 0.5 -9999 0 -1.2 213 213
COPS5 0.008 0.011 -9999 0 -10000 0 0
SMAD3/SMAD4 -0.001 0.02 -9999 0 -0.61 1 1
BNIP3 -0.41 0.46 -9999 0 -1 222 222
EGLN3 -0.42 0.46 -9999 0 -1.1 209 209
CA9 -0.45 0.48 -9999 0 -1.1 252 252
TERT -0.42 0.47 -9999 0 -1.1 228 228
ENO1 -0.41 0.46 -9999 0 -1.1 216 216
PFKL -0.41 0.46 -9999 0 -1.1 202 202
NCOA1 -0.001 0.026 -9999 0 -0.81 1 1
ADM -0.44 0.49 -9999 0 -1.1 229 229
ARNT -0.054 0.06 -9999 0 -10000 0 0
HNF4A -0.001 0.04 -9999 0 -0.28 15 15
ADFP -0.42 0.46 -9999 0 -1 269 269
SLC2A1 -0.25 0.32 -9999 0 -0.79 88 88
LEP -0.76 0.52 -9999 0 -1.2 514 514
HIF1A/ARNT/Cbp/p300 -0.34 0.33 -9999 0 -0.81 207 207
EPO -0.23 0.26 -9999 0 -0.84 34 34
CREBBP -0.053 0.12 -9999 0 -0.35 54 54
HIF1A/ARNT/Cbp/p300/HDAC7 -0.32 0.31 -9999 0 -0.84 151 151
PFKFB3 -0.41 0.47 -9999 0 -1.1 204 204
NT5E -0.41 0.46 -9999 0 -1 235 235
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.073 0.15 -10000 0 -0.38 130 130
NFATC2 -0.052 0.26 -10000 0 -0.76 103 103
NFATC3 -0.056 0.12 -10000 0 -0.31 58 58
CD40LG -0.38 0.58 -10000 0 -1.1 349 349
ITCH 0.012 0.1 -10000 0 -10000 0 0
CBLB 0.012 0.1 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.24 0.35 -10000 0 -1 106 106
JUNB 0 0.009 -10000 0 -0.28 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.037 0.1 -10000 0 -0.34 107 107
T cell anergy -0.029 0.17 -10000 0 -0.48 107 107
TLE4 -0.027 0.25 -10000 0 -0.75 82 82
Jun/NFAT1-c-4/p21SNFT -0.31 0.45 -10000 0 -0.9 315 315
AP-1/NFAT1-c-4 -0.52 0.66 -10000 0 -1.3 355 355
IKZF1 -0.016 0.2 -10000 0 -0.6 88 88
T-helper 2 cell differentiation -0.11 0.3 -10000 0 -0.82 102 102
AP-1/NFAT1 -0.23 0.33 -10000 0 -0.64 343 343
CALM1 -0.019 0.055 -10000 0 -10000 0 0
EGR2 -0.3 0.66 -10000 0 -1.2 266 266
EGR3 -0.39 0.74 -10000 0 -1.5 279 279
NFAT1/FOXP3 -0.11 0.21 -10000 0 -0.56 123 123
EGR1 -0.26 0.38 -10000 0 -0.81 316 316
JUN -0.006 0.079 -10000 0 -0.81 9 9
EGR4 -0.02 0.072 -10000 0 -0.28 71 71
mol:Ca2+ -0.022 0.064 -10000 0 -10000 0 0
GBP3 -0.021 0.22 -10000 0 -0.63 97 97
FOSL1 -0.008 0.055 -10000 0 -0.32 25 25
NFAT1-c-4/MAF/IRF4 -0.32 0.48 -10000 0 -0.94 319 319
DGKA -0.014 0.2 -10000 0 -0.58 90 90
CREM 0 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.4 0.53 -10000 0 -1.1 329 329
CTLA4 -0.081 0.23 -10000 0 -0.6 93 93
NFAT1-c-4 (dimer)/EGR1 -0.44 0.58 -10000 0 -1.2 327 327
NFAT1-c-4 (dimer)/EGR4 -0.3 0.46 -10000 0 -0.92 316 316
FOS -0.25 0.38 -10000 0 -0.82 298 298
IFNG -0.15 0.26 -10000 0 -0.84 96 96
T cell activation -0.17 0.35 -10000 0 -0.8 178 178
MAF -0.001 0.026 -10000 0 -0.81 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.17 0.37 0.68 314 -10000 0 314
TNF -0.32 0.53 -10000 0 -1 313 313
FASLG -0.37 0.69 -10000 0 -1.3 315 315
TBX21 -0.024 0.16 -10000 0 -0.67 52 52
BATF3 -0.002 0.03 -10000 0 -0.81 1 1
PRKCQ -0.025 0.16 -10000 0 -0.67 54 54
PTPN1 -0.016 0.2 -10000 0 -0.59 89 89
NFAT1-c-4/ICER1 -0.3 0.45 -10000 0 -0.91 314 314
GATA3 -0.034 0.15 -10000 0 -0.56 63 63
T-helper 1 cell differentiation -0.15 0.26 -10000 0 -0.82 96 96
IL2RA -0.23 0.34 -10000 0 -0.92 117 117
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.014 0.2 -10000 0 -0.59 89 89
E2F1 -0.077 0.14 -10000 0 -0.27 321 321
PPARG -0.19 0.34 -10000 0 -0.81 228 228
SLC3A2 -0.014 0.2 -10000 0 -0.64 65 65
IRF4 -0.072 0.23 -10000 0 -0.75 95 95
PTGS2 -0.48 0.66 -10000 0 -1.2 432 432
CSF2 -0.37 0.56 -10000 0 -1 349 349
JunB/Fra1/NFAT1-c-4 -0.29 0.44 -10000 0 -0.88 314 314
IL4 -0.12 0.31 -10000 0 -0.88 99 99
IL5 -0.36 0.56 -10000 0 -1 347 347
IL2 -0.18 0.36 -10000 0 -0.82 175 175
IL3 -0.064 0.065 -10000 0 -10000 0 0
RNF128 -0.055 0.28 -10000 0 -0.86 107 107
NFATC1 -0.17 0.37 -10000 0 -0.68 314 314
CDK4 0.088 0.23 0.54 83 -10000 0 83
PTPRK -0.019 0.22 -10000 0 -0.63 92 92
IL8 -0.37 0.57 -10000 0 -1.1 347 347
POU2F1 0.001 0.01 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.24 0.28 -9999 0 -0.77 115 115
PCK1 -1 0.71 -9999 0 -1.6 612 612
HNF4A -0.25 0.28 -9999 0 -0.85 77 77
KCNJ11 -0.27 0.31 -9999 0 -0.84 135 135
AKT1 -0.15 0.14 -9999 0 -0.38 53 53
response to starvation -0.001 0.007 -9999 0 -10000 0 0
DLK1 -0.5 0.56 -9999 0 -1.2 326 326
NKX2-1 -0.056 0.15 -9999 0 -10000 0 0
ACADM -0.24 0.28 -9999 0 -0.78 122 122
TAT -1.2 0.68 -9999 0 -1.6 725 725
CEBPB 0.004 0.006 -9999 0 -10000 0 0
CEBPA -0.002 0.077 -9999 0 -0.81 9 9
TTR -0.45 0.29 -9999 0 -0.72 413 413
PKLR -0.25 0.28 -9999 0 -0.77 118 118
APOA1 -0.3 0.3 -9999 0 -0.86 111 111
CPT1C -0.24 0.28 -9999 0 -0.75 130 130
ALAS1 -0.14 0.15 -9999 0 -10000 0 0
TFRC -0.45 0.26 -9999 0 -0.71 362 362
FOXF1 -0.004 0.057 -9999 0 -0.58 7 7
NF1 0.017 0.026 -9999 0 -0.8 1 1
HNF1A (dimer) 0.003 0.023 -9999 0 -0.28 6 6
CPT1A -0.24 0.28 -9999 0 -0.75 131 131
HMGCS1 -0.24 0.28 -9999 0 -0.76 119 119
NR3C1 -0.11 0.12 -9999 0 -0.51 36 36
CPT1B -0.24 0.28 -9999 0 -0.78 118 118
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.002 0.006 -9999 0 -10000 0 0
GCK -0.28 0.36 -9999 0 -0.93 156 156
CREB1 -0.059 0.067 -9999 0 -10000 0 0
IGFBP1 -0.46 0.6 -9999 0 -1.5 230 230
PDX1 -0.13 0.14 -9999 0 -10000 0 0
UCP2 -0.24 0.28 -9999 0 -0.77 118 118
ALDOB -0.27 0.3 -9999 0 -0.84 114 114
AFP -0.68 0.61 -9999 0 -1.3 424 424
BDH1 -0.24 0.28 -9999 0 -0.74 142 142
HADH -0.26 0.3 -9999 0 -0.82 118 118
F2 -0.29 0.3 -9999 0 -0.88 94 94
HNF1A 0.003 0.023 -9999 0 -0.28 6 6
G6PC -0.19 0.12 -9999 0 -0.64 8 8
SLC2A2 -0.16 0.17 -9999 0 -0.52 9 9
INS 0.025 0.067 -9999 0 -10000 0 0
FOXA1 -0.25 0.28 -9999 0 -0.57 293 293
FOXA3 -0.42 0.22 -9999 0 -0.53 697 697
FOXA2 -0.32 0.34 -9999 0 -0.83 196 196
ABCC8 -0.35 0.44 -9999 0 -1.1 192 192
ALB -0.94 0.65 -9999 0 -1.4 633 633
p75(NTR)-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
Sortilin/TRAF6 -0.001 0.02 -9999 0 -0.62 1 1
Necdin/E2F1 -0.081 0.15 -9999 0 -0.7 40 40
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.15 0.22 -9999 0 -0.46 318 318
NGF (dimer)/p75(NTR)/BEX1 -0.27 0.32 -9999 0 -0.63 392 392
NT-4/5 (dimer)/p75(NTR) -0.39 0.42 -9999 0 -0.78 503 503
IKBKB -0.001 0.013 -9999 0 -10000 0 0
AKT1 -0.15 0.22 -9999 0 -0.46 321 321
IKBKG 0 0 -9999 0 -10000 0 0
BDNF -0.07 0.22 -9999 0 -0.81 79 79
MGDIs/NGR/p75(NTR)/LINGO1 -0.2 0.25 -9999 0 -0.56 309 309
FURIN -0.001 0.013 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.21 0.29 -9999 0 -0.58 353 353
LINGO1 -0.065 0.12 -9999 0 -0.28 232 232
Sortilin/TRAF6/NRIF -0.001 0.026 -9999 0 -0.8 1 1
proBDNF (dimer) -0.07 0.22 -9999 0 -0.8 79 79
NTRK1 -0.01 0.063 -9999 0 -0.33 29 29
RTN4R -0.01 0.053 -9999 0 -0.28 37 37
neuron apoptosis -0.14 0.27 -9999 0 -0.54 191 191
IRAK1 -0.001 0.015 -9999 0 -0.28 3 3
SHC1 -0.16 0.27 -9999 0 -0.54 316 316
ARHGDIA 0 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase -0.001 0.015 -9999 0 -0.45 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.16 0.24 -9999 0 -0.5 316 316
MAGEH1 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.18 0.27 -9999 0 -0.53 330 330
Mammalian IAPs/DIABLO -0.006 0.047 -9999 0 -0.48 9 9
proNGF (dimer) -0.014 0.1 -9999 0 -0.8 15 15
MAGED1 -0.001 0.015 -9999 0 -0.28 3 3
APP 0 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.29 0.38 -9999 0 -0.8 351 351
ZNF274 0 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.15 0.22 -9999 0 -0.47 316 316
NGF -0.014 0.1 -9999 0 -0.81 15 15
cell cycle arrest -0.12 0.24 -9999 0 -0.45 316 316
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.11 0.16 -9999 0 -0.34 316 316
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.35 0.38 -9999 0 -0.68 503 503
NCSTN 0 0 -9999 0 -10000 0 0
mol:GTP -0.18 0.26 -9999 0 -0.56 316 316
PSENEN 0 0.009 -9999 0 -0.28 1 1
mol:ceramide -0.16 0.23 -9999 0 -0.49 316 316
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.085 0.13 -9999 0 -0.48 13 13
p75(NTR)/beta APP -0.19 0.29 -9999 0 -0.62 309 309
BEX1 -0.15 0.28 -9999 0 -0.81 134 134
mol:GDP -0.16 0.27 -9999 0 -0.55 316 316
NGF (dimer) -0.083 0.18 -9999 0 -0.5 154 154
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.18 0.23 -9999 0 -0.52 309 309
PIK3R1 -0.006 0.068 -9999 0 -0.81 7 7
RAC1/GTP -0.15 0.23 -9999 0 -0.48 316 316
MYD88 0 0 -9999 0 -10000 0 0
CHUK 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.18 0.26 -9999 0 -0.56 316 316
RHOB 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.057 0.082 -9999 0 -10000 0 0
NT3 (dimer) -0.13 0.3 -9999 0 -0.76 170 170
TP53 -0.17 0.24 -9999 0 -0.47 353 353
PRDM4 -0.16 0.23 -9999 0 -0.49 316 316
BDNF (dimer) -0.17 0.24 -9999 0 -0.58 207 207
PIK3CA 0 0.009 -9999 0 -0.28 1 1
SORT1 -0.001 0.026 -9999 0 -0.81 1 1
activation of caspase activity -0.15 0.22 -9999 0 -0.46 318 318
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.16 0.24 -9999 0 -0.5 316 316
RHOC 0 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
MAPK10 -0.16 0.27 -9999 0 -0.69 113 113
DIABLO 0 0 -9999 0 -10000 0 0
SMPD2 -0.16 0.23 -9999 0 -0.49 316 316
APH1B -0.001 0.026 -9999 0 -0.81 1 1
APH1A 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.18 0.26 -9999 0 -0.55 316 316
PSEN1 0 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.29 0.36 -9999 0 -0.7 401 401
MAPK8 -0.11 0.24 -9999 0 -0.65 51 51
MAPK9 -0.11 0.24 -9999 0 -0.65 50 50
APAF1 0 0 -9999 0 -10000 0 0
NTF3 -0.13 0.3 -9999 0 -0.77 170 170
NTF4 -0.29 0.39 -9999 0 -0.81 351 351
NDN -0.033 0.16 -9999 0 -0.81 40 40
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.14 0.21 -9999 0 -0.44 316 316
p75 CTF/Sortilin/TRAF6/NRIF 0 0.015 -9999 0 -0.48 1 1
RhoA-B-C/GTP -0.18 0.26 -9999 0 -0.55 316 316
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.18 0.25 -9999 0 -0.5 353 353
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.19 0.27 -9999 0 -0.53 353 353
PRKACB -0.016 0.074 -9999 0 -0.81 3 3
proBDNF (dimer)/p75 ECD -0.053 0.17 -9999 0 -0.62 79 79
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.01 0.081 -9999 0 -0.81 9 9
BIRC2 0 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.13 0.26 -9999 0 -0.5 269 269
BAD -0.12 0.25 -9999 0 -0.58 104 104
RIPK2 -0.001 0.02 -9999 0 -0.28 5 5
NGFR -0.25 0.37 -9999 0 -0.81 309 309
CYCS -0.15 0.22 -9999 0 -0.46 316 316
ADAM17 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.16 0.24 -9999 0 -0.5 316 316
BCL2L11 -0.12 0.25 -9999 0 -0.58 104 104
BDNF (dimer)/p75(NTR) -0.24 0.33 -9999 0 -0.67 353 353
PI3K -0.16 0.24 -9999 0 -0.5 321 321
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.16 0.24 -9999 0 -0.5 316 316
NDNL2 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
PRKCI 0 0.009 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.2 0.3 -9999 0 -0.63 316 316
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.16 0.24 -9999 0 -0.5 316 316
TRAF6 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
PRKCZ -0.001 0.026 -9999 0 -0.81 1 1
PLG -0.001 0.018 -9999 0 -0.28 4 4
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.2 0.27 -9999 0 -0.53 360 360
SQSTM1 0 0.009 -9999 0 -10000 0 0
NGFRAP1 -0.002 0.036 -9999 0 -0.81 2 2
CASP3 -0.11 0.23 -9999 0 -0.53 104 104
E2F1 -0.091 0.13 -9999 0 -0.28 321 321
CASP9 0 0 -9999 0 -10000 0 0
IKK complex -0.067 0.12 -9999 0 -0.58 19 19
NGF (dimer)/TRKA -0.017 0.088 -9999 0 -0.62 18 18
MMP7 -0.12 0.28 -9999 0 -0.81 141 141
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.15 0.22 -9999 0 -0.46 316 316
MMP3 -0.12 0.16 -9999 0 -0.3 387 387
APAF-1/Caspase 9 -0.11 0.16 -9999 0 -0.66 14 14
Glucocorticoid receptor regulatory network

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
PCK2 0.023 0.077 0.32 18 -10000 0 18
SMARCC2 0.012 0.01 -10000 0 -10000 0 0
SMARCC1 0.012 0.01 -10000 0 -10000 0 0
TBX21 -0.14 0.26 -10000 0 -0.76 90 90
SUMO2 0 0.01 -10000 0 -0.28 1 1
STAT1 (dimer) 0.013 0.039 -10000 0 -0.27 18 18
FKBP4 -0.002 0.025 -10000 0 -0.28 8 8
FKBP5 -0.013 0.1 -10000 0 -0.81 15 15
GR alpha/HSP90/FKBP51/HSP90 0.11 0.14 0.33 75 -0.44 17 92
PRL -0.089 0.12 -10000 0 -0.56 1 1
cortisol/GR alpha (dimer)/TIF2 0.28 0.28 0.53 442 -0.57 18 460
RELA -0.04 0.083 -10000 0 -10000 0 0
FGG 0.24 0.22 0.48 305 -0.53 2 307
GR beta/TIF2 0.11 0.18 0.33 134 -0.58 33 167
IFNG -0.42 0.35 -10000 0 -0.76 446 446
apoptosis -0.27 0.3 0.59 3 -0.68 241 244
CREB1 -0.007 0.028 -10000 0 -10000 0 0
histone acetylation 0.022 0.14 0.41 32 -0.41 25 57
BGLAP -0.1 0.15 -10000 0 -0.58 6 6
GR/PKAc 0.12 0.12 0.34 47 -0.56 2 49
NF kappa B1 p50/RelA -0.067 0.15 -10000 0 -0.42 34 34
SMARCD1 0.012 0.01 -10000 0 -10000 0 0
MDM2 0.12 0.1 0.25 246 -10000 0 246
GATA3 -0.026 0.16 -10000 0 -0.56 63 63
AKT1 0 0.004 -10000 0 -10000 0 0
CSF2 -0.04 0.11 0.39 1 -0.59 7 8
GSK3B 0 0.004 -10000 0 -10000 0 0
NR1I3 -0.21 0.26 0.56 3 -0.64 135 138
CSN2 0.2 0.18 0.41 223 -0.54 1 224
BRG1/BAF155/BAF170/BAF60A -0.002 0.033 -10000 0 -0.46 5 5
NFATC1 0 0.045 -10000 0 -0.81 3 3
POU2F1 0.007 0.013 -10000 0 -10000 0 0
CDKN1A 0.045 0.075 -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 -0.015 0.098 -10000 0 -0.51 30 30
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.1 0.14 0.33 59 -0.42 18 77
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.37 0.44 0.74 1 -0.92 335 336
JUN -0.32 0.29 -10000 0 -0.58 442 442
IL4 -0.13 0.16 -10000 0 -0.53 32 32
CDK5R1 -0.009 0.05 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.42 0.41 -10000 0 -0.74 541 541
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.11 0.13 0.33 60 -0.43 10 70
cortisol/GR alpha (monomer) 0.35 0.32 0.63 469 -0.55 2 471
NCOA2 -0.025 0.14 -10000 0 -0.81 31 31
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.29 0.39 -10000 0 -0.87 298 298
AP-1/NFAT1-c-4 -0.66 0.52 -10000 0 -1 620 620
AFP -0.6 0.7 -10000 0 -1.6 327 327
SUV420H1 0 0 -10000 0 -10000 0 0
IRF1 0.19 0.16 0.44 145 -10000 0 145
TP53 0.031 0.025 -10000 0 -0.51 2 2
PPP5C 0 0 -10000 0 -10000 0 0
KRT17 -0.84 0.81 -10000 0 -1.7 442 442
KRT14 -0.84 0.77 -10000 0 -1.6 526 526
TBP 0.019 0.004 -10000 0 -10000 0 0
CREBBP 0.14 0.14 0.29 294 -10000 0 294
HDAC1 0 0.003 -10000 0 -10000 0 0
HDAC2 0.001 0.004 -10000 0 -10000 0 0
AP-1 -0.66 0.53 -10000 0 -1 623 623
MAPK14 0 0.003 -10000 0 -10000 0 0
MAPK10 -0.13 0.3 -10000 0 -0.81 154 154
MAPK11 -0.002 0.045 -10000 0 -0.82 3 3
KRT5 -0.94 0.82 -10000 0 -1.7 535 535
interleukin-1 receptor activity -0.001 0.003 -10000 0 -10000 0 0
NCOA1 0.009 0.027 -10000 0 -0.8 1 1
STAT1 0.013 0.039 -10000 0 -0.27 18 18
CGA -0.16 0.18 -10000 0 -0.5 89 89
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.2 0.18 0.37 491 -10000 0 491
MAPK3 0 0.004 -10000 0 -10000 0 0
MAPK1 0 0.003 -10000 0 -10000 0 0
ICAM1 -0.18 0.25 -10000 0 -0.71 83 83
NFKB1 -0.04 0.083 -10000 0 -10000 0 0
MAPK8 -0.23 0.22 -10000 0 -0.45 385 385
MAPK9 0 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.29 0.31 0.59 3 -0.72 241 244
BAX 0.047 0.032 -10000 0 -10000 0 0
POMC -0.19 0.3 -10000 0 -0.91 83 83
EP300 0.14 0.14 0.29 288 -10000 0 288
cortisol/GR alpha (dimer)/p53 0.31 0.26 0.55 450 -0.58 1 451
proteasomal ubiquitin-dependent protein catabolic process 0.087 0.079 0.23 61 -10000 0 61
SGK1 0.23 0.2 -10000 0 -1.2 5 5
IL13 -0.32 0.28 -10000 0 -0.67 235 235
IL6 -0.5 0.63 -10000 0 -1.3 372 372
PRKACG 0 0 -10000 0 -10000 0 0
IL5 -0.27 0.22 -10000 0 -0.63 123 123
IL2 -0.42 0.35 -10000 0 -0.76 426 426
CDK5 -0.001 0.022 -10000 0 -0.28 6 6
PRKACB -0.016 0.074 -10000 0 -0.81 3 3
HSP90AA1 0 0.009 -10000 0 -0.28 1 1
IL8 -0.2 0.3 -10000 0 -0.7 170 170
CDK5R1/CDK5 -0.007 0.036 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.059 0.098 -10000 0 -0.59 4 4
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.29 0.24 0.51 444 -0.54 1 445
SMARCA4 0.012 0.013 -10000 0 -0.28 1 1
chromatin remodeling 0.2 0.16 0.39 259 -10000 0 259
NF kappa B1 p50/RelA/Cbp 0.061 0.17 0.35 47 -10000 0 47
JUN (dimer) -0.32 0.29 -10000 0 -0.58 442 442
YWHAH 0 0 -10000 0 -10000 0 0
VIPR1 -0.14 0.25 -10000 0 -0.72 100 100
NR3C1 0.2 0.2 0.46 253 -0.6 4 257
NR4A1 -0.057 0.23 -10000 0 -0.75 96 96
TIF2/SUV420H1 -0.019 0.11 -10000 0 -0.62 31 31
MAPKKK cascade -0.27 0.3 0.59 3 -0.68 241 244
cortisol/GR alpha (dimer)/Src-1 0.3 0.26 0.54 449 -0.58 1 450
PBX1 0.005 0.04 -10000 0 -0.54 4 4
POU1F1 0.003 0.015 -10000 0 -0.28 2 2
SELE -0.23 0.37 -10000 0 -0.82 185 185
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.2 0.16 0.39 257 -10000 0 257
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.29 0.24 0.51 444 -0.54 1 445
mol:cortisol 0.2 0.2 0.36 491 -10000 0 491
MMP1 -0.21 0.11 -10000 0 -10000 0 0
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.22 0.42 -10000 0 -0.86 183 183
PLK1 -0.078 0.098 -10000 0 -10000 0 0
BIRC5 -0.088 0.095 -10000 0 -10000 0 0
HSPA1B -0.22 0.42 -10000 0 -0.88 164 164
MAP2K1 0.009 0.029 -10000 0 -10000 0 0
BRCA2 -0.22 0.42 -10000 0 -0.88 175 175
FOXM1 -0.26 0.49 -10000 0 -0.97 226 226
XRCC1 -0.22 0.42 -10000 0 -0.93 131 131
FOXM1B/p19 -0.27 0.4 0.38 1 -0.86 234 235
Cyclin D1/CDK4 -0.2 0.4 -10000 0 -0.87 133 133
CDC2 -0.23 0.44 -10000 0 -0.87 213 213
TGFA -0.2 0.41 -10000 0 -0.92 130 130
SKP2 -0.22 0.42 -10000 0 -0.92 140 140
CCNE1 -0.053 0.12 -10000 0 -0.29 200 200
CKS1B -0.22 0.42 -10000 0 -0.87 173 173
RB1 -0.11 0.12 -10000 0 -1 2 2
FOXM1C/SP1 -0.27 0.43 -10000 0 -0.9 228 228
AURKB -0.07 0.099 -10000 0 -10000 0 0
CENPF -0.24 0.44 -10000 0 -0.95 151 151
CDK4 0.008 0.018 -10000 0 -0.28 2 2
MYC -0.2 0.4 -10000 0 -0.83 169 169
CHEK2 0.008 0.032 -10000 0 -0.3 2 2
ONECUT1 -0.22 0.42 -10000 0 -0.87 171 171
CDKN2A -0.035 0.11 -10000 0 -0.27 167 167
LAMA4 -0.22 0.42 -10000 0 -0.89 164 164
FOXM1B/HNF6 -0.25 0.47 -10000 0 -0.98 179 179
FOS -0.43 0.67 -10000 0 -1.3 340 340
SP1 0 0 -10000 0 -10000 0 0
CDC25B -0.22 0.42 -10000 0 -0.87 175 175
response to radiation -0.006 0.029 -10000 0 -10000 0 0
CENPB -0.22 0.42 -10000 0 -0.86 183 183
CENPA -0.24 0.44 -10000 0 -0.89 206 206
NEK2 -0.26 0.43 -10000 0 -0.9 199 199
HIST1H2BA -0.22 0.42 -10000 0 -0.9 158 158
CCNA2 -0.11 0.15 -10000 0 -0.29 407 407
EP300 0 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.25 0.47 -10000 0 -0.97 193 193
CCNB2 -0.25 0.44 -10000 0 -0.91 187 187
CCNB1 -0.24 0.44 -10000 0 -0.92 190 190
ETV5 -0.22 0.42 -10000 0 -0.93 135 135
ESR1 -0.32 0.57 -10000 0 -1.3 208 208
CCND1 -0.2 0.41 -10000 0 -0.88 137 137
GSK3A 0.014 0.021 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.079 0.14 -10000 0 -0.32 136 136
CDK2 0.006 0.009 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.009 0.035 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.31 0.36 -10000 0 -0.84 242 242
GAS1 -0.25 0.48 -10000 0 -1 191 191
MMP2 -0.22 0.43 -10000 0 -0.89 172 172
RB1/FOXM1C -0.22 0.42 -10000 0 -0.88 174 174
CREBBP 0 0 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.12 0.41 -10000 0 -0.91 204 204
NCK1/PAK1/Dok-R -0.088 0.17 -10000 0 -0.42 204 204
NCK1/Dok-R -0.24 0.47 -10000 0 -1.1 204 204
PIK3CA 0.003 0.01 -10000 0 -0.28 1 1
mol:beta2-estradiol 0.035 0.098 0.24 170 -10000 0 170
RELA 0 0 -10000 0 -10000 0 0
SHC1 0.003 0.005 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.037 0.1 0.25 167 -0.3 7 174
TNIP2 0 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.22 0.43 -10000 0 -1.1 204 204
FN1 -0.11 0.14 -10000 0 -0.28 398 398
PLD2 -0.19 0.52 -10000 0 -1.2 204 204
PTPN11 0 0 -10000 0 -10000 0 0
GRB14 -0.099 0.22 -10000 0 -0.46 212 212
ELK1 -0.15 0.46 -10000 0 -1 204 204
GRB7 -0.02 0.075 -10000 0 -0.29 70 70
PAK1 -0.006 0.041 -10000 0 -0.28 22 22
Tie2/Ang1/alpha5/beta1 Integrin -0.19 0.48 -10000 0 -1.1 204 204
CDKN1A -0.06 0.27 -10000 0 -0.64 115 115
ITGA5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.24 0.47 -10000 0 -1.1 204 204
CRK 0 0 -10000 0 -10000 0 0
mol:NO -0.064 0.31 -10000 0 -0.66 204 204
PLG -0.19 0.52 -10000 0 -1.2 204 204
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.17 0.36 -10000 0 -0.88 204 204
GRB2 0 0.009 -10000 0 -0.28 1 1
PIK3R1 -0.003 0.068 -10000 0 -0.81 7 7
ANGPT2 -0.11 0.27 -10000 0 -0.75 98 98
BMX -0.36 0.58 -10000 0 -1.4 204 204
ANGPT1 -0.23 0.56 -10000 0 -1.4 180 180
tube development -0.077 0.3 -10000 0 -0.68 164 164
ANGPT4 -0.25 0.38 -10000 0 -0.81 307 307
response to hypoxia -0.01 0.03 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.27 0.54 -10000 0 -1.3 204 204
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
FGF2 -0.32 0.4 -10000 0 -0.81 395 395
STAT5A (dimer) -0.093 0.34 -10000 0 -0.84 124 124
mol:L-citrulline -0.064 0.31 -10000 0 -0.66 204 204
AGTR1 -0.2 0.34 -10000 0 -0.7 288 288
MAPK14 -0.18 0.5 -10000 0 -1.1 204 204
Tie2/SHP2 -0.095 0.28 -10000 0 -1.3 45 45
TEK -0.1 0.32 -10000 0 -1.5 45 45
RPS6KB1 -0.11 0.39 -10000 0 -0.87 204 204
Angiotensin II/AT1 -0.15 0.26 -10000 0 -0.62 230 230
Tie2/Ang1/GRB2 -0.25 0.51 -10000 0 -1.2 204 204
MAPK3 -0.16 0.47 -10000 0 -1.1 204 204
MAPK1 -0.16 0.47 -10000 0 -1.1 204 204
Tie2/Ang1/GRB7 -0.25 0.52 -10000 0 -1.2 204 204
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.19 0.52 -10000 0 -1.2 204 204
PI3K -0.15 0.47 -10000 0 -1.1 204 204
FES -0.18 0.49 -10000 0 -1.1 204 204
Crk/Dok-R -0.24 0.47 -10000 0 -1.1 204 204
Tie2/Ang1/ABIN2 -0.25 0.51 -10000 0 -1.2 204 204
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.096 0.37 -10000 0 -0.8 204 204
STAT5A -0.007 0.072 -10000 0 -0.81 8 8
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.11 0.39 -10000 0 -0.87 204 204
Tie2/Ang2 -0.13 0.41 -10000 0 -0.97 145 145
Tie2/Ang1 -0.22 0.57 -10000 0 -1.3 204 204
FOXO1 -0.093 0.37 -10000 0 -0.81 204 204
ELF1 0.013 0.022 -10000 0 -10000 0 0
ELF2 -0.19 0.51 -10000 0 -1.2 204 204
mol:Choline -0.17 0.49 -10000 0 -1.1 204 204
cell migration -0.038 0.1 -10000 0 -0.24 169 169
FYN -0.094 0.34 -10000 0 -0.78 163 163
DOK2 -0.003 0.04 -10000 0 -0.46 6 6
negative regulation of cell cycle -0.05 0.25 -10000 0 -0.58 115 115
ETS1 -0.026 0.11 -10000 0 -0.98 4 4
PXN -0.075 0.33 -10000 0 -0.71 204 204
ITGB1 0 0 -10000 0 -10000 0 0
NOS3 -0.082 0.35 -10000 0 -0.75 204 204
RAC1 0 0 -10000 0 -10000 0 0
TNF -0.04 0.14 -10000 0 -0.83 17 17
MAPKKK cascade -0.17 0.49 -10000 0 -1.1 204 204
RASA1 0 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.23 0.52 -10000 0 -1.2 204 204
NCK1 0 0 -10000 0 -10000 0 0
vasculogenesis -0.051 0.28 -10000 0 -0.59 204 204
mol:Phosphatidic acid -0.17 0.49 -10000 0 -1.1 204 204
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.064 0.31 -10000 0 -0.66 204 204
Rac1/GTP -0.17 0.33 -10000 0 -0.81 204 204
MMP2 -0.19 0.52 -10000 0 -1.2 205 205
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.46 0.46 -10000 0 -1.1 232 232
STAT6 (cleaved dimer) -0.5 0.44 -10000 0 -0.97 384 384
IGHG1 -0.16 0.16 -10000 0 -0.35 166 166
IGHG3 -0.45 0.44 -10000 0 -0.95 345 345
AKT1 -0.21 0.24 -10000 0 -0.63 99 99
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.15 0.2 -10000 0 -0.58 62 62
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.22 0.24 -10000 0 -0.62 125 125
THY1 -0.46 0.46 -10000 0 -1.1 228 228
MYB -0.015 0.11 -10000 0 -0.75 20 20
HMGA1 -0.012 0.057 -10000 0 -0.28 43 43
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.28 0.29 -10000 0 -0.67 226 226
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.21 0.23 -10000 0 -0.58 108 108
SP1 0.018 0.004 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.024 0.03 -10000 0 -0.78 1 1
STAT6 (dimer)/ETS1 -0.49 0.44 -10000 0 -1 328 328
SOCS1 -0.3 0.31 -10000 0 -0.73 194 194
SOCS3 -0.23 0.26 -10000 0 -0.8 69 69
FCER2 -0.6 0.65 -10000 0 -1.4 330 330
PARP14 0.002 0.018 -10000 0 -0.29 3 3
CCL17 -0.47 0.46 -10000 0 -1.1 282 282
GRB2 0 0.009 -10000 0 -0.28 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.17 0.19 -10000 0 -0.58 32 32
T cell proliferation -0.46 0.48 -10000 0 -1.1 254 254
IL4R/JAK1 -0.46 0.46 -10000 0 -1.1 249 249
EGR2 -0.61 0.64 -10000 0 -1.4 318 318
JAK2 -0.008 0.037 -10000 0 -0.83 1 1
JAK3 0.008 0.037 -10000 0 -0.29 1 1
PIK3R1 -0.006 0.068 -10000 0 -0.81 7 7
JAK1 0.005 0.011 -10000 0 -10000 0 0
COL1A2 -0.14 0.16 -10000 0 -1.7 2 2
CCL26 -0.46 0.46 -10000 0 -1.1 213 213
IL4R -0.49 0.49 -10000 0 -1.2 250 250
PTPN6 0.022 0.018 -10000 0 -10000 0 0
IL13RA2 -0.46 0.46 -10000 0 -1.1 215 215
IL13RA1 -0.007 0.026 -10000 0 -10000 0 0
IRF4 -0.22 0.48 -10000 0 -1.6 103 103
ARG1 -0.11 0.12 -10000 0 -10000 0 0
CBL -0.26 0.28 -10000 0 -0.64 205 205
GTF3A 0.013 0.015 -10000 0 -10000 0 0
PIK3CA 0 0.009 -10000 0 -0.28 1 1
IL13RA1/JAK2 -0.014 0.042 -10000 0 -0.63 1 1
IRF4/BCL6 -0.2 0.43 -10000 0 -1.4 106 106
CD40LG -0.033 0.18 -10000 0 -0.7 64 64
MAPK14 -0.26 0.28 -10000 0 -0.64 200 200
mitosis -0.2 0.23 -10000 0 -0.6 99 99
STAT6 -0.53 0.54 -10000 0 -1.2 314 314
SPI1 0.006 0.024 -10000 0 -0.27 6 6
RPS6KB1 -0.19 0.22 -10000 0 -0.59 86 86
STAT6 (dimer) -0.53 0.54 -10000 0 -1.2 314 314
STAT6 (dimer)/PARP14 -0.52 0.51 -10000 0 -1.1 344 344
mast cell activation 0.012 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.21 0.23 -10000 0 -0.59 101 101
FRAP1 -0.21 0.24 -10000 0 -0.63 99 99
LTA -0.47 0.46 -10000 0 -1.1 249 249
FES -0.002 0.044 -10000 0 -0.81 3 3
T-helper 1 cell differentiation 0.52 0.52 1.1 319 -10000 0 319
CCL11 -0.48 0.44 -10000 0 -1.1 272 272
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.21 0.24 -10000 0 -0.6 103 103
IL2RG -0.005 0.09 -10000 0 -0.41 28 28
IL10 -0.46 0.46 -10000 0 -1.1 213 213
IRS1 -0.033 0.16 -10000 0 -0.81 41 41
IRS2 -0.033 0.16 -10000 0 -0.81 40 40
IL4 -0.11 0.11 -10000 0 -10000 0 0
IL5 -0.47 0.46 -10000 0 -1.1 236 236
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.38 0.36 -10000 0 -0.82 277 277
COL1A1 -0.18 0.17 -10000 0 -1.8 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.47 0.47 -10000 0 -1.2 201 201
IL2R gamma/JAK3 -0.014 0.073 -10000 0 -0.44 22 22
TFF3 -0.56 0.59 -10000 0 -1.3 299 299
ALOX15 -0.55 0.58 -10000 0 -1.3 286 286
MYBL1 -0.041 0.099 -10000 0 -0.28 146 146
T-helper 2 cell differentiation -0.4 0.38 -10000 0 -0.84 306 306
SHC1 0 0 -10000 0 -10000 0 0
CEBPB 0.008 0.009 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.21 0.24 -10000 0 -0.58 120 120
mol:PI-3-4-5-P3 -0.21 0.24 -10000 0 -0.63 99 99
PI3K -0.22 0.26 -10000 0 -0.68 97 97
DOK2 -0.003 0.04 -10000 0 -0.46 6 6
ETS1 0.019 0.052 -10000 0 -0.77 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.16 0.18 -10000 0 -0.58 24 24
ITGB3 -0.48 0.49 -10000 0 -1.2 208 208
PIGR -1 0.75 -10000 0 -1.5 637 637
IGHE 0.046 0.039 -10000 0 -10000 0 0
MAPKKK cascade -0.15 0.18 -10000 0 -0.57 24 24
BCL6 0.002 0.052 -10000 0 -0.8 4 4
OPRM1 -0.47 0.46 -10000 0 -1.1 215 215
RETNLB -0.47 0.46 -10000 0 -1.1 213 213
SELP -0.63 0.68 -10000 0 -1.5 305 305
AICDA -0.45 0.44 -10000 0 -1.1 227 227
Wnt signaling

