PARADIGM pathway analysis of mRNASeq expression and copy number data
Colorectal Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1V40TC2
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1V40TC2
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 38 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
TCGA08_retinoblastoma 164
Reelin signaling pathway 152
Ephrin A reverse signaling 106
Lissencephaly gene (LIS1) in neuronal migration and development 91
IL4-mediated signaling events 83
Glypican 1 network 83
BCR signaling pathway 74
Signaling events regulated by Ret tyrosine kinase 71
Fc-epsilon receptor I signaling in mast cells 67
Signaling events mediated by Stem cell factor receptor (c-Kit) 67
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 623 . 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 ( 623 ).

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
TCGA08_retinoblastoma 0.2632 164 1315 8 -0.091 0.082 1000 -1000 -0.003 -1000
Reelin signaling pathway 0.2440 152 8544 56 -0.35 0.075 1000 -1000 -0.047 -1000
Ephrin A reverse signaling 0.1701 106 744 7 -0.056 0 1000 -1000 -0.016 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1461 91 4924 54 -0.3 0.037 1000 -1000 -0.053 -1000
IL4-mediated signaling events 0.1332 83 7575 91 -0.79 0.57 1000 -1000 -0.17 -1000
Glypican 1 network 0.1332 83 4031 48 -0.2 0.053 1000 -1000 -0.034 -1000
BCR signaling pathway 0.1188 74 7422 99 -0.2 0.03 1000 -1000 -0.056 -1000
Signaling events regulated by Ret tyrosine kinase 0.1140 71 5868 82 -0.12 0.035 1000 -1000 -0.06 -1000
Fc-epsilon receptor I signaling in mast cells 0.1075 67 6543 97 -0.14 0.05 1000 -1000 -0.066 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1075 67 5301 78 -0.19 0.073 1000 -1000 -0.056 -1000
FOXA2 and FOXA3 transcription factor networks 0.1027 64 2946 46 -0.59 0.031 1000 -1000 -0.13 -1000
HIF-1-alpha transcription factor network 0.0963 60 4583 76 -0.56 0.036 1000 -1000 -0.16 -1000
Visual signal transduction: Rods 0.0899 56 2957 52 -0.19 0.035 1000 -1000 -0.046 -1000
p75(NTR)-mediated signaling 0.0867 54 6874 125 -0.46 0.07 1000 -1000 -0.077 -1000
Syndecan-1-mediated signaling events 0.0851 53 1810 34 -0.42 0.029 1000 -1000 -0.043 -1000
BMP receptor signaling 0.0819 51 4172 81 -0.18 0.052 1000 -1000 -0.052 -1000
Signaling events mediated by the Hedgehog family 0.0803 50 2622 52 -0.059 0.059 1000 -1000 -0.043 -1000
Syndecan-2-mediated signaling events 0.0754 47 3258 69 -0.23 0.046 1000 -1000 -0.037 -1000
Endothelins 0.0754 47 4593 96 -0.22 0.061 1000 -1000 -0.076 -1000
Visual signal transduction: Cones 0.0738 46 1756 38 -0.11 0.038 1000 -1000 -0.017 -1000
LPA receptor mediated events 0.0658 41 4204 102 -0.17 0.036 1000 -1000 -0.06 -1000
JNK signaling in the CD4+ TCR pathway 0.0642 40 694 17 -0.13 0.041 1000 -1000 -0.036 -1000
Ras signaling in the CD4+ TCR pathway 0.0626 39 667 17 -0.062 0.049 1000 -1000 -0.032 -1000
TCR signaling in naïve CD8+ T cells 0.0610 38 3615 93 -0.037 0.04 1000 -1000 -0.053 -1000
IGF1 pathway 0.0610 38 2216 57 -0.065 0.054 1000 -1000 -0.047 -1000
amb2 Integrin signaling 0.0594 37 3037 82 -0.095 0.037 1000 -1000 -0.043 -1000
Plasma membrane estrogen receptor signaling 0.0594 37 3204 86 -0.23 0.081 1000 -1000 -0.065 -1000
Canonical Wnt signaling pathway 0.0578 36 1868 51 -0.28 0.14 1000 -1000 -0.053 -1000
Effects of Botulinum toxin 0.0578 36 951 26 -0.07 0.048 1000 -1000 -0.008 -1000
Wnt signaling 0.0578 36 255 7 -0.069 0.024 1000 -1000 -0.018 -1000
Presenilin action in Notch and Wnt signaling 0.0562 35 2144 61 -0.28 0.14 1000 -1000 -0.041 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0562 35 3110 88 -0.14 0.061 1000 -1000 -0.069 -1000
LPA4-mediated signaling events 0.0530 33 407 12 -0.097 0.007 1000 -1000 -0.029 -1000
Osteopontin-mediated events 0.0530 33 1278 38 -0.17 0.04 1000 -1000 -0.057 -1000
Ephrin B reverse signaling 0.0530 33 1595 48 -0.07 0.031 1000 -1000 -0.029 -1000
EPHB forward signaling 0.0530 33 2872 85 -0.071 0.087 1000 -1000 -0.062 -1000
IL23-mediated signaling events 0.0530 33 1983 60 -0.27 0.033 1000 -1000 -0.13 -1000
Signaling events mediated by PRL 0.0514 32 1091 34 -0.062 0.086 1000 -1000 -0.051 -1000
IL1-mediated signaling events 0.0498 31 1944 62 -0.12 0.063 1000 -1000 -0.043 -1000
TCGA08_p53 0.0482 30 211 7 -0.053 0.028 1000 -1000 -0.007 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0482 30 3632 120 -0.097 0.088 1000 -1000 -0.049 -1000
Calcium signaling in the CD4+ TCR pathway 0.0465 29 905 31 -0.27 0.028 1000 -1000 -0.058 -1000
PDGFR-beta signaling pathway 0.0465 29 2825 97 -0.14 0.091 1000 -1000 -0.059 -1000
Signaling mediated by p38-alpha and p38-beta 0.0433 27 1191 44 -0.034 0.03 1000 -1000 -0.042 -1000
Syndecan-4-mediated signaling events 0.0433 27 1869 67 -0.23 0.04 1000 -1000 -0.044 -1000
Thromboxane A2 receptor signaling 0.0417 26 2732 105 -0.18 0.067 1000 -1000 -0.058 -1000
S1P5 pathway 0.0417 26 453 17 -0.12 0.052 1000 -1000 -0.02 -1000
Syndecan-3-mediated signaling events 0.0417 26 918 35 -0.23 0.07 1000 -1000 -0.035 -1000
EGFR-dependent Endothelin signaling events 0.0417 26 550 21 -0.06 0.04 1000 -1000 -0.048 -1000
Arf6 signaling events 0.0401 25 1565 62 -0.12 0.062 1000 -1000 -0.039 -1000
S1P4 pathway 0.0401 25 647 25 -0.12 0.043 1000 -1000 -0.034 -1000
IL12-mediated signaling events 0.0385 24 2145 87 -0.1 0.051 1000 -1000 -0.092 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0385 24 1270 52 -0.18 0.061 1000 -1000 -0.051 -1000
HIF-2-alpha transcription factor network 0.0385 24 1055 43 -0.33 0.16 1000 -1000 -0.078 -1000
Glucocorticoid receptor regulatory network 0.0369 23 2670 114 -0.32 0.19 1000 -1000 -0.07 -1000
Nongenotropic Androgen signaling 0.0369 23 1222 52 -0.12 0.064 1000 -1000 -0.046 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0369 23 1569 68 -0.27 0.038 1000 -1000 -0.11 -1000
Noncanonical Wnt signaling pathway 0.0353 22 574 26 -0.069 0.027 1000 -1000 -0.047 -1000
Nectin adhesion pathway 0.0353 22 1433 63 -0.4 0.076 1000 -1000 -0.055 -1000
Integrins in angiogenesis 0.0353 22 1852 84 -0.18 0.065 1000 -1000 -0.051 -1000
Caspase cascade in apoptosis 0.0337 21 1585 74 -0.084 0.064 1000 -1000 -0.039 -1000
a4b1 and a4b7 Integrin signaling 0.0337 21 107 5 0.013 0.03 1000 -1000 -0.001 -1000
VEGFR1 specific signals 0.0337 21 1213 56 -0.013 0.094 1000 -1000 -0.052 -1000
Signaling events mediated by PTP1B 0.0321 20 1523 76 -0.19 0.047 1000 -1000 -0.046 -1000
Regulation of Androgen receptor activity 0.0321 20 1456 70 -0.21 0.061 1000 -1000 -0.058 -1000
Signaling events mediated by HDAC Class III 0.0305 19 763 40 -0.13 0.052 1000 -1000 -0.019 -1000
S1P3 pathway 0.0305 19 829 42 -0.11 0.046 1000 -1000 -0.045 -1000
Ceramide signaling pathway 0.0289 18 1392 76 -0.062 0.07 1000 -1000 -0.035 -1000
S1P1 pathway 0.0289 18 651 36 -0.12 0.044 1000 -1000 -0.055 -1000
Glypican 2 network 0.0289 18 75 4 0.013 0.025 1000 -1000 0.004 -1000
PLK1 signaling events 0.0273 17 1494 85 -0.01 0.06 1000 -1000 -0.023 -1000
Regulation of p38-alpha and p38-beta 0.0273 17 965 54 -0.09 0.054 1000 -1000 -0.053 -1000
Aurora B signaling 0.0273 17 1195 67 -0.4 0.095 1000 -1000 -0.035 -1000
Coregulation of Androgen receptor activity 0.0257 16 1246 76 -0.19 0.064 1000 -1000 -0.025 -1000
FAS signaling pathway (CD95) 0.0257 16 761 47 -0.029 0.043 1000 -1000 -0.038 -1000
IL6-mediated signaling events 0.0257 16 1212 75 -0.059 0.059 1000 -1000 -0.086 -1000
Regulation of nuclear SMAD2/3 signaling 0.0241 15 2077 136 -0.43 0.067 1000 -1000 -0.059 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0241 15 531 34 -0.027 0.064 1000 -1000 -0.032 -1000
ErbB4 signaling events 0.0241 15 1055 69 -0.16 0.08 1000 -1000 -0.049 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0241 15 446 28 -0.12 0.044 1000 -1000 -0.027 -1000
Cellular roles of Anthrax toxin 0.0241 15 607 39 -0.048 0.031 1000 -1000 -0.023 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0241 15 569 37 -0.15 0.06 1000 -1000 -0.042 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0241 15 520 33 -0.061 0.066 1000 -1000 -0.028 -1000
Class I PI3K signaling events 0.0225 14 1034 73 -0.09 0.044 1000 -1000 -0.049 -1000
ErbB2/ErbB3 signaling events 0.0209 13 881 65 -0.046 0.04 1000 -1000 -0.069 -1000
Signaling mediated by p38-gamma and p38-delta 0.0209 13 201 15 -0.058 0.027 1000 -1000 -0.032 -1000
Retinoic acid receptors-mediated signaling 0.0209 13 797 58 -0.15 0.051 1000 -1000 -0.043 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0193 12 1052 83 -0.13 0.07 1000 -1000 -0.042 -1000
Arf6 downstream pathway 0.0177 11 514 43 -0.029 0.043 1000 -1000 -0.026 -1000
Insulin-mediated glucose transport 0.0177 11 359 32 -0.14 0.045 1000 -1000 -0.032 -1000
PDGFR-alpha signaling pathway 0.0177 11 515 44 -0.013 0.064 1000 -1000 -0.044 -1000
FoxO family signaling 0.0177 11 744 64 -0.056 0.064 1000 -1000 -0.063 -1000
ceramide signaling pathway 0.0161 10 494 49 0 0.045 1000 -1000 -0.038 -1000
Arf6 trafficking events 0.0161 10 778 71 -0.048 0.049 1000 -1000 -0.031 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0144 9 783 85 -0.035 0.064 1000 -1000 -0.049 -1000
EPO signaling pathway 0.0144 9 510 55 -0.004 0.065 1000 -1000 -0.053 -1000
mTOR signaling pathway 0.0144 9 482 53 -0.068 0.038 1000 -1000 -0.039 -1000
Class I PI3K signaling events mediated by Akt 0.0144 9 666 68 -0.053 0.064 1000 -1000 -0.044 -1000
IL27-mediated signaling events 0.0144 9 501 51 -0.062 0.042 1000 -1000 -0.065 -1000
TCGA08_rtk_signaling 0.0144 9 245 26 -0.031 0.061 1000 -1000 -0.025 -1000
Regulation of Telomerase 0.0144 9 1001 102 -0.2 0.065 1000 -1000 -0.075 -1000
FOXM1 transcription factor network 0.0144 9 486 51 -0.095 0.089 1000 -1000 -0.17 -1000
Hedgehog signaling events mediated by Gli proteins 0.0128 8 572 65 -0.11 0.051 1000 -1000 -0.054 -1000
IFN-gamma pathway 0.0112 7 495 68 -0.031 0.04 1000 -1000 -0.066 -1000
IL2 signaling events mediated by PI3K 0.0112 7 463 58 -0.013 0.046 1000 -1000 -0.048 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0112 7 350 45 -0.009 0.073 1000 -1000 -0.06 -1000
Rapid glucocorticoid signaling 0.0112 7 153 20 -0.016 0.026 1000 -1000 -0.006 -1000
Signaling events mediated by HDAC Class II 0.0096 6 494 75 -0.026 0.07 1000 -1000 -0.039 -1000
Aurora A signaling 0.0096 6 404 60 -0.086 0.075 1000 -1000 -0.026 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0096 6 464 74 -0.062 0.065 1000 -1000 -0.068 -1000
E-cadherin signaling in the nascent adherens junction 0.0096 6 485 76 -0.011 0.093 1000 -1000 -0.062 -1000
Arf1 pathway 0.0096 6 325 54 -0.001 0.046 1000 -1000 -0.019 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0080 5 737 125 -0.01 0.098 1000 -1000 -0.057 -1000
Class IB PI3K non-lipid kinase events 0.0080 5 15 3 -0.024 0.024 1000 -1000 -0.006 -1000
TRAIL signaling pathway 0.0064 4 224 48 -0.011 0.058 1000 -1000 -0.038 -1000
Paxillin-dependent events mediated by a4b1 0.0064 4 173 36 -0.049 0.051 1000 -1000 -0.035 -1000
p38 MAPK signaling pathway 0.0064 4 208 44 -0.013 0.058 1000 -1000 -0.032 -1000
PLK2 and PLK4 events 0.0048 3 10 3 0.01 0.027 1000 -1000 -0.018 -1000
IL2 signaling events mediated by STAT5 0.0048 3 77 22 0.006 0.042 1000 -1000 -0.057 -1000
Insulin Pathway 0.0048 3 294 74 -0.026 0.084 1000 -1000 -0.052 -1000
Canonical NF-kappaB pathway 0.0032 2 104 39 0 0.06 1000 -1000 -0.036 -1000
Signaling events mediated by HDAC Class I 0.0032 2 232 104 -0.054 0.066 1000 -1000 -0.038 -1000
Circadian rhythm pathway 0.0016 1 26 22 -0.01 0.065 1000 -1000 -0.038 -1000
Aurora C signaling 0.0016 1 9 7 0 0.041 1000 -1000 -0.013 -1000
Atypical NF-kappaB pathway 0.0016 1 31 31 0 0.057 1000 -1000 -0.033 -1000
E-cadherin signaling in keratinocytes 0.0016 1 47 43 -0.047 0.086 1000 -1000 -0.034 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 16 23 0.013 0.04 1000 -1000 -0.028 -1000
BARD1 signaling events 0.0000 0 49 57 -0.056 0.078 1000 -1000 -0.047 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 17 27 0 0.052 1000 -1000 -0.039 -1000
E-cadherin signaling events 0.0000 0 2 5 0.027 0.054 1000 -1000 0.002 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.076 1000 -1000 -0.001 -1000
Total NA 3400 197052 7203 -16 8 131000 -131000 -6.2 -131000
TCGA08_retinoblastoma

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
CDKN2B -0.091 0.17 -10000 0 -0.33 205 205
CDKN2C 0.033 0.026 -10000 0 -10000 0 0
CDKN2A -0.064 0.19 0.34 2 -0.46 114 116
CCND2 0.07 0.092 0.19 207 -10000 0 207
RB1 -0.056 0.1 0.28 9 -0.2 173 182
CDK4 0.075 0.097 0.2 202 -0.14 1 203
CDK6 0.082 0.1 0.21 217 -10000 0 217
G1/S progression 0.061 0.1 0.2 175 -0.28 10 185
Reelin signaling pathway

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
CDK5R1/CDK5 0.038 0.018 -10000 0 -0.32 1 1
VLDLR -0.003 0.1 -10000 0 -0.36 47 47
CRKL 0.027 0.006 -10000 0 -10000 0 0
LRPAP1 0.027 0.005 -10000 0 -10000 0 0
FYN 0.027 0.005 -10000 0 -10000 0 0
ITGA3 0.027 0.016 -10000 0 -0.36 1 1
RELN/VLDLR/Fyn -0.084 0.15 -10000 0 -0.24 277 277
MAPK8IP1/MKK7/MAP3K11/JNK1 0.075 0.035 -10000 0 -0.51 1 1
AKT1 -0.099 0.13 -10000 0 -0.33 78 78
MAP2K7 0.027 0.016 -10000 0 -0.36 1 1
RAPGEF1 0.027 0.016 -10000 0 -0.36 1 1
DAB1 -0.036 0.15 -10000 0 -0.45 71 71
RELN/LRP8/DAB1 -0.26 0.17 -10000 0 -0.33 505 505
LRPAP1/LRP8 -0.21 0.17 0.26 1 -0.32 422 423
RELN/LRP8/DAB1/Fyn -0.25 0.16 -10000 0 -0.33 440 440
DAB1/alpha3/beta1 Integrin -0.24 0.17 -10000 0 -0.4 248 248
long-term memory -0.35 0.21 -10000 0 -0.49 378 378
DAB1/LIS1 -0.25 0.17 -10000 0 -0.41 254 254
DAB1/CRLK/C3G -0.24 0.17 -10000 0 -0.4 252 252
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
DAB1/NCK2 -0.25 0.18 -10000 0 -0.41 254 254
ARHGEF2 0.027 0.004 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.085 0.16 -10000 0 -0.36 157 157
CDK5R1 0.026 0.02 -10000 0 -0.44 1 1
RELN -0.16 0.19 -10000 0 -0.36 282 282
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.26 0.17 0.25 1 -0.34 482 483
GRIN2A/RELN/LRP8/DAB1/Fyn -0.29 0.19 -10000 0 -0.42 349 349
MAPK8 0.027 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.1 0.15 -10000 0 -0.24 321 321
ITGB1 0.028 0.002 -10000 0 -10000 0 0
MAP1B -0.26 0.17 -10000 0 -0.42 271 271
RELN/LRP8 -0.26 0.17 0.25 1 -0.34 485 486
GRIN2B/RELN/LRP8/DAB1/Fyn -0.32 0.2 -10000 0 -0.4 472 472
PI3K 0.039 0.015 -10000 0 -0.25 1 1
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.04 0.014 -10000 0 -0.25 1 1
RAP1A -0.24 0.15 0.32 2 -0.39 247 249
PAFAH1B1 0.023 0.01 -10000 0 -10000 0 0
MAPK8IP1 0.026 0.025 -10000 0 -0.4 2 2
CRLK/C3G 0.038 0.015 -10000 0 -0.25 1 1
GRIN2B -0.13 0.22 0.36 1 -0.44 200 201
NCK2 0.028 0.002 -10000 0 -10000 0 0
neuron differentiation -0.13 0.12 0.23 1 -0.37 52 53
neuron adhesion -0.23 0.15 0.3 3 -0.38 236 239
LRP8 -0.3 0.22 0.36 1 -0.44 423 424
GSK3B -0.097 0.12 -10000 0 -0.32 76 76
RELN/VLDLR/DAB1/Fyn -0.092 0.15 -10000 0 -0.32 98 98
MAP3K11 0.026 0.016 -10000 0 -0.36 1 1
RELN/VLDLR/DAB1/P13K -0.11 0.14 -10000 0 -0.24 293 293
CDK5 0.027 0.005 -10000 0 -10000 0 0
MAPT -0.054 0.17 0.82 8 -0.31 137 145
neuron migration -0.23 0.16 0.26 4 -0.4 233 237
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.13 0.12 -10000 0 -0.38 49 49
RELN/VLDLR -0.24 0.18 0.25 1 -0.34 418 419
Ephrin A reverse signaling

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
MAPKKK cascade -0.031 0.11 -10000 0 -0.22 149 149
EFNA5 -0.056 0.16 -10000 0 -0.36 130 130
FYN -0.045 0.091 0.18 1 -0.2 137 138
neuron projection morphogenesis -0.031 0.11 -10000 0 -0.22 149 149
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.03 0.11 -10000 0 -0.22 149 149
EPHA5 -0.012 0.081 -10000 0 -0.36 29 29
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.026 0.007 -10000 0 -10000 0 0
VLDLR -0.003 0.1 -10000 0 -0.36 47 47
LRPAP1 0.027 0.005 -10000 0 -10000 0 0
NUDC 0.026 0.007 -10000 0 -10000 0 0
RELN/LRP8 -0.26 0.17 0.25 1 -0.34 485 486
CaM/Ca2+ 0.019 0.005 -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 -0.24 0.16 0.18 8 -0.33 404 412
IQGAP1/CaM 0.037 0.013 -10000 0 -10000 0 0
DAB1 -0.036 0.15 -10000 0 -0.45 71 71
IQGAP1 0.027 0.006 -10000 0 -10000 0 0
PLA2G7 0.024 0.038 -10000 0 -0.36 6 6
CALM1 0.026 0.007 -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 -0.21 0.17 0.26 1 -0.32 422 423
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.027 0.016 -10000 0 -0.36 1 1
CDK5R1 0.026 0.02 -10000 0 -0.44 1 1
LIS1/Poliovirus Protein 3A 0.007 0.005 -10000 0 -10000 0 0
CDK5R2 -0.02 0.12 -10000 0 -0.37 63 63
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.12 0.17 -10000 0 -0.26 321 321
YWHAE 0.023 0.01 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.2 0.15 0.32 6 -0.35 226 232
MAP1B 0.001 0.032 -10000 0 -0.24 11 11
RAC1 0.01 0.007 -10000 0 -10000 0 0
p35/CDK5 -0.21 0.14 0.18 2 -0.37 196 198
RELN -0.16 0.19 -10000 0 -0.36 282 282
PAFAH/LIS1 0.02 0.026 -10000 0 -0.21 4 4
LIS1/CLIP170 0.022 0.017 -10000 0 -0.21 1 1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.17 0.12 -10000 0 -0.3 177 177
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.097 0.15 -10000 0 -0.35 98 98
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.22 0.15 0.32 5 -0.37 238 243
LIS1/IQGAP1 0.022 0.014 -10000 0 -10000 0 0
RHOA 0.01 0.007 -10000 0 -10000 0 0
PAFAH1B1 0.01 0.006 -10000 0 -10000 0 0
PAFAH1B3 0.019 0.063 -10000 0 -0.44 11 11
PAFAH1B2 0.027 0.005 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.013 0.04 -10000 0 -0.23 3 3
NDEL1/Katanin 60/Dynein heavy chain -0.2 0.15 0.32 5 -0.35 227 232
LRP8 -0.3 0.22 0.36 1 -0.44 423 424
NDEL1/Katanin 60 -0.21 0.15 0.32 5 -0.36 227 232
P39/CDK5 -0.23 0.15 0.18 2 -0.39 234 236
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.022 0.014 -10000 0 -10000 0 0
CDK5 -0.23 0.14 0.18 2 -0.39 201 203
PPP2R5D 0.027 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.019 0.014 -10000 0 -0.18 1 1
CSNK2A1 0.023 0.011 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.085 0.14 -10000 0 -0.32 85 85
RELN/VLDLR -0.24 0.18 0.25 1 -0.34 418 419
CDC42 0.01 0.016 -10000 0 -0.35 1 1
IL4-mediated signaling events

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
BCL2L1 -0.45 0.49 -10000 0 -1.2 122 122
STAT6 (cleaved dimer) -0.56 0.52 -10000 0 -1.2 195 195
IGHG1 -0.16 0.16 -10000 0 -10000 0 0
IGHG3 -0.49 0.46 -10000 0 -1.1 158 158
AKT1 -0.27 0.29 -10000 0 -0.76 84 84
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.21 0.24 -10000 0 -0.86 29 29
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.26 0.28 -10000 0 -0.84 53 53
THY1 -0.52 0.48 -10000 0 -1.2 152 152
MYB 0.026 0.016 -10000 0 -0.36 1 1
HMGA1 0.027 0.023 0.36 1 -0.44 1 2
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.36 0.35 -10000 0 -0.83 154 154
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.27 0.28 -10000 0 -0.84 53 53
SP1 0.027 0.02 -10000 0 -10000 0 0
INPP5D 0.027 0.016 -10000 0 -0.36 1 1
SOCS5 0.045 0.026 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.55 0.51 -10000 0 -1.2 185 185
SOCS1 -0.37 0.31 -10000 0 -0.76 148 148
SOCS3 -0.31 0.29 -10000 0 -0.75 112 112
FCER2 -0.79 0.65 -10000 0 -1.3 326 326
PARP14 0.009 0.03 -10000 0 -10000 0 0
CCL17 -0.52 0.48 -10000 0 -1.2 132 132
GRB2 0.027 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.21 0.21 -10000 0 -0.73 26 26
T cell proliferation -0.52 0.5 -10000 0 -1.2 155 155
IL4R/JAK1 -0.52 0.49 -10000 0 -1.2 154 154
EGR2 -0.59 0.52 -10000 0 -1.3 160 160
JAK2 -0.033 0.049 -10000 0 -0.39 3 3
JAK3 0.015 0.032 -10000 0 -0.44 1 1
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
JAK1 -0.006 0.025 -10000 0 -10000 0 0
COL1A2 -0.15 0.16 -10000 0 -0.69 1 1
CCL26 -0.53 0.48 -10000 0 -1.2 155 155
IL4R -0.55 0.51 -10000 0 -1.3 152 152
PTPN6 0.038 0.014 -10000 0 -10000 0 0
IL13RA2 -0.53 0.48 -10000 0 -1.2 138 138
IL13RA1 -0.032 0.042 -10000 0 -10000 0 0
IRF4 -0.44 0.62 -10000 0 -1.4 170 170
ARG1 -0.089 0.14 -10000 0 -0.57 10 10
CBL -0.35 0.33 -10000 0 -0.8 148 148
GTF3A 0.023 0.072 0.34 23 -0.44 1 24
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
IL13RA1/JAK2 -0.037 0.061 -10000 0 -0.28 3 3
IRF4/BCL6 -0.38 0.58 -10000 0 -1.3 168 168
CD40LG -0.038 0.1 -10000 0 -0.38 42 42
MAPK14 -0.34 0.32 -10000 0 -0.81 141 141
mitosis -0.26 0.27 -10000 0 -0.71 84 84
STAT6 -0.58 0.58 -10000 0 -1.4 157 157
SPI1 0.024 0.047 -10000 0 -0.36 9 9
RPS6KB1 -0.25 0.26 -10000 0 -0.69 78 78
STAT6 (dimer) -0.58 0.57 -10000 0 -1.4 157 157
STAT6 (dimer)/PARP14 -0.59 0.55 -10000 0 -1.3 169 169
mast cell activation 0.014 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.3 0.29 -10000 0 -0.75 100 100
FRAP1 -0.27 0.29 -10000 0 -0.76 84 84
LTA -0.52 0.49 -10000 0 -1.2 148 148
FES 0.025 0.023 -10000 0 -0.36 2 2
T-helper 1 cell differentiation 0.57 0.55 1.3 157 -10000 0 157
CCL11 -0.55 0.54 -10000 0 -1.3 173 173
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.26 0.27 -10000 0 -0.73 74 74
IL2RG 0.014 0.037 -10000 0 -0.35 3 3
IL10 -0.54 0.52 -10000 0 -1.3 163 163
IRS1 0.028 0.002 -10000 0 -10000 0 0
IRS2 0.022 0.012 -10000 0 -10000 0 0
IL4 -0.14 0.2 -10000 0 -1.1 17 17
IL5 -0.52 0.48 -10000 0 -1.2 134 134
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.41 0.38 -10000 0 -0.93 129 129
COL1A1 -0.19 0.21 -10000 0 -0.64 34 34
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.53 0.5 -10000 0 -1.2 147 147
IL2R gamma/JAK3 0.018 0.045 -10000 0 -0.27 4 4
TFF3 -0.53 0.51 -10000 0 -1.2 154 154
ALOX15 -0.54 0.5 -10000 0 -1.2 162 162
MYBL1 0.022 0.028 -10000 0 -0.44 2 2
T-helper 2 cell differentiation -0.43 0.4 -10000 0 -0.96 152 152
SHC1 0.027 0.004 -10000 0 -10000 0 0
CEBPB 0.016 0.047 0.36 3 -0.44 4 7
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.24 0.27 -10000 0 -0.87 43 43
mol:PI-3-4-5-P3 -0.27 0.29 -10000 0 -0.76 84 84
PI3K -0.28 0.31 -10000 0 -0.82 84 84
DOK2 0.016 0.045 -10000 0 -0.36 8 8
ETS1 0.036 0.026 -10000 0 -0.32 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.2 0.19 -10000 0 -0.65 29 29
ITGB3 -0.52 0.49 -10000 0 -1.2 150 150
PIGR -0.69 0.65 -10000 0 -1.5 229 229
IGHE 0.083 0.073 0.18 150 -10000 0 150
MAPKKK cascade -0.19 0.19 -10000 0 -0.64 29 29
BCL6 0.034 0.011 -10000 0 -10000 0 0
OPRM1 -0.52 0.48 -10000 0 -1.2 142 142
RETNLB -0.74 0.66 -10000 0 -1.4 271 271
SELP -0.57 0.56 -10000 0 -1.4 157 157
AICDA -0.5 0.46 -10000 0 -1.2 139 139
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.029 0.069 -10000 0 -0.21 43 43
fibroblast growth factor receptor signaling pathway 0.029 0.069 -10000 0 -0.21 43 43
LAMA1 -0.055 0.15 -10000 0 -0.36 122 122
PRNP 0.021 0.024 -10000 0 -0.36 2 2
GPC1/SLIT2 -0.044 0.13 -10000 0 -0.25 175 175
SMAD2 0.011 0.021 0.18 3 -0.24 1 4
GPC1/PrPc/Cu2+ 0.029 0.025 -10000 0 -0.22 4 4
GPC1/Laminin alpha1 -0.027 0.12 -10000 0 -0.25 124 124
TDGF1 -0.2 0.24 0.36 1 -0.44 290 291
CRIPTO/GPC1 -0.13 0.18 0.26 1 -0.32 291 292
APP/GPC1 0.037 0.024 -10000 0 -0.27 3 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.12 0.14 0.2 1 -0.26 289 290
FLT1 0.021 0.012 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.053 0.023 -10000 0 -0.23 3 3
SERPINC1 0.003 0.061 -10000 0 -0.44 10 10
FYN -0.12 0.14 0.2 1 -0.27 288 289
FGR -0.12 0.14 0.2 1 -0.27 291 292
positive regulation of MAPKKK cascade -0.045 0.12 0.21 33 -0.32 46 79
SLIT2 -0.084 0.17 -10000 0 -0.36 173 173
GPC1/NRG 0.004 0.085 -10000 0 -0.25 58 58
NRG1 -0.015 0.11 -10000 0 -0.36 56 56
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.041 0.031 0.25 1 -0.24 2 3
LYN -0.11 0.14 0.2 1 -0.27 260 261
mol:Spermine 0.006 0.017 -10000 0 -0.28 2 2
cell growth 0.029 0.069 -10000 0 -0.21 43 43
BMP signaling pathway -0.026 0.025 0.4 2 -10000 0 2
SRC -0.063 0.11 0.2 1 -0.27 125 126
TGFBR1 0.027 0.016 -10000 0 -0.36 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.071 0.17 -10000 0 -0.36 151 151
GPC1 0.026 0.025 -10000 0 -0.4 2 2
TGFBR1 (dimer) 0.027 0.016 -10000 0 -0.36 1 1
VEGFA 0.028 0.019 0.36 2 -10000 0 2
BLK -0.18 0.16 0.2 1 -0.29 378 379
HCK -0.066 0.11 0.2 1 -0.27 130 131
FGF2 -0.001 0.099 -10000 0 -0.36 43 43
FGFR1 0.021 0.032 -10000 0 -0.36 4 4
VEGFR1 homodimer 0.021 0.012 -10000 0 -10000 0 0
TGFBR2 0.027 0.003 -10000 0 -10000 0 0
cell death 0.037 0.024 -10000 0 -0.27 3 3
ATIII/GPC1 0.03 0.049 -10000 0 -0.31 12 12
PLA2G2A/GPC1 -0.036 0.13 -10000 0 -0.26 153 153
LCK -0.12 0.14 0.2 1 -0.27 297 298
neuron differentiation 0.004 0.085 -10000 0 -0.25 58 58
PrPc/Cu2+ 0.016 0.017 -10000 0 -0.25 2 2
APP 0.026 0.017 -10000 0 -0.36 1 1
TGFBR2 (dimer) 0.027 0.003 -10000 0 -10000 0 0
BCR signaling pathway

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
JUN -0.11 0.2 0.48 1 -0.46 119 120
IKBKB -0.037 0.11 0.27 4 -0.29 51 55
AKT1 -0.077 0.11 0.28 7 -0.25 117 124
IKBKG -0.037 0.1 0.41 1 -0.27 55 56
CALM1 -0.098 0.21 0.29 1 -0.52 97 98
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
MAP3K1 -0.14 0.27 0.47 2 -0.63 114 116
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.1 0.23 0.26 2 -0.54 105 107
DOK1 0.028 0.001 -10000 0 -10000 0 0
AP-1 -0.067 0.11 0.24 2 -0.27 104 106
LYN 0.024 0.009 -10000 0 -10000 0 0
BLNK 0.022 0.041 -10000 0 -0.36 7 7
SHC1 0.027 0.004 -10000 0 -10000 0 0
BCR complex -0.092 0.18 -10000 0 -0.32 221 221
CD22 -0.18 0.3 -10000 0 -0.62 155 155
CAMK2G -0.092 0.19 0.28 1 -0.49 95 96
CSNK2A1 0.023 0.011 -10000 0 -10000 0 0
INPP5D 0.027 0.016 -10000 0 -0.36 1 1
SHC/GRB2/SOS1 -0.047 0.12 -10000 0 -0.32 63 63
GO:0007205 -0.11 0.23 0.26 2 -0.55 106 108
SYK 0.027 0.004 -10000 0 -10000 0 0
ELK1 -0.1 0.22 0.29 1 -0.53 100 101
NFATC1 -0.16 0.24 0.31 2 -0.51 158 160
B-cell antigen/BCR complex -0.092 0.18 -10000 0 -0.32 221 221
PAG1/CSK 0.03 0.039 -10000 0 -0.25 10 10
NFKBIB -0.001 0.048 0.17 3 -0.13 32 35
HRAS -0.082 0.18 0.25 3 -0.45 96 99
NFKBIA 0 0.047 0.15 4 -0.12 32 36
NF-kappa-B/RelA/I kappa B beta 0.005 0.04 0.17 3 -10000 0 3
RasGAP/Csk -0.055 0.18 -10000 0 -0.41 91 91
mol:GDP -0.098 0.22 0.26 2 -0.52 103 105
PTEN 0.026 0.006 -10000 0 -10000 0 0
CD79B -0.024 0.13 -10000 0 -0.36 80 80
NF-kappa-B/RelA/I kappa B alpha 0.006 0.04 0.17 3 -10000 0 3
GRB2 0.027 0.004 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.17 0.26 0.33 2 -0.54 171 173
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
mol:IP3 -0.11 0.24 0.26 2 -0.54 110 112
CSK 0.027 0.006 -10000 0 -10000 0 0
FOS -0.096 0.2 0.28 1 -0.5 98 99
CHUK -0.046 0.12 0.41 1 -0.3 70 71
IBTK 0.026 0.016 -10000 0 -0.36 1 1
CARD11/BCL10/MALT1/TAK1 -0.071 0.2 0.24 1 -0.47 92 93
PTPN6 -0.17 0.28 0.26 1 -0.59 151 152
RELA 0.027 0.004 -10000 0 -10000 0 0
BCL2A1 0.005 0.029 0.18 1 -0.13 1 2
VAV2 -0.18 0.3 -10000 0 -0.62 156 156
ubiquitin-dependent protein catabolic process 0.001 0.047 0.15 4 -0.12 31 35
BTK -0.11 0.36 -10000 0 -1.1 74 74
CD19 -0.18 0.29 -10000 0 -0.59 164 164
MAP4K1 -0.007 0.11 -10000 0 -0.36 53 53
CD72 0.026 0.016 -10000 0 -0.36 1 1
PAG1 0.017 0.05 -10000 0 -0.36 10 10
MAPK14 -0.12 0.22 0.47 3 -0.52 112 115
SH3BP5 0.024 0.035 -10000 0 -0.36 5 5
PIK3AP1 -0.098 0.23 0.27 2 -0.55 102 104
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.13 0.28 -10000 0 -0.45 205 205
RAF1 -0.079 0.17 0.24 3 -0.43 94 97
RasGAP/p62DOK/SHIP -0.051 0.18 -10000 0 -0.4 91 91
CD79A -0.11 0.19 -10000 0 -0.36 219 219
re-entry into mitotic cell cycle -0.067 0.11 0.24 2 -0.27 104 106
RASA1 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.067 0.14 0.24 5 -0.38 81 86
MAPK1 -0.067 0.14 0.22 3 -0.38 80 83
CD72/SHP1 -0.15 0.27 0.23 1 -0.56 146 147
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.12 0.22 0.45 2 -0.52 112 114
actin cytoskeleton organization -0.14 0.24 0.31 2 -0.52 145 147
NF-kappa-B/RelA 0.014 0.079 0.3 3 -0.2 13 16
Calcineurin -0.067 0.18 0.27 1 -0.46 87 88
PI3K -0.15 0.22 -10000 0 -0.46 174 174
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.1 0.24 0.29 2 -0.57 105 107
SOS1 0.028 0.002 -10000 0 -10000 0 0
Bam32/HPK1 -0.17 0.35 -10000 0 -0.84 114 114
DAPP1 -0.2 0.38 -10000 0 -0.93 114 114
cytokine secretion -0.14 0.22 0.3 2 -0.46 157 159
mol:DAG -0.11 0.24 0.26 2 -0.54 110 112
PLCG2 -0.004 0.1 -10000 0 -0.36 49 49
MAP2K1 -0.074 0.16 0.24 3 -0.42 82 85
B-cell antigen/BCR complex/FcgammaRIIB -0.084 0.2 -10000 0 -0.32 227 227
mol:PI-3-4-5-P3 -0.12 0.14 0.16 1 -0.33 146 147
ETS1 -0.085 0.18 0.26 1 -0.46 91 92
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.032 0.15 -10000 0 -0.35 65 65
B-cell antigen/BCR complex/LYN -0.14 0.27 -10000 0 -0.64 114 114
MALT1 0.02 0.02 -10000 0 -0.36 1 1
TRAF6 0.028 0.003 -10000 0 -10000 0 0
RAC1 -0.15 0.27 0.31 2 -0.57 144 146
B-cell antigen/BCR complex/LYN/SYK -0.14 0.28 0.27 1 -0.57 142 143
CARD11 -0.097 0.23 0.26 5 -0.52 107 112
FCGR2B -0.019 0.12 -10000 0 -0.36 72 72
PPP3CA 0.027 0.005 -10000 0 -10000 0 0
BCL10 0.026 0.016 -10000 0 -0.36 1 1
IKK complex -0.011 0.049 0.16 7 -0.12 13 20
PTPRC -0.003 0.1 -10000 0 -0.36 48 48
PDPK1 -0.079 0.1 0.18 7 -0.24 114 121
PPP3CB 0.027 0.004 -10000 0 -10000 0 0
PPP3CC 0.021 0.012 -10000 0 -10000 0 0
POU2F2 0.004 0.033 0.22 2 -10000 0 2
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.016 0.073 -10000 0 -0.4 14 14
Crk/p130 Cas/Paxillin -0.089 0.12 -10000 0 -0.31 57 57
JUN -0.083 0.12 -10000 0 -0.34 67 67
HRAS 0.027 0.016 -10000 0 -0.36 1 1
RET51/GFRalpha1/GDNF/GRB10 -0.06 0.15 -10000 0 -0.23 239 239
RAP1A 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.027 0.003 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.063 0.16 -10000 0 -0.23 260 260
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.028 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.023 0.01 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.042 0.12 -10000 0 -0.19 229 229
RHOA 0.027 0.004 -10000 0 -10000 0 0
RAP1A/GTP -0.055 0.14 -10000 0 -0.33 57 57
GRB7 0.035 0.049 0.36 14 -10000 0 14
RET51/GFRalpha1/GDNF -0.063 0.16 -10000 0 -0.23 257 257
MAPKKK cascade -0.078 0.14 -10000 0 -0.37 56 56
BCAR1 0.027 0.016 -10000 0 -0.36 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.042 0.12 -10000 0 -0.19 229 229
lamellipodium assembly -0.077 0.12 -10000 0 -0.28 64 64
RET51/GFRalpha1/GDNF/SHC -0.062 0.16 -10000 0 -0.36 63 63
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
RET9/GFRalpha1/GDNF/SHC -0.04 0.12 -10000 0 -0.19 223 223
RET9/GFRalpha1/GDNF/Shank3 -0.042 0.12 -10000 0 -0.19 229 229
MAPK3 -0.09 0.11 -10000 0 -0.32 57 57
DOK1 0.028 0.001 -10000 0 -10000 0 0
DOK6 0.014 0.048 -10000 0 -0.36 9 9
PXN 0.028 0.002 -10000 0 -10000 0 0
neurite development -0.066 0.1 -10000 0 -0.32 39 39
DOK5 0.012 0.047 0.36 1 -0.36 8 9
GFRA1 -0.12 0.19 -10000 0 -0.36 234 234
MAPK8 -0.087 0.13 -10000 0 -0.35 71 71
HRAS/GTP -0.076 0.16 -10000 0 -0.4 62 62
tube development -0.039 0.11 0.21 1 -0.19 82 83
MAPK1 -0.088 0.11 0.34 1 -0.32 56 57
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.056 0.1 -10000 0 -0.19 222 222
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
SRC 0.017 0.014 -10000 0 -10000 0 0
PDLIM7 0.027 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.045 0.12 -10000 0 -0.34 42 42
SHC1 0.027 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.063 0.16 -10000 0 -0.37 57 57
RET51/GFRalpha1/GDNF/Dok5 -0.049 0.13 0.25 1 -0.35 43 44
PRKCA 0.027 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.02 0.011 -10000 0 -0.25 1 1
CREB1 -0.085 0.14 -10000 0 -0.37 65 65
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.057 0.11 -10000 0 -0.2 219 219
RET51/GFRalpha1/GDNF/Grb7 -0.058 0.15 0.25 5 -0.23 246 251
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.032 0.14 -10000 0 -0.36 93 93
DOK4 0.027 0.016 -10000 0 -0.36 1 1
JNK cascade -0.082 0.12 -10000 0 -0.34 65 65
RET9/GFRalpha1/GDNF/FRS2 -0.041 0.12 -10000 0 -0.19 225 225
SHANK3 0.026 0.017 -10000 0 -0.36 1 1
RASA1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.028 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.055 0.1 -10000 0 -0.2 90 90
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.083 0.14 -10000 0 -0.37 63 63
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.086 0.14 -10000 0 -0.37 71 71
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.09 0.16 -10000 0 -0.44 65 65
PI3K -0.11 0.17 -10000 0 -0.34 187 187
SOS1 0.028 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.031 0.12 -10000 0 -0.18 209 209
GRB10 0.025 0.008 -10000 0 -10000 0 0
activation of MAPKK activity -0.07 0.12 -10000 0 -0.31 58 58
RET51/GFRalpha1/GDNF/FRS2 -0.063 0.16 -10000 0 -0.37 58 58
GAB1 0.027 0.005 -10000 0 -10000 0 0
IRS1 0.028 0.002 -10000 0 -10000 0 0
IRS2 0.022 0.012 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.09 0.16 -10000 0 -0.43 68 68
RET51/GFRalpha1/GDNF/PKC alpha -0.061 0.15 -10000 0 -0.23 249 249
GRB2 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.027 0.003 -10000 0 -10000 0 0
GDNF 0.016 0.025 -10000 0 -0.36 1 1
RAC1 0.025 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.064 0.16 -10000 0 -0.23 260 260
Rac1/GTP -0.088 0.14 -10000 0 -0.34 63 63
RET9/GFRalpha1/GDNF -0.058 0.12 -10000 0 -0.21 229 229
GFRalpha1/GDNF -0.072 0.14 -10000 0 -0.25 229 229
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.025 0.032 -10000 0 -0.36 4 4
LAT2 -0.085 0.15 -10000 0 -0.36 97 97
AP1 -0.11 0.23 -10000 0 -0.51 122 122
mol:PIP3 -0.11 0.19 0.3 8 -0.44 105 113
IKBKB -0.067 0.13 0.2 31 -0.27 123 154
AKT1 -0.079 0.11 0.34 9 -0.38 7 16
IKBKG -0.079 0.12 0.23 9 -0.27 136 145
MS4A2 -0.087 0.18 -10000 0 -0.36 177 177
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.026 0.016 -10000 0 -0.36 1 1
MAP3K1 -0.1 0.17 0.24 6 -0.4 112 118
mol:Ca2+ -0.086 0.15 0.28 8 -0.33 105 113
LYN 0.023 0.011 -10000 0 -10000 0 0
CBLB -0.086 0.15 -10000 0 -0.34 111 111
SHC1 0.027 0.004 -10000 0 -10000 0 0
RasGAP/p62DOK 0.05 0.02 -10000 0 -0.19 3 3
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.027 0.016 -10000 0 -0.36 1 1
PLD2 -0.083 0.13 0.31 12 -0.32 84 96
PTPN13 -0.096 0.18 -10000 0 -0.55 30 30
PTPN11 0.015 0.024 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.073 0.12 0.34 6 -0.31 33 39
SYK 0.026 0.009 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.1 0.2 0.18 1 -0.45 110 111
LAT -0.087 0.15 -10000 0 -0.33 119 119
PAK2 -0.11 0.19 0.25 7 -0.44 115 122
NFATC2 -0.033 0.098 -10000 0 -0.54 18 18
HRAS -0.12 0.2 0.26 5 -0.46 119 124
GAB2 0.027 0.004 -10000 0 -10000 0 0
PLA2G1B 0.019 0.12 -10000 0 -0.86 10 10
Fc epsilon R1 -0.084 0.17 -10000 0 -0.28 242 242
Antigen/IgE/Fc epsilon R1 -0.074 0.15 -10000 0 -0.25 233 233
mol:GDP -0.13 0.23 -10000 0 -0.51 126 126
JUN 0.027 0.004 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.026 0.006 -10000 0 -10000 0 0
FOS 0.022 0.039 -10000 0 -0.36 6 6
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.088 0.16 -10000 0 -0.31 159 159
CHUK -0.079 0.12 0.27 5 -0.27 137 142
KLRG1 -0.075 0.13 0.14 1 -0.33 91 92
VAV1 -0.094 0.16 -10000 0 -0.32 155 155
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.086 0.15 -10000 0 -0.31 147 147
negative regulation of mast cell degranulation -0.064 0.13 -10000 0 -0.32 86 86
BTK -0.14 0.26 -10000 0 -0.58 125 125
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.12 0.21 -10000 0 -0.49 120 120
GAB2/PI3K/SHP2 -0.093 0.1 -10000 0 -0.31 78 78
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.082 0.15 -10000 0 -0.38 91 91
RAF1 0.022 0.13 -10000 0 -0.93 10 10
Fc epsilon R1/FcgammaRIIB/SHIP -0.073 0.19 -10000 0 -0.39 115 115
FCER1G 0.028 0.041 -10000 0 -0.37 6 6
FCER1A -0.086 0.18 -10000 0 -0.37 167 167
Antigen/IgE/Fc epsilon R1/Fyn -0.061 0.15 -10000 0 -0.3 115 115
MAPK3 0.02 0.12 -10000 0 -0.85 10 10
MAPK1 0.015 0.12 -10000 0 -0.89 10 10
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.1 0.26 -10000 0 -0.66 88 88
DUSP1 0.025 0.027 -10000 0 -0.36 3 3
NF-kappa-B/RelA -0.04 0.08 -10000 0 -0.2 50 50
actin cytoskeleton reorganization -0.089 0.18 -10000 0 -0.54 27 27
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.092 0.18 -10000 0 -0.41 105 105
FER -0.084 0.15 -10000 0 -0.31 146 146
RELA 0.027 0.004 -10000 0 -10000 0 0
ITK -0.035 0.096 -10000 0 -0.38 36 36
SOS1 0.028 0.002 -10000 0 -10000 0 0
PLCG1 -0.079 0.23 0.23 28 -0.47 115 143
cytokine secretion -0.032 0.055 -10000 0 -10000 0 0
SPHK1 -0.1 0.15 -10000 0 -0.32 153 153
PTK2 -0.093 0.18 -10000 0 -0.58 26 26
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.099 0.21 0.21 5 -0.46 111 116
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.11 0.19 0.31 7 -0.43 110 117
MAP2K2 0.014 0.12 -10000 0 -0.86 10 10
MAP2K1 0.013 0.12 -10000 0 -0.87 10 10
MAP2K7 0.027 0.016 -10000 0 -0.36 1 1
KLRG1/SHP2 -0.059 0.12 0.18 3 -0.3 80 83
MAP2K4 -0.14 0.37 -10000 0 -0.9 115 115
Fc epsilon R1/FcgammaRIIB -0.086 0.19 -10000 0 -0.33 186 186
mol:Choline -0.082 0.13 0.31 12 -0.31 84 96
SHC/Grb2/SOS1 -0.058 0.16 -10000 0 -0.36 85 85
FYN 0.027 0.005 -10000 0 -10000 0 0
DOK1 0.028 0.001 -10000 0 -10000 0 0
PXN -0.088 0.17 0.41 2 -0.55 24 26
HCLS1 -0.088 0.15 -10000 0 -0.3 154 154
PRKCB -0.11 0.17 0.28 6 -0.37 146 152
FCGR2B -0.019 0.12 -10000 0 -0.36 72 72
IGHE -0.003 0.006 -10000 0 -10000 0 0
KLRG1/SHIP -0.065 0.14 -10000 0 -0.32 86 86
LCP2 0.023 0.039 -10000 0 -0.36 6 6
PLA2G4A -0.1 0.17 -10000 0 -0.33 182 182
RASA1 0.027 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.082 0.13 0.31 12 -0.31 84 96
IKK complex -0.049 0.1 0.19 28 -0.23 63 91
WIPF1 0.026 0.027 -10000 0 -0.36 3 3
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.065 0.17 -10000 0 -0.42 100 100
CRKL -0.055 0.16 -10000 0 -0.41 100 100
HRAS -0.042 0.16 -10000 0 -0.37 103 103
mol:PIP3 -0.044 0.16 0.26 2 -0.38 97 99
SPRED1 0.026 0.007 -10000 0 -10000 0 0
SPRED2 0.028 0.001 -10000 0 -10000 0 0
GAB1 -0.056 0.17 -10000 0 -0.43 100 100
FOXO3 -0.051 0.18 0.29 2 -0.41 108 110
AKT1 -0.055 0.2 0.27 1 -0.44 109 110
BAD -0.052 0.18 0.26 1 -0.41 108 109
megakaryocyte differentiation -0.074 0.18 -10000 0 -0.44 103 103
GSK3B -0.051 0.18 0.32 2 -0.41 106 108
RAF1 -0.036 0.13 0.24 1 -0.31 99 100
SHC1 0.027 0.004 -10000 0 -10000 0 0
STAT3 -0.057 0.17 -10000 0 -0.43 99 99
STAT1 -0.14 0.4 -10000 0 -0.96 110 110
HRAS/SPRED1 -0.024 0.14 -10000 0 -0.31 96 96
cell proliferation -0.055 0.17 -10000 0 -0.42 101 101
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
TEC 0.026 0.02 -10000 0 -0.44 1 1
RPS6KB1 -0.051 0.18 -10000 0 -0.43 105 105
HRAS/SPRED2 -0.023 0.14 -10000 0 -0.31 99 99
LYN/TEC/p62DOK -0.019 0.17 -10000 0 -0.41 87 87
MAPK3 -0.023 0.099 0.19 2 -0.26 37 39
STAP1 -0.093 0.19 -10000 0 -0.47 107 107
GRAP2 0.013 0.069 -10000 0 -0.36 20 20
JAK2 -0.12 0.34 -10000 0 -0.83 104 104
STAT1 (dimer) -0.14 0.38 -10000 0 -0.93 111 111
mol:Gleevec 0.002 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.033 0.2 -10000 0 -0.44 100 100
actin filament polymerization -0.057 0.17 0.2 1 -0.42 94 95
LYN 0.024 0.009 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.11 0.25 -10000 0 -0.63 105 105
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.028 0.16 -10000 0 -0.38 97 97
PI3K -0.027 0.19 -10000 0 -0.42 98 98
PTEN 0.026 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.15 0.46 -10000 0 -1.2 98 98
MAPK8 -0.057 0.17 -10000 0 -0.43 101 101
STAT3 (dimer) -0.055 0.17 -10000 0 -0.42 98 98
positive regulation of transcription -0.017 0.083 0.17 3 -0.21 37 40
mol:GDP -0.04 0.17 -10000 0 -0.39 103 103
PIK3C2B -0.057 0.17 -10000 0 -0.43 100 100
CBL/CRKL -0.04 0.16 -10000 0 -0.39 99 99
FER -0.058 0.17 -10000 0 -0.43 101 101
SH2B3 -0.057 0.17 -10000 0 -0.43 100 100
PDPK1 -0.04 0.15 0.25 5 -0.36 95 100
SNAI2 -0.056 0.16 -10000 0 -0.42 98 98
positive regulation of cell proliferation -0.097 0.29 -10000 0 -0.72 104 104
KITLG 0.011 0.066 -10000 0 -0.39 14 14
cell motility -0.097 0.29 -10000 0 -0.72 104 104
PTPN6 0.029 0.011 -10000 0 -10000 0 0
EPOR -0.012 0.14 -10000 0 -1 2 2
STAT5A (dimer) -0.076 0.24 -10000 0 -0.59 101 101
SOCS1 0.011 0.086 -10000 0 -0.44 21 21
cell migration 0.073 0.18 0.45 101 -10000 0 101
SOS1 0.028 0.002 -10000 0 -10000 0 0
EPO 0.012 0.051 0.34 2 -0.45 5 7
VAV1 0.011 0.077 -10000 0 -0.36 25 25
GRB10 -0.055 0.16 -10000 0 -0.42 94 94
PTPN11 0.029 0.007 -10000 0 -10000 0 0
SCF/KIT -0.056 0.18 -10000 0 -0.45 101 101
GO:0007205 0.003 0.009 -10000 0 -10000 0 0
MAP2K1 -0.029 0.11 0.22 1 -0.28 40 41
CBL 0.027 0.004 -10000 0 -10000 0 0
KIT -0.17 0.47 -10000 0 -1.2 100 100
MAP2K2 -0.029 0.11 0.22 1 -0.28 43 44
SHC/Grb2/SOS1 -0.018 0.18 -10000 0 -0.41 96 96
STAT5A -0.08 0.25 -10000 0 -0.61 101 101
GRB2 0.027 0.004 -10000 0 -10000 0 0
response to radiation -0.054 0.16 -10000 0 -0.41 98 98
SHC/GRAP2 0.029 0.053 -10000 0 -0.25 20 20
PTPRO -0.075 0.18 -10000 0 -0.45 103 103
SH2B2 -0.058 0.17 0.2 1 -0.43 95 96
DOK1 0.028 0.001 -10000 0 -10000 0 0
MATK -0.075 0.18 -10000 0 -0.46 101 101
CREBBP 0.016 0.057 -10000 0 -10000 0 0
BCL2 -0.19 0.42 -10000 0 -1.2 72 72
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 -0.28 0.28 -10000 0 -0.8 75 75
PCK1 -0.59 0.59 -10000 0 -1.2 268 268
HNF4A -0.26 0.29 -10000 0 -0.91 43 43
KCNJ11 -0.29 0.29 -10000 0 -0.85 64 64
AKT1 -0.2 0.18 -10000 0 -0.56 53 53
response to starvation -0.018 0.029 -10000 0 -10000 0 0
DLK1 -0.29 0.29 -10000 0 -0.87 63 63
NKX2-1 -0.12 0.14 0.34 5 -0.37 44 49
ACADM -0.29 0.28 -10000 0 -0.84 71 71
TAT -0.59 0.57 -10000 0 -1.2 247 247
CEBPB 0.004 0.052 0.36 3 -0.44 4 7
CEBPA 0.006 0.047 -10000 0 -0.36 3 3
TTR -0.34 0.47 0.52 2 -1.1 143 145
PKLR -0.34 0.34 -10000 0 -0.9 121 121
APOA1 -0.3 0.32 -10000 0 -0.98 48 48
CPT1C -0.29 0.27 -10000 0 -0.81 74 74
ALAS1 -0.14 0.14 -10000 0 -0.55 6 6
TFRC -0.27 0.23 -10000 0 -0.67 56 56
FOXF1 0.021 0.049 -10000 0 -0.36 10 10
NF1 0.031 0.006 -10000 0 -10000 0 0
HNF1A (dimer) -0.073 0.051 -10000 0 -0.27 7 7
CPT1A -0.29 0.27 -10000 0 -0.8 74 74
HMGCS1 -0.29 0.28 -10000 0 -0.81 72 72
NR3C1 -0.076 0.13 -10000 0 -0.32 82 82
CPT1B -0.29 0.28 -10000 0 -0.8 77 77
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 -0.066 0.039 -10000 0 -10000 0 0
GCK -0.29 0.29 -10000 0 -0.86 68 68
CREB1 -0.063 0.11 -10000 0 -0.21 133 133
IGFBP1 -0.22 0.2 -10000 0 -0.63 53 53
PDX1 -0.31 0.18 -10000 0 -0.64 24 24
UCP2 -0.29 0.27 -10000 0 -0.81 72 72
ALDOB -0.32 0.32 -10000 0 -0.9 86 86
AFP -0.11 0.13 -10000 0 -0.39 77 77
BDH1 -0.29 0.28 -10000 0 -0.84 65 65
HADH -0.28 0.28 -10000 0 -0.84 63 63
F2 -0.32 0.32 -10000 0 -0.99 54 54
HNF1A -0.073 0.051 -10000 0 -0.27 7 7
G6PC -0.16 0.32 -10000 0 -1.2 45 45
SLC2A2 -0.22 0.18 -10000 0 -0.68 14 14
INS -0.006 0.041 -10000 0 -10000 0 0
FOXA1 -0.036 0.12 -10000 0 -0.34 68 68
FOXA3 -0.15 0.14 -10000 0 -0.33 130 130
FOXA2 -0.33 0.32 -10000 0 -0.88 91 91
ABCC8 -0.34 0.34 -10000 0 -0.95 100 100
ALB -0.11 0.14 -10000 0 -0.39 81 81
HIF-1-alpha transcription factor network

