PARADIGM pathway analysis of mRNASeq expression and copy number data
Thyroid Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1D50KSV
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1D50KSV
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 39 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
Ephrin A reverse signaling 245
Signaling events mediated by Stem cell factor receptor (c-Kit) 166
Signaling events regulated by Ret tyrosine kinase 144
Reelin signaling pathway 128
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 110
Noncanonical Wnt signaling pathway 101
Wnt signaling 101
PDGFR-alpha signaling pathway 94
Signaling events mediated by the Hedgehog family 86
Nongenotropic Androgen signaling 86
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 494 . 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 ( 494 ).

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
Ephrin A reverse signaling 0.4960 245 1721 7 -0.42 0 1000 -1000 -0.011 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.3360 166 12971 78 -0.74 0.24 1000 -1000 -0.043 -1000
Signaling events regulated by Ret tyrosine kinase 0.2915 144 11833 82 -0.36 0.027 1000 -1000 -0.057 -1000
Reelin signaling pathway 0.2591 128 7220 56 -0.46 0.061 1000 -1000 -0.038 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2227 110 7501 68 -0.73 0.35 1000 -1000 -0.066 -1000
Noncanonical Wnt signaling pathway 0.2045 101 2650 26 -0.32 0.027 1000 -1000 -0.038 -1000
Wnt signaling 0.2045 101 709 7 -0.32 0.014 1000 -1000 -0.016 -1000
PDGFR-alpha signaling pathway 0.1903 94 4146 44 -0.4 0.043 1000 -1000 -0.045 -1000
Signaling events mediated by the Hedgehog family 0.1741 86 4515 52 -0.29 0.14 1000 -1000 -0.032 -1000
Nongenotropic Androgen signaling 0.1741 86 4517 52 -0.26 0.19 1000 -1000 -0.029 -1000
FOXA2 and FOXA3 transcription factor networks 0.1680 83 3837 46 -0.84 0.031 1000 -1000 -0.076 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1457 72 3920 54 -0.46 0.039 1000 -1000 -0.056 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1356 67 2306 34 -0.1 0.027 1000 -1000 -0.031 -1000
Calcium signaling in the CD4+ TCR pathway 0.1316 65 2039 31 -0.35 0.027 1000 -1000 -0.036 -1000
Endothelins 0.1275 63 6142 96 -0.32 0.031 1000 -1000 -0.048 -1000
IGF1 pathway 0.1275 63 3628 57 -0.14 0.064 1000 -1000 -0.041 -1000
Glypican 1 network 0.1255 62 2985 48 -0.29 0.052 1000 -1000 -0.023 -1000
IL4-mediated signaling events 0.1194 59 5432 91 -1.2 0.57 1000 -1000 -0.07 -1000
HIF-1-alpha transcription factor network 0.1154 57 4341 76 -0.47 0.041 1000 -1000 -0.052 -1000
Ephrin B reverse signaling 0.1073 53 2564 48 -0.23 0.12 1000 -1000 -0.028 -1000
EPHB forward signaling 0.1073 53 4573 85 -0.23 0.11 1000 -1000 -0.061 -1000
IL23-mediated signaling events 0.1053 52 3156 60 -0.26 0.027 1000 -1000 -0.038 -1000
BMP receptor signaling 0.1032 51 4185 81 -0.44 0.052 1000 -1000 -0.053 -1000
TCR signaling in naïve CD8+ T cells 0.0992 49 4603 93 -0.15 0.045 1000 -1000 -0.05 -1000
Coregulation of Androgen receptor activity 0.0951 47 3638 76 -0.66 0.076 1000 -1000 -0.022 -1000
Glucocorticoid receptor regulatory network 0.0951 47 5468 114 -0.45 0.25 1000 -1000 -0.057 -1000
Arf6 signaling events 0.0891 44 2779 62 -0.26 0.061 1000 -1000 -0.03 -1000
Signaling mediated by p38-alpha and p38-beta 0.0769 38 1681 44 -0.22 0.027 1000 -1000 -0.036 -1000
Thromboxane A2 receptor signaling 0.0749 37 3899 105 -0.16 0.047 1000 -1000 -0.04 -1000
Hedgehog signaling events mediated by Gli proteins 0.0729 36 2376 65 -0.58 0.064 1000 -1000 -0.04 -1000
IL12-mediated signaling events 0.0688 34 2985 87 -0.36 0.028 1000 -1000 -0.06 -1000
Ras signaling in the CD4+ TCR pathway 0.0668 33 571 17 -0.1 0.035 1000 -1000 -0.025 -1000
IL6-mediated signaling events 0.0628 31 2390 75 -0.15 0.054 1000 -1000 -0.039 -1000
EGFR-dependent Endothelin signaling events 0.0628 31 669 21 -0.076 0.038 1000 -1000 -0.045 -1000
Syndecan-1-mediated signaling events 0.0567 28 985 34 -0.075 0.027 1000 -1000 -0.037 -1000
Plasma membrane estrogen receptor signaling 0.0547 27 2385 86 -0.13 0.049 1000 -1000 -0.052 -1000
Regulation of p38-alpha and p38-beta 0.0526 26 1419 54 -0.35 0.065 1000 -1000 -0.046 -1000
Regulation of Androgen receptor activity 0.0526 26 1832 70 -0.44 0.036 1000 -1000 -0.044 -1000
Osteopontin-mediated events 0.0506 25 969 38 -0.15 0.043 1000 -1000 -0.039 -1000
ErbB2/ErbB3 signaling events 0.0486 24 1616 65 -0.17 0.037 1000 -1000 -0.049 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0486 24 2087 85 -0.22 0.13 1000 -1000 -0.043 -1000
FAS signaling pathway (CD95) 0.0486 24 1167 47 -0.2 0.044 1000 -1000 -0.029 -1000
LPA receptor mediated events 0.0466 23 2363 102 -0.15 0.035 1000 -1000 -0.058 -1000
BCR signaling pathway 0.0445 22 2196 99 -0.099 0.048 1000 -1000 -0.06 -1000
Syndecan-4-mediated signaling events 0.0445 22 1500 67 -0.16 0.039 1000 -1000 -0.038 -1000
VEGFR1 specific signals 0.0445 22 1263 56 -0.043 0.058 1000 -1000 -0.048 -1000
IFN-gamma pathway 0.0425 21 1459 68 -0.17 0.035 1000 -1000 -0.054 -1000
Ceramide signaling pathway 0.0425 21 1600 76 -0.15 0.075 1000 -1000 -0.031 -1000
Fc-epsilon receptor I signaling in mast cells 0.0385 19 1923 97 -0.15 0.044 1000 -1000 -0.056 -1000
ceramide signaling pathway 0.0364 18 923 49 -0.055 0.039 1000 -1000 -0.032 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0364 18 1623 88 -0.25 0.039 1000 -1000 -0.063 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0344 17 886 52 -0.18 0.059 1000 -1000 -0.026 -1000
Integrins in angiogenesis 0.0344 17 1453 84 -0.14 0.055 1000 -1000 -0.047 -1000
IL27-mediated signaling events 0.0344 17 889 51 -0.1 0.044 1000 -1000 -0.044 -1000
Signaling events mediated by PTP1B 0.0324 16 1264 76 -0.19 0.039 1000 -1000 -0.03 -1000
amb2 Integrin signaling 0.0324 16 1355 82 -0.18 0.036 1000 -1000 -0.035 -1000
Insulin Pathway 0.0324 16 1238 74 -0.056 0.066 1000 -1000 -0.046 -1000
JNK signaling in the CD4+ TCR pathway 0.0304 15 258 17 -0.083 0.028 1000 -1000 -0.034 -1000
mTOR signaling pathway 0.0304 15 804 53 -0.044 0.03 1000 -1000 -0.037 -1000
LPA4-mediated signaling events 0.0283 14 176 12 -0.053 0.004 1000 -1000 -0.019 -1000
Regulation of nuclear SMAD2/3 signaling 0.0283 14 1948 136 -0.26 0.052 1000 -1000 -0.036 -1000
Visual signal transduction: Cones 0.0283 14 546 38 -0.043 0.043 1000 -1000 -0.013 -1000
p75(NTR)-mediated signaling 0.0283 14 1801 125 -0.28 0.07 1000 -1000 -0.066 -1000
Caspase cascade in apoptosis 0.0263 13 984 74 -0.056 0.045 1000 -1000 -0.034 -1000
Nectin adhesion pathway 0.0263 13 867 63 -0.1 0.073 1000 -1000 -0.042 -1000
Signaling events mediated by HDAC Class III 0.0263 13 549 40 -0.28 0.046 1000 -1000 -0.019 -1000
IL1-mediated signaling events 0.0263 13 865 62 -0.083 0.061 1000 -1000 -0.047 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0263 13 598 45 -0.056 0.076 1000 -1000 -0.042 -1000
Rapid glucocorticoid signaling 0.0263 13 266 20 -0.061 0.034 1000 -1000 -0.006 -1000
Cellular roles of Anthrax toxin 0.0243 12 475 39 -0.056 0.027 1000 -1000 -0.023 -1000
Presenilin action in Notch and Wnt signaling 0.0243 12 777 61 -0.15 0.07 1000 -1000 -0.047 -1000
IL2 signaling events mediated by PI3K 0.0243 12 733 58 -0.058 0.048 1000 -1000 -0.034 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0243 12 1550 120 -0.24 0.074 1000 -1000 -0.047 -1000
FOXM1 transcription factor network 0.0243 12 656 51 -0.21 0.053 1000 -1000 -0.071 -1000
ErbB4 signaling events 0.0223 11 813 69 -0.05 0.037 1000 -1000 -0.044 -1000
Syndecan-3-mediated signaling events 0.0223 11 396 35 -0.12 0.07 1000 -1000 -0.029 -1000
Visual signal transduction: Rods 0.0223 11 588 52 -0.067 0.048 1000 -1000 -0.027 -1000
BARD1 signaling events 0.0202 10 591 57 -0.04 0.05 1000 -1000 -0.037 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0202 10 297 28 -0.13 0.056 1000 -1000 -0.022 -1000
Syndecan-2-mediated signaling events 0.0202 10 731 69 -0.16 0.05 1000 -1000 -0.025 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0202 10 743 74 -0.13 0.067 1000 -1000 -0.065 -1000
S1P3 pathway 0.0202 10 425 42 -0.13 0.048 1000 -1000 -0.033 -1000
S1P1 pathway 0.0182 9 351 36 -0.054 0.027 1000 -1000 -0.043 -1000
Retinoic acid receptors-mediated signaling 0.0182 9 537 58 -0.037 0.053 1000 -1000 -0.033 -1000
TCGA08_rtk_signaling 0.0182 9 259 26 -0.18 0.045 1000 -1000 -0.006 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0162 8 695 83 -0.17 0.048 1000 -1000 -0.033 -1000
TCGA08_p53 0.0162 8 61 7 -0.022 0.025 1000 -1000 -0.012 -1000
Class I PI3K signaling events 0.0162 8 600 73 -0.19 0.05 1000 -1000 -0.038 -1000
Regulation of Telomerase 0.0162 8 865 102 -0.19 0.071 1000 -1000 -0.03 -1000
Signaling events mediated by HDAC Class I 0.0142 7 735 104 -0.056 0.062 1000 -1000 -0.03 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0142 7 251 33 -0.11 0.055 1000 -1000 -0.033 -1000
Class IB PI3K non-lipid kinase events 0.0142 7 21 3 -0.015 0.015 1000 -1000 -0.003 -1000
a4b1 and a4b7 Integrin signaling 0.0121 6 33 5 0.004 0.034 1000 -1000 0.003 -1000
PLK1 signaling events 0.0121 6 583 85 -0.006 0.049 1000 -1000 -0.032 -1000
IL2 signaling events mediated by STAT5 0.0121 6 134 22 -0.033 0.033 1000 -1000 -0.046 -1000
Effects of Botulinum toxin 0.0101 5 130 26 -0.064 0.048 1000 -1000 -0.01 -1000
PDGFR-beta signaling pathway 0.0101 5 490 97 -0.14 0.079 1000 -1000 -0.057 -1000
Signaling events mediated by PRL 0.0101 5 175 34 -0.086 0.04 1000 -1000 -0.043 -1000
S1P4 pathway 0.0101 5 135 25 -0.003 0.047 1000 -1000 -0.029 -1000
Aurora B signaling 0.0101 5 393 67 -0.32 0.1 1000 -1000 -0.04 -1000
Insulin-mediated glucose transport 0.0081 4 151 32 -0.08 0.05 1000 -1000 -0.031 -1000
Class I PI3K signaling events mediated by Akt 0.0081 4 298 68 -0.08 0.05 1000 -1000 -0.034 -1000
S1P5 pathway 0.0081 4 84 17 -0.007 0.032 1000 -1000 -0.018 -1000
Signaling mediated by p38-gamma and p38-delta 0.0081 4 65 15 -0.002 0.027 1000 -1000 -0.027 -1000
Atypical NF-kappaB pathway 0.0081 4 126 31 -0.018 0.04 1000 -1000 -0.025 -1000
Canonical Wnt signaling pathway 0.0081 4 223 51 -0.034 0.065 1000 -1000 -0.049 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0081 4 616 125 -0.01 0.07 1000 -1000 -0.048 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0061 3 72 23 -0.016 0.049 1000 -1000 -0.027 -1000
Canonical NF-kappaB pathway 0.0061 3 151 39 -0.056 0.061 1000 -1000 -0.033 -1000
Circadian rhythm pathway 0.0061 3 83 22 -0.017 0.041 1000 -1000 -0.027 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0061 3 138 37 0 0.063 1000 -1000 -0.031 -1000
HIF-2-alpha transcription factor network 0.0061 3 165 43 -0.16 0.16 1000 -1000 -0.042 -1000
FoxO family signaling 0.0061 3 249 64 -0.08 0.1 1000 -1000 -0.04 -1000
TCGA08_retinoblastoma 0.0061 3 31 8 -0.031 0.031 1000 -1000 -0.003 -1000
E-cadherin signaling in keratinocytes 0.0061 3 131 43 -0.029 0.051 1000 -1000 -0.038 -1000
p38 MAPK signaling pathway 0.0061 3 165 44 -0.031 0.049 1000 -1000 -0.022 -1000
Aurora A signaling 0.0040 2 125 60 -0.023 0.055 1000 -1000 -0.022 -1000
EPO signaling pathway 0.0040 2 162 55 -0.013 0.059 1000 -1000 -0.04 -1000
TRAIL signaling pathway 0.0040 2 107 48 -0.012 0.074 1000 -1000 -0.038 -1000
Paxillin-dependent events mediated by a4b1 0.0040 2 99 36 -0.053 0.055 1000 -1000 -0.034 -1000
Signaling events mediated by HDAC Class II 0.0020 1 91 75 -0.036 0.074 1000 -1000 -0.025 -1000
E-cadherin signaling in the nascent adherens junction 0.0020 1 143 76 -0.054 0.066 1000 -1000 -0.06 -1000
Arf6 trafficking events 0.0020 1 103 71 -0.048 0.05 1000 -1000 -0.028 -1000
PLK2 and PLK4 events 0.0000 0 0 3 0.016 0.027 1000 -1000 -0.017 -1000
Arf6 downstream pathway 0.0000 0 9 43 -0.055 0.046 1000 -1000 -0.025 -1000
Aurora C signaling 0.0000 0 4 7 -0.005 0.046 1000 -1000 -0.012 -1000
Glypican 2 network 0.0000 0 3 4 -0.018 0.017 1000 -1000 -0.001 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 12 27 0 0.066 1000 -1000 -0.035 -1000
E-cadherin signaling events 0.0000 0 0 5 0.026 0.051 1000 -1000 0.003 -1000
Arf1 pathway 0.0000 0 25 54 -0.001 0.052 1000 -1000 -0.021 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.072 1000 -1000 -0.006 -1000
Total NA 3473 200861 7203 -22 8 131000 -131000 -4.7 -131000
Ephrin A reverse signaling

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
MAPKKK cascade -0.32 0.26 -9999 0 -0.47 337 337
EFNA5 -0.071 0.24 -9999 0 -0.67 69 69
FYN -0.29 0.24 -9999 0 -0.44 330 330
neuron projection morphogenesis -0.32 0.26 -9999 0 -0.47 337 337
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.32 0.26 -9999 0 -0.48 337 337
EPHA5 -0.42 0.33 -9999 0 -0.67 311 311
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 -0.22 0.21 0.38 1 -0.39 274 275
CRKL -0.23 0.22 -10000 0 -0.41 279 279
HRAS -0.2 0.19 -10000 0 -0.4 106 106
mol:PIP3 -0.2 0.2 -10000 0 -0.39 255 255
SPRED1 0.027 0.004 -10000 0 -10000 0 0
SPRED2 0.025 0.032 -10000 0 -0.67 1 1
GAB1 -0.24 0.23 -10000 0 -0.44 281 281
FOXO3 -0.19 0.21 0.37 2 -0.37 269 271
AKT1 -0.21 0.22 0.29 2 -0.39 273 275
BAD -0.19 0.2 0.28 2 -0.37 267 269
megakaryocyte differentiation -0.24 0.23 -10000 0 -0.43 290 290
GSK3B -0.19 0.21 0.31 3 -0.37 269 272
RAF1 -0.16 0.16 0.35 1 -0.35 71 72
SHC1 0.025 0.007 -10000 0 -10000 0 0
STAT3 -0.24 0.23 -10000 0 -0.44 275 275
STAT1 -0.59 0.56 -10000 0 -1.1 284 284
HRAS/SPRED1 -0.16 0.16 -10000 0 -0.35 71 71
cell proliferation -0.24 0.24 -10000 0 -0.44 284 284
PIK3CA 0.022 0.054 -10000 0 -0.67 3 3
TEC 0.027 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.22 0.23 -10000 0 -0.42 281 281
HRAS/SPRED2 -0.16 0.16 -10000 0 -0.35 70 70
LYN/TEC/p62DOK -0.21 0.24 -10000 0 -0.41 279 279
MAPK3 -0.11 0.12 0.26 5 -0.29 19 24
STAP1 -0.25 0.24 -10000 0 -0.44 281 281
GRAP2 -0.02 0.15 -10000 0 -0.55 33 33
JAK2 -0.49 0.48 -10000 0 -0.89 284 284
STAT1 (dimer) -0.57 0.54 -10000 0 -1 284 284
mol:Gleevec 0.008 0.011 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.21 0.24 -10000 0 -0.42 266 266
actin filament polymerization -0.23 0.23 -10000 0 -0.43 278 278
LYN 0.027 0.005 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.34 0.32 0.35 1 -0.61 282 283
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.19 0.21 -10000 0 -0.38 270 270
PI3K -0.21 0.24 -10000 0 -0.41 277 277
PTEN 0.026 0.018 -10000 0 -0.35 1 1
SCF/KIT/EPO/EPOR -0.7 0.66 -10000 0 -1.3 282 282
MAPK8 -0.25 0.24 -10000 0 -0.44 284 284
STAT3 (dimer) -0.23 0.23 -10000 0 -0.43 275 275
positive regulation of transcription -0.086 0.11 0.3 7 -0.24 18 25
mol:GDP -0.2 0.2 -10000 0 -0.38 237 237
PIK3C2B -0.23 0.23 -10000 0 -0.44 257 257
CBL/CRKL -0.2 0.22 -10000 0 -0.39 277 277
FER -0.24 0.23 -10000 0 -0.44 280 280
SH2B3 -0.24 0.23 -10000 0 -0.44 282 282
PDPK1 -0.19 0.2 0.3 3 -0.36 250 253
SNAI2 -0.24 0.24 -10000 0 -0.44 281 281
positive regulation of cell proliferation -0.41 0.4 -10000 0 -0.74 284 284
KITLG -0.017 0.093 -10000 0 -0.7 8 8
cell motility -0.41 0.4 -10000 0 -0.74 284 284
PTPN6 0.038 0.014 -10000 0 -10000 0 0
EPOR -0.15 0.19 -10000 0 -0.98 7 7
STAT5A (dimer) -0.34 0.33 -10000 0 -0.61 282 282
SOCS1 0.023 0.035 -10000 0 -0.67 1 1
cell migration 0.24 0.23 0.43 276 -10000 0 276
SOS1 0.027 0.005 -10000 0 -10000 0 0
EPO -0.007 0.03 -10000 0 -10000 0 0
VAV1 0.012 0.06 -10000 0 -0.56 3 3
GRB10 -0.24 0.23 -10000 0 -0.44 279 279
PTPN11 0.033 0.033 -10000 0 -0.65 1 1
SCF/KIT -0.25 0.25 -10000 0 -0.46 282 282
GO:0007205 0.011 0.013 -10000 0 -10000 0 0
MAP2K1 -0.13 0.13 0.27 3 -0.32 20 23
CBL 0.027 0.005 -10000 0 -10000 0 0
KIT -0.74 0.68 -10000 0 -1.3 282 282
MAP2K2 -0.12 0.13 0.28 2 -0.3 26 28
SHC/Grb2/SOS1 -0.2 0.23 -10000 0 -0.42 245 245
STAT5A -0.34 0.34 -10000 0 -0.63 281 281
GRB2 0.026 0.007 -10000 0 -10000 0 0
response to radiation -0.24 0.24 -10000 0 -0.43 281 281
SHC/GRAP2 0 0.11 -10000 0 -0.38 33 33
PTPRO -0.25 0.23 -10000 0 -0.44 290 290
SH2B2 -0.24 0.23 -10000 0 -0.44 278 278
DOK1 0.027 0.005 -10000 0 -10000 0 0
MATK -0.24 0.23 -10000 0 -0.44 276 276
CREBBP -0.043 0.077 -10000 0 -10000 0 0
BCL2 -0.22 0.4 -10000 0 -1.4 40 40
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.061 0.097 -10000 0 -0.61 7 7
Crk/p130 Cas/Paxillin -0.21 0.19 -10000 0 -0.38 253 253
JUN -0.26 0.26 -10000 0 -0.55 167 167
HRAS 0.026 0.011 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.26 0.29 -10000 0 -0.48 284 284
RAP1A 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.027 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.26 0.28 -10000 0 -0.48 291 291
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.2 0.22 -10000 0 -0.4 271 271
RHOA 0.027 0.003 -10000 0 -10000 0 0
RAP1A/GTP -0.23 0.26 -10000 0 -0.44 282 282
GRB7 0.003 0.053 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF -0.26 0.28 -10000 0 -0.47 287 287
MAPKKK cascade -0.23 0.23 -10000 0 -0.41 279 279
BCAR1 0.026 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.25 0.26 -10000 0 -0.45 288 288
lamellipodium assembly -0.19 0.18 -10000 0 -0.34 264 264
RET51/GFRalpha1/GDNF/SHC -0.25 0.28 -10000 0 -0.47 283 283
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
RET9/GFRalpha1/GDNF/SHC -0.2 0.22 -10000 0 -0.39 269 269
RET9/GFRalpha1/GDNF/Shank3 -0.21 0.21 -10000 0 -0.39 274 274
MAPK3 -0.24 0.23 -10000 0 -0.42 279 279
DOK1 0.027 0.005 -10000 0 -10000 0 0
DOK6 -0.084 0.25 -10000 0 -0.67 78 78
PXN 0.027 0.005 -10000 0 -10000 0 0
neurite development -0.26 0.24 -10000 0 -0.53 166 166
DOK5 -0.066 0.24 -10000 0 -0.66 66 66
GFRA1 -0.36 0.34 -10000 0 -0.66 279 279
MAPK8 -0.19 0.2 -10000 0 -0.34 289 289
HRAS/GTP -0.25 0.28 -10000 0 -0.46 286 286
tube development -0.19 0.2 -10000 0 -0.38 256 256
MAPK1 -0.24 0.23 0.32 3 -0.41 281 284
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.15 0.16 -10000 0 -0.29 256 256
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
PDLIM7 0.026 0.011 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.3 0.33 -10000 0 -0.53 297 297
SHC1 0.025 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.26 0.29 -10000 0 -0.48 286 286
RET51/GFRalpha1/GDNF/Dok5 -0.31 0.33 -10000 0 -0.54 300 300
PRKCA 0.002 0.13 -10000 0 -0.67 17 17
HRAS/GDP 0.019 0.007 -10000 0 -10000 0 0
CREB1 -0.19 0.21 -10000 0 -0.37 253 253
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.14 0.15 -10000 0 -0.29 240 240
RET51/GFRalpha1/GDNF/Grb7 -0.26 0.28 -10000 0 -0.49 284 284
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.1 0.25 -10000 0 -0.65 83 83
DOK4 0.026 0.009 -10000 0 -10000 0 0
JNK cascade -0.25 0.25 -10000 0 -0.54 167 167
RET9/GFRalpha1/GDNF/FRS2 -0.2 0.22 -10000 0 -0.4 272 272
SHANK3 0.02 0.012 -10000 0 -10000 0 0
RASA1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.15 0.16 -10000 0 -0.3 241 241
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.19 0.2 -10000 0 -0.35 283 283
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.2 0.2 -10000 0 -0.35 288 288
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.22 0.25 -10000 0 -0.4 273 273
PI3K -0.3 0.29 -10000 0 -0.53 271 271
SOS1 0.027 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.19 0.2 -10000 0 -0.38 257 257
GRB10 0.026 0.006 -10000 0 -10000 0 0
activation of MAPKK activity -0.17 0.18 -10000 0 -0.32 265 265
RET51/GFRalpha1/GDNF/FRS2 -0.26 0.28 -10000 0 -0.48 287 287
GAB1 0.027 0.004 -10000 0 -10000 0 0
IRS1 -0.056 0.22 -10000 0 -0.66 59 59
IRS2 0.026 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.22 0.25 -10000 0 -0.4 270 270
RET51/GFRalpha1/GDNF/PKC alpha -0.27 0.3 -10000 0 -0.5 285 285
GRB2 0.026 0.007 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
GDNF -0.007 0.023 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.31 0.32 -10000 0 -0.53 301 301
Rac1/GTP -0.23 0.22 -10000 0 -0.42 258 258
RET9/GFRalpha1/GDNF -0.23 0.23 -10000 0 -0.43 277 277
GFRalpha1/GDNF -0.27 0.26 -10000 0 -0.5 277 277
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 0.037 0.014 -10000 0 -10000 0 0
VLDLR -0.002 0.14 -10000 0 -0.65 20 20
CRKL 0.02 0.012 -10000 0 -10000 0 0
LRPAP1 0.027 0.004 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
ITGA3 0.025 0.015 -10000 0 -10000 0 0
RELN/VLDLR/Fyn -0.3 0.23 -10000 0 -0.44 346 346
MAPK8IP1/MKK7/MAP3K11/JNK1 0.061 0.067 -10000 0 -0.38 9 9
AKT1 -0.2 0.15 -10000 0 -0.29 331 331
MAP2K7 0.025 0.008 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
DAB1 0.006 0.022 -10000 0 -10000 0 0
RELN/LRP8/DAB1 -0.27 0.22 -10000 0 -0.42 335 335
LRPAP1/LRP8 0.018 0.1 -10000 0 -0.5 19 19
RELN/LRP8/DAB1/Fyn -0.26 0.22 -10000 0 -0.4 335 335
DAB1/alpha3/beta1 Integrin -0.24 0.21 -10000 0 -0.38 324 324
long-term memory -0.26 0.23 -10000 0 -0.4 334 334
DAB1/LIS1 -0.25 0.22 -10000 0 -0.39 329 329
DAB1/CRLK/C3G -0.25 0.2 -10000 0 -0.38 329 329
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
DAB1/NCK2 -0.25 0.22 -10000 0 -0.39 336 336
ARHGEF2 0.025 0.007 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.001 0.12 -10000 0 -0.67 16 16
CDK5R1 0.025 0.013 -10000 0 -10000 0 0
RELN -0.46 0.32 -10000 0 -0.67 338 338
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.3 0.24 -10000 0 -0.45 342 342
GRIN2A/RELN/LRP8/DAB1/Fyn -0.26 0.24 -10000 0 -0.41 334 334
MAPK8 0.013 0.095 -10000 0 -0.64 10 10
RELN/VLDLR/DAB1 -0.28 0.21 -10000 0 -0.41 345 345
ITGB1 0.027 0.004 -10000 0 -10000 0 0
MAP1B -0.28 0.21 -10000 0 -0.4 336 336
RELN/LRP8 -0.3 0.24 -10000 0 -0.45 341 341
GRIN2B/RELN/LRP8/DAB1/Fyn -0.26 0.22 -10000 0 -0.4 334 334
PI3K 0.036 0.043 -10000 0 -0.5 3 3
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.037 0.015 -10000 0 -10000 0 0
RAP1A -0.23 0.2 0.49 3 -0.37 246 249
PAFAH1B1 0.026 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.027 0.005 -10000 0 -10000 0 0
CRLK/C3G 0.028 0.019 -10000 0 -10000 0 0
GRIN2B -0.005 0.02 -10000 0 -10000 0 0
NCK2 0.027 0.005 -10000 0 -10000 0 0
neuron differentiation -0.13 0.13 -10000 0 -0.41 41 41
neuron adhesion -0.21 0.21 0.44 10 -0.6 27 37
LRP8 0 0.13 -10000 0 -0.67 19 19
GSK3B -0.19 0.14 -10000 0 -0.42 32 32
RELN/VLDLR/DAB1/Fyn -0.26 0.21 -10000 0 -0.39 337 337
MAP3K11 0.027 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.21 0.16 -10000 0 -0.31 336 336
CDK5 0.026 0.006 -10000 0 -10000 0 0
MAPT 0.052 0.17 0.82 20 -0.6 3 23
neuron migration -0.26 0.19 0.26 2 -0.39 316 318
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.14 0.13 -10000 0 -0.41 41 41
RELN/VLDLR -0.28 0.23 -10000 0 -0.42 338 338
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.01 0.11 -10000 0 -0.33 30 30
NFATC2 -0.22 0.33 -10000 0 -0.72 125 125
NFATC3 -0.083 0.14 -10000 0 -0.3 54 54
CD40LG -0.63 0.55 -10000 0 -1.1 265 265
ITCH 0.038 0.016 -10000 0 -10000 0 0
CBLB 0.038 0.016 -10000 0 -0.27 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.46 0.52 -10000 0 -1.2 138 138
JUNB 0.02 0.057 -10000 0 -0.59 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.042 0.018 -10000 0 -0.32 1 1
T cell anergy 0.006 0.073 0.4 5 -0.47 1 6
TLE4 -0.21 0.35 -10000 0 -0.8 109 109
Jun/NFAT1-c-4/p21SNFT -0.55 0.58 -10000 0 -1.1 238 238
AP-1/NFAT1-c-4 -0.71 0.73 -10000 0 -1.3 257 257
IKZF1 -0.17 0.28 -10000 0 -0.67 80 80
T-helper 2 cell differentiation -0.28 0.33 -10000 0 -0.82 106 106
AP-1/NFAT1 -0.32 0.41 -10000 0 -0.76 191 191
CALM1 0.038 0.012 -10000 0 -10000 0 0
EGR2 -0.73 0.77 -10000 0 -1.5 232 232
EGR3 -0.53 0.68 -10000 0 -1.4 152 152
NFAT1/FOXP3 -0.17 0.28 -10000 0 -0.56 135 135
EGR1 -0.12 0.28 -10000 0 -0.67 100 100
JUN -0.13 0.28 -10000 0 -0.67 106 106
EGR4 -0.016 0.15 -10000 0 -0.66 24 24
mol:Ca2+ 0.012 0.009 -10000 0 -0.18 1 1
GBP3 -0.16 0.26 -10000 0 -0.66 75 75
FOSL1 0.006 0.052 -10000 0 -0.35 1 1
NFAT1-c-4/MAF/IRF4 -0.49 0.55 -10000 0 -0.98 239 239
DGKA -0.15 0.25 -10000 0 -0.61 77 77
CREM 0.027 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.5 0.55 -10000 0 -0.99 240 240
CTLA4 -0.19 0.3 -10000 0 -0.68 108 108
NFAT1-c-4 (dimer)/EGR1 -0.56 0.62 -10000 0 -1.1 236 236
NFAT1-c-4 (dimer)/EGR4 -0.52 0.55 -10000 0 -1 242 242
FOS -0.16 0.3 -10000 0 -0.67 124 124
IFNG -0.37 0.5 -10000 0 -1.1 126 126
T cell activation -0.39 0.39 -10000 0 -0.87 161 161
MAF 0.026 0.006 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.35 0.4 0.73 227 -10000 0 227
TNF -0.54 0.54 -10000 0 -1 257 257
FASLG -0.7 0.75 -10000 0 -1.4 248 248
TBX21 -0.019 0.15 -10000 0 -0.68 22 22
BATF3 0.018 0.042 -10000 0 -0.67 1 1
PRKCQ 0.016 0.074 -10000 0 -0.61 6 6
PTPN1 -0.16 0.25 -10000 0 -0.58 93 93
NFAT1-c-4/ICER1 -0.49 0.54 -10000 0 -0.99 237 237
GATA3 -0.005 0.14 -10000 0 -0.63 24 24
T-helper 1 cell differentiation -0.36 0.48 -10000 0 -1.1 126 126
IL2RA -0.42 0.46 -10000 0 -1 135 135
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.15 0.25 -10000 0 -0.55 112 112
E2F1 -0.011 0.066 -10000 0 -10000 0 0
PPARG 0.016 0.083 -10000 0 -0.67 7 7
SLC3A2 -0.16 0.25 -10000 0 -0.6 85 85
IRF4 -0.046 0.18 -10000 0 -0.65 37 37
PTGS2 -0.6 0.54 -10000 0 -1.1 246 246
CSF2 -0.61 0.52 -10000 0 -1.1 256 256
JunB/Fra1/NFAT1-c-4 -0.46 0.53 -10000 0 -0.96 232 232
IL4 -0.3 0.35 -10000 0 -0.88 101 101
IL5 -0.59 0.52 -10000 0 -1.1 246 246
IL2 -0.4 0.4 -10000 0 -0.89 160 160
IL3 -0.071 0.09 -10000 0 -0.86 2 2
RNF128 0.034 0.037 -10000 0 -0.74 1 1
NFATC1 -0.35 0.41 -10000 0 -0.74 227 227
CDK4 0.24 0.25 0.58 99 -10000 0 99
PTPRK -0.15 0.25 -10000 0 -0.62 76 76
IL8 -0.6 0.53 0.5 1 -1.1 253 254
POU2F1 0.025 0.01 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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
NFATC2 -0.091 0.26 -10000 0 -0.67 83 83
GNB1/GNG2 -0.19 0.23 -10000 0 -0.52 115 115
mol:DAG -0.18 0.2 -10000 0 -0.48 112 112
PLCG1 -0.19 0.21 -10000 0 -0.5 112 112
YES1 -0.21 0.22 -10000 0 -0.37 295 295
FZD3 0.027 0.005 -10000 0 -10000 0 0
FZD6 0.027 0.005 -10000 0 -10000 0 0
G protein -0.18 0.22 -10000 0 -0.5 112 112
MAP3K7 -0.16 0.17 0.31 1 -0.41 107 108
mol:Ca2+ -0.18 0.2 -10000 0 -0.47 112 112
mol:IP3 -0.18 0.2 -10000 0 -0.48 112 112
NLK 0 0.054 -10000 0 -0.81 2 2
GNB1 0.026 0.006 -10000 0 -10000 0 0
CAMK2A -0.17 0.18 0.32 1 -0.45 108 109
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.23 0.24 -10000 0 -0.39 297 297
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
GNAS -0.21 0.22 -10000 0 -0.37 294 294
GO:0007205 -0.18 0.19 -10000 0 -0.47 112 112
WNT6 0.02 0.026 -10000 0 -10000 0 0
WNT4 -0.19 0.32 -10000 0 -0.67 154 154
NFAT1/CK1 alpha -0.24 0.24 -10000 0 -0.53 148 148
GNG2 0.025 0.032 -10000 0 -0.67 1 1
WNT5A 0.014 0.093 -10000 0 -0.67 9 9
WNT11 -0.32 0.34 -10000 0 -0.66 249 249
CDC42 -0.2 0.21 -10000 0 -0.51 114 114
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.23 0.24 -9999 0 -0.39 297 297
FZD6 0.027 0.005 -9999 0 -10000 0 0
WNT6 0.02 0.026 -9999 0 -10000 0 0
WNT4 -0.19 0.32 -9999 0 -0.67 154 154
FZD3 0.027 0.005 -9999 0 -10000 0 0
WNT5A 0.014 0.093 -9999 0 -0.67 9 9
WNT11 -0.32 0.34 -9999 0 -0.66 249 249
PDGFR-alpha signaling pathway

Figure S8.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S8.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.2 0.32 -10000 0 -0.68 148 148
PDGF/PDGFRA/CRKL -0.14 0.24 -10000 0 -0.5 147 147
positive regulation of JUN kinase activity -0.071 0.2 -10000 0 -0.39 128 128
CRKL 0.02 0.012 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.14 0.24 -10000 0 -0.51 146 146
AP1 -0.4 0.54 -10000 0 -1.2 134 134
mol:IP3 -0.16 0.24 -10000 0 -0.52 146 146
PLCG1 -0.16 0.24 -10000 0 -0.52 146 146
PDGF/PDGFRA/alphaV Integrin -0.14 0.24 -10000 0 -0.5 148 148
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.16 0.24 -10000 0 -0.52 146 146
CAV3 -0.011 0.018 -10000 0 -10000 0 0
CAV1 0.013 0.093 -10000 0 -0.67 9 9
SHC/Grb2/SOS1 -0.071 0.2 -10000 0 -0.39 128 128
PDGF/PDGFRA/Shf -0.13 0.24 -10000 0 -0.5 148 148
FOS -0.39 0.51 -10000 0 -1.2 134 134
JUN -0.14 0.22 -10000 0 -0.57 105 105
oligodendrocyte development -0.14 0.24 -10000 0 -0.5 148 148
GRB2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:DAG -0.16 0.24 -10000 0 -0.52 146 146
PDGF/PDGFRA -0.2 0.32 -10000 0 -0.68 148 148
actin cytoskeleton reorganization -0.13 0.24 -10000 0 -0.5 148 148
SRF 0.025 0.013 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
PI3K -0.094 0.22 -10000 0 -0.43 148 148
PDGF/PDGFRA/Crk/C3G -0.093 0.21 -10000 0 -0.42 144 144
JAK1 -0.15 0.23 -10000 0 -0.5 148 148
ELK1/SRF -0.12 0.19 0.32 1 -0.41 138 139
SHB 0.025 0.007 -10000 0 -10000 0 0
SHF 0.027 0.008 -10000 0 -10000 0 0
CSNK2A1 0.043 0.024 -10000 0 -10000 0 0
GO:0007205 -0.17 0.24 -10000 0 -0.54 147 147
SOS1 0.027 0.005 -10000 0 -10000 0 0
Ras protein signal transduction -0.071 0.2 -10000 0 -0.39 128 128
PDGF/PDGFRA/SHB -0.13 0.24 -10000 0 -0.5 148 148
PDGF/PDGFRA/Caveolin-1 -0.14 0.25 -10000 0 -0.51 149 149
ITGAV 0.024 0.044 -10000 0 -0.67 2 2
ELK1 -0.16 0.22 -10000 0 -0.49 144 144
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
PDGF/PDGFRA/Crk -0.13 0.24 -10000 0 -0.49 147 147
JAK-STAT cascade -0.15 0.23 -10000 0 -0.5 148 148
cell proliferation -0.13 0.24 -10000 0 -0.5 148 148
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.087 0.21 -10000 0 -0.62 30 30
IHH -0.15 0.31 -10000 0 -0.7 121 121
SHH Np/Cholesterol/GAS1 -0.051 0.16 -10000 0 -0.39 82 82
LRPAP1 0.027 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.051 0.15 0.39 82 -10000 0 82
SMO/beta Arrestin2 -0.075 0.2 -10000 0 -0.41 111 111
SMO -0.096 0.21 -10000 0 -0.43 118 118
AKT1 -0.016 0.1 -10000 0 -0.61 2 2
ARRB2 0.026 0.007 -10000 0 -10000 0 0
BOC 0.016 0.088 -10000 0 -0.67 8 8
ADRBK1 0.027 0.005 -10000 0 -10000 0 0
heart looping -0.094 0.2 -10000 0 -0.43 118 118
STIL -0.065 0.16 0.27 1 -0.34 72 73
DHH N/PTCH2 -0.05 0.2 -10000 0 -0.5 80 80
DHH N/PTCH1 -0.076 0.19 -10000 0 -0.36 144 144
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
DHH 0.021 0.063 -10000 0 -0.67 4 4
PTHLH -0.14 0.31 -10000 0 -1 32 32
determination of left/right symmetry -0.094 0.2 -10000 0 -0.43 118 118
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
skeletal system development -0.13 0.3 -10000 0 -1 32 32
IHH N/Hhip -0.29 0.33 -10000 0 -0.59 258 258
DHH N/Hhip -0.17 0.26 -10000 0 -0.5 189 189
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.094 0.2 -10000 0 -0.43 118 118
pancreas development -0.25 0.33 -10000 0 -0.66 188 188
HHAT 0.024 0.032 -10000 0 -0.67 1 1
PI3K 0.036 0.043 -10000 0 -0.5 3 3
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.097 0.26 -10000 0 -0.62 93 93
somite specification -0.094 0.2 -10000 0 -0.43 118 118
SHH Np/Cholesterol/PTCH1 -0.07 0.16 -10000 0 -0.33 111 111
SHH Np/Cholesterol/PTCH2 -0.043 0.15 -10000 0 -0.38 79 79
SHH Np/Cholesterol/Megalin -0.081 0.18 -10000 0 -0.38 126 126
SHH -0.005 0.029 -10000 0 -0.5 1 1
catabolic process -0.094 0.2 -10000 0 -0.4 141 141
SMO/Vitamin D3 -0.076 0.18 -10000 0 -0.38 109 109
SHH Np/Cholesterol/Hhip -0.14 0.2 -10000 0 -0.39 188 188
LRP2 -0.16 0.3 -10000 0 -0.66 131 131
receptor-mediated endocytosis -0.14 0.21 -10000 0 -0.57 48 48
SHH Np/Cholesterol/BOC 0.014 0.055 -10000 0 -0.37 9 9
SHH Np/Cholesterol/CDO -0.094 0.18 -10000 0 -0.37 143 143
mesenchymal cell differentiation 0.14 0.2 0.38 188 -10000 0 188
mol:Vitamin D3 -0.065 0.17 -10000 0 -0.34 111 111
IHH N/PTCH2 -0.17 0.28 -10000 0 -0.53 179 179
CDON -0.18 0.32 -10000 0 -0.66 144 144
IHH N/PTCH1 -0.091 0.21 -10000 0 -0.41 141 141
Megalin/LRPAP1 -0.1 0.24 -10000 0 -0.49 131 131
PTCH2 -0.084 0.25 -10000 0 -0.66 79 79
SHH Np/Cholesterol 0.01 0.022 -10000 0 -0.4 1 1
PTCH1 -0.094 0.2 -10000 0 -0.4 141 141
HHIP -0.25 0.33 -10000 0 -0.67 188 188
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.008 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.14 0.22 -10000 0 -0.39 200 200
regulation of S phase of mitotic cell cycle -0.1 0.16 -10000 0 -0.29 200 200
GNAO1 0.004 0.12 -10000 0 -0.67 15 15
HRAS 0.025 0.011 -10000 0 -10000 0 0
SHBG/T-DHT 0.01 0.057 -10000 0 -0.43 8 8
PELP1 0.025 0.007 -10000 0 -10000 0 0
AKT1 0.009 0.002 -10000 0 -10000 0 0
MAP2K1 -0.14 0.2 0.45 5 -0.37 195 200
T-DHT/AR -0.2 0.26 -10000 0 -0.5 206 206
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.004 -10000 0 -0.006 127 127
GNAI2 0.027 0.003 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.032 -10000 0 -0.67 1 1
mol:GDP -0.21 0.26 -10000 0 -0.52 203 203
cell proliferation -0.2 0.26 0.46 11 -0.52 140 151
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
FOS -0.26 0.37 0.47 8 -0.84 129 137
mol:Ca2+ -0.026 0.029 -10000 0 -0.066 104 104
MAPK3 -0.16 0.24 0.5 12 -0.49 97 109
MAPK1 -0.18 0.22 0.31 4 -0.42 171 175
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 115 115
cAMP biosynthetic process 0.017 0.068 0.26 10 -0.41 8 18
GNG2 0.025 0.032 -10000 0 -0.67 1 1
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 115 115
HRAS/GTP -0.14 0.2 -10000 0 -0.38 195 195
actin cytoskeleton reorganization 0.037 0.033 -10000 0 -0.36 3 3
SRC 0.026 0.009 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 115 115
PI3K 0.033 0.037 -10000 0 -0.44 3 3
apoptosis 0.19 0.25 0.52 148 -0.41 7 155
T-DHT/AR/PELP1 -0.16 0.23 -10000 0 -0.43 205 205
HRAS/GDP -0.2 0.25 -10000 0 -0.5 202 202
CREB1 -0.21 0.27 0.42 7 -0.56 148 155
RAC1-CDC42/GTP 0.047 0.035 -10000 0 -0.36 3 3
AR -0.26 0.34 -10000 0 -0.66 206 206
GNB1 0.026 0.006 -10000 0 -10000 0 0
RAF1 -0.14 0.21 0.5 6 -0.37 195 201
RAC1-CDC42/GDP -0.17 0.25 -10000 0 -0.48 201 201
T-DHT/AR/PELP1/Src -0.14 0.22 -10000 0 -0.4 196 196
MAP2K2 -0.14 0.19 0.43 2 -0.37 191 193
T-DHT/AR/PELP1/Src/PI3K -0.11 0.16 -10000 0 -0.29 200 200
GNAZ 0.02 0.012 -10000 0 -10000 0 0
SHBG 0.014 0.088 -10000 0 -0.67 8 8
Gi family/GNB1/GNG2/GDP -0.033 0.099 -10000 0 -0.45 16 16
mol:T-DHT 0 0.003 0.001 55 -0.005 67 122
RAC1 0.026 0.006 -10000 0 -10000 0 0
GNRH1 0.006 0.033 -10000 0 -0.5 2 2
Gi family/GTP -0.087 0.11 -10000 0 -0.3 48 48
CDC42 0.027 0.005 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.46 0.48 -10000 0 -0.99 189 189
PCK1 -0.3 0.44 -10000 0 -1.3 65 65
HNF4A -0.61 0.6 -10000 0 -1.2 231 231
KCNJ11 -0.44 0.47 -10000 0 -1 170 170
AKT1 -0.064 0.14 -10000 0 -0.48 8 8
response to starvation -0.018 0.042 -10000 0 -0.49 2 2
DLK1 -0.44 0.47 -10000 0 -1 166 166
NKX2-1 -0.17 0.19 -10000 0 -10000 0 0
ACADM -0.46 0.48 -10000 0 -0.98 192 192
TAT -0.18 0.2 -10000 0 -0.64 3 3
CEBPB 0.027 0.005 -10000 0 -10000 0 0
CEBPA 0.019 0.07 -10000 0 -0.67 5 5
TTR -0.14 0.22 0.65 7 -0.72 27 34
PKLR -0.46 0.48 -10000 0 -1 177 177
APOA1 -0.84 0.83 -10000 0 -1.7 232 232
CPT1C -0.47 0.48 -10000 0 -1 178 178
ALAS1 -0.16 0.19 -10000 0 -0.63 1 1
TFRC -0.23 0.27 -10000 0 -0.8 26 26
FOXF1 0.017 0.055 -10000 0 -0.67 3 3
NF1 0.031 0.008 -10000 0 -10000 0 0
HNF1A (dimer) 0.028 0.007 -10000 0 -10000 0 0
CPT1A -0.47 0.48 -10000 0 -1 172 172
HMGCS1 -0.46 0.48 -10000 0 -1 179 179
NR3C1 0.032 0.011 -10000 0 -10000 0 0
CPT1B -0.46 0.48 -10000 0 -1 163 163
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.027 0.006 -10000 0 -10000 0 0
GCK -0.59 0.62 -10000 0 -1.2 202 202
CREB1 0.008 0.066 -10000 0 -0.24 16 16
IGFBP1 -0.16 0.18 -10000 0 -10000 0 0
PDX1 -0.18 0.19 -10000 0 -0.6 3 3
UCP2 -0.47 0.48 -10000 0 -0.98 192 192
ALDOB -0.44 0.47 -10000 0 -1 169 169
AFP -0.018 0.084 -10000 0 -0.41 1 1
BDH1 -0.47 0.48 -10000 0 -1 168 168
HADH -0.44 0.47 -10000 0 -1 166 166
F2 -0.57 0.58 -10000 0 -1.2 186 186
HNF1A 0.028 0.007 -10000 0 -10000 0 0
G6PC 0 0.067 -10000 0 -10000 0 0
SLC2A2 -0.22 0.23 -10000 0 -0.53 9 9
INS -0.025 0.053 -10000 0 -0.68 3 3
FOXA1 -0.012 0.091 -10000 0 -0.31 27 27
FOXA3 -0.025 0.12 -10000 0 -0.32 37 37
FOXA2 -0.5 0.53 -10000 0 -1.1 184 184
ABCC8 -0.69 0.65 -10000 0 -1.3 249 249
ALB -0.058 0.27 -10000 0 -1.1 29 29
Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0.027 0.005 -10000 0 -10000 0 0
VLDLR -0.002 0.14 -10000 0 -0.65 20 20
LRPAP1 0.027 0.004 -10000 0 -10000 0 0
NUDC 0.027 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.3 0.24 -10000 0 -0.45 341 341
CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
KATNA1 0.027 0.004 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.28 0.21 -10000 0 -0.41 331 331
IQGAP1/CaM 0.039 0.008 -10000 0 -10000 0 0
DAB1 0.006 0.022 -10000 0 -10000 0 0
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
PLA2G7 -0.06 0.23 -10000 0 -0.67 62 62
CALM1 0.027 0.005 -10000 0 -10000 0 0
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.018 0.1 -10000 0 -0.5 19 19
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.027 0.005 -10000 0 -10000 0 0
CDK5R1 0.025 0.013 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.012 0.003 -10000 0 -10000 0 0
CDK5R2 0.001 0.023 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.3 0.23 -10000 0 -0.44 345 345
YWHAE 0.026 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.21 0.18 0.35 6 -0.53 21 27
MAP1B 0.007 0.002 -10000 0 -10000 0 0
RAC1 0.017 0.005 -10000 0 -10000 0 0
p35/CDK5 -0.24 0.19 -10000 0 -0.37 320 320
RELN -0.46 0.32 -10000 0 -0.67 338 338
PAFAH/LIS1 -0.027 0.15 -10000 0 -0.43 59 59
LIS1/CLIP170 0.031 0.009 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.17 0.15 -10000 0 -0.48 15 15
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.2 0.16 -10000 0 -0.3 324 324
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.23 0.18 0.64 1 -0.35 317 318
LIS1/IQGAP1 0.031 0.009 -10000 0 -10000 0 0
RHOA 0.017 0.005 -10000 0 -10000 0 0
PAFAH1B1 0.016 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.024 0.015 -10000 0 -10000 0 0
PAFAH1B2 0.016 0.084 -10000 0 -0.63 8 8
MAP1B/LIS1/Dynein heavy chain 0.031 0.011 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.2 0.18 0.3 5 -0.53 19 24
LRP8 0 0.13 -10000 0 -0.67 19 19
NDEL1/Katanin 60 -0.21 0.18 0.3 5 -0.53 21 26
P39/CDK5 -0.25 0.19 -10000 0 -0.37 329 329
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.03 0.01 -10000 0 -10000 0 0
CDK5 -0.26 0.19 -10000 0 -0.39 331 331
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.027 0.008 -10000 0 -10000 0 0
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.25 0.2 -10000 0 -0.39 326 326
RELN/VLDLR -0.28 0.23 -10000 0 -0.42 338 338
CDC42 0.017 0.005 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.1 0.24 0.53 115 -10000 0 115
KIRREL -0.046 0.2 -10000 0 -0.69 41 41
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.1 0.24 -10000 0 -0.53 115 115
PLCG1 0.027 0.005 -10000 0 -10000 0 0
ARRB2 0.026 0.007 -10000 0 -10000 0 0
WASL 0.026 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.056 0.2 -10000 0 -0.43 106 106
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.058 0.16 -10000 0 -0.35 103 103
FYN -0.064 0.2 0.27 25 -0.4 106 131
mol:Ca2+ -0.056 0.2 -10000 0 -0.42 105 105
mol:DAG -0.056 0.2 -10000 0 -0.43 105 105
NPHS2 -0.005 0.053 -10000 0 -0.73 1 1
mol:IP3 -0.056 0.2 -10000 0 -0.43 105 105
regulation of endocytosis -0.05 0.18 -10000 0 -0.38 103 103
Nephrin/NEPH1/podocin/Cholesterol -0.068 0.2 -10000 0 -0.42 108 108
establishment of cell polarity -0.1 0.24 -10000 0 -0.53 115 115
Nephrin/NEPH1/podocin/NCK1-2 -0.04 0.2 -10000 0 -0.4 105 105
Nephrin/NEPH1/beta Arrestin2 -0.049 0.18 -10000 0 -0.39 103 103
NPHS1 -0.1 0.26 -10000 0 -0.67 84 84
Nephrin/NEPH1/podocin -0.061 0.19 -10000 0 -0.41 106 106
TJP1 0.027 0.004 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
NCK2 0.027 0.005 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.055 0.2 -10000 0 -0.43 105 105
CD2AP 0.027 0.003 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.055 0.2 -10000 0 -0.43 103 103
GRB2 0.026 0.007 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.078 0.2 0.28 21 -0.41 107 128
cytoskeleton organization -0.082 0.2 -10000 0 -0.45 102 102
Nephrin/NEPH1 -0.072 0.18 -10000 0 -0.4 111 111
Nephrin/NEPH1/ZO-1 -0.069 0.21 -10000 0 -0.45 106 106
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.01 0.067 -9999 0 -0.45 9 9
NFATC2 -0.079 0.17 -9999 0 -0.45 83 83
NFATC3 -0.002 0.031 -9999 0 -10000 0 0
CD40LG -0.34 0.37 -9999 0 -0.75 183 183
PTGS2 -0.31 0.35 -9999 0 -0.73 164 164
JUNB 0.02 0.057 -9999 0 -0.59 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.007 0.025 -9999 0 -10000 0 0
CaM/Ca2+ 0.007 0.024 -9999 0 -10000 0 0
CALM1 0.017 0.021 -9999 0 -10000 0 0
JUN -0.13 0.28 -9999 0 -0.67 106 106
mol:Ca2+ -0.008 0.02 -9999 0 -0.19 3 3
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.011 -9999 0 -10000 0 0
FOSL1 0.006 0.052 -9999 0 -0.35 1 1
CREM 0.027 0.004 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.17 0.25 -9999 0 -0.47 158 158
FOS -0.16 0.3 -9999 0 -0.67 124 124
IFNG -0.33 0.36 -9999 0 -0.74 183 183
AP-1/NFAT1-c-4 -0.35 0.44 -9999 0 -0.86 169 169
FASLG -0.31 0.34 -9999 0 -0.72 170 170
NFAT1-c-4/ICER1 -0.079 0.17 -9999 0 -0.4 90 90
IL2RA -0.31 0.34 -9999 0 -0.72 168 168
FKBP12/FK506 0.02 0.004 -9999 0 -10000 0 0
CSF2 -0.32 0.32 -9999 0 -0.7 168 168
JunB/Fra1/NFAT1-c-4 -0.069 0.18 -9999 0 -0.4 87 87
IL4 -0.3 0.32 -9999 0 -0.68 165 165
IL2 0.003 0.071 -9999 0 -1 2 2
IL3 -0.009 0.054 -9999 0 -0.92 1 1
FKBP1A 0.027 0.005 -9999 0 -10000 0 0
BATF3 0.018 0.042 -9999 0 -0.67 1 1
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.025 0.01 -9999 0 -10000 0 0
Endothelins