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
Noncanonical Wnts/FZD -0.16 0.25 -9999 0 -0.45 347 347
FZD6 -0.007 0.072 -9999 0 -0.81 8 8
WNT6 -0.17 0.32 -9999 0 -0.72 229 229
WNT4 -0.022 0.12 -9999 0 -0.54 40 40
FZD3 -0.009 0.085 -9999 0 -0.81 11 11
WNT5A -0.013 0.096 -9999 0 -0.58 23 23
WNT11 -0.18 0.33 -9999 0 -0.78 222 222
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0 0 -9999 0 -10000 0 0
VLDLR -0.025 0.14 -9999 0 -0.81 30 30
LRPAP1 0 0 -9999 0 -10000 0 0
NUDC 0 0 -9999 0 -10000 0 0
RELN/LRP8 -0.34 0.27 -9999 0 -0.55 598 598
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0 0.009 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.3 0.24 -9999 0 -0.5 598 598
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.017 0.067 -9999 0 -0.28 60 60
IQGAP1 0 0 -9999 0 -10000 0 0
PLA2G7 -0.016 0.093 -9999 0 -0.41 39 39
CALM1 0 0 -9999 0 -10000 0 0
DYNLT1 0 0.009 -9999 0 -0.28 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.019 0.055 -9999 0 -10000 0 0
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0 0 -9999 0 -10000 0 0
CDK5R1 -0.009 0.049 -9999 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.041 0.099 -9999 0 -0.28 145 145
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.35 0.28 -9999 0 -0.56 606 606
YWHAE 0 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.24 0.19 -9999 0 -0.48 91 91
MAP1B -0.007 0.049 -9999 0 -0.38 17 17
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.27 0.22 -9999 0 -0.44 598 598
RELN -0.49 0.39 -9999 0 -0.8 601 601
PAFAH/LIS1 -0.009 0.058 -9999 0 -0.53 10 10
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 -0.43 4 4
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.21 0.17 -9999 0 -0.34 609 609
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.26 0.21 -9999 0 -0.49 172 172
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 -0.03 0.087 -9999 0 -10000 0 0
PAFAH1B2 -0.003 0.051 -9999 0 -0.81 4 4
MAP1B/LIS1/Dynein heavy chain -0.004 0.031 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.23 0.18 -9999 0 -0.5 27 27
LRP8 -0.031 0.087 -9999 0 -10000 0 0
NDEL1/Katanin 60 -0.24 0.19 -9999 0 -0.48 92 92
P39/CDK5 -0.28 0.23 -9999 0 -0.46 598 598
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -9999 0 -10000 0 0
CDK5 -0.27 0.24 -9999 0 -0.46 598 598
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 -0.3 0.24 -9999 0 -0.48 606 606
RELN/VLDLR -0.32 0.26 -9999 0 -0.52 606 606
CDC42 0 0 -9999 0 -10000 0 0
Arf6 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
CENTA1/KIF3B -0.004 0.046 -9999 0 -0.66 4 4
ARNO/beta Arrestin1-2 -0.13 0.19 -9999 0 -0.44 235 235
EGFR -0.3 0.39 -9999 0 -0.8 369 369
EPHA2 -0.005 0.063 -9999 0 -0.81 6 6
USP6 0 0 -9999 0 -10000 0 0
IQSEC1 0 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.35 0.36 -9999 0 -0.68 504 504
ARRB2 -0.057 0.16 -9999 0 -0.44 138 138
mol:GTP 0.017 0.019 -9999 0 -0.15 5 5
ARRB1 -0.002 0.037 -9999 0 -0.63 3 3
FBXO8 0 0 -9999 0 -10000 0 0
TSHR -0.036 0.16 -9999 0 -0.76 47 47
EGF -0.17 0.33 -9999 0 -0.8 206 206
somatostatin receptor activity 0 0 -9999 0 -0.001 337 337
ARAP2 -0.005 0.063 -9999 0 -0.81 6 6
mol:GDP -0.14 0.18 -9999 0 -0.35 307 307
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 234 234
ITGA2B -0.017 0.075 -9999 0 -0.81 3 3
ARF6 0 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.004 0.038 -9999 0 -0.48 6 6
ADAP1 -0.004 0.05 -9999 0 -0.44 10 10
KIF13B -0.002 0.036 -9999 0 -0.81 2 2
HGF/MET -0.14 0.28 -9999 0 -0.67 211 211
PXN 0 0 -9999 0 -10000 0 0
ARF6/GTP -0.13 0.15 -9999 0 -0.32 311 311
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.3 0.32 -9999 0 -0.59 504 504
ADRB2 -0.19 0.34 -9999 0 -0.81 234 234
receptor agonist activity 0 0 -9999 0 0 315 315
actin filament binding 0 0 -9999 0 -0.001 323 323
SRC 0 0.009 -9999 0 -10000 0 0
ITGB3 -0.024 0.14 -9999 0 -0.81 28 28
GNAQ -0.002 0.036 -9999 0 -0.81 2 2
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 292 292
ARF6/GDP -0.015 0.085 -9999 0 -0.43 17 17
ARF6/GDP/GULP/ACAP1 -0.15 0.2 -9999 0 -0.54 158 158
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.022 0.089 -9999 0 -0.49 31 31
ACAP1 -0.019 0.096 -9999 0 -0.81 10 10
ACAP2 0 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.093 0.23 -9999 0 -0.67 138 138
EFNA1 0 0 -9999 0 -10000 0 0
HGF -0.055 0.2 -9999 0 -0.81 67 67
CYTH3 0.01 0.02 -9999 0 -0.63 1 1
CYTH2 0.006 0.002 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 260 260
endosomal lumen acidification 0 0 -9999 0 -0.001 263 263
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.054 0.2 -9999 0 -0.81 66 66
GNAQ/ARNO 0.003 0.022 -9999 0 -0.46 2 2
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 325 325
MET -0.14 0.3 -9999 0 -0.81 165 165
GNA14 -0.015 0.091 -9999 0 -0.44 33 33
GNA15 -0.003 0.035 -9999 0 -0.34 8 8
GIT1 -0.001 0.02 -9999 0 -0.28 5 5
mol:PI-4-5-P2 0 0 -9999 0 -0.001 306 306
GNA11 -0.002 0.036 -9999 0 -0.81 2 2
LHCGR -0.11 0.28 -9999 0 -0.81 138 138
AGTR1 -0.2 0.34 -9999 0 -0.7 288 288
desensitization of G-protein coupled receptor protein signaling pathway -0.093 0.23 -9999 0 -0.66 138 138
IPCEF1/ARNO -0.24 0.26 -9999 0 -0.48 504 504
alphaIIb/beta3 Integrin -0.029 0.12 -9999 0 -0.63 31 31
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 -0.013 0.19 -9999 0 -0.59 80 80
PTK2B 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.02 0.19 -9999 0 -0.92 29 29
EDN1 -0.04 0.24 -9999 0 -0.82 79 79
EDN3 -0.38 0.4 -9999 0 -0.81 460 460
EDN2 -0.075 0.13 -9999 0 -0.81 6 6
HRAS/GDP -0.03 0.2 -9999 0 -0.53 88 88
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.004 0.14 -9999 0 -0.42 59 59
ADCY4 -0.15 0.29 -9999 0 -0.57 283 283
ADCY5 -0.28 0.36 -9999 0 -0.61 465 465
ADCY6 -0.13 0.27 -9999 0 -0.54 266 266
ADCY7 -0.13 0.27 -9999 0 -0.54 266 266
ADCY1 -0.15 0.29 -9999 0 -0.56 280 280
ADCY2 -0.17 0.32 -9999 0 -0.6 293 293
ADCY3 -0.13 0.27 -9999 0 -0.54 266 266
ADCY8 -0.14 0.27 -9999 0 -0.55 266 266
ADCY9 -0.13 0.27 -9999 0 -0.54 266 266
arachidonic acid secretion -0.1 0.29 -9999 0 -0.47 325 325
ETB receptor/Endothelin-1/Gq/GTP -0.032 0.17 -9999 0 -0.39 142 142
GNAO1 -0.032 0.14 -9999 0 -0.48 66 66
HRAS -0.001 0.02 -9999 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.034 0.2 -9999 0 -0.55 80 80
ETA receptor/Endothelin-1/Gs/GTP -0.095 0.32 -9999 0 -0.57 266 266
mol:GTP -0.001 0.006 -9999 0 -10000 0 0
COL3A1 -0.021 0.2 -9999 0 -0.6 80 80
EDNRB -0.066 0.24 -9999 0 -0.81 91 91
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.024 0.23 -9999 0 -0.67 93 93
CYSLTR1 -0.024 0.23 -9999 0 -0.67 93 93
SLC9A1 0 0.1 -9999 0 -0.3 79 79
mol:GDP -0.038 0.22 -9999 0 -0.56 97 97
SLC9A3 -0.049 0.28 -9999 0 -0.63 159 159
RAF1 -0.085 0.25 -9999 0 -0.54 150 150
JUN 0.024 0.18 -9999 0 -0.8 31 31
JAK2 -0.013 0.2 -9999 0 -0.6 80 80
mol:IP3 -0.029 0.17 -9999 0 -0.54 61 61
ETA receptor/Endothelin-1 0.03 0.25 -9999 0 -0.63 96 96
PLCB1 -0.055 0.2 -9999 0 -0.81 67 67
PLCB2 0.006 0.028 -9999 0 -0.81 1 1
ETA receptor/Endothelin-3 -0.28 0.32 -9999 0 -0.62 461 461
FOS -0.26 0.5 -9999 0 -0.98 308 308
Gai/GDP -0.023 0.16 -9999 0 -0.74 32 32
CRK 0 0 -9999 0 -10000 0 0
mol:Ca ++ -0.05 0.25 -9999 0 -0.67 101 101
BCAR1 0.001 0.004 -9999 0 -10000 0 0
PRKCB1 -0.032 0.17 -9999 0 -0.48 76 76
GNAQ 0.008 0.038 -9999 0 -0.81 2 2
GNAZ -0.007 0.072 -9999 0 -0.81 8 8
GNAL -0.19 0.34 -9999 0 -0.81 233 233
Gs family/GDP -0.17 0.26 -9999 0 -0.57 250 250
ETA receptor/Endothelin-1/Gq/GTP 0.015 0.13 -9999 0 -0.39 57 57
MAPK14 -0.03 0.17 -9999 0 -0.57 53 53
TRPC6 0.018 0.21 -9999 0 -1 29 29
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
GNAI1 -0.042 0.18 -9999 0 -0.81 51 51
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.038 0.18 -9999 0 -0.46 103 103
ETB receptor/Endothelin-2 -0.1 0.2 -9999 0 -0.66 96 96
ETB receptor/Endothelin-3 -0.34 0.34 -9999 0 -0.66 510 510
ETB receptor/Endothelin-1 -0.08 0.27 -9999 0 -0.66 159 159
MAPK3 -0.2 0.41 -9999 0 -0.78 314 314
MAPK1 -0.2 0.41 -9999 0 -0.78 314 314
Rac1/GDP -0.03 0.2 -9999 0 -0.53 88 88
cAMP biosynthetic process -0.18 0.3 -9999 0 -0.6 281 281
MAPK8 0.019 0.18 -9999 0 -0.68 38 38
SRC 0 0.009 -9999 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.048 0.19 -9999 0 -0.42 142 142
p130Cas/CRK/Src/PYK2 -0.015 0.21 -9999 0 -0.6 70 70
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.03 0.2 -9999 0 -0.53 88 88
COL1A2 -0.055 0.25 -9999 0 -0.68 92 92
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.031 0.11 -9999 0 -0.57 8 8
mol:DAG -0.029 0.18 -9999 0 -0.54 61 61
MAP2K2 -0.13 0.32 -9999 0 -0.56 314 314
MAP2K1 -0.13 0.32 -9999 0 -0.56 314 314
EDNRA 0.025 0.067 -9999 0 -0.44 4 4
positive regulation of muscle contraction -0.013 0.17 -9999 0 -0.52 80 80
Gq family/GDP -0.074 0.16 -9999 0 -0.6 53 53
HRAS/GTP -0.052 0.21 -9999 0 -0.48 120 120
PRKCH -0.023 0.17 -9999 0 -0.58 46 46
RAC1 0 0 -9999 0 -10000 0 0
PRKCA -0.034 0.2 -9999 0 -0.62 64 64
PRKCB -0.035 0.19 -9999 0 -0.62 58 58
PRKCE -0.024 0.17 -9999 0 -0.54 55 55
PRKCD -0.024 0.17 -9999 0 -0.54 54 54
PRKCG -0.032 0.17 -9999 0 -0.54 59 59
regulation of vascular smooth muscle contraction -0.3 0.57 -9999 0 -1.1 308 308
PRKCQ -0.045 0.21 -9999 0 -0.59 92 92
PLA2G4A -0.12 0.33 -9999 0 -0.52 325 325
GNA14 -0.006 0.093 -9999 0 -0.44 33 33
GNA15 0.006 0.036 -9999 0 -0.34 8 8
GNA12 0 0 -9999 0 -10000 0 0
GNA11 0.007 0.037 -9999 0 -0.81 2 2
Rac1/GTP 0.034 0.2 -9999 0 -0.55 80 80
MMP1 -0.12 0.12 -9999 0 -10000 0 0
Ephrin B reverse 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
EFNB2 0 0 -10000 0 -10000 0 0
EPHB2 -0.004 0.038 -10000 0 -0.28 18 18
EFNB1 0.016 0.054 -10000 0 -0.62 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.18 0.21 -10000 0 -0.42 416 416
Ephrin B2/EPHB1-2 -0.21 0.24 -10000 0 -0.49 415 415
neuron projection morphogenesis -0.17 0.2 -10000 0 -0.4 416 416
Ephrin B1/EPHB1-2/Tiam1 -0.19 0.23 -10000 0 -0.46 416 416
DNM1 -0.006 0.068 -10000 0 -0.74 8 8
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.004 0.13 -10000 0 -0.75 29 29
YES1 -0.025 0.17 -10000 0 -0.99 28 28
Ephrin B1/EPHB1-2/NCK2 -0.19 0.23 -10000 0 -0.46 416 416
PI3K -0.025 0.14 -10000 0 -0.73 34 34
mol:GDP -0.19 0.22 -10000 0 -0.45 416 416
ITGA2B -0.017 0.075 -10000 0 -0.81 3 3
endothelial cell proliferation 0 0.005 -10000 0 -10000 0 0
FYN -0.025 0.16 -10000 0 -0.99 28 28
MAP3K7 -0.022 0.14 -10000 0 -0.81 28 28
FGR -0.027 0.17 -10000 0 -1 28 28
TIAM1 -0.001 0.018 -10000 0 -10000 0 0
PIK3R1 -0.006 0.068 -10000 0 -0.81 7 7
RGS3 0 0 -10000 0 -10000 0 0
cell adhesion -0.041 0.16 -10000 0 -0.63 58 58
LYN -0.025 0.16 -10000 0 -0.99 28 28
Ephrin B1/EPHB1-2/Src Family Kinases -0.026 0.16 -10000 0 -0.93 28 28
Ephrin B1/EPHB1-2 -0.029 0.14 -10000 0 -0.88 28 28
SRC -0.027 0.17 -10000 0 -1 28 28
ITGB3 -0.024 0.14 -10000 0 -0.81 28 28
EPHB1 -0.34 0.4 -10000 0 -0.81 415 415
EPHB4 0 0.009 -10000 0 -0.28 1 1
RAC1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.029 0.12 -10000 0 -0.63 31 31
BLK -0.026 0.17 -10000 0 -1 28 28
HCK -0.027 0.17 -10000 0 -1 28 28
regulation of stress fiber formation 0.19 0.22 0.45 416 -10000 0 416
MAPK8 0.002 0.14 -10000 0 -0.73 31 31
Ephrin B1/EPHB1-2/RGS3 -0.19 0.23 -10000 0 -0.46 416 416
endothelial cell migration -0.016 0.12 -10000 0 -0.71 28 28
NCK2 0 0 -10000 0 -10000 0 0
PTPN13 -0.016 0.16 -10000 0 -0.92 28 28
regulation of focal adhesion formation 0.19 0.22 0.45 416 -10000 0 416
chemotaxis 0.19 0.22 0.45 416 -10000 0 416
PIK3CA 0 0.009 -10000 0 -0.28 1 1
Rac1/GTP -0.18 0.21 -10000 0 -0.41 416 416
angiogenesis -0.029 0.14 -10000 0 -0.87 28 28
LCK -0.029 0.17 -10000 0 -1 28 28
EPHB forward 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
Ephrin A5/EPHB2 -0.055 0.16 -10000 0 -0.54 95 95
cell-cell adhesion 0.18 0.22 0.69 71 -10000 0 71
Ephrin B/EPHB2/RasGAP -0.041 0.13 -10000 0 -0.45 85 85
ITSN1 -0.002 0.036 -10000 0 -0.81 2 2
PIK3CA 0 0.009 -10000 0 -0.28 1 1
SHC1 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.002 0.016 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.23 0.27 -10000 0 -0.54 415 415
HRAS/GDP -0.19 0.23 -10000 0 -0.67 90 90
Ephrin B/EPHB1/GRB7 -0.24 0.28 -10000 0 -0.53 434 434
Endophilin/SYNJ1 -0.038 0.12 -10000 0 -0.42 85 85
KRAS -0.001 0.013 -10000 0 -0.28 2 2
Ephrin B/EPHB1/Src -0.23 0.28 -10000 0 -0.52 433 433
endothelial cell migration -0.003 0.038 -10000 0 -0.45 7 7
GRB2 0 0.009 -10000 0 -0.28 1 1
GRB7 -0.02 0.075 -10000 0 -0.29 70 70
PAK1 -0.048 0.14 -10000 0 -0.47 94 94
HRAS -0.001 0.02 -10000 0 -10000 0 0
RRAS -0.039 0.12 -10000 0 -0.43 85 85
DNM1 -0.006 0.068 -10000 0 -0.74 8 8
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.22 0.27 -10000 0 -0.5 433 433
lamellipodium assembly -0.18 0.22 -10000 0 -0.69 71 71
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.16 0.19 -10000 0 -0.37 415 415
PIK3R1 -0.006 0.068 -10000 0 -0.81 7 7
EPHB2 -0.005 0.037 -10000 0 -0.28 18 18
EPHB3 -0.003 0.031 -10000 0 -0.28 12 12
EPHB1 -0.34 0.4 -10000 0 -0.81 415 415
EPHB4 0 0.009 -10000 0 -0.28 1 1
mol:GDP -0.16 0.22 -10000 0 -0.65 89 89
Ephrin B/EPHB2 -0.041 0.13 -10000 0 -0.46 85 85
Ephrin B/EPHB3 -0.041 0.13 -10000 0 -0.46 85 85
JNK cascade -0.19 0.22 -10000 0 -0.44 415 415
Ephrin B/EPHB1 -0.23 0.28 -10000 0 -0.53 433 433
RAP1/GDP -0.14 0.18 -10000 0 -0.56 85 85
EFNB2 0 0 -10000 0 -10000 0 0
EFNB3 -0.069 0.23 -10000 0 -0.81 85 85
EFNB1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.21 0.24 -10000 0 -0.49 415 415
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.19 0.24 -10000 0 -0.7 88 88
Rap1/GTP -0.18 0.22 -10000 0 -0.72 70 70
axon guidance -0.055 0.16 -10000 0 -0.54 95 95
MAPK3 -0.11 0.19 -10000 0 -0.53 67 67
MAPK1 -0.11 0.19 -10000 0 -0.53 67 67
Rac1/GDP -0.15 0.19 -10000 0 -0.59 86 86
actin cytoskeleton reorganization -0.14 0.17 -10000 0 -0.53 71 71
CDC42/GDP -0.15 0.19 -10000 0 -0.59 86 86
PI3K -0.003 0.039 -10000 0 -0.46 7 7
EFNA5 -0.078 0.24 -10000 0 -0.8 96 96
Ephrin B2/EPHB4 0 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.03 0.1 -10000 0 -0.34 85 85
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.18 0.22 -10000 0 -0.68 72 72
PTK2 0.045 0.051 -10000 0 -10000 0 0
MAP4K4 -0.19 0.22 -10000 0 -0.45 415 415
SRC 0 0.009 -10000 0 -10000 0 0
KALRN -0.016 0.11 -10000 0 -0.81 19 19
Intersectin/N-WASP -0.001 0.028 -10000 0 -0.62 2 2
neuron projection morphogenesis -0.14 0.18 -10000 0 -0.55 76 76
MAP2K1 -0.15 0.18 -10000 0 -0.56 68 68
WASL 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.2 0.24 -10000 0 -0.48 415 415
cell migration -0.14 0.23 -10000 0 -0.38 415 415
NRAS -0.001 0.013 -10000 0 -10000 0 0
SYNJ1 -0.039 0.12 -10000 0 -0.43 85 85
PXN 0 0 -10000 0 -10000 0 0
TF -0.25 0.27 -10000 0 -0.47 569 569
HRAS/GTP -0.2 0.24 -10000 0 -0.76 71 71
Ephrin B1/EPHB1-2 -0.21 0.24 -10000 0 -0.49 415 415
cell adhesion mediated by integrin 0.007 0.13 0.42 85 -10000 0 85
RAC1 0 0 -10000 0 -10000 0 0
mol:GTP -0.21 0.26 -10000 0 -0.48 433 433
RAC1-CDC42/GTP -0.18 0.22 -10000 0 -0.7 71 71
RASA1 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.14 0.18 -10000 0 -0.56 85 85
ruffle organization -0.18 0.22 -10000 0 -0.71 71 71
NCK1 0 0 -10000 0 -10000 0 0
receptor internalization 0.001 0.14 -10000 0 -0.43 87 87
Ephrin B/EPHB2/KALRN -0.049 0.15 -10000 0 -0.5 94 94
ROCK1 -0.002 0.02 -10000 0 -0.49 1 1
RAS family/GDP -0.12 0.16 -10000 0 -0.53 68 68
Rac1/GTP -0.19 0.24 -10000 0 -0.76 71 71
Ephrin B/EPHB1/Src/Paxillin -0.17 0.2 -10000 0 -0.38 433 433
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0 0 -10000 0 -10000 0 0
PTK2 0 0 -10000 0 -10000 0 0
CRKL -0.1 0.24 -10000 0 -0.5 239 239
GRB2/SOS1/SHC 0 0.004 -10000 0 -10000 0 0
HRAS -0.001 0.02 -10000 0 -10000 0 0
IRS1/Crk -0.12 0.23 -10000 0 -0.5 239 239
IGF-1R heterotetramer/IGF1/PTP1B -0.13 0.24 -10000 0 -0.55 225 225
AKT1 -0.067 0.22 -10000 0 -0.74 43 43
BAD -0.055 0.2 -10000 0 -0.68 43 43
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.1 0.24 -10000 0 -0.5 239 239
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.12 0.23 -10000 0 -0.5 239 239
RAF1 -0.047 0.19 -10000 0 -0.64 40 40
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.11 0.22 -10000 0 -0.47 239 239
YWHAZ -0.001 0.015 -10000 0 -0.28 3 3
IGF-1R heterotetramer/IGF1/IRS1 -0.13 0.25 -10000 0 -0.54 239 239
PIK3CA 0 0.009 -10000 0 -0.28 1 1
RPS6KB1 -0.068 0.22 -10000 0 -0.43 226 226
GNB2L1 0 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.04 0.16 -10000 0 -0.52 42 42
PXN 0 0 -10000 0 -10000 0 0
PIK3R1 -0.006 0.068 -10000 0 -0.81 7 7
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
HRAS/GTP -0.1 0.2 -10000 0 -0.75 40 40
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.099 0.19 -10000 0 -0.44 225 225
IGF-1R heterotetramer -0.036 0.14 -10000 0 -0.85 25 25
IGF-1R heterotetramer/IGF1/IRS/Nck -0.12 0.23 -10000 0 -0.5 239 239
Crk/p130 Cas/Paxillin -0.11 0.21 -10000 0 -0.46 225 225
IGF1R -0.036 0.14 -10000 0 -0.86 25 25
IGF1 -0.18 0.35 -10000 0 -0.83 215 215
IRS2/Crk -0.13 0.25 -10000 0 -0.52 251 251
PI3K -0.12 0.23 -10000 0 -0.48 240 240
apoptosis 0.08 0.15 0.56 43 -10000 0 43
HRAS/GDP -0.001 0.013 -10000 0 -10000 0 0
PRKCD -0.094 0.25 -10000 0 -0.54 225 225
RAF1/14-3-3 E -0.075 0.14 -10000 0 -0.53 40 40
BAD/14-3-3 -0.085 0.16 -10000 0 -0.61 43 43
PRKCZ -0.068 0.22 -10000 0 -0.74 44 44
Crk/p130 Cas/Paxillin/FAK1 -0.084 0.16 -10000 0 -0.64 40 40
PTPN1 -0.003 0.029 -10000 0 -0.28 11 11
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.13 0.25 -10000 0 -0.58 225 225
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.11 0.21 -10000 0 -0.48 225 225
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.12 0.23 -10000 0 -0.5 239 239
GRB10 0 0 -10000 0 -10000 0 0
PTPN11 -0.1 0.24 -10000 0 -0.5 239 239
IRS1 -0.13 0.25 -10000 0 -0.54 239 239
IRS2 -0.12 0.28 -10000 0 -0.55 251 251
IGF-1R heterotetramer/IGF1 -0.16 0.29 -10000 0 -0.68 225 225
GRB2 0 0.009 -10000 0 -0.28 1 1
PDPK1 -0.11 0.21 -10000 0 -0.46 226 226
YWHAE 0 0 -10000 0 -10000 0 0
PRKD1 -0.11 0.28 -10000 0 -0.58 237 237
SHC1 0 0 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.066 0.22 -9999 0 -0.81 81 81
GNB1/GNG2 -0.14 0.23 -9999 0 -0.65 114 114
mol:DAG -0.13 0.2 -9999 0 -0.6 102 102
PLCG1 -0.13 0.21 -9999 0 -0.63 102 102
YES1 -0.15 0.23 -9999 0 -0.67 108 108
FZD3 -0.009 0.085 -9999 0 -0.81 11 11
FZD6 -0.007 0.072 -9999 0 -0.81 8 8
G protein -0.13 0.22 -9999 0 -0.64 104 104
MAP3K7 -0.069 0.19 -9999 0 -0.49 100 100
mol:Ca2+ -0.094 0.21 -9999 0 -0.58 102 102
mol:IP3 -0.13 0.2 -9999 0 -0.6 102 102
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 -0.53 106 106
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.16 0.25 -9999 0 -0.45 347 347
CSNK1A1 0 0 -9999 0 -10000 0 0
GNAS -0.15 0.23 -9999 0 -0.41 347 347
GO:0007205 -0.094 0.22 -9999 0 -0.59 102 102
WNT6 -0.17 0.32 -9999 0 -0.72 229 229
WNT4 -0.022 0.12 -9999 0 -0.54 40 40
NFAT1/CK1 alpha -0.16 0.23 -9999 0 -0.57 171 171
GNG2 -0.009 0.085 -9999 0 -0.81 11 11
WNT5A -0.013 0.096 -9999 0 -0.58 23 23
WNT11 -0.18 0.33 -9999 0 -0.78 222 222
CDC42 -0.11 0.24 -9999 0 -0.67 94 94
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.035 0.05 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.081 0.16 -9999 0 -0.4 183 183
JUN -0.049 0.14 -9999 0 -0.42 59 59
HRAS -0.001 0.02 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.15 0.2 -9999 0 -0.54 186 186
RAP1A 0 0 -9999 0 -10000 0 0
FRS2 -0.003 0.028 -9999 0 -0.28 10 10
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.15 0.2 -9999 0 -0.54 186 186
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 -0.5 177 177
RHOA 0 0 -9999 0 -10000 0 0
RAP1A/GTP -0.13 0.18 -9999 0 -0.48 186 186
GRB7 -0.02 0.075 -9999 0 -0.29 70 70
RET51/GFRalpha1/GDNF -0.15 0.2 -9999 0 -0.54 186 186
MAPKKK cascade -0.097 0.17 -9999 0 -0.43 183 183
BCAR1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.12 0.24 -9999 0 -0.58 187 187
lamellipodium assembly -0.081 0.15 -9999 0 -0.37 187 187
RET51/GFRalpha1/GDNF/SHC -0.15 0.2 -9999 0 -0.54 186 186
PIK3CA 0 0.009 -9999 0 -0.28 1 1
RET9/GFRalpha1/GDNF/SHC -0.1 0.19 -9999 0 -0.5 177 177
RET9/GFRalpha1/GDNF/Shank3 -0.1 0.19 -9999 0 -0.5 177 177
MAPK3 -0.12 0.17 -9999 0 -0.45 183 183
DOK1 -0.001 0.013 -9999 0 -0.28 2 2
DOK6 -0.011 0.091 -9999 0 -0.63 18 18
PXN 0 0 -9999 0 -10000 0 0
neurite development -0.11 0.16 -9999 0 -0.54 52 52
DOK5 -0.019 0.12 -9999 0 -0.7 26 26
GFRA1 -0.16 0.31 -9999 0 -0.68 231 231
MAPK8 -0.074 0.13 -9999 0 -0.34 186 186
HRAS/GTP -0.1 0.2 -9999 0 -0.5 183 183
tube development -0.095 0.18 -9999 0 -0.47 177 177
MAPK1 -0.12 0.17 -9999 0 -0.45 183 183
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.064 0.13 -9999 0 -0.34 177 177
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -10000 0 0
PDLIM7 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.14 0.2 -9999 0 -0.52 191 191
SHC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.15 0.2 -9999 0 -0.54 186 186
RET51/GFRalpha1/GDNF/Dok5 -0.16 0.22 -9999 0 -0.56 199 199
PRKCA -0.02 0.12 -9999 0 -0.81 24 24
HRAS/GDP -0.001 0.013 -9999 0 -10000 0 0
CREB1 -0.071 0.15 -9999 0 -0.38 177 177
PIK3R1 -0.006 0.068 -9999 0 -0.81 7 7
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.064 0.13 -9999 0 -0.34 177 177
RET51/GFRalpha1/GDNF/Grb7 -0.16 0.21 -9999 0 -0.55 188 188
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.11 0.16 -9999 0 -0.3 371 371
DOK4 0 0 -9999 0 -10000 0 0
JNK cascade -0.048 0.14 -9999 0 -0.41 59 59
RET9/GFRalpha1/GDNF/FRS2 -0.1 0.19 -9999 0 -0.5 181 181
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 -0.064 0.13 -9999 0 -0.34 177 177
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.081 0.14 -9999 0 -0.36 183 183
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.08 0.14 -9999 0 -0.36 183 183
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.082 0.15 -9999 0 -0.37 183 183
PI3K -0.13 0.25 -9999 0 -0.58 204 204
SOS1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.095 0.18 -9999 0 -0.47 177 177
GRB10 0 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.076 0.13 -9999 0 -0.34 177 177
RET51/GFRalpha1/GDNF/FRS2 -0.15 0.2 -9999 0 -0.54 186 186
GAB1 0 0 -9999 0 -10000 0 0
IRS1 -0.033 0.16 -9999 0 -0.81 41 41
IRS2 -0.033 0.16 -9999 0 -0.81 40 40
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.082 0.15 -9999 0 -0.37 183 183
RET51/GFRalpha1/GDNF/PKC alpha -0.16 0.22 -9999 0 -0.55 208 208
GRB2 0 0.009 -9999 0 -0.28 1 1
PRKACA 0 0 -9999 0 -10000 0 0
GDNF -0.015 0.063 -9999 0 -0.28 54 54
RAC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.17 0.24 -9999 0 -0.61 195 195
Rac1/GTP -0.097 0.18 -9999 0 -0.45 184 184
RET9/GFRalpha1/GDNF -0.11 0.21 -9999 0 -0.55 181 181
GFRalpha1/GDNF -0.13 0.24 -9999 0 -0.62 181 181
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.01 0.04 -9999 0 -0.55 3 3
NFATC2 -0.035 0.16 -9999 0 -0.56 81 81
NFATC3 0.011 0.025 -9999 0 -10000 0 0
CD40LG -0.22 0.37 -9999 0 -0.71 289 289
PTGS2 -0.32 0.47 -9999 0 -0.84 401 401
JUNB 0 0.009 -9999 0 -0.28 1 1
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 -0.007 0.078 -9999 0 -0.82 9 9
mol:Ca2+ -0.006 0.009 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.005 -9999 0 -10000 0 0
FOSL1 -0.008 0.055 -9999 0 -0.32 25 25
CREM 0 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.073 0.15 -9999 0 -0.48 98 98
FOS -0.25 0.38 -9999 0 -0.82 298 298
IFNG -0.21 0.35 -9999 0 -0.68 294 294
AP-1/NFAT1-c-4 -0.31 0.38 -9999 0 -0.82 296 296
FASLG -0.21 0.35 -9999 0 -0.68 283 283
NFAT1-c-4/ICER1 -0.055 0.14 -9999 0 -0.48 84 84
IL2RA -0.21 0.35 -9999 0 -0.69 283 283
FKBP12/FK506 0 0.006 -9999 0 -10000 0 0
CSF2 -0.2 0.34 -9999 0 -0.67 287 287
JunB/Fra1/NFAT1-c-4 -0.052 0.13 -9999 0 -0.46 86 86
IL4 -0.2 0.34 -9999 0 -0.66 290 290
IL2 -0.01 0.024 -9999 0 -10000 0 0
IL3 -0.024 0.027 -9999 0 -10000 0 0
FKBP1A 0 0.009 -9999 0 -0.28 1 1
BATF3 -0.002 0.03 -9999 0 -0.81 1 1
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.001 0.01 -9999 0 -10000 0 0
Nongenotropic Androgen signaling

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 0.011 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.066 0.17 -10000 0 -0.5 131 131
regulation of S phase of mitotic cell cycle -0.04 0.12 -10000 0 -0.35 123 123
GNAO1 -0.032 0.14 -10000 0 -0.48 66 66
HRAS -0.001 0.02 -10000 0 -10000 0 0
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 -0.042 0.16 -10000 0 -0.44 121 121
T-DHT/AR -0.077 0.21 -10000 0 -0.63 122 122
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.004 -10000 0 -0.007 298 298
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.042 0.18 -10000 0 -0.81 51 51
mol:GDP -0.077 0.21 -10000 0 -0.62 123 123
cell proliferation -0.1 0.24 -10000 0 -0.42 301 301
PIK3CA 0 0.009 -10000 0 -0.28 1 1
FOS -0.23 0.42 -10000 0 -0.87 298 298
mol:Ca2+ -0.016 0.028 -10000 0 -0.077 131 131
MAPK3 -0.074 0.2 -10000 0 -0.47 121 121
MAPK1 -0.046 0.12 -10000 0 -0.31 56 56
PIK3R1 -0.006 0.068 -10000 0 -0.81 7 7
mol:IP3 -0.001 0.002 -10000 0 -0.005 298 298
cAMP biosynthetic process 0.012 0.024 -10000 0 -10000 0 0
GNG2 -0.009 0.085 -10000 0 -0.81 11 11
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.005 298 298
HRAS/GTP -0.064 0.15 -10000 0 -0.47 121 121
actin cytoskeleton reorganization -0.003 0.037 -10000 0 -0.43 7 7
SRC 0 0.009 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.005 298 298
PI3K -0.004 0.046 -10000 0 -0.54 7 7
apoptosis 0.11 0.23 0.43 300 -10000 0 300
T-DHT/AR/PELP1 -0.067 0.18 -10000 0 -0.55 121 121
HRAS/GDP -0.074 0.2 -10000 0 -0.6 121 121
CREB1 -0.12 0.24 -10000 0 -0.46 300 300
RAC1-CDC42/GTP -0.003 0.037 -10000 0 -0.44 7 7
AR -0.1 0.27 -10000 0 -0.81 122 122
GNB1 0 0 -10000 0 -10000 0 0
RAF1 -0.042 0.16 -10000 0 -0.45 121 121
RAC1-CDC42/GDP -0.07 0.19 -10000 0 -0.56 121 121
T-DHT/AR/PELP1/Src -0.062 0.16 -10000 0 -0.5 121 121
MAP2K2 -0.042 0.16 -10000 0 -0.44 121 121
T-DHT/AR/PELP1/Src/PI3K -0.043 0.12 -10000 0 -0.35 123 123
GNAZ -0.007 0.072 -10000 0 -0.81 8 8
SHBG 0 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.038 0.1 -10000 0 -0.48 35 35
mol:T-DHT -0.001 0.001 0.001 55 -0.003 243 298
RAC1 0 0 -10000 0 -10000 0 0
GNRH1 0.004 0.064 -10000 0 -0.63 10 10
Gi family/GTP -0.049 0.1 -10000 0 -0.3 84 84
CDC42 0 0 -10000 0 -10000 0 0
ErbB2/ErbB3 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
USP8 0.013 0.01 -9999 0 -10000 0 0
RAS family/GTP -0.11 0.14 -9999 0 -0.4 12 12
NFATC4 -0.089 0.16 -9999 0 -0.36 25 25
ERBB2IP 0.007 0.008 -9999 0 -10000 0 0
HSP90 (dimer) 0 0.009 -9999 0 -0.28 1 1
mammary gland morphogenesis -0.15 0.19 -9999 0 -0.4 363 363
JUN -0.018 0.08 -9999 0 -0.4 5 5
HRAS -0.001 0.02 -9999 0 -10000 0 0
DOCK7 -0.13 0.19 -9999 0 -0.39 162 162
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.18 0.23 -9999 0 -0.48 363 363
AKT1 0.007 0.006 -9999 0 -10000 0 0
BAD 0.018 0.006 -9999 0 -10000 0 0
MAPK10 -0.11 0.14 -9999 0 -0.36 155 155
mol:GTP -0.001 0.001 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.16 0.2 -9999 0 -0.43 363 363
RAF1 -0.081 0.16 -9999 0 -0.43 8 8
ErbB2/ErbB3/neuregulin 2 -0.26 0.26 -9999 0 -0.52 490 490
STAT3 0 0.004 -9999 0 -10000 0 0
cell migration -0.063 0.13 -9999 0 -0.31 79 79
mol:PI-3-4-5-P3 -0.002 0.003 -9999 0 -10000 0 0
cell proliferation -0.14 0.23 -9999 0 -0.51 156 156
FOS -0.16 0.26 -9999 0 -0.54 300 300
NRAS -0.001 0.013 -9999 0 -10000 0 0
mol:Ca2+ -0.15 0.19 -9999 0 -0.4 363 363
MAPK3 -0.11 0.19 -9999 0 -0.48 60 60
MAPK1 -0.11 0.19 -9999 0 -0.48 60 60
JAK2 -0.13 0.19 -9999 0 -0.46 23 23
NF2 -0.007 0.01 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.13 0.17 -9999 0 -0.36 363 363
NRG1 -0.3 0.39 -9999 0 -0.81 362 362
GRB2/SOS1 0 0.006 -9999 0 -10000 0 0
MAPK8 -0.11 0.17 -9999 0 -0.33 365 365
MAPK9 -0.07 0.089 -9999 0 -0.23 12 12
ERBB2 -0.016 0.053 -9999 0 -10000 0 0
ERBB3 -0.002 0.036 -9999 0 -0.81 2 2
SHC1 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
apoptosis 0.015 0.017 -9999 0 -10000 0 0
STAT3 (dimer) 0 0.004 -9999 0 -10000 0 0
RNF41 0.018 0.014 -9999 0 -10000 0 0
FRAP1 0.007 0.005 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.099 0.13 -9999 0 -0.32 23 23
ErbB2/ErbB2/HSP90 (dimer) -0.012 0.041 -9999 0 -10000 0 0
CHRNA1 -0.089 0.16 -9999 0 -0.41 54 54
myelination -0.083 0.16 -9999 0 -0.36 25 25
PPP3CB -0.13 0.17 -9999 0 -0.38 71 71
KRAS -0.001 0.013 -9999 0 -0.28 2 2
RAC1-CDC42/GDP -0.11 0.15 -9999 0 -0.36 24 24
NRG2 -0.4 0.4 -9999 0 -0.81 488 488
mol:GDP -0.13 0.17 -9999 0 -0.36 363 363
SOS1 0 0 -9999 0 -10000 0 0
MAP2K2 -0.072 0.15 -9999 0 -0.44 7 7
SRC 0 0.009 -9999 0 -10000 0 0
mol:cAMP -0.002 0.002 -9999 0 -10000 0 0
PTPN11 -0.14 0.18 -9999 0 -0.46 23 23
MAP2K1 -0.13 0.21 -9999 0 -0.49 153 153
heart morphogenesis -0.15 0.19 -9999 0 -0.4 363 363
RAS family/GDP -0.11 0.14 -9999 0 -0.51 4 4
GRB2 0 0.009 -9999 0 -0.28 1 1
PRKACA -0.011 0.014 -9999 0 -10000 0 0
CHRNE 0.007 0.023 -9999 0 -0.19 5 5
HSP90AA1 0 0.009 -9999 0 -0.28 1 1
activation of caspase activity -0.007 0.006 -9999 0 -10000 0 0
nervous system development -0.15 0.19 -9999 0 -0.4 363 363
CDC42 0 0 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.1 0.23 -10000 0 -0.62 165 165
CRKL -0.04 0.16 -10000 0 -0.36 165 165
mol:PIP3 -0.018 0.037 0.79 2 -10000 0 2
AKT1 0.003 0.023 0.49 2 -10000 0 2
PTK2B 0 0 -10000 0 -10000 0 0
RAPGEF1 -0.03 0.15 -10000 0 -0.33 165 165
RANBP10 0 0 -10000 0 -10000 0 0
PIK3CA 0 0.009 -10000 0 -0.28 1 1
HGF/MET/SHIP2 -0.12 0.25 -10000 0 -0.58 211 211
MAP3K5 -0.021 0.15 -10000 0 -0.53 24 24
HGF/MET/CIN85/CBL/ENDOPHILINS -0.11 0.23 -10000 0 -0.53 211 211
AP1 -0.19 0.27 -10000 0 -0.6 299 299
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
apoptosis -0.24 0.36 -10000 0 -0.78 299 299
STAT3 (dimer) -0.072 0.15 -10000 0 -0.34 211 211
GAB1/CRKL/SHP2/PI3K -0.064 0.13 -10000 0 -0.52 28 28
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.066 0.13 -10000 0 -0.55 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 -0.002 0.036 -10000 0 -0.81 2 2
ELK1 -0.043 0.1 -10000 0 -0.27 165 165
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.046 0.094 -10000 0 -0.42 21 21
PAK1 0.008 0.028 0.45 2 -10000 0 2
HGF/MET/RANBP10 -0.12 0.25 -10000 0 -0.58 211 211
HRAS -0.15 0.3 -10000 0 -0.78 167 167
DOCK1 -0.03 0.15 -10000 0 -0.33 165 165
GAB1 -0.05 0.16 -10000 0 -0.36 211 211
CRK -0.04 0.16 -10000 0 -0.36 165 165
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.15 0.3 -10000 0 -0.72 211 211
JUN -0.007 0.077 -10000 0 -0.81 9 9
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.077 0.15 -10000 0 -0.36 211 211
PIK3R1 -0.006 0.068 -10000 0 -0.81 7 7
cell morphogenesis -0.018 0.17 -10000 0 -0.6 25 25
GRB2/SHC -0.066 0.13 -10000 0 -0.34 165 165
FOS -0.24 0.37 -10000 0 -0.81 298 298
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.043 0.1 -10000 0 -0.27 165 165
HGF/MET/MUC20 -0.13 0.25 -10000 0 -0.59 211 211
cell migration -0.065 0.13 -10000 0 -0.33 165 165
GRB2 0 0.009 -10000 0 -0.28 1 1
CBL 0 0 -10000 0 -10000 0 0
MET/RANBP10 -0.1 0.23 -10000 0 -0.62 165 165
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.077 0.16 -10000 0 -0.36 211 211
MET/MUC20 -0.1 0.23 -10000 0 -0.63 165 165
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 0.25 -10000 0 -0.58 211 211
RAF1 -0.1 0.29 -10000 0 -0.72 165 165
STAT3 -0.073 0.15 -10000 0 -0.34 211 211
cell proliferation -0.061 0.23 -10000 0 -0.49 211 211
RPS6KB1 -0.027 0.053 -10000 0 -0.19 21 21
MAPK3 -0.044 0.092 -10000 0 -0.25 165 165
MAPK1 -0.044 0.092 -10000 0 -0.25 165 165
RANBP9 0 0 -10000 0 -10000 0 0
MAPK8 -0.002 0.13 -10000 0 -0.45 28 28
SRC -0.071 0.14 -10000 0 -0.62 21 21
PI3K -0.07 0.14 -10000 0 -0.35 171 171
MET/Glomulin -0.094 0.21 -10000 0 -0.56 165 165
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 -0.085 0.27 -10000 0 -0.65 165 165
MET -0.14 0.3 -10000 0 -0.81 165 165
MAP4K1 -0.03 0.15 -10000 0 -0.33 166 166
PTK2 0 0 -10000 0 -10000 0 0
MAP2K2 -0.085 0.27 -10000 0 -0.65 165 165
BAD 0.011 0.021 0.45 2 -10000 0 2
MAP2K4 -0.011 0.14 -10000 0 -0.47 25 25
SHP2/GRB2/SOS1/GAB1 -0.096 0.2 -10000 0 -0.51 165 165
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 -0.36 165 165
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.055 0.2 -10000 0 -0.81 67 67
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 0.14 -10000 0 -0.34 165 165
PDPK1 -0.006 0.027 0.57 2 -10000 0 2
HGF/MET/SHIP -0.12 0.25 -10000 0 -0.58 211 211
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.027 0.064 -10000 0 -0.48 3 3
epithelial cell differentiation -0.022 0.064 -10000 0 -0.49 6 6
ITCH 0.009 0.021 -10000 0 -10000 0 0
WWP1 0.007 0.069 -10000 0 -10000 0 0
FYN -0.002 0.036 -10000 0 -0.81 2 2
EGFR -0.3 0.39 -10000 0 -0.8 369 369
PRL -0.004 0.032 -10000 0 -0.28 13 13
neuron projection morphogenesis -0.11 0.21 -10000 0 -0.48 61 61
PTPRZ1 -0.42 0.4 -10000 0 -0.8 522 522
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.16 0.2 -10000 0 -0.53 68 68
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.2 0.24 -10000 0 -0.51 362 362
ADAM17 0.009 0.021 -10000 0 -10000 0 0
ErbB4/ErbB4 0 0.087 -10000 0 -0.51 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.06 0.14 -10000 0 -0.54 63 63
NCOR1 -0.001 0.026 -10000 0 -0.81 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.18 0.23 -10000 0 -0.48 362 362
GRIN2B -0.18 0.26 -10000 0 -0.47 413 413
ErbB4/ErbB2/betacellulin -0.048 0.11 -10000 0 -0.48 53 53
STAT1 -0.005 0.037 -10000 0 -0.28 18 18
HBEGF -0.002 0.036 -10000 0 -0.81 2 2
PRLR -0.006 0.066 -10000 0 -0.81 6 6
E4ICDs/ETO2 -0.036 0.095 -10000 0 -0.56 20 20
axon guidance 0.043 0.12 -10000 0 -0.42 2 2
NEDD4 0.008 0.033 -10000 0 -0.78 1 1
Prolactin receptor/Prolactin receptor/Prolactin -0.007 0.054 -10000 0 -0.62 6 6
CBFA2T3 -0.017 0.11 -10000 0 -0.7 24 24
ErbB4/ErbB2/HBEGF -0.025 0.051 -10000 0 -0.45 2 2
MAPK3 -0.15 0.19 -10000 0 -0.5 65 65
STAT1 (dimer) -0.028 0.064 -10000 0 -0.45 1 1
MAPK1 -0.15 0.19 -10000 0 -0.5 65 65
JAK2 -0.001 0.026 -10000 0 -0.81 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.19 0.23 -10000 0 -0.48 362 362
NRG1 -0.21 0.31 -10000 0 -0.62 362 362
NRG3 -0.057 0.2 -10000 0 -0.81 62 62
NRG2 -0.4 0.4 -10000 0 -0.81 488 488
NRG4 -0.005 0.037 -10000 0 -0.28 18 18
heart development 0.043 0.12 -10000 0 -0.42 2 2
neural crest cell migration -0.19 0.22 -10000 0 -0.47 362 362
ERBB2 0.01 0.056 -10000 0 -10000 0 0
WWOX/E4ICDs -0.026 0.06 -10000 0 -0.45 1 1
SHC1 0 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.2 0.22 -10000 0 -0.47 365 365
apoptosis 0.06 0.15 0.53 63 -10000 0 63
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.27 0.25 -10000 0 -0.52 489 489
ErbB4/ErbB2/epiregulin -0.083 0.15 -10000 0 -0.47 113 113
ErbB4/ErbB4/betacellulin/betacellulin -0.053 0.13 -10000 0 -0.52 54 54
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.022 0.067 -10000 0 -0.58 6 6
MDM2 0.009 0.075 -10000 0 -0.45 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.18 0.23 -10000 0 -0.48 362 362
STAT5A 0.043 0.12 -10000 0 -0.47 7 7
ErbB4/EGFR/neuregulin 1 beta -0.35 0.36 -10000 0 -0.67 501 501
DLG4 0 0 -10000 0 -10000 0 0
GRB2/SHC 0 0.006 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.024 0.057 -10000 0 -0.45 2 2
STAT5A (dimer) -0.022 0.068 -10000 0 -0.6 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.022 0.066 -10000 0 -0.45 4 4
LRIG1 -0.002 0.036 -10000 0 -0.81 2 2
EREG -0.11 0.26 -10000 0 -0.81 113 113
BTC -0.044 0.18 -10000 0 -0.79 55 55
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.043 0.12 -10000 0 -0.42 2 2
ERBB4 -0.031 0.073 -10000 0 -0.52 1 1
STAT5B -0.002 0.044 -10000 0 -0.81 3 3
YAP1 -0.01 0.045 -10000 0 -0.65 4 4
GRB2 0 0.009 -10000 0 -0.28 1 1
ErbB4/ErbB2/neuregulin 4 -0.026 0.052 -10000 0 -10000 0 0
glial cell differentiation 0.024 0.057 0.44 2 -10000 0 2
WWOX -0.001 0.013 -10000 0 -10000 0 0
cell proliferation -0.12 0.24 -10000 0 -0.58 64 64
Aurora B 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
Condensin I complex -0.05 0.059 -9999 0 -10000 0 0
STMN1 -0.1 0.12 -9999 0 -0.35 75 75
Aurora B/RasGAP/Survivin -0.17 0.13 -9999 0 -10000 0 0
Chromosomal passenger complex/Cul3 protein complex -0.15 0.15 -9999 0 -0.32 398 398
BIRC5 -0.2 0.13 -9999 0 -10000 0 0
DES -0.28 0.33 -9999 0 -0.64 454 454
Aurora C/Aurora B/INCENP -0.064 0.072 -9999 0 -0.62 1 1
Aurora B/TACC1 -0.094 0.12 -9999 0 -0.62 34 34
Aurora B/PP2A -0.094 0.091 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.006 0.015 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition -0.003 0.003 -9999 0 -10000 0 0
NDC80 -0.2 0.17 -9999 0 -0.35 510 510
Cul3 protein complex -0.22 0.26 -9999 0 -0.53 398 398
KIF2C -0.036 0.027 -9999 0 -10000 0 0
PEBP1 0.001 0.004 -9999 0 -10000 0 0
KIF20A -0.22 0.12 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.094 0.091 -9999 0 -10000 0 0
SEPT1 -0.007 0.045 -9999 0 -10000 0 0
SMC2 0 0 -9999 0 -10000 0 0
SMC4 -0.004 0.033 -9999 0 -0.28 14 14
NSUN2/NPM1/Nucleolin 0.012 0.015 -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 -0.032 0.04 -9999 0 -10000 0 0
AURKB -0.16 0.15 -9999 0 -10000 0 0
AURKC -0.004 0.041 -9999 0 -0.81 1 1
CDCA8 -0.098 0.14 -9999 0 -0.28 348 348
cytokinesis -0.1 0.069 -9999 0 -10000 0 0
Aurora B/Septin1 -0.085 0.079 -9999 0 -10000 0 0
AURKA -0.13 0.14 -9999 0 -0.28 471 471
INCENP 0.003 0.005 -9999 0 -10000 0 0
KLHL13 -0.32 0.4 -9999 0 -0.81 396 396
BUB1 -0.19 0.13 -9999 0 -0.28 679 679
hSgo1/Aurora B/Survivin -0.24 0.17 -9999 0 -0.39 504 504
EVI5 0.008 0.005 -9999 0 -10000 0 0
RhoA/GTP -0.091 0.092 -9999 0 -10000 0 0
SGOL1 -0.18 0.13 -9999 0 -0.28 640 640
CENPA -0.048 0.055 -9999 0 -10000 0 0
NCAPG -0.15 0.14 -9999 0 -0.28 516 516
Aurora B/HC8 Proteasome -0.094 0.091 -9999 0 -10000 0 0
NCAPD2 -0.002 0.025 -9999 0 -0.28 8 8
Aurora B/PP1-gamma -0.094 0.091 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
NCAPH -0.12 0.14 -9999 0 -0.28 417 417
NPM1 -0.013 0.02 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
KLHL9 -0.002 0.044 -9999 0 -0.81 3 3
mitotic prometaphase -0.006 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.094 0.091 -9999 0 -10000 0 0
PPP1CC 0 0 -9999 0 -10000 0 0
Centraspindlin -0.1 0.1 -9999 0 -0.34 35 35
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.013 0.02 -9999 0 -10000 0 0
MYLK -0.081 0.14 -9999 0 -0.47 113 113
KIF23 -0.088 0.13 -9999 0 -10000 0 0
VIM -0.09 0.1 -9999 0 -0.69 2 2
RACGAP1 -0.011 0.058 -9999 0 -0.28 42 42
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.013 0.02 -9999 0 -10000 0 0
Chromosomal passenger complex -0.072 0.069 -9999 0 -10000 0 0
Chromosomal passenger complex/EVI5 -0.15 0.17 -9999 0 -10000 0 0
TACC1 -0.028 0.15 -9999 0 -0.81 34 34
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
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.22 0.27 -10000 0 -0.54 401 401
fibroblast growth factor receptor signaling pathway -0.22 0.27 -10000 0 -0.54 401 401
LAMA1 -0.096 0.26 -10000 0 -0.81 117 117
PRNP -0.011 0.095 -10000 0 -0.81 14 14
GPC1/SLIT2 -0.065 0.19 -10000 0 -0.62 103 103
SMAD2 -0.019 0.093 -10000 0 -0.48 38 38
GPC1/PrPc/Cu2+ -0.009 0.067 -10000 0 -0.54 15 15
GPC1/Laminin alpha1 -0.075 0.2 -10000 0 -0.62 118 118
TDGF1 -0.008 0.081 -10000 0 -0.76 11 11
CRIPTO/GPC1 -0.008 0.066 -10000 0 -0.62 11 11
APP/GPC1 -0.001 0.023 -10000 0 -0.62 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.018 0.062 -10000 0 -0.53 12 12
FLT1 -0.001 0.026 -10000 0 -0.81 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.021 0.1 -10000 0 -0.53 38 38
SERPINC1 -0.014 0.061 -10000 0 -0.28 50 50
FYN 0.017 0.065 -10000 0 -0.53 13 13
FGR 0.018 0.062 -10000 0 -0.53 12 12
positive regulation of MAPKKK cascade 0.03 0.075 -10000 0 -0.53 13 13
SLIT2 -0.083 0.25 -10000 0 -0.81 102 102
GPC1/NRG -0.23 0.3 -10000 0 -0.62 363 363
NRG1 -0.3 0.39 -10000 0 -0.81 362 362
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.003 0.029 -10000 0 -0.53 2 2
LYN 0.018 0.06 -10000 0 -0.53 11 11
mol:Spermine 0.01 0.024 -10000 0 -0.63 1 1
cell growth -0.22 0.27 -10000 0 -0.54 401 401
BMP signaling pathway 0.002 0.031 0.38 5 -10000 0 5
SRC 0.018 0.06 -10000 0 -0.53 11 11
TGFBR1 0 0.009 -10000 0 -0.28 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.27 0.38 -10000 0 -0.77 352 352
GPC1 -0.002 0.031 -10000 0 -0.38 5 5
TGFBR1 (dimer) 0 0.009 -10000 0 -0.28 1 1
VEGFA -0.003 0.029 -10000 0 -0.28 11 11
BLK -0.006 0.087 -10000 0 -0.57 13 13
HCK 0.017 0.062 -10000 0 -0.53 11 11
FGF2 -0.32 0.4 -10000 0 -0.81 395 395
FGFR1 -0.01 0.086 -10000 0 -0.69 14 14
VEGFR1 homodimer -0.001 0.026 -10000 0 -0.8 1 1
TGFBR2 -0.03 0.15 -10000 0 -0.81 37 37
cell death -0.001 0.023 -10000 0 -0.62 1 1
ATIII/GPC1 -0.01 0.045 -10000 0 -0.63 1 1
PLA2G2A/GPC1 -0.21 0.29 -10000 0 -0.62 326 326
LCK 0.005 0.092 -10000 0 -0.54 24 24
neuron differentiation -0.23 0.3 -10000 0 -0.62 363 363
PrPc/Cu2+ -0.009 0.074 -10000 0 -0.63 14 14
APP 0 0 -10000 0 -10000 0 0
TGFBR2 (dimer) -0.03 0.15 -10000 0 -0.8 37 37
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.11 0.12 -10000 0 -0.34 77 77
NT3 (dimer)/TRKC -0.31 0.37 -10000 0 -0.71 425 425
NT3 (dimer)/TRKB -0.51 0.45 -10000 0 -0.8 630 630
SHC/Grb2/SOS1/GAB1/PI3K -0.002 0.027 -10000 0 -0.33 7 7
RAPGEF1 0 0 -10000 0 -10000 0 0
BDNF -0.07 0.22 -10000 0 -0.81 79 79
PIK3CA 0 0.009 -10000 0 -0.28 1 1
DYNLT1 0 0.009 -10000 0 -0.28 1 1
NTRK1 -0.01 0.063 -10000 0 -0.33 29 29
NTRK2 -0.42 0.4 -10000 0 -0.81 516 516
NTRK3 -0.28 0.38 -10000 0 -0.8 348 348
NT-4/5 (dimer)/TRKB -0.6 0.5 -10000 0 -0.88 680 680
neuron apoptosis 0.24 0.24 0.59 276 -10000 0 276
SHC 2-3/Grb2 -0.27 0.28 -10000 0 -0.66 276 276
SHC1 0 0 -10000 0 -10000 0 0
SHC2 -0.25 0.29 -10000 0 -0.68 261 261
SHC3 -0.25 0.28 -10000 0 -0.66 265 265
STAT3 (dimer) -0.005 0.027 -10000 0 -0.38 3 3
NT3 (dimer)/TRKA -0.26 0.32 -10000 0 -0.62 401 401
RIN/GDP -0.069 0.12 -10000 0 -0.28 68 68
GIPC1 -0.001 0.013 -10000 0 -0.28 2 2
KRAS -0.001 0.013 -10000 0 -0.28 2 2
DNAJA3 -0.14 0.2 -10000 0 -0.43 316 316
RIN/GTP 0 0.008 -10000 0 -10000 0 0
CCND1 0.019 0.069 -10000 0 -1 3 3
MAGED1 -0.001 0.015 -10000 0 -0.28 3 3
PTPN11 0 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.29 0.38 -10000 0 -0.8 351 351
SHC/GRB2/SOS1 0 0.004 -10000 0 -10000 0 0
GRB2 0 0.009 -10000 0 -0.28 1 1
NGF (dimer)/TRKA/MATK -0.028 0.11 -10000 0 -0.55 35 35
TRKA/NEDD4-2 -0.007 0.048 -10000 0 -0.62 4 4
ELMO1 0 0 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0 0 -10000 0 -10000 0 0
NGF -0.014 0.1 -10000 0 -0.81 15 15
HRAS -0.001 0.02 -10000 0 -10000 0 0
DOCK1 0 0 -10000 0 -10000 0 0
GAB2 -0.003 0.026 -10000 0 -0.28 9 9
RIT2 -0.001 0.013 -10000 0 -0.28 2 2
RIT1 0 0 -10000 0 -10000 0 0
FRS2 -0.003 0.028 -10000 0 -0.28 10 10
DNM1 -0.006 0.068 -10000 0 -0.74 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 -0.14 0.2 -10000 0 -0.42 316 316
mol:GDP -0.11 0.18 -10000 0 -0.37 215 215
NGF (dimer) -0.014 0.1 -10000 0 -0.8 15 15
RhoG/GDP 0 0 -10000 0 -10000 0 0
RIT1/GDP -0.065 0.12 -10000 0 -0.27 67 67
TIAM1 -0.001 0.018 -10000 0 -10000 0 0
PIK3R1 -0.006 0.068 -10000 0 -0.81 7 7
BDNF (dimer)/TRKB -0.32 0.31 -10000 0 -0.58 542 542
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 -0.001 0.013 -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 0.3 -10000 0 -0.76 170 170
RAP1/GDP -0.075 0.086 -10000 0 -0.25 39 39
KIDINS220/CRKL 0 0 -10000 0 -10000 0 0
BDNF (dimer) -0.07 0.22 -10000 0 -0.8 79 79
ubiquitin-dependent protein catabolic process -0.015 0.076 -10000 0 -0.53 19 19
Schwann cell development -0.06 0.045 -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 0.001 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.44 0.39 -10000 0 -0.88 375 375
ABL1 0 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
Rap1/GTP -0.11 0.1 -10000 0 -10000 0 0
STAT3 -0.005 0.027 -10000 0 -0.38 3 3
axon guidance -0.41 0.36 -10000 0 -0.81 375 375
MAPK3 -0.024 0.096 -10000 0 -0.5 35 35
MAPK1 -0.024 0.096 -10000 0 -0.5 35 35
CDC42/GDP -0.065 0.12 -10000 0 -0.28 54 54
NTF3 -0.13 0.3 -10000 0 -0.77 170 170
NTF4 -0.29 0.39 -10000 0 -0.81 351 351
NGF (dimer)/TRKA/FAIM -0.014 0.075 -10000 0 -0.53 18 18
PI3K -0.005 0.052 -10000 0 -0.62 7 7
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 -0.16 0.21 -10000 0 -0.45 319 319
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.25 0.34 -10000 0 -0.62 427 427
RGS19 -0.001 0.015 -10000 0 -0.28 3 3
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.003 0.082 -10000 0 -10000 0 0
Rac1/GDP -0.065 0.12 -10000 0 -0.28 51 51
NGF (dimer)/TRKA/GRIT -0.015 0.076 -10000 0 -0.54 18 18
neuron projection morphogenesis -0.11 0.21 -10000 0 -0.41 307 307
NGF (dimer)/TRKA/NEDD4-2 -0.015 0.076 -10000 0 -0.53 19 19
MAP2K1 0 0.003 -10000 0 -10000 0 0
NGFR -0.25 0.37 -10000 0 -0.81 309 309
NGF (dimer)/TRKA/GIPC/GAIP -0.009 0.054 -10000 0 -0.34 24 24
RAS family/GTP/PI3K -0.003 0.029 -10000 0 -0.34 7 7
FRS2 family/SHP2/GRB2/SOS1 -0.001 0.01 -10000 0 -10000 0 0
NRAS -0.001 0.013 -10000 0 -10000 0 0
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
PRKCI 0 0.009 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCZ -0.001 0.026 -10000 0 -0.81 1 1
MAPKKK cascade -0.065 0.11 -10000 0 -0.81 18 18
RASA1 0 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.007 0.044 -10000 0 -0.62 3 3
SQSTM1 0 0.009 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.29 0.28 -10000 0 -0.53 542 542
NGF (dimer)/TRKA/p62/Atypical PKCs -0.012 0.064 -10000 0 -0.45 19 19
MATK -0.022 0.12 -10000 0 -0.81 18 18
NEDD4L -0.001 0.026 -10000 0 -0.81 1 1
RAS family/GDP -0.067 0.08 -10000 0 -0.23 8 8
NGF (dimer)/TRKA -0.15 0.22 -10000 0 -0.46 316 316
Rac1/GTP -0.13 0.14 -10000 0 -0.34 237 237
FRS2 family/SHP2/CRK family -0.001 0.01 -10000 0 -10000 0 0
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.11 0.2 -9999 0 -0.6 121 121
SMAD6-7/SMURF1 -0.001 0.017 -9999 0 -0.53 1 1
NOG -0.023 0.12 -9999 0 -0.81 22 22
SMAD9 -0.11 0.26 -9999 0 -0.78 106 106
SMAD4 -0.001 0.026 -9999 0 -0.81 1 1
SMAD5 -0.075 0.18 -9999 0 -0.55 83 83
BMP7/USAG1 -0.35 0.35 -9999 0 -0.68 509 509
SMAD5/SKI -0.087 0.16 -9999 0 -0.54 70 70
SMAD1 0.026 0.03 -9999 0 -10000 0 0
BMP2 -0.14 0.31 -9999 0 -0.8 175 175
SMAD1/SMAD1/SMAD4 -0.002 0.015 -9999 0 -10000 0 0
BMPR1A -0.002 0.036 -9999 0 -0.81 2 2
BMPR1B -0.13 0.17 -9999 0 -0.81 23 23
BMPR1A-1B/BAMBI -0.09 0.14 -9999 0 -0.61 54 54
AHSG -0.003 0.028 -9999 0 -10000 0 0
CER1 -0.001 0.015 -9999 0 -10000 0 0
BMP2-4/CER1 -0.13 0.25 -9999 0 -0.58 220 220
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.1 0.2 -9999 0 -0.54 123 123
BMP2-4 (homodimer) -0.15 0.28 -9999 0 -0.66 220 220
RGMB -0.001 0.026 -9999 0 -0.81 1 1
BMP6/BMPR2/BMPR1A-1B -0.096 0.16 -9999 0 -0.55 99 99
RGMA -0.11 0.28 -9999 0 -0.81 133 133
SMURF1 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.11 0.2 -9999 0 -0.62 97 97
BMP2-4/USAG1 -0.38 0.37 -9999 0 -0.66 571 571
SMAD6/SMURF1/SMAD5 -0.087 0.16 -9999 0 -0.54 70 70
SOSTDC1 -0.4 0.4 -9999 0 -0.8 489 489
BMP7/BMPR2/BMPR1A-1B -0.1 0.17 -9999 0 -0.58 97 97
SKI 0 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.063 0.22 -9999 0 -0.8 76 76
HFE2 -0.002 0.025 -9999 0 -10000 0 0
ZFYVE16 0 0 -9999 0 -10000 0 0
MAP3K7 0 0.009 -9999 0 -0.28 1 1
BMP2-4/CHRD -0.14 0.27 -9999 0 -0.62 222 222
SMAD5/SMAD5/SMAD4 -0.087 0.16 -9999 0 -0.54 71 71
MAPK1 0 0 -9999 0 -10000 0 0
TAK1/TAB family -0.086 0.17 -9999 0 -0.53 94 94
BMP7 (homodimer) -0.075 0.22 -9999 0 -0.8 78 78
NUP214 0 0 -9999 0 -10000 0 0
BMP6/FETUA -0.05 0.17 -9999 0 -0.62 76 76
SMAD1/SKI -0.004 0.013 -9999 0 -10000 0 0
SMAD6 -0.001 0.026 -9999 0 -0.81 1 1
CTDSP2 0 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.13 0.25 -9999 0 -0.58 220 220
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.037 0.12 -9999 0 -0.81 12 12
BMPR2 (homodimer) 0 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.001 0.01 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.088 0.12 -9999 0 -0.63 25 25
CHRDL1 -0.55 0.38 -9999 0 -0.81 673 673
ENDOFIN/SMAD1 -0.004 0.013 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.003 0.014 -9999 0 -10000 0 0
SMAD6/SMURF1 0 0 -9999 0 -10000 0 0
BAMBI -0.035 0.14 -9999 0 -0.5 70 70
SMURF2 0 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.48 0.38 -9999 0 -0.69 690 690
BMP2-4/GREM1 -0.15 0.26 -9999 0 -0.59 224 224
SMAD7 0 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.098 0.24 -9999 0 -0.74 106 106
SMAD1/SMAD6 -0.004 0.013 -9999 0 -10000 0 0
TAK1/SMAD6 0 0.006 -9999 0 -10000 0 0
BMP7 -0.075 0.22 -9999 0 -0.81 78 78
BMP6 -0.063 0.22 -9999 0 -0.81 76 76
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.099 0.19 -9999 0 -0.6 94 94
PPM1A 0 0 -9999 0 -10000 0 0
SMAD1/SMURF2 -0.004 0.013 -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 0.02 -9999 0 -10000 0 0
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 -0.58 156 156
CHRD -0.032 0.13 -9999 0 -0.41 78 78
BMPR2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.13 0.24 -9999 0 -0.54 181 181
BMP4 -0.053 0.2 -9999 0 -0.8 66 66
FST -0.035 0.16 -9999 0 -0.76 46 46
BMP2-4/NOG -0.14 0.26 -9999 0 -0.59 233 233
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.092 0.16 -9999 0 -0.54 97 97
Visual signal transduction: Rods