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
PKM2 -0.41 0.27 -10000 0 -0.83 107 107
HDAC7 0.027 0.007 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.33 0.24 -10000 0 -0.85 39 39
SMAD4 0.02 0.013 -10000 0 -10000 0 0
ID2 -0.41 0.28 -10000 0 -0.86 89 89
AP1 0.036 0.031 -10000 0 -0.25 6 6
ABCG2 -0.55 0.3 -10000 0 -0.9 168 168
HIF1A -0.079 0.051 -10000 0 -10000 0 0
TFF3 -0.41 0.28 -10000 0 -0.87 92 92
GATA2 0.022 0.052 -10000 0 -0.36 11 11
AKT1 -0.078 0.055 -10000 0 -10000 0 0
response to hypoxia -0.081 0.046 -10000 0 -0.22 12 12
MCL1 -0.41 0.28 -10000 0 -0.86 84 84
NDRG1 -0.39 0.28 -10000 0 -0.86 80 80
SERPINE1 -0.45 0.3 -10000 0 -0.88 125 125
FECH -0.4 0.28 -10000 0 -0.86 82 82
FURIN -0.41 0.28 -10000 0 -0.86 85 85
NCOA2 0.023 0.029 -10000 0 -0.36 3 3
EP300 -0.075 0.075 -10000 0 -0.31 27 27
HMOX1 -0.41 0.28 -10000 0 -0.87 86 86
BHLHE40 -0.41 0.28 -10000 0 -0.86 87 87
BHLHE41 -0.42 0.28 -10000 0 -0.88 89 89
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.074 0.083 -10000 0 -10000 0 0
ENG -0.077 0.068 0.28 2 -10000 0 2
JUN 0.028 0.005 -10000 0 -10000 0 0
RORA -0.41 0.28 -10000 0 -0.86 89 89
ABCB1 -0.27 0.4 -10000 0 -1.1 118 118
TFRC -0.41 0.28 -10000 0 -0.86 85 85
CXCR4 -0.41 0.28 -10000 0 -0.86 87 87
TF -0.43 0.29 -10000 0 -0.89 102 102
CITED2 -0.41 0.28 -10000 0 -0.86 84 84
HIF1A/ARNT -0.44 0.32 -10000 0 -0.96 85 85
LDHA -0.04 0.055 -10000 0 -0.8 1 1
ETS1 -0.41 0.28 -10000 0 -0.86 86 86
PGK1 -0.41 0.28 -10000 0 -0.86 84 84
NOS2 -0.42 0.28 -10000 0 -0.87 98 98
ITGB2 -0.41 0.28 -10000 0 -0.86 89 89
ALDOA -0.41 0.28 -10000 0 -0.86 87 87
Cbp/p300/CITED2 -0.4 0.29 -10000 0 -0.97 60 60
FOS 0.023 0.039 -10000 0 -0.36 6 6
HK2 -0.41 0.28 -10000 0 -0.86 84 84
SP1 0.008 0.053 -10000 0 -10000 0 0
GCK -0.098 0.2 -10000 0 -1.3 12 12
HK1 -0.41 0.28 -10000 0 -0.86 86 86
NPM1 -0.41 0.28 -10000 0 -0.86 87 87
EGLN1 -0.41 0.28 -10000 0 -0.86 88 88
CREB1 0.033 0 -10000 0 -10000 0 0
PGM1 -0.41 0.28 -10000 0 -0.86 87 87
SMAD3 0.026 0.007 -10000 0 -10000 0 0
EDN1 -0.075 0.11 -10000 0 -0.68 6 6
IGFBP1 -0.43 0.3 -10000 0 -0.89 115 115
VEGFA -0.3 0.21 -10000 0 -0.76 35 35
HIF1A/JAB1 -0.04 0.044 -10000 0 -10000 0 0
CP -0.49 0.31 -10000 0 -0.89 146 146
CXCL12 -0.44 0.3 -10000 0 -0.9 109 109
COPS5 0.024 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4 0.03 0.019 -10000 0 -10000 0 0
BNIP3 -0.41 0.28 -10000 0 -0.86 89 89
EGLN3 -0.41 0.28 -10000 0 -0.86 88 88
CA9 -0.56 0.3 -10000 0 -0.87 213 213
TERT -0.42 0.29 -10000 0 -0.89 97 97
ENO1 -0.41 0.28 -10000 0 -0.86 86 86
PFKL -0.41 0.28 -10000 0 -0.86 86 86
NCOA1 0.028 0.002 -10000 0 -10000 0 0
ADM -0.41 0.28 -10000 0 -0.86 89 89
ARNT -0.083 0.05 -10000 0 -0.42 1 1
HNF4A 0.014 0.025 -10000 0 -0.36 1 1
ADFP -0.41 0.27 -10000 0 -0.83 107 107
SLC2A1 -0.31 0.22 -10000 0 -0.8 41 41
LEP -0.42 0.29 -10000 0 -0.87 105 105
HIF1A/ARNT/Cbp/p300 -0.34 0.24 -10000 0 -0.85 45 45
EPO -0.23 0.18 -10000 0 -0.82 11 11
CREBBP -0.073 0.072 -10000 0 -0.32 21 21
HIF1A/ARNT/Cbp/p300/HDAC7 -0.33 0.25 -10000 0 -0.88 39 39
PFKFB3 -0.41 0.28 -10000 0 -0.86 86 86
NT5E -0.41 0.28 -10000 0 -0.86 88 88
Visual signal transduction: Rods

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
mol:K + 0.026 0.006 -10000 0 -10000 0 0
GNAT1/GTP 0.014 0.014 -10000 0 -0.31 1 1
Metarhodopsin II/Arrestin 0.024 0.021 -10000 0 -0.27 3 3
PDE6G/GNAT1/GTP 0.017 0.057 -10000 0 -0.21 35 35
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 -0.009 0.025 -10000 0 -0.44 1 1
GRK1 -0.01 0.032 0.36 1 -0.44 2 3
CNG Channel -0.13 0.15 -10000 0 -0.36 113 113
mol:Na + -0.034 0.13 -10000 0 -0.39 32 32
mol:ADP -0.01 0.032 0.36 1 -0.44 2 3
RGS9-1/Gbeta5/R9AP 0.009 0.097 0.25 1 -0.21 95 96
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.028 0.13 -10000 0 -0.4 32 32
CNGB1 -0.047 0.13 -10000 0 -0.36 83 83
RDH5 0 0.1 -10000 0 -0.36 44 44
SAG -0.009 0.019 -10000 0 -10000 0 0
mol:Ca2+ -0.067 0.12 0.34 13 -0.38 31 44
Na + (4 Units) -0.036 0.12 -10000 0 -0.37 32 32
RGS9 -0.033 0.14 -10000 0 -0.36 93 93
GNB1/GNGT1 -0.055 0.16 0.26 14 -0.32 167 181
GNAT1/GDP 0.016 0.088 0.24 1 -0.19 67 68
GUCY2D -0.006 0.094 -10000 0 -0.46 24 24
GNGT1 -0.1 0.22 0.36 15 -0.44 167 182
GUCY2F -0.016 0.02 -10000 0 -0.44 1 1
GNB5 0.026 0.006 -10000 0 -10000 0 0
mol:GMP (4 units) -0.11 0.12 -10000 0 -0.2 351 351
mol:11-cis-retinal 0 0.1 -10000 0 -0.36 44 44
mol:cGMP 0.01 0.093 -10000 0 -0.27 54 54
GNB1 0.026 0.006 -10000 0 -10000 0 0
Rhodopsin 0.011 0.079 -10000 0 -0.26 47 47
SLC24A1 0.027 0.006 -10000 0 -10000 0 0
CNGA1 -0.007 0.11 -10000 0 -0.36 54 54
Metarhodopsin II 0.017 0.03 0.21 1 -0.3 4 5
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.019 0.098 -10000 0 -0.28 56 56
RGS9BP 0.02 0.038 0.36 1 -0.44 3 4
Metarhodopsin II/Transducin -0.023 0.068 0.15 12 -0.23 13 25
GCAP Family/Ca ++ 0.026 0.07 -10000 0 -0.25 37 37
PDE6A/B -0.14 0.15 -10000 0 -0.26 354 354
mol:Pi 0.009 0.096 0.25 1 -0.21 95 96
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin -0.033 0.14 0.23 14 -0.25 167 181
PDE6B 0.008 0.082 -10000 0 -0.36 28 28
PDE6A -0.19 0.19 -10000 0 -0.36 345 345
PDE6G 0.004 0.089 -10000 0 -0.36 34 34
RHO -0.017 0.032 -10000 0 -0.44 3 3
PDE6 -0.11 0.15 -10000 0 -0.36 90 90
GUCA1A -0.011 0.11 0.36 1 -0.44 36 37
GC2/GCAP Family 0.035 0.076 -10000 0 -0.26 37 37
GUCA1C -0.018 0.002 -10000 0 -10000 0 0
GUCA1B 0.028 0.03 0.36 3 -0.44 1 4
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.04 0.008 -10000 0 -10000 0 0
Necdin/E2F1 0.018 0.058 0.26 7 -0.27 17 24
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.001 0.12 -10000 0 -0.32 12 12
NGF (dimer)/p75(NTR)/BEX1 -0.082 0.16 -10000 0 -0.26 262 262
NT-4/5 (dimer)/p75(NTR) -0.047 0.14 -10000 0 -0.27 164 164
IKBKB 0.024 0.009 -10000 0 -10000 0 0
AKT1 -0.052 0.081 0.18 5 -0.34 8 13
IKBKG 0.027 0.016 -10000 0 -0.36 1 1
BDNF 0.019 0.06 -10000 0 -0.44 10 10
MGDIs/NGR/p75(NTR)/LINGO1 -0.034 0.13 -10000 0 -0.23 182 182
FURIN 0.026 0.017 -10000 0 -0.36 1 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.016 0.12 -10000 0 -0.22 157 157
LINGO1 0.008 0.091 -10000 0 -0.44 24 24
Sortilin/TRAF6/NRIF 0.031 0.028 -10000 0 -0.32 1 1
proBDNF (dimer) 0.019 0.06 -10000 0 -0.44 10 10
NTRK1 0.016 0.057 -10000 0 -0.43 9 9
RTN4R 0.011 0.084 -10000 0 -0.44 21 21
neuron apoptosis -0.048 0.14 0.29 4 -0.4 39 43
IRAK1 0.027 0.019 -10000 0 -0.44 1 1
SHC1 -0.045 0.1 -10000 0 -0.22 146 146
ARHGDIA 0.027 0.016 -10000 0 -0.36 1 1
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.07 0.031 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.005 0.12 -10000 0 -0.36 11 11
MAGEH1 0.024 0.038 -10000 0 -0.36 6 6
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.013 0.13 -10000 0 -0.36 25 25
Mammalian IAPs/DIABLO 0.064 0.038 -10000 0 -0.25 1 1
proNGF (dimer) 0.011 0.071 -10000 0 -0.37 20 20
MAGED1 0.027 0.003 -10000 0 -10000 0 0
APP 0.026 0.017 -10000 0 -0.36 1 1
NT-4/5 (dimer) -0.017 0.089 -10000 0 -0.45 23 23
ZNF274 0.023 0.038 -10000 0 -0.36 6 6
RhoA/GDP/RHOGDI -0.021 0.1 -10000 0 -0.32 10 10
NGF 0.011 0.071 -10000 0 -0.37 20 20
cell cycle arrest -0.031 0.089 0.2 5 -0.31 9 14
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.027 0.097 -10000 0 -0.31 16 16
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.025 0.13 -10000 0 -0.23 164 164
NCSTN 0.027 0.004 -10000 0 -10000 0 0
mol:GTP -0.046 0.14 -10000 0 -0.24 205 205
PSENEN 0.026 0.016 -10000 0 -0.36 1 1
mol:ceramide -0.039 0.096 0.18 5 -0.34 10 15
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.024 0.089 -10000 0 -0.3 22 22
p75(NTR)/beta APP -0.032 0.12 -10000 0 -0.25 149 149
BEX1 -0.085 0.17 -10000 0 -0.36 164 164
mol:GDP -0.061 0.095 -10000 0 -0.22 159 159
NGF (dimer) -0.28 0.12 -10000 0 -0.3 577 577
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.019 0.13 -10000 0 -0.29 41 41
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
RAC1/GTP -0.015 0.1 -10000 0 -0.19 143 143
MYD88 0.028 0.003 -10000 0 -10000 0 0
CHUK 0.027 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.046 0.14 -10000 0 -0.24 205 205
RHOB 0.028 0 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.024 0.043 0.26 8 -0.32 4 12
NT3 (dimer) 0.021 0.043 -10000 0 -0.37 7 7
TP53 -0.043 0.081 0.34 4 -0.34 4 8
PRDM4 -0.041 0.098 0.18 5 -0.34 10 15
BDNF (dimer) -0.46 0.15 0.4 1 -0.48 599 600
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
SORT1 0.027 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.003 0.11 -10000 0 -0.32 12 12
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.003 0.12 -10000 0 -0.34 10 10
RHOC 0.027 0.005 -10000 0 -10000 0 0
XIAP 0.028 0.002 -10000 0 -10000 0 0
MAPK10 -0.068 0.15 0.31 5 -0.41 49 54
DIABLO 0.028 0.003 -10000 0 -10000 0 0
SMPD2 -0.039 0.096 0.18 5 -0.34 10 15
APH1B 0.026 0.006 -10000 0 -10000 0 0
APH1A 0.027 0.004 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.018 0.12 -10000 0 -0.22 154 154
PSEN1 0.026 0.007 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.039 0.01 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.033 0.13 -10000 0 -0.26 148 148
MAPK8 -0.048 0.12 0.33 4 -0.33 22 26
MAPK9 -0.048 0.12 0.33 4 -0.34 19 23
APAF1 0.028 0.003 -10000 0 -10000 0 0
NTF3 0.021 0.043 -10000 0 -0.37 7 7
NTF4 -0.017 0.089 -10000 0 -0.45 23 23
NDN 0.011 0.075 -10000 0 -0.36 24 24
RAC1/GDP 0.019 0.006 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.019 0.13 -10000 0 -0.34 29 29
p75 CTF/Sortilin/TRAF6/NRIF 0.065 0.031 -10000 0 -0.19 6 6
RhoA-B-C/GTP -0.046 0.14 -10000 0 -0.24 205 205
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.008 0.12 -10000 0 -0.27 13 13
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.001 0.12 -10000 0 -0.26 10 10
PRKACB -0.019 0.12 -10000 0 -0.36 72 72
proBDNF (dimer)/p75 ECD 0.035 0.046 -10000 0 -0.32 10 10
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.02 0.05 -10000 0 -0.37 10 10
BIRC2 0.026 0.016 -10000 0 -0.36 1 1
neuron projection morphogenesis -0.053 0.12 -10000 0 -0.31 44 44
BAD -0.062 0.14 0.31 7 -0.35 47 54
RIPK2 0.024 0.01 -10000 0 -10000 0 0
NGFR -0.067 0.17 -10000 0 -0.36 148 148
CYCS -0.053 0.081 0.18 4 -0.34 8 12
ADAM17 0.028 0.002 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.004 0.11 -10000 0 -0.2 132 132
BCL2L11 -0.062 0.14 0.31 7 -0.35 47 54
BDNF (dimer)/p75(NTR) -0.037 0.13 -10000 0 -0.26 157 157
PI3K -0.005 0.12 -10000 0 -0.26 25 25
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.004 0.12 -10000 0 -0.34 10 10
NDNL2 0.026 0.007 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
PRKCI 0.026 0.022 -10000 0 -0.36 2 2
NGF (dimer)/p75(NTR) -0.04 0.13 -10000 0 -0.26 159 159
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.002 0.12 -10000 0 -0.34 10 10
TRAF6 0.027 0.003 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
PLG -0.095 0.18 0.36 1 -0.44 127 128
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.046 0.11 -10000 0 -0.23 138 138
SQSTM1 0.027 0.004 -10000 0 -10000 0 0
NGFRAP1 0.026 0.022 -10000 0 -0.36 2 2
CASP3 -0.061 0.13 0.34 5 -0.33 48 53
E2F1 0.019 0.057 0.36 9 -0.44 4 13
CASP9 0.026 0.007 -10000 0 -10000 0 0
IKK complex 0 0.11 -10000 0 -0.36 12 12
NGF (dimer)/TRKA 0.023 0.069 -10000 0 -0.28 28 28
MMP7 -0.42 0.11 0.36 3 -0.45 582 585
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.005 0.12 -10000 0 -0.33 13 13
MMP3 -0.36 0.18 0.36 1 -0.45 508 509
APAF-1/Caspase 9 -0.055 0.068 -10000 0 -0.3 11 11
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.027 0.019 -10000 0 -0.44 1 1
CCL5 0.012 0.075 -10000 0 -0.36 24 24
SDCBP 0.024 0.018 -10000 0 -0.36 1 1
FGFR/FGF2/Syndecan-1 -0.12 0.1 0.29 3 -0.32 45 48
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 -0.091 0.1 0.23 3 -0.3 41 44
Syndecan-1/Syntenin -0.11 0.1 0.28 2 -0.31 41 43
MAPK3 -0.11 0.094 0.26 2 -0.36 19 21
HGF/MET 0.029 0.059 -10000 0 -0.28 20 20
TGFB1/TGF beta receptor Type II 0.026 0.019 -10000 0 -0.44 1 1
BSG 0.027 0.016 -10000 0 -0.36 1 1
keratinocyte migration -0.091 0.1 0.22 3 -0.3 41 44
Syndecan-1/RANTES -0.12 0.11 0.26 3 -0.32 53 56
Syndecan-1/CD147 -0.11 0.1 0.35 1 -0.3 45 46
Syndecan-1/Syntenin/PIP2 -0.1 0.097 0.34 1 -0.3 41 42
LAMA5 0.017 0.036 0.36 3 -0.4 2 5
positive regulation of cell-cell adhesion -0.1 0.095 0.33 1 -0.3 41 42
MMP7 -0.42 0.11 0.36 3 -0.45 582 585
HGF 0.017 0.061 -10000 0 -0.37 15 15
Syndecan-1/CASK -0.12 0.096 0.28 2 -0.31 46 48
Syndecan-1/HGF/MET -0.11 0.1 0.35 1 -0.36 30 31
regulation of cell adhesion -0.11 0.091 0.25 2 -0.35 18 20
HPSE 0.023 0.038 -10000 0 -0.36 6 6
positive regulation of cell migration -0.12 0.1 0.29 3 -0.32 45 48
SDC1 -0.12 0.1 0.29 3 -0.32 45 48
Syndecan-1/Collagen -0.12 0.1 0.29 3 -0.32 45 48
PPIB 0.026 0.006 -10000 0 -10000 0 0
MET 0.022 0.047 -10000 0 -0.44 6 6
PRKACA 0.027 0.003 -10000 0 -10000 0 0
MMP9 0 0.12 0.36 15 -0.44 32 47
MAPK1 -0.11 0.093 0.26 2 -0.35 20 22
homophilic cell adhesion -0.12 0.1 0.29 3 -0.32 46 49
MMP1 -0.28 0.23 0.36 2 -0.44 396 398
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.008 0.17 0.25 85 -0.26 135 220
SMAD6-7/SMURF1 0.039 0.032 -10000 0 -0.23 3 3
NOG 0.014 0.033 -10000 0 -0.44 2 2
SMAD9 -0.049 0.18 -10000 0 -0.55 64 64
SMAD4 0.02 0.013 -10000 0 -10000 0 0
SMAD5 -0.033 0.12 -10000 0 -0.39 38 38
BMP7/USAG1 -0.048 0.2 0.26 76 -0.33 169 245
SMAD5/SKI -0.036 0.13 0.21 2 -0.39 44 46
SMAD1 0.011 0.05 -10000 0 -0.39 4 4
BMP2 0.007 0.075 -10000 0 -0.36 24 24
SMAD1/SMAD1/SMAD4 0.02 0.06 -10000 0 -0.36 6 6
BMPR1A 0.026 0.006 -10000 0 -10000 0 0
BMPR1B -0.013 0.12 -10000 0 -0.42 47 47
BMPR1A-1B/BAMBI 0.011 0.11 0.25 1 -0.26 78 79
AHSG -0.041 0.15 0.36 2 -0.44 73 75
CER1 -0.012 0.072 0.36 2 -0.44 14 16
BMP2-4/CER1 0.003 0.1 0.25 1 -0.26 70 71
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.04 0.13 -10000 0 -0.33 58 58
BMP2-4 (homodimer) -0.002 0.1 -10000 0 -0.3 61 61
RGMB 0.027 0.006 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.032 0.093 -10000 0 -0.25 36 36
RGMA -0.052 0.16 -10000 0 -0.36 124 124
SMURF1 0.027 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.041 0.12 -10000 0 -0.32 62 62
BMP2-4/USAG1 -0.027 0.13 -10000 0 -0.25 137 137
SMAD6/SMURF1/SMAD5 -0.037 0.13 0.2 1 -0.39 43 44
SOSTDC1 -0.041 0.14 -10000 0 -0.36 102 102
BMP7/BMPR2/BMPR1A-1B -0.007 0.17 0.25 90 -0.26 145 235
SKI 0.026 0.006 -10000 0 -10000 0 0
BMP6 (homodimer) 0.013 0.074 -10000 0 -0.36 23 23
HFE2 -0.008 0.031 -10000 0 -0.44 2 2
ZFYVE16 0.026 0.023 -10000 0 -0.36 2 2
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
BMP2-4/CHRD 0.013 0.094 -10000 0 -0.26 60 60
SMAD5/SMAD5/SMAD4 -0.033 0.13 0.21 1 -0.38 43 44
MAPK1 0.026 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.028 0.11 -10000 0 -0.31 43 43
BMP7 (homodimer) -0.025 0.25 0.36 102 -0.44 132 234
NUP214 0.027 0.004 -10000 0 -10000 0 0
BMP6/FETUA -0.014 0.13 0.26 1 -0.31 91 92
SMAD1/SKI 0.016 0.07 -10000 0 -0.43 7 7
SMAD6 0.025 0.027 -10000 0 -0.44 2 2
CTDSP2 0.028 0.002 -10000 0 -10000 0 0
BMP2-4/FETUA -0.02 0.13 0.25 1 -0.28 116 117
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.006 0.09 -10000 0 -0.39 30 30
BMPR2 (homodimer) 0.027 0.016 -10000 0 -0.36 1 1
GADD34/PP1CA 0.052 0.02 -10000 0 -0.21 2 2
BMPR1A-1B (homodimer) 0.012 0.091 -10000 0 -0.3 47 47
CHRDL1 -0.18 0.19 -10000 0 -0.36 329 329
ENDOFIN/SMAD1 0.016 0.071 -10000 0 -0.43 7 7
SMAD6-7/SMURF1/SMAD1 0.031 0.072 -10000 0 -0.39 7 7
SMAD6/SMURF1 0.026 0.006 -10000 0 -10000 0 0
BAMBI 0.001 0.11 0.36 1 -0.44 35 36
SMURF2 0.025 0.025 -10000 0 -0.4 2 2
BMP2-4/CHRDL1 -0.1 0.15 -10000 0 -0.24 314 314
BMP2-4/GREM1 -0.001 0.11 -10000 0 -0.25 86 86
SMAD7 0.02 0.02 -10000 0 -0.36 1 1
SMAD8A/SMAD8A/SMAD4 -0.045 0.18 -10000 0 -0.5 75 75
SMAD1/SMAD6 0.014 0.072 -10000 0 -0.44 7 7
TAK1/SMAD6 0.039 0.01 -10000 0 -10000 0 0
BMP7 -0.025 0.25 0.36 102 -0.44 132 234
BMP6 0.013 0.074 -10000 0 -0.36 23 23
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.048 0.13 -10000 0 -0.36 66 66
PPM1A 0.026 0.007 -10000 0 -10000 0 0
SMAD1/SMURF2 0.015 0.073 -10000 0 -0.41 9 9
SMAD7/SMURF1 0.029 0.022 -10000 0 -0.25 1 1
CTDSPL 0.028 0.003 -10000 0 -10000 0 0
PPP1CA 0.027 0.004 -10000 0 -10000 0 0
XIAP 0.028 0.002 -10000 0 -10000 0 0
CTDSP1 0.028 0.001 -10000 0 -10000 0 0
PPP1R15A 0.027 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.054 0.14 -10000 0 -0.37 73 73
CHRD 0.027 0.016 -10000 0 -0.36 1 1
BMPR2 0.027 0.016 -10000 0 -0.36 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.047 0.12 -10000 0 -0.35 59 59
BMP4 -0.005 0.12 -10000 0 -0.44 41 41
FST 0.012 0.075 -10000 0 -0.37 23 23
BMP2-4/NOG 0.011 0.095 -10000 0 -0.26 63 63
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.004 0.16 0.25 78 -0.25 131 209
Signaling events mediated by the Hedgehog family

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
TGFB2 0.014 0.099 -10000 0 -0.47 14 14
IHH 0.021 0.077 -10000 0 -0.42 16 16
SHH Np/Cholesterol/GAS1 -0.054 0.13 0.18 4 -0.25 180 184
LRPAP1 0.027 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.054 0.13 0.24 180 -0.18 4 184
SMO/beta Arrestin2 0.018 0.089 -10000 0 -0.44 9 9
SMO 0.004 0.083 -10000 0 -0.46 9 9
AKT1 0 0.11 -10000 0 -0.35 39 39
ARRB2 0.023 0.01 -10000 0 -10000 0 0
BOC 0.011 0.078 -10000 0 -0.36 26 26
ADRBK1 0.027 0.004 -10000 0 -10000 0 0
heart looping 0.006 0.083 -10000 0 -0.45 9 9
STIL -0.022 0.11 0.34 1 -0.38 10 11
DHH N/PTCH2 0.027 0.061 -10000 0 -0.26 26 26
DHH N/PTCH1 0.024 0.086 -10000 0 -0.44 8 8
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
DHH 0.011 0.073 -10000 0 -0.36 22 22
PTHLH 0.006 0.13 -10000 0 -0.73 14 14
determination of left/right symmetry 0.006 0.083 -10000 0 -0.45 9 9
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
skeletal system development 0.007 0.13 -10000 0 -0.72 14 14
IHH N/Hhip -0.022 0.13 -10000 0 -0.29 117 117
DHH N/Hhip -0.022 0.13 -10000 0 -0.27 120 120
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.006 0.083 -10000 0 -0.45 9 9
pancreas development -0.043 0.15 -10000 0 -0.36 109 109
HHAT 0.024 0.035 -10000 0 -0.36 5 5
PI3K 0.039 0.015 -10000 0 -0.25 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.035 0.14 -10000 0 -0.36 97 97
somite specification 0.006 0.083 -10000 0 -0.45 9 9
SHH Np/Cholesterol/PTCH1 -0.023 0.11 -10000 0 -0.37 12 12
SHH Np/Cholesterol/PTCH2 -0.026 0.11 0.18 5 -0.24 123 128
SHH Np/Cholesterol/Megalin -0.048 0.13 0.18 5 -0.26 158 163
SHH -0.048 0.14 0.32 6 -0.32 118 124
catabolic process 0.019 0.077 -10000 0 -0.38 13 13
SMO/Vitamin D3 -0.019 0.11 -10000 0 -0.4 13 13
SHH Np/Cholesterol/Hhip -0.059 0.13 0.18 5 -0.23 204 209
LRP2 -0.036 0.13 -10000 0 -0.44 56 56
receptor-mediated endocytosis -0.032 0.12 0.23 3 -0.41 18 21
SHH Np/Cholesterol/BOC -0.032 0.11 0.18 4 -0.24 138 142
SHH Np/Cholesterol/CDO -0.025 0.11 0.18 4 -0.24 119 123
mesenchymal cell differentiation 0.059 0.13 0.23 204 -0.18 5 209
mol:Vitamin D3 -0.017 0.12 0.36 1 -0.37 12 13
IHH N/PTCH2 0.031 0.059 -10000 0 -0.27 20 20
CDON 0.027 0.004 -10000 0 -10000 0 0
IHH N/PTCH1 0.027 0.08 -10000 0 -0.38 13 13
Megalin/LRPAP1 0.004 0.1 -10000 0 -0.32 56 56
PTCH2 0.024 0.038 -10000 0 -0.44 4 4
SHH Np/Cholesterol -0.034 0.1 -10000 0 -0.24 119 119
PTCH1 0.019 0.077 -10000 0 -0.38 13 13
HHIP -0.043 0.15 -10000 0 -0.36 109 109
Syndecan-2-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
Syndecan-2/Fibronectin 0.01 0.066 -10000 0 -0.26 34 34
EPHB2 0.024 0.033 -10000 0 -0.44 3 3
Syndecan-2/TACI -0.053 0.1 -10000 0 -0.21 192 192
LAMA1 -0.055 0.15 -10000 0 -0.36 122 122
Syndecan-2/alpha2 ITGB1 0.041 0.034 -10000 0 -0.23 1 1
HRAS 0.027 0.016 -10000 0 -0.36 1 1
Syndecan-2/CASK 0.007 0.012 -10000 0 -0.2 2 2
ITGA5 0.026 0.027 -10000 0 -0.44 2 2
BAX 0.004 0.011 -10000 0 -10000 0 0
EPB41 0.026 0.007 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.022 0.017 -10000 0 -0.18 3 3
LAMA3 0.02 0.034 -10000 0 -0.38 4 4
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 0.04 -10000 0 -0.41 5 5
Syndecan-2/MMP2 0.022 0.035 -10000 0 -0.26 8 8
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.04 0.006 -10000 0 -10000 0 0
dendrite morphogenesis 0.022 0.027 -10000 0 -0.24 5 5
Syndecan-2/GM-CSF -0.076 0.14 -10000 0 -0.26 222 222
determination of left/right symmetry 0.01 0.015 -10000 0 -0.24 2 2
Syndecan-2/PKC delta 0.025 0.017 -10000 0 -0.2 2 2
GNB2L1 0.027 0.004 -10000 0 -10000 0 0
MAPK3 -0.067 0.14 0.19 45 -0.24 218 263
MAPK1 -0.067 0.14 0.19 46 -0.24 221 267
Syndecan-2/RACK1 0.036 0.022 -10000 0 -0.17 3 3
NF1 0.027 0.005 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.01 0.015 -10000 0 -0.24 2 2
ITGA2 0.027 0.004 -10000 0 -10000 0 0
MAPK8 0.009 0.013 -10000 0 -0.2 2 2
Syndecan-2/alpha2/beta1 Integrin 0.001 0.086 -10000 0 -10000 0 0
Syndecan-2/Kininogen -0.019 0.09 -10000 0 -0.2 114 114
ITGB1 0.028 0.002 -10000 0 -10000 0 0
SRC 0.015 0.037 0.18 23 -10000 0 23
Syndecan-2/CASK/Protein 4.1 0.021 0.016 -10000 0 -0.18 2 2
extracellular matrix organization 0.024 0.02 -10000 0 -0.22 3 3
actin cytoskeleton reorganization 0.01 0.066 -10000 0 -0.26 34 34
Syndecan-2/Caveolin-2/Ras 0.036 0.03 -10000 0 -0.21 6 6
Syndecan-2/Laminin alpha3 0.019 0.023 -10000 0 -0.21 4 4
Syndecan-2/RasGAP 0.046 0.026 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.04 0.021 -10000 0 -0.32 2 2
PRKCD 0.027 0.004 -10000 0 -10000 0 0
Syndecan-2 dimer 0.022 0.027 -10000 0 -0.24 5 5
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.02 0.024 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
SDCBP 0.024 0.018 -10000 0 -0.36 1 1
TNFRSF13B -0.12 0.18 -10000 0 -0.36 214 214
RASA1 0.027 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.04 0.006 -10000 0 -10000 0 0
Syndecan-2/Synbindin 0.025 0.017 -10000 0 -0.2 2 2
TGFB1 0.027 0.019 -10000 0 -0.44 1 1
CASP3 0.033 0.058 0.19 68 -10000 0 68
FN1 0.001 0.11 -10000 0 -0.43 36 36
Syndecan-2/IL8 -0.11 0.15 -10000 0 -0.26 296 296
SDC2 0.01 0.015 -10000 0 -0.24 2 2
KNG1 -0.062 0.15 -10000 0 -0.36 128 128
Syndecan-2/Neurofibromin 0.024 0.017 -10000 0 -0.2 2 2
TRAPPC4 0.027 0.004 -10000 0 -10000 0 0
CSF2 -0.17 0.23 -10000 0 -0.45 249 249
Syndecan-2/TGFB1 0.024 0.021 -10000 0 -0.22 3 3
Syndecan-2/Syntenin/PI-4-5-P2 0.022 0.017 -10000 0 -0.18 3 3
Syndecan-2/Ezrin 0.038 0.022 -10000 0 -0.19 2 2
PRKACA 0.036 0.06 0.19 76 -0.18 2 78
angiogenesis -0.11 0.15 -10000 0 -0.26 296 296
MMP2 0.022 0.05 -10000 0 -0.41 8 8
IL8 -0.23 0.24 0.36 2 -0.44 337 339
calcineurin-NFAT signaling pathway -0.053 0.1 -10000 0 -0.21 192 192
Endothelins

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
AKT1 -0.031 0.16 0.22 2 -0.4 58 60
PTK2B 0.02 0.025 -10000 0 -0.36 2 2
mol:Ca2+ -0.01 0.23 -10000 0 -0.88 32 32
EDN1 0.019 0.12 -10000 0 -0.27 28 28
EDN3 -0.1 0.17 -10000 0 -0.36 185 185
EDN2 -0.085 0.17 -10000 0 -0.36 175 175
HRAS/GDP -0.002 0.15 0.28 16 -0.42 23 39
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.009 0.11 0.2 2 -0.38 18 20
ADCY4 -0.041 0.13 -10000 0 -0.37 50 50
ADCY5 -0.11 0.16 -10000 0 -0.38 115 115
ADCY6 -0.042 0.13 0.2 1 -0.37 51 52
ADCY7 -0.042 0.13 0.2 1 -0.37 50 51
ADCY1 -0.044 0.13 0.38 1 -0.38 48 49
ADCY2 -0.066 0.16 0.2 1 -0.39 76 77
ADCY3 -0.042 0.13 0.2 1 -0.37 51 52
ADCY8 -0.044 0.12 0.22 1 -0.37 42 43
ADCY9 -0.043 0.13 0.2 1 -0.37 50 51
arachidonic acid secretion -0.025 0.16 0.3 9 -0.46 33 42
ETB receptor/Endothelin-1/Gq/GTP 0.007 0.072 -10000 0 -0.34 12 12
GNAO1 -0.12 0.19 -10000 0 -0.36 224 224
HRAS 0.027 0.016 -10000 0 -0.36 1 1
ETA receptor/Endothelin-1/G12/GTP 0.061 0.2 0.3 5 -0.36 55 60
ETA receptor/Endothelin-1/Gs/GTP 0.033 0.19 0.29 3 -0.38 54 57
mol:GTP 0.001 0.004 -10000 0 -10000 0 0
COL3A1 -0.035 0.18 0.23 1 -0.45 57 58
EDNRB 0.009 0.063 -10000 0 -0.36 15 15
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.041 0.19 0.25 2 -0.48 71 73
CYSLTR1 -0.07 0.23 -10000 0 -0.52 112 112
SLC9A1 -0.008 0.1 -10000 0 -0.25 56 56
mol:GDP -0.013 0.15 0.28 16 -0.43 28 44
SLC9A3 -0.19 0.31 -10000 0 -0.6 152 152
RAF1 -0.016 0.13 0.31 8 -0.48 14 22
JUN 0.009 0.16 -10000 0 -0.66 10 10
JAK2 -0.031 0.16 0.22 2 -0.39 62 64
mol:IP3 0.02 0.11 0.21 9 -0.48 9 18
ETA receptor/Endothelin-1 0.042 0.25 0.34 5 -0.43 72 77
PLCB1 0.024 0.026 0.36 3 -10000 0 3
PLCB2 0.026 0.008 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.079 0.16 -10000 0 -0.28 194 194
FOS -0.016 0.16 0.38 3 -0.83 13 16
Gai/GDP -0.22 0.35 -10000 0 -0.66 229 229
CRK 0.024 0.01 -10000 0 -10000 0 0
mol:Ca ++ -0.009 0.15 0.23 9 -0.41 40 49
BCAR1 0.027 0.016 -10000 0 -0.36 1 1
PRKCB1 0.017 0.1 0.22 10 -0.44 10 20
GNAQ 0.026 0.025 -10000 0 -0.36 2 2
GNAZ 0.023 0.035 -10000 0 -0.36 5 5
GNAL 0.008 0.072 -10000 0 -0.36 22 22
Gs family/GDP -0.015 0.14 0.26 12 -0.44 22 34
ETA receptor/Endothelin-1/Gq/GTP 0.006 0.12 0.25 1 -0.41 14 15
MAPK14 0.008 0.074 0.21 1 -0.43 7 8
TRPC6 -0.014 0.24 -10000 0 -0.94 32 32
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.015 0.067 -10000 0 -0.36 19 19
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.01 0.078 -10000 0 -0.4 9 9
ETB receptor/Endothelin-2 -0.037 0.12 -10000 0 -0.26 138 138
ETB receptor/Endothelin-3 -0.065 0.13 -10000 0 -0.26 173 173
ETB receptor/Endothelin-1 0.021 0.099 -10000 0 -0.32 15 15
MAPK3 -0.013 0.14 0.36 5 -0.68 13 18
MAPK1 -0.019 0.16 0.37 4 -0.73 15 19
Rac1/GDP -0.007 0.14 0.3 8 -0.44 20 28
cAMP biosynthetic process -0.088 0.15 0.24 1 -0.39 78 79
MAPK8 0.006 0.18 0.34 1 -0.61 32 33
SRC 0.017 0.014 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.046 0.13 -10000 0 -0.33 61 61
p130Cas/CRK/Src/PYK2 -0.013 0.18 0.32 21 -0.56 30 51
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.007 0.14 0.3 8 -0.42 23 31
COL1A2 -0.002 0.17 -10000 0 -0.42 44 44
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.075 0.18 -10000 0 -0.3 199 199
mol:DAG 0.019 0.11 0.21 9 -0.48 9 18
MAP2K2 -0.017 0.13 0.33 7 -0.53 15 22
MAP2K1 -0.015 0.13 0.3 8 -0.53 15 23
EDNRA -0.013 0.17 -10000 0 -0.39 68 68
positive regulation of muscle contraction -0.012 0.15 0.25 28 -0.38 39 67
Gq family/GDP -0.005 0.13 -10000 0 -0.53 10 10
HRAS/GTP -0.017 0.13 0.29 9 -0.42 21 30
PRKCH 0.015 0.1 0.2 9 -0.48 8 17
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCA 0.017 0.11 0.22 13 -0.51 7 20
PRKCB -0.018 0.14 0.21 10 -0.38 41 51
PRKCE 0.017 0.1 0.21 10 -0.48 8 18
PRKCD 0.015 0.1 0.2 9 -0.49 8 17
PRKCG -0.053 0.15 0.23 13 -0.39 38 51
regulation of vascular smooth muscle contraction -0.021 0.18 0.42 3 -0.97 13 16
PRKCQ 0.015 0.11 0.22 11 -0.5 9 20
PLA2G4A -0.029 0.17 0.31 9 -0.5 33 42
GNA14 0.024 0.037 -10000 0 -0.36 5 5
GNA15 0.022 0.047 -10000 0 -0.44 6 6
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA11 0.024 0.033 -10000 0 -0.36 4 4
Rac1/GTP 0.06 0.2 0.3 5 -0.38 45 50
MMP1 -0.2 0.18 0.27 2 -0.35 311 313
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.035 0.051 -10000 0 -0.21 23 23
RGS9BP 0.02 0.038 0.36 1 -0.44 3 4
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 -0.01 0.032 0.36 1 -0.44 2 3
mol:Na + -0.052 0.12 0.23 6 -0.23 192 198
mol:ADP -0.013 0.035 0.27 1 -0.38 4 5
GNAT2 0.013 0.068 -10000 0 -0.44 13 13
RGS9-1/Gbeta5/R9AP 0.009 0.097 0.25 1 -0.21 95 96
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.022 0.044 -10000 0 -0.27 13 13
GRK7 0.009 0.043 -10000 0 -0.44 4 4
CNGB3 -0.017 0.099 0.36 8 -0.44 25 33
Cone Metarhodopsin II/X-Arrestin 0.013 0.023 -10000 0 -0.31 3 3
mol:Ca2+ -0.069 0.14 0.18 51 -0.23 216 267
Cone PDE6 0.022 0.094 0.25 1 -0.24 4 5
Cone Metarhodopsin II 0.02 0.031 0.22 1 -0.3 4 5
Na + (4 Units) -0.057 0.14 0.22 8 -0.23 219 227
GNAT2/GDP 0.014 0.096 0.24 1 -0.21 36 37
GNB5 0.026 0.006 -10000 0 -10000 0 0
mol:GMP (4 units) -0.018 0.039 0.18 5 -0.25 13 18
Cone Transducin 0.038 0.054 -10000 0 -0.23 23 23
SLC24A2 -0.027 0.13 0.36 5 -0.44 52 57
GNB3/GNGT2 0.034 0.042 -10000 0 -0.27 11 11
GNB3 0.024 0.037 -10000 0 -0.42 4 4
GNAT2/GTP 0.012 0.048 -10000 0 -0.31 13 13
CNGA3 -0.11 0.18 -10000 0 -0.36 199 199
ARR3 -0.008 0.037 -10000 0 -0.44 3 3
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel -0.052 0.12 0.23 6 -0.23 192 198
mol:Pi 0.009 0.096 0.25 1 -0.21 95 96
Cone CNG Channel -0.037 0.12 0.21 1 -0.27 39 40
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + -0.027 0.13 0.36 5 -0.44 52 57
RGS9 -0.033 0.14 -10000 0 -0.36 93 93
PDE6C -0.005 0.02 -10000 0 -10000 0 0
GNGT2 0.023 0.041 -10000 0 -0.36 7 7
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H -0.015 0.021 -10000 0 -0.44 1 1
LPA receptor mediated events

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
GNB1/GNG2 0.01 0.098 -10000 0 -0.34 13 13
NF kappa B1 p50/RelA/I kappa B alpha -0.004 0.09 0.31 2 -0.36 3 5
AP1 -0.031 0.085 -10000 0 -0.33 11 11
mol:PIP3 -0.027 0.073 -10000 0 -0.3 11 11
AKT1 0.005 0.076 0.24 6 -0.37 4 10
PTK2B -0.051 0.11 0.2 2 -0.31 50 52
RHOA 0.008 0.065 0.24 7 -0.33 12 19
PIK3CB 0.028 0.014 0.36 1 -10000 0 1
mol:Ca2+ -0.001 0.056 0.2 5 -0.33 2 7
MAGI3 0.026 0.016 -10000 0 -0.36 1 1
RELA 0.027 0.004 -10000 0 -10000 0 0
apoptosis -0.028 0.097 -10000 0 -0.22 111 111
HRAS/GDP 0.02 0.011 -10000 0 -0.25 1 1
positive regulation of microtubule depolymerization -0.081 0.12 0.23 5 -0.32 75 80
NF kappa B1 p50/RelA -0.032 0.082 -10000 0 -0.35 9 9
endothelial cell migration -0.014 0.088 -10000 0 -0.44 8 8
ADCY4 -0.084 0.17 0.24 1 -0.42 100 101
ADCY5 -0.17 0.23 0.24 1 -0.45 201 202
ADCY6 -0.08 0.16 0.24 1 -0.44 87 88
ADCY7 -0.079 0.16 0.24 1 -0.44 85 86
ADCY1 -0.08 0.16 -10000 0 -0.43 87 87
ADCY2 -0.11 0.2 0.24 1 -0.46 131 132
ADCY3 -0.08 0.16 0.24 1 -0.44 87 88
ADCY8 -0.077 0.16 0.24 1 -0.43 82 83
ADCY9 -0.08 0.16 0.24 1 -0.43 88 89
GSK3B -0.05 0.11 0.19 3 -0.36 29 32
arachidonic acid secretion -0.099 0.18 -10000 0 -0.43 100 100
GNG2 0.011 0.074 -10000 0 -0.36 23 23
TRIP6 0.012 0.019 -10000 0 -0.3 1 1
GNAO1 -0.089 0.14 -10000 0 -0.25 240 240
HRAS 0.027 0.016 -10000 0 -0.36 1 1
NFKBIA -0.021 0.088 0.27 4 -0.32 12 16
GAB1 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.089 0.32 -10000 0 -0.84 94 94
JUN 0.027 0.004 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.035 0.021 -10000 0 -0.24 2 2
TIAM1 -0.12 0.37 -10000 0 -0.99 94 94
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
mol:IP3 -0.01 0.052 0.21 5 -0.34 2 7
PLCB3 0.016 0.025 0.18 8 -0.21 2 10
FOS 0.022 0.039 -10000 0 -0.36 6 6
positive regulation of mitosis -0.099 0.18 -10000 0 -0.43 100 100
LPA/LPA1-2-3 0.001 0.1 -10000 0 -0.22 65 65
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade -0.001 0.001 -10000 0 -10000 0 0
BCAR1 0.027 0.016 -10000 0 -0.36 1 1
stress fiber formation -0.028 0.093 0.22 3 -0.28 30 33
GNAZ -0.013 0.08 -10000 0 -0.21 84 84
EGFR/PI3K-beta/Gab1 -0.012 0.082 -10000 0 -0.31 11 11
positive regulation of dendritic cell cytokine production -0.001 0.1 -10000 0 -0.22 65 65
LPA/LPA2/MAGI-3 0.036 0.021 -10000 0 -0.23 2 2
ARHGEF1 0.008 0.089 0.2 53 -0.33 2 55
GNAI2 -0.01 0.077 -10000 0 -0.21 75 75
GNAI3 -0.012 0.078 -10000 0 -0.21 85 85
GNAI1 -0.018 0.092 -10000 0 -0.23 89 89
LPA/LPA3 -0.001 0.072 -10000 0 -0.26 44 44
LPA/LPA2 0.02 0.018 -10000 0 -0.31 1 1
LPA/LPA1 -0.012 0.095 -10000 0 -0.24 86 86
HB-EGF/EGFR 0.004 0.072 0.2 14 -0.26 34 48
HBEGF -0.004 0.086 0.27 15 -0.31 34 49
mol:DAG -0.01 0.052 0.21 5 -0.34 2 7
cAMP biosynthetic process -0.11 0.18 0.27 5 -0.44 100 105
NFKB1 0.027 0.005 -10000 0 -10000 0 0
SRC 0.017 0.014 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
LYN -0.003 0.091 0.28 7 -0.35 6 13
GNAQ -0.001 0.058 -10000 0 -0.2 39 39
LPAR2 0.026 0.019 -10000 0 -0.44 1 1
LPAR3 -0.009 0.1 -10000 0 -0.37 44 44
LPAR1 -0.022 0.13 -10000 0 -0.36 80 80
IL8 -0.085 0.14 0.32 2 -0.38 17 19
PTK2 -0.021 0.079 0.18 4 -0.29 14 18
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
CASP3 -0.028 0.098 -10000 0 -0.22 111 111
EGFR 0.023 0.023 -10000 0 -0.36 2 2
PLCG1 -0.008 0.053 -10000 0 -0.2 26 26
PLD2 -0.022 0.081 0.19 2 -0.3 15 17
G12/G13 0.02 0.082 -10000 0 -0.19 66 66
PI3K-beta -0.004 0.073 -10000 0 -0.38 6 6
cell migration -0.017 0.11 -10000 0 -0.25 86 86
SLC9A3R2 0.026 0.016 -10000 0 -0.36 1 1
PXN -0.028 0.095 0.22 3 -0.29 30 33
HRAS/GTP -0.1 0.18 -10000 0 -0.44 99 99
RAC1 0.025 0.008 -10000 0 -10000 0 0
MMP9 0 0.12 0.36 15 -0.44 32 47
PRKCE 0.027 0.003 -10000 0 -10000 0 0
PRKCD -0.003 0.058 0.24 7 -0.4 1 8
Gi(beta/gamma) -0.085 0.17 -10000 0 -0.41 100 100
mol:LPA 0.001 0.014 -10000 0 -0.14 1 1
TRIP6/p130 Cas/FAK1/Paxillin 0.01 0.1 0.23 1 -0.36 10 11
MAPKKK cascade -0.099 0.18 -10000 0 -0.43 100 100
contractile ring contraction involved in cytokinesis 0.01 0.065 0.24 7 -0.33 12 19
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.002 0.06 -10000 0 -0.2 50 50
GNA15 -0.002 0.059 -10000 0 -0.19 51 51
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
MAPT -0.083 0.12 0.24 4 -0.33 75 79
GNA11 -0.001 0.058 -10000 0 -0.2 49 49
Rac1/GTP -0.095 0.34 -10000 0 -0.89 94 94
MMP2 -0.014 0.089 -10000 0 -0.44 8 8
JNK signaling in the CD4+ TCR pathway

Figure S22.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S22.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.034 0.096 -10000 0 -0.35 17 17
MAP4K1 -0.007 0.11 -10000 0 -0.36 53 53
MAP3K8 0.028 0.003 -10000 0 -10000 0 0
PRKCB -0.062 0.16 -10000 0 -0.36 141 141
DBNL 0.025 0.008 -10000 0 -10000 0 0
CRKL 0.027 0.006 -10000 0 -10000 0 0
MAP3K1 -0.006 0.089 -10000 0 -0.32 30 30
JUN -0.13 0.27 -10000 0 -0.58 155 155
MAP3K7 -0.006 0.089 -10000 0 -0.32 31 31
GRAP2 0.013 0.069 -10000 0 -0.36 20 20
CRK 0.023 0.01 -10000 0 -10000 0 0
MAP2K4 -0.014 0.1 0.25 3 -0.36 35 38
LAT 0.025 0.035 -10000 0 -0.4 4 4
LCP2 0.023 0.038 -10000 0 -0.36 6 6
MAPK8 -0.13 0.29 -10000 0 -0.61 156 156
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.001 0.096 -10000 0 -0.34 32 32
LAT/GRAP2/SLP76/HPK1/HIP-55 0.041 0.091 -10000 0 -0.35 11 11
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.008 0.14 -9999 0 -0.52 26 26
MAP3K8 0.028 0.003 -9999 0 -10000 0 0
FOS -0.022 0.14 -9999 0 -0.51 28 28
PRKCA 0.027 0.007 -9999 0 -10000 0 0
PTPN7 0.017 0.066 -9999 0 -0.41 14 14
HRAS 0.027 0.016 -9999 0 -0.36 1 1
PRKCB -0.062 0.16 -9999 0 -0.36 141 141
NRAS 0.026 0.023 -9999 0 -0.36 2 2
RAS family/GTP 0.049 0.024 -9999 0 -0.19 4 4
MAPK3 -0.002 0.097 -9999 0 -0.6 9 9
MAP2K1 -0.058 0.16 -9999 0 -0.34 134 134
ELK1 0.027 0.007 -9999 0 -10000 0 0
BRAF -0.052 0.14 -9999 0 -0.33 130 130
mol:GTP 0 0 -9999 0 -0.004 10 10
MAPK1 -0.022 0.15 -9999 0 -0.58 32 32
RAF1 -0.056 0.15 -9999 0 -0.33 135 135
KRAS 0.026 0.016 -9999 0 -0.36 1 1
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 0.15 0.27 9 -0.48 39 48
FYN -0.027 0.18 0.24 5 -0.54 52 57
LAT/GRAP2/SLP76 -0.006 0.16 0.19 2 -0.5 44 46
IKBKB 0.024 0.009 -10000 0 -10000 0 0
AKT1 -0.022 0.13 0.19 6 -0.4 53 59
B2M 0.025 0.018 -10000 0 -0.36 1 1
IKBKG -0.002 0.045 0.089 28 -0.14 22 50
MAP3K8 0.028 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.017 0.032 0.088 5 -0.11 52 57
integrin-mediated signaling pathway 0.033 0.025 -10000 0 -0.2 6 6
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.035 0.19 0.22 4 -0.57 52 56
TRPV6 -0.001 0.25 1.2 22 -0.44 51 73
CD28 0.012 0.078 -10000 0 -0.36 25 25
SHC1 -0.027 0.18 0.28 9 -0.54 49 58
receptor internalization -0.034 0.2 -10000 0 -0.57 57 57
PRF1 -0.032 0.22 -10000 0 -0.78 37 37
KRAS 0.026 0.016 -10000 0 -0.36 1 1
GRB2 0.027 0.004 -10000 0 -10000 0 0
COT/AKT1 -0.005 0.11 0.19 6 -0.32 48 54
LAT -0.03 0.18 0.19 4 -0.54 50 54
EntrezGene:6955 0 0.002 -10000 0 -10000 0 0
CD3D 0.017 0.064 -10000 0 -0.37 16 16
CD3E 0.014 0.072 -10000 0 -0.37 21 21
CD3G -0.003 0.1 -10000 0 -0.36 47 47
RASGRP2 -0.01 0.055 -10000 0 -0.17 61 61
RASGRP1 -0.001 0.14 0.23 6 -0.41 47 53
HLA-A 0 0.003 -10000 0 -10000 0 0
RASSF5 0.023 0.038 -10000 0 -0.36 6 6
RAP1A/GTP/RAPL 0.033 0.025 -10000 0 -0.2 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.018 0.058 0.11 46 -0.13 29 75
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.019 0.064 -10000 0 -0.22 39 39
PRKCA 0.024 0.094 0.15 36 -0.26 32 68
GRAP2 0.013 0.069 -10000 0 -0.36 20 20
mol:IP3 -0.008 0.12 0.2 49 -0.4 36 85
EntrezGene:6957 0 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.026 0.16 -10000 0 -0.52 49 49
ORAI1 -0.013 0.2 0.36 5 -0.97 22 27
CSK -0.026 0.18 0.22 3 -0.54 49 52
B7 family/CD28 -0.002 0.2 -10000 0 -0.59 45 45
CHUK 0.027 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.034 0.2 0.19 1 -0.58 56 57
PTPN6 -0.03 0.18 0.21 6 -0.54 50 56
VAV1 -0.035 0.18 0.23 4 -0.55 54 58
Monovalent TCR/CD3 -0.014 0.13 -10000 0 -0.36 58 58
CBL 0.027 0.004 -10000 0 -10000 0 0
LCK -0.03 0.18 0.22 4 -0.53 54 58
PAG1 -0.018 0.18 0.19 47 -0.54 49 96
RAP1A 0.027 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.033 0.2 0.19 1 -0.57 57 58
CD80 0.025 0.03 -10000 0 -0.39 3 3
CD86 0.019 0.057 -10000 0 -0.36 13 13
PDK1/CARD11/BCL10/MALT1 -0.013 0.08 -10000 0 -0.26 40 40
HRAS 0.027 0.016 -10000 0 -0.36 1 1
GO:0035030 -0.027 0.15 0.16 1 -0.48 47 48
CD8A -0.001 0.1 -10000 0 -0.37 45 45
CD8B 0.018 0.062 -10000 0 -0.37 15 15
PTPRC -0.004 0.1 -10000 0 -0.36 48 48
PDK1/PKC theta -0.018 0.16 0.23 8 -0.49 46 54
CSK/PAG1 -0.015 0.17 0.2 50 -0.56 41 91
SOS1 0.028 0.002 -10000 0 -10000 0 0
peptide-MHC class I 0.018 0.015 -10000 0 -0.25 1 1
GRAP2/SLP76 -0.007 0.18 -10000 0 -0.56 47 47
STIM1 0.007 0.11 1.2 4 -0.93 1 5
RAS family/GTP 0.022 0.068 0.14 20 -0.18 27 47
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.037 0.21 -10000 0 -0.61 57 57
mol:DAG -0.022 0.098 0.12 1 -0.35 38 39
RAP1A/GDP 0.011 0.028 0.077 14 -0.064 12 26
PLCG1 0.016 0.014 -10000 0 -10000 0 0
CD247 0.018 0.059 -10000 0 -0.37 14 14
cytotoxic T cell degranulation -0.029 0.21 -10000 0 -0.7 41 41
RAP1A/GTP -0.004 0.021 -10000 0 -0.063 60 60
mol:PI-3-4-5-P3 -0.026 0.16 0.2 5 -0.47 52 57
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.01 0.15 0.22 43 -0.51 36 79
NRAS 0.026 0.023 -10000 0 -0.36 2 2
ZAP70 0.019 0.06 -10000 0 -0.37 14 14
GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.015 0.16 0.21 1 -0.48 47 48
MALT1 0.02 0.02 -10000 0 -0.36 1 1
TRAF6 0.027 0.003 -10000 0 -10000 0 0
CD8 heterodimer 0.014 0.096 -10000 0 -0.29 52 52
CARD11 0.004 0.099 0.36 2 -0.41 31 33
PRKCB 0.001 0.12 0.13 62 -0.28 57 119
PRKCE 0.024 0.096 0.13 169 -0.26 32 201
PRKCQ -0.021 0.18 0.24 4 -0.54 50 54
LCP2 0.023 0.038 -10000 0 -0.36 6 6
BCL10 0.026 0.016 -10000 0 -0.36 1 1
regulation of survival gene product expression -0.017 0.12 0.19 6 -0.34 52 58
IKK complex 0.021 0.064 0.11 152 -0.11 30 182
RAS family/GDP -0.002 0.011 -10000 0 -0.06 2 2
MAP3K14 -0.007 0.086 0.16 6 -0.26 44 50
PDPK1 -0.018 0.12 0.19 9 -0.39 47 56
TCR/CD3/MHC I/CD8/Fyn -0.037 0.2 -10000 0 -0.6 55 55
IGF1 pathway