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
AKT1 -0.029 0.093 -10000 0 -0.42 11 11
PTK2B 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.15 0.28 0.46 1 -0.67 75 76
EDN1 -0.002 0.098 -10000 0 -0.52 9 9
EDN3 -0.31 0.34 -10000 0 -0.67 234 234
EDN2 0.011 0.081 -10000 0 -0.67 6 6
HRAS/GDP -0.11 0.23 0.45 3 -0.49 91 94
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.074 0.15 -10000 0 -0.34 87 87
ADCY4 -0.069 0.15 0.35 1 -0.39 69 70
ADCY5 -0.11 0.2 0.35 1 -0.44 112 113
ADCY6 -0.067 0.15 0.35 1 -0.4 67 68
ADCY7 -0.067 0.15 0.35 1 -0.4 67 68
ADCY1 -0.071 0.15 0.35 1 -0.41 68 69
ADCY2 -0.098 0.18 -10000 0 -0.43 93 93
ADCY3 -0.069 0.15 0.35 1 -0.4 70 71
ADCY8 -0.096 0.16 0.35 1 -0.42 71 72
ADCY9 -0.068 0.15 0.35 1 -0.4 67 68
arachidonic acid secretion -0.19 0.32 0.37 10 -0.61 150 160
ETB receptor/Endothelin-1/Gq/GTP -0.083 0.18 -10000 0 -0.36 119 119
GNAO1 0.004 0.12 -10000 0 -0.67 15 15
HRAS 0.025 0.011 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.03 0.1 -10000 0 -0.39 9 9
ETA receptor/Endothelin-1/Gs/GTP -0.027 0.18 -10000 0 -0.41 72 72
mol:GTP -0.003 0.009 -10000 0 -10000 0 0
COL3A1 -0.034 0.1 -10000 0 -0.46 10 10
EDNRB 0.015 0.078 -10000 0 -0.67 6 6
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.066 0.14 -10000 0 -0.59 24 24
CYSLTR1 -0.036 0.13 -10000 0 -0.66 15 15
SLC9A1 0.001 0.055 -10000 0 -0.26 9 9
mol:GDP -0.12 0.24 0.44 4 -0.51 95 99
SLC9A3 -0.055 0.21 0.37 1 -0.69 37 38
RAF1 -0.16 0.28 0.44 3 -0.55 137 140
JUN -0.29 0.49 0.45 1 -1.1 125 126
JAK2 -0.029 0.096 -10000 0 -0.42 15 15
mol:IP3 -0.1 0.2 -10000 0 -0.41 116 116
ETA receptor/Endothelin-1 0.014 0.13 -10000 0 -0.41 26 26
PLCB1 0.023 0.032 -10000 0 -0.67 1 1
PLCB2 0.02 0.024 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.23 0.28 -10000 0 -0.52 235 235
FOS -0.27 0.44 0.61 2 -0.99 127 129
Gai/GDP -0.011 0.15 -10000 0 -0.65 22 22
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.1 0.19 -10000 0 -0.44 78 78
BCAR1 0.026 0.006 -10000 0 -10000 0 0
PRKCB1 -0.1 0.2 -10000 0 -0.41 118 118
GNAQ 0.015 0.022 -10000 0 -10000 0 0
GNAZ 0.02 0.012 -10000 0 -10000 0 0
GNAL -0.061 0.23 -10000 0 -0.65 64 64
Gs family/GDP -0.15 0.25 0.28 1 -0.52 116 117
ETA receptor/Endothelin-1/Gq/GTP -0.088 0.17 -10000 0 -0.36 115 115
MAPK14 -0.071 0.15 -10000 0 -0.36 69 69
TRPC6 -0.16 0.3 0.47 1 -0.72 71 72
GNAI2 0.027 0.003 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.032 -10000 0 -0.67 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.073 0.16 -10000 0 -0.36 87 87
ETB receptor/Endothelin-2 0.021 0.087 -10000 0 -0.51 12 12
ETB receptor/Endothelin-3 -0.23 0.27 -10000 0 -0.51 237 237
ETB receptor/Endothelin-1 0.015 0.099 -10000 0 -0.54 11 11
MAPK3 -0.24 0.41 0.37 9 -0.86 131 140
MAPK1 -0.29 0.44 0.6 1 -0.96 133 134
Rac1/GDP -0.11 0.22 0.37 1 -0.48 87 88
cAMP biosynthetic process -0.074 0.18 0.47 10 -0.43 72 82
MAPK8 -0.19 0.36 0.48 1 -0.7 116 117
SRC 0.026 0.008 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.003 0.076 -10000 0 -0.28 27 27
p130Cas/CRK/Src/PYK2 -0.15 0.28 0.44 7 -0.55 130 137
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.11 0.22 0.37 1 -0.49 84 85
COL1A2 -0.006 0.11 -10000 0 -0.49 11 11
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.016 0.083 -10000 0 -0.52 7 7
mol:DAG -0.1 0.2 -10000 0 -0.42 116 116
MAP2K2 -0.19 0.33 0.41 10 -0.68 133 143
MAP2K1 -0.2 0.34 0.5 2 -0.69 138 140
EDNRA 0.002 0.072 -10000 0 -0.32 7 7
positive regulation of muscle contraction -0.022 0.078 -10000 0 -0.39 7 7
Gq family/GDP -0.14 0.28 0.38 1 -0.55 126 127
HRAS/GTP -0.14 0.24 0.48 2 -0.51 107 109
PRKCH -0.11 0.2 -10000 0 -0.44 93 93
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA -0.11 0.21 -10000 0 -0.47 99 99
PRKCB -0.11 0.2 -10000 0 -0.45 94 94
PRKCE -0.11 0.2 -10000 0 -0.46 93 93
PRKCD -0.11 0.2 -10000 0 -0.44 93 93
PRKCG -0.1 0.19 -10000 0 -0.45 89 89
regulation of vascular smooth muscle contraction -0.32 0.52 0.64 2 -1.2 127 129
PRKCQ -0.11 0.2 -10000 0 -0.45 96 96
PLA2G4A -0.21 0.35 0.37 10 -0.67 150 160
GNA14 -0.14 0.29 -10000 0 -0.64 118 118
GNA15 0.007 0.05 -10000 0 -0.67 1 1
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA11 0.008 0.085 -10000 0 -0.63 8 8
Rac1/GTP 0.031 0.1 -10000 0 -0.35 13 13
MMP1 -0.032 0.077 0.5 3 -10000 0 3
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.027 0.005 -10000 0 -10000 0 0
PTK2 0.026 0.006 -10000 0 -10000 0 0
CRKL -0.1 0.18 -10000 0 -0.35 152 152
GRB2/SOS1/SHC 0.048 0.02 -10000 0 -10000 0 0
HRAS 0.026 0.011 -10000 0 -10000 0 0
IRS1/Crk -0.091 0.19 -10000 0 -0.36 148 148
IGF-1R heterotetramer/IGF1/PTP1B -0.063 0.19 -10000 0 -0.42 106 106
AKT1 -0.089 0.17 -10000 0 -0.36 105 105
BAD -0.087 0.15 -10000 0 -0.34 100 100
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.096 0.18 -10000 0 -0.36 148 148
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.088 0.19 -10000 0 -0.36 152 152
RAF1 -0.068 0.15 0.39 1 -0.53 17 18
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.062 0.19 -10000 0 -0.34 145 145
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.095 0.2 -10000 0 -0.38 153 153
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
RPS6KB1 -0.088 0.16 -10000 0 -0.36 102 102
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.058 0.14 0.32 6 -0.44 16 22
PXN 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.07 0.16 -10000 0 -0.34 98 98
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.027 0.16 -10000 0 -0.34 96 96
IGF-1R heterotetramer -0.009 0.058 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.077 0.2 -10000 0 -0.36 152 152
Crk/p130 Cas/Paxillin -0.056 0.19 -10000 0 -0.36 103 103
IGF1R -0.009 0.058 -10000 0 -10000 0 0
IGF1 -0.14 0.29 -10000 0 -0.69 107 107
IRS2/Crk -0.085 0.18 -10000 0 -0.34 148 148
PI3K -0.065 0.2 -10000 0 -0.35 152 152
apoptosis 0.064 0.14 0.49 15 -0.39 1 16
HRAS/GDP 0.019 0.007 -10000 0 -10000 0 0
PRKCD -0.089 0.19 -10000 0 -0.44 106 106
RAF1/14-3-3 E -0.044 0.14 0.33 3 -0.45 17 20
BAD/14-3-3 -0.067 0.15 0.4 2 -0.53 15 17
PRKCZ -0.087 0.17 0.25 1 -0.35 105 106
Crk/p130 Cas/Paxillin/FAK1 -0.058 0.16 -10000 0 -0.53 15 15
PTPN1 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.092 0.2 -10000 0 -0.47 107 107
BCAR1 0.026 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.042 0.18 -10000 0 -0.37 103 103
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
IRS1/NCK2 -0.087 0.19 -10000 0 -0.36 152 152
GRB10 0.026 0.006 -10000 0 -10000 0 0
PTPN11 -0.098 0.18 -10000 0 -0.36 152 152
IRS1 -0.11 0.2 -10000 0 -0.38 153 153
IRS2 -0.098 0.18 -10000 0 -0.36 152 152
IGF-1R heterotetramer/IGF1 -0.1 0.23 -10000 0 -0.53 107 107
GRB2 0.026 0.007 -10000 0 -10000 0 0
PDPK1 -0.089 0.18 -10000 0 -0.37 106 106
YWHAE 0.026 0.007 -10000 0 -10000 0 0
PRKD1 -0.089 0.19 -10000 0 -0.44 106 106
SHC1 0.025 0.007 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.052 0.025 -9999 0 -0.44 1 1
fibroblast growth factor receptor signaling pathway 0.052 0.025 -9999 0 -0.43 1 1
LAMA1 -0.019 0.17 -9999 0 -0.66 33 33
PRNP 0.025 0.032 -9999 0 -0.67 1 1
GPC1/SLIT2 -0.041 0.19 -9999 0 -0.49 74 74
SMAD2 0.016 0.038 -9999 0 -0.39 3 3
GPC1/PrPc/Cu2+ 0.034 0.023 -9999 0 -0.44 1 1
GPC1/Laminin alpha1 0.003 0.13 -9999 0 -0.5 33 33
TDGF1 -0.27 0.34 -9999 0 -0.66 209 209
CRIPTO/GPC1 -0.19 0.27 -9999 0 -0.5 209 209
APP/GPC1 0.038 0.011 -9999 0 -10000 0 0
mol:NO 0 0 -9999 0 -10000 0 0
YES1 -0.17 0.22 -9999 0 -0.43 207 207
FLT1 0.024 0.032 -9999 0 -0.67 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.047 0.041 -9999 0 -0.43 3 3
SERPINC1 0.019 0.022 -9999 0 -10000 0 0
FYN -0.17 0.22 -9999 0 -0.43 207 207
FGR -0.17 0.22 -9999 0 -0.43 207 207
positive regulation of MAPKKK cascade -0.23 0.26 -9999 0 -0.5 209 209
SLIT2 -0.077 0.25 -9999 0 -0.66 74 74
GPC1/NRG -0.008 0.15 -9999 0 -0.49 43 43
NRG1 -0.033 0.19 -9999 0 -0.65 43 43
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.047 0.052 -9999 0 -0.56 3 3
LYN -0.17 0.22 -9999 0 -0.43 205 205
mol:Spermine 0.008 0.004 -9999 0 -10000 0 0
cell growth 0.052 0.025 -9999 0 -0.43 1 1
BMP signaling pathway -0.026 0.008 -9999 0 -10000 0 0
SRC -0.17 0.22 -9999 0 -0.43 207 207
TGFBR1 0.022 0.024 -9999 0 -10000 0 0
mol:Cu2+ 0 0 -9999 0 -10000 0 0
PLA2G2A -0.17 0.3 -9999 0 -0.66 129 129
GPC1 0.026 0.008 -9999 0 -10000 0 0
TGFBR1 (dimer) 0.022 0.023 -9999 0 -10000 0 0
VEGFA 0.023 0.054 -9999 0 -0.67 3 3
BLK -0.29 0.3 -9999 0 -0.53 279 279
HCK -0.18 0.22 -9999 0 -0.43 207 207
FGF2 0.027 0.004 -9999 0 -10000 0 0
FGFR1 0.025 0.032 -9999 0 -0.67 1 1
VEGFR1 homodimer 0.024 0.032 -9999 0 -0.67 1 1
TGFBR2 0.023 0.054 -9999 0 -0.67 3 3
cell death 0.038 0.011 -9999 0 -10000 0 0
ATIII/GPC1 0.034 0.019 -9999 0 -10000 0 0
PLA2G2A/GPC1 -0.12 0.23 -9999 0 -0.5 128 128
LCK -0.18 0.22 -9999 0 -0.43 212 212
neuron differentiation -0.008 0.15 -9999 0 -0.49 43 43
PrPc/Cu2+ 0.019 0.024 -9999 0 -0.5 1 1
APP 0.026 0.006 -9999 0 -10000 0 0
TGFBR2 (dimer) 0.023 0.054 -9999 0 -0.67 3 3
IL4-mediated signaling events

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
BCL2L1 -0.52 0.4 -10000 0 -1.1 90 90
STAT6 (cleaved dimer) -0.53 0.41 -10000 0 -0.98 153 153
IGHG1 -0.18 0.13 -10000 0 -0.38 15 15
IGHG3 -0.5 0.38 -10000 0 -0.91 164 164
AKT1 -0.27 0.28 0.62 2 -0.82 60 62
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.23 0.3 -10000 0 -0.99 48 48
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.31 0.3 -10000 0 -0.76 97 97
THY1 -0.52 0.4 -10000 0 -1.1 85 85
MYB 0.01 0.1 -10000 0 -0.64 11 11
HMGA1 0.027 0.003 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.35 0.31 -10000 0 -0.84 85 85
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.28 0.28 -10000 0 -0.88 52 52
SP1 0.031 0.01 -10000 0 -10000 0 0
INPP5D 0.019 0.032 -10000 0 -10000 0 0
SOCS5 0.041 0.018 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.52 0.41 -10000 0 -1 120 120
SOCS1 -0.36 0.26 -10000 0 -0.72 79 79
SOCS3 -0.31 0.33 0.6 2 -1.1 53 55
FCER2 -0.56 0.46 -10000 0 -1.1 138 138
PARP14 0.026 0.009 -10000 0 -10000 0 0
CCL17 -0.55 0.42 -10000 0 -1.2 96 96
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.22 0.2 -10000 0 -0.68 44 44
T cell proliferation -0.51 0.41 -10000 0 -1.1 105 105
IL4R/JAK1 -0.51 0.4 -10000 0 -1.1 94 94
EGR2 -0.86 0.68 -10000 0 -1.5 230 230
JAK2 -0.033 0.041 -10000 0 -0.38 2 2
JAK3 -0.01 0.063 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
JAK1 0.003 0.021 -10000 0 -10000 0 0
COL1A2 -0.16 0.15 -10000 0 -1.2 3 3
CCL26 -0.52 0.4 -10000 0 -1.1 83 83
IL4R -0.55 0.43 -10000 0 -1.2 93 93
PTPN6 0.04 0.012 -10000 0 -10000 0 0
IL13RA2 -0.62 0.53 -10000 0 -1.4 123 123
IL13RA1 -0.031 0.033 -10000 0 -10000 0 0
IRF4 -0.31 0.5 -10000 0 -1.2 92 92
ARG1 -0.13 0.13 -10000 0 -0.72 4 4
CBL -0.32 0.29 -10000 0 -0.81 79 79
GTF3A 0.025 0.016 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
IL13RA1/JAK2 -0.038 0.047 -10000 0 -0.25 1 1
IRF4/BCL6 -0.28 0.46 -10000 0 -1.2 88 88
CD40LG -0.08 0.24 -10000 0 -0.63 77 77
MAPK14 -0.34 0.33 -10000 0 -0.93 71 71
mitosis -0.26 0.26 0.62 2 -0.76 61 63
STAT6 -0.58 0.48 -10000 0 -1.1 145 145
SPI1 0.022 0.033 -10000 0 -10000 0 0
RPS6KB1 -0.24 0.25 0.7 3 -0.72 56 59
STAT6 (dimer) -0.58 0.48 -10000 0 -1.1 147 147
STAT6 (dimer)/PARP14 -0.55 0.44 -10000 0 -1 140 140
mast cell activation 0.015 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.28 0.3 -10000 0 -0.91 62 62
FRAP1 -0.28 0.28 0.62 2 -0.82 61 63
LTA -0.52 0.4 -10000 0 -1.2 79 79
FES 0.027 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.57 0.46 1.1 149 -10000 0 149
CCL11 -0.5 0.38 -10000 0 -1.1 78 78
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.28 0.3 -10000 0 -0.91 61 61
IL2RG -0.01 0.14 -10000 0 -0.62 21 21
IL10 -0.53 0.42 -10000 0 -1.2 82 82
IRS1 -0.056 0.22 -10000 0 -0.66 59 59
IRS2 0.026 0.006 -10000 0 -10000 0 0
IL4 -0.12 0.09 -10000 0 -10000 0 0
IL5 -0.52 0.4 -10000 0 -1.2 78 78
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.45 0.35 -10000 0 -0.94 99 99
COL1A1 -0.22 0.24 -10000 0 -1.1 22 22
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.51 0.41 -10000 0 -1.2 78 78
IL2R gamma/JAK3 -0.02 0.11 -10000 0 -0.48 20 20
TFF3 -1.2 0.57 -10000 0 -1.4 398 398
ALOX15 -0.52 0.4 -10000 0 -1 108 108
MYBL1 0.026 0.008 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.44 0.35 -10000 0 -0.93 98 98
SHC1 0.025 0.007 -10000 0 -10000 0 0
CEBPB 0.03 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.27 0.28 -10000 0 -0.9 48 48
mol:PI-3-4-5-P3 -0.27 0.28 0.62 2 -0.82 60 62
PI3K -0.29 0.3 0.67 1 -0.9 60 61
DOK2 0.019 0.051 -10000 0 -0.67 2 2
ETS1 0.039 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.2 0.19 -10000 0 -0.68 36 36
ITGB3 -0.53 0.43 -10000 0 -1.2 85 85
PIGR -0.54 0.45 -10000 0 -1.2 96 96
IGHE 0.046 0.044 0.25 8 -10000 0 8
MAPKKK cascade -0.2 0.19 0.48 2 -0.66 36 38
BCL6 0.026 0.032 -10000 0 -0.67 1 1
OPRM1 -0.53 0.4 -10000 0 -1.1 90 90
RETNLB -0.52 0.4 -10000 0 -1.1 87 87
SELP -0.52 0.41 -10000 0 -1.2 84 84
AICDA -0.5 0.38 -10000 0 -1.1 83 83
HIF-1-alpha transcription factor network

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
PKM2 -0.18 0.35 0.61 4 -0.8 55 59
HDAC7 0.028 0.006 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.23 0.4 -10000 0 -0.8 111 111
SMAD4 0.028 0.005 -10000 0 -10000 0 0
ID2 -0.19 0.34 0.62 3 -0.8 54 57
AP1 -0.19 0.36 -10000 0 -0.71 148 148
ABCG2 -0.19 0.35 0.61 1 -0.83 55 56
HIF1A -0.019 0.073 -10000 0 -0.35 1 1
TFF3 -0.47 0.42 0.62 3 -0.89 177 180
GATA2 0.028 0.01 -10000 0 -10000 0 0
AKT1 -0.052 0.11 -10000 0 -0.28 11 11
response to hypoxia -0.068 0.11 -10000 0 -0.23 95 95
MCL1 -0.18 0.34 0.61 3 -0.82 50 53
NDRG1 -0.19 0.34 0.6 2 -0.81 52 54
SERPINE1 -0.19 0.34 0.61 1 -0.83 50 51
FECH -0.18 0.35 0.61 4 -0.81 53 57
FURIN -0.18 0.35 0.61 4 -0.8 55 59
NCOA2 -0.036 0.2 -10000 0 -0.67 45 45
EP300 -0.1 0.18 -10000 0 -0.34 156 156
HMOX1 -0.2 0.33 0.62 2 -0.81 54 56
BHLHE40 -0.19 0.35 0.62 2 -0.82 52 54
BHLHE41 -0.19 0.34 0.61 1 -0.81 54 55
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.031 0.1 -10000 0 -10000 0 0
ENG 0.012 0.092 0.47 3 -10000 0 3
JUN -0.12 0.28 -10000 0 -0.66 106 106
RORA -0.19 0.35 0.61 4 -0.82 53 57
ABCB1 -0.05 0.16 -10000 0 -1.2 8 8
TFRC -0.19 0.35 0.62 2 -0.82 54 56
CXCR4 -0.19 0.35 0.62 3 -0.8 55 58
TF -0.22 0.4 0.62 2 -0.9 80 82
CITED2 -0.21 0.39 0.61 3 -0.9 68 71
HIF1A/ARNT -0.21 0.38 -10000 0 -0.89 54 54
LDHA -0.032 0.11 -10000 0 -0.69 8 8
ETS1 -0.18 0.34 0.62 3 -0.82 51 54
PGK1 -0.19 0.34 0.61 1 -0.82 51 52
NOS2 -0.19 0.34 0.62 2 -0.82 52 54
ITGB2 -0.19 0.35 0.62 3 -0.83 50 53
ALDOA -0.19 0.34 0.61 1 -0.81 52 53
Cbp/p300/CITED2 -0.29 0.46 -10000 0 -0.96 117 117
FOS -0.15 0.3 -10000 0 -0.66 124 124
HK2 -0.19 0.35 0.62 3 -0.81 56 59
SP1 0.032 0.018 -10000 0 -10000 0 0
GCK -0.39 0.63 -10000 0 -1.4 134 134
HK1 -0.19 0.34 0.62 3 -0.81 52 55
NPM1 -0.19 0.34 0.61 1 -0.82 51 52
EGLN1 -0.18 0.34 0.61 3 -0.82 50 53
CREB1 0.033 0.006 -10000 0 -10000 0 0
PGM1 -0.18 0.34 0.61 3 -0.8 55 58
SMAD3 0.028 0.004 -10000 0 -10000 0 0
EDN1 -0.19 0.29 0.49 1 -0.69 74 75
IGFBP1 -0.19 0.34 0.61 1 -0.82 50 51
VEGFA -0.2 0.35 -10000 0 -0.7 101 101
HIF1A/JAB1 0.005 0.058 -10000 0 -10000 0 0
CP -0.31 0.45 0.62 2 -0.9 138 140
CXCL12 -0.22 0.4 0.62 3 -0.91 76 79
COPS5 0.027 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4 0.041 0.009 -10000 0 -10000 0 0
BNIP3 -0.19 0.35 0.62 3 -0.81 54 57
EGLN3 -0.2 0.35 -10000 0 -0.83 58 58
CA9 -0.19 0.34 0.6 2 -0.81 57 59
TERT -0.19 0.34 0.6 1 -0.82 51 52
ENO1 -0.18 0.34 0.61 3 -0.81 53 56
PFKL -0.18 0.34 0.62 3 -0.81 53 56
NCOA1 0.027 0.005 -10000 0 -10000 0 0
ADM -0.19 0.35 0.62 3 -0.79 63 66
ARNT -0.013 0.071 -10000 0 -0.31 2 2
HNF4A -0.015 0.058 -10000 0 -10000 0 0
ADFP -0.2 0.33 -10000 0 -0.78 63 63
SLC2A1 -0.19 0.34 -10000 0 -0.7 99 99
LEP -0.19 0.34 0.61 1 -0.82 51 52
HIF1A/ARNT/Cbp/p300 -0.25 0.41 -10000 0 -0.81 120 120
EPO -0.14 0.28 -10000 0 -0.86 25 25
CREBBP -0.079 0.17 -10000 0 -0.33 131 131
HIF1A/ARNT/Cbp/p300/HDAC7 -0.22 0.4 -10000 0 -0.8 107 107
PFKFB3 -0.19 0.35 0.62 3 -0.82 52 55
NT5E -0.19 0.35 0.61 3 -0.82 55 58
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.026 0.006 -10000 0 -10000 0 0
EPHB2 0.021 0.055 -10000 0 -0.67 3 3
EFNB1 -0.002 0.085 -10000 0 -0.49 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.11 0.22 -10000 0 -0.39 183 183
Ephrin B2/EPHB1-2 -0.12 0.22 -10000 0 -0.39 184 184
neuron projection morphogenesis -0.12 0.2 -10000 0 -0.37 183 183
Ephrin B1/EPHB1-2/Tiam1 -0.12 0.23 -10000 0 -0.41 188 188
DNM1 0.004 0.11 -10000 0 -0.63 15 15
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.002 0.094 0.41 1 -0.64 8 9
YES1 0.004 0.11 -10000 0 -0.89 7 7
Ephrin B1/EPHB1-2/NCK2 -0.12 0.21 -10000 0 -0.38 184 184
PI3K 0.024 0.11 -10000 0 -0.83 7 7
mol:GDP -0.12 0.23 -10000 0 -0.4 188 188
ITGA2B -0.043 0.21 -10000 0 -0.66 49 49
endothelial cell proliferation 0.033 0.01 -10000 0 -10000 0 0
FYN 0.003 0.11 -10000 0 -0.86 8 8
MAP3K7 -0.011 0.088 -10000 0 -0.68 8 8
FGR 0.001 0.11 -10000 0 -0.85 8 8
TIAM1 -0.054 0.077 -10000 0 -0.67 1 1
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RGS3 0.025 0.008 -10000 0 -10000 0 0
cell adhesion -0.027 0.16 -10000 0 -0.43 58 58
LYN 0.003 0.11 -10000 0 -0.86 8 8
Ephrin B1/EPHB1-2/Src Family Kinases -0.006 0.1 -10000 0 -0.81 8 8
Ephrin B1/EPHB1-2 -0.01 0.092 -10000 0 -0.77 7 7
SRC 0.001 0.11 -10000 0 -0.85 8 8
ITGB3 0.011 0.099 -10000 0 -0.64 11 11
EPHB1 -0.23 0.34 -10000 0 -0.66 185 185
EPHB4 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.033 0.011 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.026 0.18 -10000 0 -0.52 56 56
BLK -0.049 0.14 -10000 0 -0.92 8 8
HCK 0.002 0.11 -10000 0 -0.85 8 8
regulation of stress fiber formation 0.12 0.21 0.38 184 -10000 0 184
MAPK8 -0.006 0.12 0.36 5 -0.66 12 17
Ephrin B1/EPHB1-2/RGS3 -0.12 0.21 -10000 0 -0.38 183 183
endothelial cell migration -0.006 0.083 0.4 2 -0.62 7 9
NCK2 0.027 0.005 -10000 0 -10000 0 0
PTPN13 0.023 0.09 -10000 0 -0.79 6 6
regulation of focal adhesion formation 0.12 0.21 0.38 184 -10000 0 184
chemotaxis 0.11 0.21 0.38 183 -10000 0 183
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
Rac1/GTP -0.11 0.21 -10000 0 -0.38 183 183
angiogenesis -0.011 0.094 -10000 0 -0.72 8 8
LCK 0 0.12 -10000 0 -0.89 8 8
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.033 0.17 -10000 0 -0.44 71 71
cell-cell adhesion 0.11 0.16 0.32 171 -10000 0 171
Ephrin B/EPHB2/RasGAP 0.065 0.06 -10000 0 -0.37 7 7
ITSN1 0.026 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
SHC1 0.025 0.007 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.024 0.046 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.14 0.22 -10000 0 -0.42 184 184
HRAS/GDP -0.078 0.16 -10000 0 -0.34 20 20
Ephrin B/EPHB1/GRB7 -0.095 0.22 -10000 0 -0.39 175 175
Endophilin/SYNJ1 0.023 0.073 0.44 6 -0.35 7 13
KRAS 0.027 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.094 0.22 -10000 0 -0.38 176 176
endothelial cell migration 0.052 0.037 -10000 0 -0.37 3 3
GRB2 0.026 0.007 -10000 0 -10000 0 0
GRB7 0.003 0.053 -10000 0 -10000 0 0
PAK1 0.024 0.074 0.47 5 -0.35 7 12
HRAS 0.026 0.011 -10000 0 -10000 0 0
RRAS 0.02 0.066 0.44 4 -0.36 6 10
DNM1 0.005 0.12 -10000 0 -0.61 16 16
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.12 0.18 -10000 0 -0.36 176 176
lamellipodium assembly -0.11 0.16 -10000 0 -0.32 171 171
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.084 0.16 -10000 0 -0.29 160 160
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
EPHB2 0.022 0.054 -10000 0 -0.67 3 3
EPHB3 -0.062 0.071 -10000 0 -10000 0 0
EPHB1 -0.23 0.34 -10000 0 -0.66 185 185
EPHB4 0.026 0.006 -10000 0 -10000 0 0
mol:GDP -0.071 0.13 0.24 1 -0.37 13 14
Ephrin B/EPHB2 0.051 0.056 -10000 0 -0.37 7 7
Ephrin B/EPHB3 0.059 0.055 -10000 0 -0.42 4 4
JNK cascade -0.12 0.19 -10000 0 -0.37 174 174
Ephrin B/EPHB1 -0.1 0.21 -10000 0 -0.38 177 177
RAP1/GDP -0.046 0.14 -10000 0 -0.33 13 13
EFNB2 0.026 0.006 -10000 0 -10000 0 0
EFNB3 0.015 0.068 -10000 0 -0.67 4 4
EFNB1 0.026 0.007 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.12 0.22 -10000 0 -0.39 185 185
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.083 0.18 -10000 0 -0.33 172 172
Rap1/GTP -0.099 0.17 -10000 0 -0.33 168 168
axon guidance -0.034 0.17 -10000 0 -0.44 71 71
MAPK3 -0.08 0.14 -10000 0 -0.44 10 10
MAPK1 -0.079 0.13 -10000 0 -0.42 11 11
Rac1/GDP -0.057 0.13 -10000 0 -0.35 12 12
actin cytoskeleton reorganization -0.078 0.12 -10000 0 -0.32 5 5
CDC42/GDP -0.055 0.14 0.4 2 -0.35 13 15
PI3K 0.057 0.038 -10000 0 -0.37 3 3
EFNA5 -0.071 0.24 -10000 0 -0.67 69 69
Ephrin B2/EPHB4 0.034 0.011 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.026 0.044 -10000 0 -0.31 7 7
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.099 0.16 -10000 0 -0.32 156 156
PTK2 0.042 0.098 0.67 10 -10000 0 10
MAP4K4 -0.12 0.19 -10000 0 -0.38 174 174
SRC 0.026 0.008 -10000 0 -10000 0 0
KALRN 0.027 0.003 -10000 0 -10000 0 0
Intersectin/N-WASP 0.038 0.01 -10000 0 -10000 0 0
neuron projection morphogenesis -0.075 0.14 0.32 5 -0.32 2 7
MAP2K1 -0.081 0.14 -10000 0 -0.45 11 11
WASL 0.026 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.11 0.22 -10000 0 -0.39 184 184
cell migration -0.082 0.18 0.58 4 -0.47 13 17
NRAS 0.027 0.005 -10000 0 -10000 0 0
SYNJ1 0.023 0.074 0.45 6 -0.35 7 13
PXN 0.027 0.005 -10000 0 -10000 0 0
TF -0.023 0.13 0.47 3 -0.37 51 54
HRAS/GTP -0.09 0.19 -10000 0 -0.34 171 171
Ephrin B1/EPHB1-2 -0.12 0.21 -10000 0 -0.39 184 184
cell adhesion mediated by integrin -0.007 0.073 0.39 4 -0.35 9 13
RAC1 0.026 0.006 -10000 0 -10000 0 0
mol:GTP -0.094 0.2 -10000 0 -0.36 174 174
RAC1-CDC42/GTP -0.14 0.16 -10000 0 -0.35 172 172
RASA1 0.027 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.047 0.13 -10000 0 -0.34 9 9
ruffle organization -0.1 0.18 0.57 5 -0.33 162 167
NCK1 0.027 0.003 -10000 0 -10000 0 0
receptor internalization 0.002 0.084 0.41 3 -0.36 17 20
Ephrin B/EPHB2/KALRN 0.065 0.06 -10000 0 -0.37 7 7
ROCK1 -0.023 0.043 -10000 0 -10000 0 0
RAS family/GDP -0.072 0.1 -10000 0 -0.32 4 4
Rac1/GTP -0.11 0.17 -10000 0 -0.34 171 171
Ephrin B/EPHB1/Src/Paxillin -0.09 0.16 -10000 0 -0.3 178 178
IL23-mediated signaling events