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
mol:K + 0 0 -9999 0 -10000 0 0
GNAT1/GTP -0.003 0.022 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.01 0.037 -9999 0 -0.3 2 2
PDE6G/GNAT1/GTP -0.008 0.034 -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 0.033 -9999 0 -0.28 14 14
GRK1 -0.003 0.028 -9999 0 -0.28 10 10
CNG Channel -0.14 0.2 -9999 0 -0.44 297 297
mol:Na + -0.14 0.19 -9999 0 -0.43 291 291
mol:ADP -0.003 0.028 -9999 0 -0.28 10 10
RGS9-1/Gbeta5/R9AP -0.065 0.17 -9999 0 -0.54 102 102
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.14 0.2 -9999 0 -0.44 291 291
CNGB1 -0.015 0.062 -9999 0 -0.28 52 52
RDH5 -0.48 0.4 -9999 0 -0.81 594 594
SAG -0.014 0.061 -9999 0 -10000 0 0
mol:Ca2+ -0.13 0.18 -9999 0 -0.41 290 290
Na + (4 Units) -0.12 0.18 -9999 0 -0.4 290 290
RGS9 -0.087 0.25 -9999 0 -0.75 115 115
GNB1/GNGT1 -0.028 0.064 -9999 0 -10000 0 0
GNAT1/GDP -0.057 0.14 -9999 0 -0.47 102 102
GUCY2D -0.006 0.049 -9999 0 -0.81 2 2
GNGT1 -0.044 0.1 -9999 0 -0.28 155 155
GUCY2F -0.001 0.013 -9999 0 -0.28 2 2
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.018 0.071 -9999 0 -0.46 20 20
mol:11-cis-retinal -0.48 0.39 -9999 0 -0.8 594 594
mol:cGMP -0.01 0.047 -9999 0 -0.47 7 7
GNB1 0 0 -9999 0 -10000 0 0
Rhodopsin -0.38 0.3 -9999 0 -0.62 594 594
SLC24A1 0 0 -9999 0 -10000 0 0
CNGA1 -0.24 0.37 -9999 0 -0.8 292 292
Metarhodopsin II -0.003 0.02 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.01 0.05 -9999 0 -0.5 7 7
RGS9BP -0.016 0.065 -9999 0 -10000 0 0
Metarhodopsin II/Transducin -0.008 0.018 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.008 0.044 -9999 0 -0.5 5 5
PDE6A/B -0.017 0.09 -9999 0 -0.62 20 20
mol:Pi -0.064 0.16 -9999 0 -0.54 102 102
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.021 0.047 -9999 0 -10000 0 0
PDE6B -0.017 0.11 -9999 0 -0.76 22 22
PDE6A -0.006 0.04 -9999 0 -0.28 21 21
PDE6G -0.012 0.056 -9999 0 -10000 0 0
RHO -0.004 0.033 -9999 0 -0.28 14 14
PDE6 -0.065 0.15 -9999 0 -0.46 118 118
GUCA1A -0.012 0.056 -9999 0 -0.28 41 41
GC2/GCAP Family -0.008 0.044 -9999 0 -0.5 5 5
GUCA1C 0 0.009 -9999 0 -0.28 1 1
GUCA1B -0.004 0.057 -9999 0 -0.81 5 5
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.097 0.18 -10000 0 -0.48 177 177
ER alpha/Gai/GDP/Gbeta gamma -0.091 0.19 -10000 0 -0.48 157 157
AKT1 -0.098 0.32 -10000 0 -0.84 149 149
PIK3CA 0 0.009 -10000 0 -0.28 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.12 0.31 -10000 0 -0.86 147 147
mol:Ca2+ -0.027 0.15 -10000 0 -0.47 78 78
IGF1R -0.022 0.12 -10000 0 -0.62 36 36
E2/ER alpha (dimer)/Striatin -0.1 0.2 -10000 0 -0.55 157 157
SHC1 0 0 -10000 0 -10000 0 0
apoptosis 0.091 0.3 0.8 149 -10000 0 149
RhoA/GTP -0.07 0.14 -10000 0 -0.4 147 147
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.091 0.21 -10000 0 -0.55 154 154
regulation of stress fiber formation 0.02 0.14 0.47 6 -10000 0 6
E2/ERA-ERB (dimer) -0.11 0.21 -10000 0 -0.55 170 170
KRAS -0.001 0.013 -10000 0 -0.28 2 2
G13/GTP -0.089 0.18 -10000 0 -0.5 147 147
pseudopodium formation -0.02 0.14 -10000 0 -0.47 6 6
E2/ER alpha (dimer)/PELP1 -0.098 0.19 -10000 0 -0.54 147 147
GRB2 0 0.009 -10000 0 -0.28 1 1
GNG2 -0.009 0.085 -10000 0 -0.81 11 11
GNAO1 -0.032 0.14 -10000 0 -0.48 66 66
HRAS -0.001 0.02 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.06 0.22 -10000 0 -0.55 156 156
E2/ER beta (dimer) -0.015 0.096 -10000 0 -0.63 24 24
mol:GDP -0.087 0.21 -10000 0 -0.54 170 170
mol:NADP -0.06 0.22 -10000 0 -0.55 156 156
PIK3R1 -0.006 0.068 -10000 0 -0.81 7 7
mol:IP3 -0.029 0.16 -10000 0 -0.49 78 78
IGF-1R heterotetramer -0.022 0.12 -10000 0 -0.62 36 36
PLCB1 -0.063 0.15 -10000 0 -0.51 77 77
PLCB2 -0.035 0.095 -10000 0 -0.67 14 14
IGF1 -0.18 0.33 -10000 0 -0.81 215 215
mol:L-citrulline -0.06 0.22 -10000 0 -0.55 156 156
RHOA 0 0 -10000 0 -10000 0 0
Gai/GDP -0.04 0.15 -10000 0 -0.86 25 25
JNK cascade -0.015 0.096 -10000 0 -0.62 24 24
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 -0.02 0.12 -10000 0 -0.81 24 24
GNAQ -0.002 0.036 -10000 0 -0.81 2 2
ESR1 -0.15 0.29 -10000 0 -0.57 264 264
Gq family/GDP/Gbeta gamma -0.007 0.072 -10000 0 -0.72 6 6
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.024 0.13 -10000 0 -0.32 147 147
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.091 0.21 -10000 0 -0.55 154 154
GNAZ -0.007 0.072 -10000 0 -0.81 8 8
E2/ER alpha (dimer) -0.12 0.22 -10000 0 -0.63 147 147
STRN -0.01 0.088 -10000 0 -0.81 12 12
GNAL -0.19 0.34 -10000 0 -0.81 233 233
PELP1 0 0 -10000 0 -10000 0 0
MAPK11 0.003 0.093 -10000 0 -0.56 26 26
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.042 0.18 -10000 0 -0.81 51 51
HBEGF -0.069 0.19 -10000 0 -0.45 160 160
cAMP biosynthetic process -0.19 0.26 -10000 0 -0.52 353 353
SRC -0.05 0.2 -10000 0 -0.45 157 157
PI3K -0.005 0.052 -10000 0 -0.62 7 7
GNB1 0 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.079 0.19 -10000 0 -0.48 162 162
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.15 0.23 -10000 0 -0.55 194 194
Gs family/GTP -0.2 0.27 -10000 0 -0.53 353 353
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.011 -10000 0 -10000 0 0
vasodilation -0.056 0.21 -10000 0 -0.52 156 156
mol:DAG -0.029 0.16 -10000 0 -0.49 78 78
Gs family/GDP/Gbeta gamma -0.16 0.23 -10000 0 -0.52 211 211
MSN -0.023 0.15 -10000 0 -0.52 6 6
Gq family/GTP -0.038 0.1 -10000 0 -0.66 15 15
mol:PI-3-4-5-P3 -0.096 0.31 -10000 0 -0.82 147 147
NRAS -0.001 0.013 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.056 0.21 0.52 156 -10000 0 156
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
RhoA/GDP -0.08 0.19 -10000 0 -0.5 170 170
NOS3 -0.064 0.24 -10000 0 -0.58 156 156
GNA11 -0.002 0.036 -10000 0 -0.81 2 2
MAPKKK cascade -0.064 0.26 -10000 0 -0.64 157 157
E2/ER alpha (dimer)/PELP1/Src -0.096 0.22 -10000 0 -0.58 154 154
ruffle organization -0.02 0.14 -10000 0 -0.47 6 6
ROCK2 -0.07 0.14 -10000 0 -0.45 20 20
GNA14 -0.015 0.09 -10000 0 -0.44 33 33
GNA15 -0.003 0.035 -10000 0 -0.34 8 8
GNA13 0 0 -10000 0 -10000 0 0
MMP9 -0.094 0.2 -10000 0 -0.53 117 117
MMP2 -0.043 0.19 -10000 0 -0.43 161 161
IL6-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
BCL2L1 -0.059 0.22 -9999 0 -0.62 55 55
CRP -0.064 0.22 -9999 0 -0.63 54 54
cell cycle arrest -0.077 0.24 -9999 0 -0.67 73 73
TIMP1 -0.057 0.2 -9999 0 -0.57 51 51
IL6ST -0.073 0.25 -9999 0 -0.8 105 105
Rac1/GDP -0.14 0.21 -9999 0 -0.66 76 76
AP1 -0.13 0.24 -9999 0 -0.49 245 245
GAB2 0.003 0.028 -9999 0 -0.28 9 9
TNFSF11 -0.069 0.22 -9999 0 -0.61 61 61
HSP90B1 0.016 0.047 -9999 0 -10000 0 0
GAB1 0 0.002 -9999 0 -10000 0 0
MAPK14 -0.12 0.24 -9999 0 -0.73 79 79
AKT1 0.04 0.034 -9999 0 -10000 0 0
FOXO1 0.048 0.056 -9999 0 -0.42 11 11
MAP2K6 -0.14 0.25 -9999 0 -0.68 99 99
mol:GTP 0 0.001 -9999 0 -10000 0 0
MAP2K4 -0.08 0.22 -9999 0 -0.63 74 74
MITF -0.13 0.25 -9999 0 -0.48 201 201
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 7 7
CEBPB 0.015 0.007 -9999 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.053 0.07 -9999 0 -10000 0 0
STAT3 -0.085 0.26 -9999 0 -0.73 72 72
STAT1 -0.013 0.022 -9999 0 -10000 0 0
CEBPD -0.061 0.22 -9999 0 -0.65 55 55
PIK3CA 0.012 0.009 -9999 0 -0.28 1 1
PI3K -0.005 0.052 -9999 0 -0.62 7 7
JUN -0.007 0.077 -9999 0 -0.81 9 9
PIAS3/MITF -0.15 0.21 -9999 0 -0.68 79 79
MAPK11 -0.12 0.25 -9999 0 -0.74 79 79
STAT3 (dimer)/FOXO1 -0.029 0.22 -9999 0 -0.57 66 66
GRB2/SOS1/GAB family -0.14 0.19 -9999 0 -0.72 55 55
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.15 0.25 -9999 0 -0.46 244 244
GRB2 0 0.009 -9999 0 -0.28 1 1
JAK2 -0.001 0.026 -9999 0 -0.81 1 1
LBP -0.22 0.44 -9999 0 -0.95 246 246
PIK3R1 0.003 0.069 -9999 0 -0.81 7 7
JAK1 0.001 0.004 -9999 0 -10000 0 0
MYC -0.073 0.26 -9999 0 -0.83 59 59
FGG -0.068 0.22 -9999 0 -0.62 60 60
macrophage differentiation -0.077 0.24 -9999 0 -0.67 73 73
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.23 0.28 -9999 0 -0.51 442 442
JUNB -0.058 0.21 -9999 0 -0.59 60 60
FOS -0.24 0.37 -9999 0 -0.81 298 298
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.15 0.26 -9999 0 -0.4 402 402
STAT1/PIAS1 -0.14 0.22 -9999 0 -0.5 149 149
GRB2/SOS1/GAB family/SHP2/PI3K 0 0.024 -9999 0 -10000 0 0
STAT3 (dimer) -0.08 0.25 -9999 0 -0.71 70 70
PRKCD -0.055 0.22 -9999 0 -0.6 68 68
IL6R -0.026 0.14 -9999 0 -0.81 33 33
SOCS3 -0.12 0.24 -9999 0 -0.76 70 70
gp130 (dimer)/JAK1/JAK1/LMO4 -0.049 0.17 -9999 0 -0.53 108 108
Rac1/GTP -0.14 0.2 -9999 0 -0.64 81 81
HCK -0.003 0.029 -9999 0 -10000 0 0
MAPKKK cascade -0.002 0.071 -9999 0 -10000 0 0
bone resorption -0.065 0.21 -9999 0 -0.58 62 62
IRF1 -0.06 0.22 -9999 0 -0.62 58 58
mol:GDP -0.12 0.24 -9999 0 -0.48 189 189
SOS1 0 0.003 -9999 0 -10000 0 0
VAV1 -0.13 0.25 -9999 0 -0.49 188 188
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.17 0.24 -9999 0 -0.8 75 75
PTPN11 -0.013 0.019 -9999 0 -10000 0 0
IL6/IL6RA -0.24 0.32 -9999 0 -0.64 377 377
gp130 (dimer)/TYK2/TYK2/LMO4 -0.052 0.17 -9999 0 -0.53 108 108
gp130 (dimer)/JAK2/JAK2/LMO4 -0.052 0.17 -9999 0 -0.54 108 108
IL6 -0.29 0.4 -9999 0 -0.8 363 363
PIAS3 0 0 -9999 0 -10000 0 0
PTPRE 0.003 0.027 -9999 0 -0.81 1 1
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 -0.4 441 441
LMO4 0.009 0.051 -9999 0 -0.45 9 9
STAT3 (dimer)/PIAS3 -0.14 0.21 -9999 0 -0.76 63 63
MCL1 0.052 0.026 -9999 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.004 0.043 -9999 0 -0.62 4 4
alphaV beta3 Integrin -0.23 0.28 -9999 0 -0.55 407 407
PTK2 -0.088 0.19 -9999 0 -0.65 35 35
IGF1R -0.022 0.12 -9999 0 -0.62 36 36
PI4KB 0 0 -9999 0 -10000 0 0
MFGE8 -0.012 0.094 -9999 0 -0.64 19 19
SRC 0 0.009 -9999 0 -10000 0 0
CDKN1B -0.086 0.12 -9999 0 -0.87 8 8
VEGFA -0.003 0.029 -9999 0 -0.28 11 11
ILK -0.083 0.11 -9999 0 -0.4 20 20
ROCK1 -0.001 0.026 -9999 0 -0.81 1 1
AKT1 -0.073 0.096 -9999 0 -0.72 5 5
PTK2B -0.016 0.088 -9999 0 -0.5 29 29
alphaV/beta3 Integrin/JAM-A -0.2 0.24 -9999 0 -0.48 410 410
CBL 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.016 0.09 -9999 0 -0.54 28 28
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.14 0.26 -9999 0 -0.56 239 239
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.01 0.056 -9999 0 -0.46 6 6
alphaV/beta3 Integrin/Syndecan-1 -0.026 0.097 -9999 0 -0.55 29 29
PI4KA 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.33 0.36 -9999 0 -0.64 483 483
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.28 1 1
alphaV/beta3 Integrin/Osteopontin -0.052 0.1 -9999 0 -0.55 28 28
RPS6KB1 -0.3 0.32 -9999 0 -0.7 314 314
TLN1 0 0 -9999 0 -10000 0 0
MAPK3 -0.33 0.39 -9999 0 -0.77 407 407
GPR124 -0.009 0.085 -9999 0 -0.81 11 11
MAPK1 -0.33 0.39 -9999 0 -0.77 407 407
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 -0.006 0.068 -9999 0 -0.81 7 7
alphaV/beta3 Integrin/Tumstatin -0.11 0.22 -9999 0 -0.54 205 205
cell adhesion -0.021 0.1 -9999 0 -0.52 38 38
ANGPTL3 -0.001 0.02 -9999 0 -0.28 5 5
VEGFR2 homodimer/VEGFA homodimer/Src -0.004 0.037 -9999 0 -0.53 4 4
IGF-1R heterotetramer -0.022 0.12 -9999 0 -0.62 36 36
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 -0.03 0.15 -9999 0 -0.81 37 37
ITGB3 -0.024 0.14 -9999 0 -0.81 28 28
IGF1 -0.18 0.33 -9999 0 -0.81 215 215
RAC1 0 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.021 0.11 -9999 0 -0.6 34 34
apoptosis 0 0 -9999 0 -10000 0 0
CD47 -0.001 0.026 -9999 0 -0.81 1 1
alphaV/beta3 Integrin/CD47 -0.016 0.09 -9999 0 -0.53 29 29
VCL 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.043 0.17 -9999 0 -0.67 60 60
CSF1 -0.006 0.068 -9999 0 -0.81 7 7
PIK3C2A -0.084 0.11 -9999 0 -0.81 6 6
PI4 Kinase/Pyk2 -0.17 0.21 -9999 0 -0.59 59 59
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.017 0.094 -9999 0 -0.54 29 29
FAK1/Vinculin -0.064 0.15 -9999 0 -0.5 33 33
alphaV beta3/Integrin/ppsTEM5 -0.021 0.12 -9999 0 -0.6 34 34
RHOA 0 0 -9999 0 -10000 0 0
VTN -0.023 0.09 -9999 0 -0.32 73 73
BCAR1 0 0 -9999 0 -10000 0 0
FGF2 -0.32 0.4 -9999 0 -0.81 395 395
F11R -0.23 0.31 -9999 0 -0.62 395 395
alphaV/beta3 Integrin/Lactadherin -0.023 0.12 -9999 0 -0.58 37 37
alphaV/beta3 Integrin/TGFBR2 -0.035 0.16 -9999 0 -0.66 51 51
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.003 0.041 -9999 0 -0.48 7 7
HSP90AA1 0 0.009 -9999 0 -0.28 1 1
alphaV/beta3 Integrin/Talin -0.014 0.082 -9999 0 -0.49 28 28
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.11 0.14 -9999 0 -0.28 398 398
alphaV/beta3 Integrin/Pyk2 -0.016 0.089 -9999 0 -0.5 29 29
SDC1 -0.021 0.076 -9999 0 -0.81 1 1
VAV3 -0.008 0.054 -9999 0 -0.45 14 14
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 -0.033 0.16 -9999 0 -0.81 41 41
FAK1/Paxillin -0.064 0.15 -9999 0 -0.5 31 31
cell migration -0.05 0.14 -9999 0 -0.45 31 31
ITGAV 0 0 -9999 0 -10000 0 0
PI3K -0.18 0.22 -9999 0 -0.44 412 412
SPP1 -0.075 0.12 -9999 0 -0.28 265 265
KDR -0.003 0.051 -9999 0 -0.81 4 4
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 -0.15 0.31 -9999 0 -0.81 181 181
angiogenesis -0.3 0.39 -9999 0 -0.74 409 409
Rac1/GTP -0.007 0.049 -9999 0 -0.41 14 14
EDIL3 -0.044 0.18 -9999 0 -0.68 64 64
cell proliferation -0.035 0.15 -9999 0 -0.66 51 51
Signaling events mediated by PTP1B

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
PDGFRB -0.003 0.051 -10000 0 -0.81 4 4
Jak2/Leptin Receptor -0.16 0.24 -10000 0 -0.54 266 266
PTP1B/AKT1 -0.071 0.11 -10000 0 -0.34 105 105
FYN -0.002 0.036 -10000 0 -0.81 2 2
p210 bcr-abl/PTP1B -0.073 0.13 -10000 0 -0.38 111 111
EGFR -0.3 0.39 -10000 0 -0.81 369 369
EGF/EGFR -0.3 0.32 -10000 0 -0.58 505 505
CSF1 -0.006 0.068 -10000 0 -0.81 7 7
AKT1 0 0.001 -10000 0 -10000 0 0
INSR 0 0.009 -10000 0 -0.28 1 1
PTP1B/N-cadherin -0.096 0.12 -10000 0 -0.37 111 111
Insulin Receptor/Insulin -0.05 0.081 -10000 0 -0.43 16 16
HCK -0.003 0.029 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
TYK2 -0.061 0.12 -10000 0 -0.36 106 106
EGF -0.17 0.33 -10000 0 -0.81 206 206
YES1 -0.001 0.026 -10000 0 -0.81 1 1
CAV1 -0.18 0.24 -10000 0 -0.51 264 264
TXN -0.001 0.015 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.088 0.15 -10000 0 -0.41 136 136
cell migration 0.073 0.13 0.38 111 -10000 0 111
STAT3 0 0 -10000 0 -10000 0 0
PRLR -0.004 0.066 -10000 0 -0.81 6 6
ITGA2B -0.017 0.076 -10000 0 -0.6 5 5
CSF1R -0.001 0.027 -10000 0 -0.54 2 2
Prolactin Receptor/Prolactin -0.006 0.054 -10000 0 -0.62 6 6
FGR -0.001 0.027 -10000 0 -0.81 1 1
PTP1B/p130 Cas -0.076 0.12 -10000 0 -0.36 105 105
Crk/p130 Cas -0.07 0.11 -10000 0 -0.36 84 84
DOK1 -0.047 0.12 -10000 0 -0.32 106 106
JAK2 -0.043 0.079 -10000 0 -0.34 20 20
Jak2/Leptin Receptor/Leptin -0.37 0.19 -10000 0 -0.5 506 506
PIK3R1 -0.006 0.068 -10000 0 -0.81 7 7
PTPN1 -0.073 0.13 -10000 0 -0.38 111 111
LYN 0 0 -10000 0 -10000 0 0
CDH2 -0.054 0.11 -10000 0 -0.28 186 186
SRC -0.014 0.047 -10000 0 -10000 0 0
ITGB3 -0.024 0.14 -10000 0 -0.81 28 28
CAT1/PTP1B -0.086 0.17 -10000 0 -0.44 101 101
CAPN1 0.001 0.002 -10000 0 -10000 0 0
CSK 0 0 -10000 0 -10000 0 0
PI3K -0.043 0.087 -10000 0 -0.57 12 12
mol:H2O2 -0.006 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.33 0.16 -10000 0 -0.44 498 498
negative regulation of transcription -0.042 0.079 -10000 0 -0.34 20 20
FCGR2A 0 0.009 -10000 0 -10000 0 0
FER -0.01 0.09 -10000 0 -0.82 12 12
alphaIIb/beta3 Integrin -0.029 0.12 -10000 0 -0.63 31 31
BLK -0.04 0.1 -10000 0 -0.81 3 3
Insulin Receptor/Insulin/Shc 0 0.005 -10000 0 -10000 0 0
RHOA 0.001 0.002 -10000 0 -10000 0 0
LEPR -0.21 0.36 -10000 0 -0.81 261 261
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0 0.009 -10000 0 -0.28 1 1
mol:NADPH -0.005 0.005 -10000 0 -10000 0 0
TRPV6 -0.031 0.13 -10000 0 -0.46 20 20
PRL -0.004 0.032 -10000 0 -0.28 13 13
SOCS3 0.017 0.12 -10000 0 -1.5 6 6
SPRY2 -0.095 0.26 -10000 0 -0.82 115 115
Insulin Receptor/Insulin/IRS1 -0.023 0.11 -10000 0 -0.55 41 41
CSF1/CSF1R -0.073 0.12 -10000 0 -0.36 109 109
Ras protein signal transduction 0.037 0.036 -10000 0 -0.19 1 1
IRS1 -0.033 0.16 -10000 0 -0.81 41 41
INS 0 0.001 -10000 0 -10000 0 0
LEP -0.65 0.32 -10000 0 -0.81 797 797
STAT5B -0.06 0.11 -10000 0 -0.31 110 110
STAT5A -0.061 0.11 -10000 0 -0.32 112 112
GRB2 0 0.009 -10000 0 -0.28 1 1
PDGFB-D/PDGFRB -0.078 0.12 -10000 0 -0.38 107 107
CSN2 0.019 0.034 -10000 0 -10000 0 0
PIK3CA 0 0.009 -10000 0 -0.28 1 1
LAT -0.015 0.053 -10000 0 -0.58 2 2
YBX1 -0.001 0.014 -10000 0 -10000 0 0
LCK -0.02 0.1 -10000 0 -0.81 13 13
SHC1 0 0 -10000 0 -10000 0 0
NOX4 -0.004 0.046 -10000 0 -0.38 11 11
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.023 0.063 -9999 0 -0.58 10 10
alphaM/beta2 Integrin/GPIbA -0.025 0.06 -9999 0 -0.56 8 8
alphaM/beta2 Integrin/proMMP-9 -0.08 0.078 -9999 0 -0.42 5 5
PLAUR -0.021 0.074 -9999 0 -10000 0 0
HMGB1 -0.013 0.018 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.018 0.028 -9999 0 -10000 0 0
AGER -0.015 0.042 -9999 0 -0.86 2 2
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 -0.075 0.097 -9999 0 -0.4 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.14 -9999 0 -0.28 444 444
CYR61 -0.044 0.18 -9999 0 -0.81 54 54
TLN1 0 0 -9999 0 -10000 0 0
Rap1/GTP -0.056 0.11 -9999 0 -0.53 20 20
RHOA 0 0 -9999 0 -10000 0 0
P-selectin oligomer -0.19 0.34 -9999 0 -0.8 233 233
MYH2 -0.067 0.16 -9999 0 -0.4 109 109
MST1R -0.011 0.085 -9999 0 -0.54 20 20
leukocyte activation during inflammatory response -0.31 0.23 -9999 0 -0.48 625 625
APOB -0.51 0.39 -9999 0 -0.81 625 625
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.008 0.081 -9999 0 -0.81 10 10
JAM3 -0.006 0.068 -9999 0 -0.81 7 7
GP1BA -0.012 0.079 -9999 0 -0.81 7 7
alphaM/beta2 Integrin/CTGF -0.025 0.071 -9999 0 -0.59 13 13
alphaM/beta2 Integrin -0.07 0.13 -9999 0 -0.36 89 89
JAM3 homodimer -0.006 0.068 -9999 0 -0.8 7 7
ICAM2 -0.004 0.057 -9999 0 -0.81 5 5
ICAM1 -0.004 0.034 -9999 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.059 0.14 -9999 0 -0.31 162 162
cell adhesion -0.025 0.059 -9999 0 -0.56 8 8
NFKB1 -0.14 0.18 -9999 0 -0.66 14 14
THY1 -0.002 0.023 -9999 0 -0.28 7 7
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.35 0.26 -9999 0 -0.55 625 625
alphaM/beta2 Integrin/LRP/tPA -0.034 0.11 -9999 0 -0.55 41 41
IL6 -0.31 0.49 -9999 0 -0.94 362 362
ITGB2 -0.017 0.036 -9999 0 -0.29 13 13
elevation of cytosolic calcium ion concentration -0.024 0.048 -9999 0 -0.38 1 1
alphaM/beta2 Integrin/JAM2/JAM3 -0.044 0.13 -9999 0 -0.56 58 58
JAM2 -0.046 0.19 -9999 0 -0.81 56 56
alphaM/beta2 Integrin/ICAM1 -0.022 0.084 -9999 0 -0.55 20 20
alphaM/beta2 Integrin/uPA/Plg -0.019 0.032 -9999 0 -10000 0 0
RhoA/GTP -0.085 0.17 -9999 0 -0.38 198 198
positive regulation of phagocytosis -0.048 0.089 -9999 0 -0.46 17 17
Ron/MSP -0.016 0.1 -9999 0 -0.68 21 21
alphaM/beta2 Integrin/uPAR/uPA -0.024 0.048 -9999 0 -0.38 1 1
alphaM/beta2 Integrin/uPAR -0.028 0.046 -9999 0 -0.42 1 1
PLAU -0.008 0.046 -9999 0 -0.28 28 28
PLAT -0.029 0.15 -9999 0 -0.81 34 34
actin filament polymerization -0.064 0.16 -9999 0 -0.38 113 113
MST1 -0.011 0.093 -9999 0 -0.71 16 16
alphaM/beta2 Integrin/lipoprotein(a) -0.31 0.23 -9999 0 -0.49 625 625
TNF -0.09 0.22 -9999 0 -0.96 18 18
RAP1B 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.021 0.035 -9999 0 -10000 0 0
fibrinolysis -0.019 0.032 -9999 0 -10000 0 0
HCK -0.003 0.029 -9999 0 -10000 0 0
dendritic cell antigen processing and presentation -0.059 0.14 -9999 0 -0.31 162 162
VTN -0.023 0.09 -9999 0 -0.32 73 73
alphaM/beta2 Integrin/CYR61 -0.047 0.13 -9999 0 -0.58 54 54
LPA -0.001 0.02 -9999 0 -0.28 5 5
LRP1 -0.008 0.081 -9999 0 -0.81 10 10
cell migration -0.071 0.082 -9999 0 -0.48 15 15
FN1 -0.11 0.14 -9999 0 -0.28 398 398
alphaM/beta2 Integrin/Thy1 -0.019 0.03 -9999 0 -10000 0 0
MPO -0.053 0.2 -9999 0 -0.78 67 67
KNG1 -0.003 0.031 -9999 0 -0.28 12 12
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.063 0.16 -9999 0 -0.4 105 105
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.001 0.018 -9999 0 -0.28 4 4
CTGF -0.011 0.093 -9999 0 -0.74 15 15
alphaM/beta2 Integrin/Hck -0.019 0.033 -9999 0 -10000 0 0
ITGAM -0.015 0.028 -9999 0 -0.31 4 4
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.13 0.22 -9999 0 -0.52 233 233
HP -0.16 0.31 -9999 0 -0.81 184 184
leukocyte adhesion -0.076 0.13 -9999 0 -0.59 41 41
SELP -0.19 0.34 -9999 0 -0.81 233 233
IL23-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
CCL2 -0.16 0.4 -9999 0 -0.98 93 93
IL23A -0.17 0.4 -9999 0 -1.1 80 80
NF kappa B1 p50/RelA/I kappa B alpha -0.24 0.32 -9999 0 -0.89 125 125
positive regulation of T cell mediated cytotoxicity -0.19 0.43 -9999 0 -0.94 152 152
ITGA3 -0.16 0.39 -9999 0 -1.1 65 65
IL17F -0.1 0.29 -9999 0 -0.66 81 81
IL12B -0.042 0.12 -9999 0 -0.28 141 141
STAT1 (dimer) -0.22 0.38 -9999 0 -0.94 130 130
CD4 -0.16 0.38 -9999 0 -0.97 81 81
IL23 -0.17 0.39 -9999 0 -1 75 75
IL23R -0.012 0.088 -9999 0 -10000 0 0
IL1B -0.18 0.42 -9999 0 -1.1 82 82
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.17 0.38 -9999 0 -0.98 84 84
TYK2 0.011 0.017 -9999 0 -10000 0 0
STAT4 -0.035 0.16 -9999 0 -0.8 43 43
STAT3 0 0 -9999 0 -10000 0 0
IL18RAP -0.028 0.15 -9999 0 -0.75 41 41
IL12RB1 0 0.064 -9999 0 -0.3 37 37
PIK3CA 0 0.009 -9999 0 -0.28 1 1
IL12Rbeta1/TYK2 -0.001 0.048 -9999 0 -0.66 1 1
IL23R/JAK2 -0.009 0.11 -9999 0 -0.65 1 1
positive regulation of chronic inflammatory response -0.19 0.43 -9999 0 -0.94 152 152
natural killer cell activation 0.002 0.008 -9999 0 -10000 0 0
JAK2 0.018 0.035 -9999 0 -0.84 1 1
PIK3R1 -0.006 0.068 -9999 0 -0.81 7 7
NFKB1 0.002 0.005 -9999 0 -10000 0 0
RELA 0.002 0.005 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.16 0.38 -9999 0 -0.96 83 83
ALOX12B -0.16 0.38 -9999 0 -0.96 86 86
CXCL1 -0.35 0.64 -9999 0 -1.4 261 261
T cell proliferation -0.19 0.43 -9999 0 -0.94 152 152
NFKBIA 0.002 0.005 -9999 0 -10000 0 0
IL17A -0.068 0.24 -9999 0 -0.54 50 50
PI3K -0.24 0.33 -9999 0 -0.9 132 132
IFNG -0.004 0.026 -9999 0 -0.091 21 21
STAT3 (dimer) -0.23 0.31 -9999 0 -0.87 122 122
IL18R1 -0.01 0.1 -9999 0 -0.8 16 16
IL23/IL23R/JAK2/TYK2/SOCS3 -0.081 0.24 -9999 0 -0.58 40 40
IL18/IL18R -0.032 0.12 -9999 0 -0.55 51 51
macrophage activation -0.013 0.017 -9999 0 -0.041 105 105
TNF -0.18 0.41 -9999 0 -1.1 81 81
STAT3/STAT4 -0.26 0.35 -9999 0 -0.9 164 164
STAT4 (dimer) -0.23 0.4 -9999 0 -0.94 164 164
IL18 -0.004 0.046 -9999 0 -0.28 26 26
IL19 -0.17 0.38 -9999 0 -0.96 91 91
STAT5A (dimer) -0.22 0.38 -9999 0 -0.94 135 135
STAT1 -0.005 0.037 -9999 0 -0.28 18 18
SOCS3 -0.005 0.063 -9999 0 -0.81 6 6
CXCL9 -0.18 0.39 -9999 0 -0.97 100 100
MPO -0.21 0.47 -9999 0 -1.2 125 125
positive regulation of humoral immune response -0.19 0.43 -9999 0 -0.94 152 152
IL23/IL23R/JAK2/TYK2 -0.19 0.45 -9999 0 -1 139 139
IL6 -0.46 0.71 -9999 0 -1.3 370 370
STAT5A -0.007 0.072 -9999 0 -0.81 8 8
IL2 0.003 0.029 -9999 0 -0.29 8 8
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.008 -9999 0 -10000 0 0
CD3E -0.17 0.42 -9999 0 -1 105 105
keratinocyte proliferation -0.19 0.43 -9999 0 -0.94 152 152
NOS2 -0.16 0.39 -9999 0 -1 85 85
RXR and RAR heterodimerization with other nuclear receptor

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
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 -0.039 0.16 -9999 0 -0.31 252 252
RXRs/LXRs/DNA/Oxysterols -0.018 0.15 -9999 0 -0.49 18 18
MED1 -0.007 0.043 -9999 0 -0.28 24 24
mol:9cRA 0.005 0.008 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.023 0.092 -9999 0 -0.36 61 61
RXRs/NUR77 -0.16 0.25 -9999 0 -0.51 306 306
RXRs/PPAR -0.13 0.23 -9999 0 -0.38 409 409
NCOR2 0 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0 0 -9999 0 -10000 0 0
RARs/VDR/DNA/Vit D3 -0.007 0.052 -9999 0 -0.46 12 12
RARA -0.004 0.033 -9999 0 -10000 0 0
NCOA1 -0.001 0.026 -9999 0 -0.81 1 1
VDR/VDR/DNA 0 0 -9999 0 -10000 0 0
RARs/RARs/DNA/9cRA -0.007 0.052 -9999 0 -0.47 12 12
RARG 0 0 -9999 0 -10000 0 0
RPS6KB1 0.03 0.053 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.022 0.088 -9999 0 -0.35 61 61
THRA -0.001 0.026 -9999 0 -0.81 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 0.21 -9999 0 -0.48 249 249
NR1H4 -0.002 0.025 -9999 0 -10000 0 0
RXRs/LXRs/DNA -0.11 0.19 -9999 0 -0.44 249 249
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 -0.12 0.2 -9999 0 -0.45 249 249
NR4A1 -0.067 0.22 -9999 0 -0.81 82 82
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.046 0.13 -9999 0 -0.27 249 249
RXRG -0.19 0.35 -9999 0 -0.8 252 252
RXR alpha/CCPG 0 0 -9999 0 -10000 0 0
RXRA 0.016 0.006 -9999 0 -10000 0 0
RXRB 0.015 0.007 -9999 0 -10000 0 0
THRB -0.043 0.18 -9999 0 -0.81 53 53
PPARG -0.19 0.34 -9999 0 -0.81 228 228
PPARD 0 0 -9999 0 -10000 0 0
TNF -0.02 0.2 -9999 0 -1.3 14 14
mol:Oxysterols 0.005 0.007 -9999 0 -10000 0 0
cholesterol transport -0.018 0.15 -9999 0 -0.49 18 18
PPARA -0.002 0.044 -9999 0 -0.81 3 3
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.01 0.088 -9999 0 -0.81 12 12
RXRs/NUR77/BCL2 -0.12 0.2 -9999 0 -0.38 326 326
SREBF1 -0.008 0.14 -9999 0 -0.63 7 7
RXRs/RXRs/DNA/9cRA -0.12 0.21 -9999 0 -0.48 249 249
ABCA1 -0.011 0.16 -9999 0 -0.98 9 9
RARs/THRs -0.032 0.12 -9999 0 -0.49 61 61
RXRs/FXR -0.12 0.21 -9999 0 -0.48 249 249
BCL2 -0.029 0.15 -9999 0 -0.81 35 35
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.053 0.16 -9999 0 -0.54 95 95
EFNA5 -0.078 0.24 -9999 0 -0.8 96 96
FYN -0.049 0.15 -9999 0 -0.5 96 96
neuron projection morphogenesis -0.053 0.16 -9999 0 -0.54 95 95
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.053 0.16 -9999 0 -0.55 95 95
EPHA5 -0.001 0.018 -9999 0 -10000 0 0
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.017 0.096 -9999 0 -0.54 28 28
NF kappa B1 p50/RelA/I kappa B alpha -0.045 0.11 -9999 0 -0.41 11 11
AP1 -0.19 0.26 -9999 0 -0.49 385 385
mol:PIP3 -0.2 0.25 -9999 0 -0.47 407 407
AKT1 -0.013 0.072 -9999 0 -0.59 8 8
PTK2B 0.014 0.061 -9999 0 -0.3 21 21
RHOA 0.028 0.027 -9999 0 -0.24 1 1
PIK3CB 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.009 0.13 -9999 0 -0.36 119 119
MAGI3 -0.001 0.026 -9999 0 -0.81 1 1
RELA 0 0 -9999 0 -10000 0 0
apoptosis -0.063 0.15 -9999 0 -0.42 142 142
HRAS/GDP -0.001 0.013 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.019 0.15 -9999 0 -0.42 108 108
NF kappa B1 p50/RelA -0.054 0.14 -9999 0 -0.5 21 21
endothelial cell migration 0.008 0.12 -9999 0 -0.66 28 28
ADCY4 -0.003 0.15 -9999 0 -0.65 35 35
ADCY5 -0.071 0.19 -9999 0 -0.62 68 68
ADCY6 0.007 0.13 -9999 0 -0.62 26 26
ADCY7 0.007 0.13 -9999 0 -0.62 26 26
ADCY1 -0.001 0.14 -9999 0 -0.65 31 31
ADCY2 -0.012 0.16 -9999 0 -0.63 40 40
ADCY3 0.007 0.13 -9999 0 -0.62 26 26
ADCY8 0.004 0.13 -9999 0 -0.62 26 26
ADCY9 0.007 0.13 -9999 0 -0.62 26 26
GSK3B 0.021 0.058 -9999 0 -0.36 9 9
arachidonic acid secretion 0.01 0.13 -9999 0 -0.58 28 28
GNG2 -0.009 0.085 -9999 0 -0.81 11 11
TRIP6 -0.001 0.017 -9999 0 -0.52 1 1
GNAO1 -0.007 0.13 -9999 0 -0.54 50 50
HRAS -0.001 0.02 -9999 0 -10000 0 0
NFKBIA -0.005 0.15 -9999 0 -0.4 119 119
GAB1 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly 0 0.03 -9999 0 -0.94 1 1
JUN -0.007 0.077 -9999 0 -0.81 9 9
LPA/LPA2/NHERF2 -0.002 0.013 -9999 0 -10000 0 0
TIAM1 0 0.036 -9999 0 -1.1 1 1
PIK3R1 -0.006 0.068 -9999 0 -0.8 7 7
mol:IP3 -0.009 0.13 -9999 0 -0.36 119 119
PLCB3 -0.001 0.011 -9999 0 -10000 0 0
FOS -0.24 0.37 -9999 0 -0.81 298 298
positive regulation of mitosis 0.01 0.13 -9999 0 -0.58 28 28
LPA/LPA1-2-3 -0.075 0.18 -9999 0 -0.5 134 134
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 0.001 0.1 -9999 0 -0.4 20 20
GNAZ 0.009 0.1 -9999 0 -0.49 35 35
EGFR/PI3K-beta/Gab1 -0.21 0.27 -9999 0 -0.49 406 406
positive regulation of dendritic cell cytokine production -0.074 0.17 -9999 0 -0.5 134 134
LPA/LPA2/MAGI-3 -0.002 0.021 -9999 0 -0.54 1 1
ARHGEF1 -0.01 0.068 -9999 0 -0.46 19 19
GNAI2 0.013 0.085 -9999 0 -0.47 28 28
GNAI3 0.013 0.085 -9999 0 -0.47 28 28
GNAI1 -0.015 0.16 -9999 0 -0.56 72 72
LPA/LPA3 -0.083 0.2 -9999 0 -0.62 119 119
LPA/LPA2 -0.002 0.016 -9999 0 -10000 0 0
LPA/LPA1 -0.015 0.094 -9999 0 -0.55 28 28
HB-EGF/EGFR -0.26 0.26 -9999 0 -0.59 364 364
HBEGF -0.069 0.1 -9999 0 -0.62 3 3
mol:DAG -0.009 0.13 -9999 0 -0.36 119 119
cAMP biosynthetic process -0.011 0.15 -9999 0 -0.56 50 50
NFKB1 0 0 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -10000 0 0
GNB1 0 0 -9999 0 -10000 0 0
LYN -0.005 0.15 -9999 0 -0.4 119 119
GNAQ -0.055 0.14 -9999 0 -0.42 121 121
LPAR2 -0.001 0.015 -9999 0 -0.28 3 3
LPAR3 -0.11 0.26 -9999 0 -0.68 156 156
LPAR1 -0.017 0.11 -9999 0 -0.81 19 19
IL8 -0.19 0.23 -9999 0 -0.44 385 385
PTK2 -0.069 0.16 -9999 0 -0.46 134 134
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.063 0.15 -9999 0 -0.42 142 142
EGFR -0.3 0.39 -9999 0 -0.8 369 369
PLCG1 -0.056 0.14 -9999 0 -0.43 120 120
PLD2 -0.069 0.16 -9999 0 -0.46 134 134
G12/G13 -0.012 0.073 -9999 0 -0.49 19 19
PI3K-beta -0.016 0.086 -9999 0 -0.72 8 8
cell migration -0.022 0.055 -9999 0 -0.24 8 8
SLC9A3R2 -0.001 0.013 -9999 0 -0.28 2 2
PXN 0.001 0.1 -9999 0 -0.41 20 20
HRAS/GTP -0.033 0.12 -9999 0 -0.6 28 28
RAC1 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.14 -9999 0 -0.28 444 444
PRKCE -0.001 0.026 -9999 0 -0.81 1 1
PRKCD -0.001 0.13 -9999 0 -0.34 119 119
Gi(beta/gamma) -0.035 0.12 -9999 0 -0.6 31 31
mol:LPA -0.002 0.021 -9999 0 -0.22 9 9
TRIP6/p130 Cas/FAK1/Paxillin -0.057 0.14 -9999 0 -0.48 28 28
MAPKKK cascade 0.01 0.13 -9999 0 -0.58 28 28
contractile ring contraction involved in cytokinesis 0.028 0.026 -9999 0 -0.23 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.06 0.15 -9999 0 -0.43 127 127
GNA15 -0.055 0.14 -9999 0 -0.42 120 120
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
MAPT -0.02 0.15 -9999 0 -0.43 108 108
GNA11 -0.055 0.14 -9999 0 -0.42 121 121
Rac1/GTP 0 0.033 -9999 0 -1 1 1
MMP2 0.008 0.12 -9999 0 -0.67 28 28
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.089 0.19 0.64 97 -10000 0 97
KIRREL -0.08 0.24 -10000 0 -0.81 97 97
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.089 0.19 -10000 0 -0.65 97 97
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 -0.064 0.15 -10000 0 -0.5 97 97
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.039 0.11 -10000 0 -0.37 97 97
FYN -0.06 0.14 -10000 0 -0.47 97 97
mol:Ca2+ -0.064 0.15 -10000 0 -0.49 97 97
mol:DAG -0.064 0.15 -10000 0 -0.49 97 97
NPHS2 -0.009 0.028 -10000 0 -0.28 4 4
mol:IP3 -0.064 0.15 -10000 0 -0.49 97 97
regulation of endocytosis -0.032 0.14 -10000 0 -0.44 97 97
Nephrin/NEPH1/podocin/Cholesterol -0.067 0.15 -10000 0 -0.5 97 97
establishment of cell polarity -0.089 0.19 -10000 0 -0.64 97 97
Nephrin/NEPH1/podocin/NCK1-2 -0.052 0.14 -10000 0 -0.45 97 97
Nephrin/NEPH1/beta Arrestin2 -0.032 0.14 -10000 0 -0.45 97 97
NPHS1 -0.05 0.1 -10000 0 -0.28 162 162
Nephrin/NEPH1/podocin -0.055 0.14 -10000 0 -0.48 97 97
TJP1 -0.001 0.026 -10000 0 -0.81 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 -0.064 0.15 -10000 0 -0.5 97 97
CD2AP 0 0.009 -10000 0 -0.28 1 1
Nephrin/NEPH1/podocin/GRB2 -0.064 0.15 -10000 0 -0.5 97 97
GRB2 0 0.009 -10000 0 -0.28 1 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.068 0.16 -10000 0 -0.51 105 105
cytoskeleton organization -0.049 0.14 -10000 0 -0.46 97 97
Nephrin/NEPH1 -0.064 0.14 -10000 0 -0.49 97 97
Nephrin/NEPH1/ZO-1 -0.07 0.16 -10000 0 -0.54 97 97
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 0.044 -9999 0 -0.63 4 4
PDGFRB 0.004 0.052 -9999 0 -0.81 4 4
SPHK1 -0.025 0.057 -9999 0 -1.1 2 2
mol:S1P -0.031 0.059 -9999 0 -0.98 2 2
S1P1/S1P/Gi -0.1 0.23 -9999 0 -0.39 341 341
GNAO1 -0.025 0.14 -9999 0 -0.49 66 66
PDGFB-D/PDGFRB/PLCgamma1 -0.12 0.18 -9999 0 -0.6 64 64
PLCG1 -0.089 0.22 -9999 0 -0.56 83 83
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.004 0.052 -9999 0 -0.81 4 4
GNAI2 0.008 0.006 -9999 0 -10000 0 0
GNAI3 0.007 0.006 -9999 0 -10000 0 0
GNAI1 -0.035 0.18 -9999 0 -0.82 51 51
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.006 0.042 -9999 0 -0.55 4 4
S1P1/S1P -0.044 0.074 -9999 0 -0.64 6 6
negative regulation of cAMP metabolic process -0.096 0.22 -9999 0 -0.38 342 342
MAPK3 -0.16 0.31 -9999 0 -0.57 331 331
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 -0.003 0.052 -9999 0 -0.82 4 4
PLCB2 -0.008 0.086 -9999 0 -0.54 7 7
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.037 0.061 -9999 0 -0.52 6 6
receptor internalization -0.042 0.069 -9999 0 -0.58 6 6
PTGS2 -0.33 0.55 -9999 0 -1.1 331 331
Rac1/GTP -0.037 0.061 -9999 0 -0.52 6 6
RHOA 0 0 -9999 0 -10000 0 0
VEGFA -0.003 0.029 -9999 0 -0.28 11 11
negative regulation of T cell proliferation -0.096 0.22 -9999 0 -0.38 342 342
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.001 0.074 -9999 0 -0.81 8 8
MAPK1 -0.16 0.31 -9999 0 -0.57 331 331
S1P1/S1P/PDGFB-D/PDGFRB -0.02 0.11 -9999 0 -0.69 8 8
ABCC1 0 0 -9999 0 -10000 0 0
Syndecan-3-mediated signaling events