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
NCK2 0.028 0.002 -10000 0 -10000 0 0
PTK2 0.023 0.01 -10000 0 -10000 0 0
CRKL -0.028 0.083 -10000 0 -0.19 129 129
GRB2/SOS1/SHC 0.054 0.012 -10000 0 -10000 0 0
HRAS 0.027 0.016 -10000 0 -0.36 1 1
IRS1/Crk -0.023 0.087 -10000 0 -0.18 133 133
IGF-1R heterotetramer/IGF1/PTP1B -0.006 0.085 -10000 0 -0.2 88 88
AKT1 -0.043 0.068 0.27 1 -0.3 1 2
BAD -0.044 0.065 0.26 1 -0.28 1 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.022 0.076 -10000 0 -0.19 106 106
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.018 0.093 -10000 0 -0.19 141 141
RAF1 -0.028 0.088 0.27 1 -0.46 9 10
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.007 0.1 -10000 0 -10000 0 0
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.019 0.1 -10000 0 -0.2 141 141
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
RPS6KB1 -0.044 0.068 0.27 1 -0.32 1 2
GNB2L1 0.027 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.011 0.082 0.25 4 -0.39 4 8
PXN 0.028 0.002 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
HRAS/GTP -0.012 0.084 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.023 0.1 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.008 0.038 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.005 0.1 -10000 0 -0.19 140 140
Crk/p130 Cas/Paxillin 0.009 0.098 -10000 0 -10000 0 0
IGF1R 0.008 0.038 -10000 0 -10000 0 0
IGF1 -0.065 0.17 -10000 0 -0.38 141 141
IRS2/Crk -0.015 0.073 -10000 0 -0.18 78 78
PI3K 0.006 0.1 -10000 0 -0.34 1 1
apoptosis 0.035 0.057 0.25 1 -0.24 1 2
HRAS/GDP 0.02 0.011 -10000 0 -0.25 1 1
PRKCD -0.055 0.13 -10000 0 -0.29 134 134
RAF1/14-3-3 E -0.011 0.082 0.26 2 -0.39 10 12
BAD/14-3-3 -0.037 0.06 0.25 1 -0.27 1 2
PRKCZ -0.043 0.068 0.2 3 -0.32 1 4
Crk/p130 Cas/Paxillin/FAK1 -0.007 0.074 -10000 0 -10000 0 0
PTPN1 0.016 0.014 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.053 0.14 -10000 0 -0.3 134 134
BCAR1 0.027 0.016 -10000 0 -0.36 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.011 0.097 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.028 0.002 -10000 0 -10000 0 0
IRS1/NCK2 -0.018 0.094 -10000 0 -0.19 140 140
GRB10 0.025 0.008 -10000 0 -10000 0 0
PTPN11 -0.031 0.086 -10000 0 -0.19 141 141
IRS1 -0.034 0.093 -10000 0 -0.2 141 141
IRS2 -0.022 0.075 -10000 0 -0.19 103 103
IGF-1R heterotetramer/IGF1 -0.033 0.13 -10000 0 -0.27 141 141
GRB2 0.027 0.004 -10000 0 -10000 0 0
PDPK1 -0.028 0.079 0.28 1 -0.33 1 2
YWHAE 0.023 0.01 -10000 0 -10000 0 0
PRKD1 -0.056 0.13 0.2 1 -0.3 133 134
SHC1 0.027 0.004 -10000 0 -10000 0 0
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.019 0.091 -10000 0 -0.27 41 41
alphaM/beta2 Integrin/GPIbA 0.013 0.085 -10000 0 -0.26 37 37
alphaM/beta2 Integrin/proMMP-9 0.003 0.1 0.25 15 -0.27 53 68
PLAUR 0.027 0.004 -10000 0 -10000 0 0
HMGB1 0.015 0.022 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.022 0.083 -10000 0 -0.26 35 35
AGER 0.018 0.033 -10000 0 -0.49 1 1
RAP1A 0.027 0.005 -10000 0 -10000 0 0
SELPLG 0.026 0.022 -10000 0 -0.36 2 2
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.021 0.094 -10000 0 -0.39 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0 0.12 0.36 15 -0.44 32 47
CYR61 0.022 0.046 -10000 0 -0.44 6 6
TLN1 0.027 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.022 0.1 -10000 0 -0.31 25 25
RHOA 0.027 0.004 -10000 0 -10000 0 0
P-selectin oligomer -0.019 0.12 -10000 0 -0.36 72 72
MYH2 -0.038 0.095 -10000 0 -0.3 32 32
MST1R 0.027 0.016 -10000 0 -0.36 1 1
leukocyte activation during inflammatory response -0.02 0.12 -10000 0 -0.26 74 74
APOB -0.046 0.14 -10000 0 -0.38 92 92
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.022 0.05 -10000 0 -0.41 8 8
JAM3 0.027 0.004 -10000 0 -10000 0 0
GP1BA 0.014 0.043 -10000 0 -0.36 7 7
alphaM/beta2 Integrin/CTGF 0.02 0.086 -10000 0 -0.26 38 38
alphaM/beta2 Integrin -0.037 0.1 -10000 0 -0.28 52 52
JAM3 homodimer 0.027 0.004 -10000 0 -10000 0 0
ICAM2 0.027 0.005 -10000 0 -10000 0 0
ICAM1 0.027 0.019 -10000 0 -0.44 1 1
phagocytosis triggered by activation of immune response cell surface activating receptor -0.037 0.1 -10000 0 -0.28 51 51
cell adhesion 0.012 0.085 -10000 0 -0.26 37 37
NFKB1 0.02 0.13 0.4 6 -0.41 16 22
THY1 0.01 0.088 -10000 0 -0.44 22 22
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
Lipoprotein(a) -0.021 0.11 -10000 0 -0.24 118 118
alphaM/beta2 Integrin/LRP/tPA 0.037 0.078 -10000 0 -0.3 12 12
IL6 -0.01 0.16 -10000 0 -0.59 12 12
ITGB2 0.012 0.055 -10000 0 -0.36 10 10
elevation of cytosolic calcium ion concentration 0.019 0.11 -10000 0 -0.27 54 54
alphaM/beta2 Integrin/JAM2/JAM3 -0.008 0.14 -10000 0 -0.36 41 41
JAM2 -0.058 0.16 -10000 0 -0.36 132 132
alphaM/beta2 Integrin/ICAM1 0.005 0.13 -10000 0 -0.26 101 101
alphaM/beta2 Integrin/uPA/Plg -0.047 0.15 -10000 0 -0.26 174 174
RhoA/GTP -0.04 0.1 -10000 0 -0.3 41 41
positive regulation of phagocytosis -0.026 0.094 0.18 1 -0.39 18 19
Ron/MSP -0.017 0.13 -10000 0 -0.32 99 99
alphaM/beta2 Integrin/uPAR/uPA 0.021 0.11 -10000 0 -0.27 54 54
alphaM/beta2 Integrin/uPAR 0.023 0.083 -10000 0 -0.26 35 35
PLAU -0.005 0.12 -10000 0 -0.44 42 42
PLAT 0.022 0.03 -10000 0 -0.39 3 3
actin filament polymerization -0.038 0.096 0.22 3 -0.28 34 37
MST1 -0.048 0.17 -10000 0 -0.44 98 98
alphaM/beta2 Integrin/lipoprotein(a) -0.017 0.12 -10000 0 -0.26 74 74
TNF 0.012 0.13 0.37 2 -0.66 7 9
RAP1B 0.028 0.003 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.002 0.11 -10000 0 -0.27 77 77
fibrinolysis -0.048 0.15 -10000 0 -0.26 175 175
HCK 0.011 0.047 -10000 0 -0.36 9 9
dendritic cell antigen processing and presentation -0.037 0.1 -10000 0 -0.28 51 51
VTN 0.006 0.082 -10000 0 -0.44 19 19
alphaM/beta2 Integrin/CYR61 0.02 0.088 -10000 0 -0.26 42 42
LPA -0.015 0.1 -10000 0 -0.45 29 29
LRP1 0.026 0.022 -10000 0 -0.36 2 2
cell migration -0.002 0.097 0.21 12 -0.3 40 52
FN1 0.001 0.11 -10000 0 -0.43 36 36
alphaM/beta2 Integrin/Thy1 0.011 0.1 -10000 0 -0.27 56 56
MPO 0.009 0.082 -10000 0 -0.44 19 19
KNG1 -0.062 0.15 -10000 0 -0.36 128 128
RAP1/GDP 0.036 0.008 -10000 0 -10000 0 0
ROCK1 -0.035 0.097 0.25 2 -0.31 24 26
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.095 0.18 0.36 1 -0.44 127 128
CTGF 0.025 0.033 -10000 0 -0.44 3 3
alphaM/beta2 Integrin/Hck 0.011 0.076 -10000 0 -0.28 27 27
ITGAM -0.002 0.092 -10000 0 -0.36 34 34
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.016 0.12 -10000 0 -0.35 30 30
HP -0.007 0.11 -10000 0 -0.44 34 34
leukocyte adhesion -0.027 0.13 -10000 0 -0.36 42 42
SELP -0.019 0.12 -10000 0 -0.36 72 72
Plasma membrane estrogen receptor signaling

Figure S27.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S27.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.027 0.085 -10000 0 -0.34 7 7
ER alpha/Gai/GDP/Gbeta gamma -0.14 0.26 -10000 0 -0.63 94 94
AKT1 -0.066 0.28 -10000 0 -0.81 73 73
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.066 0.28 -10000 0 -0.82 73 73
mol:Ca2+ 0.019 0.07 -10000 0 -0.39 7 7
IGF1R 0.027 0.006 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.014 0.071 -10000 0 -0.21 55 55
SHC1 0.027 0.004 -10000 0 -10000 0 0
apoptosis 0.062 0.26 0.76 73 -10000 0 73
RhoA/GTP 0.007 0.056 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.044 0.22 -10000 0 -0.56 59 59
regulation of stress fiber formation 0.017 0.055 0.27 2 -0.23 4 6
E2/ERA-ERB (dimer) 0.01 0.073 -10000 0 -0.21 59 59
KRAS 0.026 0.016 -10000 0 -0.36 1 1
G13/GTP 0.014 0.063 -10000 0 -0.19 54 54
pseudopodium formation -0.017 0.055 0.23 4 -0.27 2 6
E2/ER alpha (dimer)/PELP1 0.011 0.067 -10000 0 -0.2 55 55
GRB2 0.027 0.004 -10000 0 -10000 0 0
GNG2 0.011 0.074 -10000 0 -0.36 23 23
GNAO1 -0.12 0.19 -10000 0 -0.36 224 224
HRAS 0.027 0.016 -10000 0 -0.36 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.086 0.23 0.23 1 -0.61 77 78
E2/ER beta (dimer) 0.017 0.025 -10000 0 -0.25 5 5
mol:GDP -0.017 0.1 -10000 0 -0.31 57 57
mol:NADP -0.086 0.23 0.23 1 -0.61 77 78
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
mol:IP3 0.002 0.051 -10000 0 -0.4 7 7
IGF-1R heterotetramer 0.026 0.006 -10000 0 -10000 0 0
PLCB1 0.006 0.055 -10000 0 -0.41 7 7
PLCB2 0.006 0.057 -10000 0 -0.41 8 8
IGF1 -0.062 0.16 -10000 0 -0.36 141 141
mol:L-citrulline -0.086 0.23 0.23 1 -0.61 77 78
RHOA 0.027 0.004 -10000 0 -10000 0 0
Gai/GDP -0.23 0.35 -10000 0 -0.66 232 232
JNK cascade 0.017 0.025 -10000 0 -0.25 5 5
BCAR1 0.027 0.016 -10000 0 -0.36 1 1
ESR2 0.022 0.036 -10000 0 -0.36 5 5
GNAQ 0.026 0.022 -10000 0 -0.36 2 2
ESR1 -0.01 0.11 -10000 0 -0.36 55 55
Gq family/GDP/Gbeta gamma -0.004 0.14 -10000 0 -0.67 18 18
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.004 0.13 -10000 0 -0.79 8 8
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.042 0.21 -10000 0 -0.56 59 59
GNAZ 0.023 0.035 -10000 0 -0.36 5 5
E2/ER alpha (dimer) -0.005 0.077 -10000 0 -0.25 55 55
STRN 0.028 0.003 -10000 0 -10000 0 0
GNAL 0.008 0.072 -10000 0 -0.36 22 22
PELP1 0.023 0.01 -10000 0 -10000 0 0
MAPK11 0.01 0.026 -10000 0 -0.23 7 7
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.015 0.067 -10000 0 -0.36 19 19
HBEGF -0.021 0.26 0.31 128 -0.56 65 193
cAMP biosynthetic process 0 0.07 -10000 0 -0.19 57 57
SRC -0.066 0.25 0.22 1 -0.6 77 78
PI3K 0.039 0.015 -10000 0 -0.25 1 1
GNB1 0.026 0.006 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.007 0.11 -10000 0 -0.29 52 52
SOS1 0.028 0.002 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.096 0.17 -10000 0 -0.47 75 75
Gs family/GTP 0.006 0.073 -10000 0 -0.19 57 57
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.048 0.024 -10000 0 -0.19 4 4
vasodilation -0.081 0.22 0.23 1 -0.57 77 78
mol:DAG 0.002 0.051 -10000 0 -0.4 7 7
Gs family/GDP/Gbeta gamma -0.016 0.1 -10000 0 -0.31 47 47
MSN -0.018 0.058 0.24 4 -0.28 2 6
Gq family/GTP 0.013 0.062 -10000 0 -0.43 8 8
mol:PI-3-4-5-P3 -0.061 0.27 -10000 0 -0.78 73 73
NRAS 0.026 0.023 -10000 0 -0.36 2 2
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.081 0.22 0.57 77 -0.23 1 78
GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
RhoA/GDP -0.002 0.1 -10000 0 -0.3 57 57
NOS3 -0.092 0.24 0.24 1 -0.65 77 78
GNA11 0.025 0.031 -10000 0 -0.36 4 4
MAPKKK cascade -0.041 0.23 0.35 1 -0.6 71 72
E2/ER alpha (dimer)/PELP1/Src -0.044 0.23 0.27 7 -0.56 64 71
ruffle organization -0.017 0.055 0.23 4 -0.27 2 6
ROCK2 -0.017 0.063 0.25 4 -0.31 2 6
GNA14 0.024 0.035 -10000 0 -0.36 5 5
GNA15 0.023 0.046 -10000 0 -0.44 6 6
GNA13 0.027 0.005 -10000 0 -10000 0 0
MMP9 -0.023 0.27 0.37 114 -0.56 66 180
MMP2 -0.065 0.24 0.27 8 -0.58 72 80
Canonical Wnt signaling pathway

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
HDAC1 0.027 0.011 -10000 0 -10000 0 0
AES 0.027 0.009 -10000 0 -10000 0 0
FBXW11 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.038 0.02 -10000 0 -0.25 2 2
SMAD4 0.02 0.013 -10000 0 -10000 0 0
DKK2 -0.042 0.16 -10000 0 -0.44 89 89
TLE1 0.027 0.017 -10000 0 -0.35 1 1
MACF1 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.044 0.077 0.28 11 -0.31 2 13
WIF1 -0.08 0.19 0.35 1 -0.44 125 126
beta catenin/RanBP3 0.031 0.081 0.29 12 -10000 0 12
KREMEN2 -0.027 0.15 0.36 2 -0.44 72 74
DKK1 -0.076 0.19 0.36 1 -0.44 128 129
beta catenin/beta TrCP1 0.056 0.075 0.28 11 -0.32 1 12
FZD1 0.026 0.023 -10000 0 -0.36 2 2
AXIN2 -0.009 0.12 0.56 9 -10000 0 9
AXIN1 0.027 0.016 -10000 0 -0.36 1 1
RAN 0.028 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.033 0.058 -10000 0 -0.48 6 6
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.027 0.15 0.3 3 -0.5 27 30
Axin1/APC/GSK3 0.055 0.065 0.22 9 -0.29 5 14
Axin1/APC/GSK3/beta catenin/Macf1 0.025 0.07 0.25 3 -0.35 2 5
HNF1A 0.026 0.024 -10000 0 -0.36 2 2
CTBP1 0.027 0.009 -10000 0 -10000 0 0
MYC 0.097 0.21 0.56 98 -10000 0 98
RANBP3 0.027 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.029 0.14 0.25 1 -0.27 153 154
NKD1 -0.28 0.23 0.35 8 -0.44 401 409
TCF4 0.019 0.026 -10000 0 -0.36 2 2
TCF3 0.027 0.009 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.062 0.035 -10000 0 -0.24 3 3
Ran/GTP 0.02 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.013 0.09 0.31 1 -0.42 7 8
LEF1 -0.031 0.16 -10000 0 -0.45 75 75
DVL1 0.027 0.057 0.18 1 -0.37 5 6
CSNK2A1 0.023 0.011 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.021 0.1 0.34 2 -0.56 9 11
DKK1/LRP6/Kremen 2 -0.048 0.16 0.23 2 -0.29 182 184
LRP6 0.027 0.005 -10000 0 -10000 0 0
CSNK1A1 0.027 0.01 -10000 0 -10000 0 0
NLK 0.027 0.005 -10000 0 -10000 0 0
CCND1 0.003 0.049 0.55 1 -10000 0 1
WNT1 0.018 0.036 -10000 0 -0.44 3 3
GSK3A 0.028 0.004 -10000 0 -10000 0 0
GSK3B 0.028 0.002 -10000 0 -10000 0 0
FRAT1 0.026 0.005 -10000 0 -10000 0 0
PPP2R5D 0.14 0.1 0.22 344 -0.25 3 347
APC 0.008 0.067 0.22 34 -10000 0 34
WNT1/LRP6/FZD1 0.041 0.053 0.22 6 -10000 0 6
CREBBP 0.027 0.009 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A -0.008 0.073 0.26 3 -0.31 31 34
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.035 0.027 -10000 0 -0.32 3 3
STXBP1 0.022 0.05 -10000 0 -0.44 7 7
ACh/CHRNA1 -0.039 0.085 -10000 0 -0.25 52 52
RAB3GAP2/RIMS1/UNC13B 0.048 0.029 -10000 0 -0.26 4 4
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 0.009 0.042 -10000 0 -0.44 4 4
mol:ACh -0.037 0.063 0.078 50 -0.11 211 261
RAB3GAP2 0.027 0.016 -10000 0 -0.36 1 1
STX1A/SNAP25/VAMP2 -0.037 0.1 -10000 0 -0.22 40 40
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.039 0.085 -10000 0 -0.25 52 52
UNC13B 0.027 0.004 -10000 0 -10000 0 0
CHRNA1 -0.008 0.11 -10000 0 -0.36 55 55
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.045 0.095 -10000 0 -0.23 96 96
SNAP25 -0.07 0.11 0.18 1 -0.24 188 189
VAMP2 0.004 0.002 -10000 0 -10000 0 0
SYT1 -0.02 0.13 -10000 0 -0.36 75 75
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.008 0.071 0.2 3 -0.27 35 38
STX1A/SNAP25 fragment 1/VAMP2 -0.037 0.1 -10000 0 -0.22 40 40
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.033 0.1 0.17 1 -0.3 44 45
FZD6 0.024 0.01 -10000 0 -10000 0 0
WNT6 -0.011 0.11 -10000 0 -0.38 52 52
WNT4 0.013 0.072 -10000 0 -0.38 20 20
FZD3 0.021 0.035 0.36 2 -0.44 2 4
WNT5A 0.022 0.05 -10000 0 -0.44 7 7
WNT11 -0.069 0.19 -10000 0 -0.44 127 127
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.023 0.098 -10000 0 -0.35 37 37
HDAC1 0.024 0.006 -10000 0 -10000 0 0
AES 0.027 0.004 -10000 0 -10000 0 0
FBXW11 0.027 0.004 -10000 0 -10000 0 0
DTX1 0.024 0.035 -10000 0 -0.36 5 5
LRP6/FZD1 0.038 0.02 -10000 0 -0.25 2 2
TLE1 0.026 0.016 -10000 0 -0.36 1 1
AP1 -0.083 0.098 0.21 7 -0.29 57 64
NCSTN 0.027 0.004 -10000 0 -10000 0 0
ADAM10 0.026 0.006 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.041 0.079 -10000 0 -0.56 9 9
NICD/RBPSUH 0.023 0.097 -10000 0 -0.35 37 37
WIF1 -0.08 0.18 0.36 1 -0.44 125 126
NOTCH1 0.005 0.096 -10000 0 -0.37 37 37
PSENEN 0.026 0.016 -10000 0 -0.36 1 1
KREMEN2 -0.027 0.15 0.36 2 -0.44 72 74
DKK1 -0.076 0.19 0.36 1 -0.44 128 129
beta catenin/beta TrCP1 0.093 0.074 0.26 15 -0.29 1 16
APH1B 0.026 0.006 -10000 0 -10000 0 0
APH1A 0.027 0.004 -10000 0 -10000 0 0
AXIN1 -0.026 0.064 -10000 0 -0.42 7 7
CtBP/CBP/TCF1/TLE1/AES 0.019 0.025 -10000 0 -0.28 1 1
PSEN1 0.026 0.007 -10000 0 -10000 0 0
FOS 0.022 0.039 -10000 0 -0.36 6 6
JUN 0.027 0.004 -10000 0 -10000 0 0
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
CTNNB1 0.082 0.077 0.26 17 -0.3 1 18
MAPK3 0.027 0.016 -10000 0 -0.36 1 1
DKK2/LRP6/Kremen 2 -0.029 0.14 0.25 1 -0.27 153 154
HNF1A 0.026 0.022 -10000 0 -0.36 2 2
CTBP1 0.026 0.005 -10000 0 -10000 0 0
MYC 0.023 0.043 -10000 0 -10000 0 0
NKD1 -0.28 0.23 0.36 8 -0.44 401 409
FZD1 0.025 0.023 -10000 0 -0.36 2 2
NOTCH1 precursor/Deltex homolog 1 0.022 0.098 -10000 0 -0.35 37 37
apoptosis -0.083 0.098 0.21 7 -0.29 57 64
Delta 1/NOTCHprecursor 0.021 0.098 -10000 0 -0.35 37 37
DLL1 0.025 0.031 -10000 0 -0.36 4 4
PPARD 0.028 0.075 -10000 0 -0.86 4 4
Gamma Secretase 0.071 0.031 -10000 0 -10000 0 0
APC -0.05 0.12 -10000 0 -0.41 47 47
DVL1 0.001 0.081 -10000 0 -0.35 24 24
CSNK2A1 0.023 0.011 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.001 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.049 0.16 0.23 2 -0.29 182 184
LRP6 0.027 0.004 -10000 0 -10000 0 0
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
NLK 0.012 0.004 -10000 0 -10000 0 0
CCND1 0.018 0.11 -10000 0 -0.8 10 10
WNT1 0.011 0.038 -10000 0 -0.44 3 3
Axin1/APC/beta catenin 0.022 0.12 0.4 3 -0.4 22 25
DKK2 -0.042 0.16 -10000 0 -0.44 89 89
NOTCH1 precursor/DVL1 0 0.14 -10000 0 -0.48 30 30
GSK3B 0.027 0.002 -10000 0 -10000 0 0
FRAT1 0.026 0.005 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.024 0.098 -10000 0 -0.35 37 37
PPP2R5D 0.14 0.1 0.22 287 -0.27 4 291
MAPK1 0.026 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0 0.12 -10000 0 -0.25 120 120
RBPJ 0.027 0.004 -10000 0 -10000 0 0
CREBBP 0.029 0.005 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.036 0.24 0.39 3 -0.78 42 45
NCK1/PAK1/Dok-R -0.029 0.099 -10000 0 -0.39 40 40
NCK1/Dok-R 0.007 0.26 -10000 0 -0.91 41 41
PIK3CA 0.026 0.016 -10000 0 -0.36 1 1
mol:beta2-estradiol 0.004 0.053 0.25 27 -10000 0 27
RELA 0.027 0.004 -10000 0 -10000 0 0
SHC1 0.028 0.005 -10000 0 -10000 0 0
Rac/GDP 0.019 0.006 -10000 0 -10000 0 0
F2 -0.14 0.23 0.27 27 -0.46 197 224
TNIP2 0.027 0.005 -10000 0 -10000 0 0
NF kappa B/RelA 0.042 0.26 -10000 0 -0.85 42 42
FN1 0.001 0.11 -10000 0 -0.43 36 36
PLD2 -0.028 0.26 -10000 0 -0.93 42 42
PTPN11 0.028 0.002 -10000 0 -10000 0 0
GRB14 -0.005 0.1 -10000 0 -0.39 42 42
ELK1 0.009 0.25 -10000 0 -0.85 43 43
GRB7 0.035 0.049 0.36 14 -10000 0 14
PAK1 0.027 0.004 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.031 0.27 -10000 0 -0.9 42 42
CDKN1A 0.038 0.2 0.43 5 -0.6 29 34
ITGA5 0.026 0.027 -10000 0 -0.44 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.007 0.26 -10000 0 -0.91 41 41
CRK 0.023 0.01 -10000 0 -10000 0 0
mol:NO 0.05 0.2 0.4 18 -0.59 43 61
PLG -0.059 0.27 -10000 0 -0.96 43 43
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.026 0.23 -10000 0 -0.75 42 42
GRB2 0.027 0.004 -10000 0 -10000 0 0
PIK3R1 0.028 0.006 -10000 0 -10000 0 0
ANGPT2 -0.025 0.2 0.41 3 -0.6 29 32
BMX -0.063 0.28 -10000 0 -1 42 42
ANGPT1 0.007 0.25 0.34 1 -1.1 28 29
tube development 0.027 0.21 0.4 10 -0.63 35 45
ANGPT4 0.012 0.039 -10000 0 -0.44 4 4
response to hypoxia -0.003 0.017 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 0.007 0.29 -10000 0 -0.97 42 42
alpha5/beta1 Integrin 0.04 0.021 -10000 0 -0.32 2 2
FGF2 -0.001 0.099 -10000 0 -0.36 43 43
STAT5A (dimer) 0.034 0.23 0.43 1 -0.73 33 34
mol:L-citrulline 0.05 0.2 0.4 18 -0.59 43 61
AGTR1 -0.11 0.18 -10000 0 -0.36 214 214
MAPK14 -0.001 0.28 -10000 0 -0.97 43 43
Tie2/SHP2 0.019 0.2 -10000 0 -0.98 22 22
TEK -0.007 0.22 -10000 0 -1.1 22 22
RPS6KB1 0.034 0.24 0.45 4 -0.75 43 47
Angiotensin II/AT1 -0.073 0.13 -10000 0 -0.25 214 214
Tie2/Ang1/GRB2 0.018 0.28 -10000 0 -0.96 42 42
MAPK3 -0.017 0.24 -10000 0 -0.86 42 42
MAPK1 -0.018 0.24 -10000 0 -0.86 42 42
Tie2/Ang1/GRB7 0.022 0.28 -10000 0 -0.95 42 42
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.024 0.26 -10000 0 -0.94 42 42
PI3K 0.021 0.27 -10000 0 -0.89 43 43
FES -0.01 0.29 -10000 0 -0.98 43 43
Crk/Dok-R 0.003 0.26 -10000 0 -0.91 41 41
Tie2/Ang1/ABIN2 0.018 0.28 -10000 0 -0.96 42 42
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.044 0.22 0.38 4 -0.69 43 47
STAT5A 0.027 0.004 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.054 0.25 0.43 18 -0.74 41 59
Tie2/Ang2 -0.009 0.25 0.45 1 -0.87 33 34
Tie2/Ang1 -0.022 0.28 -10000 0 -1 42 42
FOXO1 0.061 0.24 0.41 19 -0.72 36 55
ELF1 0.021 0.029 -10000 0 -10000 0 0
ELF2 -0.021 0.26 -10000 0 -0.94 42 42
mol:Choline -0.026 0.25 -10000 0 -0.89 42 42
cell migration -0.014 0.06 -10000 0 -0.22 43 43
FYN 0.02 0.23 0.44 5 -0.73 34 39
DOK2 0.016 0.045 -10000 0 -0.36 8 8
negative regulation of cell cycle 0.041 0.18 0.4 11 -0.55 29 40
ETS1 0.02 0.064 -10000 0 -0.27 27 27
PXN 0.06 0.22 0.39 32 -0.62 41 73
ITGB1 0.028 0.002 -10000 0 -10000 0 0
NOS3 0.046 0.22 0.41 15 -0.67 42 57
RAC1 0.025 0.008 -10000 0 -10000 0 0
TNF 0.019 0.07 -10000 0 -0.28 29 29
MAPKKK cascade -0.026 0.25 -10000 0 -0.89 42 42
RASA1 0.027 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.02 0.28 -10000 0 -0.96 42 42
NCK1 0.028 0.003 -10000 0 -10000 0 0
vasculogenesis 0.053 0.19 0.38 23 -0.53 43 66
mol:Phosphatidic acid -0.026 0.25 -10000 0 -0.89 42 42
mol:Angiotensin II 0.001 0.002 -10000 0 -10000 0 0
mol:NADP 0.05 0.2 0.4 18 -0.59 43 61
Rac1/GTP 0.03 0.22 -10000 0 -0.71 41 41
MMP2 -0.026 0.26 -10000 0 -0.94 42 42
LPA4-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
ADCY4 -0.006 0.002 -10000 0 -10000 0 0
ADCY5 -0.097 0.1 -10000 0 -0.21 272 272
ADCY6 -0.006 0.001 -10000 0 -10000 0 0
ADCY7 -0.006 0.001 -10000 0 -10000 0 0
ADCY1 -0.011 0.039 0.21 2 -0.26 14 16
ADCY2 -0.034 0.07 -10000 0 -0.21 84 84
ADCY3 -0.006 0.001 -10000 0 -10000 0 0
ADCY8 -0.012 0.031 0.21 1 -0.27 8 9
PRKCE 0.007 0.001 -10000 0 -10000 0 0
ADCY9 -0.007 0.012 -10000 0 -0.21 2 2
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.017 0.076 0.2 19 -0.2 5 24
Osteopontin-mediated 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
IKK alpha homodimer -0.078 0.13 -10000 0 -0.28 36 36
NF kappa B1 p50/RelA/I kappa B alpha -0.063 0.13 0.32 6 -0.33 3 9
alphaV/beta3 Integrin/Osteopontin/Src -0.11 0.18 -10000 0 -0.31 262 262
AP1 -0.06 0.14 -10000 0 -0.46 7 7
ILK -0.088 0.13 -10000 0 -0.32 9 9
bone resorption -0.073 0.12 0.33 1 -0.35 4 5
PTK2B 0.02 0.025 -10000 0 -0.36 2 2
PYK2/p130Cas -0.06 0.14 -10000 0 -0.32 10 10
ITGAV 0.029 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.04 0.017 -10000 0 -0.25 2 2
alphaV/beta3 Integrin/Osteopontin -0.082 0.16 -10000 0 -0.26 258 258
MAP3K1 -0.091 0.13 -10000 0 -0.29 36 36
JUN 0.027 0.004 -10000 0 -10000 0 0
MAPK3 -0.093 0.12 0.19 1 -0.32 37 38
MAPK1 -0.092 0.12 0.19 1 -0.31 36 37
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.09 0.12 0.19 7 -0.28 35 42
ITGB3 0.025 0.041 -10000 0 -0.36 7 7
NFKBIA -0.083 0.11 0.19 1 -0.31 37 38
FOS 0.022 0.039 -10000 0 -0.36 6 6
CD44 0.027 0.003 -10000 0 -10000 0 0
CHUK 0.027 0.006 -10000 0 -10000 0 0
PLAU -0.08 0.14 0.45 1 -0.47 7 8
NF kappa B1 p50/RelA -0.061 0.14 -10000 0 -0.33 30 30
BCAR1 0.027 0.016 -10000 0 -0.36 1 1
RELA 0.027 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.04 0.033 -10000 0 -0.25 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.09 0.13 0.19 1 -0.28 36 37
VAV3 -0.1 0.13 0.19 7 -0.37 41 48
MAP3K14 -0.092 0.13 -10000 0 -0.3 36 36
ROCK2 0.026 0.022 -10000 0 -0.36 2 2
SPP1 -0.17 0.23 -10000 0 -0.44 262 262
RAC1 0.025 0.008 -10000 0 -10000 0 0
Rac1/GTP -0.085 0.13 -10000 0 -0.35 36 36
MMP2 -0.072 0.11 -10000 0 -0.53 7 7
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.022 0.011 -10000 0 -10000 0 0
EPHB2 0.024 0.034 -10000 0 -0.44 3 3
EFNB1 0.007 0.035 0.26 2 -0.31 5 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.015 0.13 -10000 0 -0.35 18 18
Ephrin B2/EPHB1-2 -0.006 0.1 0.26 1 -0.24 89 90
neuron projection morphogenesis -0.026 0.11 -10000 0 -0.28 34 34
Ephrin B1/EPHB1-2/Tiam1 -0.027 0.13 -10000 0 -0.25 118 118
DNM1 0.025 0.046 0.35 2 -0.44 5 7
cell-cell signaling 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.007 0.068 0.24 1 -0.41 15 16
YES1 -0.009 0.11 -10000 0 -0.65 16 16
Ephrin B1/EPHB1-2/NCK2 -0.004 0.12 0.28 1 -0.23 113 114
PI3K 0.031 0.083 -10000 0 -0.4 18 18
mol:GDP -0.028 0.13 -10000 0 -0.25 118 118
ITGA2B 0.006 0.09 -10000 0 -0.44 23 23
endothelial cell proliferation 0.028 0.016 -10000 0 -10000 0 0
FYN -0.007 0.11 -10000 0 -0.63 17 17
MAP3K7 -0.012 0.072 -10000 0 -0.44 16 16
FGR -0.01 0.11 -10000 0 -0.62 19 19
TIAM1 -0.011 0.11 -10000 0 -0.36 59 59
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
RGS3 0.027 0.004 -10000 0 -10000 0 0
cell adhesion 0.009 0.091 -10000 0 -0.42 15 15
LYN -0.007 0.11 -10000 0 -0.62 18 18
Ephrin B1/EPHB1-2/Src Family Kinases -0.009 0.094 -10000 0 -0.53 18 18
Ephrin B1/EPHB1-2 -0.01 0.076 -10000 0 -0.49 14 14
SRC -0.008 0.1 -10000 0 -0.61 17 17
ITGB3 0.023 0.041 -10000 0 -0.36 7 7
EPHB1 -0.07 0.19 0.35 1 -0.44 129 130
EPHB4 0.027 0.006 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.029 0.016 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.023 0.074 -10000 0 -0.3 30 30
BLK -0.044 0.12 -10000 0 -0.66 16 16
HCK -0.011 0.1 -10000 0 -0.62 16 16
regulation of stress fiber formation 0.005 0.12 0.23 113 -0.27 1 114
MAPK8 -0.007 0.068 0.22 1 -0.39 15 16
Ephrin B1/EPHB1-2/RGS3 -0.005 0.12 0.28 1 -0.23 116 117
endothelial cell migration 0.017 0.09 0.26 38 -0.36 9 47
NCK2 0.028 0.002 -10000 0 -10000 0 0
PTPN13 0.005 0.088 -10000 0 -0.4 27 27
regulation of focal adhesion formation 0.005 0.12 0.23 113 -0.27 1 114
chemotaxis 0.006 0.12 0.23 116 -0.27 1 117
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
Rac1/GTP -0.02 0.12 -10000 0 -0.28 34 34
angiogenesis -0.011 0.077 -10000 0 -0.48 15 15
LCK -0.01 0.11 -10000 0 -0.62 19 19
EPHB forward 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
Ephrin A5/EPHB2 -0.02 0.1 -10000 0 -0.21 133 133
cell-cell adhesion 0.04 0.068 0.36 3 -10000 0 3
Ephrin B/EPHB2/RasGAP 0.049 0.05 -10000 0 -0.23 4 4
ITSN1 0.027 0.006 -10000 0 -10000 0 0
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
SHC1 0.027 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.018 0.073 -10000 0 -0.27 38 38
Ephrin B1/EPHB1 -0.027 0.12 0.23 1 -0.27 129 130
HRAS/GDP -0.023 0.1 -10000 0 -0.31 20 20
Ephrin B/EPHB1/GRB7 0.011 0.11 0.25 6 -0.23 82 88
Endophilin/SYNJ1 0.029 0.08 0.18 122 -10000 0 122
KRAS 0.026 0.016 -10000 0 -0.36 1 1
Ephrin B/EPHB1/Src 0.01 0.085 -10000 0 -0.24 43 43
endothelial cell migration 0.043 0.028 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
GRB7 0.035 0.049 0.36 14 -10000 0 14
PAK1 0.03 0.085 0.26 9 -10000 0 9
HRAS 0.027 0.016 -10000 0 -0.36 1 1
RRAS 0.031 0.081 0.18 124 -0.22 4 128
DNM1 0.025 0.046 0.36 2 -0.44 5 7
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.019 0.1 0.18 73 -0.22 70 143
lamellipodium assembly -0.04 0.068 -10000 0 -0.36 3 3
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.015 0.06 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
EPHB2 0.024 0.033 -10000 0 -0.44 3 3
EPHB3 -0.002 0.11 -10000 0 -0.44 38 38
EPHB1 -0.071 0.19 0.36 1 -0.44 129 130
EPHB4 0.027 0.006 -10000 0 -10000 0 0
mol:GDP -0.012 0.09 0.27 3 -0.3 19 22
Ephrin B/EPHB2 0.039 0.043 -10000 0 -0.21 8 8
Ephrin B/EPHB3 0.026 0.073 -10000 0 -0.23 38 38
JNK cascade -0.056 0.096 0.35 4 -0.4 3 7
Ephrin B/EPHB1 -0.001 0.1 -10000 0 -0.23 92 92
RAP1/GDP 0.003 0.11 0.31 16 -0.28 16 32
EFNB2 0.022 0.011 -10000 0 -10000 0 0
EFNB3 0.018 0.045 -10000 0 -0.38 7 7
EFNB1 0.028 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.007 0.1 0.24 1 -0.24 89 90
RAP1B 0.028 0.003 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.007 0.097 -10000 0 -0.31 6 6
Rap1/GTP -0.016 0.082 -10000 0 -0.37 3 3
axon guidance -0.02 0.1 -10000 0 -0.21 133 133
MAPK3 0.007 0.054 0.2 3 -10000 0 3
MAPK1 0.008 0.051 0.17 1 -10000 0 1
Rac1/GDP -0.013 0.097 0.26 3 -0.29 15 18
actin cytoskeleton reorganization -0.034 0.076 -10000 0 -0.25 19 19
CDC42/GDP -0.003 0.11 0.31 18 -0.28 18 36
PI3K 0.048 0.031 -10000 0 -10000 0 0
EFNA5 -0.056 0.16 -10000 0 -0.36 130 130
Ephrin B2/EPHB4 0.029 0.016 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.017 0.026 -10000 0 -0.19 3 3
CDC42 0.025 0.017 -10000 0 -0.36 1 1
RAS family/GTP -0.02 0.082 -10000 0 -0.35 5 5
PTK2 0.087 0.21 0.58 89 -10000 0 89
MAP4K4 -0.056 0.097 0.35 4 -0.4 3 7
SRC 0.017 0.014 -10000 0 -10000 0 0
KALRN 0.027 0.016 -10000 0 -0.36 1 1
Intersectin/N-WASP 0.038 0.011 -10000 0 -10000 0 0
neuron projection morphogenesis -0.007 0.092 0.29 16 -0.29 3 19
MAP2K1 0.011 0.056 -10000 0 -10000 0 0
WASL 0.027 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.001 0.13 -10000 0 -0.25 130 130
cell migration 0.033 0.089 0.22 50 -10000 0 50
NRAS 0.026 0.023 -10000 0 -0.36 2 2
SYNJ1 0.029 0.08 0.18 122 -10000 0 122
PXN 0.028 0.002 -10000 0 -10000 0 0
TF 0.004 0.098 0.17 102 -0.41 1 103
HRAS/GTP -0.004 0.094 -10000 0 -0.22 70 70
Ephrin B1/EPHB1-2 -0.013 0.12 0.24 1 -0.25 130 131
cell adhesion mediated by integrin -0.034 0.091 0.24 3 -0.2 122 125
RAC1 0.025 0.008 -10000 0 -10000 0 0
mol:GTP -0.003 0.097 -10000 0 -0.22 71 71
RAC1-CDC42/GTP -0.034 0.095 -10000 0 -0.39 14 14
RASA1 0.027 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.006 0.099 0.26 3 -0.28 16 19
ruffle organization -0.003 0.13 0.39 30 -0.37 3 33
NCK1 0.028 0.003 -10000 0 -10000 0 0
receptor internalization 0.026 0.079 0.18 119 -10000 0 119
Ephrin B/EPHB2/KALRN 0.049 0.051 -10000 0 -0.23 5 5
ROCK1 -0.003 0.061 0.18 1 -0.23 39 40
RAS family/GDP -0.043 0.062 -10000 0 -0.28 5 5
Rac1/GTP -0.021 0.081 -10000 0 -0.38 3 3
Ephrin B/EPHB1/Src/Paxillin 0 0.048 -10000 0 -0.21 1 1
IL23-mediated signaling events

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
CCL2 -0.23 0.35 -10000 0 -1.1 50 50
IL23A -0.27 0.35 -10000 0 -1.1 48 48
NF kappa B1 p50/RelA/I kappa B alpha -0.24 0.34 -10000 0 -1 50 50
positive regulation of T cell mediated cytotoxicity -0.24 0.36 -10000 0 -1.1 52 52
ITGA3 -0.23 0.33 -10000 0 -1 42 42
IL17F -0.21 0.26 -10000 0 -0.68 69 69
IL12B -0.014 0.054 -10000 0 -0.47 4 4
STAT1 (dimer) -0.23 0.35 -10000 0 -1.1 52 52
CD4 -0.23 0.35 -10000 0 -1.1 50 50
IL23 -0.26 0.34 -10000 0 -1 48 48
IL23R -0.071 0.25 -10000 0 -1.1 30 30
IL1B -0.26 0.35 -10000 0 -1.1 48 48
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.27 0.34 -10000 0 -0.99 57 57
TYK2 -0.004 0.033 -10000 0 -10000 0 0
STAT4 0.011 0.08 -10000 0 -0.36 27 27
STAT3 0.026 0.006 -10000 0 -10000 0 0
IL18RAP 0.006 0.083 -10000 0 -0.36 29 29
IL12RB1 -0.016 0.076 -10000 0 -0.39 20 20
PIK3CA 0.026 0.017 -10000 0 -0.36 1 1
IL12Rbeta1/TYK2 -0.01 0.066 -10000 0 -0.28 20 20
IL23R/JAK2 -0.072 0.24 -10000 0 -1.1 27 27
positive regulation of chronic inflammatory response -0.24 0.36 -10000 0 -1.1 52 52
natural killer cell activation 0.005 0.013 0.079 15 -10000 0 15
JAK2 -0.008 0.047 -10000 0 -0.38 3 3
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
NFKB1 0.025 0.005 -10000 0 -10000 0 0
RELA 0.025 0.005 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.26 0.33 -10000 0 -0.98 49 49
ALOX12B -0.22 0.33 -10000 0 -1.1 38 38
CXCL1 -0.27 0.34 -10000 0 -1 51 51
T cell proliferation -0.24 0.36 -10000 0 -1.1 52 52
NFKBIA 0.024 0.007 -10000 0 -10000 0 0
IL17A -0.2 0.23 -10000 0 -0.56 81 81
PI3K -0.23 0.35 -10000 0 -1 56 56
IFNG -0.01 0.036 0.14 13 -0.11 7 20
STAT3 (dimer) -0.24 0.35 -10000 0 -0.98 56 56
IL18R1 0.019 0.05 -10000 0 -0.36 10 10
IL23/IL23R/JAK2/TYK2/SOCS3 -0.14 0.23 -10000 0 -0.75 39 39
IL18/IL18R 0.033 0.073 -10000 0 -0.22 37 37
macrophage activation -0.017 0.017 -10000 0 -0.044 35 35
TNF -0.25 0.35 -10000 0 -1.1 43 43
STAT3/STAT4 -0.23 0.35 -10000 0 -1 55 55
STAT4 (dimer) -0.24 0.36 -10000 0 -1.1 55 55
IL18 0.023 0.03 -10000 0 -0.36 3 3
IL19 -0.22 0.32 -10000 0 -1 38 38
STAT5A (dimer) -0.23 0.35 -10000 0 -1.1 50 50
STAT1 0.027 0.019 -10000 0 -0.44 1 1
SOCS3 0.026 0.027 -10000 0 -0.44 2 2
CXCL9 -0.24 0.34 -10000 0 -1.1 44 44
MPO -0.22 0.32 -10000 0 -1 39 39
positive regulation of humoral immune response -0.24 0.36 -10000 0 -1.1 52 52
IL23/IL23R/JAK2/TYK2 -0.25 0.38 -10000 0 -1.1 52 52
IL6 -0.24 0.36 -10000 0 -1.1 52 52
STAT5A 0.027 0.004 -10000 0 -10000 0 0
IL2 0.013 0.022 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.005 0.013 0.079 15 -10000 0 15
CD3E -0.24 0.37 -10000 0 -1.1 57 57
keratinocyte proliferation -0.24 0.36 -10000 0 -1.1 52 52
NOS2 -0.25 0.37 -10000 0 -1.1 55 55
Signaling events mediated by PRL

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
CCNE1 0.027 0.036 0.36 3 -0.44 2 5
mol:Halofuginone 0.004 0 -10000 0 -10000 0 0
ITGA1 0.027 0.003 -10000 0 -10000 0 0
CDKN1A 0.007 0.048 -10000 0 -0.31 13 13
PRL-3/alpha Tubulin 0.021 0.12 0.26 42 -0.32 53 95
mol:Ca2+ -0.062 0.13 0.18 35 -0.3 118 153
AGT -0.035 0.16 0.36 2 -0.44 82 84
CCNA2 -0.003 0.01 -10000 0 -10000 0 0
TUBA1B 0.028 0.002 -10000 0 -10000 0 0
EGR1 0.014 0.015 -10000 0 -0.24 2 2
CDK2/Cyclin E1 0.074 0.077 0.33 2 -0.34 1 3
MAPK3 0.001 0.12 0.28 42 -0.32 54 96
PRL-2 /Rab GGTase beta 0.039 0.009 -10000 0 -10000 0 0
MAPK1 0.001 0.12 0.28 41 -0.32 53 94
PTP4A1 0.002 0.011 -10000 0 -10000 0 0
PTP4A3 0.007 0.16 0.36 42 -0.44 53 95
PTP4A2 0.027 0.005 -10000 0 -10000 0 0
ITGB1 0.002 0.12 0.28 42 -0.32 53 95
SRC 0.017 0.014 -10000 0 -10000 0 0
RAC1 0.024 0.068 0.3 24 -0.3 4 28
Rab GGTase beta/Rab GGTase alpha 0.037 0.012 -10000 0 -10000 0 0
PRL-1/ATF-5 0.085 0.083 -10000 0 -10000 0 0
RABGGTA 0.026 0.007 -10000 0 -10000 0 0
BCAR1 -0.019 0.08 0.16 53 -0.25 42 95
RHOC 0.023 0.082 0.3 28 -0.32 11 39
RHOA 0.024 0.076 0.3 27 -0.3 8 35
cell motility 0.049 0.11 0.32 25 -0.33 10 35
PRL-1/alpha Tubulin 0.086 0.083 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.02 0.12 0.26 40 -0.32 53 93
ROCK1 0.05 0.1 0.32 25 -0.35 6 31
RABGGTB 0.027 0.005 -10000 0 -10000 0 0
CDK2 0.028 0.002 -10000 0 -10000 0 0
mitosis 0.002 0.011 -10000 0 -10000 0 0
ATF5 0.027 0.004 -10000 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.02 0.002 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.027 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.015 0.042 -10000 0 -10000 0 0
IRAK/TOLLIP 0.03 0.013 -10000 0 -0.24 1 1
IKBKB 0.024 0.009 -10000 0 -10000 0 0
IKBKG 0.027 0.016 -10000 0 -0.36 1 1
IL1 alpha/IL1R2 -0.12 0.18 -10000 0 -0.3 296 296
IL1A -0.1 0.21 -10000 0 -0.44 165 165
IL1B -0.018 0.096 -10000 0 -0.31 60 60
IRAK/TRAF6/p62/Atypical PKCs 0.063 0.028 -10000 0 -10000 0 0
IL1R2 -0.068 0.17 -10000 0 -0.36 151 151
IL1R1 0.023 0.041 -10000 0 -0.36 7 7
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.01 0.043 -10000 0 -10000 0 0
TOLLIP 0.027 0.003 -10000 0 -10000 0 0
TICAM2 0.014 0.055 -10000 0 -0.36 12 12
MAP3K3 0.027 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.018 0.003 -10000 0 -10000 0 0
IKK complex/ELKS 0.022 0.056 -10000 0 -0.35 1 1
JUN -0.011 0.022 0.2 4 -10000 0 4
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.038 0.091 -10000 0 -0.31 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.017 0.14 -10000 0 -0.25 169 169
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.006 0.14 -10000 0 -0.24 163 163
IL1 beta fragment/IL1R1/IL1RAP 0.015 0.088 -10000 0 -0.25 54 54
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.009 0.023 0.21 4 -10000 0 4
IRAK1 0.014 0.012 -10000 0 -0.27 1 1
IL1RN/IL1R1 0.002 0.11 -10000 0 -0.31 68 68
IRAK4 0.028 0.003 -10000 0 -10000 0 0
PRKCI 0.026 0.022 -10000 0 -0.36 2 2
TRAF6 0.027 0.003 -10000 0 -10000 0 0
PI3K 0.039 0.015 -10000 0 -0.25 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.014 0.047 -10000 0 -0.3 1 1
CHUK 0.027 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.015 0.088 -10000 0 -0.25 54 54
IL1 beta/IL1R2 -0.053 0.13 -10000 0 -0.23 200 200
IRAK/TRAF6/TAK1/TAB1/TAB2 0.038 0.014 -10000 0 -0.21 1 1
NF kappa B1 p50/RelA 0.026 0.082 -10000 0 -0.28 1 1
IRAK3 0.02 0.054 -10000 0 -0.36 12 12
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.033 0.095 -10000 0 -0.34 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.007 0.063 -10000 0 -0.3 2 2
IL1 alpha/IL1R1/IL1RAP -0.034 0.15 -10000 0 -0.27 169 169
RELA 0.027 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.027 0.004 -10000 0 -10000 0 0
MYD88 0.028 0.003 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.045 0.017 -10000 0 -0.23 1 1
IL1RAP 0.028 0.002 -10000 0 -10000 0 0
UBE2N 0.027 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 0.007 0.077 -10000 0 -0.32 2 2
CASP1 0.025 0.027 -10000 0 -0.36 3 3
IL1RN/IL1R2 -0.067 0.15 -10000 0 -0.27 211 211
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.029 0.089 -10000 0 -0.24 52 52
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.002 0.059 -10000 0 -0.3 7 7
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
IL1RN -0.019 0.14 -10000 0 -0.44 61 61
TRAF6/TAK1/TAB1/TAB2 0.039 0.008 -10000 0 -10000 0 0
MAP2K6 0.012 0.023 0.22 4 -10000 0 4
TCGA08_p53