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
CCL2 -0.18 0.53 -10000 0 -1.3 79 79
IL23A -0.2 0.55 -10000 0 -1.2 95 95
NF kappa B1 p50/RelA/I kappa B alpha -0.16 0.54 -10000 0 -1.2 87 87
positive regulation of T cell mediated cytotoxicity -0.22 0.61 -10000 0 -1.3 92 92
ITGA3 -0.17 0.5 -10000 0 -1.2 79 79
IL17F -0.094 0.33 0.65 2 -0.73 78 80
IL12B 0.004 0.092 -10000 0 -0.69 6 6
STAT1 (dimer) -0.2 0.58 -10000 0 -1.3 92 92
CD4 -0.17 0.49 -10000 0 -1.2 75 75
IL23 -0.19 0.53 -10000 0 -1.2 94 94
IL23R 0.006 0.1 -10000 0 -0.82 2 2
IL1B -0.21 0.57 -10000 0 -1.4 78 78
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.16 0.5 -10000 0 -1.2 74 74
TYK2 0.016 0.035 -10000 0 -10000 0 0
STAT4 0.004 0.098 -10000 0 -0.58 11 11
STAT3 0.026 0.007 -10000 0 -10000 0 0
IL18RAP -0.011 0.14 -10000 0 -0.67 22 22
IL12RB1 -0.003 0.088 -10000 0 -0.65 6 6
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
IL12Rbeta1/TYK2 0.013 0.077 -10000 0 -0.51 6 6
IL23R/JAK2 0.013 0.13 -10000 0 -0.72 2 2
positive regulation of chronic inflammatory response -0.22 0.61 -10000 0 -1.3 92 92
natural killer cell activation 0.001 0.009 -10000 0 -0.046 2 2
JAK2 0.016 0.051 -10000 0 -0.38 2 2
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
RELA 0.027 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.17 0.49 -10000 0 -1.1 95 95
ALOX12B -0.17 0.49 -10000 0 -1.1 82 82
CXCL1 -0.18 0.52 -10000 0 -1.2 83 83
T cell proliferation -0.22 0.61 -10000 0 -1.3 92 92
NFKBIA 0.027 0.006 -10000 0 -10000 0 0
IL17A -0.051 0.27 -10000 0 -0.56 70 70
PI3K -0.18 0.55 -10000 0 -1.2 88 88
IFNG -0.014 0.053 0.12 1 -0.13 65 66
STAT3 (dimer) -0.16 0.51 -10000 0 -1.1 85 85
IL18R1 -0.002 0.095 -10000 0 -0.58 10 10
IL23/IL23R/JAK2/TYK2/SOCS3 -0.088 0.34 -10000 0 -0.81 61 61
IL18/IL18R -0.001 0.15 -10000 0 -0.47 37 37
macrophage activation -0.008 0.021 -10000 0 -0.044 95 95
TNF -0.24 0.6 -10000 0 -1.4 97 97
STAT3/STAT4 -0.19 0.55 -10000 0 -1.2 91 91
STAT4 (dimer) -0.21 0.58 -10000 0 -1.3 92 92
IL18 -0.008 0.11 -10000 0 -0.64 11 11
IL19 -0.16 0.5 -10000 0 -1.2 75 75
STAT5A (dimer) -0.2 0.57 -10000 0 -1.3 89 89
STAT1 0.023 0.023 -10000 0 -10000 0 0
SOCS3 -0.002 0.13 -10000 0 -0.67 19 19
CXCL9 -0.26 0.62 -10000 0 -1.4 108 108
MPO -0.17 0.5 -10000 0 -1.2 80 80
positive regulation of humoral immune response -0.22 0.61 -10000 0 -1.3 92 92
IL23/IL23R/JAK2/TYK2 -0.26 0.74 -10000 0 -1.6 92 92
IL6 -0.26 0.62 -10000 0 -1.3 112 112
STAT5A 0.026 0.007 -10000 0 -10000 0 0
IL2 0.003 0.029 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.009 -10000 0 -0.046 2 2
CD3E -0.2 0.55 -10000 0 -1.3 85 85
keratinocyte proliferation -0.22 0.61 -10000 0 -1.3 92 92
NOS2 -0.17 0.49 -10000 0 -1.2 76 76
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.16 0.29 -10000 0 -0.48 207 207
SMAD6-7/SMURF1 0.052 0.014 -10000 0 -10000 0 0
NOG -0.02 0.17 -10000 0 -0.67 30 30
SMAD9 -0.18 0.27 -10000 0 -0.53 170 170
SMAD4 0.027 0.005 -10000 0 -10000 0 0
SMAD5 -0.082 0.16 -10000 0 -0.44 31 31
BMP7/USAG1 -0.23 0.27 -10000 0 -0.5 247 247
SMAD5/SKI -0.067 0.17 0.3 4 -0.42 31 35
SMAD1 -0.036 0.094 -10000 0 -0.66 1 1
BMP2 0.001 0.13 -10000 0 -0.67 18 18
SMAD1/SMAD1/SMAD4 -0.021 0.084 -10000 0 -0.53 1 1
BMPR1A 0.027 0.005 -10000 0 -10000 0 0
BMPR1B -0.2 0.32 -10000 0 -0.67 160 160
BMPR1A-1B/BAMBI -0.11 0.23 -10000 0 -0.44 160 160
AHSG -0.004 0.039 -10000 0 -10000 0 0
CER1 -0.014 0.009 -10000 0 -10000 0 0
BMP2-4/CER1 0.014 0.11 -10000 0 -0.43 29 29
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.064 0.16 -10000 0 -0.53 28 28
BMP2-4 (homodimer) 0.006 0.13 -10000 0 -0.5 29 29
RGMB 0.026 0.005 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.085 0.22 -10000 0 -0.4 159 159
RGMA 0.002 0.13 -10000 0 -0.65 18 18
SMURF1 0.026 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.077 0.16 -10000 0 -0.45 34 34
BMP2-4/USAG1 -0.22 0.26 -10000 0 -0.46 260 260
SMAD6/SMURF1/SMAD5 -0.066 0.17 0.32 1 -0.42 29 30
SOSTDC1 -0.33 0.34 -10000 0 -0.67 247 247
BMP7/BMPR2/BMPR1A-1B -0.084 0.22 -10000 0 -0.4 157 157
SKI 0.026 0.006 -10000 0 -10000 0 0
BMP6 (homodimer) 0.026 0.013 -10000 0 -10000 0 0
HFE2 -0.003 0.022 -10000 0 -10000 0 0
ZFYVE16 0.026 0.005 -10000 0 -10000 0 0
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
BMP2-4/CHRD 0.015 0.14 -10000 0 -0.44 38 38
SMAD5/SMAD5/SMAD4 -0.065 0.17 0.3 4 -0.42 31 35
MAPK1 0.02 0.012 -10000 0 -10000 0 0
TAK1/TAB family -0.052 0.15 -10000 0 -0.39 33 33
BMP7 (homodimer) 0.027 0.005 -10000 0 -10000 0 0
NUP214 0.025 0.008 -10000 0 -10000 0 0
BMP6/FETUA 0.027 0.032 -10000 0 -10000 0 0
SMAD1/SKI -0.027 0.1 0.33 1 -0.62 1 2
SMAD6 0.027 0.004 -10000 0 -10000 0 0
CTDSP2 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.022 0.12 -10000 0 -0.44 29 29
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.14 0.28 -10000 0 -0.65 112 112
BMPR2 (homodimer) 0.027 0.005 -10000 0 -10000 0 0
GADD34/PP1CA 0.046 0.047 -10000 0 -0.44 4 4
BMPR1A-1B (homodimer) -0.14 0.25 -10000 0 -0.5 160 160
CHRDL1 -0.44 0.32 -10000 0 -0.65 338 338
ENDOFIN/SMAD1 -0.028 0.098 -10000 0 -0.62 1 1
SMAD6-7/SMURF1/SMAD1 -0.012 0.1 -10000 0 -0.58 1 1
SMAD6/SMURF1 0.026 0.006 -10000 0 -10000 0 0
BAMBI 0.019 0.051 -10000 0 -0.67 2 2
SMURF2 0.026 0.007 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.3 0.24 -10000 0 -0.46 328 328
BMP2-4/GREM1 -0.077 0.23 -10000 0 -0.47 123 123
SMAD7 0.027 0.004 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.17 0.26 -10000 0 -0.51 167 167
SMAD1/SMAD6 -0.027 0.096 -10000 0 -0.62 1 1
TAK1/SMAD6 0.038 0.01 -10000 0 -10000 0 0
BMP7 0.027 0.005 -10000 0 -10000 0 0
BMP6 0.026 0.013 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.056 0.13 -10000 0 -0.4 30 30
PPM1A 0.027 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.025 0.096 0.31 1 -0.62 1 2
SMAD7/SMURF1 0.038 0.01 -10000 0 -10000 0 0
CTDSPL 0.027 0.003 -10000 0 -10000 0 0
PPP1CA 0.027 0.005 -10000 0 -10000 0 0
XIAP 0.026 0.007 -10000 0 -10000 0 0
CTDSP1 0.027 0.005 -10000 0 -10000 0 0
PPP1R15A 0.02 0.063 -10000 0 -0.67 4 4
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.16 0.26 -10000 0 -0.39 212 212
CHRD 0.013 0.098 -10000 0 -0.67 10 10
BMPR2 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.078 0.16 -10000 0 -0.28 167 167
BMP4 0.008 0.1 -10000 0 -0.64 12 12
FST -0.13 0.29 -10000 0 -0.67 111 111
BMP2-4/NOG -0.006 0.16 -10000 0 -0.44 58 58
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.07 0.21 -10000 0 -0.38 154 154
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.056 0.25 0.29 18 -0.59 72 90
FYN -0.1 0.32 0.47 1 -0.78 75 76
LAT/GRAP2/SLP76 -0.083 0.25 -10000 0 -0.62 77 77
IKBKB 0.027 0.005 -10000 0 -10000 0 0
AKT1 -0.063 0.21 0.49 8 -0.47 77 85
B2M 0.027 0.006 -10000 0 -10000 0 0
IKBKG -0.016 0.057 0.1 5 -0.16 32 37
MAP3K8 0.018 0.078 -10000 0 -0.62 7 7
mol:Ca2+ -0.03 0.042 0.092 5 -0.1 101 106
integrin-mediated signaling pathway 0.034 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.11 0.3 0.5 4 -0.72 80 84
TRPV6 -0.1 0.35 0.99 20 -0.67 101 121
CD28 -0.015 0.15 -10000 0 -0.65 25 25
SHC1 -0.1 0.32 0.31 19 -0.78 75 94
receptor internalization -0.13 0.35 -10000 0 -0.66 118 118
PRF1 -0.11 0.33 -10000 0 -0.91 60 60
KRAS 0.027 0.005 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
COT/AKT1 -0.046 0.17 0.41 5 -0.37 78 83
LAT -0.11 0.31 0.3 3 -0.78 76 79
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.049 0.21 -10000 0 -0.63 53 53
CD3E -0.031 0.19 -10000 0 -0.62 42 42
CD3G -0.098 0.26 -10000 0 -0.65 89 89
RASGRP2 -0.004 0.033 0.095 3 -0.18 12 15
RASGRP1 -0.052 0.21 0.5 10 -0.47 76 86
HLA-A 0.026 0.012 -10000 0 -10000 0 0
RASSF5 0.025 0.007 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.034 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.017 0.14 0.33 29 -0.13 43 72
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.048 0.086 -10000 0 -0.25 59 59
PRKCA -0.034 0.12 -10000 0 -0.29 74 74
GRAP2 -0.019 0.15 -10000 0 -0.55 33 33
mol:IP3 -0.032 0.21 0.26 71 -0.45 72 143
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.13 0.35 -10000 0 -0.85 77 77
ORAI1 0.045 0.21 0.7 2 -0.78 16 18
CSK -0.11 0.32 -10000 0 -0.79 77 77
B7 family/CD28 -0.11 0.35 -10000 0 -0.78 85 85
CHUK 0.027 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.14 0.38 -10000 0 -0.89 84 84
PTPN6 -0.11 0.32 0.25 1 -0.8 76 77
VAV1 -0.11 0.31 -10000 0 -0.76 78 78
Monovalent TCR/CD3 -0.12 0.31 -10000 0 -0.6 109 109
CBL 0.027 0.005 -10000 0 -10000 0 0
LCK -0.11 0.33 -10000 0 -0.82 74 74
PAG1 -0.11 0.32 -10000 0 -0.8 76 76
RAP1A 0.027 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.14 0.38 -10000 0 -0.89 83 83
CD80 -0.041 0.21 -10000 0 -0.66 48 48
CD86 0.013 0.076 -10000 0 -0.67 5 5
PDK1/CARD11/BCL10/MALT1 -0.041 0.11 -10000 0 -0.29 62 62
HRAS 0.026 0.011 -10000 0 -10000 0 0
GO:0035030 -0.1 0.26 -10000 0 -0.58 93 93
CD8A -0.026 0.18 -10000 0 -0.65 38 38
CD8B -0.052 0.22 -10000 0 -0.65 55 55
PTPRC -0.008 0.14 -10000 0 -0.67 20 20
PDK1/PKC theta -0.077 0.26 0.57 10 -0.58 78 88
CSK/PAG1 -0.11 0.31 -10000 0 -0.78 75 75
SOS1 0.027 0.005 -10000 0 -10000 0 0
peptide-MHC class I 0.038 0.014 -10000 0 -10000 0 0
GRAP2/SLP76 -0.1 0.31 -10000 0 -0.74 78 78
STIM1 0.018 0.16 1.2 2 -0.9 9 11
RAS family/GTP 0.008 0.099 0.23 24 -0.19 42 66
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.14 0.39 -10000 0 -0.72 117 117
mol:DAG -0.06 0.16 0.14 6 -0.39 75 81
RAP1A/GDP 0.008 0.06 0.19 16 -0.066 13 29
PLCG1 0.027 0.005 -10000 0 -10000 0 0
CD247 -0.003 0.13 -10000 0 -0.67 18 18
cytotoxic T cell degranulation -0.1 0.31 -10000 0 -0.85 60 60
RAP1A/GTP -0.001 0.012 -10000 0 -0.068 10 10
mol:PI-3-4-5-P3 -0.084 0.24 0.52 6 -0.57 80 86
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.05 0.26 0.28 66 -0.59 74 140
NRAS 0.027 0.005 -10000 0 -10000 0 0
ZAP70 -0.002 0.13 -10000 0 -0.65 18 18
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.081 0.24 -10000 0 -0.59 77 77
MALT1 0.027 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.044 -10000 0 -0.67 2 2
CD8 heterodimer -0.057 0.23 -10000 0 -0.58 75 75
CARD11 -0.017 0.11 -10000 0 -0.67 11 11
PRKCB -0.03 0.12 -10000 0 -0.3 64 64
PRKCE -0.03 0.12 -10000 0 -0.28 71 71
PRKCQ -0.095 0.28 0.56 7 -0.68 77 84
LCP2 0.024 0.02 -10000 0 -10000 0 0
BCL10 0.027 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression -0.048 0.18 0.51 9 -0.39 77 86
IKK complex 0.018 0.13 0.37 25 -0.12 27 52
RAS family/GDP -0.005 0.011 -10000 0 -10000 0 0
MAP3K14 -0.034 0.12 0.26 3 -0.29 63 66
PDPK1 -0.06 0.2 0.49 9 -0.44 78 87
TCR/CD3/MHC I/CD8/Fyn -0.15 0.42 -10000 0 -0.98 84 84
Coregulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 -0.006 0.052 -10000 0 -10000 0 0
SVIL -0.003 0.048 -10000 0 -10000 0 0
ZNF318 0.076 0.087 0.24 7 -0.67 1 8
JMJD2C -0.065 0.067 -10000 0 -0.12 278 278
T-DHT/AR/Ubc9 -0.22 0.24 -10000 0 -0.48 207 207
CARM1 0.023 0.009 -10000 0 -10000 0 0
PRDX1 0.029 0.006 -10000 0 -10000 0 0
PELP1 0.032 0.013 -10000 0 -10000 0 0
CTNNB1 0.002 0.04 -10000 0 -10000 0 0
AKT1 0.038 0.021 -10000 0 -10000 0 0
PTK2B 0.007 0.032 -10000 0 -10000 0 0
MED1 0.037 0.021 -10000 0 -10000 0 0
MAK 0.067 0.12 0.22 64 -0.65 7 71
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 -0.007 0.064 -10000 0 -0.67 2 2
GSN -0.001 0.045 -10000 0 -10000 0 0
NCOA2 -0.04 0.2 -10000 0 -0.67 45 45
NCOA6 -0.003 0.054 -10000 0 -0.67 1 1
DNA-PK 0.074 0.078 -10000 0 -10000 0 0
NCOA4 0.026 0.005 -10000 0 -10000 0 0
PIAS3 0.003 0.038 -10000 0 -10000 0 0
cell proliferation -0.002 0.14 -10000 0 -0.8 10 10
XRCC5 0.037 0.018 -10000 0 -10000 0 0
UBE3A -0.012 0.063 -10000 0 -0.18 1 1
T-DHT/AR/SNURF -0.25 0.26 -10000 0 -0.52 214 214
FHL2 -0.13 0.32 -10000 0 -1.1 42 42
RANBP9 -0.002 0.046 -10000 0 -10000 0 0
JMJD1A -0.001 0.035 -10000 0 -0.12 34 34
CDK6 0.023 0.054 -10000 0 -0.67 3 3
TGFB1I1 -0.003 0.048 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.24 0.24 -10000 0 -0.49 214 214
XRCC6 0.028 0.023 -10000 0 -10000 0 0
T-DHT/AR -0.28 0.26 -10000 0 -0.52 232 232
CTDSP1 0.012 0.024 -10000 0 -10000 0 0
CTDSP2 0.058 0.052 -10000 0 -10000 0 0
BRCA1 -0.003 0.047 -10000 0 -10000 0 0
TCF4 0.048 0.035 -10000 0 -10000 0 0
CDKN2A 0.006 0.08 -10000 0 -10000 0 0
SRF 0.035 0.051 -10000 0 -10000 0 0
NKX3-1 -0.11 0.14 -10000 0 -0.6 15 15
KLK3 -0.39 0.65 -10000 0 -1.4 141 141
TMF1 0.017 0.046 -10000 0 -0.67 2 2
HNRNPA1 0.044 0.029 -10000 0 -10000 0 0
AOF2 -0.02 0.033 -10000 0 -0.072 141 141
APPL1 0.042 0.042 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.22 0.24 -10000 0 -0.48 208 208
AR -0.31 0.34 -10000 0 -0.7 206 206
UBA3 0.012 0.024 -10000 0 -10000 0 0
PATZ1 0.033 0.031 -10000 0 -10000 0 0
PAWR 0.02 0.015 -10000 0 -10000 0 0
PRKDC 0.037 0.018 -10000 0 -10000 0 0
PA2G4 0.049 0.037 -10000 0 -10000 0 0
UBE2I 0.026 0.007 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.2 0.22 -10000 0 -0.45 202 202
RPS6KA3 -0.003 0.046 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.23 0.24 -10000 0 -0.49 207 207
LATS2 0.04 0.043 -10000 0 -0.67 1 1
T-DHT/AR/PRX1 -0.19 0.22 -10000 0 -0.44 204 204
Cyclin D3/CDK11 p58 0.022 0.005 -10000 0 -10000 0 0
VAV3 -0.005 0.083 -10000 0 -0.67 6 6
KLK2 -0.66 0.55 -10000 0 -1.1 280 280
CASP8 0.031 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.24 0.27 -10000 0 -0.52 211 211
TMPRSS2 -0.16 0.27 -10000 0 -1.1 32 32
CCND1 0.013 0.03 -10000 0 -10000 0 0
PIAS1 -0.012 0.063 -10000 0 -10000 0 0
mol:T-DHT -0.033 0.039 -10000 0 -0.078 170 170
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.031 0.091 -10000 0 -0.2 7 7
T-DHT/AR/CDK6 -0.22 0.24 -10000 0 -0.48 213 213
CMTM2 0.029 0.012 -10000 0 -10000 0 0
SNURF -0.015 0.16 -10000 0 -0.65 29 29
ZMIZ1 -0.024 0.056 -10000 0 -0.66 1 1
CCND3 0.028 0.004 -10000 0 -10000 0 0
TGIF1 0.044 0.029 -10000 0 -10000 0 0
FKBP4 -0.002 0.046 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 0.083 0.087 0.32 13 -10000 0 13
SMARCC2 0.026 0.018 -10000 0 -10000 0 0
SMARCC1 0.026 0.018 -10000 0 -10000 0 0
TBX21 -0.12 0.24 -10000 0 -0.76 42 42
SUMO2 0.024 0.018 -10000 0 -10000 0 0
STAT1 (dimer) 0.03 0.023 -10000 0 -10000 0 0
FKBP4 0.027 0.005 -10000 0 -10000 0 0
FKBP5 0.019 0.072 -10000 0 -0.62 6 6
GR alpha/HSP90/FKBP51/HSP90 0.12 0.11 0.32 57 -0.38 5 62
PRL -0.06 0.1 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.18 0.29 0.54 144 -0.45 21 165
RELA -0.023 0.099 -10000 0 -0.27 28 28
FGG 0.16 0.2 0.46 112 -10000 0 112
GR beta/TIF2 0.07 0.2 0.33 74 -0.45 45 119
IFNG -0.35 0.47 -10000 0 -1.1 114 114
apoptosis -0.014 0.23 0.48 47 -0.53 18 65
CREB1 0.026 0.013 -10000 0 -10000 0 0
histone acetylation -0.074 0.16 -10000 0 -0.42 59 59
BGLAP -0.075 0.13 -10000 0 -0.47 15 15
GR/PKAc 0.11 0.1 0.33 39 -0.33 1 40
NF kappa B1 p50/RelA -0.04 0.17 -10000 0 -0.38 68 68
SMARCD1 0.026 0.018 -10000 0 -10000 0 0
MDM2 0.083 0.098 0.26 79 -10000 0 79
GATA3 -0.003 0.14 -10000 0 -0.63 24 24
AKT1 0.021 0.004 -10000 0 -10000 0 0
CSF2 -0.11 0.14 -10000 0 -0.55 18 18
GSK3B 0.025 0.019 -10000 0 -10000 0 0
NR1I3 0.005 0.23 0.51 32 -0.73 4 36
CSN2 0.13 0.16 0.39 90 -10000 0 90
BRG1/BAF155/BAF170/BAF60A 0.063 0.053 -10000 0 -0.31 7 7
NFATC1 0.015 0.093 -10000 0 -0.67 9 9
POU2F1 0.026 0.01 -10000 0 -10000 0 0
CDKN1A 0.026 0.034 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.014 -10000 0 -10000 0 0
SFN -0.08 0.12 -10000 0 -0.67 15 15
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.12 0.13 0.34 49 -0.36 12 61
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.12 0.4 0.47 31 -0.83 103 134
JUN -0.24 0.27 -10000 0 -0.57 163 163
IL4 -0.097 0.16 -10000 0 -0.62 21 21
CDK5R1 0.025 0.015 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.25 0.31 -10000 0 -0.67 146 146
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.12 0.11 0.34 47 -0.38 4 51
cortisol/GR alpha (monomer) 0.25 0.3 0.64 148 -10000 0 148
NCOA2 -0.037 0.2 -10000 0 -0.67 45 45
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.18 0.3 -10000 0 -0.68 125 125
AP-1/NFAT1-c-4 -0.37 0.41 -10000 0 -0.8 193 193
AFP -0.17 0.2 -10000 0 -0.66 28 28
SUV420H1 0.027 0.005 -10000 0 -10000 0 0
IRF1 0.14 0.14 0.46 43 -10000 0 43
TP53 0.041 0.013 -10000 0 -10000 0 0
PPP5C 0.025 0.007 -10000 0 -10000 0 0
KRT17 -0.28 0.34 -10000 0 -0.79 104 104
KRT14 -0.08 0.12 -10000 0 -0.49 6 6
TBP 0.034 0.007 -10000 0 -10000 0 0
CREBBP 0.033 0.046 -10000 0 -0.26 10 10
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC2 0.03 0.005 -10000 0 -10000 0 0
AP-1 -0.37 0.41 -10000 0 -0.79 198 198
MAPK14 0.027 0.016 -10000 0 -10000 0 0
MAPK10 0.025 0.036 -10000 0 -0.67 1 1
MAPK11 0.017 0.019 -10000 0 -10000 0 0
KRT5 -0.37 0.49 -10000 0 -1.1 127 127
interleukin-1 receptor activity 0.002 0.003 -10000 0 -10000 0 0
NCOA1 0.029 0.005 -10000 0 -10000 0 0
STAT1 0.03 0.023 -10000 0 -10000 0 0
CGA -0.092 0.14 -10000 0 -0.51 15 15
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.089 0.11 0.34 37 -10000 0 37
MAPK3 0.025 0.017 -10000 0 -10000 0 0
MAPK1 0.02 0.017 -10000 0 -10000 0 0
ICAM1 -0.16 0.24 -10000 0 -0.62 75 75
NFKB1 -0.022 0.097 -10000 0 -0.26 29 29
MAPK8 -0.13 0.18 -10000 0 -0.44 96 96
MAPK9 0.027 0.014 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.019 0.24 0.47 46 -0.56 18 64
BAX 0.039 0.093 0.85 5 -10000 0 5
POMC -0.45 0.64 -10000 0 -1.3 145 145
EP300 0.025 0.043 -10000 0 -0.26 8 8
cortisol/GR alpha (dimer)/p53 0.23 0.25 0.56 135 -10000 0 135
proteasomal ubiquitin-dependent protein catabolic process 0.078 0.13 0.34 76 -10000 0 76
SGK1 0.01 0.21 0.51 1 -1.3 10 11
IL13 -0.21 0.25 -10000 0 -0.76 46 46
IL6 -0.28 0.47 -10000 0 -1.1 108 108
PRKACG -0.009 0.016 -10000 0 -10000 0 0
IL5 -0.18 0.21 -10000 0 -0.74 25 25
IL2 -0.25 0.28 -10000 0 -0.67 102 102
CDK5 0.027 0.009 -10000 0 -10000 0 0
PRKACB 0.025 0.032 -10000 0 -0.67 1 1
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
IL8 -0.17 0.29 -10000 0 -0.72 73 73
CDK5R1/CDK5 0.038 0.02 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.003 0.14 -10000 0 -0.37 27 27
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.22 0.23 0.52 149 -10000 0 149
SMARCA4 0.024 0.018 -10000 0 -10000 0 0
chromatin remodeling 0.14 0.15 0.38 93 -0.38 2 95
NF kappa B1 p50/RelA/Cbp -0.007 0.16 -10000 0 -0.41 29 29
JUN (dimer) -0.23 0.27 -10000 0 -0.56 163 163
YWHAH 0.02 0.012 -10000 0 -10000 0 0
VIPR1 -0.21 0.36 -10000 0 -0.93 88 88
NR3C1 0.15 0.19 0.43 118 -10000 0 118
NR4A1 -0.26 0.36 -10000 0 -0.66 211 211
TIF2/SUV420H1 -0.011 0.16 -10000 0 -0.5 45 45
MAPKKK cascade -0.014 0.23 0.48 47 -0.53 18 65
cortisol/GR alpha (dimer)/Src-1 0.22 0.25 0.55 146 -10000 0 146
PBX1 0.026 0.008 -10000 0 -10000 0 0
POU1F1 0.005 0.022 -10000 0 -10000 0 0
SELE -0.25 0.45 -10000 0 -1.1 92 92
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.14 0.15 0.38 92 -0.38 2 94
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.22 0.23 0.52 149 -10000 0 149
mol:cortisol 0.14 0.19 0.38 146 -10000 0 146
MMP1 -0.098 0.14 -10000 0 -0.87 10 10
Arf6 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
CENTA1/KIF3B 0.035 0.009 -10000 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.017 0.15 -10000 0 -0.66 14 14
EGFR 0.019 0.07 -10000 0 -0.67 5 5
EPHA2 0.026 0.012 -10000 0 -10000 0 0
USP6 0.025 0.013 -10000 0 -10000 0 0
IQSEC1 0.027 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.045 0.19 -10000 0 -0.5 76 76
ARRB2 -0.037 0.13 -10000 0 -0.38 61 61
mol:GTP 0.024 0.037 0.17 20 -10000 0 20
ARRB1 0.025 0.032 -10000 0 -0.67 1 1
FBXO8 0.027 0.004 -10000 0 -10000 0 0
TSHR 0.024 0.044 -10000 0 -0.67 2 2
EGF -0.076 0.24 -10000 0 -0.66 72 72
somatostatin receptor activity 0 0.001 0.002 14 -0.001 141 155
ARAP2 0.025 0.036 -10000 0 -0.51 2 2
mol:GDP -0.11 0.14 0.27 5 -0.3 120 125
mol:PI-3-4-5-P3 0 0 0.002 11 -0.001 77 88
ITGA2B -0.043 0.21 -10000 0 -0.66 49 49
ARF6 0.027 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.061 0.024 -10000 0 -10000 0 0
ADAP1 0.026 0.006 -10000 0 -10000 0 0
KIF13B 0.027 0.005 -10000 0 -10000 0 0
HGF/MET -0.075 0.19 -10000 0 -0.52 69 69
PXN 0.027 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.11 0.16 0.51 8 -0.29 150 158
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.022 0.18 -10000 0 -0.43 76 76
ADRB2 0.011 0.1 -10000 0 -0.67 11 11
receptor agonist activity 0 0 0.001 18 0 145 163
actin filament binding 0 0 0.002 15 -0.001 139 154
SRC 0.026 0.008 -10000 0 -10000 0 0
ITGB3 0.011 0.099 -10000 0 -0.64 11 11
GNAQ 0.025 0.008 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.005 16 -0.001 68 84
ARF6/GDP -0.007 0.091 0.24 2 -0.45 9 11
ARF6/GDP/GULP/ACAP1 -0.14 0.18 -10000 0 -0.4 119 119
alphaIIb/beta3 Integrin/paxillin/GIT1 0.01 0.16 -10000 0 -0.42 56 56
ACAP1 0.018 0.045 -10000 0 -0.51 2 2
ACAP2 0.027 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.051 0.19 -10000 0 -0.56 61 61
EFNA1 0.025 0.007 -10000 0 -10000 0 0
HGF -0.072 0.24 -10000 0 -0.67 69 69
CYTH3 0.006 0.033 -10000 0 -0.5 2 2
CYTH2 -0.009 0.15 -10000 0 -0.94 13 13
NCK1 0.027 0.003 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 22 0 96 118
endosomal lumen acidification 0 0 0.002 6 -0.001 145 151
microtubule-based process 0 0 -10000 0 0 7 7
GULP1 -0.091 0.26 -10000 0 -0.65 86 86
GNAQ/ARNO 0.005 0.14 -10000 0 -0.86 13 13
mol:Phosphatidic acid 0 0 0.001 13 -10000 0 13
PIP3-E 0 0 0.001 9 0 14 23
MET -0.027 0.069 -10000 0 -10000 0 0
GNA14 -0.13 0.28 -10000 0 -0.63 118 118
GNA15 0.014 0.048 -10000 0 -0.67 1 1
GIT1 0.026 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 0.003 15 -0.001 107 122
GNA11 0.014 0.084 -10000 0 -0.63 8 8
LHCGR -0.076 0.22 -10000 0 -0.67 61 61
AGTR1 -0.26 0.34 -10000 0 -0.67 199 199
desensitization of G-protein coupled receptor protein signaling pathway -0.051 0.19 -10000 0 -0.56 61 61
IPCEF1/ARNO -0.035 0.18 -10000 0 -0.75 13 13
alphaIIb/beta3 Integrin -0.026 0.18 -10000 0 -0.52 56 56
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.083 0.32 -10000 0 -1.1 39 39
MKNK1 0.027 0.005 -10000 0 -10000 0 0
MAPK14 -0.016 0.11 -10000 0 -0.35 33 33
ATF2/c-Jun -0.2 0.35 -10000 0 -0.8 119 119
MAPK11 -0.011 0.095 -10000 0 -0.35 27 27
MITF -0.022 0.12 -10000 0 -0.42 36 36
MAPKAPK5 -0.017 0.11 -10000 0 -0.41 31 31
KRT8 -0.017 0.11 -10000 0 -0.41 31 31
MAPKAPK3 0.027 0.003 -10000 0 -10000 0 0
MAPKAPK2 0.025 0.007 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.024 0.15 -10000 0 -0.51 32 32
CEBPB -0.02 0.12 -10000 0 -0.41 34 34
SLC9A1 -0.022 0.12 -10000 0 -0.41 36 36
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.075 0.19 -10000 0 -0.44 77 77
p38alpha-beta/MNK1 -0.009 0.13 -10000 0 -0.42 30 30
JUN -0.2 0.35 -10000 0 -0.79 119 119
PPARGC1A -0.22 0.25 -10000 0 -0.45 250 250
USF1 -0.022 0.12 -10000 0 -0.41 36 36
RAB5/GDP/GDI1 -0.035 0.1 -10000 0 -0.32 34 34
NOS2 -0.027 0.12 -10000 0 -0.53 6 6
DDIT3 -0.018 0.11 -10000 0 -0.41 31 31
RAB5A 0.027 0.004 -10000 0 -10000 0 0
HSPB1 -0.015 0.092 0.38 2 -0.38 15 17
p38alpha-beta/HBP1 -0.005 0.12 -10000 0 -0.41 26 26
CREB1 -0.054 0.16 -10000 0 -0.48 40 40
RAB5/GDP 0.02 0.003 -10000 0 -10000 0 0
EIF4E -0.024 0.1 -10000 0 -0.43 13 13
RPS6KA4 -0.02 0.12 -10000 0 -0.42 34 34
PLA2G4A -0.05 0.16 -10000 0 -0.5 41 41
GDI1 -0.017 0.11 -10000 0 -0.43 30 30
TP53 -0.03 0.13 -10000 0 -0.51 28 28
RPS6KA5 -0.061 0.18 -10000 0 -0.45 76 76
ESR1 -0.05 0.19 -10000 0 -0.56 48 48
HBP1 0.026 0.006 -10000 0 -10000 0 0
MEF2C -0.018 0.11 -10000 0 -0.41 32 32
MEF2A -0.024 0.12 -10000 0 -0.42 38 38
EIF4EBP1 -0.054 0.15 -10000 0 -0.46 41 41
KRT19 -0.05 0.16 -10000 0 -0.49 43 43
ELK4 -0.022 0.12 -10000 0 -0.41 36 36
ATF6 -0.022 0.12 -10000 0 -0.41 36 36
ATF1 -0.052 0.15 -10000 0 -0.47 38 38
p38alpha-beta/MAPKAPK2 -0.01 0.13 -10000 0 -0.41 31 31
p38alpha-beta/MAPKAPK3 -0.009 0.13 -10000 0 -0.41 32 32
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.006 0.05 -10000 0 -10000 0 0
GNB1/GNG2 -0.032 0.066 -10000 0 -0.19 67 67
AKT1 0.013 0.13 0.41 22 -0.22 8 30
EGF -0.076 0.24 -10000 0 -0.66 72 72
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.019 0.084 0.36 13 -0.49 2 15
mol:Ca2+ -0.014 0.15 0.38 18 -0.3 69 87
LYN 0.019 0.083 0.36 12 -0.49 2 14
RhoA/GTP -0.008 0.054 -10000 0 -0.14 32 32
mol:PGI2 0 0.001 -10000 0 -10000 0 0
SYK -0.015 0.17 0.43 18 -0.34 67 85
GNG2 0.025 0.032 -10000 0 -0.67 1 1
ARRB2 0.026 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.032 0.12 0.27 1 -0.59 12 13
G beta5/gamma2 -0.041 0.089 -10000 0 -0.25 67 67
PRKCH -0.021 0.17 0.45 14 -0.36 68 82
DNM1 0.005 0.12 -10000 0 -0.61 16 16
TXA2/TP beta/beta Arrestin3 -0.009 0.12 -10000 0 -0.42 34 34
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.002 0.14 -10000 0 -0.67 20 20
G12 family/GTP -0.032 0.12 -10000 0 -0.31 65 65
ADRBK1 0.027 0.005 -10000 0 -10000 0 0
ADRBK2 0.02 0.012 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.036 0.007 -10000 0 -10000 0 0
mol:GDP 0.047 0.14 0.39 38 -0.35 7 45
mol:NADP 0.026 0.006 -10000 0 -10000 0 0
RAB11A 0.027 0.004 -10000 0 -10000 0 0
PRKG1 -0.16 0.31 -10000 0 -0.66 136 136
mol:IP3 -0.024 0.18 0.44 14 -0.38 69 83
cell morphogenesis 0.035 0.007 -10000 0 -10000 0 0
PLCB2 -0.046 0.22 0.46 11 -0.52 69 80
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.075 0.17 0.36 9 -0.32 137 146
mol:PDG2 0 0.001 -10000 0 -10000 0 0
HCK 0.014 0.078 0.34 10 -0.49 2 12
RHOA 0.027 0.003 -10000 0 -10000 0 0
PTGIR 0.02 0.063 -10000 0 -0.67 4 4
PRKCB1 -0.025 0.17 0.43 13 -0.38 70 83
GNAQ 0.025 0.008 -10000 0 -10000 0 0
mol:L-citrulline 0.026 0.006 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.042 0.23 0.49 14 -0.53 69 83
LCK 0.015 0.096 0.36 13 -0.53 5 18
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.026 0.08 -10000 0 -0.32 18 18
TXA2-R family/G12 family/GDP/G beta/gamma 0.031 0.033 -10000 0 -0.34 2 2
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.031 0.08 -10000 0 -0.31 18 18
MAPK14 -0.003 0.12 0.35 21 -0.23 64 85
TGM2/GTP -0.041 0.18 0.34 5 -0.42 69 74
MAPK11 -0.007 0.13 0.36 21 -0.23 59 80
ARHGEF1 -0.014 0.073 0.17 1 -0.18 61 62
GNAI2 0.027 0.003 -10000 0 -10000 0 0
JNK cascade -0.022 0.18 0.44 18 -0.39 69 87
RAB11/GDP 0.027 0.006 -10000 0 -10000 0 0
ICAM1 -0.012 0.14 0.37 19 -0.29 69 88
cAMP biosynthetic process -0.026 0.17 0.43 15 -0.35 69 84
Gq family/GTP/EBP50 -0.046 0.12 0.24 2 -0.33 27 29
actin cytoskeleton reorganization 0.035 0.007 -10000 0 -10000 0 0
SRC 0.016 0.078 0.34 10 -0.49 2 12
GNB5 0.027 0.004 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
EGF/EGFR -0.02 0.13 0.43 16 -0.29 15 31
VCAM1 -0.01 0.15 0.37 18 -0.3 69 87
TP beta/Gq family/GDP/G beta5/gamma2 -0.032 0.12 0.27 1 -0.59 12 13
platelet activation -0.002 0.17 0.45 23 -0.3 67 90
PGI2/IP 0.015 0.047 -10000 0 -0.5 4 4
PRKACA 0.004 0.078 -10000 0 -0.35 21 21
Gq family/GDP/G beta5/gamma2 -0.032 0.12 0.28 1 -0.56 12 13
TXA2/TP beta/beta Arrestin2 0.006 0.1 -10000 0 -0.53 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.001 0.079 -10000 0 -0.35 19 19
mol:DAG -0.03 0.19 0.46 13 -0.43 69 82
EGFR 0.019 0.07 -10000 0 -0.67 5 5
TXA2/TP alpha -0.041 0.22 0.51 13 -0.48 69 82
Gq family/GTP -0.065 0.13 0.22 2 -0.28 121 123
YES1 0.021 0.087 0.37 14 -0.49 2 16
GNAI2/GTP 0.008 0.069 -10000 0 -0.35 7 7
PGD2/DP -0.002 0.1 -10000 0 -0.5 20 20
SLC9A3R1 0.026 0.007 -10000 0 -10000 0 0
FYN 0.022 0.088 0.36 16 -0.49 2 18
mol:NO 0.026 0.006 -10000 0 -10000 0 0
GNA15 0.014 0.048 -10000 0 -0.67 1 1
PGK/cGMP -0.092 0.21 -10000 0 -0.43 135 135
RhoA/GDP 0.027 0.004 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.04 0.091 -10000 0 -0.34 18 18
NOS3 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA -0.025 0.18 0.44 16 -0.38 70 86
PRKCB -0.023 0.17 0.43 17 -0.37 68 85
PRKCE -0.028 0.16 0.38 11 -0.37 70 81
PRKCD -0.025 0.17 0.44 12 -0.38 69 81
PRKCG -0.025 0.18 0.41 17 -0.39 66 83
muscle contraction -0.035 0.22 0.51 14 -0.49 68 82
PRKCZ -0.015 0.17 0.43 18 -0.34 68 86
ARR3 -0.002 0.02 -10000 0 -10000 0 0
TXA2/TP beta 0.016 0.08 -10000 0 -0.31 20 20
PRKCQ -0.025 0.17 0.42 13 -0.36 70 83
MAPKKK cascade -0.034 0.2 0.47 15 -0.46 69 84
SELE -0.027 0.18 0.37 18 -0.42 69 87
TP beta/GNAI2/GDP/G beta/gamma 0.039 0.089 -10000 0 -0.79 2 2
ROCK1 0.027 0.005 -10000 0 -10000 0 0
GNA14 -0.13 0.28 -10000 0 -0.63 118 118
chemotaxis -0.049 0.26 0.52 14 -0.61 69 83
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
GNA11 0.015 0.084 -10000 0 -0.63 8 8
Rac1/GTP 0.019 0.005 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.046 0.042 -10000 0 -0.81 1 1
forebrain development -0.29 0.28 0.37 3 -0.53 247 250
GNAO1 0.002 0.12 -10000 0 -0.67 15 15
SMO/beta Arrestin2 0.014 0.036 -10000 0 -0.5 1 1
SMO 0.015 0.034 -10000 0 -0.67 1 1
ARRB2 0.021 0.008 -10000 0 -10000 0 0
GLI3/SPOP 0.035 0.075 -10000 0 -0.34 5 5
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
GSK3B 0.027 0.003 -10000 0 -10000 0 0
GNAI2 0.025 0.005 -10000 0 -10000 0 0
SIN3/HDAC complex 0.064 0.033 -10000 0 -0.4 1 1
GNAI1 0.023 0.032 -10000 0 -0.68 1 1
XPO1 0.016 0.019 -10000 0 -10000 0 0
GLI1/Su(fu) -0.21 0.21 -10000 0 -0.49 134 134
SAP30 0.026 0.032 -10000 0 -0.67 1 1
mol:GDP 0.015 0.034 -10000 0 -0.67 1 1
MIM/GLI2A -0.031 0.067 -10000 0 -10000 0 0
IFT88 0.026 0.007 -10000 0 -10000 0 0
GNAI3 0.025 0.006 -10000 0 -10000 0 0
GLI2 0 0.079 0.28 2 -0.38 7 9
GLI3 0.026 0.078 0.28 3 -0.36 5 8
CSNK1D 0.026 0.007 -10000 0 -10000 0 0
CSNK1E 0.02 0.012 -10000 0 -10000 0 0
SAP18 0.026 0.007 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.026 0.007 -10000 0 -10000 0 0
GNG2 0.025 0.032 -10000 0 -0.67 1 1
Gi family/GTP -0.017 0.069 -10000 0 -0.3 17 17
SIN3B 0.026 0.008 -10000 0 -10000 0 0
SIN3A 0.028 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.036 0.067 -10000 0 -0.48 2 2
GLI2/Su(fu) 0.009 0.076 -10000 0 -0.49 3 3
FOXA2 -0.58 0.61 -10000 0 -1.2 240 240
neural tube patterning -0.29 0.28 0.37 3 -0.53 247 250
SPOP 0.026 0.007 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.034 0.03 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
CSNK1G2 0.025 0.008 -10000 0 -10000 0 0
CSNK1G3 0.026 0.006 -10000 0 -10000 0 0
MTSS1 -0.031 0.067 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.29 0.28 0.37 3 -0.53 247 250
SUFU 0.018 0.016 -10000 0 -0.23 1 1
LGALS3 -0.02 0.073 -10000 0 -0.67 1 1
catabolic process 0.031 0.1 0.29 1 -0.44 8 9
GLI3A/CBP -0.17 0.2 -10000 0 -0.38 241 241
KIF3A 0.026 0.006 -10000 0 -10000 0 0
GLI1 -0.3 0.28 0.37 3 -0.54 246 249
RAB23 0.022 0.062 -10000 0 -0.67 4 4
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
IFT172 0.027 0.005 -10000 0 -10000 0 0
RBBP7 0.026 0.008 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.021 0.051 -10000 0 -0.32 2 2
GNAZ 0.018 0.012 -10000 0 -10000 0 0
RBBP4 0.024 0.044 -10000 0 -0.67 2 2
CSNK1G1 0.027 0.004 -10000 0 -10000 0 0
PIAS1 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
GLI2/SPOP 0.01 0.081 -10000 0 -0.35 8 8
STK36 0.016 0.019 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.01 0.054 -10000 0 -0.31 6 6
PTCH1 -0.26 0.26 0.58 2 -0.59 138 140
MIM/GLI1 -0.42 0.37 0.35 1 -0.69 275 276
CREBBP -0.17 0.2 -10000 0 -0.38 241 241
Su(fu)/SIN3/HDAC complex 0.035 0.069 -10000 0 -0.53 5 5
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.028 0.14 -10000 0 -0.34 55 55
TBX21 -0.12 0.43 -10000 0 -1.2 58 58
B2M 0.023 0.018 -10000 0 -10000 0 0
TYK2 0.019 0.03 -10000 0 -10000 0 0
IL12RB1 0.001 0.087 -10000 0 -0.64 6 6
GADD45B -0.097 0.39 -10000 0 -1 60 60
IL12RB2 -0.003 0.13 -10000 0 -0.65 17 17
GADD45G -0.092 0.36 -10000 0 -0.95 53 53
natural killer cell activation 0.001 0.02 -10000 0 -10000 0 0
RELB 0.026 0.007 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
IL18 -0.002 0.11 -10000 0 -0.65 11 11
IL2RA -0.017 0.16 -10000 0 -0.63 28 28
IFNG -0.07 0.22 -10000 0 -0.67 60 60
STAT3 (dimer) -0.082 0.32 -10000 0 -0.78 64 64
HLA-DRB5 -0.008 0.08 -10000 0 -0.67 4 4
FASLG -0.14 0.46 -10000 0 -1.2 64 64
NF kappa B2 p52/RelB -0.1 0.39 -10000 0 -0.97 62 62
CD4 0.011 0.035 -10000 0 -10000 0 0
SOCS1 0.023 0.035 -10000 0 -0.67 1 1
EntrezGene:6955 -0.007 0.015 -10000 0 -10000 0 0
CD3D -0.063 0.2 -10000 0 -0.63 53 53
CD3E -0.043 0.18 -10000 0 -0.62 42 42
CD3G -0.11 0.26 -10000 0 -0.65 89 89
IL12Rbeta2/JAK2 0.011 0.11 -10000 0 -0.47 19 19
CCL3 -0.12 0.42 -10000 0 -1.2 51 51
CCL4 -0.15 0.49 -10000 0 -1.4 58 58
HLA-A 0.023 0.019 -10000 0 -10000 0 0
IL18/IL18R 0.028 0.16 -10000 0 -0.48 36 36
NOS2 -0.088 0.36 -10000 0 -1 47 47
IL12/IL12R/TYK2/JAK2/SPHK2 -0.029 0.14 -10000 0 -0.35 50 50
IL1R1 -0.1 0.38 -10000 0 -1 57 57
IL4 0.001 0.034 -10000 0 -10000 0 0
JAK2 0.017 0.039 -10000 0 -0.37 2 2
EntrezGene:6957 -0.006 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.21 0.49 -10000 0 -1.1 97 97
RAB7A -0.058 0.3 -10000 0 -0.76 53 53
lysosomal transport -0.052 0.29 -10000 0 -0.7 55 55
FOS -0.36 0.61 -10000 0 -1.2 156 156
STAT4 (dimer) -0.086 0.36 -10000 0 -0.84 70 70
STAT5A (dimer) -0.14 0.41 -10000 0 -0.95 77 77
GZMA -0.12 0.4 -10000 0 -1.1 53 53
GZMB -0.12 0.39 -10000 0 -1.1 50 50
HLX 0.022 0.023 -10000 0 -10000 0 0
LCK -0.13 0.43 -10000 0 -1.1 64 64
TCR/CD3/MHC II/CD4 -0.14 0.29 -10000 0 -0.67 84 84
IL2/IL2R -0.007 0.17 -10000 0 -0.54 37 37
MAPK14 -0.085 0.37 0.46 1 -0.89 67 68
CCR5 -0.096 0.4 -10000 0 -1.1 53 53
IL1B -0.027 0.18 -10000 0 -0.7 33 33
STAT6 -0.007 0.11 -10000 0 -0.46 5 5
STAT4 0.004 0.098 -10000 0 -0.58 11 11
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT1 0.023 0.023 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
NFKB2 0.027 0.004 -10000 0 -10000 0 0
IL12B 0.005 0.084 -10000 0 -0.68 6 6
CD8A -0.028 0.18 -10000 0 -0.65 38 38
CD8B -0.055 0.21 -10000 0 -0.64 55 55
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.028 0.14 0.34 57 -10000 0 57
IL2RB 0.004 0.089 -10000 0 -0.57 10 10
proteasomal ubiquitin-dependent protein catabolic process -0.072 0.33 -10000 0 -0.75 70 70
IL2RG -0.012 0.14 -10000 0 -0.62 21 21
IL12 -0.034 0.18 -10000 0 -0.52 56 56
STAT5A 0.026 0.007 -10000 0 -10000 0 0
CD247 -0.015 0.13 -10000 0 -0.67 18 18
IL2 -0.003 0.02 -10000 0 -10000 0 0
SPHK2 0.025 0.007 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.052 0.21 -10000 0 -0.67 51 51
IL12/IL12R/TYK2/JAK2 -0.14 0.51 -10000 0 -1.2 65 65
MAP2K3 -0.085 0.37 -10000 0 -0.89 65 65
RIPK2 0.027 0.005 -10000 0 -10000 0 0
MAP2K6 -0.093 0.38 -10000 0 -0.9 68 68
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.008 0.096 -10000 0 -0.67 8 8
IL18RAP -0.005 0.14 -10000 0 -0.67 22 22
IL12Rbeta1/TYK2 0.021 0.075 -10000 0 -0.49 6 6
EOMES -0.13 0.4 -10000 0 -1.3 49 49
STAT1 (dimer) -0.12 0.36 -10000 0 -0.79 87 87
T cell proliferation -0.052 0.27 -10000 0 -0.62 65 65
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.005 0.095 -10000 0 -0.57 10 10
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.066 0.28 -10000 0 -0.65 74 74
ATF2 -0.089 0.34 0.44 1 -0.79 70 71
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.1 0.22 -10000 0 -0.42 131 131
MAP3K8 0.015 0.078 -10000 0 -0.62 7 7
FOS -0.075 0.17 0.29 3 -0.44 59 62
PRKCA -0.008 0.13 -10000 0 -0.67 17 17
PTPN7 -0.023 0.13 -10000 0 -0.67 18 18
HRAS 0.025 0.011 -10000 0 -10000 0 0
PRKCB -0.003 0.08 -10000 0 -0.67 5 5
NRAS 0.026 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.035 0.031 -10000 0 -10000 0 0
MAPK3 -0.013 0.12 -10000 0 -0.46 22 22
MAP2K1 -0.016 0.13 -10000 0 -0.54 21 21
ELK1 0.012 0.025 -10000 0 -10000 0 0
BRAF -0.011 0.11 -10000 0 -0.52 21 21
mol:GTP -0.002 0.004 -10000 0 -0.006 127 127
MAPK1 -0.099 0.2 -10000 0 -0.41 119 119
RAF1 -0.011 0.11 -10000 0 -0.52 21 21
KRAS 0.026 0.005 -10000 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.005 0.19 0.57 7 -0.58 19 26
CRP 0.008 0.2 0.56 11 -0.58 22 33
cell cycle arrest -0.009 0.2 0.49 6 -0.64 26 32
TIMP1 -0.032 0.22 0.56 4 -0.62 35 39
IL6ST -0.065 0.24 -10000 0 -0.67 66 66
Rac1/GDP -0.041 0.2 0.31 1 -0.53 45 46
AP1 -0.11 0.27 -10000 0 -0.6 88 88
GAB2 0.027 0.005 -10000 0 -10000 0 0
TNFSF11 -0.005 0.19 0.59 5 -0.56 24 29
HSP90B1 0.043 0.052 -10000 0 -0.64 1 1
GAB1 0.027 0.004 -10000 0 -10000 0 0
MAPK14 -0.083 0.24 -10000 0 -0.69 48 48
AKT1 0.04 0.06 -10000 0 -0.97 1 1
FOXO1 0.039 0.058 -10000 0 -0.91 1 1
MAP2K6 -0.074 0.23 0.24 1 -0.59 54 55
mol:GTP 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.028 0.19 0.33 6 -0.52 39 45
MITF -0.063 0.21 -10000 0 -0.57 45 45
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.025 0.008 -10000 0 -10000 0 0
A2M 0.026 0.071 -10000 0 -1.1 2 2
CEBPB 0.033 0.006 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.009 0.093 -10000 0 -0.49 6 6
STAT3 -0.019 0.21 0.51 4 -0.68 26 30
STAT1 0.01 0.098 -10000 0 -0.92 5 5
CEBPD 0.003 0.19 0.56 4 -0.59 19 23
PIK3CA 0.024 0.054 -10000 0 -0.67 3 3
PI3K 0.038 0.043 -10000 0 -0.5 3 3
JUN -0.12 0.28 -10000 0 -0.66 106 106
PIAS3/MITF -0.047 0.2 0.27 1 -0.56 41 42
MAPK11 -0.084 0.23 -10000 0 -0.71 43 43
STAT3 (dimer)/FOXO1 0.019 0.16 0.38 1 -0.52 18 19
GRB2/SOS1/GAB family -0.025 0.2 -10000 0 -0.61 26 26
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.067 0.21 -10000 0 -0.37 127 127
GRB2 0.026 0.007 -10000 0 -10000 0 0
JAK2 0.024 0.025 -10000 0 -0.35 2 2
LBP 0.01 0.18 0.59 8 -0.55 7 15
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
JAK1 0.027 0.013 -10000 0 -10000 0 0
MYC -0.009 0.24 0.63 3 -0.87 20 23
FGG -0.004 0.19 0.68 3 -0.6 18 21
macrophage differentiation -0.009 0.2 0.49 6 -0.64 26 32
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.064 0.25 -10000 0 -0.45 127 127
JUNB 0 0.2 0.56 4 -0.66 22 26
FOS -0.15 0.3 -10000 0 -0.66 124 124
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.061 0.22 -10000 0 -0.43 91 91
STAT1/PIAS1 -0.033 0.2 -10000 0 -0.51 45 45
GRB2/SOS1/GAB family/SHP2/PI3K 0.038 0.063 -10000 0 -0.68 2 2
STAT3 (dimer) -0.012 0.21 0.5 5 -0.66 26 31
PRKCD -0.015 0.19 0.4 7 -0.55 30 37
IL6R 0.003 0.12 -10000 0 -0.67 16 16
SOCS3 -0.096 0.31 0.43 2 -1 39 41
gp130 (dimer)/JAK1/JAK1/LMO4 -0.006 0.17 -10000 0 -0.43 64 64
Rac1/GTP -0.038 0.2 -10000 0 -0.54 43 43
HCK 0.017 0.037 -10000 0 -10000 0 0
MAPKKK cascade 0.026 0.1 -10000 0 -0.61 5 5
bone resorption -0.004 0.18 0.59 5 -0.53 26 31
IRF1 0.006 0.19 0.62 7 -0.6 15 22
mol:GDP -0.059 0.2 0.24 1 -0.54 49 50
SOS1 0.027 0.005 -10000 0 -10000 0 0
VAV1 -0.059 0.2 0.25 1 -0.55 48 49
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.079 0.24 -10000 0 -0.7 48 48
PTPN11 0.014 0.074 -10000 0 -0.87 3 3
IL6/IL6RA -0.067 0.22 -10000 0 -0.52 91 91
gp130 (dimer)/TYK2/TYK2/LMO4 -0.009 0.16 -10000 0 -0.41 66 66
gp130 (dimer)/JAK2/JAK2/LMO4 -0.012 0.17 -10000 0 -0.43 64 64
IL6 -0.093 0.26 -10000 0 -0.67 80 80
PIAS3 0.026 0.007 -10000 0 -10000 0 0
PTPRE -0.023 0.074 -10000 0 -0.67 1 1
PIAS1 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.027 0.006 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.068 0.21 -10000 0 -0.38 124 124
LMO4 0.028 0.016 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.015 0.2 -10000 0 -0.68 25 25
MCL1 0.054 0.072 -10000 0 -0.82 1 1
EGFR-dependent Endothelin 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
HRAS 0.026 0.011 -9999 0 -10000 0 0
EGFR 0.019 0.07 -9999 0 -0.67 5 5
EGF/EGFR -0.017 0.15 -9999 0 -0.36 78 78
EGF/EGFR dimer/SHC/GRB2/SOS1 0.003 0.16 -9999 0 -0.38 70 70
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.024 0.034 -9999 0 -0.67 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.076 0.24 -9999 0 -0.66 72 72
EGF/EGFR dimer/SHC -0.025 0.17 -9999 0 -0.43 76 76
mol:GDP -0.002 0.16 -9999 0 -0.37 70 70
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.019 0.071 -9999 0 -0.67 5 5
GRB2/SOS1 0.038 0.011 -9999 0 -10000 0 0
HRAS/GTP -0.014 0.14 -9999 0 -0.35 70 70
SHC1 0.025 0.007 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.15 -9999 0 -0.36 70 70
FRAP1 -0.052 0.13 -9999 0 -0.36 70 70
EGF/EGFR dimer -0.045 0.19 -9999 0 -0.5 76 76
SOS1 0.027 0.005 -9999 0 -10000 0 0
GRB2 0.026 0.007 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.032 0.061 -9999 0 -0.5 6 6
Syndecan-1-mediated signaling events

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
TGFB1 0.024 0.016 -10000 0 -10000 0 0
CCL5 -0.018 0.16 -10000 0 -0.67 29 29
SDCBP 0.027 0.005 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.036 0.13 -10000 0 -0.37 52 52
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.03 0.14 -10000 0 -0.4 44 44
Syndecan-1/Syntenin -0.029 0.14 0.25 2 -0.43 37 39
MAPK3 -0.029 0.12 -10000 0 -0.49 21 21
HGF/MET -0.075 0.19 -10000 0 -0.52 69 69
TGFB1/TGF beta receptor Type II 0.024 0.016 -10000 0 -10000 0 0
BSG 0.025 0.008 -10000 0 -10000 0 0
keratinocyte migration -0.03 0.14 -10000 0 -0.4 44 44
Syndecan-1/RANTES -0.049 0.19 -10000 0 -0.49 59 59
Syndecan-1/CD147 -0.014 0.14 -10000 0 -0.46 28 28
Syndecan-1/Syntenin/PIP2 -0.029 0.13 0.23 1 -0.42 37 38
LAMA5 0.027 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.028 0.13 0.23 1 -0.41 37 38
MMP7 -0.074 0.15 -10000 0 -0.66 25 25
HGF -0.072 0.24 -10000 0 -0.67 69 69
Syndecan-1/CASK -0.043 0.13 -10000 0 -0.37 56 56
Syndecan-1/HGF/MET -0.071 0.2 -10000 0 -0.48 78 78
regulation of cell adhesion -0.031 0.11 -10000 0 -0.48 20 20
HPSE 0.01 0.093 -10000 0 -0.63 9 9
positive regulation of cell migration -0.036 0.13 -10000 0 -0.37 52 52
SDC1 -0.035 0.13 -10000 0 -0.37 52 52
Syndecan-1/Collagen -0.036 0.13 -10000 0 -0.37 52 52
PPIB 0.027 0.004 -10000 0 -10000 0 0
MET -0.027 0.069 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
MMP9 -0.041 0.19 -10000 0 -0.67 41 41
MAPK1 -0.03 0.12 -10000 0 -0.49 22 22
homophilic cell adhesion -0.035 0.13 0.21 1 -0.39 47 48
MMP1 -0.041 0.071 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.04 0.1 -10000 0 -0.41 22 22
ER alpha/Gai/GDP/Gbeta gamma -0.005 0.14 -10000 0 -0.53 23 23
AKT1 -0.014 0.2 -10000 0 -0.78 29 29
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.01 0.2 -10000 0 -0.78 29 29
mol:Ca2+ -0.097 0.19 -10000 0 -0.42 119 119
IGF1R 0.027 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.02 0.15 -10000 0 -0.44 51 51
SHC1 0.025 0.007 -10000 0 -10000 0 0
apoptosis 0.012 0.19 0.74 29 -10000 0 29
RhoA/GTP 0.006 0.071 -10000 0 -0.34 17 17
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.005 0.13 -10000 0 -0.54 20 20
regulation of stress fiber formation 0.01 0.087 0.29 34 -0.28 1 35
E2/ERA-ERB (dimer) 0.007 0.1 -10000 0 -0.43 24 24
KRAS 0.027 0.005 -10000 0 -10000 0 0
G13/GTP 0.01 0.084 -10000 0 -0.36 22 22
pseudopodium formation -0.01 0.087 0.28 1 -0.29 34 35
E2/ER alpha (dimer)/PELP1 0.009 0.093 -10000 0 -0.4 22 22
GRB2 0.026 0.007 -10000 0 -10000 0 0
GNG2 0.025 0.032 -10000 0 -0.67 1 1
GNAO1 0.004 0.12 -10000 0 -0.67 15 15
HRAS 0.026 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.009 0.15 0.47 7 -0.58 23 30
E2/ER beta (dimer) 0.017 0.041 -10000 0 -0.5 3 3
mol:GDP 0.002 0.11 -10000 0 -0.46 23 23
mol:NADP 0.009 0.15 0.47 7 -0.58 23 30
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.1 0.2 -10000 0 -0.44 119 119
IGF-1R heterotetramer 0.027 0.004 -10000 0 -10000 0 0
PLCB1 -0.1 0.2 -10000 0 -0.45 120 120
PLCB2 -0.1 0.21 -10000 0 -0.45 120 120
IGF1 -0.13 0.28 -10000 0 -0.66 107 107
mol:L-citrulline 0.009 0.15 0.47 7 -0.58 23 30
RHOA 0.027 0.003 -10000 0 -10000 0 0
Gai/GDP 0.004 0.14 -10000 0 -0.67 20 20
JNK cascade 0.017 0.041 -10000 0 -0.5 3 3
BCAR1 0.026 0.006 -10000 0 -10000 0 0
ESR2 0.022 0.054 -10000 0 -0.67 3 3
GNAQ 0.025 0.008 -10000 0 -10000 0 0
ESR1 -0.013 0.14 -10000 0 -0.64 23 23
Gq family/GDP/Gbeta gamma -0.058 0.19 -10000 0 -0.66 27 27
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.019 0.098 -10000 0 -0.6 6 6
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.003 0.13 -10000 0 -0.54 20 20
GNAZ 0.02 0.012 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.009 0.11 -10000 0 -0.48 23 23
STRN -0.016 0.17 -10000 0 -0.66 31 31
GNAL -0.061 0.23 -10000 0 -0.65 64 64
PELP1 0.026 0.007 -10000 0 -10000 0 0
MAPK11 0.01 0.035 -10000 0 -0.43 3 3
GNAI2 0.027 0.003 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.032 -10000 0 -0.67 1 1
HBEGF -0.019 0.14 0.37 3 -0.5 26 29
cAMP biosynthetic process -0.04 0.15 -10000 0 -0.38 79 79
SRC -0.004 0.13 -10000 0 -0.49 23 23
PI3K 0.036 0.043 -10000 0 -0.5 3 3
GNB1 0.026 0.006 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.031 0.11 -10000 0 -0.42 23 23
SOS1 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.069 0.16 -10000 0 -0.42 51 51
Gs family/GTP -0.03 0.16 -10000 0 -0.38 79 79
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.049 0.015 -10000 0 -10000 0 0
vasodilation 0.01 0.15 0.46 7 -0.55 23 30
mol:DAG -0.1 0.2 -10000 0 -0.44 119 119
Gs family/GDP/Gbeta gamma -0.027 0.14 -10000 0 -0.35 72 72
MSN -0.011 0.093 0.29 1 -0.31 34 35
Gq family/GTP -0.1 0.22 -10000 0 -0.47 121 121
mol:PI-3-4-5-P3 -0.008 0.19 -10000 0 -0.75 29 29
NRAS 0.027 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.01 0.15 0.55 23 -0.46 7 30
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.11 -10000 0 -0.44 23 23
NOS3 0.003 0.15 0.41 3 -0.61 23 26
GNA11 0.015 0.084 -10000 0 -0.63 8 8
MAPKKK cascade -0.016 0.18 0.37 1 -0.58 32 33
E2/ER alpha (dimer)/PELP1/Src 0 0.14 -10000 0 -0.57 20 20
ruffle organization -0.01 0.087 0.28 1 -0.29 34 35
ROCK2 -0.004 0.11 0.36 5 -0.34 35 40
GNA14 -0.13 0.28 -10000 0 -0.63 118 118
GNA15 0.014 0.048 -10000 0 -0.67 1 1
GNA13 0.026 0.007 -10000 0 -10000 0 0
MMP9 -0.033 0.16 -10000 0 -0.53 31 31
MMP2 -0.004 0.13 0.34 1 -0.48 24 25
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.035 0.01 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.027 0.003 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.011 0.098 -10000 0 -0.67 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.026 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.12 0.13 -10000 0 -0.25 252 252
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.027 0.005 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.026 0.007 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
MAP3K12 0.027 0.005 -10000 0 -10000 0 0
FGR 0.025 0.014 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.043 0.068 -10000 0 -0.28 10 10
PRKG1 -0.16 0.31 -10000 0 -0.66 136 136
DUSP8 0.019 0.064 -10000 0 -0.67 4 4
PGK/cGMP/p38 alpha -0.11 0.18 -10000 0 -0.36 132 132
apoptosis -0.042 0.065 -10000 0 -0.27 10 10
RAL/GTP 0.035 0.008 -10000 0 -10000 0 0
LYN 0.027 0.005 -10000 0 -10000 0 0
DUSP1 -0.084 0.25 -10000 0 -0.67 78 78
PAK1 0.027 0.005 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.065 0.02 -10000 0 -10000 0 0
TRAF6 0.024 0.044 -10000 0 -0.67 2 2
RAC1 0.026 0.006 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.026 0.011 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.035 0.01 -10000 0 -10000 0 0
MAPK11 -0.052 0.16 0.41 19 -0.32 33 52
BLK -0.19 0.31 -10000 0 -0.66 145 145
HCK 0.017 0.037 -10000 0 -10000 0 0
MAP2K3 0.026 0.007 -10000 0 -10000 0 0
DUSP16 0.027 0.005 -10000 0 -10000 0 0
DUSP10 0.023 0.033 -10000 0 -0.67 1 1
TRAF6/MEKK3 0.031 0.029 -10000 0 -0.4 2 2
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.01 0.12 0.35 19 -0.3 10 29
positive regulation of innate immune response -0.042 0.17 0.46 19 -0.4 14 33
LCK 0.012 0.081 -10000 0 -0.67 6 6
p38alpha-beta/MKP7 -0.044 0.14 0.34 9 -0.46 7 16
p38alpha-beta/MKP5 -0.036 0.15 0.43 14 -0.43 8 22
PGK/cGMP -0.12 0.23 -10000 0 -0.5 136 136
PAK2 0.027 0.004 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.095 0.18 0.31 4 -0.42 64 68
CDC42 0.027 0.005 -10000 0 -10000 0 0
RALB 0.027 0.005 -10000 0 -10000 0 0
RALA 0.026 0.006 -10000 0 -10000 0 0
PAK3 -0.35 0.34 -10000 0 -0.65 275 275
Regulation of Androgen receptor activity

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
HDAC1 0.009 0.013 -10000 0 -10000 0 0
SMARCC1 0.011 0.013 -10000 0 -10000 0 0
REL -0.012 0.17 -10000 0 -0.65 32 32
HDAC7 -0.07 0.12 -10000 0 -0.49 20 20
JUN -0.12 0.28 -10000 0 -0.66 106 106
EP300 0.02 0.012 -10000 0 -10000 0 0
KAT2B 0.027 0.004 -10000 0 -10000 0 0
KAT5 0.027 0.005 -10000 0 -10000 0 0
MAPK14 -0.015 0.075 -10000 0 -0.52 10 10
FOXO1 0.025 0.007 -10000 0 -10000 0 0
T-DHT/AR -0.068 0.13 -10000 0 -0.51 20 20
MAP2K6 0.004 0.099 -10000 0 -0.68 10 10
BRM/BAF57 0.017 0.033 -10000 0 -10000 0 0
MAP2K4 0.019 0.014 -10000 0 -10000 0 0
SMARCA2 0.013 0.022 -10000 0 -10000 0 0
PDE9A 0.015 0.066 -10000 0 -0.59 1 1
NCOA2 -0.043 0.2 -10000 0 -0.67 45 45
CEBPA 0.019 0.07 -10000 0 -0.67 5 5
EHMT2 0.025 0.005 -10000 0 -10000 0 0
cell proliferation -0.082 0.2 0.56 21 -0.47 23 44
NR0B1 -0.008 0.023 -10000 0 -10000 0 0
EGR1 -0.13 0.28 -10000 0 -0.67 100 100
RXRs/9cRA 0.019 0.072 -10000 0 -0.4 4 4
AR/RACK1/Src -0.13 0.15 0.33 2 -0.51 22 24
AR/GR -0.12 0.18 0.25 5 -0.32 198 203
GNB2L1 0.022 0.008 -10000 0 -10000 0 0
PKN1 0.025 0.007 -10000 0 -10000 0 0
RCHY1 0.027 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity -0.005 0.007 -10000 0 -0.012 144 144
MAPK8 -0.014 0.071 -10000 0 -0.51 9 9
T-DHT/AR/TIF2/CARM1 -0.13 0.19 0.34 3 -0.56 49 52
SRC -0.044 0.087 0.24 1 -0.46 16 17
NR3C1 0.026 0.006 -10000 0 -10000 0 0
KLK3 -0.36 0.55 0.38 2 -1.2 142 144
APPBP2 0.024 0.012 -10000 0 -10000 0 0
TRIM24 0.013 0.022 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.07 0.13 0.32 7 -0.56 16 23
TMPRSS2 -0.044 0.28 -10000 0 -1.1 30 30
RXRG -0.1 0.074 -10000 0 -0.67 4 4
mol:9cRA -0.002 0.003 -10000 0 -0.011 10 10
RXRA 0.024 0.008 -10000 0 -10000 0 0
RXRB 0.026 0.004 -10000 0 -10000 0 0
CARM1 0.02 0.009 -10000 0 -10000 0 0
NR2C2 0.012 0.098 -10000 0 -0.67 10 10
KLK2 -0.44 0.38 0.34 2 -0.76 280 282
AR -0.14 0.18 -10000 0 -0.35 202 202
SENP1 0.025 0.005 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
MDM2 0.036 0.016 -10000 0 -10000 0 0
SRY 0.009 0.015 0.032 141 -10000 0 141
GATA2 0.027 0.007 -10000 0 -10000 0 0
MYST2 0.001 0.002 -10000 0 -10000 0 0
HOXB13 -0.011 0.033 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.1 0.13 0.32 5 -0.54 18 23
positive regulation of transcription 0.027 0.007 -10000 0 -10000 0 0
DNAJA1 0.024 0.014 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.008 -10000 0 -10000 0 0
NCOA1 0.017 0.022 -10000 0 -10000 0 0
SPDEF -0.003 0.047 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.092 0.15 0.28 2 -0.44 51 53
T-DHT/AR/Hsp90 -0.071 0.13 0.32 8 -0.55 16 24
GSK3B 0.025 0.007 -10000 0 -10000 0 0
NR2C1 0.028 0.006 -10000 0 -10000 0 0
mol:T-DHT -0.037 0.091 0.26 1 -0.48 16 17
SIRT1 0.025 0.032 -10000 0 -0.67 1 1
ZMIZ2 0.036 0.017 -10000 0 -10000 0 0
POU2F1 0.032 0.036 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.075 0.13 0.32 6 -0.57 16 22
CREBBP 0.026 0.006 -10000 0 -10000 0 0
SMARCE1 0.012 0.022 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.002 0.1 -10000 0 -0.37 31 31
NF kappa B1 p50/RelA/I kappa B alpha 0.011 0.11 0.35 3 -0.51 2 5
alphaV/beta3 Integrin/Osteopontin/Src 0.004 0.12 -10000 0 -0.49 25 25
AP1 -0.14 0.3 -10000 0 -0.66 99 99
ILK -0.005 0.11 -10000 0 -0.39 30 30
bone resorption -0.007 0.12 -10000 0 -0.53 7 7
PTK2B 0.027 0.005 -10000 0 -10000 0 0
PYK2/p130Cas 0.043 0.11 -10000 0 -0.36 30 30
ITGAV 0.026 0.044 -10000 0 -0.66 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.013 0.12 -10000 0 -0.49 24 24
alphaV/beta3 Integrin/Osteopontin 0.028 0.12 -10000 0 -0.43 31 31
MAP3K1 -0.006 0.11 -10000 0 -0.4 31 31
JUN -0.12 0.28 -10000 0 -0.66 106 106
MAPK3 -0.02 0.098 -10000 0 -0.37 31 31
MAPK1 -0.021 0.095 -10000 0 -0.37 30 30
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.017 0.12 -10000 0 -0.4 37 37
ITGB3 0.013 0.099 -10000 0 -0.63 11 11
NFKBIA -0.016 0.093 -10000 0 -0.36 29 29
FOS -0.15 0.3 -10000 0 -0.66 124 124
CD44 0.027 0.005 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
PLAU -0.035 0.11 0.52 3 -0.6 1 4
NF kappa B1 p50/RelA 0.023 0.099 -10000 0 -0.5 2 2
BCAR1 0.026 0.006 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.028 0.088 -10000 0 -0.53 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.006 0.11 -10000 0 -0.4 31 31
VAV3 -0.014 0.11 0.4 1 -0.38 35 36
MAP3K14 -0.011 0.11 -10000 0 -0.4 31 31
ROCK2 -0.006 0.15 -10000 0 -0.66 24 24
SPP1 -0.027 0.15 -10000 0 -0.66 23 23
RAC1 0.026 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.003 0.11 -10000 0 -0.36 33 33
MMP2 -0.13 0.24 0.3 1 -0.55 90 91
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.004 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.004 0.12 -10000 0 -0.37 18 18
NFATC4 -0.019 0.086 0.28 4 -0.28 17 21
ERBB2IP 0.027 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.027 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.014 0.11 -10000 0 -0.35 39 39
JUN -0.005 0.094 0.33 11 -0.2 7 18
HRAS 0.025 0.011 -10000 0 -10000 0 0
DOCK7 -0.025 0.1 -10000 0 -0.34 41 41
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.003 0.12 -10000 0 -0.39 41 41
AKT1 0.007 0.006 -10000 0 -10000 0 0
BAD 0.005 0.004 -10000 0 -10000 0 0
MAPK10 -0.008 0.065 0.25 4 -0.38 1 5
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.015 0.12 -10000 0 -0.38 39 39
RAF1 -0.011 0.12 0.32 9 -0.38 19 28
ErbB2/ErbB3/neuregulin 2 -0.025 0.14 -10000 0 -0.41 59 59
STAT3 0.028 0.069 -10000 0 -0.84 3 3
cell migration 0.007 0.11 0.4 19 -0.28 4 23
mol:PI-3-4-5-P3 0 0.004 -10000 0 -10000 0 0
cell proliferation -0.15 0.32 -10000 0 -0.68 116 116
FOS -0.12 0.26 0.35 6 -0.5 150 156
NRAS 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.014 0.11 -10000 0 -0.35 39 39
MAPK3 -0.078 0.24 0.4 2 -0.52 83 85
MAPK1 -0.17 0.3 0.36 1 -0.64 119 120
JAK2 -0.024 0.097 -10000 0 -0.34 38 38
NF2 -0.011 0.11 -10000 0 -0.62 16 16
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.011 0.11 -10000 0 -0.34 43 43
NRG1 -0.034 0.19 -10000 0 -0.65 43 43
GRB2/SOS1 0.037 0.011 -10000 0 -10000 0 0
MAPK8 -0.02 0.11 -10000 0 -0.33 46 46
MAPK9 -0.009 0.061 0.23 3 -10000 0 3
ERBB2 -0.017 0.006 -10000 0 -10000 0 0
ERBB3 0.016 0.079 -10000 0 -0.62 7 7
SHC1 0.025 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
apoptosis 0.001 0.014 -10000 0 -10000 0 0
STAT3 (dimer) 0.028 0.068 -10000 0 -0.82 3 3
RNF41 0 0.008 -10000 0 -10000 0 0
FRAP1 0.002 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.017 0.075 -10000 0 -0.25 38 38
ErbB2/ErbB2/HSP90 (dimer) 0.014 0.014 -10000 0 -10000 0 0
CHRNA1 -0.075 0.19 0.33 1 -0.4 107 108
myelination -0.009 0.14 0.54 16 -0.3 1 17
PPP3CB -0.022 0.093 -10000 0 -0.32 39 39
KRAS 0.026 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.021 0.1 -10000 0 -0.3 40 40
NRG2 -0.05 0.22 -10000 0 -0.67 53 53
mol:GDP -0.011 0.11 -10000 0 -0.33 43 43
SOS1 0.026 0.005 -10000 0 -10000 0 0
MAP2K2 -0.026 0.12 0.31 5 -0.38 20 25
SRC 0.026 0.008 -10000 0 -10000 0 0
mol:cAMP 0 0.003 -10000 0 -10000 0 0
PTPN11 -0.023 0.1 0.25 1 -0.34 39 40
MAP2K1 -0.074 0.23 -10000 0 -0.62 30 30
heart morphogenesis -0.014 0.11 -10000 0 -0.35 39 39
RAS family/GDP 0.016 0.11 -10000 0 -0.36 18 18
GRB2 0.025 0.007 -10000 0 -10000 0 0
PRKACA -0.011 0.13 -10000 0 -0.65 18 18
CHRNE 0.007 0.037 0.18 12 -0.088 7 19
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.007 0.006 -10000 0 -10000 0 0
nervous system development -0.014 0.11 -10000 0 -0.35 39 39
CDC42 0.027 0.005 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.003 0.055 -10000 0 -10000 0 0
CRKL -0.013 0.091 0.36 2 -0.42 1 3
mol:PIP3 -0.002 0.017 0.33 1 -10000 0 1
AKT1 0.003 0.055 0.37 2 -0.45 3 5
PTK2B 0.027 0.005 -10000 0 -10000 0 0
RAPGEF1 0.003 0.1 0.42 8 -0.4 1 9
RANBP10 0.026 0.006 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
HGF/MET/SHIP2 -0.013 0.18 -10000 0 -0.45 69 69
MAP3K5 0.012 0.12 0.44 13 -0.4 6 19
HGF/MET/CIN85/CBL/ENDOPHILINS 0.004 0.17 -10000 0 -0.4 69 69
AP1 -0.18 0.33 -10000 0 -0.64 147 147
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
apoptosis -0.22 0.4 -10000 0 -0.81 148 148
STAT3 (dimer) -0.018 0.1 -10000 0 -0.28 63 63
GAB1/CRKL/SHP2/PI3K 0.027 0.11 0.34 1 -0.49 3 4
INPP5D 0.019 0.032 -10000 0 -10000 0 0
CBL/CRK 0.017 0.11 0.5 7 -0.41 1 8
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.027 0.005 -10000 0 -10000 0 0
PTEN 0.026 0.018 -10000 0 -0.35 1 1
ELK1 0.035 0.14 0.42 29 -0.23 4 33
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.006 0.067 -10000 0 -0.26 3 3
PAK1 0.005 0.057 0.35 5 -0.37 3 8
HGF/MET/RANBP10 -0.013 0.18 -10000 0 -0.45 69 69
HRAS -0.019 0.13 -10000 0 -0.54 3 3
DOCK1 0.001 0.11 0.44 9 -0.47 2 11
GAB1 -0.01 0.096 0.26 1 -0.35 4 5
CRK -0.005 0.097 0.31 4 -0.43 1 5
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.042 0.19 -10000 0 -0.5 69 69
JUN -0.12 0.28 -10000 0 -0.66 106 106
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.03 0.085 -10000 0 -0.24 67 67
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
cell morphogenesis -0.006 0.13 0.48 6 -0.51 3 9
GRB2/SHC 0.005 0.084 -10000 0 -0.22 23 23
FOS -0.15 0.3 -10000 0 -0.66 124 124
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility 0.035 0.14 0.42 29 -0.23 4 33
HGF/MET/MUC20 -0.063 0.16 -10000 0 -0.45 69 69
cell migration 0.004 0.083 -10000 0 -0.22 23 23
GRB2 0.026 0.007 -10000 0 -10000 0 0
CBL 0.027 0.005 -10000 0 -10000 0 0
MET/RANBP10 -0.003 0.055 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.015 0.11 -10000 0 -0.3 63 63
MET/MUC20 -0.015 0.045 -10000 0 -10000 0 0
RAP1B 0.013 0.13 0.54 13 -0.37 1 14
RAP1A 0.01 0.11 0.4 11 -0.37 1 12
HGF/MET/RANBP9 -0.012 0.18 -10000 0 -0.44 69 69
RAF1 -0.016 0.12 -10000 0 -0.46 3 3
STAT3 -0.019 0.1 -10000 0 -0.28 63 63
cell proliferation -0.022 0.15 -10000 0 -0.39 61 61
RPS6KB1 0 0.033 -10000 0 -0.22 2 2
MAPK3 -0.021 0.1 0.5 13 -10000 0 13
MAPK1 0.13 0.29 0.61 131 -10000 0 131
RANBP9 0.027 0.003 -10000 0 -10000 0 0
MAPK8 0.024 0.17 0.58 18 -0.6 9 27
SRC -0.02 0.1 -10000 0 -0.28 63 63
PI3K 0.004 0.093 -10000 0 -0.24 29 29
MET/Glomulin -0.006 0.043 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
MAP2K1 -0.01 0.12 0.32 3 -0.43 3 6
MET -0.027 0.069 -10000 0 -10000 0 0
MAP4K1 0.008 0.12 0.46 8 -0.42 6 14
PTK2 0.026 0.006 -10000 0 -10000 0 0
MAP2K2 -0.007 0.12 0.32 2 -0.41 2 4
BAD 0.005 0.057 0.35 5 -0.4 2 7
MAP2K4 0.022 0.14 0.5 20 -0.4 4 24
SHP2/GRB2/SOS1/GAB1 0.019 0.097 -10000 0 -0.36 1 1
INPPL1 0.027 0.005 -10000 0 -10000 0 0
PXN 0.027 0.005 -10000 0 -10000 0 0
SH3KBP1 0.025 0.007 -10000 0 -10000 0 0
HGS -0.027 0.076 -10000 0 -0.22 64 64
PLCgamma1/PKC 0.02 0.004 -10000 0 -10000 0 0
HGF -0.072 0.24 -10000 0 -0.67 69 69
RASA1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
PTPRJ 0.027 0.005 -10000 0 -10000 0 0
NCK/PLCgamma1 0.004 0.098 -10000 0 -0.24 66 66
PDPK1 -0.001 0.047 -10000 0 -0.48 3 3
HGF/MET/SHIP -0.016 0.18 -10000 0 -0.45 69 69
FAS signaling pathway (CD95)