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
CTTN -0.003 0.026 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.18 0.21 -9999 0 -0.42 428 428
Syndecan-3/Neurocan -0.007 0.026 -9999 0 -10000 0 0
POMC -0.023 0.12 -9999 0 -0.47 48 48
EGFR -0.3 0.39 -9999 0 -0.8 369 369
Syndecan-3/EGFR -0.17 0.22 -9999 0 -0.45 364 364
AGRP -0.003 0.028 -9999 0 -0.28 10 10
NCSTN 0 0 -9999 0 -10000 0 0
PSENEN 0 0.009 -9999 0 -0.28 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B -0.001 0.026 -9999 0 -0.81 1 1
APH1A 0 0 -9999 0 -10000 0 0
NCAN -0.019 0.07 -9999 0 -10000 0 0
long-term memory -0.002 0.021 -9999 0 -0.42 2 2
Syndecan-3/IL8 -0.015 0.066 -9999 0 -0.45 19 19
PSEN1 0 0 -9999 0 -10000 0 0
Src/Cortactin -0.002 0.018 -9999 0 -10000 0 0
FYN -0.002 0.036 -9999 0 -0.81 2 2
limb bud formation 0 0.003 -9999 0 -10000 0 0
MC4R -0.003 0.029 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -10000 0 0
PTN -0.35 0.4 -9999 0 -0.81 428 428
FGFR/FGF/Syndecan-3 0 0.003 -9999 0 -10000 0 0
neuron projection morphogenesis -0.18 0.2 -9999 0 -0.4 428 428
Syndecan-3/AgRP -0.001 0.011 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.002 0.014 -9999 0 -10000 0 0
Fyn/Cortactin -0.003 0.032 -9999 0 -0.62 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 0.066 -9999 0 -0.45 19 19
IL8 -0.033 0.13 -9999 0 -0.4 80 80
Syndecan-3/Fyn/Cortactin -0.002 0.021 -9999 0 -0.43 2 2
Syndecan-3/CASK 0 0.003 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.018 0.088 -9999 0 -0.61 18 18
Gamma Secretase -0.001 0.015 -9999 0 -0.45 1 1
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.057 0.3 -10000 0 -0.82 122 122
IHH -0.013 0.078 -10000 0 -0.35 8 8
SHH Np/Cholesterol/GAS1 -0.03 0.12 -10000 0 -0.5 55 55
LRPAP1 0 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.03 0.12 0.5 55 -10000 0 55
SMO/beta Arrestin2 -0.077 0.23 -10000 0 -0.85 74 74
SMO -0.045 0.26 -10000 0 -0.86 83 83
AKT1 0.002 0.11 -10000 0 -0.39 23 23
ARRB2 0 0 -10000 0 -10000 0 0
BOC -0.06 0.21 -10000 0 -0.81 73 73
ADRBK1 0 0 -10000 0 -10000 0 0
heart looping -0.037 0.26 -10000 0 -0.84 83 83
STIL -0.04 0.21 -10000 0 -0.72 76 76
DHH N/PTCH2 -0.067 0.2 -10000 0 -0.65 101 101
DHH N/PTCH1 -0.091 0.24 -10000 0 -0.76 104 104
PIK3CA 0 0.009 -10000 0 -0.28 1 1
DHH -0.023 0.13 -10000 0 -0.77 29 29
PTHLH -0.087 0.39 -10000 0 -1.1 122 122
determination of left/right symmetry -0.037 0.26 -10000 0 -0.84 83 83
PIK3R1 -0.006 0.068 -10000 0 -0.81 7 7
skeletal system development -0.085 0.38 -10000 0 -1.1 122 122
IHH N/Hhip -0.01 0.05 -10000 0 -0.44 5 5
DHH N/Hhip -0.02 0.11 -10000 0 -0.63 29 29
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.037 0.26 -10000 0 -0.84 83 83
pancreas development -0.004 0.045 -10000 0 -0.37 11 11
HHAT -0.001 0.026 -10000 0 -0.81 1 1
PI3K -0.005 0.052 -10000 0 -0.62 7 7
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.044 0.18 -10000 0 -0.81 54 54
somite specification -0.037 0.26 -10000 0 -0.84 83 83
SHH Np/Cholesterol/PTCH1 -0.072 0.21 -10000 0 -0.75 77 77
SHH Np/Cholesterol/PTCH2 -0.043 0.14 -10000 0 -0.5 81 81
SHH Np/Cholesterol/Megalin -0.14 0.22 -10000 0 -0.5 258 258
SHH 0.01 0.035 -10000 0 -0.63 1 1
catabolic process -0.049 0.26 -10000 0 -0.84 86 86
SMO/Vitamin D3 -0.076 0.23 -10000 0 -0.82 75 75
SHH Np/Cholesterol/Hhip -0.005 0.037 -10000 0 -0.5 3 3
LRP2 -0.22 0.35 -10000 0 -0.81 257 257
receptor-mediated endocytosis -0.15 0.26 -10000 0 -0.82 95 95
SHH Np/Cholesterol/BOC -0.04 0.13 -10000 0 -0.5 74 74
SHH Np/Cholesterol/CDO -0.01 0.061 -10000 0 -0.5 14 14
mesenchymal cell differentiation 0.005 0.037 0.5 3 -10000 0 3
mol:Vitamin D3 -0.032 0.22 -10000 0 -0.73 82 82
IHH N/PTCH2 -0.062 0.19 -10000 0 -0.68 83 83
CDON -0.011 0.092 -10000 0 -0.81 13 13
IHH N/PTCH1 -0.047 0.26 -10000 0 -0.85 86 86
Megalin/LRPAP1 -0.16 0.27 -10000 0 -0.62 257 257
PTCH2 -0.065 0.22 -10000 0 -0.81 80 80
SHH Np/Cholesterol -0.003 0.025 -10000 0 -0.51 1 1
PTCH1 -0.05 0.26 -10000 0 -0.84 86 86
HHIP -0.004 0.045 -10000 0 -0.38 11 11
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 -0.059 0.2 -9999 0 -0.82 63 63
PDGF/PDGFRA/CRKL -0.039 0.15 -9999 0 -0.62 62 62
positive regulation of JUN kinase activity -0.03 0.12 -9999 0 -0.48 62 62
CRKL 0 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.043 0.15 -9999 0 -0.63 62 62
AP1 -0.37 0.54 -9999 0 -1.1 332 332
mol:IP3 -0.034 0.16 -9999 0 -0.64 62 62
PLCG1 -0.034 0.16 -9999 0 -0.65 62 62
PDGF/PDGFRA/alphaV Integrin -0.039 0.15 -9999 0 -0.62 62 62
RAPGEF1 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.034 0.16 -9999 0 -0.64 62 62
CAV3 -0.001 0.015 -9999 0 -0.28 3 3
CAV1 -0.17 0.33 -9999 0 -0.81 208 208
SHC/Grb2/SOS1 -0.03 0.12 -9999 0 -0.48 62 62
PDGF/PDGFRA/Shf -0.04 0.15 -9999 0 -0.63 62 62
FOS -0.33 0.55 -9999 0 -1.1 332 332
JUN -0.026 0.07 -9999 0 -0.69 9 9
oligodendrocyte development -0.039 0.15 -9999 0 -0.62 62 62
GRB2 0 0.009 -9999 0 -0.28 1 1
PIK3R1 -0.006 0.068 -9999 0 -0.81 7 7
mol:DAG -0.034 0.16 -9999 0 -0.64 62 62
PDGF/PDGFRA -0.059 0.2 -9999 0 -0.82 63 63
actin cytoskeleton reorganization -0.04 0.15 -9999 0 -0.62 63 63
SRF 0.015 0.021 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
PI3K -0.037 0.14 -9999 0 -0.53 69 69
PDGF/PDGFRA/Crk/C3G -0.033 0.13 -9999 0 -0.53 62 62
JAK1 -0.023 0.16 -9999 0 -0.62 62 62
ELK1/SRF -0.026 0.12 -9999 0 -0.49 62 62
SHB -0.001 0.027 -9999 0 -0.54 2 2
SHF -0.001 0.027 -9999 0 -0.81 1 1
CSNK2A1 0.019 0.027 -9999 0 -10000 0 0
GO:0007205 -0.036 0.17 -9999 0 -0.66 62 62
SOS1 0 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.03 0.12 -9999 0 -0.48 62 62
PDGF/PDGFRA/SHB -0.04 0.15 -9999 0 -0.62 63 63
PDGF/PDGFRA/Caveolin-1 -0.17 0.32 -9999 0 -0.72 231 231
ITGAV 0 0 -9999 0 -10000 0 0
ELK1 -0.034 0.15 -9999 0 -0.6 62 62
PIK3CA 0 0.009 -9999 0 -0.28 1 1
PDGF/PDGFRA/Crk -0.039 0.15 -9999 0 -0.62 62 62
JAK-STAT cascade -0.023 0.15 -9999 0 -0.62 62 62
cell proliferation -0.04 0.15 -9999 0 -0.63 62 62
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0 0.009 -9999 0 -10000 0 0
CCL5 -0.014 0.077 -9999 0 -0.81 5 5
SDCBP 0 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.074 0.11 -9999 0 -0.34 98 98
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 -0.068 0.097 -9999 0 -0.35 41 41
Syndecan-1/Syntenin -0.068 0.097 -9999 0 -0.5 5 5
MAPK3 -0.043 0.095 -9999 0 -0.48 5 5
HGF/MET -0.14 0.28 -9999 0 -0.67 211 211
TGFB1/TGF beta receptor Type II 0 0.009 -9999 0 -10000 0 0
BSG 0 0 -9999 0 -10000 0 0
keratinocyte migration -0.067 0.096 -9999 0 -0.34 41 41
Syndecan-1/RANTES -0.075 0.11 -9999 0 -0.39 44 44
Syndecan-1/CD147 -0.059 0.094 -9999 0 -0.52 5 5
Syndecan-1/Syntenin/PIP2 -0.065 0.094 -9999 0 -0.48 5 5
LAMA5 0 0.009 -9999 0 -0.28 1 1
positive regulation of cell-cell adhesion -0.064 0.092 -9999 0 -0.47 5 5
MMP7 -0.12 0.28 -9999 0 -0.81 141 141
HGF -0.055 0.2 -9999 0 -0.81 67 67
Syndecan-1/CASK -0.07 0.1 -9999 0 -0.32 98 98
Syndecan-1/HGF/MET -0.16 0.25 -9999 0 -0.6 213 213
regulation of cell adhesion -0.037 0.092 -9999 0 -0.49 4 4
HPSE -0.007 0.052 -9999 0 -0.81 2 2
positive regulation of cell migration -0.074 0.11 -9999 0 -0.34 98 98
SDC1 -0.074 0.11 -9999 0 -0.34 98 98
Syndecan-1/Collagen -0.074 0.11 -9999 0 -0.34 98 98
PPIB -0.001 0.015 -9999 0 -0.28 3 3
MET -0.14 0.3 -9999 0 -0.81 165 165
PRKACA 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.14 -9999 0 -0.28 444 444
MAPK1 -0.043 0.095 -9999 0 -0.48 5 5
homophilic cell adhesion -0.073 0.11 -9999 0 -0.34 98 98
MMP1 -0.21 0.12 -9999 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.002 0.036 -9999 0 -0.81 2 2
LAT2 -0.062 0.14 -9999 0 -0.43 81 81
AP1 -0.16 0.22 -9999 0 -0.58 139 139
mol:PIP3 -0.027 0.2 -9999 0 -0.48 94 94
IKBKB 0.002 0.12 -9999 0 -0.32 46 46
AKT1 -0.081 0.17 -9999 0 -0.68 35 35
IKBKG 0.002 0.12 -9999 0 -0.32 48 48
MS4A2 -0.066 0.22 -9999 0 -0.81 80 80
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.28 1 1
MAP3K1 0.007 0.13 -9999 0 -0.44 34 34
mol:Ca2+ -0.013 0.15 -9999 0 -0.31 194 194
LYN 0.011 0.004 -9999 0 -10000 0 0
CBLB -0.061 0.14 -9999 0 -0.53 41 41
SHC1 0 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.067 0.17 -9999 0 -0.49 134 134
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0 0 -9999 0 -10000 0 0
PLD2 -0.097 0.21 -9999 0 -0.49 194 194
PTPN13 -0.03 0.17 -9999 0 -0.54 57 57
PTPN11 0.01 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.007 0.14 -9999 0 -0.42 35 35
SYK 0.011 0.01 -9999 0 -0.28 1 1
GRB2 0 0.009 -9999 0 -0.28 1 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.085 0.18 -9999 0 -0.43 194 194
LAT -0.063 0.14 -9999 0 -0.43 82 82
PAK2 -0.002 0.14 -9999 0 -0.49 35 35
NFATC2 -0.095 0.24 -9999 0 -0.83 81 81
HRAS -0.012 0.15 -9999 0 -0.55 35 35
GAB2 -0.003 0.026 -9999 0 -0.28 9 9
PLA2G1B 0.027 0.018 -9999 0 -10000 0 0
Fc epsilon R1 -0.12 0.25 -9999 0 -0.61 194 194
Antigen/IgE/Fc epsilon R1 -0.11 0.24 -9999 0 -0.56 194 194
mol:GDP -0.018 0.15 -9999 0 -0.56 35 35
JUN -0.007 0.077 -9999 0 -0.81 9 9
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 -0.006 0.068 -9999 0 -0.81 7 7
FOS -0.24 0.37 -9999 0 -0.81 298 298
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.066 0.14 -9999 0 -0.45 82 82
CHUK 0.002 0.12 -9999 0 -0.32 46 46
KLRG1 -0.061 0.13 -9999 0 -0.55 36 36
VAV1 -0.062 0.14 -9999 0 -0.43 82 82
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.061 0.14 -9999 0 -0.53 41 41
negative regulation of mast cell degranulation -0.055 0.12 -9999 0 -0.51 35 35
BTK -0.06 0.13 -9999 0 -0.57 34 34
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.085 0.2 -9999 0 -0.43 196 196
GAB2/PI3K/SHP2 -0.089 0.19 -9999 0 -0.74 38 38
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.068 0.16 -9999 0 -0.35 194 194
RAF1 0.015 0.022 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.1 0.22 -9999 0 -0.52 196 196
FCER1G 0.002 0.015 -9999 0 -0.28 2 2
FCER1A -0.11 0.29 -9999 0 -0.82 145 145
Antigen/IgE/Fc epsilon R1/Fyn -0.1 0.22 -9999 0 -0.53 194 194
MAPK3 0.026 0.018 -9999 0 -10000 0 0
MAPK1 0.026 0.018 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 0.011 0.066 -9999 0 -0.61 6 6
DUSP1 -0.11 0.28 -9999 0 -0.81 134 134
NF-kappa-B/RelA -0.027 0.054 -9999 0 -0.23 4 4
actin cytoskeleton reorganization -0.026 0.15 -9999 0 -0.55 35 35
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.055 0.12 -9999 0 -0.51 41 41
FER -0.066 0.15 -9999 0 -0.45 89 89
RELA 0 0 -9999 0 -10000 0 0
ITK -0.034 0.11 -9999 0 -0.61 34 34
SOS1 0 0 -9999 0 -10000 0 0
PLCG1 -0.016 0.16 -9999 0 -0.58 35 35
cytokine secretion -0.019 0.04 -9999 0 -10000 0 0
SPHK1 -0.064 0.14 -9999 0 -0.43 84 84
PTK2 -0.028 0.15 -9999 0 -0.57 35 35
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.088 0.19 -9999 0 -0.45 194 194
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.022 0.2 -9999 0 -0.41 194 194
MAP2K2 0.022 0.019 -9999 0 -10000 0 0
MAP2K1 0.022 0.019 -9999 0 -10000 0 0
MAP2K7 0 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.057 0.12 -9999 0 -0.51 35 35
MAP2K4 0.016 0.034 -9999 0 -1 1 1
Fc epsilon R1/FcgammaRIIB -0.11 0.23 -9999 0 -0.55 196 196
mol:Choline -0.095 0.2 -9999 0 -0.48 194 194
SHC/Grb2/SOS1 -0.055 0.12 -9999 0 -0.54 33 33
FYN -0.002 0.036 -9999 0 -0.81 2 2
DOK1 -0.001 0.013 -9999 0 -0.28 2 2
PXN -0.018 0.14 -9999 0 -0.53 33 33
HCLS1 -0.061 0.14 -9999 0 -0.42 81 81
PRKCB -0.015 0.16 -9999 0 -0.37 98 98
FCGR2B -0.004 0.052 -9999 0 -0.81 4 4
IGHE 0 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.056 0.12 -9999 0 -0.52 35 35
LCP2 0 0.009 -9999 0 -0.28 1 1
PLA2G4A -0.11 0.21 -9999 0 -0.55 143 143
RASA1 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.095 0.2 -9999 0 -0.48 194 194
IKK complex 0.019 0.093 -9999 0 -0.23 44 44
WIPF1 0 0 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.008 0.045 -10000 0 -0.43 7 7
adherens junction organization 0.031 0.066 -10000 0 -0.31 30 30
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.14 0.18 -10000 0 -0.38 369 369
FMN1 0.022 0.094 -10000 0 -0.47 22 22
mol:IP3 -0.008 0.044 -10000 0 -0.4 7 7
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.011 0.055 -10000 0 -0.32 30 30
CTNNB1 0.001 0.004 -10000 0 -10000 0 0
AKT1 -0.009 0.046 -10000 0 -0.39 7 7
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.015 0.086 -10000 0 -0.51 29 29
CTNND1 0.011 0.009 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.032 0.059 -10000 0 -10000 0 0
VASP 0.032 0.06 -10000 0 -10000 0 0
ZYX 0.032 0.06 -10000 0 -10000 0 0
JUB 0.03 0.066 -10000 0 -0.42 4 4
EGFR(dimer) -0.17 0.21 -10000 0 -0.43 379 379
E-cadherin/beta catenin-gamma catenin -0.016 0.089 -10000 0 -0.52 30 30
mol:PI-3-4-5-P3 -0.009 0.05 -10000 0 -0.42 7 7
PIK3CA 0 0.009 -10000 0 -10000 0 0
PI3K -0.009 0.05 -10000 0 -0.43 7 7
FYN 0.041 0.05 -10000 0 -0.35 9 9
mol:Ca2+ -0.008 0.043 -10000 0 -0.39 7 7
JUP -0.001 0.029 -10000 0 -0.81 1 1
PIK3R1 -0.006 0.068 -10000 0 -0.81 7 7
mol:DAG -0.008 0.044 -10000 0 -0.4 7 7
CDH1 -0.024 0.14 -10000 0 -0.81 29 29
RhoA/GDP -0.14 0.18 -10000 0 -0.38 369 369
establishment of polarity of embryonic epithelium 0.032 0.059 -10000 0 -10000 0 0
SRC 0 0.009 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
EGFR -0.3 0.39 -10000 0 -0.8 369 369
CASR -0.008 0.041 -10000 0 -0.37 7 7
RhoA/GTP -0.007 0.038 -10000 0 -0.36 7 7
AKT2 -0.009 0.046 -10000 0 -0.39 7 7
actin cable formation 0.029 0.092 -10000 0 -0.44 22 22
apoptosis 0.009 0.046 0.41 7 -10000 0 7
CTNNA1 0.011 0.002 -10000 0 -10000 0 0
mol:GDP -0.16 0.2 -10000 0 -0.41 369 369
PIP5K1A 0.032 0.06 -10000 0 -10000 0 0
PLCG1 -0.008 0.044 -10000 0 -0.41 7 7
Rac1/GTP -0.15 0.2 -10000 0 -0.4 365 365
homophilic cell adhesion 0.001 0.002 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA -0.051 0.2 -10000 0 -0.81 62 62
HRAS -0.001 0.02 -10000 0 -10000 0 0
EGFR -0.3 0.39 -10000 0 -0.8 369 369
AKT 0.015 0.074 -10000 0 -0.56 14 14
FOXO3 -0.002 0.036 -10000 0 -0.81 2 2
AKT1 0 0 -10000 0 -10000 0 0
FOXO1 -0.009 0.085 -10000 0 -0.81 11 11
AKT3 -0.011 0.095 -10000 0 -0.81 14 14
FOXO4 0 0 -10000 0 -10000 0 0
MET -0.14 0.3 -10000 0 -0.81 165 165
PIK3CA 0 0.009 -10000 0 -0.28 1 1
PIK3CB 0 0 -10000 0 -10000 0 0
NRAS -0.001 0.013 -10000 0 -10000 0 0
PIK3CG -0.011 0.09 -10000 0 -0.7 15 15
PIK3R3 0 0.009 -10000 0 -0.28 1 1
PIK3R2 0 0 -10000 0 -10000 0 0
NF1 -0.001 0.026 -10000 0 -0.81 1 1
RAS -0.094 0.16 0.26 1 -0.37 187 188
ERBB2 -0.023 0.076 -10000 0 -0.28 80 80
proliferation/survival/translation -0.005 0.056 0.26 9 -10000 0 9
PI3K -0.084 0.16 -10000 0 -0.26 378 378
PIK3R1 -0.006 0.068 -10000 0 -0.81 7 7
KRAS -0.001 0.013 -10000 0 -0.28 2 2
FOXO 0.026 0.029 -10000 0 -0.5 1 1
AKT2 0 0 -10000 0 -10000 0 0
PTEN -0.002 0.036 -10000 0 -0.81 2 2
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.008 0.058 -9999 0 -0.47 15 15
RGS9BP -0.016 0.065 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.003 0.028 -9999 0 -0.28 10 10
mol:Na + -0.019 0.05 -9999 0 -10000 0 0
mol:ADP 0.007 0.028 -9999 0 -10000 0 0
GNAT2 -0.001 0.018 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.065 0.17 -9999 0 -0.54 102 102
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.014 -9999 0 -10000 0 0
GRK7 -0.003 0.028 -9999 0 -10000 0 0
CNGB3 -0.01 0.052 -9999 0 -0.28 35 35
Cone Metarhodopsin II/X-Arrestin -0.002 0.017 -9999 0 -10000 0 0
mol:Ca2+ -0.093 0.077 -9999 0 -10000 0 0
Cone PDE6 -0.056 0.14 -9999 0 -0.47 102 102
Cone Metarhodopsin II -0.003 0.019 -9999 0 -10000 0 0
Na + (4 Units) -0.093 0.076 -9999 0 -10000 0 0
GNAT2/GDP -0.055 0.14 -9999 0 -0.47 102 102
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.005 0.015 -9999 0 -10000 0 0
Cone Transducin -0.008 0.061 -9999 0 -0.49 15 15
SLC24A2 -0.17 0.14 -9999 0 -0.28 603 603
GNB3/GNGT2 -0.01 0.076 -9999 0 -0.62 15 15
GNB3 -0.011 0.093 -9999 0 -0.81 13 13
GNAT2/GTP -0.001 0.012 -9999 0 -10000 0 0
CNGA3 -0.026 0.081 -9999 0 -10000 0 0
ARR3 -0.002 0.025 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.019 0.05 -9999 0 -10000 0 0
mol:Pi -0.064 0.16 -9999 0 -0.54 102 102
Cone CNG Channel -0.015 0.037 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.17 0.14 -9999 0 -0.28 603 603
RGS9 -0.087 0.25 -9999 0 -0.75 115 115
PDE6C 0 0.009 -9999 0 -10000 0 0
GNGT2 -0.002 0.036 -9999 0 -0.81 2 2
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.001 0.02 -9999 0 -0.28 5 5
Nectin adhesion 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
PDGFRB -0.003 0.051 -9999 0 -0.81 4 4
alphaV beta3 Integrin -0.018 0.1 -9999 0 -0.62 28 28
PTK2 -0.063 0.18 -9999 0 -0.56 105 105
positive regulation of JNK cascade -0.036 0.1 -9999 0 -0.34 105 105
CDC42/GDP 0 0.16 -9999 0 -0.46 105 105
Rac1/GDP 0.002 0.16 -9999 0 -0.45 105 105
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 -0.045 0.13 -9999 0 -0.42 105 105
nectin-3/I-afadin -0.068 0.2 -9999 0 -0.64 105 105
RAPGEF1 -0.008 0.18 -9999 0 -0.52 105 105
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.022 0.21 -9999 0 -0.61 105 105
PDGFB-D/PDGFRB -0.003 0.051 -9999 0 -0.8 4 4
TLN1 0.001 0.1 -9999 0 -0.55 13 13
Rap1/GTP -0.039 0.11 -9999 0 -0.36 105 105
IQGAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.003 0.038 -9999 0 -0.49 6 6
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.068 0.2 -9999 0 -0.64 105 105
PVR 0 0 -9999 0 -10000 0 0
Necl-5(dimer) 0 0 -9999 0 -10000 0 0
mol:GDP -0.011 0.2 -9999 0 -0.58 105 105
MLLT4 -0.005 0.063 -9999 0 -0.73 7 7
PIK3CA 0 0.009 -9999 0 -0.28 1 1
PI3K -0.055 0.17 -9999 0 -0.5 109 109
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.004 0.048 -9999 0 -0.62 6 6
positive regulation of lamellipodium assembly -0.038 0.11 -9999 0 -0.35 105 105
PVRL1 0 0 -9999 0 -10000 0 0
PVRL3 -0.085 0.25 -9999 0 -0.81 104 104
PVRL2 -0.001 0.013 -9999 0 -0.28 2 2
PIK3R1 -0.006 0.068 -9999 0 -0.81 7 7
CDH1 -0.024 0.14 -9999 0 -0.81 29 29
CLDN1 -0.036 0.16 -9999 0 -0.58 62 62
JAM-A/CLDN1 -0.074 0.19 -9999 0 -0.54 131 131
SRC -0.075 0.22 -9999 0 -0.69 105 105
ITGB3 -0.024 0.14 -9999 0 -0.81 28 28
nectin-1(dimer)/I-afadin/I-afadin -0.004 0.048 -9999 0 -0.62 6 6
FARP2 -0.016 0.19 -9999 0 -0.57 105 105
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) -0.059 0.18 -9999 0 -0.56 105 105
nectin-1/I-afadin -0.004 0.048 -9999 0 -0.62 6 6
nectin-2/I-afadin -0.004 0.049 -9999 0 -0.62 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 -0.059 0.18 -9999 0 -0.56 105 105
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 -0.036 0.1 -9999 0 -0.34 105 105
alphaV/beta3 Integrin/Talin -0.037 0.12 -9999 0 -0.6 33 33
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.004 0.049 -9999 0 -0.62 6 6
nectin-2(dimer)/I-afadin/I-afadin -0.004 0.049 -9999 0 -0.62 6 6
PIP5K1C -0.032 0.1 -9999 0 -0.59 13 13
VAV2 -0.017 0.2 -9999 0 -0.58 105 105
RAP1/GDP -0.045 0.13 -9999 0 -0.42 105 105
ITGAV 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.059 0.18 -9999 0 -0.56 105 105
nectin-3(dimer)/I-afadin/I-afadin -0.068 0.2 -9999 0 -0.64 105 105
Rac1/GTP -0.047 0.14 -9999 0 -0.44 105 105
PTPRM -0.036 0.12 -9999 0 -0.33 109 109
E-cadherin/beta catenin/alpha catenin -0.015 0.082 -9999 0 -0.44 34 34
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.01 0.058 -10000 0 -0.33 31 31
epithelial cell differentiation -0.013 0.077 -10000 0 -0.45 29 29
CYFIP2 -0.01 0.063 -10000 0 -0.33 29 29
ENAH 0.056 0.062 -10000 0 -10000 0 0
EGFR -0.3 0.39 -10000 0 -0.8 369 369
EPHA2 -0.005 0.063 -10000 0 -0.81 6 6
MYO6 -0.013 0.074 -10000 0 -0.43 30 30
CTNNB1 0 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.005 0.036 -10000 0 -0.53 3 3
AQP5 -0.24 0.3 -10000 0 -0.6 395 395
CTNND1 0 0.009 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.012 0.071 -10000 0 -0.42 29 29
regulation of calcium-dependent cell-cell adhesion -0.035 0.12 -10000 0 -0.43 78 78
EGF -0.17 0.33 -10000 0 -0.8 206 206
NCKAP1 0 0 -10000 0 -10000 0 0
AQP3 -0.038 0.14 -10000 0 -0.59 49 49
cortical microtubule organization -0.013 0.077 -10000 0 -0.45 29 29
GO:0000145 0.024 0.074 -10000 0 -0.4 29 29
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.014 0.078 -10000 0 -0.46 29 29
MLLT4 -0.005 0.063 -10000 0 -0.73 7 7
ARF6/GDP -0.013 0.065 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.004 0.038 -10000 0 -0.48 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.035 0.078 -10000 0 -0.4 29 29
PVRL2 -0.001 0.013 -10000 0 -0.28 2 2
ZYX -0.013 0.073 -10000 0 -0.43 29 29
ARF6/GTP -0.003 0.035 -10000 0 -0.44 6 6
CDH1 -0.024 0.14 -10000 0 -0.81 29 29
EGFR/EGFR/EGF/EGF -0.25 0.27 -10000 0 -0.48 518 518
RhoA/GDP -0.013 0.072 -10000 0 -0.42 29 29
actin cytoskeleton organization 0.031 0.077 -10000 0 -0.4 30 30
IGF-1R heterotetramer -0.022 0.12 -10000 0 -0.62 36 36
GIT1 -0.001 0.02 -10000 0 -0.28 5 5
IGF1R -0.022 0.12 -10000 0 -0.62 36 36
IGF1 -0.18 0.33 -10000 0 -0.81 215 215
DIAPH1 -0.001 0.038 -10000 0 -0.67 3 3
Wnt receptor signaling pathway 0.013 0.077 0.45 29 -10000 0 29
RHOA 0 0 -10000 0 -10000 0 0
RhoA/GTP -0.013 0.066 -10000 0 -10000 0 0
CTNNA1 0 0 -10000 0 -10000 0 0
VCL 0.031 0.079 -10000 0 -0.42 30 30
EFNA1 0 0 -10000 0 -10000 0 0
LPP 0.029 0.083 -10000 0 -0.4 35 35
Ephrin A1/EPHA2 -0.015 0.076 -10000 0 -0.41 35 35
SEC6/SEC8 -0.014 0.072 -10000 0 -0.77 1 1
MGAT3 -0.035 0.12 -10000 0 -0.44 78 78
HGF/MET -0.11 0.21 -10000 0 -0.47 232 232
HGF -0.055 0.2 -10000 0 -0.81 67 67
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.01 0.058 -10000 0 -0.33 31 31
actin cable formation 0.07 0.059 -10000 0 -10000 0 0
KIAA1543 0.031 0.087 -10000 0 -0.44 29 29
KIFC3 -0.014 0.075 -10000 0 -0.43 31 31
NCK1 0 0 -10000 0 -10000 0 0
EXOC3 0 0 -10000 0 -10000 0 0
ACTN1 -0.013 0.074 -10000 0 -0.43 30 30
NCK1/GIT1 -0.001 0.012 -10000 0 -10000 0 0
mol:GDP -0.013 0.077 -10000 0 -0.45 29 29
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.013 0.073 -10000 0 -0.43 29 29
PIP5K1C -0.013 0.073 -10000 0 -0.43 29 29
LIMA1 -0.002 0.036 -10000 0 -0.81 2 2
ABI1 0 0 -10000 0 -10000 0 0
ROCK1 -0.012 0.058 -10000 0 -10000 0 0
adherens junction assembly 0.046 0.084 -10000 0 -0.65 4 4
IGF-1R heterotetramer/IGF1 -0.11 0.2 -10000 0 -0.44 250 250
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.004 0.049 -10000 0 -0.62 6 6
MET -0.14 0.3 -10000 0 -0.81 165 165
PLEKHA7 -0.014 0.08 -10000 0 -0.46 29 29
mol:GTP -0.003 0.038 -10000 0 -0.48 6 6
establishment of epithelial cell apical/basal polarity -0.013 0.068 -10000 0 -0.72 1 1
cortical actin cytoskeleton stabilization -0.01 0.058 -10000 0 -0.33 31 31
regulation of cell-cell adhesion 0.031 0.077 -10000 0 -0.4 30 30
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.01 0.058 -10000 0 -0.33 31 31
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.12 0.21 -10000 0 -0.48 236 236
MAPK9 0.008 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.001 0.02 -10000 0 -10000 0 0
GNB1/GNG2 -0.006 0.057 -10000 0 -0.54 11 11
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 0.22 -10000 0 -0.51 233 233
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 0.049 0.12 233 -10000 0 233
GNAL -0.19 0.34 -10000 0 -0.81 233 233
GNG2 -0.009 0.085 -10000 0 -0.81 11 11
CRH -0.003 0.029 -10000 0 -0.28 11 11
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.006 0.033 -10000 0 -0.45 5 5
MAPK11 0.007 0.025 -10000 0 -0.45 3 3
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.12 0.18 -9999 0 -0.39 300 300
MAP3K8 -0.004 0.058 -9999 0 -0.81 5 5
FOS -0.035 0.13 -9999 0 -0.46 32 32
PRKCA -0.012 0.13 -9999 0 -0.78 26 26
PTPN7 -0.007 0.068 -9999 0 -0.32 17 17
HRAS -0.001 0.02 -9999 0 -10000 0 0
PRKCB -0.012 0.12 -9999 0 -0.71 24 24
NRAS -0.001 0.013 -9999 0 -10000 0 0
RAS family/GTP -0.001 0.012 -9999 0 -10000 0 0
MAPK3 -0.008 0.072 -9999 0 -10000 0 0
MAP2K1 -0.013 0.14 -9999 0 -0.61 41 41
ELK1 -0.003 0.005 -9999 0 -10000 0 0
BRAF -0.032 0.12 -9999 0 -0.59 41 41
mol:GTP -0.002 0.003 -9999 0 -0.006 298 298
MAPK1 -0.008 0.072 -9999 0 -10000 0 0
RAF1 -0.032 0.12 -9999 0 -0.59 41 41
KRAS -0.001 0.013 -9999 0 -0.28 2 2
FAS signaling pathway (CD95)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPTAN1 0.011 0.053 0.29 35 -10000 0 35
RFC1 0.011 0.053 0.29 35 -10000 0 35
PRKDC 0.01 0.054 0.29 35 -10000 0 35
RIPK1 0 0 -10000 0 -10000 0 0
CASP7 -0.023 0.036 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 -0.016 0.065 0.25 15 -0.38 13 28
MAP2K4 -0.058 0.16 -10000 0 -0.41 29 29
mol:ceramide -0.03 0.11 -10000 0 -0.57 16 16
GSN 0.004 0.079 0.29 34 -0.5 13 47
FASLG/FAS/FADD/FAF1/Caspase 8 -0.029 0.069 -10000 0 -0.46 13 13
FAS 0.004 0.046 -10000 0 -0.82 3 3
BID 0.001 0.005 -10000 0 -10000 0 0
MAP3K1 -0.021 0.093 -10000 0 -0.29 13 13
MAP3K7 0 0.009 -10000 0 -0.28 1 1
RB1 0.01 0.056 0.29 34 -0.42 2 36
CFLAR 0 0 -10000 0 -10000 0 0
HGF/MET -0.14 0.27 -10000 0 -0.61 224 224
ARHGDIB 0.01 0.054 0.29 35 -10000 0 35
FADD 0.002 0.039 -10000 0 -0.3 10 10
actin filament polymerization -0.004 0.079 0.5 13 -0.29 34 47
NFKB1 -0.076 0.1 -10000 0 -0.29 14 14
MAPK8 -0.12 0.24 -10000 0 -0.43 365 365
DFFA 0.011 0.053 0.29 35 -10000 0 35
DNA fragmentation during apoptosis 0.011 0.053 0.29 35 -10000 0 35
FAS/FADD/MET -0.095 0.21 -10000 0 -0.56 165 165
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.001 0.046 -10000 0 -0.28 22 22
FAF1 0.008 0.006 -10000 0 -10000 0 0
PARP1 0.01 0.053 0.29 35 -10000 0 35
DFFB 0.011 0.053 0.29 35 -10000 0 35
CHUK -0.066 0.088 -10000 0 -10000 0 0
FASLG -0.013 0.1 -10000 0 -0.4 48 48
FAS/FADD -0.005 0.045 -10000 0 -0.69 3 3
HGF -0.055 0.2 -10000 0 -0.81 67 67
LMNA 0.01 0.048 0.26 35 -10000 0 35
CASP6 0.01 0.053 0.29 35 -10000 0 35
CASP10 0.004 0.053 -10000 0 -0.82 4 4
CASP3 0.013 0.064 0.35 35 -10000 0 35
PTPN13 -0.023 0.13 -10000 0 -0.81 28 28
CASP8 0.002 0.013 -10000 0 -10000 0 0
IL6 -0.47 0.67 -10000 0 -1.4 362 362
MET -0.14 0.3 -10000 0 -0.81 165 165
ICAD/CAD 0.01 0.049 0.26 35 -10000 0 35
FASLG/FAS/FADD/FAF1/Caspase 10 -0.03 0.12 -10000 0 -0.58 16 16
activation of caspase activity by cytochrome c 0.001 0.005 -10000 0 -10000 0 0
PAK2 0.011 0.053 0.28 35 -10000 0 35
BCL2 -0.024 0.15 -10000 0 -0.81 35 35
Glypican 2 network

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
MDK -0.011 0.054 -9999 0 -0.28 39 39
GPC2 -0.034 0.098 -9999 0 -0.29 114 114
GPC2/Midkine -0.029 0.077 -9999 0 -0.4 18 18
neuron projection morphogenesis -0.029 0.077 -9999 0 -0.39 18 18
Signaling events mediated by HDAC Class III

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
EP300 0 0 -10000 0 -10000 0 0
HDAC4 -0.001 0.026 -10000 0 -0.81 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.011 0.074 0.62 1 -10000 0 1
CDKN1A -0.002 0.043 -10000 0 -0.96 2 2
KAT2B -0.001 0.026 -10000 0 -0.81 1 1
BAX -0.001 0.018 -10000 0 -0.28 4 4
FOXO3 -0.001 0.015 -10000 0 -0.33 2 2
FOXO1 -0.009 0.085 -10000 0 -0.81 11 11
FOXO4 0 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 -0.57 0.36 -10000 0 -0.79 716 716
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.01 0.03 -10000 0 -0.62 1 1
PPARGC1A -0.17 0.33 -10000 0 -0.81 208 208
FHL2 -0.005 0.063 -10000 0 -0.81 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 0.074 -10000 0 -0.62 1 1
SIRT1/FOXO3a 0 0.013 -10000 0 -0.25 2 2
SIRT1 0 0.009 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0.018 -10000 0 -0.53 1 1
SIRT1/Histone H1b -0.002 0.011 -10000 0 -10000 0 0
apoptosis 0 0.011 -10000 0 -10000 0 0
SIRT1/PGC1A -0.12 0.22 -10000 0 -0.54 208 208
p53/SIRT1 0.001 0.02 0.43 2 -10000 0 2
SIRT1/FOXO4 0 0.008 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.008 0.064 -10000 0 -0.49 17 17
HIST1H1E -0.004 0.012 -10000 0 -10000 0 0
SIRT1/p300 0 0.007 -10000 0 -10000 0 0
muscle cell differentiation 0.002 0.024 0.53 1 -10000 0 1
TP53 0 0.009 -10000 0 -10000 0 0
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 -0.44 0.28 -10000 0 -0.62 689 689
ACSS2 0.019 0.021 -10000 0 -0.62 1 1
SIRT1/PCAF/MYOD -0.002 0.024 -10000 0 -0.53 1 1
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.55 0.38 -9999 0 -0.81 677 677
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 -0.004 0.032 -9999 0 -10000 0 0
TCEB1 -0.001 0.015 -9999 0 -0.28 3 3
HIF1A/p53 -0.001 0.005 -9999 0 -10000 0 0
HIF1A -0.002 0.007 -9999 0 -10000 0 0
COPS5 0 0.009 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.002 0.012 -9999 0 -10000 0 0
FIH (dimer) 0 0 -9999 0 -10000 0 0
CDKN2A -0.047 0.1 -9999 0 -0.28 167 167
ARNT/IPAS -0.42 0.29 -9999 0 -0.62 677 677
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 0.009 -9999 0 -0.28 1 1
RACK1/Elongin B/Elongin C -0.002 0.017 -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 -0.01 0.037 -9999 0 -0.48 2 2
HIF1A/RACK1/Elongin B/Elongin C 0 0.012 -9999 0 -10000 0 0
VHL 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.009 -9999 0 -0.28 1 1
HIF1A/JAB1 -0.001 0.007 -9999 0 -10000 0 0
EGLN3 -0.022 0.078 -9999 0 -0.81 1 1
EGLN2 -0.001 0.02 -9999 0 -0.28 5 5
EGLN1 -0.001 0.026 -9999 0 -0.81 1 1
TP53 0 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0 0.004 -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 -0.017 0.037 -9999 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.003 0.11 -9999 0 -0.54 40 40
ADCY5 -0.16 0.26 -9999 0 -0.54 316 316
ADCY6 0.019 0.018 -9999 0 -0.54 1 1
ADCY7 0.019 0.018 -9999 0 -0.54 1 1
ADCY1 -0.007 0.097 -9999 0 -0.54 25 25
ADCY2 -0.03 0.15 -9999 0 -0.54 76 76
ADCY3 0.019 0.019 -9999 0 -0.54 1 1
ADCY8 0.009 0.032 -9999 0 -0.54 1 1
PRKCE 0.01 0.02 -9999 0 -0.63 1 1
ADCY9 0.019 0.018 -9999 0 -0.54 1 1
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.032 0.1 -9999 0 -0.32 66 66
Signaling events mediated by PRL

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
CCNE1 -0.056 0.11 -9999 0 -0.28 200 200
mol:Halofuginone 0 0.002 -9999 0 -10000 0 0
ITGA1 -0.006 0.068 -9999 0 -0.81 7 7
CDKN1A -0.059 0.091 -9999 0 -0.86 2 2
PRL-3/alpha Tubulin -0.002 0.017 -9999 0 -10000 0 0
mol:Ca2+ -0.034 0.097 -9999 0 -0.63 14 14
AGT -0.048 0.13 -9999 0 -0.33 143 143
CCNA2 -0.17 0.24 -9999 0 -0.56 175 175
TUBA1B 0 0 -9999 0 -10000 0 0
EGR1 -0.18 0.3 -9999 0 -0.61 316 316
CDK2/Cyclin E1 -0.068 0.091 -9999 0 -0.82 2 2
MAPK3 0.02 0.019 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0.006 -9999 0 -10000 0 0
MAPK1 0.02 0.019 -9999 0 -10000 0 0
PTP4A1 -0.13 0.24 -9999 0 -0.47 316 316
PTP4A3 -0.003 0.026 -9999 0 -0.28 9 9
PTP4A2 0 0.009 -9999 0 -0.28 1 1
ITGB1 0.02 0.019 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -10000 0 0
RAC1 -0.057 0.084 -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 -0.6 3 3
RABGGTA 0 0 -9999 0 -10000 0 0
BCAR1 0.001 0.008 -9999 0 -10000 0 0
RHOC -0.057 0.084 -9999 0 -10000 0 0
RHOA -0.057 0.084 -9999 0 -10000 0 0
cell motility -0.037 0.11 -9999 0 -10000 0 0
PRL-1/alpha Tubulin -0.14 0.2 -9999 0 -0.62 2 2
PRL-3/alpha1 Integrin -0.006 0.054 -9999 0 -0.62 7 7
ROCK1 -0.037 0.11 -9999 0 -10000 0 0
RABGGTB 0 0 -9999 0 -10000 0 0
CDK2 0 0 -9999 0 -10000 0 0
mitosis -0.12 0.24 -9999 0 -0.47 316 316
ATF5 -0.001 0.018 -9999 0 -0.28 4 4
Presenilin action in Notch and Wnt signaling