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
CDKN2A -0.053 0.13 0.26 2 -0.32 114 116
TP53 -0.017 0.062 -10000 0 -0.27 28 28
Senescence -0.016 0.062 -10000 0 -0.27 28 28
Apoptosis -0.016 0.062 -10000 0 -0.27 28 28
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.022 0.068 0.31 7 -0.18 3 10
MDM4 0.028 0.014 0.36 1 -10000 0 1
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.027 0.006 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.029 0.093 -10000 0 -0.23 78 78
NT3 (dimer)/TRKC -0.024 0.12 -10000 0 -0.26 124 124
NT3 (dimer)/TRKB -0.078 0.17 -10000 0 -0.27 248 248
SHC/Grb2/SOS1/GAB1/PI3K 0.028 0.016 -10000 0 -0.27 1 1
RAPGEF1 0.027 0.016 -10000 0 -0.36 1 1
BDNF 0.019 0.06 -10000 0 -0.44 10 10
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
NTRK1 0.016 0.057 -10000 0 -0.43 9 9
NTRK2 -0.086 0.18 -10000 0 -0.37 176 176
NTRK3 -0.058 0.15 -10000 0 -0.36 123 123
NT-4/5 (dimer)/TRKB -0.092 0.17 -10000 0 -0.27 267 267
neuron apoptosis 0.088 0.16 0.38 92 -10000 0 92
SHC 2-3/Grb2 -0.094 0.17 -10000 0 -0.41 92 92
SHC1 0.027 0.004 -10000 0 -10000 0 0
SHC2 -0.093 0.16 -10000 0 -0.42 93 93
SHC3 -0.097 0.16 -10000 0 -0.41 91 91
STAT3 (dimer) 0.031 0.024 -10000 0 -0.35 1 1
NT3 (dimer)/TRKA -0.015 0.12 -10000 0 -0.22 150 150
RIN/GDP -0.005 0.08 0.27 7 -0.25 6 13
GIPC1 0.027 0.016 -10000 0 -0.36 1 1
KRAS 0.026 0.016 -10000 0 -0.36 1 1
DNAJA3 -0.061 0.12 -10000 0 -0.27 135 135
RIN/GTP 0.009 0.014 -10000 0 -0.31 1 1
CCND1 0.017 0.03 -10000 0 -0.35 4 4
MAGED1 0.027 0.003 -10000 0 -10000 0 0
PTPN11 0.028 0.002 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.017 0.089 -10000 0 -0.45 23 23
SHC/GRB2/SOS1 0.054 0.012 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.009 0.1 -10000 0 -0.23 91 91
TRKA/NEDD4-2 0.024 0.045 -10000 0 -0.3 10 10
ELMO1 0.023 0.028 -10000 0 -0.36 3 3
RhoG/GTP/ELMO1/DOCK1 0.032 0.023 -10000 0 -0.21 4 4
NGF 0.011 0.071 -10000 0 -0.37 20 20
HRAS 0.027 0.016 -10000 0 -0.36 1 1
DOCK1 0.026 0.016 -10000 0 -0.36 1 1
GAB2 0.027 0.004 -10000 0 -10000 0 0
RIT2 -0.012 0.021 -10000 0 -0.44 1 1
RIT1 0.027 0.004 -10000 0 -10000 0 0
FRS2 0.027 0.003 -10000 0 -10000 0 0
DNM1 0.025 0.046 0.36 2 -0.44 5 7
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.023 0.01 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.046 0.12 -10000 0 -0.26 130 130
mol:GDP -0.012 0.12 0.3 11 -0.36 11 22
NGF (dimer) 0.011 0.071 -10000 0 -0.37 20 20
RhoG/GDP 0.017 0.02 -10000 0 -0.25 3 3
RIT1/GDP -0.003 0.084 0.2 8 -0.24 9 17
TIAM1 -0.011 0.11 -10000 0 -0.36 59 59
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.03 0.13 -10000 0 -0.22 184 184
KIDINS220/CRKL/C3G 0.038 0.015 -10000 0 -0.25 1 1
SHC/RasGAP 0.039 0.009 -10000 0 -10000 0 0
FRS2 family/SHP2 0.055 0.012 0.24 1 -10000 0 1
SHC/GRB2/SOS1/GAB1 0.066 0.019 -10000 0 -10000 0 0
RIT1/GTP 0.02 0.003 -10000 0 -10000 0 0
NT3 (dimer) 0.021 0.043 -10000 0 -0.37 7 7
RAP1/GDP -0.005 0.069 0.14 2 -0.23 4 6
KIDINS220/CRKL 0.026 0.006 -10000 0 -10000 0 0
BDNF (dimer) 0.019 0.06 -10000 0 -0.44 10 10
ubiquitin-dependent protein catabolic process 0.026 0.064 -10000 0 -0.23 29 29
Schwann cell development -0.026 0.027 -10000 0 -10000 0 0
EHD4 0.026 0.007 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.068 0.018 0.25 1 -10000 0 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.016 0.042 0.25 1 -0.24 2 3
RAP1B 0.028 0.003 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.051 0.12 -10000 0 -0.33 35 35
ABL1 0.027 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
Rap1/GTP -0.013 0.095 -10000 0 -0.42 17 17
STAT3 0.031 0.024 -10000 0 -0.35 1 1
axon guidance -0.054 0.11 -10000 0 -0.32 35 35
MAPK3 -0.02 0.083 0.18 8 -0.31 10 18
MAPK1 -0.019 0.082 0.18 6 -0.31 10 16
CDC42/GDP 0.001 0.088 0.24 13 -0.24 8 21
NTF3 0.021 0.043 -10000 0 -0.37 7 7
NTF4 -0.017 0.089 -10000 0 -0.45 23 23
NGF (dimer)/TRKA/FAIM 0.039 0.064 0.25 1 -0.24 28 29
PI3K 0.039 0.015 -10000 0 -0.25 1 1
FRS3 0.028 0.014 0.36 1 -10000 0 1
FAIM 0.028 0.014 0.36 1 -10000 0 1
GAB1 0.027 0.005 -10000 0 -10000 0 0
RASGRF1 -0.077 0.13 -10000 0 -0.27 169 169
SOS1 0.028 0.002 -10000 0 -10000 0 0
MCF2L -0.031 0.086 -10000 0 -0.22 101 101
RGS19 0.017 0.014 -10000 0 -10000 0 0
CDC42 0.025 0.017 -10000 0 -0.36 1 1
RAS family/GTP 0.007 0.078 0.47 1 -0.42 4 5
Rac1/GDP -0.005 0.082 0.25 8 -0.24 9 17
NGF (dimer)/TRKA/GRIT 0.022 0.058 -10000 0 -0.24 28 28
neuron projection morphogenesis -0.047 0.14 -10000 0 -0.78 4 4
NGF (dimer)/TRKA/NEDD4-2 0.026 0.064 -10000 0 -0.23 29 29
MAP2K1 -0.006 0.033 0.18 19 -10000 0 19
NGFR -0.067 0.17 -10000 0 -0.36 148 148
NGF (dimer)/TRKA/GIPC/GAIP 0.01 0.038 -10000 0 -10000 0 0
RAS family/GTP/PI3K 0.022 0.026 -10000 0 -0.26 4 4
FRS2 family/SHP2/GRB2/SOS1 0.078 0.02 0.25 1 -10000 0 1
NRAS 0.026 0.023 -10000 0 -0.36 2 2
GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
PRKCI 0.026 0.022 -10000 0 -0.36 2 2
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
MAPKKK cascade -0.042 0.14 -10000 0 -0.57 37 37
RASA1 0.027 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.034 0.043 -10000 0 -0.31 9 9
SQSTM1 0.027 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.012 0.12 -10000 0 -0.2 176 176
NGF (dimer)/TRKA/p62/Atypical PKCs 0.059 0.067 -10000 0 -0.28 8 8
MATK -0.02 0.13 -10000 0 -0.36 74 74
NEDD4L 0.02 0.02 -10000 0 -0.36 1 1
RAS family/GDP -0.027 0.044 -10000 0 -0.2 2 2
NGF (dimer)/TRKA -0.058 0.13 -10000 0 -0.27 150 150
Rac1/GTP -0.064 0.1 -10000 0 -0.26 73 73
FRS2 family/SHP2/CRK family 0.067 0.034 0.25 1 -10000 0 1
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.013 0.036 -10000 0 -0.22 3 3
NFATC2 -0.015 0.044 -10000 0 -0.23 16 16
NFATC3 -0.014 0.037 -10000 0 -10000 0 0
CD40LG -0.058 0.2 0.37 2 -0.56 30 32
PTGS2 -0.056 0.2 0.36 1 -0.57 34 35
JUNB 0.026 0.022 -10000 0 -0.36 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.029 -10000 0 -10000 0 0
CaM/Ca2+ -0.005 0.029 -10000 0 -10000 0 0
CALM1 0.009 0.026 -10000 0 -10000 0 0
JUN 0.009 0.027 -10000 0 -10000 0 0
mol:Ca2+ -0.009 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.013 -10000 0 -10000 0 0
FOSL1 -0.27 0.23 0.36 1 -0.44 384 385
CREM 0.028 0.002 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.013 0.13 -10000 0 -0.41 9 9
FOS 0.005 0.045 -10000 0 -0.36 6 6
IFNG -0.065 0.21 0.36 1 -0.54 47 48
AP-1/NFAT1-c-4 -0.054 0.2 -10000 0 -0.48 57 57
FASLG -0.055 0.2 0.36 1 -0.55 23 24
NFAT1-c-4/ICER1 -0.018 0.077 -10000 0 -0.34 2 2
IL2RA -0.051 0.19 0.37 2 -0.58 16 18
FKBP12/FK506 0.017 0.008 -10000 0 -10000 0 0
CSF2 -0.12 0.25 0.37 2 -0.54 75 77
JunB/Fra1/NFAT1-c-4 -0.097 0.16 -10000 0 -0.32 137 137
IL4 -0.052 0.18 0.36 2 -0.54 15 17
IL2 -0.016 0.14 -10000 0 -0.84 18 18
IL3 0 0.086 -10000 0 -0.6 11 11
FKBP1A 0.023 0.011 -10000 0 -10000 0 0
BATF3 0.022 0.049 -10000 0 -0.43 7 7
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.026 0.02 -10000 0 -0.44 1 1
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.044 0.11 0.21 86 -0.29 8 94
PDGFB-D/PDGFRB/SLAP 0.03 0.045 -10000 0 -0.3 10 10
PDGFB-D/PDGFRB/APS/CBL 0.045 0.054 0.25 1 -0.26 16 17
AKT1 0.055 0.095 0.28 16 -10000 0 16
mol:PI-4-5-P2 0.001 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.067 0.13 0.24 109 -0.32 9 118
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
FGR 0.01 0.12 -10000 0 -0.46 26 26
mol:Ca2+ 0.061 0.12 0.24 88 -0.42 5 93
MYC 0.091 0.16 0.39 81 -0.4 1 82
SHC1 0.027 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.063 0.076 -10000 0 -0.22 6 6
LRP1/PDGFRB/PDGFB 0.05 0.04 -10000 0 -0.25 9 9
GRB10 0.025 0.008 -10000 0 -10000 0 0
PTPN11 0.028 0.002 -10000 0 -10000 0 0
GO:0007205 0.061 0.12 0.24 84 -0.42 5 89
PTEN 0.026 0.006 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
GRB7 0.035 0.049 0.36 14 -10000 0 14
PDGFB-D/PDGFRB/SHP2 0.038 0.038 -10000 0 -0.31 7 7
PDGFB-D/PDGFRB/GRB10 0.035 0.037 -10000 0 -0.31 6 6
cell cycle arrest 0.03 0.045 -10000 0 -0.29 10 10
HRAS 0.027 0.016 -10000 0 -0.36 1 1
HIF1A 0.048 0.088 0.24 23 -10000 0 23
GAB1 0.044 0.12 0.22 74 -0.34 9 83
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.058 0.12 0.23 98 -0.33 4 102
PDGFB-D/PDGFRB 0.026 0.042 -10000 0 -0.27 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.038 0.038 -10000 0 -0.31 7 7
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.004 0.062 0.2 1 -0.28 3 4
positive regulation of MAPKKK cascade 0.037 0.038 -10000 0 -0.31 7 7
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
mol:IP3 0.062 0.12 0.24 84 -0.43 5 89
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.024 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.042 0.051 0.26 14 -0.31 7 21
SHB 0.026 0.03 0.36 1 -0.44 2 3
BLK -0.14 0.23 -10000 0 -0.46 200 200
PTPN2 0.024 0.012 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.037 0.039 -10000 0 -0.31 7 7
BCAR1 0.027 0.016 -10000 0 -0.36 1 1
VAV2 0.054 0.13 0.25 90 -0.37 8 98
CBL 0.027 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.037 0.038 -10000 0 -0.31 7 7
LCK 0.019 0.11 -10000 0 -0.44 18 18
PDGFRB 0.024 0.05 -10000 0 -0.44 7 7
ACP1 0.028 0.002 -10000 0 -10000 0 0
HCK 0.005 0.076 -10000 0 -0.48 10 10
ABL1 0.038 0.13 0.23 81 -0.34 15 96
PDGFB-D/PDGFRB/CBL 0.032 0.12 0.29 2 -0.4 10 12
PTPN1 0.016 0.014 -10000 0 -10000 0 0
SNX15 0.027 0.004 -10000 0 -10000 0 0
STAT3 0.027 0.004 -10000 0 -10000 0 0
STAT1 0.027 0.019 -10000 0 -0.44 1 1
cell proliferation 0.089 0.15 0.38 85 -0.36 1 86
SLA 0.022 0.029 -10000 0 -0.36 3 3
actin cytoskeleton reorganization 0.086 0.089 0.34 7 -10000 0 7
SRC 0.009 0.04 -10000 0 -10000 0 0
PI3K -0.003 0.026 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.054 0.046 0.25 12 -0.26 7 19
SH2B2 0.02 0.058 0.36 1 -0.44 9 10
PLCgamma1/SPHK1 0.068 0.13 0.24 93 -0.33 9 102
LYN 0.023 0.077 -10000 0 -0.47 5 5
LRP1 0.026 0.022 -10000 0 -0.36 2 2
SOS1 0.028 0.002 -10000 0 -10000 0 0
STAT5B 0.027 0.004 -10000 0 -10000 0 0
STAT5A 0.027 0.004 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.039 0.051 -10000 0 -10000 0 0
SPHK1 0 0.12 -10000 0 -0.44 40 40
EDG1 0.003 0.004 -10000 0 -10000 0 0
mol:DAG 0.062 0.12 0.24 84 -0.43 5 89
PLCG1 0.062 0.12 0.24 82 -0.44 5 87
NHERF/PDGFRB 0.05 0.038 -10000 0 -0.26 8 8
YES1 -0.002 0.15 -10000 0 -0.51 39 39
cell migration 0.05 0.038 -10000 0 -0.26 8 8
SHC/Grb2/SOS1 0.038 0.05 -10000 0 -10000 0 0
SLC9A3R2 0.027 0.016 -10000 0 -0.36 1 1
SLC9A3R1 0.027 0.004 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.062 0.041 -10000 0 -0.23 8 8
FYN 0.019 0.093 -10000 0 -0.47 11 11
DOK1 0.057 0.084 0.18 159 -0.24 6 165
HRAS/GTP 0.02 0.011 -10000 0 -0.25 1 1
PDGFB 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.068 0.15 0.34 59 -0.45 3 62
PRKCD 0.058 0.086 0.18 175 -0.24 6 181
FER 0.056 0.086 0.18 175 -0.24 6 181
MAPKKK cascade 0.063 0.099 0.3 12 -10000 0 12
RASA1 0.058 0.086 0.18 178 -0.24 6 184
NCK1 0.028 0.003 -10000 0 -10000 0 0
NCK2 0.028 0.002 -10000 0 -10000 0 0
p62DOK/Csk 0.065 0.075 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.036 0.044 0.26 1 -0.31 9 10
chemotaxis 0.038 0.12 0.23 81 -0.33 15 96
STAT1-3-5/STAT1-3-5 0.032 0.044 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.018 0.036 -10000 0 -0.31 7 7
PTPRJ 0.028 0.003 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.014 0.16 -10000 0 -0.86 15 15
MKNK1 0.027 0.004 -10000 0 -10000 0 0
MAPK14 0.01 0.088 -10000 0 -0.3 33 33
ATF2/c-Jun 0.004 0.068 -10000 0 -0.41 2 2
MAPK11 0.01 0.088 -10000 0 -0.3 35 35
MITF -0.005 0.11 -10000 0 -0.36 39 39
MAPKAPK5 0.002 0.096 -10000 0 -0.34 37 37
KRT8 0.002 0.095 -10000 0 -0.34 37 37
MAPKAPK3 0.027 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.027 0.004 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.012 0.13 -10000 0 -0.43 35 35
CEBPB -0.002 0.081 0.25 3 -0.35 23 26
SLC9A1 -0.001 0.099 -10000 0 -0.35 37 37
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.003 0.097 -10000 0 -0.33 35 35
p38alpha-beta/MNK1 0.029 0.11 -10000 0 -0.35 34 34
JUN 0.002 0.066 -10000 0 -0.4 2 2
PPARGC1A -0.034 0.14 -10000 0 -0.4 44 44
USF1 0.004 0.091 -10000 0 -0.34 34 34
RAB5/GDP/GDI1 0.008 0.076 -10000 0 -0.41 2 2
NOS2 -0.028 0.21 -10000 0 -0.92 28 28
DDIT3 0.002 0.096 -10000 0 -0.34 37 37
RAB5A 0.026 0.022 -10000 0 -0.36 2 2
HSPB1 0.003 0.089 0.28 17 -0.28 34 51
p38alpha-beta/HBP1 0.028 0.11 -10000 0 -0.35 31 31
CREB1 0.002 0.1 -10000 0 -0.37 36 36
RAB5/GDP 0.019 0.016 -10000 0 -0.25 2 2
EIF4E -0.004 0.087 -10000 0 -0.31 34 34
RPS6KA4 0.002 0.095 -10000 0 -0.34 36 36
PLA2G4A -0.026 0.11 -10000 0 -0.35 33 33
GDI1 0.003 0.092 -10000 0 -0.34 35 35
TP53 -0.013 0.11 -10000 0 -0.42 32 32
RPS6KA5 0 0.1 -10000 0 -0.36 36 36
ESR1 -0.021 0.13 -10000 0 -0.41 38 38
HBP1 0.027 0.005 -10000 0 -10000 0 0
MEF2C -0.005 0.11 -10000 0 -0.37 37 37
MEF2A 0.001 0.1 -10000 0 -0.36 36 36
EIF4EBP1 -0.001 0.1 -10000 0 -0.39 34 34
KRT19 0.002 0.094 -10000 0 -0.34 35 35
ELK4 0.003 0.092 -10000 0 -0.34 35 35
ATF6 0.004 0.091 -10000 0 -0.34 34 34
ATF1 0.002 0.1 -10000 0 -0.37 36 36
p38alpha-beta/MAPKAPK2 0.03 0.1 -10000 0 -0.35 32 32
p38alpha-beta/MAPKAPK3 0.029 0.11 -10000 0 -0.35 34 34
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 0.017 0.072 -10000 0 -0.37 7 7
Syndecan-4/Syndesmos 0.026 0.13 0.31 9 -0.4 8 17
positive regulation of JNK cascade 0.001 0.14 0.3 8 -0.44 8 16
Syndecan-4/ADAM12 -0.069 0.18 0.3 9 -0.42 37 46
CCL5 0.012 0.075 -10000 0 -0.36 24 24
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
DNM2 0.027 0.003 -10000 0 -10000 0 0
ITGA5 0.026 0.027 -10000 0 -0.44 2 2
SDCBP 0.024 0.018 -10000 0 -0.36 1 1
PLG -0.1 0.19 0.35 1 -0.46 127 128
ADAM12 -0.23 0.24 -10000 0 -0.45 329 329
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.043 0.05 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.011 0.13 0.31 7 -0.39 14 21
Syndecan-4/CXCL12/CXCR4 0.002 0.15 0.32 8 -0.47 8 16
Syndecan-4/Laminin alpha3 0.017 0.12 0.32 9 -0.41 7 16
MDK 0.023 0.046 -10000 0 -0.44 6 6
Syndecan-4/FZD7 0.028 0.13 0.32 10 -0.4 8 18
Syndecan-4/Midkine 0.026 0.14 0.32 10 -0.4 8 18
FZD7 0.028 0 -10000 0 -10000 0 0
Syndecan-4/FGFR1/FGF 0.008 0.13 0.3 7 -0.4 7 14
THBS1 0.025 0.025 -10000 0 -0.4 2 2
integrin-mediated signaling pathway 0.023 0.13 0.31 10 -0.39 11 21
positive regulation of MAPKKK cascade 0.001 0.14 0.3 8 -0.44 8 16
Syndecan-4/TACI -0.028 0.14 0.33 6 -0.39 22 28
CXCR4 0.028 0.002 -10000 0 -10000 0 0
cell adhesion 0.009 0.048 0.2 13 -0.22 8 21
Syndecan-4/Dynamin 0.028 0.13 0.32 10 -0.4 8 18
Syndecan-4/TSP1 0.027 0.13 0.32 11 -0.41 8 19
Syndecan-4/GIPC 0.028 0.13 0.32 11 -0.4 8 19
Syndecan-4/RANTES 0.021 0.14 0.32 8 -0.41 9 17
ITGB1 0.028 0.002 -10000 0 -10000 0 0
LAMA1 -0.055 0.15 -10000 0 -0.36 122 122
LAMA3 0.02 0.034 -10000 0 -0.38 4 4
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCA 0.019 0.12 0.79 14 -10000 0 14
Syndecan-4/alpha-Actinin 0.024 0.13 0.31 10 -0.41 7 17
TFPI 0.025 0.035 -10000 0 -0.36 5 5
F2 -0.12 0.22 -10000 0 -0.43 210 210
alpha5/beta1 Integrin 0.04 0.021 -10000 0 -0.32 2 2
positive regulation of cell adhesion -0.018 0.13 0.3 8 -0.4 10 18
ACTN1 0.026 0.007 -10000 0 -10000 0 0
TNC 0.018 0.064 -10000 0 -0.4 14 14
Syndecan-4/CXCL12 0.004 0.15 0.31 9 -0.44 11 20
FGF6 -0.017 0.024 0.36 1 -0.44 1 2
RHOA 0.027 0.004 -10000 0 -10000 0 0
CXCL12 -0.046 0.15 -10000 0 -0.36 116 116
TNFRSF13B -0.12 0.18 -10000 0 -0.36 214 214
FGF2 -0.001 0.099 -10000 0 -0.36 43 43
FGFR1 0.021 0.032 -10000 0 -0.36 4 4
Syndecan-4/PI-4-5-P2 -0.016 0.099 0.29 7 -0.4 8 15
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.012 0.11 -10000 0 -0.43 36 36
cell migration -0.022 0.02 -10000 0 -10000 0 0
PRKCD 0.015 0.024 -10000 0 -10000 0 0
vasculogenesis 0.027 0.13 0.31 11 -0.4 8 19
SDC4 -0.014 0.1 0.32 7 -0.42 8 15
Syndecan-4/Tenascin C 0.023 0.14 0.32 9 -0.4 11 20
Syndecan-4/PI-4-5-P2/PKC alpha -0.035 0.038 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.02 0.12 0.32 7 -0.41 7 14
MMP9 -0.001 0.12 0.37 15 -0.44 32 47
Rac1/GTP 0.009 0.049 0.2 13 -0.22 8 21
cytoskeleton organization 0.026 0.13 0.3 9 -0.39 8 17
GIPC1 0.027 0.016 -10000 0 -0.36 1 1
Syndecan-4/TFPI 0.027 0.14 0.32 10 -0.4 9 19
Thromboxane A2 receptor signaling

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
TGM2 0.013 0.039 -10000 0 -0.44 4 4
GNB1/GNG2 -0.053 0.049 -10000 0 -0.2 18 18
AKT1 -0.042 0.093 0.29 5 -0.29 38 43
EGF -0.06 0.16 -10000 0 -0.37 127 127
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.069 0.077 0.39 1 -0.28 2 3
mol:Ca2+ -0.054 0.098 0.31 4 -0.29 36 40
LYN -0.06 0.075 0.39 1 -10000 0 1
RhoA/GTP -0.024 0.043 -10000 0 -0.14 9 9
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.06 0.1 0.31 5 -0.34 17 22
GNG2 0.011 0.074 -10000 0 -0.36 23 23
ARRB2 0.023 0.01 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.027 0.11 -10000 0 -0.59 15 15
G beta5/gamma2 -0.061 0.066 -10000 0 -0.26 16 16
PRKCH -0.057 0.1 0.3 4 -0.34 21 25
DNM1 0.025 0.046 0.36 2 -0.44 5 7
TXA2/TP beta/beta Arrestin3 -0.01 0.049 -10000 0 -0.62 3 3
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.18 0.19 -10000 0 -0.36 317 317
G12 family/GTP -0.055 0.088 -10000 0 -0.3 18 18
ADRBK1 0.027 0.004 -10000 0 -10000 0 0
ADRBK2 0.027 0.005 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.03 0.018 -10000 0 -0.21 1 1
mol:GDP 0.067 0.098 0.32 38 -0.31 2 40
mol:NADP 0.02 0.058 0.35 1 -0.44 9 10
RAB11A 0.027 0.006 -10000 0 -10000 0 0
PRKG1 0.012 0.071 -10000 0 -0.36 21 21
mol:IP3 -0.066 0.12 0.33 4 -0.36 36 40
cell morphogenesis 0.029 0.017 -10000 0 -0.21 1 1
PLCB2 -0.09 0.15 0.41 2 -0.48 36 38
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.099 0.11 -10000 0 -0.28 101 101
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.041 0.069 -10000 0 -0.28 5 5
RHOA 0.027 0.004 -10000 0 -10000 0 0
PTGIR 0.026 0.027 -10000 0 -0.44 2 2
PRKCB1 -0.06 0.11 0.31 4 -0.35 24 28
GNAQ 0.026 0.022 -10000 0 -0.36 2 2
mol:L-citrulline 0.02 0.058 0.35 1 -0.44 9 10
TXA2/TXA2-R family -0.086 0.14 0.43 2 -0.5 21 23
LCK -0.072 0.079 0.39 1 -0.3 6 7
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.078 0.097 -10000 0 -0.23 4 4
TXA2-R family/G12 family/GDP/G beta/gamma -0.028 0.11 -10000 0 -0.48 30 30
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.071 0.096 -10000 0 -0.23 2 2
MAPK14 -0.042 0.076 0.32 5 -0.23 15 20
TGM2/GTP -0.077 0.12 0.33 3 -0.42 22 25
MAPK11 -0.042 0.073 0.26 5 -0.23 15 20
ARHGEF1 -0.034 0.057 0.25 1 -0.18 15 16
GNAI2 0.027 0.004 -10000 0 -10000 0 0
JNK cascade -0.066 0.11 0.33 4 -0.38 19 23
RAB11/GDP 0.027 0.006 -10000 0 -10000 0 0
ICAM1 -0.045 0.085 0.28 4 -0.28 14 18
cAMP biosynthetic process -0.07 0.11 0.32 4 -0.35 32 36
Gq family/GTP/EBP50 0.015 0.045 0.24 4 -0.29 7 11
actin cytoskeleton reorganization 0.029 0.017 -10000 0 -0.21 1 1
SRC -0.04 0.066 -10000 0 -10000 0 0
GNB5 0.026 0.006 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
EGF/EGFR -0.061 0.099 0.21 7 -0.28 31 38
VCAM1 -0.05 0.093 0.29 4 -0.36 15 19
TP beta/Gq family/GDP/G beta5/gamma2 -0.027 0.11 -10000 0 -0.59 15 15
platelet activation -0.055 0.099 0.37 5 -0.3 17 22
PGI2/IP 0.019 0.019 -10000 0 -0.31 2 2
PRKACA -0.09 0.1 -10000 0 -0.19 308 308
Gq family/GDP/G beta5/gamma2 -0.033 0.1 -10000 0 -0.5 16 16
TXA2/TP beta/beta Arrestin2 -0.026 0.061 -10000 0 -0.34 6 6
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.091 0.094 -10000 0 -0.18 303 303
mol:DAG -0.068 0.12 0.33 4 -0.4 24 28
EGFR 0.024 0.023 -10000 0 -0.36 2 2
TXA2/TP alpha -0.09 0.15 0.37 4 -0.47 32 36
Gq family/GTP 0.009 0.054 0.3 4 -0.24 15 19
YES1 -0.06 0.076 0.39 1 -10000 0 1
GNAI2/GTP -0.071 0.089 -10000 0 -0.24 1 1
PGD2/DP -0.12 0.13 -10000 0 -0.25 317 317
SLC9A3R1 0.027 0.004 -10000 0 -10000 0 0
FYN -0.07 0.076 0.39 1 -10000 0 1
mol:NO 0.02 0.058 0.35 1 -0.44 9 10
GNA15 0.023 0.046 -10000 0 -0.44 6 6
PGK/cGMP 0.021 0.058 -10000 0 -0.23 28 28
RhoA/GDP 0.028 0.005 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.038 0.096 -10000 0 -0.31 12 12
NOS3 0.02 0.058 0.36 1 -0.44 9 10
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCA -0.056 0.1 0.34 4 -0.33 21 25
PRKCB -0.077 0.12 0.35 4 -0.39 30 34
PRKCE -0.054 0.1 0.33 2 -0.34 18 20
PRKCD -0.059 0.11 0.3 4 -0.36 17 21
PRKCG -0.086 0.13 0.34 4 -0.4 26 30
muscle contraction -0.084 0.14 0.37 4 -0.48 21 25
PRKCZ -0.061 0.1 0.31 4 -0.34 17 21
ARR3 -0.008 0.037 -10000 0 -0.44 3 3
TXA2/TP beta -0.073 0.1 -10000 0 -0.24 2 2
PRKCQ -0.056 0.1 0.34 4 -0.34 20 24
MAPKKK cascade -0.079 0.13 0.34 4 -0.44 28 32
SELE -0.059 0.1 0.29 4 -0.29 20 24
TP beta/GNAI2/GDP/G beta/gamma -0.072 0.11 -10000 0 -0.3 17 17
ROCK1 0.022 0.019 -10000 0 -0.36 1 1
GNA14 0.024 0.035 -10000 0 -0.36 5 5
chemotaxis -0.088 0.15 0.44 2 -0.59 16 18
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
GNA11 0.025 0.031 -10000 0 -0.36 4 4
Rac1/GTP 0.018 0.006 -10000 0 -10000 0 0
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.052 0.12 0.29 45 -10000 0 45
GNAI2 0.027 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.027 0.046 -10000 0 -0.27 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.12 0.19 -10000 0 -0.36 224 224
RhoA/GTP -0.052 0.12 -10000 0 -0.3 45 45
negative regulation of cAMP metabolic process -0.063 0.12 -10000 0 -0.33 43 43
GNAZ 0.023 0.035 -10000 0 -0.36 5 5
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNA12 0.025 0.008 -10000 0 -10000 0 0
S1PR5 0.016 0.073 -10000 0 -0.44 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.063 0.12 -10000 0 -0.33 43 43
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
GNAI1 0.015 0.067 -10000 0 -0.36 19 19
Syndecan-3-mediated signaling events

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
CTTN 0.027 0.004 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.001 0.098 -10000 0 -0.38 20 20
Syndecan-3/Neurocan 0.007 0.088 -10000 0 -0.36 31 31
POMC 0.011 0.075 -10000 0 -0.36 23 23
EGFR 0.024 0.023 -10000 0 -0.36 2 2
Syndecan-3/EGFR 0.008 0.087 -10000 0 -0.36 31 31
AGRP -0.006 0.049 -10000 0 -0.44 6 6
NCSTN 0.027 0.004 -10000 0 -10000 0 0
PSENEN 0.026 0.016 -10000 0 -0.36 1 1
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.026 0.006 -10000 0 -10000 0 0
APH1A 0.027 0.004 -10000 0 -10000 0 0
NCAN 0.002 0.034 -10000 0 -0.44 2 2
long-term memory 0.027 0.088 -10000 0 -0.35 30 30
Syndecan-3/IL8 -0.12 0.14 0.23 2 -0.44 33 35
PSEN1 0.026 0.007 -10000 0 -10000 0 0
Src/Cortactin 0.024 0.02 -10000 0 -10000 0 0
FYN 0.027 0.005 -10000 0 -10000 0 0
limb bud formation -0.005 0.084 -10000 0 -0.38 30 30
MC4R -0.008 0.039 -10000 0 -0.44 4 4
SRC 0.017 0.014 -10000 0 -10000 0 0
PTN -0.034 0.14 -10000 0 -0.36 95 95
FGFR/FGF/Syndecan-3 -0.006 0.085 -10000 0 -0.38 30 30
neuron projection morphogenesis 0.031 0.12 -10000 0 -0.37 20 20
Syndecan-3/AgRP 0.005 0.09 -10000 0 -0.36 32 32
Syndecan-3/AgRP/MC4R 0.008 0.089 -10000 0 -0.34 32 32
Fyn/Cortactin 0.039 0.009 -10000 0 -10000 0 0
SDC3 -0.006 0.086 -10000 0 -0.38 30 30
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration -0.12 0.14 0.22 2 -0.43 33 35
IL8 -0.23 0.24 0.36 2 -0.44 337 339
Syndecan-3/Fyn/Cortactin 0.027 0.09 -10000 0 -0.36 30 30
Syndecan-3/CASK -0.007 0.083 -10000 0 -0.35 33 33
alpha-MSH/MC4R 0.013 0.06 -10000 0 -0.26 27 27
Gamma Secretase 0.07 0.031 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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
HRAS 0.027 0.016 -9999 0 -0.36 1 1
EGFR 0.024 0.023 -9999 0 -0.36 2 2
EGF/EGFR -0.011 0.11 -9999 0 -0.26 51 51
EGF/EGFR dimer/SHC/GRB2/SOS1 0.019 0.1 -9999 0 -0.23 20 20
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.003 0.12 -9999 0 -0.45 39 39
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.06 0.16 -9999 0 -0.37 127 127
EGF/EGFR dimer/SHC -0.003 0.11 -9999 0 -0.22 113 113
mol:GDP 0.015 0.1 -9999 0 -0.23 20 20
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.027 0.016 -9999 0 -0.36 1 1
GRB2/SOS1 0.04 0.007 -9999 0 -10000 0 0
HRAS/GTP 0.002 0.089 -9999 0 -10000 0 0
SHC1 0.027 0.004 -9999 0 -10000 0 0
HRAS/GDP 0.014 0.098 -9999 0 -10000 0 0
FRAP1 -0.042 0.067 -9999 0 -0.22 20 20
EGF/EGFR dimer -0.022 0.12 -9999 0 -0.26 116 116
SOS1 0.028 0.002 -9999 0 -10000 0 0
GRB2 0.027 0.004 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.016 0.089 -9999 0 -0.32 40 40
Arf6 signaling events

Figure S50.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S50.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.026 0.024 -10000 0 -0.39 1 1
ARNO/beta Arrestin1-2 0.006 0.092 -10000 0 -0.83 3 3
EGFR 0.024 0.023 -10000 0 -0.36 2 2
EPHA2 0.025 0.028 -10000 0 -0.44 2 2
USP6 0.022 0.026 -10000 0 -0.4 2 2
IQSEC1 0.027 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.022 0.12 -10000 0 -0.26 116 116
ARRB2 0.008 0.004 -10000 0 -10000 0 0
mol:GTP 0.004 0.041 0.13 10 -0.17 6 16
ARRB1 0.027 0.016 -10000 0 -0.36 1 1
FBXO8 0.026 0.017 -10000 0 -0.36 1 1
TSHR 0.013 0.033 -10000 0 -0.44 2 2
EGF -0.06 0.16 -10000 0 -0.37 127 127
somatostatin receptor activity 0 0 0.001 32 -0.001 31 63
ARAP2 0.026 0.023 -10000 0 -0.36 2 2
mol:GDP -0.034 0.11 0.17 14 -0.28 43 57
mol:PI-3-4-5-P3 0 0 0.001 13 -0.001 7 20
ITGA2B 0.006 0.09 -10000 0 -0.44 23 23
ARF6 0.026 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.062 0.031 -10000 0 -0.25 2 2
ADAP1 0.025 0.017 -10000 0 -0.36 1 1
KIF13B 0.021 0.019 -10000 0 -0.36 1 1
HGF/MET 0.029 0.059 -10000 0 -0.28 20 20
PXN 0.028 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.023 0.11 0.22 29 -0.27 32 61
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.003 0.11 -10000 0 -0.22 116 116
ADRB2 -0.033 0.14 -10000 0 -0.36 93 93
receptor agonist activity 0 0 0 13 0 29 42
actin filament binding 0 0 0 32 -0.001 33 65
SRC 0.017 0.014 -10000 0 -10000 0 0
ITGB3 0.023 0.041 -10000 0 -0.36 7 7
GNAQ 0.026 0.022 -10000 0 -0.36 2 2
EFA6/PI-4-5-P2 0 0.001 0.001 36 -0.001 13 49
ARF6/GDP -0.047 0.16 0.21 4 -0.42 76 80
ARF6/GDP/GULP/ACAP1 -0.023 0.12 0.22 3 -0.37 21 24
alphaIIb/beta3 Integrin/paxillin/GIT1 0.054 0.066 -10000 0 -0.24 29 29
ACAP1 0.013 0.06 -10000 0 -0.36 15 15
ACAP2 0.027 0.016 -10000 0 -0.36 1 1
LHCGR/beta Arrestin2 0.007 0.026 -10000 0 -10000 0 0
EFNA1 0.027 0.004 -10000 0 -10000 0 0
HGF 0.017 0.061 -10000 0 -0.37 15 15
CYTH3 0.006 0.002 -10000 0 -10000 0 0
CYTH2 0.015 0.071 -10000 0 -1 3 3
NCK1 0.028 0.003 -10000 0 -10000 0 0
fibronectin binding 0 0 0 43 0 13 56
endosomal lumen acidification 0 0 0 46 -0.001 15 61
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 0.007 0.088 -10000 0 -0.36 33 33
GNAQ/ARNO 0.03 0.068 -10000 0 -0.92 3 3
mol:Phosphatidic acid 0 0 0 8 -10000 0 8
PIP3-E 0 0 0 13 0 5 18
MET 0.022 0.047 -10000 0 -0.44 6 6
GNA14 0.024 0.035 -10000 0 -0.36 5 5
GNA15 0.023 0.046 -10000 0 -0.44 6 6
GIT1 0.026 0.016 -10000 0 -0.36 1 1
mol:PI-4-5-P2 0 0 0.001 32 -0.001 20 52
GNA11 0.025 0.032 -10000 0 -0.36 4 4
LHCGR -0.012 0.015 -10000 0 -10000 0 0
AGTR1 -0.12 0.18 -10000 0 -0.36 214 214
desensitization of G-protein coupled receptor protein signaling pathway 0.007 0.026 -10000 0 -10000 0 0
IPCEF1/ARNO 0.001 0.098 -10000 0 -0.89 3 3
alphaIIb/beta3 Integrin 0.023 0.074 -10000 0 -0.3 30 30
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.12 0.19 -10000 0 -0.36 224 224
CDC42/GTP -0.054 0.12 -10000 0 -0.32 47 47
PLCG1 -0.042 0.1 -10000 0 -0.34 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
G12/G13 0.036 0.013 -10000 0 -10000 0 0
cell migration -0.054 0.12 -10000 0 -0.31 47 47
S1PR5 0.016 0.073 -10000 0 -0.44 15 15
S1PR4 0.021 0.049 -10000 0 -0.36 10 10
MAPK3 -0.068 0.12 -10000 0 -0.33 49 49
MAPK1 -0.059 0.11 -10000 0 -0.35 33 33
S1P/S1P5/Gi -0.063 0.12 -10000 0 -0.33 43 43
GNAI1 0.015 0.067 -10000 0 -0.36 19 19
CDC42/GDP 0.019 0.012 -10000 0 -0.25 1 1
S1P/S1P5/G12 0.027 0.046 -10000 0 -0.27 14 14
RHOA 0.027 0.059 0.19 59 -10000 0 59
S1P/S1P4/Gi -0.063 0.13 -10000 0 -0.36 43 43
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.023 0.035 -10000 0 -0.36 5 5
S1P/S1P4/G12/G13 0.043 0.032 -10000 0 -0.19 8 8
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
CDC42 0.025 0.017 -10000 0 -0.36 1 1
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.002 0.1 0.22 2 -0.36 20 22
TBX21 -0.086 0.38 0.44 1 -1.1 54 55
B2M 0.023 0.022 -10000 0 -0.36 1 1
TYK2 0.02 0.031 -10000 0 -10000 0 0
IL12RB1 0.008 0.079 -10000 0 -0.39 20 20
GADD45B -0.028 0.26 -10000 0 -0.88 32 32
IL12RB2 0.012 0.066 -10000 0 -0.4 12 12
GADD45G -0.029 0.26 -10000 0 -0.91 28 28
natural killer cell activation 0 0.018 0.046 8 -0.041 46 54
RELB 0.027 0.003 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
IL18 0.026 0.03 -10000 0 -0.36 3 3
IL2RA 0.019 0.056 -10000 0 -0.36 13 13
IFNG -0.026 0.14 -10000 0 -0.44 59 59
STAT3 (dimer) -0.032 0.26 -10000 0 -0.72 51 51
HLA-DRB5 0 0.002 -10000 0 -0.021 4 4
FASLG -0.084 0.38 0.58 1 -1.2 52 53
NF kappa B2 p52/RelB -0.05 0.3 -10000 0 -0.87 50 50
CD4 0.016 0.064 -10000 0 -0.36 17 17
SOCS1 0.011 0.086 -10000 0 -0.44 21 21
EntrezGene:6955 0 0.009 -10000 0 -0.034 34 34
CD3D 0.015 0.064 -10000 0 -0.36 16 16
CD3E 0.012 0.073 -10000 0 -0.36 21 21
CD3G -0.004 0.11 -10000 0 -0.37 47 47
IL12Rbeta2/JAK2 0.024 0.066 -10000 0 -0.29 15 15
CCL3 -0.062 0.31 -10000 0 -0.94 44 44
CCL4 -0.057 0.3 -10000 0 -0.93 44 44
HLA-A -0.001 0.008 -10000 0 -0.036 29 29
IL18/IL18R 0.051 0.084 -10000 0 -0.23 35 35
NOS2 -0.072 0.36 -10000 0 -1.2 45 45
IL12/IL12R/TYK2/JAK2/SPHK2 0.007 0.097 0.22 2 -0.35 20 22
IL1R1 -0.064 0.32 -10000 0 -0.98 46 46
IL4 -0.003 0.034 -10000 0 -10000 0 0
JAK2 0.017 0.042 -10000 0 -0.39 3 3
EntrezGene:6957 0 0.009 -10000 0 -0.035 33 33
TCR/CD3/MHC I/CD8 -0.054 0.25 -10000 0 -0.8 52 52
RAB7A -0.018 0.23 0.52 1 -0.77 26 27
lysosomal transport -0.015 0.22 0.51 1 -0.72 27 28
FOS -0.061 0.29 -10000 0 -0.89 48 48
STAT4 (dimer) -0.03 0.28 0.44 2 -0.83 46 48
STAT5A (dimer) -0.067 0.31 -10000 0 -0.84 56 56
GZMA -0.1 0.4 -10000 0 -1.2 61 61
GZMB -0.086 0.31 -10000 0 -0.94 44 44
HLX 0.027 0.016 -10000 0 -0.36 1 1
LCK -0.069 0.32 -10000 0 -0.93 53 53
TCR/CD3/MHC II/CD4 -0.017 0.14 -10000 0 -0.44 43 43
IL2/IL2R 0.05 0.065 -10000 0 -0.26 22 22
MAPK14 -0.031 0.28 -10000 0 -0.88 36 36
CCR5 -0.038 0.29 -10000 0 -0.97 34 34
IL1B -0.022 0.14 -10000 0 -0.44 57 57
STAT6 0.008 0.091 -10000 0 -0.27 1 1
STAT4 0.011 0.08 -10000 0 -0.36 27 27
STAT3 0.027 0.004 -10000 0 -10000 0 0
STAT1 0.027 0.019 -10000 0 -0.44 1 1
NFKB1 0.027 0.005 -10000 0 -10000 0 0
NFKB2 0.027 0.006 -10000 0 -10000 0 0
IL12B 0.012 0.05 -10000 0 -0.44 4 4
CD8A -0.003 0.1 -10000 0 -0.37 45 45
CD8B 0.016 0.063 -10000 0 -0.37 15 15
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.002 0.1 0.36 20 -0.22 2 22
IL2RB 0.018 0.058 -10000 0 -0.36 14 14
proteasomal ubiquitin-dependent protein catabolic process -0.023 0.26 0.43 2 -0.76 45 47
IL2RG 0.026 0.027 -10000 0 -0.36 3 3
IL12 0.022 0.065 -10000 0 -0.29 12 12
STAT5A 0.027 0.004 -10000 0 -10000 0 0
CD247 0.017 0.06 -10000 0 -0.36 14 14
IL2 -0.006 0.02 -10000 0 -10000 0 0
SPHK2 0.027 0.016 -10000 0 -0.36 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.014 0.056 -10000 0 -0.38 8 8
IL12/IL12R/TYK2/JAK2 -0.069 0.35 0.41 2 -0.99 54 56
MAP2K3 -0.051 0.3 -10000 0 -0.88 46 46
RIPK2 0.024 0.01 -10000 0 -10000 0 0
MAP2K6 -0.025 0.27 -10000 0 -0.86 35 35
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.001 0.002 -10000 0 -0.023 5 5
IL18RAP 0.009 0.086 -10000 0 -0.37 29 29
IL12Rbeta1/TYK2 0.022 0.07 -10000 0 -0.29 20 20
EOMES -0.043 0.25 -10000 0 -1.1 32 32
STAT1 (dimer) -0.029 0.25 -10000 0 -0.73 43 43
T cell proliferation -0.012 0.22 0.38 2 -0.62 42 44
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.022 0.052 -10000 0 -0.37 10 10
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.019 0.24 -10000 0 -0.68 40 40
ATF2 -0.029 0.26 -10000 0 -0.84 32 32
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.017 0.074 0.82 3 -10000 0 3
VDR 0.028 0.003 -10000 0 -10000 0 0
FAM120B 0.027 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.051 0.11 -10000 0 -0.35 6 6
RXRs/LXRs/DNA/Oxysterols -0.038 0.11 -10000 0 -0.4 10 10
MED1 0.028 0.019 0.36 2 -10000 0 2
mol:9cRA 0.003 0.007 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.033 0.1 0.17 1 -0.34 6 7
RXRs/NUR77 -0.041 0.13 -10000 0 -0.32 12 12
RXRs/PPAR -0.061 0.11 -10000 0 -0.28 29 29
NCOR2 0.027 0.016 -10000 0 -0.36 1 1
VDR/VDR/Vit D3 0.02 0.002 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.061 0.028 0.24 1 -10000 0 1
RARA 0.027 0.021 0.36 1 -0.36 1 2
NCOA1 0.028 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.028 0.002 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.046 0.026 0.22 1 -0.18 5 6
RARG 0.028 0.002 -10000 0 -10000 0 0
RPS6KB1 0.031 0.072 0.57 9 -0.34 1 10
RARs/THRs/DNA/SMRT -0.033 0.1 0.17 1 -0.34 7 8
THRA 0.027 0.014 0.36 1 -10000 0 1
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.02 0.002 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.042 0.12 -10000 0 -0.29 2 2
NR1H4 -0.18 0.19 -10000 0 -0.36 308 308
RXRs/LXRs/DNA -0.021 0.13 -10000 0 -0.34 3 3
NR1H2 0.029 0.019 -10000 0 -0.36 1 1
NR1H3 0.03 0.012 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.035 0.12 -10000 0 -0.24 2 2
NR4A1 0.02 0.059 -10000 0 -0.43 10 10
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.15 0.14 -10000 0 -0.35 147 147
RXRG -0.13 0.19 -10000 0 -0.36 253 253
RXR alpha/CCPG 0.041 0.017 -10000 0 -0.25 1 1
RXRA 0.029 0.019 -10000 0 -0.36 1 1
RXRB 0.03 0.012 -10000 0 -10000 0 0
THRB -0.085 0.18 -10000 0 -0.36 177 177
PPARG 0.026 0.022 -10000 0 -0.36 2 2
PPARD 0.027 0.016 -10000 0 -0.36 1 1
TNF -0.041 0.12 -10000 0 -0.85 6 6
mol:Oxysterols 0.003 0.006 -10000 0 -10000 0 0
cholesterol transport -0.037 0.1 -10000 0 -0.4 10 10
PPARA 0.026 0.006 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.025 0.032 -10000 0 -0.36 4 4
RXRs/NUR77/BCL2 -0.085 0.12 -10000 0 -0.3 78 78
SREBF1 -0.03 0.09 -10000 0 -0.49 2 2
RXRs/RXRs/DNA/9cRA -0.042 0.12 -10000 0 -0.29 2 2
ABCA1 -0.043 0.13 -10000 0 -0.89 7 7
RARs/THRs 0.003 0.12 0.25 1 -0.35 2 3
RXRs/FXR -0.15 0.16 -10000 0 -0.36 141 141
BCL2 0.013 0.052 -10000 0 -0.36 11 11
HIF-2-alpha transcription factor network

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
MMP14 -0.029 0.16 -10000 0 -0.62 35 35
oxygen homeostasis -0.01 0.01 -10000 0 -10000 0 0
TCEB2 0.026 0.027 -10000 0 -0.44 2 2
TCEB1 0.024 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.041 0.074 -10000 0 -10000 0 0
EPO -0.14 0.16 -10000 0 -0.56 15 15
FIH (dimer) 0.008 0.023 -10000 0 -10000 0 0
APEX1 -0.015 0.024 -10000 0 -10000 0 0
SERPINE1 -0.19 0.23 -10000 0 -0.58 115 115
FLT1 -0.002 0.089 -10000 0 -0.59 12 12
ADORA2A -0.15 0.17 0.36 1 -0.53 49 50
germ cell development -0.15 0.17 -10000 0 -0.53 53 53
SLC11A2 -0.15 0.17 -10000 0 -0.55 49 49
BHLHE40 -0.16 0.18 -10000 0 -0.55 50 50
HIF1AN 0.008 0.023 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.084 0.11 -10000 0 -0.39 4 4
ETS1 0.036 0.018 -10000 0 -0.36 1 1
CITED2 -0.007 0.11 -10000 0 -0.71 12 12
KDR -0.01 0.13 -10000 0 -0.62 22 22
PGK1 -0.15 0.18 -10000 0 -0.55 49 49
SIRT1 0.027 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT -0.17 0.21 -10000 0 -0.62 50 50
EPAS1 -0.047 0.066 -10000 0 -0.28 6 6
SP1 0.031 0.01 -10000 0 -10000 0 0
ABCG2 -0.33 0.24 -10000 0 -0.62 146 146
EFNA1 -0.15 0.17 -10000 0 -0.55 49 49
FXN -0.15 0.17 0.36 1 -0.53 49 50
POU5F1 -0.16 0.18 -10000 0 -0.55 53 53
neuron apoptosis 0.16 0.2 0.61 50 -10000 0 50
EP300 0.026 0.006 -10000 0 -10000 0 0
EGLN3 0.005 0.035 -10000 0 -0.36 3 3
EGLN2 0.008 0.028 -10000 0 -0.37 1 1
EGLN1 0.009 0.024 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.047 0.024 -10000 0 -0.27 1 1
VHL 0.027 0.004 -10000 0 -10000 0 0
ARNT -0.013 0.029 -10000 0 -0.38 1 1
SLC2A1 -0.16 0.18 0.36 1 -0.55 64 65
TWIST1 -0.16 0.19 0.36 1 -0.61 58 59
ELK1 0.032 0.006 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.085 0.11 -10000 0 -0.39 3 3
VEGFA -0.15 0.17 -10000 0 -0.55 49 49
CREBBP 0.027 0.004 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.055 0.062 -10000 0 -10000 0 0
SMARCC2 0.025 0.017 -10000 0 -10000 0 0
SMARCC1 0.025 0.018 -10000 0 -10000 0 0
TBX21 -0.095 0.17 0.29 2 -0.63 43 45
SUMO2 0.027 0.008 -10000 0 -10000 0 0
STAT1 (dimer) 0.033 0.019 -10000 0 -0.43 1 1
FKBP4 0.027 0.014 0.36 1 -10000 0 1
FKBP5 0.027 0.016 -10000 0 -0.36 1 1
GR alpha/HSP90/FKBP51/HSP90 0.087 0.1 0.3 19 -0.27 11 30
PRL -0.041 0.087 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.16 0.19 0.5 56 -0.39 6 62
RELA -0.039 0.073 -10000 0 -0.22 2 2
FGG 0.075 0.18 0.44 24 -0.46 19 43
GR beta/TIF2 0.073 0.11 0.29 24 -0.3 23 47
IFNG -0.19 0.16 -10000 0 -0.59 43 43
apoptosis -0.001 0.14 0.46 16 -0.5 9 25
CREB1 0.028 0.018 -10000 0 -10000 0 0
histone acetylation -0.042 0.098 0.32 5 -0.34 20 25
BGLAP -0.044 0.088 -10000 0 -0.44 2 2
GR/PKAc 0.066 0.13 0.29 13 -0.32 20 33
NF kappa B1 p50/RelA -0.064 0.12 -10000 0 -0.31 37 37
SMARCD1 0.025 0.018 -10000 0 -10000 0 0
MDM2 0.057 0.059 0.22 31 -0.24 1 32
GATA3 0.023 0.044 -10000 0 -0.38 5 5
AKT1 0.022 0.006 -10000 0 -10000 0 0
CSF2 -0.12 0.12 0.29 1 -0.41 18 19
GSK3B 0.028 0.007 -10000 0 -10000 0 0
NR1I3 0.003 0.15 0.46 15 -0.62 8 23
CSN2 0.072 0.12 0.35 25 -0.36 5 30
BRG1/BAF155/BAF170/BAF60A 0.064 0.052 -10000 0 -0.26 4 4
NFATC1 0.019 0.03 -10000 0 -0.36 3 3
POU2F1 0.026 0.025 -10000 0 -0.44 1 1
CDKN1A -0.009 0.085 -10000 0 -1.3 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.006 -10000 0 -10000 0 0
SFN 0.025 0.023 -10000 0 -0.36 2 2
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.092 0.1 0.32 9 -0.28 5 14
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.001 0.13 0.44 13 -0.56 6 19
JUN -0.18 0.12 -10000 0 -0.42 51 51
IL4 -0.05 0.082 -10000 0 -0.43 8 8
CDK5R1 0.027 0.02 -10000 0 -0.44 1 1
PRKACA 0.027 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.22 0.16 -10000 0 -0.41 163 163
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.097 0.1 0.3 16 -0.27 8 24
cortisol/GR alpha (monomer) 0.19 0.21 0.58 60 -0.45 5 65
NCOA2 0.022 0.028 -10000 0 -0.36 3 3
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.074 0.054 -10000 0 -0.42 6 6
AP-1/NFAT1-c-4 -0.28 0.17 -10000 0 -0.56 89 89
AFP -0.13 0.11 -10000 0 -0.49 9 9
SUV420H1 0.027 0.004 -10000 0 -10000 0 0
IRF1 0.092 0.1 0.4 10 -0.35 1 11
TP53 0.034 0.026 -10000 0 -0.48 1 1
PPP5C 0.027 0.004 -10000 0 -10000 0 0
KRT17 -0.32 0.17 -10000 0 -0.56 116 116
KRT14 -0.076 0.18 0.39 10 -0.84 19 29
TBP 0.033 0.011 -10000 0 -10000 0 0
CREBBP 0.034 0.069 0.32 9 -0.25 21 30
HDAC1 0.026 0.008 -10000 0 -10000 0 0
HDAC2 0.036 0.014 -10000 0 -10000 0 0
AP-1 -0.28 0.17 -10000 0 -0.56 95 95
MAPK14 0.028 0.007 -10000 0 -10000 0 0
MAPK10 -0.019 0.12 -10000 0 -0.36 73 73
MAPK11 0.025 0.029 -10000 0 -0.45 2 2
KRT5 -0.2 0.18 -10000 0 -0.6 61 61
interleukin-1 receptor activity 0.009 0.012 -10000 0 -10000 0 0
NCOA1 0.03 0.001 -10000 0 -10000 0 0
STAT1 0.033 0.019 -10000 0 -0.44 1 1
CGA -0.055 0.094 -10000 0 -0.4 10 10
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.083 0.14 0.35 35 -0.4 14 49
MAPK3 0.027 0.018 -10000 0 -0.36 1 1
MAPK1 0.027 0.009 -10000 0 -10000 0 0
ICAM1 -0.1 0.14 -10000 0 -0.56 8 8
NFKB1 -0.039 0.073 -10000 0 -0.25 3 3
MAPK8 -0.13 0.11 -10000 0 -0.37 43 43
MAPK9 0.028 0.007 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.003 0.15 0.47 16 -0.52 9 25
BAX -0.006 0.072 -10000 0 -10000 0 0
POMC -0.099 0.25 -10000 0 -1.3 22 22
EP300 0.034 0.07 0.32 10 -0.25 21 31
cortisol/GR alpha (dimer)/p53 0.16 0.19 0.52 50 -0.41 3 53
proteasomal ubiquitin-dependent protein catabolic process 0.035 0.059 0.26 19 -0.21 1 20
SGK1 0.001 0.26 -10000 0 -1.2 25 25
IL13 -0.14 0.13 -10000 0 -0.57 4 4
IL6 -0.13 0.19 -10000 0 -0.52 80 80
PRKACG -0.006 0.032 -10000 0 -0.44 2 2
IL5 -0.12 0.11 -10000 0 -0.65 2 2
IL2 -0.18 0.14 -10000 0 -0.54 33 33
CDK5 0.027 0.006 -10000 0 -10000 0 0
PRKACB -0.019 0.12 -10000 0 -0.36 72 72
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
IL8 -0.21 0.21 -10000 0 -0.48 125 125
CDK5R1/CDK5 0.039 0.019 -10000 0 -0.31 1 1
NF kappa B1 p50/RelA/PKAc -0.056 0.12 -10000 0 -0.32 18 18
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.17 0.18 0.49 59 -0.37 4 63
SMARCA4 0.025 0.017 -10000 0 -10000 0 0
chromatin remodeling 0.081 0.15 0.35 28 -0.49 20 48
NF kappa B1 p50/RelA/Cbp -0.011 0.13 0.35 6 -0.38 6 12
JUN (dimer) -0.18 0.12 -10000 0 -0.42 51 51
YWHAH 0.027 0.006 -10000 0 -10000 0 0
VIPR1 -0.09 0.17 -10000 0 -0.71 31 31
NR3C1 0.092 0.15 0.4 34 -0.37 32 66
NR4A1 0.006 0.12 -10000 0 -0.5 30 30
TIF2/SUV420H1 0.034 0.025 -10000 0 -0.25 3 3
MAPKKK cascade -0.001 0.14 0.46 16 -0.5 9 25
cortisol/GR alpha (dimer)/Src-1 0.18 0.19 0.52 60 -0.4 4 64
PBX1 0.019 0.058 -10000 0 -0.36 13 13
POU1F1 0.002 0.033 -10000 0 -0.53 1 1
SELE -0.13 0.18 -10000 0 -0.52 60 60
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.081 0.15 0.35 28 -0.5 20 48
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.17 0.18 0.49 59 -0.37 4 63
mol:cortisol 0.093 0.11 0.31 65 -10000 0 65
MMP1 -0.24 0.17 -10000 0 -0.82 12 12
Nongenotropic Androgen 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
PTK2 0.006 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.02 0.079 -10000 0 -0.2 62 62
regulation of S phase of mitotic cell cycle 0.003 0.047 -10000 0 -0.2 30 30
GNAO1 -0.12 0.19 -10000 0 -0.36 224 224
HRAS 0.027 0.016 -10000 0 -0.36 1 1
SHBG/T-DHT 0.011 0.037 -10000 0 -0.32 7 7
PELP1 0.023 0.01 -10000 0 -10000 0 0
AKT1 0.007 0.002 -10000 0 -10000 0 0
MAP2K1 0.049 0.097 0.19 49 -10000 0 49
T-DHT/AR -0.002 0.072 -10000 0 -0.25 47 47
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.009 10 10
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.015 0.067 -10000 0 -0.36 19 19
mol:GDP -0.019 0.078 -10000 0 -0.28 45 45
cell proliferation 0.041 0.11 0.26 9 -0.37 6 15
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
FOS 0.034 0.12 0.26 1 -0.73 10 11
mol:Ca2+ -0.017 0.03 -10000 0 -0.078 68 68
MAPK3 0.046 0.1 0.27 10 -0.28 2 12
MAPK1 0.021 0.1 0.21 1 -0.41 21 22
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.005 10 10
cAMP biosynthetic process 0.002 0.039 0.11 2 -0.3 7 9
GNG2 0.011 0.074 -10000 0 -0.36 23 23
potassium channel inhibitor activity 0 0.001 -10000 0 -0.005 10 10
HRAS/GTP 0.017 0.051 -10000 0 -0.22 1 1
actin cytoskeleton reorganization 0.035 0.021 -10000 0 -0.17 1 1
SRC 0.017 0.014 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.005 10 10
PI3K 0.035 0.013 -10000 0 -0.21 1 1
apoptosis -0.042 0.096 0.35 12 -0.22 5 17
T-DHT/AR/PELP1 0.012 0.064 -10000 0 -0.2 47 47
HRAS/GDP -0.008 0.078 -10000 0 -0.29 39 39
CREB1 0.042 0.1 0.24 3 -0.37 12 15
RAC1-CDC42/GTP 0.044 0.025 -10000 0 -0.18 1 1
AR -0.009 0.1 -10000 0 -0.36 47 47
GNB1 0.026 0.006 -10000 0 -10000 0 0
RAF1 0.064 0.097 0.2 53 -10000 0 53
RAC1-CDC42/GDP 0.033 0.094 -10000 0 -0.31 29 29
T-DHT/AR/PELP1/Src 0.016 0.054 -10000 0 -0.19 28 28
MAP2K2 0.049 0.098 0.19 51 -0.31 1 52
T-DHT/AR/PELP1/Src/PI3K 0.003 0.048 -10000 0 -0.2 30 30
GNAZ 0.023 0.035 -10000 0 -0.36 5 5
SHBG 0.01 0.061 -10000 0 -0.52 7 7
Gi family/GNB1/GNG2/GDP -0.1 0.19 -10000 0 -0.46 85 85
mol:T-DHT 0 0.001 -10000 0 -0.004 10 10
RAC1 0.025 0.008 -10000 0 -10000 0 0
GNRH1 0.005 0.011 -10000 0 -0.25 1 1
Gi family/GTP -0.062 0.11 -10000 0 -0.3 67 67
CDC42 0.025 0.017 -10000 0 -0.36 1 1
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.006 0.11 -10000 0 -0.46 29 29
NFATC2 -0.004 0.12 -10000 0 -0.55 11 11
NFATC3 -0.018 0.066 -10000 0 -0.28 6 6
CD40LG -0.18 0.27 -10000 0 -0.82 37 37
ITCH 0.018 0.018 -10000 0 -10000 0 0
CBLB 0.029 0.026 -10000 0 -0.36 2 2
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.11 0.2 -10000 0 -0.8 25 25
JUNB 0.026 0.022 -10000 0 -0.36 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.037 0.023 -10000 0 -0.26 3 3
T cell anergy 0.037 0.055 0.24 1 -0.31 1 2
TLE4 -0.004 0.085 -10000 0 -0.46 8 8
Jun/NFAT1-c-4/p21SNFT -0.078 0.18 -10000 0 -0.78 10 10
AP-1/NFAT1-c-4 -0.2 0.27 -10000 0 -0.88 31 31
IKZF1 -0.014 0.13 -10000 0 -0.62 21 21
T-helper 2 cell differentiation -0.053 0.16 0.4 1 -0.67 20 21
AP-1/NFAT1 -0.032 0.1 -10000 0 -0.41 7 7
CALM1 0.034 0.017 -10000 0 -10000 0 0
EGR2 -0.039 0.16 -10000 0 -1 9 9
EGR3 -0.041 0.17 -10000 0 -0.9 14 14
NFAT1/FOXP3 -0.002 0.12 -10000 0 -0.48 16 16
EGR1 0.027 0.023 -10000 0 -0.36 2 2
JUN -0.032 0.047 -10000 0 -10000 0 0
EGR4 -0.051 0.17 -10000 0 -0.44 101 101
mol:Ca2+ 0.009 0.011 -10000 0 -10000 0 0
GBP3 -0.024 0.15 -10000 0 -0.58 34 34
FOSL1 -0.27 0.23 0.36 1 -0.44 384 385
NFAT1-c-4/MAF/IRF4 -0.069 0.18 -10000 0 -0.75 21 21
DGKA -0.003 0.082 -10000 0 -0.44 6 6
CREM 0.027 0.002 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.041 0.15 -10000 0 -0.78 8 8
CTLA4 -0.017 0.11 -10000 0 -0.48 22 22
NFAT1-c-4 (dimer)/EGR1 -0.04 0.15 -10000 0 -0.78 8 8
NFAT1-c-4 (dimer)/EGR4 -0.071 0.17 -10000 0 -0.82 9 9
FOS -0.033 0.057 -10000 0 -0.37 6 6
IFNG -0.061 0.18 -10000 0 -0.7 21 21
T cell activation -0.021 0.14 -10000 0 -0.57 2 2
MAF 0.019 0.058 -10000 0 -0.36 14 14
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.038 0.14 0.78 11 -10000 0 11
TNF -0.066 0.15 -10000 0 -0.81 9 9
FASLG -0.085 0.34 -10000 0 -1.2 44 44
TBX21 -0.001 0.093 -10000 0 -0.36 34 34
BATF3 0.022 0.049 -10000 0 -0.43 7 7
PRKCQ 0.019 0.052 -10000 0 -0.36 8 8
PTPN1 -0.003 0.082 -10000 0 -0.44 6 6
NFAT1-c-4/ICER1 -0.041 0.15 -10000 0 -0.76 9 9
GATA3 0.024 0.037 -10000 0 -0.38 5 5
T-helper 1 cell differentiation -0.06 0.18 -10000 0 -0.68 21 21
IL2RA -0.1 0.2 -10000 0 -0.76 28 28
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.004 0.08 -10000 0 -0.42 7 7
E2F1 0.021 0.057 0.36 9 -0.44 4 13
PPARG 0.026 0.022 -10000 0 -0.36 2 2
SLC3A2 -0.003 0.08 -10000 0 -0.44 6 6
IRF4 -0.072 0.17 -10000 0 -0.36 156 156
PTGS2 -0.18 0.27 -10000 0 -0.81 41 41
CSF2 -0.25 0.32 -10000 0 -0.76 80 80
JunB/Fra1/NFAT1-c-4 -0.16 0.18 -10000 0 -0.77 17 17
IL4 -0.054 0.17 0.4 1 -0.7 20 21
IL5 -0.17 0.26 -10000 0 -0.79 33 33
IL2 -0.022 0.14 -10000 0 -0.58 2 2
IL3 -0.033 0.089 -10000 0 -0.67 8 8
RNF128 0.029 0.026 -10000 0 -0.46 1 1
NFATC1 -0.038 0.14 -10000 0 -0.79 11 11
CDK4 0.024 0.096 0.57 7 -10000 0 7
PTPRK -0.004 0.081 -10000 0 -0.42 7 7
IL8 -0.27 0.32 -10000 0 -0.77 81 81
POU2F1 0.026 0.02 -10000 0 -0.44 1 1
Noncanonical Wnt signaling 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
NFATC2 0.005 0.063 -10000 0 -0.36 17 17
GNB1/GNG2 -0.028 0.12 -10000 0 -0.33 25 25
mol:DAG -0.026 0.082 0.19 1 -0.34 15 16
PLCG1 -0.027 0.084 0.19 1 -0.34 15 16
YES1 -0.035 0.091 0.15 1 -0.29 37 38
FZD3 0.021 0.035 0.36 2 -0.44 2 4
FZD6 0.024 0.01 -10000 0 -10000 0 0
G protein 0.021 0.13 0.28 13 -0.36 15 28
MAP3K7 -0.033 0.076 -10000 0 -0.32 17 17
mol:Ca2+ -0.026 0.08 0.19 1 -0.33 15 16
mol:IP3 -0.026 0.082 0.19 1 -0.34 15 16
NLK -0.003 0.094 -10000 0 -0.77 9 9
GNB1 0.026 0.006 -10000 0 -10000 0 0
CAMK2A -0.032 0.082 0.18 1 -0.34 17 18
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.033 0.1 0.17 1 -0.3 44 45
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
GNAS -0.022 0.086 0.33 1 -0.32 22 23
GO:0007205 -0.029 0.08 0.19 1 -0.33 15 16
WNT6 -0.011 0.11 -10000 0 -0.38 52 52
WNT4 0.013 0.072 -10000 0 -0.38 20 20
NFAT1/CK1 alpha -0.019 0.092 -10000 0 -0.39 12 12
GNG2 0.011 0.074 -10000 0 -0.36 23 23
WNT5A 0.022 0.05 -10000 0 -0.44 7 7
WNT11 -0.069 0.19 -10000 0 -0.44 127 127
CDC42 -0.035 0.087 0.19 1 -0.28 28 29
Nectin adhesion 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
PDGFRB 0.022 0.05 -10000 0 -0.44 7 7
alphaV beta3 Integrin 0.037 0.032 -10000 0 -0.25 7 7
PTK2 0.016 0.066 -10000 0 -0.34 12 12
positive regulation of JNK cascade 0.028 0.068 -10000 0 -0.28 9 9
CDC42/GDP 0.059 0.097 0.32 3 -0.36 10 13
Rac1/GDP 0.052 0.095 0.32 2 -0.36 10 12
RAP1B 0.028 0.003 -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 0.047 0.084 -10000 0 -0.34 9 9
nectin-3/I-afadin 0.032 0.047 -10000 0 -0.25 16 16
RAPGEF1 0.033 0.092 0.32 3 -0.4 9 12
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.023 0.088 -10000 0 -0.44 9 9
PDGFB-D/PDGFRB 0.022 0.05 -10000 0 -0.44 7 7
TLN1 -0.001 0.025 -10000 0 -0.3 2 2
Rap1/GTP 0.022 0.065 -10000 0 -0.3 7 7
IQGAP1 0.027 0.006 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.05 0.013 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.032 0.047 -10000 0 -0.25 16 16
PVR 0.027 0.003 -10000 0 -10000 0 0
Necl-5(dimer) 0.027 0.003 -10000 0 -10000 0 0
mol:GDP 0.052 0.11 0.33 3 -0.43 11 14
MLLT4 0.027 0.004 -10000 0 -10000 0 0
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
PI3K 0.066 0.057 -10000 0 -0.23 7 7
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.039 0.008 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.029 0.077 -10000 0 -0.29 10 10
PVRL1 0.027 0.004 -10000 0 -10000 0 0
PVRL3 0.017 0.062 -10000 0 -0.36 16 16
PVRL2 0.027 0.003 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
CDH1 0.028 0.003 -10000 0 -10000 0 0
CLDN1 -0.4 0.14 0.36 3 -0.44 556 559
JAM-A/CLDN1 -0.22 0.096 -10000 0 -0.25 542 542
SRC 0.006 0.095 -10000 0 -0.44 16 16
ITGB3 0.023 0.041 -10000 0 -0.36 7 7
nectin-1(dimer)/I-afadin/I-afadin 0.039 0.008 -10000 0 -10000 0 0
FARP2 0.053 0.11 0.35 2 -0.52 3 5
RAC1 0.025 0.008 -10000 0 -10000 0 0
CTNNA1 0.027 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.047 0.044 -10000 0 -0.21 16 16
nectin-1/I-afadin 0.039 0.008 -10000 0 -10000 0 0
nectin-2/I-afadin 0.04 0.008 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.033 0.013 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.046 0.044 -10000 0 -0.21 16 16
CDC42/GTP/IQGAP1/filamentous actin 0.033 0.015 -10000 0 -0.21 1 1
F11R 0.027 0.004 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.028 0.068 -10000 0 -0.28 9 9
alphaV/beta3 Integrin/Talin 0.008 0.069 -10000 0 -0.28 4 4
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.04 0.008 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.04 0.008 -10000 0 -10000 0 0
PIP5K1C 0.002 0.028 -10000 0 -0.27 3 3
VAV2 0.047 0.12 0.34 2 -0.44 11 13
RAP1/GDP 0.061 0.09 0.29 2 -0.34 8 10
ITGAV 0.028 0.002 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.047 0.044 -10000 0 -0.21 16 16
nectin-3(dimer)/I-afadin/I-afadin 0.032 0.047 -10000 0 -0.25 16 16
Rac1/GTP 0.037 0.093 -10000 0 -0.35 10 10
PTPRM 0.007 0.034 -10000 0 -0.34 3 3
E-cadherin/beta catenin/alpha catenin 0.076 0.023 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.025 0.017 -10000 0 -0.36 1 1
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.039 0.019 0.26 2 -0.25 1 3
alphaV beta3 Integrin 0.032 0.075 -10000 0 -0.22 46 46
PTK2 0.031 0.11 0.31 19 -0.39 5 24
IGF1R 0.027 0.006 -10000 0 -10000 0 0
PI4KB 0.027 0.004 -10000 0 -10000 0 0
MFGE8 0.027 0.006 -10000 0 -10000 0 0
SRC 0.017 0.014 -10000 0 -10000 0 0
CDKN1B 0.01 0.044 -10000 0 -0.38 2 2
VEGFA 0.028 0.019 0.36 2 -10000 0 2
ILK 0.011 0.039 -10000 0 -10000 0 0
ROCK1 0.022 0.019 -10000 0 -0.36 1 1
AKT1 0.004 0.033 -10000 0 -10000 0 0
PTK2B -0.007 0.037 0.19 14 -10000 0 14
alphaV/beta3 Integrin/JAM-A 0.03 0.08 -10000 0 -0.24 20 20
CBL 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.045 0.037 -10000 0 -0.23 10 10
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.008 0.11 -10000 0 -0.19 131 131
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.016 0.039 0.15 1 -0.32 4 5
alphaV/beta3 Integrin/Syndecan-1 0.052 0.03 -10000 0 -0.21 7 7
PI4KA 0.027 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.021 0.13 -10000 0 -0.35 40 40
PI4 Kinase 0.039 0.01 -10000 0 -10000 0 0
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
alphaV/beta3 Integrin/Osteopontin -0.088 0.16 -10000 0 -0.27 268 268
RPS6KB1 -0.069 0.1 -10000 0 -0.34 40 40
TLN1 0.027 0.004 -10000 0 -10000 0 0
MAPK3 -0.042 0.15 -10000 0 -0.48 53 53
GPR124 0.023 0.018 -10000 0 -0.36 1 1
MAPK1 -0.041 0.15 -10000 0 -0.48 53 53
PXN 0.028 0.002 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.028 0.081 -10000 0 -0.22 58 58
cell adhesion 0.04 0.036 -10000 0 -0.22 5 5
ANGPTL3 -0.003 0.038 -10000 0 -0.44 3 3
VEGFR2 homodimer/VEGFA homodimer/Src 0.033 0.029 0.25 1 -10000 0 1
IGF-1R heterotetramer 0.026 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
TGFBR2 0.027 0.003 -10000 0 -10000 0 0
ITGB3 0.023 0.041 -10000 0 -0.36 7 7
IGF1 -0.062 0.16 -10000 0 -0.36 141 141
RAC1 0.025 0.008 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.043 0.035 -10000 0 -0.2 8 8
apoptosis 0.028 0.002 -10000 0 -10000 0 0
CD47 0.027 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.051 0.03 -10000 0 -0.21 7 7
VCL 0.027 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.006 0.11 -10000 0 -0.22 104 104
CSF1 0.025 0.027 -10000 0 -0.36 3 3
PIK3C2A 0.01 0.044 -10000 0 -0.38 2 2
PI4 Kinase/Pyk2 0.01 0.068 -10000 0 -0.31 2 2
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.064 0.034 0.25 2 -0.19 6 8
FAK1/Vinculin 0.045 0.1 0.25 32 -0.34 3 35
alphaV beta3/Integrin/ppsTEM5 0.044 0.035 -10000 0 -0.21 8 8
RHOA 0.027 0.004 -10000 0 -10000 0 0
VTN 0.006 0.082 -10000 0 -0.44 19 19
BCAR1 0.027 0.016 -10000 0 -0.36 1 1
FGF2 -0.001 0.099 -10000 0 -0.36 43 43
F11R -0.005 0.067 -10000 0 -0.25 42 42
alphaV/beta3 Integrin/Lactadherin 0.05 0.031 -10000 0 -0.21 7 7
alphaV/beta3 Integrin/TGFBR2 0.051 0.03 -10000 0 -0.21 7 7
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.065 0.027 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.048 0.028 -10000 0 -0.19 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.001 0.11 -10000 0 -0.43 36 36
alphaV/beta3 Integrin/Pyk2 0.036 0.039 -10000 0 -10000 0 0
SDC1 0.028 0 -10000 0 -10000 0 0
VAV3 -0.025 0.049 0.18 3 -10000 0 3
PTPN11 0.028 0.002 -10000 0 -10000 0 0
IRS1 0.028 0.002 -10000 0 -10000 0 0
FAK1/Paxillin 0.045 0.1 0.25 31 -0.33 4 35
cell migration 0.039 0.096 0.22 52 -0.31 3 55
ITGAV 0.028 0.002 -10000 0 -10000 0 0
PI3K 0.041 0.083 -10000 0 -0.33 2 2
SPP1 -0.18 0.23 -10000 0 -0.44 262 262
KDR 0.026 0.016 -10000 0 -0.36 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.028 0.002 -10000 0 -10000 0 0
COL4A3 -0.013 0.11 -10000 0 -0.38 51 51
angiogenesis -0.038 0.15 0.24 1 -0.48 54 55
Rac1/GTP 0.009 0.054 -10000 0 -10000 0 0
EDIL3 -0.04 0.15 -10000 0 -0.36 106 106
cell proliferation 0.051 0.03 -10000 0 -0.21 7 7
Caspase cascade in apoptosis