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
SPTAN1 0.013 0.061 0.24 33 -10000 0 33
RFC1 0.014 0.063 0.24 35 -10000 0 35
PRKDC 0.016 0.069 0.26 35 -10000 0 35
RIPK1 0.029 0.005 -10000 0 -10000 0 0
CASP7 -0.003 0.096 -10000 0 -0.74 6 6
FASLG/FAS/FADD/FAF1 -0.015 0.096 0.23 5 -0.34 33 38
MAP2K4 -0.027 0.16 0.32 2 -0.49 26 28
mol:ceramide -0.02 0.13 -10000 0 -0.42 35 35
GSN 0.013 0.061 0.24 33 -10000 0 33
FASLG/FAS/FADD/FAF1/Caspase 8 -0.02 0.12 -10000 0 -0.42 33 33
FAS 0.02 0.018 -10000 0 -10000 0 0
BID -0.017 0.035 0.26 4 -10000 0 4
MAP3K1 -0.009 0.12 0.26 4 -0.41 18 22
MAP3K7 0.026 0.005 -10000 0 -10000 0 0
RB1 0.013 0.064 0.25 31 -0.21 1 32
CFLAR 0.028 0.006 -10000 0 -10000 0 0
HGF/MET -0.018 0.19 -10000 0 -0.46 72 72
ARHGDIB 0.015 0.068 0.24 37 -10000 0 37
FADD 0.02 0.018 -10000 0 -10000 0 0
actin filament polymerization -0.013 0.061 -10000 0 -0.24 33 33
NFKB1 -0.015 0.098 -10000 0 -0.57 3 3
MAPK8 -0.063 0.22 0.4 2 -0.47 93 95
DFFA 0.014 0.063 0.24 35 -10000 0 35
DNA fragmentation during apoptosis 0.014 0.063 0.24 35 -10000 0 35
FAS/FADD/MET 0.044 0.04 -10000 0 -10000 0 0
CFLAR/RIP1 0.042 0.01 -10000 0 -10000 0 0
FAIM3 0.017 0.06 -10000 0 -0.67 3 3
FAF1 0.019 0.02 -10000 0 -10000 0 0
PARP1 0.017 0.079 0.28 36 -10000 0 36
DFFB 0.014 0.063 0.24 35 -10000 0 35
CHUK -0.015 0.089 -10000 0 -0.62 2 2
FASLG -0.034 0.18 -10000 0 -0.68 33 33
FAS/FADD 0.029 0.026 -10000 0 -10000 0 0
HGF -0.072 0.24 -10000 0 -0.67 69 69
LMNA 0.013 0.067 0.24 33 -10000 0 33
CASP6 0.014 0.063 0.24 35 -10000 0 35
CASP10 0.02 0.018 -10000 0 -10000 0 0
CASP3 0.018 0.078 0.3 35 -0.19 1 36
PTPN13 0.018 0.076 -10000 0 -0.67 6 6
CASP8 -0.014 0.033 0.4 3 -10000 0 3
IL6 -0.2 0.5 -10000 0 -1.2 90 90
MET -0.027 0.069 -10000 0 -10000 0 0
ICAD/CAD 0.012 0.056 0.22 33 -10000 0 33
FASLG/FAS/FADD/FAF1/Caspase 10 -0.02 0.14 -10000 0 -0.43 35 35
activation of caspase activity by cytochrome c -0.017 0.035 0.26 4 -10000 0 4
PAK2 0.014 0.063 0.24 34 -10000 0 34
BCL2 -0.023 0.18 -10000 0 -0.66 36 36
LPA receptor mediated events

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
GNB1/GNG2 0.019 0.12 -10000 0 -0.41 33 33
NF kappa B1 p50/RelA/I kappa B alpha 0.01 0.086 0.35 2 -10000 0 2
AP1 -0.15 0.3 -10000 0 -0.55 156 156
mol:PIP3 -0.011 0.091 -10000 0 -0.35 30 30
AKT1 0.03 0.096 0.29 11 -0.56 2 13
PTK2B -0.009 0.085 0.26 1 -0.28 30 31
RHOA 0.014 0.042 0.25 1 -10000 0 1
PIK3CB 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.009 0.072 0.27 8 -10000 0 8
MAGI3 0.025 0.032 -10000 0 -0.67 1 1
RELA 0.027 0.005 -10000 0 -10000 0 0
apoptosis -0.008 0.1 -10000 0 -0.34 39 39
HRAS/GDP 0.019 0.007 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0 0.099 0.35 11 -0.32 14 25
NF kappa B1 p50/RelA -0.019 0.1 -10000 0 -0.42 10 10
endothelial cell migration -0.015 0.14 -10000 0 -0.52 33 33
ADCY4 -0.029 0.14 -10000 0 -0.49 38 38
ADCY5 -0.054 0.16 -10000 0 -0.53 41 41
ADCY6 -0.029 0.14 -10000 0 -0.49 38 38
ADCY7 -0.029 0.15 -10000 0 -0.5 38 38
ADCY1 -0.031 0.15 -10000 0 -0.48 40 40
ADCY2 -0.048 0.16 -10000 0 -0.52 41 41
ADCY3 -0.029 0.14 -10000 0 -0.5 37 37
ADCY8 -0.037 0.15 -10000 0 -0.5 39 39
ADCY9 -0.029 0.15 -10000 0 -0.5 38 38
GSK3B -0.008 0.084 0.37 2 -0.34 12 14
arachidonic acid secretion -0.029 0.14 -10000 0 -0.43 48 48
GNG2 0.025 0.031 -10000 0 -0.66 1 1
TRIP6 0.024 0.01 -10000 0 -10000 0 0
GNAO1 -0.025 0.15 -10000 0 -0.46 46 46
HRAS 0.026 0.011 -10000 0 -10000 0 0
NFKBIA -0.006 0.094 0.4 7 -0.49 1 8
GAB1 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.016 0.18 -10000 0 -0.79 22 22
JUN -0.12 0.28 -10000 0 -0.66 106 106
LPA/LPA2/NHERF2 0.035 0.017 -10000 0 -10000 0 0
TIAM1 0.001 0.21 -10000 0 -0.92 23 23
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.012 0.065 0.32 1 -10000 0 1
PLCB3 0.027 0.035 -10000 0 -10000 0 0
FOS -0.15 0.3 -10000 0 -0.66 124 124
positive regulation of mitosis -0.029 0.14 -10000 0 -0.43 48 48
LPA/LPA1-2-3 0.019 0.11 -10000 0 -0.38 33 33
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.026 0.006 -10000 0 -10000 0 0
stress fiber formation 0.002 0.1 0.45 2 -0.32 28 30
GNAZ -0.015 0.12 -10000 0 -0.42 35 35
EGFR/PI3K-beta/Gab1 0.001 0.098 -10000 0 -0.36 30 30
positive regulation of dendritic cell cytokine production 0.018 0.11 -10000 0 -0.38 33 33
LPA/LPA2/MAGI-3 0.034 0.027 -10000 0 -0.44 1 1
ARHGEF1 0.006 0.1 0.36 3 -0.39 23 26
GNAI2 -0.012 0.12 -10000 0 -0.44 34 34
GNAI3 -0.011 0.12 -10000 0 -0.42 37 37
GNAI1 -0.012 0.12 -10000 0 -0.41 38 38
LPA/LPA3 0.015 0.024 -10000 0 -10000 0 0
LPA/LPA2 0.02 0.013 -10000 0 -10000 0 0
LPA/LPA1 -0.014 0.14 -10000 0 -0.47 40 40
HB-EGF/EGFR -0.021 0.13 -10000 0 -0.44 43 43
HBEGF -0.036 0.14 -10000 0 -0.49 41 41
mol:DAG -0.012 0.065 0.32 1 -10000 0 1
cAMP biosynthetic process -0.035 0.16 0.42 10 -0.46 49 59
NFKB1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
LYN -0.008 0.09 0.36 6 -0.4 2 8
GNAQ 0.016 0.015 -10000 0 -10000 0 0
LPAR2 0.025 0.007 -10000 0 -10000 0 0
LPAR3 0.013 0.032 -10000 0 -10000 0 0
LPAR1 -0.022 0.18 -10000 0 -0.59 40 40
IL8 -0.082 0.17 0.37 1 -0.46 40 41
PTK2 -0.002 0.1 -10000 0 -0.38 28 28
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
CASP3 -0.008 0.1 -10000 0 -0.34 39 39
EGFR 0.019 0.07 -10000 0 -0.67 5 5
PLCG1 -0.013 0.064 -10000 0 -0.26 5 5
PLD2 -0.001 0.1 -10000 0 -0.37 28 28
G12/G13 0.022 0.11 -10000 0 -0.39 32 32
PI3K-beta 0.005 0.087 -10000 0 -0.37 12 12
cell migration 0.019 0.072 -10000 0 -0.24 17 17
SLC9A3R2 0.026 0.006 -10000 0 -10000 0 0
PXN 0 0.097 0.26 1 -0.33 28 29
HRAS/GTP -0.029 0.14 -10000 0 -0.44 48 48
RAC1 0.026 0.006 -10000 0 -10000 0 0
MMP9 -0.041 0.19 -10000 0 -0.67 41 41
PRKCE 0.02 0.07 -10000 0 -0.67 5 5
PRKCD -0.009 0.085 0.32 12 -10000 0 12
Gi(beta/gamma) -0.024 0.14 -10000 0 -0.47 38 38
mol:LPA 0.002 0.016 -10000 0 -0.19 2 2
TRIP6/p130 Cas/FAK1/Paxillin 0.019 0.11 -10000 0 -0.38 26 26
MAPKKK cascade -0.029 0.14 -10000 0 -0.43 48 48
contractile ring contraction involved in cytokinesis 0.017 0.047 0.27 3 -10000 0 3
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.067 0.15 -10000 0 -0.34 116 116
GNA15 0.014 0.026 -10000 0 -0.36 1 1
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
MAPT -0.003 0.094 0.33 8 -0.34 14 22
GNA11 0.012 0.046 -10000 0 -0.32 8 8
Rac1/GTP 0.015 0.19 -10000 0 -0.83 22 22
MMP2 -0.015 0.15 -10000 0 -0.52 33 33
BCR signaling pathway

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
JUN -0.066 0.17 0.44 9 -0.44 36 45
IKBKB 0.011 0.12 0.5 15 -0.34 5 20
AKT1 -0.001 0.17 0.53 26 -0.24 15 41
IKBKG -0.002 0.13 0.47 15 -0.36 12 27
CALM1 -0.021 0.093 0.39 3 -0.44 6 9
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
MAP3K1 -0.013 0.17 0.46 11 -0.53 21 32
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.023 0.093 0.32 2 -0.42 8 10
DOK1 0.027 0.005 -10000 0 -10000 0 0
AP-1 -0.058 0.15 0.53 11 -0.26 92 103
LYN 0.027 0.005 -10000 0 -10000 0 0
BLNK 0.027 0.004 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
BCR complex -0.068 0.18 -10000 0 -0.5 64 64
CD22 -0.068 0.18 -10000 0 -0.42 82 82
CAMK2G -0.018 0.09 0.34 4 -0.43 5 9
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
INPP5D 0.019 0.032 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.038 0.12 -10000 0 -0.34 57 57
GO:0007205 -0.024 0.095 0.32 2 -0.43 8 10
SYK 0.025 0.008 -10000 0 -10000 0 0
ELK1 -0.019 0.092 0.31 4 -0.42 7 11
NFATC1 -0.039 0.14 0.36 6 -0.43 24 30
B-cell antigen/BCR complex -0.068 0.18 -10000 0 -0.5 64 64
PAG1/CSK 0.038 0.026 -10000 0 -0.5 1 1
NFKBIB 0.019 0.044 0.2 12 -0.13 6 18
HRAS -0.017 0.095 0.29 4 -0.36 7 11
NFKBIA 0.019 0.044 0.2 12 -0.13 6 18
NF-kappa-B/RelA/I kappa B beta 0.024 0.04 0.2 12 -10000 0 12
RasGAP/Csk -0.003 0.18 -10000 0 -0.4 73 73
mol:GDP -0.022 0.092 0.29 2 -0.41 9 11
PTEN 0.026 0.018 -10000 0 -0.35 1 1
CD79B 0.007 0.049 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha 0.024 0.04 0.2 12 -10000 0 12
GRB2 0.026 0.007 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.036 0.16 0.44 4 -0.48 20 24
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.023 0.092 0.32 2 -0.42 7 9
CSK 0.027 0.008 -10000 0 -10000 0 0
FOS -0.096 0.18 0.47 8 -0.36 124 132
CHUK 0.008 0.1 0.4 15 -0.38 5 20
IBTK 0.027 0.004 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.012 0.11 -10000 0 -0.45 11 11
PTPN6 -0.063 0.16 -10000 0 -0.48 41 41
RELA 0.027 0.005 -10000 0 -10000 0 0
BCL2A1 0.015 0.035 0.17 5 -0.13 6 11
VAV2 -0.054 0.15 -10000 0 -0.63 16 16
ubiquitin-dependent protein catabolic process 0.023 0.043 0.2 12 -0.12 6 18
BTK -0.038 0.24 -10000 0 -0.98 30 30
CD19 -0.06 0.15 -10000 0 -0.4 67 67
MAP4K1 0.008 0.078 -10000 0 -0.67 5 5
CD72 0.024 0.015 -10000 0 -10000 0 0
PAG1 0.025 0.032 -10000 0 -0.67 1 1
MAPK14 -0.006 0.15 0.43 13 -0.46 19 32
SH3BP5 0.027 0.004 -10000 0 -10000 0 0
PIK3AP1 -0.016 0.094 -10000 0 -0.6 4 4
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.047 0.18 -10000 0 -0.43 70 70
RAF1 -0.014 0.096 0.34 7 -0.48 2 9
RasGAP/p62DOK/SHIP -0.005 0.17 -10000 0 -0.38 73 73
CD79A -0.099 0.23 -10000 0 -0.65 66 66
re-entry into mitotic cell cycle -0.057 0.15 0.53 11 -0.26 93 104
RASA1 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.003 0.1 0.39 15 -0.4 2 17
MAPK1 -0.009 0.09 0.4 7 -0.39 2 9
CD72/SHP1 -0.045 0.17 0.31 1 -0.56 23 24
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.012 0.16 0.47 12 -0.49 21 33
actin cytoskeleton organization -0.043 0.14 0.34 2 -0.53 15 17
NF-kappa-B/RelA 0.048 0.073 0.34 12 -0.22 1 13
Calcineurin 0.008 0.09 -10000 0 -0.41 4 4
PI3K -0.061 0.14 -10000 0 -0.48 19 19
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.018 0.097 -10000 0 -0.44 10 10
SOS1 0.027 0.005 -10000 0 -10000 0 0
Bam32/HPK1 -0.022 0.22 -10000 0 -0.93 20 20
DAPP1 -0.043 0.25 -10000 0 -1.1 20 20
cytokine secretion -0.036 0.13 0.36 6 -0.4 24 30
mol:DAG -0.023 0.092 0.32 2 -0.42 7 9
PLCG2 0.026 0.006 -10000 0 -10000 0 0
MAP2K1 -0.012 0.091 0.34 6 -0.45 2 8
B-cell antigen/BCR complex/FcgammaRIIB -0.054 0.19 -10000 0 -0.44 80 80
mol:PI-3-4-5-P3 -0.051 0.099 -10000 0 -0.36 15 15
ETS1 -0.015 0.086 0.34 5 -0.42 4 9
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.012 0.15 -10000 0 -0.38 62 62
B-cell antigen/BCR complex/LYN -0.048 0.16 -10000 0 -0.42 68 68
MALT1 0.027 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.044 -10000 0 -0.67 2 2
RAC1 -0.047 0.15 0.37 1 -0.57 15 16
B-cell antigen/BCR complex/LYN/SYK -0.037 0.19 -10000 0 -0.45 65 65
CARD11 -0.035 0.12 0.34 5 -0.45 17 22
FCGR2B -0.009 0.15 -10000 0 -0.67 24 24
PPP3CA 0.027 0.004 -10000 0 -10000 0 0
BCL10 0.027 0.005 -10000 0 -10000 0 0
IKK complex 0.019 0.096 0.45 17 -0.13 5 22
PTPRC -0.008 0.14 -10000 0 -0.67 20 20
PDPK1 -0.028 0.087 0.23 11 -0.25 17 28
PPP3CB 0.027 0.005 -10000 0 -10000 0 0
PPP3CC 0.027 0.005 -10000 0 -10000 0 0
POU2F2 0.019 0.032 0.16 13 -10000 0 13
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.007 0.1 -10000 0 -0.81 6 6
Syndecan-4/Syndesmos -0.035 0.16 -10000 0 -0.54 41 41
positive regulation of JNK cascade -0.049 0.19 -10000 0 -0.55 45 45
Syndecan-4/ADAM12 -0.044 0.16 -10000 0 -0.54 41 41
CCL5 -0.018 0.16 -10000 0 -0.67 29 29
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
DNM2 0.025 0.008 -10000 0 -10000 0 0
ITGA5 0.027 0.005 -10000 0 -10000 0 0
SDCBP 0.027 0.005 -10000 0 -10000 0 0
PLG 0.008 0.031 -10000 0 -0.17 1 1
ADAM12 -0.009 0.063 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.026 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.056 0.029 -10000 0 -0.17 4 4
Syndecan-4/Laminin alpha1 -0.056 0.18 -10000 0 -0.57 41 41
Syndecan-4/CXCL12/CXCR4 -0.052 0.2 -10000 0 -0.59 43 43
Syndecan-4/Laminin alpha3 -0.046 0.17 -10000 0 -0.56 40 40
MDK -0.018 0.073 -10000 0 -0.67 1 1
Syndecan-4/FZD7 -0.035 0.16 -10000 0 -0.54 41 41
Syndecan-4/Midkine -0.046 0.16 -10000 0 -0.55 40 40
FZD7 0.022 0.05 -10000 0 -0.51 4 4
Syndecan-4/FGFR1/FGF -0.01 0.15 -10000 0 -0.5 40 40
THBS1 0.013 0.043 -10000 0 -10000 0 0
integrin-mediated signaling pathway -0.05 0.16 -10000 0 -0.55 41 41
positive regulation of MAPKKK cascade -0.049 0.19 -10000 0 -0.55 45 45
Syndecan-4/TACI -0.12 0.21 -10000 0 -0.6 41 41
CXCR4 0.026 0.012 -10000 0 -10000 0 0
cell adhesion 0 0.066 0.2 5 -0.31 17 22
Syndecan-4/Dynamin -0.035 0.16 -10000 0 -0.54 40 40
Syndecan-4/TSP1 -0.037 0.16 -10000 0 -0.54 41 41
Syndecan-4/GIPC -0.035 0.16 -10000 0 -0.54 40 40
Syndecan-4/RANTES -0.055 0.2 -10000 0 -0.65 41 41
ITGB1 0.027 0.004 -10000 0 -10000 0 0
LAMA1 -0.019 0.17 -10000 0 -0.66 33 33
LAMA3 0 0.12 -10000 0 -0.67 16 16
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA 0.018 0.19 0.75 21 -0.62 17 38
Syndecan-4/alpha-Actinin -0.033 0.16 -10000 0 -0.54 40 40
TFPI -0.012 0.16 -10000 0 -0.66 28 28
F2 0.01 0.029 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.039 0.009 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.069 0.18 -10000 0 -0.58 40 40
ACTN1 0.026 0.008 -10000 0 -10000 0 0
TNC -0.03 0.093 -10000 0 -0.67 5 5
Syndecan-4/CXCL12 -0.07 0.2 -10000 0 -0.59 47 47
FGF6 -0.016 0.005 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
CXCL12 -0.046 0.21 -10000 0 -0.66 52 52
TNFRSF13B -0.16 0.29 -10000 0 -0.66 120 120
FGF2 0.027 0.004 -10000 0 -10000 0 0
FGFR1 0.025 0.032 -10000 0 -0.67 1 1
Syndecan-4/PI-4-5-P2 -0.047 0.15 -10000 0 -0.54 41 41
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.075 0.071 -10000 0 -0.23 1 1
cell migration -0.026 0.012 -10000 0 -10000 0 0
PRKCD 0.025 0.022 -10000 0 -10000 0 0
vasculogenesis -0.036 0.15 -10000 0 -0.52 41 41
SDC4 -0.046 0.16 -10000 0 -0.57 41 41
Syndecan-4/Tenascin C -0.052 0.17 -10000 0 -0.57 41 41
Syndecan-4/PI-4-5-P2/PKC alpha -0.045 0.023 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.034 0.16 -10000 0 -0.54 41 41
MMP9 -0.041 0.19 -10000 0 -0.66 41 41
Rac1/GTP 0 0.067 0.2 4 -0.31 17 21
cytoskeleton organization -0.033 0.15 -10000 0 -0.52 41 41
GIPC1 0.025 0.008 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.053 0.18 -10000 0 -0.56 43 43
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.033 0.04 -10000 0 -0.81 1 1
VEGFR1 homodimer/NRP1 0.015 0.038 -10000 0 -0.81 1 1
mol:DAG -0.021 0.13 -10000 0 -0.4 50 50
VEGFR1 homodimer/NRP1/VEGFR 121 0.028 0.059 -10000 0 -0.63 3 3
CaM/Ca2+ -0.006 0.13 -10000 0 -0.38 50 50
HIF1A 0.032 0.019 -10000 0 -0.37 1 1
GAB1 0.027 0.004 -10000 0 -10000 0 0
AKT1 -0.02 0.13 -10000 0 -0.39 51 51
PLCG1 -0.021 0.13 -10000 0 -0.4 50 50
NOS3 -0.012 0.12 -10000 0 -0.36 46 46
CBL 0.027 0.005 -10000 0 -10000 0 0
mol:NO -0.008 0.12 0.47 3 -0.35 46 49
FLT1 0.02 0.042 -10000 0 -0.91 1 1
PGF -0.043 0.21 -10000 0 -0.66 50 50
VEGFR1 homodimer/NRP2/VEGFR121 0.045 0.062 -10000 0 -0.63 3 3
CALM1 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
eNOS/Hsp90 0.005 0.12 0.3 1 -0.48 3 4
endothelial cell proliferation -0.037 0.15 0.36 2 -0.42 50 52
mol:Ca2+ -0.021 0.13 -10000 0 -0.39 50 50
MAPK3 -0.038 0.13 0.35 2 -0.36 64 66
MAPK1 -0.041 0.12 -10000 0 -0.36 63 63
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
PLGF homodimer -0.043 0.21 -10000 0 -0.66 50 50
PRKACA 0.025 0.008 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.013 0.093 -10000 0 -0.67 9 9
VEGFA homodimer 0.023 0.054 -10000 0 -0.67 3 3
VEGFR1 homodimer/VEGFA homodimer 0.031 0.062 -10000 0 -0.68 3 3
platelet activating factor biosynthetic process -0.042 0.12 -10000 0 -0.35 52 52
PI3K 0.015 0.14 -10000 0 -0.38 51 51
PRKCA -0.038 0.14 -10000 0 -0.38 64 64
PRKCB -0.034 0.12 -10000 0 -0.38 54 54
VEGFR1 homodimer/PLGF homodimer -0.013 0.14 -10000 0 -0.44 50 50
VEGFA 0.023 0.054 -10000 0 -0.67 3 3
VEGFB 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.021 0.13 -10000 0 -0.4 50 50
RASA1 0.02 0.038 -10000 0 -0.76 1 1
NRP2 0.015 0.04 -10000 0 -10000 0 0
VEGFR1 homodimer 0.02 0.042 -10000 0 -0.9 1 1
VEGFB homodimer 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.002 0.14 0.55 4 -0.53 6 10
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
mol:PI-3-4-5-P3 0.014 0.14 -10000 0 -0.38 51 51
mol:L-citrulline -0.008 0.12 0.47 3 -0.35 46 49
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.058 0.061 -10000 0 -0.6 3 3
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.045 0.061 -10000 0 -0.63 3 3
CD2AP 0.027 0.003 -10000 0 -10000 0 0
PI3K/GAB1 0.026 0.14 -10000 0 -0.37 51 51
PDPK1 -0.017 0.13 0.34 3 -0.37 51 54
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.044 0.074 -10000 0 -0.74 3 3
mol:NADP -0.008 0.12 0.47 3 -0.35 46 49
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.056 0.06 -10000 0 -0.59 3 3
VEGFR1 homodimer/NRP2 0.034 0.041 -10000 0 -0.81 1 1
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.01 0.14 -10000 0 -0.35 60 60
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.02 0.012 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.002 0.12 -10000 0 -0.43 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.035 0.052 -10000 0 -0.29 1 1
antigen processing and presentation of peptide antigen via MHC class I 0.008 0.07 -10000 0 -0.25 2 2
CaM/Ca2+ 0.015 0.13 -10000 0 -0.33 60 60
RAP1A 0.027 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.011 0.12 -10000 0 -0.34 60 60
AKT1 -0.016 0.12 0.38 5 -0.36 8 13
MAP2K1 -0.024 0.11 0.29 2 -0.32 57 59
MAP3K11 -0.021 0.12 0.3 5 -0.34 60 65
IFNGR1 0.02 0.025 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.018 0.072 -10000 0 -0.4 3 3
Rap1/GTP -0.019 0.093 -10000 0 -0.35 1 1
CRKL/C3G 0.028 0.019 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.018 0.15 -10000 0 -0.37 59 59
CEBPB -0.057 0.19 0.52 6 -0.53 35 41
STAT3 0.026 0.007 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.018 0.16 -10000 0 -0.71 6 6
STAT1 -0.021 0.12 0.3 5 -0.34 60 65
CALM1 0.027 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.064 0.23 -10000 0 -0.67 60 60
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
STAT1 (dimer)/PIAS1 -0.005 0.12 0.3 4 -0.32 55 59
CEBPB/PTGES2/Cbp/p300 -0.023 0.12 -10000 0 -0.39 13 13
mol:Ca2+ 0.008 0.14 -10000 0 -0.35 60 60
MAPK3 -0.008 0.12 -10000 0 -0.65 4 4
STAT1 (dimer) 0.018 0.096 -10000 0 -0.35 2 2
MAPK1 -0.17 0.3 0.44 1 -0.67 119 120
JAK2 0.017 0.035 -10000 0 -0.38 2 2
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
JAK1 0.02 0.025 -10000 0 -10000 0 0
CAMK2D 0.027 0.004 -10000 0 -10000 0 0
DAPK1 -0.039 0.18 0.48 9 -0.6 26 35
SMAD7 0.018 0.064 0.42 6 -10000 0 6
CBL/CRKL/C3G -0.008 0.12 0.3 2 -0.32 42 44
PI3K 0.013 0.13 -10000 0 -0.33 60 60
IFNG -0.064 0.23 -10000 0 -0.67 60 60
apoptosis -0.037 0.15 0.56 4 -0.46 35 39
CAMK2G 0.027 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.026 0.007 -10000 0 -10000 0 0
CAMK2A 0.012 0.033 -10000 0 -10000 0 0
CAMK2B 0.021 0.063 -10000 0 -0.67 4 4
FRAP1 -0.023 0.11 0.37 5 -0.35 7 12
PRKCD -0.012 0.13 0.42 9 -0.37 8 17
RAP1B 0.027 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.008 0.07 -10000 0 -0.25 2 2
PTPN2 0.027 0.004 -10000 0 -10000 0 0
EP300 0.02 0.013 -10000 0 -10000 0 0
IRF1 -0.014 0.084 -10000 0 -10000 0 0
STAT1 (dimer)/PIASy -0.01 0.12 0.3 2 -0.32 53 55
SOCS1 0.017 0.12 -10000 0 -1 6 6
mol:GDP -0.009 0.11 0.28 2 -0.3 42 44
CASP1 0.016 0.063 0.45 4 -0.32 2 6
PTGES2 0.025 0.008 -10000 0 -10000 0 0
IRF9 -0.001 0.057 0.34 1 -10000 0 1
mol:PI-3-4-5-P3 -0.001 0.12 -10000 0 -0.32 60 60
RAP1/GDP -0.004 0.1 -10000 0 -0.36 1 1
CBL -0.021 0.12 0.29 6 -0.34 60 66
MAP3K1 -0.022 0.12 0.3 2 -0.34 58 60
PIAS1 0.027 0.004 -10000 0 -10000 0 0
PIAS4 0.025 0.008 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.008 0.07 -10000 0 -0.25 2 2
PTPN11 -0.024 0.12 -10000 0 -0.35 60 60
CREBBP 0.027 0.006 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 0.016 0.005 -10000 0 -10000 0 0
MAP4K4 -0.014 0.12 -10000 0 -0.48 16 16
BAG4 0.025 0.032 -10000 0 -0.67 1 1
PKC zeta/ceramide -0.02 0.097 -10000 0 -0.28 36 36
NFKBIA 0.027 0.005 -10000 0 -10000 0 0
BIRC3 -0.009 0.14 -10000 0 -0.62 25 25
BAX -0.013 0.076 -10000 0 -0.34 20 20
RIPK1 0.027 0.003 -10000 0 -10000 0 0
AKT1 0.028 0.14 0.79 16 -10000 0 16
BAD -0.033 0.088 0.18 1 -0.31 27 28
SMPD1 -0.012 0.088 0.26 6 -0.23 61 67
RB1 -0.033 0.09 0.19 1 -0.31 29 30
FADD/Caspase 8 -0.005 0.12 -10000 0 -0.5 14 14
MAP2K4 -0.02 0.072 0.2 3 -0.37 8 11
NSMAF 0.027 0.005 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.024 0.082 0.19 1 -0.41 12 13
EGF -0.076 0.24 -10000 0 -0.66 72 72
mol:ceramide -0.037 0.098 -10000 0 -0.29 39 39
MADD 0.027 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.015 0.024 -10000 0 -0.5 1 1
ASAH1 0.025 0.032 -10000 0 -0.67 1 1
negative regulation of cell cycle -0.032 0.089 0.19 1 -0.31 29 30
cell proliferation -0.059 0.15 -10000 0 -0.32 104 104
BID -0.15 0.28 -10000 0 -0.6 125 125
MAP3K1 -0.028 0.079 0.19 1 -0.28 27 28
EIF2A -0.03 0.078 -10000 0 -0.45 10 10
TRADD 0.026 0.006 -10000 0 -10000 0 0
CRADD 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.015 0.07 -10000 0 -0.35 10 10
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.043 0.086 -10000 0 -0.38 13 13
Cathepsin D/ceramide -0.019 0.093 -10000 0 -0.27 36 36
FADD -0.013 0.12 -10000 0 -0.49 15 15
KSR1 -0.027 0.087 0.18 9 -0.3 28 37
MAPK8 -0.019 0.091 -10000 0 -0.37 19 19
PRKRA -0.035 0.091 -10000 0 -0.35 22 22
PDGFA 0.026 0.006 -10000 0 -10000 0 0
TRAF2 0.025 0.008 -10000 0 -10000 0 0
IGF1 -0.13 0.28 -10000 0 -0.66 107 107
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.037 0.097 -10000 0 -0.29 39 39
CTSD 0.026 0.008 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.039 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.062 0.16 -10000 0 -0.34 104 104
PRKCD 0.027 0.003 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.015 0.024 -10000 0 -0.5 1 1
RelA/NF kappa B1 0.039 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.027 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.013 0.12 -10000 0 -0.51 16 16
TNFR1A/BAG4/TNF-alpha -0.003 0.16 -10000 0 -0.44 57 57
mol:Sphingosine-1-phosphate 0.016 0.005 -10000 0 -10000 0 0
MAP2K1 -0.023 0.078 -10000 0 -0.38 12 12
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
CYCS -0.007 0.071 0.17 26 -0.24 20 46
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.026 -10000 0 -0.5 1 1
EIF2AK2 -0.032 0.084 -10000 0 -0.47 11 11
TNF-alpha/TNFR1A/FAN -0.002 0.16 -10000 0 -0.44 56 56
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.012 0.088 -10000 0 -0.48 7 7
MAP2K2 -0.016 0.067 -10000 0 -0.36 8 8
SMPD3 -0.017 0.1 -10000 0 -0.26 65 65
TNF -0.056 0.22 -10000 0 -0.67 56 56
PKC zeta/PAR4 0.038 0.01 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.016 0.11 0.25 70 -0.25 18 88
NF kappa B1/RelA/I kappa B alpha 0.075 0.023 -10000 0 -10000 0 0
AIFM1 -0.011 0.082 0.17 25 -0.26 26 51
BCL2 -0.023 0.18 -10000 0 -0.66 36 36
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.026 0.009 -10000 0 -10000 0 0
LAT2 -0.002 0.065 -10000 0 -0.27 3 3
AP1 -0.11 0.25 -10000 0 -0.55 103 103
mol:PIP3 0.028 0.17 0.6 21 -0.36 25 46
IKBKB 0.039 0.17 0.59 27 -0.26 7 34
AKT1 -0.007 0.12 0.32 25 -0.44 7 32
IKBKG 0.041 0.17 0.63 27 -0.26 7 34
MS4A2 -0.013 0.06 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
MAP3K1 0.024 0.11 0.45 12 -0.4 7 19
mol:Ca2+ 0.034 0.16 0.44 37 -0.29 20 57
LYN 0.027 0.011 -10000 0 -10000 0 0
CBLB 0 0.062 -10000 0 -0.24 5 5
SHC1 0.025 0.007 -10000 0 -10000 0 0
RasGAP/p62DOK -0.021 0.16 -10000 0 -0.4 78 78
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.019 0.032 -10000 0 -10000 0 0
PLD2 -0.008 0.13 0.32 33 -0.37 29 62
PTPN13 0.012 0.13 0.53 1 -0.62 13 14
PTPN11 0.023 0.036 -10000 0 -0.69 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.032 0.16 0.62 21 -0.36 7 28
SYK 0.025 0.012 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs 0.001 0.1 -10000 0 -0.37 27 27
LAT -0.003 0.068 -10000 0 -0.32 4 4
PAK2 0.017 0.1 0.35 6 -0.43 8 14
NFATC2 -0.1 0.23 -10000 0 -0.6 83 83
HRAS 0.013 0.099 0.26 1 -0.43 10 11
GAB2 0.027 0.005 -10000 0 -10000 0 0
PLA2G1B 0.005 0.097 -10000 0 -0.68 7 7
Fc epsilon R1 0.01 0.13 -10000 0 -0.45 31 31
Antigen/IgE/Fc epsilon R1 0.012 0.12 -10000 0 -0.4 31 31
mol:GDP 0.003 0.1 -10000 0 -0.47 13 13
JUN -0.12 0.28 -10000 0 -0.66 106 106
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
FOS -0.15 0.3 -10000 0 -0.66 124 124
Antigen/IgE/Fc epsilon R1/LYN/SYK 0.005 0.068 -10000 0 -0.24 18 18
CHUK 0.037 0.16 0.56 27 -0.26 7 34
KLRG1 -0.007 0.076 -10000 0 -0.3 14 14
VAV1 -0.003 0.072 0.22 1 -0.36 6 7
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL 0 0.062 -10000 0 -0.25 1 1
negative regulation of mast cell degranulation 0.007 0.079 -10000 0 -0.3 10 10
BTK -0.005 0.12 -10000 0 -0.56 16 16
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.017 0.15 -10000 0 -0.47 40 40
GAB2/PI3K/SHP2 -0.027 0.096 -10000 0 -0.38 28 28
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP 0 0.071 -10000 0 -0.26 28 28
RAF1 0.014 0.085 -10000 0 -0.85 4 4
Fc epsilon R1/FcgammaRIIB/SHIP 0.025 0.17 -10000 0 -0.5 41 41
FCER1G 0.018 0.034 -10000 0 -10000 0 0
FCER1A -0.031 0.17 -10000 0 -0.67 32 32
Antigen/IgE/Fc epsilon R1/Fyn 0.027 0.12 -10000 0 -0.38 31 31
MAPK3 0.018 0.091 -10000 0 -0.7 6 6
MAPK1 -0.015 0.11 -10000 0 -0.72 7 7
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 0 0.18 -10000 0 -0.63 31 31
DUSP1 -0.084 0.25 -10000 0 -0.67 78 78
NF-kappa-B/RelA 0.016 0.047 0.14 1 -0.18 2 3
actin cytoskeleton reorganization 0.015 0.13 0.37 1 -0.71 10 11
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.024 0.097 -10000 0 -0.46 7 7
FER -0.003 0.07 -10000 0 -0.38 4 4
RELA 0.027 0.005 -10000 0 -10000 0 0
ITK -0.043 0.15 -10000 0 -0.46 55 55
SOS1 0.027 0.005 -10000 0 -10000 0 0
PLCG1 0.012 0.12 0.4 8 -0.5 10 18
cytokine secretion 0.005 0.029 -10000 0 -10000 0 0
SPHK1 0 0.064 0.27 1 -0.28 2 3
PTK2 0.014 0.13 0.37 1 -0.75 10 11
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.007 0.11 -10000 0 -0.38 27 27
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.036 0.18 0.66 20 -0.41 11 31
MAP2K2 0.018 0.09 -10000 0 -0.79 4 4
MAP2K1 0.009 0.083 -10000 0 -0.76 5 5
MAP2K7 0.025 0.008 -10000 0 -10000 0 0
KLRG1/SHP2 0 0.081 -10000 0 -0.34 10 10
MAP2K4 -0.006 0.19 -10000 0 -0.85 23 23
Fc epsilon R1/FcgammaRIIB 0.009 0.18 -10000 0 -0.53 41 41
mol:Choline -0.008 0.13 0.32 33 -0.36 29 62
SHC/Grb2/SOS1 0.038 0.075 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
DOK1 0.027 0.005 -10000 0 -10000 0 0
PXN 0.019 0.13 0.42 4 -0.67 10 14
HCLS1 -0.001 0.063 -10000 0 -0.28 2 2
PRKCB 0.036 0.18 0.63 25 -0.33 12 37
FCGR2B -0.009 0.15 -10000 0 -0.67 24 24
IGHE 0.001 0.011 -10000 0 -10000 0 0
KLRG1/SHIP 0.008 0.081 -10000 0 -0.31 10 10
LCP2 0.024 0.02 -10000 0 -10000 0 0
PLA2G4A -0.022 0.12 -10000 0 -0.42 31 31
RASA1 0.027 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.008 0.13 0.32 33 -0.36 29 62
IKK complex 0.044 0.18 0.62 29 -0.21 3 32
WIPF1 0.027 0.005 -10000 0 -10000 0 0
ceramide signaling pathway

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
MAP4K4 -0.015 0.12 -10000 0 -0.44 20 20
BAG4 0.025 0.032 -10000 0 -0.67 1 1
BAD 0.007 0.065 0.34 9 -10000 0 9
NFKBIA 0.027 0.005 -10000 0 -10000 0 0
BIRC3 -0.01 0.14 -10000 0 -0.62 25 25
BAX 0.012 0.07 0.24 25 -0.15 11 36
EnzymeConsortium:3.1.4.12 0.002 0.039 0.16 10 -0.1 17 27
IKBKB -0.013 0.12 0.29 1 -0.42 19 20
MAP2K2 0.017 0.094 0.33 24 -0.3 2 26
MAP2K1 0.011 0.084 0.32 19 -0.3 2 21
SMPD1 0.005 0.046 0.22 8 -0.13 6 14
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.01 0.12 -10000 0 -0.45 20 20
MAP2K4 0.017 0.096 0.35 26 -10000 0 26
protein ubiquitination -0.012 0.12 0.32 4 -0.43 18 22
EnzymeConsortium:2.7.1.37 0.017 0.11 0.38 25 -0.3 2 27
response to UV 0 0.002 0.006 27 -0.002 12 39
RAF1 0.012 0.085 0.31 21 -0.31 2 23
CRADD 0.027 0.005 -10000 0 -10000 0 0
mol:ceramide 0.004 0.059 0.22 12 -0.15 16 28
I-kappa-B-alpha/RELA/p50/ubiquitin 0.036 0.008 -10000 0 -10000 0 0
MADD 0.027 0.005 -10000 0 -10000 0 0
MAP3K1 0.01 0.077 0.31 18 -0.16 10 28
TRADD 0.026 0.006 -10000 0 -10000 0 0
RELA/p50 0.027 0.005 -10000 0 -10000 0 0
MAPK3 0.017 0.088 0.34 19 -0.29 2 21
MAPK1 -0.005 0.09 0.33 16 -0.27 4 20
p50/RELA/I-kappa-B-alpha 0.039 0.009 -10000 0 -10000 0 0
FADD -0.015 0.12 -10000 0 -0.44 19 19
KSR1 0.01 0.08 0.27 24 -0.19 12 36
MAPK8 0.011 0.11 0.38 22 -0.35 9 31
TRAF2 0.025 0.008 -10000 0 -10000 0 0
response to radiation 0 0.001 0.006 13 -10000 0 13
CHUK -0.014 0.12 0.33 1 -0.42 20 21
TNF R/SODD 0.038 0.026 -10000 0 -0.5 1 1
TNF -0.055 0.22 -10000 0 -0.67 56 56
CYCS 0.019 0.08 0.24 29 -0.15 10 39
IKBKG -0.013 0.12 0.32 2 -0.42 18 20
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.016 0.13 -10000 0 -0.41 29 29
RELA 0.027 0.005 -10000 0 -10000 0 0
RIPK1 0.027 0.003 -10000 0 -10000 0 0
AIFM1 0.017 0.079 0.25 24 -0.17 3 27
TNF/TNF R/SODD -0.003 0.16 -10000 0 -0.43 57 57
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
response to heat 0 0.001 0.006 13 -10000 0 13
CASP8 0.008 0.13 -10000 0 -0.72 14 14
NSMAF -0.014 0.12 -10000 0 -0.44 19 19
response to hydrogen peroxide 0 0.002 0.006 27 -0.002 12 39
BCL2 -0.023 0.18 -10000 0 -0.66 36 36
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.014 0.2 -10000 0 -0.94 20 20
NCK1/PAK1/Dok-R -0.028 0.088 -10000 0 -0.43 20 20
NCK1/Dok-R -0.004 0.25 -10000 0 -1.1 20 20
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
mol:beta2-estradiol 0 0.045 0.23 18 -10000 0 18
RELA 0.027 0.005 -10000 0 -10000 0 0
SHC1 0.026 0.008 -10000 0 -10000 0 0
Rac/GDP 0.019 0.004 -10000 0 -10000 0 0
F2 -0.011 0.056 0.27 13 -10000 0 13
TNIP2 0.027 0.004 -10000 0 -10000 0 0
NF kappa B/RelA 0.01 0.23 -10000 0 -1 20 20
FN1 -0.078 0.065 -10000 0 -10000 0 0
PLD2 -0.026 0.25 -10000 0 -1.2 20 20
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
GRB14 0.007 0.12 -10000 0 -0.67 14 14
ELK1 -0.025 0.22 -10000 0 -1 20 20
GRB7 0.003 0.053 -10000 0 -10000 0 0
PAK1 0.027 0.005 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.008 0.25 -10000 0 -1.1 20 20
CDKN1A -0.023 0.16 0.49 4 -0.63 20 24
ITGA5 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.005 0.25 -10000 0 -1.1 20 20
CRK 0.026 0.007 -10000 0 -10000 0 0
mol:NO 0.01 0.17 0.57 8 -0.67 20 28
PLG -0.032 0.25 -10000 0 -1.2 20 20
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.012 0.19 -10000 0 -0.89 20 20
GRB2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.006 -10000 0 -10000 0 0
ANGPT2 -0.1 0.2 0.42 1 -0.79 16 17
BMX -0.035 0.26 -10000 0 -1.2 20 20
ANGPT1 -0.044 0.26 -10000 0 -1.3 18 18
tube development -0.038 0.17 0.48 2 -0.73 20 22
ANGPT4 -0.033 0.19 -10000 0 -0.67 41 41
response to hypoxia -0.004 0.015 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.028 0.27 -10000 0 -1.2 20 20
alpha5/beta1 Integrin 0.039 0.009 -10000 0 -10000 0 0
FGF2 0.026 0.004 -10000 0 -10000 0 0
STAT5A (dimer) -0.038 0.19 -10000 0 -0.83 20 20
mol:L-citrulline 0.01 0.17 0.57 8 -0.67 20 28
AGTR1 -0.25 0.34 -10000 0 -0.66 199 199
MAPK14 -0.027 0.25 -10000 0 -1.2 20 20
Tie2/SHP2 -0.004 0.18 -10000 0 -1.2 8 8
TEK 0.004 0.19 -10000 0 -1.4 8 8
RPS6KB1 -0.007 0.2 0.5 2 -0.89 20 22
Angiotensin II/AT1 -0.19 0.26 -10000 0 -0.5 199 199
Tie2/Ang1/GRB2 -0.017 0.26 -10000 0 -1.2 20 20
MAPK3 -0.021 0.22 -10000 0 -1.1 20 20
MAPK1 -0.03 0.22 -10000 0 -1.1 20 20
Tie2/Ang1/GRB7 -0.017 0.26 -10000 0 -1.2 20 20
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.033 0.26 -10000 0 -1.2 20 20
PI3K -0.021 0.23 -10000 0 -1.1 20 20
FES -0.028 0.25 -10000 0 -1.2 20 20
Crk/Dok-R -0.004 0.25 -10000 0 -1.1 20 20
Tie2/Ang1/ABIN2 -0.016 0.26 -10000 0 -1.2 20 20
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.004 0.19 0.5 4 -0.83 20 24
STAT5A 0.026 0.007 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.011 0.2 0.48 1 -0.9 20 21
Tie2/Ang2 -0.057 0.22 -10000 0 -1 20 20
Tie2/Ang1 -0.028 0.28 -10000 0 -1.3 20 20
FOXO1 -0.001 0.19 0.56 4 -0.83 20 24
ELF1 0.028 0.052 -10000 0 -0.58 3 3
ELF2 -0.025 0.24 -10000 0 -1.2 20 20
mol:Choline -0.023 0.23 -10000 0 -1.1 20 20
cell migration -0.009 0.056 -10000 0 -0.24 20 20
FYN -0.047 0.19 0.52 1 -0.84 20 21
DOK2 0.019 0.051 -10000 0 -0.67 2 2
negative regulation of cell cycle -0.02 0.15 0.48 4 -0.57 20 24
ETS1 0.026 0.047 -10000 0 -10000 0 0
PXN 0.001 0.18 0.59 5 -0.73 20 25
ITGB1 0.027 0.004 -10000 0 -10000 0 0
NOS3 0.003 0.19 0.57 7 -0.77 20 27
RAC1 0.026 0.006 -10000 0 -10000 0 0
TNF -0.057 0.23 -10000 0 -0.59 71 71
MAPKKK cascade -0.023 0.23 -10000 0 -1.1 20 20
RASA1 0.027 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.019 0.26 -10000 0 -1.2 20 20
NCK1 0.027 0.003 -10000 0 -10000 0 0
vasculogenesis 0.013 0.16 0.52 10 -0.6 20 30
mol:Phosphatidic acid -0.023 0.23 -10000 0 -1.1 20 20
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.01 0.17 0.57 8 -0.67 20 28
Rac1/GTP -0.005 0.18 -10000 0 -0.83 20 20
MMP2 -0.031 0.26 -10000 0 -1.2 20 20
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.04 0.12 0.89 7 -10000 0 7
VDR 0.026 0.008 -10000 0 -10000 0 0
FAM120B 0.027 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.004 0.11 -10000 0 -0.3 41 41
RXRs/LXRs/DNA/Oxysterols -0.009 0.15 -10000 0 -0.41 54 54
MED1 0.026 0.007 -10000 0 -10000 0 0
mol:9cRA -0.001 0.018 -10000 0 -0.14 1 1
RARs/THRs/DNA/Src-1 0.02 0.069 -10000 0 -0.3 21 21
RXRs/NUR77 -0.088 0.23 -10000 0 -0.44 135 135
RXRs/PPAR -0.019 0.081 -10000 0 -0.38 11 11
NCOR2 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.02 0.006 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.048 0.074 -10000 0 -0.38 13 13
RARA 0.026 0.007 -10000 0 -10000 0 0
NCOA1 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.008 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.032 0.071 -10000 0 -0.36 14 14
RARG 0.027 0.005 -10000 0 -10000 0 0
RPS6KB1 0.051 0.12 0.56 27 -10000 0 27
RARs/THRs/DNA/SMRT 0.02 0.069 -10000 0 -0.3 21 21
THRA 0.026 0.007 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.02 0.006 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.039 0.097 -10000 0 -0.35 8 8
NR1H4 -0.004 0.022 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.059 0.12 -10000 0 -0.5 4 4
NR1H2 0.022 0.024 -10000 0 -10000 0 0
NR1H3 0.023 0.026 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.05 0.08 -10000 0 -0.45 3 3
NR4A1 -0.18 0.32 -10000 0 -0.67 145 145
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.004 0.054 -10000 0 -0.31 3 3
RXRG -0.1 0.075 -10000 0 -0.6 5 5
RXR alpha/CCPG 0.032 0.025 -10000 0 -10000 0 0
RXRA 0.02 0.025 -10000 0 -10000 0 0
RXRB 0.023 0.027 -10000 0 -10000 0 0
THRB 0.014 0.095 -10000 0 -0.64 10 10
PPARG 0.016 0.083 -10000 0 -0.67 7 7
PPARD 0.027 0.003 -10000 0 -10000 0 0
TNF -0.097 0.37 -10000 0 -1.1 57 57
mol:Oxysterols -0.001 0.016 -10000 0 -10000 0 0
cholesterol transport -0.008 0.15 -10000 0 -0.41 54 54
PPARA 0.02 0.012 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.007 0.12 -10000 0 -0.67 14 14
RXRs/NUR77/BCL2 -0.11 0.17 -10000 0 -0.34 149 149
SREBF1 -0.01 0.14 -10000 0 -0.52 7 7
RXRs/RXRs/DNA/9cRA 0.039 0.097 -10000 0 -0.35 8 8
ABCA1 -0.009 0.14 -10000 0 -0.51 8 8
RARs/THRs 0.056 0.097 -10000 0 -0.4 20 20
RXRs/FXR 0.05 0.085 -10000 0 -0.48 3 3
BCL2 -0.023 0.18 -10000 0 -0.66 36 36
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.032 0.069 -10000 0 -0.57 6 6
alphaV beta3 Integrin 0.039 0.081 -10000 0 -0.47 11 11
PTK2 0.012 0.14 0.41 11 -0.5 11 22
IGF1R 0.027 0.004 -10000 0 -10000 0 0
PI4KB 0.025 0.007 -10000 0 -10000 0 0
MFGE8 0.01 0.047 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
CDKN1B -0.027 0.16 -10000 0 -0.53 45 45
VEGFA 0.023 0.054 -10000 0 -0.67 3 3
ILK -0.028 0.16 -10000 0 -0.53 46 46
ROCK1 0.027 0.005 -10000 0 -10000 0 0
AKT1 -0.029 0.15 -10000 0 -0.5 45 45
PTK2B 0.012 0.089 0.36 1 -0.42 16 17
alphaV/beta3 Integrin/JAM-A 0.007 0.14 -10000 0 -0.39 51 51
CBL 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.036 0.079 -10000 0 -0.48 10 10
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.088 0.24 -10000 0 -0.43 152 152
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0 0.092 -10000 0 -0.41 5 5
alphaV/beta3 Integrin/Syndecan-1 0.04 0.081 -10000 0 -0.47 11 11
PI4KA 0.02 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.092 0.23 -10000 0 -0.42 152 152
PI4 Kinase 0.028 0.019 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
alphaV/beta3 Integrin/Osteopontin 0.02 0.13 -10000 0 -0.45 31 31
RPS6KB1 -0.14 0.19 0.42 2 -0.42 113 115
TLN1 0.025 0.007 -10000 0 -10000 0 0
MAPK3 -0.05 0.13 -10000 0 -0.64 12 12
GPR124 0.027 0.005 -10000 0 -10000 0 0
MAPK1 -0.059 0.14 -10000 0 -0.6 17 17
PXN 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.028 0.12 -10000 0 -0.51 20 20
cell adhesion 0.03 0.077 -10000 0 -0.45 10 10
ANGPTL3 0.007 0.024 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.047 0.064 -10000 0 -0.5 6 6
IGF-1R heterotetramer 0.027 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
TGFBR2 0.023 0.054 -10000 0 -0.67 3 3
ITGB3 0.011 0.099 -10000 0 -0.64 11 11
IGF1 -0.13 0.28 -10000 0 -0.66 107 107
RAC1 0.026 0.006 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.039 0.08 -10000 0 -0.47 11 11
apoptosis 0.024 0.044 -10000 0 -0.66 2 2
CD47 0.027 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.04 0.081 -10000 0 -0.47 11 11
VCL 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.032 0.1 -10000 0 -0.48 18 18
CSF1 0.015 0.088 -10000 0 -0.67 8 8
PIK3C2A -0.029 0.17 -10000 0 -0.53 47 47
PI4 Kinase/Pyk2 -0.014 0.12 -10000 0 -0.36 42 42
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.048 0.096 -10000 0 -0.44 16 16
FAK1/Vinculin 0.023 0.12 0.39 9 -0.41 9 18
alphaV beta3/Integrin/ppsTEM5 0.039 0.081 -10000 0 -0.47 11 11
RHOA 0.027 0.003 -10000 0 -10000 0 0
VTN -0.038 0.2 -10000 0 -0.67 44 44
BCAR1 0.026 0.006 -10000 0 -10000 0 0
FGF2 0.027 0.004 -10000 0 -10000 0 0
F11R 0.016 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin 0.041 0.081 -10000 0 -0.47 11 11
alphaV/beta3 Integrin/TGFBR2 0.037 0.086 -10000 0 -0.44 14 14
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.055 0.072 -10000 0 -0.44 9 9
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.035 0.075 -10000 0 -0.43 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.078 0.065 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 0.033 0.088 -10000 0 -0.42 16 16
SDC1 0.025 0.014 -10000 0 -10000 0 0
VAV3 0.009 0.08 -10000 0 -0.42 14 14
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
IRS1 -0.056 0.22 -10000 0 -0.66 59 59
FAK1/Paxillin 0.022 0.12 0.35 8 -0.41 9 17
cell migration 0.017 0.11 0.34 6 -0.4 6 12
ITGAV 0.024 0.044 -10000 0 -0.67 2 2
PI3K 0.016 0.14 -10000 0 -0.38 52 52
SPP1 -0.029 0.15 -10000 0 -0.67 23 23
KDR 0.021 0.063 -10000 0 -0.67 4 4
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.024 0.044 -10000 0 -0.67 2 2
COL4A3 0.008 0.11 -10000 0 -0.62 14 14
angiogenesis -0.054 0.15 -10000 0 -0.61 17 17
Rac1/GTP 0.021 0.074 -10000 0 -0.39 14 14
EDIL3 0.006 0.093 -10000 0 -0.67 8 8
cell proliferation 0.037 0.085 -10000 0 -0.44 14 14
IL27-mediated signaling events