Figure S62.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S62.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.004 0.048 -10000 0 -0.52 8 8
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 -0.074 0.23 -10000 0 -0.81 90 90
LRP6/FZD1 0 0.006 -10000 0 -10000 0 0
TLE1 -0.006 0.072 -10000 0 -0.81 8 8
AP1 -0.12 0.18 -10000 0 -0.38 302 302
NCSTN 0 0 -10000 0 -10000 0 0
ADAM10 -0.001 0.036 -10000 0 -0.81 2 2
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.008 0.045 -10000 0 -10000 0 0
NICD/RBPSUH -0.001 0.032 -10000 0 -0.71 2 2
WIF1 -0.42 0.4 -10000 0 -0.79 524 524
NOTCH1 -0.002 0.034 -10000 0 -0.76 2 2
PSENEN 0 0.009 -10000 0 -0.28 1 1
KREMEN2 -0.13 0.14 -10000 0 -10000 0 0
DKK1 -0.078 0.19 -10000 0 -0.81 49 49
beta catenin/beta TrCP1 -0.009 0.024 0.22 2 -10000 0 2
APH1B -0.001 0.026 -10000 0 -0.81 1 1
APH1A 0 0 -10000 0 -10000 0 0
AXIN1 0.003 0.013 -10000 0 -0.22 2 2
CtBP/CBP/TCF1/TLE1/AES 0.003 0.041 -10000 0 -0.35 6 6
PSEN1 0 0 -10000 0 -10000 0 0
FOS -0.24 0.37 -10000 0 -0.81 298 298
JUN -0.007 0.077 -10000 0 -0.81 9 9
MAP3K7 0.001 0.01 -10000 0 -0.28 1 1
CTNNB1 -0.003 0.035 0.23 3 -10000 0 3
MAPK3 0 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.078 0.11 -10000 0 -0.61 25 25
HNF1A -0.001 0.022 -10000 0 -0.28 6 6
CTBP1 0.001 0.004 -10000 0 -10000 0 0
MYC -0.035 0.23 -10000 0 -1.5 23 23
NKD1 -0.009 0.072 -10000 0 -0.42 22 22
FZD1 0 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.042 0.13 -10000 0 -0.45 92 92
apoptosis -0.11 0.18 -10000 0 -0.37 302 302
Delta 1/NOTCHprecursor -0.004 0.047 -10000 0 -0.51 8 8
DLL1 -0.005 0.063 -10000 0 -0.81 6 6
PPARD -0.001 0.013 -10000 0 -10000 0 0
Gamma Secretase -0.001 0.015 -10000 0 -0.45 1 1
APC 0.003 0.013 -10000 0 -0.22 2 2
DVL1 -0.038 0.037 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.11 0.14 -10000 0 -0.58 50 50
LRP6 0 0.009 -10000 0 -0.28 1 1
CSNK1A1 0 0 -10000 0 -10000 0 0
NLK 0.002 0.01 -10000 0 -10000 0 0
CCND1 -0.01 0.086 -10000 0 -1.5 3 3
WNT1 -0.001 0.013 -10000 0 -0.28 2 2
Axin1/APC/beta catenin 0.01 0.037 -10000 0 -10000 0 0
DKK2 -0.021 0.13 -10000 0 -0.81 25 25
NOTCH1 precursor/DVL1 -0.019 0.033 -10000 0 -0.64 2 2
GSK3B 0 0.002 -10000 0 -10000 0 0
FRAT1 0 0.003 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.042 0.13 -10000 0 -0.45 92 92
PPP2R5D -0.015 0.039 0.36 6 -10000 0 6
MAPK1 0 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.25 0.24 -10000 0 -0.48 511 511
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.014 0.004 -10000 0 -10000 0 0
Syndecan-4-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
PTK2 0.002 0.031 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.019 0.033 -9999 0 -0.64 1 1
positive regulation of JNK cascade -0.045 0.11 -9999 0 -0.46 6 6
Syndecan-4/ADAM12 -0.027 0.051 -9999 0 -0.55 2 2
CCL5 -0.014 0.077 -9999 0 -0.81 5 5
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0 0 -9999 0 -10000 0 0
ITGA5 0 0 -9999 0 -10000 0 0
SDCBP 0 0 -9999 0 -10000 0 0
PLG 0 0.019 -9999 0 -0.28 4 4
ADAM12 -0.019 0.077 -9999 0 -0.3 65 65
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 -0.001 0.015 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.054 0.043 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.07 0.14 -9999 0 -0.46 63 63
Syndecan-4/CXCL12/CXCR4 -0.047 0.11 -9999 0 -0.49 6 6
Syndecan-4/Laminin alpha3 -0.13 0.2 -9999 0 -0.5 118 118
MDK -0.011 0.054 -9999 0 -0.28 39 39
Syndecan-4/FZD7 -0.028 0.069 -9999 0 -0.47 14 14
Syndecan-4/Midkine -0.021 0.039 -9999 0 -0.64 1 1
FZD7 -0.017 0.12 -9999 0 -0.81 21 21
Syndecan-4/FGFR1/FGF -0.18 0.21 -9999 0 -0.5 107 107
THBS1 -0.002 0.044 -9999 0 -0.81 3 3
integrin-mediated signaling pathway -0.027 0.069 -9999 0 -0.48 13 13
positive regulation of MAPKKK cascade -0.045 0.11 -9999 0 -0.46 6 6
Syndecan-4/TACI -0.029 0.066 -9999 0 -0.5 7 7
CXCR4 -0.008 0.045 -9999 0 -10000 0 0
cell adhesion -0.025 0.055 -9999 0 -0.34 24 24
Syndecan-4/Dynamin -0.018 0.032 -9999 0 -0.64 1 1
Syndecan-4/TSP1 -0.02 0.04 -9999 0 -0.52 3 3
Syndecan-4/GIPC -0.019 0.033 -9999 0 -0.64 1 1
Syndecan-4/RANTES -0.025 0.05 -9999 0 -0.51 5 5
ITGB1 0 0 -9999 0 -10000 0 0
LAMA1 -0.096 0.26 -9999 0 -0.81 117 117
LAMA3 -0.2 0.35 -9999 0 -0.81 245 245
RAC1 0 0 -9999 0 -10000 0 0
PRKCA 0.004 0.12 -9999 0 -0.77 24 24
Syndecan-4/alpha-Actinin -0.019 0.035 -9999 0 -0.55 2 2
TFPI -0.038 0.17 -9999 0 -0.81 46 46
F2 0.001 0.028 -9999 0 -0.28 9 9
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.16 0.24 -9999 0 -0.6 106 106
ACTN1 -0.001 0.026 -9999 0 -0.81 1 1
TNC -0.018 0.12 -9999 0 -0.67 27 27
Syndecan-4/CXCL12 -0.051 0.11 -9999 0 -0.46 35 35
FGF6 -0.002 0.036 -9999 0 -0.81 2 2
RHOA 0 0 -9999 0 -10000 0 0
CXCL12 -0.061 0.21 -9999 0 -0.81 75 75
TNFRSF13B -0.026 0.11 -9999 0 -0.81 15 15
FGF2 -0.32 0.4 -9999 0 -0.81 395 395
FGFR1 -0.01 0.086 -9999 0 -0.69 14 14
Syndecan-4/PI-4-5-P2 -0.013 0.043 -9999 0 -0.65 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.11 0.14 -9999 0 -0.29 398 398
cell migration -0.025 0.019 -9999 0 -10000 0 0
PRKCD 0.005 0.013 -9999 0 -0.27 1 1
vasculogenesis -0.019 0.038 -9999 0 -0.5 3 3
SDC4 -0.013 0.046 -9999 0 -0.69 1 1
Syndecan-4/Tenascin C -0.028 0.072 -9999 0 -0.5 13 13
Syndecan-4/PI-4-5-P2/PKC alpha -0.043 0.034 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.018 0.032 -9999 0 -0.64 1 1
MMP9 -0.12 0.15 -9999 0 -0.28 444 444
Rac1/GTP -0.025 0.056 -9999 0 -0.35 24 24
cytoskeleton organization -0.018 0.032 -9999 0 -0.62 1 1
GIPC1 -0.001 0.013 -9999 0 -0.28 2 2
Syndecan-4/TFPI -0.039 0.096 -9999 0 -0.47 30 30
Regulation of Androgen receptor activity

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
HDAC1 0.02 0.006 -9999 0 -10000 0 0
SMARCC1 0.004 0.02 -9999 0 -0.57 1 1
REL -0.003 0.078 -9999 0 -0.81 9 9
HDAC7 0.009 0.13 -9999 0 -0.6 13 13
JUN -0.007 0.077 -9999 0 -0.81 9 9
EP300 0 0 -9999 0 -10000 0 0
KAT2B -0.001 0.026 -9999 0 -0.81 1 1
KAT5 0.002 0.004 -9999 0 -10000 0 0
MAPK14 0.006 0.095 -9999 0 -0.63 21 21
FOXO1 -0.009 0.085 -9999 0 -0.81 11 11
T-DHT/AR -0.005 0.14 -9999 0 -0.56 21 21
MAP2K6 -0.017 0.12 -9999 0 -0.79 22 22
BRM/BAF57 -0.001 0.011 -9999 0 -10000 0 0
MAP2K4 0 0.026 -9999 0 -0.81 1 1
SMARCA2 0 0 -9999 0 -10000 0 0
PDE9A -0.093 0.3 -9999 0 -1.2 61 61
NCOA2 -0.025 0.14 -9999 0 -0.81 31 31
CEBPA -0.006 0.077 -9999 0 -0.81 9 9
EHMT2 0 0 -9999 0 -10000 0 0
cell proliferation 0.015 0.14 -9999 0 -0.5 24 24
NR0B1 -0.01 0.052 -9999 0 -0.28 36 36
EGR1 -0.26 0.38 -9999 0 -0.81 316 316
RXRs/9cRA -0.12 0.21 -9999 0 -0.49 249 249
AR/RACK1/Src -0.004 0.11 -9999 0 -0.49 26 26
AR/GR -0.05 0.12 -9999 0 -0.44 45 45
GNB2L1 0.001 0.003 -9999 0 -10000 0 0
PKN1 0 0.009 -9999 0 -0.28 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 0.016 0.052 -9999 0 -0.62 6 6
T-DHT/AR/TIF2/CARM1 -0.009 0.14 -9999 0 -0.51 52 52
SRC 0.022 0.091 -9999 0 -0.48 26 26
NR3C1 -0.01 0.088 -9999 0 -0.81 12 12
KLK3 -0.22 0.43 -9999 0 -1.2 155 155
APPBP2 -0.001 0.015 -9999 0 -10000 0 0
TRIM24 0.001 0.01 -9999 0 -0.28 1 1
T-DHT/AR/TIP60 -0.026 0.094 -9999 0 -0.52 26 26
TMPRSS2 -0.17 0.42 -9999 0 -1.2 132 132
RXRG -0.2 0.35 -9999 0 -0.8 252 252
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 0.001 0.003 -9999 0 -10000 0 0
NR2C2 -0.005 0.063 -9999 0 -0.81 6 6
KLK2 -0.041 0.25 -9999 0 -0.78 86 86
AR -0.025 0.14 -9999 0 -0.34 143 143
SENP1 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.009 -9999 0 -0.28 1 1
MDM2 0.005 0.023 -9999 0 -0.28 4 4
SRY 0.003 0.01 -9999 0 -10000 0 0
GATA2 -0.025 0.13 -9999 0 -0.65 38 38
MYST2 0.001 0.01 -9999 0 -0.28 1 1
HOXB13 -0.13 0.14 -9999 0 -0.28 456 456
T-DHT/AR/RACK1/Src -0.026 0.093 -9999 0 -0.5 26 26
positive regulation of transcription -0.025 0.13 -9999 0 -0.65 38 38
DNAJA1 0 0.002 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.013 -9999 0 -10000 0 0
NCOA1 0.012 0.028 -9999 0 -0.84 1 1
SPDEF -0.056 0.2 -9999 0 -0.81 65 65
T-DHT/AR/TIF2 0.016 0.09 -9999 0 -0.49 13 13
T-DHT/AR/Hsp90 -0.033 0.091 -9999 0 -0.52 26 26
GSK3B 0.001 0.004 -9999 0 -10000 0 0
NR2C1 0.002 0.006 -9999 0 -10000 0 0
mol:T-DHT 0.015 0.096 -9999 0 -0.52 26 26
SIRT1 0 0 -9999 0 -10000 0 0
ZMIZ2 0.006 0.014 -9999 0 -10000 0 0
POU2F1 0.021 0.027 -9999 0 -0.41 1 1
T-DHT/AR/DAX-1 -0.034 0.096 -9999 0 -0.53 26 26
CREBBP 0 0 -9999 0 -10000 0 0
SMARCE1 -0.001 0.016 -9999 0 -0.29 3 3
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.002 0.13 -10000 0 -0.41 49 49
TBX21 -0.011 0.34 -10000 0 -1.3 50 50
B2M 0.011 0.005 -10000 0 -10000 0 0
TYK2 0.017 0.015 -10000 0 -10000 0 0
IL12RB1 0.005 0.066 -10000 0 -0.31 36 36
GADD45B 0.034 0.22 -10000 0 -0.85 30 30
IL12RB2 -0.058 0.2 -10000 0 -0.44 164 164
GADD45G 0.026 0.22 -10000 0 -0.86 30 30
natural killer cell activation 0.007 0.017 -10000 0 -10000 0 0
RELB -0.003 0.026 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
IL18 0.007 0.047 -10000 0 -0.28 26 26
IL2RA -0.028 0.11 -10000 0 -0.36 77 77
IFNG -0.039 0.096 -10000 0 -0.28 137 137
STAT3 (dimer) 0.028 0.21 -10000 0 -0.66 49 49
HLA-DRB5 -0.017 0.094 -10000 0 -0.49 14 14
FASLG 0.008 0.28 -10000 0 -1.1 38 38
NF kappa B2 p52/RelB -0.077 0.2 -10000 0 -0.81 47 47
CD4 0.008 0.006 -10000 0 -10000 0 0
SOCS1 -0.005 0.042 -10000 0 -0.81 1 1
EntrezGene:6955 -0.006 0.014 -10000 0 -10000 0 0
CD3D -0.026 0.14 -10000 0 -0.67 38 38
CD3E -0.022 0.14 -10000 0 -0.51 58 58
CD3G -0.035 0.17 -10000 0 -0.57 74 74
IL12Rbeta2/JAK2 -0.027 0.16 -10000 0 -0.64 50 50
CCL3 0.015 0.26 -10000 0 -0.99 36 36
CCL4 0.018 0.25 -10000 0 -0.9 39 39
HLA-A 0.009 0.026 -10000 0 -0.34 1 1
IL18/IL18R 0.021 0.14 -10000 0 -0.56 51 51
NOS2 0.021 0.25 -10000 0 -1 33 33
IL12/IL12R/TYK2/JAK2/SPHK2 -0.001 0.13 -10000 0 -0.42 46 46
IL1R1 0.005 0.3 -10000 0 -1.2 40 40
IL4 -0.005 0.018 -10000 0 -10000 0 0
JAK2 0.016 0.031 -10000 0 -0.82 1 1
EntrezGene:6957 -0.005 0.012 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.032 0.26 -10000 0 -1 45 45
RAB7A 0.049 0.19 -10000 0 -0.73 26 26
lysosomal transport 0.05 0.19 -10000 0 -0.68 27 27
FOS -0.36 0.67 -10000 0 -1.3 313 313
STAT4 (dimer) 0.023 0.26 -10000 0 -0.91 47 47
STAT5A (dimer) -0.081 0.21 -10000 0 -0.74 63 63
GZMA 0.006 0.28 -10000 0 -1.1 35 35
GZMB -0.004 0.3 -10000 0 -1.1 42 42
HLX -0.001 0.013 -10000 0 -0.28 2 2
LCK 0.007 0.29 -10000 0 -0.87 60 60
TCR/CD3/MHC II/CD4 -0.066 0.2 -10000 0 -0.57 79 79
IL2/IL2R -0.029 0.097 -10000 0 -0.46 38 38
MAPK14 0.038 0.22 -10000 0 -0.82 35 35
CCR5 0.028 0.22 -10000 0 -0.87 32 32
IL1B 0.003 0.1 -10000 0 -0.73 18 18
STAT6 0.027 0.086 -10000 0 -0.26 5 5
STAT4 -0.035 0.16 -10000 0 -0.8 43 43
STAT3 0 0 -10000 0 -10000 0 0
STAT1 -0.005 0.037 -10000 0 -0.28 18 18
NFKB1 0 0 -10000 0 -10000 0 0
NFKB2 0 0.009 -10000 0 -0.28 1 1
IL12B -0.04 0.12 -10000 0 -0.27 179 179
CD8A -0.001 0.074 -10000 0 -0.37 30 30
CD8B -0.024 0.15 -10000 0 -0.56 61 61
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.002 0.13 0.41 49 -10000 0 49
IL2RB -0.011 0.055 -10000 0 -0.28 40 40
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.24 -10000 0 -0.81 47 47
IL2RG -0.018 0.087 -10000 0 -0.81 7 7
IL12 -0.047 0.16 -10000 0 -0.6 58 58
STAT5A -0.007 0.072 -10000 0 -0.81 8 8
CD247 -0.014 0.12 -10000 0 -0.6 36 36
IL2 -0.003 0.026 -10000 0 -10000 0 0
SPHK2 0 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.032 0.19 -10000 0 -0.7 68 68
IL12/IL12R/TYK2/JAK2 0.011 0.29 -10000 0 -0.85 62 62
MAP2K3 0.034 0.22 -10000 0 -0.84 34 34
RIPK2 -0.001 0.02 -10000 0 -0.28 5 5
MAP2K6 0.03 0.23 -10000 0 -0.83 37 37
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.007 0.028 -10000 0 -0.81 1 1
IL18RAP -0.018 0.16 -10000 0 -0.77 40 40
IL12Rbeta1/TYK2 0.014 0.051 -10000 0 -0.67 1 1
EOMES -0.022 0.18 -10000 0 -1.5 14 14
STAT1 (dimer) 0.032 0.21 -10000 0 -0.71 38 38
T cell proliferation 0.034 0.2 -10000 0 -0.63 49 49
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.001 0.1 -10000 0 -0.81 16 16
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.061 0.17 -10000 0 -0.77 40 40
ATF2 0.046 0.21 -10000 0 -0.78 32 32
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.036 0.13 -10000 0 -0.62 36 36
FYN 0.015 0.18 -10000 0 -0.75 42 42
LAT/GRAP2/SLP76 -0.029 0.15 -10000 0 -0.65 42 42
IKBKB -0.001 0.013 -10000 0 -10000 0 0
AKT1 0.03 0.12 -10000 0 -0.47 41 41
B2M 0.011 0.004 -10000 0 -10000 0 0
IKBKG -0.008 0.027 -10000 0 -0.13 23 23
MAP3K8 -0.004 0.058 -10000 0 -0.81 5 5
mol:Ca2+ -0.025 0.048 -10000 0 -0.12 191 191
integrin-mediated signaling pathway -0.002 0.03 -10000 0 -0.54 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.021 0.18 -10000 0 -0.71 43 43
TRPV6 -0.16 0.32 -10000 0 -0.78 205 205
CD28 -0.007 0.063 -10000 0 -0.47 14 14
SHC1 0.01 0.19 -10000 0 -0.8 39 39
receptor internalization -0.003 0.21 -10000 0 -0.82 47 47
PRF1 -0.003 0.23 -10000 0 -1.2 32 32
KRAS -0.001 0.013 -10000 0 -0.28 2 2
GRB2 0 0.009 -10000 0 -0.28 1 1
COT/AKT1 0.032 0.1 -10000 0 -0.38 40 40
LAT 0.007 0.19 -10000 0 -0.79 42 42
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D -0.023 0.14 -10000 0 -0.82 27 27
CD3E -0.018 0.14 -10000 0 -0.5 58 58
CD3G -0.034 0.17 -10000 0 -0.56 74 74
RASGRP2 -0.006 0.04 -10000 0 -0.18 44 44
RASGRP1 0.036 0.12 -10000 0 -0.47 41 41
HLA-A 0.009 0.025 -10000 0 -10000 0 0
RASSF5 -0.003 0.045 -10000 0 -0.68 4 4
RAP1A/GTP/RAPL -0.002 0.03 -10000 0 -0.54 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 -0.015 0.048 -10000 0 -0.23 31 31
PRKCA -0.012 0.085 -10000 0 -0.32 51 51
GRAP2 -0.015 0.11 -10000 0 -0.81 17 17
mol:IP3 0.018 0.15 0.27 164 -0.45 40 204
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.008 0.22 -10000 0 -0.94 38 38
ORAI1 0.078 0.15 0.38 191 -10000 0 191
CSK 0.007 0.19 -10000 0 -0.82 39 39
B7 family/CD28 -0.023 0.18 -10000 0 -0.72 47 47
CHUK 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.004 0.22 -10000 0 -0.81 54 54
PTPN6 0.006 0.19 -10000 0 -0.8 41 41
VAV1 0.009 0.19 -10000 0 -0.79 41 41
Monovalent TCR/CD3 -0.032 0.21 -10000 0 -0.71 63 63
CBL 0 0 -10000 0 -10000 0 0
LCK 0.008 0.2 -10000 0 -0.82 41 41
PAG1 0.007 0.19 -10000 0 -0.8 41 41
RAP1A 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.004 0.22 -10000 0 -0.82 51 51
CD80 -0.076 0.12 -10000 0 -10000 0 0
CD86 -0.001 0.02 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1 -0.018 0.058 -10000 0 -0.27 35 35
HRAS -0.001 0.02 -10000 0 -10000 0 0
GO:0035030 -0.046 0.14 -10000 0 -0.58 47 47
CD8A 0 0.074 -10000 0 -0.37 30 30
CD8B -0.024 0.15 -10000 0 -0.56 61 61
PTPRC -0.01 0.078 -10000 0 -0.5 19 19
PDK1/PKC theta 0.033 0.16 -10000 0 -0.59 44 44
CSK/PAG1 0.012 0.18 -10000 0 -0.79 39 39
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I -0.001 0.015 -10000 0 -10000 0 0
GRAP2/SLP76 -0.036 0.17 -10000 0 -0.77 42 42
STIM1 0.041 0.079 -10000 0 -10000 0 0
RAS family/GTP 0.041 0.054 -10000 0 -0.18 29 29
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.008 0.23 -10000 0 -0.91 47 47
mol:DAG -0.007 0.1 -10000 0 -0.41 40 40
RAP1A/GDP 0.015 0.018 -10000 0 -10000 0 0
PLCG1 0 0 -10000 0 -10000 0 0
CD247 -0.014 0.12 -10000 0 -0.73 25 25
cytotoxic T cell degranulation 0 0.22 -10000 0 -1 35 35
RAP1A/GTP -0.003 0.014 -10000 0 -0.07 15 15
mol:PI-3-4-5-P3 0.026 0.14 -10000 0 -0.56 43 43
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.012 0.18 0.29 155 -0.61 40 195
NRAS -0.001 0.013 -10000 0 -10000 0 0
ZAP70 -0.03 0.13 -10000 0 -0.44 68 68
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.026 0.14 -10000 0 -0.63 40 40
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
CD8 heterodimer -0.032 0.14 -10000 0 -0.58 50 50
CARD11 -0.008 0.055 -10000 0 -0.32 24 24
PRKCB -0.012 0.087 -10000 0 -0.34 46 46
PRKCE -0.007 0.069 -10000 0 -0.28 38 38
PRKCQ 0.023 0.18 -10000 0 -0.68 46 46
LCP2 0 0.009 -10000 0 -0.28 1 1
BCL10 0 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.031 0.1 -10000 0 -0.4 41 41
IKK complex 0.041 0.044 -10000 0 -0.12 27 27
RAS family/GDP -0.002 0.006 -10000 0 -10000 0 0
MAP3K14 0.036 0.08 -10000 0 -0.3 35 35
PDPK1 0.033 0.12 -10000 0 -0.46 38 38
TCR/CD3/MHC I/CD8/Fyn -0.008 0.24 -10000 0 -0.96 47 47
Coregulation of Androgen receptor activity

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
NRIP1 -0.003 0.034 -10000 0 -0.81 1 1
SVIL -0.004 0.049 -10000 0 -0.81 3 3
ZNF318 0.024 0.059 0.2 7 -10000 0 7
JMJD2C -0.003 0.042 -10000 0 -0.14 77 77
T-DHT/AR/Ubc9 -0.078 0.18 -10000 0 -0.56 122 122
CARM1 0 0 -10000 0 -10000 0 0
PRDX1 0.002 0.012 -10000 0 -0.28 1 1
PELP1 0.005 0.013 -10000 0 -10000 0 0
CTNNB1 -0.001 0.015 -10000 0 -10000 0 0
AKT1 0.008 0.019 -10000 0 -10000 0 0
PTK2B -0.004 0.01 -10000 0 -10000 0 0
MED1 0.002 0.048 -10000 0 -0.28 20 20
MAK 0.013 0.11 0.28 2 -0.78 11 13
response to oxidative stress 0.001 0.004 -10000 0 -10000 0 0
HIP1 -0.005 0.055 -10000 0 -0.81 4 4
GSN -0.013 0.094 -10000 0 -0.81 13 13
NCOA2 -0.025 0.14 -10000 0 -0.81 31 31
NCOA6 -0.002 0.021 -10000 0 -0.28 1 1
DNA-PK 0.022 0.06 0.23 1 -10000 0 1
NCOA4 0 0 -10000 0 -10000 0 0
PIAS3 -0.001 0.015 -10000 0 -10000 0 0
cell proliferation -0.007 0.12 -10000 0 -0.89 11 11
XRCC5 0.007 0.016 -10000 0 -10000 0 0
UBE3A -0.006 0.032 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.091 0.21 -10000 0 -0.6 134 134
FHL2 -0.017 0.13 -10000 0 -1.3 6 6
RANBP9 -0.001 0.019 -10000 0 -10000 0 0
JMJD1A -0.012 0.056 -10000 0 -0.14 141 141
CDK6 -0.006 0.078 -10000 0 -0.71 11 11
TGFB1I1 -0.004 0.049 -10000 0 -0.81 3 3
T-DHT/AR/CyclinD1 -0.09 0.19 -10000 0 -0.56 129 129
XRCC6 0.007 0.016 -10000 0 -10000 0 0
T-DHT/AR -0.065 0.21 -10000 0 -0.55 137 137
CTDSP1 0 0 -10000 0 -10000 0 0
CTDSP2 0.016 0.04 -10000 0 -10000 0 0
BRCA1 -0.003 0.036 -10000 0 -0.48 3 3
TCF4 0.004 0.087 -10000 0 -0.8 10 10
CDKN2A -0.038 0.11 -10000 0 -0.28 143 143
SRF 0.024 0.02 -10000 0 -10000 0 0
NKX3-1 -0.081 0.2 -10000 0 -1.3 18 18
KLK3 -0.19 0.52 -10000 0 -1.6 127 127
TMF1 0 0 -10000 0 -10000 0 0
HNRNPA1 0.009 0.022 -10000 0 -10000 0 0
AOF2 -0.009 0.024 -10000 0 -0.072 127 127
APPL1 0.035 0.034 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.07 0.19 -10000 0 -0.55 122 122
AR -0.097 0.27 -10000 0 -0.81 122 122
UBA3 0 0 -10000 0 -10000 0 0
PATZ1 0.009 0.022 -10000 0 -10000 0 0
PAWR -0.001 0.026 -10000 0 -0.81 1 1
PRKDC 0.006 0.022 -10000 0 -0.28 2 2
PA2G4 0.012 0.029 -10000 0 -10000 0 0
UBE2I 0 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.066 0.17 -10000 0 -0.51 121 121
RPS6KA3 -0.006 0.056 -10000 0 -0.81 4 4
T-DHT/AR/ARA70 -0.082 0.18 -10000 0 -0.56 121 121
LATS2 0.01 0.024 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.061 0.18 0.19 1 -0.51 121 122
Cyclin D3/CDK11 p58 0 0.006 -10000 0 -10000 0 0
VAV3 -0.011 0.078 -10000 0 -0.7 9 9
KLK2 -0.12 0.33 -10000 0 -1.2 77 77
CASP8 0.004 0.011 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.089 0.19 -10000 0 -0.54 143 143
TMPRSS2 -0.18 0.4 -10000 0 -1.2 132 132
CCND1 -0.015 0.069 -10000 0 -0.32 39 39
PIAS1 -0.006 0.032 -10000 0 -10000 0 0
mol:T-DHT -0.009 0.034 -10000 0 -0.079 172 172
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.013 0.051 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.08 0.19 -10000 0 -0.56 131 131
CMTM2 0.003 0.013 -10000 0 -0.28 1 1
SNURF -0.02 0.13 -10000 0 -0.81 25 25
ZMIZ1 0.003 0.031 -10000 0 -0.35 1 1
CCND3 0.002 0.01 -10000 0 -10000 0 0
TGIF1 0.009 0.022 -10000 0 -10000 0 0
FKBP4 -0.004 0.032 -10000 0 -0.29 8 8
BCR signaling pathway

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
JUN 0.003 0.12 -10000 0 -0.45 34 34
IKBKB 0.015 0.054 -10000 0 -0.27 3 3
AKT1 0.004 0.081 0.25 1 -0.26 32 33
IKBKG 0.017 0.056 -10000 0 -0.24 17 17
CALM1 -0.012 0.096 -10000 0 -0.46 29 29
PIK3CA 0 0.009 -10000 0 -0.28 1 1
MAP3K1 -0.01 0.15 -10000 0 -0.63 35 35
MAP3K7 0 0.009 -10000 0 -0.28 1 1
mol:Ca2+ -0.021 0.1 -10000 0 -0.49 29 29
DOK1 -0.001 0.013 -10000 0 -0.28 2 2
AP-1 -0.043 0.11 -10000 0 -0.25 86 86
LYN 0 0 -10000 0 -10000 0 0
BLNK 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
BCR complex -0.081 0.22 -10000 0 -0.64 110 110
CD22 -0.063 0.19 -10000 0 -0.56 94 94
CAMK2G -0.003 0.09 -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 -0.049 0.14 -10000 0 -0.46 91 91
GO:0007205 -0.021 0.1 -10000 0 -0.5 29 29
SYK 0 0.009 -10000 0 -0.28 1 1
ELK1 -0.012 0.097 -10000 0 -0.47 29 29
NFATC1 -0.018 0.14 -10000 0 -0.39 92 92
B-cell antigen/BCR complex -0.081 0.22 -10000 0 -0.64 110 110
PAG1/CSK -0.001 0.012 -10000 0 -10000 0 0
NFKBIB 0.015 0.02 -10000 0 -10000 0 0
HRAS -0.01 0.1 -10000 0 -0.48 29 29
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 -0.06 0.17 -10000 0 -0.54 93 93
mol:GDP -0.021 0.094 -10000 0 -0.47 29 29
PTEN -0.002 0.036 -10000 0 -0.81 2 2
CD79B -0.029 0.14 -10000 0 -0.59 49 49
NF-kappa-B/RelA/I kappa B alpha 0.019 0.016 -10000 0 -10000 0 0
GRB2 0 0.009 -10000 0 -0.28 1 1
PI3K/BCAP/CD19 -0.027 0.16 -10000 0 -0.48 92 92
PIK3R1 -0.006 0.068 -10000 0 -0.81 7 7
mol:IP3 -0.031 0.1 -10000 0 -0.51 29 29
CSK 0 0 -10000 0 -10000 0 0
FOS -0.14 0.23 -10000 0 -0.45 318 318
CHUK 0.017 0.056 -10000 0 -0.24 16 16
IBTK 0 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.024 0.081 -10000 0 -0.49 17 17
PTPN6 -0.059 0.17 -10000 0 -0.76 39 39
RELA 0 0 -10000 0 -10000 0 0
BCL2A1 0.015 0.02 -10000 0 -0.12 1 1
VAV2 -0.071 0.17 -10000 0 -0.54 91 91
ubiquitin-dependent protein catabolic process 0.019 0.019 -10000 0 -10000 0 0
BTK -0.004 0.006 -10000 0 -10000 0 0
CD19 -0.081 0.18 -10000 0 -0.55 91 91
MAP4K1 -0.012 0.064 -10000 0 -0.81 2 2
CD72 -0.008 0.051 -10000 0 -0.3 26 26
PAG1 -0.001 0.02 -10000 0 -0.28 5 5
MAPK14 0.001 0.13 -10000 0 -0.52 34 34
SH3BP5 0 0 -10000 0 -10000 0 0
PIK3AP1 -0.012 0.11 -10000 0 -0.55 29 29
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.043 0.14 -10000 0 -0.48 80 80
RAF1 -0.002 0.1 -10000 0 -0.45 29 29
RasGAP/p62DOK/SHIP -0.056 0.16 -10000 0 -0.51 93 93
CD79A -0.083 0.22 -10000 0 -0.56 147 147
re-entry into mitotic cell cycle -0.042 0.11 -10000 0 -0.26 81 81
RASA1 0 0 -10000 0 -10000 0 0
MAPK3 0.015 0.085 -10000 0 -0.43 17 17
MAPK1 0.015 0.085 -10000 0 -0.43 17 17
CD72/SHP1 -0.055 0.16 -10000 0 -0.7 40 40
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.001 0.13 -10000 0 -0.52 37 37
actin cytoskeleton organization -0.026 0.15 -10000 0 -0.45 91 91
NF-kappa-B/RelA 0.042 0.032 -10000 0 -10000 0 0
Calcineurin -0.021 0.074 -10000 0 -0.45 17 17
PI3K -0.058 0.13 -10000 0 -0.54 39 39
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.033 0.11 -10000 0 -0.58 29 29
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.049 0.18 -10000 0 -0.84 34 34
DAPP1 -0.053 0.2 -10000 0 -0.98 34 34
cytokine secretion -0.015 0.13 -10000 0 -0.36 92 92
mol:DAG -0.031 0.1 -10000 0 -0.51 29 29
PLCG2 -0.002 0.037 -10000 0 -0.63 3 3
MAP2K1 0.007 0.093 -10000 0 -0.48 17 17
B-cell antigen/BCR complex/FcgammaRIIB -0.071 0.2 -10000 0 -0.62 93 93
mol:PI-3-4-5-P3 -0.043 0.093 0.34 1 -0.37 38 39
ETS1 0.003 0.091 -10000 0 -0.49 19 19
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.058 0.16 -10000 0 -0.53 91 91
B-cell antigen/BCR complex/LYN -0.06 0.19 -10000 0 -0.57 96 96
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0 0.001 -10000 0 -10000 0 0
RAC1 -0.03 0.17 -10000 0 -0.48 91 91
B-cell antigen/BCR complex/LYN/SYK -0.059 0.18 -10000 0 -0.57 93 93
CARD11 -0.016 0.1 -10000 0 -0.5 29 29
FCGR2B -0.004 0.052 -10000 0 -0.81 4 4
PPP3CA -0.001 0.013 -10000 0 -0.28 2 2
BCL10 0 0 -10000 0 -10000 0 0
IKK complex 0.017 0.027 -10000 0 -0.097 2 2
PTPRC -0.01 0.078 -10000 0 -0.5 19 19
PDPK1 -0.028 0.062 0.22 1 -0.27 22 23
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
Insulin Pathway

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
CBL/APS/CAP -0.13 0.22 -9999 0 -0.48 256 256
TC10/GTP -0.1 0.18 -9999 0 -0.42 242 242
Insulin Receptor/Insulin/IRS1/Shp2 -0.021 0.1 -9999 0 -0.5 41 41
HRAS -0.001 0.02 -9999 0 -10000 0 0
APS homodimer -0.012 0.057 -9999 0 -0.28 43 43
GRB14 -0.099 0.22 -9999 0 -0.46 212 212
FOXO3 -0.013 0.063 -9999 0 -0.7 7 7
AKT1 -0.056 0.13 -9999 0 -0.52 10 10
INSR 0 0.009 -9999 0 -0.27 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 -0.81 242 242
CRK 0 0 -9999 0 -10000 0 0
PTPN1 0.033 0.03 -9999 0 -10000 0 0
CAV1 -0.12 0.23 -9999 0 -0.52 225 225
CBL/APS/CAP/Crk-II/C3G -0.12 0.2 -9999 0 -0.46 242 242
Insulin Receptor/Insulin/IRS1/NCK2 -0.021 0.1 -9999 0 -0.5 41 41
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.021 0.094 -9999 0 -0.44 48 48
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.012 0.056 -9999 0 -10000 0 0
RPS6KB1 -0.007 0.13 -9999 0 -0.47 10 10
PARD6A -0.001 0.02 -9999 0 -0.28 5 5
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 -0.006 0.068 -9999 0 -0.81 7 7
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.049 0.11 -9999 0 -0.49 10 10
HRAS/GTP -0.016 0.076 -9999 0 -0.47 2 2
Insulin Receptor 0 0.009 -9999 0 -0.27 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.019 0.093 -9999 0 -0.47 41 41
PRKCI -0.013 0.032 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.061 0.14 -9999 0 -0.42 120 120
SHC1 0 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0.002 -9999 0 -10000 0 0
PI3K -0.022 0.096 -9999 0 -0.45 48 48
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 -0.001 0.013 -9999 0 -10000 0 0
AKT2 -0.056 0.13 -9999 0 -0.38 120 120
PRKCZ -0.013 0.037 -9999 0 -0.61 1 1
SH2B2 -0.012 0.057 -9999 0 -0.28 43 43
SHC/SHIP -0.018 0.088 -9999 0 -0.44 41 41
F2RL2 -0.058 0.15 -9999 0 -0.81 21 21
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 -0.12 0.21 -9999 0 -0.49 242 242
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0 0.003 -9999 0 -10000 0 0
INPP5D -0.02 0.094 -9999 0 -0.47 41 41
SOS1 0 0 -9999 0 -10000 0 0
SGK1 -0.008 0.071 -9999 0 -1 5 5
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 -0.033 0.16 -9999 0 -0.81 41 41
p62DOK/RasGAP 0 0.002 -9999 0 -10000 0 0
INS 0.003 0.004 -9999 0 -10000 0 0
mol:PI-3-4-P2 -0.019 0.093 -9999 0 -0.47 41 41
GRB2 0 0.009 -9999 0 -0.28 1 1
EIF4EBP1 -0.013 0.14 -9999 0 -0.46 23 23
PTPRA 0 0.001 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.28 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 -0.014 0.066 -9999 0 -0.33 41 41
Insulin Receptor/Insulin/IRS1 -0.021 0.1 -9999 0 -0.51 41 41
Insulin Receptor/Insulin/IRS3 -0.001 0.007 -9999 0 -10000 0 0
Par3/Par6 -0.025 0.075 -9999 0 -0.46 21 21
Osteopontin-mediated 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
IKK alpha homodimer -0.033 0.079 -9999 0 -0.44 28 28
NF kappa B1 p50/RelA/I kappa B alpha -0.02 0.065 -9999 0 -0.44 6 6
alphaV/beta3 Integrin/Osteopontin/Src -0.044 0.072 -9999 0 -10000 0 0
AP1 -0.14 0.21 -9999 0 -0.56 116 116
ILK -0.003 0.1 -9999 0 -0.48 28 28
bone resorption -0.031 0.093 -9999 0 -0.63 11 11
PTK2B 0 0 -9999 0 -10000 0 0
PYK2/p130Cas 0.008 0.087 -9999 0 -0.43 28 28
ITGAV 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.012 0.083 -9999 0 -0.62 18 18
alphaV/beta3 Integrin/Osteopontin -0.046 0.099 -9999 0 -0.53 28 28
MAP3K1 -0.004 0.11 -9999 0 -0.5 28 28
JUN -0.007 0.077 -9999 0 -0.81 9 9
MAPK3 0.012 0.1 -9999 0 -0.44 28 28
MAPK1 0.012 0.1 -9999 0 -0.44 28 28
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 0.006 0.12 -9999 0 -0.52 30 30
ITGB3 -0.024 0.13 -9999 0 -0.8 28 28
NFKBIA 0.025 0.096 -9999 0 -0.42 28 28
FOS -0.24 0.37 -9999 0 -0.81 298 298
CD44 -0.001 0.015 -9999 0 -0.28 3 3
CHUK 0 0 -9999 0 -10000 0 0
PLAU 0.023 0.096 -9999 0 -0.5 2 2
NF kappa B1 p50/RelA -0.019 0.062 -9999 0 -0.45 4 4
BCAR1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.018 0.1 -9999 0 -0.61 28 28
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.005 0.1 -9999 0 -0.48 28 28
VAV3 0.001 0.11 -9999 0 -0.46 35 35
MAP3K14 -0.001 0.1 -9999 0 -0.48 28 28
ROCK2 -0.015 0.11 -9999 0 -0.81 18 18
SPP1 -0.072 0.12 -9999 0 -0.27 265 265
RAC1 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.033 0.08 -9999 0 -0.41 35 35
MMP2 -0.076 0.21 -9999 0 -0.67 34 34
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.002 0.011 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.028 0.12 0.55 10 -10000 0 10
IL27/IL27R/JAK1 -0.065 0.18 -10000 0 -0.74 23 23
TBX21 -0.038 0.21 -10000 0 -0.65 60 60
IL12B -0.048 0.11 -10000 0 -0.28 191 191
IL12A -0.028 0.14 -10000 0 -0.53 68 68
IL6ST -0.081 0.25 -10000 0 -0.82 105 105
IL27RA/JAK1 -0.006 0.062 -10000 0 -1.3 2 2
IL27 -0.023 0.086 -10000 0 -0.28 63 63
TYK2 0.01 0.006 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.13 0.18 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.028 0.12 0.55 10 -10000 0 10
T cell proliferation during immune response 0.028 0.12 0.55 10 -10000 0 10
MAPKKK cascade -0.028 0.12 -10000 0 -0.55 10 10
STAT3 0 0 -10000 0 -10000 0 0
STAT2 0 0 -10000 0 -10000 0 0
STAT1 -0.005 0.038 -10000 0 -0.28 18 18
IL12RB1 -0.011 0.059 -10000 0 -0.3 38 38
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.053 0.23 -10000 0 -0.63 85 85
IL27/IL27R/JAK2/TYK2 -0.029 0.12 -10000 0 -0.56 10 10
positive regulation of T cell mediated cytotoxicity -0.028 0.12 -10000 0 -0.55 10 10
STAT1 (dimer) -0.084 0.22 0.52 8 -0.8 36 44
JAK2 0.004 0.027 -10000 0 -0.81 1 1
JAK1 0.001 0.003 -10000 0 -10000 0 0
STAT2 (dimer) -0.039 0.11 -10000 0 -0.55 8 8
T cell proliferation -0.18 0.25 -10000 0 -0.5 272 272
IL12/IL12R/TYK2/JAK2 0.014 0.069 -10000 0 -10000 0 0
IL17A -0.13 0.18 -10000 0 -10000 0 0
mast cell activation 0.028 0.12 0.55 10 -10000 0 10
IFNG 0.001 0.023 -10000 0 -0.085 3 3
T cell differentiation -0.003 0.006 -10000 0 -0.02 9 9
STAT3 (dimer) -0.039 0.11 -10000 0 -0.55 8 8
STAT5A (dimer) -0.043 0.12 -10000 0 -0.55 15 15
STAT4 (dimer) -0.059 0.14 -10000 0 -0.53 50 50
STAT4 -0.035 0.16 -10000 0 -0.8 43 43
T cell activation -0.008 0.008 0.13 2 -10000 0 2
IL27R/JAK2/TYK2 -0.054 0.16 -10000 0 -0.94 5 5
GATA3 -0.038 0.27 -10000 0 -1.5 34 34
IL18 0.006 0.032 -10000 0 -10000 0 0
positive regulation of mast cell cytokine production -0.039 0.1 -10000 0 -0.54 8 8
IL27/EBI3 -0.025 0.083 -10000 0 -0.5 16 16
IL27RA 0 0.069 -10000 0 -1.4 2 2
IL6 -0.29 0.39 -10000 0 -0.81 362 362
STAT5A -0.007 0.072 -10000 0 -0.81 8 8
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.003 0.027 0.48 2 -10000 0 2
IL1B 0.001 0.079 -10000 0 -0.63 15 15
EBI3 -0.006 0.081 -10000 0 -0.49 21 21
TNF -0.002 0.08 -10000 0 -0.63 14 14
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.026 0.027 -9999 0 -10000 0 0
BUB1B -0.036 0.047 -9999 0 -10000 0 0
PLK1 -0.006 0.021 -9999 0 -10000 0 0
PLK1S1 0.001 0.012 -9999 0 -10000 0 0
KIF2A 0.004 0.019 -9999 0 -10000 0 0
regulation of mitotic centrosome separation -0.006 0.021 -9999 0 -10000 0 0
GOLGA2 0 0 -9999 0 -10000 0 0
Hec1/SPC24 -0.16 0.11 -9999 0 -0.27 463 463
WEE1 -0.001 0.022 -9999 0 -10000 0 0
cytokinesis -0.045 0.05 -9999 0 -0.26 3 3
PP2A-alpha B56 0.033 0.022 -9999 0 -10000 0 0
AURKA 0.003 0.011 -9999 0 -10000 0 0
PICH/PLK1 -0.071 0.091 -9999 0 -0.32 10 10
CENPE -0.047 0.082 -9999 0 -0.2 2 2
RhoA/GTP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.004 0.019 -9999 0 -10000 0 0
PPP2CA 0 0 -9999 0 -10000 0 0
FZR1 0 0 -9999 0 -10000 0 0
TPX2 -0.002 0.014 -9999 0 -10000 0 0
PAK1 -0.006 0.041 -9999 0 -0.28 22 22
SPC24 -0.17 0.14 -9999 0 -0.28 610 610
FBXW11 0 0 -9999 0 -10000 0 0
CLSPN -0.002 0.015 -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 -0.004 0.012 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle -0.001 0.002 -9999 0 -10000 0 0
STAG2 -0.001 0.026 -9999 0 -0.81 1 1
GRASP65/GM130/RAB1/GTP 0.008 0.009 -9999 0 -10000 0 0
spindle elongation -0.006 0.021 -9999 0 -10000 0 0
ODF2 0 0 -9999 0 -10000 0 0
BUB1 0.028 0.019 -9999 0 -10000 0 0
TPT1 0.001 0.012 -9999 0 -10000 0 0
CDC25C -0.002 0.013 -9999 0 -10000 0 0
CDC25B -0.003 0.038 -9999 0 -0.28 18 18
SGOL1 -0.026 0.027 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.02 0.039 -9999 0 -10000 0 0
CDC14B -0.009 0.11 -9999 0 -0.64 30 30
CDC20 -0.15 0.14 -9999 0 -0.28 540 540
PLK1/PBIP1 -0.027 0.051 -9999 0 -0.17 4 4
mitosis -0.006 0.007 -9999 0 -0.022 2 2
FBXO5 0.002 0.021 -9999 0 -10000 0 0
CDC2 -0.001 0.002 -9999 0 -10000 0 0
NDC80 -0.17 0.14 -9999 0 -10000 0 0
metaphase plate congression -0.001 0.014 -9999 0 -10000 0 0
ERCC6L -0.062 0.083 -9999 0 -10000 0 0
NLP/gamma Tubulin 0 0.012 -9999 0 -10000 0 0
microtubule cytoskeleton organization 0.001 0.012 -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 -0.13 0.096 -9999 0 -0.27 229 229
GRASP65/GM130/RAB1/GTP/PLK1 -0.001 0.002 -9999 0 -10000 0 0
RAB1A 0 0 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
Aurora A/BORA -0.001 0.022 -9999 0 -10000 0 0
mitotic prometaphase -0.002 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.01 0.049 -9999 0 -0.29 25 25
microtubule-based process -0.11 0.063 -9999 0 -10000 0 0
Golgi organization -0.006 0.021 -9999 0 -10000 0 0
Cohesin/SA2 -0.008 0.017 -9999 0 -0.47 1 1
PPP1CB/MYPT1 0 0 -9999 0 -10000 0 0
KIF20A -0.21 0.12 -9999 0 -10000 0 0
APC/C/CDC20 -0.083 0.075 -9999 0 -0.2 2 2
PPP2R1A 0 0 -9999 0 -10000 0 0
chromosome segregation -0.027 0.051 -9999 0 -0.17 4 4
PRC1 -0.072 0.12 -9999 0 -0.28 256 256
ECT2 -0.002 0.037 -9999 0 -10000 0 0
C13orf34 0.001 0.02 -9999 0 -10000 0 0
NUDC -0.001 0.014 -9999 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.036 0.047 -9999 0 -10000 0 0
spindle assembly -0.002 0.018 -9999 0 -10000 0 0
spindle stabilization 0.001 0.012 -9999 0 -10000 0 0
APC/C/HCDH1 -0.017 0.094 -9999 0 -0.55 30 30
MKLP2/PLK1 -0.11 0.063 -9999 0 -10000 0 0
CCNB1 -0.058 0.11 -9999 0 -0.28 207 207
PPP1CB 0 0 -9999 0 -10000 0 0
BTRC 0 0 -9999 0 -10000 0 0
ROCK2 -0.003 0.071 -9999 0 -0.52 18 18
TUBG1 0.001 0.013 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.02 0.038 -9999 0 -10000 0 0
MLF1IP -0.027 0.073 -9999 0 -0.19 158 158
INCENP 0 0.001 -9999 0 -10000 0 0
Syndecan-2-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
Syndecan-2/Fibronectin -0.057 0.073 -9999 0 -0.41 6 6
EPHB2 -0.005 0.037 -9999 0 -0.28 18 18
Syndecan-2/TACI -0.017 0.077 -9999 0 -0.54 18 18
LAMA1 -0.096 0.26 -9999 0 -0.81 117 117
Syndecan-2/alpha2 ITGB1 -0.13 0.22 -9999 0 -0.48 260 260
HRAS -0.001 0.02 -9999 0 -10000 0 0
Syndecan-2/CASK -0.002 0.031 -9999 0 -0.54 3 3
ITGA5 0 0 -9999 0 -10000 0 0
BAX 0.035 0.053 -9999 0 -0.53 8 8
EPB41 0 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.002 0.028 -9999 0 -0.49 3 3
LAMA3 -0.2 0.35 -9999 0 -0.81 245 245
EZR -0.001 0.015 -9999 0 -0.28 3 3
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.1 0.27 -9999 0 -0.81 127 127
Syndecan-2/MMP2 -0.007 0.072 -9999 0 -0.68 10 10
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.016 0.097 -9999 0 -0.62 25 25
dendrite morphogenesis -0.005 0.035 -9999 0 -0.53 3 3
Syndecan-2/GM-CSF -0.005 0.037 -9999 0 -0.54 3 3
determination of left/right symmetry 0.017 0.037 -9999 0 -0.36 7 7
Syndecan-2/PKC delta -0.002 0.031 -9999 0 -0.53 3 3
GNB2L1 0 0 -9999 0 -10000 0 0
MAPK3 0.022 0.037 -9999 0 -0.48 3 3
MAPK1 0.022 0.037 -9999 0 -0.48 3 3
Syndecan-2/RACK1 -0.002 0.027 -9999 0 -0.46 3 3
NF1 -0.001 0.026 -9999 0 -0.81 1 1
FGFR/FGF/Syndecan-2 0.017 0.037 -9999 0 -0.36 7 7
ITGA2 -0.02 0.13 -9999 0 -0.81 25 25
MAPK8 0.029 0.055 -9999 0 -0.57 8 8
Syndecan-2/alpha2/beta1 Integrin -0.067 0.18 -9999 0 -0.52 128 128
Syndecan-2/Kininogen -0.004 0.034 -9999 0 -0.54 3 3
ITGB1 0 0 -9999 0 -10000 0 0
SRC -0.002 0.025 -9999 0 -0.43 3 3
Syndecan-2/CASK/Protein 4.1 -0.002 0.028 -9999 0 -0.49 3 3
extracellular matrix organization -0.002 0.031 -9999 0 -0.53 3 3
actin cytoskeleton reorganization -0.057 0.073 -9999 0 -0.41 6 6
Syndecan-2/Caveolin-2/Ras -0.065 0.17 -9999 0 -0.5 127 127
Syndecan-2/Laminin alpha3 -0.14 0.23 -9999 0 -0.54 248 248
Syndecan-2/RasGAP -0.002 0.025 -9999 0 -0.43 3 3
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
PRKCD 0 0.009 -9999 0 -0.28 1 1
Syndecan-2 dimer -0.005 0.035 -9999 0 -0.53 3 3
GO:0007205 0 0.001 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.002 0.024 -9999 0 -0.41 3 3
RHOA 0 0 -9999 0 -10000 0 0
SDCBP 0 0 -9999 0 -10000 0 0
TNFRSF13B -0.026 0.11 -9999 0 -0.81 15 15
RASA1 0 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.016 0.097 -9999 0 -0.62 25 25
Syndecan-2/Synbindin -0.002 0.03 -9999 0 -0.53 3 3
TGFB1 0 0.009 -9999 0 -10000 0 0
CASP3 0.03 0.03 -9999 0 -0.48 3 3
FN1 -0.11 0.14 -9999 0 -0.28 398 398
Syndecan-2/IL8 -0.021 0.085 -9999 0 -0.53 22 22
SDC2 0.017 0.037 -9999 0 -0.37 7 7
KNG1 -0.003 0.031 -9999 0 -0.28 12 12
Syndecan-2/Neurofibromin -0.003 0.035 -9999 0 -0.53 4 4
TRAPPC4 0 0 -9999 0 -10000 0 0
CSF2 -0.006 0.042 -9999 0 -0.28 23 23
Syndecan-2/TGFB1 -0.002 0.031 -9999 0 -0.53 3 3
Syndecan-2/Syntenin/PI-4-5-P2 -0.002 0.028 -9999 0 -0.49 3 3
Syndecan-2/Ezrin -0.002 0.028 -9999 0 -0.48 3 3
PRKACA 0.029 0.034 -9999 0 -0.48 4 4
angiogenesis -0.021 0.084 -9999 0 -0.53 22 22
MMP2 -0.008 0.081 -9999 0 -0.81 10 10
IL8 -0.033 0.13 -9999 0 -0.4 80 80
calcineurin-NFAT signaling pathway -0.017 0.077 -9999 0 -0.53 18 18
TCGA08_retinoblastoma