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
TOP1 -0.037 0.1 -10000 0 -0.33 38 38
ACTA1 -0.054 0.1 -10000 0 -0.34 34 34
NUMA1 -0.037 0.11 0.2 1 -0.36 38 39
SPTAN1 -0.054 0.1 0.21 1 -0.35 30 31
LIMK1 -0.048 0.11 0.26 7 -0.34 30 37
BIRC3 0.02 0.05 -10000 0 -0.37 10 10
BIRC2 0.026 0.016 -10000 0 -0.36 1 1
BAX 0.027 0.004 -10000 0 -10000 0 0
CASP10 -0.077 0.12 -10000 0 -0.28 152 152
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.028 0.002 -10000 0 -10000 0 0
PTK2 -0.035 0.11 -10000 0 -0.33 41 41
DIABLO 0.028 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes -0.053 0.1 0.21 1 -0.34 30 31
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.027 0.003 -10000 0 -10000 0 0
GSN -0.057 0.11 0.19 5 -0.35 35 40
MADD 0.028 0.003 -10000 0 -10000 0 0
TFAP2A -0.001 0.095 0.34 1 -0.57 13 14
BID -0.028 0.064 -10000 0 -0.24 19 19
MAP3K1 -0.019 0.08 -10000 0 -0.43 16 16
TRADD 0.028 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.039 0.01 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.053 0.1 0.22 5 -0.34 33 38
CASP9 0.026 0.007 -10000 0 -10000 0 0
DNA repair 0.008 0.04 0.19 3 -10000 0 3
neuron apoptosis -0.021 0.17 -10000 0 -0.66 37 37
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.048 0.11 -10000 0 -0.34 44 44
APAF1 0.028 0.003 -10000 0 -10000 0 0
CASP6 -0.025 0.16 0.34 1 -0.87 19 20
TRAF2 0.027 0.016 -10000 0 -0.36 1 1
ICAD/CAD -0.054 0.097 -10000 0 -0.34 28 28
CASP7 0.002 0.056 0.23 6 -0.25 12 18
KRT18 0.011 0.038 -10000 0 -0.51 1 1
apoptosis -0.051 0.12 0.31 1 -0.37 41 42
DFFA -0.054 0.1 -10000 0 -0.34 32 32
DFFB -0.054 0.1 0.19 1 -0.34 32 33
PARP1 -0.008 0.04 -10000 0 -0.19 3 3
actin filament polymerization 0.048 0.1 0.33 29 -0.27 3 32
TNF 0.024 0.035 -10000 0 -0.36 5 5
CYCS -0.014 0.056 0.19 1 -0.17 16 17
SATB1 -0.027 0.15 0.32 1 -0.81 19 20
SLK -0.055 0.1 -10000 0 -0.34 33 33
p15 BID/BAX -0.018 0.07 -10000 0 -0.22 20 20
CASP2 0.021 0.045 0.21 16 -0.22 1 17
JNK cascade 0.019 0.079 0.43 16 -10000 0 16
CASP3 -0.056 0.11 -10000 0 -0.35 34 34
LMNB2 0.011 0.11 0.41 3 -0.62 10 13
RIPK1 0.027 0.004 -10000 0 -10000 0 0
CASP4 0.027 0.004 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.064 0.038 -10000 0 -0.24 1 1
negative regulation of DNA binding -0.001 0.094 0.34 1 -0.56 13 14
stress fiber formation -0.055 0.1 -10000 0 -0.34 33 33
GZMB -0.074 0.15 -10000 0 -0.34 152 152
CASP1 0.013 0.019 -10000 0 -0.26 3 3
LMNB1 0.007 0.11 0.35 4 -0.44 22 26
APP -0.022 0.17 -10000 0 -0.68 37 37
TNFRSF1A 0.027 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.007 0 -10000 0 -10000 0 0
VIM -0.047 0.12 0.32 1 -0.38 39 40
LMNA 0.018 0.069 0.35 4 -0.26 16 20
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.022 0.034 -10000 0 -0.23 2 2
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.051 0.098 -10000 0 -0.33 33 33
APAF-1/Caspase 9 -0.02 0.14 -10000 0 -0.61 33 33
nuclear fragmentation during apoptosis -0.036 0.11 0.2 1 -0.35 38 39
CFL2 -0.049 0.1 0.27 3 -0.34 29 32
GAS2 -0.084 0.13 -10000 0 -0.37 68 68
positive regulation of apoptosis 0.016 0.099 0.25 11 -0.43 19 30
PRF1 0.019 0.058 -10000 0 -0.39 12 12
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.028 0.002 -9999 0 -10000 0 0
ITGB7 0.013 0.074 -9999 0 -0.36 23 23
ITGA4 0.014 0.072 -9999 0 -0.36 22 22
alpha4/beta7 Integrin 0.02 0.081 -9999 0 -0.28 40 40
alpha4/beta1 Integrin 0.03 0.055 -9999 0 -0.25 22 22
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.025 0.016 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.01 0.007 -10000 0 -10000 0 0
mol:DAG 0.015 0.061 0.2 42 -10000 0 42
VEGFR1 homodimer/NRP1/VEGFR 121 0.023 0.017 0.22 1 -10000 0 1
CaM/Ca2+ 0.024 0.06 -10000 0 -10000 0 0
HIF1A 0.032 0.009 -10000 0 -10000 0 0
GAB1 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.037 0.076 0.33 2 -10000 0 2
PLCG1 0.015 0.061 0.2 42 -10000 0 42
NOS3 0.081 0.11 0.3 85 -10000 0 85
CBL 0.027 0.004 -10000 0 -10000 0 0
mol:NO 0.083 0.11 0.3 91 -0.4 1 92
FLT1 0.014 0.009 -10000 0 -10000 0 0
PGF 0.011 0.084 -10000 0 -0.44 20 20
VEGFR1 homodimer/NRP2/VEGFR121 0.035 0.029 0.24 1 -10000 0 1
CALM1 0.026 0.007 -10000 0 -10000 0 0
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
eNOS/Hsp90 0.094 0.11 0.3 91 -0.37 1 92
endothelial cell proliferation 0.048 0.12 0.33 57 -10000 0 57
mol:Ca2+ 0.015 0.061 0.2 42 -10000 0 42
MAPK3 0.002 0.056 0.17 41 -10000 0 41
MAPK1 0.001 0.054 0.17 38 -10000 0 38
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
PLGF homodimer 0.01 0.083 -10000 0 -0.44 20 20
PRKACA 0.027 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.019 0.054 -10000 0 -0.36 12 12
VEGFA homodimer 0.028 0.019 0.36 2 -10000 0 2
VEGFR1 homodimer/VEGFA homodimer 0.026 0.024 0.32 2 -10000 0 2
platelet activating factor biosynthetic process 0.074 0.13 0.34 77 -10000 0 77
PI3K 0.038 0.054 -10000 0 -10000 0 0
PRKCA 0.004 0.059 0.18 42 -10000 0 42
PRKCB -0.013 0.074 0.18 33 -10000 0 33
VEGFR1 homodimer/PLGF homodimer 0.018 0.049 -10000 0 -0.26 16 16
VEGFA 0.028 0.019 0.36 2 -10000 0 2
VEGFB 0.027 0.004 -10000 0 -10000 0 0
mol:IP3 0.015 0.061 0.2 42 -10000 0 42
RASA1 0.051 0.074 0.2 126 -10000 0 126
NRP2 0.026 0.027 -10000 0 -0.36 3 3
VEGFR1 homodimer 0.014 0.009 -10000 0 -10000 0 0
VEGFB homodimer 0.027 0.004 -10000 0 -10000 0 0
NCK1 0.028 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.083 0.11 0.29 72 -0.39 1 73
PTPN11 0.028 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.036 0.053 -10000 0 -10000 0 0
mol:L-citrulline 0.083 0.11 0.3 91 -0.4 1 92
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.041 0.045 0.25 1 -10000 0 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.036 0.025 0.24 1 -10000 0 1
CD2AP 0.016 0.066 -10000 0 -0.36 18 18
PI3K/GAB1 0.08 0.072 -10000 0 -10000 0 0
PDPK1 0.039 0.081 0.34 2 -10000 0 2
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.036 0.025 0.24 1 -10000 0 1
mol:NADP 0.083 0.11 0.3 91 -0.4 1 92
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.04 0.044 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.024 0.023 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.022 0.05 -10000 0 -0.44 7 7
Jak2/Leptin Receptor 0.022 0.087 -10000 0 -0.38 10 10
PTP1B/AKT1 0.017 0.078 0.18 12 -0.32 7 19
FYN 0.027 0.005 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.012 0.084 0.2 15 -0.34 7 22
EGFR 0.017 0.029 -10000 0 -0.37 2 2
EGF/EGFR -0.013 0.11 -10000 0 -0.26 44 44
CSF1 0.025 0.027 -10000 0 -0.36 3 3
AKT1 0.026 0.008 -10000 0 -10000 0 0
INSR 0.028 0.004 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.007 0.08 0.2 8 -0.32 10 18
Insulin Receptor/Insulin 0.025 0.074 0.23 1 -0.38 3 4
HCK 0.011 0.047 -10000 0 -0.36 9 9
CRK 0.023 0.01 -10000 0 -10000 0 0
TYK2 0.01 0.082 0.22 16 -0.33 6 22
EGF -0.057 0.16 -10000 0 -0.38 127 127
YES1 0.022 0.019 -10000 0 -0.36 1 1
CAV1 0.02 0.11 0.21 60 -0.3 9 69
TXN 0.027 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.027 0.088 0.2 11 -0.32 6 17
cell migration -0.012 0.084 0.34 7 -0.2 15 22
STAT3 0.027 0.004 -10000 0 -10000 0 0
PRLR 0.017 0.062 -10000 0 -0.36 16 16
ITGA2B 0.006 0.089 -10000 0 -0.44 23 23
CSF1R 0.006 0.088 -10000 0 -0.36 33 33
Prolactin Receptor/Prolactin 0.02 0.069 -10000 0 -0.29 27 27
FGR 0.023 0.034 -10000 0 -0.38 4 4
PTP1B/p130 Cas 0.018 0.084 0.19 10 -0.32 7 17
Crk/p130 Cas 0.018 0.081 0.19 6 -0.33 5 11
DOK1 0.014 0.078 0.2 9 -0.34 5 14
JAK2 0.014 0.088 0.24 3 -0.38 11 14
Jak2/Leptin Receptor/Leptin 0.01 0.097 -10000 0 -0.33 6 6
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
PTPN1 0.012 0.084 0.2 15 -0.34 7 22
LYN 0.024 0.009 -10000 0 -10000 0 0
CDH2 0.005 0.077 -10000 0 -0.37 24 24
SRC 0.025 0.089 -10000 0 -0.41 16 16
ITGB3 0.022 0.042 -10000 0 -0.36 7 7
CAT1/PTP1B 0.005 0.16 0.24 81 -0.41 24 105
CAPN1 0.027 0.005 -10000 0 -10000 0 0
CSK 0.027 0.006 -10000 0 -10000 0 0
PI3K 0.04 0.07 0.21 1 -0.41 2 3
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.014 0.089 -10000 0 -0.31 5 5
negative regulation of transcription 0.014 0.088 0.24 3 -0.37 11 14
FCGR2A 0.023 0.041 -10000 0 -0.43 5 5
FER 0.024 0.025 -10000 0 -0.4 2 2
alphaIIb/beta3 Integrin 0.022 0.074 -10000 0 -0.3 30 30
BLK -0.09 0.17 -10000 0 -0.36 172 172
Insulin Receptor/Insulin/Shc 0.046 0.013 -10000 0 -10000 0 0
RHOA 0.027 0.005 -10000 0 -10000 0 0
LEPR 0.021 0.044 -10000 0 -0.36 8 8
BCAR1 0.027 0.016 -10000 0 -0.36 1 1
p210 bcr-abl/Grb2 0.027 0.004 -10000 0 -10000 0 0
mol:NADPH -0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.065 0.17 0.24 18 -0.41 67 85
PRL -0.005 0.066 -10000 0 -0.44 12 12
SOCS3 0.009 0.12 -10000 0 -1.1 8 8
SPRY2 0.023 0.012 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.047 0.012 -10000 0 -10000 0 0
CSF1/CSF1R 0.017 0.098 0.22 7 -0.33 11 18
Ras protein signal transduction -0.006 0.053 0.44 6 -10000 0 6
IRS1 0.028 0.002 -10000 0 -10000 0 0
INS 0.003 0.018 -10000 0 -10000 0 0
LEP -0.021 0.11 -10000 0 -0.37 54 54
STAT5B 0.018 0.082 0.2 13 -0.33 9 22
STAT5A 0.018 0.082 0.2 13 -0.33 9 22
GRB2 0.027 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.017 0.089 0.2 13 -0.31 12 25
CSN2 -0.007 0.052 -10000 0 -10000 0 0
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
LAT 0.029 0.058 -10000 0 -0.45 5 5
YBX1 0.036 0.008 -10000 0 -10000 0 0
LCK 0.019 0.058 -10000 0 -0.43 10 10
SHC1 0.027 0.004 -10000 0 -10000 0 0
NOX4 -0.19 0.24 0.35 1 -0.44 279 280
Regulation of Androgen receptor activity

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
HDAC1 0.008 0.012 -10000 0 -10000 0 0
SMARCC1 0.013 0.01 -10000 0 -10000 0 0
REL 0.03 0.008 -10000 0 -10000 0 0
HDAC7 -0.022 0.085 0.46 1 -0.36 4 5
JUN 0.026 0.006 -10000 0 -10000 0 0
EP300 0.026 0.006 -10000 0 -10000 0 0
KAT2B 0.01 0.078 -10000 0 -0.36 26 26
KAT5 0.027 0.005 -10000 0 -10000 0 0
MAPK14 0.001 0.03 -10000 0 -0.27 4 4
FOXO1 0.02 0.019 -10000 0 -0.36 1 1
T-DHT/AR -0.004 0.097 -10000 0 -0.37 4 4
MAP2K6 0.016 0.037 -10000 0 -0.37 4 4
BRM/BAF57 0.028 0.031 -10000 0 -0.28 1 1
MAP2K4 0.016 0.02 -10000 0 -10000 0 0
SMARCA2 0.019 0.025 -10000 0 -0.38 1 1
PDE9A -0.15 0.38 -10000 0 -0.88 123 123
NCOA2 0.022 0.028 -10000 0 -0.36 3 3
CEBPA 0.026 0.027 -10000 0 -0.36 3 3
EHMT2 0.026 0.015 0.36 1 -10000 0 1
cell proliferation 0.034 0.13 0.28 37 -0.4 3 40
NR0B1 -0.005 0.045 -10000 0 -0.44 5 5
EGR1 0.019 0.028 -10000 0 -0.36 2 2
RXRs/9cRA -0.059 0.12 -10000 0 -0.19 248 248
AR/RACK1/Src 0.052 0.1 0.28 10 -0.33 1 11
AR/GR -0.019 0.089 -10000 0 -0.3 21 21
GNB2L1 0.027 0.004 -10000 0 -10000 0 0
PKN1 0.027 0.003 -10000 0 -10000 0 0
RCHY1 0.027 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.002 -10000 0 -0.014 2 2
MAPK8 0.003 0.018 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.004 0.061 -10000 0 -0.34 1 1
SRC 0.025 0.084 0.19 119 -10000 0 119
NR3C1 -0.001 0.1 -10000 0 -0.36 44 44
KLK3 -0.21 0.42 -10000 0 -1.1 103 103
APPBP2 0.018 0.025 -10000 0 -0.36 1 1
TRIM24 0.02 0.019 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.005 0.058 0.34 1 -0.3 3 4
TMPRSS2 -0.023 0.15 -10000 0 -0.6 28 28
RXRG -0.15 0.18 -10000 0 -0.36 253 253
mol:9cRA -0.001 0.002 -10000 0 -0.014 2 2
RXRA 0.026 0.016 -10000 0 -0.36 1 1
RXRB 0.027 0.004 -10000 0 -10000 0 0
CARM1 0.028 0.003 -10000 0 -10000 0 0
NR2C2 0.026 0.016 -10000 0 -0.36 1 1
KLK2 0.022 0.09 0.28 2 -0.35 3 5
AR -0.011 0.064 0.16 1 -0.24 38 39
SENP1 0.027 0.003 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
MDM2 0.031 0.02 -10000 0 -0.36 1 1
SRY 0.004 0.011 0.028 105 -10000 0 105
GATA2 0.021 0.052 -10000 0 -0.36 11 11
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 -0.008 0.1 -10000 0 -0.36 42 42
T-DHT/AR/RACK1/Src 0.061 0.1 0.3 13 -0.34 1 14
positive regulation of transcription 0.021 0.052 -10000 0 -0.36 11 11
DNAJA1 0.019 0.02 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.014 -10000 0 -0.28 1 1
NCOA1 0.025 0.02 -10000 0 -10000 0 0
SPDEF -0.065 0.16 -10000 0 -0.36 138 138
T-DHT/AR/TIF2 -0.003 0.068 0.26 3 -0.27 9 12
T-DHT/AR/Hsp90 -0.006 0.055 0.32 1 -0.3 3 4
GSK3B 0.027 0.004 -10000 0 -10000 0 0
NR2C1 0.028 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.016 0.033 0.22 2 -0.25 3 5
SIRT1 0.027 0.005 -10000 0 -10000 0 0
ZMIZ2 0.029 0.014 -10000 0 -10000 0 0
POU2F1 0.015 0.055 -10000 0 -0.44 1 1
T-DHT/AR/DAX-1 -0.014 0.059 0.32 1 -0.3 4 5
CREBBP 0.027 0.004 -10000 0 -10000 0 0
SMARCE1 0.019 0.019 -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 0.026 0.006 -10000 0 -10000 0 0
HDAC4 0.028 0.002 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.007 0.039 0.31 8 -0.27 1 9
CDKN1A -0.008 0.024 -10000 0 -0.59 1 1
KAT2B 0.011 0.078 -10000 0 -0.36 26 26
BAX 0.027 0.004 -10000 0 -10000 0 0
FOXO3 -0.005 0.003 -10000 0 -10000 0 0
FOXO1 0.021 0.019 -10000 0 -0.36 1 1
FOXO4 0.015 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.026 0.006 -10000 0 -10000 0 0
TAT -0.13 0.18 -10000 0 -0.36 224 224
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.025 0.049 -10000 0 -0.26 26 26
PPARGC1A -0.026 0.13 -10000 0 -0.36 84 84
FHL2 0.028 0.001 -10000 0 -10000 0 0
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.037 0.011 -10000 0 -10000 0 0
HIST2H4A 0.007 0.039 0.27 1 -0.31 8 9
SIRT1/FOXO3a 0.019 0.02 -10000 0 -10000 0 0
SIRT1 0.024 0.008 0.19 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.052 0.013 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.015 0.046 -10000 0 -0.21 7 7
apoptosis -0.05 0.016 -10000 0 -10000 0 0
SIRT1/PGC1A 0 0.084 -10000 0 -0.21 83 83
p53/SIRT1 0.027 0.019 0.37 1 -10000 0 1
SIRT1/FOXO4 0.023 0.031 -10000 0 -0.2 2 2
FOXO1/FHL2/SIRT1 0.039 0.025 -10000 0 -0.19 1 1
HIST1H1E 0.006 0.038 0.19 2 -0.25 4 6
SIRT1/p300 0.037 0.011 -10000 0 -10000 0 0
muscle cell differentiation -0.02 0.052 0.22 26 -0.22 3 29
TP53 0.02 0.012 0.19 1 -10000 0 1
KU70/SIRT1/BAX 0.05 0.016 -10000 0 -10000 0 0
CREBBP 0.027 0.004 -10000 0 -10000 0 0
MEF2D 0.027 0.004 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.07 0.14 -10000 0 -0.25 222 222
ACSS2 0.007 0.013 -10000 0 -0.25 1 1
SIRT1/PCAF/MYOD 0.02 0.052 0.22 3 -0.22 26 29
S1P3 pathway

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
PDGFRB 0.022 0.05 -10000 0 -0.44 7 7
mol:S1P 0.001 0.002 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.055 0.11 -10000 0 -0.29 52 52
GNAO1 -0.11 0.19 -10000 0 -0.36 224 224
S1P/S1P3/G12/G13 0.046 0.024 -10000 0 -0.24 1 1
AKT1 -0.034 0.14 -10000 0 -0.47 48 48
AKT3 -0.012 0.15 -10000 0 -1.1 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.022 0.05 -10000 0 -0.44 7 7
GNAI2 0.027 0.009 -10000 0 -10000 0 0
GNAI3 0.027 0.008 -10000 0 -10000 0 0
GNAI1 0.015 0.068 -10000 0 -0.36 19 19
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.027 0.021 -10000 0 -0.44 1 1
S1PR2 0.027 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.055 0.13 -10000 0 -0.34 47 47
MAPK3 -0.059 0.12 -10000 0 -0.33 52 52
MAPK1 -0.051 0.12 -10000 0 -0.34 36 36
JAK2 -0.012 0.14 0.23 5 -0.38 27 32
CXCR4 -0.058 0.12 -10000 0 -0.33 51 51
FLT1 0.021 0.015 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
SRC -0.038 0.1 -10000 0 -0.33 33 33
S1P/S1P3/Gi -0.056 0.13 -10000 0 -0.35 47 47
RAC1 0.025 0.008 -10000 0 -10000 0 0
RhoA/GTP -0.046 0.13 -10000 0 -0.31 51 51
VEGFA 0.029 0.021 0.36 2 -10000 0 2
S1P/S1P2/Gi -0.058 0.12 -10000 0 -0.33 48 48
VEGFR1 homodimer/VEGFA homodimer 0.034 0.025 0.26 1 -10000 0 1
RHOA 0.027 0.004 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.021 0.041 -10000 0 -0.41 3 3
GNAQ 0.026 0.022 -10000 0 -0.36 2 2
GNAZ 0.023 0.036 -10000 0 -0.36 5 5
G12/G13 0.036 0.013 -10000 0 -10000 0 0
GNA14 0.024 0.035 -10000 0 -0.36 5 5
GNA15 0.023 0.046 -10000 0 -0.44 6 6
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
GNA11 0.025 0.031 -10000 0 -0.36 4 4
Rac1/GTP -0.045 0.12 -10000 0 -0.34 36 36
Ceramide signaling pathway

Figure S68.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S68.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.012 0.011 -10000 0 -0.25 1 1
MAP4K4 0.017 0.037 -10000 0 -0.26 1 1
BAG4 0.024 0.01 -10000 0 -10000 0 0
PKC zeta/ceramide -0.014 0.073 -10000 0 -0.21 57 57
NFKBIA 0.026 0.007 -10000 0 -10000 0 0
BIRC3 0.02 0.05 -10000 0 -0.37 10 10
BAX -0.002 0.04 -10000 0 -0.3 6 6
RIPK1 0.027 0.004 -10000 0 -10000 0 0
AKT1 -0.002 0.012 -10000 0 -10000 0 0
BAD -0.029 0.066 -10000 0 -0.21 57 57
SMPD1 0.02 0.047 0.22 7 -0.22 5 12
RB1 0.011 0.087 0.19 82 -0.2 28 110
FADD/Caspase 8 0.024 0.04 0.2 2 -0.26 1 3
MAP2K4 -0.027 0.062 -10000 0 -0.26 16 16
NSMAF 0.024 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.024 0.066 0.18 12 -0.26 14 26
EGF -0.06 0.16 -10000 0 -0.37 127 127
mol:ceramide -0.029 0.07 -10000 0 -0.22 58 58
MADD 0.028 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.01 0.006 -10000 0 -10000 0 0
ASAH1 0.021 0.012 -10000 0 -10000 0 0
negative regulation of cell cycle 0.01 0.087 0.19 82 -0.2 28 110
cell proliferation -0.035 0.094 -10000 0 -0.31 15 15
BID 0 0.13 -10000 0 -0.58 27 27
MAP3K1 -0.029 0.066 -10000 0 -0.21 56 56
EIF2A -0.03 0.062 0.17 3 -0.26 15 18
TRADD 0.028 0.003 -10000 0 -10000 0 0
CRADD 0.027 0.003 -10000 0 -10000 0 0
MAPK3 -0.021 0.063 0.17 12 -0.26 11 23
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.025 0.064 0.17 10 -0.26 12 22
Cathepsin D/ceramide -0.014 0.073 -10000 0 -0.21 58 58
FADD 0.018 0.036 0.21 2 -10000 0 2
KSR1 -0.024 0.069 0.19 10 -0.21 53 63
MAPK8 -0.023 0.07 -10000 0 -0.25 20 20
PRKRA -0.029 0.066 -10000 0 -0.21 58 58
PDGFA 0.025 0.008 -10000 0 -10000 0 0
TRAF2 0.027 0.016 -10000 0 -0.36 1 1
IGF1 -0.062 0.16 -10000 0 -0.36 141 141
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.028 0.07 -10000 0 -0.22 58 58
CTSD 0.027 0.016 -10000 0 -0.36 1 1
regulation of nitric oxide biosynthetic process 0.039 0.009 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.037 0.1 -10000 0 -0.33 15 15
PRKCD 0.027 0.004 -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 0.01 0.006 -10000 0 -10000 0 0
RelA/NF kappa B1 0.039 0.009 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.028 0.003 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.023 0.031 -10000 0 -0.26 2 2
TNFR1A/BAG4/TNF-alpha 0.045 0.031 -10000 0 -0.21 4 4
mol:Sphingosine-1-phosphate 0.012 0.011 -10000 0 -0.25 1 1
MAP2K1 -0.025 0.063 0.18 5 -0.26 12 17
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
CYCS 0.02 0.051 0.15 9 -0.18 3 12
TNFRSF1A 0.027 0.004 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.035 0.015 -10000 0 -10000 0 0
EIF2AK2 -0.03 0.063 -10000 0 -0.27 16 16
TNF-alpha/TNFR1A/FAN 0.046 0.03 -10000 0 -0.21 4 4
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.028 0.052 -10000 0 -0.32 3 3
MAP2K2 -0.025 0.063 0.18 4 -0.26 12 16
SMPD3 0.018 0.055 0.17 2 -0.27 15 17
TNF 0.024 0.035 -10000 0 -0.36 5 5
PKC zeta/PAR4 0.039 0.01 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.03 0.08 0.18 97 -0.16 4 101
NF kappa B1/RelA/I kappa B alpha 0.07 0.03 -10000 0 -10000 0 0
AIFM1 0.013 0.06 0.14 9 -0.28 2 11
BCL2 0.013 0.052 -10000 0 -0.36 11 11
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.041 0.02 0.26 2 -0.25 1 3
PDGFRB 0.023 0.05 -10000 0 -0.44 7 7
SPHK1 -0.005 0.068 -10000 0 -0.64 6 6
mol:S1P -0.007 0.061 -10000 0 -0.54 6 6
S1P1/S1P/Gi -0.059 0.16 -10000 0 -0.43 47 47
GNAO1 -0.12 0.19 -10000 0 -0.36 224 224
PDGFB-D/PDGFRB/PLCgamma1 -0.005 0.17 0.29 14 -0.43 30 44
PLCG1 -0.055 0.13 0.28 5 -0.45 31 36
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.023 0.05 -10000 0 -0.44 7 7
GNAI2 0.028 0.008 -10000 0 -10000 0 0
GNAI3 0.027 0.008 -10000 0 -10000 0 0
GNAI1 0.014 0.068 -10000 0 -0.36 19 19
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.006 0.016 0.19 2 -0.2 1 3
S1P1/S1P 0.021 0.065 0.22 4 -0.38 4 8
negative regulation of cAMP metabolic process -0.058 0.16 -10000 0 -0.42 48 48
MAPK3 -0.063 0.17 0.26 2 -0.55 32 34
calcium-dependent phospholipase C activity -0.001 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
KDR 0.027 0.017 -10000 0 -0.36 1 1
PLCB2 0.022 0.069 0.25 12 -0.34 4 16
RAC1 0.025 0.008 -10000 0 -10000 0 0
RhoA/GTP 0.017 0.053 -10000 0 -0.32 4 4
receptor internalization 0.019 0.061 0.2 4 -0.35 4 8
PTGS2 -0.059 0.2 0.38 2 -0.88 19 21
Rac1/GTP 0.015 0.051 -10000 0 -0.34 3 3
RHOA 0.027 0.004 -10000 0 -10000 0 0
VEGFA 0.029 0.019 0.36 2 -10000 0 2
negative regulation of T cell proliferation -0.058 0.16 -10000 0 -0.42 48 48
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.024 0.036 -10000 0 -0.37 5 5
MAPK1 -0.059 0.16 -10000 0 -0.55 31 31
S1P1/S1P/PDGFB-D/PDGFRB 0.044 0.09 0.28 15 -0.31 5 20
ABCC1 0.028 0.004 -10000 0 -10000 0 0
Glypican 2 network

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
MDK 0.023 0.046 -10000 0 -0.44 6 6
GPC2 0.013 0.081 0.36 1 -0.44 18 19
GPC2/Midkine 0.025 0.07 0.26 1 -0.32 24 25
neuron projection morphogenesis 0.025 0.07 0.26 1 -0.32 24 25
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.01 0.021 0.12 8 -0.11 2 10
BUB1B 0.017 0.041 0.12 4 -0.14 4 8
PLK1 0.023 0.028 0.072 71 -0.099 3 74
PLK1S1 0.021 0.049 0.1 63 -0.17 22 85
KIF2A 0.018 0.027 0.18 2 -10000 0 2
regulation of mitotic centrosome separation 0.023 0.028 0.071 71 -0.098 3 74
GOLGA2 0.027 0.004 -10000 0 -10000 0 0
Hec1/SPC24 0.038 0.043 -10000 0 -0.21 10 10
WEE1 0.029 0.038 -10000 0 -0.31 2 2
cytokinesis 0.025 0.036 -10000 0 -0.18 1 1
PP2A-alpha B56 0.055 0.083 -10000 0 -0.49 13 13
AURKA 0.025 0.023 0.11 1 -10000 0 1
PICH/PLK1 0.016 0.056 0.18 20 -0.18 25 45
CENPE 0.017 0.027 0.11 1 -0.23 1 2
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.018 0.027 0.18 2 -10000 0 2
PPP2CA 0.027 0.005 -10000 0 -10000 0 0
FZR1 0.027 0.016 -10000 0 -0.36 1 1
TPX2 0.04 0.04 0.1 76 -10000 0 76
PAK1 0.028 0.004 -10000 0 -10000 0 0
SPC24 0.02 0.061 0.36 1 -0.44 10 11
FBXW11 0.027 0.004 -10000 0 -10000 0 0
CLSPN 0.015 0.042 -10000 0 -0.22 17 17
GORASP1 0.028 0.003 -10000 0 -10000 0 0
metaphase 0 0.002 0.017 8 -0.011 1 9
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.011 0.015 0.039 71 -0.052 3 74
G2 phase of mitotic cell cycle 0.001 0.003 0.014 9 -10000 0 9
STAG2 0.027 0.003 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.016 0.047 -10000 0 -0.48 5 5
spindle elongation 0.023 0.028 0.071 71 -0.098 3 74
ODF2 0.03 0.005 -10000 0 -10000 0 0
BUB1 0.018 0.081 -10000 0 -0.54 12 12
TPT1 0.026 0.037 0.1 22 -0.17 8 30
CDC25C 0.018 0.04 -10000 0 -0.24 12 12
CDC25B 0.012 0.11 0.35 17 -0.44 27 44
SGOL1 0.01 0.021 0.11 2 -0.12 8 10
RHOA 0.027 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.035 0.056 0.23 17 -0.16 1 18
CDC14B 0.007 0.011 -10000 0 -0.25 1 1
CDC20 0.026 0.019 -10000 0 -0.44 1 1
PLK1/PBIP1 0.018 0.021 0.099 2 -10000 0 2
mitosis -0.002 0.002 -10000 0 -10000 0 0
FBXO5 0.016 0.031 0.15 5 -10000 0 5
CDC2 0.002 0.003 0.015 17 -0.009 2 19
NDC80 0.022 0.011 -10000 0 -10000 0 0
metaphase plate congression 0.007 0.064 -10000 0 -0.22 43 43
ERCC6L 0.017 0.054 0.19 17 -0.2 5 22
NLP/gamma Tubulin 0.012 0.017 0.076 8 -0.086 1 9
microtubule cytoskeleton organization 0.026 0.037 0.1 22 -0.17 8 30
G2/M transition DNA damage checkpoint 0 0.002 0.013 10 -10000 0 10
PPP1R12A 0.027 0.023 -10000 0 -0.36 2 2
interphase 0 0.002 0.013 10 -10000 0 10
PLK1/PRC1-2 0.05 0.027 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.06 0.025 -10000 0 -10000 0 0
RAB1A 0.028 0.001 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.026 0.031 0.064 218 -10000 0 218
mitotic prometaphase 0.001 0.005 0.018 43 -10000 0 43
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.026 0.17 3 -0.21 1 4
microtubule-based process 0.035 0.027 0.12 1 -10000 0 1
Golgi organization 0.023 0.028 0.071 71 -0.098 3 74
Cohesin/SA2 0.034 0.023 0.12 1 -10000 0 1
PPP1CB/MYPT1 0.04 0.024 -10000 0 -0.36 2 2
KIF20A 0.027 0.004 -10000 0 -10000 0 0
APC/C/CDC20 0.036 0.029 0.12 1 -0.23 1 2
PPP2R1A 0.027 0.004 -10000 0 -10000 0 0
chromosome segregation 0.017 0.021 0.098 2 -10000 0 2
PRC1 0.027 0.006 -10000 0 -10000 0 0
ECT2 0.017 0.034 0.19 4 -0.2 4 8
C13orf34 0.022 0.026 0.066 71 -0.071 2 73
NUDC 0.007 0.065 -10000 0 -0.22 43 43
regulation of attachment of spindle microtubules to kinetochore 0.017 0.04 0.12 4 -0.14 4 8
spindle assembly 0.018 0.024 0.097 12 -0.085 3 15
spindle stabilization 0.021 0.049 0.1 63 -0.17 22 85
APC/C/HCDH1 0.025 0.014 -10000 0 -0.21 2 2
MKLP2/PLK1 0.036 0.027 0.12 1 -10000 0 1
CCNB1 0.027 0.009 -10000 0 -10000 0 0
PPP1CB 0.028 0.016 -10000 0 -0.37 1 1
BTRC 0.027 0.006 -10000 0 -10000 0 0
ROCK2 0.025 0.036 -10000 0 -0.31 3 3
TUBG1 0.018 0.021 0.11 2 -0.16 3 5
G2/M transition of mitotic cell cycle 0.01 0.047 0.18 17 -0.16 1 18
MLF1IP 0.007 0.003 -10000 0 -10000 0 0
INCENP 0.028 0.004 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.036 0.008 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.027 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.024 0.032 -10000 0 -0.36 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.023 0.011 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.014 0.011 -10000 0 -0.17 1 1
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.022 0.019 -10000 0 -0.36 1 1
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.027 0.005 -10000 0 -10000 0 0
FYN 0.027 0.005 -10000 0 -10000 0 0
MAP3K12 0.028 0.002 -10000 0 -10000 0 0
FGR 0.023 0.034 -10000 0 -0.38 4 4
p38 alpha/TAB1 -0.061 0.11 -10000 0 -0.32 70 70
PRKG1 0.012 0.071 -10000 0 -0.36 21 21
DUSP8 0.026 0.022 -10000 0 -0.36 2 2
PGK/cGMP/p38 alpha -0.026 0.14 0.16 10 -0.35 55 65
apoptosis -0.058 0.1 -10000 0 -0.31 70 70
RAL/GTP 0.034 0.011 -10000 0 -10000 0 0
LYN 0.024 0.009 -10000 0 -10000 0 0
DUSP1 0.025 0.027 -10000 0 -0.36 3 3
PAK1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.017 0.014 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.054 0.032 -10000 0 -10000 0 0
TRAF6 0.027 0.003 -10000 0 -10000 0 0
RAC1 0.025 0.008 -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 0.025 0.017 -10000 0 -0.36 1 1
RAC1-CDC42/GTP 0.032 0.017 -10000 0 -0.21 1 1
MAPK11 -0.009 0.14 0.24 41 -0.36 30 71
BLK -0.09 0.17 -10000 0 -0.36 172 172
HCK 0.011 0.047 -10000 0 -0.36 9 9
MAP2K3 0.024 0.01 -10000 0 -10000 0 0
DUSP16 0.027 0.005 -10000 0 -10000 0 0
DUSP10 0.025 0.036 0.36 1 -0.44 3 4
TRAF6/MEKK3 0.034 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.02 0.15 0.22 36 -0.36 62 98
positive regulation of innate immune response -0.02 0.17 0.26 41 -0.41 47 88
LCK 0.019 0.058 -10000 0 -0.43 10 10
p38alpha-beta/MKP7 -0.013 0.16 0.26 38 -0.4 43 81
p38alpha-beta/MKP5 -0.012 0.17 0.26 40 -0.4 44 84
PGK/cGMP 0.01 0.049 -10000 0 -0.25 21 21
PAK2 0.028 0.003 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.012 0.17 0.26 41 -0.41 42 83
CDC42 0.025 0.017 -10000 0 -0.36 1 1
RALB 0.028 0.001 -10000 0 -10000 0 0
RALA 0.025 0.008 -10000 0 -10000 0 0
PAK3 0.01 0.022 -10000 0 -10000 0 0
Aurora B 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
Condensin I complex 0.01 0.046 -10000 0 -0.35 1 1
STMN1 0.013 0.013 -10000 0 -0.25 1 1
Aurora B/RasGAP/Survivin 0.053 0.03 0.25 1 -0.26 1 2
Chromosomal passenger complex/Cul3 protein complex -0.012 0.082 0.15 1 -0.27 25 26
BIRC5 0.029 0.023 0.35 1 -0.44 1 2
DES -0.4 0.3 -10000 0 -0.58 434 434
Aurora C/Aurora B/INCENP 0.048 0.032 -10000 0 -0.19 4 4
Aurora B/TACC1 0.031 0.018 -10000 0 -10000 0 0
Aurora B/PP2A 0.037 0.018 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.009 0.005 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition 0.001 0.004 -10000 0 -10000 0 0
NDC80 0.013 0.008 -10000 0 -10000 0 0
Cul3 protein complex 0.018 0.092 -10000 0 -0.21 82 82
KIF2C 0.015 0.049 -10000 0 -0.35 8 8
PEBP1 0.029 0.003 -10000 0 -10000 0 0
KIF20A 0.029 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.038 0.018 -10000 0 -10000 0 0
SEPT1 0.023 0.041 -10000 0 -0.36 7 7
SMC2 0.027 0.016 -10000 0 -0.36 1 1
SMC4 0.026 0.022 -10000 0 -0.36 2 2
NSUN2/NPM1/Nucleolin -0.071 0.2 -10000 0 -0.5 105 105
PSMA3 0.026 0.007 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B 0.015 0.007 -10000 0 -10000 0 0
AURKB 0.028 0.014 -10000 0 -10000 0 0
AURKC 0.023 0.033 -10000 0 -0.36 4 4
CDCA8 0.03 0.005 -10000 0 -10000 0 0
cytokinesis 0.005 0.039 -10000 0 -0.37 3 3
Aurora B/Septin1 0.005 0.11 -10000 0 -0.3 13 13
AURKA 0.017 0.014 -10000 0 -10000 0 0
INCENP 0.03 0.005 -10000 0 -10000 0 0
KLHL13 -0.026 0.13 -10000 0 -0.36 83 83
BUB1 0.03 0.004 -10000 0 -10000 0 0
hSgo1/Aurora B/Survivin 0.05 0.033 0.24 1 -0.24 3 4
EVI5 0.028 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.049 0.065 -10000 0 -0.29 1 1
SGOL1 0.026 0.027 -10000 0 -0.44 2 2
CENPA 0.033 0.059 0.14 1 -0.19 11 12
NCAPG 0.027 0.005 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.038 0.018 -10000 0 -10000 0 0
NCAPD2 0.027 0.005 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.038 0.018 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
NCAPH 0.028 0 -10000 0 -10000 0 0
NPM1 -0.042 0.15 -10000 0 -0.34 99 99
RASA1 0.027 0.005 -10000 0 -10000 0 0
KLHL9 0.027 0.005 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.018 -10000 0 -10000 0 0
PPP1CC 0.028 0.002 -10000 0 -10000 0 0
Centraspindlin 0.044 0.065 -10000 0 -0.26 3 3
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
NSUN2 -0.032 0.11 -10000 0 -0.28 97 97
MYLK -0.022 0.092 -10000 0 -0.26 82 82
KIF23 0.027 0.02 -10000 0 -0.44 1 1
VIM 0.014 0.008 -10000 0 -10000 0 0
RACGAP1 0.028 0.004 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.032 0.11 -10000 0 -0.28 98 98
Chromosomal passenger complex 0.02 0.052 0.17 1 -0.18 15 16
Chromosomal passenger complex/EVI5 0.095 0.057 0.3 1 -0.22 1 2
TACC1 0.024 0.01 -10000 0 -10000 0 0
PPP2R5D 0.027 0.004 -10000 0 -10000 0 0
CUL3 0.028 0.001 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.007 0.047 -10000 0 -0.36 2 2
SVIL 0.011 0.04 -10000 0 -0.36 1 1
ZNF318 0.05 0.057 0.2 3 -10000 0 3
JMJD2C 0.004 0.02 0.048 2 -0.073 28 30
T-DHT/AR/Ubc9 0.019 0.069 -10000 0 -0.21 47 47
CARM1 0.02 0.019 -10000 0 -10000 0 0
PRDX1 0.029 0.006 -10000 0 -10000 0 0
PELP1 0.026 0.015 -10000 0 -10000 0 0
CTNNB1 0.013 0.035 -10000 0 -10000 0 0
AKT1 0.032 0.019 -10000 0 -10000 0 0
PTK2B 0.011 0.034 -10000 0 -0.36 2 2
MED1 0.036 0.029 0.38 2 -10000 0 2
MAK 0.033 0.11 0.19 68 -0.43 21 89
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 0.011 0.039 -10000 0 -0.36 1 1
GSN 0.001 0.07 -10000 0 -0.38 13 13
NCOA2 0.017 0.032 -10000 0 -0.36 3 3
NCOA6 0.009 0.028 -10000 0 -10000 0 0
DNA-PK 0.064 0.055 0.22 5 -10000 0 5
NCOA4 0.024 0.019 -10000 0 -0.36 1 1
PIAS3 0.012 0.034 -10000 0 -10000 0 0
cell proliferation 0.028 0.071 0.25 3 -0.38 5 8
XRCC5 0.033 0.013 -10000 0 -10000 0 0
UBE3A 0.007 0.05 -10000 0 -0.36 1 1
T-DHT/AR/SNURF -0.007 0.1 -10000 0 -0.23 97 97
FHL2 0.042 0.053 -10000 0 -10000 0 0
RANBP9 0.009 0.044 -10000 0 -0.36 1 1
JMJD1A 0.002 0.012 -10000 0 -0.12 4 4
CDK6 0.027 0.007 -10000 0 -10000 0 0
TGFB1I1 0.012 0.037 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 0.005 0.077 0.18 1 -0.22 51 52
XRCC6 0.032 0.015 -10000 0 -10000 0 0
T-DHT/AR 0.027 0.076 -10000 0 -0.2 45 45
CTDSP1 0.018 0.024 -10000 0 -10000 0 0
CTDSP2 0.043 0.038 -10000 0 -10000 0 0
BRCA1 0.012 0.036 -10000 0 -10000 0 0
TCF4 0.026 0.035 -10000 0 -0.36 2 2
CDKN2A -0.052 0.19 0.38 2 -0.44 114 116
SRF 0.04 0.021 -10000 0 -10000 0 0
NKX3-1 -0.004 0.033 -10000 0 -0.14 12 12
KLK3 -0.19 0.48 -10000 0 -1.3 99 99
TMF1 0.019 0.024 -10000 0 -0.36 1 1
HNRNPA1 0.037 0.022 -10000 0 -10000 0 0
AOF2 -0.012 0.029 -10000 0 -0.078 99 99
APPL1 0.025 0.041 0.15 3 -0.25 3 6
T-DHT/AR/Caspase 8 0.029 0.074 -10000 0 -0.2 47 47
AR -0.004 0.1 -10000 0 -0.36 47 47
UBA3 0.017 0.023 -10000 0 -10000 0 0
PATZ1 0.035 0.022 -10000 0 -10000 0 0
PAWR 0.02 0.019 -10000 0 -10000 0 0
PRKDC 0.029 0.02 0.36 1 -10000 0 1
PA2G4 0.038 0.025 -10000 0 -10000 0 0
UBE2I 0.027 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.026 0.065 -10000 0 -0.18 46 46
RPS6KA3 0.009 0.043 -10000 0 -10000 0 0
T-DHT/AR/ARA70 0.014 0.07 -10000 0 -0.21 48 48
LATS2 0.028 0.024 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.032 0.072 0.16 13 -0.18 38 51
Cyclin D3/CDK11 p58 0.022 0.005 -10000 0 -10000 0 0
VAV3 -0.017 0.11 -10000 0 -0.37 48 48
KLK2 -0.002 0.071 -10000 0 -0.3 27 27
CASP8 0.031 0.008 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.018 0.072 -10000 0 -0.2 43 43
TMPRSS2 0.004 0.072 -10000 0 -0.62 6 6
CCND1 0.014 0.047 0.35 1 -0.44 4 5
PIAS1 0.007 0.049 -10000 0 -10000 0 0
mol:T-DHT 0.001 0.01 -10000 0 -0.056 6 6
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.002 0.07 -10000 0 -10000 0 0
T-DHT/AR/CDK6 0.023 0.07 -10000 0 -0.2 45 45
CMTM2 0.011 0.09 -10000 0 -0.44 23 23
SNURF -0.024 0.12 -10000 0 -0.37 60 60
ZMIZ1 0.027 0.018 -10000 0 -10000 0 0
CCND3 0.028 0.005 -10000 0 -10000 0 0
TGIF1 0.028 0.023 -10000 0 -10000 0 0
FKBP4 0.01 0.044 0.36 1 -10000 0 1
FAS signaling pathway (CD95)