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
TGFB1 0.026 0.017 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.044 0.13 0.47 15 -10000 0 15
IL27/IL27R/JAK1 -0.013 0.17 -10000 0 -0.47 13 13
TBX21 -0.066 0.18 0.39 4 -0.57 28 32
IL12B 0.005 0.079 -10000 0 -0.67 6 6
IL12A -0.047 0.16 -10000 0 -0.5 51 51
IL6ST -0.072 0.24 -10000 0 -0.67 66 66
IL27RA/JAK1 0.019 0.053 0.56 1 -10000 0 1
IL27 0.011 0.027 -10000 0 -10000 0 0
TYK2 0.019 0.02 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.039 0.13 -10000 0 -0.49 3 3
T-helper 2 cell differentiation 0.044 0.13 0.47 15 -10000 0 15
T cell proliferation during immune response 0.044 0.13 0.47 15 -10000 0 15
MAPKKK cascade -0.044 0.13 -10000 0 -0.47 15 15
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT2 0.027 0.005 -10000 0 -10000 0 0
STAT1 0.023 0.023 -10000 0 -10000 0 0
IL12RB1 0.004 0.081 -10000 0 -0.62 6 6
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.058 0.19 0.49 11 -0.54 27 38
IL27/IL27R/JAK2/TYK2 -0.045 0.13 -10000 0 -0.48 15 15
positive regulation of T cell mediated cytotoxicity -0.044 0.13 -10000 0 -0.47 15 15
STAT1 (dimer) -0.026 0.21 0.53 11 -0.6 17 28
JAK2 0.019 0.031 -10000 0 -0.36 2 2
JAK1 0.027 0.008 -10000 0 -10000 0 0
STAT2 (dimer) -0.033 0.14 -10000 0 -0.46 14 14
T cell proliferation -0.1 0.19 -10000 0 -0.5 59 59
IL12/IL12R/TYK2/JAK2 -0.07 0.23 -10000 0 -0.81 30 30
IL17A -0.04 0.13 -10000 0 -0.49 3 3
mast cell activation 0.044 0.13 0.47 15 -10000 0 15
IFNG -0.016 0.051 0.089 4 -0.13 67 71
T cell differentiation -0.004 0.008 0.014 1 -0.022 64 65
STAT3 (dimer) -0.032 0.13 -10000 0 -0.44 15 15
STAT5A (dimer) -0.032 0.13 -10000 0 -0.46 13 13
STAT4 (dimer) -0.038 0.15 0.33 1 -0.45 22 23
STAT4 0.004 0.098 -10000 0 -0.58 11 11
T cell activation -0.008 0.005 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.024 0.15 -10000 0 -0.46 11 11
GATA3 -0.056 0.29 -10000 0 -1.3 24 24
IL18 -0.012 0.076 -10000 0 -0.48 11 11
positive regulation of mast cell cytokine production -0.031 0.13 -10000 0 -0.44 15 15
IL27/EBI3 -0.027 0.058 -10000 0 -0.25 1 1
IL27RA 0 0.024 -10000 0 -10000 0 0
IL6 -0.094 0.26 -10000 0 -0.67 80 80
STAT5A 0.026 0.007 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.003 -10000 0 -0.023 2 2
IL2 -0.011 0.018 -10000 0 -10000 0 0
IL1B -0.028 0.13 -10000 0 -0.5 33 33
EBI3 -0.048 0.071 -10000 0 -0.36 1 1
TNF -0.053 0.16 -10000 0 -0.5 56 56
Signaling events mediated by PTP1B

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
PDGFRB 0.025 0.032 -10000 0 -0.67 1 1
Jak2/Leptin Receptor -0.006 0.12 0.29 2 -0.37 29 31
PTP1B/AKT1 0.006 0.071 0.32 2 -0.28 6 8
FYN 0.027 0.004 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0 0.082 0.32 10 -0.28 9 19
EGFR 0.013 0.072 -10000 0 -0.68 5 5
EGF/EGFR -0.035 0.16 0.24 1 -0.38 74 75
CSF1 0.015 0.088 -10000 0 -0.67 8 8
AKT1 0.027 0.006 -10000 0 -10000 0 0
INSR 0.026 0.008 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.002 0.11 0.32 6 -0.33 20 26
Insulin Receptor/Insulin 0.015 0.072 -10000 0 -0.35 4 4
HCK 0.017 0.037 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
TYK2 0.008 0.092 0.31 20 -0.28 7 27
EGF -0.076 0.25 -10000 0 -0.67 72 72
YES1 0.027 0.005 -10000 0 -10000 0 0
CAV1 -0.004 0.11 0.4 12 -0.31 10 22
TXN 0.024 0.011 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.03 0.14 -10000 0 -0.38 60 60
cell migration 0 0.082 0.28 9 -0.32 10 19
STAT3 0.026 0.007 -10000 0 -10000 0 0
PRLR -0.014 0.15 -10000 0 -0.67 25 25
ITGA2B -0.043 0.21 -10000 0 -0.66 49 49
CSF1R 0.024 0.035 -10000 0 -0.67 1 1
Prolactin Receptor/Prolactin 0.001 0.12 -10000 0 -0.5 25 25
FGR 0.025 0.014 -10000 0 -10000 0 0
PTP1B/p130 Cas 0.006 0.072 0.28 3 -0.28 6 9
Crk/p130 Cas 0.013 0.071 -10000 0 -0.29 4 4
DOK1 0.012 0.087 0.36 12 -0.34 3 15
JAK2 -0.012 0.12 0.31 7 -0.37 34 41
Jak2/Leptin Receptor/Leptin -0.007 0.13 -10000 0 -0.49 19 19
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
PTPN1 0 0.083 0.32 10 -0.28 9 19
LYN 0.027 0.005 -10000 0 -10000 0 0
CDH2 -0.068 0.12 -10000 0 -0.62 14 14
SRC 0.023 0.057 0.32 1 -0.39 5 6
ITGB3 0.01 0.1 -10000 0 -0.64 11 11
CAT1/PTP1B -0.058 0.16 0.4 14 -0.36 43 57
CAPN1 0.027 0.006 -10000 0 -10000 0 0
CSK 0.027 0.008 -10000 0 -10000 0 0
PI3K 0.021 0.082 -10000 0 -0.42 6 6
mol:H2O2 -0.001 0.007 -10000 0 -10000 0 0
STAT3 (dimer) -0.007 0.13 -10000 0 -0.52 19 19
negative regulation of transcription -0.01 0.12 0.31 7 -0.36 34 41
FCGR2A 0.017 0.044 -10000 0 -0.67 1 1
FER 0.021 0.055 -10000 0 -0.68 3 3
alphaIIb/beta3 Integrin -0.027 0.18 -10000 0 -0.53 56 56
BLK -0.19 0.31 -10000 0 -0.66 145 145
Insulin Receptor/Insulin/Shc 0.039 0.04 -10000 0 -0.42 3 3
RHOA 0.028 0.006 -10000 0 -10000 0 0
LEPR 0.021 0.06 -10000 0 -0.54 5 5
BCAR1 0.026 0.006 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.026 0.007 -10000 0 -10000 0 0
mol:NADPH 0 0.005 -10000 0 -10000 0 0
TRPV6 -0.088 0.17 0.38 3 -0.47 41 44
PRL -0.006 0.019 -10000 0 -10000 0 0
SOCS3 -0.039 0.3 -10000 0 -1.3 26 26
SPRY2 0.022 0.046 -10000 0 -0.68 2 2
Insulin Receptor/Insulin/IRS1 -0.017 0.16 -10000 0 -0.44 61 61
CSF1/CSF1R 0.008 0.095 0.28 1 -0.45 10 11
Ras protein signal transduction 0.027 0.11 0.44 28 -10000 0 28
IRS1 -0.056 0.22 -10000 0 -0.66 59 59
INS 0.007 0.055 -10000 0 -0.67 3 3
LEP 0.009 0.032 -10000 0 -10000 0 0
STAT5B 0.002 0.091 0.29 11 -0.28 14 25
STAT5A 0.002 0.091 0.29 11 -0.28 14 25
GRB2 0.026 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.004 0.073 0.28 1 -0.3 9 10
CSN2 0.001 0.063 0.81 1 -10000 0 1
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
LAT 0.02 0.073 0.32 1 -0.45 8 9
YBX1 0.033 0.007 -10000 0 -10000 0 0
LCK 0.012 0.081 -10000 0 -0.67 6 6
SHC1 0.025 0.007 -10000 0 -10000 0 0
NOX4 -0.036 0.072 -10000 0 -10000 0 0
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.011 0.1 -10000 0 -0.51 11 11
alphaM/beta2 Integrin/GPIbA 0.002 0.12 -10000 0 -0.49 18 18
alphaM/beta2 Integrin/proMMP-9 -0.021 0.16 -10000 0 -0.5 43 43
PLAUR -0.02 0.067 -10000 0 -10000 0 0
HMGB1 0.009 0.035 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.015 0.085 -10000 0 -0.56 5 5
AGER -0.037 0.18 -10000 0 -0.69 32 32
RAP1A 0.027 0.005 -10000 0 -10000 0 0
SELPLG 0.017 0.037 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.031 0.19 -10000 0 -0.47 54 54
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.041 0.19 -10000 0 -0.67 41 41
CYR61 -0.18 0.31 -10000 0 -0.66 143 143
TLN1 0.025 0.007 -10000 0 -10000 0 0
Rap1/GTP 0.001 0.087 -10000 0 -0.37 9 9
RHOA 0.027 0.003 -10000 0 -10000 0 0
P-selectin oligomer 0.015 0.078 -10000 0 -0.67 6 6
MYH2 -0.028 0.097 -10000 0 -0.4 10 10
MST1R 0.02 0.064 -10000 0 -0.67 4 4
leukocyte activation during inflammatory response 0.015 0.08 -10000 0 -0.49 5 5
APOB 0.007 0.038 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.017 0.079 -10000 0 -0.62 7 7
JAM3 0.027 0.005 -10000 0 -10000 0 0
GP1BA 0.002 0.12 -10000 0 -0.63 15 15
alphaM/beta2 Integrin/CTGF -0.05 0.19 -10000 0 -0.46 75 75
alphaM/beta2 Integrin -0.021 0.089 -10000 0 -0.32 21 21
JAM3 homodimer 0.027 0.005 -10000 0 -10000 0 0
ICAM2 0.026 0.007 -10000 0 -10000 0 0
ICAM1 -0.009 0.061 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.022 0.089 -10000 0 -0.32 22 22
cell adhesion 0.001 0.12 -10000 0 -0.48 18 18
NFKB1 -0.11 0.26 0.33 1 -0.5 130 131
THY1 0.026 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
Lipoprotein(a) 0.021 0.027 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.03 0.093 -10000 0 -0.48 9 9
IL6 -0.18 0.38 -10000 0 -0.95 87 87
ITGB2 -0.001 0.057 -10000 0 -0.7 1 1
elevation of cytosolic calcium ion concentration 0.016 0.1 -10000 0 -0.51 5 5
alphaM/beta2 Integrin/JAM2/JAM3 0.03 0.093 -10000 0 -0.47 9 9
JAM2 0.02 0.063 -10000 0 -0.67 4 4
alphaM/beta2 Integrin/ICAM1 0.036 0.1 -10000 0 -0.48 9 9
alphaM/beta2 Integrin/uPA/Plg 0.017 0.096 -10000 0 -0.47 6 6
RhoA/GTP -0.023 0.1 -10000 0 -0.36 17 17
positive regulation of phagocytosis -0.005 0.096 -10000 0 -0.46 8 8
Ron/MSP 0.034 0.056 -10000 0 -0.5 5 5
alphaM/beta2 Integrin/uPAR/uPA 0.018 0.11 -10000 0 -0.51 5 5
alphaM/beta2 Integrin/uPAR 0.013 0.092 -10000 0 -0.54 5 5
PLAU -0.04 0.072 -10000 0 -10000 0 0
PLAT 0.02 0.057 -10000 0 -0.67 3 3
actin filament polymerization -0.027 0.094 -10000 0 -0.39 9 9
MST1 0.026 0.031 -10000 0 -0.67 1 1
alphaM/beta2 Integrin/lipoprotein(a) 0.02 0.082 -10000 0 -0.5 5 5
TNF -0.16 0.34 0.33 1 -0.89 76 77
RAP1B 0.027 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.01 0.097 -10000 0 -0.51 6 6
fibrinolysis 0.015 0.095 -10000 0 -0.47 6 6
HCK 0.017 0.037 -10000 0 -10000 0 0
dendritic cell antigen processing and presentation -0.022 0.089 -10000 0 -0.32 22 22
VTN -0.038 0.2 -10000 0 -0.67 44 44
alphaM/beta2 Integrin/CYR61 -0.12 0.23 -10000 0 -0.46 145 145
LPA -0.005 0.025 -10000 0 -10000 0 0
LRP1 0.025 0.032 -10000 0 -0.67 1 1
cell migration -0.03 0.16 -10000 0 -0.48 45 45
FN1 -0.078 0.065 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 0.017 0.086 -10000 0 -0.56 5 5
MPO 0.012 0.077 -10000 0 -0.67 6 6
KNG1 -0.005 0.037 -10000 0 -10000 0 0
RAP1/GDP 0.035 0.009 -10000 0 -10000 0 0
ROCK1 -0.022 0.097 -10000 0 -0.43 7 7
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.014 0.019 -10000 0 -10000 0 0
CTGF -0.077 0.25 -10000 0 -0.66 75 75
alphaM/beta2 Integrin/Hck 0.012 0.09 -10000 0 -0.51 6 6
ITGAM -0.005 0.08 -10000 0 -0.54 6 6
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.024 0.1 -10000 0 -0.52 10 10
HP -0.021 0.095 -10000 0 -0.67 6 6
leukocyte adhesion -0.025 0.16 -10000 0 -0.52 24 24
SELP 0.015 0.078 -10000 0 -0.67 6 6
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.004 0.14 -10000 0 -0.36 62 62
TC10/GTP 0.042 0.038 -10000 0 -0.35 3 3
Insulin Receptor/Insulin/IRS1/Shp2 -0.001 0.16 -10000 0 -0.42 61 61
HRAS 0.026 0.011 -10000 0 -10000 0 0
APS homodimer 0.026 0.009 -10000 0 -10000 0 0
GRB14 0.007 0.12 -10000 0 -0.67 14 14
FOXO3 0.001 0.12 -10000 0 -0.65 14 14
AKT1 -0.029 0.14 0.36 5 -0.34 68 73
INSR 0.027 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.05 0.035 -10000 0 -0.34 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.026 0.006 -10000 0 -10000 0 0
SORBS1 0.021 0.063 -10000 0 -0.67 4 4
CRK 0.026 0.007 -10000 0 -10000 0 0
PTPN1 0.015 0.038 -10000 0 -0.33 3 3
CAV1 -0.037 0.14 -10000 0 -0.38 67 67
CBL/APS/CAP/Crk-II/C3G 0.066 0.047 -10000 0 -0.38 3 3
Insulin Receptor/Insulin/IRS1/NCK2 0.001 0.16 -10000 0 -0.41 61 61
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.005 0.14 -10000 0 -0.37 63 63
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.008 0.1 -10000 0 -0.43 8 8
RPS6KB1 -0.033 0.12 0.29 3 -0.36 13 16
PARD6A 0.026 0.006 -10000 0 -10000 0 0
CBL 0.027 0.005 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.018 0.036 -10000 0 -0.52 2 2
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.012 0.13 -10000 0 -0.33 56 56
HRAS/GTP -0.024 0.11 -10000 0 -0.33 47 47
Insulin Receptor 0.027 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.014 0.14 -10000 0 -0.38 48 48
PRKCI 0.012 0.075 -10000 0 -0.49 5 5
Insulin Receptor/Insulin/GRB14/PDK1 -0.027 0.14 -10000 0 -0.36 72 72
SHC1 0.025 0.007 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.045 0.046 -10000 0 -0.37 4 4
PI3K 0.003 0.15 -10000 0 -0.37 63 63
NCK2 0.027 0.005 -10000 0 -10000 0 0
RHOQ 0.027 0.005 -10000 0 -10000 0 0
mol:H2O2 0.001 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.007 -10000 0 -10000 0 0
AKT2 -0.031 0.14 0.38 7 -0.34 67 74
PRKCZ 0.012 0.074 -10000 0 -0.51 5 5
SH2B2 0.026 0.009 -10000 0 -10000 0 0
SHC/SHIP -0.014 0.13 0.3 1 -0.36 51 52
F2RL2 -0.017 0.082 -10000 0 -0.67 3 3
TRIP10 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.039 0.036 -10000 0 -0.36 3 3
TC10/GTP/CIP4/Exocyst 0.034 0.011 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.062 0.041 -10000 0 -0.34 2 2
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
RASA1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.06 0.044 -10000 0 -0.4 3 3
TC10/GDP 0.02 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.053 0.041 -10000 0 -0.36 3 3
INPP5D -0.032 0.14 0.31 1 -0.38 61 62
SOS1 0.027 0.005 -10000 0 -10000 0 0
SGK1 -0.013 0.15 -10000 0 -0.83 15 15
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
IRS1 -0.056 0.22 -10000 0 -0.66 59 59
p62DOK/RasGAP 0.046 0.046 -10000 0 -0.38 4 4
INS 0.015 0.054 -10000 0 -0.67 3 3
mol:PI-3-4-P2 -0.032 0.14 0.31 1 -0.38 61 62
GRB2 0.026 0.007 -10000 0 -10000 0 0
EIF4EBP1 -0.033 0.12 0.36 3 -0.37 13 16
PTPRA 0.028 0.008 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
TC10/GTP/CIP4 0.034 0.011 -10000 0 -10000 0 0
PDPK1 0.023 0.045 -10000 0 -0.67 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.01 0.1 -10000 0 -0.29 48 48
Insulin Receptor/Insulin/IRS1 -0.013 0.15 -10000 0 -0.41 61 61
Insulin Receptor/Insulin/IRS3 0.03 0.043 -10000 0 -0.5 3 3
Par3/Par6 0.059 0.039 -10000 0 -0.38 2 2
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.018 0.12 -10000 0 -0.45 24 24
MAP4K1 0.008 0.078 -10000 0 -0.67 5 5
MAP3K8 0.018 0.078 -10000 0 -0.62 7 7
PRKCB 0.008 0.079 -10000 0 -0.67 5 5
DBNL 0.026 0.006 -10000 0 -10000 0 0
CRKL 0.02 0.012 -10000 0 -10000 0 0
MAP3K1 0.002 0.08 -10000 0 -0.32 25 25
JUN -0.083 0.21 0.37 1 -0.51 52 53
MAP3K7 0.002 0.08 -10000 0 -0.41 9 9
GRAP2 -0.02 0.15 -10000 0 -0.55 33 33
CRK 0.026 0.007 -10000 0 -10000 0 0
MAP2K4 -0.003 0.097 0.34 3 -0.36 17 20
LAT 0.021 0.058 -10000 0 -0.59 4 4
LCP2 0.024 0.02 -10000 0 -10000 0 0
MAPK8 -0.007 0.15 -10000 0 -0.61 25 25
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.005 0.085 -10000 0 -0.33 25 25
LAT/GRAP2/SLP76/HPK1/HIP-55 0.028 0.12 -10000 0 -0.44 23 23
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.027 0.005 -10000 0 -10000 0 0
mol:PIP3 -0.031 0.11 -10000 0 -0.33 59 59
FRAP1 0.01 0.047 0.36 3 -0.42 1 4
AKT1 -0.027 0.096 -10000 0 -0.28 56 56
INSR 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.024 0.037 -10000 0 -0.43 3 3
mol:GTP 0.003 0.089 -10000 0 -0.42 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.006 0.036 -10000 0 -0.24 1 1
TSC2 0.026 0.006 -10000 0 -10000 0 0
RHEB/GDP -0.002 0.075 -10000 0 -0.38 3 3
TSC1 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.024 0.13 -10000 0 -0.37 61 61
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.016 0.044 -10000 0 -0.27 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.027 0.004 -10000 0 -10000 0 0
RPS6KB1 0.018 0.098 0.39 18 -0.37 3 21
MAP3K5 0.006 0.028 0.18 1 -0.22 6 7
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
apoptosis 0.006 0.029 0.18 1 -0.21 7 8
mol:LY294002 0 0.001 0.001 1 -0.002 73 74
EIF4B 0.023 0.11 0.46 21 -0.32 3 24
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.027 0.069 0.38 4 -0.33 2 6
eIF4E/eIF4G1/eIF4A1 0.016 0.024 -10000 0 -0.25 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.009 0.13 -10000 0 -0.36 60 60
mTOR/RHEB/GTP/Raptor/GBL 0.004 0.047 0.28 3 -0.24 2 5
FKBP1A 0.027 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.011 0.081 -10000 0 -0.38 3 3
mol:Amino Acids 0 0.001 0.001 1 -0.002 73 74
FKBP12/Rapamycin 0.02 0.004 -10000 0 -10000 0 0
PDPK1 -0.033 0.11 -10000 0 -0.32 58 58
EIF4E 0.027 0.004 -10000 0 -10000 0 0
ASK1/PP5C 0.025 0.074 -10000 0 -0.5 8 8
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.018 0.008 -10000 0 -10000 0 0
TSC1/TSC2 0.005 0.097 0.28 1 -0.46 3 4
tumor necrosis factor receptor activity 0 0.001 0.002 73 -0.001 1 74
RPS6 0.025 0.008 -10000 0 -10000 0 0
PPP5C 0.025 0.007 -10000 0 -10000 0 0
EIF4G1 0.027 0.004 -10000 0 -10000 0 0
IRS1 -0.044 0.14 -10000 0 -0.37 68 68
INS -0.02 0.051 -10000 0 -0.67 3 3
PTEN 0.025 0.018 -10000 0 -0.35 1 1
PDK2 -0.031 0.1 0.22 3 -0.31 56 59
EIF4EBP1 0.016 0.097 -10000 0 -0.93 5 5
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
PPP2R5D 0.02 0.074 0.39 13 -0.38 1 14
peptide biosynthetic process 0.011 0.034 -10000 0 -0.38 3 3
RHEB 0.026 0.006 -10000 0 -10000 0 0
EIF4A1 0.026 0.007 -10000 0 -10000 0 0
mol:Rapamycin 0 0.002 0.009 19 -0.003 3 22
EEF2 0.011 0.034 -10000 0 -0.38 3 3
eIF4E/4E-BP1 0.03 0.088 -10000 0 -0.83 5 5
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 0.002 0.044 -10000 0 -0.43 5 5
ADCY5 -0.053 0.15 -10000 0 -0.44 65 65
ADCY6 0.002 0.044 -10000 0 -0.43 5 5
ADCY7 0.002 0.044 -10000 0 -0.43 5 5
ADCY1 -0.002 0.065 -10000 0 -0.49 8 8
ADCY2 -0.037 0.13 -10000 0 -0.44 45 45
ADCY3 0.002 0.044 -10000 0 -0.43 5 5
ADCY8 -0.047 0.052 -10000 0 -0.48 5 5
PRKCE 0.004 0.051 -10000 0 -0.5 5 5
ADCY9 0.002 0.044 -10000 0 -0.43 5 5
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.034 0.095 0.34 7 -0.36 16 23
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.025 0.025 0.37 1 -10000 0 1
HSPA8 0.02 0.057 -10000 0 -0.59 4 4
SMAD3/SMAD4/ER alpha -0.002 0.13 -10000 0 -0.46 22 22
AKT1 0.026 0.006 -10000 0 -10000 0 0
GSC -0.17 0.49 -10000 0 -1.4 67 67
NKX2-5 0.018 0.014 -10000 0 -10000 0 0
muscle cell differentiation -0.01 0.082 0.38 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.038 0.095 -10000 0 -0.31 1 1
SMAD4 -0.007 0.071 -10000 0 -0.22 5 5
CBFB 0.026 0.006 -10000 0 -10000 0 0
SAP18 0.025 0.007 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.041 0.069 -10000 0 -0.38 4 4
SMAD3/SMAD4/VDR 0.048 0.074 -10000 0 -10000 0 0
MYC 0.013 0.1 -10000 0 -0.64 11 11
CDKN2B -0.018 0.1 0.35 1 -0.4 12 13
AP1 -0.19 0.41 -10000 0 -0.76 148 148
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.028 0.063 -10000 0 -0.5 3 3
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.011 0.034 -10000 0 -10000 0 0
SP3 0.029 0.005 -10000 0 -10000 0 0
CREB1 0.027 0.005 -10000 0 -10000 0 0
FOXH1 0.005 0.053 -10000 0 -0.22 1 1
SMAD3/SMAD4/GR 0.021 0.079 -10000 0 -10000 0 0
GATA3 -0.008 0.14 -10000 0 -0.62 24 24
SKI/SIN3/HDAC complex/NCoR1 0.028 0.04 -10000 0 -0.65 1 1
MEF2C/TIF2 -0.032 0.15 0.32 3 -0.4 40 43
endothelial cell migration -0.023 0.078 1.3 1 -10000 0 1
MAX 0.026 0.005 -10000 0 -10000 0 0
RBBP7 0.025 0.007 -10000 0 -10000 0 0
RBBP4 0.023 0.044 -10000 0 -0.67 2 2
RUNX2 -0.013 0.076 -10000 0 -0.67 2 2
RUNX3 0.009 0.1 -10000 0 -0.67 11 11
RUNX1 -0.036 0.072 -10000 0 -10000 0 0
CTBP1 0.027 0.004 -10000 0 -10000 0 0
NR3C1 0.025 0.006 -10000 0 -10000 0 0
VDR 0.026 0.008 -10000 0 -10000 0 0
CDKN1A 0.019 0.046 -10000 0 -10000 0 0
KAT2B 0.029 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.014 0.12 -10000 0 -0.29 37 37
DCP1A 0.027 0.003 -10000 0 -10000 0 0
SKI 0.026 0.006 -10000 0 -10000 0 0
SERPINE1 0.022 0.079 -10000 0 -1.3 1 1
SMAD3/SMAD4/ATF2 0.002 0.13 -10000 0 -0.48 20 20
SMAD3/SMAD4/ATF3 -0.077 0.24 -10000 0 -0.5 109 109
SAP30 0.025 0.032 -10000 0 -0.67 1 1
Cbp/p300/PIAS3 0.048 0.044 -10000 0 -10000 0 0
JUN -0.19 0.4 0.3 1 -0.75 147 148
SMAD3/SMAD4/IRF7 0.024 0.08 -10000 0 -10000 0 0
TFE3 0.03 0.009 -10000 0 -10000 0 0
COL1A2 0.026 0.062 -10000 0 -1.1 1 1
mesenchymal cell differentiation -0.015 0.096 0.31 7 -10000 0 7
DLX1 -0.009 0.15 -10000 0 -0.64 26 26
TCF3 0.025 0.008 -10000 0 -10000 0 0
FOS -0.16 0.33 -10000 0 -0.73 124 124
SMAD3/SMAD4/Max 0.02 0.08 -10000 0 -0.25 4 4
Cbp/p300/SNIP1 0.042 0.036 -10000 0 -0.42 1 1
ZBTB17 0.027 0.006 -10000 0 -10000 0 0
LAMC1 0.012 0.06 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.022 0.08 -10000 0 -0.24 4 4
IRF7 0.027 0.01 -10000 0 -10000 0 0
ESR1 -0.015 0.14 -10000 0 -0.64 23 23
HNF4A -0.008 0.024 -10000 0 -10000 0 0
MEF2C -0.012 0.1 0.37 4 -0.88 1 5
SMAD2-3/SMAD4 0.012 0.095 -10000 0 -0.29 2 2
Cbp/p300/Src-1 0.046 0.034 -10000 0 -10000 0 0
IGHV3OR16-13 0.001 0.034 -10000 0 -0.34 3 3
TGIF2/HDAC complex 0.027 0.005 -10000 0 -10000 0 0
CREBBP 0.029 0.011 -10000 0 -10000 0 0
SKIL 0.026 0.031 -10000 0 -0.67 1 1
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC2 0.027 0.004 -10000 0 -10000 0 0
SNIP1 0.024 0.032 -10000 0 -0.67 1 1
GCN5L2 0.004 0.013 0.2 1 -10000 0 1
SMAD3/SMAD4/TFE3 0.03 0.08 -10000 0 -0.27 1 1
MSG1/HSC70 -0.061 0.069 -10000 0 -0.44 9 9
SMAD2 0.012 0.047 -10000 0 -10000 0 0
SMAD3 0.005 0.06 -10000 0 -0.22 1 1
SMAD3/E2F4-5/DP1/p107/SMAD4 0.013 0.066 -10000 0 -0.44 4 4
SMAD2/SMAD2/SMAD4 0.003 0.036 0.23 3 -10000 0 3
NCOR1 0.025 0.007 -10000 0 -10000 0 0
NCOA2 -0.037 0.2 -10000 0 -0.67 45 45
NCOA1 0.027 0.005 -10000 0 -10000 0 0
MYOD/E2A 0.029 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.046 0.095 -10000 0 -10000 0 0
IFNB1 0 0.058 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.005 0.11 -10000 0 -0.62 2 2
CITED1 -0.094 0.078 -10000 0 -0.6 5 5
SMAD2-3/SMAD4/ARC105 0.013 0.085 -10000 0 -10000 0 0
RBL1 0.014 0.093 -10000 0 -0.67 9 9
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.013 0.034 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 0.045 0.077 -10000 0 -0.44 10 10
SMAD7 -0.086 0.25 -10000 0 -0.54 90 90
MYC/MIZ-1 0.029 0.079 -10000 0 -0.5 10 10
SMAD3/SMAD4 0.022 0.11 0.29 33 -0.52 1 34
IL10 -0.029 0.15 -10000 0 -0.52 34 34
PIASy/HDAC complex 0.018 0.02 -10000 0 -10000 0 0
PIAS3 0.027 0.008 -10000 0 -10000 0 0
CDK2 0.03 0.011 -10000 0 -10000 0 0
IL5 -0.022 0.1 -10000 0 -0.4 22 22
CDK4 0.03 0.011 -10000 0 -10000 0 0
PIAS4 0.018 0.02 -10000 0 -10000 0 0
ATF3 -0.13 0.29 -10000 0 -0.66 109 109
SMAD3/SMAD4/SP1 0.033 0.083 -10000 0 -0.29 1 1
FOXG1 0.008 0.041 -10000 0 -0.67 1 1
FOXO3 0.016 0.007 -10000 0 -10000 0 0
FOXO1 0.015 0.007 -10000 0 -10000 0 0
FOXO4 0.015 0.007 -10000 0 -10000 0 0
heart looping -0.012 0.1 0.37 4 -0.86 1 5
CEBPB 0.026 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.003 0.14 -10000 0 -0.47 25 25
MYOD1 -0.013 0.015 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.016 0.081 -10000 0 -0.3 1 1
SMAD3/SMAD4/GATA3 0.001 0.14 -10000 0 -0.41 34 34
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.031 -10000 0 -0.67 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.03 0.12 -10000 0 -0.47 10 10
SMAD3/SMAD4/SP1-3 0.052 0.081 -10000 0 -10000 0 0
MED15 0.02 0.012 -10000 0 -10000 0 0
SP1 0.032 0.011 -10000 0 -10000 0 0
SIN3B 0.025 0.007 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.029 0.11 -10000 0 -0.41 3 3
ITGB5 0.015 0.06 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.031 0.034 -10000 0 -0.49 1 1
SMAD3/SMAD4/AR -0.18 0.25 -10000 0 -0.48 200 200
AR -0.26 0.34 -10000 0 -0.66 206 206
negative regulation of cell growth -0.023 0.12 -10000 0 -0.44 5 5
SMAD3/SMAD4/MYOD 0.016 0.08 -10000 0 -0.25 4 4
E2F5 0.025 0.032 -10000 0 -0.67 1 1
E2F4 0.026 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.028 0.096 -10000 0 -0.33 2 2
SMAD2-3/SMAD4/FOXO1-3a-4 0.014 0.035 -10000 0 -10000 0 0
TFDP1 0.025 0.018 -10000 0 -0.35 1 1
SMAD3/SMAD4/AP1 -0.18 0.42 -10000 0 -0.77 147 147
SMAD3/SMAD4/RUNX2 0.016 0.096 -10000 0 -0.31 7 7
TGIF2 0.027 0.005 -10000 0 -10000 0 0
TGIF1 0.027 0.005 -10000 0 -10000 0 0
ATF2 -0.002 0.14 -10000 0 -0.65 21 21
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.03 0.074 -9999 0 -0.38 15 15
RGS9BP -0.015 0.16 -9999 0 -0.66 29 29
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.038 0.2 -9999 0 -0.65 46 46
mol:Na + 0.018 0.032 -9999 0 -10000 0 0
mol:ADP -0.043 0.14 -9999 0 -0.5 45 45
GNAT2 0.016 0.02 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.021 0.18 -9999 0 -0.44 70 70
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.028 0.01 -9999 0 -10000 0 0
GRK7 0.006 0.022 -9999 0 -10000 0 0
CNGB3 -0.008 0.017 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.014 0.005 -9999 0 -10000 0 0
mol:Ca2+ -0.009 0.027 -9999 0 -10000 0 0
Cone PDE6 -0.002 0.16 -9999 0 -0.39 69 69
Cone Metarhodopsin II -0.01 0.12 -9999 0 -0.39 46 46
Na + (4 Units) 0.032 0.03 -9999 0 -10000 0 0
GNAT2/GDP -0.007 0.16 -9999 0 -0.39 67 67
GNB5 0.027 0.004 -9999 0 -10000 0 0
mol:GMP (4 units) -0.003 0.022 -9999 0 -10000 0 0
Cone Transducin 0.033 0.078 -9999 0 -0.4 15 15
SLC24A2 -0.007 0.029 -9999 0 -10000 0 0
GNB3/GNGT2 0.02 0.094 -9999 0 -0.5 15 15
GNB3 0.007 0.12 -9999 0 -0.67 14 14
GNAT2/GTP 0.018 0.006 -9999 0 -10000 0 0
CNGA3 0.008 0.048 -9999 0 -10000 0 0
ARR3 -0.002 0.02 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel 0.018 0.032 -9999 0 -10000 0 0
mol:Pi -0.021 0.17 -9999 0 -0.44 70 70
Cone CNG Channel 0.043 0.033 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.007 0.029 -9999 0 -10000 0 0
RGS9 -0.037 0.2 -9999 0 -0.67 44 44
PDE6C -0.005 0.02 -9999 0 -10000 0 0
GNGT2 0.023 0.034 -9999 0 -0.67 1 1
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.003 0.02 -9999 0 -10000 0 0
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.037 0.036 -10000 0 -0.5 2 2
Necdin/E2F1 0 0.076 -10000 0 -0.55 5 5
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.057 0.091 -10000 0 -0.4 16 16
NGF (dimer)/p75(NTR)/BEX1 -0.18 0.25 -10000 0 -0.45 214 214
NT-4/5 (dimer)/p75(NTR) -0.012 0.13 -10000 0 -0.52 30 30
IKBKB 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.005 0.096 0.36 1 -0.4 19 20
IKBKG 0.025 0.008 -10000 0 -10000 0 0
BDNF 0.009 0.1 -10000 0 -0.67 11 11
MGDIs/NGR/p75(NTR)/LINGO1 0.023 0.091 -10000 0 -0.44 16 16
FURIN 0.027 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.027 0.11 -10000 0 -0.42 27 27
LINGO1 0.02 0.03 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.031 0.028 -10000 0 -0.34 2 2
proBDNF (dimer) 0.009 0.1 -10000 0 -0.67 11 11
NTRK1 0.01 0.03 -10000 0 -10000 0 0
RTN4R 0.02 0.012 -10000 0 -10000 0 0
neuron apoptosis 0.023 0.13 0.4 16 -0.42 17 33
IRAK1 0.025 0.008 -10000 0 -10000 0 0
SHC1 -0.006 0.089 -10000 0 -0.46 15 15
ARHGDIA 0.026 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.07 0.03 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.047 0.092 -10000 0 -0.42 16 16
MAGEH1 0.026 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.045 0.1 -10000 0 -0.42 20 20
Mammalian IAPs/DIABLO 0.046 0.093 -10000 0 -0.4 19 19
proNGF (dimer) 0.021 0.055 -10000 0 -0.67 3 3
MAGED1 0.026 0.007 -10000 0 -10000 0 0
APP 0.026 0.006 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.002 0.12 -10000 0 -0.65 15 15
ZNF274 0.025 0.007 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.012 0.084 -10000 0 -0.4 16 16
NGF 0.021 0.055 -10000 0 -0.67 3 3
cell cycle arrest 0.057 0.14 0.46 16 -0.38 16 32
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.016 0.069 -10000 0 -0.32 18 18
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.018 0.12 -10000 0 -0.45 32 32
NCSTN 0.025 0.007 -10000 0 -10000 0 0
mol:GTP 0.034 0.097 -10000 0 -0.44 18 18
PSENEN 0.026 0.007 -10000 0 -10000 0 0
mol:ceramide 0.003 0.091 -10000 0 -0.42 16 16
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.019 0.059 -10000 0 -0.38 4 4
p75(NTR)/beta APP 0.005 0.1 -10000 0 -0.5 16 16
BEX1 -0.28 0.34 -10000 0 -0.66 215 215
mol:GDP -0.017 0.087 -10000 0 -0.43 18 18
NGF (dimer) 0.038 0.11 -10000 0 -0.41 26 26
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.035 0.089 -10000 0 -0.4 16 16
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RAC1/GTP 0.031 0.082 -10000 0 -0.38 17 17
MYD88 0.027 0.003 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.035 0.097 -10000 0 -0.44 18 18
RHOB 0.027 0.005 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.005 0.053 -10000 0 -10000 0 0
NT3 (dimer) -0.016 0.15 -10000 0 -0.67 25 25
TP53 -0.003 0.098 0.35 1 -0.36 26 27
PRDM4 0.001 0.089 -10000 0 -0.42 16 16
BDNF (dimer) 0.007 0.14 -10000 0 -0.43 33 33
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
SORT1 0.027 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.051 0.088 -10000 0 -0.4 16 16
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.048 0.096 -10000 0 -0.42 18 18
RHOC 0.027 0.005 -10000 0 -10000 0 0
XIAP 0.026 0.007 -10000 0 -10000 0 0
MAPK10 0.015 0.11 0.34 16 -0.4 14 30
DIABLO 0.027 0.005 -10000 0 -10000 0 0
SMPD2 0.003 0.092 -10000 0 -0.42 16 16
APH1B 0.027 0.004 -10000 0 -10000 0 0
APH1A 0.025 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.036 0.095 -10000 0 -0.46 16 16
PSEN1 0.027 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.037 0.026 -10000 0 -0.5 1 1
NT3 (dimer)/p75(NTR) -0.025 0.15 -10000 0 -0.51 40 40
MAPK8 0.01 0.12 0.34 15 -0.4 16 31
MAPK9 0.01 0.1 0.34 10 -0.39 13 23
APAF1 0.025 0.032 -10000 0 -0.67 1 1
NTF3 -0.016 0.15 -10000 0 -0.67 25 25
NTF4 0.002 0.12 -10000 0 -0.65 15 15
NDN 0.02 0.07 -10000 0 -0.67 5 5
RAC1/GDP 0.019 0.004 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.052 0.085 -10000 0 -0.37 17 17
p75 CTF/Sortilin/TRAF6/NRIF 0.059 0.052 -10000 0 -0.51 3 3
RhoA-B-C/GTP 0.034 0.096 -10000 0 -0.44 18 18
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.048 0.11 -10000 0 -0.38 26 26
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.039 0.11 -10000 0 -0.4 27 27
PRKACB 0.025 0.032 -10000 0 -0.67 1 1
proBDNF (dimer)/p75 ECD 0.023 0.088 -10000 0 -0.5 13 13
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.009 0.14 -10000 0 -0.62 25 25
BIRC2 0.027 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis 0.07 0.14 0.48 12 -0.39 16 28
BAD 0.027 0.14 0.44 25 -0.4 15 40
RIPK2 0.027 0.005 -10000 0 -10000 0 0
NGFR -0.015 0.13 -10000 0 -0.67 16 16
CYCS 0.008 0.1 0.36 12 -0.4 16 28
ADAM17 0.024 0.044 -10000 0 -0.67 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.046 0.097 -10000 0 -0.42 18 18
BCL2L11 0.027 0.14 0.44 25 -0.4 15 40
BDNF (dimer)/p75(NTR) -0.008 0.13 -10000 0 -0.5 27 27
PI3K 0.046 0.099 -10000 0 -0.42 19 19
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.05 0.092 -10000 0 -0.42 16 16
NDNL2 0.027 0.004 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
PRKCI 0.027 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.002 0.11 -10000 0 -0.5 18 18
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.047 0.092 -10000 0 -0.42 16 16
TRAF6 0.024 0.044 -10000 0 -0.67 2 2
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
PLG -0.014 0.019 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.005 0.099 -10000 0 -0.4 26 26
SQSTM1 0.026 0.006 -10000 0 -10000 0 0
NGFRAP1 0.026 0.007 -10000 0 -10000 0 0
CASP3 0.03 0.14 0.43 25 -0.36 15 40
E2F1 -0.016 0.066 -10000 0 -10000 0 0
CASP9 0.027 0.005 -10000 0 -10000 0 0
IKK complex 0.05 0.074 -10000 0 -0.46 3 3
NGF (dimer)/TRKA 0.028 0.048 -10000 0 -0.5 3 3
MMP7 -0.074 0.15 -10000 0 -0.66 25 25
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.055 0.095 -10000 0 -0.4 18 18
MMP3 -0.016 0.046 -10000 0 -10000 0 0
APAF-1/Caspase 9 -0.014 0.095 -10000 0 -0.57 5 5
Caspase cascade in apoptosis

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
TOP1 0.02 0.088 0.34 4 -0.41 12 16
ACTA1 0.008 0.1 0.34 6 -0.48 12 18
NUMA1 0.016 0.097 0.29 5 -0.47 13 18
SPTAN1 0.006 0.1 0.35 6 -0.49 11 17
LIMK1 0.012 0.11 0.45 8 -0.51 10 18
BIRC3 -0.01 0.14 -10000 0 -0.62 25 25
BIRC2 0.027 0.005 -10000 0 -10000 0 0
BAX 0.025 0.01 -10000 0 -10000 0 0
CASP10 -0.011 0.088 -10000 0 -0.53 12 12
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.026 0.007 -10000 0 -10000 0 0
PTK2 0.014 0.099 0.39 2 -0.42 17 19
DIABLO 0.027 0.005 -10000 0 -10000 0 0
apoptotic nuclear changes 0.006 0.1 0.35 6 -0.48 11 17
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.027 0.005 -10000 0 -10000 0 0
GSN 0.006 0.1 0.36 5 -0.48 12 17
MADD 0.027 0.005 -10000 0 -10000 0 0
TFAP2A -0.042 0.22 -10000 0 -0.61 62 62
BID -0.011 0.061 -10000 0 -0.32 12 12
MAP3K1 0.018 0.042 0.27 3 -0.21 2 5
TRADD 0.026 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.026 -10000 0 -0.5 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.009 0.11 0.45 8 -0.51 10 18
CASP9 0.026 0.006 -10000 0 -10000 0 0
DNA repair -0.017 0.063 0.42 4 -0.21 19 23
neuron apoptosis 0.009 0.11 -10000 0 -0.55 15 15
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.016 0.11 0.35 4 -0.51 13 17
APAF1 0.025 0.032 -10000 0 -0.67 1 1
CASP6 0.02 0.086 0.38 1 -0.59 4 5
TRAF2 0.025 0.008 -10000 0 -10000 0 0
ICAD/CAD 0.011 0.11 0.4 13 -0.49 10 23
CASP7 0.007 0.097 0.31 22 -0.43 9 31
KRT18 0.021 0.04 -10000 0 -0.44 2 2
apoptosis 0.015 0.1 0.48 4 -0.47 10 14
DFFA 0.008 0.1 0.36 6 -0.49 11 17
DFFB 0.008 0.1 0.36 6 -0.49 11 17
PARP1 0.017 0.064 0.21 19 -0.43 4 23
actin filament polymerization -0.017 0.12 0.47 10 -0.54 11 21
TNF -0.056 0.22 -10000 0 -0.67 56 56
CYCS 0 0.048 0.24 3 -0.22 11 14
SATB1 0.02 0.085 0.52 2 -0.55 4 6
SLK 0.004 0.1 0.46 3 -0.48 13 16
p15 BID/BAX -0.01 0.07 -10000 0 -0.29 12 12
CASP2 -0.014 0.1 0.21 4 -0.37 18 22
JNK cascade -0.018 0.041 0.21 2 -0.27 3 5
CASP3 0.005 0.1 0.35 5 -0.48 13 18
LMNB2 0.006 0.11 0.36 9 -0.41 12 21
RIPK1 0.027 0.003 -10000 0 -10000 0 0
CASP4 0.027 0.005 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.045 0.093 -10000 0 -0.4 19 19
negative regulation of DNA binding -0.042 0.22 -10000 0 -0.6 62 62
stress fiber formation 0.004 0.1 0.46 3 -0.47 13 16
GZMB -0.007 0.1 -10000 0 -0.6 12 12
CASP1 0.015 0.026 -10000 0 -0.39 2 2
LMNB1 0.019 0.087 0.34 10 -0.3 3 13
APP 0.008 0.11 -10000 0 -0.56 15 15
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
response to stress 0 0.001 -10000 0 -10000 0 0
CASP8 0.009 0.002 -10000 0 -10000 0 0
VIM 0.017 0.095 0.45 3 -0.48 9 12
LMNA 0.015 0.098 0.35 11 -0.42 5 16
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.013 0.11 -10000 0 -0.27 59 59
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.014 0.11 0.43 9 -0.52 9 18
APAF-1/Caspase 9 0.013 0.063 -10000 0 -0.55 4 4
nuclear fragmentation during apoptosis 0.016 0.096 0.28 6 -0.47 13 19
CFL2 0.017 0.12 0.54 11 -0.48 10 21
GAS2 0.002 0.1 0.36 4 -0.47 14 18
positive regulation of apoptosis 0.016 0.1 0.36 9 -0.38 7 16
PRF1 0.014 0.089 -10000 0 -0.67 8 8
Nectin adhesion pathway

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
PDGFRB 0.025 0.032 -10000 0 -0.67 1 1
alphaV beta3 Integrin 0.024 0.088 -10000 0 -0.54 11 11
PTK2 0.008 0.15 -10000 0 -0.55 27 27
positive regulation of JNK cascade 0.012 0.099 -10000 0 -0.32 32 32
CDC42/GDP 0.029 0.14 0.44 1 -0.44 34 35
Rac1/GDP 0.029 0.14 -10000 0 -0.45 30 30
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
CDC42/GTP 0.022 0.12 -10000 0 -0.4 32 32
nectin-3/I-afadin 0.007 0.13 -10000 0 -0.5 30 30
RAPGEF1 0.011 0.14 0.35 2 -0.5 30 32
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.008 0.16 -10000 0 -0.57 30 30
PDGFB-D/PDGFRB 0.025 0.032 -10000 0 -0.67 1 1
TLN1 -0.005 0.061 -10000 0 -0.78 1 1
Rap1/GTP 0.01 0.097 -10000 0 -0.35 29 29
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.05 0.014 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.007 0.13 -10000 0 -0.5 30 30
PVR 0.026 0.007 -10000 0 -10000 0 0
Necl-5(dimer) 0.025 0.007 -10000 0 -10000 0 0
mol:GDP 0.014 0.17 0.47 1 -0.54 37 38
MLLT4 0.027 0.004 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
PI3K 0.048 0.12 -10000 0 -0.41 29 29
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.036 0.019 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.008 0.11 -10000 0 -0.35 30 30
PVRL1 0.023 0.024 -10000 0 -10000 0 0
PVRL3 -0.016 0.17 -10000 0 -0.66 31 31
PVRL2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
CLDN1 -0.1 0.093 -10000 0 -0.6 10 10
JAM-A/CLDN1 0.039 0.13 -10000 0 -0.41 35 35
SRC 0.003 0.17 -10000 0 -0.64 31 31
ITGB3 0.011 0.099 -10000 0 -0.64 11 11
nectin-1(dimer)/I-afadin/I-afadin 0.036 0.019 -10000 0 -10000 0 0
FARP2 0.017 0.16 -10000 0 -0.53 35 35
RAC1 0.026 0.006 -10000 0 -10000 0 0
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.022 0.12 -10000 0 -0.43 30 30
nectin-1/I-afadin 0.036 0.019 -10000 0 -10000 0 0
nectin-2/I-afadin 0.038 0.011 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.035 0.009 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.024 0.12 -10000 0 -0.44 30 30
CDC42/GTP/IQGAP1/filamentous actin 0.036 0.008 -10000 0 -10000 0 0
F11R 0.025 0.007 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.012 0.099 -10000 0 -0.32 32 32
alphaV/beta3 Integrin/Talin 0.022 0.11 -10000 0 -0.55 11 11
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.011 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.038 0.011 -10000 0 -10000 0 0
PIP5K1C -0.003 0.066 -10000 0 -0.82 1 1
VAV2 -0.002 0.19 0.37 1 -0.59 34 35
RAP1/GDP 0.032 0.13 0.28 1 -0.41 32 33
ITGAV 0.024 0.044 -10000 0 -0.67 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.022 0.12 -10000 0 -0.43 30 30
nectin-3(dimer)/I-afadin/I-afadin 0.007 0.13 -10000 0 -0.5 30 30
Rac1/GTP 0.013 0.13 -10000 0 -0.43 30 30
PTPRM 0 0.073 -10000 0 -0.27 29 29
E-cadherin/beta catenin/alpha catenin 0.073 0.027 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.02 0.012 -10000 0 -10000 0 0
HDAC4 0.027 0.005 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.013 0.024 0.5 1 -10000 0 1
CDKN1A -0.006 0.011 -10000 0 -10000 0 0
KAT2B 0.027 0.004 -10000 0 -10000 0 0
BAX 0.025 0.01 -10000 0 -10000 0 0
FOXO3 -0.004 0.007 -10000 0 -10000 0 0
FOXO1 0.026 0.007 -10000 0 -10000 0 0
FOXO4 0.014 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.02 0.012 -10000 0 -10000 0 0
TAT 0.011 0.024 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.008 0.009 -10000 0 -10000 0 0
PPARGC1A -0.28 0.34 -10000 0 -0.67 217 217
FHL2 -0.027 0.18 -10000 0 -0.67 38 38
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.026 0.03 -10000 0 -0.5 1 1
HIST2H4A 0.013 0.024 -10000 0 -0.5 1 1
SIRT1/FOXO3a 0.038 0.052 -10000 0 -0.3 2 2
SIRT1 0.022 0.032 -10000 0 -0.67 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.046 0.028 -10000 0 -0.44 1 1
SIRT1/Histone H1b -0.006 0.07 -10000 0 -0.3 11 11
apoptosis -0.036 0.032 0.43 1 -10000 0 1
SIRT1/PGC1A -0.17 0.23 -10000 0 -0.44 217 217
p53/SIRT1 0.028 0.027 -10000 0 -0.5 1 1
SIRT1/FOXO4 -0.004 0.064 -10000 0 -0.31 4 4
FOXO1/FHL2/SIRT1 0.01 0.12 -10000 0 -0.4 39 39
HIST1H1E 0.008 0.046 -10000 0 -0.34 8 8
SIRT1/p300 0.026 0.03 -10000 0 -0.5 1 1
muscle cell differentiation -0.029 0.028 0.44 1 -10000 0 1
TP53 0.022 0.006 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.037 0.033 -10000 0 -0.44 1 1
CREBBP 0.026 0.006 -10000 0 -10000 0 0
MEF2D 0.025 0.007 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.031 0.028 -10000 0 -0.5 1 1
ACSS2 0.013 0.024 -10000 0 -0.5 1 1
SIRT1/PCAF/MYOD 0.029 0.028 -10000 0 -0.44 1 1
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.034 0.008 -9999 0 -10000 0 0
PRKCZ 0.026 0.006 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.027 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.016 0.06 -9999 0 -0.38 2 2
IRAK/TOLLIP 0.029 0.011 -9999 0 -10000 0 0
IKBKB 0.027 0.005 -9999 0 -10000 0 0
IKBKG 0.025 0.008 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.053 0.2 -9999 0 -0.54 69 69
IL1A -0.03 0.18 -9999 0 -0.66 38 38
IL1B -0.021 0.14 -9999 0 -0.51 34 34
IRAK/TRAF6/p62/Atypical PKCs 0.061 0.037 -9999 0 -0.36 2 2
IL1R2 -0.04 0.19 -9999 0 -0.65 40 40
IL1R1 0.027 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.007 0.048 -9999 0 -0.27 1 1
TOLLIP 0.026 0.005 -9999 0 -10000 0 0
TICAM2 0.019 0.07 -9999 0 -0.67 5 5
MAP3K3 0.026 0.007 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0.018 0.003 -9999 0 -10000 0 0
IKK complex/ELKS 0.034 0.058 -9999 0 -10000 0 0
JUN -0.083 0.16 -9999 0 -0.37 110 110
MAP3K7 0.027 0.004 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.041 0.12 -9999 0 -0.38 33 33
IL1 alpha/IL1R1/IL1RAP/MYD88 0.036 0.13 -9999 0 -0.4 37 37
PIK3R1 0.026 0.005 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.047 0.12 -9999 0 -0.38 37 37
IL1 beta fragment/IL1R1/IL1RAP 0.017 0.12 -9999 0 -0.42 33 33
NFKB1 0.027 0.004 -9999 0 -10000 0 0
MAPK8 -0.014 0.085 -9999 0 -0.44 16 16
IRAK1 0.015 0.006 -9999 0 -10000 0 0
IL1RN/IL1R1 0.012 0.085 -9999 0 -0.48 11 11
IRAK4 0.027 0.005 -9999 0 -10000 0 0
PRKCI 0.027 0.003 -9999 0 -10000 0 0
TRAF6 0.024 0.044 -9999 0 -0.67 2 2
PI3K 0.036 0.043 -9999 0 -0.5 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.015 0.066 -9999 0 -0.35 4 4
CHUK 0.027 0.004 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.017 0.12 -9999 0 -0.42 33 33
IL1 beta/IL1R2 -0.04 0.18 -9999 0 -0.48 65 65
IRAK/TRAF6/TAK1/TAB1/TAB2 0.035 0.028 -9999 0 -0.36 2 2
NF kappa B1 p50/RelA 0.029 0.11 -9999 0 -0.35 33 33
IRAK3 0.027 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.04 0.12 -9999 0 -0.38 35 35
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.006 0.085 -9999 0 -0.29 37 37
IL1 alpha/IL1R1/IL1RAP 0.019 0.13 -9999 0 -0.44 37 37
RELA 0.027 0.005 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.026 0.006 -9999 0 -10000 0 0
MYD88 0.027 0.003 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.042 0.033 -9999 0 -0.38 2 2
IL1RAP -0.01 0.064 -9999 0 -10000 0 0
UBE2N 0.027 0.005 -9999 0 -10000 0 0
IRAK/TRAF6 -0.006 0.1 -9999 0 -0.34 34 34
CASP1 0.022 0.047 -9999 0 -0.67 2 2
IL1RN/IL1R2 -0.038 0.17 -9999 0 -0.53 45 45
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.032 0.12 -9999 0 -0.39 33 33
TMEM189-UBE2V1 -0.003 0.02 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.01 0.071 -9999 0 -0.37 2 2
PIK3CA 0.023 0.054 -9999 0 -0.67 3 3
IL1RN -0.009 0.11 -9999 0 -0.64 11 11
TRAF6/TAK1/TAB1/TAB2 0.045 0.029 -9999 0 -0.37 2 2
MAP2K6 0.006 0.06 -9999 0 -0.36 12 12
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.025 0.032 -10000 0 -0.67 1 1
Caspase 8 (4 units) 0.022 0.09 -10000 0 -0.44 5 5
NEF -0.014 0.067 -10000 0 -0.25 29 29
NFKBIA 0.021 0.032 -10000 0 -10000 0 0
BIRC3 -0.004 0.15 -10000 0 -0.64 23 23
CYCS -0.009 0.092 0.22 1 -0.37 10 11
RIPK1 0.027 0.003 -10000 0 -10000 0 0
CD247 -0.016 0.16 -10000 0 -0.76 18 18
MAP2K7 -0.002 0.16 -10000 0 -0.62 23 23
protein ubiquitination 0.009 0.099 0.36 6 -0.35 5 11
CRADD 0.027 0.005 -10000 0 -10000 0 0
DAXX 0.027 0.003 -10000 0 -10000 0 0
FAS 0.027 0.005 -10000 0 -10000 0 0
BID -0.009 0.098 0.22 1 -0.32 29 30
NF-kappa-B/RelA/I kappa B alpha 0.043 0.078 -10000 0 -0.32 19 19
TRADD 0.026 0.006 -10000 0 -10000 0 0
MAP3K5 0.026 0.032 -10000 0 -0.67 1 1
CFLAR 0.027 0.005 -10000 0 -10000 0 0
FADD 0.027 0.005 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.043 0.079 -10000 0 -0.32 19 19
MAPK8 -0.006 0.16 0.35 1 -0.58 24 25
APAF1 0.025 0.032 -10000 0 -0.67 1 1
TRAF1 0.025 0.008 -10000 0 -10000 0 0
TRAF2 0.025 0.008 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.001 0.098 -10000 0 -0.32 35 35
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0 0.11 -10000 0 -0.36 20 20
CHUK 0.004 0.098 0.28 3 -0.38 5 8
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.076 0.029 -10000 0 -0.38 1 1
TCRz/NEF -0.024 0.15 -10000 0 -0.45 47 47
TNF -0.056 0.22 -10000 0 -0.67 56 56
FASLG -0.049 0.23 -10000 0 -0.76 42 42
NFKB1 0.021 0.033 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.003 0.16 -10000 0 -0.44 57 57
CASP6 0.038 0.096 -10000 0 -0.66 5 5
CASP7 0.009 0.15 0.39 2 -0.57 26 28
RELA 0.021 0.033 -10000 0 -10000 0 0
CASP2 0.026 0.006 -10000 0 -10000 0 0
CASP3 0.009 0.15 0.32 2 -0.56 26 28
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.026 -10000 0 -0.5 1 1
CASP8 0.027 0.005 -10000 0 -10000 0 0
CASP9 0.027 0.005 -10000 0 -10000 0 0
MAP3K14 0.003 0.1 -10000 0 -0.39 7 7
APAF-1/Caspase 9 -0.002 0.12 -10000 0 -0.47 22 22
BCL2 -0.027 0.16 0.34 1 -0.56 24 25
Rapid glucocorticoid signaling