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
CDKN2B -0.003 0.063 -10000 0 -0.66 8 8
CDKN2C 0.006 0.04 -10000 0 -0.8 2 2
CDKN2A -0.049 0.11 -10000 0 -0.29 167 167
CCND2 0.006 0.031 0.23 8 -0.16 11 19
RB1 -0.007 0.03 0.15 6 -0.23 8 14
CDK4 0.009 0.029 0.25 8 -10000 0 8
CDK6 0.006 0.035 0.27 7 -0.22 8 15
G1/S progression -0.007 0.034 0.23 8 -0.19 3 11
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.002 0.01 -10000 0 -10000 0 0
HSPA8 0 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.1 0.21 0.26 1 -0.57 147 148
AKT1 0.013 0.006 -10000 0 -10000 0 0
GSC -0.041 0.31 -10000 0 -1.5 41 41
NKX2-5 -0.042 0.098 -10000 0 -0.28 149 149
muscle cell differentiation 0.006 0.05 0.77 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.003 0.037 -10000 0 -0.46 2 2
SMAD4 0.013 0.043 -10000 0 -0.85 1 1
CBFB 0 0 -10000 0 -10000 0 0
SAP18 0 0 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.2 0.26 -10000 0 -0.53 379 379
SMAD3/SMAD4/VDR 0.005 0.031 -10000 0 -0.45 2 2
MYC -0.018 0.12 -10000 0 -0.81 23 23
CDKN2B 0.029 0.12 -10000 0 -1.5 6 6
AP1 -0.13 0.21 -10000 0 -0.43 299 299
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.001 0.015 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0 0.042 -10000 0 -0.35 1 1
SP3 0 0 -10000 0 -10000 0 0
CREB1 0 0 -10000 0 -10000 0 0
FOXH1 -0.037 0.11 -10000 0 -0.4 4 4
SMAD3/SMAD4/GR -0.009 0.07 -10000 0 -0.58 13 13
GATA3 -0.036 0.15 -10000 0 -0.57 60 60
SKI/SIN3/HDAC complex/NCoR1 0.002 0.014 -10000 0 -10000 0 0
MEF2C/TIF2 -0.044 0.11 -10000 0 -0.6 25 25
endothelial cell migration -0.01 0.037 -10000 0 -10000 0 0
MAX 0.001 0.004 -10000 0 -10000 0 0
RBBP7 -0.002 0.025 -10000 0 -0.28 8 8
RBBP4 -0.001 0.026 -10000 0 -0.81 1 1
RUNX2 -0.004 0.032 -10000 0 -10000 0 0
RUNX3 -0.005 0.059 -10000 0 -0.61 8 8
RUNX1 -0.001 0.026 -10000 0 -0.81 1 1
CTBP1 0 0 -10000 0 -10000 0 0
NR3C1 -0.009 0.089 -10000 0 -0.81 12 12
VDR 0 0 -10000 0 -10000 0 0
CDKN1A 0.049 0.081 -10000 0 -1.5 2 2
KAT2B 0 0.026 -10000 0 -0.81 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.022 0.071 -10000 0 -0.46 5 5
DCP1A 0 0 -10000 0 -10000 0 0
SKI 0 0 -10000 0 -10000 0 0
SERPINE1 0.009 0.037 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF2 -0.002 0.034 -10000 0 -0.55 2 2
SMAD3/SMAD4/ATF3 -0.086 0.2 -10000 0 -0.57 148 148
SAP30 -0.001 0.018 -10000 0 -0.28 4 4
Cbp/p300/PIAS3 0.006 0.023 -10000 0 -10000 0 0
JUN -0.081 0.23 -10000 0 -0.42 299 299
SMAD3/SMAD4/IRF7 -0.01 0.063 -10000 0 -0.55 1 1
TFE3 0.017 0.006 -10000 0 -10000 0 0
COL1A2 0.028 0.1 -10000 0 -1.3 2 2
mesenchymal cell differentiation 0.004 0.034 0.55 1 -10000 0 1
DLX1 -0.052 0.13 -10000 0 -0.81 10 10
TCF3 0 0.009 -10000 0 -0.28 1 1
FOS -0.23 0.38 -10000 0 -0.8 298 298
SMAD3/SMAD4/Max -0.002 0.03 -10000 0 -0.56 1 1
Cbp/p300/SNIP1 0 0 -10000 0 -10000 0 0
ZBTB17 0 0.005 -10000 0 -10000 0 0
LAMC1 0.042 0.049 -10000 0 -0.64 2 2
TGIF2/HDAC complex/SMAD3/SMAD4 -0.001 0.029 -10000 0 -0.56 1 1
IRF7 -0.026 0.082 -10000 0 -0.35 22 22
ESR1 -0.15 0.29 -10000 0 -0.58 263 263
HNF4A -0.004 0.034 -10000 0 -0.28 15 15
MEF2C -0.002 0.092 -10000 0 -0.69 4 4
SMAD2-3/SMAD4 -0.003 0.034 -10000 0 -0.55 1 1
Cbp/p300/Src-1 0.003 0.023 -10000 0 -0.53 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 0.028 -10000 0 -0.28 10 10
HDAC1 0 0 -10000 0 -10000 0 0
HDAC2 0 0 -10000 0 -10000 0 0
SNIP1 0 0.002 -10000 0 -10000 0 0
GCN5L2 0.001 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.001 0.031 -10000 0 -0.55 1 1
MSG1/HSC70 -0.24 0.3 -10000 0 -0.62 379 379
SMAD2 0.014 0.021 -10000 0 -10000 0 0
SMAD3 0.014 0.029 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.007 0.026 -10000 0 -0.36 1 1
SMAD2/SMAD2/SMAD4 0.026 0.041 -10000 0 -1.1 1 1
NCOR1 -0.001 0.026 -10000 0 -0.81 1 1
NCOA2 -0.025 0.14 -10000 0 -0.81 31 31
NCOA1 -0.001 0.026 -10000 0 -0.81 1 1
MYOD/E2A -0.003 0.021 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.008 0.04 -10000 0 -0.42 2 2
IFNB1 0.014 0.085 -10000 0 -0.48 1 1
SMAD3/SMAD4/MEF2C -0.025 0.074 -10000 0 -0.77 3 3
CITED1 -0.31 0.39 -10000 0 -0.79 393 393
SMAD2-3/SMAD4/ARC105 -0.001 0.03 -10000 0 -0.49 1 1
RBL1 -0.001 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.038 0.063 -10000 0 -0.49 6 6
RUNX1-3/PEBPB2 -0.004 0.047 -10000 0 -0.63 5 5
SMAD7 -0.078 0.14 -10000 0 -0.59 10 10
MYC/MIZ-1 -0.014 0.095 -10000 0 -0.62 23 23
SMAD3/SMAD4 0.019 0.06 0.27 38 -0.45 1 39
IL10 0.018 0.12 -10000 0 -0.53 36 36
PIASy/HDAC complex 0.001 0.003 -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 -0.52 34 34
CDK4 0.001 0.015 -10000 0 -0.28 2 2
PIAS4 0.001 0.003 -10000 0 -10000 0 0
ATF3 -0.12 0.29 -10000 0 -0.81 147 147
SMAD3/SMAD4/SP1 0 0.034 -10000 0 -0.53 2 2
FOXG1 -0.021 0.073 -10000 0 -10000 0 0
FOXO3 0.025 0.03 -10000 0 -0.62 2 2
FOXO1 0.019 0.068 -10000 0 -0.62 11 11
FOXO4 0.026 0.008 -10000 0 -10000 0 0
heart looping -0.002 0.091 -10000 0 -0.68 4 4
CEBPB 0.012 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.029 0.082 -10000 0 -0.57 11 11
MYOD1 -0.004 0.032 -10000 0 -0.28 13 13
SMAD3/SMAD4/HNF4 -0.006 0.036 -10000 0 -0.69 1 1
SMAD3/SMAD4/GATA3 -0.023 0.11 -10000 0 -0.58 34 34
SnoN/SIN3/HDAC complex/NCoR1 -0.003 0.028 -10000 0 -0.28 10 10
SMAD3/SMAD4/RUNX1-3/PEBPB2 0 0.05 -10000 0 -0.56 6 6
SMAD3/SMAD4/SP1-3 0.003 0.03 -10000 0 -0.46 2 2
MED15 0 0 -10000 0 -10000 0 0
SP1 0.019 0.013 -10000 0 -10000 0 0
SIN3B 0 0 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.007 0.088 -10000 0 -0.49 5 5
ITGB5 0.051 0.046 -10000 0 -0.43 1 1
TGIF/SIN3/HDAC complex/CtBP 0 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.071 0.19 -10000 0 -0.57 122 122
AR -0.099 0.26 -10000 0 -0.8 122 122
negative regulation of cell growth -0.026 0.074 -10000 0 -0.45 1 1
SMAD3/SMAD4/MYOD -0.007 0.035 -10000 0 -0.56 1 1
E2F5 -0.006 0.039 -10000 0 -0.28 20 20
E2F4 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.002 0.056 -10000 0 -0.55 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0 0.044 -10000 0 -0.35 3 3
TFDP1 -0.001 0.018 -10000 0 -0.28 4 4
SMAD3/SMAD4/AP1 -0.12 0.22 -10000 0 -0.43 299 299
SMAD3/SMAD4/RUNX2 -0.004 0.034 -10000 0 -0.56 1 1
TGIF2 0 0 -10000 0 -10000 0 0
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 -0.001 0.026 -10000 0 -0.81 1 1
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.004 0.017 -10000 0 -10000 0 0
AES 0.004 0.014 -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 0.026 -10000 0 -0.81 1 1
DKK2 -0.021 0.13 -10000 0 -0.81 25 25
TLE1 -0.003 0.074 -10000 0 -0.81 8 8
MACF1 0 0.001 -10000 0 -10000 0 0
CTNNB1 0.1 0.087 -10000 0 -10000 0 0
WIF1 -0.42 0.4 -10000 0 -0.79 524 524
beta catenin/RanBP3 0.014 0.076 0.37 38 -10000 0 38
KREMEN2 -0.13 0.14 -10000 0 -10000 0 0
DKK1 -0.078 0.19 -10000 0 -0.81 49 49
beta catenin/beta TrCP1 0.1 0.084 -10000 0 -10000 0 0
FZD1 0 0.001 -10000 0 -10000 0 0
AXIN2 -0.011 0.2 -10000 0 -1.5 16 16
AXIN1 0.006 0.006 -10000 0 -10000 0 0
RAN 0 0.002 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.005 0.019 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.092 0.079 -10000 0 -0.5 6 6
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 0.026 -10000 0 -0.28 2 2
CTBP1 0.004 0.015 -10000 0 -10000 0 0
MYC -0.02 0.24 -10000 0 -1.6 23 23
RANBP3 0 0.002 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.078 0.11 -10000 0 -0.61 25 25
NKD1 -0.009 0.072 -10000 0 -0.42 22 22
TCF4 -0.004 0.082 -10000 0 -0.8 10 10
TCF3 0.003 0.016 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0 0.006 -10000 0 -10000 0 0
Ran/GTP 0 0 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.013 0.095 0.44 40 -0.43 1 41
LEF1 -0.035 0.1 -10000 0 -0.29 120 120
DVL1 0.071 0.065 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.099 0.091 -10000 0 -0.64 4 4
DKK1/LRP6/Kremen 2 -0.11 0.14 -10000 0 -0.58 50 50
LRP6 0 0.009 -10000 0 -0.28 1 1
CSNK1A1 0.004 0.017 -10000 0 -10000 0 0
NLK 0.01 0.014 -10000 0 -10000 0 0
CCND1 0.003 0.1 -10000 0 -1.6 3 3
WNT1 0 0.012 -10000 0 -0.28 2 2
GSK3A 0.006 0.006 -10000 0 -10000 0 0
GSK3B 0 0 -10000 0 -10000 0 0
FRAT1 0 0 -10000 0 -10000 0 0
PPP2R5D 0.043 0.046 0.34 7 -10000 0 7
APC 0 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.14 0.13 0.27 511 -10000 0 511
CREBBP 0.004 0.015 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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
TGM2 0.005 0.035 -10000 0 -10000 0 0
GNB1/GNG2 -0.015 0.048 -10000 0 -0.21 35 35
AKT1 0.05 0.072 -10000 0 -0.22 16 16
EGF -0.17 0.33 -10000 0 -0.8 206 206
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.01 0.052 -10000 0 -0.56 2 2
mol:Ca2+ 0.046 0.099 -10000 0 -0.3 59 59
LYN -0.01 0.049 -10000 0 -0.52 1 1
RhoA/GTP -0.009 0.03 -10000 0 -0.14 2 2
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.052 0.11 -10000 0 -0.35 59 59
GNG2 -0.009 0.085 -10000 0 -0.81 11 11
ARRB2 0 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.029 0.056 -10000 0 -0.54 6 6
G beta5/gamma2 -0.019 0.065 -10000 0 -0.29 31 31
PRKCH 0.048 0.11 -10000 0 -0.36 53 53
DNM1 -0.006 0.068 -10000 0 -0.74 8 8
TXA2/TP beta/beta Arrestin3 -0.004 0.028 -10000 0 -0.31 7 7
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.031 0.15 -10000 0 -0.72 42 42
G12 family/GTP -0.022 0.074 -10000 0 -0.31 59 59
ADRBK1 0 0 -10000 0 -10000 0 0
ADRBK2 -0.003 0.051 -10000 0 -0.81 4 4
RhoA/GTP/ROCK1 -0.001 0.017 -10000 0 -0.54 1 1
mol:GDP -0.036 0.079 0.36 20 -10000 0 20
mol:NADP 0 0 -10000 0 -10000 0 0
RAB11A -0.001 0.013 -10000 0 -0.28 2 2
PRKG1 -0.048 0.19 -10000 0 -0.81 59 59
mol:IP3 0.047 0.12 -10000 0 -0.38 59 59
cell morphogenesis -0.001 0.017 -10000 0 -0.54 1 1
PLCB2 0.044 0.15 -10000 0 -0.52 59 59
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.001 0.063 -10000 0 -0.44 5 5
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.009 0.05 -10000 0 -0.52 1 1
RHOA 0 0 -10000 0 -10000 0 0
PTGIR -0.003 0.026 -10000 0 -0.28 9 9
PRKCB1 0.045 0.12 -10000 0 -0.38 59 59
GNAQ -0.002 0.036 -10000 0 -0.81 2 2
mol:L-citrulline 0 0 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.046 0.16 -10000 0 -0.54 59 59
LCK -0.013 0.074 -10000 0 -0.48 14 14
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.012 0.057 -10000 0 -0.35 1 1
TXA2-R family/G12 family/GDP/G beta/gamma 0.024 0.034 -10000 0 -0.29 6 6
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.011 0.055 -10000 0 -0.34 1 1
MAPK14 0.051 0.079 -10000 0 -0.24 28 28
TGM2/GTP 0.047 0.13 -10000 0 -0.43 59 59
MAPK11 0.05 0.082 -10000 0 -0.26 28 28
ARHGEF1 0.038 0.061 -10000 0 -0.19 14 14
GNAI2 0 0 -10000 0 -10000 0 0
JNK cascade 0.049 0.12 -10000 0 -0.4 59 59
RAB11/GDP -0.001 0.012 -10000 0 -0.28 2 2
ICAM1 0.046 0.093 -10000 0 -0.28 59 59
cAMP biosynthetic process 0.043 0.12 -10000 0 -0.36 59 59
Gq family/GTP/EBP50 -0.006 0.032 -10000 0 -0.25 15 15
actin cytoskeleton reorganization -0.001 0.017 -10000 0 -0.54 1 1
SRC -0.01 0.049 -10000 0 -0.52 1 1
GNB5 0 0 -10000 0 -10000 0 0
GNB1 0 0 -10000 0 -10000 0 0
EGF/EGFR -0.031 0.11 -10000 0 -0.35 23 23
VCAM1 0.044 0.1 -10000 0 -0.32 59 59
TP beta/Gq family/GDP/G beta5/gamma2 0.029 0.056 -10000 0 -0.54 6 6
platelet activation 0.066 0.1 -10000 0 -0.31 59 59
PGI2/IP -0.002 0.018 -10000 0 -10000 0 0
PRKACA -0.014 0.07 -10000 0 -0.38 35 35
Gq family/GDP/G beta5/gamma2 0.026 0.058 -10000 0 -0.54 6 6
TXA2/TP beta/beta Arrestin2 -0.006 0.056 -10000 0 -0.66 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.013 0.065 -10000 0 -0.35 35 35
mol:DAG 0.046 0.13 -10000 0 -0.42 59 59
EGFR -0.3 0.39 -10000 0 -0.8 369 369
TXA2/TP alpha 0.048 0.15 -10000 0 -0.5 59 59
Gq family/GTP -0.004 0.035 -10000 0 -0.28 15 15
YES1 -0.01 0.05 -10000 0 -0.44 2 2
GNAI2/GTP -0.011 0.057 -10000 0 -0.46 3 3
PGD2/DP -0.024 0.12 -10000 0 -0.63 35 35
SLC9A3R1 -0.023 0.077 -10000 0 -0.28 83 83
FYN -0.011 0.053 -10000 0 -0.5 3 3
mol:NO 0 0 -10000 0 -10000 0 0
GNA15 -0.003 0.035 -10000 0 -0.34 8 8
PGK/cGMP -0.032 0.13 -10000 0 -0.54 59 59
RhoA/GDP 0 0 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.014 0.079 -10000 0 -0.66 7 7
NOS3 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCA 0.042 0.12 -10000 0 -0.38 59 59
PRKCB 0.043 0.12 -10000 0 -0.38 64 64
PRKCE 0.049 0.11 -10000 0 -0.36 53 53
PRKCD 0.048 0.12 -10000 0 -0.38 59 59
PRKCG 0.044 0.12 -10000 0 -0.39 59 59
muscle contraction 0.05 0.15 -10000 0 -0.5 59 59
PRKCZ 0.052 0.11 -10000 0 -0.35 60 60
ARR3 -0.002 0.025 -10000 0 -10000 0 0
TXA2/TP beta -0.013 0.064 -10000 0 -0.49 4 4
PRKCQ 0.037 0.14 -10000 0 -0.4 69 69
MAPKKK cascade 0.044 0.14 -10000 0 -0.47 59 59
SELE 0.038 0.12 -10000 0 -0.42 59 59
TP beta/GNAI2/GDP/G beta/gamma -0.015 0.078 -10000 0 -0.58 10 10
ROCK1 -0.001 0.026 -10000 0 -0.81 1 1
GNA14 -0.015 0.09 -10000 0 -0.44 33 33
chemotaxis 0.045 0.18 -10000 0 -0.63 59 59
GNA12 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
GNA11 -0.002 0.036 -10000 0 -0.81 2 2
Rac1/GTP 0 0 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
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 -0.017 0.12 -9999 0 -0.81 21 21
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 -0.001 0.026 -9999 0 -0.81 1 1
RAC1-CDC42/GTP/PAK family -0.13 0.14 -9999 0 -0.28 457 457
response to UV 0 0 -9999 0 -10000 0 0
YES1 -0.001 0.026 -9999 0 -0.81 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 -0.002 0.036 -9999 0 -0.81 2 2
MAP3K12 0 0 -9999 0 -10000 0 0
FGR -0.001 0.027 -9999 0 -0.81 1 1
p38 alpha/TAB1 -0.007 0.034 -9999 0 -0.32 4 4
PRKG1 -0.048 0.19 -9999 0 -0.81 59 59
DUSP8 -0.003 0.045 -9999 0 -0.68 4 4
PGK/cGMP/p38 alpha -0.03 0.1 -9999 0 -0.4 62 62
apoptosis -0.007 0.033 -9999 0 -0.34 3 3
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0 0 -9999 0 -10000 0 0
DUSP1 -0.11 0.28 -9999 0 -0.81 134 134
PAK1 -0.006 0.041 -9999 0 -0.28 22 22
SRC 0 0.009 -9999 0 -10000 0 0
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 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.016 0.069 -9999 0 -0.35 18 18
BLK -0.04 0.1 -9999 0 -0.81 3 3
HCK -0.003 0.029 -9999 0 -10000 0 0
MAP2K3 0 0.009 -9999 0 -0.28 1 1
DUSP16 0 0 -9999 0 -10000 0 0
DUSP10 -0.001 0.015 -9999 0 -0.28 3 3
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.027 0.049 -9999 0 -0.35 4 4
positive regulation of innate immune response 0.022 0.075 -9999 0 -0.37 18 18
LCK -0.02 0.1 -9999 0 -0.81 13 13
p38alpha-beta/MKP7 -0.012 0.055 -9999 0 -0.35 17 17
p38alpha-beta/MKP5 -0.012 0.056 -9999 0 -0.35 17 17
PGK/cGMP -0.037 0.15 -9999 0 -0.63 59 59
PAK2 0 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.062 0.14 -9999 0 -0.42 89 89
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 -0.37 0.4 -9999 0 -0.81 457 457
Regulation of Telomerase

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
Telomerase catalytic core complex -0.05 0.11 -9999 0 -0.64 3 3
RAD9A 0 0.009 -9999 0 -0.28 1 1
AP1 -0.19 0.29 -9999 0 -0.63 299 299
IFNAR2 0.01 0.005 -9999 0 -10000 0 0
AKT1 -0.037 0.11 -9999 0 -0.29 147 147
ER alpha/Oestrogen -0.12 0.22 -9999 0 -0.63 147 147
NFX1/SIN3/HDAC complex 0 0.007 -9999 0 -10000 0 0
EGF -0.17 0.33 -9999 0 -0.8 206 206
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 -0.063 0.084 -9999 0 -0.6 3 3
SAP18 0 0 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.14 0.14 -9999 0 -10000 0 0
WRN 0 0 -9999 0 -10000 0 0
SP1 0.011 0.005 -9999 0 -10000 0 0
SP3 0 0.002 -9999 0 -10000 0 0
TERF2IP 0 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.048 0.074 -9999 0 -0.57 2 2
Mad/Max 0 0.006 -9999 0 -10000 0 0
TERT -0.051 0.12 -9999 0 -0.66 3 3
CCND1 -0.043 0.12 -9999 0 -1.3 3 3
MAX 0.001 0.004 -9999 0 -10000 0 0
RBBP7 -0.002 0.025 -9999 0 -0.28 8 8
RBBP4 -0.001 0.026 -9999 0 -0.81 1 1
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0 0 -9999 0 -10000 0 0
SIN3A 0 0 -9999 0 -10000 0 0
Telomerase/911 0.004 0.016 -9999 0 -10000 0 0
CDKN1B 0.008 0.074 -9999 0 -0.88 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 -0.001 0.018 -9999 0 -0.28 4 4
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0 0 -9999 0 -10000 0 0
JUN -0.006 0.077 -9999 0 -0.81 9 9
E6 0 0.001 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0 0 -9999 0 -10000 0 0
FOS -0.24 0.37 -9999 0 -0.81 298 298
IFN-gamma/IRF1 -0.024 0.06 -9999 0 -0.35 5 5
PARP2 0 0 -9999 0 -10000 0 0
BLM -0.03 0.087 -9999 0 -0.28 107 107
Telomerase -0.004 0.025 -9999 0 -10000 0 0
IRF1 -0.001 0.018 -9999 0 -0.27 3 3
ESR1 -0.15 0.29 -9999 0 -0.57 264 264
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 0.008 -9999 0 -10000 0 0
HDAC1 0 0 -9999 0 -10000 0 0
HDAC2 0.01 0.006 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.021 0.006 -9999 0 -10000 0 0
ABL1 0 0 -9999 0 -10000 0 0
MXD1 0.001 0.01 -9999 0 -0.28 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 -0.28 3 3
TERT/NF kappa B1/14-3-3 -0.062 0.099 -9999 0 -0.66 3 3
NR2F2 0 0.045 -9999 0 -0.81 3 3
MAPK3 0.014 0.02 -9999 0 -10000 0 0
MAPK1 0.014 0.02 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0 0.009 -9999 0 -10000 0 0
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 -0.3 0.39 -9999 0 -0.8 369 369
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.35 0.36 -9999 0 -0.68 504 504
MYC -0.01 0.12 -9999 0 -0.81 23 23
IL2 0.004 0.028 -9999 0 -0.28 6 6
KU 0 0 -9999 0 -10000 0 0
RAD50 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.009 -9999 0 -0.28 1 1
TGFB1 0 0.009 -9999 0 -10000 0 0
TRF2/BLM -0.017 0.049 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.059 0.082 -9999 0 -0.59 3 3
SP1/HDAC2 0 0 -9999 0 -10000 0 0
PINX1 0 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.048 0.074 -9999 0 -0.57 2 2
Smad3/Myc -0.012 0.08 -9999 0 -0.53 23 23
911 complex 0 0.004 -9999 0 -10000 0 0
IFNG -0.037 0.094 -9999 0 -10000 0 0
Telomerase/PinX1 -0.048 0.074 -9999 0 -0.57 2 2
Telomerase/AKT1/mTOR/p70S6K 0.004 0.054 -9999 0 -10000 0 0
SIN3B 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.048 0.074 -9999 0 -0.57 2 2
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 -0.048 0.074 -9999 0 -0.57 2 2
E2F1 -0.083 0.14 -9999 0 -0.28 321 321
ZNFX1 0 0 -9999 0 -10000 0 0
PIF1 -0.056 0.11 -9999 0 -10000 0 0
NCL 0 0 -9999 0 -10000 0 0
DKC1 -0.001 0.013 -9999 0 -0.28 2 2
telomeric DNA binding 0 0 -9999 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 -0.003 0.026 -9999 0 -0.28 9 9
ELF1 -0.011 0.047 -9999 0 -0.38 12 12
CCNA2 -0.12 0.14 -9999 0 -0.28 407 407
PIK3CA 0 0.009 -9999 0 -0.28 1 1
JAK3 -0.005 0.035 -9999 0 -10000 0 0
PIK3R1 -0.006 0.068 -9999 0 -0.81 7 7
JAK1 0 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.059 0.073 -9999 0 -0.61 6 6
SHC1 0 0 -9999 0 -10000 0 0
SP1 -0.005 0.042 -9999 0 -0.38 12 12
IL2RA 0.004 0.12 -9999 0 -1 12 12
IL2RB -0.011 0.055 -9999 0 -0.28 40 40
SOS1 0 0 -9999 0 -10000 0 0
IL2RG -0.018 0.087 -9999 0 -0.81 7 7
G1/S transition of mitotic cell cycle 0.008 0.12 -9999 0 -0.83 18 18
PTPN11 0 0 -9999 0 -10000 0 0
CCND2 0.016 0.12 -9999 0 -1 12 12
LCK -0.02 0.1 -9999 0 -0.81 13 13
GRB2 0 0.009 -9999 0 -0.28 1 1
IL2 -0.002 0.026 -9999 0 -10000 0 0
CDK6 -0.008 0.078 -9999 0 -0.71 11 11
CCND3 0.064 0.064 -9999 0 -0.58 4 4
Arf6 trafficking events

Figure S81.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S81.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.45 0.4 -10000 0 -0.81 553 553
CLTC 0.027 0.016 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.024 0.018 -10000 0 -10000 0 0
Dynamin 2/GTP -0.006 0.026 -10000 0 -10000 0 0
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.025 0.016 -10000 0 -10000 0 0
CPE 0.005 0.083 -10000 0 -0.54 22 22
CTNNB1 0 0 -10000 0 -10000 0 0
membrane fusion -0.001 0.017 -10000 0 -10000 0 0
CTNND1 -0.005 0.023 -10000 0 -10000 0 0
DNM2 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.029 0.013 -10000 0 -10000 0 0
TSHR -0.007 0.12 -10000 0 -0.54 43 43
INS 0.011 0.005 -10000 0 -10000 0 0
BIN1 -0.008 0.077 -10000 0 -0.75 10 10
mol:Choline -0.001 0.017 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.01 0.035 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.006 0.026 -10000 0 -10000 0 0
JUP 0.025 0.016 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.005 0.049 -10000 0 -0.49 10 10
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.016 0.052 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0 0.009 -10000 0 -0.28 1 1
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 -0.004 0.034 -10000 0 -0.28 15 15
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 0.009 0.033 -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 0.018 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.02 0.014 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.032 0.02 -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 -0.005 0.022 -10000 0 -10000 0 0
NME1 0.01 0.035 -10000 0 -10000 0 0
clathrin coat assembly 0.027 0.016 -10000 0 -10000 0 0
IL2RA 0.018 0.042 -10000 0 -0.37 6 6
VAMP3 0.018 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.23 0.2 -10000 0 -0.41 553 553
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 -0.002 0.029 -10000 0 -0.34 7 7
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0 0 -10000 0 -10000 0 0
PIP5K1C 0.03 0.013 -10000 0 -10000 0 0
SDC1 0.021 0.023 -10000 0 -0.35 1 1
ARF6/GDP -0.007 0.031 -10000 0 -10000 0 0
EXOC7 0 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.009 0.034 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.001 0.017 -10000 0 -10000 0 0
endocytosis 0.005 0.049 0.49 10 -10000 0 10
SCAMP2 0 0 -10000 0 -10000 0 0
ADRB2 -0.077 0.2 -10000 0 -0.44 234 234
EXOC3 0 0 -10000 0 -10000 0 0
ASAP2 -0.001 0.026 -10000 0 -0.81 1 1
Dynamin 2/GDP -0.006 0.026 -10000 0 -10000 0 0
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 -0.15 0.23 -10000 0 -0.43 380 380
RALA 0 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.007 0.029 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.023 0.074 -9999 0 -0.19 167 167
TP53 -0.008 0.018 -9999 0 -10000 0 0
Senescence -0.008 0.018 -9999 0 -10000 0 0
Apoptosis -0.008 0.018 -9999 0 -10000 0 0
Activated_Oncogenes 0 0 -9999 0 -10000 0 0
MDM2 0.015 0.038 -9999 0 -10000 0 0
MDM4 0 0 -9999 0 -10000 0 0
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.023 0.078 0.32 35 -10000 0 35
GNAI2 0 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.005 0.036 -10000 0 -0.54 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.032 0.14 -10000 0 -0.48 66 66
RhoA/GTP -0.024 0.079 -10000 0 -0.33 35 35
negative regulation of cAMP metabolic process -0.027 0.088 -10000 0 -0.31 82 82
GNAZ -0.007 0.072 -10000 0 -0.81 8 8
GNAI3 0 0 -10000 0 -10000 0 0
GNA12 0 0 -10000 0 -10000 0 0
S1PR5 -0.008 0.059 -10000 0 -0.81 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.027 0.089 -10000 0 -0.31 82 82
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
GNAI1 -0.042 0.18 -10000 0 -0.81 51 51
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.001 0.003 -9999 0 -10000 0 0
HDAC2 0.001 0.004 -9999 0 -10000 0 0
GNB1/GNG2 -0.01 0.076 -9999 0 -0.56 18 18
forebrain development -0.027 0.2 -9999 0 -0.52 124 124
GNAO1 -0.032 0.14 -9999 0 -0.48 66 66
SMO/beta Arrestin2 -0.005 0.056 -9999 0 -0.62 8 8
SMO 0.004 0.074 -9999 0 -0.75 9 9
ARRB2 0.003 0.005 -9999 0 -10000 0 0
GLI3/SPOP -0.002 0.036 -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 0.001 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0.007 -9999 0 -10000 0 0
GNAI1 -0.042 0.18 -9999 0 -0.81 51 51
XPO1 0.011 0.005 -9999 0 -10000 0 0
GLI1/Su(fu) -0.056 0.16 -9999 0 -0.52 75 75
SAP30 0 0.018 -9999 0 -0.28 4 4
mol:GDP 0.004 0.074 -9999 0 -0.75 9 9
MIM/GLI2A 0.002 0.028 -9999 0 -0.28 9 9
IFT88 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
GLI2 0.04 0.034 -9999 0 -10000 0 0
GLI3 0.039 0.041 -9999 0 -0.3 12 12
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
SAP18 0.001 0.003 -9999 0 -10000 0 0
embryonic digit morphogenesis 0 0 -9999 0 -10000 0 0
GNG2 -0.009 0.085 -9999 0 -0.81 11 11
Gi family/GTP -0.024 0.097 -9999 0 -0.35 52 52
SIN3B 0.001 0.004 -9999 0 -10000 0 0
SIN3A 0.001 0.003 -9999 0 -10000 0 0
GLI3/Su(fu) -0.003 0.027 -9999 0 -0.45 1 1
GLI2/Su(fu) -0.005 0.038 -9999 0 -0.4 6 6
FOXA2 -0.013 0.032 -9999 0 -10000 0 0
neural tube patterning -0.027 0.2 -9999 0 -0.52 124 124
SPOP 0 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 -0.003 0.027 -9999 0 -0.46 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 -0.28 9 9
embryonic limb morphogenesis -0.027 0.2 -9999 0 -0.52 124 124
SUFU -0.003 0.03 -9999 0 -0.31 9 9
LGALS3 -0.011 0.092 -9999 0 -0.81 13 13
catabolic process -0.004 0.028 -9999 0 -10000 0 0
GLI3A/CBP -0.026 0.096 -9999 0 -0.38 67 67
KIF3A 0 0 -9999 0 -10000 0 0
GLI1 -0.029 0.21 -9999 0 -0.54 124 124
RAB23 0 0 -9999 0 -10000 0 0
CSNK1A1 0 0 -9999 0 -10000 0 0
IFT172 -0.001 0.026 -9999 0 -0.81 1 1
RBBP7 -0.001 0.025 -9999 0 -0.28 8 8
Su(fu)/Galectin3 -0.009 0.067 -9999 0 -0.54 14 14
GNAZ -0.007 0.072 -9999 0 -0.81 8 8
RBBP4 0 0.026 -9999 0 -0.81 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 -0.003 0.025 -9999 0 -10000 0 0
STK36 0.01 0.026 -9999 0 -0.81 1 1
Gi family/GNB1/GNG2/GDP -0.028 0.097 -9999 0 -0.55 14 14
PTCH1 -0.069 0.35 -9999 0 -1.1 85 85
MIM/GLI1 -0.055 0.19 -9999 0 -0.52 104 104
CREBBP -0.026 0.096 -9999 0 -0.38 67 67
Su(fu)/SIN3/HDAC complex 0.006 0.021 -9999 0 -10000 0 0
S1P4 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 -9999 0 -10000 0 0
GNAO1 -0.032 0.14 -9999 0 -0.48 66 66
CDC42/GTP -0.025 0.078 -9999 0 -0.5 4 4
PLCG1 -0.026 0.081 -9999 0 -0.32 37 37
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 -0.024 0.077 -9999 0 -0.48 4 4
S1PR5 -0.008 0.059 -9999 0 -0.81 3 3
S1PR4 -0.014 0.08 -9999 0 -0.36 40 40
MAPK3 -0.026 0.081 -9999 0 -0.32 37 37
MAPK1 -0.026 0.081 -9999 0 -0.32 37 37
S1P/S1P5/Gi -0.027 0.089 -9999 0 -0.31 82 82
GNAI1 -0.042 0.18 -9999 0 -0.81 51 51
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.005 0.036 -9999 0 -0.54 3 3
RHOA -0.006 0.04 -9999 0 -0.46 6 6
S1P/S1P4/Gi -0.029 0.088 -9999 0 -0.3 87 87
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.007 0.072 -9999 0 -0.81 8 8
S1P/S1P4/G12/G13 -0.007 0.044 -9999 0 -0.49 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
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.022 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0.007 -10000 0 -10000 0 0
CDKN1B 0.035 0.026 -10000 0 -0.43 3 3
CDKN1A 0.036 0.022 -10000 0 -0.43 2 2
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC -0.001 0.015 -10000 0 -0.28 3 3
FOXO3 0.036 0.021 -10000 0 -0.43 2 2
AKT1 0 0.001 -10000 0 -10000 0 0
BAD 0 0.009 -10000 0 -0.28 1 1
AKT3 0.01 0.054 -10000 0 -0.44 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.037 0.002 -10000 0 -10000 0 0
AKT1/ASK1 -0.001 0.023 -10000 0 -0.42 3 3
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 0.022 0.41 3 -10000 0 3
TSC1 0.037 0.002 -10000 0 -10000 0 0
YWHAZ -0.001 0.015 -10000 0 -0.28 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 0.002 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
TBC1D4 0.022 0.039 -10000 0 -0.53 5 5
MAP3K5 -0.002 0.044 -10000 0 -0.81 3 3
MAPKAP1 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.039 0.022 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
AKT1S1 0.037 0.002 -10000 0 -10000 0 0
CASP9 0.037 0.002 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 -0.001 0.022 -10000 0 -0.41 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 -10000 0 0
AKT2/p21CIP1 -0.001 0.019 -10000 0 -0.42 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.001 -10000 0 -10000 0 0
CHUK 0.037 0.002 -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 0.016 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 0.008 -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 0.043 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0.004 -10000 0 -10000 0 0
glucose import -0.26 0.26 -10000 0 -0.48 555 555
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 -0.26 0.26 -10000 0 -0.49 555 555
GSK3A 0.037 0.002 -10000 0 -10000 0 0
FOXO1 0.031 0.049 -10000 0 -0.43 11 11
GSK3B 0.037 0.002 -10000 0 -10000 0 0
SFN -0.015 0.098 -10000 0 -0.51 30 30
G1/S transition of mitotic cell cycle 0.043 0.002 -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 -0.28 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 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
SPHK2 0.021 0.02 -10000 0 -0.62 1 1
MAP4K4 0.04 0.048 -10000 0 -0.69 1 1
BAG4 -0.004 0.046 -10000 0 -0.37 12 12
PKC zeta/ceramide -0.025 0.049 -10000 0 -0.59 1 1
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.081 -10000 0 -0.81 9 9
BAX -0.009 0.022 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
AKT1 0.024 0.01 -10000 0 -10000 0 0
BAD -0.023 0.047 0.2 1 -0.24 1 2
SMPD1 0.025 0.035 -10000 0 -0.25 14 14
RB1 -0.024 0.051 0.2 1 -0.48 2 3
FADD/Caspase 8 0.047 0.049 -10000 0 -0.66 1 1
MAP2K4 -0.016 0.048 0.2 1 -0.46 2 3
NSMAF 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.015 0.047 0.2 1 -0.3 3 4
EGF -0.17 0.33 -10000 0 -0.8 206 206
mol:ceramide -0.034 0.049 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 -0.62 1 1
ASAH1 -0.001 0.015 -10000 0 -0.28 3 3
negative regulation of cell cycle -0.024 0.05 0.2 1 -0.48 2 3
cell proliferation -0.095 0.16 -10000 0 -0.39 215 215
BID 0.022 0.036 -10000 0 -0.4 1 1
MAP3K1 -0.024 0.049 0.2 1 -0.48 1 2
EIF2A -0.006 0.042 -10000 0 -10000 0 0
TRADD 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
MAPK3 -0.003 0.044 -10000 0 -0.42 1 1
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.003 0.044 -10000 0 -0.42 1 1
Cathepsin D/ceramide -0.029 0.05 -10000 0 -0.24 1 1
FADD 0.038 0.052 -10000 0 -0.47 3 3
KSR1 -0.024 0.049 0.2 1 -0.33 3 4
MAPK8 -0.013 0.054 0.2 1 -0.37 7 8
PRKRA -0.023 0.046 0.2 1 -10000 0 1
PDGFA -0.001 0.026 -10000 0 -0.81 1 1
TRAF2 -0.001 0.018 -10000 0 -0.28 4 4
IGF1 -0.18 0.33 -10000 0 -0.81 215 215
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.034 0.049 0.21 1 -10000 0 1
CTSD -0.01 0.053 -10000 0 -10000 0 0
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 -0.42 215 215
PRKCD 0 0.009 -10000 0 -0.28 1 1
PRKCZ -0.001 0.026 -10000 0 -0.81 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.021 0.023 -10000 0 -0.62 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 0.026 -10000 0 -0.81 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.006 0.044 -10000 0 -0.74 1 1
TNFR1A/BAG4/TNF-alpha -0.013 0.072 -10000 0 -0.54 16 16
mol:Sphingosine-1-phosphate 0.021 0.02 -10000 0 -0.62 1 1
MAP2K1 -0.007 0.045 -10000 0 -0.43 1 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
CYCS -0.008 0.045 0.18 24 -10000 0 24
TNFRSF1A 0 0 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.003 0.033 -10000 0 -0.62 2 2
EIF2AK2 -0.015 0.044 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.01 0.066 -10000 0 -0.53 14 14
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.003 0.022 -10000 0 -0.33 1 1
MAP2K2 -0.007 0.045 -10000 0 -0.43 1 1
SMPD3 0.024 0.044 -10000 0 -0.28 18 18
TNF -0.017 0.1 -10000 0 -0.81 14 14
PKC zeta/PAR4 -0.001 0.028 -10000 0 -0.62 2 2
mol:PHOSPHOCHOLINE 0.048 0.12 0.27 205 -10000 0 205
NF kappa B1/RelA/I kappa B alpha -0.001 0.02 -10000 0 -0.45 2 2
AIFM1 -0.008 0.045 0.18 24 -10000 0 24
BCL2 -0.029 0.15 -10000 0 -0.81 35 35
TRAIL signaling 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
TNFSF10 -0.008 0.077 -10000 0 -0.75 10 10
positive regulation of NF-kappaB transcription factor activity -0.064 0.19 -10000 0 -0.62 102 102
MAP2K4 0.041 0.04 -10000 0 -0.43 1 1
IKBKB -0.001 0.013 -10000 0 -10000 0 0
TNFRSF10B 0 0 -10000 0 -10000 0 0
TNFRSF10A -0.005 0.063 -10000 0 -0.81 6 6
SMPD1 -0.003 0.027 -10000 0 -0.29 9 9
IKBKG 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.076 0.24 -10000 0 -0.8 94 94
TRAIL/TRAILR2 -0.006 0.059 -10000 0 -0.62 9 9
TRAIL/TRAILR3 -0.009 0.073 -10000 0 -0.66 11 11
TRAIL/TRAILR1 -0.01 0.076 -10000 0 -0.62 15 15
TRAIL/TRAILR4 -0.064 0.19 -10000 0 -0.62 102 102
TRAIL/TRAILR1/DAP3/GTP -0.008 0.06 -10000 0 -0.49 15 15
IKK complex -0.003 0.021 -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 -10000 0 0
MAPK3 0.016 0.061 -10000 0 -0.62 9 9
MAP3K1 -0.004 0.034 -10000 0 -0.32 10 10
TRAILR4 (trimer) -0.076 0.24 -10000 0 -0.8 94 94
TRADD 0 0 -10000 0 -10000 0 0
TRAILR1 (trimer) -0.005 0.063 -10000 0 -0.8 6 6
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.006 0.04 -10000 0 -0.33 15 15
CFLAR 0 0 -10000 0 -10000 0 0
MAPK1 0.016 0.061 -10000 0 -0.62 9 9
TRAIL/TRAILR1/FADD/TRADD/RIP -0.009 0.057 -10000 0 -0.46 15 15
mol:ceramide -0.003 0.027 -10000 0 -0.29 9 9
FADD -0.005 0.035 -10000 0 -10000 0 0
MAPK8 0.045 0.053 -10000 0 -0.47 6 6
TRAF2 -0.001 0.018 -10000 0 -0.28 4 4
TRAILR3 (trimer) -0.005 0.051 -10000 0 -0.42 11 11
CHUK 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.01 0.068 -10000 0 -0.54 15 15
DAP3 0 0.009 -10000 0 -0.28 1 1
CASP10 0.02 0.11 0.31 88 -0.5 13 101
JNK cascade -0.064 0.19 -10000 0 -0.62 102 102
TRAIL (trimer) -0.008 0.077 -10000 0 -0.75 10 10
TNFRSF10C -0.005 0.051 -10000 0 -0.42 11 11
TRAIL/TRAILR1/DAP3/GTP/FADD -0.009 0.059 -10000 0 -0.47 15 15
TRAIL/TRAILR2/FADD -0.007 0.053 -10000 0 -0.53 9 9
cell death -0.003 0.027 -10000 0 -0.29 9 9
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.004 0.031 -10000 0 -0.33 9 9
TRAILR2 (trimer) 0 0 -10000 0 -10000 0 0
CASP8 0.001 0.015 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.006 0.044 -10000 0 -0.45 9 9
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.016 0.092 -9999 0 -0.53 30 30
E-cadherin/beta catenin -0.018 0.1 -9999 0 -0.62 29 29
CTNNB1 0 0 -9999 0 -10000 0 0
JUP -0.001 0.029 -9999 0 -0.81 1 1
CDH1 -0.024 0.14 -9999 0 -0.81 29 29
Effects of Botulinum toxin

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
STX1A 0.003 0.039 -9999 0 -0.19 40 40
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.046 0.13 -9999 0 -0.62 42 42
STXBP1 -0.004 0.057 -9999 0 -0.81 5 5
ACh/CHRNA1 -0.059 0.078 -9999 0 -0.27 9 9
RAB3GAP2/RIMS1/UNC13B -0.038 0.11 -9999 0 -0.53 42 42
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 -0.81 42 42
mol:ACh 0.001 0.031 -9999 0 -0.15 33 33
RAB3GAP2 0 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.037 0.093 -9999 0 -0.4 47 47
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.058 0.077 -9999 0 -0.27 9 9
UNC13B 0 0 -9999 0 -10000 0 0
CHRNA1 -0.094 0.13 -9999 0 -10000 0 0
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.06 0.13 -9999 0 -0.53 47 47
SNAP25 -0.016 0.069 -9999 0 -0.38 33 33
VAMP2 0 0 -9999 0 -10000 0 0
SYT1 -0.089 0.18 -9999 0 -0.81 40 40
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.009 0.047 -9999 0 -0.54 5 5
STX1A/SNAP25 fragment 1/VAMP2 -0.037 0.093 -9999 0 -0.4 47 47
Caspase cascade in apoptosis