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
SPTAN1 0.001 0.035 0.22 11 -10000 0 11
RFC1 0 0.029 0.19 9 -10000 0 9
PRKDC 0.015 0.065 0.22 51 -10000 0 51
RIPK1 0.028 0.004 -10000 0 -10000 0 0
CASP7 0.006 0.098 -10000 0 -0.54 16 16
FASLG/FAS/FADD/FAF1 0.008 0.063 0.2 16 -0.22 27 43
MAP2K4 -0.014 0.098 0.25 1 -0.38 16 17
mol:ceramide 0.005 0.079 -10000 0 -0.35 10 10
GSN 0 0.039 0.2 17 -0.19 5 22
FASLG/FAS/FADD/FAF1/Caspase 8 0.004 0.072 0.26 1 -0.28 24 25
FAS 0.02 0.045 -10000 0 -0.36 8 8
BID -0.01 0.05 0.25 21 -0.28 1 22
MAP3K1 0.007 0.081 0.22 3 -0.35 15 18
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
RB1 0.023 0.075 0.22 69 -10000 0 69
CFLAR 0.028 0.002 -10000 0 -10000 0 0
HGF/MET 0.03 0.084 -10000 0 -0.26 43 43
ARHGDIB 0.001 0.036 0.21 15 -10000 0 15
FADD 0.026 0.008 -10000 0 -10000 0 0
actin filament polymerization 0.004 0.047 0.2 1 -0.2 17 18
NFKB1 -0.007 0.12 -10000 0 -0.68 18 18
MAPK8 -0.022 0.11 0.24 1 -0.42 19 20
DFFA 0 0.029 0.19 8 -10000 0 8
DNA fragmentation during apoptosis -0.003 0.04 0.19 11 -10000 0 11
FAS/FADD/MET 0.043 0.046 -10000 0 -0.24 13 13
CFLAR/RIP1 0.041 0.007 -10000 0 -10000 0 0
FAIM3 0.009 0.081 -10000 0 -0.36 28 28
FAF1 0.022 0.017 -10000 0 -10000 0 0
PARP1 0 0.029 0.19 8 -10000 0 8
DFFB 0.001 0.03 0.18 16 -10000 0 16
CHUK -0.011 0.12 -10000 0 -0.62 19 19
FASLG 0.001 0.087 -10000 0 -0.36 32 32
FAS/FADD 0.033 0.036 -10000 0 -0.26 8 8
HGF 0.017 0.061 -10000 0 -0.37 15 15
LMNA -0.003 0.039 0.24 5 -10000 0 5
CASP6 0 0.029 0.19 10 -10000 0 10
CASP10 0.027 0.007 -10000 0 -10000 0 0
CASP3 0.003 0.035 0.22 15 -10000 0 15
PTPN13 0.007 0.094 -10000 0 -0.43 27 27
CASP8 -0.006 0.068 0.31 27 -10000 0 27
IL6 -0.029 0.19 -10000 0 -0.84 21 21
MET 0.022 0.047 -10000 0 -0.44 6 6
ICAD/CAD -0.001 0.027 0.24 2 -10000 0 2
FASLG/FAS/FADD/FAF1/Caspase 10 0.005 0.08 -10000 0 -0.36 10 10
activation of caspase activity by cytochrome c -0.01 0.05 0.25 21 -0.28 1 22
PAK2 0.001 0.032 0.19 12 -10000 0 12
BCL2 0.013 0.052 -10000 0 -0.36 11 11
IL6-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
BCL2L1 0.063 0.16 0.42 2 -0.84 1 3
CRP -0.003 0.14 0.43 1 -0.68 4 5
cell cycle arrest -0.003 0.14 -10000 0 -0.73 4 4
TIMP1 0.007 0.14 -10000 0 -0.57 6 6
IL6ST 0.019 0.061 -10000 0 -0.36 15 15
Rac1/GDP -0.03 0.12 0.3 1 -0.37 32 33
AP1 0.048 0.09 -10000 0 -0.46 5 5
GAB2 0.028 0.004 -10000 0 -10000 0 0
TNFSF11 0.028 0.17 -10000 0 -0.86 5 5
HSP90B1 0.035 0.049 -10000 0 -0.57 1 1
GAB1 0.027 0.005 -10000 0 -10000 0 0
MAPK14 -0.029 0.11 -10000 0 -0.37 22 22
AKT1 0.032 0.037 -10000 0 -0.4 1 1
FOXO1 0.059 0.078 0.26 2 -0.36 1 3
MAP2K6 -0.037 0.11 -10000 0 -0.36 30 30
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 -0.028 0.12 0.29 2 -0.42 16 18
MITF -0.037 0.12 0.18 4 -0.37 34 38
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.027 0.004 -10000 0 -10000 0 0
A2M 0.008 0.15 -10000 0 -1.1 10 10
CEBPB 0.017 0.047 0.35 3 -0.44 4 7
GRB2/SOS1/GAB family/SHP2 0.025 0.079 -10000 0 -0.42 7 7
STAT3 -0.008 0.14 -10000 0 -0.78 4 4
STAT1 0.021 0.017 -10000 0 -10000 0 0
CEBPD 0.015 0.14 -10000 0 -0.96 2 2
PIK3CA 0.028 0.016 -10000 0 -0.36 1 1
PI3K 0.04 0.015 -10000 0 -0.25 1 1
JUN 0.027 0.004 -10000 0 -10000 0 0
PIAS3/MITF -0.025 0.12 0.22 1 -0.37 30 31
MAPK11 -0.028 0.11 -10000 0 -0.37 21 21
STAT3 (dimer)/FOXO1 0.039 0.14 0.36 16 -0.62 2 18
GRB2/SOS1/GAB family 0.026 0.13 0.24 3 -0.37 16 19
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.026 0.1 0.24 3 -0.37 27 30
GRB2 0.027 0.004 -10000 0 -10000 0 0
JAK2 0.025 0.028 -10000 0 -0.36 3 3
LBP 0.054 0.17 0.39 17 -0.6 1 18
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
JAK1 0.028 0.009 -10000 0 -10000 0 0
MYC 0.026 0.15 0.4 3 -0.75 2 5
FGG -0.017 0.15 -10000 0 -0.65 5 5
macrophage differentiation -0.003 0.14 -10000 0 -0.73 4 4
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.011 0.14 0.26 4 -0.32 40 44
JUNB -0.002 0.14 -10000 0 -0.93 3 3
FOS 0.022 0.039 -10000 0 -0.36 6 6
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.034 0.12 0.2 3 -0.37 33 36
STAT1/PIAS1 -0.005 0.12 -10000 0 -0.38 15 15
GRB2/SOS1/GAB family/SHP2/PI3K 0.036 0.039 -10000 0 -0.36 2 2
STAT3 (dimer) -0.004 0.14 -10000 0 -0.76 4 4
PRKCD -0.012 0.14 0.32 24 -0.48 9 33
IL6R -0.052 0.16 -10000 0 -0.36 128 128
SOCS3 -0.025 0.11 0.4 1 -0.47 6 7
gp130 (dimer)/JAK1/JAK1/LMO4 0.052 0.047 -10000 0 -0.21 4 4
Rac1/GTP -0.029 0.12 -10000 0 -0.42 19 19
HCK 0.011 0.047 -10000 0 -0.36 9 9
MAPKKK cascade 0.038 0.081 -10000 0 -0.5 6 6
bone resorption 0.029 0.17 0.42 1 -0.8 5 6
IRF1 -0.001 0.13 -10000 0 -0.74 2 2
mol:GDP -0.035 0.12 0.19 1 -0.36 38 39
SOS1 0.028 0.002 -10000 0 -10000 0 0
VAV1 -0.038 0.12 0.18 3 -0.37 39 42
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.059 0.16 0.33 1 -0.36 108 109
PTPN11 0.019 0.048 -10000 0 -0.77 2 2
IL6/IL6RA -0.054 0.15 0.26 4 -0.29 175 179
gp130 (dimer)/TYK2/TYK2/LMO4 0.05 0.044 -10000 0 -10000 0 0
gp130 (dimer)/JAK2/JAK2/LMO4 0.047 0.048 -10000 0 -0.21 18 18
IL6 -0.026 0.16 0.36 7 -0.43 76 83
PIAS3 0.027 0.005 -10000 0 -10000 0 0
PTPRE 0.022 0.011 -10000 0 -10000 0 0
PIAS1 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.037 0.11 0.18 3 -0.34 34 37
LMO4 0.029 0.01 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 0.001 0.14 -10000 0 -0.73 4 4
MCL1 0.032 0.045 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

Figure S77.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S77.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.026 0.023 -10000 0 -10000 0 0
HSPA8 0.026 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0 0.1 -10000 0 -0.29 30 30
AKT1 -0.008 0.054 -10000 0 -10000 0 0
GSC -0.038 0.13 -10000 0 -0.53 7 7
NKX2-5 -0.001 0.011 -10000 0 -10000 0 0
muscle cell differentiation 0.041 0.12 0.37 18 -10000 0 18
SMAD2-3/SMAD4/SP1 -0.01 0.11 -10000 0 -0.3 1 1
SMAD4 0.001 0.047 -10000 0 -10000 0 0
CBFB 0.028 0.003 -10000 0 -10000 0 0
SAP18 0.021 0.011 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.018 0.14 -10000 0 -0.27 136 136
SMAD3/SMAD4/VDR 0.057 0.06 -10000 0 -10000 0 0
MYC 0.048 0.06 0.36 9 -0.38 2 11
CDKN2B -0.43 0.61 -10000 0 -1.3 218 218
AP1 0.013 0.053 -10000 0 -0.3 1 1
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.019 0.12 -10000 0 -0.36 40 40
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.15 0.22 -10000 0 -0.43 206 206
SP3 0.029 0.001 -10000 0 -10000 0 0
CREB1 0.028 0 -10000 0 -10000 0 0
FOXH1 0.008 0.07 0.36 3 -0.38 15 18
SMAD3/SMAD4/GR 0.01 0.1 -10000 0 -0.29 26 26
GATA3 0.017 0.051 -10000 0 -0.39 5 5
SKI/SIN3/HDAC complex/NCoR1 0.021 0.064 -10000 0 -0.42 5 5
MEF2C/TIF2 0 0.087 -10000 0 -0.37 14 14
endothelial cell migration 0.025 0.12 0.54 1 -10000 0 1
MAX 0.03 0.012 -10000 0 -10000 0 0
RBBP7 0.027 0.004 -10000 0 -10000 0 0
RBBP4 0.026 0.005 -10000 0 -10000 0 0
RUNX2 0.027 0.004 -10000 0 -10000 0 0
RUNX3 0.025 0.017 -10000 0 -0.36 1 1
RUNX1 0.026 0.007 -10000 0 -10000 0 0
CTBP1 0.027 0.005 -10000 0 -10000 0 0
NR3C1 0.003 0.1 -10000 0 -0.36 44 44
VDR 0.028 0.003 -10000 0 -10000 0 0
CDKN1A -0.009 0.081 -10000 0 -0.88 2 2
KAT2B 0.012 0.077 -10000 0 -0.35 26 26
SMAD2/SMAD2/SMAD4/FOXH1 -0.001 0.078 0.27 2 -0.28 9 11
DCP1A 0.027 0.004 -10000 0 -10000 0 0
SKI 0.026 0.006 -10000 0 -10000 0 0
SERPINE1 -0.026 0.12 -10000 0 -0.55 1 1
SMAD3/SMAD4/ATF2 0.018 0.064 -10000 0 -0.27 1 1
SMAD3/SMAD4/ATF3 0.018 0.065 -10000 0 -0.3 2 2
SAP30 0.026 0.006 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.054 0.048 -10000 0 -10000 0 0
JUN 0.003 0.045 -10000 0 -0.3 1 1
SMAD3/SMAD4/IRF7 0.018 0.064 -10000 0 -10000 0 0
TFE3 0.018 0.025 -10000 0 -10000 0 0
COL1A2 0.002 0.083 -10000 0 -0.32 2 2
mesenchymal cell differentiation -0.018 0.063 -10000 0 -10000 0 0
DLX1 0.002 0.081 -10000 0 -0.43 19 19
TCF3 0.027 0.004 -10000 0 -10000 0 0
FOS 0.02 0.042 -10000 0 -0.37 6 6
SMAD3/SMAD4/Max 0.026 0.069 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.055 0.019 -10000 0 -10000 0 0
ZBTB17 0.044 0.036 -10000 0 -0.36 1 1
LAMC1 -0.003 0.041 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.015 0.052 0.28 2 -10000 0 2
IRF7 0.027 0.016 -10000 0 -0.36 1 1
ESR1 -0.01 0.11 -10000 0 -0.36 55 55
HNF4A 0.015 0.02 -10000 0 -0.36 1 1
MEF2C -0.003 0.093 -10000 0 -0.39 14 14
SMAD2-3/SMAD4 -0.003 0.089 -10000 0 -0.28 3 3
Cbp/p300/Src-1 0.058 0.025 -10000 0 -10000 0 0
IGHV3OR16-13 0.01 0.01 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.02 0.036 0.36 6 -10000 0 6
CREBBP 0.027 0.017 -10000 0 -10000 0 0
SKIL 0.027 0.016 -10000 0 -0.36 1 1
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC2 0.027 0.005 -10000 0 -10000 0 0
SNIP1 0.026 0.006 -10000 0 -10000 0 0
GCN5L2 0.004 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.015 0.061 -10000 0 -10000 0 0
MSG1/HSC70 -0.042 0.15 -10000 0 -0.32 137 137
SMAD2 -0.009 0.049 -10000 0 -0.21 1 1
SMAD3 0.002 0.05 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.004 0.048 0.21 6 -0.24 3 9
SMAD2/SMAD2/SMAD4 -0.06 0.12 -10000 0 -0.35 57 57
NCOR1 0.023 0.01 -10000 0 -10000 0 0
NCOA2 0.022 0.028 -10000 0 -0.36 3 3
NCOA1 0.028 0 -10000 0 -10000 0 0
MYOD/E2A 0.032 0.006 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 -0.001 0.12 -10000 0 -0.32 1 1
IFNB1 -0.007 0.043 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.003 0.11 -10000 0 -0.4 13 13
CITED1 -0.079 0.2 -10000 0 -0.44 137 137
SMAD2-3/SMAD4/ARC105 0.008 0.089 -10000 0 -10000 0 0
RBL1 0.017 0.014 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.15 0.27 -10000 0 -0.51 199 199
RUNX1-3/PEBPB2 0.049 0.021 -10000 0 -0.21 1 1
SMAD7 -0.005 0.086 -10000 0 -0.64 1 1
MYC/MIZ-1 0.067 0.075 0.2 67 -0.29 2 69
SMAD3/SMAD4 -0.001 0.11 0.26 8 -0.35 7 15
IL10 -0.02 0.11 -10000 0 -0.41 38 38
PIASy/HDAC complex 0.013 0.025 -10000 0 -10000 0 0
PIAS3 0.028 0.007 -10000 0 -10000 0 0
CDK2 0.029 0.012 -10000 0 -10000 0 0
IL5 -0.013 0.074 -10000 0 -0.38 7 7
CDK4 0.026 0.027 -10000 0 -0.43 1 1
PIAS4 0.013 0.025 -10000 0 -10000 0 0
ATF3 0.026 0.027 -10000 0 -0.44 2 2
SMAD3/SMAD4/SP1 0.002 0.082 -10000 0 -10000 0 0
FOXG1 -0.069 0.16 -10000 0 -0.46 82 82
FOXO3 -0.023 0.059 -10000 0 -10000 0 0
FOXO1 -0.016 0.05 -10000 0 -0.32 1 1
FOXO4 -0.022 0.057 -10000 0 -10000 0 0
heart looping -0.003 0.092 -10000 0 -0.38 14 14
CEBPB 0 0.052 0.33 3 -0.45 4 7
SMAD3/SMAD4/DLX1 0.008 0.08 -10000 0 -0.27 15 15
MYOD1 -0.018 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.013 0.048 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 0.012 0.089 -10000 0 -0.32 6 6
SnoN/SIN3/HDAC complex/NCoR1 0.027 0.016 -10000 0 -0.36 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.035 0.069 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.015 0.083 -10000 0 -10000 0 0
MED15 0.026 0.017 -10000 0 -0.36 1 1
SP1 0.003 0.04 -10000 0 -10000 0 0
SIN3B 0.027 0.003 -10000 0 -10000 0 0
SIN3A 0.026 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.001 0.076 0.26 2 -0.26 13 15
ITGB5 -0.01 0.053 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.025 0.053 -10000 0 -0.44 2 2
SMAD3/SMAD4/AR -0.001 0.094 -10000 0 -0.29 23 23
AR -0.009 0.1 -10000 0 -0.36 47 47
negative regulation of cell growth -0.011 0.076 0.22 1 -0.32 12 13
SMAD3/SMAD4/MYOD 0.013 0.063 -10000 0 -10000 0 0
E2F5 0.027 0.051 0.36 9 -0.42 3 12
E2F4 0.028 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.022 0.073 0.27 2 -0.3 1 3
SMAD2-3/SMAD4/FOXO1-3a-4 -0.12 0.23 -10000 0 -0.43 199 199
TFDP1 0.022 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.025 0.064 -10000 0 -0.3 1 1
SMAD3/SMAD4/RUNX2 0.018 0.063 -10000 0 -10000 0 0
TGIF2 0.02 0.036 0.36 6 -10000 0 6
TGIF1 0.022 0.011 -10000 0 -10000 0 0
ATF2 0.027 0.016 -10000 0 -0.36 1 1
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.027 0.067 0.3 23 -0.24 2 25
KIRREL 0.021 0.048 -10000 0 -0.38 8 8
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.027 0.067 0.24 2 -0.3 23 25
PLCG1 0.016 0.014 -10000 0 -10000 0 0
ARRB2 0.023 0.01 -10000 0 -10000 0 0
WASL 0.027 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.043 0.079 -10000 0 -0.24 37 37
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.02 0.037 0.2 2 -0.22 7 9
FYN 0.01 0.063 0.28 12 -0.21 25 37
mol:Ca2+ 0.027 0.061 0.22 1 -0.24 21 22
mol:DAG 0.027 0.062 0.22 1 -0.24 21 22
NPHS2 0.013 0.049 -10000 0 -0.45 6 6
mol:IP3 0.027 0.062 0.22 1 -0.24 21 22
regulation of endocytosis 0.036 0.054 0.21 2 -0.2 18 20
Nephrin/NEPH1/podocin/Cholesterol 0.035 0.059 0.21 2 -0.23 25 27
establishment of cell polarity 0.027 0.067 0.24 2 -0.3 23 25
Nephrin/NEPH1/podocin/NCK1-2 0.064 0.063 -10000 0 -0.39 2 2
Nephrin/NEPH1/beta Arrestin2 0.037 0.056 0.22 2 -0.2 18 20
NPHS1 0.013 0.076 0.32 2 -0.44 15 17
Nephrin/NEPH1/podocin 0.037 0.054 0.21 2 -0.21 25 27
TJP1 0.026 0.007 -10000 0 -10000 0 0
NCK1 0.028 0.003 -10000 0 -10000 0 0
NCK2 0.028 0.002 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.028 0.062 0.23 1 -0.24 21 22
CD2AP 0.016 0.066 -10000 0 -0.36 18 18
Nephrin/NEPH1/podocin/GRB2 0.05 0.064 0.23 2 -0.24 25 27
GRB2 0.027 0.004 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.011 0.076 0.3 12 -0.21 43 55
cytoskeleton organization 0.009 0.046 0.2 7 -0.35 2 9
Nephrin/NEPH1 0.025 0.048 0.19 2 -0.2 23 25
Nephrin/NEPH1/ZO-1 0.04 0.059 0.22 2 -0.24 22 24
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.056 0.05 -10000 0 -0.58 1 1
epithelial cell differentiation 0.049 0.073 -10000 0 -0.62 1 1
ITCH 0.018 0.016 -10000 0 -10000 0 0
WWP1 0.014 0.06 -10000 0 -1.1 1 1
FYN 0.027 0.005 -10000 0 -10000 0 0
EGFR 0.024 0.023 -10000 0 -0.36 2 2
PRL -0.007 0.066 -10000 0 -0.44 12 12
neuron projection morphogenesis 0.025 0.074 0.26 11 -0.43 1 12
PTPRZ1 -0.12 0.18 -10000 0 -0.36 221 221
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.037 0.074 -10000 0 -0.46 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.012 0.06 -10000 0 -0.51 1 1
ADAM17 0.021 0.016 -10000 0 -10000 0 0
ErbB4/ErbB4 0.015 0.036 -10000 0 -0.63 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.053 0.049 -10000 0 -0.58 1 1
NCOR1 0.023 0.011 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.023 0.067 -10000 0 -0.48 1 1
GRIN2B -0.052 0.12 0.3 3 -0.36 13 16
ErbB4/ErbB2/betacellulin 0.053 0.049 0.24 6 -0.48 1 7
STAT1 0.027 0.019 -10000 0 -0.44 1 1
HBEGF 0.026 0.027 -10000 0 -0.44 2 2
PRLR 0.017 0.062 -10000 0 -0.36 16 16
E4ICDs/ETO2 0.037 0.077 -10000 0 -0.58 1 1
axon guidance 0.046 0.084 0.28 19 -0.72 1 20
NEDD4 0.019 0.015 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.021 0.068 -10000 0 -0.29 27 27
CBFA2T3 -0.022 0.13 -10000 0 -0.36 77 77
ErbB4/ErbB2/HBEGF 0.055 0.047 0.24 6 -0.48 1 7
MAPK3 0.023 0.071 0.25 9 -0.37 2 11
STAT1 (dimer) 0.057 0.049 -10000 0 -0.57 1 1
MAPK1 0.023 0.07 0.25 8 -0.44 1 9
JAK2 0.025 0.028 -10000 0 -0.36 3 3
ErbB4/ErbB2/neuregulin 1 beta 0.012 0.063 0.23 6 -0.48 1 7
NRG1 -0.02 0.076 -10000 0 -0.26 56 56
NRG3 0.005 0.032 -10000 0 -0.4 2 2
NRG2 -0.04 0.13 -10000 0 -0.36 88 88
NRG4 -0.015 0.1 -10000 0 -0.36 50 50
heart development 0.046 0.084 0.28 19 -0.72 1 20
neural crest cell migration 0.012 0.063 0.23 6 -0.48 1 7
ERBB2 0.012 0.038 0.27 11 -10000 0 11
WWOX/E4ICDs 0.053 0.049 -10000 0 -0.58 1 1
SHC1 0.027 0.004 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.042 0.072 -10000 0 -0.55 1 1
apoptosis -0.038 0.076 0.39 10 -10000 0 10
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.031 0.079 -10000 0 -0.58 1 1
ErbB4/ErbB2/epiregulin -0.036 0.12 0.29 5 -0.33 6 11
ErbB4/ErbB4/betacellulin/betacellulin 0.054 0.052 -10000 0 -0.58 1 1
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.07 0.075 -10000 0 -0.44 2 2
MDM2 0.011 0.032 0.25 1 -0.58 1 2
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.005 0.054 -10000 0 -0.4 1 1
STAT5A 0.05 0.08 0.28 10 -0.69 1 11
ErbB4/EGFR/neuregulin 1 beta 0.02 0.066 -10000 0 -0.48 1 1
DLG4 0.022 0.022 -10000 0 -0.44 1 1
GRB2/SHC 0.039 0.009 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.042 0.043 -10000 0 -0.54 1 1
STAT5A (dimer) 0.075 0.091 0.3 2 -0.68 1 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.08 0.083 0.28 14 -0.69 1 15
LRIG1 0.027 0.016 -10000 0 -0.36 1 1
EREG -0.16 0.23 0.36 3 -0.44 249 252
BTC 0.021 0.047 -10000 0 -0.36 9 9
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.028 0.07 0.28 9 -0.72 1 10
ERBB4 0.011 0.029 -10000 0 -0.64 1 1
STAT5B 0.027 0.004 -10000 0 -10000 0 0
YAP1 0.009 0.06 -10000 0 -0.42 10 10
GRB2 0.027 0.004 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.039 0.067 0.25 4 -0.49 1 5
glial cell differentiation -0.042 0.043 0.54 1 -10000 0 1
WWOX 0.025 0.008 -10000 0 -10000 0 0
cell proliferation 0.023 0.087 0.28 9 -0.52 1 10
Sphingosine 1-phosphate (S1P) pathway

Figure S80.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S80.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.027 0.016 -9999 0 -0.36 1 1
SPHK1 -0.004 0.12 -9999 0 -0.44 40 40
GNAI2 0.027 0.004 -9999 0 -10000 0 0
mol:S1P 0.006 0.034 -9999 0 -0.23 1 1
GNAO1 -0.12 0.19 -9999 0 -0.36 224 224
mol:Sphinganine-1-P -0.009 0.082 -9999 0 -0.32 41 41
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.044 0.046 -9999 0 -10000 0 0
GNAI3 0.027 0.005 -9999 0 -10000 0 0
G12/G13 0.036 0.013 -9999 0 -10000 0 0
S1PR3 0.027 0.019 -9999 0 -0.44 1 1
S1PR2 0.027 0.004 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0.001 0.031 -9999 0 -0.2 1 1
S1PR5 0.016 0.073 -9999 0 -0.44 15 15
S1PR4 0.021 0.049 -9999 0 -0.36 10 10
GNAI1 0.015 0.067 -9999 0 -0.36 19 19
S1P/S1P5/G12 0.027 0.061 -9999 0 -0.27 14 14
S1P/S1P3/Gq 0.023 0.056 -9999 0 -0.36 9 9
S1P/S1P4/Gi -0.063 0.13 -9999 0 -0.36 48 48
GNAQ 0.026 0.022 -9999 0 -0.36 2 2
GNAZ 0.023 0.035 -9999 0 -0.36 5 5
GNA14 0.024 0.035 -9999 0 -0.36 5 5
GNA15 0.023 0.046 -9999 0 -0.44 6 6
GNA12 0.025 0.008 -9999 0 -10000 0 0
GNA13 0.027 0.005 -9999 0 -10000 0 0
GNA11 0.025 0.031 -9999 0 -0.36 4 4
ABCC1 0.027 0.003 -9999 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.021 0.056 -10000 0 -0.43 9 9
ANTXR2 0.026 0.023 -10000 0 -0.36 2 2
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.007 -10000 0 -0.052 11 11
monocyte activation -0.002 0.091 -10000 0 -0.34 41 41
MAP2K2 0.006 0.078 -10000 0 -0.57 11 11
MAP2K1 -0.004 0.006 -10000 0 -10000 0 0
MAP2K7 -0.004 0.009 -10000 0 -0.18 1 1
MAP2K6 -0.005 0.015 -10000 0 -0.18 4 4
CYAA -0.009 0.028 -10000 0 -0.21 11 11
MAP2K4 -0.003 0.007 -10000 0 -10000 0 0
IL1B -0.022 0.063 -10000 0 -0.22 56 56
Channel 0.03 0.035 -10000 0 -0.23 11 11
NLRP1 -0.005 0.016 -10000 0 -0.21 3 3
CALM1 0.026 0.007 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.016 0.1 -10000 0 -0.38 44 44
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.007 0.052 11 -10000 0 11
MAPK3 -0.004 0.011 0.14 1 -0.18 1 2
MAPK1 -0.004 0.006 -10000 0 -10000 0 0
PGR -0.048 0.075 -10000 0 -0.18 156 156
PA/Cellular Receptors 0.031 0.039 -10000 0 -0.25 11 11
apoptosis -0.002 0.007 -10000 0 -0.052 11 11
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.03 0.032 -10000 0 -0.2 11 11
macrophage activation -0.003 0.024 0.17 10 -0.17 1 11
TNF 0.024 0.035 -10000 0 -0.36 5 5
VCAM1 -0.002 0.09 -10000 0 -0.34 40 40
platelet activation -0.016 0.1 -10000 0 -0.38 44 44
MAPKKK cascade 0.001 0.014 0.13 1 -0.086 4 5
IL18 -0.003 0.016 -10000 0 -0.17 3 3
negative regulation of macrophage activation -0.002 0.007 -10000 0 -0.052 11 11
LEF -0.002 0.007 -10000 0 -0.052 11 11
CASP1 -0.001 0.011 -10000 0 -0.095 5 5
mol:cAMP -0.017 0.1 -10000 0 -0.38 44 44
necrosis -0.002 0.007 -10000 0 -0.052 11 11
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.03 0.033 -10000 0 -0.21 11 11
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.007 0.064 -10000 0 -0.29 22 22
CRKL 0.027 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
DOCK1 0.026 0.016 -10000 0 -0.36 1 1
ITGA4 0.014 0.072 -10000 0 -0.36 22 22
alpha4/beta7 Integrin/MAdCAM1 -0.063 0.15 -10000 0 -0.39 29 29
EPO 0.005 0.05 0.36 2 -0.44 5 7
alpha4/beta7 Integrin 0.02 0.081 -10000 0 -0.28 40 40
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.023 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.03 0.055 -10000 0 -0.25 22 22
EPO/EPOR (dimer) 0.033 0.038 0.26 2 -0.32 6 8
lamellipodium assembly 0.006 0.081 -10000 0 -0.38 12 12
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
PI3K 0.039 0.015 -10000 0 -0.25 1 1
ARF6 0.026 0.007 -10000 0 -10000 0 0
JAK2 0.015 0.051 0.17 1 -0.41 3 4
PXN 0.028 0.002 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
MADCAM1 -0.15 0.19 -10000 0 -0.36 274 274
cell adhesion -0.064 0.14 -10000 0 -0.39 29 29
CRKL/CBL 0.039 0.01 -10000 0 -10000 0 0
ITGB1 0.028 0.002 -10000 0 -10000 0 0
SRC 0.002 0.046 -10000 0 -0.36 7 7
ITGB7 0.013 0.074 -10000 0 -0.36 23 23
RAC1 0.025 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.04 0.07 -10000 0 -0.28 25 25
p130Cas/Crk/Dock1 0.056 0.076 -10000 0 -0.31 7 7
VCAM1 0.019 0.056 -10000 0 -0.36 13 13
RHOA 0.027 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.06 0.049 -10000 0 -10000 0 0
BCAR1 -0.013 0.042 0.18 1 -0.34 7 8
EPOR 0.027 0.019 -10000 0 -0.44 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.027 0.004 -10000 0 -10000 0 0
GIT1 0.026 0.016 -10000 0 -0.36 1 1
Rac1/GTP 0.006 0.083 -10000 0 -0.39 12 12
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.047 0.15 -10000 0 -0.36 116 116
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.026 0.027 -10000 0 -0.44 2 2
TCEB1 0.024 0.009 -10000 0 -10000 0 0
HIF1A/p53 0.013 0.058 0.26 1 -0.25 23 24
HIF1A 0.003 0.046 -10000 0 -0.26 17 17
COPS5 0.024 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.066 0.035 -10000 0 -0.23 1 1
FIH (dimer) 0.027 0.006 -10000 0 -10000 0 0
CDKN2A -0.061 0.19 0.36 2 -0.45 114 116
ARNT/IPAS -0.014 0.11 -10000 0 -0.25 113 113
HIF1AN 0.027 0.006 -10000 0 -10000 0 0
GNB2L1 0.027 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.011 0.062 -10000 0 -0.26 24 24
CUL2 0.028 0.002 -10000 0 -10000 0 0
OS9 0.028 0.002 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.047 0.024 -10000 0 -0.27 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.016 0.06 0.26 1 -0.26 24 25
PHD1-3/OS9 0.062 0.031 -10000 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C 0.03 0.066 -10000 0 -0.29 7 7
VHL 0.027 0.004 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
HIF1A/JAB1 0.011 0.061 0.26 1 -0.26 22 23
EGLN3 0.024 0.028 -10000 0 -0.36 3 3
EGLN2 0.027 0.016 -10000 0 -0.36 1 1
EGLN1 0.027 0.005 -10000 0 -10000 0 0
TP53 0.023 0.011 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.029 0.078 -10000 0 -0.5 12 12
ARNT 0.027 0.016 -10000 0 -0.36 1 1
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.026 0.017 -10000 0 -0.36 1 1
HIF1A/p19ARF -0.029 0.11 0.24 2 -0.29 31 33
Class I PI3K signaling events

Figure S84.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S84.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.007 0.049 0.29 1 -10000 0 1
DAPP1 -0.012 0.14 0.22 22 -0.38 33 55
Src family/SYK family/BLNK-LAT/BTK-ITK -0.06 0.18 0.24 13 -0.5 50 63
mol:DAG 0 0.094 0.18 72 -0.23 17 89
HRAS 0.027 0.017 -10000 0 -0.36 1 1
RAP1A 0.027 0.007 -10000 0 -10000 0 0
ARF5/GDP 0.027 0.12 0.2 4 -0.4 21 25
PLCG2 -0.004 0.1 -10000 0 -0.36 49 49
PLCG1 0.016 0.014 -10000 0 -10000 0 0
ARF5 0.027 0.005 -10000 0 -10000 0 0
mol:GTP -0.014 0.031 0.3 1 -10000 0 1
ARF1/GTP 0.002 0.04 0.25 3 -10000 0 3
RHOA 0.027 0.004 -10000 0 -10000 0 0
YES1 0.022 0.019 -10000 0 -0.36 1 1
RAP1A/GTP -0.014 0.03 0.16 14 -10000 0 14
ADAP1 -0.015 0.03 0.28 1 -0.33 1 2
ARAP3 -0.014 0.031 0.3 1 -10000 0 1
INPPL1 0.027 0.004 -10000 0 -10000 0 0
PREX1 0.015 0.025 -10000 0 -0.36 2 2
ARHGEF6 0.019 0.056 -10000 0 -0.36 13 13
ARHGEF7 0.022 0.012 -10000 0 -10000 0 0
ARF1 0.027 0.004 -10000 0 -10000 0 0
NRAS 0.026 0.023 -10000 0 -0.36 2 2
FYN 0.027 0.005 -10000 0 -10000 0 0
ARF6 0.026 0.007 -10000 0 -10000 0 0
FGR 0.023 0.034 -10000 0 -0.38 4 4
mol:Ca2+ 0.004 0.057 0.16 18 -10000 0 18
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.011 0.11 -10000 0 -0.36 59 59
ZAP70 0.018 0.06 -10000 0 -0.37 14 14
mol:IP3 -0.002 0.07 0.18 20 -0.18 7 27
LYN 0.024 0.009 -10000 0 -10000 0 0
ARF1/GDP 0.028 0.12 0.21 4 -0.4 23 27
RhoA/GDP 0.04 0.069 0.23 9 -0.26 6 15
PDK1/Src/Hsp90 0.032 0.028 -10000 0 -10000 0 0
BLNK 0.022 0.042 -10000 0 -0.36 7 7
actin cytoskeleton reorganization 0.035 0.093 0.23 36 -0.34 8 44
SRC 0.017 0.014 -10000 0 -10000 0 0
PLEKHA2 -0.008 0.003 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
PTEN 0.026 0.01 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
ARF6/GTP -0.014 0.035 0.29 1 -10000 0 1
RhoA/GTP -0.014 0.033 0.3 1 -10000 0 1
Src family/SYK family/BLNK-LAT -0.032 0.1 -10000 0 -0.36 26 26
BLK -0.09 0.17 -10000 0 -0.36 172 172
PDPK1 0.027 0.004 -10000 0 -10000 0 0
CYTH1 -0.015 0.029 0.28 1 -10000 0 1
HCK 0.011 0.047 -10000 0 -0.36 9 9
CYTH3 -0.015 0.028 0.28 1 -10000 0 1
CYTH2 -0.015 0.029 0.28 1 -10000 0 1
KRAS 0.027 0.017 -10000 0 -0.36 1 1
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.013 0.079 -10000 0 -0.36 22 22
SGK1 -0.003 0.082 -10000 0 -0.37 26 26
INPP5D 0.027 0.016 -10000 0 -0.36 1 1
mol:GDP 0.016 0.12 0.2 6 -0.42 23 29
SOS1 0.028 0.002 -10000 0 -10000 0 0
SYK 0.027 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.026 0.066 0.24 9 -0.29 3 12
mol:PI-3-4-5-P3 -0.014 0.03 0.28 1 -10000 0 1
ARAP3/RAP1A/GTP -0.014 0.03 0.16 14 -10000 0 14
VAV1 0.011 0.077 -10000 0 -0.36 25 25
mol:PI-3-4-P2 0.013 0.011 -10000 0 -0.25 1 1
RAS family/GTP/PI3K Class I 0.044 0.039 -10000 0 -10000 0 0
PLEKHA1 -0.009 0.008 -10000 0 -0.21 1 1
Rac1/GDP 0.022 0.11 0.2 4 -0.41 20 24
LAT 0.025 0.035 -10000 0 -0.4 4 4
Rac1/GTP -0.016 0.1 -10000 0 -0.46 21 21
ITK -0.022 0.041 0.28 1 -10000 0 1
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.009 0.11 0.2 66 -0.3 25 91
LCK 0.019 0.058 -10000 0 -0.43 10 10
BTK -0.032 0.056 0.28 1 -10000 0 1
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.007 0.013 -10000 0 -0.2 2 2
RAS family/GTP 0.011 0.088 -10000 0 -0.26 9 9
NFATC4 -0.022 0.055 0.24 1 -10000 0 1
ERBB2IP 0.023 0.041 -10000 0 -0.36 7 7
HSP90 (dimer) 0.026 0.007 -10000 0 -10000 0 0
mammary gland morphogenesis 0.003 0.069 -10000 0 -10000 0 0
JUN 0.005 0.067 0.21 3 -0.26 2 5
HRAS 0.027 0.016 -10000 0 -0.36 1 1
DOCK7 -0.026 0.061 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.02 0.074 0.22 3 -10000 0 3
AKT1 0.004 0.006 -10000 0 -10000 0 0
BAD -0.006 0.009 -10000 0 -0.21 1 1
MAPK10 -0.02 0.064 0.21 4 -0.22 12 16
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.006 0.074 -10000 0 -10000 0 0
RAF1 -0.005 0.086 0.29 4 -0.29 8 12
ErbB2/ErbB3/neuregulin 2 -0.002 0.084 0.2 12 -0.2 74 86
STAT3 0.017 0.06 -10000 0 -0.79 3 3
cell migration -0.013 0.066 0.21 10 -0.2 12 22
mol:PI-3-4-5-P3 -0.001 0.001 -10000 0 -10000 0 0
cell proliferation -0.042 0.22 0.37 2 -0.59 68 70
FOS -0.017 0.14 0.33 2 -0.36 62 64
NRAS 0.026 0.023 -10000 0 -0.36 2 2
mol:Ca2+ 0.003 0.069 -10000 0 -10000 0 0
MAPK3 -0.025 0.17 0.35 2 -0.49 51 53
MAPK1 -0.039 0.19 0.36 2 -0.53 61 63
JAK2 -0.026 0.062 -10000 0 -10000 0 0
NF2 0.004 0.06 -10000 0 -0.59 6 6
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.003 0.067 0.18 2 -0.21 52 54
NRG1 -0.015 0.11 -10000 0 -0.36 56 56
GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
MAPK8 -0.018 0.089 -10000 0 -0.25 11 11
MAPK9 -0.008 0.052 0.2 5 -10000 0 5
ERBB2 -0.012 0.05 0.27 18 -10000 0 18
ERBB3 0.027 0.003 -10000 0 -10000 0 0
SHC1 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
apoptosis 0.005 0.011 0.2 1 -10000 0 1
STAT3 (dimer) 0.017 0.059 -10000 0 -0.78 3 3
RNF41 -0.009 0.012 -10000 0 -0.18 2 2
FRAP1 -0.003 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.01 0.047 -10000 0 -10000 0 0
ErbB2/ErbB2/HSP90 (dimer) 0.012 0.039 0.21 18 -10000 0 18
CHRNA1 -0.033 0.2 0.34 2 -0.6 56 58
myelination -0.018 0.061 0.28 4 -10000 0 4
PPP3CB -0.025 0.058 -10000 0 -10000 0 0
KRAS 0.026 0.016 -10000 0 -0.36 1 1
RAC1-CDC42/GDP 0.009 0.077 -10000 0 -10000 0 0
NRG2 -0.04 0.13 -10000 0 -0.36 88 88
mol:GDP -0.003 0.067 0.18 2 -0.21 52 54
SOS1 0.028 0.002 -10000 0 -10000 0 0
MAP2K2 -0.014 0.09 0.3 3 -0.32 11 14
SRC 0.017 0.014 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.027 0.062 -10000 0 -10000 0 0
MAP2K1 -0.046 0.2 0.36 1 -0.58 47 48
heart morphogenesis 0.003 0.069 -10000 0 -10000 0 0
RAS family/GDP 0.015 0.089 -10000 0 -0.28 1 1
GRB2 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.007 0.063 -10000 0 -0.62 6 6
CHRNE 0.005 0.025 0.077 1 -0.14 11 12
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
activation of caspase activity -0.004 0.006 -10000 0 -10000 0 0
nervous system development 0.003 0.069 -10000 0 -10000 0 0
CDC42 0.025 0.017 -10000 0 -0.36 1 1
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.008 0.004 -10000 0 -10000 0 0
SNTA1 0.016 0.02 -10000 0 -0.36 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.008 0.009 -10000 0 -0.21 1 1
MAPK12 -0.007 0.035 -10000 0 -0.26 11 11
CCND1 0.006 0.039 0.19 1 -0.32 6 7
p38 gamma/SNTA1 0.008 0.041 0.19 5 -0.26 9 14
MAP2K3 0.024 0.01 -10000 0 -10000 0 0
PKN1 0.027 0.003 -10000 0 -10000 0 0
G2/M transition checkpoint -0.004 0.043 0.2 9 -0.25 11 20
MAP2K6 0.001 0.016 -10000 0 -0.2 4 4
MAPT -0.058 0.12 0.24 5 -0.27 138 143
MAPK13 0.011 0.005 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.001 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC3 0.027 0.004 -10000 0 -10000 0 0
VDR 0.028 0.003 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.041 0.054 -10000 0 -0.21 24 24
EP300 0.026 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0 0.041 -10000 0 -0.29 3 3
KAT2B 0.011 0.078 -10000 0 -0.36 26 26
MAPK14 0.027 0.003 -10000 0 -10000 0 0
AKT1 -0.002 0.05 0.18 3 -0.23 3 6
RAR alpha/9cRA/Cyclin H 0.008 0.072 0.22 1 -10000 0 1
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.006 0.054 0.2 3 -0.22 14 17
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.004 0.059 -10000 0 -0.25 4 4
NCOR2 0.027 0.016 -10000 0 -0.36 1 1
VDR/VDR/Vit D3 0.02 0.002 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.031 0.087 0.4 3 -0.42 7 10
NCOA2 0.022 0.028 -10000 0 -0.36 3 3
NCOA3 0.016 0.014 -10000 0 -10000 0 0
NCOA1 0.028 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.028 0.002 -10000 0 -10000 0 0
RARG 0.028 0.004 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.037 0.005 -10000 0 -10000 0 0
MAPK3 0.027 0.016 -10000 0 -0.36 1 1
MAPK1 0.026 0.006 -10000 0 -10000 0 0
MAPK8 0.028 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.035 0.085 0.26 1 -0.36 10 11
RARA -0.016 0.061 0.18 4 -0.23 12 16
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.003 0.053 0.2 3 -0.23 15 18
PRKCA 0.028 0.008 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.036 0.092 0.36 4 -0.44 6 10
RXRG -0.15 0.16 0.3 4 -0.31 254 258
RXRA -0.013 0.058 0.25 2 -0.23 1 3
RXRB -0.033 0.089 0.29 5 -0.35 7 12
VDR/Vit D3/DNA 0.02 0.002 -10000 0 -10000 0 0
RBP1 -0.003 0.12 0.36 1 -0.44 40 41
CRBP1/9-cic-RA -0.001 0.083 0.24 1 -0.31 40 41
RARB 0.026 0.032 -10000 0 -0.36 4 4
PRKCG -0.13 0.23 0.36 5 -0.44 208 213
MNAT1 0.026 0.007 -10000 0 -10000 0 0
RAR alpha/RXRs -0.031 0.081 -10000 0 -0.4 10 10
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.023 0.079 0.4 3 -0.36 5 8
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.077 0.25 10 -0.28 5 15
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.036 0.092 0.36 4 -0.43 7 11
positive regulation of DNA binding 0.001 0.063 -10000 0 -0.24 1 1
NRIP1 -0.036 0.1 0.37 1 -1.1 2 3
RXRs/RARs -0.037 0.091 0.37 2 -0.37 10 12
RXRs/RXRs/DNA/9cRA -0.043 0.077 -10000 0 -0.37 10 10
PRKACA 0.027 0.003 -10000 0 -10000 0 0
CDK7 0.027 0.005 -10000 0 -10000 0 0
TFIIH 0.051 0.017 -10000 0 -10000 0 0
RAR alpha/9cRA 0.017 0.068 0.22 2 -0.25 2 4
CCNH 0.027 0.004 -10000 0 -10000 0 0
CREBBP 0.027 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.049 0.018 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.017 0.014 -10000 0 -10000 0 0
NFATC1 -0.02 0.13 0.31 3 -0.38 43 46
NFATC2 0.034 0.053 0.16 6 -0.23 3 9
NFATC3 0.02 0.008 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.054 0.1 0.24 2 -0.28 66 68
Exportin 1/Ran/NUP214 0.055 0.009 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.037 0.12 0.24 1 -0.33 38 39
BCL2/BAX 0.024 0.042 -10000 0 -0.25 11 11
CaM/Ca2+/Calcineurin A alpha-beta B1 0.019 0.007 -10000 0 -10000 0 0
CaM/Ca2+ 0.019 0.007 -10000 0 -10000 0 0
BAX 0.027 0.004 -10000 0 -10000 0 0
MAPK14 0.028 0.003 -10000 0 -10000 0 0
BAD 0.027 0.016 -10000 0 -0.36 1 1
CABIN1/MEF2D -0.043 0.1 0.26 1 -0.32 32 33
Calcineurin A alpha-beta B1/BCL2 0.013 0.052 -10000 0 -0.36 11 11
FKBP8 0.027 0.016 -10000 0 -0.36 1 1
activation-induced cell death of T cells 0.043 0.1 0.32 32 -0.26 1 33
KPNB1 0.027 0.004 -10000 0 -10000 0 0
KPNA2 0.027 0.014 0.36 1 -10000 0 1
XPO1 0.028 0 -10000 0 -10000 0 0
SFN 0.025 0.023 -10000 0 -0.36 2 2
MAP3K8 0.028 0.003 -10000 0 -10000 0 0
NFAT4/CK1 alpha 0.028 0.023 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.07 0.067 -10000 0 -0.3 2 2
CABIN1 -0.055 0.1 0.19 1 -0.28 66 67
CALM1 0.026 0.007 -10000 0 -10000 0 0
RAN 0.028 0.003 -10000 0 -10000 0 0
MAP3K1 0.026 0.016 -10000 0 -0.36 1 1
CAMK4 0.006 0.085 -10000 0 -0.36 31 31
mol:Ca2+ 0 0.002 -10000 0 -10000 0 0
MAPK3 0.027 0.016 -10000 0 -0.36 1 1
YWHAH 0.027 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.027 0.057 -10000 0 -0.25 24 24
YWHAB 0.016 0.014 -10000 0 -10000 0 0
MAPK8 0.027 0.004 -10000 0 -10000 0 0
MAPK9 0.027 0.004 -10000 0 -10000 0 0
YWHAG 0.027 0.005 -10000 0 -10000 0 0
FKBP1A 0.023 0.011 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.009 0.13 0.27 4 -0.37 32 36
PRKCH 0.025 0.017 -10000 0 -0.36 1 1
CABIN1/Cbp/p300 0.038 0.013 -10000 0 -10000 0 0
CASP3 0.026 0.007 -10000 0 -10000 0 0
PIM1 0.027 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.016 0.007 -10000 0 -10000 0 0
apoptosis 0.01 0.014 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.035 0.045 -10000 0 -0.35 1 1
PRKCB -0.062 0.16 -10000 0 -0.36 141 141
PRKCE 0.028 0.002 -10000 0 -10000 0 0
JNK2/NFAT4 0.025 0.038 -10000 0 -10000 0 0
BAD/BCL-XL 0.024 0.023 -10000 0 -0.25 1 1
PRKCD 0.027 0.004 -10000 0 -10000 0 0
NUP214 0.027 0.004 -10000 0 -10000 0 0
PRKCZ 0.027 0.006 -10000 0 -10000 0 0
PRKCA 0.027 0.005 -10000 0 -10000 0 0
PRKCG -0.13 0.23 0.36 5 -0.44 208 213
PRKCQ 0.022 0.044 -10000 0 -0.36 8 8
FKBP38/BCL2 0.024 0.043 -10000 0 -0.25 12 12
EP300 0.026 0.008 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.023 0.011 -10000 0 -10000 0 0
NFATc/JNK1 -0.006 0.13 0.29 4 -0.36 41 45
CaM/Ca2+/FKBP38 0.035 0.015 -10000 0 -0.22 1 1
FKBP12/FK506 0.017 0.008 -10000 0 -10000 0 0
CSNK1A1 0.014 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.022 0.053 -10000 0 -0.2 31 31
NFATc/ERK1 -0.007 0.13 0.33 2 -0.36 40 42
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.039 0.12 0.24 1 -0.32 45 46
NR4A1 0.039 0.073 0.26 4 -0.38 10 14
GSK3B 0.028 0.002 -10000 0 -10000 0 0
positive T cell selection 0.02 0.008 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.031 0.039 0.16 1 -10000 0 1
RCH1/ KPNB1 0.04 0.008 -10000 0 -10000 0 0
YWHAQ 0.028 0.002 -10000 0 -10000 0 0
PRKACA 0.028 0.003 -10000 0 -10000 0 0
AKAP5 0.011 0.075 -10000 0 -0.36 24 24
MEF2D 0.027 0.007 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
NFATc/p38 alpha -0.008 0.13 0.34 2 -0.36 41 43
CREBBP 0.027 0.007 -10000 0 -10000 0 0
BCL2 0.013 0.052 -10000 0 -0.36 11 11
Arf6 downstream pathway

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
PLAUR 0.015 0.028 -10000 0 -10000 0 0
regulation of axonogenesis -0.009 0.027 0.23 7 -10000 0 7
myoblast fusion -0.029 0.019 -10000 0 -10000 0 0
mol:GTP 0.016 0.032 -10000 0 -0.15 22 22
regulation of calcium-dependent cell-cell adhesion -0.019 0.086 0.21 63 -10000 0 63
ARF1/GTP 0.029 0.036 -10000 0 -10000 0 0
mol:GM1 0.004 0.027 -10000 0 -10000 0 0
mol:Choline 0.008 0.015 -10000 0 -0.19 1 1
lamellipodium assembly 0.004 0.082 -10000 0 -0.34 32 32
MAPK3 0.018 0.026 -10000 0 -0.22 1 1
ARF6/GTP/NME1/Tiam1 0.02 0.086 -10000 0 -0.21 63 63
ARF1 0.027 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.029 0.019 -10000 0 -10000 0 0
ARF1/GDP 0.024 0.058 -10000 0 -0.24 8 8
ARF6 0.032 0.009 -10000 0 -10000 0 0
RAB11A 0.027 0.006 -10000 0 -10000 0 0
TIAM1 -0.01 0.11 -10000 0 -0.36 59 59
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.018 0.024 -10000 0 -10000 0 0
actin filament bundle formation -0.026 0.058 0.24 8 -10000 0 8
KALRN 0.02 0.017 -10000 0 -0.18 1 1
RAB11FIP3/RAB11A 0.039 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.027 0.058 -10000 0 -0.24 8 8
NME1 0.023 0.057 0.36 2 -0.44 8 10
Rac1/GDP 0.025 0.056 -10000 0 -0.24 7 7
substrate adhesion-dependent cell spreading 0.016 0.032 -10000 0 -0.15 22 22
cortical actin cytoskeleton organization 0.005 0.081 -10000 0 -0.34 30 30
RAC1 0.025 0.008 -10000 0 -10000 0 0
liver development 0.016 0.032 -10000 0 -0.15 22 22
ARF6/GTP 0.016 0.032 -10000 0 -0.15 22 22
RhoA/GTP 0.029 0.036 -10000 0 -10000 0 0
mol:GDP 0.012 0.05 -10000 0 -0.2 27 27
ARF6/GTP/RAB11FIP3/RAB11A 0.043 0.037 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
PLD1 0.012 0.034 -10000 0 -0.22 2 2
RAB11FIP3 0.027 0.004 -10000 0 -10000 0 0
tube morphogenesis 0.004 0.082 -10000 0 -0.34 32 32
ruffle organization 0.009 0.027 -10000 0 -0.23 7 7
regulation of epithelial cell migration 0.016 0.032 -10000 0 -0.15 22 22
PLD2 0.016 0.017 -10000 0 -10000 0 0
PIP5K1A 0.009 0.027 -10000 0 -0.23 7 7
mol:Phosphatidic acid 0.008 0.015 -10000 0 -0.19 1 1
Rac1/GTP 0.005 0.081 -10000 0 -0.34 30 30
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.1 0.17 -10000 0 -0.38 108 108
CaM/Ca2+ 0.019 0.005 -10000 0 -10000 0 0
AKT1 0.026 0.007 -10000 0 -10000 0 0
AKT2 0.027 0.004 -10000 0 -10000 0 0
STXBP4 0.026 0.016 -10000 0 -0.36 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.12 0.17 -10000 0 -0.4 118 118
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
CALM1 0.026 0.007 -10000 0 -10000 0 0
YWHAQ 0.028 0.002 -10000 0 -10000 0 0
TBC1D4 0.01 0.012 -10000 0 -0.25 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.027 0.006 -10000 0 -10000 0 0
YWHAB 0.016 0.014 -10000 0 -10000 0 0
SNARE/Synip 0.045 0.025 -10000 0 -0.21 1 1
YWHAG 0.027 0.005 -10000 0 -10000 0 0
ASIP 0.005 0.044 0.36 5 -0.44 2 7
PRKCI 0.026 0.022 -10000 0 -0.36 2 2
AS160/CaM/Ca2+ 0.019 0.005 -10000 0 -10000 0 0
RHOQ 0.028 0.002 -10000 0 -10000 0 0
GYS1 0.011 0.004 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
TRIP10 0.027 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.037 0.006 -10000 0 -10000 0 0
AS160/14-3-3 0.012 0.042 -10000 0 -0.3 1 1
VAMP2 0.023 0.011 -10000 0 -10000 0 0
SLC2A4 -0.14 0.19 -10000 0 -0.45 118 118
STX4 0.027 0.003 -10000 0 -10000 0 0
GSK3B 0.02 0.007 -10000 0 -10000 0 0
SFN 0.025 0.023 -10000 0 -0.36 2 2
LNPEP 0.026 0.006 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

Figure S91.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S91.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.024 0.058 -10000 0 -0.36 13 13
PDGF/PDGFRA/CRKL 0.036 0.043 -10000 0 -0.24 13 13
positive regulation of JUN kinase activity 0.062 0.041 -10000 0 -10000 0 0
CRKL 0.027 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.029 0.049 -10000 0 -0.26 16 16
AP1 0.023 0.098 0.3 5 -0.6 6 11
mol:IP3 0.003 0.036 -10000 0 -0.25 11 11
PLCG1 0.003 0.036 -10000 0 -0.25 11 11
PDGF/PDGFRA/alphaV Integrin 0.038 0.043 -10000 0 -0.24 13 13
RAPGEF1 0.027 0.016 -10000 0 -0.36 1 1
CRK 0.023 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0.003 0.036 -10000 0 -0.25 11 11
CAV3 -0.013 0.035 -10000 0 -0.44 3 3
CAV1 0.019 0.054 -10000 0 -0.36 12 12
SHC/Grb2/SOS1 0.064 0.042 -10000 0 -10000 0 0
PDGF/PDGFRA/Shf 0.027 0.07 -10000 0 -0.28 28 28
FOS -0.004 0.08 0.31 14 -0.63 5 19
JUN -0.006 0.021 -10000 0 -10000 0 0
oligodendrocyte development 0.037 0.043 -10000 0 -0.24 13 13
GRB2 0.027 0.004 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
mol:DAG 0.003 0.036 -10000 0 -0.25 11 11
PDGF/PDGFRA 0.024 0.058 -10000 0 -0.36 13 13
actin cytoskeleton reorganization 0.036 0.048 0.26 1 -0.25 15 16
SRF 0.004 0.012 -10000 0 -10000 0 0
SHC1 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.051 0.04 -10000 0 -0.2 11 11
PDGF/PDGFRA/Crk/C3G 0.044 0.042 -10000 0 -0.2 10 10
JAK1 0.012 0.037 -10000 0 -0.24 12 12
ELK1/SRF 0.026 0.077 0.16 137 -10000 0 137
SHB 0.026 0.03 0.36 1 -0.44 2 3
SHF 0.015 0.072 -10000 0 -0.44 15 15
CSNK2A1 0.012 0.021 -10000 0 -10000 0 0
GO:0007205 -0.002 0.038 -10000 0 -0.28 11 11
SOS1 0.028 0.002 -10000 0 -10000 0 0
Ras protein signal transduction 0.062 0.041 -10000 0 -10000 0 0
PDGF/PDGFRA/SHB 0.036 0.048 0.26 1 -0.25 15 16
PDGF/PDGFRA/Caveolin-1 0.032 0.057 -10000 0 -0.26 20 20
ITGAV 0.028 0.002 -10000 0 -10000 0 0
ELK1 -0.006 0.034 0.25 1 -0.24 10 11
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
PDGF/PDGFRA/Crk 0.031 0.043 -10000 0 -0.23 13 13
JAK-STAT cascade 0.012 0.037 -10000 0 -0.24 12 12
cell proliferation 0.027 0.069 -10000 0 -0.28 28 28
FoxO family signaling