Figure S69.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S69.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.007 0.14 -10000 0 -0.37 62 62
MAPK9 0.008 0.002 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.004 0.02 -10000 0 -10000 0 0
GNB1/GNG2 0.034 0.023 -10000 0 -0.44 1 1
GNB1 0.026 0.006 -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 0.009 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.035 0.14 -10000 0 -0.39 64 64
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 0.012 0.032 0.095 64 -10000 0 64
GNAL -0.061 0.23 -10000 0 -0.65 64 64
GNG2 0.025 0.032 -10000 0 -0.67 1 1
CRH 0 0.037 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0 0.055 -10000 0 -0.38 10 10
MAPK11 0.006 0.004 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.014 0.091 -10000 0 -0.6 10 10
ANTXR2 0.023 0.054 -10000 0 -0.67 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.013 -10000 0 -0.081 13 13
monocyte activation -0.036 0.16 -10000 0 -0.44 62 62
MAP2K2 -0.009 0.12 -10000 0 -0.54 22 22
MAP2K1 -0.001 0.012 -10000 0 -10000 0 0
MAP2K7 -0.001 0.012 -10000 0 -10000 0 0
MAP2K6 -0.009 0.056 0.11 1 -0.39 10 11
CYAA -0.007 0.057 -10000 0 -0.34 13 13
MAP2K4 -0.001 0.012 0.11 1 -10000 0 1
IL1B -0.022 0.094 0.18 1 -0.35 35 36
Channel 0.024 0.066 -10000 0 -0.36 13 13
NLRP1 -0.002 0.027 0.11 1 -0.38 2 3
CALM1 0.027 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.011 0.028 -10000 0 -0.51 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.013 0.081 13 -10000 0 13
MAPK3 -0.001 0.012 -10000 0 -10000 0 0
MAPK1 -0.001 0.012 -10000 0 -10000 0 0
PGR -0.012 0.054 -10000 0 -0.35 11 11
PA/Cellular Receptors 0.025 0.071 -10000 0 -0.4 13 13
apoptosis -0.002 0.013 -10000 0 -0.081 13 13
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.023 0.062 -10000 0 -0.34 13 13
macrophage activation -0.002 0.011 -10000 0 -10000 0 0
TNF -0.056 0.22 -10000 0 -0.67 56 56
VCAM1 -0.036 0.16 -10000 0 -0.44 62 62
platelet activation 0.011 0.028 -10000 0 -0.51 1 1
MAPKKK cascade -0.003 0.029 0.095 19 -0.1 17 36
IL18 -0.009 0.059 -10000 0 -0.32 13 13
negative regulation of macrophage activation -0.002 0.013 -10000 0 -0.081 13 13
LEF -0.002 0.013 -10000 0 -0.081 13 13
CASP1 0.001 0.018 -10000 0 -0.17 3 3
mol:cAMP 0.011 0.029 -10000 0 -0.51 1 1
necrosis -0.002 0.013 -10000 0 -0.081 13 13
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.024 0.062 -10000 0 -0.34 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.005 0.14 -10000 0 -0.68 11 11
HDAC1 0.024 0.007 -10000 0 -10000 0 0
AES 0.025 0.008 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
DTX1 0.024 0.044 -10000 0 -0.67 2 2
LRP6/FZD1 0.039 0.009 -10000 0 -10000 0 0
TLE1 0.02 0.055 -10000 0 -0.67 3 3
AP1 -0.13 0.24 -10000 0 -0.49 136 136
NCSTN 0.025 0.007 -10000 0 -10000 0 0
ADAM10 0.011 0.1 -10000 0 -0.67 11 11
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.028 0.075 -10000 0 -0.55 4 4
NICD/RBPSUH 0.006 0.13 -10000 0 -0.64 11 11
WIF1 -0.014 0.044 -10000 0 -10000 0 0
NOTCH1 -0.004 0.13 -10000 0 -0.47 32 32
PSENEN 0.026 0.007 -10000 0 -10000 0 0
KREMEN2 0.016 0.036 -10000 0 -10000 0 0
DKK1 0 0.068 -10000 0 -0.67 2 2
beta catenin/beta TrCP1 0.046 0.047 0.28 3 -10000 0 3
APH1B 0.027 0.004 -10000 0 -10000 0 0
APH1A 0.025 0.007 -10000 0 -10000 0 0
AXIN1 -0.006 0.082 0.38 1 -0.4 11 12
CtBP/CBP/TCF1/TLE1/AES 0.019 0.031 -10000 0 -0.29 3 3
PSEN1 0.027 0.005 -10000 0 -10000 0 0
FOS -0.15 0.3 -10000 0 -0.66 124 124
JUN -0.12 0.28 -10000 0 -0.66 106 106
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
CTNNB1 0.038 0.062 0.31 12 -10000 0 12
MAPK3 0.026 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.035 0.092 -10000 0 -0.43 18 18
HNF1A 0.026 0.005 -10000 0 -10000 0 0
CTBP1 0.026 0.004 -10000 0 -10000 0 0
MYC -0.015 0.24 -10000 0 -1.2 18 18
NKD1 0.006 0.11 -10000 0 -0.67 13 13
FZD1 0.026 0.006 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.005 0.14 -10000 0 -0.64 13 13
apoptosis -0.13 0.24 -10000 0 -0.48 136 136
Delta 1/NOTCHprecursor 0.006 0.14 -10000 0 -0.67 11 11
DLL1 0.025 0.032 -10000 0 -0.67 1 1
PPARD 0.021 0.081 -10000 0 -0.84 4 4
Gamma Secretase 0.07 0.03 -10000 0 -10000 0 0
APC 0 0.073 0.33 2 -0.55 3 5
DVL1 0.025 0.009 -10000 0 -10000 0 0
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.049 0.044 -10000 0 -0.46 2 2
LRP6 0.027 0.005 -10000 0 -10000 0 0
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
NLK 0.013 0.007 -10000 0 -10000 0 0
CCND1 0.01 0.13 -10000 0 -0.85 10 10
WNT1 0.018 0.022 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.045 0.096 0.41 13 -0.47 2 15
DKK2 -0.002 0.13 -10000 0 -0.65 19 19
NOTCH1 precursor/DVL1 0.012 0.12 -10000 0 -0.59 11 11
GSK3B 0.027 0.003 -10000 0 -10000 0 0
FRAT1 0.026 0.005 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.005 0.14 -10000 0 -0.65 13 13
PPP2R5D 0.028 0.058 0.33 13 -0.32 3 16
MAPK1 0.02 0.012 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.065 0.018 -10000 0 -10000 0 0
RBPJ 0.027 0.008 -10000 0 -10000 0 0
CREBBP 0.028 0.008 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.001 0.1 -10000 0 -0.61 8 8
UGCG -0.058 0.22 -10000 0 -0.64 57 57
AKT1/mTOR/p70S6K/Hsp90/TERT 0.014 0.14 0.42 5 -0.41 23 28
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.058 0.22 -10000 0 -0.62 59 59
mol:DAG -0.01 0.12 -10000 0 -0.77 12 12
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.17 -10000 0 -0.44 47 47
FRAP1 -0.015 0.19 0.44 2 -0.51 48 50
FOXO3 -0.002 0.17 0.44 2 -0.63 20 22
AKT1 -0.006 0.18 -10000 0 -0.67 22 22
GAB2 0.027 0.006 -10000 0 -10000 0 0
SMPD1 0.01 0.085 -10000 0 -0.77 5 5
SGMS1 0.002 0.11 -10000 0 -0.64 12 12
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 0.007 0.036 -10000 0 -0.44 3 3
CALM1 0.027 0.005 -10000 0 -10000 0 0
cell proliferation -0.029 0.19 0.33 5 -0.52 41 46
EIF3A 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.039 0.044 -10000 0 -0.51 3 3
RPS6KB1 0.016 0.067 -10000 0 -0.82 2 2
mol:sphingomyelin -0.01 0.12 -10000 0 -0.77 12 12
natural killer cell activation 0 0.002 -10000 0 -0.012 4 4
JAK3 -0.009 0.062 -10000 0 -10000 0 0
PIK3R1 0.028 0.006 -10000 0 -10000 0 0
JAK1 0.028 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MYC -0.004 0.2 0.47 4 -0.94 16 20
MYB 0.002 0.19 -10000 0 -1.2 11 11
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.004 0.15 -10000 0 -0.56 22 22
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.042 0.068 -10000 0 -0.74 2 2
mol:PI-3-4-5-P3 -0.003 0.14 -10000 0 -0.54 22 22
Rac1/GDP 0.023 0.036 -10000 0 -0.4 3 3
T cell proliferation -0.003 0.13 -10000 0 -0.52 20 20
SHC1 0.026 0.008 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.01 -10000 0 -0.066 11 11
PRKCZ -0.004 0.14 -10000 0 -0.54 20 20
NF kappa B1 p50/RelA 0.012 0.17 -10000 0 -0.5 27 27
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.001 0.11 -10000 0 -0.49 16 16
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
IL2RA -0.017 0.16 -10000 0 -0.63 28 28
IL2RB 0.005 0.09 -10000 0 -0.57 10 10
TERT -0.006 0.023 -10000 0 -10000 0 0
E2F1 0.023 0.07 -10000 0 -0.43 11 11
SOS1 0.027 0.005 -10000 0 -10000 0 0
RPS6 0.025 0.008 -10000 0 -10000 0 0
mol:cAMP -0.001 0.005 0.031 11 -10000 0 11
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
IL2RG -0.01 0.14 -10000 0 -0.62 21 21
actin cytoskeleton organization -0.003 0.13 -10000 0 -0.52 20 20
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL2 0.018 0.013 -10000 0 -10000 0 0
PIK3CA 0.025 0.055 -10000 0 -0.67 3 3
Rac1/GTP 0.048 0.041 -10000 0 -0.39 3 3
LCK 0.014 0.081 -10000 0 -0.67 6 6
BCL2 -0.039 0.27 0.47 4 -0.79 49 53
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.02 0.012 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.001 0.064 -10000 0 -0.37 2 2
NT3 (dimer)/TRKC -0.02 0.14 -10000 0 -0.5 36 36
NT3 (dimer)/TRKB 0.005 0.14 -10000 0 -0.45 42 42
SHC/Grb2/SOS1/GAB1/PI3K 0.03 0.028 -10000 0 -0.28 3 3
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
BDNF 0.009 0.1 -10000 0 -0.67 11 11
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
NTRK1 0.01 0.03 -10000 0 -10000 0 0
NTRK2 0.019 0.065 -10000 0 -0.6 5 5
NTRK3 -0.01 0.11 -10000 0 -0.64 12 12
NT-4/5 (dimer)/TRKB 0.013 0.13 -10000 0 -0.44 34 34
neuron apoptosis -0.011 0.11 0.38 18 -10000 0 18
SHC 2-3/Grb2 0.011 0.12 -10000 0 -0.41 18 18
SHC1 0.025 0.007 -10000 0 -10000 0 0
SHC2 0.002 0.1 -10000 0 -0.48 14 14
SHC3 -0.005 0.12 -10000 0 -0.45 21 21
STAT3 (dimer) 0.03 0.015 -10000 0 -10000 0 0
NT3 (dimer)/TRKA 0.004 0.14 -10000 0 -0.43 39 39
RIN/GDP -0.003 0.077 0.3 7 -0.26 4 11
GIPC1 0.025 0.008 -10000 0 -10000 0 0
KRAS 0.027 0.005 -10000 0 -10000 0 0
DNAJA3 -0.005 0.071 -10000 0 -0.38 15 15
RIN/GTP 0.013 0.004 -10000 0 -10000 0 0
CCND1 0.02 0.017 -10000 0 -10000 0 0
MAGED1 0.026 0.007 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.002 0.12 -10000 0 -0.65 15 15
SHC/GRB2/SOS1 0.048 0.02 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.038 0.063 -10000 0 -0.44 7 7
TRKA/NEDD4-2 0.031 0.022 -10000 0 -10000 0 0
ELMO1 -0.24 0.34 -10000 0 -0.67 188 188
RhoG/GTP/ELMO1/DOCK1 -0.15 0.23 -10000 0 -0.44 188 188
NGF 0.021 0.055 -10000 0 -0.67 3 3
HRAS 0.026 0.011 -10000 0 -10000 0 0
DOCK1 0.023 0.054 -10000 0 -0.67 3 3
GAB2 0.027 0.005 -10000 0 -10000 0 0
RIT2 -0.009 0.016 -10000 0 -10000 0 0
RIT1 0.025 0.007 -10000 0 -10000 0 0
FRS2 0.027 0.005 -10000 0 -10000 0 0
DNM1 0.005 0.12 -10000 0 -0.61 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.12 0.18 -10000 0 -0.35 191 191
mol:GDP -0.012 0.1 0.35 8 -0.38 5 13
NGF (dimer) 0.021 0.055 -10000 0 -0.67 3 3
RhoG/GDP -0.18 0.25 -10000 0 -0.5 188 188
RIT1/GDP -0.002 0.076 0.3 7 -0.26 3 10
TIAM1 -0.054 0.077 -10000 0 -0.67 1 1
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB 0.036 0.087 -10000 0 -0.44 15 15
KIDINS220/CRKL/C3G 0.028 0.019 -10000 0 -10000 0 0
SHC/RasGAP 0.037 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2 0.053 0.025 -10000 0 -0.44 1 1
SHC/GRB2/SOS1/GAB1 0.06 0.025 -10000 0 -10000 0 0
RIT1/GTP 0.019 0.005 -10000 0 -10000 0 0
NT3 (dimer) -0.016 0.15 -10000 0 -0.67 25 25
RAP1/GDP -0.005 0.057 -10000 0 -0.23 3 3
KIDINS220/CRKL 0.02 0.012 -10000 0 -10000 0 0
BDNF (dimer) 0.009 0.1 -10000 0 -0.67 11 11
ubiquitin-dependent protein catabolic process 0.045 0.042 -10000 0 -0.44 3 3
Schwann cell development -0.03 0.028 -10000 0 -10000 0 0
EHD4 0.027 0.004 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.065 0.021 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.02 0.037 -10000 0 -0.28 1 1
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.007 0.12 -10000 0 -0.35 38 38
ABL1 0.025 0.008 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
Rap1/GTP -0.008 0.1 -10000 0 -0.5 6 6
STAT3 0.03 0.015 -10000 0 -10000 0 0
axon guidance -0.015 0.11 -10000 0 -0.34 38 38
MAPK3 0.017 0.069 -10000 0 -0.4 7 7
MAPK1 0.01 0.062 -10000 0 -0.4 7 7
CDC42/GDP -0.001 0.078 0.3 7 -0.26 3 10
NTF3 -0.016 0.15 -10000 0 -0.67 25 25
NTF4 0.002 0.12 -10000 0 -0.65 15 15
NGF (dimer)/TRKA/FAIM 0.046 0.042 -10000 0 -0.44 3 3
PI3K 0.036 0.043 -10000 0 -0.5 3 3
FRS3 0.027 0.003 -10000 0 -10000 0 0
FAIM 0.027 0.003 -10000 0 -10000 0 0
GAB1 0.027 0.004 -10000 0 -10000 0 0
RASGRF1 -0.04 0.082 -10000 0 -0.37 22 22
SOS1 0.027 0.005 -10000 0 -10000 0 0
MCF2L -0.026 0.12 -10000 0 -0.43 35 35
RGS19 0.026 0.008 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.036 0.07 -10000 0 -0.48 2 2
Rac1/GDP -0.004 0.067 0.22 1 -0.25 3 4
NGF (dimer)/TRKA/GRIT 0.026 0.042 -10000 0 -0.44 3 3
neuron projection morphogenesis 0.023 0.088 -10000 0 -0.7 2 2
NGF (dimer)/TRKA/NEDD4-2 0.046 0.043 -10000 0 -0.44 3 3
MAP2K1 0.039 0.058 0.36 4 -10000 0 4
NGFR -0.015 0.13 -10000 0 -0.67 16 16
NGF (dimer)/TRKA/GIPC/GAIP 0.016 0.07 -10000 0 -0.34 15 15
RAS family/GTP/PI3K 0.026 0.027 -10000 0 -0.3 3 3
FRS2 family/SHP2/GRB2/SOS1 0.074 0.031 -10000 0 -0.38 1 1
NRAS 0.027 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
PRKCI 0.027 0.003 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
MAPKKK cascade 0.021 0.074 -10000 0 -0.54 6 6
RASA1 0.027 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.03 0.024 -10000 0 -10000 0 0
SQSTM1 0.026 0.006 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.047 0.083 -10000 0 -0.4 14 14
NGF (dimer)/TRKA/p62/Atypical PKCs 0.068 0.045 -10000 0 -0.38 3 3
MATK 0.016 0.068 -10000 0 -0.6 5 5
NEDD4L 0.027 0.004 -10000 0 -10000 0 0
RAS family/GDP -0.019 0.041 -10000 0 -10000 0 0
NGF (dimer)/TRKA 0 0.076 -10000 0 -0.38 17 17
Rac1/GTP -0.11 0.12 -10000 0 -0.29 72 72
FRS2 family/SHP2/CRK family 0.057 0.043 -10000 0 -0.38 1 1
FOXM1 transcription factor network

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
NFATC3 -0.005 0.31 0.79 2 -0.93 11 13
PLK1 0.03 0.095 -10000 0 -0.81 5 5
BIRC5 0.027 0.1 -10000 0 -0.93 4 4
HSPA1B -0.011 0.31 -10000 0 -0.93 11 11
MAP2K1 0.026 0.045 -10000 0 -10000 0 0
BRCA2 -0.014 0.32 0.8 1 -0.99 14 15
FOXM1 -0.037 0.34 -10000 0 -1.1 13 13
XRCC1 -0.003 0.31 -10000 0 -0.91 11 11
FOXM1B/p19 -0.035 0.33 -10000 0 -0.93 20 20
Cyclin D1/CDK4 0.011 0.29 -10000 0 -0.83 10 10
CDC2 -0.015 0.32 -10000 0 -0.9 16 16
TGFA -0.003 0.29 -10000 0 -0.82 11 11
SKP2 -0.007 0.32 0.79 2 -0.98 14 16
CCNE1 0.027 0.01 -10000 0 -10000 0 0
CKS1B 0 0.31 0.79 1 -0.92 11 12
RB1 0.031 0.19 -10000 0 -0.68 8 8
FOXM1C/SP1 -0.017 0.33 -10000 0 -1 13 13
AURKB 0.011 0.13 -10000 0 -0.79 10 10
CENPF -0.001 0.31 0.79 1 -0.94 10 11
CDK4 0.028 0.019 -10000 0 -10000 0 0
MYC -0.018 0.31 -10000 0 -0.94 16 16
CHEK2 0.021 0.04 -10000 0 -10000 0 0
ONECUT1 -0.001 0.3 -10000 0 -0.89 11 11
CDKN2A -0.03 0.069 -10000 0 -10000 0 0
LAMA4 -0.011 0.31 -10000 0 -0.93 11 11
FOXM1B/HNF6 -0.007 0.32 -10000 0 -1 11 11
FOS -0.21 0.59 0.79 2 -1.2 127 129
SP1 0.027 0.009 -10000 0 -10000 0 0
CDC25B -0.006 0.31 0.8 1 -0.92 11 12
response to radiation 0.007 0.026 -10000 0 -10000 0 0
CENPB -0.006 0.31 0.8 1 -0.92 11 12
CENPA -0.021 0.32 -10000 0 -0.97 15 15
NEK2 -0.002 0.31 0.79 1 -0.94 10 11
HIST1H2BA -0.017 0.31 -10000 0 -0.94 11 11
CCNA2 0.026 0.022 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
CCNB1/CDK1 -0.021 0.33 -10000 0 -1.1 11 11
CCNB2 -0.013 0.31 -10000 0 -0.93 11 11
CCNB1 -0.013 0.32 -10000 0 -0.98 11 11
ETV5 -0.011 0.31 -10000 0 -0.93 11 11
ESR1 -0.048 0.38 -10000 0 -1.1 28 28
CCND1 0.004 0.29 -10000 0 -0.85 11 11
GSK3A 0.023 0.038 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.053 0.043 -10000 0 -10000 0 0
CDK2 0.028 0.008 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.01 0.032 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.027 0.31 -10000 0 -0.97 12 12
GAS1 -0.16 0.54 0.8 1 -1.2 97 98
MMP2 -0.013 0.34 0.79 2 -1.2 12 14
RB1/FOXM1C 0.004 0.29 -10000 0 -0.89 11 11
CREBBP 0.026 0.006 -10000 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.002 0.086 -10000 0 -0.36 2 2
epithelial cell differentiation -0.004 0.098 -10000 0 -0.4 7 7
ITCH 0.037 0.019 -10000 0 -10000 0 0
WWP1 -0.009 0.069 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
EGFR 0.019 0.07 -10000 0 -0.67 5 5
PRL -0.012 0.014 -10000 0 -10000 0 0
neuron projection morphogenesis -0.018 0.11 0.34 3 -0.48 5 8
PTPRZ1 0.002 0.1 -10000 0 -0.67 10 10
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.001 0.13 -10000 0 -0.5 6 6
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.037 0.13 -10000 0 -0.41 44 44
ADAM17 0.033 0.049 -10000 0 -0.67 2 2
ErbB4/ErbB4 -0.015 0.087 -10000 0 -0.38 2 2
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.029 0.14 -10000 0 -0.44 34 34
NCOR1 0.026 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.025 0.13 -10000 0 -0.39 42 42
GRIN2B -0.034 0.12 -10000 0 -0.38 41 41
ErbB4/ErbB2/betacellulin -0.001 0.11 -10000 0 -0.47 16 16
STAT1 0.023 0.023 -10000 0 -10000 0 0
HBEGF 0.019 0.033 -10000 0 -10000 0 0
PRLR -0.015 0.15 -10000 0 -0.67 25 25
E4ICDs/ETO2 -0.003 0.086 -10000 0 -0.43 3 3
axon guidance -0.006 0.071 -10000 0 -0.4 2 2
NEDD4 0.034 0.048 -10000 0 -0.66 2 2
Prolactin receptor/Prolactin receptor/Prolactin 0 0.12 -10000 0 -0.5 25 25
CBFA2T3 0.024 0.033 -10000 0 -0.67 1 1
ErbB4/ErbB2/HBEGF 0.01 0.073 -10000 0 -0.4 3 3
MAPK3 -0.013 0.11 -10000 0 -0.47 6 6
STAT1 (dimer) -0.001 0.085 -10000 0 -0.35 2 2
MAPK1 -0.016 0.11 -10000 0 -0.47 6 6
JAK2 0.024 0.025 -10000 0 -0.35 2 2
ErbB4/ErbB2/neuregulin 1 beta -0.03 0.12 -10000 0 -0.39 40 40
NRG1 -0.025 0.15 -10000 0 -0.52 42 42
NRG3 -0.022 0.17 -10000 0 -0.64 35 35
NRG2 -0.05 0.22 -10000 0 -0.67 53 53
NRG4 0.021 0.02 -10000 0 -10000 0 0
heart development -0.006 0.071 -10000 0 -0.4 2 2
neural crest cell migration -0.03 0.12 -10000 0 -0.38 40 40
ERBB2 0.019 0.035 -10000 0 -0.49 2 2
WWOX/E4ICDs -0.003 0.089 -10000 0 -0.55 2 2
SHC1 0.025 0.007 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.008 0.097 -10000 0 -0.48 5 5
apoptosis 0.022 0.13 0.4 35 -10000 0 35
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.048 0.16 -10000 0 -0.43 55 55
ErbB4/ErbB2/epiregulin 0.011 0.084 -10000 0 -0.42 3 3
ErbB4/ErbB4/betacellulin/betacellulin -0.015 0.12 -10000 0 -0.5 17 17
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.005 0.12 -10000 0 -0.36 27 27
MDM2 -0.013 0.077 0.26 2 -0.41 1 3
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.021 0.13 -10000 0 -0.4 41 41
STAT5A -0.001 0.071 -10000 0 -0.45 1 1
ErbB4/EGFR/neuregulin 1 beta -0.027 0.14 -10000 0 -0.4 46 46
DLG4 0.026 0.007 -10000 0 -10000 0 0
GRB2/SHC 0.035 0.014 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.002 0.076 -10000 0 -0.33 2 2
STAT5A (dimer) 0.005 0.11 -10000 0 -0.43 7 7
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.006 0.072 -10000 0 -0.45 1 1
LRIG1 0.016 0.084 -10000 0 -0.63 8 8
EREG -0.048 0.068 -10000 0 -10000 0 0
BTC 0.004 0.12 -10000 0 -0.67 16 16
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.006 0.069 -10000 0 -0.4 2 2
ERBB4 -0.015 0.088 -10000 0 -0.38 2 2
STAT5B 0.026 0.007 -10000 0 -10000 0 0
YAP1 0.005 0.066 -10000 0 -0.47 8 8
GRB2 0.026 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.01 0.071 -10000 0 -0.38 3 3
glial cell differentiation 0.002 0.075 0.33 2 -10000 0 2
WWOX 0.025 0.032 -10000 0 -0.67 1 1
cell proliferation -0.025 0.14 -10000 0 -0.48 16 16
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.027 0.005 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.027 0.11 -9999 0 -0.34 35 35
Syndecan-3/Neurocan 0.005 0.093 -9999 0 -0.35 28 28
POMC -0.12 0.28 -9999 0 -0.66 102 102
EGFR 0.019 0.07 -9999 0 -0.67 5 5
Syndecan-3/EGFR 0.027 0.043 -9999 0 -0.33 6 6
AGRP 0.003 0.033 -9999 0 -10000 0 0
NCSTN 0.025 0.007 -9999 0 -10000 0 0
PSENEN 0.026 0.007 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.027 0.004 -9999 0 -10000 0 0
APH1A 0.025 0.007 -9999 0 -10000 0 0
NCAN -0.024 0.17 -9999 0 -0.66 33 33
long-term memory 0.05 0.029 -9999 0 -10000 0 0
Syndecan-3/IL8 0.03 0.066 -9999 0 -0.36 11 11
PSEN1 0.027 0.005 -9999 0 -10000 0 0
Src/Cortactin 0.039 0.01 -9999 0 -10000 0 0
FYN 0.027 0.004 -9999 0 -10000 0 0
limb bud formation 0.015 0.006 -9999 0 -10000 0 0
MC4R 0 0.027 -9999 0 -10000 0 0
SRC 0.026 0.008 -9999 0 -10000 0 0
PTN -0.036 0.2 -9999 0 -0.67 44 44
FGFR/FGF/Syndecan-3 0.015 0.006 -9999 0 -10000 0 0
neuron projection morphogenesis -0.021 0.12 -9999 0 -0.4 5 5
Syndecan-3/AgRP 0.031 0.024 -9999 0 -0.31 1 1
Syndecan-3/AgRP/MC4R 0.046 0.029 -9999 0 -0.29 1 1
Fyn/Cortactin 0.039 0.008 -9999 0 -10000 0 0
SDC3 0.015 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.03 0.065 -9999 0 -0.35 11 11
IL8 -0.023 0.12 -9999 0 -0.67 11 11
Syndecan-3/Fyn/Cortactin 0.052 0.03 -9999 0 -10000 0 0
Syndecan-3/CASK 0.011 0.024 -9999 0 -0.3 1 1
alpha-MSH/MC4R -0.078 0.22 -9999 0 -0.5 102 102
Gamma Secretase 0.07 0.03 -9999 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.027 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.014 0.008 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.026 0.009 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.02 0.048 -10000 0 -0.43 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 -0.001 0.023 -10000 0 -10000 0 0
GRK1 -0.038 0.2 -10000 0 -0.65 46 46
CNG Channel 0.038 0.057 -10000 0 -0.37 7 7
mol:Na + 0.029 0.069 -10000 0 -0.39 9 9
mol:ADP -0.038 0.2 -10000 0 -0.65 46 46
RGS9-1/Gbeta5/R9AP -0.021 0.18 -10000 0 -0.44 70 70
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.041 0.072 -10000 0 -0.4 9 9
CNGB1 0.017 0.03 -10000 0 -10000 0 0
RDH5 -0.067 0.069 -10000 0 -10000 0 0
SAG -0.009 0.017 -10000 0 -10000 0 0
mol:Ca2+ -0.007 0.1 0.49 11 -0.38 9 20
Na + (4 Units) 0.022 0.065 -10000 0 -0.37 9 9
RGS9 -0.037 0.2 -10000 0 -0.67 44 44
GNB1/GNGT1 0.029 0.013 -10000 0 -10000 0 0
GNAT1/GDP -0.009 0.16 -10000 0 -0.39 69 69
GUCY2D 0.013 0.076 -10000 0 -0.62 6 6
GNGT1 -0.015 0.013 -10000 0 -10000 0 0
GUCY2F -0.013 0.01 -10000 0 -10000 0 0
GNB5 0.027 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) 0.015 0.043 -10000 0 -0.38 3 3
mol:11-cis-retinal -0.067 0.069 -10000 0 -10000 0 0
mol:cGMP 0.032 0.057 -10000 0 -0.39 6 6
GNB1 0.026 0.006 -10000 0 -10000 0 0
Rhodopsin -0.039 0.054 -10000 0 -10000 0 0
SLC24A1 0.027 0.004 -10000 0 -10000 0 0
CNGA1 0.018 0.071 -10000 0 -0.67 5 5
Metarhodopsin II -0.009 0.12 -10000 0 -0.39 46 46
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.048 0.062 -10000 0 -0.4 8 8
RGS9BP -0.015 0.16 -10000 0 -0.66 29 29
Metarhodopsin II/Transducin 0.013 0.006 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.039 0.036 -10000 0 -0.41 3 3
PDE6A/B 0.032 0.027 -10000 0 -10000 0 0
mol:Pi -0.021 0.17 -10000 0 -0.44 70 70
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.038 0.014 -10000 0 -10000 0 0
PDE6B 0.027 0.004 -10000 0 -10000 0 0
PDE6A 0.013 0.035 -10000 0 -10000 0 0
PDE6G 0.01 0.071 -10000 0 -0.67 4 4
RHO 0.006 0.023 -10000 0 -10000 0 0
PDE6 0.005 0.16 -10000 0 -0.38 70 70
GUCA1A 0.005 0.025 -10000 0 -10000 0 0
GC2/GCAP Family 0.046 0.036 -10000 0 -0.41 2 2
GUCA1C -0.016 0.002 -10000 0 -10000 0 0
GUCA1B 0.023 0.055 -10000 0 -0.67 3 3
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.011 0.12 -10000 0 -0.47 27 27
ATM 0.025 0.032 -10000 0 -0.67 1 1
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
PRKDC 0.027 0.005 -10000 0 -10000 0 0
ATR 0.026 0.032 -10000 0 -0.67 1 1
UBE2L3 0.02 0.012 -10000 0 -10000 0 0
FANCD2 0.023 0.026 -10000 0 -0.38 2 2
protein ubiquitination 0.044 0.095 -10000 0 -0.37 21 21
XRCC5 0.027 0.005 -10000 0 -10000 0 0
XRCC6 0.02 0.012 -10000 0 -10000 0 0
M/R/N Complex 0.05 0.034 -10000 0 -0.44 2 2
MRE11A 0.024 0.044 -10000 0 -0.67 2 2
DNA-PK 0.04 0.026 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.008 0.12 -10000 0 -0.49 23 23
FANCF 0.027 0.005 -10000 0 -10000 0 0
BRCA1 0.026 0.007 -10000 0 -10000 0 0
CCNE1 0.025 0.008 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.037 0.012 -10000 0 -10000 0 0
FANCG 0.025 0.007 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.011 0.11 -10000 0 -0.45 27 27
FANCE 0.027 0.003 -10000 0 -10000 0 0
FANCC 0.025 0.008 -10000 0 -10000 0 0
NBN 0.027 0.005 -10000 0 -10000 0 0
FANCA 0.02 0.029 -10000 0 -10000 0 0
DNA repair 0.017 0.09 0.41 2 -0.44 6 8
BRCA1/BARD1/ubiquitin 0.011 0.11 -10000 0 -0.45 27 27
BARD1/DNA-PK 0.028 0.1 -10000 0 -0.39 23 23
FANCL 0.027 0.005 -10000 0 -10000 0 0
mRNA polyadenylation -0.011 0.12 0.46 27 -10000 0 27
BRCA1/BARD1/CTIP/M/R/N Complex 0.014 0.075 -10000 0 -0.29 23 23
BRCA1/BACH1/BARD1/TopBP1 0.028 0.1 -10000 0 -0.39 27 27
BRCA1/BARD1/P53 0.042 0.1 -10000 0 -0.4 22 22
BARD1/CSTF1/BRCA1 0.028 0.1 -10000 0 -0.39 26 26
BRCA1/BACH1 0.026 0.007 -10000 0 -10000 0 0
BARD1 -0.011 0.15 -10000 0 -0.62 28 28
PCNA 0.027 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.028 0.1 -10000 0 -0.4 26 26
BRCA1/BARD1/UbcH7 0.017 0.1 -10000 0 -0.39 26 26
BRCA1/BARD1/RAD51/PCNA 0.043 0.099 -10000 0 -0.38 23 23
BARD1/DNA-PK/P53 0.037 0.097 -10000 0 -0.37 21 21
BRCA1/BARD1/Ubiquitin 0.011 0.11 -10000 0 -0.45 27 27
BRCA1/BARD1/CTIP 0.022 0.095 -10000 0 -0.38 24 24
FA complex 0.028 0.033 -10000 0 -10000 0 0
BARD1/EWS 0.002 0.12 -10000 0 -0.46 28 28
RBBP8 0.016 0.024 -10000 0 -0.5 1 1
TP53 0.026 0.007 -10000 0 -10000 0 0
TOPBP1 0.027 0.003 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.04 0.099 0.4 22 -10000 0 22
BRCA1/BARD1 0.05 0.098 -10000 0 -0.38 21 21
CSTF1 0.027 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.008 0.12 -10000 0 -0.47 28 28
CDK2 0.027 0.005 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.026 0.012 -10000 0 -10000 0 0
RAD50 0.026 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.011 0.11 -10000 0 -0.45 27 27
EWSR1 0.02 0.012 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.025 0.007 -9999 0 -10000 0 0
SPHK1 0.022 0.022 -9999 0 -10000 0 0
GNAI2 0.027 0.003 -9999 0 -10000 0 0
mol:S1P 0.017 0.007 -9999 0 -10000 0 0
GNAO1 0.004 0.12 -9999 0 -0.67 15 15
mol:Sphinganine-1-P 0.014 0.014 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.056 0.028 -9999 0 -10000 0 0
GNAI3 0.027 0.005 -9999 0 -10000 0 0
G12/G13 0.037 0.011 -9999 0 -10000 0 0
S1PR3 0.025 0.008 -9999 0 -10000 0 0
S1PR2 0.024 0.014 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0.01 0.018 -9999 0 -0.2 2 2
S1PR5 0.023 0.034 -9999 0 -0.67 1 1
S1PR4 0.023 0.019 -9999 0 -10000 0 0
GNAI1 0.025 0.032 -9999 0 -0.67 1 1
S1P/S1P5/G12 0.043 0.03 -9999 0 -0.38 1 1
S1P/S1P3/Gq -0.056 0.16 -9999 0 -0.3 133 133
S1P/S1P4/Gi 0.003 0.079 -9999 0 -0.32 17 17
GNAQ 0.025 0.008 -9999 0 -10000 0 0
GNAZ 0.02 0.012 -9999 0 -10000 0 0
GNA14 -0.13 0.28 -9999 0 -0.63 118 118
GNA15 0.014 0.048 -9999 0 -0.67 1 1
GNA12 0.026 0.006 -9999 0 -10000 0 0
GNA13 0.026 0.007 -9999 0 -10000 0 0
GNA11 0.015 0.084 -9999 0 -0.63 8 8
ABCC1 0.026 0.006 -9999 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.034 0.059 -10000 0 -0.39 6 6
EPHB2 0.022 0.054 -10000 0 -0.67 3 3
Syndecan-2/TACI -0.088 0.2 -10000 0 -0.44 121 121
LAMA1 -0.019 0.17 -10000 0 -0.66 33 33
Syndecan-2/alpha2 ITGB1 0.048 0.089 -10000 0 -0.38 19 19
HRAS 0.026 0.011 -10000 0 -10000 0 0
Syndecan-2/CASK 0.007 0.042 -10000 0 -0.33 7 7
ITGA5 0.027 0.005 -10000 0 -10000 0 0
BAX 0.002 0.064 -10000 0 -0.38 13 13
EPB41 0.027 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.024 0.04 -10000 0 -0.39 4 4
LAMA3 0 0.12 -10000 0 -0.67 16 16
EZR 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.023 0.045 -10000 0 -0.67 2 2
Syndecan-2/MMP2 0.021 0.07 -10000 0 -0.47 9 9
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 -0.006 0.056 -10000 0 -10000 0 0
dendrite morphogenesis 0.022 0.057 -10000 0 -0.35 10 10
Syndecan-2/GM-CSF -0.03 0.056 -10000 0 -0.39 5 5
determination of left/right symmetry 0.01 0.05 -10000 0 -0.38 7 7
Syndecan-2/PKC delta 0.026 0.045 -10000 0 -0.33 7 7
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
MAPK3 -0.029 0.047 -10000 0 -0.4 4 4
MAPK1 -0.023 0.046 -10000 0 -0.4 4 4
Syndecan-2/RACK1 0.038 0.041 -10000 0 -0.37 4 4
NF1 0.026 0.007 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.01 0.05 -10000 0 -0.38 7 7
ITGA2 -0.03 0.071 -10000 0 -10000 0 0
MAPK8 0.004 0.073 -10000 0 -0.42 14 14
Syndecan-2/alpha2/beta1 Integrin 0.034 0.12 -10000 0 -0.41 31 31
Syndecan-2/Kininogen 0.017 0.049 -10000 0 -0.33 7 7
ITGB1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.022 0.044 0.35 1 -0.35 4 5
Syndecan-2/CASK/Protein 4.1 0.023 0.041 -10000 0 -0.32 6 6
extracellular matrix organization 0.024 0.044 -10000 0 -0.42 4 4
actin cytoskeleton reorganization -0.033 0.059 -10000 0 -0.39 6 6
Syndecan-2/Caveolin-2/Ras 0.039 0.049 -10000 0 -0.39 6 6
Syndecan-2/Laminin alpha3 0.009 0.093 -10000 0 -0.42 21 21
Syndecan-2/RasGAP 0.05 0.042 -10000 0 -0.36 4 4
alpha5/beta1 Integrin 0.039 0.009 -10000 0 -10000 0 0
PRKCD 0.027 0.003 -10000 0 -10000 0 0
Syndecan-2 dimer 0.023 0.057 -10000 0 -0.36 10 10
GO:0007205 0.003 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.04 0.041 -10000 0 -0.35 4 4
RHOA 0.027 0.003 -10000 0 -10000 0 0
SDCBP 0.027 0.005 -10000 0 -10000 0 0
TNFRSF13B -0.16 0.29 -10000 0 -0.66 120 120
RASA1 0.027 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin -0.006 0.056 -10000 0 -10000 0 0
Syndecan-2/Synbindin 0.026 0.044 -10000 0 -0.35 6 6
TGFB1 0.024 0.016 -10000 0 -10000 0 0
CASP3 0.018 0.044 -10000 0 -0.39 4 4
FN1 -0.078 0.065 -10000 0 -10000 0 0
Syndecan-2/IL8 -0.004 0.086 -10000 0 -0.39 18 18
SDC2 0.01 0.05 -10000 0 -0.38 7 7
KNG1 -0.005 0.037 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.026 0.043 -10000 0 -0.43 4 4
TRAPPC4 0.027 0.005 -10000 0 -10000 0 0
CSF2 -0.076 0.062 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.024 0.044 -10000 0 -0.43 4 4
Syndecan-2/Syntenin/PI-4-5-P2 0.024 0.041 -10000 0 -0.39 4 4
Syndecan-2/Ezrin 0.042 0.043 -10000 0 -0.39 4 4
PRKACA 0.017 0.041 -10000 0 -0.39 4 4
angiogenesis -0.004 0.085 -10000 0 -0.39 18 18
MMP2 0.017 0.079 -10000 0 -0.62 7 7
IL8 -0.023 0.12 -10000 0 -0.67 11 11
calcineurin-NFAT signaling pathway -0.088 0.2 -10000 0 -0.43 121 121
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.029 0.008 -10000 0 -10000 0 0
epithelial cell differentiation 0.055 0.016 -10000 0 -10000 0 0
CYFIP2 0.026 0.006 -10000 0 -10000 0 0
ENAH 0.022 0.078 0.46 11 -10000 0 11
EGFR 0.019 0.07 -10000 0 -0.67 5 5
EPHA2 0.026 0.012 -10000 0 -10000 0 0
MYO6 0.031 0.065 0.42 11 -10000 0 11
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.053 0.013 -10000 0 -10000 0 0
AQP5 0.002 0.11 -10000 0 -0.53 19 19
CTNND1 0.027 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.024 0.047 0.38 7 -10000 0 7
regulation of calcium-dependent cell-cell adhesion -0.01 0.054 0.4 5 -10000 0 5
EGF -0.076 0.24 -10000 0 -0.66 72 72
NCKAP1 0.027 0.005 -10000 0 -10000 0 0
AQP3 -0.041 0.17 -10000 0 -0.53 49 49
cortical microtubule organization 0.055 0.016 -10000 0 -10000 0 0
GO:0000145 0.012 0.047 0.37 7 -10000 0 7
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.061 0.017 -10000 0 -10000 0 0
MLLT4 0.027 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.006 0.004 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.062 0.024 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.012 0.03 -10000 0 -10000 0 0
PVRL2 0.026 0.007 -10000 0 -10000 0 0
ZYX 0.02 0.021 -10000 0 -10000 0 0
ARF6/GTP 0.067 0.027 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.011 0.14 -10000 0 -0.35 74 74
RhoA/GDP 0.057 0.016 -10000 0 -10000 0 0
actin cytoskeleton organization 0.02 0.051 0.38 8 -10000 0 8
IGF-1R heterotetramer 0.027 0.004 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
IGF1R 0.027 0.004 -10000 0 -10000 0 0
IGF1 -0.13 0.28 -10000 0 -0.66 107 107
DIAPH1 0.05 0.05 -10000 0 -10000 0 0
Wnt receptor signaling pathway -0.055 0.016 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
RhoA/GTP 0.006 0.004 -10000 0 -10000 0 0
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
VCL 0.021 0.051 0.39 8 -10000 0 8
EFNA1 0.025 0.007 -10000 0 -10000 0 0
LPP 0.01 0.06 0.35 4 -0.35 8 12
Ephrin A1/EPHA2 0.047 0.019 -10000 0 -10000 0 0
SEC6/SEC8 0.014 0.006 -10000 0 -10000 0 0
MGAT3 -0.01 0.054 0.4 5 -10000 0 5
HGF/MET -0.004 0.14 -10000 0 -0.37 63 63
HGF -0.072 0.24 -10000 0 -0.67 69 69
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.029 0.009 -10000 0 -10000 0 0
actin cable formation 0.066 0.13 0.49 30 -0.33 1 31
KIAA1543 0.013 0.053 0.37 8 -0.35 1 9
KIFC3 0.021 0.023 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
EXOC3 0.026 0.007 -10000 0 -10000 0 0
ACTN1 0.024 0.038 0.36 4 -10000 0 4
NCK1/GIT1 0.038 0.01 -10000 0 -10000 0 0
mol:GDP 0.055 0.016 -10000 0 -10000 0 0
EXOC4 0.026 0.006 -10000 0 -10000 0 0
STX4 0.021 0.023 -10000 0 -10000 0 0
PIP5K1C 0.024 0.047 0.38 7 -10000 0 7
LIMA1 0.027 0.005 -10000 0 -10000 0 0
ABI1 0.027 0.004 -10000 0 -10000 0 0
ROCK1 0.044 0.1 0.44 22 -10000 0 22
adherens junction assembly 0.026 0.086 0.46 12 -0.56 1 13
IGF-1R heterotetramer/IGF1 -0.036 0.16 -10000 0 -0.35 101 101
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.011 -10000 0 -10000 0 0
MET -0.027 0.069 -10000 0 -10000 0 0
PLEKHA7 0.026 0.053 0.38 8 -0.36 1 9
mol:GTP 0.059 0.024 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.032 0.067 0.48 7 -10000 0 7
cortical actin cytoskeleton stabilization 0.029 0.008 -10000 0 -10000 0 0
regulation of cell-cell adhesion 0.02 0.051 0.38 8 -10000 0 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.029 0.009 -10000 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.025 0.032 -9999 0 -0.67 1 1
mol:S1P 0.001 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.013 0.053 -9999 0 -0.26 16 16
GNAO1 0.005 0.12 -9999 0 -0.67 15 15
S1P/S1P3/G12/G13 0.048 0.02 -9999 0 -10000 0 0
AKT1 0.023 0.041 -9999 0 -0.35 3 3
AKT3 0.019 0.067 -9999 0 -0.47 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.032 -9999 0 -0.67 1 1
GNAI2 0.029 0.004 -9999 0 -10000 0 0
GNAI3 0.028 0.005 -9999 0 -10000 0 0
GNAI1 0.026 0.032 -9999 0 -0.67 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.026 0.008 -9999 0 -10000 0 0
S1PR2 0.024 0.014 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.006 0.07 -9999 0 -0.3 16 16
MAPK3 0.003 0.065 -9999 0 -0.39 3 3
MAPK1 0.013 0.058 -9999 0 -0.38 3 3
JAK2 0.006 0.067 -9999 0 -0.28 15 15
CXCR4 0.003 0.064 -9999 0 -0.29 15 15
FLT1 0.027 0.032 -9999 0 -0.67 1 1
RhoA/GDP 0.02 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.019 0.004 -9999 0 -10000 0 0
SRC 0.003 0.063 -9999 0 -0.28 15 15
S1P/S1P3/Gi 0.006 0.07 -9999 0 -0.3 16 16
RAC1 0.026 0.006 -9999 0 -10000 0 0
RhoA/GTP 0.01 0.073 -9999 0 -0.28 15 15
VEGFA 0.025 0.054 -9999 0 -0.67 3 3
S1P/S1P2/Gi 0.004 0.074 -9999 0 -0.31 17 17
VEGFR1 homodimer/VEGFA homodimer 0.04 0.056 -9999 0 -0.63 3 3
RHOA 0.027 0.003 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.056 0.15 -9999 0 -0.31 121 121
GNAQ 0.025 0.008 -9999 0 -10000 0 0
GNAZ 0.021 0.013 -9999 0 -10000 0 0
G12/G13 0.037 0.011 -9999 0 -10000 0 0
GNA14 -0.13 0.28 -9999 0 -0.63 118 118
GNA15 0.014 0.048 -9999 0 -0.67 1 1
GNA12 0.026 0.006 -9999 0 -10000 0 0
GNA13 0.026 0.007 -9999 0 -10000 0 0
GNA11 0.015 0.084 -9999 0 -0.63 8 8
Rac1/GTP 0.01 0.072 -9999 0 -0.28 15 15
S1P1 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
VEGFR2 homodimer/VEGFA homodimer 0.03 0.07 -10000 0 -0.57 6 6
PDGFRB 0.025 0.032 -10000 0 -0.67 1 1
SPHK1 0.01 0.06 -10000 0 -0.86 2 2
mol:S1P 0.008 0.058 -10000 0 -0.79 2 2
S1P1/S1P/Gi -0.007 0.13 -10000 0 -0.4 38 38
GNAO1 0.002 0.12 -10000 0 -0.67 15 15
PDGFB-D/PDGFRB/PLCgamma1 -0.006 0.12 -10000 0 -0.46 15 15
PLCG1 -0.008 0.12 -10000 0 -0.4 30 30
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.032 -10000 0 -0.67 1 1
GNAI2 0.025 0.013 -10000 0 -10000 0 0
GNAI3 0.025 0.013 -10000 0 -10000 0 0
GNAI1 0.023 0.033 -10000 0 -0.67 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.001 0.058 -10000 0 -0.49 6 6
S1P1/S1P 0.003 0.07 -10000 0 -0.45 7 7
negative regulation of cAMP metabolic process -0.007 0.12 -10000 0 -0.39 38 38
MAPK3 -0.019 0.16 -10000 0 -0.59 32 32
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
KDR 0.021 0.063 -10000 0 -0.67 4 4
PLCB2 0.014 0.077 0.4 5 -0.49 4 9
RAC1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.009 0.06 -10000 0 -0.46 4 4
receptor internalization 0.003 0.065 -10000 0 -0.42 7 7
PTGS2 -0.054 0.29 0.64 3 -0.99 40 43
Rac1/GTP 0.01 0.059 -10000 0 -0.38 7 7
RHOA 0.027 0.003 -10000 0 -10000 0 0
VEGFA 0.023 0.054 -10000 0 -0.67 3 3
negative regulation of T cell proliferation -0.007 0.12 -10000 0 -0.39 38 38
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.019 0.015 -10000 0 -10000 0 0
MAPK1 -0.021 0.17 -10000 0 -0.6 34 34
S1P1/S1P/PDGFB-D/PDGFRB 0.012 0.079 -10000 0 -0.44 8 8
ABCC1 0.026 0.006 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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 0.027 0.005 -10000 0 -10000 0 0
HDAC3 0.026 0.006 -10000 0 -10000 0 0
VDR 0.026 0.008 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.04 0.026 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.003 0.07 -10000 0 -0.31 10 10
KAT2B 0.027 0.004 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
AKT1 0.013 0.082 0.25 13 -0.36 14 27
RAR alpha/9cRA/Cyclin H 0.034 0.097 -10000 0 -0.38 19 19
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.013 0.066 0.24 1 -0.29 15 16
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.011 0.097 -10000 0 -0.36 25 25
NCOR2 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.02 0.006 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.002 0.13 -10000 0 -0.54 22 22
NCOA2 -0.037 0.2 -10000 0 -0.67 45 45
NCOA3 0.027 0.005 -10000 0 -10000 0 0
NCOA1 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.008 -10000 0 -10000 0 0
RARG 0.027 0.005 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.034 0.011 -10000 0 -10000 0 0
MAPK3 0.027 0.006 -10000 0 -10000 0 0
MAPK1 0.02 0.012 -10000 0 -10000 0 0
MAPK8 0.014 0.095 -10000 0 -0.64 10 10
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.01 0.12 -10000 0 -0.53 19 19
RARA 0.005 0.075 -10000 0 -0.31 24 24
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.016 0.13 -10000 0 -0.46 26 26
PRKCA 0.004 0.13 -10000 0 -0.67 17 17
RXRs/RARs/NRIP1/9cRA/HDAC1 0.012 0.14 0.38 5 -0.53 23 28
RXRG -0.018 0.081 -10000 0 -0.4 21 21
RXRA 0.007 0.075 -10000 0 -0.3 24 24
RXRB 0.009 0.074 -10000 0 -0.38 17 17
VDR/Vit D3/DNA 0.02 0.006 -10000 0 -10000 0 0
RBP1 0.015 0.089 -10000 0 -0.67 8 8
CRBP1/9-cic-RA 0.011 0.067 -10000 0 -0.5 8 8
RARB 0.009 0.12 -10000 0 -0.67 14 14
PRKCG 0.021 0.015 -10000 0 -10000 0 0
MNAT1 0.027 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.006 0.13 -10000 0 -0.57 22 22
RXRs/RARs/SMRT(N-CoR2)/9cRA 0 0.12 -10000 0 -0.48 22 22
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.09 0.36 3 -0.42 11 14
RXRs/RARs/NRIP1/9cRA/HDAC3 0.012 0.14 0.42 5 -0.53 23 28
positive regulation of DNA binding 0.022 0.087 -10000 0 -0.35 19 19
NRIP1 0.013 0.13 0.5 1 -0.68 6 7
RXRs/RARs 0.005 0.13 -10000 0 -0.53 23 23
RXRs/RXRs/DNA/9cRA -0.01 0.11 -10000 0 -0.54 19 19
PRKACA 0.025 0.008 -10000 0 -10000 0 0
CDK7 0.026 0.005 -10000 0 -10000 0 0
TFIIH 0.053 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.047 0.068 -10000 0 -0.41 3 3
CCNH 0.027 0.005 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.049 0.018 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA -0.18 0.32 -10000 0 -0.66 149 149
HRAS 0.026 0.011 -10000 0 -10000 0 0
EGFR 0.019 0.07 -10000 0 -0.67 5 5
AKT 0.015 0.084 0.32 10 -10000 0 10
FOXO3 0.027 0.004 -10000 0 -10000 0 0
AKT1 0.027 0.005 -10000 0 -10000 0 0
FOXO1 0.026 0.007 -10000 0 -10000 0 0
AKT3 0.025 0.008 -10000 0 -10000 0 0
FOXO4 0.026 0.007 -10000 0 -10000 0 0
MET -0.027 0.069 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
PIK3CB 0.027 0.003 -10000 0 -10000 0 0
NRAS 0.027 0.005 -10000 0 -10000 0 0
PIK3CG 0.005 0.12 -10000 0 -0.67 14 14
PIK3R3 0.027 0.005 -10000 0 -10000 0 0
PIK3R2 0.025 0.008 -10000 0 -10000 0 0
NF1 0.026 0.007 -10000 0 -10000 0 0
RAS -0.031 0.086 -10000 0 -0.19 41 41
ERBB2 0.026 0.007 -10000 0 -10000 0 0
proliferation/survival/translation -0.037 0.06 0.32 7 -10000 0 7
PI3K -0.015 0.099 0.39 8 -0.24 13 21
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
KRAS 0.027 0.005 -10000 0 -10000 0 0
FOXO 0.045 0.059 0.31 8 -10000 0 8
AKT2 0.026 0.007 -10000 0 -10000 0 0
PTEN 0.026 0.018 -10000 0 -0.35 1 1
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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 0.027 0.005 -10000 0 -10000 0 0
NFATC1 0.035 0.095 0.46 9 -0.38 9 18
NFATC2 -0.023 0.097 0.28 9 -0.27 31 40
NFATC3 0.018 0.01 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.008 0.086 0.28 1 -0.31 23 24
Exportin 1/Ran/NUP214 0.047 0.018 -10000 0 -10000 0 0
mol:DAG -0.002 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.004 0.097 -10000 0 -0.39 12 12
BCL2/BAX -0.001 0.14 -10000 0 -0.48 36 36
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.02 -10000 0 -10000 0 0
CaM/Ca2+ 0.008 0.02 -10000 0 -10000 0 0
BAX 0.025 0.01 -10000 0 -10000 0 0
MAPK14 0.025 0.005 -10000 0 -10000 0 0
BAD 0.027 0.005 -10000 0 -10000 0 0
CABIN1/MEF2D 0.006 0.091 0.34 3 -0.38 10 13
Calcineurin A alpha-beta B1/BCL2 -0.023 0.18 -10000 0 -0.66 36 36
FKBP8 0.025 0.008 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.006 0.09 0.38 10 -0.34 3 13
KPNB1 0.026 0.007 -10000 0 -10000 0 0
KPNA2 0.026 0.007 -10000 0 -10000 0 0
XPO1 0.026 0.005 -10000 0 -10000 0 0
SFN -0.08 0.12 -10000 0 -0.67 15 15
MAP3K8 0.016 0.078 -10000 0 -0.62 7 7
NFAT4/CK1 alpha 0.019 0.029 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.073 0.17 -10000 0 -0.34 108 108
CABIN1 -0.007 0.084 0.28 1 -0.3 22 23
CALM1 0.023 0.009 -10000 0 -10000 0 0
RAN 0.026 0.005 -10000 0 -10000 0 0
MAP3K1 0.026 0.005 -10000 0 -10000 0 0
CAMK4 0.013 0.084 -10000 0 -0.67 7 7
mol:Ca2+ -0.004 0.008 -10000 0 -10000 0 0
MAPK3 0.026 0.006 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.036 0.012 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.01 0.095 -10000 0 -0.64 10 10
MAPK9 0.026 0.006 -10000 0 -10000 0 0
YWHAG 0.026 0.006 -10000 0 -10000 0 0
FKBP1A 0.027 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.021 0.087 0.37 2 -0.47 3 5
PRKCH 0.027 0.005 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.013 0.031 -10000 0 -10000 0 0
CASP3 0.025 0.005 -10000 0 -10000 0 0
PIM1 0.027 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.011 0.012 -10000 0 -10000 0 0
apoptosis 0.01 0.043 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.004 0.053 -10000 0 -0.32 5 5
PRKCB 0.008 0.079 -10000 0 -0.67 5 5
PRKCE 0.02 0.07 -10000 0 -0.67 5 5
JNK2/NFAT4 0.031 0.025 -10000 0 -10000 0 0
BAD/BCL-XL 0.039 0.009 -10000 0 -10000 0 0
PRKCD 0.027 0.003 -10000 0 -10000 0 0
NUP214 0.025 0.008 -10000 0 -10000 0 0
PRKCZ 0.024 0.007 -10000 0 -10000 0 0
PRKCA 0.002 0.13 -10000 0 -0.67 17 17
PRKCG 0.005 0.023 -10000 0 -10000 0 0
PRKCQ 0.019 0.072 -10000 0 -0.62 6 6
FKBP38/BCL2 -0.001 0.14 -10000 0 -0.48 36 36
EP300 0.01 0.02 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.037 0.1 0.41 7 -0.38 11 18
CaM/Ca2+/FKBP38 0.019 0.025 -10000 0 -10000 0 0
FKBP12/FK506 0.02 0.004 -10000 0 -10000 0 0
CSNK1A1 0.005 0.02 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.013 0.062 -10000 0 -0.44 7 7
NFATc/ERK1 0.042 0.08 0.44 3 -0.41 4 7
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.009 0.1 -10000 0 -0.37 15 15
NR4A1 -0.17 0.29 -10000 0 -0.61 147 147
GSK3B 0.024 0.007 -10000 0 -10000 0 0
positive T cell selection 0.018 0.01 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.023 0.072 -10000 0 -0.31 10 10
RCH1/ KPNB1 0.038 0.01 -10000 0 -10000 0 0
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
PRKACA 0.023 0.008 -10000 0 -10000 0 0
AKAP5 0.027 0.005 -10000 0 -10000 0 0
MEF2D 0.014 0.021 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
NFATc/p38 alpha 0.048 0.094 0.43 10 -0.41 4 14
CREBBP 0.013 0.022 -10000 0 -10000 0 0
BCL2 -0.023 0.18 -10000 0 -0.66 36 36
TCGA08_p53

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
CDKN2A -0.022 0.04 -10000 0 -10000 0 0
TP53 -0.008 0.037 -10000 0 -0.18 20 20
Senescence -0.008 0.037 -10000 0 -0.18 20 20
Apoptosis -0.008 0.037 -10000 0 -0.18 20 20
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.01 0.024 0.34 1 -10000 0 1
MDM4 0.025 0.007 -10000 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.026 0.046 0.29 10 -0.35 1 11
DAPP1 -0.036 0.13 0.33 4 -0.47 12 16
Src family/SYK family/BLNK-LAT/BTK-ITK -0.052 0.17 0.29 7 -0.48 27 34
mol:DAG -0.016 0.095 0.35 11 -0.26 13 24
HRAS 0.027 0.012 -10000 0 -10000 0 0
RAP1A 0.028 0.007 -10000 0 -10000 0 0
ARF5/GDP 0.035 0.064 0.28 2 -0.35 4 6
PLCG2 0.026 0.006 -10000 0 -10000 0 0
PLCG1 0.027 0.005 -10000 0 -10000 0 0
ARF5 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.048 0.3 10 -10000 0 10
ARF1/GTP 0.004 0.017 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
YES1 0.027 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.019 0.017 -10000 0 -10000 0 0
ADAP1 -0.001 0.045 0.29 10 -10000 0 10
ARAP3 0 0.048 0.3 10 -10000 0 10
INPPL1 0.027 0.005 -10000 0 -10000 0 0
PREX1 0.027 0.005 -10000 0 -10000 0 0
ARHGEF6 0.025 0.018 -10000 0 -0.35 1 1
ARHGEF7 0.026 0.006 -10000 0 -10000 0 0
ARF1 0.025 0.008 -10000 0 -10000 0 0
NRAS 0.028 0.007 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
FGR 0.025 0.014 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0.065 0.3 10 -10000 0 10
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.054 0.077 -10000 0 -0.67 1 1
ZAP70 -0.002 0.13 -10000 0 -0.65 18 18
mol:IP3 -0.013 0.069 0.24 12 -0.21 4 16
LYN 0.027 0.005 -10000 0 -10000 0 0
ARF1/GDP 0.034 0.073 0.3 7 -0.35 6 13
RhoA/GDP 0.038 0.044 0.35 2 -10000 0 2
PDK1/Src/Hsp90 0.05 0.034 -10000 0 -0.44 2 2
BLNK 0.027 0.004 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.034 0.076 0.4 10 -10000 0 10
SRC 0.026 0.008 -10000 0 -10000 0 0
PLEKHA2 0.005 0.015 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
PTEN 0.023 0.02 -10000 0 -0.33 1 1
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.025 0.039 0.29 9 -10000 0 9
RhoA/GTP 0.024 0.042 0.3 9 -10000 0 9
Src family/SYK family/BLNK-LAT -0.045 0.14 -10000 0 -0.44 24 24
BLK -0.19 0.31 -10000 0 -0.66 145 145
PDPK1 0.023 0.045 -10000 0 -0.67 2 2
CYTH1 0.002 0.054 0.31 12 -10000 0 12
HCK 0.017 0.037 -10000 0 -10000 0 0
CYTH3 -0.002 0.049 0.29 10 -0.36 1 11
CYTH2 0.003 0.057 0.31 14 -10000 0 14
KRAS 0.028 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.017 0.088 -10000 0 -0.54 10 10
SGK1 0.017 0.098 -10000 0 -0.52 13 13
INPP5D 0.019 0.032 -10000 0 -10000 0 0
mol:GDP 0.027 0.081 0.29 13 -0.32 9 22
SOS1 0.027 0.005 -10000 0 -10000 0 0
SYK 0.025 0.008 -10000 0 -10000 0 0
ARF6/GDP 0.03 0.051 0.29 8 -10000 0 8
mol:PI-3-4-5-P3 -0.008 0.015 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP 0.019 0.017 -10000 0 -10000 0 0
VAV1 0.012 0.06 -10000 0 -0.56 3 3
mol:PI-3-4-P2 0.012 0.02 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.044 0.03 0.33 1 -10000 0 1
PLEKHA1 0.005 0.015 -10000 0 -10000 0 0
Rac1/GDP 0.034 0.065 0.35 1 -0.32 6 7
LAT 0.021 0.058 -10000 0 -0.59 4 4
Rac1/GTP 0.018 0.06 0.27 1 -0.48 3 4
ITK -0.04 0.12 0.28 9 -0.36 49 58
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.028 0.12 0.38 9 -0.36 15 24
LCK 0.012 0.081 -10000 0 -0.67 6 6
BTK -0.005 0.066 0.3 13 -0.36 6 19
Regulation of Telomerase

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
Telomerase catalytic core complex -0.001 0.099 0.44 8 -10000 0 8
RAD9A 0.027 0.005 -10000 0 -10000 0 0
AP1 -0.19 0.36 -10000 0 -0.71 148 148
IFNAR2 0.027 0.006 -10000 0 -10000 0 0
AKT1 0.007 0.053 -10000 0 -0.24 20 20
ER alpha/Oestrogen -0.009 0.11 -10000 0 -0.48 23 23
NFX1/SIN3/HDAC complex 0.031 0.036 -10000 0 -0.49 1 1
EGF -0.075 0.24 -10000 0 -0.66 72 72
SMG5 0.025 0.007 -10000 0 -10000 0 0
SMG6 0.026 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.041 0.008 -10000 0 -10000 0 0
TERT/c-Abl -0.002 0.08 0.47 1 -10000 0 1
SAP18 0.026 0.007 -10000 0 -10000 0 0
MRN complex 0.05 0.034 -10000 0 -0.44 2 2
WT1 0.008 0.044 -10000 0 -10000 0 0
WRN 0.025 0.032 -10000 0 -0.67 1 1
SP1 0.028 0.006 -10000 0 -10000 0 0
SP3 0.027 0.005 -10000 0 -10000 0 0
TERF2IP 0.026 0.006 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.012 0.081 -10000 0 -10000 0 0
Mad/Max 0.04 0.009 -10000 0 -10000 0 0
TERT -0.001 0.099 0.44 8 -10000 0 8
CCND1 0.002 0.099 0.53 6 -10000 0 6
MAX 0.027 0.005 -10000 0 -10000 0 0
RBBP7 0.026 0.007 -10000 0 -10000 0 0
RBBP4 0.024 0.044 -10000 0 -0.67 2 2
TERF2 0.024 0.009 -10000 0 -10000 0 0
PTGES3 0.027 0.005 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
Telomerase/911 0.026 0.058 -10000 0 -0.3 3 3
CDKN1B -0.028 0.14 -10000 0 -0.42 55 55
RAD1 0.026 0.006 -10000 0 -10000 0 0
XRCC5 0.027 0.005 -10000 0 -10000 0 0
XRCC6 0.02 0.012 -10000 0 -10000 0 0
SAP30 0.026 0.032 -10000 0 -0.67 1 1
TRF2/PARP2 0.037 0.011 -10000 0 -10000 0 0
UBE3A 0.027 0.004 -10000 0 -10000 0 0
JUN -0.12 0.28 -10000 0 -0.66 106 106
E6 0 0 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.021 0.003 -10000 0 -10000 0 0
FOS -0.15 0.3 -10000 0 -0.66 124 124
IFN-gamma/IRF1 -0.017 0.17 -10000 0 -0.47 60 60
PARP2 0.027 0.005 -10000 0 -10000 0 0
BLM 0.027 0.008 -10000 0 -10000 0 0
Telomerase 0.014 0.1 0.26 1 -0.46 13 14
IRF1 0.03 0.009 -10000 0 -10000 0 0
ESR1 -0.013 0.14 -10000 0 -0.64 23 23
KU/TER 0.029 0.019 -10000 0 -10000 0 0
ATM/TRF2 0.038 0.024 -10000 0 -0.45 1 1
ubiquitin-dependent protein catabolic process 0.037 0.039 -10000 0 -0.33 3 3
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.037 0.04 -10000 0 -0.34 3 3
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.004 -10000 0 -10000 0 0
ATM 0.009 0.023 -10000 0 -0.48 1 1
SMAD3 0.015 0.01 -10000 0 -10000 0 0
ABL1 0.025 0.008 -10000 0 -10000 0 0
MXD1 0.027 0.005 -10000 0 -10000 0 0
MRE11A 0.024 0.044 -10000 0 -0.67 2 2
HUS1 0.026 0.006 -10000 0 -10000 0 0
RPS6KB1 0.026 0.007 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.018 0.08 -10000 0 -10000 0 0
NR2F2 0.026 0.004 -10000 0 -10000 0 0
MAPK3 0.002 0.013 -10000 0 -10000 0 0
MAPK1 0.002 0.011 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.024 0.016 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
HNRNPC 0.027 0.005 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.009 0.023 -10000 0 -0.48 1 1
NBN 0.027 0.005 -10000 0 -10000 0 0
EGFR 0.02 0.07 -10000 0 -0.67 5 5
mol:Oestrogen 0 0 -10000 0 -10000 0 0
EGF/EGFR -0.044 0.19 -10000 0 -0.5 76 76
MYC 0.012 0.1 -10000 0 -0.64 11 11
IL2 0.02 0.009 -10000 0 -10000 0 0
KU 0.029 0.019 -10000 0 -10000 0 0
RAD50 0.026 0.006 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
TGFB1 0.024 0.016 -10000 0 -10000 0 0
TRF2/BLM 0.037 0.012 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.003 0.084 0.5 2 -10000 0 2
SP1/HDAC2 0.042 0.009 -10000 0 -10000 0 0
PINX1 0.027 0.005 -10000 0 -10000 0 0
Telomerase/EST1A 0.012 0.079 -10000 0 -10000 0 0
Smad3/Myc 0.019 0.065 -10000 0 -0.41 10 10
911 complex 0.052 0.015 -10000 0 -10000 0 0
IFNG -0.06 0.22 -10000 0 -0.66 60 60
Telomerase/PinX1 0.011 0.081 -10000 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K 0.014 0.061 0.37 1 -0.42 2 3
SIN3B 0.026 0.008 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.01 0.078 -10000 0 -10000 0 0
response to DNA damage stimulus 0.003 0.019 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.071 0.036 -10000 0 -0.38 2 2
TRF2/WRN 0.037 0.025 -10000 0 -0.48 1 1
Telomerase/hnRNP C1/C2 0.012 0.081 -10000 0 -10000 0 0
E2F1 -0.015 0.066 -10000 0 -10000 0 0
ZNFX1 0.027 0.005 -10000 0 -10000 0 0
PIF1 0.017 0.077 -10000 0 -0.67 6 6
NCL 0.027 0.005 -10000 0 -10000 0 0
DKC1 0.025 0.008 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.006 0.16 -10000 0 -0.43 56 56
Ran/GTP/Exportin 1/HDAC1 0.007 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.018 0.14 -10000 0 -0.38 55 55
SUMO1 0.027 0.005 -10000 0 -10000 0 0
ZFPM1 0.026 0.007 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.009 -10000 0 -10000 0 0
FKBP3 0.027 0.005 -10000 0 -10000 0 0
Histones 0.036 0.083 -10000 0 -10000 0 0
YY1/LSF 0.006 0.065 -10000 0 -0.43 4 4
SMG5 0.025 0.007 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.007 0.11 -10000 0 -0.31 54 54
I kappa B alpha/HDAC1 0.011 0.08 -10000 0 -10000 0 0
SAP18 0.026 0.007 -10000 0 -10000 0 0
RELA -0.016 0.11 -10000 0 -0.31 56 56
HDAC1/Smad7 0.051 0.016 -10000 0 -10000 0 0
RANGAP1 0.02 0.012 -10000 0 -10000 0 0
HDAC3/TR2 0.012 0.08 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.031 0.037 -10000 0 -0.44 2 2
NF kappa B1 p50/RelA -0.024 0.12 0.32 1 -0.29 57 58
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.027 0.007 -10000 0 -10000 0 0
GATA1 0.012 0.021 -10000 0 -10000 0 0
Mad/Max 0.039 0.008 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.034 0.067 -10000 0 -0.49 5 5
RBBP7 0.026 0.007 -10000 0 -10000 0 0
NPC 0.016 0.003 -10000 0 -10000 0 0
RBBP4 0.024 0.044 -10000 0 -0.67 2 2
MAX 0.027 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
NFKBIA -0.003 0.082 -10000 0 -0.23 55 55
KAT2B 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.029 0.034 -10000 0 -0.55 1 1
SIN3 complex 0.061 0.031 -10000 0 -0.4 1 1
SMURF1 0.026 0.006 -10000 0 -10000 0 0
CHD3 0.026 0.007 -10000 0 -10000 0 0
SAP30 0.025 0.032 -10000 0 -0.67 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.026 0.007 -10000 0 -10000 0 0
YY1/HDAC3 -0.008 0.079 -10000 0 -0.26 11 11
YY1/HDAC2 0.009 0.054 -10000 0 -0.28 1 1
YY1/HDAC1 0.009 0.054 -10000 0 -0.28 1 1
NuRD/MBD2 Complex (MeCP1) 0.031 0.031 -10000 0 -0.4 1 1
PPARG -0.021 0.14 -10000 0 -0.38 60 60
HDAC8/hEST1B 0.046 0.021 -10000 0 -10000 0 0
UBE2I 0.026 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.012 0.08 -10000 0 -10000 0 0
MBD3L2 -0.015 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.051 0.015 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.035 0.061 -10000 0 -0.45 4 4
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC3 -0.003 0.083 -10000 0 -0.23 55 55
HDAC2 0.027 0.004 -10000 0 -10000 0 0
YY1 0.018 0.012 -10000 0 -10000 0 0
HDAC8 0.026 0.007 -10000 0 -10000 0 0
SMAD7 0.027 0.004 -10000 0 -10000 0 0
NCOR2 0.027 0.005 -10000 0 -10000 0 0
MXD1 0.027 0.005 -10000 0 -10000 0 0
STAT3 0.018 0.012 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.027 0.005 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.019 0.066 -10000 0 -0.4 4 4
YY1/SAP30/HDAC1 0.021 0.058 -10000 0 -0.3 1 1
EP300 0.02 0.012 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.018 0.012 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.082 -10000 0 -0.23 55 55
histone deacetylation 0.038 0.034 -10000 0 -0.39 1 1
STAT3 (dimer non-phopshorylated)/HDAC3 0.003 0.073 -10000 0 -0.27 9 9
nuclear export -0.046 0.021 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
GATAD2B 0.025 0.007 -10000 0 -10000 0 0
GATAD2A 0.025 0.008 -10000 0 -10000 0 0
GATA2/HDAC3 0.012 0.08 -10000 0 -10000 0 0
GATA1/HDAC1 0.034 0.013 -10000 0 -10000 0 0
GATA1/HDAC3 0.009 0.079 -10000 0 -10000 0 0
CHD4 0.027 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A -0.024 0.17 -10000 0 -0.5 56 56
SIN3/HDAC complex/Mad/Max 0.032 0.034 -10000 0 -0.49 1 1
NuRD Complex 0.041 0.052 -10000 0 -0.49 2 2
positive regulation of chromatin silencing 0.034 0.081 -10000 0 -10000 0 0
SIN3B 0.025 0.008 -10000 0 -10000 0 0
MTA2 0.027 0.005 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
XPO1 0.027 0.005 -10000 0 -10000 0 0
SUMO1/HDAC1 0.014 0.058 -10000 0 -0.31 1 1
HDAC complex 0.062 0.036 -10000 0 -0.39 2 2
GATA1/Fog1 0.034 0.014 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.053 0.014 -10000 0 -10000 0 0
TNF -0.056 0.22 -10000 0 -0.67 56 56
negative regulation of cell growth 0.035 0.035 -10000 0 -0.48 1 1
NuRD/MBD2/PRMT5 Complex 0.031 0.031 -10000 0 -0.4 1 1
Ran/GTP/Exportin 1 0.017 0.052 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.03 0.14 -10000 0 -0.39 56 56
SIN3/HDAC complex/NCoR1 0.031 0.044 -10000 0 -0.44 2 2
TFCP2 0.021 0.063 -10000 0 -0.67 4 4
NR2C1 0.027 0.005 -10000 0 -10000 0 0
MBD3 0.025 0.008 -10000 0 -10000 0 0
MBD2 0.027 0.004 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.11 0.28 -10000 0 -0.66 98 98
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.025 0.013 -10000 0 -10000 0 0
TCEB1 0.027 0.005 -10000 0 -10000 0 0
HIF1A/p53 0.033 0.038 0.35 1 -10000 0 1
HIF1A 0.009 0.024 -10000 0 -0.25 2 2
COPS5 0.027 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.055 0.051 -10000 0 -0.39 3 3
FIH (dimer) 0.027 0.004 -10000 0 -10000 0 0
CDKN2A -0.028 0.069 -10000 0 -10000 0 0
ARNT/IPAS -0.068 0.21 -10000 0 -0.48 98 98
HIF1AN 0.027 0.004 -10000 0 -10000 0 0
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
HIF1A/ARNT 0.032 0.048 0.31 7 -10000 0 7
CUL2 0.027 0.004 -10000 0 -10000 0 0
OS9 0.027 0.005 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.052 0.015 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.032 0.037 0.28 1 -10000 0 1
PHD1-3/OS9 0.05 0.073 -10000 0 -0.4 11 11
HIF1A/RACK1/Elongin B/Elongin C 0.055 0.039 -10000 0 -10000 0 0
VHL 0.023 0.054 -10000 0 -0.67 3 3
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.036 0.046 0.34 4 -10000 0 4
EGLN3 0.007 0.1 -10000 0 -0.67 10 10
EGLN2 0.026 0.007 -10000 0 -10000 0 0
EGLN1 0.024 0.032 -10000 0 -0.67 1 1
TP53 0.026 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.025 0.075 -10000 0 -0.57 6 6
ARNT 0.025 0.007 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.02 0.012 -10000 0 -10000 0 0
HIF1A/p19ARF 0.038 0.051 0.32 6 -10000 0 6
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.015 0.08 0.62 7 -10000 0 7
PI3K Class IB/PDE3B 0.015 0.08 -10000 0 -0.62 7 7
PDE3B 0.015 0.08 -10000 0 -0.62 7 7
a4b1 and a4b7 Integrin 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
ITGB1 0.027 0.004 -9999 0 -10000 0 0
ITGB7 0.004 0.11 -9999 0 -0.64 12 12
ITGA4 0.02 0.057 -9999 0 -0.67 3 3
alpha4/beta7 Integrin 0.016 0.095 -9999 0 -0.49 15 15
alpha4/beta1 Integrin 0.034 0.045 -9999 0 -0.5 3 3
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.006 0.016 0.12 1 -0.13 3 4
BUB1B 0.014 0.031 0.18 10 -0.15 1 11
PLK1 0.012 0.03 0.16 13 -0.1 1 14
PLK1S1 0.015 0.026 0.18 9 -10000 0 9
KIF2A 0.018 0.067 0.32 20 -0.38 1 21
regulation of mitotic centrosome separation 0.012 0.03 0.16 13 -0.1 1 14
GOLGA2 0.025 0.008 -10000 0 -10000 0 0
Hec1/SPC24 0.034 0.036 0.17 1 -10000 0 1
WEE1 0.022 0.046 0.29 5 -0.34 2 7
cytokinesis 0.011 0.062 0.27 8 -0.24 4 12
PP2A-alpha B56 0.048 0.096 -10000 0 -0.55 9 9
AURKA 0.014 0.023 0.17 7 -10000 0 7
PICH/PLK1 0.019 0.015 -10000 0 -10000 0 0
CENPE 0.01 0.051 0.25 11 -0.38 3 14
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.018 0.067 0.32 20 -0.38 1 21
PPP2CA 0.026 0.006 -10000 0 -10000 0 0
FZR1 0.025 0.008 -10000 0 -10000 0 0
TPX2 0.015 0.027 0.17 11 -10000 0 11
PAK1 0.026 0.005 -10000 0 -10000 0 0
SPC24 0.016 0.035 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
CLSPN 0.012 0.029 0.13 2 -0.29 3 5
GORASP1 0.027 0.004 -10000 0 -10000 0 0
metaphase 0.001 0.006 0.022 27 -10000 0 27
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.006 0.019 0.091 15 -0.05 1 16
G2 phase of mitotic cell cycle 0 0.004 0.012 41 -10000 0 41
STAG2 0.026 0.007 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.024 0.03 -10000 0 -0.41 2 2
spindle elongation 0.012 0.03 0.16 13 -0.1 1 14
ODF2 0.025 0.008 -10000 0 -10000 0 0
BUB1 0.023 0.1 -10000 0 -0.55 14 14
TPT1 0.004 0.045 0.14 4 -0.18 24 28
CDC25C 0.019 0.025 0.19 5 -10000 0 5
CDC25B 0.027 0.011 -10000 0 -10000 0 0
SGOL1 0.006 0.016 0.13 3 -0.12 1 4
RHOA 0.027 0.003 -10000 0 -10000 0 0
CCNB1/CDK1 0.042 0.014 -10000 0 -10000 0 0
CDC14B 0.003 0.045 -10000 0 -0.38 6 6
CDC20 0.025 0.018 -10000 0 -10000 0 0
PLK1/PBIP1 0.01 0.019 0.14 3 -10000 0 3
mitosis -0.001 0.003 0.019 5 -10000 0 5
FBXO5 0.013 0.037 0.21 9 -0.34 1 10
CDC2 0.002 0.001 0.01 1 -10000 0 1
NDC80 0.01 0.047 -10000 0 -10000 0 0
metaphase plate congression 0.014 0.025 0.14 1 -0.24 3 4
ERCC6L 0.025 0.014 -10000 0 -10000 0 0
NLP/gamma Tubulin 0.011 0.027 0.14 15 -10000 0 15
microtubule cytoskeleton organization 0.004 0.045 0.14 4 -0.18 24 28
G2/M transition DNA damage checkpoint 0 0.004 0.018 17 -10000 0 17
PPP1R12A 0.027 0.005 -10000 0 -10000 0 0
interphase 0 0.004 0.018 17 -10000 0 17
PLK1/PRC1-2 0.038 0.027 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.049 0.021 -10000 0 -10000 0 0
RAB1A 0.027 0.005 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.009 0.027 0.14 14 -10000 0 14
mitotic prometaphase 0 0.004 0.027 7 -10000 0 7
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.026 -10000 0 -10000 0 0
microtubule-based process 0.022 0.025 -10000 0 -10000 0 0
Golgi organization 0.012 0.03 0.16 13 -0.1 1 14
Cohesin/SA2 0.021 0.02 0.18 3 -10000 0 3
PPP1CB/MYPT1 0.039 0.009 -10000 0 -10000 0 0
KIF20A 0.005 0.051 -10000 0 -10000 0 0
APC/C/CDC20 0.025 0.024 0.16 3 -10000 0 3
PPP2R1A 0.025 0.007 -10000 0 -10000 0 0
chromosome segregation 0.01 0.019 0.13 3 -10000 0 3
PRC1 0.027 0.004 -10000 0 -10000 0 0
ECT2 0.01 0.041 0.21 9 -0.4 2 11
C13orf34 0.009 0.026 0.13 14 -0.081 1 15
NUDC 0.014 0.025 0.14 1 -0.24 3 4
regulation of attachment of spindle microtubules to kinetochore 0.014 0.031 0.18 10 -0.14 1 11
spindle assembly 0.014 0.037 0.17 18 -0.079 1 19
spindle stabilization 0.015 0.026 0.18 9 -10000 0 9
APC/C/HCDH1 0.019 0.041 -10000 0 -0.32 6 6
MKLP2/PLK1 0.022 0.025 -10000 0 -10000 0 0
CCNB1 0.027 0.006 -10000 0 -10000 0 0
PPP1CB 0.027 0.005 -10000 0 -10000 0 0
BTRC 0.027 0.004 -10000 0 -10000 0 0
ROCK2 -0.006 0.11 0.22 2 -0.4 32 34
TUBG1 0.015 0.029 0.18 9 -0.16 2 11
G2/M transition of mitotic cell cycle 0.013 0.01 -10000 0 -10000 0 0
MLF1IP 0.007 0.012 -10000 0 -10000 0 0
INCENP 0.024 0.045 -10000 0 -0.67 2 2
IL2 signaling events mediated by STAT5

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
GAB2 0.027 0.005 -10000 0 -10000 0 0
ELF1 0.004 0.1 -10000 0 -0.39 29 29
CCNA2 0.024 0.02 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
JAK3 -0.01 0.062 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
JAK1 0.027 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.003 0.13 -10000 0 -0.58 16 16
SHC1 0.026 0.008 -10000 0 -10000 0 0
SP1 0.033 0.006 -10000 0 -10000 0 0
IL2RA -0.033 0.21 -10000 0 -0.87 28 28
IL2RB 0.004 0.09 -10000 0 -0.57 10 10
SOS1 0.027 0.005 -10000 0 -10000 0 0
IL2RG -0.011 0.14 -10000 0 -0.62 21 21
G1/S transition of mitotic cell cycle 0.03 0.063 0.42 5 -0.5 3 8
PTPN11 0.026 0.032 -10000 0 -0.67 1 1
CCND2 0.023 0.005 -10000 0 -10000 0 0
LCK 0.013 0.081 -10000 0 -0.67 6 6
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL2 0.02 0.006 -10000 0 -10000 0 0
CDK6 0.022 0.054 -10000 0 -0.67 3 3
CCND3 0.007 0.12 -10000 0 -0.59 9 9
Effects of Botulinum toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A 0.009 0.002 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.036 0.013 -10000 0 -10000 0 0
STXBP1 0.025 0.008 -10000 0 -10000 0 0
ACh/CHRNA1 0.01 0.043 -10000 0 -0.24 4 4
RAB3GAP2/RIMS1/UNC13B 0.048 0.019 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.021 0.017 -10000 0 -10000 0 0
mol:ACh 0.002 0.044 0.14 21 -0.14 24 45
RAB3GAP2 0.025 0.008 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.031 0.055 -10000 0 -0.26 1 1
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.01 0.043 -10000 0 -0.24 4 4
UNC13B 0.025 0.008 -10000 0 -10000 0 0
CHRNA1 0.009 0.05 -10000 0 -0.67 1 1
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.039 0.11 -10000 0 -0.47 25 25
SNAP25 -0.015 0.075 -10000 0 -0.34 25 25
VAMP2 0.006 0.001 -10000 0 -10000 0 0
SYT1 -0.064 0.15 -10000 0 -0.67 24 24
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.024 0.009 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.031 0.055 -10000 0 -0.26 1 1
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.025 0.052 0.31 1 -0.66 1 2
PDGFB-D/PDGFRB/SLAP 0.037 0.027 -10000 0 -0.51 1 1
PDGFB-D/PDGFRB/APS/CBL 0.052 0.026 -10000 0 -0.42 1 1
AKT1 0.029 0.087 0.5 11 -10000 0 11
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.029 0.054 0.34 1 -0.7 1 2
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
FGR 0.018 0.045 0.33 2 -0.53 2 4
mol:Ca2+ 0.034 0.083 0.41 13 -0.74 1 14
MYC 0.032 0.18 0.58 18 -0.77 13 31
SHC1 0.025 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.035 0.025 -10000 0 -0.37 1 1
LRP1/PDGFRB/PDGFB 0.038 0.04 -10000 0 -0.44 2 2
GRB10 0.026 0.006 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
GO:0007205 0.034 0.083 0.4 13 -0.75 1 14
PTEN 0.026 0.018 -10000 0 -0.35 1 1
GRB2 0.026 0.007 -10000 0 -10000 0 0
GRB7 0.003 0.053 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.037 0.036 -10000 0 -0.51 2 2
PDGFB-D/PDGFRB/GRB10 0.038 0.026 -10000 0 -0.51 1 1
cell cycle arrest 0.037 0.027 -10000 0 -0.5 1 1
HRAS 0.026 0.011 -10000 0 -10000 0 0
HIF1A 0.023 0.084 0.48 11 -10000 0 11
GAB1 0.029 0.094 0.45 11 -0.56 2 13
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.034 0.11 0.5 16 -0.7 1 17
PDGFB-D/PDGFRB 0.054 0.029 -10000 0 -0.45 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.038 0.026 -10000 0 -0.51 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.032 0.052 -10000 0 -0.66 1 1
positive regulation of MAPKKK cascade 0.037 0.036 -10000 0 -0.51 2 2
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 0.034 0.083 0.41 13 -0.76 1 14
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.025 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.019 0.05 -10000 0 -0.56 1 1
SHB 0.025 0.007 -10000 0 -10000 0 0
BLK -0.14 0.26 -10000 0 -0.55 141 141
PTPN2 0.028 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.038 0.026 -10000 0 -0.48 1 1
BCAR1 0.026 0.006 -10000 0 -10000 0 0
VAV2 0.034 0.11 0.49 14 -0.57 3 17
CBL 0.027 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.038 0.026 -10000 0 -0.51 1 1
LCK 0.011 0.081 -10000 0 -0.65 6 6
PDGFRB 0.026 0.032 -10000 0 -0.68 1 1
ACP1 0.027 0.005 -10000 0 -10000 0 0
HCK 0.024 0.032 0.29 1 -0.43 1 2
ABL1 0.027 0.097 0.42 14 -0.58 2 16
PDGFB-D/PDGFRB/CBL 0.024 0.083 0.45 4 -0.64 2 6
PTPN1 0.028 0.005 -10000 0 -10000 0 0
SNX15 0.027 0.005 -10000 0 -10000 0 0
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT1 0.023 0.023 -10000 0 -10000 0 0
cell proliferation 0.033 0.17 0.54 20 -0.68 13 33
SLA 0.026 0.009 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.033 0.027 -10000 0 -0.36 1 1
SRC 0.019 0.036 0.29 1 -0.45 1 2
PI3K 0.012 0.034 -10000 0 -0.34 4 4
PDGFB-D/PDGFRB/GRB7/SHC 0.049 0.028 -10000 0 -0.3 1 1
SH2B2 0.026 0.009 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.029 0.055 0.34 1 -0.74 1 2
LYN 0.018 0.036 -10000 0 -0.44 2 2
LRP1 0.025 0.032 -10000 0 -0.67 1 1
SOS1 0.027 0.005 -10000 0 -10000 0 0
STAT5B 0.026 0.007 -10000 0 -10000 0 0
STAT5A 0.026 0.007 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.079 0.032 -10000 0 -0.37 1 1
SPHK1 0.023 0.022 -10000 0 -10000 0 0
EDG1 0.001 0.005 -10000 0 -10000 0 0
mol:DAG 0.034 0.083 0.41 13 -0.76 1 14
PLCG1 0.034 0.084 0.41 13 -0.79 1 14
NHERF/PDGFRB 0.05 0.028 -10000 0 -0.44 1 1
YES1 0.015 0.056 0.37 1 -0.51 4 5
cell migration 0.049 0.027 -10000 0 -0.44 1 1
SHC/Grb2/SOS1 0.072 0.035 -10000 0 -10000 0 0
SLC9A3R2 0.026 0.006 -10000 0 -10000 0 0
SLC9A3R1 0.026 0.007 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.062 0.033 -10000 0 -0.4 1 1
FYN 0.016 0.051 -10000 0 -0.48 3 3
DOK1 0.024 0.03 -10000 0 -0.41 1 1
HRAS/GTP 0.019 0.007 -10000 0 -10000 0 0
PDGFB 0.02 0.012 -10000 0 -10000 0 0
RAC1 0.04 0.14 0.52 21 -0.46 11 32
PRKCD 0.024 0.031 -10000 0 -0.41 1 1
FER 0.02 0.044 -10000 0 -0.41 4 4
MAPKKK cascade 0.015 0.056 0.37 1 -10000 0 1
RASA1 0.023 0.029 -10000 0 -0.41 1 1
NCK1 0.027 0.003 -10000 0 -10000 0 0
NCK2 0.027 0.005 -10000 0 -10000 0 0
p62DOK/Csk 0.039 0.029 -10000 0 -0.38 1 1
PDGFB-D/PDGFRB/SHB 0.036 0.028 -10000 0 -0.51 1 1
chemotaxis 0.027 0.096 0.42 14 -0.56 2 16
STAT1-3-5/STAT1-3-5 0.063 0.029 -10000 0 -0.36 1 1
Bovine Papilomavirus E5/PDGFRB 0.019 0.025 -10000 0 -0.51 1 1
PTPRJ 0.027 0.005 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.025 0.008 -10000 0 -10000 0 0
mol:Halofuginone 0.004 0.001 -10000 0 -10000 0 0
ITGA1 0.017 0.082 -10000 0 -0.67 7 7
CDKN1A -0.007 0.071 -10000 0 -0.61 1 1
PRL-3/alpha Tubulin 0.028 0.033 -10000 0 -10000 0 0
mol:Ca2+ -0.027 0.077 0.24 5 -0.51 10 15
AGT 0.005 0.1 -10000 0 -0.67 10 10
CCNA2 -0.067 0.15 -10000 0 -0.41 4 4
TUBA1B 0.027 0.005 -10000 0 -10000 0 0
EGR1 -0.086 0.2 -10000 0 -0.49 100 100
CDK2/Cyclin E1 0.018 0.077 -10000 0 -0.53 1 1
MAPK3 0.009 0.025 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.04 0.007 -10000 0 -10000 0 0
MAPK1 0.007 0.022 -10000 0 -10000 0 0
PTP4A1 -0.069 0.16 -10000 0 -10000 0 0
PTP4A3 0.014 0.041 -10000 0 -10000 0 0
PTP4A2 0.027 0.005 -10000 0 -10000 0 0
ITGB1 0.008 0.026 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
RAC1 -0.011 0.081 -10000 0 -0.37 8 8
Rab GGTase beta/Rab GGTase alpha 0.039 0.009 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.051 0.16 -10000 0 -0.41 3 3
RABGGTA 0.027 0.005 -10000 0 -10000 0 0
BCAR1 -0.017 0.006 -10000 0 -10000 0 0
RHOC -0.011 0.083 -10000 0 -0.4 7 7
RHOA -0.01 0.08 -10000 0 -0.61 2 2
cell motility -0.004 0.095 0.31 4 -0.71 2 6
PRL-1/alpha Tubulin -0.049 0.16 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.021 0.073 -10000 0 -0.52 7 7
ROCK1 -0.005 0.093 0.33 2 -0.72 2 4
RABGGTB 0.027 0.005 -10000 0 -10000 0 0
CDK2 0.027 0.005 -10000 0 -10000 0 0
mitosis -0.069 0.16 -10000 0 -10000 0 0
ATF5 0.02 0.027 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.004 0.12 -10000 0 -0.67 15 15
CDC42/GTP 0.007 0.074 -10000 0 -0.3 14 14
PLCG1 -0.002 0.067 -10000 0 -0.32 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.027 0.003 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
G12/G13 0.037 0.011 -10000 0 -10000 0 0
cell migration 0.007 0.073 -10000 0 -0.3 14 14
S1PR5 0.023 0.034 -10000 0 -0.67 1 1
S1PR4 0.023 0.019 -10000 0 -10000 0 0
MAPK3 -0.003 0.068 -10000 0 -0.32 14 14
MAPK1 0.009 0.06 -10000 0 -0.31 14 14
S1P/S1P5/Gi -0.001 0.074 -10000 0 -0.32 18 18
GNAI1 0.025 0.032 -10000 0 -0.67 1 1
CDC42/GDP 0.02 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.025 -10000 0 -0.44 1 1
RHOA 0.034 0.07 0.41 12 -10000 0 12
S1P/S1P4/Gi 0 0.073 -10000 0 -0.32 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.02 0.012 -10000 0 -10000 0 0
S1P/S1P4/G12/G13 0.047 0.018 -10000 0 -10000 0 0
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
Aurora B signaling

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
Condensin I complex 0.018 0.04 -10000 0 -0.25 2 2
STMN1 0.001 0.04 0.19 3 -10000 0 3
Aurora B/RasGAP/Survivin 0.053 0.05 -10000 0 -0.44 1 1
Chromosomal passenger complex/Cul3 protein complex 0.014 0.05 -10000 0 -0.25 11 11
BIRC5 0.017 0.047 -10000 0 -0.68 1 1
DES -0.32 0.3 -10000 0 -0.56 287 287
Aurora C/Aurora B/INCENP 0.055 0.044 -10000 0 -0.44 2 2
Aurora B/TACC1 0.032 0.041 -10000 0 -0.49 1 1
Aurora B/PP2A 0.033 0.041 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.011 0.006 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition -0.001 0.002 -10000 0 -10000 0 0
NDC80 -0.007 0.057 0.19 2 -10000 0 2
Cul3 protein complex 0.038 0.072 -10000 0 -0.43 10 10
KIF2C 0.016 0.027 -10000 0 -0.47 1 1
PEBP1 0.027 0.006 -10000 0 -10000 0 0
KIF20A 0.005 0.051 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.033 0.041 -10000 0 -10000 0 0
SEPT1 0.024 0.02 -10000 0 -10000 0 0
SMC2 0.025 0.008 -10000 0 -10000 0 0
SMC4 0.027 0.003 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.017 0.079 0.28 2 -0.54 8 10
PSMA3 0.027 0.005 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B 0.012 0.016 -10000 0 -10000 0 0
AURKB 0.003 0.062 -10000 0 -10000 0 0
AURKC 0.02 0.028 -10000 0 -10000 0 0
CDCA8 0.027 0.015 -10000 0 -10000 0 0
cytokinesis -0.017 0.053 -10000 0 -0.36 4 4
Aurora B/Septin1 0.046 0.065 0.27 1 -0.34 5 6
AURKA 0.026 0.005 -10000 0 -10000 0 0
INCENP 0.026 0.046 -10000 0 -0.68 2 2
KLHL13 0.006 0.1 -10000 0 -0.62 12 12
BUB1 -0.025 0.075 -10000 0 -0.67 1 1
hSgo1/Aurora B/Survivin 0.051 0.052 -10000 0 -0.4 1 1
EVI5 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.052 0.046 -10000 0 -10000 0 0
SGOL1 0.021 0.028 -10000 0 -10000 0 0
CENPA 0.019 0.04 0.2 2 -0.23 4 6
NCAPG 0.013 0.043 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.033 0.041 -10000 0 -10000 0 0
NCAPD2 0.027 0.005 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.033 0.041 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
NCAPH 0.006 0.051 -10000 0 -10000 0 0
NPM1 0.012 0.04 -10000 0 -0.3 7 7
RASA1 0.027 0.005 -10000 0 -10000 0 0
KLHL9 0.025 0.008 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.032 0.041 -10000 0 -10000 0 0
PPP1CC 0.027 0.005 -10000 0 -10000 0 0
Centraspindlin 0.044 0.047 -10000 0 -0.25 1 1
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
NSUN2 0.012 0.043 -10000 0 -0.3 6 6
MYLK 0.011 0.024 -10000 0 -0.4 1 1
KIF23 0.021 0.032 -10000 0 -10000 0 0
VIM 0.001 0.037 -10000 0 -10000 0 0
RACGAP1 0.028 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.005 0.08 -10000 0 -0.51 8 8
Chromosomal passenger complex 0.016 0.035 -10000 0 -0.26 3 3
Chromosomal passenger complex/EVI5 0.1 0.066 -10000 0 -0.41 3 3
TACC1 0.025 0.032 -10000 0 -0.67 1 1
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
CUL3 0.027 0.005 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.029 0.1 -10000 0 -0.48 8 8
CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
AKT1 0.027 0.005 -10000 0 -10000 0 0
AKT2 0.026 0.007 -10000 0 -10000 0 0
STXBP4 0.024 0.032 -10000 0 -0.67 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.023 0.1 0.33 7 -0.5 7 14
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
TBC1D4 -0.053 0.17 -10000 0 -0.49 67 67
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.05 0.027 -10000 0 -0.44 1 1
YWHAG 0.026 0.006 -10000 0 -10000 0 0
ASIP 0.005 0.047 -10000 0 -10000 0 0
PRKCI 0.027 0.003 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
RHOQ 0.027 0.005 -10000 0 -10000 0 0
GYS1 0.017 0.012 0.25 1 -10000 0 1
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
TRIP10 0.025 0.008 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.034 0.011 -10000 0 -10000 0 0
AS160/14-3-3 -0.034 0.094 -10000 0 -0.35 15 15
VAMP2 0.026 0.007 -10000 0 -10000 0 0
SLC2A4 0.022 0.11 0.33 6 -0.57 7 13
STX4 0.026 0.006 -10000 0 -10000 0 0
GSK3B 0.023 0.008 -10000 0 -10000 0 0
SFN -0.08 0.12 -10000 0 -0.67 15 15
LNPEP 0.004 0.12 -10000 0 -0.67 16 16
YWHAE 0.026 0.007 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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 0.016 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.044 0.016 -10000 0 -10000 0 0
CDKN1B 0.022 0.024 -10000 0 -10000 0 0
CDKN1A 0.02 0.024 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.027 0.005 -10000 0 -10000 0 0
FOXO3 0.022 0.023 -10000 0 -10000 0 0
AKT1 0.021 0.023 -10000 0 -10000 0 0
BAD 0.027 0.005 -10000 0 -10000 0 0
AKT3 0.013 0.026 -10000 0 -0.38 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.022 0.026 -10000 0 -10000 0 0
AKT1/ASK1 0.038 0.036 -10000 0 -0.33 1 1
BAD/YWHAZ 0.05 0.018 -10000 0 -10000 0 0
RICTOR 0.025 0.032 -10000 0 -0.67 1 1
RAF1 0.027 0.004 -10000 0 -10000 0 0
JNK cascade -0.036 0.034 0.32 1 -10000 0 1
TSC1 0.02 0.025 -10000 0 -10000 0 0
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
AKT1/RAF1 0.041 0.035 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
mol:GDP 0.022 0.023 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.021 0.023 -10000 0 -10000 0 0
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
TBC1D4 -0.046 0.15 -10000 0 -0.43 63 63
MAP3K5 0.026 0.032 -10000 0 -0.67 1 1
MAPKAP1 0.025 0.008 -10000 0 -10000 0 0
negative regulation of cell cycle -0.012 0.076 0.39 5 -0.32 8 13
YWHAH 0.02 0.012 -10000 0 -10000 0 0
AKT1S1 0.026 0.038 -10000 0 -10000 0 0
CASP9 0.023 0.03 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.044 0.048 0.36 6 -10000 0 6
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.05 0.034 -10000 0 -0.44 2 2
YWHAE 0.026 0.007 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
AKT2/p21CIP1 0.022 0.029 -10000 0 -0.35 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.011 -10000 0 -10000 0 0
CHUK 0.022 0.023 -10000 0 -10000 0 0
BAD/BCL-XL 0.046 0.034 0.28 1 -10000 0 1
mTORC2 0.03 0.023 -10000 0 -0.4 1 1
AKT2 0.014 0.026 -10000 0 -0.38 2 2
FOXO1-3a-4/14-3-3 family 0.02 0.081 0.37 8 -0.36 4 12
PDPK1 0.023 0.045 -10000 0 -0.67 2 2
MDM2 0.022 0.025 -10000 0 -10000 0 0
MAPKKK cascade -0.04 0.035 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.039 0.034 -10000 0 -10000 0 0
TSC1/TSC2 0.023 0.039 0.3 4 -10000 0 4
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.033 -10000 0 -10000 0 0
glucose import -0.057 0.16 0.21 5 -0.41 78 83
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.026 0.028 0.21 2 -10000 0 2
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.059 0.16 -10000 0 -0.41 78 78
GSK3A 0.026 0.037 -10000 0 -10000 0 0
FOXO1 0.021 0.025 -10000 0 -10000 0 0
GSK3B 0.022 0.023 -10000 0 -10000 0 0
SFN -0.08 0.12 -10000 0 -0.67 15 15
G1/S transition of mitotic cell cycle 0.028 0.043 0.32 2 -10000 0 2
p27Kip1/14-3-3 family 0.017 0.052 -10000 0 -0.34 5 5
PRKACA 0.025 0.008 -10000 0 -10000 0 0
KPNA1 0.027 0.003 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
YWHAG 0.026 0.006 -10000 0 -10000 0 0
RHEB 0.026 0.006 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.007 0.074 0.3 15 -10000 0 15
GNAI2 0.027 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.025 -10000 0 -0.44 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.004 0.12 -10000 0 -0.67 15 15
RhoA/GTP 0.007 0.075 -10000 0 -0.3 15 15
negative regulation of cAMP metabolic process -0.001 0.074 -10000 0 -0.31 18 18
GNAZ 0.02 0.012 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNA12 0.026 0.006 -10000 0 -10000 0 0
S1PR5 0.023 0.034 -10000 0 -0.67 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.001 0.074 -10000 0 -0.32 18 18
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
GNAI1 0.025 0.032 -10000 0 -0.67 1 1
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.008 0.003 -10000 0 -10000 0 0
SNTA1 0.027 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.008 0.004 -10000 0 -10000 0 0
MAPK12 -0.002 0.054 -10000 0 -0.38 10 10
CCND1 0.007 0.046 -10000 0 -0.4 4 4
p38 gamma/SNTA1 0.02 0.067 -10000 0 -0.36 11 11
MAP2K3 0.026 0.007 -10000 0 -10000 0 0
PKN1 0.025 0.008 -10000 0 -10000 0 0
G2/M transition checkpoint 0.001 0.063 0.21 8 -0.38 11 19
MAP2K6 0.001 0.064 -10000 0 -0.42 11 11
MAPT 0.009 0.047 0.28 6 -0.36 3 9
MAPK13 0.016 0.005 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.015 0.019 -10000 0 -0.39 1 1
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.037 0.013 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.003 0.11 -10000 0 -0.43 31 31
NF kappa B1 p50/RelA/I kappa B alpha 0.036 0.038 -10000 0 -10000 0 0
NFKBIA 0.014 0.029 -10000 0 -0.24 5 5
MAPK14 0.027 0.003 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.032 0.008 -10000 0 -10000 0 0
ARRB2 0.016 0.005 -10000 0 -10000 0 0
REL -0.018 0.17 -10000 0 -0.66 32 32
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.03 0.01 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.032 0.008 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
NF kappa B1 p50 dimer 0.025 0.023 0.25 5 -10000 0 5
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
NFKB1 0.017 0.003 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.02 0.038 -10000 0 -0.31 5 5
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.04 0.039 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
PI3K 0.036 0.043 -10000 0 -0.5 3 3
NF kappa B1 p50/RelA 0.02 0.038 -10000 0 -0.31 5 5
IKBKB 0.027 0.005 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -10000 0 -10000 0 0
SYK 0.025 0.008 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.028 0.038 -10000 0 -10000 0 0
cell death 0.038 0.038 -10000 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.003 0.11 -10000 0 -0.43 31 31
LCK 0.012 0.081 -10000 0 -0.67 6 6
BCL3 0.025 0.01 -10000 0 -10000 0 0
Canonical Wnt 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
HDAC1 0.027 0.022 0.25 1 -10000 0 1
AES 0.025 0.018 0.2 1 -10000 0 1
FBXW11 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.039 0.009 -10000 0 -10000 0 0
SMAD4 0.027 0.005 -10000 0 -10000 0 0
DKK2 -0.002 0.13 -10000 0 -0.65 19 19
TLE1 0.021 0.056 -10000 0 -0.65 3 3
MACF1 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.048 0.088 0.46 16 -10000 0 16
WIF1 -0.013 0.044 -10000 0 -10000 0 0
beta catenin/RanBP3 0.03 0.085 0.38 24 -10000 0 24
KREMEN2 0.016 0.036 -10000 0 -10000 0 0
DKK1 0.001 0.068 -10000 0 -0.67 2 2
beta catenin/beta TrCP1 0.048 0.045 0.38 2 -10000 0 2
FZD1 0.026 0.006 -10000 0 -10000 0 0
AXIN2 -0.028 0.3 0.61 13 -1.4 18 31
AXIN1 0.026 0.007 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.03 0.067 -10000 0 -0.51 2 2
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.039 0.094 0.29 1 -0.56 4 5
Axin1/APC/GSK3 0.034 0.045 0.34 4 -10000 0 4
Axin1/APC/GSK3/beta catenin/Macf1 0.034 0.029 0.32 1 -10000 0 1
HNF1A 0.027 0.02 0.21 2 -10000 0 2
CTBP1 0.027 0.02 0.24 1 -10000 0 1
MYC -0.034 0.23 0.55 5 -1.3 13 18
RANBP3 0.025 0.008 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.035 0.092 -10000 0 -0.43 18 18
NKD1 0.007 0.11 -10000 0 -0.67 13 13
TCF4 0.027 0.019 0.22 1 -10000 0 1
TCF3 0.025 0.02 0.23 1 -10000 0 1
WNT1/LRP6/FZD1/Axin1 0.065 0.02 -10000 0 -10000 0 0
Ran/GTP 0.02 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.02 0.11 0.49 21 -10000 0 21
LEF1 0.022 0.049 0.22 1 -0.62 2 3
DVL1 0.027 0.015 -10000 0 -10000 0 0
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.039 0.11 -10000 0 -0.53 8 8
DKK1/LRP6/Kremen 2 0.049 0.043 -10000 0 -0.46 2 2
LRP6 0.027 0.005 -10000 0 -10000 0 0
CSNK1A1 0.026 0.019 -10000 0 -10000 0 0
NLK 0.026 0.008 -10000 0 -10000 0 0
CCND1 -0.01 0.08 0.58 2 -0.68 2 4
WNT1 0.023 0.017 -10000 0 -10000 0 0
GSK3A 0.026 0.008 -10000 0 -10000 0 0
GSK3B 0.027 0.004 -10000 0 -10000 0 0
FRAT1 0.027 0.005 -10000 0 -10000 0 0
PPP2R5D 0.032 0.055 0.33 13 -0.29 2 15
APC 0.022 0.039 0.36 3 -0.38 1 4
WNT1/LRP6/FZD1 0.031 0.02 -10000 0 -10000 0 0
CREBBP 0.027 0.02 0.23 1 -10000 0 1
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.024 0.088 -10000 0 -0.54 11 11
AKT1 0.039 0.09 0.36 3 -0.58 7 10
PTK2B 0.017 0.11 0.35 1 -0.79 5 6
VEGFR2 homodimer/Frs2 0.032 0.083 -10000 0 -0.87 4 4
CAV1 0.013 0.093 -10000 0 -0.67 9 9
CALM1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.047 0.094 -10000 0 -0.73 6 6
endothelial cell proliferation 0.053 0.14 0.57 19 -0.55 6 25
mol:Ca2+ 0.023 0.09 -10000 0 -0.86 4 4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.06 0.091 -10000 0 -0.76 5 5
RP11-342D11.1 0.012 0.088 -10000 0 -0.64 7 7
CDH5 0.026 0.006 -10000 0 -10000 0 0
VEGFA homodimer 0.059 0.058 -10000 0 -0.49 4 4
SHC1 0.025 0.007 -10000 0 -10000 0 0
SHC2 0.021 0.055 -10000 0 -0.67 3 3
HRAS/GDP 0.039 0.078 -10000 0 -0.7 4 4
SH2D2A -0.01 0.14 -10000 0 -0.67 22 22
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.057 0.095 -10000 0 -0.65 4 4
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.024 0.13 -10000 0 -0.46 28 28
VEGFR1 homodimer 0.024 0.032 -10000 0 -0.67 1 1
SHC/GRB2/SOS1 0.065 0.095 -10000 0 -0.81 4 4
GRB10 0.023 0.088 -10000 0 -0.86 4 4
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
GRB2 0.026 0.007 -10000 0 -10000 0 0
PAK1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.07 0.092 -10000 0 -0.68 6 6
HRAS 0.026 0.011 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.027 0.065 -10000 0 -0.41 6 6
HIF1A 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.027 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.058 0.089 -10000 0 -0.75 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.018 0.076 -10000 0 -0.67 6 6
Nck/Pak 0.039 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.047 0.094 -10000 0 -0.73 6 6
mol:GDP 0.052 0.086 -10000 0 -0.76 4 4
mol:NADP 0.04 0.097 0.46 7 -0.48 6 13
eNOS/Hsp90 0.043 0.079 -10000 0 -0.45 6 6
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 0.023 0.092 -10000 0 -0.88 4 4
HIF1A/ARNT 0.037 0.012 -10000 0 -10000 0 0
SHB 0.025 0.007 -10000 0 -10000 0 0
VEGFA 0.025 0.054 -10000 0 -0.66 3 3
VEGFC 0.025 0.032 -10000 0 -0.67 1 1
FAK1/Vinculin 0.04 0.1 -10000 0 -0.68 6 6
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.048 0.12 -10000 0 -0.51 16 16
PTPN6 0.027 0.005 -10000 0 -10000 0 0
EPAS1 0.03 0.056 -10000 0 -0.53 4 4
mol:L-citrulline 0.04 0.097 0.46 7 -0.48 6 13
ITGAV 0.024 0.044 -10000 0 -0.67 2 2
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.058 0.092 -10000 0 -0.76 5 5
VEGFR2 homodimer/VEGFA homodimer 0.05 0.11 -10000 0 -0.72 7 7
VEGFR2/3 heterodimer 0.026 0.11 -10000 0 -0.83 7 7
VEGFB 0.027 0.005 -10000 0 -10000 0 0
MAPK11 0.006 0.098 0.38 1 -0.74 6 7
VEGFR2 homodimer 0.019 0.09 -10000 0 -0.97 4 4
FLT1 0.024 0.032 -10000 0 -0.67 1 1
NEDD4 0.026 0.044 -10000 0 -0.67 2 2
MAPK3 0.002 0.091 0.37 1 -0.73 5 6
MAPK1 -0.003 0.09 0.37 1 -0.73 5 6
VEGFA145/NRP2 0.028 0.052 -10000 0 -0.5 3 3
VEGFR1/2 heterodimer 0.03 0.093 -10000 0 -0.95 4 4
KDR 0.019 0.09 -10000 0 -0.97 4 4
VEGFA165/NRP1/VEGFR2 homodimer 0.054 0.099 -10000 0 -0.67 7 7
SRC 0.026 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.01 0.11 0.38 10 -0.86 4 14
PI3K 0.042 0.098 -10000 0 -0.78 5 5
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.047 0.094 -10000 0 -0.73 6 6
FES 0.024 0.096 -10000 0 -0.91 4 4
GAB1 0.029 0.093 -10000 0 -0.77 5 5
VEGFR2 homodimer/VEGFA homodimer/Src 0.047 0.094 -10000 0 -0.73 6 6
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
ARNT 0.025 0.007 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.039 0.09 0.4 1 -0.5 6 7
VEGFR2 homodimer/VEGFA homodimer/Yes 0.046 0.094 -10000 0 -0.73 6 6
PI3K/GAB1 0.05 0.085 -10000 0 -0.62 5 5
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.07 0.092 -10000 0 -0.68 6 6
PRKACA 0.025 0.008 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.04 0.11 -10000 0 -0.73 8 8
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
CDC42 0.022 0.096 -10000 0 -0.91 4 4
actin cytoskeleton reorganization 0.024 0.13 -10000 0 -0.45 28 28
PTK2 0.025 0.1 -10000 0 -0.75 6 6
EDG1 0.012 0.088 -10000 0 -0.64 7 7
mol:DAG 0.023 0.092 -10000 0 -0.88 4 4
CaM/Ca2+ 0.036 0.085 -10000 0 -0.8 4 4
MAP2K3 0.009 0.1 0.37 1 -0.89 4 5
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.052 0.1 -10000 0 -0.93 4 4
PLCG1 0.023 0.096 -10000 0 -0.91 4 4
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.057 0.093 -10000 0 -0.7 6 6
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
YES1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.046 0.1 -10000 0 -0.78 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.047 0.094 -10000 0 -0.73 6 6
cell migration 0.046 0.084 0.34 1 -0.66 4 5
mol:PI-3-4-5-P3 0.041 0.086 -10000 0 -0.68 5 5
FYN 0.027 0.004 -10000 0 -10000 0 0
VEGFB/NRP1 0.028 0.085 -10000 0 -0.6 7 7
mol:NO 0.04 0.097 0.46 7 -0.48 6 13
PXN 0.027 0.005 -10000 0 -10000 0 0
HRAS/GTP 0.021 0.075 -10000 0 -0.7 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.043 0.099 -10000 0 -0.93 4 4
VHL 0.023 0.054 -10000 0 -0.67 3 3
ITGB3 0.011 0.099 -10000 0 -0.64 11 11
NOS3 0.039 0.1 0.49 6 -0.55 6 12
VEGFR2 homodimer/VEGFA homodimer/Sck 0.041 0.099 -10000 0 -0.64 8 8
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA 0.002 0.12 0.36 1 -0.95 4 5
PRKCB 0.006 0.093 0.36 1 -0.81 4 5
VCL 0.027 0.005 -10000 0 -10000 0 0
VEGFA165/NRP1 0.029 0.095 -10000 0 -0.66 7 7
VEGFR1/2 heterodimer/VEGFA homodimer 0.044 0.1 -10000 0 -0.78 6 6
VEGFA165/NRP2 0.028 0.052 -10000 0 -0.5 3 3
MAPKKK cascade 0.053 0.091 0.36 2 -0.71 4 6
NRP2 0.015 0.04 -10000 0 -10000 0 0
VEGFC homodimer 0.025 0.032 -10000 0 -0.67 1 1
NCK1 0.027 0.003 -10000 0 -10000 0 0
ROCK1 0.027 0.005 -10000 0 -10000 0 0
FAK1/Paxillin 0.04 0.1 -10000 0 -0.68 6 6
MAP3K13 0.016 0.12 -10000 0 -0.54 14 14
PDPK1 0.028 0.081 -10000 0 -0.61 6 6
Regulation of cytoplasmic and nuclear SMAD2/3 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
SMAD4 0.027 0.005 -9999 0 -10000 0 0
SMAD2 -0.016 0.044 -9999 0 -0.24 1 1
SMAD3 0.021 0.016 -9999 0 -10000 0 0
SMAD3/SMAD4 0.032 0.05 -9999 0 -0.41 5 5
SMAD4/Ubc9/PIASy 0.049 0.019 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.027 0.063 -9999 0 -0.41 1 1
PPM1A 0.027 0.005 -9999 0 -10000 0 0
CALM1 0.027 0.005 -9999 0 -10000 0 0
SMAD2/SMAD4 -0.004 0.054 -9999 0 -0.34 2 2
MAP3K1 0.026 0.005 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.006 0.13 -9999 0 -0.49 31 31
MAPK3 0.026 0.006 -9999 0 -10000 0 0
MAPK1 0.02 0.012 -9999 0 -10000 0 0
NUP214 0.025 0.008 -9999 0 -10000 0 0
CTDSP1 0.027 0.005 -9999 0 -10000 0 0
CTDSP2 0.027 0.005 -9999 0 -10000 0 0
CTDSPL 0.027 0.003 -9999 0 -10000 0 0
KPNB1 0.026 0.007 -9999 0 -10000 0 0
TGFBRAP1 -0.016 0.17 -9999 0 -0.66 31 31
UBE2I 0.026 0.007 -9999 0 -10000 0 0
NUP153 0.026 0.031 -9999 0 -0.67 1 1
KPNA2 0.026 0.007 -9999 0 -10000 0 0
PIAS4 0.025 0.008 -9999 0 -10000 0 0
Canonical NF-kappaB pathway