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
TOP1 0.006 0.095 -10000 0 -0.46 32 32
ACTA1 -0.016 0.13 -10000 0 -0.66 31 31
NUMA1 0.006 0.095 -10000 0 -0.48 29 29
SPTAN1 -0.004 0.13 -10000 0 -0.65 29 29
LIMK1 -0.004 0.13 -10000 0 -0.65 29 29
BIRC3 -0.01 0.081 -10000 0 -0.81 9 9
BIRC2 0 0 -10000 0 -10000 0 0
BAX -0.001 0.018 -10000 0 -0.28 4 4
CASP10 -0.014 0.15 -10000 0 -0.69 33 33
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0.006 0.095 -10000 0 -0.46 32 32
DIABLO 0 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.003 0.12 -10000 0 -0.63 29 29
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
GSN -0.01 0.14 -10000 0 -0.65 38 38
MADD 0 0 -10000 0 -10000 0 0
TFAP2A 0.012 0.09 -10000 0 -0.69 15 15
BID 0.005 0.062 -10000 0 -0.3 32 32
MAP3K1 0.004 0.042 -10000 0 -0.27 9 9
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 -0.004 0.13 -10000 0 -0.65 29 29
CASP9 0.001 0.002 -10000 0 -10000 0 0
DNA repair -0.002 0.03 0.18 7 -0.22 4 11
neuron apoptosis 0.021 0.013 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.004 0.12 -10000 0 -0.62 29 29
APAF1 0 0.001 -10000 0 -10000 0 0
CASP6 0.023 0.058 -10000 0 -0.42 4 4
TRAF2 -0.001 0.018 -10000 0 -0.28 4 4
ICAD/CAD 0.004 0.12 -10000 0 -0.62 29 29
CASP7 -0.007 0.038 0.36 9 -10000 0 9
KRT18 0.016 0.016 -10000 0 -10000 0 0
apoptosis 0.009 0.11 -10000 0 -0.55 29 29
DFFA -0.004 0.13 -10000 0 -0.65 29 29
DFFB -0.004 0.13 -10000 0 -0.65 29 29
PARP1 0.002 0.031 0.22 4 -0.18 7 11
actin filament polymerization -0.003 0.12 0.58 32 -10000 0 32
TNF -0.017 0.1 -10000 0 -0.81 14 14
CYCS 0.008 0.049 -10000 0 -0.22 30 30
SATB1 0.018 0.098 -10000 0 -0.49 25 25
SLK -0.004 0.13 -10000 0 -0.65 29 29
p15 BID/BAX -0.013 0.048 -10000 0 -0.35 8 8
CASP2 0.042 0.042 -10000 0 -0.46 1 1
JNK cascade -0.004 0.041 0.27 9 -10000 0 9
CASP3 -0.012 0.13 -10000 0 -0.65 33 33
LMNB2 0.04 0.039 -10000 0 -0.35 3 3
RIPK1 0 0 -10000 0 -10000 0 0
CASP4 -0.001 0.026 -10000 0 -0.81 1 1
Mammalian IAPs/DIABLO -0.006 0.047 -10000 0 -0.48 9 9
negative regulation of DNA binding 0.012 0.089 -10000 0 -0.68 15 15
stress fiber formation -0.003 0.12 -10000 0 -0.63 29 29
GZMB -0.027 0.15 -10000 0 -0.67 40 40
CASP1 0.013 0.033 -10000 0 -0.44 5 5
LMNB1 0.044 0.04 -10000 0 -0.35 3 3
APP 0.021 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 0.004 0.1 -10000 0 -0.53 29 29
LMNA 0.039 0.039 -10000 0 -0.35 3 3
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.005 0.038 -10000 0 -0.49 1 1
LRDD -0.001 0.015 -10000 0 -0.28 3 3
SREBF1 -0.006 0.13 -10000 0 -0.65 29 29
APAF-1/Caspase 9 -0.003 0.02 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.006 0.093 -10000 0 -0.46 31 31
CFL2 0.003 0.12 -10000 0 -0.6 32 32
GAS2 -0.05 0.19 -10000 0 -0.53 118 118
positive regulation of apoptosis 0.045 0.039 -10000 0 -0.34 3 3
PRF1 -0.019 0.12 -10000 0 -0.81 20 20
Cellular roles of Anthrax toxin

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
ANTXR1 -0.001 0.027 -10000 0 -0.54 2 2
ANTXR2 -0.008 0.081 -10000 0 -0.81 10 10
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.011 -10000 0 -0.1 11 11
monocyte activation 0.003 0.074 -10000 0 -0.46 25 25
MAP2K2 0 0.004 -10000 0 -10000 0 0
MAP2K1 -0.001 0.009 -10000 0 -10000 0 0
MAP2K7 -0.001 0.009 -10000 0 -10000 0 0
MAP2K6 -0.011 0.07 -10000 0 -0.48 21 21
CYAA -0.005 0.05 -10000 0 -0.47 11 11
MAP2K4 -0.001 0.018 -10000 0 -0.48 1 1
IL1B 0.006 0.067 -10000 0 -0.35 29 29
Channel -0.006 0.053 -10000 0 -0.5 11 11
NLRP1 -0.008 0.059 -10000 0 -0.49 14 14
CALM1 0 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.013 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.011 0.1 11 -10000 0 11
MAPK3 -0.001 0.009 -10000 0 -10000 0 0
MAPK1 -0.001 0.009 -10000 0 -10000 0 0
PGR -0.14 0.21 -10000 0 -0.48 275 275
PA/Cellular Receptors -0.006 0.057 -10000 0 -0.54 11 11
apoptosis -0.001 0.011 -10000 0 -0.1 11 11
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.005 0.049 -10000 0 -0.47 11 11
macrophage activation 0.019 0.01 -10000 0 -10000 0 0
TNF -0.017 0.1 -10000 0 -0.81 14 14
VCAM1 -0.012 0.072 -10000 0 -0.46 25 25
platelet activation -0.001 0.013 -10000 0 -10000 0 0
MAPKKK cascade -0.013 0.022 0.11 21 -10000 0 21
IL18 0.011 0.036 -10000 0 -0.21 14 14
negative regulation of macrophage activation -0.001 0.011 -10000 0 -0.1 11 11
LEF -0.001 0.011 -10000 0 -0.1 11 11
CASP1 -0.004 0.029 -10000 0 -0.23 14 14
mol:cAMP -0.001 0.013 -10000 0 -10000 0 0
necrosis -0.001 0.011 -10000 0 -0.1 11 11
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.005 0.05 -10000 0 -0.48 11 11
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
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 -0.001 0.017 -10000 0 -0.53 1 1
EP300 0 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.037 0.038 -10000 0 -0.32 3 3
KAT2B -0.001 0.026 -10000 0 -0.81 1 1
MAPK14 0 0 -10000 0 -10000 0 0
AKT1 0.02 0.048 0.24 4 -0.35 10 14
RAR alpha/9cRA/Cyclin H -0.011 0.06 -10000 0 -0.37 24 24
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.034 0.048 -10000 0 -0.32 13 13
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 -0.01 0.059 -10000 0 -0.59 6 6
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 0.12 -10000 0 -0.58 26 26
NCOA2 -0.025 0.14 -10000 0 -0.81 31 31
NCOA3 0 0.009 -10000 0 -10000 0 0
NCOA1 -0.001 0.026 -10000 0 -0.81 1 1
VDR/VDR/DNA 0 0 -10000 0 -10000 0 0
RARG 0.008 0.005 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
MAPK1 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.058 -10000 0 -0.81 5 5
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.042 0.11 -10000 0 -0.62 24 24
RARA 0.015 0.057 -10000 0 -0.3 29 29
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.025 0.073 -10000 0 -0.29 42 42
PRKCA -0.006 0.13 -10000 0 -0.8 24 24
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.006 0.12 -10000 0 -0.61 26 26
RXRG -0.11 0.21 -10000 0 -0.45 268 268
RXRA 0.023 0.061 -10000 0 -0.32 29 29
RXRB 0.011 0.073 -10000 0 -0.44 24 24
VDR/Vit D3/DNA 0 0 -10000 0 -10000 0 0
RBP1 -0.023 0.094 -10000 0 -0.33 68 68
CRBP1/9-cic-RA -0.016 0.068 -10000 0 -0.63 7 7
RARB 0.003 0.09 -10000 0 -0.81 12 12
PRKCG -0.002 0.057 -10000 0 -0.28 41 41
MNAT1 0 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.028 0.11 -10000 0 -0.62 26 26
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.013 0.1 -10000 0 -0.49 27 27
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.052 -10000 0 -0.42 3 3
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.006 0.12 -10000 0 -0.61 26 26
positive regulation of DNA binding -0.01 0.057 -10000 0 -0.35 24 24
NRIP1 -0.004 0.12 -10000 0 -0.86 7 7
RXRs/RARs -0.012 0.12 -10000 0 -0.58 29 29
RXRs/RXRs/DNA/9cRA -0.045 0.11 -10000 0 -0.65 24 24
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 -0.005 0.031 -10000 0 -10000 0 0
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
Aurora A signaling

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
Aurora A/GADD45A -0.025 0.029 -9999 0 -10000 0 0
BIRC5 -0.2 0.13 -9999 0 -10000 0 0
NFKBIA -0.023 0.032 -9999 0 -10000 0 0
CPEB1 -0.15 0.32 -9999 0 -0.81 189 189
AKT1 -0.023 0.032 -9999 0 -10000 0 0
NDEL1 0 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.023 0.032 -9999 0 -0.56 1 1
NDEL1/TACC3 -0.037 0.056 -9999 0 -10000 0 0
GADD45A 0 0 -9999 0 -10000 0 0
GSK3B 0.003 0.003 -9999 0 -10000 0 0
PAK1/Aurora A -0.028 0.037 -9999 0 -10000 0 0
MDM2 -0.001 0.018 -9999 0 -0.28 4 4
JUB -0.003 0.051 -9999 0 -0.81 4 4
TPX2 -0.1 0.096 -9999 0 -10000 0 0
TP53 -0.01 0.015 -9999 0 -10000 0 0
DLG7 -0.029 0.034 -9999 0 -10000 0 0
AURKAIP1 -0.002 0.022 -9999 0 -10000 0 0
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 -0.04 0.06 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.022 0.032 -9999 0 -0.55 1 1
AURKA -0.036 0.043 -9999 0 -10000 0 0
AURKB -0.003 0.008 -9999 0 -10000 0 0
CDC25B -0.017 0.024 -9999 0 -10000 0 0
G2/M transition checkpoint -0.024 0.04 -9999 0 -0.5 4 4
mRNA polyadenylation -0.12 0.2 -9999 0 -0.53 189 189
Aurora A/CPEB -0.12 0.2 -9999 0 -0.54 189 189
Aurora A/TACC1/TRAP/chTOG -0.029 0.087 -9999 0 -0.48 34 34
BRCA1 -0.001 0.029 -9999 0 -0.81 1 1
centrosome duplication -0.028 0.036 -9999 0 -10000 0 0
regulation of centrosome cycle -0.037 0.056 -9999 0 -10000 0 0
spindle assembly -0.029 0.086 -9999 0 -0.48 34 34
TDRD7 0 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.098 0.068 -9999 0 -0.62 1 1
CENPA 0 0.01 -9999 0 -10000 0 0
Aurora A/PP2A -0.025 0.029 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.007 0.027 -9999 0 -10000 0 0
negative regulation of DNA binding -0.01 0.015 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX -0.001 0.012 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.024 0.04 -9999 0 -0.51 4 4
mitotic prometaphase -0.013 0.011 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.036 0.043 -9999 0 -10000 0 0
TACC1 -0.028 0.15 -9999 0 -0.81 34 34
TACC3 -0.043 0.1 -9999 0 -0.28 152 152
Aurora A/Antizyme1 -0.019 0.022 -9999 0 -10000 0 0
Aurora A/RasGAP -0.025 0.029 -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 0.003 -9999 0 -10000 0 0
GIT1 -0.001 0.02 -9999 0 -0.28 5 5
GIT1/beta-PIX/PAK1 -0.004 0.022 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.1 0.096 -9999 0 -10000 0 0
PPP2R5D 0 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.1 0.084 -9999 0 -10000 0 0
PAK1 -0.006 0.041 -9999 0 -0.28 22 22
CKAP5 0 0 -9999 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0 0.009 -9999 0 -0.28 1 1
PLK4 -0.011 0.054 -9999 0 -0.28 39 39
regulation of centriole replication 0.014 0.039 -9999 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
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 0.044 -9999 0 -10000 0 0
MAPK12 0.017 0.082 -9999 0 -0.48 25 25
CCND1 0.015 0.041 -9999 0 -0.41 4 4
p38 gamma/SNTA1 -0.012 0.072 -9999 0 -0.47 21 21
MAP2K3 0 0.009 -9999 0 -0.28 1 1
PKN1 0 0.009 -9999 0 -0.28 1 1
G2/M transition checkpoint 0.017 0.081 -9999 0 -0.47 25 25
MAP2K6 0.011 0.084 -9999 0 -0.5 25 25
MAPT -0.017 0.14 -9999 0 -0.41 102 102
MAPK13 0.022 0.009 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.014 0.029 -9999 0 -0.44 4 4
E-cadherin signaling in the nascent adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.018 0.1 -9999 0 -0.59 29 29
KLHL20 -0.008 0.033 -9999 0 -0.24 3 3
CYFIP2 -0.01 0.063 -9999 0 -0.33 29 29
Rac1/GDP 0.048 0.07 -9999 0 -0.35 29 29
ENAH -0.018 0.099 -9999 0 -0.58 29 29
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 -0.009 0.05 -9999 0 -0.5 1 1
ABI1/Sra1/Nap1 -0.006 0.024 -9999 0 -0.17 3 3
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.018 0.086 -9999 0 -0.48 31 31
RAPGEF1 0.037 0.092 -9999 0 -0.49 29 29
CTNND1 0 0.009 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.018 0.1 -9999 0 -0.61 29 29
CRK 0.029 0.1 -9999 0 -0.54 29 29
E-cadherin/gamma catenin/alpha catenin -0.016 0.092 -9999 0 -0.53 30 30
alphaE/beta7 Integrin -0.006 0.039 -9999 0 -0.62 2 2
IQGAP1 0 0 -9999 0 -10000 0 0
NCKAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.003 0.038 -9999 0 -0.49 6 6
DLG1 -0.018 0.099 -9999 0 -0.58 29 29
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.008 0.04 -9999 0 -0.32 2 2
MLLT4 -0.005 0.063 -9999 0 -0.73 7 7
ARF6/GTP/NME1/Tiam1 -0.006 0.027 -9999 0 -10000 0 0
PI3K -0.01 0.051 -9999 0 -0.43 2 2
ARF6 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.019 0.11 -9999 0 -0.62 30 30
TIAM1 -0.001 0.018 -9999 0 -10000 0 0
E-cadherin(dimer)/Ca2+ -0.014 0.078 -9999 0 -0.46 29 29
AKT1 -0.006 0.029 -9999 0 -0.24 1 1
PIK3R1 -0.006 0.068 -9999 0 -0.81 7 7
CDH1 -0.024 0.14 -9999 0 -0.81 29 29
RhoA/GDP 0.047 0.07 -9999 0 -0.35 29 29
actin cytoskeleton organization -0.006 0.024 -9999 0 -0.18 3 3
CDC42/GDP 0.047 0.07 -9999 0 -0.35 29 29
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.01 0.058 -9999 0 -0.34 30 30
ITGB7 -0.008 0.056 -9999 0 -0.32 26 26
RAC1 0 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.014 0.082 -9999 0 -0.48 29 29
E-cadherin/Ca2+/beta catenin/alpha catenin -0.014 0.079 -9999 0 -0.47 29 29
mol:GDP 0.045 0.082 -9999 0 -0.42 29 29
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP -0.001 0.029 -9999 0 -0.81 1 1
p120 catenin/RhoA/GDP -0.011 0.061 -9999 0 -0.36 29 29
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 0.028 -9999 0 -0.21 6 6
NME1 -0.014 0.061 -9999 0 -0.28 49 49
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.018 0.1 -9999 0 -0.58 30 30
regulation of cell-cell adhesion -0.008 0.044 -9999 0 -0.42 1 1
WASF2 -0.003 0.012 -9999 0 -10000 0 0
Rap1/GTP -0.011 0.058 -9999 0 -0.6 1 1
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.017 0.081 -9999 0 -0.45 32 32
CCND1 -0.008 0.034 -9999 0 -0.26 6 6
VAV2 0.033 0.096 -9999 0 -0.52 29 29
RAP1/GDP -0.01 0.058 -9999 0 -0.57 1 1
adherens junction assembly -0.017 0.096 -9999 0 -0.56 30 30
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 -0.016 0.076 -9999 0 -0.43 32 32
E-cadherin/beta catenin -0.015 0.084 -9999 0 -0.5 29 29
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.018 0.099 -9999 0 -0.58 29 29
PIK3CA 0 0.009 -9999 0 -0.28 1 1
Rac1/GTP -0.011 0.053 -9999 0 -0.37 5 5
E-cadherin/beta catenin/alpha catenin -0.016 0.09 -9999 0 -0.53 29 29
ITGAE 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.019 0.11 -9999 0 -0.62 29 29
S1P3 pathway

Figure S98.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S98.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.003 0.051 -9999 0 -0.81 4 4
mol:S1P 0.001 0.003 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.029 0.094 -9999 0 -0.34 81 81
GNAO1 -0.021 0.14 -9999 0 -0.48 66 66
S1P/S1P3/G12/G13 -0.001 0.012 -9999 0 -10000 0 0
AKT1 -0.011 0.053 -9999 0 -0.68 4 4
AKT3 0.017 0.18 -9999 0 -1.4 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.003 0.051 -9999 0 -0.8 4 4
GNAI2 0.012 0.003 -9999 0 -10000 0 0
GNAI3 0.012 0.002 -9999 0 -10000 0 0
GNAI1 -0.03 0.18 -9999 0 -0.81 51 51
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.009 0.028 -9999 0 -0.28 9 9
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.01 0.1 -9999 0 -0.39 36 36
MAPK3 0.018 0.099 -9999 0 -0.52 11 11
MAPK1 0.018 0.099 -9999 0 -0.52 11 11
JAK2 0.02 0.1 -9999 0 -0.45 17 17
CXCR4 0.015 0.1 -9999 0 -0.48 16 16
FLT1 0.013 0.027 -9999 0 -0.82 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.018 0.099 -9999 0 -0.52 11 11
S1P/S1P3/Gi 0.01 0.1 -9999 0 -0.39 36 36
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.024 0.083 -9999 0 -0.5 11 11
VEGFA 0.01 0.031 -9999 0 -0.28 11 11
S1P/S1P2/Gi -0.026 0.088 -9999 0 -0.31 81 81
VEGFR1 homodimer/VEGFA homodimer 0.021 0.031 -9999 0 -0.64 1 1
RHOA 0 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.006 0.042 -9999 0 -0.34 15 15
GNAQ -0.002 0.036 -9999 0 -0.81 2 2
GNAZ 0.005 0.074 -9999 0 -0.81 8 8
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.015 0.09 -9999 0 -0.44 33 33
GNA15 -0.003 0.035 -9999 0 -0.34 8 8
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 -0.002 0.036 -9999 0 -0.81 2 2
Rac1/GTP -0.024 0.083 -9999 0 -0.5 11 11
IL1-mediated signaling events

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
UBC13/UEV1A 0 0.008 -10000 0 -10000 0 0
PRKCZ -0.001 0.026 -10000 0 -0.81 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 0.039 -10000 0 -0.42 3 3
IRAK/TOLLIP -0.001 0.009 -10000 0 -10000 0 0
IKBKB -0.001 0.013 -10000 0 -10000 0 0
IKBKG 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.03 0.12 -10000 0 -0.6 38 38
IL1A -0.005 0.038 -10000 0 -0.28 19 19
IL1B 0.009 0.097 -10000 0 -0.71 16 16
IRAK/TRAF6/p62/Atypical PKCs -0.001 0.014 -10000 0 -0.41 1 1
IL1R2 -0.037 0.16 -10000 0 -0.57 64 64
IL1R1 -0.015 0.11 -10000 0 -0.81 18 18
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.001 0.061 0.24 29 -0.32 15 44
TOLLIP 0 0.009 -10000 0 -0.28 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 -0.39 34 34
MAP3K7 0 0.009 -10000 0 -0.28 1 1
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.019 0.098 -10000 0 -0.47 40 40
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.011 0.066 -10000 0 -0.48 18 18
PIK3R1 -0.006 0.068 -10000 0 -0.81 7 7
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.01 0.062 -10000 0 -0.45 18 18
IL1 beta fragment/IL1R1/IL1RAP -0.018 0.1 -10000 0 -0.54 33 33
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 0.028 0.071 -10000 0 -0.4 26 26
IRAK1 0.021 0.012 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.019 0.092 -10000 0 -0.62 20 20
IRAK4 0 0 -10000 0 -10000 0 0
PRKCI 0 0.009 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
PI3K -0.005 0.052 -10000 0 -0.62 7 7
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.01 0.057 -10000 0 -0.34 20 20
CHUK 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.018 0.1 -10000 0 -0.54 33 33
IL1 beta/IL1R2 -0.033 0.13 -10000 0 -0.57 50 50
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.001 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.017 0.087 -10000 0 -0.88 3 3
IRAK3 -0.029 0.15 -10000 0 -0.79 36 36
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.016 0.092 -10000 0 -0.48 33 33
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.006 0.044 -10000 0 -0.33 18 18
IL1 alpha/IL1R1/IL1RAP -0.012 0.073 -10000 0 -0.53 18 18
RELA 0 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0 0.009 -10000 0 -10000 0 0
MYD88 0 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0 0.007 -10000 0 -10000 0 0
IL1RAP 0 0 -10000 0 -10000 0 0
UBE2N 0 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.013 0.074 -10000 0 -0.78 3 3
CASP1 -0.003 0.051 -10000 0 -0.81 4 4
IL1RN/IL1R2 -0.035 0.12 -10000 0 -0.59 42 42
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.017 0.097 -10000 0 -0.5 33 33
TMEM189-UBE2V1 -0.001 0.013 -10000 0 -0.28 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.007 0.05 -10000 0 -0.38 18 18
PIK3CA 0 0.009 -10000 0 -0.28 1 1
IL1RN -0.012 0.064 -10000 0 -0.81 2 2
TRAF6/TAK1/TAB1/TAB2 0 0.005 -10000 0 -10000 0 0
MAP2K6 -0.009 0.062 -10000 0 -0.43 21 21
BARD1 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
BARD1/CSTF1 -0.007 0.065 -10000 0 -0.62 11 11
ATM 0 0 -10000 0 -10000 0 0
UBE2D3 0 0 -10000 0 -10000 0 0
PRKDC -0.001 0.015 -10000 0 -0.28 3 3
ATR 0 0 -10000 0 -10000 0 0
UBE2L3 0 0 -10000 0 -10000 0 0
FANCD2 0.023 0.01 -10000 0 -10000 0 0
protein ubiquitination -0.025 0.066 -10000 0 -0.51 12 12
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 0.007 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.002 0.011 -10000 0 -10000 0 0
FANCF 0 0.009 -10000 0 -10000 0 0
BRCA1 -0.001 0.029 -10000 0 -0.81 1 1
CCNE1 -0.056 0.11 -10000 0 -0.28 200 200
CDK2/Cyclin E1 -0.036 0.071 -10000 0 -10000 0 0
FANCG 0 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.008 0.068 -10000 0 -0.62 12 12
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 -0.28 182 182
DNA repair 0.011 0.087 -10000 0 -0.46 6 6
BRCA1/BARD1/ubiquitin -0.008 0.068 -10000 0 -0.62 12 12
BARD1/DNA-PK -0.006 0.051 -10000 0 -0.48 11 11
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.007 0.065 0.62 11 -10000 0 11
BRCA1/BARD1/CTIP/M/R/N Complex -0.004 0.034 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 -0.007 0.059 -10000 0 -0.53 12 12
BRCA1/BARD1/P53 -0.006 0.053 -10000 0 -0.48 12 12
BARD1/CSTF1/BRCA1 -0.007 0.059 -10000 0 -0.53 12 12
BRCA1/BACH1 -0.001 0.028 -10000 0 -0.45 3 3
BARD1 -0.009 0.085 -10000 0 -0.81 11 11
PCNA -0.001 0.015 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.007 0.059 -10000 0 -0.53 12 12
BRCA1/BARD1/UbcH7 -0.007 0.059 -10000 0 -0.53 12 12
BRCA1/BARD1/RAD51/PCNA -0.049 0.078 -10000 0 -0.54 12 12
BARD1/DNA-PK/P53 -0.005 0.048 -10000 0 -0.45 11 11
BRCA1/BARD1/Ubiquitin -0.008 0.068 -10000 0 -0.62 12 12
BRCA1/BARD1/CTIP -0.006 0.053 -10000 0 -0.48 12 12
FA complex -0.004 0.009 -10000 0 -10000 0 0
BARD1/EWS -0.007 0.065 -10000 0 -0.62 11 11
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 0.006 0.053 0.48 12 -10000 0 12
BRCA1/BARD1 -0.025 0.067 -10000 0 -0.51 12 12
CSTF1 0 0.009 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.007 0.066 -10000 0 -0.63 11 11
CDK2 0 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.11 0.14 -10000 0 -10000 0 0
RAD50 0 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.008 0.068 -10000 0 -0.62 12 12
EWSR1 0 0 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.017 0.085 -9999 0 -0.52 22 22
MAP4K1 -0.012 0.064 -9999 0 -0.81 2 2
MAP3K8 -0.004 0.058 -9999 0 -0.81 5 5
PRKCB -0.02 0.12 -9999 0 -0.81 19 19
DBNL 0 0 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
MAP3K1 -0.007 0.048 -9999 0 -0.48 4 4
JUN 0.016 0.11 -9999 0 -0.58 33 33
MAP3K7 -0.007 0.046 -9999 0 -0.49 3 3
GRAP2 -0.015 0.11 -9999 0 -0.81 17 17
CRK 0 0 -9999 0 -10000 0 0
MAP2K4 0.043 0.057 -9999 0 -0.46 5 5
LAT -0.006 0.049 -9999 0 -0.34 16 16
LCP2 0 0.009 -9999 0 -0.28 1 1
MAPK8 0.013 0.11 -9999 0 -0.66 24 24
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.008 0.05 -9999 0 -0.36 17 17
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.016 0.079 -9999 0 -0.5 20 20
IL2 signaling events mediated by PI3K

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
BCL2L1 0.046 0.059 -10000 0 -0.48 4 4
UGCG -0.008 0.083 -10000 0 -0.8 10 10
AKT1/mTOR/p70S6K/Hsp90/TERT 0.054 0.09 -10000 0 -0.39 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.016 0.085 -10000 0 -0.79 10 10
mol:DAG 0 0.002 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.025 0.089 -10000 0 -0.48 13 13
FRAP1 0.052 0.13 -10000 0 -0.44 40 40
FOXO3 0.061 0.11 -10000 0 -0.57 9 9
AKT1 0.056 0.11 -10000 0 -0.44 30 30
GAB2 0.007 0.028 -10000 0 -0.28 9 9
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 0.018 0.048 -10000 0 -0.54 7 7
CALM1 0 0 -10000 0 -10000 0 0
cell proliferation 0.034 0.083 -10000 0 -0.49 12 12
EIF3A 0 0 -10000 0 -10000 0 0
PI3K -0.005 0.052 -10000 0 -0.62 7 7
RPS6KB1 0.021 0.032 -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 23 23
JAK3 0.008 0.037 -10000 0 -10000 0 0
PIK3R1 0.007 0.069 -10000 0 -0.81 7 7
JAK1 0.013 0.004 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
MYC 0.046 0.18 -10000 0 -0.98 26 26
MYB 0.012 0.18 -10000 0 -1.3 18 18
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.054 0.089 -10000 0 -0.61 7 7
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.003 0.021 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.053 0.087 -10000 0 -0.59 7 7
Rac1/GDP -0.004 0.041 -10000 0 -0.49 7 7
T cell proliferation 0.059 0.083 -10000 0 -0.52 8 8
SHC1 0.01 0.004 -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 -0.062 20 20
PRKCZ 0.059 0.086 -10000 0 -0.54 8 8
NF kappa B1 p50/RelA -0.025 0.087 -10000 0 -0.52 10 10
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.04 0.063 -10000 0 -0.53 4 4
HSP90AA1 0 0.009 -10000 0 -0.28 1 1
RELA 0 0 -10000 0 -10000 0 0
IL2RA -0.019 0.11 -10000 0 -0.36 77 77
IL2RB 0.001 0.057 -10000 0 -0.28 40 40
TERT -0.038 0.096 -10000 0 -0.28 135 135
E2F1 0.024 0.063 -10000 0 -0.44 18 18
SOS1 0.01 0.004 -10000 0 -10000 0 0
RPS6 0 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.004 0.027 20 -10000 0 20
PTPN11 0.01 0.004 -10000 0 -10000 0 0
IL2RG -0.005 0.089 -10000 0 -0.81 7 7
actin cytoskeleton organization 0.059 0.083 -10000 0 -0.52 8 8
GRB2 0.009 0.01 -10000 0 -0.28 1 1
IL2 0.006 0.028 -10000 0 -0.28 3 3
PIK3CA 0.013 0.01 -10000 0 -0.28 1 1
Rac1/GTP 0.027 0.043 -10000 0 -0.47 7 7
LCK -0.008 0.11 -10000 0 -0.8 13 13
BCL2 0.038 0.2 -10000 0 -0.9 38 38
Sphingosine 1-phosphate (S1P) pathway

Figure S103.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S103.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0 0 -9999 0 -10000 0 0
SPHK1 -0.006 0.051 -9999 0 -0.81 2 2
GNAI2 0 0 -9999 0 -10000 0 0
mol:S1P -0.001 0.017 -9999 0 -0.36 2 2
GNAO1 -0.032 0.14 -9999 0 -0.48 66 66
mol:Sphinganine-1-P 0.017 0.038 -9999 0 -0.62 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 0.026 -9999 0 -0.28 9 9
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.001 0.015 -9999 0 -0.31 2 2
S1PR5 -0.008 0.059 -9999 0 -0.81 3 3
S1PR4 -0.014 0.08 -9999 0 -0.36 40 40
GNAI1 -0.042 0.18 -9999 0 -0.81 51 51
S1P/S1P5/G12 -0.005 0.033 -9999 0 -0.48 3 3
S1P/S1P3/Gq -0.005 0.037 -9999 0 -0.29 15 15
S1P/S1P4/Gi -0.027 0.085 -9999 0 -0.34 39 39
GNAQ -0.002 0.036 -9999 0 -0.81 2 2
GNAZ -0.007 0.072 -9999 0 -0.81 8 8
GNA14 -0.015 0.09 -9999 0 -0.44 33 33
GNA15 -0.003 0.035 -9999 0 -0.34 8 8
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 -0.002 0.036 -9999 0 -0.81 2 2
ABCC1 0 0 -9999 0 -10000 0 0
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 -0.017 0.078 0.33 1 -0.36 47 48
FRAP1 0.011 0.02 -10000 0 -10000 0 0
AKT1 -0.015 0.067 0.24 1 -0.3 47 48
INSR 0 0.009 -10000 0 -0.28 1 1
Insulin Receptor/Insulin 0 0.005 -10000 0 -10000 0 0
mol:GTP -0.012 0.051 -10000 0 -0.34 8 8
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.004 0.016 -10000 0 -10000 0 0
TSC2 0 0.001 -10000 0 -10000 0 0
RHEB/GDP -0.01 0.044 -10000 0 -0.31 8 8
TSC1 0 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.017 0.084 -10000 0 -0.42 41 41
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.004 0.019 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.019 0.042 -10000 0 -0.26 8 8
MAP3K5 0.009 0.025 -10000 0 -0.44 3 3
PIK3R1 -0.006 0.068 -10000 0 -0.81 7 7
apoptosis 0.009 0.025 -10000 0 -0.44 3 3
mol:LY294002 0 0 -10000 0 -0.002 41 41
EIF4B 0.025 0.038 0.19 1 -0.22 8 9
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.006 0.028 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 -0.001 0.007 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.019 0.083 -10000 0 -0.38 48 48
mTOR/RHEB/GTP/Raptor/GBL 0.026 0.029 0.18 1 -0.19 7 8
FKBP1A 0 0.009 -10000 0 -0.28 1 1
RHEB/GTP -0.01 0.044 -10000 0 -0.31 8 8
mol:Amino Acids 0 0 -10000 0 -0.002 41 41
FKBP12/Rapamycin 0 0.006 -10000 0 -10000 0 0
PDPK1 -0.015 0.07 0.26 1 -0.32 47 48
EIF4E 0 0 -10000 0 -10000 0 0
ASK1/PP5C -0.003 0.036 -10000 0 -0.63 3 3
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.016 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.012 0.055 -10000 0 -0.37 8 8
tumor necrosis factor receptor activity 0 0 0.002 41 -10000 0 41
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 0.092 -10000 0 -0.45 41 41
INS 0 0 -10000 0 -10000 0 0
PTEN -0.001 0.036 -10000 0 -0.8 2 2
PDK2 -0.017 0.076 0.26 1 -0.34 50 51
EIF4EBP1 0.014 0.014 -10000 0 -10000 0 0
PIK3CA 0 0.009 -10000 0 -0.28 1 1
PPP2R5D 0.018 0.019 -10000 0 -10000 0 0
peptide biosynthetic process 0 0.004 -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 7 9
EEF2 0 0.004 -10000 0 -10000 0 0
eIF4E/4E-BP1 0 0 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0 0 -10000 0 -10000 0 0
NFATC1 0.048 0.03 -10000 0 -0.36 4 4
NFATC2 0.018 0.06 -10000 0 -0.3 8 8
NFATC3 -0.001 0.016 -10000 0 -0.52 1 1
YWHAE 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.012 0.096 -10000 0 -0.4 32 32
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 -0.018 0.075 -10000 0 -0.5 14 14
BCL2/BAX -0.023 0.12 -10000 0 -0.62 35 35
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 -0.28 4 4
MAPK14 0 0 -10000 0 -10000 0 0
BAD 0 0.009 -10000 0 -0.28 1 1
CABIN1/MEF2D -0.02 0.082 -10000 0 -0.56 14 14
Calcineurin A alpha-beta B1/BCL2 -0.029 0.15 -10000 0 -0.8 35 35
FKBP8 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.02 0.081 0.55 14 -10000 0 14
KPNB1 0 0 -10000 0 -10000 0 0
KPNA2 -0.029 0.085 -10000 0 -0.28 103 103
XPO1 0 0 -10000 0 -10000 0 0
SFN -0.015 0.098 -10000 0 -0.51 30 30
MAP3K8 -0.004 0.058 -10000 0 -0.81 5 5
NFAT4/CK1 alpha -0.001 0.018 -10000 0 -0.39 2 2
MEF2D/NFAT1/Cbp/p300 -0.035 0.091 -10000 0 -0.47 3 3
CABIN1 0.012 0.097 -10000 0 -0.41 32 32
CALM1 0 0 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
MAP3K1 -0.001 0.026 -10000 0 -0.81 1 1
CAMK4 -0.01 0.051 -10000 0 -0.28 34 34
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 0.043 -10000 0 -0.62 1 1
YWHAB 0 0 -10000 0 -10000 0 0
MAPK8 -0.004 0.057 -10000 0 -0.81 5 5
MAPK9 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0 0.009 -10000 0 -0.28 1 1
NFAT1-c-4/YWHAQ -0.002 0.022 -10000 0 -0.41 1 1
PRKCH -0.001 0.026 -10000 0 -0.81 1 1
CABIN1/Cbp/p300 -0.001 0.003 -10000 0 -10000 0 0
CASP3 0 0 -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 0.036 -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 -0.02 0.12 -10000 0 -0.81 19 19
PRKCE -0.001 0.026 -10000 0 -0.81 1 1
JNK2/NFAT4 0 0.015 -10000 0 -0.47 1 1
BAD/BCL-XL 0 0.006 -10000 0 -10000 0 0
PRKCD 0 0.009 -10000 0 -0.28 1 1
NUP214 0 0 -10000 0 -10000 0 0
PRKCZ -0.001 0.026 -10000 0 -0.81 1 1
PRKCA -0.02 0.12 -10000 0 -0.81 24 24
PRKCG -0.012 0.056 -10000 0 -0.28 41 41
PRKCQ -0.037 0.16 -10000 0 -0.67 54 54
FKBP38/BCL2 -0.022 0.11 -10000 0 -0.62 35 35
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 0.048 0.044 -10000 0 -0.38 6 6
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0.006 -10000 0 -10000 0 0
CSNK1A1 0.018 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.005 0.026 -10000 0 -10000 0 0
NFATc/ERK1 0.048 0.033 -10000 0 -0.36 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.018 0.074 -10000 0 -0.5 14 14
NR4A1 -0.066 0.2 -10000 0 -0.72 82 82
GSK3B 0 0 -10000 0 -10000 0 0
positive T cell selection -0.001 0.016 -10000 0 -0.52 1 1
NFAT1/CK1 alpha -0.014 0.036 -10000 0 -0.26 5 5
RCH1/ KPNB1 -0.018 0.054 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
AKAP5 -0.015 0.066 -10000 0 -0.29 51 51
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 -0.28 3 3
NFATc/p38 alpha 0.05 0.031 -10000 0 -0.36 1 1
CREBBP 0 0.001 -10000 0 -10000 0 0
BCL2 -0.029 0.15 -10000 0 -0.81 35 35
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 -0.001 0.026 -10000 0 -0.47 3 3
TRAF2/ASK1 -0.002 0.031 -10000 0 -0.54 3 3
ATM 0 0 -10000 0 -10000 0 0
MAP2K3 0.025 0.044 -10000 0 -0.42 2 2
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.027 0.06 -10000 0 -0.36 7 7
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.03 0.087 -10000 0 -0.28 108 108
TXN 0.008 0.005 -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 0.026 -10000 0 -0.81 1 1
MAP3K6 -0.001 0.026 -10000 0 -0.81 1 1
MAP3K7 0 0.009 -10000 0 -0.28 1 1
MAP3K4 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.002 0.039 -10000 0 -0.62 4 4
TAK1/TAB family 0.001 0.012 0.22 3 -10000 0 3
RAC1/OSM/MEKK3 0 0.005 -10000 0 -10000 0 0
TRAF2 -0.001 0.018 -10000 0 -0.28 4 4
RAC1/OSM/MEKK3/MKK3 -0.006 0.022 -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 -0.073 0.22 -10000 0 -0.81 74 74
CCM2 -0.001 0.013 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.047 0.14 -10000 0 -0.54 74 74
MAPK11 -0.002 0.044 -10000 0 -0.81 3 3
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.044 0.13 -10000 0 -0.5 76 76
OSM/MEKK3 0 0.008 -10000 0 -10000 0 0
TAOK1 0 0.084 -10000 0 -0.44 34 34
TAOK2 0.016 0 -10000 0 -10000 0 0
TAOK3 0.016 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 -0.002 0.044 -10000 0 -0.81 3 3
MAP3K10 0 0.009 -10000 0 -0.28 1 1
MAP3K3 0 0 -10000 0 -10000 0 0
TRX/ASK1 -0.002 0.029 -10000 0 -0.53 3 3
GADD45/MTK1/MTK1 -0.011 0.032 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 -0.005 0.051 -10000 0 -0.48 11 11
HDAC3 0 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.013 -10000 0 -0.41 1 1
GATA1/HDAC4 -0.003 0.028 -10000 0 -0.62 1 1
GATA1/HDAC5 -0.002 0.02 -10000 0 -10000 0 0
GATA2/HDAC5 -0.019 0.1 -10000 0 -0.62 27 27
HDAC5/BCL6/BCoR -0.003 0.041 -10000 0 -0.53 6 6
HDAC9 -0.01 0.078 -10000 0 -0.81 8 8
Glucocorticoid receptor/Hsp90/HDAC6 -0.007 0.058 -10000 0 -0.53 12 12
HDAC4/ANKRA2 -0.001 0.02 -10000 0 -0.62 1 1
HDAC5/YWHAB 0 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0 0 -10000 0 -10000 0 0
GATA2 -0.025 0.13 -10000 0 -0.65 38 38
HDAC4/RFXANK -0.001 0.023 -10000 0 -0.62 1 1
BCOR -0.002 0.036 -10000 0 -0.81 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0 0 -10000 0 -10000 0 0
HDAC5 0 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.007 0.065 -10000 0 -0.62 11 11
Histones -0.003 0.025 -10000 0 -10000 0 0
ADRBK1 0 0 -10000 0 -10000 0 0
HDAC4 -0.001 0.026 -10000 0 -0.81 1 1
XPO1 0 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 0 0 -10000 0 -10000 0 0
HDAC4/Ubc9 -0.001 0.02 -10000 0 -0.62 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 0.011 -10000 0 -10000 0 0
CAMK4 -0.01 0.051 -10000 0 -0.28 34 34
Tubulin/HDAC6 0 0.006 -10000 0 -10000 0 0
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 -0.004 0.032 -10000 0 -0.28 13 13
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
NR3C1 -0.01 0.088 -10000 0 -0.81 12 12
SUMO1/HDAC4 0 0.014 -10000 0 -0.45 1 1
SRF 0 0 -10000 0 -10000 0 0
HDAC4/YWHAB -0.001 0.02 -10000 0 -0.62 1 1
Tubulin 0 0.008 -10000 0 -10000 0 0
HDAC4/14-3-3 E -0.001 0.02 -10000 0 -0.62 1 1
GNB1 0 0 -10000 0 -10000 0 0
RANGAP1 0 0 -10000 0 -10000 0 0
BCL6/BCoR -0.004 0.048 -10000 0 -0.62 6 6
HDAC4/HDAC3/SMRT (N-CoR2) -0.001 0.017 -10000 0 -0.53 1 1
HDAC4/SRF -0.005 0.03 -10000 0 -0.53 1 1
HDAC4/ER alpha -0.11 0.22 -10000 0 -0.62 148 148
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.002 0.025 -10000 0 -10000 0 0
cell motility 0 0.006 -10000 0 -10000 0 0
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 -0.003 0.051 -10000 0 -0.81 4 4
HDAC4/CaMK II delta B -0.001 0.026 -10000 0 -0.8 1 1
Hsp90/HDAC6 0 0.006 -10000 0 -10000 0 0
ESR1 -0.15 0.29 -10000 0 -0.57 264 264
HDAC6/HDAC11 0 0.008 -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 -0.002 0.036 -10000 0 -0.81 2 2
RAN 0 0 -10000 0 -10000 0 0
HDAC4/MEF2C -0.001 0.025 -10000 0 -0.45 3 3
GNG2 -0.009 0.085 -10000 0 -0.81 11 11
NCOR2 0 0 -10000 0 -10000 0 0
TUBB2A -0.001 0.013 -10000 0 -0.28 2 2
HDAC11 -0.001 0.013 -10000 0 -10000 0 0
HSP90AA1 0 0.009 -10000 0 -0.28 1 1
RANBP2 0 0 -10000 0 -10000 0 0
ANKRA2 0 0 -10000 0 -10000 0 0
RFXANK -0.001 0.018 -10000 0 -0.28 4 4
nuclear import 0 0.014 0.44 1 -10000 0 1
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0 0 -9999 0 -10000 0 0
ITGB7 -0.008 0.056 -9999 0 -0.32 26 26
ITGA4 -0.003 0.026 -9999 0 -0.28 9 9
alpha4/beta7 Integrin -0.007 0.044 -9999 0 -0.46 5 5
alpha4/beta1 Integrin -0.002 0.017 -9999 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.003 0.024 -9999 0 -0.41 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 0.026 -9999 0 -0.28 9 9
alpha4/beta7 Integrin/MAdCAM1 -0.009 0.041 -9999 0 -0.45 3 3
EPO -0.046 0.1 -9999 0 -0.28 163 163
alpha4/beta7 Integrin -0.007 0.044 -9999 0 -0.46 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.002 0.017 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.029 0.065 -9999 0 -10000 0 0
lamellipodium assembly -0.002 0.035 -9999 0 -0.41 7 7
PIK3CA 0 0.009 -9999 0 -0.28 1 1
PI3K -0.005 0.052 -9999 0 -0.62 7 7
ARF6 0 0 -9999 0 -10000 0 0
JAK2 -0.009 0.024 -9999 0 -0.51 1 1
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 -0.006 0.068 -9999 0 -0.81 7 7
MADCAM1 -0.011 0.054 -9999 0 -0.28 39 39
cell adhesion -0.009 0.041 -9999 0 -0.45 3 3
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0 0 -9999 0 -10000 0 0
SRC -0.007 0.052 -9999 0 -0.48 11 11
ITGB7 -0.008 0.056 -9999 0 -0.32 26 26
RAC1 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.008 0.058 -9999 0 -0.53 11 11
p130Cas/Crk/Dock1 -0.006 0.043 -9999 0 -10000 0 0
VCAM1 -0.011 0.087 -9999 0 -0.81 11 11
RHOA 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.002 0.013 -9999 0 -10000 0 0
BCAR1 0.033 0.054 -9999 0 -0.45 11 11
EPOR 0 0.009 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
GIT1 -0.001 0.02 -9999 0 -0.28 5 5
Rac1/GTP -0.002 0.036 -9999 0 -0.42 7 7
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.001 0.029 -9999 0 -0.91 1 1
VEGFR1 homodimer/NRP1 -0.001 0.029 -9999 0 -0.92 1 1
mol:DAG 0.038 0.033 -9999 0 -0.65 2 2
VEGFR1 homodimer/NRP1/VEGFR 121 -0.002 0.03 -9999 0 -0.86 1 1
CaM/Ca2+ -0.002 0.029 -9999 0 -0.62 2 2
HIF1A 0 0.012 -9999 0 -0.38 1 1
GAB1 0 0 -9999 0 -10000 0 0
AKT1 -0.004 0.044 -9999 0 -0.72 1 1
PLCG1 0.038 0.033 -9999 0 -0.66 2 2
NOS3 0.061 0.032 -9999 0 -0.56 2 2
CBL 0 0 -9999 0 -10000 0 0
mol:NO 0.061 0.031 -9999 0 -0.54 2 2
FLT1 0.028 0.033 -9999 0 -1 1 1
PGF -0.002 0.03 -9999 0 -0.41 4 4
VEGFR1 homodimer/NRP2/VEGFR121 -0.004 0.049 -9999 0 -0.79 3 3
CALM1 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.28 1 1
eNOS/Hsp90 -0.002 0.025 -9999 0 -0.65 1 1
endothelial cell proliferation 0.036 0.091 -9999 0 -0.7 5 5
mol:Ca2+ 0.037 0.033 -9999 0 -0.65 2 2
MAPK3 0.039 0.082 -9999 0 -0.45 24 24
MAPK1 0.039 0.082 -9999 0 -0.45 25 25
PIK3R1 -0.006 0.068 -9999 0 -0.81 7 7
PLGF homodimer -0.002 0.03 -9999 0 -0.41 4 4
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 -0.81 208 208
VEGFA homodimer -0.003 0.029 -9999 0 -0.28 11 11
VEGFR1 homodimer/VEGFA homodimer -0.002 0.032 -9999 0 -0.91 1 1
platelet activating factor biosynthetic process 0.046 0.08 -9999 0 -1.1 1 1
PI3K -0.005 0.048 -9999 0 -0.49 9 9
PRKCA 0.033 0.086 -9999 0 -0.48 25 25
PRKCB 0.033 0.08 -9999 0 -0.49 20 20
VEGFR1 homodimer/PLGF homodimer -0.002 0.034 -9999 0 -0.72 2 2
VEGFA -0.003 0.029 -9999 0 -0.28 11 11
VEGFB 0 0 -9999 0 -10000 0 0
mol:IP3 0.038 0.033 -9999 0 -0.65 2 2
RASA1 0.039 0.028 -9999 0 -0.84 1 1
NRP2 -0.003 0.045 -9999 0 -0.68 4 4
VEGFR1 homodimer 0.028 0.033 -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 -0.081 0.16 -9999 0 -0.67 5 5
PTPN11 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.005 0.047 -9999 0 -0.48 9 9
mol:L-citrulline 0.061 0.031 -9999 0 -0.54 2 2
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.002 0.028 -9999 0 -0.81 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.002 0.029 -9999 0 -0.85 1 1
CD2AP 0 0.009 -9999 0 -0.28 1 1
PI3K/GAB1 -0.004 0.045 -9999 0 -0.46 9 9
PDPK1 -0.004 0.044 -9999 0 -0.45 9 9
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.002 0.029 -9999 0 -0.85 1 1
mol:NADP 0.061 0.031 -9999 0 -0.54 2 2
HSP90AA1 0 0.009 -9999 0 -0.28 1 1
ubiquitin-dependent protein catabolic process -0.002 0.028 -9999 0 -0.79 1 1
VEGFR1 homodimer/NRP2 -0.003 0.05 -9999 0 -0.81 3 3
Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin -0.018 0.1 -9999 0 -0.62 28 28
AKT1 0.081 0.066 -9999 0 -0.68 6 6
PTK2B -0.017 0.1 -9999 0 -1 6 6
VEGFR2 homodimer/Frs2 -0.006 0.074 -9999 0 -0.98 5 5
CAV1 -0.17 0.33 -9999 0 -0.81 208 208
CALM1 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.007 0.07 -9999 0 -0.92 5 5
endothelial cell proliferation 0.083 0.083 -9999 0 -0.64 7 7
mol:Ca2+ 0.051 0.067 -9999 0 -0.92 4 4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.003 0.066 -9999 0 -0.99 4 4
RP11-342D11.1 0.043 0.067 -9999 0 -0.76 6 6
CDH5 -0.007 0.072 -9999 0 -0.81 8 8
VEGFA homodimer -0.001 0.011 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
SHC2 -0.02 0.13 -9999 0 -0.81 25 25
HRAS/GDP -0.003 0.052 -9999 0 -0.77 4 4
SH2D2A -0.033 0.094 -9999 0 -0.81 2 2
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.002 0.05 -9999 0 -0.71 4 4
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.018 0.08 -9999 0 -0.83 7 7
VEGFR1 homodimer -0.001 0.026 -9999 0 -0.8 1 1
SHC/GRB2/SOS1 -0.003 0.061 -9999 0 -0.89 4 4
GRB10 0.051 0.067 -9999 0 -0.92 4 4
PTPN11 0 0 -9999 0 -10000 0 0
GRB2 0 0.009 -9999 0 -0.28 1 1
PAK1 -0.006 0.041 -9999 0 -0.28 22 22
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.007 0.089 -9999 0 -1.1 6 6
HRAS -0.001 0.02 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.009 0.059 -9999 0 -0.59 6 6
HIF1A 0 0 -9999 0 -10000 0 0
FRS2 -0.003 0.028 -9999 0 -0.28 10 10
oxygen and reactive oxygen species metabolic process -0.003 0.064 -9999 0 -0.96 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.002 0.044 -9999 0 -0.81 3 3
Nck/Pak -0.004 0.026 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.007 0.078 -9999 0 -0.94 6 6
mol:GDP -0.003 0.057 -9999 0 -0.84 4 4
mol:NADP 0.074 0.047 -9999 0 -0.57 4 4
eNOS/Hsp90 0.075 0.044 -9999 0 -0.53 4 4
PIK3R1 -0.006 0.068 -9999 0 -0.81 7 7
mol:IP3 0.051 0.069 -9999 0 -0.94 4 4
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB -0.001 0.027 -9999 0 -0.54 2 2
VEGFA -0.003 0.029 -9999 0 -0.27 11 11
VEGFC 0 0 -9999 0 -10000 0 0
FAK1/Vinculin -0.011 0.081 -9999 0 -0.96 5 5
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.016 0.11 -9999 0 -0.58 29 29
PTPN6 -0.001 0.013 -9999 0 -0.28 2 2
EPAS1 -0.004 0.061 -9999 0 -0.78 5 5
mol:L-citrulline 0.074 0.047 -9999 0 -0.57 4 4
ITGAV 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.28 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.002 0.067 -9999 0 -0.88 5 5
VEGFR2 homodimer/VEGFA homodimer -0.004 0.07 -9999 0 -0.84 6 6
VEGFR2/3 heterodimer -0.006 0.086 -9999 0 -1.1 6 6
VEGFB 0 0 -9999 0 -10000 0 0
MAPK11 0.056 0.073 -9999 0 -0.99 4 4
VEGFR2 homodimer 0.029 0.083 -9999 0 -1.1 5 5
FLT1 -0.001 0.026 -9999 0 -0.81 1 1
NEDD4 -0.001 0.026 -9999 0 -0.8 1 1
MAPK3 0.051 0.08 -9999 0 -0.81 6 6
MAPK1 0.051 0.08 -9999 0 -0.81 6 6
VEGFA145/NRP2 -0.004 0.041 -9999 0 -0.66 3 3
VEGFR1/2 heterodimer -0.005 0.08 -9999 0 -1.1 5 5
KDR 0.029 0.083 -9999 0 -1.1 5 5
VEGFA165/NRP1/VEGFR2 homodimer -0.005 0.079 -9999 0 -1 5 5
SRC 0 0.009 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.054 0.081 -9999 0 -0.92 5 5
PI3K -0.007 0.075 -9999 0 -0.9 6 6
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.006 0.069 -9999 0 -0.92 5 5
FES 0.05 0.076 -9999 0 -0.96 4 4
GAB1 -0.004 0.065 -9999 0 -0.99 4 4
VEGFR2 homodimer/VEGFA homodimer/Src -0.006 0.069 -9999 0 -0.92 5 5
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 -0.009 0.17 -9999 0 -0.59 10 10
VEGFR2 homodimer/VEGFA homodimer/Yes -0.006 0.071 -9999 0 -0.84 6 6
PI3K/GAB1 0.08 0.071 -9999 0 -0.72 6 6
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0 0.065 -9999 0 -0.95 4 4
PRKACA 0 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.006 0.081 -9999 0 -1 6 6
HSP90AA1 0 0.009 -9999 0 -0.28 1 1
CDC42 0.051 0.071 -9999 0 -0.96 4 4
actin cytoskeleton reorganization -0.017 0.078 -9999 0 -0.81 7 7
PTK2 0.054 0.1 -9999 0 -1 6 6
EDG1 0.043 0.067 -9999 0 -0.76 6 6
mol:DAG 0.051 0.069 -9999 0 -0.94 4 4
CaM/Ca2+ -0.005 0.058 -9999 0 -0.85 4 4
MAP2K3 0.058 0.07 -9999 0 -0.9 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.004 0.067 -9999 0 -0.98 4 4
PLCG1 0.051 0.071 -9999 0 -0.96 4 4
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.004 0.068 -9999 0 -0.99 4 4
IQGAP1 0 0 -9999 0 -10000 0 0
YES1 -0.001 0.026 -9999 0 -0.81 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.006 0.069 -9999 0 -0.92 5 5
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.006 0.069 -9999 0 -0.92 5 5
cell migration 0.08 0.081 -9999 0 -0.8 5 5
mol:PI-3-4-5-P3 -0.006 0.066 -9999 0 -0.79 6 6
FYN -0.002 0.036 -9999 0 -0.81 2 2
VEGFB/NRP1 -0.005 0.059 -9999 0 -0.87 4 4
mol:NO 0.074 0.047 -9999 0 -0.57 4 4
PXN 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.005 0.053 -9999 0 -0.78 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.004 0.067 -9999 0 -0.98 4 4
VHL 0 0 -9999 0 -10000 0 0
ITGB3 -0.024 0.14 -9999 0 -0.81 28 28
NOS3 0.076 0.053 -9999 0 -0.67 4 4
VEGFR2 homodimer/VEGFA homodimer/Sck -0.018 0.1 -9999 0 -0.55 30 30
RAC1 0 0 -9999 0 -10000 0 0
PRKCA 0.047 0.1 -9999 0 -1.1 4 4
PRKCB 0.047 0.1 -9999 0 -0.94 6 6
VCL 0 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.004 0.064 -9999 0 -0.76 6 6
VEGFR1/2 heterodimer/VEGFA homodimer -0.006 0.076 -9999 0 -1 5 5
VEGFA165/NRP2 -0.004 0.041 -9999 0 -0.66 3 3
MAPKKK cascade -0.003 0.054 -9999 0 -0.78 4 4
NRP2 -0.003 0.045 -9999 0 -0.68 4 4
VEGFC homodimer 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
ROCK1 -0.001 0.026 -9999 0 -0.81 1 1
FAK1/Paxillin -0.011 0.081 -9999 0 -0.96 5 5
MAP3K13 0.05 0.074 -9999 0 -0.96 4 4
PDPK1 0.074 0.064 -9999 0 -0.67 6 6
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.005 0.048 -9999 0 -0.57 6 6
PDGFB-D/PDGFRB/SLAP -0.004 0.042 -9999 0 -0.62 4 4
PDGFB-D/PDGFRB/APS/CBL -0.008 0.043 -9999 0 -0.53 4 4
AKT1 -0.01 0.046 -9999 0 -0.56 2 2
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.005 0.05 -9999 0 -0.6 6 6
PIK3CA 0 0.009 -9999 0 -0.28 1 1
FGR -0.003 0.04 -9999 0 -0.54 5 5
mol:Ca2+ 0.032 0.05 -9999 0 -0.69 4 4
MYC 0.037 0.14 -9999 0 -0.83 25 25
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.003 0.03 -9999 0 -0.43 4 4
LRP1/PDGFRB/PDGFB -0.007 0.07 -9999 0 -0.61 12 12
GRB10 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
GO:0007205 0.032 0.051 -9999 0 -0.7 4 4
PTEN -0.002 0.036 -9999 0 -0.81 2 2
GRB2 0 0.009 -9999 0 -0.28 1 1
GRB7 -0.02 0.075 -9999 0 -0.29 70 70
PDGFB-D/PDGFRB/SHP2 -0.002 0.039 -9999 0 -0.62 4 4
PDGFB-D/PDGFRB/GRB10 -0.002 0.039 -9999 0 -0.62 4 4
cell cycle arrest -0.004 0.042 -9999 0 -0.61 4 4
HRAS -0.001 0.02 -9999 0 -10000 0 0
HIF1A 0.052 0.055 -9999 0 -0.48 2 2
GAB1 0.035 0.058 -9999 0 -0.68 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.039 0.055 -9999 0 -0.62 4 4
PDGFB-D/PDGFRB -0.003 0.037 -9999 0 -0.54 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.002 0.039 -9999 0 -0.62 4 4
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.006 0.052 -9999 0 -0.58 6 6
positive regulation of MAPKKK cascade -0.002 0.039 -9999 0 -0.61 4 4
PIK3R1 -0.006 0.068 -9999 0 -0.81 7 7
mol:IP3 0.032 0.052 -9999 0 -0.71 4 4
E5 0 0.001 -9999 0 -10000 0 0
CSK 0 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.016 0.062 -9999 0 -0.62 5 5
SHB -0.001 0.027 -9999 0 -0.54 2 2
BLK -0.002 0.053 -9999 0 -0.59 7 7
PTPN2 0.001 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.002 0.039 -9999 0 -0.62 4 4
BCAR1 0 0 -9999 0 -10000 0 0
VAV2 0.039 0.065 -9999 0 -0.62 5 5
CBL 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.002 0.039 -9999 0 -0.62 4 4
LCK -0.011 0.085 -9999 0 -0.64 16 16
PDGFRB 0.008 0.052 -9999 0 -0.81 4 4
ACP1 0 0 -9999 0 -10000 0 0
HCK -0.003 0.035 -9999 0 -0.52 4 4
ABL1 0.033 0.052 -9999 0 -0.64 4 4
PDGFB-D/PDGFRB/CBL 0.033 0.064 -9999 0 -0.8 4 4
PTPN1 -0.003 0.029 -9999 0 -0.28 11 11
SNX15 0 0 -9999 0 -10000 0 0
STAT3 0 0 -9999 0 -10000 0 0
STAT1 -0.005 0.037 -9999 0 -0.28 18 18
cell proliferation 0.039 0.12 -9999 0 -0.72 25 25
SLA -0.003 0.026 -9999 0 -0.28 9 9
actin cytoskeleton reorganization -0.003 0.03 -9999 0 -0.41 5 5
SRC -0.003 0.035 -9999 0 -0.52 4 4
PI3K -0.011 0.052 -9999 0 -0.64 2 2
PDGFB-D/PDGFRB/GRB7/SHC -0.012 0.051 -9999 0 -0.53 5 5
SH2B2 -0.012 0.057 -9999 0 -0.28 43 43
PLCgamma1/SPHK1 -0.005 0.052 -9999 0 -0.62 6 6
LYN -0.003 0.035 -9999 0 -0.52 4 4
LRP1 -0.008 0.081 -9999 0 -0.81 10 10
SOS1 0 0 -9999 0 -10000 0 0
STAT5B -0.002 0.044 -9999 0 -0.81 3 3
STAT5A -0.007 0.072 -9999 0 -0.81 8 8
NCK1-2/p130 Cas -0.003 0.028 -9999 0 -0.43 4 4
SPHK1 -0.006 0.051 -9999 0 -0.81 2 2
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.032 0.052 -9999 0 -0.71 4 4
PLCG1 0.032 0.054 -9999 0 -0.74 4 4
NHERF/PDGFRB -0.014 0.05 -9999 0 -0.53 4 4
YES1 -0.003 0.04 -9999 0 -0.54 5 5
cell migration -0.014 0.05 -9999 0 -0.53 4 4
SHC/Grb2/SOS1 -0.003 0.029 -9999 0 -0.43 4 4
SLC9A3R2 -0.001 0.013 -9999 0 -0.28 2 2
SLC9A3R1 -0.023 0.077 -9999 0 -0.28 83 83
NHERF1-2/PDGFRB/PTEN -0.012 0.048 -9999 0 -0.48 6 6
FYN -0.004 0.064 -9999 0 -0.91 4 4
DOK1 0.002 0.036 -9999 0 -0.48 4 4
HRAS/GTP -0.001 0.013 -9999 0 -10000 0 0
PDGFB 0 0 -9999 0 -10000 0 0
RAC1 0.045 0.085 -9999 0 -0.45 27 27
PRKCD 0.029 0.037 -9999 0 -0.49 4 4
FER 0.023 0.071 -9999 0 -0.52 15 15
MAPKKK cascade -0.002 0.029 -9999 0 -0.42 4 4
RASA1 0.029 0.037 -9999 0 -0.49 4 4
NCK1 0 0 -9999 0 -10000 0 0
NCK2 0 0 -9999 0 -10000 0 0
p62DOK/Csk -0.002 0.03 -9999 0 -0.44 4 4
PDGFB-D/PDGFRB/SHB -0.003 0.044 -9999 0 -0.62 5 5
chemotaxis 0.033 0.05 -9999 0 -0.62 4 4
STAT1-3-5/STAT1-3-5 -0.008 0.058 -9999 0 -0.48 13 13
Bovine Papilomavirus E5/PDGFRB -0.003 0.04 -9999 0 -0.63 4 4
PTPRJ 0 0 -9999 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 -0.001 0.026 -9999 0 -0.81 1 1
SMAD2 0.014 0.005 -9999 0 -10000 0 0
SMAD3 0.041 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.005 0.017 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy -0.001 0.017 -9999 0 -0.53 1 1
SMAD2/SMAD2/SMAD4 -0.009 0.03 -9999 0 -0.53 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 -0.48 1 1
MAP3K1 -0.001 0.026 -9999 0 -0.81 1 1
TRAP-1/SMAD4 -0.007 0.065 -9999 0 -0.62 11 11
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 -0.008 0.081 -9999 0 -0.81 10 10
UBE2I 0 0 -9999 0 -10000 0 0
NUP153 0 0.009 -9999 0 -0.28 1 1
KPNA2 -0.029 0.085 -9999 0 -0.28 103 103
PIAS4 0 0 -9999 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 -0.004 0.046 -9999 0 -0.37 12 12
Caspase 8 (4 units) -0.008 0.046 -9999 0 -1 1 1
NEF -0.005 0.024 -9999 0 -10000 0 0
NFKBIA -0.001 0.011 -9999 0 -10000 0 0
BIRC3 0.034 0.085 -9999 0 -0.81 9 9
CYCS 0.041 0.057 -9999 0 -0.95 1 1
RIPK1 0 0 -9999 0 -10000 0 0
CD247 -0.027 0.13 -9999 0 -0.7 30 30
MAP2K7 0.042 0.047 -9999 0 -0.81 1 1
protein ubiquitination 0.065 0.035 -9999 0 -10000 0 0
CRADD 0 0 -9999 0 -10000 0 0
DAXX 0 0 -9999 0 -10000 0 0
FAS -0.002 0.044 -9999 0 -0.81 3 3
BID -0.009 0.051 -9999 0 -1 1 1
NF-kappa-B/RelA/I kappa B alpha -0.004 0.034 -9999 0 -10000 0 0
TRADD 0 0 -9999 0 -10000 0 0
MAP3K5 -0.002 0.044 -9999 0 -0.81 3 3
CFLAR 0 0 -9999 0 -10000 0 0
FADD -0.005 0.035 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.004 0.034 -9999 0 -10000 0 0
MAPK8 0.046 0.055 -9999 0 -0.46 6 6
APAF1 0 0 -9999 0 -10000 0 0
TRAF1 -0.001 0.018 -9999 0 -0.28 4 4
TRAF2 -0.001 0.018 -9999 0 -0.28 4 4
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.01 0.055 -9999 0 -0.38 12 12
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.002 0.033 -9999 0 -0.37 2 2
CHUK 0.067 0.037 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.004 0.045 -9999 0 -0.57 5 5
TCRz/NEF -0.025 0.11 -9999 0 -0.54 37 37
TNF -0.017 0.1 -9999 0 -0.81 14 14
FASLG -0.006 0.14 -9999 0 -0.64 37 37
NFKB1 -0.001 0.011 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.013 0.072 -9999 0 -0.54 16 16
CASP6 -0.004 0.031 -9999 0 -0.71 1 1
CASP7 0.073 0.077 -9999 0 -0.63 9 9
RELA -0.001 0.011 -9999 0 -10000 0 0
CASP2 0 0 -9999 0 -10000 0 0
CASP3 0.073 0.077 -9999 0 -0.63 9 9
TNFRSF1A 0 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.003 0.033 -9999 0 -0.62 2 2
CASP8 0 0 -9999 0 -10000 0 0
CASP9 0 0 -9999 0 -10000 0 0
MAP3K14 0.062 0.039 -9999 0 -0.35 1 1
APAF-1/Caspase 9 -0.009 0.055 -9999 0 -0.52 9 9
BCL2 0.037 0.1 -9999 0 -0.42 39 39
ceramide 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
MAP4K4 0.044 0.049 -10000 0 -0.56 1 1
BAG4 -0.004 0.046 -10000 0 -0.37 12 12
BAD 0.032 0.018 -10000 0 -10000 0 0
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.081 -10000 0 -0.81 9 9
BAX 0.031 0.019 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.015 0.013 -10000 0 -0.1 2 2
IKBKB 0.05 0.047 -10000 0 -0.52 1 1
MAP2K2 0.044 0.025 -10000 0 -0.47 1 1
MAP2K1 0.044 0.025 -10000 0 -0.47 1 1
SMPD1 0.02 0.013 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.049 0.051 -10000 0 -0.45 3 3
MAP2K4 0.038 0.026 -10000 0 -0.39 2 2
protein ubiquitination 0.052 0.047 -10000 0 -0.52 1 1
EnzymeConsortium:2.7.1.37 0.049 0.028 -10000 0 -0.5 1 1
response to UV 0 0 -10000 0 -0.003 1 1
RAF1 0.038 0.026 -10000 0 -0.5 1 1
CRADD 0 0 -10000 0 -10000 0 0
mol:ceramide 0.025 0.019 -10000 0 -0.15 2 2
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0 0 -10000 0 -10000 0 0
MAP3K1 0.031 0.023 -10000 0 -0.42 1 1
TRADD 0 0 -10000 0 -10000 0 0
RELA/p50 0 0 -10000 0 -10000 0 0
MAPK3 0.046 0.025 -10000 0 -0.46 1 1
MAPK1 0.046 0.025 -10000 0 -0.46 1 1
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.042 0.053 -10000 0 -0.47 3 3
KSR1 0.032 0.026 -10000 0 -0.53 1 1
MAPK8 0.041 0.043 -10000 0 -0.46 6 6
TRAF2 -0.001 0.018 -10000 0 -0.28 4 4
response to radiation 0 0 -10000 0 -0.002 1 1
CHUK 0.051 0.046 -10000 0 -0.52 1 1
TNF R/SODD -0.003 0.033 -10000 0 -0.62 2 2
TNF -0.017 0.1 -10000 0 -0.81 14 14
CYCS 0.037 0.027 0.15 30 -10000 0 30
IKBKG 0.051 0.046 -10000 0 -0.52 1 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.038 0.051 -10000 0 -0.36 9 9
RELA 0 0 -10000 0 -10000 0 0
RIPK1 0 0.001 -10000 0 -10000 0 0
AIFM1 0.037 0.027 0.15 30 -10000 0 30
TNF/TNF R/SODD -0.013 0.072 -10000 0 -0.54 16 16
TNFRSF1A 0 0.001 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -0.002 1 1
CASP8 0.027 0.013 -10000 0 -10000 0 0
NSMAF 0.044 0.048 -10000 0 -0.55 1 1
response to hydrogen peroxide 0 0 -10000 0 -0.003 1 1
BCL2 -0.029 0.15 -10000 0 -0.81 35 35
HIF-2-alpha transcription factor network

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
MMP14 0 0.016 -10000 0 -10000 0 0
oxygen homeostasis 0.012 0.012 -10000 0 -10000 0 0
TCEB2 -0.004 0.032 -10000 0 -10000 0 0
TCEB1 -0.001 0.015 -10000 0 -0.28 3 3
VHL/Elongin B/Elongin C/HIF2A -0.004 0.034 -10000 0 -0.43 2 2
EPO 0.15 0.15 -10000 0 -0.71 2 2
FIH (dimer) 0.023 0.011 -10000 0 -10000 0 0
APEX1 0.022 0.014 -10000 0 -0.3 1 1
SERPINE1 0.16 0.15 -10000 0 -0.68 4 4
FLT1 -0.002 0.079 -10000 0 -1.1 4 4
ADORA2A 0.14 0.16 -10000 0 -0.67 4 4
germ cell development 0.16 0.15 -10000 0 -0.64 7 7
SLC11A2 0.16 0.15 -10000 0 -0.68 4 4
BHLHE40 0.16 0.15 -10000 0 -0.81 5 5
HIF1AN 0.023 0.011 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.017 0.07 -10000 0 -0.44 4 4
ETS1 0.022 0.054 -10000 0 -0.82 4 4
CITED2 0.001 0.01 -10000 0 -10000 0 0
KDR -0.005 0.11 -10000 0 -1.3 6 6
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 0.095 0.079 -10000 0 -0.42 4 4
SP1 0.018 0.002 -10000 0 -10000 0 0
ABCG2 0.13 0.25 -10000 0 -0.7 68 68
EFNA1 0.16 0.15 -10000 0 -0.68 4 4
FXN 0.16 0.14 -10000 0 -0.67 4 4
POU5F1 0.16 0.15 -10000 0 -0.67 7 7
neuron apoptosis -0.16 0.16 0.74 5 -10000 0 5
EP300 0 0 -10000 0 -10000 0 0
EGLN3 0 0.082 -10000 0 -0.39 6 6
EGLN2 0.021 0.023 -10000 0 -0.26 5 5
EGLN1 0.022 0.029 -10000 0 -0.82 1 1
VHL/Elongin B/Elongin C -0.002 0.017 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.023 0.009 -10000 0 -10000 0 0
SLC2A1 0.15 0.15 -10000 0 -0.66 5 5
TWIST1 0.14 0.2 -10000 0 -0.72 34 34
ELK1 0.018 0 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.01 0.063 -10000 0 -0.61 1 1
VEGFA 0.16 0.15 -10000 0 -0.71 4 4
CREBBP 0 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA -0.005 0.059 -9999 0 -0.49 14 14
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.006 0.049 -9999 0 -0.41 14 14
SUMO1 0 0 -9999 0 -10000 0 0
ZFPM1 -0.002 0.023 -9999 0 -0.28 7 7
NPC/RanGAP1/SUMO1/Ubc9 0 0 -9999 0 -10000 0 0
FKBP3 0 0 -9999 0 -10000 0 0
Histones -0.003 0.024 -9999 0 -10000 0 0
YY1/LSF 0 0.009 -9999 0 -0.3 1 1
SMG5 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.006 0.043 -9999 0 -0.36 14 14
I kappa B alpha/HDAC1 -0.004 0.029 -9999 0 -10000 0 0
SAP18 0 0 -9999 0 -10000 0 0
RELA -0.005 0.038 -9999 0 -0.32 14 14
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0 0 -9999 0 -10000 0 0
HDAC3/TR2 -0.004 0.029 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0 0.007 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.004 0.034 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.025 0.13 -9999 0 -0.65 38 38
GATA1 -0.004 0.032 -9999 0 -0.28 13 13
Mad/Max 0 0.006 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0 0.008 -9999 0 -10000 0 0
RBBP7 -0.002 0.025 -9999 0 -0.28 8 8
NPC 0 0 -9999 0 -10000 0 0
RBBP4 -0.001 0.026 -9999 0 -0.81 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 -0.005 0.034 -9999 0 -10000 0 0
KAT2B -0.001 0.026 -9999 0 -0.81 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 -0.28 4 4
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 -0.001 0.026 -9999 0 -0.81 1 1
YY1/HDAC3 -0.004 0.027 -9999 0 -10000 0 0
YY1/HDAC2 0 0.009 -9999 0 -0.3 1 1
YY1/HDAC1 0 0.009 -9999 0 -0.3 1 1
NuRD/MBD2 Complex (MeCP1) 0 0.007 -9999 0 -10000 0 0
PPARG -0.093 0.17 -9999 0 -0.38 237 237
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 0.029 -9999 0 -10000 0 0
MBD3L2 -0.001 0.013 -9999 0 -0.28 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 -0.005 0.034 -9999 0 -10000 0 0
HDAC2 0 0 -9999 0 -10000 0 0
YY1 0 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 -0.28 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 0.008 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 -0.001 0.011 -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 -0.005 0.033 -9999 0 -10000 0 0
histone deacetylation 0.045 0.008 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.004 0.026 -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 -0.019 0.084 -9999 0 -0.48 27 27
GATA1/HDAC1 -0.002 0.02 -9999 0 -10000 0 0
GATA1/HDAC3 -0.006 0.032 -9999 0 -10000 0 0
CHD4 0 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.012 0.077 -9999 0 -0.62 14 14
SIN3/HDAC complex/Mad/Max 0 0.007 -9999 0 -10000 0 0
NuRD Complex 0 0.007 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.003 0.024 -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 -9999 0 -10000 0 0
HDAC complex -0.001 0.018 -9999 0 -0.48 1 1
GATA1/Fog1 -0.004 0.025 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.017 0.1 -9999 0 -0.81 14 14
negative regulation of cell growth 0.045 0.009 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0 0.007 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.007 0.051 -9999 0 -0.43 14 14
SIN3/HDAC complex/NCoR1 0 0.011 -9999 0 -10000 0 0
TFCP2 0 0 -9999 0 -10000 0 0
NR2C1 0 0 -9999 0 -10000 0 0
MBD3 0 0.009 -9999 0 -0.28 1 1
MBD2 0 0 -9999 0 -10000 0 0
FoxO family 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
G6PC 0.029 0.039 -9999 0 -10000 0 0
PLK1 0.014 0.11 -9999 0 -0.63 4 4
CDKN1B 0.083 0.066 -9999 0 -0.54 3 3
FOXO3 0.045 0.1 -9999 0 -0.56 8 8
KAT2B 0.008 0.03 -9999 0 -0.84 1 1
FOXO1/SIRT1 0.006 0.04 -9999 0 -0.33 10 10
CAT 0.048 0.11 -9999 0 -1 4 4
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 11 11
MAPK10 -0.04 0.18 -9999 0 -0.46 154 154
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.063 0.087 -9999 0 -10000 0 0
response to oxidative stress 0.005 0.011 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.012 0.062 -9999 0 -0.5 6 6
XPO1 0 0 -9999 0 -10000 0 0
EP300 0.005 0.006 -9999 0 -10000 0 0
BCL2L11 0.029 0.018 -9999 0 -10000 0 0
FOXO1/SKP2 -0.004 0.034 -9999 0 -0.33 10 10
mol:GDP 0.005 0.011 -9999 0 -10000 0 0
RAN 0.012 0.003 -9999 0 -10000 0 0
GADD45A 0.07 0.059 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.068 0.027 -9999 0 -10000 0 0
MST1 -0.003 0.095 -9999 0 -0.77 14 14
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.002 0.04 -9999 0 -0.35 4 4
YWHAB 0 0 -9999 0 -10000 0 0
MAPK8 0.034 0.036 -9999 0 -0.46 5 5
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 -0.28 3 3
SIRT1 0.002 0.008 -9999 0 -10000 0 0
SOD2 0.093 0.071 -9999 0 -10000 0 0
RBL2 0.063 0.076 -9999 0 -0.55 1 1
RAL/GDP 0.011 0.015 -9999 0 -10000 0 0
CHUK 0.009 0.012 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
CSNK1G2 0 0 -9999 0 -10000 0 0
RAL/GTP 0.03 0.009 -9999 0 -10000 0 0
CSNK1G1 0 0 -9999 0 -10000 0 0
FASLG 0.008 0.17 -9999 0 -1.5 11 11
SKP2 0 0 -9999 0 -10000 0 0
USP7 0.01 0.005 -9999 0 -10000 0 0
IKBKB 0.008 0.017 -9999 0 -10000 0 0
CCNB1 0.039 0.11 -9999 0 -0.71 2 2
FOXO1-3a-4/beta catenin -0.008 0.037 -9999 0 -0.42 4 4
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.034 -9999 0 -0.32 10 10
CSNK1A1 0 0 -9999 0 -10000 0 0
SGK1 0.004 0.06 -9999 0 -0.82 5 5
CSNK1G3 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
ZFAND5 0.068 0.077 -9999 0 -10000 0 0
SFN -0.015 0.098 -9999 0 -0.51 30 30
CDK2 0.002 0.005 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.023 0.05 -9999 0 -10000 0 0
CREBBP 0.002 0.005 -9999 0 -10000 0 0
FBXO32 0.047 0.12 -9999 0 -1.2 4 4
BCL6 0.059 0.11 -9999 0 -1.3 4 4
RALB 0 0 -9999 0 -10000 0 0
RALA 0 0 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP -0.001 0.026 0.3 2 -10000 0 2
DAPP1 0.035 0.055 -10000 0 -0.59 4 4
Src family/SYK family/BLNK-LAT/BTK-ITK 0.046 0.081 -10000 0 -0.57 10 10
mol:DAG 0.052 0.05 0.21 1 -0.27 7 8
HRAS -0.001 0.02 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
ARF5/GDP -0.003 0.024 -10000 0 -0.3 1 1
PLCG2 -0.002 0.037 -10000 0 -0.63 3 3
PLCG1 0 0 -10000 0 -10000 0 0
ARF5 0 0.009 -10000 0 -0.28 1 1
mol:GTP -0.001 0.023 0.27 2 -0.4 2 4
ARF1/GTP -0.001 0.023 0.28 2 -0.38 2 4
RHOA 0 0 -10000 0 -10000 0 0
YES1 -0.001 0.026 -10000 0 -0.81 1 1
RAP1A/GTP -0.001 0.022 0.25 2 -0.39 2 4
ADAP1 -0.003 0.033 -10000 0 -0.42 3 3
ARAP3 -0.001 0.023 0.26 2 -0.4 2 4
INPPL1 0 0 -10000 0 -10000 0 0
PREX1 -0.01 0.056 -10000 0 -0.29 34 34
ARHGEF6 -0.011 0.092 -10000 0 -0.81 13 13
ARHGEF7 0 0 -10000 0 -10000 0 0
ARF1 0 0 -10000 0 -10000 0 0
NRAS -0.001 0.012 -10000 0 -10000 0 0
FYN -0.002 0.036 -10000 0 -0.81 2 2
ARF6 0 0 -10000 0 -10000 0 0
FGR -0.001 0.027 -10000 0 -0.81 1 1
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 -10000 0 0
ZAP70 -0.03 0.13 -10000 0 -0.43 68 68
mol:IP3 0.047 0.038 -10000 0 -0.22 1 1
LYN 0 0 -10000 0 -10000 0 0
ARF1/GDP -0.003 0.024 -10000 0 -0.3 1 1
RhoA/GDP -0.002 0.022 0.28 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 0.033 -10000 0 -10000 0 0
SRC 0 0.009 -10000 0 -10000 0 0
PLEKHA2 0.03 0.007 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PTEN -0.001 0.035 -10000 0 -0.78 2 2
HSP90AA1 0 0.009 -10000 0 -0.28 1 1
ARF6/GTP -0.001 0.022 0.3 2 -10000 0 2
RhoA/GTP -0.001 0.021 -10000 0 -0.37 2 2
Src family/SYK family/BLNK-LAT -0.01 0.059 -10000 0 -0.55 6 6
BLK -0.04 0.1 -10000 0 -0.81 3 3
PDPK1 0 0 -10000 0 -10000 0 0
CYTH1 -0.001 0.021 -10000 0 -10000 0 0
HCK -0.003 0.029 -10000 0 -10000 0 0
CYTH3 -0.001 0.025 -10000 0 -0.42 1 1
CYTH2 -0.001 0.021 -10000 0 -10000 0 0
KRAS -0.001 0.012 -10000 0 -0.28 2 2
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.004 0.051 -10000 0 -0.57 7 7
SGK1 -0.003 0.053 -10000 0 -0.72 5 5
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.034 0.031 -10000 0 -0.27 3 3
SOS1 0 0 -10000 0 -10000 0 0
SYK 0 0.009 -10000 0 -0.28 1 1
ARF6/GDP -0.001 0.023 0.29 2 -10000 0 2
mol:PI-3-4-5-P3 -0.001 0.025 0.36 2 -0.4 2 4
ARAP3/RAP1A/GTP -0.001 0.023 -10000 0 -0.4 2 2
VAV1 -0.001 0.029 -10000 0 -0.46 3 3
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 -0.4 2 2
PLEKHA1 0.029 0.019 -10000 0 -0.53 1 1
Rac1/GDP -0.003 0.024 -10000 0 -0.3 1 1
LAT -0.006 0.049 -10000 0 -0.34 16 16
Rac1/GTP -0.005 0.043 -10000 0 -0.36 13 13
ITK -0.018 0.084 0.26 1 -0.45 33 34
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.059 0.065 0.24 1 -0.4 7 8
LCK -0.02 0.1 -10000 0 -0.81 13 13
BTK -0.001 0.022 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

Figure S120.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S120.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.076 0.035 -9999 0 -10000 0 0
ERC1 0 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.006 0.038 -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 -10000 0 0
RIPK2 -0.001 0.02 -9999 0 -0.28 5 5
IKBKG 0 0.008 -9999 0 -10000 0 0
IKK complex/A20 -0.004 0.048 -9999 0 -0.38 14 14
NEMO/A20/RIP2 -0.001 0.02 -9999 0 -0.28 5 5
XPO1 0 0 -9999 0 -10000 0 0
NEMO/ATM 0 0.008 -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 -0.009 0.053 -9999 0 -0.3 29 29
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 -0.012 0.077 -9999 0 -0.62 14 14
TRAF6 0 0 -9999 0 -10000 0 0
PRKCA -0.02 0.12 -9999 0 -0.81 24 24
CHUK 0 0 -9999 0 -10000 0 0
UBE2D3 0 0 -9999 0 -10000 0 0
TNF -0.017 0.1 -9999 0 -0.81 14 14
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 0.009 -9999 0 -10000 0 0
CYLD 0 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.009 0.059 -9999 0 -0.38 24 24
Circadian rhythm 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
chromatin modification 0 0.019 -9999 0 -10000 0 0
CLOCK 0.008 0.068 -9999 0 -0.8 7 7
TIMELESS/CRY2 -0.001 0.009 -9999 0 -10000 0 0
DEC1/BMAL1 -0.001 0.011 -9999 0 -10000 0 0
ATR 0 0 -9999 0 -10000 0 0
NR1D1 0.041 0.015 -9999 0 -10000 0 0
ARNTL 0.014 0.002 -9999 0 -10000 0 0
TIMELESS 0.04 0.018 -9999 0 -10000 0 0
NPAS2 0.008 0.065 -9999 0 -0.8 6 6
CRY2 0 0 -9999 0 -10000 0 0
mol:CO -0.013 0.003 -9999 0 -10000 0 0
CHEK1 -0.007 0.045 -9999 0 -10000 0 0
mol:HEME 0.013 0.003 -9999 0 -10000 0 0
PER1 -0.016 0.11 -9999 0 -0.81 20 20
BMAL/CLOCK/NPAS2 -0.007 0.06 -9999 0 -0.52 13 13
BMAL1/CLOCK 0.042 0.047 -9999 0 -10000 0 0
S phase of mitotic cell cycle 0 0.019 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0 0.019 -9999 0 -10000 0 0
mol:NADPH 0.013 0.003 -9999 0 -10000 0 0
PER1/TIMELESS -0.011 0.067 -9999 0 -0.47 20 20
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.001 0.018 -9999 0 -0.28 4 4
EPO signaling 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
BCL2L1 0.057 0.078 -9999 0 -0.52 1 1
CRKL 0.028 0.048 -9999 0 -0.5 1 1
mol:DAG -0.002 0.028 -9999 0 -0.4 1 1
HRAS -0.005 0.021 -9999 0 -10000 0 0
MAPK8 0.012 0.063 -9999 0 -0.53 5 5
RAP1A 0.028 0.048 -9999 0 -0.5 1 1
GAB1 0.028 0.048 -9999 0 -0.5 1 1
MAPK14 0.015 0.049 -9999 0 -10000 0 0
EPO -0.035 0.11 -9999 0 -0.3 10 10
PLCG1 -0.002 0.028 -9999 0 -0.4 1 1
EPOR/TRPC2/IP3 Receptors 0.012 0.01 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.023 0.065 -9999 0 -0.64 6 6
GAB1/SHC/GRB2/SOS1 -0.007 0.022 -9999 0 -0.42 1 1
EPO/EPOR (dimer) -0.028 0.063 -9999 0 -10000 0 0
IRS2 0.009 0.11 -9999 0 -0.48 41 41
STAT1 0.048 0.057 -9999 0 -0.51 1 1
STAT5B -0.003 0.045 -9999 0 -0.44 4 4
cell proliferation 0.021 0.059 -9999 0 -0.49 5 5
GAB1/SHIP/PIK3R1/SHP2/SHC -0.008 0.037 -9999 0 -0.43 3 3
TEC 0.027 0.056 -9999 0 -0.49 4 4
SOCS3 -0.005 0.063 -9999 0 -0.81 6 6
STAT1 (dimer) 0.048 0.056 -9999 0 -0.5 1 1
JAK2 0 0.026 -9999 0 -0.82 1 1
PIK3R1 -0.006 0.068 -9999 0 -0.81 7 7
EPO/EPOR (dimer)/JAK2 0.054 0.042 -9999 0 -0.53 1 1
EPO/EPOR -0.028 0.063 -9999 0 -10000 0 0
LYN 0.012 0.002 -9999 0 -10000 0 0
TEC/VAV2 -0.012 0.037 -9999 0 -0.47 4 4
elevation of cytosolic calcium ion concentration 0.012 0.01 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.017 0.047 -9999 0 -10000 0 0
mol:IP3 -0.002 0.028 -9999 0 -0.4 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.028 0.093 -9999 0 -0.49 20 20
SH2B3 0.001 0.002 -9999 0 -10000 0 0
NFKB1 0.015 0.049 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 -0.009 0.031 -9999 0 -0.32 7 7
PTPN6 0.021 0.05 -9999 0 -0.52 1 1
TEC/VAV2/GRB2 -0.01 0.035 -9999 0 -0.45 4 4
EPOR 0.012 0.01 -9999 0 -10000 0 0
INPP5D 0 0 -9999 0 -10000 0 0
mol:GDP -0.007 0.022 -9999 0 -0.43 1 1
SOS1 0 0 -9999 0 -10000 0 0
PLCG2 -0.002 0.037 -9999 0 -0.63 3 3
CRKL/CBL/C3G -0.009 0.025 -9999 0 -0.45 1 1
VAV2 0.028 0.049 -9999 0 -0.5 1 1
CBL 0.028 0.048 -9999 0 -0.5 1 1
SHC/Grb2/SOS1 0.005 0.029 -9999 0 -0.45 1 1
STAT5A -0.006 0.058 -9999 0 -0.48 9 9
GRB2 0 0.009 -9999 0 -0.28 1 1
STAT5 (dimer) 0.056 0.088 -9999 0 -0.57 5 5
LYN/PLCgamma2 -0.001 0.028 -9999 0 -0.62 2 2
PTPN11 0 0 -9999 0 -10000 0 0
BTK 0.028 0.049 -9999 0 -0.5 1 1
BCL2 0.034 0.2 -9999 0 -0.99 35 35
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.13 0.12 -9999 0 -0.53 7 7
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 -0.28 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose -0.12 0.15 -9999 0 -0.31 20 20
YWHAZ -0.001 0.015 -9999 0 -0.28 3 3
CALM1 0 0 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
TBC1D4 0.019 0.045 -9999 0 -0.62 5 5
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 -0.002 0.023 -9999 0 -0.28 7 7
PRKCI 0 0.009 -9999 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -9999 0 -10000 0 0
RHOQ 0 0 -9999 0 -10000 0 0
GYS1 0.031 0 -9999 0 -10000 0 0
PRKCZ -0.001 0.026 -9999 0 -0.81 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 -0.34 20 20
STX4 0 0 -9999 0 -10000 0 0
GSK3B 0.025 0 -9999 0 -10000 0 0
SFN -0.015 0.098 -9999 0 -0.51 30 30
LNPEP -0.005 0.063 -9999 0 -0.81 6 6
YWHAE 0 0 -9999 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0 0.008 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.005 0.051 -9999 0 -0.53 9 9
NF kappa B1 p50/RelA/I kappa B alpha -0.003 0.025 -9999 0 -10000 0 0
NFKBIA 0.023 0.035 -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 0.016 0 -9999 0 -10000 0 0
REL -0.007 0.077 -9999 0 -0.81 9 9
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.001 0.009 -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 -0.28 1 1
NF kappa B1 p50 dimer 0 0.008 -9999 0 -10000 0 0
PIK3R1 -0.006 0.068 -9999 0 -0.81 7 7
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 0.035 -9999 0 -0.27 13 13
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.003 0.024 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -10000 0 0
PI3K -0.005 0.052 -9999 0 -0.62 7 7
NF kappa B1 p50/RelA -0.004 0.031 -9999 0 -0.27 13 13
IKBKB -0.001 0.013 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
SYK 0 0.009 -9999 0 -0.28 1 1
I kappa B alpha/PIK3R1 -0.007 0.047 -9999 0 -0.45 7 7
cell death -0.003 0.023 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel -0.005 0.051 -9999 0 -0.53 9 9
LCK -0.02 0.1 -9999 0 -0.81 13 13
BCL3 -0.001 0.013 -9999 0 -0.28 2 2
Arf6 downstream 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
PLAUR 0.028 0.042 -10000 0 -10000 0 0
regulation of axonogenesis 0.003 0.027 0.32 7 -10000 0 7
myoblast fusion 0.008 0.025 -10000 0 -10000 0 0
mol:GTP -0.005 0.015 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.008 0.028 -10000 0 -10000 0 0
ARF1/GTP -0.002 0.007 -10000 0 -10000 0 0
mol:GM1 0.006 0.014 -10000 0 -10000 0 0
mol:Choline 0.021 0.047 -10000 0 -0.52 7 7
lamellipodium assembly -0.004 0.031 -10000 0 -10000 0 0
MAPK3 0.02 0.023 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.008 0.028 -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 0.007 -10000 0 -10000 0 0
RAB11A -0.001 0.013 -10000 0 -0.28 2 2
TIAM1 0.01 0.019 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.02 0.023 -10000 0 -10000 0 0
actin filament bundle formation 0.006 0.021 -10000 0 -10000 0 0
KALRN -0.011 0.069 -10000 0 -0.49 19 19
RAB11FIP3/RAB11A 0 0.008 -10000 0 -10000 0 0
RhoA/GDP -0.006 0.021 -10000 0 -10000 0 0
NME1 -0.003 0.063 -10000 0 -0.28 49 49
Rac1/GDP -0.006 0.021 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.005 0.015 -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 0.015 -10000 0 -10000 0 0
ARF6/GTP -0.005 0.015 -10000 0 -10000 0 0
RhoA/GTP -0.002 0.007 -10000 0 -10000 0 0
mol:GDP -0.005 0.028 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A -0.001 0.006 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
PLD1 0.012 0.053 -10000 0 -0.59 7 7
RAB11FIP3 0 0 -10000 0 -10000 0 0
tube morphogenesis -0.004 0.031 -10000 0 -10000 0 0
ruffle organization -0.003 0.027 -10000 0 -0.32 7 7
regulation of epithelial cell migration -0.005 0.015 -10000 0 -10000 0 0
PLD2 0.016 0.013 -10000 0 -10000 0 0
PIP5K1A -0.003 0.027 -10000 0 -0.32 7 7
mol:Phosphatidic acid 0.021 0.047 -10000 0 -0.52 7 7
Rac1/GTP -0.004 0.031 -10000 0 -10000 0 0
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.012 0.035 -9999 0 -0.43 1 1
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 -0.006 0.025 -9999 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.001 0.017 -9999 0 -0.54 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.006 0.039 -9999 0 -0.4 1 1
CaM/Ca2+ 0.01 0.031 -9999 0 -0.4 1 1
RAP1A 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.011 0.032 -9999 0 -0.41 1 1
AKT1 -0.008 0.037 -9999 0 -0.46 1 1
MAP2K1 0.04 0.041 -9999 0 -0.4 1 1
MAP3K11 0.031 0.039 -9999 0 -0.4 1 1
IFNGR1 0.001 0.002 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.025 0.099 -9999 0 -0.41 21 21
Rap1/GTP -0.003 0.012 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.011 0.034 -9999 0 -0.45 1 1
CEBPB 0.075 0.038 -9999 0 -0.42 1 1
STAT3 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.009 0.056 -9999 0 -1.3 1 1
STAT1 -0.01 0.032 -9999 0 -0.41 1 1
CALM1 0 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.037 0.094 -9999 0 -0.28 1 1
PIK3CA 0 0.009 -9999 0 -0.28 1 1
STAT1 (dimer)/PIAS1 -0.008 0.029 -9999 0 -10000 0 0
CEBPB/PTGES2/Cbp/p300 -0.001 0.013 -9999 0 -10000 0 0
mol:Ca2+ 0.011 0.033 -9999 0 -0.43 1 1
MAPK3 0.054 0.038 -9999 0 -10000 0 0
STAT1 (dimer) -0.005 0.053 -9999 0 -0.6 1 1
MAPK1 0.054 0.038 -9999 0 -0.44 1 1
JAK2 0 0.026 -9999 0 -0.8 1 1
PIK3R1 -0.006 0.068 -9999 0 -0.81 7 7
JAK1 0.001 0.002 -9999 0 -10000 0 0
CAMK2D -0.002 0.044 -9999 0 -0.81 3 3
DAPK1 0.069 0.032 -9999 0 -10000 0 0
SMAD7 0.05 0.037 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.006 0.018 -9999 0 -10000 0 0
PI3K 0.006 0.046 -9999 0 -0.42 7 7
IFNG -0.037 0.094 -9999 0 -0.28 1 1
apoptosis 0.053 0.028 -9999 0 -10000 0 0
CAMK2G 0 0 -9999 0 -10000 0 0
STAT3 (dimer) 0 0 -9999 0 -10000 0 0
CAMK2A -0.009 0.049 -9999 0 -0.28 31 31
CAMK2B -0.073 0.22 -9999 0 -0.81 74 74
FRAP1 0.04 0.048 -9999 0 -0.43 1 1
PRKCD -0.008 0.037 -9999 0 -0.46 1 1
RAP1B 0 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.006 0.039 -9999 0 -0.4 1 1
PTPN2 0 0 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
IRF1 0.064 0.044 -9999 0 -10000 0 0
STAT1 (dimer)/PIASy -0.008 0.03 -9999 0 -10000 0 0
SOCS1 0 0.051 -9999 0 -1.5 1 1
mol:GDP -0.006 0.018 -9999 0 -10000 0 0
CASP1 0.049 0.044 -9999 0 -0.36 4 4
PTGES2 0 0.009 -9999 0 -0.28 1 1
IRF9 0.057 0.02 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.003 0.042 -9999 0 -0.41 7 7
RAP1/GDP -0.003 0.012 -9999 0 -10000 0 0
CBL -0.009 0.025 -9999 0 -0.4 1 1
MAP3K1 0.031 0.042 -9999 0 -0.42 2 2
PIAS1 0 0 -9999 0 -10000 0 0
PIAS4 0 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.006 0.039 -9999 0 -0.4 1 1
PTPN11 -0.01 0.028 -9999 0 -0.43 1 1
CREBBP 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
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 0.026 -9999 0 -0.28 9 9
RAC1 0 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.007 0.044 -9999 0 -0.46 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.001 0.013 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin -0.005 0.031 -9999 0 -0.48 2 2
lamellipodium assembly -0.003 0.039 -9999 0 -0.46 7 7
PIK3CA 0 0.009 -9999 0 -0.28 1 1
PI3K -0.005 0.052 -9999 0 -0.62 7 7
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 -0.006 0.068 -9999 0 -0.81 7 7
ARF6/GTP -0.001 0.009 -9999 0 -10000 0 0
cell adhesion -0.001 0.009 -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 -0.008 0.056 -9999 0 -0.32 26 26
ARF6/GDP 0 0.003 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.006 0.049 -9999 0 -0.45 11 11
p130Cas/Crk/Dock1 0 0 -9999 0 -10000 0 0
VCAM1 -0.011 0.087 -9999 0 -0.81 11 11
alpha4/beta1 Integrin/Paxillin/Talin -0.001 0.009 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.001 0.011 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
mol:GDP 0.001 0.011 -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 -0.28 5 5
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.001 0.009 -9999 0 -10000 0 0
Rac1/GTP -0.003 0.044 -9999 0 -0.52 7 7
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.071 0.064 -9999 0 -0.62 1 1
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.018 0.016 -9999 0 -10000 0 0
AURKB -0.16 0.14 -9999 0 -10000 0 0
AURKC -0.004 0.041 -9999 0 -0.81 1 1
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 0.012 -9999 0 -0.38 1 1
MDM2/SUMO1 0 0.006 -9999 0 -10000 0 0
HDAC4 -0.001 0.026 -9999 0 -0.81 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 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.028 0 -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 0.014 -9999 0 -0.45 1 1
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
RANGAP1 0 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0 0.007 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0 0 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 -0.001 0.018 -9999 0 -0.28 4 4
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 0.02 -9999 0 -0.28 5 5
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 0.015 -9999 0 -10000 0 0
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 0.007 -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 0.008 -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 0.009 -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 0.015 -9999 0 -10000 0 0
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 0.015 -9999 0 -10000 0 0
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 0.017 -9999 0 -10000 0 0
RELB -0.003 0.026 -9999 0 -10000 0 0
NFKB2 0 0.009 -9999 0 -0.28 1 1
NF kappa B2 p52/RelB -0.001 0.014 -9999 0 -10000 0 0
regulation of B cell activation -0.001 0.014 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 988 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.PE.A5DE TCGA.PE.A5DD TCGA.PE.A5DC TCGA.OL.A66K
109_MAP3K5 0.042 0.053 0.053 0.053
47_PPARGC1A 0 0 -0.81 0
105_BMP4 0 0 0 0
105_BMP6 0 0 0 0
105_BMP7 0 0 0 0
105_BMP2 0 0 0 0
131_RELN/VLDLR -0.48 -0.48 -0.48 -0.48
30_TGFB1/TGF beta receptor Type II 0 0 0 0
84_STAT5B -0.1 -0.075 -0.13 -0.1
84_STAT5A -0.1 -0.075 -0.13 -0.1
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/4397369/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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