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
G6PC -0.056 0.32 0.51 2 -1.2 44 46
PLK1 0.02 0.12 0.4 1 -0.58 6 7
CDKN1B 0.057 0.12 0.39 7 -0.37 7 14
FOXO3 0.026 0.13 -10000 0 -0.56 9 9
KAT2B 0.015 0.08 -10000 0 -0.36 26 26
FOXO1/SIRT1 0.019 0.12 0.27 3 -0.38 34 37
CAT 0.02 0.12 -10000 0 -0.58 5 5
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
AKT1 0.025 0.029 -10000 0 -10000 0 0
FOXO1 0.009 0.13 0.39 5 -0.38 44 49
MAPK10 0.012 0.08 0.19 46 -0.19 11 57
mol:GTP 0.001 0 -10000 0 -10000 0 0
FOXO4 0.037 0.076 0.31 7 -10000 0 7
response to oxidative stress 0.004 0.017 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.038 0.12 -10000 0 -0.5 9 9
XPO1 0.028 0 -10000 0 -10000 0 0
EP300 0.02 0.026 -10000 0 -10000 0 0
BCL2L11 0.031 0.024 -10000 0 -10000 0 0
FOXO1/SKP2 0.017 0.12 0.27 4 -0.38 35 39
mol:GDP 0.004 0.017 -10000 0 -10000 0 0
RAN 0.029 0.003 -10000 0 -10000 0 0
GADD45A 0.042 0.13 -10000 0 -0.55 20 20
YWHAQ 0.028 0.002 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.041 0.12 0.23 11 -0.42 18 29
MST1 -0.043 0.17 -10000 0 -0.44 98 98
CSNK1D 0.027 0.004 -10000 0 -10000 0 0
CSNK1E 0.027 0.006 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.006 0.11 -10000 0 -0.4 26 26
YWHAB 0.016 0.014 -10000 0 -10000 0 0
MAPK8 0.036 0.05 0.19 54 -10000 0 54
MAPK9 0.036 0.05 0.19 54 -10000 0 54
YWHAG 0.027 0.005 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
SIRT1 0.028 0.014 -10000 0 -10000 0 0
SOD2 0.053 0.11 0.42 5 -0.54 1 6
RBL2 0.044 0.11 -10000 0 -0.95 1 1
RAL/GDP 0.037 0.023 -10000 0 -10000 0 0
CHUK 0.031 0.017 -10000 0 -10000 0 0
Ran/GTP 0.023 0.002 -10000 0 -10000 0 0
CSNK1G2 0.027 0.016 -10000 0 -0.36 1 1
RAL/GTP 0.041 0.022 -10000 0 -10000 0 0
CSNK1G1 0.026 0.017 -10000 0 -0.36 1 1
FASLG -0.035 0.29 -10000 0 -1.2 33 33
SKP2 0.027 0.004 -10000 0 -10000 0 0
USP7 0.028 0.004 -10000 0 -10000 0 0
IKBKB 0.029 0.018 -10000 0 -10000 0 0
CCNB1 0.022 0.12 -10000 0 -0.58 5 5
FOXO1-3a-4/beta catenin 0.064 0.12 0.34 20 -10000 0 20
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.12 0.27 4 -0.38 35 39
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
SGK1 0.017 0.077 -10000 0 -0.36 24 24
CSNK1G3 0.027 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.042 0.004 -10000 0 -10000 0 0
ZFAND5 0.035 0.071 0.34 4 -10000 0 4
SFN 0.025 0.023 -10000 0 -0.36 2 2
CDK2 0.019 0.034 -10000 0 -10000 0 0
FOXO3A/14-3-3 -0.001 0.097 -10000 0 -0.42 17 17
CREBBP 0.018 0.034 -10000 0 -10000 0 0
FBXO32 0.048 0.16 -10000 0 -0.76 4 4
BCL6 0.044 0.11 -10000 0 -0.82 1 1
RALB 0.029 0.001 -10000 0 -10000 0 0
RALA 0.026 0.008 -10000 0 -10000 0 0
YWHAH 0.027 0.006 -10000 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.021 0.054 -10000 0 -0.29 4 4
BAG4 0.024 0.01 -10000 0 -10000 0 0
BAD 0.013 0.029 0.16 4 -0.33 1 5
NFKBIA 0.026 0.007 -10000 0 -10000 0 0
BIRC3 0.02 0.05 -10000 0 -0.37 10 10
BAX 0.014 0.037 0.2 11 -0.18 1 12
EnzymeConsortium:3.1.4.12 0.008 0.017 0.097 5 -0.073 3 8
IKBKB 0.033 0.067 0.24 7 -0.31 1 8
MAP2K2 0.013 0.042 0.19 19 -0.28 1 20
MAP2K1 0.012 0.04 0.19 18 -10000 0 18
SMPD1 0.009 0.026 0.14 4 -0.16 7 11
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.026 0.058 0.22 1 -0.32 3 4
MAP2K4 0.009 0.026 0.19 3 -0.21 1 4
protein ubiquitination 0.027 0.06 0.33 3 -0.3 2 5
EnzymeConsortium:2.7.1.37 0.014 0.043 0.19 20 -0.22 1 21
response to UV 0 0 0.002 20 -10000 0 20
RAF1 0.015 0.041 0.19 19 -10000 0 19
CRADD 0.027 0.003 -10000 0 -10000 0 0
mol:ceramide 0.015 0.029 0.13 9 -0.18 1 10
I-kappa-B-alpha/RELA/p50/ubiquitin 0.034 0.011 -10000 0 -10000 0 0
MADD 0.028 0.003 -10000 0 -10000 0 0
MAP3K1 0.012 0.03 0.17 4 -0.2 2 6
TRADD 0.028 0.003 -10000 0 -10000 0 0
RELA/p50 0.027 0.004 -10000 0 -10000 0 0
MAPK3 0.017 0.042 0.19 19 -0.23 1 20
MAPK1 0.013 0.044 0.19 17 -0.23 1 18
p50/RELA/I-kappa-B-alpha 0.038 0.012 -10000 0 -10000 0 0
FADD 0.023 0.052 0.21 2 -0.28 3 5
KSR1 0.016 0.04 0.19 18 -0.18 1 19
MAPK8 0.009 0.03 0.2 4 -0.2 1 5
TRAF2 0.027 0.016 -10000 0 -0.36 1 1
response to radiation 0 0 0.002 6 -10000 0 6
CHUK 0.019 0.051 0.26 1 -0.29 1 2
TNF R/SODD 0.035 0.015 -10000 0 -10000 0 0
TNF 0.024 0.035 -10000 0 -0.36 5 5
CYCS 0.037 0.05 0.13 64 -0.26 1 65
IKBKG 0.021 0.056 0.24 2 -0.35 2 4
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.026 0.055 -10000 0 -0.29 4 4
RELA 0.027 0.004 -10000 0 -10000 0 0
RIPK1 0.027 0.004 -10000 0 -10000 0 0
AIFM1 0.032 0.047 0.14 39 -0.26 1 40
TNF/TNF R/SODD 0.045 0.031 -10000 0 -0.21 4 4
TNFRSF1A 0.027 0.004 -10000 0 -10000 0 0
response to heat 0 0 0.002 6 -10000 0 6
CASP8 0.023 0.098 -10000 0 -0.56 16 16
NSMAF 0.038 0.072 0.21 57 -0.32 1 58
response to hydrogen peroxide 0 0 0.002 20 -10000 0 20
BCL2 0.013 0.052 -10000 0 -0.36 11 11
Arf6 trafficking 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
SLC2A4 -0.018 0.12 -10000 0 -0.36 64 64
CLTC -0.002 0.1 0.23 1 -0.4 37 38
calcium ion-dependent exocytosis 0.012 0.042 -10000 0 -10000 0 0
Dynamin 2/GTP 0.023 0.031 0.18 1 -0.23 8 9
EXOC4 0.027 0.006 -10000 0 -10000 0 0
CD59 0.002 0.075 -10000 0 -0.32 29 29
CPE -0.002 0.057 -10000 0 -0.21 42 42
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
membrane fusion 0.018 0.027 -10000 0 -10000 0 0
CTNND1 0.009 0.032 0.18 7 -0.22 8 15
DNM2 0.027 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.004 0.064 -10000 0 -0.24 28 28
TSHR 0.006 0.019 -10000 0 -0.27 2 2
INS 0.006 0.045 -10000 0 -0.49 4 4
BIN1 0.027 0.016 -10000 0 -0.36 1 1
mol:Choline 0.018 0.027 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.01 0.032 0.23 1 -0.26 8 9
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.022 0.031 0.18 1 -0.23 8 9
JUP 0.002 0.074 0.21 1 -0.32 29 30
ASAP2/amphiphysin II 0.049 0.017 -10000 0 -0.19 1 1
ARF6/GTP 0.019 0.005 -10000 0 -10000 0 0
CDH1 0.002 0.074 -10000 0 -0.32 29 29
clathrin-independent pinocytosis 0.019 0.005 -10000 0 -10000 0 0
MAPK8IP3 0.026 0.025 -10000 0 -0.4 2 2
positive regulation of endocytosis 0.019 0.005 -10000 0 -10000 0 0
EXOC2 0.027 0.016 -10000 0 -0.36 1 1
substrate adhesion-dependent cell spreading 0.024 0.041 -10000 0 -0.37 4 4
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.027 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.019 0.093 0.32 35 -10000 0 35
positive regulation of phagocytosis 0.013 0.005 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.034 0.019 -10000 0 -0.24 2 2
ACAP1 0.018 0.03 -10000 0 -0.28 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.037 0.11 -10000 0 -0.4 31 31
clathrin heavy chain/ACAP1 0.001 0.09 0.22 4 -0.33 35 39
JIP4/KLC1 0.048 0.016 -10000 0 -10000 0 0
EXOC1 0.026 0.016 -10000 0 -0.36 1 1
exocyst 0.024 0.042 -10000 0 -0.37 4 4
RALA/GTP 0.019 0.006 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.035 0.01 -10000 0 -10000 0 0
receptor recycling 0.019 0.005 -10000 0 -10000 0 0
CTNNA1 0.009 0.032 0.18 7 -0.22 8 15
NME1 0.01 0.032 0.23 1 -0.26 8 9
clathrin coat assembly -0.002 0.1 0.22 1 -0.39 37 38
IL2RA -0.001 0.076 -10000 0 -0.32 29 29
VAMP3 0.013 0.005 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.007 0.098 0.2 1 -0.3 38 39
EXOC6 0.027 0.006 -10000 0 -10000 0 0
PLD1 0.013 0.011 -10000 0 -0.23 1 1
PLD2 0.012 0.007 -10000 0 -10000 0 0
EXOC5 0.024 0.028 -10000 0 -0.36 3 3
PIP5K1C 0.007 0.055 -10000 0 -0.22 23 23
SDC1 0.002 0.074 -10000 0 -0.32 29 29
ARF6/GDP 0.021 0.033 0.2 1 -0.26 8 9
EXOC7 0.027 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.022 0.096 -10000 0 -0.33 35 35
mol:Phosphatidic acid 0.018 0.027 -10000 0 -10000 0 0
endocytosis -0.048 0.016 0.19 1 -10000 0 1
SCAMP2 0.027 0.006 -10000 0 -10000 0 0
ADRB2 -0.028 0.12 0.39 1 -0.41 39 40
EXOC3 0.027 0.004 -10000 0 -10000 0 0
ASAP2 0.028 0.002 -10000 0 -10000 0 0
Dynamin 2/GDP 0.026 0.032 0.21 1 -0.23 8 9
KLC1 0.026 0.007 -10000 0 -10000 0 0
AVPR2 -0.014 0.11 0.28 6 -0.39 38 44
RALA 0.025 0.008 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.017 0.09 -10000 0 -0.34 24 24
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.035 0.038 -10000 0 -0.31 7 7
CRKL 0.026 0.096 0.27 10 -0.44 14 24
mol:PIP3 -0.002 0.011 -10000 0 -10000 0 0
AKT1 -0.007 0.02 -10000 0 -10000 0 0
PTK2B 0.02 0.025 -10000 0 -0.36 2 2
RAPGEF1 0.029 0.095 0.3 9 -0.42 14 23
RANBP10 0.028 0.003 -10000 0 -10000 0 0
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
HGF/MET/SHIP2 0.043 0.055 -10000 0 -0.24 20 20
MAP3K5 0.017 0.12 0.35 5 -0.44 19 24
HGF/MET/CIN85/CBL/ENDOPHILINS 0.057 0.054 -10000 0 -0.27 7 7
AP1 0.029 0.036 -10000 0 -0.22 4 4
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.027 0.004 -10000 0 -10000 0 0
apoptosis -0.035 0.23 -10000 0 -0.72 58 58
STAT3 (dimer) 0.003 0.052 -10000 0 -0.33 6 6
GAB1/CRKL/SHP2/PI3K 0.064 0.093 0.3 4 -0.41 12 16
INPP5D 0.027 0.016 -10000 0 -0.36 1 1
CBL/CRK 0.047 0.093 0.26 9 -0.41 14 23
PTPN11 0.028 0.002 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.016 0.014 -10000 0 -10000 0 0
PTEN 0.026 0.006 -10000 0 -10000 0 0
ELK1 0.004 0.094 0.36 29 -10000 0 29
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.007 0.04 -10000 0 -0.23 6 6
PAK1 -0.008 0.022 -10000 0 -10000 0 0
HGF/MET/RANBP10 0.044 0.055 -10000 0 -0.24 20 20
HRAS 0.019 0.06 -10000 0 -0.47 3 3
DOCK1 0.028 0.091 0.3 5 -0.42 14 19
GAB1 0.018 0.088 -10000 0 -0.45 15 15
CRK 0.024 0.09 0.27 9 -0.45 12 21
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.018 0.079 -10000 0 -0.43 15 15
JUN 0.027 0.004 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.013 0.04 -10000 0 -0.17 18 18
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
cell morphogenesis 0.048 0.1 0.26 40 -0.42 4 44
GRB2/SHC 0.008 0.054 -10000 0 -0.21 5 5
FOS 0.022 0.039 -10000 0 -0.36 6 6
GLMN 0.001 0.012 -10000 0 -0.21 2 2
cell motility 0.004 0.093 0.35 29 -10000 0 29
HGF/MET/MUC20 0.027 0.05 -10000 0 -0.24 20 20
cell migration 0.008 0.053 -10000 0 -0.2 5 5
GRB2 0.027 0.004 -10000 0 -10000 0 0
CBL 0.027 0.004 -10000 0 -10000 0 0
MET/RANBP10 0.036 0.036 -10000 0 -0.32 6 6
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.013 0.048 -10000 0 -0.3 9 9
MET/MUC20 0.017 0.033 -10000 0 -0.31 6 6
RAP1B 0.028 0.092 0.3 10 -0.41 13 23
RAP1A 0.027 0.09 0.29 8 -0.4 14 22
HGF/MET/RANBP9 0.043 0.056 -10000 0 -0.24 21 21
RAF1 0.022 0.064 0.27 1 -0.44 3 4
STAT3 0.003 0.051 -10000 0 -0.35 5 5
cell proliferation 0.03 0.074 0.33 2 -0.39 5 7
RPS6KB1 0.003 0.036 -10000 0 -0.29 7 7
MAPK3 -0.013 0.083 0.56 7 -10000 0 7
MAPK1 0.015 0.16 0.65 32 -10000 0 32
RANBP9 0.027 0.016 -10000 0 -0.36 1 1
MAPK8 0.027 0.11 0.35 5 -0.46 10 15
SRC 0.004 0.039 -10000 0 -0.3 6 6
PI3K 0.008 0.054 -10000 0 -0.2 4 4
MET/Glomulin -0.015 0.053 -10000 0 -0.2 18 18
SOS1 0.028 0.002 -10000 0 -10000 0 0
MAP2K1 0.021 0.061 0.29 2 -0.46 2 4
MET 0.022 0.047 -10000 0 -0.44 6 6
MAP4K1 0.018 0.12 0.29 5 -0.46 21 26
PTK2 0.023 0.01 -10000 0 -10000 0 0
MAP2K2 0.021 0.064 0.29 2 -0.46 2 4
BAD -0.008 0.021 -10000 0 -10000 0 0
MAP2K4 0.013 0.11 0.34 5 -0.43 14 19
SHP2/GRB2/SOS1/GAB1 0.049 0.083 -10000 0 -0.39 13 13
INPPL1 0.027 0.004 -10000 0 -10000 0 0
PXN 0.028 0.002 -10000 0 -10000 0 0
SH3KBP1 0.027 0.004 -10000 0 -10000 0 0
HGS -0.015 0.036 -10000 0 -0.19 8 8
PLCgamma1/PKC 0.012 0.01 -10000 0 -10000 0 0
HGF 0.017 0.061 -10000 0 -0.37 15 15
RASA1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.028 0.003 -10000 0 -10000 0 0
PTPRJ 0.028 0.003 -10000 0 -10000 0 0
NCK/PLCgamma1 0.025 0.039 -10000 0 -0.26 1 1
PDPK1 -0.005 0.023 -10000 0 -10000 0 0
HGF/MET/SHIP 0.043 0.056 -10000 0 -0.24 21 21
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.022 0.06 -10000 0 -10000 0 0
CRKL 0.021 0.052 0.3 4 -0.34 1 5
mol:DAG 0.018 0.031 -10000 0 -10000 0 0
HRAS 0.008 0.06 0.3 6 -10000 0 6
MAPK8 0.034 0.063 0.19 60 -0.23 4 64
RAP1A 0.021 0.052 0.33 3 -0.29 2 5
GAB1 0.02 0.052 0.31 3 -0.34 1 4
MAPK14 0.033 0.063 0.19 57 -0.23 4 61
EPO 0.02 0.048 0.33 2 -0.45 5 7
PLCG1 0.018 0.032 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.027 0.022 -10000 0 -0.41 1 1
RAPGEF1 0.027 0.016 -10000 0 -0.36 1 1
EPO/EPOR (dimer)/SOCS3 0.047 0.042 0.23 2 -0.26 8 10
GAB1/SHC/GRB2/SOS1 0.051 0.05 0.26 1 -0.31 1 2
EPO/EPOR (dimer) 0.034 0.041 0.24 2 -0.31 6 8
IRS2 0.014 0.039 0.23 1 -0.34 1 2
STAT1 0.029 0.05 -10000 0 -10000 0 0
STAT5B 0.027 0.045 -10000 0 -10000 0 0
cell proliferation 0.014 0.074 0.19 79 -10000 0 79
GAB1/SHIP/PIK3R1/SHP2/SHC 0.041 0.044 -10000 0 -10000 0 0
TEC 0.02 0.052 0.31 3 -0.34 1 4
SOCS3 0.026 0.027 -10000 0 -0.44 2 2
STAT1 (dimer) 0.031 0.05 -10000 0 -10000 0 0
JAK2 0.025 0.03 -10000 0 -0.37 3 3
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.065 0.053 0.24 1 -0.3 2 3
EPO/EPOR 0.034 0.041 0.24 2 -0.31 6 8
LYN 0.024 0.013 -10000 0 -10000 0 0
TEC/VAV2 0.03 0.052 -10000 0 -0.26 1 1
elevation of cytosolic calcium ion concentration 0.027 0.022 -10000 0 -0.41 1 1
SHC1 0.027 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.046 0.041 0.24 2 -0.25 5 7
mol:IP3 0.018 0.031 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.034 0.046 0.24 1 -0.32 1 2
SH2B3 0.028 0.011 -10000 0 -10000 0 0
NFKB1 0.033 0.063 0.19 58 -0.23 4 62
EPO/EPOR (dimer)/JAK2/SOCS3 0.011 0.028 -10000 0 -0.24 3 3
PTPN6 0.02 0.05 0.3 2 -0.3 2 4
TEC/VAV2/GRB2 0.043 0.056 0.26 1 -10000 0 1
EPOR 0.027 0.022 -10000 0 -0.41 1 1
INPP5D 0.027 0.016 -10000 0 -0.36 1 1
mol:GDP 0.05 0.05 0.26 1 -0.32 1 2
SOS1 0.028 0.002 -10000 0 -10000 0 0
PLCG2 -0.004 0.1 -10000 0 -0.36 49 49
CRKL/CBL/C3G 0.047 0.049 0.25 3 -10000 0 3
VAV2 0.018 0.056 0.3 4 -0.26 1 5
CBL 0.02 0.052 0.3 4 -0.34 1 5
SHC/Grb2/SOS1 0.038 0.042 -10000 0 -0.32 1 1
STAT5A 0.027 0.046 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
STAT5 (dimer) 0.041 0.069 -10000 0 -0.32 1 1
LYN/PLCgamma2 0.016 0.075 -10000 0 -0.25 43 43
PTPN11 0.028 0.002 -10000 0 -10000 0 0
BTK 0.001 0.079 0.3 4 -0.31 6 10
BCL2 0.007 0.17 0.34 1 -0.68 32 33
mTOR 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.027 0.004 -10000 0 -10000 0 0
mol:PIP3 0.007 0.016 -10000 0 -0.2 1 1
FRAP1 -0.012 0.11 -10000 0 -0.44 38 38
AKT1 0.002 0.036 0.15 18 -0.31 1 19
INSR 0.027 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.029 0.007 -10000 0 -10000 0 0
mol:GTP 0.03 0.042 0.23 1 -0.24 1 2
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.006 0.04 -10000 0 -0.22 7 7
TSC2 0.027 0.004 -10000 0 -10000 0 0
RHEB/GDP 0.02 0.03 -10000 0 -0.22 1 1
TSC1 0.027 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.024 0.015 -10000 0 -0.18 2 2
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.017 0.05 -10000 0 -0.25 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.027 0.004 -10000 0 -10000 0 0
RPS6KB1 0.007 0.077 0.23 5 -0.3 21 26
MAP3K5 0.005 0.029 0.2 4 -0.17 11 15
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
apoptosis 0.006 0.029 0.2 4 -0.17 11 15
mol:LY294002 0 0 0.001 1 -0.001 2 3
EIF4B 0.006 0.071 0.27 5 -0.32 10 15
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.026 0.069 0.23 3 -0.32 8 11
eIF4E/eIF4G1/eIF4A1 0.002 0.069 -10000 0 -0.26 35 35
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.038 0.023 -10000 0 -0.18 3 3
mTOR/RHEB/GTP/Raptor/GBL 0.009 0.034 0.2 9 -0.15 1 10
FKBP1A 0.023 0.011 -10000 0 -10000 0 0
RHEB/GTP 0.034 0.038 0.2 1 -0.22 1 2
mol:Amino Acids 0 0 0.001 1 -0.001 2 3
FKBP12/Rapamycin 0.017 0.008 -10000 0 -10000 0 0
PDPK1 -0.006 0.018 0.16 3 -0.2 1 4
EIF4E 0.026 0.023 -10000 0 -0.36 2 2
ASK1/PP5C 0.006 0.13 -10000 0 -0.43 45 45
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.009 0.047 -10000 0 -0.3 4 4
TSC1/TSC2 0.033 0.045 0.24 1 -0.26 1 2
tumor necrosis factor receptor activity 0 0 0.001 2 -0.001 1 3
RPS6 0.026 0.02 -10000 0 -0.44 1 1
PPP5C 0.027 0.004 -10000 0 -10000 0 0
EIF4G1 0.028 0.002 -10000 0 -10000 0 0
IRS1 0.007 0.013 -10000 0 -0.21 2 2
INS -0.017 0.003 -10000 0 -10000 0 0
PTEN 0.026 0.006 -10000 0 -10000 0 0
PDK2 -0.006 0.02 0.16 3 -0.2 1 4
EIF4EBP1 -0.068 0.3 -10000 0 -1 53 53
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
PPP2R5D -0.008 0.11 0.25 4 -0.4 38 42
peptide biosynthetic process -0.007 0.035 0.18 19 -0.25 1 20
RHEB 0.027 0.005 -10000 0 -10000 0 0
EIF4A1 0.023 0.011 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 10 -0.003 1 11
EEF2 -0.007 0.035 0.18 19 -0.25 1 20
eIF4E/4E-BP1 -0.051 0.28 -10000 0 -0.97 53 53
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.008 0.007 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.025 0.025 -10000 0 -10000 0 0
CDKN1B 0.026 0.068 0.26 3 -0.6 2 5
CDKN1A 0.024 0.069 0.24 1 -0.6 2 3
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.025 0.016 0.36 1 -10000 0 1
FOXO3 0.026 0.06 0.24 1 -0.59 1 2
AKT1 0.002 0.061 0.26 1 -0.34 14 15
BAD 0.027 0.016 -10000 0 -0.36 1 1
AKT3 0.01 0.033 -10000 0 -0.26 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.025 0.067 0.24 1 -0.6 2 3
AKT1/ASK1 0.042 0.091 0.24 2 -0.53 3 5
BAD/YWHAZ 0.046 0.024 -10000 0 -0.21 1 1
RICTOR 0.024 0.035 -10000 0 -0.36 5 5
RAF1 0.027 0.004 -10000 0 -10000 0 0
JNK cascade -0.04 0.087 0.51 3 -0.23 1 4
TSC1 0.023 0.069 0.24 1 -0.6 2 3
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
AKT1/RAF1 0.046 0.094 0.25 3 -0.56 3 6
EP300 0.026 0.006 -10000 0 -10000 0 0
mol:GDP 0.027 0.071 0.26 1 -0.33 14 15
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.025 0.067 0.26 2 -0.6 2 4
YWHAQ 0.028 0.002 -10000 0 -10000 0 0
TBC1D4 0.053 0.093 0.24 122 -0.2 1 123
MAP3K5 0.027 0.004 -10000 0 -10000 0 0
MAPKAP1 0.027 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.053 0.093 0.3 10 -0.21 58 68
YWHAH 0.027 0.006 -10000 0 -10000 0 0
AKT1S1 0.026 0.071 0.26 5 -0.6 2 7
CASP9 0.025 0.062 0.24 1 -0.6 2 3
YWHAB 0.016 0.014 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.046 0.094 0.31 7 -0.53 3 10
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.032 0.028 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
SRC 0.017 0.014 -10000 0 -10000 0 0
AKT2/p21CIP1 0.022 0.075 0.23 1 -0.42 5 6
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.032 -10000 0 -0.27 2 2
CHUK 0.027 0.053 0.24 1 -10000 0 1
BAD/BCL-XL 0.017 0.065 -10000 0 -0.57 2 2
mTORC2 0.032 0.021 -10000 0 -0.19 5 5
AKT2 0.014 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.064 0.12 0.27 61 -0.41 11 72
PDPK1 0.027 0.004 -10000 0 -10000 0 0
MDM2 0.025 0.069 0.26 2 -0.6 2 4
MAPKKK cascade -0.046 0.093 0.54 3 -0.25 3 6
MDM2/Cbp/p300 0.052 0.091 0.27 1 -0.51 3 4
TSC1/TSC2 0.023 0.067 0.27 4 -0.59 2 6
proteasomal ubiquitin-dependent protein catabolic process 0.049 0.088 0.26 1 -0.48 3 4
glucose import 0.013 0.093 0.21 83 -10000 0 83
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.025 0.049 0.18 6 -0.33 2 8
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.013 0.093 0.21 83 -10000 0 83
GSK3A 0.027 0.07 0.26 5 -0.6 2 7
FOXO1 0.053 0.097 0.27 60 -0.61 1 61
GSK3B 0.025 0.07 0.26 2 -0.6 2 4
SFN 0.025 0.023 -10000 0 -0.36 2 2
G1/S transition of mitotic cell cycle 0.036 0.081 0.27 9 -0.54 3 12
p27Kip1/14-3-3 family 0.049 0.054 0.28 1 -10000 0 1
PRKACA 0.027 0.003 -10000 0 -10000 0 0
KPNA1 0.028 0.003 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
YWHAG 0.027 0.005 -10000 0 -10000 0 0
RHEB 0.027 0.005 -10000 0 -10000 0 0
CREBBP 0.027 0.004 -10000 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.011 0.071 -10000 0 -0.44 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.004 0.088 0.41 4 -10000 0 4
IL27/IL27R/JAK1 0.036 0.11 -10000 0 -0.54 1 1
TBX21 -0.02 0.12 -10000 0 -0.47 19 19
IL12B 0.015 0.041 -10000 0 -0.45 4 4
IL12A 0.002 0.03 -10000 0 -0.26 8 8
IL6ST 0.016 0.062 -10000 0 -0.37 15 15
IL27RA/JAK1 0.023 0.027 -10000 0 -10000 0 0
IL27 0.003 0.089 -10000 0 -0.44 23 23
TYK2 0.024 0.015 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.054 0.16 0.77 3 -10000 0 3
T-helper 2 cell differentiation 0.004 0.088 0.41 4 -10000 0 4
T cell proliferation during immune response 0.004 0.088 0.41 4 -10000 0 4
MAPKKK cascade -0.004 0.088 -10000 0 -0.41 4 4
STAT3 0.027 0.004 -10000 0 -10000 0 0
STAT2 0.028 0.002 -10000 0 -10000 0 0
STAT1 0.027 0.019 -10000 0 -0.45 1 1
IL12RB1 0.014 0.07 -10000 0 -0.36 20 20
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.014 0.11 0.37 1 -0.5 11 12
IL27/IL27R/JAK2/TYK2 -0.004 0.089 -10000 0 -0.41 4 4
positive regulation of T cell mediated cytotoxicity -0.004 0.088 -10000 0 -0.41 4 4
STAT1 (dimer) 0.042 0.15 -10000 0 -0.54 7 7
JAK2 0.022 0.031 -10000 0 -0.36 3 3
JAK1 0.027 0.005 -10000 0 -10000 0 0
STAT2 (dimer) 0.007 0.093 -10000 0 -0.4 4 4
T cell proliferation -0.043 0.11 0.45 1 -0.4 14 15
IL12/IL12R/TYK2/JAK2 0.003 0.15 -10000 0 -0.76 19 19
IL17A -0.054 0.16 0.78 3 -10000 0 3
mast cell activation 0.004 0.088 0.41 4 -10000 0 4
IFNG 0.002 0.026 -10000 0 -0.11 2 2
T cell differentiation -0.001 0.004 -10000 0 -0.017 4 4
STAT3 (dimer) 0.008 0.093 -10000 0 -0.4 4 4
STAT5A (dimer) 0.008 0.093 -10000 0 -0.4 4 4
STAT4 (dimer) 0.001 0.11 -10000 0 -0.37 16 16
STAT4 0.011 0.08 -10000 0 -0.36 27 27
T cell activation -0.006 0.003 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.038 0.059 -10000 0 -10000 0 0
GATA3 -0.011 0.1 0.52 2 -1.2 4 6
IL18 0.004 0.018 -10000 0 -0.25 3 3
positive regulation of mast cell cytokine production 0.008 0.092 -10000 0 -0.39 4 4
IL27/EBI3 0.004 0.098 -10000 0 -0.28 61 61
IL27RA 0.008 0.022 -10000 0 -10000 0 0
IL6 -0.062 0.17 0.33 7 -0.46 76 83
STAT5A 0.027 0.004 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 -0.016 0.013 -10000 0 -10000 0 0
IL1B -0.023 0.092 -10000 0 -0.31 57 57
EBI3 0.002 0.095 -10000 0 -0.36 39 39
TNF 0.004 0.023 -10000 0 -0.25 5 5
TCGA08_rtk_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
PDGFRA 0.019 0.056 -10000 0 -0.36 13 13
HRAS 0.027 0.016 -10000 0 -0.36 1 1
EGFR 0.024 0.023 -10000 0 -0.36 2 2
AKT 0.038 0.072 0.26 14 -0.28 6 20
FOXO3 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.026 0.007 -10000 0 -10000 0 0
FOXO1 0.021 0.019 -10000 0 -0.36 1 1
AKT3 0.021 0.047 -10000 0 -0.36 9 9
FOXO4 0.028 0.002 -10000 0 -10000 0 0
MET 0.022 0.047 -10000 0 -0.44 6 6
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
PIK3CB 0.028 0.014 0.36 1 -10000 0 1
NRAS 0.026 0.023 -10000 0 -0.36 2 2
PIK3CG -0.031 0.14 -10000 0 -0.36 91 91
PIK3R3 0.027 0.004 -10000 0 -10000 0 0
PIK3R2 0.027 0.003 -10000 0 -10000 0 0
NF1 0.027 0.005 -10000 0 -10000 0 0
RAS 0.022 0.037 0.14 10 -0.28 1 11
ERBB2 0.033 0.044 0.36 11 -10000 0 11
proliferation/survival/translation -0.025 0.071 0.26 17 -0.23 3 20
PI3K 0.024 0.064 0.22 24 -0.21 6 30
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
KRAS 0.026 0.016 -10000 0 -0.36 1 1
FOXO 0.061 0.054 0.22 25 -10000 0 25
AKT2 0.027 0.004 -10000 0 -10000 0 0
PTEN 0.026 0.006 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.001 0.13 -10000 0 -1.1 2 2
RAD9A 0.027 0.004 -10000 0 -10000 0 0
AP1 0.035 0.031 -10000 0 -0.25 6 6
IFNAR2 0.024 0.013 -10000 0 -10000 0 0
AKT1 -0.002 0.063 -10000 0 -0.29 15 15
ER alpha/Oestrogen -0.005 0.077 -10000 0 -0.25 55 55
NFX1/SIN3/HDAC complex 0.039 0.047 -10000 0 -0.29 2 2
EGF -0.058 0.16 -10000 0 -0.37 127 127
SMG5 0.027 0.004 -10000 0 -10000 0 0
SMG6 0.023 0.01 -10000 0 -10000 0 0
SP3/HDAC2 0.037 0.02 -10000 0 -10000 0 0
TERT/c-Abl 0.008 0.13 -10000 0 -1 2 2
SAP18 0.022 0.012 -10000 0 -10000 0 0
MRN complex 0.046 0.024 -10000 0 -0.21 1 1
WT1 -0.2 0.24 0.35 3 -0.44 299 302
WRN 0.021 0.019 -10000 0 -0.36 1 1
SP1 0.025 0.016 -10000 0 -10000 0 0
SP3 0.028 0.004 -10000 0 -10000 0 0
TERF2IP 0.027 0.003 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.027 0.12 -10000 0 -0.9 2 2
Mad/Max 0.037 0.021 -10000 0 -0.25 2 2
TERT -0.002 0.13 -10000 0 -1.1 2 2
CCND1 -0.001 0.12 -10000 0 -0.92 2 2
MAX 0.026 0.008 -10000 0 -10000 0 0
RBBP7 0.027 0.004 -10000 0 -10000 0 0
RBBP4 0.027 0.005 -10000 0 -10000 0 0
TERF2 0.025 0.009 -10000 0 -10000 0 0
PTGES3 0.028 0.002 -10000 0 -10000 0 0
SIN3A 0.027 0.006 -10000 0 -10000 0 0
Telomerase/911 0.041 0.046 -10000 0 -0.32 2 2
CDKN1B -0.007 0.083 -10000 0 -0.26 59 59
RAD1 0.028 0.014 0.36 1 -10000 0 1
XRCC5 0.028 0.001 -10000 0 -10000 0 0
XRCC6 0.026 0.006 -10000 0 -10000 0 0
SAP30 0.027 0.006 -10000 0 -10000 0 0
TRF2/PARP2 0.037 0.012 -10000 0 -10000 0 0
UBE3A 0.025 0.017 -10000 0 -0.36 1 1
JUN 0.027 0.005 -10000 0 -10000 0 0
E6 0 0.002 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.017 0.015 -10000 0 -0.25 1 1
FOS 0.022 0.039 -10000 0 -0.36 6 6
IFN-gamma/IRF1 0.011 0.11 -10000 0 -0.31 59 59
PARP2 0.026 0.007 -10000 0 -10000 0 0
BLM 0.027 0.014 0.36 1 -10000 0 1
Telomerase -0.001 0.11 -10000 0 -0.61 12 12
IRF1 0.03 0.006 -10000 0 -10000 0 0
ESR1 -0.008 0.11 -10000 0 -0.36 55 55
KU/TER 0.039 0.009 -10000 0 -10000 0 0
ATM/TRF2 0.04 0.009 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.032 0.06 -10000 0 -0.3 5 5
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.033 0.061 -10000 0 -0.31 5 5
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.024 0.016 -10000 0 -10000 0 0
ATM 0.011 0.003 -10000 0 -10000 0 0
SMAD3 0.012 0.014 -10000 0 -0.32 1 1
ABL1 0.027 0.004 -10000 0 -10000 0 0
MXD1 0.026 0.022 -10000 0 -0.36 2 2
MRE11A 0.027 0.004 -10000 0 -10000 0 0
HUS1 0.025 0.008 -10000 0 -10000 0 0
RPS6KB1 0.026 0.016 -10000 0 -0.36 1 1
TERT/NF kappa B1/14-3-3 0.012 0.14 -10000 0 -0.86 3 3
NR2F2 0.026 0.007 -10000 0 -10000 0 0
MAPK3 -0.008 0.017 -10000 0 -0.27 1 1
MAPK1 -0.007 0.013 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.026 0.019 -10000 0 -0.44 1 1
NFKB1 0.027 0.005 -10000 0 -10000 0 0
HNRNPC 0.026 0.007 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.011 0.003 -10000 0 -10000 0 0
NBN 0.023 0.018 -10000 0 -0.36 1 1
EGFR 0.024 0.024 -10000 0 -0.36 2 2
mol:Oestrogen 0 0.001 -10000 0 -10000 0 0
EGF/EGFR -0.022 0.12 -10000 0 -0.26 116 116
MYC 0.027 0.049 0.36 9 -0.44 2 11
IL2 0.017 0.017 -10000 0 -10000 0 0
KU 0.039 0.009 -10000 0 -10000 0 0
RAD50 0.027 0.005 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
TGFB1 0.026 0.019 -10000 0 -0.44 1 1
TRF2/BLM 0.039 0.014 0.24 1 -10000 0 1
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.021 0.13 -10000 0 -1 2 2
SP1/HDAC2 0.037 0.024 -10000 0 -10000 0 0
PINX1 0.021 0.012 -10000 0 -10000 0 0
Telomerase/EST1A 0.024 0.12 -10000 0 -0.9 2 2
Smad3/Myc 0.025 0.036 0.25 9 -0.27 3 12
911 complex 0.05 0.02 0.25 1 -10000 0 1
IFNG -0.017 0.14 -10000 0 -0.44 59 59
Telomerase/PinX1 0.016 0.12 -10000 0 -0.9 2 2
Telomerase/AKT1/mTOR/p70S6K 0.001 0.1 0.27 1 -0.43 18 19
SIN3B 0.027 0.003 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
Telomerase/EST1B 0.026 0.12 -10000 0 -0.9 2 2
response to DNA damage stimulus 0.002 0.017 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.065 0.032 -10000 0 -10000 0 0
TRF2/WRN 0.03 0.021 -10000 0 -0.24 1 1
Telomerase/hnRNP C1/C2 0.028 0.12 -10000 0 -0.9 2 2
E2F1 0.017 0.058 0.36 9 -0.45 4 13
ZNFX1 0.016 0.014 -10000 0 -10000 0 0
PIF1 0.013 0.077 -10000 0 -0.44 17 17
NCL 0.028 0.002 -10000 0 -10000 0 0
DKC1 0.027 0.003 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 0.05 0.24 -10000 0 -1 1 1
PLK1 0.039 0.081 -10000 0 -0.84 4 4
BIRC5 0.034 0.1 -10000 0 -0.81 8 8
HSPA1B 0.04 0.25 -10000 0 -0.94 2 2
MAP2K1 0.031 0.038 -10000 0 -10000 0 0
BRCA2 0.089 0.25 0.61 1 -1 1 2
FOXM1 0.05 0.26 -10000 0 -1.1 3 3
XRCC1 0.052 0.24 0.61 1 -0.91 3 4
FOXM1B/p19 0.016 0.27 -10000 0 -1 5 5
Cyclin D1/CDK4 0.058 0.23 -10000 0 -0.92 3 3
CDC2 0.051 0.25 -10000 0 -1 3 3
TGFA 0.047 0.23 -10000 0 -0.96 3 3
SKP2 0.053 0.24 -10000 0 -0.99 2 2
CCNE1 0.028 0.037 0.35 3 -0.44 2 5
CKS1B 0.05 0.24 -10000 0 -0.95 3 3
RB1 0.049 0.13 -10000 0 -0.67 3 3
FOXM1C/SP1 0.055 0.26 -10000 0 -1 3 3
AURKB -0.095 0.33 -10000 0 -0.8 104 104
CENPF 0.053 0.24 -10000 0 -0.95 3 3
CDK4 0.029 0.026 -10000 0 -0.42 1 1
MYC 0.039 0.21 -10000 0 -0.89 1 1
CHEK2 0.032 0.038 -10000 0 -10000 0 0
ONECUT1 0.048 0.23 -10000 0 -0.96 3 3
CDKN2A -0.063 0.19 0.35 2 -0.45 114 116
LAMA4 0.05 0.24 -10000 0 -1 1 1
FOXM1B/HNF6 0.046 0.25 -10000 0 -1.1 3 3
FOS 0.04 0.27 -10000 0 -1 12 12
SP1 0.027 0.009 -10000 0 -10000 0 0
CDC25B 0.067 0.25 0.61 1 -1.1 2 3
response to radiation 0.011 0.021 -10000 0 -10000 0 0
CENPB 0.073 0.24 0.61 1 -1 1 2
CENPA 0.049 0.24 -10000 0 -0.99 2 2
NEK2 0.053 0.24 -10000 0 -0.99 2 2
HIST1H2BA 0.046 0.24 -10000 0 -0.91 3 3
CCNA2 0.028 0.012 -10000 0 -10000 0 0
EP300 0.026 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.046 0.26 -10000 0 -1.1 3 3
CCNB2 0.05 0.24 -10000 0 -0.99 2 2
CCNB1 0.05 0.25 -10000 0 -1 3 3
ETV5 0.049 0.24 -10000 0 -0.99 2 2
ESR1 -0.011 0.39 -10000 0 -1.1 57 57
CCND1 0.047 0.23 -10000 0 -0.93 3 3
GSK3A 0.03 0.034 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.061 0.044 0.24 3 -0.26 2 5
CDK2 0.029 0.011 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.012 0.025 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 0.06 0.25 -10000 0 -0.97 3 3
GAS1 -0.057 0.45 -10000 0 -1 93 93
MMP2 0.047 0.25 -10000 0 -1.2 3 3
RB1/FOXM1C 0.041 0.22 -10000 0 -0.96 2 2
CREBBP 0.027 0.004 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.027 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.04 0.05 -10000 0 -0.21 18 18
forebrain development 0.001 0.085 0.38 1 -0.53 5 6
GNAO1 -0.11 0.19 -10000 0 -0.36 224 224
SMO/beta Arrestin2 0.034 0.018 -10000 0 -10000 0 0
SMO 0.027 0.007 -10000 0 -10000 0 0
ARRB2 0.024 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.038 0.093 0.22 3 -0.34 8 11
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.028 0.002 -10000 0 -10000 0 0
GNAI2 0.028 0.005 -10000 0 -10000 0 0
SIN3/HDAC complex 0.051 0.032 -10000 0 -10000 0 0
GNAI1 0.015 0.067 -10000 0 -0.36 19 19
XPO1 0.029 0.008 -10000 0 -10000 0 0
GLI1/Su(fu) 0 0.088 -10000 0 -0.57 3 3
SAP30 0.026 0.006 -10000 0 -10000 0 0
mol:GDP 0.027 0.007 -10000 0 -10000 0 0
MIM/GLI2A 0.022 0.039 -10000 0 -0.36 5 5
IFT88 0.021 0.012 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GLI2 0.012 0.058 -10000 0 -0.26 16 16
GLI3 0.026 0.095 0.2 19 -0.34 9 28
CSNK1D 0.027 0.004 -10000 0 -10000 0 0
CSNK1E 0.027 0.006 -10000 0 -10000 0 0
SAP18 0.022 0.012 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.021 0.012 -10000 0 -10000 0 0
GNG2 0.011 0.074 -10000 0 -0.36 23 23
Gi family/GTP -0.058 0.12 -10000 0 -0.32 42 42
SIN3B 0.027 0.003 -10000 0 -10000 0 0
SIN3A 0.026 0.006 -10000 0 -10000 0 0
GLI3/Su(fu) 0.033 0.084 0.27 3 -0.35 6 9
GLI2/Su(fu) 0.021 0.063 -10000 0 -0.35 8 8
FOXA2 0 0.14 -10000 0 -0.59 24 24
neural tube patterning 0.001 0.085 0.38 1 -0.53 5 6
SPOP 0.027 0.004 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.028 0.039 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
CSNK1G2 0.027 0.016 -10000 0 -0.36 1 1
CSNK1G3 0.027 0.005 -10000 0 -10000 0 0
MTSS1 0.022 0.039 -10000 0 -0.36 5 5
embryonic limb morphogenesis 0.001 0.085 0.38 1 -0.53 5 6
SUFU 0.021 0.011 -10000 0 -10000 0 0
LGALS3 0.025 0.017 -10000 0 -0.36 1 1
catabolic process 0.042 0.1 -10000 0 -0.38 12 12
GLI3A/CBP 0.032 0.025 -10000 0 -0.31 3 3
KIF3A 0.027 0.005 -10000 0 -10000 0 0
GLI1 0.001 0.087 0.38 1 -0.54 5 6
RAB23 0.026 0.022 -10000 0 -0.36 2 2
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
IFT172 0.028 0 -10000 0 -10000 0 0
RBBP7 0.027 0.004 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.029 0.039 -10000 0 -10000 0 0
GNAZ 0.024 0.035 -10000 0 -0.36 5 5
RBBP4 0.027 0.005 -10000 0 -10000 0 0
CSNK1G1 0.026 0.017 -10000 0 -0.36 1 1
PIAS1 0.026 0.006 -10000 0 -10000 0 0
PRKACA 0.027 0.003 -10000 0 -10000 0 0
GLI2/SPOP 0.026 0.058 -10000 0 -0.32 4 4
STK36 0.029 0.008 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.06 0.13 -10000 0 -0.37 52 52
PTCH1 0 0.097 -10000 0 -0.98 3 3
MIM/GLI1 0.008 0.098 0.37 1 -0.54 6 7
CREBBP 0.032 0.024 -10000 0 -0.31 3 3
Su(fu)/SIN3/HDAC complex 0.027 0.081 -10000 0 -0.34 19 19
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.035 0.081 -10000 0 -0.21 1 1
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.027 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.029 0.074 0.3 1 -0.36 1 2
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.04 0.041 -10000 0 -0.22 3 3
antigen processing and presentation of peptide antigen via MHC class I -0.005 0.054 -10000 0 -0.26 1 1
CaM/Ca2+ 0.035 0.079 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.012 0.072 -10000 0 -0.39 1 1
AKT1 -0.007 0.064 0.32 3 -10000 0 3
MAP2K1 -0.022 0.064 0.35 2 -10000 0 2
MAP3K11 -0.004 0.069 0.35 2 -10000 0 2
IFNGR1 0.022 0.019 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.025 0.13 -10000 0 -0.36 57 57
Rap1/GTP 0.001 0.056 -10000 0 -10000 0 0
CRKL/C3G 0.038 0.015 -10000 0 -0.25 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.034 0.09 -10000 0 -10000 0 0
CEBPB 0.022 0.14 0.32 7 -0.56 11 18
STAT3 0.027 0.004 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.036 0.11 -10000 0 -0.68 5 5
STAT1 -0.002 0.07 0.35 2 -0.39 1 3
CALM1 0.026 0.007 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.02 0.14 -10000 0 -0.44 59 59
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
STAT1 (dimer)/PIAS1 0.011 0.072 0.35 2 -0.38 1 3
CEBPB/PTGES2/Cbp/p300 0.028 0.092 -10000 0 -0.4 6 6
mol:Ca2+ 0.032 0.079 -10000 0 -0.21 1 1
MAPK3 -0.003 0.09 0.39 1 -0.69 4 5
STAT1 (dimer) 0.002 0.075 -10000 0 -0.36 1 1
MAPK1 -0.031 0.17 0.41 1 -0.72 28 29
JAK2 0.02 0.033 -10000 0 -0.37 3 3
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
JAK1 0.022 0.02 -10000 0 -10000 0 0
CAMK2D 0.026 0.023 -10000 0 -0.36 2 2
DAPK1 0.013 0.14 0.32 9 -0.54 28 37
SMAD7 0.002 0.034 0.18 3 -0.22 1 4
CBL/CRKL/C3G 0.021 0.074 0.34 2 -10000 0 2
PI3K 0.034 0.078 -10000 0 -10000 0 0
IFNG -0.02 0.14 -10000 0 -0.44 59 59
apoptosis 0.009 0.12 0.29 8 -0.42 33 41
CAMK2G 0.027 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.027 0.004 -10000 0 -10000 0 0
CAMK2A -0.007 0.1 -10000 0 -0.36 49 49
CAMK2B -0.013 0.11 0.36 1 -0.37 50 51
FRAP1 -0.019 0.057 0.3 3 -10000 0 3
PRKCD -0.017 0.064 0.32 3 -10000 0 3
RAP1B 0.028 0.003 -10000 0 -10000 0 0
negative regulation of cell growth -0.005 0.054 -10000 0 -0.26 1 1
PTPN2 0.022 0.011 -10000 0 -10000 0 0
EP300 0.027 0.006 -10000 0 -10000 0 0
IRF1 -0.007 0.063 0.33 4 -10000 0 4
STAT1 (dimer)/PIASy 0.011 0.072 0.4 1 -0.38 1 2
SOCS1 0.012 0.11 -10000 0 -1 5 5
mol:GDP 0.018 0.069 0.27 1 -10000 0 1
CASP1 0.001 0.038 0.18 3 -0.22 3 6
PTGES2 0.027 0.004 -10000 0 -10000 0 0
IRF9 0.024 0.052 0.2 11 -0.19 1 12
mol:PI-3-4-5-P3 0.021 0.071 -10000 0 -10000 0 0
RAP1/GDP 0.019 0.065 -10000 0 -10000 0 0
CBL -0.006 0.068 0.35 2 -10000 0 2
MAP3K1 -0.003 0.069 0.36 2 -10000 0 2
PIAS1 0.026 0.006 -10000 0 -10000 0 0
PIAS4 0.027 0.004 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.005 0.054 -10000 0 -0.26 1 1
PTPN11 -0.003 0.068 -10000 0 -10000 0 0
CREBBP 0.027 0.004 -10000 0 -10000 0 0
RAPGEF1 0.027 0.016 -10000 0 -0.36 1 1
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.081 0.1 -10000 0 -0.52 1 1
UGCG 0.019 0.061 -10000 0 -0.62 5 5
AKT1/mTOR/p70S6K/Hsp90/TERT 0.01 0.13 0.22 1 -0.45 26 27
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.019 0.06 -10000 0 -0.61 5 5
mol:DAG -0.002 0.11 -10000 0 -0.82 11 11
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.13 0.23 1 -0.4 36 37
FRAP1 0.011 0.14 0.24 1 -0.45 40 41
FOXO3 0.016 0.11 0.3 3 -0.41 14 17
AKT1 0.018 0.11 0.25 1 -0.41 18 19
GAB2 0.027 0.004 -10000 0 -10000 0 0
SMPD1 0.014 0.084 -10000 0 -0.65 9 9
SGMS1 0.013 0.087 -10000 0 -0.61 11 11
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.006 0.011 -10000 0 -0.21 1 1
CALM1 0.026 0.007 -10000 0 -10000 0 0
cell proliferation 0.034 0.083 -10000 0 -0.41 10 10
EIF3A 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.042 0.016 -10000 0 -0.25 1 1
RPS6KB1 0.014 0.1 -10000 0 -0.8 9 9
mol:sphingomyelin -0.002 0.11 -10000 0 -0.82 11 11
natural killer cell activation 0 0.002 -10000 0 -0.01 5 5
JAK3 0.028 0.019 -10000 0 -0.44 1 1
PIK3R1 0.028 0.006 -10000 0 -10000 0 0
JAK1 0.029 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MYC 0.046 0.12 0.29 5 -0.43 5 10
MYB 0.03 0.073 -10000 0 -1.1 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.025 0.09 -10000 0 -0.4 11 11
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.042 0.1 -10000 0 -0.74 9 9
mol:PI-3-4-5-P3 0.024 0.089 -10000 0 -0.39 11 11
Rac1/GDP 0.02 0.016 -10000 0 -0.19 1 1
T cell proliferation 0.024 0.076 0.24 1 -0.4 6 7
SHC1 0.027 0.005 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.004 -10000 0 -0.066 2 2
PRKCZ 0.024 0.078 0.24 1 -0.42 6 7
NF kappa B1 p50/RelA 0.035 0.13 -10000 0 -0.42 32 32
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.025 0.053 -10000 0 -0.36 6 6
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
IL2RA 0.019 0.056 -10000 0 -0.36 13 13
IL2RB 0.019 0.058 -10000 0 -0.36 14 14
TERT -0.013 0.14 0.36 3 -0.44 54 57
E2F1 0.032 0.044 -10000 0 -0.43 2 2
SOS1 0.028 0.002 -10000 0 -10000 0 0
RPS6 0.026 0.02 -10000 0 -0.44 1 1
mol:cAMP -0.002 0.002 0.031 2 -10000 0 2
PTPN11 0.028 0.003 -10000 0 -10000 0 0
IL2RG 0.028 0.027 -10000 0 -0.36 3 3
actin cytoskeleton organization 0.024 0.076 0.24 1 -0.4 6 7
GRB2 0.027 0.005 -10000 0 -10000 0 0
IL2 0.019 0.012 -10000 0 -10000 0 0
PIK3CA 0.029 0.016 -10000 0 -0.36 1 1
Rac1/GTP 0.046 0.027 -10000 0 -0.18 1 1
LCK 0.021 0.058 -10000 0 -0.42 10 10
BCL2 -0.004 0.2 -10000 0 -0.79 33 33
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.024 0.01 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.03 0.069 -10000 0 -0.34 6 6
NEF -0.004 0.033 -10000 0 -0.23 2 2
NFKBIA 0.026 0.016 -10000 0 -10000 0 0
BIRC3 0.013 0.056 -10000 0 -0.4 10 10
CYCS 0.012 0.078 0.18 49 -0.37 5 54
RIPK1 0.027 0.004 -10000 0 -10000 0 0
CD247 0.013 0.077 -10000 0 -0.43 14 14
MAP2K7 0.018 0.11 -10000 0 -0.64 11 11
protein ubiquitination 0.027 0.054 0.38 4 -0.29 1 5
CRADD 0.027 0.003 -10000 0 -10000 0 0
DAXX 0.027 0.004 -10000 0 -10000 0 0
FAS 0.021 0.044 -10000 0 -0.36 8 8
BID 0.004 0.069 0.19 9 -0.36 7 16
NF-kappa-B/RelA/I kappa B alpha 0.052 0.041 -10000 0 -0.23 9 9
TRADD 0.028 0.003 -10000 0 -10000 0 0
MAP3K5 0.027 0.004 -10000 0 -10000 0 0
CFLAR 0.028 0 -10000 0 -10000 0 0
FADD 0.027 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.052 0.041 -10000 0 -0.23 9 9
MAPK8 0.017 0.1 0.36 2 -0.59 11 13
APAF1 0.028 0.003 -10000 0 -10000 0 0
TRAF1 0.027 0.004 -10000 0 -10000 0 0
TRAF2 0.027 0.016 -10000 0 -0.36 1 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.01 0.073 0.2 9 -0.26 32 41
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.033 0.048 -10000 0 -0.36 2 2
CHUK 0.026 0.051 0.33 3 -0.3 2 5
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.073 0.037 -10000 0 -10000 0 0
TCRz/NEF 0.007 0.079 -10000 0 -0.29 38 38
TNF 0.024 0.035 -10000 0 -0.36 5 5
FASLG -0.009 0.12 -10000 0 -0.49 32 32
NFKB1 0.027 0.016 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.045 0.031 -10000 0 -0.21 4 4
CASP6 0.033 0.1 -10000 0 -0.47 11 11
CASP7 0.015 0.09 0.35 2 -0.39 15 17
RELA 0.027 0.016 -10000 0 -10000 0 0
CASP2 0.027 0.005 -10000 0 -10000 0 0
CASP3 0.012 0.091 0.35 2 -0.42 14 16
TNFRSF1A 0.027 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.035 0.015 -10000 0 -10000 0 0
CASP8 0.028 0.001 -10000 0 -10000 0 0
CASP9 0.026 0.007 -10000 0 -10000 0 0
MAP3K14 0.029 0.05 0.2 6 -0.33 2 8
APAF-1/Caspase 9 0.023 0.072 -10000 0 -0.39 1 1
BCL2 0.008 0.093 0.35 2 -0.54 10 12
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.023 0.06 -10000 0 -0.19 35 35
MAPK9 0.007 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.01 0.018 -10000 0 -0.31 2 2
GNB1/GNG2 0.024 0.047 -10000 0 -0.21 23 23
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 0.007 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.007 0.038 -10000 0 -0.19 22 22
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 0.003 0.01 0.053 22 -10000 0 22
GNAL 0.008 0.072 -10000 0 -0.36 22 22
GNG2 0.011 0.074 -10000 0 -0.36 23 23
CRH -0.016 0.026 -10000 0 -0.44 2 2
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.007 0.001 -10000 0 -10000 0 0
MAPK11 0.007 0.01 -10000 0 -0.16 2 2
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0.052 0.054 -10000 0 -10000 0 0
HDAC3 0.027 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.009 0.001 -10000 0 -10000 0 0
GATA1/HDAC4 0.038 0.006 -10000 0 -10000 0 0
GATA1/HDAC5 0.037 0.014 -10000 0 -0.26 1 1
GATA2/HDAC5 0.034 0.041 -10000 0 -0.25 12 12
HDAC5/BCL6/BCoR 0.054 0.016 -10000 0 -0.21 1 1
HDAC9 -0.026 0.13 -10000 0 -0.36 80 80
Glucocorticoid receptor/Hsp90/HDAC6 0.033 0.069 -10000 0 -0.21 36 36
HDAC4/ANKRA2 0.04 0.007 -10000 0 -10000 0 0
HDAC5/YWHAB 0.023 0.023 -10000 0 -0.25 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.014 0.012 -10000 0 -0.17 2 2
GATA2 0.021 0.052 -10000 0 -0.36 11 11
HDAC4/RFXANK 0.04 0.015 -10000 0 -0.32 1 1
BCOR 0.027 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.026 0.017 -10000 0 -0.36 1 1
HDAC5 0.027 0.016 -10000 0 -0.36 1 1
GNB1/GNG2 0.026 0.056 -10000 0 -0.25 23 23
Histones 0.003 0.081 -10000 0 -0.3 13 13
ADRBK1 0.027 0.004 -10000 0 -10000 0 0
HDAC4 0.028 0.002 -10000 0 -10000 0 0
XPO1 0.028 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.039 0.015 -10000 0 -0.25 1 1
HDAC4/Ubc9 0.04 0.007 -10000 0 -10000 0 0
HDAC7 0.028 0.002 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.034 0.019 -10000 0 -0.25 1 1
TUBA1B 0.028 0.002 -10000 0 -10000 0 0
HDAC6 0.027 0.003 -10000 0 -10000 0 0
HDAC5/RFXANK 0.039 0.02 -10000 0 -0.28 2 2
CAMK4 0.006 0.085 -10000 0 -0.36 31 31
Tubulin/HDAC6 0.051 0.036 -10000 0 -0.27 7 7
SUMO1 0.027 0.022 -10000 0 -0.36 2 2
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.016 0.014 -10000 0 -10000 0 0
GATA1 0.011 0.022 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
NR3C1 -0.001 0.1 -10000 0 -0.36 44 44
SUMO1/HDAC4 0.038 0.034 -10000 0 -0.26 2 2
SRF 0.027 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.023 0.02 -10000 0 -10000 0 0
Tubulin 0.036 0.038 -10000 0 -0.32 7 7
HDAC4/14-3-3 E 0.034 0.016 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
RANGAP1 0.026 0.02 -10000 0 -0.44 1 1
BCL6/BCoR 0.04 0.006 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.054 0.015 -10000 0 -0.21 1 1
HDAC4/SRF 0.038 0.06 -10000 0 -0.21 31 31
HDAC4/ER alpha 0.013 0.084 -10000 0 -0.25 55 55
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.003 0.081 -10000 0 -0.3 13 13
cell motility 0.05 0.036 -10000 0 -0.27 7 7
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.027 0.004 -10000 0 -10000 0 0
HDAC7/HDAC3 0.04 0.007 -10000 0 -10000 0 0
BCL6 0.028 0.003 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.028 0.002 -10000 0 -10000 0 0
Hsp90/HDAC6 0.038 0.011 -10000 0 -10000 0 0
ESR1 -0.01 0.11 -10000 0 -0.36 55 55
HDAC6/HDAC11 0.04 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.039 0.031 -10000 0 -10000 0 0
NPC 0.016 0 -10000 0 -10000 0 0
MEF2C 0.015 0.066 -10000 0 -0.36 18 18
RAN 0.028 0.003 -10000 0 -10000 0 0
HDAC4/MEF2C 0.07 0.048 -10000 0 -10000 0 0
GNG2 0.011 0.074 -10000 0 -0.36 23 23
NCOR2 0.027 0.016 -10000 0 -0.36 1 1
TUBB2A 0.022 0.05 -10000 0 -0.44 7 7
HDAC11 0.027 0.004 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
RANBP2 0.028 0 -10000 0 -10000 0 0
ANKRA2 0.027 0.005 -10000 0 -10000 0 0
RFXANK 0.027 0.019 -10000 0 -0.44 1 1
nuclear import -0.018 0.021 0.23 1 -10000 0 1
Aurora A signaling