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
FBXW11 0.029 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.048 0.065 0.38 1 -10000 0 1
ERC1 0.027 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.022 0.052 -10000 0 -0.5 2 2
NFKBIA 0.022 0.014 -10000 0 -10000 0 0
BIRC2 0.027 0.005 -10000 0 -10000 0 0
IKBKB 0.027 0.005 -10000 0 -10000 0 0
RIPK2 0.027 0.005 -10000 0 -10000 0 0
IKBKG 0.033 0.025 -10000 0 -10000 0 0
IKK complex/A20 0.015 0.14 0.33 1 -0.48 6 7
NEMO/A20/RIP2 0.027 0.005 -10000 0 -10000 0 0
XPO1 0.027 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.033 0.074 -10000 0 -0.56 1 1
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.036 0.008 -10000 0 -10000 0 0
IKK complex/ELKS 0.045 0.068 -10000 0 -0.38 1 1
BCL10/MALT1/TRAF6 0.05 0.034 -10000 0 -0.44 2 2
NOD2 0.004 0.065 -10000 0 -0.67 2 2
NFKB1 0.03 0.004 -10000 0 -10000 0 0
RELA 0.029 0.005 -10000 0 -10000 0 0
MALT1 0.027 0.004 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.039 0.008 -10000 0 -10000 0 0
ATM 0.025 0.032 -10000 0 -0.67 1 1
TNF/TNFR1A -0.024 0.17 -10000 0 -0.5 56 56
TRAF6 0.024 0.044 -10000 0 -0.67 2 2
PRKCA 0.002 0.13 -10000 0 -0.67 17 17
CHUK 0.027 0.004 -10000 0 -10000 0 0
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
TNF -0.056 0.22 -10000 0 -0.67 56 56
NF kappa B1 p50/RelA 0.061 0.016 -10000 0 -10000 0 0
BCL10 0.027 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.014 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.029 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
IKK complex 0.047 0.072 -10000 0 -0.4 1 1
CYLD 0.026 0.006 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.043 0.099 -10000 0 -0.46 2 2
Circadian rhythm pathway

Figure S110.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S110.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.04 0.042 -9999 0 -0.45 1 1
CLOCK -0.017 0.17 -9999 0 -0.67 32 32
TIMELESS/CRY2 0.027 0.035 -9999 0 -10000 0 0
DEC1/BMAL1 0.018 0.037 -9999 0 -10000 0 0
ATR 0.026 0.032 -9999 0 -0.67 1 1
NR1D1 0.002 0.039 -9999 0 -10000 0 0
ARNTL 0.012 0.046 -9999 0 -10000 0 0
TIMELESS 0.011 0.03 -9999 0 -10000 0 0
NPAS2 0.027 0.019 -9999 0 -0.35 1 1
CRY2 0.027 0.005 -9999 0 -10000 0 0
mol:CO -0.005 0.008 -9999 0 -10000 0 0
CHEK1 0.027 0.005 -9999 0 -10000 0 0
mol:HEME 0.005 0.008 -9999 0 -10000 0 0
PER1 0.026 0.007 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.024 0.12 -9999 0 -0.43 32 32
BMAL1/CLOCK -0.003 0.11 -9999 0 -0.43 14 14
S phase of mitotic cell cycle 0.04 0.042 -9999 0 -0.45 1 1
TIMELESS/CHEK1/ATR 0.041 0.042 -9999 0 -0.45 1 1
mol:NADPH 0.005 0.008 -9999 0 -10000 0 0
PER1/TIMELESS 0.026 0.033 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.012 0.013 -9999 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.012 0.069 -9999 0 -0.38 14 14
CRKL 0.02 0.012 -9999 0 -10000 0 0
Rac1/GDP 0.019 0.004 -9999 0 -10000 0 0
DOCK1 0.023 0.054 -9999 0 -0.67 3 3
ITGA4 0.02 0.057 -9999 0 -0.67 3 3
alpha4/beta7 Integrin/MAdCAM1 0.045 0.088 -9999 0 -0.4 16 16
EPO 0.004 0.026 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.016 0.095 -9999 0 -0.49 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.026 0.007 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.034 0.045 -9999 0 -0.5 3 3
EPO/EPOR (dimer) 0.03 0.021 -9999 0 -10000 0 0
lamellipodium assembly 0.02 0.037 -9999 0 -0.4 3 3
PIK3CA 0.023 0.054 -9999 0 -0.67 3 3
PI3K 0.036 0.043 -9999 0 -0.5 3 3
ARF6 0.027 0.005 -9999 0 -10000 0 0
JAK2 0.022 0.045 -9999 0 -0.5 3 3
PXN 0.027 0.005 -9999 0 -10000 0 0
PIK3R1 0.026 0.005 -9999 0 -10000 0 0
MADCAM1 0.005 0.063 -9999 0 -0.67 3 3
cell adhesion 0.043 0.087 -9999 0 -0.4 16 16
CRKL/CBL 0.029 0.018 -9999 0 -10000 0 0
ITGB1 0.027 0.004 -9999 0 -10000 0 0
SRC 0.016 0.065 -9999 0 -0.45 7 7
ITGB7 0.004 0.11 -9999 0 -0.64 12 12
RAC1 0.026 0.006 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.045 0.068 -9999 0 -0.49 7 7
p130Cas/Crk/Dock1 0.035 0.065 -9999 0 -0.36 10 10
VCAM1 0.018 0.071 -9999 0 -0.67 5 5
RHOA 0.027 0.003 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.063 0.038 -9999 0 -0.4 2 2
BCAR1 0.008 0.06 -9999 0 -0.42 7 7
EPOR 0.024 0.016 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.027 0.005 -9999 0 -10000 0 0
GIT1 0.026 0.007 -9999 0 -10000 0 0
Rac1/GTP 0.02 0.038 -9999 0 -0.41 3 3
HIF-2-alpha transcription factor network

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
MMP14 0.015 0.034 -10000 0 -10000 0 0
oxygen homeostasis 0.011 0.009 -10000 0 -10000 0 0
TCEB2 0.025 0.013 -10000 0 -10000 0 0
TCEB1 0.027 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.1 0.086 -10000 0 -0.53 3 3
EPO 0.12 0.11 -10000 0 -0.68 2 2
FIH (dimer) 0.036 0.012 -10000 0 -10000 0 0
APEX1 0.035 0.015 -10000 0 -10000 0 0
SERPINE1 0.12 0.12 -10000 0 -0.67 3 3
FLT1 0.019 0.12 -10000 0 -0.68 10 10
ADORA2A 0.099 0.12 0.43 1 -0.72 2 3
germ cell development 0.12 0.11 -10000 0 -0.71 2 2
SLC11A2 0.12 0.11 -10000 0 -0.75 2 2
BHLHE40 0.13 0.11 -10000 0 -0.75 2 2
HIF1AN 0.036 0.012 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.11 0.095 -10000 0 -0.65 2 2
ETS1 0.037 0.015 -10000 0 -10000 0 0
CITED2 -0.037 0.31 -10000 0 -1 41 41
KDR 0.025 0.13 -10000 0 -1 6 6
PGK1 0.12 0.11 -10000 0 -0.75 2 2
SIRT1 0.026 0.032 -10000 0 -0.67 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.16 0.14 -10000 0 -0.94 2 2
EPAS1 0.06 0.069 -10000 0 -0.46 2 2
SP1 0.032 0.007 -10000 0 -10000 0 0
ABCG2 0.12 0.13 -10000 0 -0.78 4 4
EFNA1 0.12 0.11 -10000 0 -0.75 2 2
FXN 0.12 0.12 0.45 4 -0.72 2 6
POU5F1 0.12 0.11 -10000 0 -0.75 2 2
neuron apoptosis -0.16 0.13 0.89 2 -10000 0 2
EP300 0.02 0.012 -10000 0 -10000 0 0
EGLN3 0.016 0.1 -10000 0 -0.66 10 10
EGLN2 0.035 0.014 -10000 0 -10000 0 0
EGLN1 0.033 0.034 -10000 0 -0.67 1 1
VHL/Elongin B/Elongin C 0.049 0.042 -10000 0 -0.45 3 3
VHL 0.023 0.054 -10000 0 -0.67 3 3
ARNT 0.034 0.015 -10000 0 -10000 0 0
SLC2A1 0.13 0.12 0.42 17 -0.72 2 19
TWIST1 0.12 0.14 0.4 17 -0.57 8 25
ELK1 0.022 0.036 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.088 0.098 -10000 0 -0.63 1 1
VEGFA 0.12 0.12 -10000 0 -0.7 4 4
CREBBP 0.026 0.006 -10000 0 -10000 0 0
FoxO family 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
G6PC 0.025 0.11 0.66 10 -10000 0 10
PLK1 0.068 0.11 0.6 2 -0.58 4 6
CDKN1B 0.073 0.09 0.47 3 -0.4 1 4
FOXO3 0.065 0.11 -10000 0 -0.63 4 4
KAT2B 0.032 0.019 -10000 0 -10000 0 0
FOXO1/SIRT1 0.019 0.056 0.42 2 -0.39 1 3
CAT 0.061 0.13 -10000 0 -1.4 2 2
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
AKT1 0.033 0.02 -10000 0 -10000 0 0
FOXO1 0.017 0.082 0.44 12 -10000 0 12
MAPK10 0.032 0.032 -10000 0 -0.4 1 1
mol:GTP 0.002 0.001 -10000 0 -10000 0 0
FOXO4 0.068 0.085 0.49 9 -0.51 3 12
response to oxidative stress 0.01 0.012 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.086 0.087 -10000 0 -0.59 4 4
XPO1 0.027 0.005 -10000 0 -10000 0 0
EP300 0.021 0.013 -10000 0 -10000 0 0
BCL2L11 0.026 0.099 -10000 0 -0.66 8 8
FOXO1/SKP2 0.015 0.055 -10000 0 -0.43 3 3
mol:GDP 0.01 0.012 -10000 0 -10000 0 0
RAN 0.028 0.006 -10000 0 -10000 0 0
GADD45A 0.098 0.091 0.45 6 -0.58 3 9
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.001 0.1 -10000 0 -0.48 7 7
MST1 0.031 0.036 -10000 0 -0.66 1 1
CSNK1D 0.026 0.007 -10000 0 -10000 0 0
CSNK1E 0.02 0.012 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.008 0.11 -10000 0 -0.56 10 10
YWHAB 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.026 0.062 0.21 2 -0.38 9 11
MAPK9 0.03 0.018 -10000 0 -10000 0 0
YWHAG 0.026 0.006 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
SIRT1 0.026 0.037 -10000 0 -0.66 1 1
SOD2 0.1 0.1 0.58 9 -0.62 2 11
RBL2 0.076 0.15 0.57 1 -0.89 7 8
RAL/GDP 0.045 0.015 -10000 0 -10000 0 0
CHUK 0.032 0.019 -10000 0 -10000 0 0
Ran/GTP 0.023 0.005 -10000 0 -10000 0 0
CSNK1G2 0.025 0.008 -10000 0 -10000 0 0
RAL/GTP 0.049 0.016 -10000 0 -10000 0 0
CSNK1G1 0.027 0.004 -10000 0 -10000 0 0
FASLG -0.071 0.38 -10000 0 -1.3 40 40
SKP2 0.022 0.054 -10000 0 -0.67 3 3
USP7 0.027 0.006 -10000 0 -10000 0 0
IKBKB 0.031 0.02 -10000 0 -10000 0 0
CCNB1 0.069 0.11 0.6 2 -0.63 2 4
FOXO1-3a-4/beta catenin 0.097 0.099 0.44 7 -0.42 4 11
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.055 -10000 0 -0.42 3 3
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
SGK1 0.018 0.1 -10000 0 -0.67 10 10
CSNK1G3 0.026 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.04 0.01 -10000 0 -10000 0 0
ZFAND5 0.075 0.11 0.56 15 -0.44 2 17
SFN -0.08 0.12 -10000 0 -0.67 15 15
CDK2 0.027 0.005 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.009 0.1 -10000 0 -0.51 10 10
CREBBP 0.026 0.006 -10000 0 -10000 0 0
FBXO32 0.065 0.11 0.58 1 -0.6 3 4
BCL6 0.082 0.12 0.57 1 -0.82 4 5
RALB 0.028 0.005 -10000 0 -10000 0 0
RALA 0.027 0.006 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B -0.031 0.073 -10000 0 -0.14 1 1
CDKN2C 0.031 0.019 -10000 0 -10000 0 0
CDKN2A -0.029 0.073 -10000 0 -10000 0 0
CCND2 0.009 0.022 -10000 0 -10000 0 0
RB1 -0.012 0.045 0.32 2 -0.24 10 12
CDK4 0.008 0.022 -10000 0 -10000 0 0
CDK6 0.009 0.024 -10000 0 -0.16 1 1
G1/S progression 0.014 0.05 0.24 15 -0.32 2 17
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.028 0.041 0.29 3 -0.38 3 6
adherens junction organization 0.02 0.04 0.25 4 -10000 0 4
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.036 0.051 -10000 0 -0.6 1 1
FMN1 0.008 0.082 -10000 0 -0.34 24 24
mol:IP3 0.027 0.032 -10000 0 -0.33 3 3
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.029 0.022 -10000 0 -10000 0 0
CTNNB1 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.033 0.035 0.25 1 -0.32 3 4
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.035 0.029 -10000 0 -10000 0 0
CTNND1 0.028 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.023 0.032 -10000 0 -0.38 2 2
VASP 0.025 0.018 -10000 0 -10000 0 0
ZYX 0.025 0.021 -10000 0 -10000 0 0
JUB 0.025 0.02 -10000 0 -10000 0 0
EGFR(dimer) 0.039 0.047 -10000 0 -0.36 5 5
E-cadherin/beta catenin-gamma catenin 0.051 0.016 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.048 0.038 0.25 1 -0.34 3 4
PIK3CA 0.024 0.055 -10000 0 -0.67 3 3
PI3K 0.05 0.039 0.26 1 -0.34 3 4
FYN 0.026 0.036 0.29 3 -10000 0 3
mol:Ca2+ 0.027 0.032 -10000 0 -0.32 3 3
JUP 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
mol:DAG 0.027 0.032 -10000 0 -0.33 3 3
CDH1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.037 0.053 -10000 0 -0.6 1 1
establishment of polarity of embryonic epithelium 0.025 0.018 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
EGFR 0.019 0.07 -10000 0 -0.67 5 5
CASR 0.018 0.031 -10000 0 -0.31 3 3
RhoA/GTP 0.039 0.032 -10000 0 -0.3 3 3
AKT2 0.031 0.033 -10000 0 -0.32 3 3
actin cable formation 0.006 0.077 -10000 0 -0.33 23 23
apoptosis -0.029 0.043 0.35 3 -0.32 4 7
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
mol:GDP 0.021 0.052 -10000 0 -0.37 7 7
PIP5K1A 0.023 0.033 -10000 0 -0.39 2 2
PLCG1 0.027 0.033 -10000 0 -0.34 3 3
Rac1/GTP 0.048 0.047 -10000 0 -0.33 5 5
homophilic cell adhesion 0.001 0.005 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.019 0.03 -10000 0 -0.32 3 3
TRAF2/ASK1 0.032 0.024 -10000 0 -0.44 1 1
ATM 0.025 0.032 -10000 0 -0.67 1 1
MAP2K3 0.036 0.094 0.42 15 -0.38 3 18
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.025 0.095 0.34 14 -0.38 8 22
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.014 0.083 -10000 0 -0.67 7 7
TXN 0.008 0.003 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
GADD45A 0.027 0.005 -10000 0 -10000 0 0
GADD45B 0.006 0.11 -10000 0 -0.6 15 15
MAP3K1 0.026 0.005 -10000 0 -10000 0 0
MAP3K6 0.027 0.005 -10000 0 -10000 0 0
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
MAP3K4 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.038 0.026 -10000 0 -0.5 1 1
TAK1/TAB family 0.011 0.033 -10000 0 -0.19 3 3
RAC1/OSM/MEKK3 0.049 0.015 -10000 0 -10000 0 0
TRAF2 0.025 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.036 0.055 -10000 0 -0.33 2 2
TRAF6 0.007 0.026 -10000 0 -0.39 2 2
RAC1 0.026 0.006 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.021 0.063 -10000 0 -0.67 4 4
CCM2 0.026 0.011 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.031 0.043 -10000 0 -0.44 4 4
MAPK11 0.02 0.012 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.046 0.052 -10000 0 -0.49 4 4
OSM/MEKK3 0.037 0.013 -10000 0 -10000 0 0
TAOK1 -0.031 0.13 -10000 0 -0.4 56 56
TAOK2 0.015 0.019 -10000 0 -0.38 1 1
TAOK3 0.015 0.018 -10000 0 -0.38 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.026 0.032 -10000 0 -0.67 1 1
MAP3K10 0.026 0.007 -10000 0 -10000 0 0
MAP3K3 0.026 0.007 -10000 0 -10000 0 0
TRX/ASK1 0.017 0.036 -10000 0 -0.42 1 1
GADD45/MTK1/MTK1 0.038 0.09 -10000 0 -0.4 18 18
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.03 0.025 -10000 0 -10000 0 0
BIRC5 0.016 0.046 -10000 0 -0.67 1 1
NFKBIA 0.015 0.022 0.25 3 -10000 0 3
CPEB1 -0.023 0.18 -10000 0 -0.64 37 37
AKT1 0.015 0.024 0.25 4 -10000 0 4
NDEL1 0.026 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.027 0.021 -10000 0 -10000 0 0
NDEL1/TACC3 0.044 0.024 -10000 0 -10000 0 0
GADD45A 0.027 0.005 -10000 0 -10000 0 0
GSK3B 0.027 0.009 -10000 0 -10000 0 0
PAK1/Aurora A 0.03 0.025 -10000 0 -10000 0 0
MDM2 0.027 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.008 0.027 -10000 0 -10000 0 0
TP53 0.025 0.012 -10000 0 -10000 0 0
DLG7 0.013 0.011 -10000 0 -10000 0 0
AURKAIP1 0.026 0.011 -10000 0 -10000 0 0
ARHGEF7 0.026 0.006 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.046 0.024 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.026 0.021 -10000 0 -10000 0 0
AURKA 0.02 0.016 -10000 0 -10000 0 0
AURKB 0.012 0.023 -10000 0 -0.16 3 3
CDC25B 0.021 0.012 -10000 0 -10000 0 0
G2/M transition checkpoint 0.01 0.018 -10000 0 -10000 0 0
mRNA polyadenylation -0.002 0.11 -10000 0 -0.4 33 33
Aurora A/CPEB -0.002 0.11 -10000 0 -0.4 33 33
Aurora A/TACC1/TRAP/chTOG 0.054 0.038 -10000 0 -0.37 1 1
BRCA1 0.026 0.007 -10000 0 -10000 0 0
centrosome duplication 0.03 0.025 -10000 0 -10000 0 0
regulation of centrosome cycle 0.042 0.023 -10000 0 -10000 0 0
spindle assembly 0.053 0.038 -10000 0 -0.37 1 1
TDRD7 0.025 0.008 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.055 0.033 -10000 0 -0.36 1 1
CENPA 0.016 0.033 -10000 0 -0.25 7 7
Aurora A/PP2A 0.03 0.024 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.021 0.018 -10000 0 -10000 0 0
negative regulation of DNA binding 0.025 0.012 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.037 0.012 -10000 0 -10000 0 0
RASA1 0.027 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A 0.01 0.019 -10000 0 -10000 0 0
mitotic prometaphase -0.004 0.011 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.016 -10000 0 -10000 0 0
TACC1 0.025 0.032 -10000 0 -0.67 1 1
TACC3 0.026 0.01 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.046 0.021 -10000 0 -10000 0 0
Aurora A/RasGAP 0.03 0.025 -10000 0 -10000 0 0
OAZ1 0.025 0.008 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.025 0.01 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.05 0.018 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.008 0.027 -10000 0 -10000 0 0
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
Aurora A/TPX2 0.017 0.031 -10000 0 -10000 0 0
PAK1 0.027 0.005 -10000 0 -10000 0 0
CKAP5 0.027 0.005 -10000 0 -10000 0 0
EPO signaling pathway

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
BCL2L1 0.031 0.097 0.34 2 -10000 0 2
CRKL 0.014 0.047 0.46 3 -10000 0 3
mol:DAG 0.028 0.047 -10000 0 -10000 0 0
HRAS 0.034 0.063 0.35 6 -10000 0 6
MAPK8 0.013 0.068 -10000 0 -0.43 9 9
RAP1A 0.023 0.062 0.49 5 -10000 0 5
GAB1 0.021 0.053 0.46 3 -10000 0 3
MAPK14 0.021 0.033 -10000 0 -10000 0 0
EPO 0.019 0.022 -10000 0 -10000 0 0
PLCG1 0.028 0.048 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.024 0.021 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.028 0.092 -10000 0 -0.41 19 19
GAB1/SHC/GRB2/SOS1 0.047 0.044 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.03 0.027 -10000 0 -10000 0 0
IRS2 0.02 0.054 0.5 3 -10000 0 3
STAT1 0.029 0.071 -10000 0 -10000 0 0
STAT5B 0.028 0.06 -10000 0 -10000 0 0
cell proliferation 0.011 0.076 0.34 7 -0.4 9 16
GAB1/SHIP/PIK3R1/SHP2/SHC 0.036 0.042 -10000 0 -0.4 1 1
TEC 0.021 0.053 0.46 3 -10000 0 3
SOCS3 -0.002 0.13 -10000 0 -0.67 19 19
STAT1 (dimer) 0.029 0.07 -10000 0 -10000 0 0
JAK2 0.026 0.026 -10000 0 -0.34 2 2
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.059 0.053 -10000 0 -10000 0 0
EPO/EPOR 0.03 0.027 -10000 0 -10000 0 0
LYN 0.025 0.013 -10000 0 -10000 0 0
TEC/VAV2 0.032 0.041 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.023 0.021 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.049 0.032 -10000 0 -10000 0 0
mol:IP3 0.028 0.047 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.044 0.046 -10000 0 -10000 0 0
SH2B3 0.028 0.008 -10000 0 -10000 0 0
NFKB1 0.021 0.033 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 0.002 0.056 -10000 0 -0.26 16 16
PTPN6 0.022 0.047 0.31 1 -10000 0 1
TEC/VAV2/GRB2 0.042 0.044 -10000 0 -10000 0 0
EPOR 0.024 0.021 -10000 0 -10000 0 0
INPP5D 0.019 0.032 -10000 0 -10000 0 0
mol:GDP 0.046 0.044 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
PLCG2 0.026 0.006 -10000 0 -10000 0 0
CRKL/CBL/C3G 0.03 0.042 -10000 0 -10000 0 0
VAV2 0.023 0.059 0.47 5 -10000 0 5
CBL 0.021 0.056 0.45 4 -10000 0 4
SHC/Grb2/SOS1 0.036 0.039 -10000 0 -10000 0 0
STAT5A 0.028 0.06 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
STAT5 (dimer) 0.039 0.096 -10000 0 -0.42 1 1
LYN/PLCgamma2 0.039 0.011 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
BTK 0.01 0.058 -10000 0 -0.35 6 6
BCL2 -0.013 0.25 0.34 2 -0.9 35 37
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.023 0.055 -10000 0 -0.67 3 3
positive regulation of NF-kappaB transcription factor activity 0.036 0.043 -10000 0 -0.5 3 3
MAP2K4 0.027 0.046 -10000 0 -0.44 1 1
IKBKB 0.027 0.005 -10000 0 -10000 0 0
TNFRSF10B 0.027 0.005 -10000 0 -10000 0 0
TNFRSF10A 0.022 0.054 -10000 0 -0.67 3 3
SMPD1 0.015 0.03 -10000 0 -0.34 3 3
IKBKG 0.025 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.027 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.036 0.043 -10000 0 -0.5 3 3
TRAIL/TRAILR3 0.005 0.065 -10000 0 -0.5 3 3
TRAIL/TRAILR1 0.033 0.06 -10000 0 -0.5 6 6
TRAIL/TRAILR4 0.036 0.043 -10000 0 -0.5 3 3
TRAIL/TRAILR1/DAP3/GTP 0.042 0.052 -10000 0 -0.4 6 6
IKK complex 0.023 0.054 -10000 0 -0.4 2 2
RIPK1 0.027 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.019 0.006 -10000 0 -10000 0 0
MAPK3 0.013 0.041 -10000 0 -0.5 3 3
MAP3K1 0.027 0.047 -10000 0 -0.47 2 2
TRAILR4 (trimer) 0.027 0.005 -10000 0 -10000 0 0
TRADD 0.026 0.006 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.022 0.054 -10000 0 -0.67 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.028 0.043 -10000 0 -0.33 6 6
CFLAR 0.027 0.005 -10000 0 -10000 0 0
MAPK1 0.009 0.04 -10000 0 -0.5 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP 0.071 0.054 -10000 0 -0.38 6 6
mol:ceramide 0.015 0.03 -10000 0 -0.34 3 3
FADD 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.016 0.071 0.28 1 -0.36 10 11
TRAF2 0.025 0.008 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.012 0.064 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.047 0.055 -10000 0 -0.43 6 6
DAP3 0.025 0.007 -10000 0 -10000 0 0
CASP10 0.01 0.04 -10000 0 -0.43 3 3
JNK cascade 0.036 0.043 -10000 0 -0.5 3 3
TRAIL (trimer) 0.023 0.054 -10000 0 -0.67 3 3
TNFRSF10C -0.012 0.064 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.053 0.052 -10000 0 -0.37 6 6
TRAIL/TRAILR2/FADD 0.05 0.04 -10000 0 -0.43 3 3
cell death 0.015 0.03 -10000 0 -0.34 3 3
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.029 0.035 -10000 0 -0.37 3 3
TRAILR2 (trimer) 0.027 0.005 -10000 0 -10000 0 0
CASP8 0.011 0.032 -10000 0 -0.58 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.074 0.041 -10000 0 -0.37 3 3
Paxillin-dependent events mediated by a4b1

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
CRKL 0.02 0.012 -10000 0 -10000 0 0
Rac1/GDP 0.024 0.009 -10000 0 -10000 0 0
DOCK1 0.023 0.054 -10000 0 -0.67 3 3
ITGA4 0.02 0.057 -10000 0 -0.67 3 3
RAC1 0.026 0.006 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.016 0.095 -10000 0 -0.49 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.048 0.041 -10000 0 -0.44 3 3
alpha4/beta7 Integrin/Paxillin 0.032 0.077 -10000 0 -0.4 14 14
lamellipodium assembly 0.025 0.063 -10000 0 -0.52 5 5
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
PI3K 0.036 0.043 -10000 0 -0.5 3 3
ARF6 0.027 0.005 -10000 0 -10000 0 0
TLN1 0.025 0.007 -10000 0 -10000 0 0
PXN 0.016 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.052 0.035 -10000 0 -0.35 2 2
cell adhesion 0.05 0.04 -10000 0 -0.36 3 3
CRKL/CBL 0.029 0.018 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.042 0.038 -10000 0 -0.4 3 3
ITGB1 0.027 0.004 -10000 0 -10000 0 0
ITGB7 0.004 0.11 -10000 0 -0.64 12 12
ARF6/GDP 0.024 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.05 0.063 -10000 0 -0.42 7 7
p130Cas/Crk/Dock1 0.048 0.041 -10000 0 -0.44 3 3
VCAM1 0.018 0.071 -10000 0 -0.67 5 5
alpha4/beta1 Integrin/Paxillin/Talin 0.052 0.04 -10000 0 -0.37 3 3
alpha4/beta1 Integrin/Paxillin/GIT1 0.055 0.037 -10000 0 -0.38 2 2
BCAR1 0.026 0.006 -10000 0 -10000 0 0
mol:GDP -0.053 0.036 0.37 2 -10000 0 2
CBL 0.027 0.005 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.052 0.04 -10000 0 -0.37 3 3
Rac1/GTP 0.025 0.071 -10000 0 -0.6 5 5
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.063 0.03 -9999 0 -0.38 1 1
HDAC3 0.026 0.006 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.002 -9999 0 -10000 0 0
GATA1/HDAC4 0.035 0.012 -9999 0 -10000 0 0
GATA1/HDAC5 0.034 0.013 -9999 0 -10000 0 0
GATA2/HDAC5 0.038 0.011 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR 0.049 0.028 -9999 0 -0.44 1 1
HDAC9 0.013 0.041 -9999 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.051 0.016 -9999 0 -10000 0 0
HDAC4/ANKRA2 0.039 0.01 -9999 0 -10000 0 0
HDAC5/YWHAB 0.038 0.01 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.009 -9999 0 -10000 0 0
GATA2 0.027 0.007 -9999 0 -10000 0 0
HDAC4/RFXANK 0.037 0.014 -9999 0 -10000 0 0
BCOR 0.026 0.007 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.02 0.012 -9999 0 -10000 0 0
HDAC5 0.026 0.007 -9999 0 -10000 0 0
GNB1/GNG2 0.037 0.026 -9999 0 -0.5 1 1
Histones 0.008 0.048 -9999 0 -0.24 1 1
ADRBK1 0.027 0.005 -9999 0 -10000 0 0
HDAC4 0.027 0.005 -9999 0 -10000 0 0
XPO1 0.027 0.005 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.038 0.011 -9999 0 -10000 0 0
HDAC4/Ubc9 0.038 0.011 -9999 0 -10000 0 0
HDAC7 0.027 0.005 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.038 0.011 -9999 0 -10000 0 0
TUBA1B 0.027 0.005 -9999 0 -10000 0 0
HDAC6 0.026 0.007 -9999 0 -10000 0 0
HDAC5/RFXANK 0.036 0.015 -9999 0 -10000 0 0
CAMK4 0.013 0.084 -9999 0 -0.67 7 7
Tubulin/HDAC6 0.047 0.048 -9999 0 -0.39 5 5
SUMO1 0.027 0.005 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.027 0.005 -9999 0 -10000 0 0
GATA1 0.012 0.021 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.026 0.007 -9999 0 -10000 0 0
NR3C1 0.026 0.006 -9999 0 -10000 0 0
SUMO1/HDAC4 0.014 0.058 -9999 0 -0.3 1 1
SRF 0.027 0.003 -9999 0 -10000 0 0
HDAC4/YWHAB 0.039 0.009 -9999 0 -10000 0 0
Tubulin 0.034 0.055 -9999 0 -0.5 5 5
HDAC4/14-3-3 E 0.038 0.011 -9999 0 -10000 0 0
GNB1 0.026 0.006 -9999 0 -10000 0 0
RANGAP1 0.02 0.012 -9999 0 -10000 0 0
BCL6/BCoR 0.037 0.027 -9999 0 -0.5 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0.052 0.014 -9999 0 -10000 0 0
HDAC4/SRF 0.046 0.059 -9999 0 -0.44 7 7
HDAC4/ER alpha 0.008 0.11 -9999 0 -0.48 23 23
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.008 0.048 -9999 0 -0.24 1 1
cell motility 0.046 0.048 -9999 0 -0.39 5 5
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.026 0.007 -9999 0 -10000 0 0
HDAC7/HDAC3 0.039 0.009 -9999 0 -10000 0 0
BCL6 0.026 0.031 -9999 0 -0.67 1 1
HDAC4/CaMK II delta B 0.027 0.005 -9999 0 -10000 0 0
Hsp90/HDAC6 0.037 0.012 -9999 0 -10000 0 0
ESR1 -0.013 0.14 -9999 0 -0.64 23 23
HDAC6/HDAC11 0.038 0.011 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.017 0.052 -9999 0 -10000 0 0
NPC 0.016 0.003 -9999 0 -10000 0 0
MEF2C 0.025 0.032 -9999 0 -0.67 1 1
RAN 0.027 0.005 -9999 0 -10000 0 0
HDAC4/MEF2C 0.074 0.031 -9999 0 -0.38 1 1
GNG2 0.025 0.032 -9999 0 -0.67 1 1
NCOR2 0.027 0.005 -9999 0 -10000 0 0
TUBB2A 0.02 0.07 -9999 0 -0.67 5 5
HDAC11 0.027 0.004 -9999 0 -10000 0 0
HSP90AA1 0.027 0.005 -9999 0 -10000 0 0
RANBP2 0.027 0.005 -9999 0 -10000 0 0
ANKRA2 0.026 0.005 -9999 0 -10000 0 0
RFXANK 0.025 0.012 -9999 0 -10000 0 0
nuclear import -0.036 0.011 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.03 0.029 -10000 0 -10000 0 0
KLHL20 0.014 0.05 -10000 0 -10000 0 0
CYFIP2 0.026 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.038 0.041 0.26 2 -10000 0 2
ENAH 0.027 0.027 -10000 0 -10000 0 0
AP1M1 0.025 0.008 -10000 0 -10000 0 0
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
CDC42/GTP 0.035 0.015 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.008 0.032 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.055 0.072 -10000 0 -0.4 11 11
RAPGEF1 0.026 0.033 0.27 1 -10000 0 1
CTNND1 0.027 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.032 0.034 -10000 0 -0.31 1 1
CRK 0.026 0.026 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin 0.051 0.016 -10000 0 -10000 0 0
alphaE/beta7 Integrin 0.021 0.083 -10000 0 -0.5 11 11
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
NCKAP1 0.027 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.05 0.014 -10000 0 -10000 0 0
DLG1 0.029 0.033 -10000 0 -10000 0 0
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.008 0.016 -10000 0 -10000 0 0
MLLT4 0.027 0.004 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.055 0.03 -10000 0 -0.4 1 1
PI3K 0.016 0.022 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.038 0.011 -10000 0 -10000 0 0
TIAM1 -0.054 0.077 -10000 0 -0.67 1 1
E-cadherin(dimer)/Ca2+ 0.061 0.017 -10000 0 -10000 0 0
AKT1 0.018 0.021 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.045 0.067 0.42 8 -10000 0 8
actin cytoskeleton organization 0.013 0.041 0.19 3 -10000 0 3
CDC42/GDP 0.046 0.075 0.46 10 -10000 0 10
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.023 0.008 -10000 0 -10000 0 0
ITGB7 0.004 0.11 -10000 0 -0.64 12 12
RAC1 0.026 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.066 0.019 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.046 0.012 -10000 0 -10000 0 0
mol:GDP 0.035 0.081 0.48 10 -10000 0 10
CDC42/GTP/IQGAP1 0.036 0.008 -10000 0 -10000 0 0
JUP 0.026 0.007 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.045 0.043 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1 0.035 0.009 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.037 0.012 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.012 0.036 0.2 5 -10000 0 5
NME1 0.026 0.007 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.029 0.033 -10000 0 -10000 0 0
regulation of cell-cell adhesion 0.025 0.011 -10000 0 -10000 0 0
WASF2 0.007 0.022 -10000 0 -10000 0 0
Rap1/GTP 0.042 0.027 0.24 2 -10000 0 2
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.064 0.072 -10000 0 -0.38 11 11
CCND1 0.013 0.039 0.19 4 -10000 0 4
VAV2 0.007 0.14 -10000 0 -0.53 27 27
RAP1/GDP 0.048 0.04 0.3 5 -10000 0 5
adherens junction assembly 0.029 0.032 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.027 0.004 -10000 0 -10000 0 0
PIP5K1C 0.025 0.008 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.053 0.067 -10000 0 -0.36 11 11
E-cadherin/beta catenin 0.015 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SRC 0.03 0.03 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
Rac1/GTP -0.006 0.076 -10000 0 -0.31 3 3
E-cadherin/beta catenin/alpha catenin 0.053 0.014 -10000 0 -10000 0 0
ITGAE 0.026 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.033 0.034 -10000 0 -0.32 1 1
Arf6 trafficking events

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
SLC2A4 -0.003 0.14 -10000 0 -0.65 20 20
CLTC 0.028 0.022 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.019 0.015 -10000 0 -10000 0 0
Dynamin 2/GTP 0.027 0.01 -10000 0 -10000 0 0
EXOC4 0.026 0.006 -10000 0 -10000 0 0
CD59 0.021 0.011 -10000 0 -10000 0 0
CPE 0.01 0.053 -10000 0 -0.43 7 7
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
membrane fusion 0.019 0.013 -10000 0 -10000 0 0
CTNND1 0.022 0.037 0.36 3 -10000 0 3
DNM2 0.025 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.022 0.03 0.24 1 -10000 0 1
TSHR 0.015 0.029 -10000 0 -0.44 2 2
INS 0.007 0.073 -10000 0 -0.48 10 10
BIN1 0.027 0.005 -10000 0 -10000 0 0
mol:Choline 0.019 0.013 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.005 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.027 0.01 -10000 0 -10000 0 0
JUP 0.021 0.01 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0.05 0.023 -10000 0 -0.4 1 1
ARF6/GTP 0.02 0.004 -10000 0 -10000 0 0
CDH1 0.021 0.011 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0.02 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.026 0.009 -10000 0 -10000 0 0
positive regulation of endocytosis 0.02 0.003 -10000 0 -10000 0 0
EXOC2 0.027 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.033 0.014 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.026 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.047 0.025 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.016 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.035 0.01 -10000 0 -10000 0 0
ACAP1 0.023 0.014 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.017 0.01 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.028 0.024 -10000 0 -10000 0 0
JIP4/KLC1 0.049 0.014 -10000 0 -10000 0 0
EXOC1 0.027 0.004 -10000 0 -10000 0 0
exocyst 0.033 0.014 -10000 0 -10000 0 0
RALA/GTP 0.019 0.004 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.035 0.01 -10000 0 -10000 0 0
receptor recycling 0.02 0.003 -10000 0 -10000 0 0
CTNNA1 0.02 0.029 0.36 1 -10000 0 1
NME1 0.016 0.005 -10000 0 -10000 0 0
clathrin coat assembly 0.032 0.036 0.34 3 -10000 0 3
IL2RA 0.008 0.055 -10000 0 -10000 0 0
VAMP3 0.016 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.024 0.07 -10000 0 -0.31 19 19
EXOC6 0.027 0.005 -10000 0 -10000 0 0
PLD1 0.018 0.005 -10000 0 -10000 0 0
PLD2 0.017 0.006 -10000 0 -10000 0 0
EXOC5 0.027 0.005 -10000 0 -10000 0 0
PIP5K1C 0.021 0.012 -10000 0 -10000 0 0
SDC1 0.021 0.012 -10000 0 -10000 0 0
ARF6/GDP 0.025 0.007 -10000 0 -10000 0 0
EXOC7 0.026 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.049 0.026 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.019 0.013 -10000 0 -10000 0 0
endocytosis -0.048 0.023 0.4 1 -10000 0 1
SCAMP2 0.027 0.004 -10000 0 -10000 0 0
ADRB2 0.03 0.084 0.43 9 -0.33 9 18
EXOC3 0.026 0.007 -10000 0 -10000 0 0
ASAP2 0.025 0.032 -10000 0 -0.67 1 1
Dynamin 2/GDP 0.03 0.011 -10000 0 -10000 0 0
KLC1 0.027 0.005 -10000 0 -10000 0 0
AVPR2 0.029 0.079 0.46 7 -0.33 9 16
RALA 0.026 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.046 0.025 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.025 0.017 -9999 0 -9999 0 0
PLK4 0.027 0.004 -9999 0 -9999 0 0
regulation of centriole replication 0.016 0.011 -9999 0 -9999 0 0
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 -0.001 0.039 -10000 0 -10000 0 0
regulation of axonogenesis -0.012 0.02 0.27 2 -10000 0 2
myoblast fusion -0.011 0.027 -10000 0 -10000 0 0
mol:GTP 0.01 0.017 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.026 0.061 0.41 1 -10000 0 1
ARF1/GTP 0.03 0.013 -10000 0 -10000 0 0
mol:GM1 0.005 0.011 -10000 0 -10000 0 0
mol:Choline 0.009 0.013 -10000 0 -10000 0 0
lamellipodium assembly 0.015 0.026 -10000 0 -10000 0 0
MAPK3 0.009 0.025 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.027 0.062 -10000 0 -0.41 1 1
ARF1 0.025 0.008 -10000 0 -10000 0 0
ARF6/GDP 0.011 0.027 -10000 0 -10000 0 0
ARF1/GDP 0.02 0.029 -10000 0 -10000 0 0
ARF6 0.03 0.008 -10000 0 -10000 0 0
RAB11A 0.027 0.004 -10000 0 -10000 0 0
TIAM1 -0.055 0.077 -10000 0 -0.67 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.007 0.023 -10000 0 -10000 0 0
actin filament bundle formation -0.024 0.029 -10000 0 -10000 0 0
KALRN 0.009 0.02 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0.038 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.029 -10000 0 -10000 0 0
NME1 0.025 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.024 0.026 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.01 0.017 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.015 0.026 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
liver development 0.01 0.017 -10000 0 -10000 0 0
ARF6/GTP 0.01 0.017 -10000 0 -10000 0 0
RhoA/GTP 0.032 0.011 -10000 0 -10000 0 0
mol:GDP 0.009 0.019 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.046 0.016 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
PLD1 0.013 0.016 -10000 0 -10000 0 0
RAB11FIP3 0.026 0.007 -10000 0 -10000 0 0
tube morphogenesis 0.015 0.026 -10000 0 -10000 0 0
ruffle organization 0.012 0.02 -10000 0 -0.27 2 2
regulation of epithelial cell migration 0.01 0.017 -10000 0 -10000 0 0
PLD2 0.012 0.016 -10000 0 -10000 0 0
PIP5K1A 0.012 0.02 -10000 0 -0.27 2 2
mol:Phosphatidic acid 0.009 0.013 -10000 0 -10000 0 0
Rac1/GTP 0.015 0.026 -10000 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.024 0.044 -9999 0 -0.67 2 2
Aurora C/Aurora B/INCENP 0.046 0.041 -9999 0 -0.44 2 2
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.009 0.013 -9999 0 -10000 0 0
AURKB -0.005 0.059 -9999 0 -10000 0 0
AURKC 0.02 0.028 -9999 0 -10000 0 0
Glypican 2 network

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
MDK -0.018 0.073 -9999 0 -0.67 1 1
GPC2 0.017 0.036 -9999 0 -10000 0 0
GPC2/Midkine -0.003 0.058 -9999 0 -0.29 1 1
neuron projection morphogenesis -0.003 0.058 -9999 0 -0.29 1 1
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.005 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.014 -9999 0 -10000 0 0
MDM2/SUMO1 0.014 0.054 -9999 0 -10000 0 0
HDAC4 0.027 0.005 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.001 0.014 -9999 0 -10000 0 0
SUMO1 0.027 0.005 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.006 0.036 -9999 0 -0.24 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.012 0.008 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.027 0.005 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.027 0.005 -9999 0 -10000 0 0
SUMO1/HDAC4 0.014 0.058 -9999 0 -0.3 1 1
SUMO1/HDAC1 0.014 0.058 -9999 0 -0.31 1 1
RANGAP1 0.02 0.012 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.066 0.018 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.013 0.009 -9999 0 -10000 0 0
Ran/GTP 0.006 0.048 -9999 0 -0.23 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.027 0.005 -9999 0 -10000 0 0
UBE2I 0.026 0.007 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.006 0.046 -9999 0 -10000 0 0
NPC 0.016 0.003 -9999 0 -10000 0 0
PIAS2 0.027 0.004 -9999 0 -10000 0 0
PIAS1 0.027 0.004 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.051 0.016 -9999 0 -9999 0 0
E-cadherin/beta catenin 0.039 0.009 -9999 0 -9999 0 0
CTNNB1 0.027 0.003 -9999 0 -9999 0 0
JUP 0.026 0.007 -9999 0 -9999 0 0
CDH1 0.026 0.006 -9999 0 -9999 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 0.011 0.017 -10000 0 -10000 0 0
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.025 0.033 0.2 1 -0.17 2 3
AP2 0.038 0.011 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.036 0.011 -10000 0 -10000 0 0
CLTB 0.026 0.006 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.021 0.009 -10000 0 -10000 0 0
CD4 0.021 0.028 -10000 0 -10000 0 0
CLTA 0.025 0.007 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.009 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.006 0.024 -10000 0 -0.37 2 2
ARF1/GTP 0.028 0.02 -10000 0 -0.19 2 2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.015 0.007 -10000 0 -10000 0 0
mol:Choline 0.006 0.024 -10000 0 -0.36 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.026 0.009 -10000 0 -10000 0 0
DDEF1 0.007 0.027 -10000 0 -0.37 2 2
ARF1/GDP 0.004 0.017 -10000 0 -10000 0 0
AP2M1 0.027 0.003 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.014 0.006 -10000 0 -10000 0 0
Rac/GTP 0.021 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.036 0.015 -10000 0 -10000 0 0
ARFIP2 0.022 0.013 -10000 0 -10000 0 0
COPA 0.025 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.014 0.034 -10000 0 -0.48 1 1
ARF1/GTP/ARHGAP10 0.018 0.007 -10000 0 -10000 0 0
GGA3 0.026 0.007 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.024 0.022 -10000 0 -0.28 1 1
AP2A1 0.025 0.007 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.019 0.008 -10000 0 -10000 0 0
ARF1/GDP/Membrin 0.026 0.024 -10000 0 -0.25 2 2
Arfaptin 2/Rac/GDP 0.034 0.011 -10000 0 -10000 0 0
CYTH2 0.028 0.01 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.033 0.014 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.019 0.004 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.024 0.025 -10000 0 -10000 0 0
PLD2 0.006 0.024 -10000 0 -0.37 2 2
ARF-GAP1/v-SNARE 0.009 0.002 -10000 0 -10000 0 0
PIP5K1A 0.006 0.024 -10000 0 -0.37 2 2
ARF1/GTP/Membrin/GBF1/p115 0.023 0.02 -10000 0 -0.19 2 2
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.006 0.024 -10000 0 -0.36 2 2
KDEL Receptor/Ligand/ARF-GAP1 0.009 0.002 -10000 0 -10000 0 0
GOSR2 0.014 0.013 -10000 0 -10000 0 0
USO1 0.014 0.013 -10000 0 -10000 0 0
GBF1 0.013 0.024 -10000 0 -0.3 2 2
ARF1/GTP/Arfaptin 2 0.035 0.014 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.052 0.017 -10000 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 0.038 0.011 -9999 0 -9999 0 0
FBXW11 0.026 0.006 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -9999 0 -9999 0 0
CHUK 0.027 0.004 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.072 0.027 -9999 0 -9999 0 0
NFKB1 0.027 0.004 -9999 0 -9999 0 0
MAP3K14 0.026 0.007 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.038 0.011 -9999 0 -9999 0 0
RELB 0.026 0.007 -9999 0 -9999 0 0
NFKB2 0.027 0.004 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.034 0.01 -9999 0 -9999 0 0
regulation of B cell activation 0.034 0.01 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 492 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.MK.A4N9 TCGA.MK.A4N7 TCGA.MK.A4N6 TCGA.L6.A4EU
109_MAP3K5 -0.2 0.027 0.027 0.027
47_PPARGC1A -0.67 -0.67 -0.67 0.028
105_BMP4 0.028 -0.12 0.028 0.028
105_BMP6 0.028 0.028 0.028 0.028
105_BMP7 0.028 0.028 0.028 0.028
105_BMP2 0.028 0.028 0.028 0.028
131_RELN/VLDLR -0.4 -0.4 -0.4 -0.4
30_TGFB1/TGF beta receptor Type II 0.027 0.027 0.027 0.028
84_STAT5B 0.04 -0.049 0.033 -0.048
84_STAT5A 0.04 -0.049 0.033 -0.048
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/THCA-TP/9830962/THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/THCA-TP/10006309/Gistic2_Analysis_10006450/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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