Figure S109.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S109.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.048 0.036 -10000 0 -10000 0 0
BIRC5 0.027 0.024 0.36 1 -0.44 1 2
NFKBIA 0.005 0.011 0.25 1 -10000 0 1
CPEB1 -0.086 0.17 -10000 0 -0.36 165 165
AKT1 0.004 0.004 -10000 0 -10000 0 0
NDEL1 0.023 0.01 -10000 0 -10000 0 0
Aurora A/BRCA1 0.017 0.016 -10000 0 -10000 0 0
NDEL1/TACC3 0.054 0.038 -10000 0 -0.22 1 1
GADD45A 0.027 0.005 -10000 0 -10000 0 0
GSK3B 0.025 0.002 -10000 0 -10000 0 0
PAK1/Aurora A 0.049 0.036 -10000 0 -10000 0 0
MDM2 0.027 0.016 -10000 0 -0.36 1 1
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.011 0.027 0.27 6 -10000 0 6
TP53 0.013 0.012 -10000 0 -10000 0 0
DLG7 0.006 0.005 -10000 0 -10000 0 0
AURKAIP1 0.026 0.02 -10000 0 -0.44 1 1
ARHGEF7 0.022 0.012 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.057 0.04 -10000 0 -0.24 1 1
G2/M transition of mitotic cell cycle 0.017 0.016 -10000 0 -10000 0 0
AURKA 0.01 0.009 -10000 0 -10000 0 0
AURKB 0.009 0.009 -10000 0 -10000 0 0
CDC25B 0.013 0.049 0.29 15 -10000 0 15
G2/M transition checkpoint 0.006 0.007 -10000 0 -10000 0 0
mRNA polyadenylation -0.027 0.075 -10000 0 -0.18 95 95
Aurora A/CPEB -0.027 0.075 -10000 0 -0.18 95 95
Aurora A/TACC1/TRAP/chTOG 0.071 0.041 -10000 0 -10000 0 0
BRCA1 0.027 0.004 -10000 0 -10000 0 0
centrosome duplication 0.049 0.036 -10000 0 -10000 0 0
regulation of centrosome cycle 0.052 0.037 -10000 0 -0.22 1 1
spindle assembly 0.069 0.04 -10000 0 -10000 0 0
TDRD7 0.027 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.075 0.036 -10000 0 -0.22 1 1
CENPA 0.011 0.011 -10000 0 -10000 0 0
Aurora A/PP2A 0.048 0.036 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.036 0.041 0.2 2 -10000 0 2
negative regulation of DNA binding 0.012 0.016 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.031 0.021 -10000 0 -0.25 1 1
RASA1 0.027 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A 0.006 0.007 -10000 0 -10000 0 0
mitotic prometaphase 0.01 0.027 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.009 -10000 0 -10000 0 0
TACC1 0.024 0.01 -10000 0 -10000 0 0
TACC3 0.026 0.02 -10000 0 -0.44 1 1
Aurora A/Antizyme1 0.067 0.036 -10000 0 -0.24 1 1
Aurora A/RasGAP 0.049 0.036 -10000 0 -10000 0 0
OAZ1 0.027 0.004 -10000 0 -10000 0 0
RAN 0.028 0.003 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.025 0.003 -10000 0 -10000 0 0
GIT1 0.026 0.016 -10000 0 -0.36 1 1
GIT1/beta-PIX/PAK1 0.042 0.027 -10000 0 -0.21 1 1
Importin alpha/Importin beta/TPX2 0.011 0.027 0.27 6 -10000 0 6
PPP2R5D 0.027 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.015 0.027 0.25 6 -10000 0 6
PAK1 0.027 0.004 -10000 0 -10000 0 0
CKAP5 0.027 0.003 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.022 0.028 -10000 0 -0.2 9 9
epithelial cell differentiation 0.057 0.014 -10000 0 -10000 0 0
CYFIP2 0.027 0.016 -10000 0 -0.36 1 1
ENAH -0.012 0.029 0.27 2 -10000 0 2
EGFR 0.024 0.023 -10000 0 -0.36 2 2
EPHA2 0.025 0.028 -10000 0 -0.44 2 2
MYO6 -0.009 0.015 0.18 3 -10000 0 3
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.054 0.015 -10000 0 -0.21 1 1
AQP5 -0.006 0.047 -10000 0 -0.51 1 1
CTNND1 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.009 0.019 0.18 5 -10000 0 5
regulation of calcium-dependent cell-cell adhesion -0.015 0.037 -10000 0 -10000 0 0
EGF -0.06 0.16 -10000 0 -0.37 127 127
NCKAP1 0.028 0 -10000 0 -10000 0 0
AQP3 0.009 0.036 -10000 0 -0.41 2 2
cortical microtubule organization 0.057 0.014 -10000 0 -10000 0 0
GO:0000145 -0.009 0.018 0.16 5 -10000 0 5
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.062 0.016 -10000 0 -10000 0 0
MLLT4 0.027 0.004 -10000 0 -10000 0 0
ARF6/GDP -0.016 0.014 -10000 0 -10000 0 0
ARF6 0.026 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.062 0.031 -10000 0 -0.25 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.006 0.009 -10000 0 -10000 0 0
PVRL2 0.027 0.003 -10000 0 -10000 0 0
ZYX -0.01 0.011 0.18 1 -10000 0 1
ARF6/GTP 0.065 0.035 -10000 0 -0.23 2 2
CDH1 0.028 0.003 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.003 0.09 -10000 0 -0.22 18 18
RhoA/GDP 0.058 0.016 -10000 0 -10000 0 0
actin cytoskeleton organization -0.009 0.011 0.16 2 -10000 0 2
IGF-1R heterotetramer 0.026 0.006 -10000 0 -10000 0 0
GIT1 0.026 0.016 -10000 0 -0.36 1 1
IGF1R 0.027 0.006 -10000 0 -10000 0 0
IGF1 -0.062 0.16 -10000 0 -0.36 141 141
DIAPH1 0.044 0.096 -10000 0 -0.52 12 12
Wnt receptor signaling pathway -0.057 0.014 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.017 0.014 -10000 0 -10000 0 0
CTNNA1 0.027 0.004 -10000 0 -10000 0 0
VCL -0.009 0.011 0.17 2 -10000 0 2
EFNA1 0.027 0.004 -10000 0 -10000 0 0
LPP -0.01 0.019 0.17 5 -10000 0 5
Ephrin A1/EPHA2 0.047 0.023 -10000 0 -10000 0 0
SEC6/SEC8 -0.015 0.006 -10000 0 -10000 0 0
MGAT3 -0.015 0.037 -10000 0 -10000 0 0
HGF/MET 0.042 0.047 -10000 0 -0.37 1 1
HGF 0.017 0.061 -10000 0 -0.37 15 15
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.022 0.028 -10000 0 -0.2 9 9
actin cable formation 0.009 0.058 0.24 19 -0.29 1 20
KIAA1543 -0.009 0.018 0.16 5 -10000 0 5
KIFC3 -0.016 0.037 0.18 1 -10000 0 1
NCK1 0.028 0.003 -10000 0 -10000 0 0
EXOC3 0.027 0.004 -10000 0 -10000 0 0
ACTN1 -0.008 0.018 0.18 5 -10000 0 5
NCK1/GIT1 0.039 0.014 -10000 0 -0.25 1 1
mol:GDP 0.057 0.014 -10000 0 -10000 0 0
EXOC4 0.027 0.006 -10000 0 -10000 0 0
STX4 -0.01 0.013 0.18 2 -10000 0 2
PIP5K1C -0.009 0.02 0.18 5 -10000 0 5
LIMA1 0.022 0.047 -10000 0 -0.36 9 9
ABI1 0.028 0.003 -10000 0 -10000 0 0
ROCK1 -0.008 0.04 0.29 4 -10000 0 4
adherens junction assembly 0.003 0.041 0.28 4 -0.28 1 5
IGF-1R heterotetramer/IGF1 0 0.093 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.04 0.008 -10000 0 -10000 0 0
MET 0.022 0.047 -10000 0 -0.44 6 6
PLEKHA7 -0.009 0.02 0.18 5 -10000 0 5
mol:GTP 0.06 0.03 -10000 0 -0.24 2 2
establishment of epithelial cell apical/basal polarity -0.005 0.047 0.32 3 -10000 0 3
cortical actin cytoskeleton stabilization 0.022 0.028 -10000 0 -0.2 9 9
regulation of cell-cell adhesion -0.009 0.011 0.16 2 -10000 0 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.022 0.028 -10000 0 -0.2 9 9
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.022 0.031 -10000 0 -0.31 2 2
KLHL20 0.041 0.07 0.2 29 -0.24 8 37
CYFIP2 0.027 0.016 -10000 0 -0.36 1 1
Rac1/GDP 0.071 0.08 0.29 8 -10000 0 8
ENAH 0.022 0.032 -10000 0 -0.31 2 2
AP1M1 0.027 0.003 -10000 0 -10000 0 0
RAP1B 0.028 0.003 -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 0.017 0.022 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.007 0.025 -10000 0 -0.16 8 8
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.052 0.05 -10000 0 -10000 0 0
RAPGEF1 0.06 0.083 0.29 10 -10000 0 10
CTNND1 0.027 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.03 0.033 -10000 0 -0.32 2 2
CRK 0.06 0.078 -10000 0 -0.3 1 1
E-cadherin/gamma catenin/alpha catenin 0.053 0.016 -10000 0 -0.21 1 1
alphaE/beta7 Integrin 0.024 0.054 -10000 0 -0.24 23 23
IQGAP1 0.027 0.006 -10000 0 -10000 0 0
NCKAP1 0.028 0 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.051 0.013 -10000 0 -10000 0 0
DLG1 0.022 0.032 -10000 0 -0.31 2 2
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.004 0.01 -10000 0 -10000 0 0
MLLT4 0.027 0.004 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.021 0.077 -10000 0 -0.2 64 64
PI3K 0.008 0.015 -10000 0 -10000 0 0
ARF6 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.04 0.014 -10000 0 -0.25 1 1
TIAM1 -0.011 0.11 -10000 0 -0.36 59 59
E-cadherin(dimer)/Ca2+ 0.063 0.016 -10000 0 -10000 0 0
AKT1 0.025 0.045 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
CDH1 0.028 0.003 -10000 0 -10000 0 0
RhoA/GDP 0.084 0.083 0.3 12 -10000 0 12
actin cytoskeleton organization 0.039 0.058 0.17 34 -0.17 8 42
CDC42/GDP 0.08 0.083 0.3 12 -10000 0 12
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.02 0.01 -10000 0 -0.19 1 1
ITGB7 0.013 0.074 -10000 0 -0.36 23 23
RAC1 0.025 0.008 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.068 0.017 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.048 0.01 -10000 0 -10000 0 0
mol:GDP 0.076 0.09 0.31 13 -10000 0 13
CDC42/GTP/IQGAP1 0.033 0.015 -10000 0 -0.21 1 1
JUP 0.027 0.016 -10000 0 -0.36 1 1
p120 catenin/RhoA/GDP 0.093 0.082 0.31 12 -10000 0 12
RAC1/GTP/IQGAP1 0.033 0.013 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.04 0.013 -10000 0 -0.25 1 1
RHOA 0.027 0.004 -10000 0 -10000 0 0
CDC42 0.025 0.017 -10000 0 -0.36 1 1
CTNNA1 0.027 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.033 0.048 0.14 41 -0.16 5 46
NME1 0.022 0.057 0.36 2 -0.44 8 10
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.021 0.031 -10000 0 -0.31 2 2
regulation of cell-cell adhesion 0.011 0.016 -10000 0 -10000 0 0
WASF2 0.015 0.026 -10000 0 -10000 0 0
Rap1/GTP 0.081 0.072 0.31 5 -10000 0 5
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.06 0.053 -10000 0 -10000 0 0
CCND1 0.038 0.055 0.16 39 -0.2 5 44
VAV2 0.077 0.13 0.41 1 -0.62 10 11
RAP1/GDP 0.091 0.079 0.31 10 -10000 0 10
adherens junction assembly 0.021 0.031 -10000 0 -0.3 2 2
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.028 0.003 -10000 0 -10000 0 0
PIP5K1C 0.027 0.016 -10000 0 -0.36 1 1
regulation of heterotypic cell-cell adhesion 0.046 0.047 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.014 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SRC 0.013 0.027 -10000 0 -0.31 2 2
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
Rac1/GTP -0.002 0.061 -10000 0 -0.38 9 9
E-cadherin/beta catenin/alpha catenin 0.054 0.011 -10000 0 -10000 0 0
ITGAE 0.023 0.01 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.031 0.033 -10000 0 -0.32 2 2
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.059 0.07 0.15 229 -0.29 1 230
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.011 0.035 0.15 11 -0.17 2 13
AP2 0.04 0.013 -10000 0 -0.25 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.033 0.013 -10000 0 -10000 0 0
CLTB 0.027 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.02 0.006 -10000 0 -10000 0 0
CD4 0.016 0.064 -10000 0 -0.36 17 17
CLTA 0.027 0.004 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
ARFGAP1 0.005 0.018 0.26 2 -0.25 1 3
mol:PI-4-5-P2 0.006 0.007 -10000 0 -10000 0 0
ARF1/GTP 0.036 0.01 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.007 0.015 0.18 2 -0.23 1 3
mol:Choline 0.006 0.007 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.028 0.006 -10000 0 -10000 0 0
DDEF1 0.005 0.007 -10000 0 -10000 0 0
ARF1/GDP 0.002 0.016 0.18 2 -0.21 1 3
AP2M1 0.028 0.003 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.012 0.006 -10000 0 -10000 0 0
Rac/GTP 0.02 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.024 0.024 0.19 2 -0.18 1 3
ARFIP2 0.017 0.021 -10000 0 -10000 0 0
COPA 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.014 0.018 0.14 1 -0.17 1 2
ARF1/GTP/ARHGAP10 0.02 0.006 -10000 0 -10000 0 0
GGA3 0.027 0.004 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.025 0.027 -10000 0 -0.24 5 5
AP2A1 0.027 0.016 -10000 0 -0.36 1 1
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.009 0.019 0.13 2 -0.21 1 3
ARF1/GDP/Membrin 0.018 0.034 -10000 0 -0.27 6 6
Arfaptin 2/Rac/GDP 0.032 0.012 -10000 0 -10000 0 0
CYTH2 0.029 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.037 0.01 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.019 0.006 -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 0.019 0.035 -10000 0 -10000 0 0
PLD2 0.006 0.007 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.005 0.018 0.26 2 -0.25 1 3
PIP5K1A 0.006 0.007 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.013 0.027 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.005 0.007 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.005 0.018 0.26 2 -0.25 1 3
GOSR2 0.011 0.006 -10000 0 -10000 0 0
USO1 0.01 0.023 -10000 0 -0.31 3 3
GBF1 0.007 0.037 -10000 0 -0.31 8 8
ARF1/GTP/Arfaptin 2 0.037 0.009 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.046 0.047 -10000 0 -0.21 18 18
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.037 0.032 -10000 0 -0.25 7 7
AKT1 0.089 0.096 0.26 84 -0.38 2 86
PTK2B 0.014 0.041 0.34 1 -0.38 2 3
VEGFR2 homodimer/Frs2 0.034 0.026 -10000 0 -0.55 1 1
CAV1 0.019 0.054 -10000 0 -0.36 12 12
CALM1 0.026 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.051 0.03 0.25 2 -0.51 1 3
endothelial cell proliferation 0.098 0.13 0.28 160 -0.34 2 162
mol:Ca2+ 0.012 0.018 -10000 0 -0.3 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.058 0.037 0.25 2 -0.48 1 3
RP11-342D11.1 0.01 0.025 -10000 0 -0.47 1 1
CDH5 0.028 0.003 -10000 0 -10000 0 0
VEGFA homodimer 0.064 0.024 0.25 1 -10000 0 1
SHC1 0.027 0.004 -10000 0 -10000 0 0
SHC2 0.019 0.059 -10000 0 -0.41 11 11
HRAS/GDP 0.046 0.03 -10000 0 -0.42 1 1
SH2D2A 0.026 0.019 -10000 0 -0.44 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.097 0.084 0.27 12 -0.36 3 15
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.05 0.032 0.25 2 -0.51 1 3
VEGFR1 homodimer 0.021 0.012 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.074 0.039 -10000 0 -0.45 1 1
GRB10 0.02 0.026 -10000 0 -0.47 1 1
PTPN11 0.028 0.002 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
PAK1 0.027 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.074 0.036 -10000 0 -0.47 1 1
HRAS 0.027 0.016 -10000 0 -0.36 1 1
VEGF/Rho/ROCK1/Integrin Complex 0.004 0.079 -10000 0 -0.39 5 5
HIF1A 0.026 0.007 -10000 0 -10000 0 0
FRS2 0.027 0.003 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.056 0.036 -10000 0 -0.48 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.025 0.031 -10000 0 -0.36 4 4
Nck/Pak 0.04 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.05 0.03 0.25 2 -0.51 1 3
mol:GDP 0.059 0.033 -10000 0 -0.44 1 1
mol:NADP 0.088 0.09 0.3 24 -0.35 3 27
eNOS/Hsp90 0.092 0.087 0.3 23 -0.36 1 24
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
mol:IP3 0.013 0.019 -10000 0 -0.3 1 1
HIF1A/ARNT 0.037 0.017 -10000 0 -0.25 1 1
SHB 0.026 0.03 0.36 1 -0.44 2 3
VEGFA 0.03 0.019 0.36 2 -10000 0 2
VEGFC 0.02 0.049 -10000 0 -0.36 10 10
FAK1/Vinculin 0.055 0.075 0.29 7 -0.54 1 8
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.062 0.041 0.25 2 -0.4 2 4
PTPN6 0.027 0.004 -10000 0 -10000 0 0
EPAS1 0.034 0.021 -10000 0 -0.33 2 2
mol:L-citrulline 0.088 0.09 0.3 24 -0.35 3 27
ITGAV 0.028 0.002 -10000 0 -10000 0 0
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.064 0.032 -10000 0 -0.48 1 1
VEGFR2 homodimer/VEGFA homodimer 0.053 0.032 0.25 2 -0.51 1 3
VEGFR2/3 heterodimer 0.033 0.033 -10000 0 -0.55 1 1
VEGFB 0.027 0.004 -10000 0 -10000 0 0
MAPK11 0.006 0.036 0.25 1 -0.43 2 3
VEGFR2 homodimer 0.021 0.026 -10000 0 -0.62 1 1
FLT1 0.021 0.012 -10000 0 -10000 0 0
NEDD4 0.028 0.007 -10000 0 -10000 0 0
MAPK3 0.034 0.081 0.3 7 -0.3 1 8
MAPK1 0.034 0.08 0.3 7 -0.3 1 8
VEGFA145/NRP2 0.041 0.025 0.26 2 -0.25 3 5
VEGFR1/2 heterodimer 0.026 0.03 -10000 0 -0.55 1 1
KDR 0.021 0.026 -10000 0 -0.62 1 1
VEGFA165/NRP1/VEGFR2 homodimer 0.053 0.034 0.24 2 -0.47 1 3
SRC 0.017 0.014 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.048 0.088 0.31 13 -0.31 1 14
PI3K 0.056 0.058 0.3 1 -0.39 1 2
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.051 0.03 0.25 2 -0.51 1 3
FES 0.021 0.027 -10000 0 -0.48 1 1
GAB1 0.028 0.036 -10000 0 -0.53 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.031 0.032 0.25 1 -0.33 1 2
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
SOS1 0.028 0.002 -10000 0 -10000 0 0
ARNT 0.027 0.016 -10000 0 -0.36 1 1
eNOS/Caveolin-1 0.087 0.082 0.28 11 -0.35 2 13
VEGFR2 homodimer/VEGFA homodimer/Yes 0.042 0.038 0.25 1 -0.67 1 2
PI3K/GAB1 0.053 0.055 0.25 3 -0.42 1 4
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.076 0.034 -10000 0 -0.47 1 1
PRKACA 0.027 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.042 0.046 -10000 0 -0.43 2 2
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
CDC42 0.021 0.026 -10000 0 -0.48 1 1
actin cytoskeleton reorganization 0.049 0.032 0.24 2 -0.5 1 3
PTK2 0.029 0.054 0.25 5 -0.45 2 7
EDG1 0.01 0.025 -10000 0 -0.47 1 1
mol:DAG 0.013 0.019 -10000 0 -0.3 1 1
CaM/Ca2+ 0.021 0.026 -10000 0 -0.28 1 1
MAP2K3 0.012 0.034 -10000 0 -0.46 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.063 0.056 -10000 0 -0.48 1 1
PLCG1 0.013 0.019 -10000 0 -0.31 1 1
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.039 0.041 0.25 2 -0.31 1 3
IQGAP1 0.027 0.006 -10000 0 -10000 0 0
YES1 0.022 0.019 -10000 0 -0.36 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.051 0.03 0.25 2 -0.51 1 3
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.05 0.029 0.25 1 -0.51 1 2
cell migration 0.061 0.078 0.29 10 -0.48 1 11
mol:PI-3-4-5-P3 0.054 0.056 0.29 1 -0.36 1 2
FYN 0.027 0.005 -10000 0 -10000 0 0
VEGFB/NRP1 0.027 0.026 -10000 0 -0.45 1 1
mol:NO 0.088 0.09 0.3 24 -0.35 3 27
PXN 0.028 0.002 -10000 0 -10000 0 0
HRAS/GTP 0.027 0.024 -10000 0 -0.42 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.04 0.031 -10000 0 -0.48 1 1
VHL 0.027 0.004 -10000 0 -10000 0 0
ITGB3 0.023 0.041 -10000 0 -0.36 7 7
NOS3 0.09 0.094 0.34 16 -0.38 3 19
VEGFR2 homodimer/VEGFA homodimer/Sck 0.046 0.046 0.25 1 -0.51 1 2
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCA 0.007 0.02 -10000 0 -0.29 1 1
PRKCB -0.01 0.052 -10000 0 -0.29 1 1
VCL 0.027 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 0.03 0.028 0.23 2 -0.47 1 3
VEGFR1/2 heterodimer/VEGFA homodimer 0.038 0.035 0.25 1 -0.51 1 2
VEGFA165/NRP2 0.041 0.025 0.26 2 -0.25 3 5
MAPKKK cascade 0.033 0.037 -10000 0 -0.42 1 1
NRP2 0.026 0.027 -10000 0 -0.36 3 3
VEGFC homodimer 0.02 0.049 -10000 0 -0.36 10 10
NCK1 0.028 0.003 -10000 0 -10000 0 0
ROCK1 0.022 0.019 -10000 0 -0.36 1 1
FAK1/Paxillin 0.055 0.076 0.29 6 -0.54 1 7
MAP3K13 0.022 0.028 -10000 0 -0.48 1 1
PDPK1 0.078 0.086 0.25 84 -0.34 1 85
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.024 0.035 0.36 5 -10000 0 5
PI3K Class IB/PDE3B 0.024 0.035 -10000 0 -0.36 5 5
PDE3B 0.024 0.035 -10000 0 -0.36 5 5
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.024 0.035 -9999 0 -0.36 5 5
positive regulation of NF-kappaB transcription factor activity 0.028 0.031 -9999 0 -0.25 5 5
MAP2K4 0.017 0.026 -9999 0 -10000 0 0
IKBKB 0.024 0.009 -9999 0 -10000 0 0
TNFRSF10B 0.021 0.012 -9999 0 -10000 0 0
TNFRSF10A 0.021 0.012 -9999 0 -10000 0 0
SMPD1 0.007 0.037 -9999 0 -0.26 9 9
IKBKG 0.027 0.016 -9999 0 -0.36 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.021 0.012 -9999 0 -10000 0 0
TRAIL/TRAILR2 0.029 0.031 -9999 0 -0.25 5 5
TRAIL/TRAILR3 0.005 0.091 -9999 0 -0.31 46 46
TRAIL/TRAILR1 0.029 0.031 -9999 0 -0.25 5 5
TRAIL/TRAILR4 0.029 0.031 -9999 0 -0.25 5 5
TRAIL/TRAILR1/DAP3/GTP 0.037 0.031 -9999 0 -0.19 5 5
IKK complex 0.019 0.042 -9999 0 -0.33 2 2
RIPK1 0.027 0.004 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0.02 0.003 -9999 0 -10000 0 0
MAPK3 0.011 0.024 -9999 0 -0.25 5 5
MAP3K1 0.02 0.029 -9999 0 -10000 0 0
TRAILR4 (trimer) 0.021 0.012 -9999 0 -10000 0 0
TRADD 0.028 0.003 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.021 0.012 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.021 0.024 -9999 0 -10000 0 0
CFLAR 0.028 0 -9999 0 -10000 0 0
MAPK1 0.011 0.022 -9999 0 -0.25 4 4
TRAIL/TRAILR1/FADD/TRADD/RIP 0.058 0.042 -9999 0 -10000 0 0
mol:ceramide 0.007 0.037 -9999 0 -0.26 9 9
FADD 0.027 0.004 -9999 0 -10000 0 0
MAPK8 0.014 0.03 -9999 0 -10000 0 0
TRAF2 0.027 0.016 -9999 0 -0.36 1 1
TRAILR3 (trimer) -0.011 0.12 -9999 0 -0.44 41 41
CHUK 0.027 0.006 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.04 0.034 -9999 0 -0.21 5 5
DAP3 0.027 0.004 -9999 0 -10000 0 0
CASP10 0.005 0.025 -9999 0 -0.24 5 5
JNK cascade 0.028 0.031 -9999 0 -0.25 5 5
TRAIL (trimer) 0.024 0.035 -9999 0 -0.36 5 5
TNFRSF10C -0.011 0.12 -9999 0 -0.44 41 41
TRAIL/TRAILR1/DAP3/GTP/FADD 0.046 0.036 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD 0.04 0.034 -9999 0 -0.21 5 5
cell death 0.007 0.037 -9999 0 -0.26 9 9
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.021 0.024 -9999 0 -10000 0 0
TRAILR2 (trimer) 0.021 0.012 -9999 0 -10000 0 0
CASP8 0.015 0.023 -9999 0 -0.47 1 1
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.058 0.042 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.027 0.006 -9999 0 -10000 0 0
Rac1/GDP 0.026 0.01 -9999 0 -10000 0 0
DOCK1 0.026 0.016 -9999 0 -0.36 1 1
ITGA4 0.014 0.072 -9999 0 -0.36 22 22
RAC1 0.025 0.008 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.02 0.081 -9999 0 -0.28 40 40
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.023 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.046 0.05 -9999 0 -0.21 22 22
alpha4/beta7 Integrin/Paxillin 0.029 0.066 -9999 0 -0.36 5 5
lamellipodium assembly 0.007 0.081 -9999 0 -0.4 16 16
PIK3CA 0.027 0.016 -9999 0 -0.36 1 1
PI3K 0.039 0.015 -9999 0 -0.25 1 1
ARF6 0.026 0.007 -9999 0 -10000 0 0
TLN1 0.027 0.004 -9999 0 -10000 0 0
PXN 0.013 0.002 -9999 0 -10000 0 0
PIK3R1 0.027 0.006 -9999 0 -10000 0 0
ARF6/GTP 0.047 0.044 -9999 0 -10000 0 0
cell adhesion 0.049 0.046 -9999 0 -10000 0 0
CRKL/CBL 0.039 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.037 0.045 -9999 0 -10000 0 0
ITGB1 0.028 0.002 -9999 0 -10000 0 0
ITGB7 0.013 0.074 -9999 0 -0.36 23 23
ARF6/GDP 0.027 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.046 0.064 -9999 0 -0.35 9 9
p130Cas/Crk/Dock1 0.045 0.026 -9999 0 -0.21 2 2
VCAM1 0.019 0.056 -9999 0 -0.36 13 13
alpha4/beta1 Integrin/Paxillin/Talin 0.051 0.047 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.051 0.045 -9999 0 -10000 0 0
BCAR1 0.027 0.016 -9999 0 -0.36 1 1
mol:GDP -0.049 0.045 -9999 0 -10000 0 0
CBL 0.027 0.004 -9999 0 -10000 0 0
PRKACA 0.027 0.003 -9999 0 -10000 0 0
GIT1 0.026 0.016 -9999 0 -0.36 1 1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.051 0.047 -9999 0 -10000 0 0
Rac1/GTP 0.006 0.089 -9999 0 -0.45 16 16
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.021 0.009 -10000 0 -10000 0 0
TRAF2/ASK1 0.036 0.013 -10000 0 -0.21 1 1
ATM 0.027 0.005 -10000 0 -10000 0 0
MAP2K3 0.008 0.075 0.29 3 -0.31 13 16
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.016 0.064 0.26 5 -0.34 6 11
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.023 0.047 0.36 1 -0.43 6 7
TXN 0.007 0.001 -10000 0 -10000 0 0
CALM1 0.026 0.007 -10000 0 -10000 0 0
GADD45A 0.027 0.005 -10000 0 -10000 0 0
GADD45B 0.027 0.004 -10000 0 -10000 0 0
MAP3K1 0.026 0.016 -10000 0 -0.36 1 1
MAP3K6 0.025 0.017 -10000 0 -0.36 1 1
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 0.037 0.017 -10000 0 -0.25 1 1
TAK1/TAB family 0 0.014 -10000 0 -10000 0 0
RAC1/OSM/MEKK3 0.047 0.02 -10000 0 -0.19 1 1
TRAF2 0.027 0.016 -10000 0 -0.36 1 1
RAC1/OSM/MEKK3/MKK3 0.019 0.064 -10000 0 -0.3 5 5
TRAF6 0.007 0.001 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.013 0.11 0.36 1 -0.37 50 51
CCM2 0.025 0.017 -10000 0 -0.36 1 1
CaM/Ca2+/CAMKIIB 0.011 0.07 0.23 1 -0.22 50 51
MAPK11 0.025 0.027 -10000 0 -0.44 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.025 0.069 0.24 1 -0.2 49 50
OSM/MEKK3 0.036 0.017 -10000 0 -0.25 1 1
TAOK1 0.014 0.004 -10000 0 -10000 0 0
TAOK2 0.014 0.003 -10000 0 -10000 0 0
TAOK3 0.014 0.003 -10000 0 -10000 0 0
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 0.027 0.004 -10000 0 -10000 0 0
MAP3K10 0.028 0.014 0.36 1 -10000 0 1
MAP3K3 0.027 0.005 -10000 0 -10000 0 0
TRX/ASK1 0.025 0.009 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.058 0.034 0.24 1 -0.23 5 6
PLK2 and PLK4 events

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
PLK2 0.023 0.042 -9999 0 -0.44 5 5
PLK4 0.027 0.005 -9999 0 -10000 0 0
regulation of centriole replication 0.01 0.03 -9999 0 -0.32 5 5
IL2 signaling events mediated by STAT5

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
GAB2 0.028 0.004 -10000 0 -10000 0 0
ELF1 0.021 0.042 -10000 0 -0.31 9 9
CCNA2 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
JAK3 0.027 0.019 -10000 0 -0.44 1 1
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 0.042 0.086 -10000 0 -0.48 6 6
SHC1 0.028 0.004 -10000 0 -10000 0 0
SP1 0.03 0.036 -10000 0 -0.3 7 7
IL2RA 0.006 0.078 -10000 0 -0.63 9 9
IL2RB 0.018 0.058 -10000 0 -0.36 14 14
SOS1 0.028 0.002 -10000 0 -10000 0 0
IL2RG 0.026 0.027 -10000 0 -0.36 3 3
G1/S transition of mitotic cell cycle 0.024 0.084 0.4 2 -0.59 6 8
PTPN11 0.028 0.002 -10000 0 -10000 0 0
CCND2 0.013 0.058 -10000 0 -0.63 5 5
LCK 0.02 0.058 -10000 0 -0.43 10 10
GRB2 0.028 0.004 -10000 0 -10000 0 0
IL2 0.018 0.01 -10000 0 -10000 0 0
CDK6 0.026 0.006 -10000 0 -10000 0 0
CCND3 0.041 0.085 0.39 2 -0.56 2 4
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.048 0.052 -10000 0 -10000 0 0
TC10/GTP 0.033 0.049 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.077 0.027 -10000 0 -10000 0 0
HRAS 0.027 0.016 -10000 0 -0.36 1 1
APS homodimer 0.02 0.058 0.36 1 -0.44 9 10
GRB14 -0.005 0.1 -10000 0 -0.39 42 42
FOXO3 -0.01 0.15 -10000 0 -0.57 38 38
AKT1 -0.002 0.06 0.21 3 -10000 0 3
INSR 0.039 0.014 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.078 0.072 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.025 0.008 -10000 0 -10000 0 0
SORBS1 0.017 0.06 -10000 0 -0.36 15 15
CRK 0.023 0.01 -10000 0 -10000 0 0
PTPN1 0.006 0.023 -10000 0 -10000 0 0
CAV1 0.012 0.046 0.18 10 -10000 0 10
CBL/APS/CAP/Crk-II/C3G 0.054 0.061 0.25 1 -0.23 6 7
Insulin Receptor/Insulin/IRS1/NCK2 0.077 0.027 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.058 0.025 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.063 0.07 -10000 0 -0.3 5 5
RPS6KB1 -0.007 0.053 0.19 3 -10000 0 3
PARD6A 0.026 0.027 -10000 0 -0.44 2 2
CBL 0.027 0.004 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.019 0.008 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.03 0.057 -10000 0 -10000 0 0
HRAS/GTP 0.022 0.013 -10000 0 -10000 0 0
Insulin Receptor 0.039 0.014 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.084 0.032 -10000 0 -10000 0 0
PRKCI 0.027 0.055 -10000 0 -0.4 4 4
Insulin Receptor/Insulin/GRB14/PDK1 0.022 0.055 -10000 0 -10000 0 0
SHC1 0.027 0.004 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.043 0.028 -10000 0 -0.35 1 1
PI3K 0.071 0.03 -10000 0 -10000 0 0
NCK2 0.028 0.002 -10000 0 -10000 0 0
RHOQ 0.028 0.002 -10000 0 -10000 0 0
mol:H2O2 0.001 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.02 0.011 -10000 0 -0.25 1 1
AKT2 -0.003 0.059 0.21 1 -10000 0 1
PRKCZ 0.018 0.076 -10000 0 -0.4 4 4
SH2B2 0.02 0.058 0.36 1 -0.44 9 10
SHC/SHIP 0.044 0.03 -10000 0 -10000 0 0
F2RL2 0.002 0.1 -10000 0 -0.43 33 33
TRIP10 0.027 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.059 0.025 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.037 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.084 0.032 -10000 0 -10000 0 0
RAPGEF1 0.027 0.016 -10000 0 -0.36 1 1
RASA1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.028 0.003 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.046 0.058 0.25 1 -0.24 9 10
TC10/GDP 0.02 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.068 0.034 -10000 0 -10000 0 0
INPP5D 0.016 0.041 0.18 10 -10000 0 10
SOS1 0.028 0.002 -10000 0 -10000 0 0
SGK1 -0.026 0.18 -10000 0 -0.74 35 35
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.028 0.002 -10000 0 -10000 0 0
IRS1 0.028 0.002 -10000 0 -10000 0 0
p62DOK/RasGAP 0.044 0.028 -10000 0 -0.35 1 1
INS 0.028 0.014 -10000 0 -10000 0 0
mol:PI-3-4-P2 0.016 0.041 0.18 10 -10000 0 10
GRB2 0.027 0.004 -10000 0 -10000 0 0
EIF4EBP1 -0.007 0.054 0.22 5 -10000 0 5
PTPRA 0.029 0.016 -10000 0 -10000 0 0
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
TC10/GTP/CIP4 0.037 0.006 -10000 0 -10000 0 0
PDPK1 0.027 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.036 0.019 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.06 0.023 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0.051 0.025 -10000 0 -10000 0 0
Par3/Par6 0.046 0.068 -10000 0 -0.23 31 31
Canonical NF-kappaB pathway

Figure S121.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S121.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.029 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.05 0.077 0.23 29 -0.27 1 30
ERC1 0.027 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.026 0.058 -10000 0 -0.31 16 16
NFKBIA 0.012 0.01 0.21 1 -10000 0 1
BIRC2 0.026 0.016 -10000 0 -0.36 1 1
IKBKB 0.024 0.009 -10000 0 -10000 0 0
RIPK2 0.024 0.01 -10000 0 -10000 0 0
IKBKG 0.025 0.044 -10000 0 -0.33 4 4
IKK complex/A20 0.053 0.061 -10000 0 -0.32 3 3
NEMO/A20/RIP2 0.024 0.01 -10000 0 -10000 0 0
XPO1 0.028 0 -10000 0 -10000 0 0
NEMO/ATM 0.045 0.055 0.27 2 -0.32 5 7
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.028 0.003 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.037 0.003 -10000 0 -10000 0 0
IKK complex/ELKS 0.043 0.051 -10000 0 -0.31 2 2
BCL10/MALT1/TRAF6 0.04 0.029 -10000 0 -0.21 2 2
NOD2 0.014 0.077 -10000 0 -0.44 17 17
NFKB1 0.029 0.005 -10000 0 -10000 0 0
RELA 0.029 0.005 -10000 0 -10000 0 0
MALT1 0.02 0.02 -10000 0 -0.36 1 1
cIAP1/UbcH5C 0.039 0.015 -10000 0 -0.25 1 1
ATM 0.027 0.005 -10000 0 -10000 0 0
TNF/TNFR1A 0.037 0.027 -10000 0 -0.25 5 5
TRAF6 0.027 0.003 -10000 0 -10000 0 0
PRKCA 0.027 0.005 -10000 0 -10000 0 0
CHUK 0.027 0.006 -10000 0 -10000 0 0
UBE2D3 0.027 0.005 -10000 0 -10000 0 0
TNF 0.024 0.035 -10000 0 -0.36 5 5
NF kappa B1 p50/RelA 0.06 0.016 -10000 0 -10000 0 0
BCL10 0.026 0.016 -10000 0 -0.36 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.01 0.21 1 -10000 0 1
beta TrCP1/SCF ubiquitin ligase complex 0.029 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.004 -10000 0 -10000 0 0
IKK complex 0.047 0.054 -10000 0 -0.31 4 4
CYLD 0.027 0.016 -10000 0 -0.36 1 1
IKK complex/PKC alpha 0.054 0.057 -10000 0 -0.32 2 2
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.058 0.049 -10000 0 -0.27 5 5
Ran/GTP/Exportin 1/HDAC1 -0.008 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.031 0.057 -10000 0 -0.34 3 3
SUMO1 0.027 0.022 -10000 0 -0.36 2 2
ZFPM1 0.018 0.065 -10000 0 -0.44 12 12
NPC/RanGAP1/SUMO1/Ubc9 0.014 0.012 -10000 0 -0.17 2 2
FKBP3 0.025 0.017 -10000 0 -0.36 1 1
Histones 0.061 0.038 -10000 0 -10000 0 0
YY1/LSF 0.009 0.068 -10000 0 -0.31 6 6
SMG5 0.027 0.004 -10000 0 -10000 0 0
RAN 0.028 0.003 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.024 0.022 -10000 0 -10000 0 0
I kappa B alpha/HDAC1 0.026 0.047 -10000 0 -10000 0 0
SAP18 0.022 0.012 -10000 0 -10000 0 0
RELA 0.023 0.033 -10000 0 -0.51 1 1
HDAC1/Smad7 0.039 0.028 -10000 0 -0.21 1 1
RANGAP1 0.026 0.02 -10000 0 -0.44 1 1
HDAC3/TR2 0.035 0.033 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.019 0.043 -10000 0 -0.33 1 1
NF kappa B1 p50/RelA 0.028 0.061 0.31 1 -0.31 7 8
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.021 0.052 -10000 0 -0.36 11 11
GATA1 0.011 0.022 -10000 0 -10000 0 0
Mad/Max 0.037 0.02 -10000 0 -0.25 2 2
NuRD/MBD3 Complex/GATA1/Fog1 0.013 0.066 -10000 0 -0.31 5 5
RBBP7 0.027 0.004 -10000 0 -10000 0 0
NPC 0.016 0 -10000 0 -10000 0 0
RBBP4 0.027 0.005 -10000 0 -10000 0 0
MAX 0.026 0.007 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.027 0.004 -10000 0 -10000 0 0
NFKBIA 0.021 0.017 -10000 0 -10000 0 0
KAT2B 0.011 0.078 -10000 0 -0.36 26 26
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.021 0.014 -10000 0 -10000 0 0
SIN3 complex 0.051 0.032 -10000 0 -10000 0 0
SMURF1 0.027 0.006 -10000 0 -10000 0 0
CHD3 0.023 0.011 -10000 0 -10000 0 0
SAP30 0.027 0.006 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.023 0.011 -10000 0 -10000 0 0
YY1/HDAC3 0.012 0.058 -10000 0 -0.29 5 5
YY1/HDAC2 0.011 0.067 -10000 0 -0.31 6 6
YY1/HDAC1 0.011 0.066 -10000 0 -0.31 6 6
NuRD/MBD2 Complex (MeCP1) 0.016 0.039 -10000 0 -0.33 1 1
PPARG 0.021 0.036 -10000 0 -0.24 2 2
HDAC8/hEST1B 0.054 0.011 -10000 0 -10000 0 0
UBE2I 0.027 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.004 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.035 0.034 -10000 0 -10000 0 0
MBD3L2 -0.018 0.003 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.039 0.027 -10000 0 -0.21 1 1
CREBBP 0.027 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.013 0.069 -10000 0 -0.31 9 9
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC3 0.022 0.016 -10000 0 -10000 0 0
HDAC2 0.027 0.005 -10000 0 -10000 0 0
YY1 0.01 0.044 -10000 0 -0.22 21 21
HDAC8 0.028 0.002 -10000 0 -10000 0 0
SMAD7 0.02 0.02 -10000 0 -0.36 1 1
NCOR2 0.027 0.016 -10000 0 -0.36 1 1
MXD1 0.026 0.022 -10000 0 -0.36 2 2
STAT3 0.021 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.028 0 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.024 0.068 -10000 0 -0.29 6 6
YY1/SAP30/HDAC1 0.025 0.066 -10000 0 -0.29 6 6
EP300 0.026 0.006 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.021 0.006 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.017 -10000 0 -10000 0 0
histone deacetylation 0.014 0.046 -10000 0 -0.4 3 3
STAT3 (dimer non-phopshorylated)/HDAC3 0.03 0.022 -10000 0 -10000 0 0
nuclear export -0.054 0.011 -10000 0 -10000 0 0
PRKACA 0.027 0.003 -10000 0 -10000 0 0
GATAD2B 0.027 0.004 -10000 0 -10000 0 0
GATAD2A 0.027 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.031 0.044 -10000 0 -0.3 1 1
GATA1/HDAC1 0.037 0.009 -10000 0 -10000 0 0
GATA1/HDAC3 0.033 0.032 -10000 0 -10000 0 0
CHD4 0.027 0.004 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.037 0.027 -10000 0 -0.25 5 5
SIN3/HDAC complex/Mad/Max 0.033 0.046 -10000 0 -0.33 2 2
NuRD Complex -0.007 0.091 -10000 0 -0.3 24 24
positive regulation of chromatin silencing 0.058 0.037 -10000 0 -10000 0 0
SIN3B 0.027 0.003 -10000 0 -10000 0 0
MTA2 0.027 0.004 -10000 0 -10000 0 0
SIN3A 0.027 0.006 -10000 0 -10000 0 0
XPO1 0.028 0 -10000 0 -10000 0 0
SUMO1/HDAC1 0.038 0.031 -10000 0 -0.26 2 2
HDAC complex 0.066 0.02 -10000 0 -10000 0 0
GATA1/Fog1 0.031 0.05 -10000 0 -0.32 12 12
FKBP25/HDAC1/HDAC2 0.049 0.021 -10000 0 -0.21 1 1
TNF 0.024 0.035 -10000 0 -0.36 5 5
negative regulation of cell growth 0.033 0.046 -10000 0 -0.32 2 2
NuRD/MBD2/PRMT5 Complex 0.016 0.039 -10000 0 -0.33 1 1
Ran/GTP/Exportin 1 0.039 0.031 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.018 0.047 -10000 0 -0.29 7 7
SIN3/HDAC complex/NCoR1 0.01 0.05 -10000 0 -0.3 10 10
TFCP2 0.027 0.016 -10000 0 -0.36 1 1
NR2C1 0.028 0.003 -10000 0 -10000 0 0
MBD3 0.026 0.025 -10000 0 -0.4 2 2
MBD2 0.02 0.012 -10000 0 -10000 0 0
Circadian rhythm pathway

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
chromatin modification 0.053 0.015 -10000 0 -10000 0 0
CLOCK 0.029 0.006 -10000 0 -10000 0 0
TIMELESS/CRY2 0.039 0.013 -10000 0 -10000 0 0
DEC1/BMAL1 0.03 0.05 -10000 0 -0.33 11 11
ATR 0.028 0.003 -10000 0 -10000 0 0
NR1D1 0.023 0.01 -10000 0 -10000 0 0
ARNTL 0.03 0.004 -10000 0 -10000 0 0
TIMELESS 0.023 0.009 -10000 0 -10000 0 0
NPAS2 0.03 0.003 -10000 0 -10000 0 0
CRY2 0.027 0.003 -10000 0 -10000 0 0
mol:CO -0.009 0.003 0.069 1 -10000 0 1
CHEK1 0.027 0.004 -10000 0 -10000 0 0
mol:HEME 0.009 0.003 -10000 0 -0.069 1 1
PER1 0.022 0.019 -10000 0 -0.36 1 1
BMAL/CLOCK/NPAS2 0.065 0.014 -10000 0 -10000 0 0
BMAL1/CLOCK 0.024 0.046 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.053 0.015 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.054 0.015 -10000 0 -10000 0 0
mol:NADPH 0.009 0.003 -10000 0 -0.069 1 1
PER1/TIMELESS 0.033 0.019 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.01 0.065 -10000 0 -0.46 11 11
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.027 0.004 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.041 0.028 -9999 0 -0.19 4 4
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.01 0.015 -9999 0 -0.3 1 1
AURKB 0.023 0.01 -9999 0 -10000 0 0
AURKC 0.023 0.033 -9999 0 -0.36 4 4
Atypical NF-kappaB 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
BCL3/RelA 0.04 0.008 -10000 0 -10000 0 0
FBXW11 0.027 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.026 0.011 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.054 0.055 0.21 6 -10000 0 6
NFKBIA 0.047 0.055 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.026 0.011 -10000 0 -10000 0 0
ARRB2 0.012 0.006 -10000 0 -10000 0 0
REL 0.028 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.026 0.011 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.026 0.011 -10000 0 -10000 0 0
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
NF kappa B1 p50 dimer 0.019 0.008 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
NFKB1 0.012 0.005 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.038 0.045 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.046 0.054 0.22 1 -10000 0 1
SRC 0.017 0.014 -10000 0 -10000 0 0
PI3K 0.039 0.015 -10000 0 -0.25 1 1
NF kappa B1 p50/RelA 0.038 0.045 -10000 0 -10000 0 0
IKBKB 0.024 0.009 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.004 -10000 0 -10000 0 0
SYK 0.027 0.004 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.057 0.059 0.22 7 -10000 0 7
cell death 0.044 0.053 0.19 5 -10000 0 5
NF kappa B1 p105/c-Rel 0.026 0.011 -10000 0 -10000 0 0
LCK 0.019 0.058 -10000 0 -0.43 10 10
BCL3 0.027 0.003 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.01 0.023 -10000 0 -0.25 1 1
adherens junction organization 0.036 0.039 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.027 -10000 0 -10000 0 0
FMN1 0.038 0.037 -10000 0 -10000 0 0
mol:IP3 0.011 0.02 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.043 0.036 -10000 0 -10000 0 0
CTNNB1 0.028 0.004 -10000 0 -10000 0 0
AKT1 0.051 0.05 0.19 8 -10000 0 8
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.065 0.062 -10000 0 -0.48 1 1
CTNND1 0.03 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.038 0.037 -10000 0 -10000 0 0
VASP 0.038 0.037 -10000 0 -10000 0 0
ZYX 0.037 0.036 -10000 0 -10000 0 0
JUB 0.039 0.035 -10000 0 -10000 0 0
EGFR(dimer) 0.05 0.042 -10000 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin 0.051 0.015 -10000 0 -0.2 1 1
mol:PI-3-4-5-P3 0.085 0.062 0.22 9 -10000 0 9
PIK3CA 0.03 0.017 -10000 0 -0.36 1 1
PI3K 0.086 0.063 0.22 9 -10000 0 9
FYN -0.004 0.044 -10000 0 -10000 0 0
mol:Ca2+ 0.011 0.019 -10000 0 -10000 0 0
JUP 0.027 0.016 -10000 0 -0.36 1 1
PIK3R1 0.03 0.008 -10000 0 -10000 0 0
mol:DAG 0.011 0.02 -10000 0 -10000 0 0
CDH1 0.028 0.003 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.033 -10000 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.038 0.036 -10000 0 -10000 0 0
SRC 0.017 0.014 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
EGFR 0.024 0.023 -10000 0 -0.36 2 2
CASR -0.006 0.044 -10000 0 -10000 0 0
RhoA/GTP 0.019 0.024 -10000 0 -10000 0 0
AKT2 0.054 0.049 0.18 6 -10000 0 6
actin cable formation 0.033 0.036 -10000 0 -10000 0 0
apoptosis -0.047 0.05 0.24 1 -0.19 7 8
CTNNA1 0.03 0.006 -10000 0 -10000 0 0
mol:GDP 0.008 0.02 -10000 0 -10000 0 0
PIP5K1A 0.039 0.037 -10000 0 -10000 0 0
PLCG1 0.011 0.02 -10000 0 -10000 0 0
Rac1/GTP 0.055 0.042 -10000 0 -10000 0 0
homophilic cell adhesion 0.002 0.004 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.02 0.013 -10000 0 -10000 0 0
SMAD2 0.013 0.032 -10000 0 -0.2 1 1
SMAD3 0.019 0.017 -10000 0 -10000 0 0
SMAD3/SMAD4 0.023 0.061 -10000 0 -0.42 10 10
SMAD4/Ubc9/PIASy 0.04 0.026 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.04 0.045 -10000 0 -10000 0 0
PPM1A 0.026 0.007 -10000 0 -10000 0 0
CALM1 0.026 0.007 -10000 0 -10000 0 0
SMAD2/SMAD4 0.015 0.022 -10000 0 -10000 0 0
MAP3K1 0.026 0.016 -10000 0 -0.36 1 1
TRAP-1/SMAD4 0.029 0.022 -10000 0 -0.25 1 1
MAPK3 0.027 0.016 -10000 0 -0.36 1 1
MAPK1 0.026 0.006 -10000 0 -10000 0 0
NUP214 0.027 0.004 -10000 0 -10000 0 0
CTDSP1 0.028 0.001 -10000 0 -10000 0 0
CTDSP2 0.028 0.002 -10000 0 -10000 0 0
CTDSPL 0.028 0.003 -10000 0 -10000 0 0
KPNB1 0.027 0.004 -10000 0 -10000 0 0
TGFBRAP1 0.027 0.016 -10000 0 -0.36 1 1
UBE2I 0.027 0.004 -10000 0 -10000 0 0
NUP153 0.027 0.004 -10000 0 -10000 0 0
KPNA2 0.027 0.014 0.36 1 -10000 0 1
PIAS4 0.027 0.004 -10000 0 -10000 0 0
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.024 0.02 -10000 0 -10000 0 0
ATM 0.027 0.005 -10000 0 -10000 0 0
UBE2D3 0.027 0.005 -10000 0 -10000 0 0
PRKDC 0.025 0.016 0.36 1 -10000 0 1
ATR 0.028 0.003 -10000 0 -10000 0 0
UBE2L3 0.027 0.006 -10000 0 -10000 0 0
FANCD2 0.021 0.012 -10000 0 -0.26 1 1
protein ubiquitination 0.071 0.027 0.24 3 -0.23 1 4
XRCC5 0.028 0.001 -10000 0 -10000 0 0
XRCC6 0.026 0.006 -10000 0 -10000 0 0
M/R/N Complex 0.046 0.024 -10000 0 -0.21 1 1
MRE11A 0.027 0.004 -10000 0 -10000 0 0
DNA-PK 0.048 0.022 0.25 1 -10000 0 1
FA complex/FANCD2/Ubiquitin 0.03 0.043 -10000 0 -0.39 4 4
FANCF 0.027 0.003 -10000 0 -10000 0 0
BRCA1 0.027 0.004 -10000 0 -10000 0 0
CCNE1 0.027 0.036 0.36 3 -0.44 2 5
CDK2/Cyclin E1 0.04 0.026 0.26 3 -0.32 2 5
FANCG 0.028 0.014 0.36 1 -10000 0 1
BRCA1/BACH1/BARD1 0.041 0.005 -10000 0 -10000 0 0
FANCE 0.027 0.003 -10000 0 -10000 0 0
FANCC 0.027 0.004 -10000 0 -10000 0 0
NBN 0.023 0.018 -10000 0 -0.36 1 1
FANCA 0.027 0.004 -10000 0 -10000 0 0
DNA repair 0.042 0.062 0.24 10 -10000 0 10
BRCA1/BARD1/ubiquitin 0.041 0.005 -10000 0 -10000 0 0
BARD1/DNA-PK 0.061 0.027 0.25 1 -10000 0 1
FANCL 0.028 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.024 0.02 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.024 0.044 -10000 0 -0.25 7 7
BRCA1/BACH1/BARD1/TopBP1 0.055 0.009 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.058 0.028 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.033 0.028 -10000 0 -10000 0 0
BRCA1/BACH1 0.027 0.004 -10000 0 -10000 0 0
BARD1 0.028 0.001 -10000 0 -10000 0 0
PCNA 0.023 0.011 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.054 0.012 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.053 0.013 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.054 0.031 -10000 0 -10000 0 0
BARD1/DNA-PK/P53 0.061 0.038 0.25 1 -10000 0 1
BRCA1/BARD1/Ubiquitin 0.041 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP 0.036 0.022 -10000 0 -10000 0 0
FA complex 0.03 0.016 0.17 1 -10000 0 1
BARD1/EWS 0.039 0.009 -10000 0 -10000 0 0
RBBP8 0.01 0.012 -10000 0 -0.25 1 1
TP53 0.023 0.011 -10000 0 -10000 0 0
TOPBP1 0.028 0.003 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.056 0.027 -10000 0 -10000 0 0
BRCA1/BARD1 0.078 0.028 0.25 3 -0.23 1 4
CSTF1 0.016 0.014 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.021 0.001 -10000 0 -10000 0 0
CDK2 0.028 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.026 0.007 -10000 0 -10000 0 0
RAD50 0.027 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.041 0.005 -10000 0 -10000 0 0
EWSR1 0.027 0.006 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

Figure S129.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S129.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.005 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.006 0.01 -9999 0 -10000 0 0
MDM2/SUMO1 0.038 0.036 -9999 0 -0.33 2 2
HDAC4 0.028 0.002 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.006 0.009 -9999 0 -10000 0 0
SUMO1 0.027 0.022 -9999 0 -0.36 2 2
NPC/RanGAP1/SUMO1 0.012 0.012 -9999 0 -0.17 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.01 0.011 -9999 0 -0.16 2 2
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.028 0.003 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.028 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.038 0.034 -9999 0 -0.26 2 2
SUMO1/HDAC1 0.038 0.031 -9999 0 -0.26 2 2
RANGAP1 0.026 0.02 -9999 0 -0.44 1 1
MDM2/SUMO1/SUMO1 0.052 0.037 -9999 0 -0.37 1 1
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.014 0.012 -9999 0 -0.17 2 2
Ran/GTP 0.025 0.027 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.027 0.016 -9999 0 -0.36 1 1
UBE2I 0.027 0.004 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.022 0.026 -9999 0 -10000 0 0
NPC 0.016 0 -9999 0 -10000 0 0
PIAS2 0.021 0.012 -9999 0 -10000 0 0
PIAS1 0.026 0.006 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.054 0.016 -9999 0 -0.21 1 1
E-cadherin/beta catenin 0.04 0.006 -9999 0 -10000 0 0
CTNNB1 0.027 0.003 -9999 0 -10000 0 0
JUP 0.027 0.016 -9999 0 -0.36 1 1
CDH1 0.028 0.003 -9999 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.039 0.01 -9999 0 -9999 0 0
FBXW11 0.027 0.004 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.004 -9999 0 -9999 0 0
CHUK 0.027 0.006 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.076 0.023 -9999 0 -9999 0 0
NFKB1 0.027 0.005 -9999 0 -9999 0 0
MAP3K14 0.027 0.004 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.04 0.008 -9999 0 -9999 0 0
RELB 0.027 0.003 -9999 0 -9999 0 0
NFKB2 0.027 0.006 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.036 0.009 -9999 0 -9999 0 0
regulation of B cell activation 0.035 0.009 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 612 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.WS.AB45 TCGA.T9.A92H TCGA.SS.A7HO TCGA.RU.A8FL
109_MAP3K5 0.031 0.031 -0.19 -0.17
47_PPARGC1A 0.028 0.028 0.028 0.028
105_BMP4 0.028 0 0 0.028
105_BMP6 0.028 0.028 0.028 0.028
105_BMP7 -0.36 0.028 0.028 0.36
105_BMP2 0.028 0.028 0 -0.36
131_RELN/VLDLR -0.25 -0.41 -0.058 -0.23
30_TGFB1/TGF beta receptor Type II 0.027 0.027 0.03 0.032
84_STAT5B 0.0059 0.028 0 0.04
84_STAT5A 0.0059 0.028 0 0.04
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/COADREAD-TP/19438829/COADREAD-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/COADREAD-TP/19775091/Gistic2_Analysis_19775756/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)
Copyright © 2015 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle