PARADIGM pathway analysis of mRNASeq expression and copy number data
Glioma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1PN951R
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1PN951R
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
Ephrin A reverse signaling 136
FOXM1 transcription factor network 123
Aurora B signaling 121
Glypican 2 network 113
Effects of Botulinum toxin 112
Retinoic acid receptors-mediated signaling 105
Reelin signaling pathway 94
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 85
Signaling mediated by p38-alpha and p38-beta 81
Ephrin B reverse signaling 79
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 669 . 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 ( 669 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Ephrin A reverse signaling 0.2033 136 954 7 -0.058 0.018 1000 -1000 -0.013 -1000
FOXM1 transcription factor network 0.1839 123 6278 51 0.02 0.3 1000 -1000 -0.15 -1000
Aurora B signaling 0.1809 121 8117 67 -0.049 0.16 1000 -1000 -0.032 -1000
Glypican 2 network 0.1689 113 455 4 0.047 0.057 1000 -1000 0.021 -1000
Effects of Botulinum toxin 0.1674 112 2937 26 -0.096 0.041 1000 -1000 -0.005 -1000
Retinoic acid receptors-mediated signaling 0.1570 105 6114 58 -0.25 0.041 1000 -1000 -0.033 -1000
Reelin signaling pathway 0.1405 94 5271 56 -0.11 0.053 1000 -1000 -0.021 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.1271 85 7265 85 -0.17 0.041 1000 -1000 -0.036 -1000
Signaling mediated by p38-alpha and p38-beta 0.1211 81 3571 44 -0.096 0.021 1000 -1000 -0.021 -1000
Ephrin B reverse signaling 0.1181 79 3821 48 -0.044 0.044 1000 -1000 -0.027 -1000
Visual signal transduction: Rods 0.1181 79 4158 52 -0.11 0.063 1000 -1000 -0.015 -1000
Aurora C signaling 0.1166 78 551 7 0 0.1 1000 -1000 -0.014 -1000
Glucocorticoid receptor regulatory network 0.1151 77 8784 114 -0.45 0.24 1000 -1000 -0.043 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1106 74 5086 68 -0.21 0.1 1000 -1000 -0.086 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1091 73 2485 34 -0.034 0.027 1000 -1000 -0.024 -1000
IL23-mediated signaling events 0.1076 72 4328 60 -0.42 0.056 1000 -1000 -0.13 -1000
PLK1 signaling events 0.1061 71 6090 85 -0.02 0.098 1000 -1000 -0.033 -1000
TCGA08_retinoblastoma 0.1061 71 569 8 -0.01 0.044 1000 -1000 -0.002 -1000
Thromboxane A2 receptor signaling 0.0927 62 6523 105 -0.2 0.053 1000 -1000 -0.042 -1000
a4b1 and a4b7 Integrin signaling 0.0792 53 269 5 0.021 0.042 1000 -1000 0.02 -1000
Arf6 signaling events 0.0792 53 3320 62 -0.083 0.079 1000 -1000 -0.033 -1000
HIF-1-alpha transcription factor network 0.0703 47 3614 76 -0.004 0.23 1000 -1000 -0.064 -1000
Syndecan-1-mediated signaling events 0.0688 46 1584 34 -0.042 0.057 1000 -1000 -0.024 -1000
FAS signaling pathway (CD95) 0.0673 45 2146 47 -0.18 0.046 1000 -1000 -0.044 -1000
LPA receptor mediated events 0.0673 45 4625 102 -0.045 0.052 1000 -1000 -0.06 -1000
S1P1 pathway 0.0643 43 1548 36 -0.1 0.027 1000 -1000 -0.035 -1000
Ceramide signaling pathway 0.0628 42 3217 76 -0.078 0.035 1000 -1000 -0.03 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0613 41 2265 54 -0.074 0.03 1000 -1000 -0.028 -1000
Signaling events mediated by the Hedgehog family 0.0613 41 2133 52 -0.023 0.037 1000 -1000 -0.035 -1000
p75(NTR)-mediated signaling 0.0613 41 5241 125 -0.08 0.057 1000 -1000 -0.036 -1000
amb2 Integrin signaling 0.0613 41 3370 82 -0.088 0.05 1000 -1000 -0.023 -1000
Ras signaling in the CD4+ TCR pathway 0.0583 39 673 17 -0.074 0.036 1000 -1000 -0.028 -1000
EPO signaling pathway 0.0568 38 2142 55 -0.004 0.058 1000 -1000 -0.017 -1000
Syndecan-3-mediated signaling events 0.0568 38 1337 35 -0.035 0.053 1000 -1000 -0.016 -1000
Syndecan-4-mediated signaling events 0.0568 38 2573 67 -0.03 0.083 1000 -1000 -0.038 -1000
TCGA08_p53 0.0553 37 259 7 -0.007 0.02 1000 -1000 -0.006 -1000
TCGA08_rtk_signaling 0.0538 36 951 26 -0.013 0.055 1000 -1000 0.002 -1000
EGFR-dependent Endothelin signaling events 0.0508 34 734 21 -0.009 0.066 1000 -1000 -0.022 -1000
ErbB2/ErbB3 signaling events 0.0493 33 2162 65 -0.042 0.03 1000 -1000 -0.058 -1000
Coregulation of Androgen receptor activity 0.0493 33 2550 76 -0.023 0.07 1000 -1000 -0.016 -1000
IL1-mediated signaling events 0.0493 33 2071 62 -0.019 0.064 1000 -1000 -0.03 -1000
PDGFR-alpha signaling pathway 0.0463 31 1379 44 -0.017 0.055 1000 -1000 -0.023 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0463 31 2640 83 -0.16 0.15 1000 -1000 -0.026 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0463 31 3830 120 -0.085 0.068 1000 -1000 -0.037 -1000
Osteopontin-mediated events 0.0448 30 1166 38 -0.007 0.073 1000 -1000 -0.025 -1000
JNK signaling in the CD4+ TCR pathway 0.0448 30 520 17 -0.18 0.048 1000 -1000 -0.03 -1000
BARD1 signaling events 0.0433 29 1691 57 -0.066 0.084 1000 -1000 -0.036 -1000
IL4-mediated signaling events 0.0419 28 2633 91 -0.58 0.18 1000 -1000 -0.16 -1000
BMP receptor signaling 0.0419 28 2297 81 -0.051 0.089 1000 -1000 -0.02 -1000
Glypican 1 network 0.0419 28 1350 48 -0.03 0.046 1000 -1000 -0.022 -1000
IL12-mediated signaling events 0.0404 27 2404 87 -0.11 0.077 1000 -1000 -0.086 -1000
Cellular roles of Anthrax toxin 0.0404 27 1073 39 -0.026 0.041 1000 -1000 -0.019 -1000
TCR signaling in naïve CD8+ T cells 0.0404 27 2583 93 -0.19 0.21 1000 -1000 -0.032 -1000
IL2 signaling events mediated by STAT5 0.0404 27 598 22 -0.009 0.056 1000 -1000 -0.035 -1000
Nongenotropic Androgen signaling 0.0389 26 1382 52 -0.011 0.072 1000 -1000 -0.021 -1000
IL6-mediated signaling events 0.0389 26 1969 75 -0.089 0.071 1000 -1000 -0.046 -1000
Visual signal transduction: Cones 0.0374 25 955 38 -0.011 0.056 1000 -1000 -0.012 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0374 25 1336 52 -0.05 0.05 1000 -1000 -0.035 -1000
Regulation of nuclear SMAD2/3 signaling 0.0359 24 3353 136 -0.062 0.093 1000 -1000 -0.036 -1000
Signaling events regulated by Ret tyrosine kinase 0.0359 24 2027 82 -0.02 0.054 1000 -1000 -0.032 -1000
IL2 signaling events mediated by PI3K 0.0344 23 1348 58 -0.062 0.059 1000 -1000 -0.04 -1000
Canonical Wnt signaling pathway 0.0344 23 1203 51 -0.026 0.074 1000 -1000 -0.042 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0344 23 1759 74 -0.076 0.053 1000 -1000 -0.043 -1000
Rapid glucocorticoid signaling 0.0344 23 471 20 -0.016 0.024 1000 -1000 -0.004 -1000
Aurora A signaling 0.0329 22 1354 60 -0.012 0.078 1000 -1000 -0.015 -1000
Fc-epsilon receptor I signaling in mast cells 0.0329 22 2166 97 -0.013 0.098 1000 -1000 -0.047 -1000
Insulin-mediated glucose transport 0.0329 22 723 32 -0.063 0.055 1000 -1000 -0.024 -1000
Caspase cascade in apoptosis 0.0314 21 1622 74 -0.04 0.051 1000 -1000 -0.034 -1000
PLK2 and PLK4 events 0.0314 21 63 3 -0.009 0.026 1000 -1000 -0.009 -1000
Signaling events mediated by PTP1B 0.0314 21 1622 76 -0.076 0.064 1000 -1000 -0.031 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0299 20 756 37 -0.004 0.061 1000 -1000 -0.017 -1000
E-cadherin signaling in keratinocytes 0.0284 19 833 43 -0.007 0.053 1000 -1000 -0.019 -1000
IFN-gamma pathway 0.0269 18 1231 68 -0.21 0.058 1000 -1000 -0.041 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0269 18 614 33 -0.009 0.052 1000 -1000 -0.022 -1000
Presenilin action in Notch and Wnt signaling 0.0254 17 1076 61 -0.049 0.054 1000 -1000 -0.033 -1000
Regulation of p38-alpha and p38-beta 0.0254 17 930 54 -0.07 0.044 1000 -1000 -0.035 -1000
Syndecan-2-mediated signaling events 0.0239 16 1163 69 -0.007 0.044 1000 -1000 -0.027 -1000
S1P5 pathway 0.0239 16 272 17 -0.016 0.021 1000 -1000 -0.012 -1000
Class I PI3K signaling events 0.0239 16 1189 73 -0.016 0.039 1000 -1000 -0.026 -1000
BCR signaling pathway 0.0239 16 1625 99 -0.018 0.073 1000 -1000 -0.038 -1000
VEGFR1 specific signals 0.0239 16 928 56 -0.019 0.072 1000 -1000 -0.026 -1000
Signaling events mediated by PRL 0.0239 16 557 34 -0.026 0.051 1000 -1000 -0.024 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0239 16 1316 78 -0.003 0.052 1000 -1000 -0.041 -1000
EPHB forward signaling 0.0224 15 1295 85 -0.026 0.056 1000 -1000 -0.038 -1000
Plasma membrane estrogen receptor signaling 0.0224 15 1333 86 -0.022 0.042 1000 -1000 -0.042 -1000
p38 MAPK signaling pathway 0.0224 15 683 44 -0.016 0.058 1000 -1000 -0.025 -1000
Endothelins 0.0209 14 1401 96 -0.043 0.064 1000 -1000 -0.045 -1000
Paxillin-dependent events mediated by a4b1 0.0209 14 504 36 -0.046 0.061 1000 -1000 -0.023 -1000
Calcium signaling in the CD4+ TCR pathway 0.0209 14 442 31 -0.026 0.04 1000 -1000 -0.049 -1000
E-cadherin signaling in the nascent adherens junction 0.0209 14 1134 76 -0.024 0.055 1000 -1000 -0.038 -1000
Regulation of Telomerase 0.0209 14 1481 102 -0.013 0.076 1000 -1000 -0.049 -1000
Noncanonical Wnt signaling pathway 0.0194 13 359 26 -0.016 0.03 1000 -1000 -0.029 -1000
PDGFR-beta signaling pathway 0.0194 13 1308 97 -0.022 0.083 1000 -1000 -0.03 -1000
E-cadherin signaling events 0.0194 13 68 5 0.021 0.036 1000 -1000 0.021 -1000
Integrins in angiogenesis 0.0179 12 1050 84 -0.019 0.069 1000 -1000 -0.031 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0179 12 1534 125 -0.018 0.073 1000 -1000 -0.036 -1000
S1P4 pathway 0.0179 12 323 25 -0.016 0.033 1000 -1000 -0.013 -1000
FOXA2 and FOXA3 transcription factor networks 0.0164 11 510 46 -0.032 0.047 1000 -1000 -0.1 -1000
Class I PI3K signaling events mediated by Akt 0.0164 11 805 68 -0.017 0.039 1000 -1000 -0.029 -1000
Nectin adhesion pathway 0.0164 11 703 63 -0.011 0.055 1000 -1000 -0.048 -1000
Signaling events mediated by HDAC Class III 0.0164 11 461 40 -0.025 0.034 1000 -1000 -0.027 -1000
TRAIL signaling pathway 0.0164 11 569 48 -0.012 0.061 1000 -1000 -0.021 -1000
ceramide signaling pathway 0.0164 11 547 49 -0.008 0.03 1000 -1000 -0.032 -1000
FoxO family signaling 0.0164 11 760 64 -0.023 0.065 1000 -1000 -0.064 -1000
Wnt signaling 0.0164 11 81 7 0.013 0.028 1000 -1000 -0.004 -1000
Canonical NF-kappaB pathway 0.0149 10 423 39 -0.012 0.047 1000 -1000 -0.019 -1000
Arf6 trafficking events 0.0149 10 762 71 -0.038 0.039 1000 -1000 -0.027 -1000
Insulin Pathway 0.0149 10 803 74 -0.061 0.059 1000 -1000 -0.033 -1000
Regulation of Androgen receptor activity 0.0149 10 741 70 -0.048 0.042 1000 -1000 -0.039 -1000
ErbB4 signaling events 0.0135 9 631 69 -0.032 0.053 1000 -1000 -0.027 -1000
Arf6 downstream pathway 0.0135 9 413 43 -0.034 0.039 1000 -1000 -0.022 -1000
IL27-mediated signaling events 0.0135 9 479 51 -0.15 0.034 1000 -1000 -0.044 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0135 9 826 88 -0.017 0.068 1000 -1000 -0.065 -1000
mTOR signaling pathway 0.0120 8 458 53 -0.013 0.047 1000 -1000 -0.031 -1000
Atypical NF-kappaB pathway 0.0120 8 263 31 -0.012 0.039 1000 -1000 -0.011 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0120 8 380 45 -0.017 0.058 1000 -1000 -0.04 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0105 7 200 28 -0.01 0.04 1000 -1000 -0.014 -1000
Hedgehog signaling events mediated by Gli proteins 0.0105 7 456 65 -0.009 0.048 1000 -1000 -0.046 -1000
HIF-2-alpha transcription factor network 0.0105 7 307 43 -0.099 0.1 1000 -1000 -0.05 -1000
IGF1 pathway 0.0105 7 418 57 -0.026 0.057 1000 -1000 -0.027 -1000
S1P3 pathway 0.0105 7 322 42 0 0.042 1000 -1000 -0.037 -1000
Signaling events mediated by HDAC Class I 0.0075 5 527 104 -0.04 0.048 1000 -1000 -0.03 -1000
LPA4-mediated signaling events 0.0060 4 57 12 -0.01 0 1000 -1000 -0.01 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0045 3 88 23 -0.007 0.04 1000 -1000 -0.017 -1000
Signaling events mediated by HDAC Class II 0.0045 3 226 75 -0.024 0.056 1000 -1000 -0.016 -1000
Arf1 pathway 0.0045 3 213 54 -0.015 0.036 1000 -1000 -0.011 -1000
Circadian rhythm pathway 0.0030 2 64 22 -0.007 0.044 1000 -1000 -0.035 -1000
Signaling mediated by p38-gamma and p38-delta 0.0030 2 36 15 -0.014 0.021 1000 -1000 -0.012 -1000
Class IB PI3K non-lipid kinase events 0.0015 1 3 3 -0.021 0.021 1000 -1000 -0.021 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 6 27 -0.014 0.05 1000 -1000 -0.019 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.05 1000 -1000 0 -1000
Total NA 4005 218601 7203 -7 8 131000 -131000 -4.2 -131000
Ephrin A reverse signaling

Figure S1.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S1.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.039 0.092 -9999 0 -0.15 240 240
EFNA5 0.018 0.007 -9999 0 -10000 0 0
FYN -0.058 0.067 -9999 0 -0.14 234 234
neuron projection morphogenesis -0.039 0.092 -9999 0 -0.15 240 240
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.038 0.092 -9999 0 -0.15 240 240
EPHA5 0.014 0.01 -9999 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 0.27 0.21 0.6 114 -10000 0 114
PLK1 0.1 0.1 -10000 0 -0.55 1 1
BIRC5 0.13 0.1 -10000 0 -0.88 1 1
HSPA1B 0.27 0.21 0.6 116 -10000 0 116
MAP2K1 0.068 0.045 0.12 203 -10000 0 203
BRCA2 0.28 0.22 0.62 122 -10000 0 122
FOXM1 0.3 0.23 0.65 121 -10000 0 121
XRCC1 0.28 0.22 0.63 116 -10000 0 116
FOXM1B/p19 0.11 0.17 0.56 33 -10000 0 33
Cyclin D1/CDK4 0.23 0.2 0.55 102 -10000 0 102
CDC2 0.29 0.22 0.6 140 -10000 0 140
TGFA 0.25 0.2 0.54 142 -10000 0 142
SKP2 0.27 0.21 0.59 129 -10000 0 129
CCNE1 0.029 0.015 0.067 2 -10000 0 2
CKS1B 0.27 0.21 0.57 144 -10000 0 144
RB1 0.14 0.16 0.41 121 -0.53 1 122
FOXM1C/SP1 0.28 0.2 0.59 106 -10000 0 106
AURKB 0.14 0.11 -10000 0 -0.71 3 3
CENPF 0.28 0.22 0.63 115 -10000 0 115
CDK4 0.04 0.037 0.13 69 -10000 0 69
MYC 0.25 0.2 0.54 144 -10000 0 144
CHEK2 0.084 0.074 0.18 205 -10000 0 205
ONECUT1 0.26 0.2 0.56 138 -10000 0 138
CDKN2A 0.024 0.053 0.1 180 -0.03 125 305
LAMA4 0.27 0.21 0.6 119 -10000 0 119
FOXM1B/HNF6 0.27 0.21 0.6 110 -10000 0 110
FOS 0.26 0.24 0.6 121 -0.92 6 127
SP1 0.025 0.007 -10000 0 -10000 0 0
CDC25B 0.28 0.22 0.63 124 -10000 0 124
response to radiation 0.042 0.034 0.069 321 -10000 0 321
CENPB 0.28 0.22 0.62 125 -10000 0 125
CENPA 0.29 0.22 0.61 135 -10000 0 135
NEK2 0.27 0.25 0.63 119 -0.99 8 127
HIST1H2BA 0.27 0.21 0.6 115 -10000 0 115
CCNA2 0.066 0.058 0.15 223 -10000 0 223
EP300 0.02 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.28 0.21 0.64 104 -10000 0 104
CCNB2 0.3 0.22 0.6 147 -10000 0 147
CCNB1 0.29 0.22 0.62 126 -10000 0 126
ETV5 0.27 0.21 0.61 114 -10000 0 114
ESR1 0.27 0.21 0.6 118 -0.83 1 119
CCND1 0.26 0.21 0.56 142 -10000 0 142
GSK3A 0.055 0.039 0.11 144 -10000 0 144
Cyclin A-E1/CDK1-2 0.11 0.097 0.24 208 -10000 0 208
CDK2 0.061 0.057 0.15 198 -10000 0 198
G2/M transition of mitotic cell cycle 0.049 0.042 0.083 313 -10000 0 313
FOXM1B/Cbp/p300 0.25 0.19 0.56 96 -10000 0 96
GAS1 0.28 0.22 0.61 126 -10000 0 126
MMP2 0.28 0.22 0.62 119 -10000 0 119
RB1/FOXM1C 0.21 0.2 0.55 103 -10000 0 103
CREBBP 0.021 0.002 -10000 0 -10000 0 0
Aurora B 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
Condensin I complex 0.063 0.043 0.13 102 -0.16 1 103
STMN1 0.034 0.026 0.051 460 -10000 0 460
Aurora B/RasGAP/Survivin 0.13 0.058 0.17 365 -10000 0 365
Chromosomal passenger complex/Cul3 protein complex 0.027 0.047 0.14 3 -0.3 2 5
BIRC5 0.081 0.053 0.13 369 -10000 0 369
DES -0.049 0.25 -10000 0 -0.49 153 153
Aurora C/Aurora B/INCENP 0.08 0.042 0.14 40 -10000 0 40
Aurora B/TACC1 0.078 0.03 0.1 79 -10000 0 79
Aurora B/PP2A 0.087 0.032 0.12 3 -10000 0 3
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.018 0.008 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition -0.003 0.002 -10000 0 -10000 0 0
NDC80 0.072 0.047 0.092 522 -10000 0 522
Cul3 protein complex 0.036 0.016 -10000 0 -10000 0 0
KIF2C 0.061 0.046 0.11 146 -0.18 2 148
PEBP1 0.022 0.003 -10000 0 -10000 0 0
KIF20A 0.088 0.049 0.12 439 -0.017 1 440
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.087 0.032 0.11 9 -10000 0 9
SEPT1 0.021 0.004 0.12 1 -10000 0 1
SMC2 0.021 0.003 -10000 0 -10000 0 0
SMC4 0.037 0.037 0.12 101 -10000 0 101
NSUN2/NPM1/Nucleolin 0.058 0.068 0.29 2 -0.5 6 8
PSMA3 0.02 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.002 0.002 -10000 0 -10000 0 0
H3F3B 0.039 0.018 -10000 0 -10000 0 0
AURKB 0.1 0.043 0.12 514 -10000 0 514
AURKC 0.022 0.019 0.12 20 -10000 0 20
CDCA8 0.058 0.052 0.13 233 -10000 0 233
cytokinesis 0.067 0.07 0.16 145 -0.21 1 146
Aurora B/Septin1 0.1 0.08 0.21 54 -0.24 2 56
AURKA 0.04 0.042 0.12 134 -10000 0 134
INCENP 0.023 0.004 -10000 0 -10000 0 0
KLHL13 0.022 0.008 0.12 4 -10000 0 4
BUB1 0.089 0.048 0.12 446 -10000 0 446
hSgo1/Aurora B/Survivin 0.16 0.082 0.21 438 -10000 0 438
EVI5 0.02 0.008 -10000 0 -10000 0 0
RhoA/GTP 0.1 0.067 0.18 230 -0.26 1 231
SGOL1 0.087 0.05 0.12 421 -10000 0 421
CENPA 0.074 0.052 0.14 150 -0.29 2 152
NCAPG 0.1 0.041 0.12 537 -10000 0 537
Aurora B/HC8 Proteasome 0.085 0.034 0.11 20 -10000 0 20
NCAPD2 0.02 0.006 0.12 1 -10000 0 1
Aurora B/PP1-gamma 0.087 0.032 0.11 100 -10000 0 100
RHOA 0.021 0.003 -10000 0 -10000 0 0
NCAPH 0.061 0.05 0.12 255 -10000 0 255
NPM1 0.046 0.053 -10000 0 -0.34 7 7
RASA1 0.021 0.002 -10000 0 -10000 0 0
KLHL9 0.018 0.008 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.085 0.034 0.11 20 -10000 0 20
PPP1CC 0.021 0.003 -10000 0 -10000 0 0
Centraspindlin 0.1 0.074 0.19 237 -0.3 1 238
RhoA/GDP 0.015 0.002 -10000 0 -10000 0 0
NSUN2 0.046 0.053 -10000 0 -0.36 6 6
MYLK 0.04 0.017 -10000 0 -10000 0 0
KIF23 0.067 0.052 0.13 277 -10000 0 277
VIM 0.042 0.038 0.064 450 -10000 0 450
RACGAP1 0.025 0.015 0.13 12 -10000 0 12
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.046 0.055 -10000 0 -0.34 7 7
Chromosomal passenger complex 0.068 0.053 0.12 236 -0.27 2 238
Chromosomal passenger complex/EVI5 0.14 0.088 0.22 348 -10000 0 348
TACC1 0.021 0.003 -10000 0 -10000 0 0
PPP2R5D 0.021 0.002 -10000 0 -10000 0 0
CUL3 0.021 0.002 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Glypican 2 network

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
MDK 0.05 0.047 0.12 188 -9999 0 188
GPC2 0.047 0.05 0.12 193 -9999 0 193
GPC2/Midkine 0.057 0.051 0.18 37 -9999 0 37
neuron projection morphogenesis 0.057 0.051 0.18 37 -9999 0 37
Effects of Botulinum toxin

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
STX1A -0.002 0.003 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B -0.03 0.086 -10000 0 -0.16 212 212
STXBP1 0.018 0.008 -10000 0 -10000 0 0
ACh/CHRNA1 -0.015 0.069 0.1 92 -0.088 253 345
RAB3GAP2/RIMS1/UNC13B -0.014 0.08 -10000 0 -0.13 208 208
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 0.014 0.01 -10000 0 -10000 0 0
mol:ACh -0.041 0.064 0.097 45 -0.11 255 300
RAB3GAP2 0.021 0.003 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.096 0.13 -10000 0 -0.24 271 271
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.015 0.069 0.1 92 -0.087 253 345
UNC13B 0.02 0.005 -10000 0 -10000 0 0
CHRNA1 0.041 0.042 0.12 132 -10000 0 132
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.072 0.11 0.099 1 -0.21 249 250
SNAP25 -0.092 0.098 -10000 0 -0.19 318 318
VAMP2 0.003 0 -10000 0 -10000 0 0
SYT1 0.007 0.01 -10000 0 -10000 0 0
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 -0.056 0.084 -10000 0 -0.15 285 285
STX1A/SNAP25 fragment 1/VAMP2 -0.096 0.13 -10000 0 -0.24 271 271
Retinoic acid receptors-mediated signaling

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
HDAC1 0.019 0.006 -10000 0 -10000 0 0
HDAC3 0.021 0.002 -10000 0 -10000 0 0
VDR 0.023 0.017 0.12 16 -10000 0 16
Cbp/p300/PCAF 0.041 0.01 -10000 0 -10000 0 0
EP300 0.02 0.004 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.041 0.058 -10000 0 -0.25 22 22
KAT2B 0.021 0.005 0.12 1 -10000 0 1
MAPK14 0.021 0.002 -10000 0 -10000 0 0
AKT1 -0.065 0.059 -10000 0 -0.22 33 33
RAR alpha/9cRA/Cyclin H -0.12 0.1 -10000 0 -0.3 55 55
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.043 0.05 -10000 0 -0.23 18 18
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.098 0.086 -10000 0 -0.15 419 419
NCOR2 0.021 0.002 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.014 0.025 0.089 16 -0.15 11 27
RXRs/RARs/NRIP1/9cRA -0.23 0.15 -10000 0 -0.33 411 411
NCOA2 0.02 0.005 -10000 0 -10000 0 0
NCOA3 0.02 0.004 -10000 0 -10000 0 0
NCOA1 0.021 0.002 -10000 0 -10000 0 0
VDR/VDR/DNA 0.023 0.017 0.12 16 -10000 0 16
RARG 0.021 0.008 0.12 3 -10000 0 3
RAR gamma1/9cRA 0.027 0.007 0.096 2 -10000 0 2
MAPK3 0.021 0.002 -10000 0 -10000 0 0
MAPK1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 0.019 0.006 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.23 0.15 -10000 0 -0.32 476 476
RARA -0.095 0.09 -10000 0 -0.17 372 372
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.044 0.055 -10000 0 -0.23 28 28
PRKCA 0.021 0.004 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.22 0.15 -10000 0 -0.32 410 410
RXRG -0.14 0.12 -10000 0 -0.23 414 414
RXRA -0.092 0.083 -10000 0 -0.15 400 400
RXRB -0.13 0.11 -10000 0 -0.21 414 414
VDR/Vit D3/DNA 0.014 0.025 0.089 16 -0.15 11 27
RBP1 0.033 0.034 0.12 80 -10000 0 80
CRBP1/9-cic-RA 0.024 0.024 0.089 80 -10000 0 80
RARB 0.021 0.002 -10000 0 -10000 0 0
PRKCG 0.005 0.009 -10000 0 -10000 0 0
MNAT1 0.02 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.25 0.16 -10000 0 -0.35 460 460
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.2 0.14 -10000 0 -0.28 419 419
proteasomal ubiquitin-dependent protein catabolic process -0.087 0.078 -10000 0 -0.26 53 53
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.22 0.15 -10000 0 -0.32 409 409
positive regulation of DNA binding -0.11 0.093 -10000 0 -0.28 55 55
NRIP1 -0.2 0.14 -10000 0 -0.43 48 48
RXRs/RARs -0.22 0.15 -10000 0 -0.31 421 421
RXRs/RXRs/DNA/9cRA -0.24 0.15 -10000 0 -0.32 477 477
PRKACA 0.02 0.004 -10000 0 -10000 0 0
CDK7 0.021 0.003 -10000 0 -10000 0 0
TFIIH 0.04 0.01 -10000 0 -10000 0 0
RAR alpha/9cRA -0.085 0.084 -10000 0 -0.23 48 48
CCNH 0.021 0.002 -10000 0 -10000 0 0
CREBBP 0.021 0.002 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.037 0.014 -10000 0 -10000 0 0
Reelin 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
CDK5R1/CDK5 0.012 0.047 -10000 0 -0.16 44 44
VLDLR 0.02 0.006 -10000 0 -10000 0 0
CRKL 0.021 0.005 0.12 1 -10000 0 1
LRPAP1 0.021 0.003 -10000 0 -10000 0 0
FYN 0.02 0.004 -10000 0 -10000 0 0
ITGA3 0.023 0.016 0.12 16 -10000 0 16
RELN/VLDLR/Fyn -0.018 0.075 -10000 0 -0.13 191 191
MAPK8IP1/MKK7/MAP3K11/JNK1 0.053 0.027 -10000 0 -0.12 5 5
AKT1 -0.068 0.099 -10000 0 -0.19 228 228
MAP2K7 0.021 0.003 -10000 0 -10000 0 0
RAPGEF1 0.021 0.003 -10000 0 -10000 0 0
DAB1 0.015 0.01 -10000 0 -10000 0 0
RELN/LRP8/DAB1 -0.033 0.081 -10000 0 -0.13 245 245
LRPAP1/LRP8 0.028 0.01 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.028 0.081 -10000 0 -0.13 242 242
DAB1/alpha3/beta1 Integrin -0.028 0.078 -10000 0 -0.13 205 205
long-term memory -0.11 0.13 -10000 0 -0.22 365 365
DAB1/LIS1 -0.024 0.085 -10000 0 -0.13 212 212
DAB1/CRLK/C3G -0.028 0.08 -10000 0 -0.13 209 209
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
DAB1/NCK2 -0.024 0.085 -10000 0 -0.13 238 238
ARHGEF2 0.021 0.003 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.01 0.011 -10000 0 -10000 0 0
CDK5R1 0.019 0.006 -10000 0 -10000 0 0
RELN 0.011 0.011 -10000 0 -10000 0 0
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.018 0.073 -10000 0 -0.13 189 189
GRIN2A/RELN/LRP8/DAB1/Fyn -0.067 0.12 -10000 0 -0.18 305 305
MAPK8 0.019 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.034 0.08 -10000 0 -0.13 246 246
ITGB1 0.021 0.016 0.12 12 -10000 0 12
MAP1B -0.058 0.069 0.15 1 -0.15 212 213
RELN/LRP8 -0.017 0.073 -10000 0 -0.13 189 189
GRIN2B/RELN/LRP8/DAB1/Fyn -0.075 0.11 -10000 0 -0.17 337 337
PI3K 0.03 0.006 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.031 0.021 0.13 20 -10000 0 20
RAP1A -0.023 0.1 0.17 91 -0.2 40 131
PAFAH1B1 0.021 0.002 -10000 0 -10000 0 0
MAPK8IP1 0.02 0.004 -10000 0 -10000 0 0
CRLK/C3G 0.03 0.007 0.11 1 -10000 0 1
GRIN2B 0.009 0.01 -10000 0 -10000 0 0
NCK2 0.021 0.001 -10000 0 -10000 0 0
neuron differentiation -0.062 0.11 -10000 0 -0.27 101 101
neuron adhesion -0.023 0.1 0.2 43 -0.19 38 81
LRP8 0.019 0.007 -10000 0 -10000 0 0
GSK3B -0.07 0.093 -10000 0 -0.19 227 227
RELN/VLDLR/DAB1/Fyn -0.029 0.081 -10000 0 -0.13 245 245
MAP3K11 0.021 0.003 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.067 0.11 -10000 0 -0.2 240 240
CDK5 0.017 0.009 -10000 0 -10000 0 0
MAPT 0.009 0.072 0.8 5 -10000 0 5
neuron migration -0.085 0.13 0.2 34 -0.24 232 266
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.049 0.099 -10000 0 -0.26 72 72
RELN/VLDLR -0.01 0.072 -10000 0 -0.12 190 190
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.042 0.086 0.11 1 -0.16 233 234
CRKL -0.045 0.14 0.22 22 -0.41 23 45
mol:PIP3 0.008 0.037 -10000 0 -0.91 1 1
AKT1 0.002 0.041 -10000 0 -0.8 1 1
PTK2B 0.021 0.003 -10000 0 -10000 0 0
RAPGEF1 -0.042 0.13 0.27 12 -0.39 23 35
RANBP10 0.021 0.002 -10000 0 -10000 0 0
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.028 0.081 -10000 0 -0.14 229 229
MAP3K5 -0.047 0.14 0.23 12 -0.38 51 63
HGF/MET/CIN85/CBL/ENDOPHILINS -0.019 0.08 -10000 0 -0.12 226 226
AP1 0.013 0.063 0.13 94 -0.16 6 100
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.023 0.016 0.12 16 -10000 0 16
apoptosis -0.094 0.3 -10000 0 -0.78 100 100
STAT3 (dimer) -0.049 0.086 -10000 0 -0.17 208 208
GAB1/CRKL/SHP2/PI3K -0.028 0.14 0.29 3 -0.38 23 26
INPP5D 0.021 0.009 0.12 5 -10000 0 5
CBL/CRK -0.033 0.14 0.22 16 -0.38 24 40
PTPN11 0.021 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.02 0.004 -10000 0 -10000 0 0
PTEN 0.018 0.007 -10000 0 -10000 0 0
ELK1 0.041 0.17 0.35 142 -0.25 1 143
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.035 0.063 -10000 0 -0.21 23 23
PAK1 -0.023 0.059 -10000 0 -0.85 1 1
HGF/MET/RANBP10 -0.029 0.082 -10000 0 -0.14 231 231
HRAS -0.17 0.24 -10000 0 -0.49 236 236
DOCK1 -0.044 0.13 0.23 17 -0.39 23 40
GAB1 -0.051 0.13 -10000 0 -0.43 22 22
CRK -0.045 0.14 0.22 19 -0.41 23 42
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.14 0.21 -10000 0 -0.43 234 234
JUN 0.019 0.007 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.055 0.084 -10000 0 -0.17 228 228
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
cell morphogenesis -0.05 0.14 0.28 26 -0.36 19 45
GRB2/SHC -0.037 0.09 0.22 2 -0.16 223 225
FOS 0.021 0.013 0.12 8 -10000 0 8
GLMN 0.002 0.001 -10000 0 -10000 0 0
cell motility 0.04 0.17 0.35 142 -0.25 1 143
HGF/MET/MUC20 -0.033 0.074 0.096 6 -0.13 232 238
cell migration -0.036 0.089 0.21 2 -0.16 223 225
GRB2 0.02 0.004 -10000 0 -10000 0 0
CBL 0.021 0.003 -10000 0 -10000 0 0
MET/RANBP10 -0.042 0.086 0.11 1 -0.16 233 234
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.045 0.084 -10000 0 -0.16 214 214
MET/MUC20 -0.047 0.078 0.089 1 -0.15 234 235
RAP1B -0.039 0.13 0.31 16 -0.37 23 39
RAP1A -0.04 0.13 0.29 10 -0.36 23 33
HGF/MET/RANBP9 -0.029 0.082 -10000 0 -0.14 231 231
RAF1 -0.16 0.24 -10000 0 -0.46 239 239
STAT3 -0.049 0.086 -10000 0 -0.17 208 208
cell proliferation -0.085 0.14 0.21 14 -0.28 217 231
RPS6KB1 -0.024 0.047 -10000 0 -0.2 5 5
MAPK3 0.03 0.16 0.4 38 -10000 0 38
MAPK1 0.038 0.18 0.39 88 -10000 0 88
RANBP9 0.021 0.003 -10000 0 -10000 0 0
MAPK8 -0.062 0.13 0.27 3 -0.39 32 35
SRC -0.047 0.078 -10000 0 -0.16 210 210
PI3K -0.04 0.089 -10000 0 -0.16 231 231
MET/Glomulin -0.011 0.06 0.097 1 -0.17 70 71
SOS1 0.021 0.001 -10000 0 -10000 0 0
MAP2K1 -0.15 0.22 0.28 2 -0.43 238 240
MET 0.009 0.011 0.12 1 -10000 0 1
MAP4K1 -0.048 0.15 0.22 16 -0.4 52 68
PTK2 0.019 0.006 -10000 0 -10000 0 0
MAP2K2 -0.15 0.23 0.28 10 -0.43 238 248
BAD 0 0.043 -10000 0 -0.76 1 1
MAP2K4 -0.046 0.14 0.25 10 -0.35 51 61
SHP2/GRB2/SOS1/GAB1 -0.065 0.13 -10000 0 -0.24 207 207
INPPL1 0.021 0.003 -10000 0 -10000 0 0
PXN 0.021 0.002 -10000 0 -10000 0 0
SH3KBP1 0.021 0.001 -10000 0 -10000 0 0
HGS -0.053 0.075 0.073 1 -0.16 217 218
PLCgamma1/PKC 0.015 0.003 -10000 0 -10000 0 0
HGF 0.018 0.013 0.12 5 -10000 0 5
RASA1 0.021 0.002 -10000 0 -10000 0 0
NCK1 0.021 0.005 0.12 1 -10000 0 1
PTPRJ 0.021 0.003 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.039 0.088 -10000 0 -0.16 227 227
PDPK1 0.006 0.041 -10000 0 -0.84 1 1
HGF/MET/SHIP -0.028 0.082 -10000 0 -0.14 232 232
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.096 0.29 -10000 0 -0.79 95 95
MKNK1 0.019 0.006 -10000 0 -10000 0 0
MAPK14 -0.012 0.11 -10000 0 -0.27 96 96
ATF2/c-Jun -0.021 0.077 -10000 0 -0.22 75 75
MAPK11 -0.014 0.11 -10000 0 -0.27 96 96
MITF -0.027 0.12 -10000 0 -0.31 95 95
MAPKAPK5 -0.027 0.12 -10000 0 -0.31 96 96
KRT8 -0.023 0.12 -10000 0 -0.31 95 95
MAPKAPK3 0.021 0.003 -10000 0 -10000 0 0
MAPKAPK2 0.021 0.005 0.12 1 -10000 0 1
p38alpha-beta/CK2 -0.021 0.15 -10000 0 -0.38 96 96
CEBPB -0.026 0.12 -10000 0 -0.31 93 93
SLC9A1 -0.035 0.13 -10000 0 -0.34 96 96
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.021 0.12 -10000 0 -0.29 96 96
p38alpha-beta/MNK1 -0.007 0.12 -10000 0 -0.3 96 96
JUN -0.019 0.074 -10000 0 -0.22 75 75
PPARGC1A -0.029 0.12 -10000 0 -0.32 98 98
USF1 -0.027 0.12 -10000 0 -0.31 96 96
RAB5/GDP/GDI1 -0.016 0.092 -10000 0 -0.23 97 97
NOS2 -0.032 0.15 -10000 0 -0.36 93 93
DDIT3 -0.026 0.12 -10000 0 -0.31 92 92
RAB5A 0.021 0.002 -10000 0 -10000 0 0
HSPB1 0.01 0.14 0.27 90 -0.26 85 175
p38alpha-beta/HBP1 -0.006 0.12 -10000 0 -0.3 80 80
CREB1 -0.03 0.13 -10000 0 -0.34 94 94
RAB5/GDP 0.015 0.002 -10000 0 -10000 0 0
EIF4E -0.048 0.092 -10000 0 -0.27 95 95
RPS6KA4 -0.027 0.12 -10000 0 -0.31 95 95
PLA2G4A -0.047 0.092 -10000 0 -0.27 95 95
GDI1 -0.027 0.12 -10000 0 -0.31 96 96
TP53 -0.044 0.14 -10000 0 -0.38 95 95
RPS6KA5 -0.029 0.12 -10000 0 -0.32 95 95
ESR1 -0.029 0.12 -10000 0 -0.32 96 96
HBP1 0.017 0.01 0.12 1 -10000 0 1
MEF2C -0.031 0.13 -10000 0 -0.34 93 93
MEF2A -0.028 0.12 -10000 0 -0.32 96 96
EIF4EBP1 -0.024 0.13 -10000 0 -0.34 95 95
KRT19 -0.038 0.13 -10000 0 -0.31 116 116
ELK4 -0.027 0.12 -10000 0 -0.31 95 95
ATF6 -0.027 0.12 -10000 0 -0.31 96 96
ATF1 -0.032 0.13 -10000 0 -0.34 95 95
p38alpha-beta/MAPKAPK2 -0.003 0.13 -10000 0 -0.3 96 96
p38alpha-beta/MAPKAPK3 -0.002 0.13 -10000 0 -0.3 95 95
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.02 0.004 -10000 0 -10000 0 0
EPHB2 0.018 0.006 -10000 0 -10000 0 0
EFNB1 -0.007 0.014 0.051 1 -0.14 5 6
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.033 0.074 -10000 0 -0.11 290 290
Ephrin B2/EPHB1-2 0.033 0.02 -10000 0 -0.11 6 6
neuron projection morphogenesis -0.037 0.065 -10000 0 -0.11 290 290
Ephrin B1/EPHB1-2/Tiam1 -0.043 0.078 -10000 0 -0.12 338 338
DNM1 0.009 0.01 -10000 0 -10000 0 0
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.007 0.042 -10000 0 -0.41 7 7
YES1 0.005 0.068 -10000 0 -0.64 7 7
Ephrin B1/EPHB1-2/NCK2 -0.044 0.078 -10000 0 -0.12 344 344
PI3K 0.027 0.047 -10000 0 -0.39 8 8
mol:GDP -0.043 0.077 -10000 0 -0.12 338 338
ITGA2B 0.021 0.003 -10000 0 -10000 0 0
endothelial cell proliferation 0.023 0.016 0.095 12 -0.13 1 13
FYN 0.003 0.07 -10000 0 -0.63 7 7
MAP3K7 -0.005 0.044 -10000 0 -0.43 7 7
FGR 0.006 0.068 -10000 0 -0.64 7 7
TIAM1 0.02 0.004 -10000 0 -10000 0 0
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
RGS3 0.021 0.003 -10000 0 -10000 0 0
cell adhesion 0.019 0.048 -10000 0 -0.39 7 7
LYN 0.007 0.066 -10000 0 -0.62 7 7
Ephrin B1/EPHB1-2/Src Family Kinases 0.001 0.059 -10000 0 -0.56 7 7
Ephrin B1/EPHB1-2 -0.001 0.048 -10000 0 -0.47 7 7
SRC 0.006 0.065 -10000 0 -0.62 7 7
ITGB3 0.04 0.04 0.12 124 -10000 0 124
EPHB1 0.022 0.011 0.13 7 -10000 0 7
EPHB4 0.019 0.017 0.12 13 -10000 0 13
RAC1 0.018 0.008 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.023 0.017 0.096 12 -0.13 1 13
alphaIIb/beta3 Integrin 0.043 0.036 0.11 123 -0.15 7 130
BLK 0.011 0.066 -10000 0 -0.62 7 7
HCK 0.008 0.065 -10000 0 -0.62 7 7
regulation of stress fiber formation 0.044 0.077 0.12 344 -10000 0 344
MAPK8 -0.01 0.042 0.18 2 -0.39 7 9
Ephrin B1/EPHB1-2/RGS3 -0.044 0.078 -10000 0 -0.12 344 344
endothelial cell migration 0.027 0.083 0.19 121 -0.35 6 127
NCK2 0.021 0.001 -10000 0 -10000 0 0
PTPN13 0.023 0.007 0.13 1 -10000 0 1
regulation of focal adhesion formation 0.044 0.077 0.12 344 -10000 0 344
chemotaxis 0.044 0.077 0.12 344 -10000 0 344
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
Rac1/GTP -0.035 0.069 -10000 0 -0.11 290 290
angiogenesis -0.001 0.048 -10000 0 -0.46 7 7
LCK 0.011 0.069 -10000 0 -0.64 7 7
Visual signal transduction: Rods

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
mol:K + 0.021 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.015 0.004 0.089 1 -10000 0 1
Metarhodopsin II/Arrestin -0.019 0.069 -10000 0 -0.13 186 186
PDE6G/GNAT1/GTP 0.039 0.027 0.096 87 -10000 0 87
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.02 0.005 0.12 1 -10000 0 1
GRK1 0.02 0.006 0.12 1 -10000 0 1
CNG Channel -0.049 0.076 -10000 0 -0.11 369 369
mol:Na + -0.092 0.09 -10000 0 -0.15 465 465
mol:ADP 0.02 0.006 0.12 1 -10000 0 1
RGS9-1/Gbeta5/R9AP 0.04 0.026 -10000 0 -0.12 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.092 0.095 -10000 0 -0.15 465 465
CNGB1 0.007 0.009 -10000 0 -10000 0 0
RDH5 0.028 0.028 0.12 51 -10000 0 51
SAG 0.016 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.11 0.073 0.19 9 -0.2 170 179
Na + (4 Units) -0.092 0.085 -10000 0 -0.14 435 435
RGS9 0.027 0.026 0.12 43 -10000 0 43
GNB1/GNGT1 0.019 0.012 -10000 0 -10000 0 0
GNAT1/GDP 0.045 0.026 -10000 0 -0.1 4 4
GUCY2D 0.021 0.014 0.12 11 -10000 0 11
GNGT1 0.012 0.006 -10000 0 -10000 0 0
GUCY2F 0.02 0.01 0.12 6 -10000 0 6
GNB5 0.021 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) 0.016 0.032 0.095 22 -0.11 18 40
mol:11-cis-retinal 0.028 0.028 0.12 51 -10000 0 51
mol:cGMP -0.021 0.077 -10000 0 -0.12 250 250
GNB1 0.019 0.007 -10000 0 -10000 0 0
Rhodopsin -0.019 0.086 0.1 24 -0.16 184 208
SLC24A1 0.021 0.003 -10000 0 -10000 0 0
CNGA1 0.021 0.009 0.12 4 -10000 0 4
Metarhodopsin II -0.014 0.062 0.091 1 -0.11 183 184
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family -0.016 0.085 -10000 0 -0.12 251 251
RGS9BP 0.019 0.006 -10000 0 -10000 0 0
Metarhodopsin II/Transducin -0.024 0.064 -10000 0 -0.16 123 123
GCAP Family/Ca ++ -0.022 0.076 -10000 0 -0.12 251 251
PDE6A/B 0.03 0.038 -10000 0 -0.16 19 19
mol:Pi 0.04 0.026 -10000 0 -0.12 4 4
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.026 0.017 -10000 0 -10000 0 0
PDE6B 0.02 0.004 -10000 0 -10000 0 0
PDE6A 0.029 0.028 0.12 52 -10000 0 52
PDE6G 0.039 0.04 0.12 120 -10000 0 120
RHO 0.014 0.009 -10000 0 -10000 0 0
PDE6 0.063 0.05 0.17 22 -0.11 19 41
GUCA1A 0.012 0.01 -10000 0 -10000 0 0
GC2/GCAP Family -0.016 0.084 -10000 0 -0.12 250 250
GUCA1C 0.017 0.005 0.12 1 -10000 0 1
GUCA1B 0.021 0.002 -10000 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.021 0.003 -10000 0 -9999 0 0
Aurora C/Aurora B/INCENP 0.079 0.042 0.17 17 -9999 0 17
metaphase 0 0 -10000 0 -9999 0 0
mitosis 0 0 -10000 0 -9999 0 0
H3F3B 0.011 0.005 -10000 0 -9999 0 0
AURKB 0.1 0.043 0.12 514 -9999 0 514
AURKC 0.022 0.019 0.12 20 -9999 0 20
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.081 0.074 0.26 2 -0.26 2 4
SMARCC2 0.021 0.004 -10000 0 -10000 0 0
SMARCC1 0.021 0.005 0.12 1 -10000 0 1
TBX21 -0.049 0.093 -10000 0 -0.25 60 60
SUMO2 0.019 0.009 -10000 0 -0.026 19 19
STAT1 (dimer) 0.027 0.016 0.15 7 -10000 0 7
FKBP4 0.02 0.005 -10000 0 -10000 0 0
FKBP5 0.026 0.023 0.12 35 -10000 0 35
GR alpha/HSP90/FKBP51/HSP90 0.11 0.081 0.22 158 -10000 0 158
PRL -0.084 0.08 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.21 0.18 0.41 217 -10000 0 217
RELA -0.04 0.094 -10000 0 -0.16 250 250
FGG 0.19 0.16 0.37 206 -10000 0 206
GR beta/TIF2 0.11 0.09 0.22 180 -0.18 3 183
IFNG -0.21 0.2 -10000 0 -0.44 236 236
apoptosis 0.039 0.086 0.45 2 -0.38 2 4
CREB1 0.023 0.007 -10000 0 -10000 0 0
histone acetylation -0.1 0.097 -10000 0 -0.26 97 97
BGLAP -0.097 0.098 -10000 0 -0.32 18 18
GR/PKAc 0.1 0.08 0.22 114 -10000 0 114
NF kappa B1 p50/RelA -0.064 0.16 0.22 2 -0.26 242 244
SMARCD1 0.021 0.004 -10000 0 -10000 0 0
MDM2 0.085 0.073 0.17 203 -10000 0 203
GATA3 0.039 0.043 0.13 122 -10000 0 122
AKT1 0.019 0.005 -10000 0 -0.049 1 1
CSF2 -0.11 0.094 -10000 0 -0.48 1 1
GSK3B 0.019 0.009 -10000 0 -0.026 20 20
NR1I3 0.041 0.083 0.42 2 -10000 0 2
CSN2 0.16 0.14 0.31 235 -10000 0 235
BRG1/BAF155/BAF170/BAF60A 0.052 0.015 -10000 0 -10000 0 0
NFATC1 0.02 0.004 -10000 0 -10000 0 0
POU2F1 0.022 0.008 0.12 3 -10000 0 3
CDKN1A 0.021 0.042 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.003 -10000 0 -10000 0 0
SFN 0.022 0.02 0.12 23 -10000 0 23
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.11 0.081 0.22 138 -10000 0 138
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.025 0.14 0.41 2 -0.67 20 22
JUN -0.11 0.14 -10000 0 -0.29 208 208
IL4 -0.11 0.098 -10000 0 -0.33 20 20
CDK5R1 0.018 0.009 -10000 0 -0.019 20 20
PRKACA 0.02 0.004 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.04 0.057 -10000 0 -0.18 56 56
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.11 0.081 0.22 124 -10000 0 124
cortisol/GR alpha (monomer) 0.24 0.2 0.47 200 -10000 0 200
NCOA2 0.02 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.04 0.071 0.13 5 -0.11 279 284
AP-1/NFAT1-c-4 -0.21 0.22 -10000 0 -0.42 314 314
AFP -0.14 0.12 -10000 0 -0.5 3 3
SUV420H1 0.021 0.003 -10000 0 -10000 0 0
IRF1 0.15 0.11 0.31 104 -10000 0 104
TP53 0.043 0.036 -10000 0 -10000 0 0
PPP5C 0.019 0.007 -10000 0 -10000 0 0
KRT17 -0.45 0.43 -10000 0 -0.9 303 303
KRT14 -0.095 0.093 -10000 0 -0.41 1 1
TBP 0.022 0.006 -10000 0 -10000 0 0
CREBBP 0.017 0.018 -10000 0 -10000 0 0
HDAC1 0.018 0.007 -10000 0 -10000 0 0
HDAC2 0.02 0.004 -10000 0 -10000 0 0
AP-1 -0.21 0.22 -10000 0 -0.42 315 315
MAPK14 0.019 0.008 -10000 0 -0.024 20 20
MAPK10 0.019 0.008 -10000 0 -0.024 19 19
MAPK11 0.019 0.009 -10000 0 -0.026 20 20
KRT5 -0.3 0.35 -10000 0 -0.74 210 210
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
NCOA1 0.022 0.002 -10000 0 -10000 0 0
STAT1 0.027 0.016 0.15 7 -10000 0 7
CGA -0.1 0.099 -10000 0 -0.32 25 25
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.084 0.086 0.27 16 -10000 0 16
MAPK3 0.02 0.008 -10000 0 -0.024 20 20
MAPK1 0.019 0.008 -10000 0 -0.024 20 20
ICAM1 -0.16 0.18 -10000 0 -0.42 147 147
NFKB1 -0.04 0.095 -10000 0 -0.16 250 250
MAPK8 -0.11 0.12 -10000 0 -0.25 223 223
MAPK9 0.019 0.008 -10000 0 -0.024 11 11
cortisol/GR alpha (dimer) 0.038 0.087 0.46 2 -0.39 2 4
BAX -0.001 0.064 -10000 0 -10000 0 0
POMC -0.13 0.14 0.93 1 -1.2 4 5
EP300 0.016 0.018 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.23 0.18 0.43 209 -10000 0 209
proteasomal ubiquitin-dependent protein catabolic process 0.065 0.077 0.2 83 -10000 0 83
SGK1 0.037 0.058 -10000 0 -10000 0 0
IL13 -0.17 0.18 -10000 0 -0.48 88 88
IL6 -0.21 0.3 -10000 0 -0.67 161 161
PRKACG 0.019 0.009 0.12 4 -10000 0 4
IL5 -0.14 0.15 -10000 0 -0.54 21 21
IL2 -0.22 0.2 -10000 0 -0.47 171 171
CDK5 0.015 0.01 -10000 0 -10000 0 0
PRKACB 0.018 0.007 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
IL8 -0.22 0.28 -10000 0 -0.65 157 157
CDK5R1/CDK5 0.01 0.047 -10000 0 -0.16 44 44
NF kappa B1 p50/RelA/PKAc -0.026 0.13 0.21 2 -0.21 170 172
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.19 0.18 0.39 213 -10000 0 213
SMARCA4 0.021 0.004 -10000 0 -10000 0 0
chromatin remodeling 0.13 0.11 0.28 167 -10000 0 167
NF kappa B1 p50/RelA/Cbp -0.036 0.14 -10000 0 -0.27 82 82
JUN (dimer) -0.11 0.14 -10000 0 -0.29 205 205
YWHAH 0.02 0.005 -10000 0 -10000 0 0
VIPR1 -0.17 0.26 -10000 0 -0.56 203 203
NR3C1 0.14 0.13 0.29 204 -10000 0 204
NR4A1 0.021 0.032 -10000 0 -0.43 3 3
TIF2/SUV420H1 0.027 0.025 -10000 0 -0.16 11 11
MAPKKK cascade 0.039 0.086 0.45 2 -0.38 2 4
cortisol/GR alpha (dimer)/Src-1 0.22 0.18 0.42 200 -10000 0 200
PBX1 0.021 0.003 -10000 0 -10000 0 0
POU1F1 0.018 0.004 -10000 0 -10000 0 0
SELE -0.27 0.33 -10000 0 -0.68 222 222
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.13 0.11 0.28 166 -10000 0 166
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.19 0.18 0.39 213 -10000 0 213
mol:cortisol 0.13 0.12 0.27 208 -10000 0 208
MMP1 -0.035 0.072 -10000 0 -0.44 1 1
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.028 0.013 0.17 2 -10000 0 2
NFATC2 0.01 0.12 0.32 4 -0.34 3 7
NFATC3 -0.045 0.11 -10000 0 -0.25 131 131
CD40LG -0.12 0.3 0.35 1 -0.7 132 133
ITCH -0.055 0.084 -10000 0 -0.16 249 249
CBLB -0.054 0.085 -10000 0 -0.16 240 240
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.047 0.2 0.33 3 -0.65 26 29
JUNB 0.021 0.006 0.12 1 -10000 0 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.063 0.1 -10000 0 -0.19 273 273
T cell anergy -0.11 0.14 -10000 0 -0.28 266 266
TLE4 -0.001 0.069 -10000 0 -0.25 1 1
Jun/NFAT1-c-4/p21SNFT -0.09 0.33 -10000 0 -0.73 132 132
AP-1/NFAT1-c-4 -0.093 0.36 0.43 3 -0.77 133 136
IKZF1 0 0.068 0.26 5 -0.25 1 6
T-helper 2 cell differentiation -0.015 0.16 -10000 0 -0.65 19 19
AP-1/NFAT1 0.025 0.092 0.26 5 -0.24 5 10
CALM1 -0.034 0.072 -10000 0 -0.12 257 257
EGR2 -0.11 0.29 -10000 0 -0.64 132 132
EGR3 -0.21 0.47 -10000 0 -1.1 133 133
NFAT1/FOXP3 0.032 0.094 0.29 7 -0.24 2 9
EGR1 0.019 0.012 0.12 2 -0.038 20 22
JUN 0.015 0.018 -10000 0 -0.053 5 5
EGR4 0.009 0.014 0.12 1 -0.039 17 18
mol:Ca2+ -0.044 0.057 -10000 0 -0.11 276 276
GBP3 0.019 0.081 0.24 10 -0.25 1 11
FOSL1 0.04 0.041 0.12 126 -10000 0 126
NFAT1-c-4/MAF/IRF4 -0.084 0.32 -10000 0 -0.71 132 132
DGKA -0.002 0.07 -10000 0 -0.25 1 1
CREM 0.019 0.007 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.098 0.33 -10000 0 -0.73 132 132
CTLA4 0.004 0.068 0.22 7 -10000 0 7
NFAT1-c-4 (dimer)/EGR1 -0.1 0.34 0.37 1 -0.75 132 133
NFAT1-c-4 (dimer)/EGR4 -0.17 0.33 -10000 0 -0.8 133 133
FOS 0.016 0.025 0.13 8 -0.09 6 14
IFNG -0.017 0.1 -10000 0 -0.46 5 5
T cell activation -0.025 0.14 -10000 0 -0.48 6 6
MAF 0.021 0.002 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.1 0.24 0.57 134 -10000 0 134
TNF -0.18 0.32 -10000 0 -0.77 135 135
FASLG -0.18 0.41 -10000 0 -0.97 133 133
TBX21 0.028 0.026 0.13 41 -10000 0 41
BATF3 0.022 0.013 0.12 10 -10000 0 10
PRKCQ 0.019 0.009 0.12 1 -10000 0 1
PTPN1 -0.002 0.071 -10000 0 -0.25 1 1
NFAT1-c-4/ICER1 -0.1 0.32 -10000 0 -0.73 131 131
GATA3 0.037 0.042 0.12 122 -10000 0 122
T-helper 1 cell differentiation -0.017 0.1 -10000 0 -0.45 5 5
IL2RA -0.04 0.21 0.33 4 -0.57 39 43
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.001 0.07 -10000 0 -10000 0 0
E2F1 0.026 0.016 0.15 7 -10000 0 7
PPARG 0.021 0.006 0.12 2 -10000 0 2
SLC3A2 -0.002 0.07 -10000 0 -0.25 1 1
IRF4 0.023 0.016 0.12 16 -10000 0 16
PTGS2 -0.14 0.32 0.35 1 -0.74 133 134
CSF2 -0.13 0.3 0.34 1 -0.7 133 134
JunB/Fra1/NFAT1-c-4 -0.075 0.32 0.4 1 -0.7 132 133
IL4 -0.016 0.17 -10000 0 -0.68 19 19
IL5 -0.13 0.3 0.34 1 -0.69 133 134
IL2 -0.026 0.14 -10000 0 -0.48 6 6
IL3 -0.011 0.075 -10000 0 -0.66 4 4
RNF128 -0.12 0.17 -10000 0 -0.34 257 257
NFATC1 -0.1 0.24 -10000 0 -0.58 134 134
CDK4 0.071 0.16 0.52 23 -10000 0 23
PTPRK -0.001 0.068 -10000 0 -0.23 1 1
IL8 -0.13 0.32 0.39 2 -0.72 133 135
POU2F1 0.021 0.007 0.12 3 -10000 0 3
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.002 0.076 0.16 110 -0.14 2 112
KIRREL 0.018 0.036 0.12 42 -0.037 102 144
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.002 0.076 0.14 2 -0.16 110 112
PLCG1 0.02 0.004 -10000 0 -10000 0 0
ARRB2 0.021 0.002 -10000 0 -10000 0 0
WASL 0.017 0.008 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.018 0.068 0.17 1 -0.12 110 111
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.016 0.066 -10000 0 -0.18 86 86
FYN -0.026 0.051 0.14 17 -0.12 108 125
mol:Ca2+ 0.016 0.066 0.17 2 -0.12 108 110
mol:DAG 0.017 0.067 0.17 2 -0.12 108 110
NPHS2 0.006 0.022 -10000 0 -0.039 110 110
mol:IP3 0.017 0.067 0.17 2 -0.12 108 110
regulation of endocytosis 0.011 0.062 -10000 0 -0.12 110 110
Nephrin/NEPH1/podocin/Cholesterol 0.009 0.061 0.16 2 -0.12 110 112
establishment of cell polarity -0.002 0.076 0.14 2 -0.16 110 112
Nephrin/NEPH1/podocin/NCK1-2 0.027 0.069 0.18 2 -0.12 109 111
Nephrin/NEPH1/beta Arrestin2 0.012 0.063 -10000 0 -0.12 110 110
NPHS1 0.015 0.01 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin 0.008 0.062 -10000 0 -0.12 110 110
TJP1 0.021 0.003 -10000 0 -10000 0 0
NCK1 0.021 0.005 0.12 1 -10000 0 1
NCK2 0.021 0.001 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.017 0.067 0.18 2 -0.12 108 110
CD2AP 0.021 0.002 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.018 0.067 0.18 2 -0.12 106 108
GRB2 0.02 0.004 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.024 0.048 0.14 18 -0.11 108 126
cytoskeleton organization -0.034 0.076 0.2 11 -0.21 84 95
Nephrin/NEPH1 0.004 0.052 0.088 29 -0.11 110 139
Nephrin/NEPH1/ZO-1 0.011 0.066 0.13 1 -0.13 110 111
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.27 0.44 -10000 0 -1.1 103 103
IL23A -0.29 0.46 -10000 0 -1.2 85 85
NF kappa B1 p50/RelA/I kappa B alpha -0.26 0.44 -10000 0 -1 126 126
positive regulation of T cell mediated cytotoxicity -0.3 0.48 -10000 0 -1.1 127 127
ITGA3 -0.27 0.42 -10000 0 -1.1 92 92
IL17F -0.19 0.29 0.4 1 -0.66 128 129
IL12B -0.007 0.045 0.12 11 -0.067 30 41
STAT1 (dimer) -0.28 0.47 -10000 0 -1.1 127 127
CD4 -0.26 0.42 -10000 0 -1 101 101
IL23 -0.28 0.45 -10000 0 -1.2 84 84
IL23R -0.12 0.31 -10000 0 -0.97 67 67
IL1B -0.31 0.5 -10000 0 -1.3 101 101
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.26 0.42 -10000 0 -1.1 92 92
TYK2 -0.006 0.036 -10000 0 -10000 0 0
STAT4 0.009 0.01 -10000 0 -10000 0 0
STAT3 0.021 0.002 -10000 0 -10000 0 0
IL18RAP 0.033 0.033 0.12 76 -0.016 3 79
IL12RB1 -0.006 0.036 0.09 2 -0.056 1 3
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.005 0.047 -10000 0 -0.19 1 1
IL23R/JAK2 -0.11 0.3 -10000 0 -1 50 50
positive regulation of chronic inflammatory response -0.3 0.48 -10000 0 -1.1 127 127
natural killer cell activation 0.004 0.007 -10000 0 -10000 0 0
JAK2 -0.005 0.045 0.1 10 -0.068 5 15
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
NFKB1 0.012 0.017 -10000 0 -10000 0 0
RELA 0.012 0.017 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.26 0.42 -10000 0 -1.1 85 85
ALOX12B -0.34 0.49 -10000 0 -1.1 158 158
CXCL1 -0.28 0.44 -10000 0 -1.1 105 105
T cell proliferation -0.3 0.48 -10000 0 -1.1 127 127
NFKBIA 0.012 0.019 0.13 3 -10000 0 3
IL17A -0.14 0.23 -10000 0 -0.53 97 97
PI3K -0.27 0.45 -10000 0 -1 127 127
IFNG -0.006 0.025 0.076 2 -0.091 19 21
STAT3 (dimer) -0.26 0.43 -10000 0 -0.99 127 127
IL18R1 0.024 0.016 0.12 16 -10000 0 16
IL23/IL23R/JAK2/TYK2/SOCS3 -0.18 0.3 -10000 0 -0.74 89 89
IL18/IL18R 0.056 0.036 0.19 22 -0.13 3 25
macrophage activation -0.015 0.02 -10000 0 -0.044 82 82
TNF -0.3 0.48 -10000 0 -1.2 95 95
STAT3/STAT4 -0.32 0.46 -10000 0 -1.1 137 137
STAT4 (dimer) -0.33 0.48 -10000 0 -1.1 137 137
IL18 0.026 0.021 0.12 29 -10000 0 29
IL19 -0.26 0.42 -10000 0 -1 99 99
STAT5A (dimer) -0.28 0.47 -10000 0 -1.1 127 127
STAT1 0.022 0.011 0.12 7 -10000 0 7
SOCS3 0.021 0.017 0.12 14 -10000 0 14
CXCL9 -0.26 0.42 -10000 0 -1 98 98
MPO -0.42 0.56 -10000 0 -1.1 238 238
positive regulation of humoral immune response -0.3 0.48 -10000 0 -1.1 127 127
IL23/IL23R/JAK2/TYK2 -0.31 0.51 -10000 0 -1.2 125 125
IL6 -0.32 0.53 0.54 1 -1.2 143 144
STAT5A 0.021 0.002 -10000 0 -10000 0 0
IL2 0.011 0.016 -10000 0 -0.024 11 11
positive regulation of tyrosine phosphorylation of STAT protein 0.004 0.007 -10000 0 -10000 0 0
CD3E -0.26 0.43 -10000 0 -1.1 96 96
keratinocyte proliferation -0.3 0.48 -10000 0 -1.1 127 127
NOS2 -0.27 0.43 -10000 0 -1.1 105 105
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.015 0.025 0.14 4 -0.092 6 10
BUB1B 0.011 0.043 0.1 32 -0.13 7 39
PLK1 -0.009 0.042 0.079 30 -0.077 145 175
PLK1S1 -0.001 0.03 0.098 4 -0.2 5 9
KIF2A -0.011 0.044 0.19 8 -0.099 15 23
regulation of mitotic centrosome separation -0.009 0.042 0.08 29 -0.077 145 174
GOLGA2 0.021 0.003 -10000 0 -10000 0 0
Hec1/SPC24 0.062 0.085 0.16 168 -0.098 7 175
WEE1 0.013 0.072 0.15 9 -0.3 19 28
cytokinesis 0.019 0.047 0.15 8 -0.16 6 14
PP2A-alpha B56 0.071 0.069 -10000 0 -0.51 6 6
AURKA 0.007 0.029 0.098 6 -10000 0 6
PICH/PLK1 0.018 0.066 0.1 169 -0.088 10 179
CENPE -0.01 0.04 0.082 15 -0.095 25 40
RhoA/GTP 0.015 0.002 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.011 0.044 0.19 8 -0.099 15 23
PPP2CA 0.021 0.002 -10000 0 -10000 0 0
FZR1 0.02 0.004 -10000 0 -10000 0 0
TPX2 0.01 0.034 0.11 24 -10000 0 24
PAK1 0.015 0.009 -10000 0 -10000 0 0
SPC24 0.044 0.044 0.12 154 -10000 0 154
FBXW11 0.021 0.003 -10000 0 -10000 0 0
CLSPN -0.018 0.082 0.1 5 -0.25 65 70
GORASP1 0.021 0.002 -10000 0 -10000 0 0
metaphase 0 0.002 0.014 4 -0.01 2 6
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.007 0.022 0.043 30 -0.041 147 177
G2 phase of mitotic cell cycle 0 0.002 0.012 10 -10000 0 10
STAG2 0.021 0.001 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.011 0.051 -10000 0 -0.51 6 6
spindle elongation -0.009 0.042 0.08 29 -0.077 145 174
ODF2 0.022 0.004 -10000 0 -10000 0 0
BUB1 0.064 0.069 -10000 0 -0.55 6 6
TPT1 -0.009 0.044 0.1 1 -0.19 28 29
CDC25C 0.023 0.044 0.13 1 -0.24 6 7
CDC25B 0.021 0.006 -10000 0 -0.02 4 4
SGOL1 0.015 0.025 0.092 6 -0.14 4 10
RHOA 0.021 0.003 -10000 0 -10000 0 0
CCNB1/CDK1 0.03 0.052 0.13 58 -0.12 6 64
CDC14B -0.006 0.004 0.015 1 -10000 0 1
CDC20 0.064 0.053 0.12 286 -10000 0 286
PLK1/PBIP1 0.003 0.039 0.073 37 -0.079 24 61
mitosis -0.003 0.003 0.016 2 -10000 0 2
FBXO5 -0.007 0.038 0.11 15 -0.11 12 27
CDC2 0.001 0.002 -10000 0 -0.01 6 6
NDC80 0.098 0.046 0.12 494 -10000 0 494
metaphase plate congression -0.02 0.079 -10000 0 -0.25 64 64
ERCC6L 0.025 0.061 0.14 82 -0.12 5 87
NLP/gamma Tubulin -0.007 0.026 0.057 11 -0.064 31 42
microtubule cytoskeleton organization -0.009 0.044 0.1 1 -0.19 28 29
G2/M transition DNA damage checkpoint 0.002 0.005 0.009 154 -10000 0 154
PPP1R12A 0.021 0.003 -10000 0 -10000 0 0
interphase 0.002 0.005 0.009 154 -10000 0 154
PLK1/PRC1-2 0.049 0.074 0.13 156 -0.094 14 170
GRASP65/GM130/RAB1/GTP/PLK1 0.014 0.05 -10000 0 -0.11 2 2
RAB1A 0.021 0.002 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.005 0.032 0.076 32 -0.067 31 63
mitotic prometaphase 0.002 0.005 0.018 64 -10000 0 64
proteasomal ubiquitin-dependent protein catabolic process 0.008 0.043 0.16 3 -0.22 13 16
microtubule-based process 0.04 0.069 0.1 321 -0.076 80 401
Golgi organization -0.009 0.042 0.08 29 -0.077 145 174
Cohesin/SA2 0.003 0.038 0.084 7 -0.084 6 13
PPP1CB/MYPT1 0.032 0.005 -10000 0 -10000 0 0
KIF20A 0.09 0.049 0.12 439 -10000 0 439
APC/C/CDC20 0.033 0.064 0.1 240 -0.069 95 335
PPP2R1A 0.019 0.007 -10000 0 -10000 0 0
chromosome segregation 0.003 0.039 0.072 37 -0.078 24 61
PRC1 0.025 0.02 0.12 26 -10000 0 26
ECT2 -0.01 0.044 0.15 14 -0.095 26 40
C13orf34 -0.008 0.035 0.07 30 -0.064 146 176
NUDC -0.02 0.079 -10000 0 -0.25 64 64
regulation of attachment of spindle microtubules to kinetochore 0.011 0.042 0.1 32 -0.13 7 39
spindle assembly -0.01 0.035 0.064 31 -0.066 144 175
spindle stabilization -0.001 0.03 0.098 4 -0.2 5 9
APC/C/HCDH1 0.017 0.004 -10000 0 -10000 0 0
MKLP2/PLK1 0.041 0.07 0.1 321 -0.076 80 401
CCNB1 0.032 0.032 0.13 69 -0.02 2 71
PPP1CB 0.022 0.002 -10000 0 -10000 0 0
BTRC 0.019 0.006 -10000 0 -10000 0 0
ROCK2 0 0.042 -10000 0 -0.29 6 6
TUBG1 -0.001 0.024 -10000 0 -0.25 1 1
G2/M transition of mitotic cell cycle 0.001 0.033 -10000 0 -0.12 6 6
MLF1IP 0.018 0.027 0.049 289 -10000 0 289
INCENP 0.022 0.003 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B 0.034 0.043 0.13 106 -10000 0 106
CDKN2C 0.041 0.043 0.11 172 -0.075 1 173
CDKN2A 0.044 0.052 0.13 180 -10000 0 180
CCND2 -0.009 0.021 0.077 1 -0.11 8 9
RB1 0.001 0.032 0.17 1 -0.16 5 6
CDK4 -0.01 0.024 0.098 2 -0.14 7 9
CDK6 -0.009 0.024 0.096 3 -0.14 6 9
G1/S progression 0.015 0.064 0.17 74 -0.26 3 77
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.02 0.007 0.13 2 -10000 0 2
GNB1/GNG2 -0.054 0.072 -10000 0 -0.18 152 152
AKT1 -0.041 0.11 0.24 15 -0.29 25 40
EGF 0.024 0.019 0.12 22 -10000 0 22
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.003 0.057 0.22 31 -10000 0 31
mol:Ca2+ -0.047 0.14 0.28 14 -0.28 153 167
LYN -0.007 0.061 0.22 33 -10000 0 33
RhoA/GTP -0.027 0.056 0.093 2 -0.13 121 123
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.065 0.16 0.27 14 -0.33 153 167
GNG2 0.02 0.004 -10000 0 -10000 0 0
ARRB2 0.021 0.002 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.004 0.062 -10000 0 -0.46 7 7
G beta5/gamma2 -0.062 0.097 -10000 0 -0.23 150 150
PRKCH -0.058 0.16 0.28 14 -0.32 154 168
DNM1 0.009 0.01 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 0 0.023 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.024 0.02 0.12 25 -10000 0 25
G12 family/GTP -0.064 0.12 -10000 0 -0.29 126 126
ADRBK1 0.021 0.003 -10000 0 -10000 0 0
ADRBK2 0.02 0.004 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.027 0.006 0.096 1 -10000 0 1
mol:GDP 0.026 0.097 0.27 14 -0.24 15 29
mol:NADP 0.017 0.01 0.12 1 -10000 0 1
RAB11A 0.021 0.003 -10000 0 -10000 0 0
PRKG1 0.019 0.009 0.12 2 -10000 0 2
mol:IP3 -0.062 0.17 0.31 12 -0.34 153 165
cell morphogenesis 0.027 0.006 0.095 1 -10000 0 1
PLCB2 -0.089 0.22 0.36 8 -0.46 153 161
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.001 0.064 0.22 34 -10000 0 34
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.011 0.048 0.19 23 -10000 0 23
RHOA 0.021 0.003 -10000 0 -10000 0 0
PTGIR 0.021 0.017 0.12 14 -10000 0 14
PRKCB1 -0.062 0.17 0.29 12 -0.34 155 167
GNAQ 0.021 0.003 -10000 0 -10000 0 0
mol:L-citrulline 0.017 0.01 0.12 1 -10000 0 1
TXA2/TXA2-R family -0.1 0.23 0.34 9 -0.49 155 164
LCK 0.009 0.064 0.23 33 -10000 0 33
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.013 0.03 0.16 1 -10000 0 1
TXA2-R family/G12 family/GDP/G beta/gamma -0.027 0.14 -10000 0 -0.42 68 68
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.015 0.031 0.16 1 -10000 0 1
MAPK14 -0.042 0.11 0.21 16 -0.22 149 165
TGM2/GTP -0.074 0.18 0.32 7 -0.39 150 157
MAPK11 -0.043 0.11 0.21 17 -0.22 150 167
ARHGEF1 -0.038 0.075 0.13 2 -0.17 121 123
GNAI2 0.021 0.003 -10000 0 -10000 0 0
JNK cascade -0.073 0.18 0.3 13 -0.36 155 168
RAB11/GDP 0.02 0.006 -10000 0 -0.023 9 9
ICAM1 -0.051 0.13 0.24 15 -0.27 154 169
cAMP biosynthetic process -0.064 0.16 0.3 12 -0.32 152 164
Gq family/GTP/EBP50 0.01 0.03 0.24 6 -0.17 9 15
actin cytoskeleton reorganization 0.027 0.006 0.095 1 -10000 0 1
SRC -0.012 0.047 0.19 23 -10000 0 23
GNB5 0.021 0.003 -10000 0 -10000 0 0
GNB1 0.019 0.007 -10000 0 -10000 0 0
EGF/EGFR 0.023 0.083 0.22 54 -0.19 9 63
VCAM1 -0.054 0.14 0.24 15 -0.28 154 169
TP beta/Gq family/GDP/G beta5/gamma2 0.004 0.062 -10000 0 -0.46 7 7
platelet activation -0.054 0.14 0.28 15 -0.28 153 168
PGI2/IP 0.015 0.012 0.09 14 -10000 0 14
PRKACA 0.011 0.008 -10000 0 -10000 0 0
Gq family/GDP/G beta5/gamma2 0.006 0.05 -10000 0 -0.38 6 6
TXA2/TP beta/beta Arrestin2 -0.2 0.2 -10000 0 -0.39 335 335
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.002 0.016 -10000 0 -10000 0 0
mol:DAG -0.069 0.19 0.32 12 -0.38 154 166
EGFR 0.053 0.054 0.12 235 -10000 0 235
TXA2/TP alpha -0.088 0.21 0.35 11 -0.44 152 163
Gq family/GTP 0.005 0.026 0.21 4 -0.19 6 10
YES1 -0.006 0.061 0.22 33 -10000 0 33
GNAI2/GTP 0.002 0.031 -10000 0 -0.12 1 1
PGD2/DP 0.017 0.015 0.089 25 -10000 0 25
SLC9A3R1 0.021 0.003 -10000 0 -10000 0 0
FYN -0.006 0.06 0.22 33 -10000 0 33
mol:NO 0.017 0.01 0.12 1 -10000 0 1
GNA15 0.021 0.006 0.12 1 -10000 0 1
PGK/cGMP 0.02 0.019 0.097 3 -0.13 6 9
RhoA/GDP 0.02 0.006 -10000 0 -0.023 9 9
TP alpha/TGM2/GDP/G beta/gamma 0.027 0.035 0.17 3 -0.16 1 4
NOS3 0.017 0.01 0.12 1 -10000 0 1
RAC1 0.018 0.008 -10000 0 -10000 0 0
PRKCA -0.056 0.16 0.29 13 -0.32 143 156
PRKCB -0.076 0.16 0.25 8 -0.34 160 168
PRKCE -0.058 0.16 0.29 11 -0.32 151 162
PRKCD -0.066 0.17 0.28 13 -0.36 158 171
PRKCG -0.084 0.17 0.32 9 -0.38 156 165
muscle contraction -0.098 0.21 0.33 9 -0.46 156 165
PRKCZ -0.072 0.16 0.27 14 -0.33 154 168
ARR3 0.016 0.001 -10000 0 -10000 0 0
TXA2/TP beta 0.009 0.036 0.16 3 -0.12 1 4
PRKCQ -0.061 0.16 0.27 17 -0.33 152 169
MAPKKK cascade -0.084 0.2 0.32 10 -0.41 155 165
SELE -0.07 0.16 0.24 15 -0.35 154 169
TP beta/GNAI2/GDP/G beta/gamma 0.028 0.035 0.17 4 -0.15 1 5
ROCK1 0.021 0.005 0.12 1 -10000 0 1
GNA14 0.021 0.003 -10000 0 -10000 0 0
chemotaxis -0.12 0.26 0.35 8 -0.58 154 162
GNA12 0.018 0.008 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
GNA11 0.02 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.006 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.021 0.016 0.12 12 0 72 84
ITGB7 0.022 0.012 0.12 8 -9999 0 8
ITGA4 0.036 0.036 0.12 95 -9999 0 95
alpha4/beta7 Integrin 0.042 0.029 0.18 4 -9999 0 4
alpha4/beta1 Integrin 0.038 0.031 0.12 78 -9999 0 78
Arf6 signaling 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
CENTA1/KIF3B 0.012 0.041 -10000 0 -0.13 48 48
ARNO/beta Arrestin1-2 -0.045 0.24 -10000 0 -0.75 67 67
EGFR 0.053 0.054 0.12 235 -10000 0 235
EPHA2 0.02 0.013 0.12 8 -10000 0 8
USP6 0.021 0.007 0.12 3 -10000 0 3
IQSEC1 0.021 0.003 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.05 0.045 0.11 237 -10000 0 237
ARRB2 0.008 0.004 -10000 0 -10000 0 0
mol:GTP -0.003 0.042 0.12 6 -0.12 44 50
ARRB1 0.02 0.004 -10000 0 -10000 0 0
FBXO8 0.021 0.006 0.12 1 -10000 0 1
TSHR 0.079 0.053 0.12 374 -10000 0 374
EGF 0.024 0.019 0.12 22 -10000 0 22
somatostatin receptor activity 0 0 0.001 115 -0.001 8 123
ARAP2 0.021 0.003 -10000 0 -10000 0 0
mol:GDP 0.032 0.092 0.19 101 -0.25 16 117
mol:PI-3-4-5-P3 0 0 0.001 133 -0.001 4 137
ITGA2B 0.021 0.003 -10000 0 -10000 0 0
ARF6 0.021 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.048 0.02 -10000 0 -10000 0 0
ADAP1 0.016 0.009 -10000 0 -10000 0 0
KIF13B 0.021 0.003 -10000 0 -10000 0 0
HGF/MET -0.042 0.089 0.11 6 -0.16 232 238
PXN 0.021 0.002 -10000 0 -10000 0 0
ARF6/GTP 0.05 0.1 0.24 107 -0.23 10 117
EGFR/EGFR/EGF/EGF/ARFGEP100 0.054 0.048 0.18 4 -0.13 5 9
ADRB2 0.021 0.003 -10000 0 -10000 0 0
receptor agonist activity 0 0 0 95 0 9 104
actin filament binding 0 0 0.001 109 0 8 117
SRC 0.02 0.004 -10000 0 -10000 0 0
ITGB3 0.04 0.04 0.12 124 -10000 0 124
GNAQ 0.021 0.003 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 135 -0.001 8 143
ARF6/GDP -0.01 0.1 0.19 4 -0.31 41 45
ARF6/GDP/GULP/ACAP1 0.047 0.09 0.2 69 -0.26 15 84
alphaIIb/beta3 Integrin/paxillin/GIT1 0.063 0.033 -10000 0 -0.12 7 7
ACAP1 0.022 0.009 0.12 5 -10000 0 5
ACAP2 0.021 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.018 0.01 0.11 6 -10000 0 6
EFNA1 0.021 0.003 -10000 0 -10000 0 0
HGF 0.018 0.013 0.12 5 -10000 0 5
CYTH3 -0.005 0.002 -10000 0 -10000 0 0
CYTH2 -0.083 0.29 -10000 0 -0.95 67 67
NCK1 0.021 0.005 0.12 1 -10000 0 1
fibronectin binding 0 0 0.001 113 0 8 121
endosomal lumen acidification 0 0 0.001 114 0 7 121
microtubule-based process 0 0 -10000 0 0 17 17
GULP1 0.021 0.006 0.12 1 -10000 0 1
GNAQ/ARNO -0.064 0.27 -10000 0 -0.88 67 67
mol:Phosphatidic acid 0 0 0 38 -10000 0 38
PIP3-E 0 0 0 87 0 1 88
MET 0.009 0.011 0.12 1 -10000 0 1
GNA14 0.021 0.003 -10000 0 -10000 0 0
GNA15 0.021 0.006 0.12 1 -10000 0 1
GIT1 0.021 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 117 -0.001 8 125
GNA11 0.02 0.004 -10000 0 -10000 0 0
LHCGR 0.02 0.01 0.12 6 -10000 0 6
AGTR1 0.027 0.024 0.12 37 -10000 0 37
desensitization of G-protein coupled receptor protein signaling pathway 0.018 0.01 0.11 6 -10000 0 6
IPCEF1/ARNO -0.037 0.26 -10000 0 -0.78 67 67
alphaIIb/beta3 Integrin 0.043 0.036 0.11 123 -0.15 7 130
HIF-1-alpha transcription factor network

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
PKM2 0.076 0.11 0.24 64 -0.4 8 72
HDAC7 0.021 0.004 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.15 0.2 0.38 93 -0.57 31 124
SMAD4 0.021 0.003 -10000 0 -10000 0 0
ID2 0.087 0.11 0.28 45 -0.44 6 51
AP1 0.026 0.023 0.12 2 -0.15 7 9
ABCG2 0.088 0.11 0.28 49 -0.44 6 55
HIF1A 0.041 0.032 0.11 33 -10000 0 33
TFF3 0.09 0.12 0.28 60 -0.43 6 66
GATA2 0.022 0.009 0.12 4 -10000 0 4
AKT1 0.036 0.048 0.11 27 -0.15 29 56
response to hypoxia 0.019 0.042 0.072 62 -0.14 32 94
MCL1 0.086 0.11 0.28 40 -0.44 6 46
NDRG1 0.082 0.11 0.28 46 -0.44 6 52
SERPINE1 0.076 0.12 0.29 68 -0.41 6 74
FECH 0.086 0.11 0.28 48 -0.44 6 54
FURIN 0.087 0.11 0.28 47 -0.43 6 53
NCOA2 0.022 0.006 -10000 0 -10000 0 0
EP300 0.028 0.076 0.13 10 -0.29 31 41
HMOX1 0.091 0.12 0.29 64 -0.44 5 69
BHLHE40 0.087 0.12 0.28 46 -0.44 8 54
BHLHE41 0.085 0.11 0.28 43 -0.44 7 50
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.096 0.055 0.21 36 -10000 0 36
ENG 0.031 0.048 0.22 24 -10000 0 24
JUN 0.019 0.007 -10000 0 -10000 0 0
RORA 0.087 0.11 0.28 45 -0.43 6 51
ABCB1 0.037 0.049 -10000 0 -0.4 2 2
TFRC 0.086 0.11 0.28 42 -0.46 5 47
CXCR4 0.1 0.12 0.3 81 -0.44 6 87
TF 0.085 0.12 0.28 42 -0.48 6 48
CITED2 0.085 0.11 0.28 43 -0.46 5 48
HIF1A/ARNT 0.23 0.2 0.51 129 -0.68 2 131
LDHA 0.039 0.079 -10000 0 -0.56 5 5
ETS1 0.09 0.11 0.28 52 -0.43 6 58
PGK1 0.088 0.11 0.28 49 -0.44 6 55
NOS2 0.09 0.12 0.29 49 -0.43 7 56
ITGB2 0.087 0.12 0.28 50 -0.44 6 56
ALDOA 0.088 0.11 0.28 45 -0.44 6 51
Cbp/p300/CITED2 0.09 0.18 0.31 57 -0.6 31 88
FOS 0.021 0.013 0.13 8 -10000 0 8
HK2 0.09 0.12 0.28 47 -0.45 6 53
SP1 0.023 0.004 -10000 0 -10000 0 0
GCK -0.004 0.27 -10000 0 -1.2 32 32
HK1 0.075 0.11 0.27 39 -0.44 6 45
NPM1 0.088 0.11 0.28 48 -0.44 6 54
EGLN1 0.086 0.11 0.27 45 -0.44 6 51
CREB1 0.023 0.001 -10000 0 -10000 0 0
PGM1 0.082 0.11 0.27 46 -0.48 4 50
SMAD3 0.021 0.003 -10000 0 -10000 0 0
EDN1 0.016 0.11 -10000 0 -0.48 15 15
IGFBP1 0.086 0.12 0.29 59 -0.42 5 64
VEGFA 0.078 0.16 0.29 62 -0.51 31 93
HIF1A/JAB1 0.047 0.027 0.12 14 -10000 0 14
CP 0.097 0.13 0.29 77 -0.47 7 84
CXCL12 0.076 0.11 0.28 37 -0.44 6 43
COPS5 0.022 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4 0.031 0.006 -10000 0 -10000 0 0
BNIP3 0.074 0.11 0.28 35 -0.44 6 41
EGLN3 0.087 0.11 0.28 47 -0.43 6 53
CA9 0.1 0.12 0.29 94 -0.44 6 100
TERT 0.11 0.13 0.29 92 -0.45 5 97
ENO1 0.079 0.11 0.27 43 -0.48 4 47
PFKL 0.086 0.11 0.28 47 -0.44 6 53
NCOA1 0.021 0.002 -10000 0 -10000 0 0
ADM 0.09 0.12 0.3 60 -0.44 8 68
ARNT 0.04 0.03 0.11 23 -10000 0 23
HNF4A 0.012 0.028 0.12 1 -0.11 29 30
ADFP 0.076 0.11 0.24 64 -0.4 8 72
SLC2A1 0.064 0.15 0.27 36 -0.5 31 67
LEP 0.065 0.1 0.27 30 -0.41 6 36
HIF1A/ARNT/Cbp/p300 0.14 0.2 0.38 91 -0.59 31 122
EPO 0.075 0.12 0.33 36 -0.55 5 41
CREBBP 0.029 0.079 0.13 10 -0.3 32 42
HIF1A/ARNT/Cbp/p300/HDAC7 0.14 0.2 0.4 91 -0.57 31 122
PFKFB3 0.074 0.11 0.27 37 -0.44 6 43
NT5E 0.088 0.12 0.29 45 -0.44 6 51
Syndecan-1-mediated signaling events

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
TGFB1 0.019 0.008 0.12 1 -10000 0 1
CCL5 0.036 0.037 0.12 97 -10000 0 97
SDCBP 0.02 0.004 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.029 0.05 0.18 20 -10000 0 20
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 0.035 0.054 0.18 17 -0.21 6 23
Syndecan-1/Syntenin 0.041 0.062 0.21 30 -0.21 6 36
MAPK3 0.028 0.051 0.16 21 -0.2 6 27
HGF/MET -0.042 0.089 0.11 6 -0.16 232 238
TGFB1/TGF beta receptor Type II 0.019 0.008 0.12 1 -10000 0 1
BSG 0.02 0.004 -10000 0 -10000 0 0
keratinocyte migration 0.034 0.053 0.18 17 -0.2 6 23
Syndecan-1/RANTES 0.052 0.072 0.18 81 -0.22 7 88
Syndecan-1/CD147 0.046 0.057 0.2 17 -0.2 6 23
Syndecan-1/Syntenin/PIP2 0.039 0.058 0.2 30 -0.2 6 36
LAMA5 0.02 0.006 0.12 1 -10000 0 1
positive regulation of cell-cell adhesion 0.037 0.056 0.19 29 -0.2 6 35
MMP7 0.057 0.051 0.12 238 -10000 0 238
HGF 0.018 0.013 0.12 5 -10000 0 5
Syndecan-1/CASK 0.02 0.046 0.12 28 -0.2 6 34
Syndecan-1/HGF/MET -0.006 0.08 0.19 9 -0.19 35 44
regulation of cell adhesion 0.021 0.068 0.22 35 -0.19 6 41
HPSE 0.043 0.043 0.12 141 -10000 0 141
positive regulation of cell migration 0.029 0.05 0.18 20 -10000 0 20
SDC1 0.031 0.041 0.14 30 -0.14 2 32
Syndecan-1/Collagen 0.029 0.05 0.18 20 -10000 0 20
PPIB 0.021 0.008 0.12 4 -10000 0 4
MET 0.009 0.011 0.12 1 -10000 0 1
PRKACA 0.02 0.004 -10000 0 -10000 0 0
MMP9 0.05 0.048 0.12 193 -10000 0 193
MAPK1 0.027 0.051 0.16 20 -0.2 6 26
homophilic cell adhesion 0.03 0.057 0.2 26 -0.18 5 31
MMP1 0.035 0.039 0.12 105 -10000 0 105
FAS signaling pathway (CD95)

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
SPTAN1 -0.014 0.027 0.2 4 -0.2 6 10
RFC1 -0.015 0.019 -10000 0 -0.2 4 4
PRKDC -0.012 0.034 0.2 10 -0.2 5 15
RIPK1 0.022 0.005 -10000 0 -0.019 3 3
CASP7 -0.074 0.19 -10000 0 -0.59 75 75
FASLG/FAS/FADD/FAF1 -0.025 0.048 -10000 0 -0.13 31 31
MAP2K4 -0.069 0.13 0.19 1 -0.3 120 121
mol:ceramide -0.027 0.084 -10000 0 -0.2 64 64
GSN -0.014 0.027 0.2 4 -0.2 6 10
FASLG/FAS/FADD/FAF1/Caspase 8 -0.018 0.053 -10000 0 -0.21 13 13
FAS 0.016 0.028 0.13 25 -0.029 100 125
BID -0.032 0.023 -10000 0 -10000 0 0
MAP3K1 -0.071 0.14 -10000 0 -0.39 77 77
MAP3K7 0.014 0.015 -10000 0 -0.019 100 100
RB1 -0.014 0.023 0.22 2 -0.2 4 6
CFLAR 0.022 0.005 -10000 0 -0.019 3 3
HGF/MET -0.029 0.082 -10000 0 -0.14 232 232
ARHGDIB -0.009 0.04 0.21 16 -0.19 5 21
FADD 0.013 0.018 -10000 0 -0.029 100 100
actin filament polymerization 0.018 0.039 0.18 22 -0.2 6 28
NFKB1 -0.021 0.11 -10000 0 -0.76 8 8
MAPK8 -0.094 0.18 -10000 0 -0.44 116 116
DFFA -0.014 0.022 0.22 1 -0.2 4 5
DNA fragmentation during apoptosis -0.016 0.032 0.2 2 -0.18 16 18
FAS/FADD/MET -0.031 0.081 0.18 1 -0.14 231 232
CFLAR/RIP1 0.033 0.008 -10000 0 -10000 0 0
FAIM3 0.046 0.044 0.12 158 -10000 0 158
FAF1 0.012 0.019 -10000 0 -0.036 74 74
PARP1 -0.015 0.023 0.22 1 -0.2 6 7
DFFB -0.013 0.023 0.2 2 -0.2 4 6
CHUK -0.022 0.1 -10000 0 -0.72 8 8
FASLG 0.014 0.027 0.12 17 -0.035 104 121
FAS/FADD 0.021 0.031 0.11 25 -0.062 1 26
HGF 0.018 0.013 0.12 5 -10000 0 5
LMNA -0.019 0.032 0.19 4 -0.17 17 21
CASP6 -0.014 0.02 -10000 0 -0.19 5 5
CASP10 0.014 0.018 -10000 0 -0.029 103 103
CASP3 -0.012 0.019 -10000 0 -0.24 2 2
PTPN13 0.021 0.005 0.12 1 -10000 0 1
CASP8 -0.034 0.028 -10000 0 -10000 0 0
IL6 -0.18 0.41 -10000 0 -1.1 109 109
MET 0.009 0.011 0.12 1 -10000 0 1
ICAD/CAD -0.015 0.026 0.29 2 -0.19 4 6
FASLG/FAS/FADD/FAF1/Caspase 10 -0.028 0.085 -10000 0 -0.21 64 64
activation of caspase activity by cytochrome c -0.032 0.023 -10000 0 -10000 0 0
PAK2 -0.014 0.031 0.21 6 -0.2 6 12
BCL2 0.021 0.003 -10000 0 -10000 0 0
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.039 0.039 -10000 0 -0.1 28 28
NF kappa B1 p50/RelA/I kappa B alpha -0.032 0.1 0.22 16 -0.22 26 42
AP1 -0.006 0.063 -10000 0 -0.11 120 120
mol:PIP3 -0.019 0.041 -10000 0 -0.11 44 44
AKT1 0.002 0.071 0.23 21 -0.24 6 27
PTK2B 0.001 0.058 0.18 17 -0.18 23 40
RHOA 0.012 0.053 0.18 11 -0.34 4 15
PIK3CB 0.021 0.003 -10000 0 -0.022 2 2
mol:Ca2+ -0.029 0.066 0.18 20 -0.2 4 24
MAGI3 0.019 0.007 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
apoptosis -0.026 0.07 -10000 0 -0.15 158 158
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.005 0.056 0.18 19 -0.25 5 24
NF kappa B1 p50/RelA -0.027 0.08 -10000 0 -0.19 29 29
endothelial cell migration 0.021 0.051 0.27 3 -0.13 5 8
ADCY4 0.002 0.068 0.12 42 -0.29 25 67
ADCY5 -0.003 0.072 0.12 37 -0.28 32 69
ADCY6 0.002 0.068 0.12 18 -0.29 25 43
ADCY7 0.003 0.066 0.12 45 -0.28 25 70
ADCY1 -0.027 0.082 0.13 10 -0.32 28 38
ADCY2 0.001 0.068 0.12 44 -0.29 25 69
ADCY3 0.003 0.067 0.12 48 -0.28 26 74
ADCY8 0.003 0.067 0.12 46 -0.28 25 71
ADCY9 0.003 0.066 0.12 47 -0.28 24 71
GSK3B -0.002 0.056 0.18 17 -0.21 11 28
arachidonic acid secretion 0.002 0.071 0.12 1 -0.27 28 29
GNG2 0.02 0.005 -10000 0 -0.022 2 2
TRIP6 0.013 0.01 -10000 0 -10000 0 0
GNAO1 0.007 0.031 -10000 0 -0.12 29 29
HRAS 0.02 0.005 -10000 0 -10000 0 0
NFKBIA -0.045 0.098 0.21 21 -0.2 115 136
GAB1 0.021 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.005 0.17 -10000 0 -0.79 29 29
JUN 0.019 0.007 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.031 0.011 0.11 1 -10000 0 1
TIAM1 -0.019 0.2 -10000 0 -0.96 29 29
PIK3R1 0.021 0.003 -10000 0 -0.019 1 1
mol:IP3 -0.031 0.062 0.16 16 -0.26 2 18
PLCB3 -0.006 0.012 -10000 0 -10000 0 0
FOS 0.021 0.013 0.12 8 -10000 0 8
positive regulation of mitosis 0.002 0.071 0.12 1 -0.27 28 29
LPA/LPA1-2-3 0.003 0.07 0.15 1 -0.11 163 164
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -10000 0 0
BCAR1 0.021 0.003 -10000 0 -10000 0 0
stress fiber formation -0.001 0.065 0.2 13 -0.37 4 17
GNAZ 0.007 0.031 -10000 0 -0.12 28 28
EGFR/PI3K-beta/Gab1 -0.01 0.049 -10000 0 -0.12 4 4
positive regulation of dendritic cell cytokine production 0.002 0.069 0.15 1 -0.11 163 164
LPA/LPA2/MAGI-3 0.029 0.015 0.1 4 -10000 0 4
ARHGEF1 0.021 0.074 0.19 96 -10000 0 96
GNAI2 0.007 0.031 -10000 0 -0.12 28 28
GNAI3 0.011 0.021 -10000 0 -0.12 8 8
GNAI1 0.005 0.028 -10000 0 -0.12 24 24
LPA/LPA3 -0.021 0.067 -10000 0 -0.15 141 141
LPA/LPA2 0.02 0.011 0.092 7 -10000 0 7
LPA/LPA1 0.021 0.042 0.1 1 -0.15 29 30
HB-EGF/EGFR 0.043 0.043 0.098 205 -10000 0 205
HBEGF 0.006 0.029 0.051 188 -10000 0 188
mol:DAG -0.031 0.062 0.16 16 -0.26 2 18
cAMP biosynthetic process 0.002 0.084 0.2 16 -0.28 29 45
NFKB1 0.021 0.002 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
GNB1 0.019 0.007 -10000 0 -10000 0 0
LYN -0.039 0.097 0.2 25 -0.19 110 135
GNAQ -0.024 0.064 -10000 0 -0.15 136 136
LPAR2 0.021 0.011 0.12 7 -0.023 1 8
LPAR3 0.01 0.011 -10000 0 -0.015 37 37
LPAR1 0.025 0.011 -10000 0 -10000 0 0
IL8 -0.032 0.18 0.32 19 -0.42 97 116
PTK2 -0.021 0.06 0.18 24 -0.2 1 25
Rac1/GDP 0.013 0.006 -10000 0 -10000 0 0
CASP3 -0.026 0.071 -10000 0 -0.15 158 158
EGFR 0.052 0.054 0.12 235 -10000 0 235
PLCG1 -0.034 0.07 0.15 5 -0.16 134 139
PLD2 -0.024 0.061 0.18 25 -0.2 1 26
G12/G13 0.035 0.038 -10000 0 -0.11 24 24
PI3K-beta 0.002 0.049 -10000 0 -0.2 19 19
cell migration -0.004 0.055 -10000 0 -0.24 22 22
SLC9A3R2 0.021 0.002 -10000 0 -10000 0 0
PXN -0.001 0.066 0.2 13 -0.38 4 17
HRAS/GTP -0.004 0.069 0.11 40 -0.28 28 68
RAC1 0.018 0.008 -10000 0 -10000 0 0
MMP9 0.05 0.048 0.12 193 -0.015 2 195
PRKCE 0.02 0.005 -10000 0 -0.022 2 2
PRKCD -0.028 0.076 0.21 26 -0.25 3 29
Gi(beta/gamma) 0 0.083 0.12 36 -0.3 27 63
mol:LPA 0.005 0.009 -10000 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.003 0.065 0.18 2 -0.37 3 5
MAPKKK cascade 0.002 0.071 0.12 1 -0.27 28 29
contractile ring contraction involved in cytokinesis 0.012 0.063 0.22 19 -0.34 4 23
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.024 0.064 -10000 0 -0.15 136 136
GNA15 -0.024 0.064 -10000 0 -0.15 137 137
GNA12 0.018 0.008 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
MAPT -0.005 0.057 0.18 19 -0.26 5 24
GNA11 -0.024 0.064 -10000 0 -0.15 137 137
Rac1/GTP -0.005 0.18 -10000 0 -0.84 29 29
MMP2 0.022 0.052 0.27 3 -0.13 5 8
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.03 0.035 0.18 1 -10000 0 1
PDGFRB 0.017 0.016 0.12 4 -0.018 17 21
SPHK1 -0.002 0.056 -10000 0 -0.91 2 2
mol:S1P -0.006 0.057 -10000 0 -0.83 2 2
S1P1/S1P/Gi -0.035 0.13 0.2 2 -0.34 86 88
GNAO1 0.014 0.017 -10000 0 -0.028 88 88
PDGFB-D/PDGFRB/PLCgamma1 -0.024 0.13 0.19 5 -0.32 85 90
PLCG1 -0.037 0.12 0.18 2 -0.33 84 86
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.017 0.016 0.12 4 -0.018 17 21
GNAI2 0.015 0.017 -10000 0 -0.028 86 86
GNAI3 0.014 0.016 0.12 1 -0.027 66 67
GNAI1 0.012 0.016 -10000 0 -0.027 77 77
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.008 0.017 0.058 1 -10000 0 1
S1P1/S1P -0.008 0.065 -10000 0 -0.62 2 2
negative regulation of cAMP metabolic process -0.034 0.12 0.2 2 -0.33 86 88
MAPK3 -0.062 0.18 0.21 1 -0.51 90 91
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.013 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.002 -10000 0 -10000 0 0
KDR 0.016 0.019 0.12 8 -0.023 87 95
PLCB2 -0.001 0.069 0.18 16 -0.55 2 18
RAC1 0.018 0.008 -10000 0 -10000 0 0
RhoA/GTP -0.007 0.056 -10000 0 -0.51 2 2
receptor internalization -0.008 0.061 -10000 0 -0.57 2 2
PTGS2 -0.1 0.32 0.3 1 -0.9 89 90
Rac1/GTP -0.008 0.053 -10000 0 -0.51 2 2
RHOA 0.021 0.003 -10000 0 -10000 0 0
VEGFA 0.027 0.039 0.12 79 -0.023 87 166
negative regulation of T cell proliferation -0.034 0.12 0.2 2 -0.33 86 88
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.014 0.017 -10000 0 -0.027 88 88
MAPK1 -0.063 0.18 0.21 1 -0.51 91 92
S1P1/S1P/PDGFB-D/PDGFRB 0 0.079 0.18 11 -0.45 3 14
ABCC1 0.016 0.015 0.12 1 -0.022 79 80
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.009 0.006 -10000 0 -10000 0 0
MAP4K4 -0.006 0.049 -10000 0 -0.25 9 9
BAG4 0.02 0.004 -10000 0 -10000 0 0
PKC zeta/ceramide -0.029 0.12 -10000 0 -0.25 105 105
NFKBIA 0.021 0.008 0.12 3 -10000 0 3
BIRC3 0.023 0.017 0.12 16 -10000 0 16
BAX -0.043 0.12 -10000 0 -0.35 76 76
RIPK1 0.021 0.003 -10000 0 -10000 0 0
AKT1 0 0.05 0.68 3 -10000 0 3
BAD -0.035 0.1 0.19 5 -0.22 106 111
SMPD1 -0.002 0.046 0.12 10 -0.17 17 27
RB1 -0.036 0.1 0.19 2 -0.22 108 110
FADD/Caspase 8 0 0.054 0.19 1 -0.3 8 9
MAP2K4 -0.038 0.095 0.18 1 -0.22 107 108
NSMAF 0.02 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.037 0.098 0.18 7 -0.22 106 113
EGF 0.024 0.019 0.12 22 -10000 0 22
mol:ceramide -0.035 0.11 -10000 0 -0.23 108 108
MADD 0.02 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.01 0.005 -10000 0 -10000 0 0
ASAH1 0.02 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.036 0.1 0.19 2 -0.22 108 110
cell proliferation -0.017 0.087 0.17 3 -0.19 101 104
BID -0.005 0.11 -10000 0 -0.68 12 12
MAP3K1 -0.036 0.1 0.2 1 -0.22 108 109
EIF2A -0.039 0.092 0.17 5 -0.21 107 112
TRADD 0.021 0.002 -10000 0 -10000 0 0
CRADD 0.021 0.002 -10000 0 -10000 0 0
MAPK3 -0.032 0.086 0.17 6 -0.2 98 104
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.034 0.089 0.17 6 -0.21 100 106
Cathepsin D/ceramide -0.022 0.11 -10000 0 -0.22 106 106
FADD -0.005 0.048 -10000 0 -0.25 8 8
KSR1 -0.036 0.1 0.2 1 -0.22 106 107
MAPK8 -0.078 0.15 -10000 0 -0.25 216 216
PRKRA -0.037 0.1 0.2 1 -0.22 108 109
PDGFA 0.018 0.008 -10000 0 -10000 0 0
TRAF2 0.021 0.003 -10000 0 -10000 0 0
IGF1 0.021 0.005 0.12 1 -10000 0 1
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.035 0.11 -10000 0 -0.23 108 108
CTSD 0.02 0.005 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.03 0.005 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.018 0.094 0.18 3 -0.21 101 104
PRKCD 0.02 0.004 -10000 0 -10000 0 0
PRKCZ 0.016 0.009 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.01 0.005 -10000 0 -10000 0 0
RelA/NF kappa B1 0.03 0.005 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.023 0.016 0.12 15 -10000 0 15
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0 0.05 -10000 0 -0.26 7 7
TNFR1A/BAG4/TNF-alpha 0.028 0.049 -10000 0 -0.14 49 49
mol:Sphingosine-1-phosphate -0.009 0.006 -10000 0 -10000 0 0
MAP2K1 -0.038 0.093 0.17 8 -0.21 105 113
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
CYCS -0.022 0.071 0.19 1 -0.2 77 78
TNFRSF1A 0.021 0.01 0.12 5 -10000 0 5
NFKB1 0.021 0.002 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.022 -10000 0 -0.16 7 7
EIF2AK2 -0.038 0.097 0.17 4 -0.22 108 112
TNF-alpha/TNFR1A/FAN 0.029 0.046 -10000 0 -0.13 43 43
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.015 0.057 -10000 0 -0.41 6 6
MAP2K2 -0.034 0.086 0.17 11 -0.21 98 109
SMPD3 -0.006 0.067 -10000 0 -0.26 27 27
TNF 0.021 0.015 0.12 11 -10000 0 11
PKC zeta/PAR4 0.008 0.059 0.11 11 -0.16 72 83
mol:PHOSPHOCHOLINE -0.019 0.062 0.11 6 -0.15 103 109
NF kappa B1/RelA/I kappa B alpha 0.035 0.058 -10000 0 -0.12 71 71
AIFM1 -0.035 0.083 0.19 1 -0.17 135 136
BCL2 0.021 0.003 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.02 0.004 -10000 0 -10000 0 0
VLDLR 0.02 0.006 -10000 0 -10000 0 0
LRPAP1 0.021 0.003 -10000 0 -10000 0 0
NUDC 0.019 0.006 -10000 0 -10000 0 0
RELN/LRP8 -0.017 0.073 -10000 0 -0.13 189 189
CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
KATNA1 0.02 0.005 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.041 0.049 -10000 0 -0.12 182 182
IQGAP1/CaM 0.03 0.011 0.11 6 -10000 0 6
DAB1 0.015 0.01 -10000 0 -10000 0 0
IQGAP1 0.022 0.01 0.12 6 -10000 0 6
PLA2G7 0.021 0.006 0.12 2 -10000 0 2
CALM1 0.02 0.005 -10000 0 -10000 0 0
DYNLT1 0.03 0.031 0.12 63 -10000 0 63
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.028 0.01 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.021 0.002 -10000 0 -10000 0 0
CDK5R1 0.019 0.006 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A -0.01 0.002 -10000 0 -10000 0 0
CDK5R2 0.014 0.01 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.039 0.089 -10000 0 -0.15 246 246
YWHAE 0.021 0.002 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.041 0.15 0.28 72 -0.26 100 172
MAP1B 0.004 0.001 -10000 0 -10000 0 0
RAC1 0.007 0.004 -10000 0 -10000 0 0
p35/CDK5 -0.044 0.061 0.17 10 -0.21 30 40
RELN 0.011 0.011 -10000 0 -10000 0 0
PAFAH/LIS1 0.018 0.015 0.094 2 -0.13 5 7
LIS1/CLIP170 0.019 0.005 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.065 0.085 0.12 6 -0.23 95 101
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.074 0.12 -10000 0 -0.32 92 92
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.071 0.1 0.16 7 -0.23 154 161
LIS1/IQGAP1 0.02 0.009 0.094 6 -10000 0 6
RHOA 0.007 0.003 -10000 0 -10000 0 0
PAFAH1B1 -0.012 0.003 -10000 0 -10000 0 0
PAFAH1B3 0.019 0.007 -10000 0 -10000 0 0
PAFAH1B2 0.021 0.003 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.018 0.014 -10000 0 -0.11 3 3
NDEL1/Katanin 60/Dynein heavy chain -0.03 0.14 0.28 64 -0.26 99 163
LRP8 0.019 0.007 -10000 0 -10000 0 0
NDEL1/Katanin 60 -0.043 0.14 0.28 67 -0.26 100 167
P39/CDK5 -0.059 0.071 0.17 7 -0.21 73 80
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.017 0.007 -10000 0 -10000 0 0
CDK5 -0.038 0.05 0.17 6 -0.12 146 152
PPP2R5D 0.021 0.002 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.017 0.004 -10000 0 -10000 0 0
CSNK2A1 0.02 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.03 0.079 -10000 0 -0.13 237 237
RELN/VLDLR -0.01 0.072 -10000 0 -0.12 190 190
CDC42 0.007 0.004 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.006 0.11 -10000 0 -0.45 35 35
IHH 0.018 0.034 0.11 7 -0.12 35 42
SHH Np/Cholesterol/GAS1 0.01 0.043 0.09 53 -0.12 50 103
LRPAP1 0.021 0.003 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.01 0.042 0.12 50 -0.089 53 103
SMO/beta Arrestin2 0.012 0.072 -10000 0 -0.28 26 26
SMO 0 0.065 -10000 0 -0.29 27 27
AKT1 0.004 0.076 -10000 0 -0.4 16 16
ARRB2 0.021 0.002 -10000 0 -10000 0 0
BOC 0.027 0.025 0.12 42 -10000 0 42
ADRBK1 0.021 0.003 -10000 0 -10000 0 0
heart looping 0 0.064 -10000 0 -0.28 27 27
STIL 0.004 0.087 0.17 101 -0.22 29 130
DHH N/PTCH2 0.029 0.02 -10000 0 -0.16 2 2
DHH N/PTCH1 0.017 0.065 -10000 0 -0.25 34 34
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
DHH 0.023 0.018 0.12 19 -10000 0 19
PTHLH -0.023 0.17 -10000 0 -0.72 35 35
determination of left/right symmetry 0 0.064 -10000 0 -0.28 27 27
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
skeletal system development -0.023 0.16 -10000 0 -0.71 35 35
IHH N/Hhip -0.005 0.079 0.12 1 -0.18 106 107
DHH N/Hhip 0.002 0.07 0.11 15 -0.16 105 120
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0 0.064 -10000 0 -0.28 27 27
pancreas development 0.017 0.009 0.12 1 -10000 0 1
HHAT 0.021 0.002 -10000 0 -10000 0 0
PI3K 0.03 0.006 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.037 0.038 0.12 107 -10000 0 107
somite specification 0 0.064 -10000 0 -0.28 27 27
SHH Np/Cholesterol/PTCH1 -0.005 0.059 -10000 0 -0.24 29 29
SHH Np/Cholesterol/PTCH2 0.002 0.037 -10000 0 -0.12 53 53
SHH Np/Cholesterol/Megalin -0.003 0.05 0.086 16 -0.12 92 108
SHH -0.009 0.008 0.051 4 -10000 0 4
catabolic process 0.004 0.068 -10000 0 -0.28 34 34
SMO/Vitamin D3 -0.004 0.071 0.24 6 -0.27 27 33
SHH Np/Cholesterol/Hhip -0.012 0.055 -10000 0 -0.13 119 119
LRP2 0.022 0.018 0.12 18 -10000 0 18
receptor-mediated endocytosis -0.016 0.074 0.2 2 -0.28 32 34
SHH Np/Cholesterol/BOC 0.007 0.04 0.086 32 -0.12 52 84
SHH Np/Cholesterol/CDO 0.004 0.036 0.086 3 -0.12 51 54
mesenchymal cell differentiation 0.012 0.055 0.12 119 -10000 0 119
mol:Vitamin D3 0.022 0.092 0.18 108 -0.24 29 137
IHH N/PTCH2 0.026 0.024 -10000 0 -0.22 2 2
CDON 0.022 0.012 0.12 8 -10000 0 8
IHH N/PTCH1 0.012 0.071 -10000 0 -0.28 34 34
Megalin/LRPAP1 0.014 0.058 0.11 18 -0.16 66 84
PTCH2 0.019 0.007 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.003 0.033 -10000 0 -0.11 52 52
PTCH1 0.004 0.068 -10000 0 -0.28 34 34
HHIP 0.017 0.009 0.12 1 -10000 0 1
p75(NTR)-mediated 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
Sortilin/TRAF6 0.027 0.011 -10000 0 -10000 0 0
Necdin/E2F1 0.025 0.032 -10000 0 -0.16 18 18
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.05 0.053 0.18 1 -0.12 41 42
NGF (dimer)/p75(NTR)/BEX1 0.031 0.055 -10000 0 -0.13 53 53
NT-4/5 (dimer)/p75(NTR) 0.036 0.031 0.11 94 -10000 0 94
IKBKB 0.021 0.003 -10000 0 -10000 0 0
AKT1 -0.013 0.043 0.18 18 -10000 0 18
IKBKG 0.021 0.002 -10000 0 -10000 0 0
BDNF 0.01 0.011 -10000 0 -10000 0 0
MGDIs/NGR/p75(NTR)/LINGO1 0.003 0.087 -10000 0 -0.15 150 150
FURIN 0.021 0.003 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.044 0.089 -10000 0 -0.13 335 335
LINGO1 0.02 0.005 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.021 0.015 -10000 0 -10000 0 0
proBDNF (dimer) 0.01 0.01 -10000 0 -10000 0 0
NTRK1 0.026 0.023 0.12 35 -10000 0 35
RTN4R 0.016 0.009 -10000 0 -10000 0 0
neuron apoptosis -0.077 0.12 0.28 6 -0.37 63 69
IRAK1 0.021 0.002 -10000 0 -10000 0 0
SHC1 -0.013 0.036 0.072 15 -0.13 40 55
ARHGDIA 0.021 0.003 -10000 0 -10000 0 0
RhoA/GTP 0.015 0.002 -10000 0 -10000 0 0
Gamma Secretase 0.053 0.023 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.043 0.052 0.18 1 -0.12 41 42
MAGEH1 0.021 0.003 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.037 0.06 0.18 1 -0.13 60 61
Mammalian IAPs/DIABLO 0.051 0.028 -10000 0 -0.12 13 13
proNGF (dimer) 0.017 0.009 0.12 1 -10000 0 1
MAGED1 0.021 0 -10000 0 -10000 0 0
APP 0.021 0.003 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.019 0.02 0.12 22 -10000 0 22
ZNF274 0.018 0.007 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.018 0.035 -10000 0 -0.11 39 39
NGF 0.017 0.009 0.12 1 -10000 0 1
cell cycle arrest -0.017 0.043 0.27 9 -10000 0 9
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.011 0.045 -10000 0 -0.16 35 35
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.045 0.031 0.18 4 -10000 0 4
NCSTN 0.021 0.002 -10000 0 -10000 0 0
mol:GTP 0.033 0.05 0.18 1 -0.13 41 42
PSENEN 0.019 0.006 -10000 0 -10000 0 0
mol:ceramide -0.016 0.029 0.045 1 -0.12 37 38
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.026 0.076 -10000 0 -0.18 72 72
p75(NTR)/beta APP 0.04 0.026 -10000 0 -10000 0 0
BEX1 0.021 0.003 -10000 0 -10000 0 0
mol:GDP -0.012 0.032 0.058 1 -0.13 41 42
NGF (dimer) 0.05 0.059 0.18 1 -0.12 41 42
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.013 0.086 -10000 0 -0.14 149 149
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
RAC1/GTP 0.025 0.039 0.16 1 -0.11 32 33
MYD88 0.027 0.024 0.12 38 -10000 0 38
CHUK 0.019 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.034 0.051 0.18 1 -0.13 41 42
RHOB 0.021 0.002 -10000 0 -10000 0 0
RHOA 0.021 0.003 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.03 0.011 -10000 0 -10000 0 0
NT3 (dimer) 0.019 0.011 0.12 6 -10000 0 6
TP53 -0.05 0.074 0.22 19 -10000 0 19
PRDM4 -0.017 0.03 -10000 0 -0.12 40 40
BDNF (dimer) -0.08 0.1 -10000 0 -0.14 457 457
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
SORT1 0.019 0.007 -10000 0 -10000 0 0
activation of caspase activity 0.045 0.05 0.17 1 -0.12 41 42
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.043 0.052 0.18 1 -0.12 41 42
RHOC 0.022 0.021 0.12 23 -10000 0 23
XIAP 0.021 0.001 -10000 0 -10000 0 0
MAPK10 -0.033 0.093 0.19 51 -0.23 25 76
DIABLO 0.021 0.002 -10000 0 -10000 0 0
SMPD2 -0.016 0.029 0.045 1 -0.12 37 38
APH1B 0.021 0.003 -10000 0 -10000 0 0
APH1A 0.021 0.002 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.034 0.051 0.18 1 -0.13 41 42
PSEN1 0.02 0.004 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.028 0.01 0.11 1 -10000 0 1
NT3 (dimer)/p75(NTR) 0.037 0.027 0.18 3 -10000 0 3
MAPK8 -0.041 0.08 0.23 16 -0.22 28 44
MAPK9 -0.033 0.091 0.19 51 -0.22 24 75
APAF1 0.021 0.002 -10000 0 -10000 0 0
NTF3 0.019 0.011 0.12 6 -10000 0 6
NTF4 0.019 0.021 0.12 22 -10000 0 22
NDN 0.02 0.005 -10000 0 -10000 0 0
RAC1/GDP 0.013 0.006 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.044 0.049 0.15 7 -0.11 40 47
p75 CTF/Sortilin/TRAF6/NRIF 0.044 0.022 -10000 0 -10000 0 0
RhoA-B-C/GTP 0.033 0.05 0.17 1 -0.13 41 42
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.028 0.088 -10000 0 -0.11 328 328
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.034 0.089 -10000 0 -0.12 334 334
PRKACB 0.018 0.007 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.067 0.093 -10000 0 -0.16 340 340
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.023 0.017 0.12 16 -10000 0 16
BIRC2 0.021 0.003 -10000 0 -10000 0 0
neuron projection morphogenesis -0.015 0.049 0.16 12 -0.15 38 50
BAD -0.036 0.093 0.26 25 -0.23 26 51
RIPK2 0.02 0.007 0.12 2 -10000 0 2
NGFR 0.034 0.035 0.12 84 -10000 0 84
CYCS -0.014 0.039 0.25 7 -10000 0 7
ADAM17 0.021 0.002 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.042 0.051 0.18 1 -0.12 38 39
BCL2L11 -0.036 0.091 0.25 24 -0.23 26 50
BDNF (dimer)/p75(NTR) -0.06 0.099 0.11 44 -0.16 339 383
PI3K 0.043 0.051 0.18 1 -0.12 39 40
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.043 0.051 0.18 1 -0.12 41 42
NDNL2 0.021 0.003 -10000 0 -10000 0 0
YWHAE 0.021 0.002 -10000 0 -10000 0 0
PRKCI 0.021 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.024 0.054 0.18 1 -0.16 41 42
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.044 0.051 0.18 1 -0.12 41 42
TRAF6 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.018 0.008 -10000 0 -10000 0 0
PRKCZ 0.016 0.009 -10000 0 -10000 0 0
PLG 0.016 0.008 0.12 3 -10000 0 3
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.071 0.075 0.09 5 -0.14 342 347
SQSTM1 0.021 0.003 -10000 0 -10000 0 0
NGFRAP1 0.021 0.001 -10000 0 -10000 0 0
CASP3 -0.034 0.089 0.24 25 -0.22 27 52
E2F1 0.021 0.011 0.12 7 -10000 0 7
CASP9 0.019 0.008 0.12 1 -10000 0 1
IKK complex -0.004 0.095 -10000 0 -0.22 34 34
NGF (dimer)/TRKA 0.02 0.05 0.18 1 -0.16 41 42
MMP7 0.057 0.051 0.12 238 -10000 0 238
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.046 0.053 0.18 1 -0.11 40 41
MMP3 0.012 0.012 0.12 3 -10000 0 3
APAF-1/Caspase 9 -0.028 0.029 -10000 0 -0.19 4 4
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 0.037 0.058 0.2 6 -0.1 19 25
alphaM/beta2 Integrin/GPIbA 0.022 0.048 0.19 1 -0.1 24 25
alphaM/beta2 Integrin/proMMP-9 0.04 0.062 0.19 6 -0.099 21 27
PLAUR 0.026 0.028 0.12 46 -10000 0 46
HMGB1 0.007 0.029 -10000 0 -0.053 125 125
alphaM/beta2 Integrin/Talin 0.021 0.047 0.19 1 -0.092 27 28
AGER 0.015 0.043 0.12 52 -0.053 124 176
RAP1A 0.019 0.007 -10000 0 -10000 0 0
SELPLG 0.021 0.005 0.12 1 -10000 0 1
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.013 0.1 0.2 2 -0.19 128 130
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.05 0.048 0.12 193 -10000 0 193
CYR61 0.022 0.021 0.12 23 -10000 0 23
TLN1 0.02 0.005 -10000 0 -10000 0 0
Rap1/GTP -0.005 0.074 -10000 0 -0.27 10 10
RHOA 0.021 0.003 -10000 0 -10000 0 0
P-selectin oligomer 0.022 0.015 0.12 14 -10000 0 14
MYH2 -0.018 0.078 0.17 5 -0.29 10 15
MST1R 0.021 0.005 0.12 1 -10000 0 1
leukocyte activation during inflammatory response -0.006 0.072 0.16 1 -0.12 142 143
APOB 0.02 0.01 0.12 4 -10000 0 4
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.044 0.043 0.12 145 -10000 0 145
JAM3 0.02 0.004 -10000 0 -10000 0 0
GP1BA 0.021 0.005 0.12 1 -10000 0 1
alphaM/beta2 Integrin/CTGF 0.023 0.049 0.19 1 -0.097 23 24
alphaM/beta2 Integrin -0.017 0.075 0.12 2 -0.32 9 11
JAM3 homodimer 0.02 0.004 -10000 0 -10000 0 0
ICAM2 0.021 0.003 -10000 0 -10000 0 0
ICAM1 0.027 0.025 0.12 40 -10000 0 40
phagocytosis triggered by activation of immune response cell surface activating receptor -0.016 0.075 -10000 0 -0.32 9 9
cell adhesion 0.021 0.048 0.18 1 -0.1 24 25
NFKB1 -0.062 0.13 0.19 13 -0.32 127 140
THY1 0.02 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.002 -10000 0 -10000 0 0
Lipoprotein(a) -0.007 0.065 0.096 3 -0.13 137 140
alphaM/beta2 Integrin/LRP/tPA 0.034 0.054 0.19 1 -0.097 18 19
IL6 -0.088 0.19 0.18 1 -0.49 114 115
ITGB2 0.008 0.033 0.13 9 -0.053 130 139
elevation of cytosolic calcium ion concentration 0.041 0.067 0.19 44 -0.1 12 56
alphaM/beta2 Integrin/JAM2/JAM3 0.031 0.05 0.19 1 -0.098 17 18
JAM2 0.021 0.009 0.12 4 -10000 0 4
alphaM/beta2 Integrin/ICAM1 0.049 0.058 0.2 5 -0.13 5 10
alphaM/beta2 Integrin/uPA/Plg 0.038 0.062 0.19 7 -0.099 16 23
RhoA/GTP -0.015 0.081 -10000 0 -0.3 11 11
positive regulation of phagocytosis -0.007 0.066 0.16 6 -0.26 8 14
Ron/MSP 0.039 0.027 -10000 0 -0.16 2 2
alphaM/beta2 Integrin/uPAR/uPA 0.042 0.069 0.19 44 -0.1 12 56
alphaM/beta2 Integrin/uPAR 0.024 0.052 0.21 3 -0.095 21 24
PLAU 0.041 0.044 0.12 138 -10000 0 138
PLAT 0.029 0.028 0.12 52 -10000 0 52
actin filament polymerization -0.016 0.077 0.17 5 -0.35 6 11
MST1 0.033 0.034 0.12 78 -10000 0 78
alphaM/beta2 Integrin/lipoprotein(a) -0.004 0.075 0.18 1 -0.12 142 143
TNF -0.076 0.16 0.2 3 -0.37 128 131
RAP1B 0.021 0.009 0.12 4 -10000 0 4
alphaM/beta2 Integrin/uPA 0.033 0.061 0.19 7 -0.1 21 28
fibrinolysis 0.036 0.06 0.19 7 -0.099 16 23
HCK 0.022 0.014 0.12 11 -10000 0 11
dendritic cell antigen processing and presentation -0.016 0.075 -10000 0 -0.32 9 9
VTN 0.021 0.006 0.12 2 -10000 0 2
alphaM/beta2 Integrin/CYR61 0.022 0.05 0.19 2 -0.11 21 23
LPA 0.015 0.009 0.12 1 -10000 0 1
LRP1 0.02 0.004 -10000 0 -10000 0 0
cell migration 0.027 0.05 0.16 7 -0.096 17 24
FN1 0.036 0.036 0.12 94 -10000 0 94
alphaM/beta2 Integrin/Thy1 0.019 0.051 0.19 1 -0.12 30 31
MPO 0.015 0.01 -10000 0 -10000 0 0
KNG1 0.018 0.014 0.12 10 -10000 0 10
RAP1/GDP 0.025 0.012 0.096 4 -10000 0 4
ROCK1 -0.016 0.079 0.19 7 -0.27 12 19
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.016 0.008 0.12 3 -10000 0 3
CTGF 0.023 0.018 0.12 20 -10000 0 20
alphaM/beta2 Integrin/Hck 0.022 0.05 0.19 7 -0.1 22 29
ITGAM 0.007 0.031 0.13 1 -0.054 130 131
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.031 0.052 0.21 3 -0.098 18 21
HP 0.05 0.047 0.12 188 -10000 0 188
leukocyte adhesion 0.002 0.085 0.2 1 -0.16 115 116
SELP 0.022 0.015 0.12 14 -10000 0 14
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.02 0.11 -10000 0 -0.43 12 12
MAP3K8 0.02 0.016 0.12 12 -0.019 6 18
FOS -0.028 0.1 -10000 0 -0.44 12 12
PRKCA 0.02 0.006 -10000 0 -0.025 7 7
PTPN7 0.036 0.037 0.12 96 -0.031 7 103
HRAS 0.02 0.005 -10000 0 -10000 0 0
PRKCB 0.014 0.011 -10000 0 -0.025 7 7
NRAS 0.019 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.033 0.017 -10000 0 -10000 0 0
MAPK3 -0.006 0.073 -10000 0 -0.49 6 6
MAP2K1 -0.065 0.14 -10000 0 -0.29 169 169
ELK1 0.021 0.006 -10000 0 -0.034 7 7
BRAF -0.045 0.12 -10000 0 -0.28 121 121
mol:GTP 0 0 -10000 0 -0.004 7 7
MAPK1 -0.012 0.094 -10000 0 -0.5 14 14
RAF1 -0.074 0.14 -10000 0 -0.28 190 190
KRAS 0.02 0.004 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.041 0.044 0.29 2 -10000 0 2
CRKL 0.022 0.073 0.16 134 -10000 0 134
mol:DAG 0.02 0.026 0.16 4 -10000 0 4
HRAS 0.02 0.083 0.2 68 -10000 0 68
MAPK8 -0.004 0.033 0.15 22 -10000 0 22
RAP1A 0.021 0.07 0.16 125 -10000 0 125
GAB1 0.022 0.073 0.16 135 -10000 0 135
MAPK14 0.001 0.043 0.16 41 -10000 0 41
EPO 0.026 0.031 0.13 50 -10000 0 50
PLCG1 0.02 0.026 0.17 4 -10000 0 4
EPOR/TRPC2/IP3 Receptors 0.025 0.008 0.079 2 -10000 0 2
RAPGEF1 0.021 0.003 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.028 0.053 0.15 5 -0.14 43 48
GAB1/SHC/GRB2/SOS1 0.054 0.048 0.18 23 -10000 0 23
EPO/EPOR (dimer) 0.032 0.027 0.11 46 -10000 0 46
IRS2 0.021 0.071 0.16 133 -10000 0 133
STAT1 0.023 0.028 0.18 4 -10000 0 4
STAT5B 0.022 0.027 0.17 4 -10000 0 4
cell proliferation 0.012 0.07 0.17 97 -10000 0 97
GAB1/SHIP/PIK3R1/SHP2/SHC 0.04 0.035 0.13 19 -10000 0 19
TEC 0.022 0.073 0.16 133 -10000 0 133
SOCS3 0.021 0.017 0.12 14 -10000 0 14
STAT1 (dimer) 0.023 0.028 0.18 4 -10000 0 4
JAK2 0.024 0.01 0.079 3 -10000 0 3
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.05 0.041 0.2 19 -10000 0 19
EPO/EPOR 0.032 0.027 0.11 46 -10000 0 46
LYN 0.021 0.008 0.12 3 -10000 0 3
TEC/VAV2 0.013 0.058 0.13 114 -10000 0 114
elevation of cytosolic calcium ion concentration 0.025 0.008 0.079 2 -10000 0 2
SHC1 0.023 0.016 0.12 16 -10000 0 16
EPO/EPOR (dimer)/LYN 0.041 0.029 0.14 5 -10000 0 5
mol:IP3 0.02 0.026 0.16 4 -10000 0 4
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.058 0.062 0.19 61 -10000 0 61
SH2B3 0.026 0.009 0.1 2 -10000 0 2
NFKB1 0.001 0.043 0.15 45 -10000 0 45
EPO/EPOR (dimer)/JAK2/SOCS3 0.001 0.043 -10000 0 -0.15 43 43
PTPN6 0.026 0.074 0.16 137 -10000 0 137
TEC/VAV2/GRB2 0.045 0.046 0.18 23 -10000 0 23
EPOR 0.025 0.008 0.08 2 -10000 0 2
INPP5D 0.021 0.009 0.12 5 -10000 0 5
mol:GDP 0.053 0.049 0.18 23 -10000 0 23
SOS1 0.021 0.001 -10000 0 -10000 0 0
PLCG2 0.022 0.009 0.12 5 -10000 0 5
CRKL/CBL/C3G 0.046 0.047 0.16 47 -10000 0 47
VAV2 0.022 0.073 0.16 134 -10000 0 134
CBL 0.023 0.074 0.16 136 -10000 0 136
SHC/Grb2/SOS1 0.028 0.021 -10000 0 -10000 0 0
STAT5A 0.022 0.027 0.17 4 -10000 0 4
GRB2 0.02 0.004 -10000 0 -10000 0 0
STAT5 (dimer) 0.032 0.032 0.2 4 -10000 0 4
LYN/PLCgamma2 0.031 0.013 0.15 5 -10000 0 5
PTPN11 0.021 0.003 -10000 0 -10000 0 0
BTK 0.026 0.075 0.16 140 -10000 0 140
BCL2 0.042 0.047 0.29 2 -10000 0 2
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.021 0.003 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0 0.11 -10000 0 -0.35 59 59
Syndecan-3/Neurocan -0.016 0.12 -10000 0 -0.38 62 62
POMC 0.021 0.005 0.12 1 -10000 0 1
EGFR 0.053 0.054 0.12 235 -10000 0 235
Syndecan-3/EGFR 0.001 0.12 -10000 0 -0.36 61 61
AGRP 0.02 0.009 0.12 4 -10000 0 4
NCSTN 0.021 0.002 -10000 0 -10000 0 0
PSENEN 0.019 0.006 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.021 0.003 -10000 0 -10000 0 0
APH1A 0.021 0.002 -10000 0 -10000 0 0
NCAN 0.02 0.007 0.12 2 -10000 0 2
long-term memory -0.003 0.12 -10000 0 -0.36 61 61
Syndecan-3/IL8 -0.012 0.13 -10000 0 -0.4 62 62
PSEN1 0.02 0.004 -10000 0 -10000 0 0
Src/Cortactin 0.03 0.007 -10000 0 -10000 0 0
FYN 0.02 0.004 -10000 0 -10000 0 0
limb bud formation -0.029 0.12 -10000 0 -0.39 62 62
MC4R 0.015 0.01 0.12 1 -10000 0 1
SRC 0.02 0.004 -10000 0 -10000 0 0
PTN 0.017 0.013 0.12 5 -10000 0 5
FGFR/FGF/Syndecan-3 -0.029 0.12 -10000 0 -0.39 62 62
neuron projection morphogenesis 0 0.12 -10000 0 -0.35 55 55
Syndecan-3/AgRP -0.015 0.12 -10000 0 -0.38 62 62
Syndecan-3/AgRP/MC4R -0.035 0.12 -10000 0 -0.38 62 62
Fyn/Cortactin 0.03 0.007 -10000 0 -10000 0 0
SDC3 -0.029 0.12 -10000 0 -0.39 62 62
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration -0.012 0.12 -10000 0 -0.39 62 62
IL8 0.027 0.032 0.12 60 -10000 0 60
Syndecan-3/Fyn/Cortactin -0.003 0.12 -10000 0 -0.37 61 61
Syndecan-3/CASK -0.028 0.11 -10000 0 -0.37 62 62
alpha-MSH/MC4R -0.019 0.082 -10000 0 -0.16 174 174
Gamma Secretase 0.053 0.023 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.023 0.042 -10000 0 -0.28 3 3
Syndecan-4/Syndesmos 0.022 0.1 -10000 0 -0.38 22 22
positive regulation of JNK cascade 0.031 0.1 -10000 0 -0.36 23 23
Syndecan-4/ADAM12 0.022 0.1 0.26 1 -0.38 23 24
CCL5 0.036 0.037 0.12 97 -10000 0 97
Rac1/GDP 0.013 0.006 -10000 0 -10000 0 0
DNM2 0.02 0.004 -10000 0 -10000 0 0
ITGA5 0.034 0.036 0.12 89 -10000 0 89
SDCBP 0.02 0.004 -10000 0 -10000 0 0
PLG 0.012 0.016 0.11 3 -0.04 44 47
ADAM12 0.032 0.036 0.12 85 -10000 0 85
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.021 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.03 0.015 -10000 0 -0.056 1 1
Syndecan-4/Laminin alpha1 0.024 0.1 0.27 3 -0.39 23 26
Syndecan-4/CXCL12/CXCR4 0.033 0.1 -10000 0 -0.38 22 22
Syndecan-4/Laminin alpha3 0.017 0.1 -10000 0 -0.39 25 25
MDK 0.05 0.047 0.12 188 -10000 0 188
Syndecan-4/FZD7 0.028 0.11 0.26 4 -0.39 24 28
Syndecan-4/Midkine 0.04 0.11 0.26 9 -0.38 22 31
FZD7 0.032 0.033 0.12 73 -10000 0 73
Syndecan-4/FGFR1/FGF 0.03 0.098 -10000 0 -0.37 22 22
THBS1 0.024 0.02 0.12 24 -10000 0 24
integrin-mediated signaling pathway 0.058 0.11 0.26 9 -0.37 23 32
positive regulation of MAPKKK cascade 0.031 0.1 -10000 0 -0.36 23 23
Syndecan-4/TACI 0.019 0.1 -10000 0 -0.38 24 24
CXCR4 0.039 0.039 0.12 113 -10000 0 113
cell adhesion 0.016 0.032 0.2 15 -10000 0 15
Syndecan-4/Dynamin 0.018 0.099 -10000 0 -0.39 22 22
Syndecan-4/TSP1 0.022 0.1 0.26 1 -0.4 22 23
Syndecan-4/GIPC 0.018 0.099 -10000 0 -0.38 24 24
Syndecan-4/RANTES 0.03 0.11 -10000 0 -0.38 24 24
ITGB1 0.021 0.016 0.12 12 -10000 0 12
LAMA1 0.025 0.022 0.12 30 -10000 0 30
LAMA3 0.02 0.006 0.12 1 -10000 0 1
RAC1 0.018 0.008 -10000 0 -10000 0 0
PRKCA 0.009 0.14 0.83 17 -10000 0 17
Syndecan-4/alpha-Actinin 0.021 0.099 -10000 0 -0.38 22 22
TFPI 0.065 0.051 0.12 282 -10000 0 282
F2 0.018 0.016 0.1 5 -0.035 22 27
alpha5/beta1 Integrin 0.037 0.031 0.18 10 -10000 0 10
positive regulation of cell adhesion 0.011 0.099 0.24 1 -0.39 25 26
ACTN1 0.02 0.005 -10000 0 -10000 0 0
TNC 0.083 0.051 0.12 401 -10000 0 401
Syndecan-4/CXCL12 0.015 0.097 -10000 0 -0.38 22 22
FGF6 0.015 0.004 -10000 0 -10000 0 0
RHOA 0.021 0.003 -10000 0 -10000 0 0
CXCL12 0.02 0.01 0.12 4 -10000 0 4
TNFRSF13B 0.018 0.008 0.12 3 -10000 0 3
FGF2 0.021 0.005 0.12 1 -10000 0 1
FGFR1 0.021 0.003 -10000 0 -10000 0 0
Syndecan-4/PI-4-5-P2 0.002 0.091 -10000 0 -0.37 24 24
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.032 0.039 0.12 94 -0.041 35 129
cell migration -0.017 0.009 -10000 0 -0.039 1 1
PRKCD 0.016 0.016 -10000 0 -0.039 43 43
vasculogenesis 0.022 0.1 0.26 1 -0.38 23 24
SDC4 0.007 0.094 -10000 0 -0.39 24 24
Syndecan-4/Tenascin C 0.059 0.12 0.26 9 -0.38 23 32
Syndecan-4/PI-4-5-P2/PKC alpha -0.024 0.012 -10000 0 -0.045 1 1
Syndecan-4/Syntenin 0.021 0.099 -10000 0 -0.38 23 23
MMP9 0.047 0.05 0.12 192 -0.033 23 215
Rac1/GTP 0.016 0.033 0.2 15 -10000 0 15
cytoskeleton organization 0.021 0.097 -10000 0 -0.37 23 23
GIPC1 0.02 0.004 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.048 0.12 0.26 9 -0.38 22 31
TCGA08_p53

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
CDKN2A 0.011 0.024 0.05 182 -10000 0 182
TP53 0.005 0.031 -10000 0 -0.16 20 20
Senescence 0.005 0.031 -10000 0 -0.15 21 21
Apoptosis 0.005 0.031 -10000 0 -0.15 21 21
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.007 0.045 0.28 15 -10000 0 15
MDM4 0.02 0.005 -10000 0 -10000 0 0
TCGA08_rtk_signaling

Figure S37.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S37.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.031 0.033 0.12 72 -10000 0 72
HRAS 0.02 0.005 -10000 0 -10000 0 0
EGFR 0.053 0.054 0.12 235 -10000 0 235
AKT 0.04 0.11 0.22 125 -0.14 18 143
FOXO3 0.02 0.004 -10000 0 -10000 0 0
AKT1 0.02 0.004 -10000 0 -10000 0 0
FOXO1 0.02 0.004 -10000 0 -10000 0 0
AKT3 0.021 0.003 -10000 0 -10000 0 0
FOXO4 0.021 0.002 -10000 0 -10000 0 0
MET 0.009 0.011 0.12 1 -10000 0 1
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
PIK3CB 0.021 0.002 -10000 0 -10000 0 0
NRAS 0.019 0.007 -10000 0 -10000 0 0
PIK3CG 0.019 0.018 0.12 14 -10000 0 14
PIK3R3 0.019 0.006 -10000 0 -10000 0 0
PIK3R2 0.02 0.004 -10000 0 -10000 0 0
NF1 0.021 0.002 -10000 0 -10000 0 0
RAS -0.007 0.052 0.11 10 -0.095 127 137
ERBB2 0.022 0.011 0.12 8 -10000 0 8
proliferation/survival/translation -0.013 0.065 0.35 9 -0.21 13 22
PI3K 0.015 0.1 0.2 100 -0.11 83 183
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
KRAS 0.02 0.004 -10000 0 -10000 0 0
FOXO 0.055 0.09 0.2 136 -10000 0 136
AKT2 0.019 0.007 -10000 0 -10000 0 0
PTEN 0.018 0.007 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.02 0.005 -10000 0 -9999 0 0
EGFR 0.053 0.054 0.12 235 -9999 0 235
EGF/EGFR 0.053 0.043 0.14 33 -9999 0 33
EGF/EGFR dimer/SHC/GRB2/SOS1 0.066 0.05 0.18 5 -9999 0 5
mol:GTP 0 0 -10000 0 -9999 0 0
EDNRA 0.032 0.033 0.12 75 -9999 0 75
response to oxidative stress 0 0 -10000 0 -9999 0 0
EGF 0.024 0.019 0.12 22 -9999 0 22
EGF/EGFR dimer/SHC 0.057 0.046 0.18 7 -9999 0 7
mol:GDP 0.06 0.046 0.17 5 -9999 0 5
mol:Ca2+ 0 0 -10000 0 -9999 0 0
EDN1 0.023 0.015 0.12 13 -9999 0 13
GRB2/SOS1 0.03 0.006 -10000 0 -9999 0 0
HRAS/GTP 0.039 0.031 -10000 0 -9999 0 0
SHC1 0.023 0.016 0.12 16 -9999 0 16
HRAS/GDP 0.052 0.042 -10000 0 -9999 0 0
FRAP1 -0.009 0.008 -10000 0 -9999 0 0
EGF/EGFR dimer 0.05 0.045 0.11 237 -9999 0 237
SOS1 0.021 0.001 -10000 0 -9999 0 0
GRB2 0.02 0.004 -10000 0 -9999 0 0
ETA receptor/Endothelin-1 0.04 0.027 0.11 86 -9999 0 86
ErbB2/ErbB3 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
USP8 -0.011 0.006 0.024 5 -10000 0 5
RAS family/GTP 0.003 0.08 0.22 1 -0.16 89 90
NFATC4 -0.034 0.052 0.2 8 -0.18 4 12
ERBB2IP 0.022 0.007 0.13 2 -10000 0 2
HSP90 (dimer) 0.02 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis -0.035 0.058 0.15 2 -0.15 118 120
JUN 0 0.051 0.18 5 -10000 0 5
HRAS 0.02 0.005 -10000 0 -10000 0 0
DOCK7 -0.039 0.055 0.13 11 -0.15 103 114
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.006 0.067 -10000 0 -0.13 126 126
AKT1 -0.007 0.005 0.027 2 -10000 0 2
BAD -0.01 0.004 0.018 2 -10000 0 2
MAPK10 -0.018 0.048 0.11 14 -0.13 2 16
mol:GTP 0 0 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.036 0.062 0.16 2 -0.16 118 120
RAF1 -0.015 0.08 0.22 22 -0.28 5 27
ErbB2/ErbB3/neuregulin 2 0.015 0.032 0.2 1 -0.13 13 14
STAT3 0.023 0.037 -10000 0 -0.89 1 1
cell migration -0.016 0.052 0.22 8 -0.16 1 9
mol:PI-3-4-5-P3 -0.001 0.001 -10000 0 -10000 0 0
cell proliferation 0.013 0.11 0.43 3 -0.59 4 7
FOS 0.012 0.091 0.34 6 -0.39 11 17
NRAS 0.019 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.035 0.058 0.15 2 -0.15 118 120
MAPK3 0.011 0.097 0.41 3 -0.53 4 7
MAPK1 0.008 0.1 0.41 3 -0.53 5 8
JAK2 -0.039 0.052 0.12 11 -0.15 99 110
NF2 0.003 0.028 -10000 0 -0.69 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.022 0.075 0.15 2 -0.18 120 122
NRG1 0.016 0.009 -10000 0 -10000 0 0
GRB2/SOS1 0.03 0.006 -10000 0 -10000 0 0
MAPK8 -0.032 0.082 -10000 0 -0.21 108 108
MAPK9 -0.018 0.047 0.11 10 -0.13 2 12
ERBB2 -0.019 0.009 -10000 0 -10000 0 0
ERBB3 0.02 0.009 0.12 4 -10000 0 4
SHC1 0.023 0.016 0.12 16 -10000 0 16
RAC1 0.018 0.008 -10000 0 -10000 0 0
apoptosis 0.006 0.009 -10000 0 -0.22 1 1
STAT3 (dimer) 0.023 0.036 -10000 0 -0.87 1 1
RNF41 -0.014 0.006 0.018 1 -10000 0 1
FRAP1 -0.006 0.003 0.013 5 -10000 0 5
RAC1-CDC42/GTP -0.033 0.039 -10000 0 -0.12 100 100
ErbB2/ErbB2/HSP90 (dimer) -0.018 0.011 -10000 0 -10000 0 0
CHRNA1 0.021 0.088 0.34 5 -0.51 4 9
myelination -0.034 0.056 0.28 6 -0.18 4 10
PPP3CB -0.039 0.049 0.12 7 -0.14 98 105
KRAS 0.02 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.006 0.074 -10000 0 -0.16 106 106
NRG2 0.021 0.003 -10000 0 -10000 0 0
mol:GDP -0.022 0.075 0.15 2 -0.17 120 122
SOS1 0.021 0.001 -10000 0 -10000 0 0
MAP2K2 -0.012 0.079 0.2 30 -0.24 6 36
SRC 0.02 0.004 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.042 0.054 0.12 12 -0.15 105 117
MAP2K1 -0.005 0.12 0.61 1 -0.57 11 12
heart morphogenesis -0.035 0.058 0.15 2 -0.15 118 120
RAS family/GDP 0.002 0.082 0.22 1 -0.16 90 91
GRB2 0.02 0.004 -10000 0 -10000 0 0
PRKACA 0.008 0.03 -10000 0 -0.73 1 1
CHRNE 0.002 0.013 0.064 6 -10000 0 6
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.007 0.005 -10000 0 -0.027 2 2
nervous system development -0.035 0.058 0.15 2 -0.15 118 120
CDC42 0.019 0.006 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.019 0.014 -10000 0 -0.088 11 11
SVIL 0.018 0.018 0.12 6 -0.08 12 18
ZNF318 0.022 0.022 0.17 12 -10000 0 12
JMJD2C 0.002 0.007 0.041 1 -10000 0 1
T-DHT/AR/Ubc9 0.057 0.047 0.12 44 -0.076 25 69
CARM1 0.019 0.007 -10000 0 -0.026 12 12
PRDX1 0.019 0.007 -10000 0 -10000 0 0
PELP1 0.021 0.004 -10000 0 -10000 0 0
CTNNB1 0.019 0.012 -10000 0 -0.068 12 12
AKT1 0.021 0.008 0.066 12 -0.017 1 13
PTK2B 0.019 0.011 -10000 0 -0.061 11 11
MED1 0.022 0.007 0.072 11 -10000 0 11
MAK 0.033 0.039 0.13 80 -10000 0 80
response to oxidative stress 0 0.002 -10000 0 -10000 0 0
HIP1 0.017 0.019 0.12 8 -0.08 11 19
GSN 0.019 0.015 -10000 0 -0.09 12 12
NCOA2 0.019 0.007 -10000 0 -0.026 11 11
NCOA6 0.019 0.014 -10000 0 -0.076 12 12
DNA-PK 0.042 0.02 0.18 10 -10000 0 10
NCOA4 0.018 0.008 -10000 0 -0.021 12 12
PIAS3 0.018 0.013 -10000 0 -0.068 11 11
cell proliferation 0.017 0.058 0.23 1 -0.39 9 10
XRCC5 0.021 0.005 0.063 1 -10000 0 1
UBE3A 0.019 0.018 -10000 0 -0.11 11 11
T-DHT/AR/SNURF 0.051 0.056 0.12 42 -0.097 45 87
FHL2 -0.023 0.18 -10000 0 -0.69 44 44
RANBP9 0.019 0.013 -10000 0 -0.076 12 12
JMJD1A 0.005 0.011 0.039 56 -10000 0 56
CDK6 0.024 0.028 0.12 43 -10000 0 43
TGFB1I1 0.049 0.049 0.12 186 -0.078 11 197
T-DHT/AR/CyclinD1 0.06 0.049 0.13 52 -0.075 21 73
XRCC6 0.021 0.006 0.063 1 -10000 0 1
T-DHT/AR 0.052 0.065 0.15 36 -0.14 42 78
CTDSP1 0.02 0.009 0.12 1 -0.037 12 13
CTDSP2 0.02 0.016 0.12 11 -10000 0 11
BRCA1 0.022 0.022 0.12 18 -0.08 12 30
TCF4 0.021 0.013 0.1 12 -0.018 22 34
CDKN2A 0.045 0.05 0.12 190 -0.017 2 192
SRF 0.013 0.041 -10000 0 -0.14 44 44
NKX3-1 0.005 0.021 0.06 4 -0.086 1 5
KLK3 -0.015 0.17 -10000 0 -1.2 12 12
TMF1 0.02 0.007 -10000 0 -0.026 12 12
HNRNPA1 0.021 0.01 0.079 12 -0.017 6 18
AOF2 -0.001 0.009 -10000 0 -0.064 12 12
APPL1 -0.01 0.016 0.1 12 -10000 0 12
T-DHT/AR/Caspase 8 0.061 0.05 0.13 56 -0.076 24 80
AR 0.07 0.057 0.12 329 -0.063 25 354
UBA3 0.02 0.008 -10000 0 -0.037 12 12
PATZ1 0.021 0.009 0.076 12 -0.017 6 18
PAWR 0.022 0.017 0.12 15 -0.026 11 26
PRKDC 0.021 0.005 0.054 9 -10000 0 9
PA2G4 0.02 0.011 0.089 11 -10000 0 11
UBE2I 0.021 0.002 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.055 0.044 0.11 45 -0.066 24 69
RPS6KA3 0.019 0.015 -10000 0 -0.09 12 12
T-DHT/AR/ARA70 0.05 0.049 0.12 35 -0.076 25 60
LATS2 0.021 0.01 0.085 11 -0.016 6 17
T-DHT/AR/PRX1 0.053 0.047 0.12 49 -0.068 14 63
Cyclin D3/CDK11 p58 0.016 0.002 -10000 0 -10000 0 0
VAV3 0.018 0.02 0.12 11 -0.068 11 22
KLK2 0.005 0.047 -10000 0 -0.32 10 10
CASP8 0.025 0.019 0.12 23 -10000 0 23
T-DHT/AR/TIF2/CARM1 0.059 0.055 0.13 33 -0.12 12 45
TMPRSS2 0.016 0.032 -10000 0 -10000 0 0
CCND1 0.026 0.027 0.12 43 -0.047 10 53
PIAS1 0.019 0.018 -10000 0 -0.11 11 11
mol:T-DHT -0.002 0.014 -10000 0 -0.052 45 45
CDC2L1 0 0.001 -10000 0 -10000 0 0
PIAS4 0.018 0.025 -10000 0 -0.16 12 12
T-DHT/AR/CDK6 0.047 0.053 0.13 48 -0.075 24 72
CMTM2 0.021 0.006 0.12 2 -10000 0 2
SNURF 0.02 0.004 -10000 0 -10000 0 0
ZMIZ1 0.015 0.022 -10000 0 -0.064 42 42
CCND3 0.021 0.002 -10000 0 -10000 0 0
TGIF1 0.038 0.04 0.12 122 -0.017 4 126
FKBP4 0.019 0.013 -10000 0 -0.075 11 11
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.015 0.002 -10000 0 -10000 0 0
PRKCZ 0.016 0.009 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.02 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.012 0.049 -10000 0 -0.22 10 10
IRAK/TOLLIP 0.021 0.005 -10000 0 -10000 0 0
IKBKB 0.021 0.003 -10000 0 -10000 0 0
IKBKG 0.021 0.002 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.049 0.056 0.11 227 -0.15 28 255
IL1A 0.02 0.007 0.12 2 -10000 0 2
IL1B 0 0.025 0.051 114 -0.14 1 115
IRAK/TRAF6/p62/Atypical PKCs 0.026 0.052 0.16 2 -0.11 70 72
IL1R2 0.058 0.05 0.12 238 -10000 0 238
IL1R1 0.025 0.019 0.12 24 -10000 0 24
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0 0.052 -10000 0 -0.28 8 8
TOLLIP 0.02 0.005 -10000 0 -10000 0 0
TICAM2 0.021 0.002 -10000 0 -10000 0 0
MAP3K3 0.021 0.003 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.014 0.003 -10000 0 -10000 0 0
IKK complex/ELKS -0.001 0.061 -10000 0 -0.27 6 6
JUN -0.014 0.014 0.15 3 -10000 0 3
MAP3K7 0.02 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.046 0.063 0.2 3 -0.12 69 72
IL1 alpha/IL1R1/IL1RAP/MYD88 0.058 0.049 0.19 21 -0.12 27 48
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.064 0.05 0.19 22 -0.12 27 49
IL1 beta fragment/IL1R1/IL1RAP 0.03 0.061 0.14 47 -0.12 70 117
NFKB1 0.021 0.002 -10000 0 -10000 0 0
MAPK8 -0.013 0.018 0.16 6 -10000 0 6
IRAK1 -0.01 0.001 -10000 0 -10000 0 0
IL1RN/IL1R1 0.021 0.055 0.18 4 -0.16 52 56
IRAK4 0.021 0.007 0.12 2 -10000 0 2
PRKCI 0.021 0.003 -10000 0 -10000 0 0
TRAF6 0.021 0.003 -10000 0 -10000 0 0
PI3K 0.03 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.011 0.048 -10000 0 -0.19 12 12
CHUK 0.019 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.03 0.061 0.14 47 -0.12 70 117
IL1 beta/IL1R2 0.044 0.077 0.17 74 -0.13 71 145
IRAK/TRAF6/TAK1/TAB1/TAB2 0.027 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.031 0.053 0.13 3 -0.12 60 63
IRAK3 0.024 0.019 0.12 23 -10000 0 23
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.045 0.064 0.2 5 -0.12 70 75
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.015 0.042 -10000 0 -0.16 28 28
IL1 alpha/IL1R1/IL1RAP 0.044 0.045 0.18 3 -0.13 28 31
RELA 0.021 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.021 0.003 -10000 0 -10000 0 0
MYD88 0.027 0.024 0.12 38 -10000 0 38
IRAK/TRAF6/MEKK3 0.032 0.009 -10000 0 -10000 0 0
IL1RAP 0.031 0.032 0.12 68 -10000 0 68
UBE2N 0.021 0.002 -10000 0 -10000 0 0
IRAK/TRAF6 -0.019 0.046 0.068 46 -10000 0 46
CASP1 0.038 0.039 0.12 112 -10000 0 112
IL1RN/IL1R2 0.044 0.07 0.18 12 -0.16 52 64
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.043 0.067 0.16 66 -0.12 69 135
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.012 0.051 -10000 0 -0.27 9 9
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
IL1RN 0.021 0.016 0.12 13 -10000 0 13
TRAF6/TAK1/TAB1/TAB2 0.029 0.008 -10000 0 -10000 0 0
MAP2K6 -0.01 0.022 0.17 9 -10000 0 9
PDGFR-alpha signaling 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
PDGFRA 0.031 0.034 0.12 73 -0.047 4 77
PDGF/PDGFRA/CRKL 0.036 0.027 0.11 69 -0.14 1 70
positive regulation of JUN kinase activity 0.054 0.029 -10000 0 -0.11 1 1
CRKL 0.021 0.005 0.12 1 -10000 0 1
PDGF/PDGFRA/Caveolin-3 0.035 0.027 0.11 40 -0.14 1 41
AP1 -0.006 0.075 0.26 2 -0.58 7 9
mol:IP3 -0.005 0.021 0.052 69 -0.066 4 73
PLCG1 -0.005 0.021 0.052 69 -0.066 4 73
PDGF/PDGFRA/alphaV Integrin 0.037 0.026 0.1 68 -0.14 1 69
RAPGEF1 0.021 0.003 -10000 0 -10000 0 0
CRK 0.021 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.005 0.021 0.052 69 -0.066 4 73
CAV3 0.02 0.014 0.12 11 -10000 0 11
CAV1 0.028 0.035 0.12 73 -10000 0 73
SHC/Grb2/SOS1 0.055 0.03 -10000 0 -0.11 1 1
PDGF/PDGFRA/Shf 0.036 0.027 0.1 68 -0.14 1 69
FOS -0.017 0.063 0.21 1 -0.58 7 8
JUN -0.014 0.014 -10000 0 -10000 0 0
oligodendrocyte development 0.036 0.026 0.1 68 -0.14 1 69
GRB2 0.02 0.004 -10000 0 -10000 0 0
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
mol:DAG -0.005 0.021 0.052 69 -0.066 4 73
PDGF/PDGFRA 0.031 0.034 0.12 73 -0.047 4 77
actin cytoskeleton reorganization 0.035 0.027 0.1 68 -0.12 1 69
SRF -0.013 0.005 -10000 0 -10000 0 0
SHC1 0.023 0.016 0.12 16 -10000 0 16
PI3K 0.045 0.027 -10000 0 -0.12 1 1
PDGF/PDGFRA/Crk/C3G 0.045 0.027 -10000 0 -0.12 1 1
JAK1 -0.005 0.018 0.049 53 -10000 0 53
ELK1/SRF -0.003 0.043 0.14 47 -0.12 1 48
SHB 0.02 0.004 -10000 0 -10000 0 0
SHF 0.021 0.003 -10000 0 -10000 0 0
CSNK2A1 0.018 0.013 -10000 0 -0.033 2 2
GO:0007205 -0.003 0.015 -10000 0 -10000 0 0
SOS1 0.021 0.001 -10000 0 -10000 0 0
Ras protein signal transduction 0.054 0.029 -10000 0 -0.11 1 1
PDGF/PDGFRA/SHB 0.035 0.027 0.1 68 -0.12 1 69
PDGF/PDGFRA/Caveolin-1 0.037 0.036 0.11 123 -10000 0 123
ITGAV 0.021 0.001 -10000 0 -10000 0 0
ELK1 -0.008 0.013 0.059 1 -0.1 3 4
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.036 0.027 0.11 1 -0.14 1 2
JAK-STAT cascade -0.005 0.018 0.049 53 -10000 0 53
cell proliferation 0.036 0.027 0.1 68 -0.14 1 69
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.02 0.004 -10000 0 -10000 0 0
NFATC1 -0.013 0.078 0.24 1 -0.31 13 14
NFATC2 -0.025 0.072 -10000 0 -0.22 52 52
NFATC3 -0.016 0.081 -10000 0 -0.25 71 71
YWHAE 0.021 0.002 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.16 0.15 0.16 1 -0.34 241 242
Exportin 1/Ran/NUP214 0.042 0.008 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.16 0.16 -10000 0 -0.3 304 304
BCL2/BAX 0.027 0.011 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.015 0.004 -10000 0 -10000 0 0
CaM/Ca2+ 0.015 0.004 -10000 0 -10000 0 0
BAX 0.019 0.007 -10000 0 -10000 0 0
MAPK14 0.021 0.002 -10000 0 -10000 0 0
BAD 0.021 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D -0.15 0.15 0.15 1 -0.33 230 231
Calcineurin A alpha-beta B1/BCL2 0.021 0.003 -10000 0 -10000 0 0
FKBP8 0.02 0.004 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.15 0.15 0.32 230 -0.15 1 231
KPNB1 0.021 0.002 -10000 0 -10000 0 0
KPNA2 0.021 0.003 -10000 0 -10000 0 0
XPO1 0.021 0.001 -10000 0 -10000 0 0
SFN 0.022 0.02 0.12 23 -10000 0 23
MAP3K8 0.021 0.016 0.12 12 -10000 0 12
NFAT4/CK1 alpha 0.002 0.046 -10000 0 -0.12 71 71
MEF2D/NFAT1/Cbp/p300 0.004 0.08 -10000 0 -0.22 37 37
CABIN1 -0.16 0.16 0.16 1 -0.34 242 243
CALM1 0.02 0.005 -10000 0 -10000 0 0
RAN 0.021 0.002 -10000 0 -10000 0 0
MAP3K1 0.024 0.018 0.12 21 -10000 0 21
CAMK4 0.015 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
MAPK3 0.021 0.002 -10000 0 -10000 0 0
YWHAH 0.02 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.034 0.088 -10000 0 -0.16 221 221
YWHAB 0.02 0.004 -10000 0 -10000 0 0
MAPK8 0.019 0.006 -10000 0 -10000 0 0
MAPK9 0.021 0.003 -10000 0 -10000 0 0
YWHAG 0.017 0.008 -10000 0 -10000 0 0
FKBP1A 0.02 0.004 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.021 0.1 -10000 0 -0.28 33 33
PRKCH 0.02 0.004 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.03 0.007 -10000 0 -10000 0 0
CASP3 0.021 0.009 0.12 4 -10000 0 4
PIM1 0.021 0.007 0.12 3 -10000 0 3
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.003 -10000 0 -10000 0 0
apoptosis 0.008 0.021 -10000 0 -0.12 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0 0.04 -10000 0 -0.22 6 6
PRKCB 0.014 0.01 -10000 0 -10000 0 0
PRKCE 0.02 0.004 -10000 0 -10000 0 0
JNK2/NFAT4 -0.021 0.089 -10000 0 -0.19 141 141
BAD/BCL-XL 0.03 0.007 -10000 0 -10000 0 0
PRKCD 0.02 0.004 -10000 0 -10000 0 0
NUP214 0.021 0.003 -10000 0 -10000 0 0
PRKCZ 0.017 0.009 -10000 0 -10000 0 0
PRKCA 0.02 0.004 -10000 0 -10000 0 0
PRKCG 0.005 0.009 -10000 0 -10000 0 0
PRKCQ 0.018 0.008 0.12 1 -10000 0 1
FKBP38/BCL2 0.029 0.007 -10000 0 -10000 0 0
EP300 0.02 0.004 -10000 0 -0.021 1 1
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.02 0.004 -10000 0 -10000 0 0
NFATc/JNK1 -0.005 0.076 -10000 0 -0.3 13 13
CaM/Ca2+/FKBP38 0.026 0.008 -10000 0 -10000 0 0
FKBP12/FK506 0.015 0.003 -10000 0 -10000 0 0
CSNK1A1 -0.009 0.003 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.015 0.069 -10000 0 -0.13 181 181
NFATc/ERK1 -0.003 0.081 0.24 1 -0.3 13 14
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.16 0.16 -10000 0 -0.3 310 310
NR4A1 -0.017 0.062 -10000 0 -0.2 34 34
GSK3B 0.021 0.003 -10000 0 -10000 0 0
positive T cell selection -0.016 0.081 -10000 0 -0.25 71 71
NFAT1/CK1 alpha -0.014 0.05 -10000 0 -0.17 38 38
RCH1/ KPNB1 0.031 0.005 -10000 0 -10000 0 0
YWHAQ 0.021 0.002 -10000 0 -10000 0 0
PRKACA 0.02 0.004 -10000 0 -10000 0 0
AKAP5 0.013 0.01 -10000 0 -10000 0 0
MEF2D 0.021 0.003 -10000 0 -0.021 1 1
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.02 0.005 -10000 0 -10000 0 0
NFATc/p38 alpha -0.003 0.08 0.24 1 -0.3 13 14
CREBBP 0.021 0.003 -10000 0 -0.021 1 1
BCL2 0.021 0.003 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.021 0.005 0.12 1 -10000 0 1
RAS family/GTP/Tiam1 0.001 0.034 -10000 0 -0.2 1 1
NT3 (dimer)/TRKC 0.027 0.017 -10000 0 -0.15 4 4
NT3 (dimer)/TRKB 0.045 0.029 0.18 2 -0.12 3 5
SHC/Grb2/SOS1/GAB1/PI3K 0.018 0.007 -10000 0 -10000 0 0
RAPGEF1 0.021 0.003 -10000 0 -10000 0 0
BDNF 0.01 0.011 -10000 0 -10000 0 0
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
DYNLT1 0.03 0.031 0.12 63 -10000 0 63
NTRK1 0.026 0.023 0.12 35 -10000 0 35
NTRK2 0.021 0.005 0.12 1 -10000 0 1
NTRK3 0.021 0.003 -10000 0 -10000 0 0
NT-4/5 (dimer)/TRKB 0.044 0.032 0.18 3 -0.13 2 5
neuron apoptosis 0.068 0.11 0.31 66 -10000 0 66
SHC 2-3/Grb2 -0.073 0.12 -10000 0 -0.33 66 66
SHC1 0.023 0.016 0.12 16 -10000 0 16
SHC2 -0.06 0.088 -10000 0 -0.24 66 66
SHC3 -0.085 0.14 -10000 0 -0.42 65 65
STAT3 (dimer) 0.027 0.013 -10000 0 -10000 0 0
NT3 (dimer)/TRKA 0.049 0.03 0.18 6 -10000 0 6
RIN/GDP -0.001 0.048 0.17 6 -0.25 4 10
GIPC1 0.02 0.004 -10000 0 -10000 0 0
KRAS 0.02 0.004 -10000 0 -10000 0 0
DNAJA3 -0.014 0.045 0.12 5 -0.15 34 39
RIN/GTP -0.027 0.072 -10000 0 -0.15 168 168
CCND1 -0.002 0.031 0.27 2 -10000 0 2
MAGED1 0.021 0 -10000 0 -10000 0 0
PTPN11 0.021 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.019 0.02 0.12 22 -10000 0 22
SHC/GRB2/SOS1 0.042 0.014 -10000 0 -10000 0 0
GRB2 0.02 0.004 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.015 0.085 0.18 1 -0.14 197 198
TRKA/NEDD4-2 0.03 0.033 -10000 0 -0.16 15 15
ELMO1 0.018 0.008 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.022 0.012 -10000 0 -10000 0 0
NGF 0.017 0.009 0.12 1 -10000 0 1
HRAS 0.02 0.005 -10000 0 -10000 0 0
DOCK1 0.018 0.007 -10000 0 -10000 0 0
GAB2 0.021 0.003 -10000 0 -10000 0 0
RIT2 0.015 0.009 -10000 0 -10000 0 0
RIT1 0.021 0.003 -10000 0 -10000 0 0
FRS2 0.02 0.004 -10000 0 -10000 0 0
DNM1 0.009 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.021 0.002 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.007 0.049 0.14 1 -0.14 29 30
mol:GDP 0 0.065 0.23 9 -0.37 4 13
NGF (dimer) 0.017 0.009 0.12 1 -10000 0 1
RhoG/GDP 0.013 0.006 -10000 0 -10000 0 0
RIT1/GDP 0.005 0.05 0.2 8 -0.24 4 12
TIAM1 0.02 0.004 -10000 0 -10000 0 0
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.048 0.087 -10000 0 -0.13 340 340
KIDINS220/CRKL/C3G 0.03 0.007 0.11 1 -10000 0 1
SHC/RasGAP 0.032 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2 0.041 0.009 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.052 0.017 -10000 0 -10000 0 0
RIT1/GTP 0.015 0.002 -10000 0 -10000 0 0
NT3 (dimer) 0.019 0.011 0.12 6 -10000 0 6
RAP1/GDP 0.004 0.037 0.11 1 -0.21 4 5
KIDINS220/CRKL 0.021 0.005 0.12 1 -10000 0 1
BDNF (dimer) 0.01 0.01 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.026 0.053 0.18 1 -0.13 55 56
Schwann cell development -0.018 0.015 -10000 0 -0.044 91 91
EHD4 0.022 0.012 0.12 8 -10000 0 8
FRS2 family/GRB2/SOS1 0.051 0.014 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.016 0.03 -10000 0 -0.2 7 7
RAP1B 0.021 0.009 0.12 4 -10000 0 4
RAP1A 0.019 0.007 -10000 0 -10000 0 0
CDC42/GTP -0.038 0.071 -10000 0 -0.11 304 304
ABL1 0.021 0.003 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.03 0.006 -10000 0 -10000 0 0
Rap1/GTP -0.042 0.082 -10000 0 -0.25 54 54
STAT3 0.027 0.013 -10000 0 -10000 0 0
axon guidance -0.041 0.065 -10000 0 -0.11 304 304
MAPK3 -0.046 0.057 0.14 3 -0.13 194 197
MAPK1 -0.045 0.057 0.18 2 -0.13 188 190
CDC42/GDP 0.009 0.045 0.17 8 -0.24 4 12
NTF3 0.019 0.011 0.12 6 -10000 0 6
NTF4 0.019 0.021 0.12 22 -10000 0 22
NGF (dimer)/TRKA/FAIM 0.03 0.047 0.18 1 -0.13 40 41
PI3K 0.03 0.006 -10000 0 -10000 0 0
FRS3 0.021 0.002 -10000 0 -10000 0 0
FAIM 0.021 0.002 -10000 0 -10000 0 0
GAB1 0.021 0.003 -10000 0 -10000 0 0
RASGRF1 -0.016 0.049 0.13 2 -0.18 38 40
SOS1 0.021 0.001 -10000 0 -10000 0 0
MCF2L -0.014 0.011 -10000 0 -0.13 4 4
RGS19 0.02 0.004 -10000 0 -10000 0 0
CDC42 0.019 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.003 0.053 -10000 0 -0.4 4 4
Rac1/GDP 0.005 0.044 0.2 5 -0.35 1 6
NGF (dimer)/TRKA/GRIT 0.019 0.042 0.098 35 -0.13 41 76
neuron projection morphogenesis 0.009 0.065 -10000 0 -0.93 1 1
NGF (dimer)/TRKA/NEDD4-2 0.026 0.053 0.18 1 -0.13 55 56
MAP2K1 -0.009 0.042 0.17 33 -10000 0 33
NGFR 0.034 0.035 0.12 84 -10000 0 84
NGF (dimer)/TRKA/GIPC/GAIP -0.082 0.11 -10000 0 -0.18 320 320
RAS family/GTP/PI3K 0.012 0.012 -10000 0 -0.17 2 2
FRS2 family/SHP2/GRB2/SOS1 0.058 0.017 -10000 0 -10000 0 0
NRAS 0.019 0.007 -10000 0 -10000 0 0
GRB2/SOS1 0.03 0.006 -10000 0 -10000 0 0
PRKCI 0.021 0.003 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.018 0.008 -10000 0 -10000 0 0
PRKCZ 0.016 0.009 -10000 0 -10000 0 0
MAPKKK cascade -0.046 0.19 -10000 0 -0.44 114 114
RASA1 0.021 0.002 -10000 0 -10000 0 0
TRKA/c-Abl 0.034 0.018 0.11 35 -10000 0 35
SQSTM1 0.021 0.003 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.035 0.087 -10000 0 -0.12 331 331
NGF (dimer)/TRKA/p62/Atypical PKCs 0.027 0.07 -10000 0 -0.12 99 99
MATK 0.015 0.01 -10000 0 -10000 0 0
NEDD4L 0.02 0.005 -10000 0 -10000 0 0
RAS family/GDP -0.007 0.026 -10000 0 -0.16 5 5
NGF (dimer)/TRKA 0 0.05 0.14 3 -0.15 34 37
Rac1/GTP -0.019 0.05 -10000 0 -0.16 23 23
FRS2 family/SHP2/CRK family 0.059 0.016 -10000 0 -10000 0 0
Osteopontin-mediated 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
IKK alpha homodimer 0.03 0.025 0.17 1 -10000 0 1
NF kappa B1 p50/RelA/I kappa B alpha 0.032 0.039 0.27 4 -10000 0 4
alphaV/beta3 Integrin/Osteopontin/Src 0.045 0.032 0.12 44 -0.15 3 47
AP1 0.052 0.053 0.2 5 -0.18 1 6
ILK 0.006 0.031 0.19 2 -10000 0 2
bone resorption 0.023 0.06 0.18 22 -10000 0 22
PTK2B 0.021 0.003 -10000 0 -10000 0 0
PYK2/p130Cas 0.069 0.04 0.17 33 -0.11 3 36
ITGAV 0.023 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.058 0.039 0.11 248 -0.15 2 250
alphaV/beta3 Integrin/Osteopontin 0.073 0.051 0.2 58 -0.13 3 61
MAP3K1 0.008 0.035 0.084 49 -0.12 3 52
JUN 0.019 0.007 -10000 0 -10000 0 0
MAPK3 0.005 0.033 0.18 1 -10000 0 1
MAPK1 0.004 0.033 0.18 1 -10000 0 1
Rac1/GDP 0.013 0.006 -10000 0 -10000 0 0
NFKB1 0.021 0.002 -10000 0 -10000 0 0
MAPK8 -0.002 0.025 0.18 2 -10000 0 2
ITGB3 0.043 0.042 0.13 124 -10000 0 124
NFKBIA 0.007 0.028 0.17 1 -0.17 1 2
FOS 0.022 0.013 0.12 8 -10000 0 8
CD44 0.06 0.051 0.12 252 -10000 0 252
CHUK 0.019 0.006 -10000 0 -10000 0 0
PLAU 0.018 0.05 0.28 2 -10000 0 2
NF kappa B1 p50/RelA 0.046 0.035 0.19 5 -10000 0 5
BCAR1 0.021 0.003 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.05 0.032 0.12 101 -10000 0 101
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.005 0.031 0.1 11 -0.12 3 14
VAV3 0.001 0.025 0.19 4 -10000 0 4
MAP3K14 0.009 0.035 0.08 55 -0.12 3 58
ROCK2 0.021 0.002 -10000 0 -10000 0 0
SPP1 0.038 0.038 0.13 96 -10000 0 96
RAC1 0.018 0.008 -10000 0 -10000 0 0
Rac1/GTP -0.007 0.036 0.16 2 -10000 0 2
MMP2 0.015 0.059 0.21 13 -10000 0 13
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.048 0.028 0.21 5 -0.12 1 6
MAP4K1 0.02 0.011 0.12 5 -10000 0 5
MAP3K8 0.021 0.016 0.12 12 -10000 0 12
PRKCB 0.014 0.01 -10000 0 -10000 0 0
DBNL 0.018 0.008 -10000 0 -10000 0 0
CRKL 0.021 0.005 0.12 1 -10000 0 1
MAP3K1 0.011 0.039 0.12 1 -0.26 2 3
JUN -0.17 0.27 -10000 0 -0.53 224 224
MAP3K7 0.01 0.035 -10000 0 -0.16 2 2
GRAP2 0.023 0.018 0.12 19 -10000 0 19
CRK 0.021 0.002 -10000 0 -10000 0 0
MAP2K4 0.007 0.044 0.18 5 -0.52 1 6
LAT 0.021 0.006 0.12 2 -10000 0 2
LCP2 0.021 0.009 0.12 4 -10000 0 4
MAPK8 -0.18 0.28 -10000 0 -0.56 226 226
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.018 0.042 -10000 0 -0.22 4 4
LAT/GRAP2/SLP76/HPK1/HIP-55 0.048 0.034 0.21 5 -0.12 1 6
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.038 0.029 0.11 83 -0.16 3 86
ATM 0.021 0.003 -10000 0 -10000 0 0
UBE2D3 0.021 0.002 -10000 0 -10000 0 0
PRKDC 0.021 0.003 -10000 0 -10000 0 0
ATR 0.021 0.003 -10000 0 -10000 0 0
UBE2L3 0.021 0.003 -10000 0 -10000 0 0
FANCD2 0.023 0.018 -10000 0 -10000 0 0
protein ubiquitination 0.07 0.05 0.18 65 -0.12 3 68
XRCC5 0.021 0.001 -10000 0 -10000 0 0
XRCC6 0.02 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.04 0.012 -10000 0 -10000 0 0
MRE11A 0.021 0.003 -10000 0 -10000 0 0
DNA-PK 0.04 0.01 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.019 0.063 0.19 1 -0.47 7 8
FANCF 0.021 0.003 -10000 0 -10000 0 0
BRCA1 0.024 0.017 0.12 18 -10000 0 18
CCNE1 0.019 0.007 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.048 0.037 -10000 0 -10000 0 0
FANCG 0.02 0.006 0.12 1 -10000 0 1
BRCA1/BACH1/BARD1 0.043 0.034 0.18 11 -0.16 3 14
FANCE 0.021 0.002 -10000 0 -10000 0 0
FANCC 0.034 0.035 0.12 85 -10000 0 85
NBN 0.02 0.005 -10000 0 -10000 0 0
FANCA 0.022 0.01 0.12 6 -10000 0 6
DNA repair 0.018 0.057 0.23 22 -0.4 2 24
BRCA1/BARD1/ubiquitin 0.043 0.034 0.18 11 -0.16 3 14
BARD1/DNA-PK 0.059 0.028 -10000 0 -0.12 2 2
FANCL 0.021 0.002 -10000 0 -10000 0 0
mRNA polyadenylation -0.038 0.029 0.16 3 -0.1 83 86
BRCA1/BARD1/CTIP/M/R/N Complex 0.017 0.02 0.15 3 -0.16 2 5
BRCA1/BACH1/BARD1/TopBP1 0.052 0.031 0.18 10 -0.13 3 13
BRCA1/BARD1/P53 0.068 0.041 0.19 33 -0.12 3 36
BARD1/CSTF1/BRCA1 0.05 0.032 0.18 11 -0.13 3 14
BRCA1/BACH1 0.024 0.017 0.12 18 -10000 0 18
BARD1 0.036 0.036 0.12 95 -10000 0 95
PCNA 0.027 0.027 0.12 46 -10000 0 46
BRCA1/BARD1/UbcH5C 0.052 0.031 0.18 9 -0.13 3 12
BRCA1/BARD1/UbcH7 0.051 0.031 0.18 8 -0.13 3 11
BRCA1/BARD1/RAD51/PCNA 0.084 0.06 0.2 90 -0.11 3 93
BARD1/DNA-PK/P53 0.07 0.036 0.18 20 -0.11 2 22
BRCA1/BARD1/Ubiquitin 0.043 0.034 0.18 11 -0.16 3 14
BRCA1/BARD1/CTIP 0.045 0.037 0.17 29 -0.12 3 32
FA complex 0.017 0.024 -10000 0 -0.17 5 5
BARD1/EWS 0.04 0.03 0.11 90 -0.16 3 93
RBBP8 -0.008 0.016 0.051 47 -10000 0 47
TP53 0.031 0.031 0.12 67 -10000 0 67
TOPBP1 0.021 0.003 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.066 0.04 0.12 3 -0.19 33 36
BRCA1/BARD1 0.076 0.054 0.19 65 -0.12 3 68
CSTF1 0.02 0.004 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.025 0.029 0.089 95 -0.15 3 98
CDK2 0.051 0.048 0.12 198 -10000 0 198
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.059 0.05 0.12 242 -10000 0 242
RAD50 0.021 0.002 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.043 0.034 0.18 11 -0.16 3 14
EWSR1 0.02 0.004 -10000 0 -10000 0 0
IL4-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
BCL2L1 -0.16 0.31 0.62 2 -0.99 8 10
STAT6 (cleaved dimer) -0.2 0.32 -10000 0 -0.91 34 34
IGHG1 -0.058 0.14 0.38 2 -10000 0 2
IGHG3 -0.16 0.29 -10000 0 -0.96 8 8
AKT1 -0.12 0.25 0.4 3 -0.75 38 41
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.092 0.22 0.39 2 -0.79 25 27
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.12 0.25 0.42 2 -0.74 42 44
THY1 -0.18 0.33 -10000 0 -1.1 18 18
MYB 0.03 0.031 0.12 63 -10000 0 63
HMGA1 0.021 0.005 0.12 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.14 0.26 0.41 7 -0.69 44 51
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.12 0.25 0.42 2 -0.74 42 44
SP1 0.027 0.012 -10000 0 -10000 0 0
INPP5D 0.021 0.009 0.12 5 -10000 0 5
SOCS5 0.021 0.029 -10000 0 -0.056 7 7
STAT6 (dimer)/ETS1 -0.18 0.33 0.6 1 -0.94 26 27
SOCS1 -0.14 0.28 0.42 12 -0.65 39 51
SOCS3 -0.18 0.36 0.52 2 -1.1 57 59
FCER2 -0.58 0.62 0.5 1 -1.2 339 340
PARP14 -0.009 0.045 0.11 29 -0.048 325 354
CCL17 -0.17 0.3 -10000 0 -0.99 8 8
GRB2 0.02 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.088 0.19 0.38 3 -0.58 23 26
T cell proliferation -0.18 0.32 -10000 0 -0.98 14 14
IL4R/JAK1 -0.17 0.31 -10000 0 -1 8 8
EGR2 -0.28 0.4 -10000 0 -1.1 42 42
JAK2 -0.006 0.045 0.11 8 -10000 0 8
JAK3 0.01 0.02 -10000 0 -0.041 24 24
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
JAK1 0.004 0.028 0.077 7 -10000 0 7
COL1A2 -0.044 0.15 -10000 0 -0.73 2 2
CCL26 -0.13 0.34 0.6 10 -1 7 17
IL4R -0.18 0.32 0.61 1 -1 8 9
PTPN6 0.017 0.024 0.11 4 -0.046 1 5
IL13RA2 -0.33 0.55 -10000 0 -1.2 153 153
IL13RA1 -0.003 0.048 0.12 10 -10000 0 10
IRF4 -0.065 0.15 0.4 1 -0.79 8 9
ARG1 -0.047 0.13 0.36 1 -0.93 1 2
CBL -0.13 0.24 0.39 4 -0.66 43 47
GTF3A 0.029 0.024 -10000 0 -0.12 8 8
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
IL13RA1/JAK2 0 0.066 0.16 14 -10000 0 14
IRF4/BCL6 -0.017 0.13 -10000 0 -0.78 6 6
CD40LG 0.002 0.033 0.12 22 -0.078 2 24
MAPK14 -0.15 0.28 0.41 4 -0.77 55 59
mitosis -0.11 0.24 0.39 3 -0.7 38 41
STAT6 -0.18 0.34 0.62 2 -1.1 8 10
SPI1 0.024 0.014 0.13 10 -10000 0 10
RPS6KB1 -0.11 0.23 0.4 4 -0.69 36 40
STAT6 (dimer) -0.18 0.33 0.62 2 -1.1 8 10
STAT6 (dimer)/PARP14 -0.24 0.36 -10000 0 -0.94 30 30
mast cell activation 0.005 0.013 -10000 0 -0.034 5 5
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.1 0.23 0.42 3 -0.74 25 28
FRAP1 -0.12 0.25 0.4 3 -0.75 38 41
LTA -0.17 0.3 0.57 1 -0.99 8 9
FES 0.021 0.005 0.12 1 -10000 0 1
T-helper 1 cell differentiation 0.18 0.33 1.1 8 -0.62 2 10
CCL11 -0.17 0.29 -10000 0 -0.96 8 8
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.11 0.23 0.43 2 -0.75 25 27
IL2RG 0.024 0.04 0.12 78 -0.042 24 102
IL10 -0.16 0.31 0.57 2 -0.99 8 10
IRS1 0.021 0.001 -10000 0 -10000 0 0
IRS2 0.02 0.004 -10000 0 -10000 0 0
IL4 -0.041 0.13 -10000 0 -0.93 4 4
IL5 -0.17 0.3 -10000 0 -0.99 8 8
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.15 0.28 0.55 2 -0.79 11 13
COL1A1 -0.066 0.23 0.43 2 -0.92 24 26
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.17 0.3 -10000 0 -1 8 8
IL2R gamma/JAK3 0.018 0.05 0.11 40 -0.15 21 61
TFF3 -0.17 0.31 0.58 2 -0.99 8 10
ALOX15 -0.17 0.3 -10000 0 -0.99 8 8
MYBL1 0.021 0.01 0.12 5 -10000 0 5
T-helper 2 cell differentiation -0.17 0.3 0.5 2 -0.8 28 30
SHC1 0.023 0.016 0.12 16 -10000 0 16
CEBPB 0.022 0.008 0.13 2 -10000 0 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.12 0.25 0.42 2 -0.72 45 47
mol:PI-3-4-5-P3 -0.12 0.25 0.4 3 -0.75 38 41
PI3K -0.12 0.26 0.4 3 -0.8 38 41
DOK2 0.026 0.024 0.12 36 -10000 0 36
ETS1 0.021 0.033 0.13 22 -0.054 5 27
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.08 0.18 0.33 8 -0.52 26 34
ITGB3 -0.16 0.31 0.57 1 -0.99 8 9
PIGR -0.16 0.31 0.57 1 -0.99 8 9
IGHE 0.017 0.044 0.15 13 -0.12 3 16
MAPKKK cascade -0.079 0.18 0.33 8 -0.52 26 34
BCL6 0.032 0.014 0.061 29 -0.018 1 30
OPRM1 -0.19 0.35 -10000 0 -1.3 22 22
RETNLB -0.17 0.3 -10000 0 -0.99 8 8
SELP -0.17 0.31 0.57 2 -0.99 8 10
AICDA -0.16 0.29 -10000 0 -0.94 8 8
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.059 0.031 -10000 0 -0.11 2 2
SMAD6-7/SMURF1 0.033 0.018 -10000 0 -10000 0 0
NOG 0.04 0.041 0.12 124 -10000 0 124
SMAD9 0 0.11 -10000 0 -0.4 42 42
SMAD4 0.021 0.003 -10000 0 -10000 0 0
SMAD5 0.004 0.054 -10000 0 -0.27 16 16
BMP7/USAG1 -0.051 0.089 -10000 0 -0.16 268 268
SMAD5/SKI 0.011 0.063 -10000 0 -0.28 19 19
SMAD1 0.006 0.05 -10000 0 -0.34 6 6
BMP2 0.079 0.052 0.12 378 -10000 0 378
SMAD1/SMAD1/SMAD4 0.018 0.045 -10000 0 -0.25 10 10
BMPR1A 0.019 0.006 -10000 0 -10000 0 0
BMPR1B 0.021 0.003 -10000 0 -10000 0 0
BMPR1A-1B/BAMBI 0.036 0.018 -10000 0 -0.13 2 2
AHSG 0.023 0.016 0.12 15 -10000 0 15
CER1 0.027 0.031 0.12 60 -10000 0 60
BMP2-4/CER1 0.078 0.044 0.18 17 -0.13 1 18
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA 0.015 0.054 -10000 0 -0.24 8 8
BMP2-4 (homodimer) 0.072 0.044 0.11 374 -0.16 1 375
RGMB 0.021 0.002 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.047 0.021 -10000 0 -0.11 2 2
RGMA 0.023 0.014 0.12 12 -10000 0 12
SMURF1 0.017 0.009 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP 0.016 0.04 -10000 0 -0.2 3 3
BMP2-4/USAG1 -0.014 0.098 0.18 5 -0.12 269 274
SMAD6/SMURF1/SMAD5 0.011 0.057 -10000 0 -0.28 14 14
SOSTDC1 0.009 0.01 -10000 0 -10000 0 0
BMP7/BMPR2/BMPR1A-1B 0.047 0.021 -10000 0 -0.11 2 2
SKI 0.019 0.007 -10000 0 -10000 0 0
BMP6 (homodimer) 0.021 0.009 0.12 5 -10000 0 5
HFE2 0.018 0.005 -10000 0 -10000 0 0
ZFYVE16 0.021 0.002 -10000 0 -10000 0 0
MAP3K7 0.02 0.004 -10000 0 -10000 0 0
BMP2-4/CHRD 0.076 0.047 0.18 13 -0.13 7 20
SMAD5/SMAD5/SMAD4 0.01 0.066 -10000 0 -0.27 22 22
MAPK1 0.021 0.003 -10000 0 -10000 0 0
TAK1/TAB family 0.022 0.041 -10000 0 -0.22 2 2
BMP7 (homodimer) 0.02 0.004 -10000 0 -10000 0 0
NUP214 0.021 0.003 -10000 0 -10000 0 0
BMP6/FETUA 0.032 0.014 -10000 0 -10000 0 0
SMAD1/SKI 0.014 0.057 -10000 0 -0.3 11 11
SMAD6 0.021 0.006 0.12 2 -10000 0 2
CTDSP2 0.019 0.006 -10000 0 -10000 0 0
BMP2-4/FETUA 0.08 0.044 0.18 27 -0.13 1 28
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.017 0.01 0.12 1 -10000 0 1
BMPR2 (homodimer) 0.021 0.001 -10000 0 -10000 0 0
GADD34/PP1CA 0.037 0.015 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.027 0.014 -10000 0 -0.16 2 2
CHRDL1 0.02 0.009 0.12 3 -10000 0 3
ENDOFIN/SMAD1 0.016 0.058 -10000 0 -0.3 11 11
SMAD6-7/SMURF1/SMAD1 0.027 0.054 -10000 0 -0.28 10 10
SMAD6/SMURF1 0.017 0.008 -10000 0 -10000 0 0
BAMBI 0.019 0.009 0.12 2 -10000 0 2
SMURF2 0.021 0.003 -10000 0 -10000 0 0
BMP2-4/CHRDL1 0.062 0.07 0.18 14 -0.13 55 69
BMP2-4/GREM1 0.038 0.087 0.18 9 -0.12 127 136
SMAD7 0.021 0.003 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 0.003 0.12 -10000 0 -0.37 53 53
SMAD1/SMAD6 0.013 0.05 -10000 0 -0.29 10 10
TAK1/SMAD6 0.024 0.013 -10000 0 -10000 0 0
BMP7 0.02 0.004 -10000 0 -10000 0 0
BMP6 0.021 0.009 0.12 5 -10000 0 5
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 0.02 0.044 -10000 0 -0.23 4 4
PPM1A 0.02 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.016 0.058 -10000 0 -0.3 11 11
SMAD7/SMURF1 0.024 0.013 -10000 0 -10000 0 0
CTDSPL 0.021 0.002 -10000 0 -10000 0 0
PPP1CA 0.021 0.003 -10000 0 -10000 0 0
XIAP 0.021 0.001 -10000 0 -10000 0 0
CTDSP1 0.021 0.004 0.12 1 -10000 0 1
PPP1R15A 0.019 0.007 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS 0.015 0.044 -10000 0 -0.2 2 2
CHRD 0.02 0.004 -10000 0 -10000 0 0
BMPR2 0.021 0.001 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM 0.016 0.04 0.13 1 -0.16 9 10
BMP4 0.023 0.017 0.12 18 -10000 0 18
FST 0.033 0.034 0.12 79 -10000 0 79
BMP2-4/NOG 0.089 0.059 0.18 126 -0.13 2 128
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.047 0.029 -10000 0 -0.1 2 2
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.04 0.011 -10000 0 -10000 0 0
fibroblast growth factor receptor signaling pathway 0.04 0.011 -10000 0 -10000 0 0
LAMA1 0.025 0.022 0.12 30 -10000 0 30
PRNP 0.02 0.004 -10000 0 -10000 0 0
GPC1/SLIT2 -0.03 0.088 0.11 3 -0.16 214 217
SMAD2 -0.016 0.008 -10000 0 -0.12 1 1
GPC1/PrPc/Cu2+ 0.026 0.01 0.096 1 -0.13 1 2
GPC1/Laminin alpha1 0.031 0.026 -10000 0 -0.15 7 7
TDGF1 0.02 0.006 0.12 1 -10000 0 1
CRIPTO/GPC1 0.025 0.034 -10000 0 -0.16 19 19
APP/GPC1 0.03 0.011 -10000 0 -0.16 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.017 0.022 -10000 0 -0.14 19 19
FLT1 0.02 0.005 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.041 0.014 -10000 0 -0.13 1 1
SERPINC1 0.026 0.025 0.12 40 -10000 0 40
FYN -0.017 0.019 -10000 0 -0.13 16 16
FGR -0.015 0.022 0.062 6 -0.14 16 22
positive regulation of MAPKKK cascade -0.002 0.066 0.18 32 -0.23 22 54
SLIT2 0.014 0.012 0.12 2 -10000 0 2
GPC1/NRG -0.006 0.074 -10000 0 -0.16 128 128
NRG1 0.016 0.009 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.046 0.026 0.18 1 -0.13 1 2
LYN -0.017 0.021 0.062 3 -0.13 18 21
mol:Spermine -0.006 0.002 0.049 1 -10000 0 1
cell growth 0.04 0.011 -10000 0 -10000 0 0
BMP signaling pathway -0.021 0.005 -10000 0 -0.12 1 1
SRC -0.017 0.02 -10000 0 -0.14 16 16
TGFBR1 0.021 0.009 0.12 4 -10000 0 4
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.032 0.041 0.12 105 -10000 0 105
GPC1 0.021 0.005 0.12 1 -10000 0 1
TGFBR1 (dimer) 0.021 0.009 0.12 4 -10000 0 4
VEGFA 0.033 0.034 0.12 79 -10000 0 79
BLK -0.006 0.034 0.062 98 -0.13 18 116
HCK -0.015 0.023 0.062 11 -0.14 16 27
FGF2 0.021 0.005 0.12 1 -10000 0 1
FGFR1 0.021 0.003 -10000 0 -10000 0 0
VEGFR1 homodimer 0.02 0.005 -10000 0 -10000 0 0
TGFBR2 0.021 0.007 0.12 3 -10000 0 3
cell death 0.029 0.01 -10000 0 -0.16 1 1
ATIII/GPC1 0.034 0.019 -10000 0 -10000 0 0
PLA2G2A/GPC1 0.028 0.054 0.11 104 -0.16 35 139
LCK -0.002 0.036 0.062 122 -0.14 16 138
neuron differentiation -0.006 0.074 -10000 0 -0.16 128 128
PrPc/Cu2+ 0.015 0.003 -10000 0 -10000 0 0
APP 0.021 0.003 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.021 0.007 0.12 3 -10000 0 3
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.057 0.088 0.18 6 -0.24 32 38
TBX21 -0.045 0.18 -10000 0 -0.79 20 20
B2M 0.032 0.032 0.12 68 -10000 0 68
TYK2 0.024 0.018 -10000 0 -10000 0 0
IL12RB1 0.024 0.019 0.097 3 -0.054 3 6
GADD45B -0.007 0.14 -10000 0 -0.6 10 10
IL12RB2 0.007 0.015 0.081 1 -0.055 2 3
GADD45G 0.004 0.14 -10000 0 -0.62 8 8
natural killer cell activation 0.014 0.013 0.038 54 -0.039 4 58
RELB 0.019 0.007 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
IL18 0.028 0.025 0.13 29 -0.032 2 31
IL2RA 0.039 0.045 0.12 139 -10000 0 139
IFNG 0.017 0.01 0.12 5 -10000 0 5
STAT3 (dimer) -0.016 0.15 0.34 4 -0.63 23 27
HLA-DRB5 0 0.002 -10000 0 -0.02 4 4
FASLG -0.046 0.18 0.57 1 -0.79 21 22
NF kappa B2 p52/RelB -0.042 0.18 -10000 0 -0.74 26 26
CD4 0.021 0.015 0.12 11 -0.03 7 18
SOCS1 0.052 0.048 0.12 202 -10000 0 202
EntrezGene:6955 0.001 0.003 -10000 0 -0.022 7 7
CD3D 0.033 0.036 0.13 83 -0.034 7 90
CD3E 0.03 0.032 0.13 60 -0.03 7 67
CD3G 0.028 0.031 0.13 55 -0.035 7 62
IL12Rbeta2/JAK2 -0.083 0.088 0.13 1 -0.15 417 418
CCL3 -0.061 0.25 -10000 0 -1.1 26 26
CCL4 -0.061 0.25 0.41 1 -1.1 26 27
HLA-A 0.001 0.001 -10000 0 -10000 0 0
IL18/IL18R 0.077 0.051 0.2 51 -0.13 3 54
NOS2 -0.007 0.18 -10000 0 -0.78 25 25
IL12/IL12R/TYK2/JAK2/SPHK2 -0.058 0.09 0.17 3 -0.24 38 41
IL1R1 -0.047 0.18 -10000 0 -0.8 20 20
IL4 -0.025 0.019 -10000 0 -0.061 19 19
JAK2 0.024 0.018 0.078 1 -0.055 2 3
EntrezGene:6957 0.001 0.002 -10000 0 -0.02 4 4
TCR/CD3/MHC I/CD8 0.011 0.057 -10000 0 -0.48 1 1
RAB7A 0.01 0.13 -10000 0 -0.67 3 3
lysosomal transport 0.011 0.13 -10000 0 -0.6 4 4
FOS -0.03 0.2 -10000 0 -0.72 38 38
STAT4 (dimer) -0.11 0.19 0.4 4 -0.7 28 32
STAT5A (dimer) -0.042 0.18 0.38 2 -0.73 27 29
GZMA -0.028 0.18 -10000 0 -0.79 19 19
GZMB -0.032 0.18 -10000 0 -0.77 21 21
HLX 0.022 0.012 0.12 9 -10000 0 9
LCK -0.044 0.19 0.38 3 -0.78 26 29
TCR/CD3/MHC II/CD4 0.014 0.038 0.12 8 -0.17 7 15
IL2/IL2R 0.067 0.06 0.22 69 -0.12 1 70
MAPK14 0.01 0.15 0.38 1 -0.63 13 14
CCR5 -0.009 0.15 0.39 4 -0.66 14 18
IL1B 0.025 0.019 0.15 4 -10000 0 4
STAT6 -0.009 0.078 0.22 2 -0.41 10 12
STAT4 0.009 0.01 -10000 0 -10000 0 0
STAT3 0.021 0.002 -10000 0 -10000 0 0
STAT1 0.022 0.011 0.12 7 -10000 0 7
NFKB1 0.021 0.002 -10000 0 -10000 0 0
NFKB2 0.019 0.006 -10000 0 -10000 0 0
IL12B 0.029 0.021 0.11 6 -0.056 2 8
CD8A 0.02 0.008 0.13 2 -10000 0 2
CD8B 0.025 0.018 0.13 19 -10000 0 19
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.058 0.088 0.24 32 -0.18 6 38
IL2RB 0.03 0.031 0.12 63 -10000 0 63
proteasomal ubiquitin-dependent protein catabolic process -0.11 0.18 0.39 4 -0.65 28 32
IL2RG 0.033 0.033 0.12 78 -10000 0 78
IL12 0.046 0.031 0.14 10 -10000 0 10
STAT5A 0.021 0.002 -10000 0 -10000 0 0
CD247 0.021 0.006 -10000 0 -0.03 7 7
IL2 0.015 0.002 -10000 0 -10000 0 0
SPHK2 0.019 0.007 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.027 0.022 0.12 12 -0.055 2 14
IL12/IL12R/TYK2/JAK2 -0.048 0.19 0.4 3 -0.81 26 29
MAP2K3 0.006 0.15 0.39 1 -0.62 13 14
RIPK2 0.02 0.007 0.12 2 -10000 0 2
MAP2K6 0.005 0.15 -10000 0 -0.61 13 13
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0 0.002 -10000 0 -0.023 7 7
IL18RAP 0.035 0.036 0.13 76 -0.032 2 78
IL12Rbeta1/TYK2 0.036 0.027 -10000 0 -0.15 1 1
EOMES 0.017 0.052 -10000 0 -0.59 3 3
STAT1 (dimer) -0.013 0.16 0.37 4 -0.62 22 26
T cell proliferation -0.027 0.15 0.34 5 -0.52 22 27
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.026 0.02 0.13 16 -10000 0 16
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.07 0.16 0.33 3 -0.56 27 30
ATF2 0.006 0.14 0.36 1 -0.59 13 14
Cellular roles of Anthrax toxin

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
ANTXR1 0.027 0.024 0.12 39 -10000 0 39
ANTXR2 0.034 0.035 0.12 86 -10000 0 86
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.002 -10000 0 -10000 0 0
monocyte activation -0.026 0.14 -10000 0 -0.34 109 109
MAP2K2 0.01 0.039 -10000 0 -0.56 3 3
MAP2K1 -0.005 0.002 -10000 0 -10000 0 0
MAP2K7 -0.005 0.002 -10000 0 -10000 0 0
MAP2K6 -0.005 0.002 -10000 0 -10000 0 0
CYAA -0.005 0.007 -10000 0 -10000 0 0
MAP2K4 -0.005 0.002 -10000 0 -10000 0 0
IL1B -0.013 0.031 -10000 0 -0.1 70 70
Channel 0.039 0.027 0.095 118 -10000 0 118
NLRP1 -0.005 0.002 -10000 0 -10000 0 0
CALM1 0.02 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.009 0.084 -10000 0 -0.38 31 31
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.002 -10000 0 -10000 0 0
MAPK3 -0.005 0.002 -10000 0 -10000 0 0
MAPK1 -0.005 0.002 -10000 0 -10000 0 0
PGR -0.005 0.002 0.013 1 -10000 0 1
PA/Cellular Receptors 0.041 0.029 0.1 118 -10000 0 118
apoptosis -0.001 0.002 -10000 0 -10000 0 0
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.038 0.027 0.092 118 -10000 0 118
macrophage activation -0.008 0.002 -10000 0 -10000 0 0
TNF 0.021 0.015 0.12 11 -10000 0 11
VCAM1 -0.026 0.14 -10000 0 -0.34 108 108
platelet activation -0.009 0.084 -10000 0 -0.38 31 31
MAPKKK cascade 0 0.017 -10000 0 -0.07 36 36
IL18 -0.002 0.01 0.19 1 -10000 0 1
negative regulation of macrophage activation -0.001 0.002 -10000 0 -10000 0 0
LEF -0.001 0.002 -10000 0 -10000 0 0
CASP1 0.001 0.006 0.017 44 -10000 0 44
mol:cAMP -0.01 0.084 -10000 0 -0.39 31 31
necrosis -0.001 0.002 -10000 0 -10000 0 0
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.038 0.027 0.093 118 -10000 0 118
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.032 0.071 0.21 22 -0.28 5 27
FYN 0.018 0.077 0.19 34 -0.31 6 40
LAT/GRAP2/SLP76 0.024 0.07 0.2 25 -0.27 6 31
IKBKB 0.021 0.003 -10000 0 -10000 0 0
AKT1 0.017 0.07 0.18 38 -0.3 4 42
B2M 0.032 0.032 0.13 68 -0.032 2 70
IKBKG 0.003 0.027 0.072 40 -0.12 1 41
MAP3K8 0.021 0.016 0.12 12 -10000 0 12
mol:Ca2+ -0.01 0.008 -10000 0 -0.041 2 2
integrin-mediated signaling pathway 0.025 0.009 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.019 0.081 0.2 33 -0.4 4 37
TRPV6 0.21 0.53 1.2 136 -10000 0 136
CD28 0.026 0.022 0.13 30 -0.016 3 33
SHC1 0.015 0.075 0.23 19 -0.28 9 28
receptor internalization 0.015 0.067 0.19 7 -0.25 13 20
PRF1 -0.033 0.2 -10000 0 -0.58 68 68
KRAS 0.02 0.004 -10000 0 -10000 0 0
GRB2 0.02 0.004 -10000 0 -10000 0 0
COT/AKT1 0.02 0.062 0.18 32 -0.25 3 35
LAT 0.012 0.069 0.18 16 -0.28 9 25
EntrezGene:6955 0 0.002 -10000 0 -0.022 2 2
CD3D 0.033 0.036 0.13 83 -0.034 2 85
CD3E 0.03 0.032 0.13 60 -0.019 5 65
CD3G 0.027 0.031 0.13 55 -0.016 29 84
RASGRP2 0.006 0.012 0.061 4 -0.15 1 5
RASGRP1 0.008 0.088 0.21 26 -0.25 29 55
HLA-A 0.001 0.003 -10000 0 -0.023 2 2
RASSF5 0.021 0.003 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.025 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.024 0.046 0.13 57 -0.12 2 59
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.002 0.024 -10000 0 -0.15 3 3
PRKCA 0 0.041 0.12 24 -0.16 4 28
GRAP2 0.023 0.018 0.12 19 -10000 0 19
mol:IP3 0.022 0.067 0.14 100 -0.19 9 109
EntrezGene:6957 0.001 0.002 -10000 0 -0.022 1 1
TCR/CD3/MHC I/CD8 0.01 0.058 0.14 14 -0.32 4 18
ORAI1 -0.19 0.44 0.49 3 -1 135 138
CSK 0.014 0.069 0.19 17 -0.28 9 26
B7 family/CD28 0.049 0.089 0.25 38 -0.3 5 43
CHUK 0.019 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.016 0.073 0.19 13 -0.29 10 23
PTPN6 0.011 0.07 0.2 21 -0.26 10 31
VAV1 0.014 0.072 0.19 22 -0.28 9 31
Monovalent TCR/CD3 0.018 0.039 0.11 37 -0.16 15 52
CBL 0.021 0.003 -10000 0 -10000 0 0
LCK 0.016 0.08 0.2 34 -0.28 9 43
PAG1 0.013 0.07 0.21 18 -0.28 9 27
RAP1A 0.019 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.016 0.072 0.18 19 -0.28 10 29
CD80 0.026 0.026 0.13 39 -0.015 10 49
CD86 0.025 0.019 0.13 22 -10000 0 22
PDK1/CARD11/BCL10/MALT1 0.005 0.031 0.11 1 -0.18 3 4
HRAS 0.02 0.005 -10000 0 -10000 0 0
GO:0035030 0.015 0.066 0.18 34 -0.27 5 39
CD8A 0.021 0.009 0.13 2 -0.034 2 4
CD8B 0.025 0.018 0.13 19 -0.024 4 23
PTPRC 0.024 0.016 0.13 15 -10000 0 15
PDK1/PKC theta 0.02 0.081 0.22 35 -0.33 4 39
CSK/PAG1 0.013 0.072 0.2 27 -0.27 9 36
SOS1 0.021 0.001 -10000 0 -10000 0 0
peptide-MHC class I 0.024 0.024 0.094 68 -10000 0 68
GRAP2/SLP76 0.031 0.077 0.22 24 -0.3 6 30
STIM1 -0.018 0.14 1.1 6 -1 2 8
RAS family/GTP 0.016 0.049 0.13 33 -0.17 6 39
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.015 0.069 0.19 7 -0.26 13 20
mol:DAG -0.003 0.04 0.1 4 -0.18 9 13
RAP1A/GDP 0.013 0.02 0.07 35 -0.067 1 36
PLCG1 0.02 0.004 -10000 0 -10000 0 0
CD247 0.021 0.005 -10000 0 -0.033 2 2
cytotoxic T cell degranulation -0.031 0.19 -10000 0 -0.56 68 68
RAP1A/GTP 0.002 0.004 -10000 0 -0.049 2 2
mol:PI-3-4-5-P3 0.02 0.074 0.19 34 -0.34 4 38
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.029 0.078 0.19 47 -0.24 8 55
NRAS 0.019 0.007 -10000 0 -10000 0 0
ZAP70 0.023 0.013 0.12 11 -10000 0 11
GRB2/SOS1 0.03 0.006 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.014 0.065 0.2 18 -0.26 6 24
MALT1 0.02 0.004 -10000 0 -10000 0 0
TRAF6 0.021 0.003 -10000 0 -10000 0 0
CD8 heterodimer 0.022 0.052 0.15 6 -0.16 45 51
CARD11 0.018 0.009 0.12 1 -10000 0 1
PRKCB -0.008 0.04 0.11 14 -0.15 20 34
PRKCE -0.001 0.04 0.12 23 -0.16 4 27
PRKCQ 0.02 0.082 0.21 38 -0.36 4 42
LCP2 0.021 0.009 0.12 4 -10000 0 4
BCL10 0.019 0.007 -10000 0 -10000 0 0
regulation of survival gene product expression 0.017 0.065 0.17 39 -0.26 4 43
IKK complex -0.003 0.034 0.11 15 -0.1 3 18
RAS family/GDP 0.001 0.006 -10000 0 -0.038 1 1
MAP3K14 0.012 0.049 0.14 31 -0.19 3 34
PDPK1 0.017 0.068 0.18 39 -0.28 4 43
TCR/CD3/MHC I/CD8/Fyn 0.018 0.077 0.22 6 -0.36 9 15
IL2 signaling events mediated by STAT5

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
GAB2 0.021 0.003 -10000 0 -10000 0 0
ELF1 0.035 0.025 0.11 2 -10000 0 2
CCNA2 0.056 0.049 0.12 223 -10000 0 223
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
JAK3 0.02 0.005 -10000 0 -10000 0 0
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
JAK1 0.019 0.007 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.019 0.075 -10000 0 -0.29 12 12
SHC1 0.023 0.016 0.12 16 -10000 0 16
SP1 0.023 0.014 0.11 3 -0.27 1 4
IL2RA 0.014 0.048 0.27 3 -10000 0 3
IL2RB 0.03 0.031 0.12 63 -10000 0 63
SOS1 0.021 0.001 -10000 0 -10000 0 0
IL2RG 0.033 0.033 0.12 78 -10000 0 78
G1/S transition of mitotic cell cycle 0.049 0.09 0.3 17 -0.52 3 20
PTPN11 0.021 0.003 -10000 0 -10000 0 0
CCND2 -0.009 0.028 0.27 3 -0.5 1 4
LCK 0.039 0.042 0.12 129 -10000 0 129
GRB2 0.02 0.004 -10000 0 -10000 0 0
IL2 0.015 0.002 -10000 0 -10000 0 0
CDK6 0.024 0.028 0.12 43 -10000 0 43
CCND3 0.014 0.075 -10000 0 -0.43 1 1
Nongenotropic Androgen signaling

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
PTK2 -0.006 0.002 -10000 0 -10000 0 0
GNB1/GNG2 0.064 0.04 -10000 0 -0.11 2 2
regulation of S phase of mitotic cell cycle 0.027 0.018 -10000 0 -0.17 1 1
GNAO1 0.021 0.003 -10000 0 -10000 0 0
HRAS 0.02 0.005 -10000 0 -0.02 2 2
SHBG/T-DHT 0.014 0.003 0.081 1 -10000 0 1
PELP1 0.021 0.003 -10000 0 -0.02 2 2
AKT1 -0.006 0.001 -10000 0 -10000 0 0
MAP2K1 -0.005 0.043 0.17 35 -0.14 6 41
T-DHT/AR 0.052 0.037 0.09 329 -10000 0 329
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 0.003 1 -0.007 7 8
GNAI2 0.021 0.003 -10000 0 -10000 0 0
GNAI3 0.019 0.008 0.12 1 -10000 0 1
GNAI1 0.017 0.008 -10000 0 -10000 0 0
mol:GDP 0.016 0.023 -10000 0 -10000 0 0
cell proliferation 0.006 0.067 0.24 18 -0.36 8 26
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
FOS 0.006 0.089 0.34 4 -0.67 8 12
mol:Ca2+ 0 0.01 -10000 0 -0.049 4 4
MAPK3 0.005 0.059 0.19 41 -0.26 7 48
MAPK1 0.006 0.062 0.18 4 -0.35 12 16
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
mol:IP3 0 0 0.002 1 -0.005 7 8
cAMP biosynthetic process -0.004 0.008 -10000 0 -10000 0 0
GNG2 0.02 0.004 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0 0.002 1 -0.005 7 8
HRAS/GTP 0.058 0.033 -10000 0 -0.071 4 4
actin cytoskeleton reorganization 0.024 0.015 -10000 0 -10000 0 0
SRC 0.02 0.005 -10000 0 -0.018 1 1
voltage-gated calcium channel activity 0 0 0.002 1 -0.005 7 8
PI3K 0.028 0.005 -10000 0 -10000 0 0
apoptosis -0.011 0.063 0.39 8 -0.23 10 18
T-DHT/AR/PELP1 0.061 0.035 0.096 325 -10000 0 325
HRAS/GDP 0.03 0.024 0.13 8 -10000 0 8
CREB1 0.011 0.066 0.23 10 -0.42 8 18
RAC1-CDC42/GTP 0.03 0.018 -10000 0 -10000 0 0
AR 0.072 0.052 0.12 329 -0.018 1 330
GNB1 0.019 0.007 -10000 0 -10000 0 0
RAF1 0.008 0.045 0.18 37 -10000 0 37
RAC1-CDC42/GDP 0.036 0.03 0.14 4 -10000 0 4
T-DHT/AR/PELP1/Src 0.068 0.036 -10000 0 -10000 0 0
MAP2K2 -0.006 0.039 0.17 28 -0.14 6 34
T-DHT/AR/PELP1/Src/PI3K 0.028 0.018 -10000 0 -0.17 1 1
GNAZ 0.02 0.004 -10000 0 -10000 0 0
SHBG 0.021 0.005 0.12 1 -10000 0 1
Gi family/GNB1/GNG2/GDP -0.011 0.09 -10000 0 -0.26 67 67
mol:T-DHT 0 0 -10000 0 -0.002 7 7
RAC1 0.018 0.008 -10000 0 -10000 0 0
GNRH1 -0.006 0.004 0.05 3 -10000 0 3
Gi family/GTP 0 0.036 0.096 3 -0.22 4 7
CDC42 0.019 0.006 -10000 0 -10000 0 0
IL6-mediated signaling events

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
BCL2L1 0.057 0.14 0.46 28 -0.52 1 29
CRP 0.049 0.13 0.48 9 -0.52 1 10
cell cycle arrest 0.054 0.13 0.42 17 -0.58 1 18
TIMP1 0.069 0.13 0.41 23 -0.53 2 25
IL6ST 0.02 0.018 -10000 0 -0.039 35 35
Rac1/GDP -0.018 0.12 0.19 3 -0.32 50 53
AP1 0.052 0.07 0.29 1 -0.41 3 4
GAB2 0.021 0.003 -10000 0 -10000 0 0
TNFSF11 0.049 0.12 0.41 13 -0.52 1 14
HSP90B1 0.038 0.049 -10000 0 -0.48 2 2
GAB1 0.021 0.003 -10000 0 -10000 0 0
MAPK14 -0.066 0.18 0.31 1 -0.5 77 78
AKT1 0.02 0.037 0.22 1 -0.3 5 6
FOXO1 0.016 0.035 -10000 0 -0.29 4 4
MAP2K6 -0.049 0.14 0.23 3 -0.38 76 79
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
MAP2K4 -0.007 0.12 0.29 16 -0.31 38 54
MITF -0.03 0.11 0.16 6 -0.34 48 54
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.02 0.004 -10000 0 -10000 0 0
A2M 0.006 0.1 -10000 0 -1.1 5 5
CEBPB 0.022 0.007 0.13 2 -10000 0 2
GRB2/SOS1/GAB family/SHP2 0.013 0.056 -10000 0 -0.35 5 5
STAT3 0.052 0.13 0.43 15 -0.61 1 16
STAT1 0.017 0.033 -10000 0 -0.71 1 1
CEBPD 0.054 0.13 0.44 15 -0.52 1 16
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
PI3K 0.031 0.006 -10000 0 -10000 0 0
JUN 0.019 0.007 -10000 0 -10000 0 0
PIAS3/MITF -0.001 0.13 0.2 46 -0.31 51 97
MAPK11 -0.065 0.18 0.24 2 -0.49 77 79
STAT3 (dimer)/FOXO1 0.025 0.084 0.31 2 -0.45 1 3
GRB2/SOS1/GAB family 0.005 0.11 -10000 0 -0.28 47 47
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.025 0.1 0.15 2 -0.25 83 85
GRB2 0.02 0.004 -10000 0 -10000 0 0
JAK2 0.02 0.005 -10000 0 -10000 0 0
LBP 0.058 0.12 0.41 26 -0.43 1 27
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
JAK1 0.017 0.015 -10000 0 -0.038 27 27
MYC 0.071 0.14 0.44 21 -0.49 1 22
FGG 0.049 0.12 0.42 12 -0.52 1 13
macrophage differentiation 0.054 0.13 0.42 17 -0.58 1 18
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.016 0.076 0.18 4 -0.18 24 28
JUNB 0.052 0.13 0.44 25 -0.94 1 26
FOS 0.021 0.013 0.12 8 -10000 0 8
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.027 0.12 0.18 4 -0.33 57 61
STAT1/PIAS1 0.003 0.1 0.21 3 -0.26 43 46
GRB2/SOS1/GAB family/SHP2/PI3K 0.026 0.036 -10000 0 -0.29 7 7
STAT3 (dimer) 0.053 0.13 0.43 15 -0.6 1 16
PRKCD 0.044 0.17 0.34 101 -0.43 10 111
IL6R 0.018 0.016 -10000 0 -0.039 32 32
SOCS3 -0.089 0.3 0.45 1 -1 55 56
gp130 (dimer)/JAK1/JAK1/LMO4 0.036 0.041 -10000 0 -0.12 14 14
Rac1/GTP -0.014 0.11 0.2 4 -0.31 49 53
HCK 0.022 0.014 0.12 11 -10000 0 11
MAPKKK cascade 0.032 0.064 -10000 0 -0.46 3 3
bone resorption 0.05 0.12 0.41 13 -0.5 1 14
IRF1 0.052 0.13 0.44 15 -0.52 1 16
mol:GDP -0.029 0.11 0.17 5 -0.33 50 55
SOS1 0.021 0.002 -10000 0 -10000 0 0
VAV1 -0.03 0.11 0.17 5 -0.33 50 55
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.073 0.23 -10000 0 -0.52 105 105
PTPN11 0.009 0.074 -10000 0 -0.69 7 7
IL6/IL6RA -0.001 0.072 0.13 13 -0.16 98 111
gp130 (dimer)/TYK2/TYK2/LMO4 0.033 0.036 -10000 0 -0.12 14 14
gp130 (dimer)/JAK2/JAK2/LMO4 0.031 0.036 -10000 0 -0.12 14 14
IL6 0.017 0.024 0.14 14 -0.039 19 33
PIAS3 0.02 0.005 -10000 0 -10000 0 0
PTPRE 0.005 0.021 -10000 0 -0.042 6 6
PIAS1 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.018 0.008 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.02 0.087 -10000 0 -0.2 105 105
LMO4 0.019 0.017 -10000 0 -0.039 32 32
STAT3 (dimer)/PIAS3 0.024 0.1 0.36 1 -0.59 1 2
MCL1 0.02 0.043 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.034 0.021 0.16 1 -10000 0 1
RGS9BP 0.019 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.02 0.006 0.12 1 -10000 0 1
mol:Na + 0.047 0.034 0.093 217 -0.13 2 219
mol:ADP -0.011 0.009 0.05 13 -10000 0 13
GNAT2 0.018 0.008 0.12 1 -10000 0 1
RGS9-1/Gbeta5/R9AP 0.04 0.026 -10000 0 -0.12 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.023 0.011 0.16 1 -10000 0 1
GRK7 0.022 0.014 0.12 12 -10000 0 12
CNGB3 0.018 0.005 -10000 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.012 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0 0.024 0.19 4 -0.17 2 6
Cone PDE6 0.049 0.033 -10000 0 -0.1 4 4
Cone Metarhodopsin II 0.026 0.011 0.09 13 -10000 0 13
Na + (4 Units) 0.026 0.066 -10000 0 -0.12 96 96
GNAT2/GDP 0.043 0.027 -10000 0 -0.094 4 4
GNB5 0.021 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) -0.011 0.007 0.055 2 -10000 0 2
Cone Transducin 0.037 0.022 0.17 1 -10000 0 1
SLC24A2 0.016 0.009 -10000 0 -10000 0 0
GNB3/GNGT2 0.034 0.02 0.11 40 -10000 0 40
GNB3 0.023 0.019 0.12 21 -10000 0 21
GNAT2/GTP 0.013 0.006 0.089 1 -10000 0 1
CNGA3 0.056 0.049 0.12 222 -10000 0 222
ARR3 0.016 0.001 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.048 0.034 0.094 217 -0.13 2 219
mol:Pi 0.04 0.026 -10000 0 -0.12 4 4
Cone CNG Channel 0.045 0.037 -10000 0 -0.11 2 2
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.016 0.009 -10000 0 -10000 0 0
RGS9 0.027 0.026 0.12 43 -10000 0 43
PDE6C 0.017 0.007 0.12 1 -10000 0 1
GNGT2 0.025 0.019 0.12 23 -10000 0 23
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.019 0.006 0.12 1 -10000 0 1
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.008 0.074 0.34 29 -10000 0 29
VDR 0.023 0.017 0.12 16 -10000 0 16
FAM120B 0.02 0.005 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.004 0.087 -10000 0 -0.27 47 47
RXRs/LXRs/DNA/Oxysterols -0.016 0.12 -10000 0 -0.39 47 47
MED1 0.021 0.002 -10000 0 -10000 0 0
mol:9cRA 0 0.013 -10000 0 -0.045 44 44
RARs/THRs/DNA/Src-1 0.008 0.043 -10000 0 -0.16 40 40
RXRs/NUR77 0.038 0.058 -10000 0 -0.12 39 39
RXRs/PPAR 0.004 0.052 -10000 0 -0.18 36 36
NCOR2 0.021 0.002 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.014 0.025 0.089 16 -0.15 11 27
RARs/VDR/DNA/Vit D3 0.047 0.025 0.17 2 -0.11 10 12
RARA 0.021 0.002 -10000 0 -10000 0 0
NCOA1 0.021 0.002 -10000 0 -10000 0 0
VDR/VDR/DNA 0.023 0.017 0.12 16 -10000 0 16
RARs/RARs/DNA/9cRA 0.033 0.019 -10000 0 -10000 0 0
RARG 0.021 0.008 0.12 3 -10000 0 3
RPS6KB1 0.009 0.087 0.55 16 -10000 0 16
RARs/THRs/DNA/SMRT 0.008 0.043 -10000 0 -0.16 39 39
THRA 0.021 0.002 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.014 0.025 0.089 16 -0.15 11 27
RXRs/PPAR/9cRA/PGJ2/DNA 0.028 0.062 -10000 0 -0.13 74 74
NR1H4 0.041 0.042 0.12 134 -10000 0 134
RXRs/LXRs/DNA 0.04 0.076 -10000 0 -0.18 43 43
NR1H2 0.018 0.018 -10000 0 -0.052 31 31
NR1H3 0.019 0.021 0.13 3 -0.053 42 45
RXRs/VDR/DNA/Vit D3 0.033 0.057 -10000 0 -0.12 50 50
NR4A1 0.021 0.009 0.12 4 -10000 0 4
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.006 0.052 -10000 0 -0.24 7 7
RXRG 0.017 0.02 0.13 1 -0.052 43 44
RXR alpha/CCPG 0.027 0.019 -10000 0 -10000 0 0
RXRA 0.018 0.019 -10000 0 -0.051 45 45
RXRB 0.019 0.02 -10000 0 -0.054 45 45
THRB 0.019 0.006 -10000 0 -10000 0 0
PPARG 0.021 0.006 0.12 2 -10000 0 2
PPARD 0.021 0.002 -10000 0 -10000 0 0
TNF -0.05 0.22 -10000 0 -0.86 45 45
mol:Oxysterols 0 0.011 -10000 0 -0.04 46 46
cholesterol transport -0.016 0.12 -10000 0 -0.39 47 47
PPARA 0.02 0.004 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.021 0.002 -10000 0 -10000 0 0
RXRs/NUR77/BCL2 0.002 0.046 -10000 0 -0.16 44 44
SREBF1 -0.018 0.11 -10000 0 -0.43 18 18
RXRs/RXRs/DNA/9cRA 0.028 0.062 -10000 0 -0.13 74 74
ABCA1 -0.013 0.11 0.28 2 -0.43 18 20
RARs/THRs 0.05 0.043 -10000 0 -0.12 38 38
RXRs/FXR 0.049 0.066 0.16 1 -0.12 41 42
BCL2 0.021 0.003 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.01 0.015 -10000 0 -0.037 5 5
HSPA8 0.021 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.049 0.028 -10000 0 -0.15 1 1
AKT1 0.023 0.006 -10000 0 -10000 0 0
GSC 0.069 0.094 -10000 0 -10000 0 0
NKX2-5 0 0.006 -10000 0 -0.043 13 13
muscle cell differentiation -0.062 0.061 0.37 2 -10000 0 2
SMAD2-3/SMAD4/SP1 0.093 0.042 0.21 7 -10000 0 7
SMAD4 0.035 0.016 -10000 0 -10000 0 0
CBFB 0.021 0.006 0.12 2 -10000 0 2
SAP18 0.02 0.005 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.036 0.02 -10000 0 -0.13 2 2
SMAD3/SMAD4/VDR 0.061 0.04 0.18 3 -0.13 2 5
MYC 0.041 0.052 0.12 180 -0.031 74 254
CDKN2B -0.058 0.16 -10000 0 -0.49 3 3
AP1 0.032 0.024 0.14 2 -0.13 1 3
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.009 0.062 -10000 0 -0.26 21 21
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.015 0.041 0.18 1 -0.36 2 3
SP3 0.021 0.001 -10000 0 -10000 0 0
CREB1 0.021 0.001 -10000 0 -10000 0 0
FOXH1 0.027 0.014 0.14 1 -0.051 3 4
SMAD3/SMAD4/GR 0.053 0.024 0.18 1 -10000 0 1
GATA3 0.039 0.044 0.13 122 -10000 0 122
SKI/SIN3/HDAC complex/NCoR1 -0.013 0.083 -10000 0 -0.27 55 55
MEF2C/TIF2 0.042 0.056 0.2 31 -0.23 13 44
endothelial cell migration -0.018 0.089 1 4 -10000 0 4
MAX 0.011 0.019 0.071 3 -0.026 132 135
RBBP7 0.021 0.002 -10000 0 -10000 0 0
RBBP4 0.019 0.006 -10000 0 -10000 0 0
RUNX2 0.022 0.012 0.12 9 -10000 0 9
RUNX3 0.025 0.025 0.12 36 -10000 0 36
RUNX1 0.029 0.029 0.12 54 -10000 0 54
CTBP1 0.021 0.003 -10000 0 -10000 0 0
NR3C1 0.011 0.019 0.071 3 -0.026 139 142
VDR 0.023 0.017 0.12 16 -10000 0 16
CDKN1A 0.035 0.045 0.36 1 -10000 0 1
KAT2B 0.02 0.006 0.12 1 -0.029 3 4
SMAD2/SMAD2/SMAD4/FOXH1 0.08 0.04 -10000 0 -10000 0 0
DCP1A 0.021 0.003 -10000 0 -10000 0 0
SKI 0.019 0.007 -10000 0 -10000 0 0
SERPINE1 0.018 0.09 -10000 0 -1 4 4
SMAD3/SMAD4/ATF2 0.058 0.024 -10000 0 -0.12 1 1
SMAD3/SMAD4/ATF3 0.058 0.026 0.17 6 -10000 0 6
SAP30 0.021 0.006 0.12 1 -10000 0 1
Cbp/p300/PIAS3 0.025 0.022 -10000 0 -10000 0 0
JUN 0.018 0.024 0.16 9 -10000 0 9
SMAD3/SMAD4/IRF7 0.059 0.03 0.18 5 -10000 0 5
TFE3 0.025 0.009 -10000 0 -0.073 3 3
COL1A2 0.023 0.029 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.058 0.026 -10000 0 -0.17 5 5
DLX1 0.014 0.011 0.12 1 -10000 0 1
TCF3 0.021 0.01 0.12 5 -10000 0 5
FOS 0.025 0.014 0.13 8 -10000 0 8
SMAD3/SMAD4/Max 0.052 0.026 0.17 2 -10000 0 2
Cbp/p300/SNIP1 0.034 0.015 -10000 0 -10000 0 0
ZBTB17 0.011 0.018 -10000 0 -0.027 107 107
LAMC1 0.028 0.036 0.13 56 -10000 0 56
TGIF2/HDAC complex/SMAD3/SMAD4 0.058 0.028 0.17 2 -10000 0 2
IRF7 0.024 0.02 0.13 22 -10000 0 22
ESR1 0.011 0.021 -10000 0 -0.038 94 94
HNF4A 0.017 0.007 0.12 1 -10000 0 1
MEF2C 0.036 0.062 0.2 47 -0.24 13 60
SMAD2-3/SMAD4 0.071 0.028 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.035 0.012 -10000 0 -10000 0 0
IGHV3OR16-13 0.01 0.014 -10000 0 -0.35 1 1
TGIF2/HDAC complex 0.023 0.019 0.12 21 -10000 0 21
CREBBP 0.015 0.011 -10000 0 -0.033 4 4
SKIL 0.021 0.003 -10000 0 -10000 0 0
HDAC1 0.019 0.006 -10000 0 -10000 0 0
HDAC2 0.02 0.005 -10000 0 -10000 0 0
SNIP1 0.02 0.007 -10000 0 -10000 0 0
GCN5L2 -0.003 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.069 0.034 0.17 12 -10000 0 12
MSG1/HSC70 0.034 0.018 0.11 12 -0.14 2 14
SMAD2 0.031 0.012 -10000 0 -10000 0 0
SMAD3 0.029 0.012 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.026 0.018 0.15 1 -0.17 1 2
SMAD2/SMAD2/SMAD4 0.011 0.032 0.16 5 -0.16 3 8
NCOR1 0.021 0.002 -10000 0 -10000 0 0
NCOA2 0.02 0.005 -10000 0 -10000 0 0
NCOA1 0.021 0.002 -10000 0 -10000 0 0
MYOD/E2A 0.056 0.039 0.1 246 -10000 0 246
SMAD2-3/SMAD4/SP1/MIZ-1 0.093 0.05 0.22 7 -10000 0 7
IFNB1 0.006 0.023 0.15 6 -10000 0 6
SMAD3/SMAD4/MEF2C 0.07 0.059 0.2 40 -0.23 13 53
CITED1 0.025 0.019 0.12 24 -10000 0 24
SMAD2-3/SMAD4/ARC105 0.079 0.031 -10000 0 -10000 0 0
RBL1 0.023 0.017 0.12 18 -10000 0 18
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.026 0.036 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 0.046 0.032 0.18 13 -10000 0 13
SMAD7 0.037 0.041 -10000 0 -10000 0 0
MYC/MIZ-1 0.033 0.043 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.012 0.056 -10000 0 -0.37 5 5
IL10 0.027 0.04 0.14 46 -10000 0 46
PIASy/HDAC complex 0.023 0.005 -10000 0 -10000 0 0
PIAS3 0.018 0.006 -10000 0 -0.028 2 2
CDK2 0.049 0.049 0.12 198 -0.035 3 201
IL5 0.018 0.028 0.2 6 -10000 0 6
CDK4 0.021 0.029 0.12 42 -0.038 3 45
PIAS4 0.023 0.005 -10000 0 -10000 0 0
ATF3 0.022 0.012 0.12 9 -10000 0 9
SMAD3/SMAD4/SP1 0.071 0.036 0.18 11 -10000 0 11
FOXG1 0.017 0.011 -10000 0 -0.017 46 46
FOXO3 -0.003 0.014 -10000 0 -10000 0 0
FOXO1 -0.003 0.013 -10000 0 -10000 0 0
FOXO4 -0.003 0.014 -10000 0 -10000 0 0
heart looping 0.035 0.061 0.2 47 -0.24 13 60
CEBPB 0.022 0.008 0.12 2 -10000 0 2
SMAD3/SMAD4/DLX1 -0.008 0.092 -10000 0 -0.13 214 214
MYOD1 0.057 0.052 0.12 244 -10000 0 244
SMAD3/SMAD4/HNF4 0.046 0.045 -10000 0 -0.13 29 29
SMAD3/SMAD4/GATA3 0.068 0.05 0.2 36 -10000 0 36
SnoN/SIN3/HDAC complex/NCoR1 0.021 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.076 0.046 0.21 23 -10000 0 23
SMAD3/SMAD4/SP1-3 0.082 0.036 0.19 4 -10000 0 4
MED15 0.021 0.003 -10000 0 -10000 0 0
SP1 0.027 0.008 -10000 0 -10000 0 0
SIN3B 0.021 0.004 -10000 0 -10000 0 0
SIN3A 0.021 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.076 0.044 -10000 0 -0.15 4 4
ITGB5 0.017 0.032 0.19 12 -10000 0 12
TGIF/SIN3/HDAC complex/CtBP 0.009 0.052 -10000 0 -0.32 10 10
SMAD3/SMAD4/AR 0.091 0.044 0.16 44 -10000 0 44
AR 0.072 0.052 0.12 329 -10000 0 329
negative regulation of cell growth 0.023 0.036 -10000 0 -0.22 2 2
SMAD3/SMAD4/MYOD 0.081 0.041 0.15 41 -10000 0 41
E2F5 0.023 0.017 0.12 18 -10000 0 18
E2F4 0.021 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.084 0.044 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 0.027 0.026 0.19 1 -10000 0 1
TFDP1 0.02 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.057 0.031 0.21 2 -0.13 1 3
SMAD3/SMAD4/RUNX2 0.059 0.026 0.18 5 -10000 0 5
TGIF2 0.023 0.019 0.12 21 -10000 0 21
TGIF1 0.038 0.039 0.12 111 -10000 0 111
ATF2 0.021 0.001 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.011 0.035 -10000 0 -0.3 7 7
Crk/p130 Cas/Paxillin -0.011 0.059 -10000 0 -0.2 28 28
JUN -0.01 0.046 -10000 0 -0.25 8 8
HRAS 0.02 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.05 0.058 0.18 17 -0.12 30 47
RAP1A 0.019 0.007 -10000 0 -10000 0 0
FRS2 0.02 0.004 -10000 0 -10000 0 0
RAP1A/GDP 0.014 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.053 0.063 0.18 18 -0.13 41 59
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.021 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.021 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.046 0.048 0.17 14 -0.12 24 38
RHOA 0.021 0.003 -10000 0 -10000 0 0
RAP1A/GTP 0.037 0.053 0.15 8 -0.12 39 47
GRB7 0.02 0.009 0.12 4 -10000 0 4
RET51/GFRalpha1/GDNF 0.052 0.062 0.18 17 -0.13 40 57
MAPKKK cascade 0.015 0.065 -10000 0 -0.18 38 38
BCAR1 0.021 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.046 0.048 0.17 14 -0.12 24 38
lamellipodium assembly 0.002 0.05 -10000 0 -0.19 19 19
RET51/GFRalpha1/GDNF/SHC 0.054 0.062 0.18 17 -0.13 38 55
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC 0.046 0.048 0.17 14 -0.12 23 37
RET9/GFRalpha1/GDNF/Shank3 0.042 0.054 0.17 14 -0.14 30 44
MAPK3 -0.015 0.036 0.17 5 -0.2 4 9
DOK1 0.022 0.007 0.12 3 -10000 0 3
DOK6 0.016 0.009 -10000 0 -10000 0 0
PXN 0.021 0.002 -10000 0 -10000 0 0
neurite development -0.02 0.041 0.15 4 -0.17 29 33
DOK5 0.02 0.004 -10000 0 -10000 0 0
GFRA1 0.021 0.02 0.12 20 -10000 0 20
MAPK8 0.001 0.05 -10000 0 -0.26 8 8
HRAS/GTP 0.035 0.074 -10000 0 -0.17 39 39
tube development 0.041 0.056 0.19 28 -0.13 29 57
MAPK1 -0.015 0.036 0.17 6 -0.2 4 10
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.014 0.037 -10000 0 -0.16 23 23
Rac1/GDP 0.013 0.006 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
PDLIM7 0.022 0.014 0.12 11 -10000 0 11
RET51/GFRalpha1/GDNF/Dok6 0.036 0.091 0.18 16 -0.14 101 117
SHC1 0.023 0.016 0.12 16 -10000 0 16
RET51/GFRalpha1/GDNF/Dok4 0.052 0.062 0.18 17 -0.13 41 58
RET51/GFRalpha1/GDNF/Dok5 0.053 0.061 0.18 17 -0.13 38 55
PRKCA 0.02 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
CREB1 0.011 0.051 0.14 1 -0.21 22 23
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.014 0.037 -10000 0 -0.16 23 23
RET51/GFRalpha1/GDNF/Grb7 0.052 0.062 0.18 17 -0.13 41 58
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.021 0.017 0.12 15 -10000 0 15
DOK4 0.021 0.002 -10000 0 -10000 0 0
JNK cascade -0.01 0.045 -10000 0 -0.24 8 8
RET9/GFRalpha1/GDNF/FRS2 0.045 0.048 0.17 14 -0.12 23 37
SHANK3 0.02 0.005 -10000 0 -10000 0 0
RASA1 0.021 0.002 -10000 0 -10000 0 0
NCK1 0.021 0.005 0.12 1 -10000 0 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.015 0.037 -10000 0 -0.16 23 23
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.007 0.059 -10000 0 -0.17 56 56
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.006 0.063 -10000 0 -0.18 63 63
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.012 0.053 -10000 0 -0.18 39 39
PI3K -0.006 0.083 0.18 1 -0.26 28 29
SOS1 0.021 0.001 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.048 0.054 0.17 14 -0.13 29 43
GRB10 0.017 0.008 -10000 0 -10000 0 0
activation of MAPKK activity 0.012 0.044 0.13 4 -0.17 23 27
RET51/GFRalpha1/GDNF/FRS2 0.052 0.062 0.18 17 -0.13 39 56
GAB1 0.021 0.003 -10000 0 -10000 0 0
IRS1 0.021 0.001 -10000 0 -10000 0 0
IRS2 0.02 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.012 0.052 -10000 0 -0.18 39 39
RET51/GFRalpha1/GDNF/PKC alpha 0.051 0.062 0.18 17 -0.13 41 58
GRB2 0.02 0.004 -10000 0 -10000 0 0
PRKACA 0.02 0.004 -10000 0 -10000 0 0
GDNF 0.044 0.044 0.12 155 -10000 0 155
RAC1 0.018 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.053 0.062 0.18 17 -0.13 40 57
Rac1/GTP 0.007 0.06 0.15 1 -0.22 19 20
RET9/GFRalpha1/GDNF 0.036 0.048 0.1 150 -0.13 24 174
GFRalpha1/GDNF 0.039 0.055 0.18 14 -0.16 24 38
IL2 signaling events mediated by PI3K

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
BCL2L1 0.014 0.068 0.26 2 -0.3 14 16
UGCG 0.003 0.11 -10000 0 -0.58 20 20
AKT1/mTOR/p70S6K/Hsp90/TERT 0.044 0.082 0.21 7 -0.33 9 16
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.004 0.1 -10000 0 -0.58 20 20
mol:DAG -0.062 0.24 -10000 0 -0.79 62 62
CaM/Ca2+/Calcineurin A alpha-beta B1 0.042 0.078 0.24 3 -0.33 3 6
FRAP1 0.039 0.084 0.26 3 -0.37 3 6
FOXO3 0.034 0.083 0.23 6 -0.38 3 9
AKT1 0.038 0.086 0.25 4 -0.4 3 7
GAB2 0.022 0.003 -10000 0 -10000 0 0
SMPD1 0.004 0.1 -10000 0 -0.52 22 22
SGMS1 -0.03 0.17 -10000 0 -0.55 61 61
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 -0.004 0.007 -10000 0 -10000 0 0
CALM1 0.02 0.005 -10000 0 -10000 0 0
cell proliferation 0.01 0.12 0.22 15 -0.32 55 70
EIF3A 0.019 0.007 -10000 0 -10000 0 0
PI3K 0.034 0.007 -10000 0 -10000 0 0
RPS6KB1 0.022 0.05 -10000 0 -0.82 2 2
mol:sphingomyelin -0.062 0.24 -10000 0 -0.79 62 62
natural killer cell activation 0.001 0.001 -10000 0 -10000 0 0
JAK3 0.021 0.006 -10000 0 -10000 0 0
PIK3R1 0.022 0.003 -10000 0 -10000 0 0
JAK1 0.02 0.007 -10000 0 -10000 0 0
NFKB1 0.021 0.002 -10000 0 -10000 0 0
MYC 0.056 0.1 0.3 41 -0.47 1 42
MYB 0.023 0.031 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.032 0.076 0.18 9 -0.26 13 22
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.039 0.051 -10000 0 -0.74 2 2
mol:PI-3-4-5-P3 0.032 0.076 0.18 9 -0.26 13 22
Rac1/GDP 0.015 0.007 -10000 0 -10000 0 0
T cell proliferation 0.028 0.062 0.22 4 -0.25 9 13
SHC1 0.024 0.016 0.13 16 -10000 0 16
RAC1 0.018 0.008 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.007 0.024 65 -10000 0 65
PRKCZ 0.03 0.057 0.22 4 -0.33 3 7
NF kappa B1 p50/RelA 0.05 0.083 0.25 3 -0.33 3 6
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.018 0.059 0.16 1 -0.3 15 16
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
IL2RA 0.04 0.045 0.13 139 -10000 0 139
IL2RB 0.032 0.031 0.13 63 -10000 0 63
TERT 0.059 0.052 0.12 258 -10000 0 258
E2F1 0.026 0.025 -10000 0 -10000 0 0
SOS1 0.022 0.002 -10000 0 -10000 0 0
RPS6 0.021 0.015 0.12 11 -10000 0 11
mol:cAMP -0.002 0.004 -10000 0 -0.013 64 64
PTPN11 0.022 0.003 -10000 0 -10000 0 0
IL2RG 0.035 0.033 0.13 78 -10000 0 78
actin cytoskeleton organization 0.028 0.062 0.22 4 -0.25 9 13
GRB2 0.021 0.004 -10000 0 -10000 0 0
IL2 0.017 0.003 -10000 0 -10000 0 0
PIK3CA 0.022 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.041 0.022 -10000 0 -10000 0 0
LCK 0.041 0.043 0.13 129 -10000 0 129
BCL2 0.036 0.075 0.34 2 -0.42 1 3
Canonical Wnt signaling pathway

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
HDAC1 0.005 0.018 -10000 0 -0.036 1 1
AES 0.005 0.018 -10000 0 -10000 0 0
FBXW11 0.021 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.025 0.015 0.11 4 -10000 0 4
SMAD4 0.021 0.003 -10000 0 -10000 0 0
DKK2 0.018 0.012 0.12 5 -10000 0 5
TLE1 0.006 0.018 -10000 0 -0.032 1 1
MACF1 0.019 0.007 -10000 0 -10000 0 0
CTNNB1 0.068 0.11 0.25 96 -0.29 10 106
WIF1 0.007 0.01 -10000 0 -0.015 4 4
beta catenin/RanBP3 0.005 0.064 -10000 0 -0.3 7 7
KREMEN2 0.022 0.009 0.12 5 -10000 0 5
DKK1 0.028 0.031 0.12 60 -10000 0 60
beta catenin/beta TrCP1 0.074 0.1 0.25 92 -0.28 9 101
FZD1 0.018 0.012 0.12 4 -10000 0 4
AXIN2 0.019 0.097 0.6 17 -10000 0 17
AXIN1 0.022 0.002 -10000 0 -10000 0 0
RAN 0.021 0.002 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.02 0.069 -10000 0 -0.62 6 6
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.057 0.08 0.27 15 -0.51 4 19
Axin1/APC/GSK3 0.025 0.069 0.17 36 -0.25 6 42
Axin1/APC/GSK3/beta catenin/Macf1 0.043 0.085 0.21 76 -0.36 5 81
HNF1A 0.006 0.019 -10000 0 -0.033 1 1
CTBP1 0.006 0.019 -10000 0 -0.033 1 1
MYC 0.073 0.17 0.63 54 -10000 0 54
RANBP3 0.02 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.017 0.061 -10000 0 -0.13 88 88
NKD1 0.037 0.038 0.12 106 -0.016 1 107
TCF4 0.005 0.019 -10000 0 -0.027 6 6
TCF3 0.006 0.021 0.12 5 -10000 0 5
WNT1/LRP6/FZD1/Axin1 0.032 0.045 -10000 0 -0.12 39 39
Ran/GTP 0.015 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.026 0.058 -10000 0 -0.38 4 4
LEF1 0.008 0.026 0.12 17 -0.033 1 18
DVL1 0.024 0.037 -10000 0 -0.21 1 1
CSNK2A1 0.02 0.004 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.071 0.077 0.28 16 -0.68 2 18
DKK1/LRP6/Kremen 2 0.041 0.033 -10000 0 -0.13 9 9
LRP6 0.021 0.005 -10000 0 -10000 0 0
CSNK1A1 0.006 0.019 -10000 0 -10000 0 0
NLK 0.022 0.002 -10000 0 -10000 0 0
CCND1 0.017 0.076 0.6 9 -10000 0 9
WNT1 0.019 0.008 0.12 1 -0.015 2 3
GSK3A 0.019 0.007 -10000 0 -10000 0 0
GSK3B 0.021 0.003 -10000 0 -10000 0 0
FRAT1 0.019 0.006 -10000 0 -10000 0 0
PPP2R5D 0.023 0.041 -10000 0 -0.27 3 3
APC 0.012 0.081 0.18 118 -0.12 9 127
WNT1/LRP6/FZD1 0.051 0.077 0.14 241 -0.21 6 247
CREBBP 0.006 0.019 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.016 0.038 -10000 0 -0.15 26 26
epithelial cell differentiation 0.038 0.032 -10000 0 -0.11 24 24
CYFIP2 0.021 0.003 -10000 0 -10000 0 0
ENAH -0.023 0.042 0.28 6 -10000 0 6
EGFR 0.053 0.054 0.12 235 -10000 0 235
EPHA2 0.02 0.013 0.12 8 -10000 0 8
MYO6 -0.017 0.034 0.17 15 -10000 0 15
CTNNB1 0.021 0.002 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.036 0.019 -10000 0 -0.13 3 3
AQP5 -0.076 0.15 0.21 1 -0.37 134 135
CTNND1 0.021 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.017 0.032 0.17 13 -10000 0 13
regulation of calcium-dependent cell-cell adhesion -0.017 0.034 0.17 14 -0.2 2 16
EGF 0.024 0.019 0.12 22 -10000 0 22
NCKAP1 0.021 0.001 -10000 0 -10000 0 0
AQP3 -0.063 0.14 -10000 0 -0.36 107 107
cortical microtubule organization 0.038 0.032 -10000 0 -0.11 24 24
GO:0000145 -0.017 0.03 0.16 13 -10000 0 13
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.043 0.033 -10000 0 -0.11 24 24
MLLT4 0.02 0.005 -10000 0 -10000 0 0
ARF6/GDP -0.03 0.017 -10000 0 -10000 0 0
ARF6 0.02 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.048 0.02 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.008 0.026 0.16 3 -0.25 4 7
PVRL2 0.019 0.007 -10000 0 -10000 0 0
ZYX -0.015 0.028 0.17 7 -10000 0 7
ARF6/GTP 0.051 0.023 -10000 0 -10000 0 0
CDH1 0.022 0.013 0.12 9 -10000 0 9
EGFR/EGFR/EGF/EGF 0.038 0.04 -10000 0 -0.11 19 19
RhoA/GDP 0.039 0.031 -10000 0 -0.11 24 24
actin cytoskeleton organization -0.016 0.032 0.16 14 -10000 0 14
IGF-1R heterotetramer 0.021 0.003 -10000 0 -10000 0 0
GIT1 0.021 0.002 -10000 0 -10000 0 0
IGF1R 0.021 0.003 -10000 0 -10000 0 0
IGF1 0.021 0.005 0.12 1 -10000 0 1
DIAPH1 -0.013 0.16 -10000 0 -0.46 63 63
Wnt receptor signaling pathway -0.038 0.032 0.11 24 -10000 0 24
RHOA 0.021 0.003 -10000 0 -10000 0 0
RhoA/GTP -0.03 0.017 -10000 0 -10000 0 0
CTNNA1 0.021 0.003 -10000 0 -10000 0 0
VCL -0.017 0.032 0.16 14 -10000 0 14
EFNA1 0.021 0.003 -10000 0 -10000 0 0
LPP -0.019 0.03 0.16 12 -10000 0 12
Ephrin A1/EPHA2 0.03 0.031 -10000 0 -0.1 23 23
SEC6/SEC8 -0.022 0.02 -10000 0 -0.11 14 14
MGAT3 -0.017 0.034 0.17 14 -0.2 2 16
HGF/MET -0.026 0.074 -10000 0 -0.12 236 236
HGF 0.018 0.013 0.12 5 -10000 0 5
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.016 0.037 -10000 0 -0.15 26 26
actin cable formation -0.011 0.059 0.22 15 -0.24 4 19
KIAA1543 -0.017 0.029 0.16 11 -10000 0 11
KIFC3 -0.019 0.03 0.17 10 -10000 0 10
NCK1 0.021 0.005 0.12 1 -10000 0 1
EXOC3 0.021 0.003 -10000 0 -10000 0 0
ACTN1 -0.017 0.032 0.17 13 -10000 0 13
NCK1/GIT1 0.031 0.005 -10000 0 -10000 0 0
mol:GDP 0.038 0.032 -10000 0 -0.11 24 24
EXOC4 0.017 0.009 -10000 0 -10000 0 0
STX4 -0.018 0.033 0.17 14 -10000 0 14
PIP5K1C -0.017 0.032 0.17 13 -10000 0 13
LIMA1 0.05 0.048 0.12 192 -10000 0 192
ABI1 0.019 0.007 -10000 0 -10000 0 0
ROCK1 -0.022 0.047 0.3 6 -10000 0 6
adherens junction assembly -0.006 0.044 0.25 9 -0.25 3 12
IGF-1R heterotetramer/IGF1 0.031 0.034 -10000 0 -0.11 31 31
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.026 0.011 -10000 0 -10000 0 0
MET 0.009 0.011 0.12 1 -10000 0 1
PLEKHA7 -0.018 0.031 0.17 11 -10000 0 11
mol:GTP 0.046 0.02 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.016 0.094 0.18 150 -10000 0 150
cortical actin cytoskeleton stabilization 0.016 0.038 -10000 0 -0.15 26 26
regulation of cell-cell adhesion -0.016 0.032 0.16 14 -10000 0 14
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.016 0.037 -10000 0 -0.15 26 26
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.001 0.061 -10000 0 -0.11 153 153
MAPK9 0.004 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.004 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.024 0.013 -10000 0 -0.13 2 2
GNB1 0.019 0.007 -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 0.004 0 -10000 0 -10000 0 0
Gs family/GTP -0.016 0.052 -10000 0 -0.11 155 155
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 0.009 0.013 0.033 155 -10000 0 155
GNAL 0.016 0.009 -10000 0 -10000 0 0
GNG2 0.02 0.004 -10000 0 -10000 0 0
CRH 0.011 0.01 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.002 0.019 -10000 0 -0.21 5 5
MAPK11 0.004 0.008 -10000 0 -0.21 1 1
Aurora A signaling

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
Aurora A/GADD45A 0.017 0.037 0.18 7 -0.12 2 9
BIRC5 0.078 0.052 0.12 369 -10000 0 369
NFKBIA -0.006 0.013 0.12 2 -10000 0 2
CPEB1 0.02 0.004 -10000 0 -10000 0 0
AKT1 -0.005 0.02 0.19 4 -10000 0 4
NDEL1 0.021 0.002 -10000 0 -10000 0 0
Aurora A/BRCA1 0.011 0.027 0.12 1 -10000 0 1
NDEL1/TACC3 0.046 0.039 0.16 19 -10000 0 19
GADD45A 0.026 0.028 0.12 46 -10000 0 46
GSK3B -0.002 0.021 0.07 2 -10000 0 2
PAK1/Aurora A 0.009 0.027 -10000 0 -0.16 4 4
MDM2 0.02 0.004 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.004 0.028 0.051 167 -10000 0 167
TP53 0.014 0.032 0.16 4 -0.19 9 13
DLG7 0 0.013 0.12 2 -10000 0 2
AURKAIP1 0.019 0.007 -10000 0 -10000 0 0
ARHGEF7 0.02 0.004 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.039 0.054 0.18 25 -10000 0 25
G2/M transition of mitotic cell cycle 0.011 0.027 0.12 1 -10000 0 1
AURKA 0.005 0.02 0.16 2 -10000 0 2
AURKB 0.049 0.028 0.096 27 -0.091 3 30
CDC25B 0.006 0.014 0.12 2 -0.18 1 3
G2/M transition checkpoint 0.001 0.015 0.093 2 -10000 0 2
mRNA polyadenylation 0.007 0.029 -10000 0 -0.14 7 7
Aurora A/CPEB 0.007 0.029 -10000 0 -0.14 7 7
Aurora A/TACC1/TRAP/chTOG 0.043 0.022 -10000 0 -10000 0 0
BRCA1 0.024 0.017 0.12 18 -10000 0 18
centrosome duplication 0.009 0.027 -10000 0 -0.16 4 4
regulation of centrosome cycle 0.034 0.047 0.15 19 -10000 0 19
spindle assembly 0.042 0.021 -10000 0 -10000 0 0
TDRD7 0.021 0.003 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.078 0.044 0.17 43 -10000 0 43
CENPA 0.05 0.034 0.12 21 -0.2 2 23
Aurora A/PP2A 0.011 0.027 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.005 0.023 0.15 2 -10000 0 2
negative regulation of DNA binding 0.014 0.033 0.16 4 -0.19 10 14
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.03 0.006 -10000 0 -10000 0 0
RASA1 0.021 0.002 -10000 0 -10000 0 0
Ajuba/Aurora A 0.001 0.015 0.094 2 -10000 0 2
mitotic prometaphase -0.012 0.009 0.072 5 -10000 0 5
proteasomal ubiquitin-dependent protein catabolic process 0.005 0.02 0.16 2 -10000 0 2
TACC1 0.021 0.003 -10000 0 -10000 0 0
TACC3 0.046 0.045 0.12 160 -10000 0 160
Aurora A/Antizyme1 0.018 0.032 -10000 0 -10000 0 0
Aurora A/RasGAP 0.011 0.027 -10000 0 -10000 0 0
OAZ1 0.02 0.004 -10000 0 -10000 0 0
RAN 0.021 0.002 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.002 0.021 0.07 2 -10000 0 2
GIT1 0.021 0.002 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 -0.003 0.075 -10000 0 -0.13 167 167
Importin alpha/Importin beta/TPX2 0.004 0.028 0.051 167 -10000 0 167
PPP2R5D 0.021 0.002 -10000 0 -10000 0 0
Aurora A/TPX2 0.013 0.032 0.12 11 -10000 0 11
PAK1 0.015 0.009 -10000 0 -10000 0 0
CKAP5 0.021 0.003 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.021 0.002 -10000 0 -10000 0 0
LAT2 0.018 0.039 0.17 30 -10000 0 30
AP1 0.031 0.078 0.26 1 -0.32 4 5
mol:PIP3 0.046 0.085 0.23 80 -0.2 1 81
IKBKB 0.01 0.068 0.2 39 -0.16 2 41
AKT1 -0.013 0.058 0.22 31 -10000 0 31
IKBKG 0.008 0.062 0.17 42 -0.17 2 44
MS4A2 0.011 0.012 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
MAP3K1 0.022 0.054 0.23 20 -0.32 1 21
mol:Ca2+ 0.042 0.077 0.2 84 -10000 0 84
LYN 0.021 0.009 0.13 3 -10000 0 3
CBLB 0.019 0.03 0.13 22 -0.13 1 23
SHC1 0.023 0.016 0.12 16 -10000 0 16
RasGAP/p62DOK 0.041 0.009 -10000 0 -10000 0 0
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.021 0.009 0.12 5 -10000 0 5
PLD2 -0.003 0.044 0.28 11 -10000 0 11
PTPN13 0.025 0.072 -10000 0 -0.62 6 6
PTPN11 0.022 0.007 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.011 0.063 0.24 25 -0.3 6 31
SYK 0.022 0.014 0.12 10 -0.019 3 13
GRB2 0.021 0.004 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs 0.042 0.041 0.17 25 -0.2 1 26
LAT 0.018 0.032 0.13 22 -0.2 2 24
PAK2 0.026 0.055 0.21 25 -0.28 2 27
NFATC2 0.008 0.037 -10000 0 -0.36 6 6
HRAS 0.028 0.051 0.19 25 -0.27 3 28
GAB2 0.021 0.003 -10000 0 -10000 0 0
PLA2G1B 0.01 0.074 -10000 0 -0.85 4 4
Fc epsilon R1 0.066 0.043 0.17 51 -10000 0 51
Antigen/IgE/Fc epsilon R1 0.063 0.041 0.15 69 -10000 0 69
mol:GDP 0.032 0.045 0.2 13 -0.35 1 14
JUN 0.019 0.007 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
FOS 0.021 0.013 0.12 8 -10000 0 8
Antigen/IgE/Fc epsilon R1/LYN/SYK 0.024 0.03 0.16 6 -0.2 2 8
CHUK 0.006 0.059 0.17 39 -0.16 2 41
KLRG1 0.015 0.025 0.25 1 -0.22 1 2
VAV1 0.018 0.03 0.13 21 -0.13 1 22
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL 0.019 0.03 0.13 22 -0.13 1 23
negative regulation of mast cell degranulation 0.032 0.038 0.18 24 -0.17 2 26
BTK 0.032 0.038 0.26 1 -0.34 1 2
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK 0.032 0.033 0.14 1 -0.2 2 3
GAB2/PI3K/SHP2 -0.013 0.025 -10000 0 -10000 0 0
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP 0.023 0.02 0.12 5 -10000 0 5
RAF1 0.009 0.075 -10000 0 -0.93 4 4
Fc epsilon R1/FcgammaRIIB/SHIP 0.098 0.06 0.2 122 -10000 0 122
FCER1G 0.036 0.036 0.13 87 -10000 0 87
FCER1A 0.05 0.048 0.13 184 -0.019 2 186
Antigen/IgE/Fc epsilon R1/Fyn 0.069 0.041 0.17 51 -10000 0 51
MAPK3 0.009 0.073 -10000 0 -0.85 4 4
MAPK1 0.007 0.077 -10000 0 -0.88 4 4
NFKB1 0.021 0.002 -10000 0 -10000 0 0
MAPK8 -0.013 0.16 -10000 0 -0.5 64 64
DUSP1 0.021 0.008 0.12 4 -10000 0 4
NF-kappa-B/RelA 0.009 0.035 0.096 17 -0.11 1 18
actin cytoskeleton reorganization 0.03 0.074 -10000 0 -0.64 6 6
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.044 0.044 0.22 10 -0.26 2 12
FER 0.018 0.032 0.13 22 -0.2 2 24
RELA 0.021 0.003 -10000 0 -10000 0 0
ITK -0.009 0.072 0.087 1 -0.27 47 48
SOS1 0.021 0.001 -10000 0 -10000 0 0
PLCG1 0.04 0.062 0.24 30 -0.32 1 31
cytokine secretion -0.003 0.022 -10000 0 -0.078 2 2
SPHK1 0.018 0.03 0.13 22 -0.13 1 23
PTK2 0.03 0.078 -10000 0 -0.67 6 6
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.044 0.05 0.22 31 -0.2 1 32
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.044 0.079 0.23 62 -0.21 1 63
MAP2K2 0.008 0.078 -10000 0 -0.86 4 4
MAP2K1 0.003 0.071 -10000 0 -0.87 4 4
MAP2K7 0.021 0.003 -10000 0 -10000 0 0
KLRG1/SHP2 0.03 0.037 0.19 23 -0.18 1 24
MAP2K4 0.025 0.072 -10000 0 -1 3 3
Fc epsilon R1/FcgammaRIIB 0.093 0.061 0.2 123 -10000 0 123
mol:Choline -0.003 0.043 0.28 11 -10000 0 11
SHC/Grb2/SOS1 0.058 0.037 0.19 5 -0.2 1 6
FYN 0.02 0.004 -10000 0 -10000 0 0
DOK1 0.022 0.007 0.12 3 -10000 0 3
PXN 0.027 0.074 0.36 2 -0.62 6 8
HCLS1 0.019 0.03 0.13 22 -0.13 1 23
PRKCB 0.01 0.072 0.19 39 -0.22 2 41
FCGR2B 0.05 0.047 0.12 186 -10000 0 186
IGHE 0 0.004 -10000 0 -10000 0 0
KLRG1/SHIP 0.032 0.039 0.18 24 -0.17 2 26
LCP2 0.022 0.009 0.12 4 -10000 0 4
PLA2G4A 0.019 0.032 0.13 22 -0.2 2 24
RASA1 0.021 0.002 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.003 0.043 0.28 11 -10000 0 11
IKK complex 0.008 0.062 0.19 39 -10000 0 39
WIPF1 0.021 0.004 0.12 1 -10000 0 1
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.037 0.14 -10000 0 -0.28 139 139
CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
AKT1 0.02 0.004 -10000 0 -10000 0 0
AKT2 0.019 0.007 -10000 0 -10000 0 0
STXBP4 0.022 0.012 0.12 9 -10000 0 9
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.056 0.14 0.2 1 -0.3 145 146
YWHAZ 0.02 0.005 -10000 0 -10000 0 0
CALM1 0.02 0.005 -10000 0 -10000 0 0
YWHAQ 0.021 0.002 -10000 0 -10000 0 0
TBC1D4 -0.012 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.02 0.005 -10000 0 -10000 0 0
YWHAB 0.02 0.004 -10000 0 -10000 0 0
SNARE/Synip 0.043 0.011 -10000 0 -10000 0 0
YWHAG 0.017 0.008 -10000 0 -10000 0 0
ASIP 0.055 0.05 0.12 223 -10000 0 223
PRKCI 0.021 0.003 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
RHOQ 0.021 0.001 -10000 0 -10000 0 0
GYS1 0.003 0.001 -10000 0 -10000 0 0
PRKCZ 0.016 0.009 -10000 0 -10000 0 0
TRIP10 0.023 0.016 0.12 15 -10000 0 15
TC10/GTP/CIP4/Exocyst 0.029 0.011 0.096 15 -10000 0 15
AS160/14-3-3 0.008 0.039 -10000 0 -0.28 7 7
VAMP2 0.021 0.002 -10000 0 -10000 0 0
SLC2A4 -0.063 0.16 0.2 1 -0.33 145 146
STX4 0.021 0.002 -10000 0 -10000 0 0
GSK3B 0.011 0.005 -10000 0 -10000 0 0
SFN 0.022 0.02 0.12 23 -10000 0 23
LNPEP 0.021 0.002 -10000 0 -10000 0 0
YWHAE 0.021 0.002 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.001 0.065 -10000 0 -0.3 17 17
ACTA1 -0.023 0.065 0.18 2 -0.28 23 25
NUMA1 0.002 0.064 0.18 1 -0.28 20 21
SPTAN1 -0.021 0.064 0.18 7 -0.29 20 27
LIMK1 0.004 0.076 0.18 56 -0.3 10 66
BIRC3 0.023 0.017 0.12 16 -10000 0 16
BIRC2 0.021 0.003 -10000 0 -10000 0 0
BAX 0.019 0.007 -10000 0 -10000 0 0
CASP10 -0.009 0.013 0.043 18 -10000 0 18
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.021 0.001 -10000 0 -10000 0 0
PTK2 -0.002 0.069 0.18 1 -0.3 22 23
DIABLO 0.021 0.002 -10000 0 -10000 0 0
apoptotic nuclear changes -0.02 0.064 0.18 7 -0.29 20 27
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.021 0.002 -10000 0 -10000 0 0
GSN -0.021 0.064 0.19 5 -0.29 20 25
MADD 0.02 0.004 -10000 0 -10000 0 0
TFAP2A 0.018 0.17 -10000 0 -0.54 53 53
BID 0.002 0.01 -10000 0 -0.11 2 2
MAP3K1 0 0.046 -10000 0 -0.42 5 5
TRADD 0.021 0.002 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.028 0.011 0.11 1 -10000 0 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.017 0.069 0.18 16 -0.29 21 37
CASP9 0.019 0.008 0.12 1 -10000 0 1
DNA repair 0.01 0.048 0.19 20 -0.16 1 21
neuron apoptosis 0.017 0.058 -10000 0 -0.64 4 4
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.009 0.068 0.22 3 -0.29 22 25
APAF1 0.021 0.002 -10000 0 -10000 0 0
CASP6 0.014 0.12 -10000 0 -0.83 10 10
TRAF2 0.021 0.003 -10000 0 -10000 0 0
ICAD/CAD -0.022 0.063 0.26 4 -0.28 21 25
CASP7 -0.027 0.087 0.19 6 -0.23 76 82
KRT18 -0.001 0.1 -10000 0 -0.49 27 27
apoptosis -0.012 0.076 0.22 2 -0.31 24 26
DFFA -0.02 0.063 0.2 2 -0.29 21 23
DFFB -0.02 0.063 0.21 3 -0.29 21 24
PARP1 -0.01 0.048 0.16 1 -0.19 20 21
actin filament polymerization -0.006 0.074 0.27 10 -0.17 56 66
TNF 0.021 0.015 0.12 11 -10000 0 11
CYCS 0.006 0.028 0.16 2 -0.35 1 3
SATB1 0.011 0.11 -10000 0 -0.78 10 10
SLK -0.017 0.059 0.21 1 -0.28 21 22
p15 BID/BAX 0.008 0.034 -10000 0 -0.16 18 18
CASP2 0.002 0.048 0.22 7 -0.28 4 11
JNK cascade 0 0.046 0.42 5 -10000 0 5
CASP3 -0.02 0.066 0.18 3 -0.29 23 26
LMNB2 0.035 0.083 0.22 21 -0.36 8 29
RIPK1 0.021 0.003 -10000 0 -10000 0 0
CASP4 0.036 0.037 0.12 96 -10000 0 96
Mammalian IAPs/DIABLO 0.051 0.028 -10000 0 -0.12 13 13
negative regulation of DNA binding 0.018 0.17 -10000 0 -0.53 53 53
stress fiber formation -0.021 0.059 0.21 1 -0.27 21 22
GZMB -0.004 0.022 0.062 62 -10000 0 62
CASP1 0.021 0.027 -10000 0 -10000 0 0
LMNB1 0.046 0.096 0.21 71 -0.37 13 84
APP 0.017 0.058 -10000 0 -0.65 4 4
TNFRSF1A 0.021 0.01 0.12 5 -10000 0 5
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.004 0.01 0.05 23 -10000 0 23
VIM -0.009 0.08 0.24 2 -0.32 24 26
LMNA 0.037 0.08 0.22 24 -0.31 8 32
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.004 0.053 -10000 0 -0.27 8 8
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.023 0.063 0.17 2 -0.29 21 23
APAF-1/Caspase 9 -0.04 0.18 -10000 0 -0.6 64 64
nuclear fragmentation during apoptosis 0.002 0.063 0.18 1 -0.28 20 21
CFL2 0.006 0.073 0.18 56 -0.28 10 66
GAS2 -0.022 0.063 0.18 3 -0.28 22 25
positive regulation of apoptosis 0.045 0.089 0.19 90 -0.37 10 100
PRF1 0.025 0.027 0.12 42 -10000 0 42
PLK2 and PLK4 events

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
PLK2 0.018 0.007 -10000 0 -10000 0 0
PLK4 0.026 0.022 0.12 32 -10000 0 32
regulation of centriole replication -0.009 0.016 0.051 28 -0.14 3 31
Signaling events mediated by PTP1B

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
PDGFRB 0.021 0.008 0.12 4 -10000 0 4
Jak2/Leptin Receptor 0.022 0.094 0.23 6 -0.3 30 36
PTP1B/AKT1 0.043 0.047 0.19 8 -0.51 1 9
FYN 0.02 0.004 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.038 0.051 0.19 13 -0.5 1 14
EGFR 0.053 0.055 0.13 235 -10000 0 235
EGF/EGFR 0.051 0.053 0.18 1 -0.42 1 2
CSF1 0.02 0.015 0.12 10 -10000 0 10
AKT1 0.021 0.005 -10000 0 -0.021 2 2
INSR 0.021 0.005 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.046 0.048 0.19 7 -0.48 1 8
Insulin Receptor/Insulin 0.048 0.044 0.2 1 -0.54 1 2
HCK 0.022 0.014 0.12 11 -10000 0 11
CRK 0.021 0.002 -10000 0 -10000 0 0
TYK2 0.038 0.066 0.27 26 -0.47 1 27
EGF 0.028 0.019 0.13 22 -0.028 1 23
YES1 0.02 0.004 -10000 0 -10000 0 0
CAV1 0.064 0.077 0.22 82 -0.52 1 83
TXN 0.023 0.004 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.054 0.048 0.2 3 -0.45 1 4
cell migration -0.038 0.051 0.5 1 -0.19 13 14
STAT3 0.021 0.002 -10000 0 -10000 0 0
PRLR 0.022 0.009 0.12 3 -10000 0 3
ITGA2B 0.022 0.003 -10000 0 -10000 0 0
CSF1R 0.021 0.009 0.12 5 -10000 0 5
Prolactin Receptor/Prolactin 0.029 0.027 -10000 0 -0.16 9 9
FGR 0.02 0.012 0.12 6 -10000 0 6
PTP1B/p130 Cas 0.045 0.048 0.19 8 -0.48 1 9
Crk/p130 Cas 0.055 0.048 0.2 6 -0.46 1 7
DOK1 0.034 0.053 0.21 11 -0.56 1 12
JAK2 0.021 0.098 0.21 4 -0.32 30 34
Jak2/Leptin Receptor/Leptin 0.021 0.061 -10000 0 -0.33 4 4
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
PTPN1 0.038 0.052 0.19 13 -0.5 1 14
LYN 0.021 0.008 0.12 3 -10000 0 3
CDH2 0.021 0.003 -10000 0 -10000 0 0
SRC 0.032 0.043 -10000 0 -0.32 6 6
ITGB3 0.041 0.04 0.12 124 -10000 0 124
CAT1/PTP1B 0.023 0.11 0.28 38 -0.29 24 62
CAPN1 0.022 0.003 -10000 0 -10000 0 0
CSK 0.021 0.003 -10000 0 -10000 0 0
PI3K 0.05 0.043 -10000 0 -0.5 1 1
mol:H2O2 0.001 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.018 0.061 -10000 0 -0.35 3 3
negative regulation of transcription 0.021 0.097 0.21 4 -0.32 30 34
FCGR2A 0.033 0.033 0.12 77 -10000 0 77
FER 0.023 0.004 -10000 0 -0.018 1 1
alphaIIb/beta3 Integrin 0.044 0.036 0.11 11 -0.16 7 18
BLK 0.036 0.039 0.12 104 -10000 0 104
Insulin Receptor/Insulin/Shc 0.038 0.016 -10000 0 -10000 0 0
RHOA 0.022 0.004 -10000 0 -10000 0 0
LEPR 0.019 0.01 0.12 3 -10000 0 3
BCAR1 0.021 0.003 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.02 0.004 -10000 0 -10000 0 0
mol:NADPH 0.002 0.003 -10000 0 -10000 0 0
TRPV6 -0.004 0.12 0.22 23 -0.3 46 69
PRL 0.018 0.011 0.13 4 -10000 0 4
SOCS3 -0.076 0.3 -10000 0 -1.1 55 55
SPRY2 0.022 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.037 0.011 -10000 0 -10000 0 0
CSF1/CSF1R 0.052 0.05 0.2 4 -0.47 1 5
Ras protein signal transduction -0.003 0.1 0.51 23 -10000 0 23
IRS1 0.021 0.001 -10000 0 -10000 0 0
INS 0.015 0.008 0.12 1 -0.015 26 27
LEP 0.014 0.009 0.12 1 -0.015 9 10
STAT5B 0.036 0.064 0.2 8 -0.33 5 13
STAT5A 0.036 0.064 0.2 8 -0.36 4 12
GRB2 0.02 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.047 0.048 0.19 7 -0.47 1 8
CSN2 -0.013 0.041 -10000 0 -10000 0 0
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
LAT 0.039 0.043 -10000 0 -0.34 4 4
YBX1 0.024 0.015 0.13 9 -10000 0 9
LCK 0.039 0.042 0.12 129 -10000 0 129
SHC1 0.023 0.016 0.12 16 -10000 0 16
NOX4 0.057 0.05 0.13 215 -10000 0 215
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.013 0.026 0.13 2 -10000 0 2
CRKL 0.021 0.005 0.12 1 -10000 0 1
Rac1/GDP 0.013 0.006 -10000 0 -10000 0 0
DOCK1 0.018 0.007 -10000 0 -10000 0 0
ITGA4 0.036 0.036 0.12 95 -10000 0 95
alpha4/beta7 Integrin/MAdCAM1 0.045 0.056 0.18 3 -0.12 54 57
EPO 0.024 0.03 0.12 50 -10000 0 50
alpha4/beta7 Integrin 0.042 0.029 0.18 4 -10000 0 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.021 0.002 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.038 0.031 0.12 78 -10000 0 78
EPO/EPOR (dimer) 0.03 0.025 0.11 48 -10000 0 48
lamellipodium assembly 0.005 0.045 -10000 0 -0.27 9 9
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
PI3K 0.03 0.006 -10000 0 -10000 0 0
ARF6 0.02 0.004 -10000 0 -10000 0 0
JAK2 0.017 0.016 -10000 0 -10000 0 0
PXN 0.021 0.002 -10000 0 -10000 0 0
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
MADCAM1 0.018 0.007 -10000 0 -10000 0 0
cell adhesion 0.043 0.055 0.18 3 -0.12 54 57
CRKL/CBL 0.03 0.007 0.11 1 -10000 0 1
ITGB1 0.021 0.016 0.12 12 -10000 0 12
SRC 0.005 0.03 0.16 12 -10000 0 12
ITGB7 0.022 0.012 0.12 8 -10000 0 8
RAC1 0.018 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.061 0.052 0.18 42 -10000 0 42
p130Cas/Crk/Dock1 0.008 0.039 0.18 17 -10000 0 17
VCAM1 0.054 0.051 0.12 226 -10000 0 226
RHOA 0.021 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.056 0.032 0.18 10 -10000 0 10
BCAR1 -0.004 0.033 0.18 18 -10000 0 18
EPOR 0.02 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.021 0.003 -10000 0 -10000 0 0
GIT1 0.021 0.002 -10000 0 -10000 0 0
Rac1/GTP 0.005 0.045 -10000 0 -0.28 9 9
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.004 0.033 0.19 3 -0.22 3 6
adherens junction organization 0.001 0.044 0.14 4 -0.2 21 25
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.029 0.05 0.16 58 -0.17 1 59
FMN1 0.002 0.046 0.14 4 -0.2 24 28
mol:IP3 0.005 0.026 -10000 0 -0.2 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.008 0.044 0.17 1 -0.19 24 25
CTNNB1 0.021 0.003 -10000 0 -10000 0 0
AKT1 0.01 0.034 0.16 2 -0.24 1 3
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.011 0.064 -10000 0 -0.27 24 24
CTNND1 0.021 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.003 0.042 0.14 4 -0.18 23 27
VASP 0.002 0.041 0.14 4 -0.18 23 27
ZYX 0.001 0.038 0.14 2 -0.19 21 23
JUB 0.005 0.042 0.15 2 -0.18 23 25
EGFR(dimer) 0.036 0.058 0.15 1 -0.18 20 21
E-cadherin/beta catenin-gamma catenin 0.037 0.032 -10000 0 -0.12 24 24
mol:PI-3-4-5-P3 0.03 0.042 0.19 2 -0.25 1 3
PIK3CA 0.021 0.005 -10000 0 -10000 0 0
PI3K 0.031 0.043 0.2 2 -0.25 1 3
FYN 0.001 0.032 0.14 7 -0.22 5 12
mol:Ca2+ 0.005 0.026 -10000 0 -0.19 1 1
JUP 0.022 0.006 0.13 2 -10000 0 2
PIK3R1 0.021 0.004 -10000 0 -10000 0 0
mol:DAG 0.005 0.026 -10000 0 -0.2 1 1
CDH1 0.022 0.013 0.12 9 -10000 0 9
RhoA/GDP 0.046 0.063 0.16 124 -0.17 1 125
establishment of polarity of embryonic epithelium 0.002 0.04 0.14 4 -0.18 23 27
SRC 0.02 0.004 -10000 0 -10000 0 0
RAC1 0.018 0.008 -10000 0 -10000 0 0
RHOA 0.021 0.003 -10000 0 -10000 0 0
EGFR 0.053 0.054 0.12 235 -10000 0 235
CASR -0.007 0.027 0.14 7 -10000 0 7
RhoA/GTP 0.016 0.027 -10000 0 -0.17 1 1
AKT2 0.01 0.031 0.16 2 -0.23 1 3
actin cable formation -0.003 0.042 0.13 4 -0.2 22 26
apoptosis -0.007 0.034 0.18 6 -0.18 3 9
CTNNA1 0.021 0.003 -10000 0 -10000 0 0
mol:GDP 0.002 0.027 0.14 2 -0.19 1 3
PIP5K1A 0.003 0.043 0.14 4 -0.19 23 27
PLCG1 0.005 0.026 -10000 0 -0.2 1 1
Rac1/GTP 0.039 0.056 -10000 0 -0.17 20 20
homophilic cell adhesion 0 0.002 -10000 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.036 0.027 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.021 0.005 0.12 1 -10000 0 1
STAT1 (dimer)/Cbp/p300 0.029 0.037 0.21 10 -10000 0 10
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.034 0.019 0.13 1 -10000 0 1
antigen processing and presentation of peptide antigen via MHC class I -0.053 0.058 -10000 0 -0.14 125 125
CaM/Ca2+ 0.037 0.028 -10000 0 -10000 0 0
RAP1A 0.019 0.007 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.011 0.026 0.13 10 -10000 0 10
AKT1 -0.015 0.043 0.17 24 -10000 0 24
MAP2K1 -0.017 0.028 0.15 15 -10000 0 15
MAP3K11 -0.015 0.03 0.17 13 -10000 0 13
IFNGR1 0.02 0.007 0.1 2 -10000 0 2
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.21 0.18 -10000 0 -0.34 410 410
Rap1/GTP -0.025 0.012 -10000 0 -10000 0 0
CRKL/C3G 0.03 0.007 0.11 1 -10000 0 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.046 0.031 -10000 0 -10000 0 0
CEBPB 0.003 0.064 0.38 3 -0.52 3 6
STAT3 0.021 0.002 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.058 0.057 -10000 0 -0.66 2 2
STAT1 -0.016 0.031 0.17 13 -10000 0 13
CALM1 0.02 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.01 0.018 0.13 5 -10000 0 5
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.016 0.036 0.17 16 -10000 0 16
CEBPB/PTGES2/Cbp/p300 0.02 0.04 -10000 0 -0.38 2 2
mol:Ca2+ 0.034 0.026 -10000 0 -10000 0 0
MAPK3 -0.001 0.064 0.5 1 -0.68 4 5
STAT1 (dimer) -0.066 0.076 -10000 0 -0.18 120 120
MAPK1 -0.011 0.1 0.5 1 -0.69 13 14
JAK2 0.02 0.006 0.078 1 -10000 0 1
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
JAK1 0.019 0.007 -10000 0 -10000 0 0
CAMK2D 0.021 0.003 -10000 0 -10000 0 0
DAPK1 0.004 0.05 0.3 6 -0.34 2 8
SMAD7 -0.033 0.031 0.11 3 -0.1 4 7
CBL/CRKL/C3G 0.009 0.038 0.19 13 -10000 0 13
PI3K 0.034 0.03 -10000 0 -10000 0 0
IFNG 0.01 0.018 0.13 5 -10000 0 5
apoptosis 0 0.055 0.29 4 -0.42 5 9
CAMK2G 0.019 0.006 -10000 0 -10000 0 0
STAT3 (dimer) 0.021 0.002 -10000 0 -10000 0 0
CAMK2A 0.006 0.01 -10000 0 -10000 0 0
CAMK2B 0.012 0.01 -10000 0 -10000 0 0
FRAP1 -0.014 0.04 0.16 24 -10000 0 24
PRKCD -0.016 0.042 0.17 26 -10000 0 26
RAP1B 0.021 0.009 0.12 4 -10000 0 4
negative regulation of cell growth -0.053 0.058 -10000 0 -0.14 125 125
PTPN2 0.021 0.003 -10000 0 -10000 0 0
EP300 0.021 0.004 -10000 0 -10000 0 0
IRF1 0.002 0.044 0.22 11 -10000 0 11
STAT1 (dimer)/PIASy -0.022 0.029 0.16 8 -10000 0 8
SOCS1 0.042 0.069 -10000 0 -0.98 2 2
mol:GDP -0.011 0.031 0.15 11 -10000 0 11
CASP1 -0.027 0.038 0.1 9 -0.1 1 10
PTGES2 0.021 0.003 -10000 0 -10000 0 0
IRF9 0.008 0.026 0.16 5 -0.15 2 7
mol:PI-3-4-5-P3 0.024 0.024 -10000 0 -10000 0 0
RAP1/GDP 0.008 0.029 0.098 2 -10000 0 2
CBL -0.015 0.03 0.17 13 -10000 0 13
MAP3K1 -0.014 0.027 0.15 12 -10000 0 12
PIAS1 0.021 0.003 -10000 0 -10000 0 0
PIAS4 0.02 0.004 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.053 0.058 -10000 0 -0.14 125 125
PTPN11 -0.013 0.027 0.17 13 -10000 0 13
CREBBP 0.021 0.002 -10000 0 -10000 0 0
RAPGEF1 0.021 0.003 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.023 0.023 0.12 28 -10000 0 28
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.021 0.002 -10000 0 -10000 0 0
TCEB1 0.02 0.004 -10000 0 -10000 0 0
HIF1A/p53 0.001 0.077 0.2 2 -0.26 40 42
HIF1A -0.009 0.055 -10000 0 -0.27 28 28
COPS5 0.021 0.003 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.052 0.024 -10000 0 -10000 0 0
FIH (dimer) 0.019 0.006 -10000 0 -10000 0 0
CDKN2A 0.044 0.05 0.12 182 -10000 0 182
ARNT/IPAS 0.026 0.034 0.11 27 -0.16 15 42
HIF1AN 0.019 0.006 -10000 0 -10000 0 0
GNB2L1 0.023 0.016 0.12 15 -10000 0 15
HIF1A/ARNT -0.003 0.074 0.16 1 -0.27 38 39
CUL2 0.019 0.007 -10000 0 -10000 0 0
OS9 0.019 0.006 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.042 0.014 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.002 0.073 0.16 2 -0.27 39 41
PHD1-3/OS9 0.043 0.022 -10000 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C 0.014 0.078 -10000 0 -0.26 40 40
VHL 0.021 0.003 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
HIF1A/JAB1 -0.004 0.074 0.16 1 -0.26 40 41
EGLN3 0.02 0.004 -10000 0 -10000 0 0
EGLN2 0.019 0.007 -10000 0 -10000 0 0
EGLN1 0.021 0.002 -10000 0 -10000 0 0
TP53 0.031 0.031 0.12 67 -10000 0 67
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.02 0.052 -10000 0 -0.49 6 6
ARNT 0.021 0.002 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.02 0.004 -10000 0 -10000 0 0
HIF1A/p19ARF 0.014 0.082 0.27 3 -0.26 40 43
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.045 0.074 -10000 0 -0.37 15 15
HDAC1 0.006 0.018 -10000 0 -0.024 22 22
AES 0.02 0.004 -10000 0 -0.016 1 1
FBXW11 0.021 0.003 -10000 0 -10000 0 0
DTX1 0.021 0.003 -10000 0 -10000 0 0
LRP6/FZD1 0.025 0.014 0.11 4 -10000 0 4
TLE1 0.02 0.003 -10000 0 -0.02 1 1
AP1 0.002 0.043 -10000 0 -0.19 13 13
NCSTN 0.021 0.002 -10000 0 -10000 0 0
ADAM10 0.021 0.003 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.033 0.03 -10000 0 -0.45 1 1
NICD/RBPSUH 0.024 0.064 -10000 0 -0.37 15 15
WIF1 0.007 0.01 -10000 0 -10000 0 0
NOTCH1 0.012 0.063 -10000 0 -0.39 15 15
PSENEN 0.019 0.006 -10000 0 -10000 0 0
KREMEN2 0.022 0.009 0.12 5 -10000 0 5
DKK1 0.028 0.031 0.12 60 -10000 0 60
beta catenin/beta TrCP1 0.011 0.067 0.24 9 -0.26 2 11
APH1B 0.021 0.003 -10000 0 -10000 0 0
APH1A 0.021 0.002 -10000 0 -10000 0 0
AXIN1 0.011 0.033 0.24 2 -10000 0 2
CtBP/CBP/TCF1/TLE1/AES -0.006 0.037 -10000 0 -0.2 7 7
PSEN1 0.02 0.004 -10000 0 -10000 0 0
FOS 0.021 0.013 0.12 8 -10000 0 8
JUN 0.019 0.007 -10000 0 -10000 0 0
MAP3K7 0.018 0.007 -10000 0 -0.017 21 21
CTNNB1 0.005 0.067 0.23 13 -0.27 2 15
MAPK3 0.021 0.002 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.017 0.061 -10000 0 -0.13 88 88
HNF1A 0.02 0.003 -10000 0 -0.018 2 2
CTBP1 0.02 0.003 -10000 0 -0.018 2 2
MYC 0.041 0.065 -10000 0 -0.81 2 2
NKD1 0.037 0.038 0.12 106 -10000 0 106
FZD1 0.018 0.012 0.12 4 -10000 0 4
NOTCH1 precursor/Deltex homolog 1 0.024 0.065 -10000 0 -0.38 15 15
apoptosis 0.002 0.043 -10000 0 -0.19 13 13
Delta 1/NOTCHprecursor 0.042 0.073 -10000 0 -0.37 15 15
DLL1 0.048 0.047 0.12 176 -10000 0 176
PPARD 0.022 0.057 -10000 0 -0.8 3 3
Gamma Secretase 0.054 0.023 -10000 0 -10000 0 0
APC 0.009 0.039 0.24 1 -0.31 4 5
DVL1 -0.021 0.065 -10000 0 -0.24 50 50
CSNK2A1 0.021 0.004 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.041 0.033 -10000 0 -0.13 9 9
LRP6 0.02 0.004 -10000 0 -10000 0 0
CSNK1A1 0.021 0.003 -10000 0 -10000 0 0
NLK 0.003 0.007 -10000 0 -10000 0 0
CCND1 0.027 0.053 -10000 0 -0.8 2 2
WNT1 0.018 0.008 0.12 1 -10000 0 1
Axin1/APC/beta catenin 0.002 0.072 0.3 5 -0.39 1 6
DKK2 0.019 0.012 0.12 5 -10000 0 5
NOTCH1 precursor/DVL1 -0.012 0.085 -10000 0 -0.42 13 13
GSK3B 0.02 0.003 -10000 0 -10000 0 0
FRAT1 0.019 0.006 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.028 0.065 -10000 0 -0.38 15 15
PPP2R5D -0.005 0.046 -10000 0 -0.31 6 6
MAPK1 0.021 0.003 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.049 0.085 -10000 0 -0.13 322 322
RBPJ 0.021 0.003 -10000 0 -10000 0 0
CREBBP 0.024 0.004 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0.027 0.006 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.021 0.003 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.02 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.021 0.002 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.07 0.1 -10000 0 -0.18 272 272
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.02 0.004 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.021 0.003 -10000 0 -10000 0 0
FYN 0.02 0.004 -10000 0 -10000 0 0
MAP3K12 0.021 0.003 -10000 0 -10000 0 0
FGR 0.02 0.012 0.12 6 -10000 0 6
p38 alpha/TAB1 -0.02 0.054 -10000 0 -0.26 14 14
PRKG1 0.019 0.009 0.12 2 -10000 0 2
DUSP8 0.019 0.006 -10000 0 -10000 0 0
PGK/cGMP/p38 alpha 0.004 0.069 0.14 3 -0.25 15 18
apoptosis -0.019 0.051 -10000 0 -0.25 14 14
RAL/GTP 0.024 0.011 -10000 0 -10000 0 0
LYN 0.021 0.008 0.12 3 -10000 0 3
DUSP1 0.021 0.008 0.12 4 -10000 0 4
PAK1 0.015 0.009 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.044 0.022 -10000 0 -10000 0 0
TRAF6 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.018 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 0.018 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.022 0.012 -10000 0 -10000 0 0
MAPK11 0.004 0.094 0.19 49 -0.3 13 62
BLK 0.036 0.039 0.12 104 -10000 0 104
HCK 0.022 0.014 0.12 11 -10000 0 11
MAP2K3 0.021 0.004 0.12 1 -10000 0 1
DUSP16 0.02 0.004 -10000 0 -10000 0 0
DUSP10 0.021 0.003 -10000 0 -10000 0 0
TRAF6/MEKK3 0.026 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.011 0.084 0.18 30 -0.29 13 43
positive regulation of innate immune response 0.006 0.11 0.21 47 -0.34 14 61
LCK 0.039 0.042 0.12 129 -10000 0 129
p38alpha-beta/MKP7 0.011 0.1 0.22 44 -0.33 14 58
p38alpha-beta/MKP5 0.011 0.11 0.21 44 -0.33 14 58
PGK/cGMP 0.012 0.02 0.089 2 -0.15 9 11
PAK2 0.02 0.004 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.011 0.11 0.22 45 -0.33 14 59
CDC42 0.019 0.006 -10000 0 -10000 0 0
RALB 0.021 0.001 -10000 0 -10000 0 0
RALA 0.018 0.008 -10000 0 -10000 0 0
PAK3 0.015 0.01 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.029 0.027 0.094 90 -10000 0 90
EPHB2 0.019 0.006 -10000 0 -10000 0 0
Syndecan-2/TACI 0.016 0.007 0.094 3 -10000 0 3
LAMA1 0.025 0.022 0.12 30 -10000 0 30
Syndecan-2/alpha2 ITGB1 0.034 0.035 0.19 2 -0.1 23 25
HRAS 0.02 0.005 -10000 0 -10000 0 0
Syndecan-2/CASK 0.004 0.002 -10000 0 -10000 0 0
ITGA5 0.034 0.036 0.12 89 -10000 0 89
BAX -0.007 0.004 -10000 0 -10000 0 0
EPB41 0.02 0.013 0.12 8 -10000 0 8
positive regulation of cell-cell adhesion 0.017 0.005 -10000 0 -10000 0 0
LAMA3 0.02 0.006 0.12 1 -10000 0 1
EZR 0.02 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.018 0.016 0.12 10 -10000 0 10
Syndecan-2/MMP2 0.034 0.031 0.13 1 -10000 0 1
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.03 0.019 0.11 24 -10000 0 24
dendrite morphogenesis 0.016 0.008 -10000 0 -10000 0 0
Syndecan-2/GM-CSF 0.015 0.004 -10000 0 -10000 0 0
determination of left/right symmetry 0.005 0.002 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.017 0.017 -10000 0 -0.13 8 8
GNB2L1 0.023 0.016 0.12 15 -10000 0 15
MAPK3 -0.001 0.045 0.18 38 -10000 0 38
MAPK1 -0.002 0.044 0.18 35 -10000 0 35
Syndecan-2/RACK1 0.029 0.014 -10000 0 -10000 0 0
NF1 0.021 0.002 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.005 0.002 -10000 0 -10000 0 0
ITGA2 0.023 0.016 0.12 15 -10000 0 15
MAPK8 -0.006 0.003 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.04 0.03 0.19 3 -0.11 5 8
Syndecan-2/Kininogen 0.017 0.011 0.094 10 -10000 0 10
ITGB1 0.021 0.016 0.12 12 -10000 0 12
SRC -0.003 0.04 0.17 32 -10000 0 32
Syndecan-2/CASK/Protein 4.1 0.016 0.01 -10000 0 -10000 0 0
extracellular matrix organization 0.016 0.008 0.093 1 -10000 0 1
actin cytoskeleton reorganization 0.029 0.026 0.094 90 -10000 0 90
Syndecan-2/Caveolin-2/Ras 0.025 0.017 -10000 0 -10000 0 0
Syndecan-2/Laminin alpha3 0.013 0.027 -10000 0 -0.13 22 22
Syndecan-2/RasGAP 0.038 0.016 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.037 0.031 0.18 10 -10000 0 10
PRKCD 0.02 0.004 -10000 0 -10000 0 0
Syndecan-2 dimer 0.017 0.008 -10000 0 -10000 0 0
GO:0007205 0.001 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.022 0.015 0.17 5 -10000 0 5
RHOA 0.021 0.003 -10000 0 -10000 0 0
SDCBP 0.02 0.004 -10000 0 -10000 0 0
TNFRSF13B 0.018 0.008 0.12 3 -10000 0 3
RASA1 0.021 0.002 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.03 0.019 0.11 24 -10000 0 24
Syndecan-2/Synbindin 0.018 0.006 -10000 0 -10000 0 0
TGFB1 0.019 0.008 0.12 1 -10000 0 1
CASP3 -0.002 0.045 0.18 34 -0.12 7 41
FN1 0.036 0.036 0.12 94 -10000 0 94
Syndecan-2/IL8 0.008 0.054 0.11 3 -0.13 77 80
SDC2 0.005 0.002 -10000 0 -10000 0 0
KNG1 0.018 0.014 0.12 10 -10000 0 10
Syndecan-2/Neurofibromin 0.018 0.005 -10000 0 -10000 0 0
TRAPPC4 0.021 0.003 -10000 0 -10000 0 0
CSF2 0.015 0.002 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.017 0.008 0.094 1 -10000 0 1
Syndecan-2/Syntenin/PI-4-5-P2 0.017 0.005 -10000 0 -10000 0 0
Syndecan-2/Ezrin 0.029 0.011 -10000 0 -10000 0 0
PRKACA 0 0.046 0.18 39 -10000 0 39
angiogenesis 0.008 0.054 0.11 3 -0.13 77 80
MMP2 0.044 0.043 0.12 145 -10000 0 145
IL8 0.027 0.032 0.12 60 -10000 0 60
calcineurin-NFAT signaling pathway 0.016 0.007 0.093 3 -10000 0 3
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.005 0.074 0.22 27 -10000 0 27
GNAI2 0.021 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.006 0.048 -10000 0 -0.13 73 73
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.021 0.003 -10000 0 -10000 0 0
RhoA/GTP -0.004 0.075 -10000 0 -0.22 27 27
negative regulation of cAMP metabolic process -0.016 0.064 -10000 0 -0.18 72 72
GNAZ 0.02 0.004 -10000 0 -10000 0 0
GNAI3 0.019 0.008 0.12 1 -10000 0 1
GNA12 0.018 0.008 -10000 0 -10000 0 0
S1PR5 0.017 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.016 0.064 -10000 0 -0.18 72 72
RhoA/GDP 0.015 0.002 -10000 0 -10000 0 0
RHOA 0.021 0.003 -10000 0 -10000 0 0
GNAI1 0.017 0.008 -10000 0 -10000 0 0
Class I PI3K 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
ARF5/GTP -0.015 0.034 0.15 20 -10000 0 20
DAPP1 0.007 0.077 0.16 17 -0.28 13 30
Src family/SYK family/BLNK-LAT/BTK-ITK 0.003 0.1 0.24 6 -0.31 32 38
mol:DAG 0.007 0.06 0.17 36 -0.16 4 40
HRAS 0.022 0.007 0.064 1 -10000 0 1
RAP1A 0.02 0.009 -10000 0 -10000 0 0
ARF5/GDP 0.021 0.04 0.18 6 -0.26 5 11
PLCG2 0.022 0.009 0.12 5 -10000 0 5
PLCG1 0.02 0.004 -10000 0 -10000 0 0
ARF5 0.017 0.009 -10000 0 -10000 0 0
mol:GTP -0.011 0.042 0.18 26 -10000 0 26
ARF1/GTP -0.007 0.035 0.16 21 -10000 0 21
RHOA 0.021 0.003 -10000 0 -10000 0 0
YES1 0.02 0.004 -10000 0 -10000 0 0
RAP1A/GTP -0.009 0.039 0.16 30 -10000 0 30
ADAP1 -0.014 0.032 0.18 13 -10000 0 13
ARAP3 -0.011 0.041 0.17 26 -10000 0 26
INPPL1 0.021 0.003 -10000 0 -10000 0 0
PREX1 0.02 0.004 -10000 0 -10000 0 0
ARHGEF6 0.022 0.009 0.12 5 -10000 0 5
ARHGEF7 0.02 0.004 -10000 0 -10000 0 0
ARF1 0.021 0.002 -10000 0 -10000 0 0
NRAS 0.02 0.009 -10000 0 -10000 0 0
FYN 0.02 0.004 -10000 0 -10000 0 0
ARF6 0.02 0.004 -10000 0 -10000 0 0
FGR 0.02 0.012 0.12 6 -10000 0 6
mol:Ca2+ 0.003 0.044 0.15 36 -0.099 2 38
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.02 0.004 -10000 0 -10000 0 0
ZAP70 0.023 0.013 0.12 11 -10000 0 11
mol:IP3 0.002 0.053 0.17 36 -0.14 2 38
LYN 0.021 0.008 0.12 3 -10000 0 3
ARF1/GDP 0.034 0.048 0.19 11 -0.24 6 17
RhoA/GDP 0.025 0.043 0.17 33 -0.21 1 34
PDK1/Src/Hsp90 0.039 0.013 -10000 0 -10000 0 0
BLNK 0.019 0.01 0.12 3 -10000 0 3
actin cytoskeleton reorganization 0.023 0.084 0.23 60 -0.37 1 61
SRC 0.02 0.004 -10000 0 -10000 0 0
PLEKHA2 -0.014 0.005 0.02 5 -10000 0 5
RAC1 0.018 0.008 -10000 0 -10000 0 0
PTEN 0.018 0.012 -10000 0 -0.03 14 14
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.014 0.041 0.17 26 -10000 0 26
RhoA/GTP -0.008 0.047 0.17 36 -10000 0 36
Src family/SYK family/BLNK-LAT 0.001 0.065 -10000 0 -0.25 15 15
BLK 0.036 0.039 0.12 104 -10000 0 104
PDPK1 0.021 0.002 -10000 0 -10000 0 0
CYTH1 -0.014 0.038 0.17 22 -10000 0 22
HCK 0.022 0.014 0.12 11 -10000 0 11
CYTH3 -0.014 0.037 0.18 18 -10000 0 18
CYTH2 -0.013 0.039 0.17 21 -10000 0 21
KRAS 0.021 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.006 0.038 0.23 4 -0.31 4 8
SGK1 0.004 0.06 0.21 2 -0.33 16 18
INPP5D 0.021 0.009 0.12 5 -10000 0 5
mol:GDP 0.023 0.05 0.18 16 -0.25 6 22
SOS1 0.021 0.001 -10000 0 -10000 0 0
SYK 0.022 0.013 0.12 10 -10000 0 10
ARF6/GDP 0.001 0.053 0.18 35 -0.22 1 36
mol:PI-3-4-5-P3 -0.016 0.022 0.2 5 -10000 0 5
ARAP3/RAP1A/GTP -0.009 0.039 0.16 30 -10000 0 30
VAV1 0.021 0.007 0.12 2 -10000 0 2
mol:PI-3-4-P2 -0.012 0.006 0.051 5 -10000 0 5
RAS family/GTP/PI3K Class I 0.039 0.051 0.18 72 -10000 0 72
PLEKHA1 -0.013 0.006 0.02 4 -10000 0 4
Rac1/GDP 0.023 0.04 0.19 6 -0.24 6 12
LAT 0.021 0.006 0.12 2 -10000 0 2
Rac1/GTP 0.023 0.037 0.18 1 -0.39 2 3
ITK -0.013 0.037 0.17 20 -10000 0 20
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.005 0.07 0.21 30 -0.21 4 34
LCK 0.039 0.042 0.12 129 -10000 0 129
BTK -0.014 0.04 0.17 23 -10000 0 23
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.009 0.11 0.23 9 -0.32 44 53
IKBKB 0.031 0.07 0.22 29 -0.3 5 34
AKT1 0.006 0.072 0.24 35 -10000 0 35
IKBKG 0.023 0.06 0.21 16 -0.26 4 20
CALM1 0.004 0.044 0.18 4 -0.24 4 8
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
MAP3K1 0.023 0.086 0.28 13 -0.37 6 19
MAP3K7 0.02 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.006 0.048 0.19 3 -0.25 4 7
DOK1 0.022 0.007 0.12 3 -10000 0 3
AP-1 -0.012 0.078 0.22 5 -0.21 50 55
LYN 0.021 0.008 0.12 3 -10000 0 3
BLNK 0.019 0.01 0.12 3 -10000 0 3
SHC1 0.023 0.016 0.12 16 -10000 0 16
BCR complex 0.033 0.028 0.12 47 -10000 0 47
CD22 0.008 0.017 -10000 0 -10000 0 0
CAMK2G 0.005 0.04 0.18 5 -0.23 4 9
CSNK2A1 0.02 0.004 -10000 0 -10000 0 0
INPP5D 0.021 0.01 0.12 5 -10000 0 5
SHC/GRB2/SOS1 -0.009 0.029 0.098 4 -10000 0 4
GO:0007205 0.006 0.048 0.19 3 -0.26 4 7
SYK 0.022 0.013 0.12 10 -10000 0 10
ELK1 0.003 0.048 0.2 5 -0.25 4 9
NFATC1 0.001 0.053 0.29 6 -0.29 4 10
B-cell antigen/BCR complex 0.033 0.028 0.12 47 -10000 0 47
PAG1/CSK 0.03 0.007 -10000 0 -10000 0 0
NFKBIB 0.02 0.034 0.13 10 -0.13 12 22
HRAS 0.005 0.05 0.21 10 -0.25 3 13
NFKBIA 0.019 0.034 0.13 10 -0.12 12 22
NF-kappa-B/RelA/I kappa B beta 0.022 0.03 0.11 20 -0.09 8 28
RasGAP/Csk 0.073 0.047 0.19 36 -10000 0 36
mol:GDP 0.008 0.048 0.18 3 -0.25 4 7
PTEN 0.018 0.007 -10000 0 -10000 0 0
CD79B 0.025 0.021 0.12 28 -10000 0 28
NF-kappa-B/RelA/I kappa B alpha 0.022 0.03 0.11 20 -0.089 8 28
GRB2 0.02 0.004 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.002 0.074 0.32 4 -0.41 2 6
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
mol:IP3 0.006 0.043 0.19 2 -0.25 3 5
CSK 0.021 0.003 -10000 0 -10000 0 0
FOS 0 0.047 0.22 4 -0.28 2 6
CHUK -0.003 0.089 0.25 6 -0.26 42 48
IBTK 0.02 0.004 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.041 0.058 0.2 12 -0.25 2 14
PTPN6 0.001 0.015 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
BCL2A1 0.017 0.023 0.077 26 -0.071 10 36
VAV2 0.003 0.041 0.2 1 -0.22 2 3
ubiquitin-dependent protein catabolic process 0.02 0.034 0.13 10 -0.13 12 22
BTK 0.022 0.017 -10000 0 -10000 0 0
CD19 0.006 0.035 0.15 2 -0.28 1 3
MAP4K1 0.02 0.011 0.12 5 -10000 0 5
CD72 0.034 0.036 0.12 89 -10000 0 89
PAG1 0.02 0.004 -10000 0 -10000 0 0
MAPK14 0.02 0.079 0.26 14 -0.33 5 19
SH3BP5 0.021 0.002 -10000 0 -10000 0 0
PIK3AP1 0.01 0.039 0.18 1 -0.27 4 5
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.009 0.075 0.17 1 -0.32 14 15
RAF1 0.002 0.047 0.21 8 -0.27 2 10
RasGAP/p62DOK/SHIP 0.07 0.046 0.18 38 -10000 0 38
CD79A 0.024 0.024 0.12 34 -10000 0 34
re-entry into mitotic cell cycle -0.012 0.076 0.21 5 -0.21 48 53
RASA1 0.021 0.002 -10000 0 -10000 0 0
MAPK3 -0.003 0.044 0.19 11 -0.3 1 12
MAPK1 -0.002 0.044 0.18 12 -0.29 1 13
CD72/SHP1 0.006 0.071 0.24 17 -0.2 2 19
NFKB1 0.021 0.002 -10000 0 -10000 0 0
MAPK8 0.019 0.08 0.26 15 -0.32 6 21
actin cytoskeleton organization 0.022 0.07 0.25 22 -0.24 1 23
NF-kappa-B/RelA 0.043 0.06 0.22 14 -0.2 10 24
Calcineurin 0.025 0.048 -10000 0 -0.22 4 4
PI3K -0.009 0.05 -10000 0 -0.18 1 1
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.018 0.033 0.19 1 -0.3 3 4
SOS1 0.021 0.001 -10000 0 -10000 0 0
Bam32/HPK1 0.027 0.095 -10000 0 -0.64 11 11
DAPP1 0.011 0.1 -10000 0 -0.76 9 9
cytokine secretion 0.002 0.051 0.26 7 -0.27 4 11
mol:DAG 0.006 0.043 0.19 2 -0.25 3 5
PLCG2 0.022 0.009 0.12 5 -10000 0 5
MAP2K1 0 0.046 0.2 10 -0.33 1 11
B-cell antigen/BCR complex/FcgammaRIIB 0.06 0.047 0.19 36 -10000 0 36
mol:PI-3-4-5-P3 -0.018 0.04 0.14 7 -10000 0 7
ETS1 0.002 0.049 0.19 16 -0.25 2 18
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.053 0.039 0.2 13 -0.1 2 15
B-cell antigen/BCR complex/LYN 0.014 0.036 -10000 0 -0.3 1 1
MALT1 0.02 0.004 -10000 0 -10000 0 0
TRAF6 0.02 0.003 -10000 0 -10000 0 0
RAC1 0.015 0.06 0.22 14 -0.25 1 15
B-cell antigen/BCR complex/LYN/SYK 0.017 0.074 0.21 20 -10000 0 20
CARD11 0.024 0.07 0.2 68 -0.3 2 70
FCGR2B 0.05 0.047 0.12 186 -10000 0 186
PPP3CA 0.021 0.002 -10000 0 -10000 0 0
BCL10 0.018 0.007 -10000 0 -10000 0 0
IKK complex 0.012 0.039 0.14 24 -0.11 10 34
PTPRC 0.023 0.016 0.12 15 -10000 0 15
PDPK1 -0.012 0.042 0.18 15 -10000 0 15
PPP3CB 0.019 0.006 -10000 0 -10000 0 0
PPP3CC 0.02 0.004 -10000 0 -10000 0 0
POU2F2 0.017 0.023 0.12 18 -0.068 3 21
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.02 0.007 -10000 0 -9999 0 0
VEGFR1 homodimer/NRP1 -0.007 0.004 -10000 0 -9999 0 0
mol:DAG 0.008 0.026 0.19 3 -9999 0 3
VEGFR1 homodimer/NRP1/VEGFR 121 0.025 0.021 -10000 0 -9999 0 0
CaM/Ca2+ 0.012 0.032 0.18 3 -9999 0 3
HIF1A 0.023 0.009 0.13 3 -9999 0 3
GAB1 0.021 0.003 -10000 0 -9999 0 0
AKT1 0.003 0.029 0.16 11 -9999 0 11
PLCG1 0.008 0.026 0.19 3 -9999 0 3
NOS3 0.009 0.02 0.2 2 -9999 0 2
CBL 0.021 0.003 -10000 0 -9999 0 0
mol:NO 0.02 0.038 0.2 2 -9999 0 2
FLT1 -0.009 0.005 -10000 0 -9999 0 0
PGF 0.067 0.053 0.12 298 -9999 0 298
VEGFR1 homodimer/NRP2/VEGFR121 0.038 0.025 0.18 3 -9999 0 3
CALM1 0.02 0.005 -10000 0 -9999 0 0
PIK3CA 0.021 0.003 -10000 0 -9999 0 0
eNOS/Hsp90 0.037 0.044 0.24 5 -9999 0 5
endothelial cell proliferation -0.019 0.053 0.22 2 -9999 0 2
mol:Ca2+ 0.008 0.026 0.19 3 -9999 0 3
MAPK3 -0.013 0.014 0.17 3 -9999 0 3
MAPK1 -0.013 0.014 0.17 3 -9999 0 3
PIK3R1 0.021 0.003 -10000 0 -9999 0 0
PLGF homodimer 0.067 0.052 0.12 298 -9999 0 298
PRKACA 0.02 0.004 -10000 0 -9999 0 0
RP11-342D11.1 0 0 -10000 0 -9999 0 0
CAV1 0.028 0.035 0.12 73 -9999 0 73
VEGFA homodimer 0.033 0.034 0.12 79 -9999 0 79
VEGFR1 homodimer/VEGFA homodimer 0.027 0.024 0.22 1 -9999 0 1
platelet activating factor biosynthetic process -0.014 0.021 0.16 8 -9999 0 8
PI3K 0.068 0.039 0.21 1 -9999 0 1
PRKCA -0.003 0.019 0.18 3 -9999 0 3
PRKCB -0.002 0.014 0.19 1 -9999 0 1
VEGFR1 homodimer/PLGF homodimer 0.053 0.04 0.22 1 -9999 0 1
VEGFA 0.033 0.034 0.12 79 -9999 0 79
VEGFB 0.021 0.003 -10000 0 -9999 0 0
mol:IP3 0.008 0.026 0.19 3 -9999 0 3
RASA1 -0.013 0.016 0.18 4 -9999 0 4
NRP2 0.022 0.01 0.12 6 -9999 0 6
VEGFR1 homodimer -0.009 0.005 -10000 0 -9999 0 0
VEGFB homodimer 0.021 0.003 -10000 0 -9999 0 0
NCK1 0.021 0.005 0.12 1 -9999 0 1
eNOS/Caveolin-1 0.025 0.041 0.19 1 -9999 0 1
PTPN11 0.021 0.003 -10000 0 -9999 0 0
mol:PI-3-4-5-P3 0.065 0.038 0.2 1 -9999 0 1
mol:L-citrulline 0.02 0.038 0.2 2 -9999 0 2
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.047 0.026 0.21 1 -9999 0 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.037 0.023 -10000 0 -9999 0 0
CD2AP 0.021 0.002 -10000 0 -9999 0 0
PI3K/GAB1 0.072 0.04 0.21 1 -9999 0 1
PDPK1 0.001 0.032 0.17 17 -9999 0 17
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.037 0.023 -10000 0 -9999 0 0
mol:NADP 0.02 0.038 0.2 2 -9999 0 2
HSP90AA1 0.02 0.004 -10000 0 -9999 0 0
ubiquitin-dependent protein catabolic process 0.046 0.025 0.2 1 -9999 0 1
VEGFR1 homodimer/NRP2 0.021 0.01 -10000 0 -9999 0 0
Signaling events mediated by PRL

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
CCNE1 0.019 0.007 -10000 0 -10000 0 0
mol:Halofuginone 0.001 0 -10000 0 -10000 0 0
ITGA1 0.031 0.031 0.12 65 -10000 0 65
CDKN1A -0.012 0.1 -10000 0 -0.32 63 63
PRL-3/alpha Tubulin 0.028 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.017 0.007 -10000 0 -10000 0 0
AGT 0.021 0.006 0.12 2 -10000 0 2
CCNA2 -0.003 0.044 0.2 25 -10000 0 25
TUBA1B 0.02 0.004 -10000 0 -10000 0 0
EGR1 0.007 0.003 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.028 0.11 0.22 5 -0.28 66 71
MAPK3 -0.012 0.005 0.051 2 -10000 0 2
PRL-2 /Rab GGTase beta 0.028 0.01 -10000 0 -10000 0 0
MAPK1 -0.011 0.005 0.051 2 -10000 0 2
PTP4A1 -0.009 0.003 -10000 0 -10000 0 0
PTP4A3 0.02 0.008 0.12 2 -10000 0 2
PTP4A2 0.019 0.006 -10000 0 -10000 0 0
ITGB1 -0.009 0.01 0.051 12 -10000 0 12
SRC 0.02 0.004 -10000 0 -10000 0 0
RAC1 0.009 0.019 -10000 0 -0.31 2 2
Rab GGTase beta/Rab GGTase alpha 0.027 0.011 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.007 0.039 -10000 0 -10000 0 0
RABGGTA 0.02 0.004 -10000 0 -10000 0 0
BCAR1 -0.018 0.007 -10000 0 -10000 0 0
RHOC -0.026 0.11 -10000 0 -0.33 76 76
RHOA 0.006 0.04 -10000 0 -0.32 10 10
cell motility -0.001 0.071 0.27 1 -0.32 12 13
PRL-1/alpha Tubulin -0.008 0.042 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.036 0.025 0.18 1 -10000 0 1
ROCK1 -0.001 0.071 0.27 1 -0.32 12 13
RABGGTB 0.019 0.007 -10000 0 -10000 0 0
CDK2 0.051 0.048 0.12 198 -10000 0 198
mitosis -0.009 0.003 -10000 0 -10000 0 0
ATF5 0.019 0.007 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0 0.064 0.21 9 -0.36 15 24
CRKL 0 0.06 -10000 0 -0.38 15 15
HRAS 0.018 0.061 -10000 0 -0.31 15 15
mol:PIP3 0.023 0.084 0.27 12 -0.35 15 27
SPRED1 0.021 0.003 -10000 0 -10000 0 0
SPRED2 0.021 0.002 -10000 0 -10000 0 0
GAB1 0.004 0.063 -10000 0 -0.39 15 15
FOXO3 0.021 0.11 0.27 9 -0.36 24 33
AKT1 0.023 0.11 0.28 6 -0.38 24 30
BAD 0.022 0.11 0.28 8 -0.36 24 32
megakaryocyte differentiation 0.004 0.062 -10000 0 -0.38 15 15
GSK3B 0.021 0.11 0.27 12 -0.36 24 36
RAF1 0.015 0.057 0.23 2 -0.26 14 16
SHC1 0.023 0.016 0.12 16 -10000 0 16
STAT3 0.003 0.063 -10000 0 -0.39 15 15
STAT1 -0.001 0.14 -10000 0 -0.9 14 14
HRAS/SPRED1 0.026 0.06 0.19 1 -0.26 15 16
cell proliferation 0.001 0.062 -10000 0 -0.39 15 15
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
TEC 0.022 0.011 0.12 7 -10000 0 7
RPS6KB1 0.018 0.08 -10000 0 -0.39 14 14
HRAS/SPRED2 0.026 0.061 0.19 1 -0.26 15 16
LYN/TEC/p62DOK 0.036 0.071 -10000 0 -0.38 15 15
MAPK3 0.012 0.057 0.21 15 -0.2 17 32
STAP1 0.005 0.063 -10000 0 -0.39 15 15
GRAP2 0.023 0.018 0.12 19 -10000 0 19
JAK2 -0.003 0.12 -10000 0 -0.78 14 14
STAT1 (dimer) -0.001 0.14 -10000 0 -0.88 14 14
mol:Gleevec -0.001 0.003 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.05 0.078 -10000 0 -0.36 15 15
actin filament polymerization -0.001 0.053 -10000 0 -0.33 15 15
LYN 0.021 0.008 0.12 3 -10000 0 3
STAP1/STAT5A (dimer) -0.003 0.089 -10000 0 -0.54 15 15
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.021 0.065 -10000 0 -0.36 14 14
PI3K 0.037 0.082 -10000 0 -0.38 13 13
PTEN 0.018 0.007 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR 0.014 0.16 -10000 0 -1 14 14
MAPK8 0.001 0.063 -10000 0 -0.4 15 15
STAT3 (dimer) 0.004 0.062 -10000 0 -0.38 15 15
positive regulation of transcription 0.012 0.051 0.19 18 -0.16 14 32
mol:GDP 0.025 0.063 -10000 0 -0.32 15 15
PIK3C2B 0.002 0.063 -10000 0 -0.39 15 15
CBL/CRKL 0.011 0.063 0.21 1 -0.37 14 15
FER 0.004 0.063 -10000 0 -0.39 15 15
SH2B3 0.004 0.063 -10000 0 -0.4 14 14
PDPK1 0.021 0.081 0.27 15 -0.33 14 29
SNAI2 0.003 0.063 -10000 0 -0.39 15 15
positive regulation of cell proliferation 0.001 0.11 -10000 0 -0.68 14 14
KITLG 0.021 0.012 -10000 0 -0.042 14 14
cell motility 0.001 0.11 -10000 0 -0.68 14 14
PTPN6 0.019 0.011 0.12 4 -10000 0 4
EPOR 0.022 0.053 -10000 0 -0.54 2 2
STAT5A (dimer) 0.005 0.093 -10000 0 -0.55 15 15
SOCS1 0.052 0.048 0.12 202 -10000 0 202
cell migration 0.003 0.069 0.44 15 -10000 0 15
SOS1 0.021 0.001 -10000 0 -10000 0 0
EPO 0.024 0.031 0.13 50 -0.029 8 58
VAV1 0.021 0.007 0.12 2 -10000 0 2
GRB10 0 0.055 -10000 0 -0.36 12 12
PTPN11 0.019 0.008 -10000 0 -0.019 25 25
SCF/KIT 0.008 0.066 -10000 0 -0.41 15 15
GO:0007205 0 0.003 -10000 0 -10000 0 0
MAP2K1 0.01 0.05 0.19 5 -0.22 14 19
CBL 0.021 0.003 -10000 0 -10000 0 0
KIT -0.001 0.17 -10000 0 -1 16 16
MAP2K2 0.012 0.059 0.25 15 -0.22 14 29
SHC/Grb2/SOS1 0.036 0.071 -10000 0 -0.38 15 15
STAT5A 0.007 0.094 -10000 0 -0.56 15 15
GRB2 0.02 0.004 -10000 0 -10000 0 0
response to radiation 0.004 0.062 -10000 0 -0.38 15 15
SHC/GRAP2 0.033 0.019 0.18 2 -10000 0 2
PTPRO 0.004 0.063 -10000 0 -0.39 15 15
SH2B2 -0.001 0.054 -10000 0 -0.35 13 13
DOK1 0.022 0.007 0.12 3 -10000 0 3
MATK -0.003 0.07 -10000 0 -0.44 15 15
CREBBP 0.024 0.02 -10000 0 -0.11 14 14
BCL2 0.014 0.088 -10000 0 -0.69 4 4
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.005 0.052 -10000 0 -0.12 90 90
cell-cell adhesion 0.02 0.017 0.11 9 -10000 0 9
Ephrin B/EPHB2/RasGAP 0.052 0.031 -10000 0 -0.11 10 10
ITSN1 0.021 0.003 -10000 0 -10000 0 0
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
SHC1 0.023 0.016 0.12 16 -10000 0 16
Ephrin B1/EPHB3 0.029 0.01 0.1 9 -10000 0 9
Ephrin B1/EPHB1 0.028 0.017 0.096 12 -0.13 5 17
HRAS/GDP 0.022 0.035 -10000 0 -0.14 15 15
Ephrin B/EPHB1/GRB7 0.056 0.031 -10000 0 -0.11 14 14
Endophilin/SYNJ1 -0.014 0.03 0.17 14 -10000 0 14
KRAS 0.02 0.004 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.055 0.031 -10000 0 -0.11 12 12
endothelial cell migration 0.035 0.022 -10000 0 -0.11 1 1
GRB2 0.02 0.004 -10000 0 -10000 0 0
GRB7 0.02 0.009 0.12 4 -10000 0 4
PAK1 -0.015 0.037 0.2 12 -0.2 3 15
HRAS 0.02 0.005 -10000 0 -10000 0 0
RRAS -0.011 0.034 0.19 14 -10000 0 14
DNM1 0.009 0.01 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.016 0.033 0.18 14 -10000 0 14
lamellipodium assembly -0.02 0.017 -10000 0 -0.11 9 9
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.019 0.03 -10000 0 -0.16 7 7
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
EPHB2 0.019 0.006 -10000 0 -10000 0 0
EPHB3 0.021 0.009 0.12 4 -10000 0 4
EPHB1 0.022 0.011 0.12 7 -10000 0 7
EPHB4 0.019 0.017 0.12 13 -10000 0 13
mol:GDP -0.006 0.031 0.16 9 -0.15 14 23
Ephrin B/EPHB2 0.041 0.026 -10000 0 -0.11 10 10
Ephrin B/EPHB3 0.045 0.024 -10000 0 -0.11 10 10
JNK cascade -0.014 0.036 0.21 13 -10000 0 13
Ephrin B/EPHB1 0.045 0.028 -10000 0 -0.11 15 15
RAP1/GDP 0.043 0.078 0.21 98 -0.16 2 100
EFNB2 0.02 0.004 -10000 0 -10000 0 0
EFNB3 0.021 0.003 -10000 0 -10000 0 0
EFNB1 0.022 0.01 0.12 6 -10000 0 6
Ephrin B2/EPHB1-2 0.034 0.021 -10000 0 -0.11 6 6
RAP1B 0.021 0.009 0.12 4 -10000 0 4
RAP1A 0.019 0.007 -10000 0 -10000 0 0
CDC42/GTP 0.025 0.037 -10000 0 -0.16 8 8
Rap1/GTP -0.026 0.019 -10000 0 -10000 0 0
axon guidance 0.005 0.052 -10000 0 -0.12 90 90
MAPK3 0.004 0.026 -10000 0 -0.15 7 7
MAPK1 0.005 0.024 -10000 0 -0.13 6 6
Rac1/GDP 0.003 0.063 0.21 45 -0.17 2 47
actin cytoskeleton reorganization -0.021 0.02 -10000 0 -0.13 7 7
CDC42/GDP 0.027 0.088 0.21 115 -0.16 2 117
PI3K 0.039 0.024 -10000 0 -0.11 1 1
EFNA5 0.018 0.007 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.023 0.017 0.096 12 -0.13 1 13
Ephrin B/EPHB2/Intersectin/N-WASP 0.011 0.025 -10000 0 -0.17 10 10
CDC42 0.019 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.026 0.018 -10000 0 -10000 0 0
PTK2 0.024 0.13 0.54 41 -10000 0 41
MAP4K4 -0.014 0.036 0.21 13 -10000 0 13
SRC 0.02 0.004 -10000 0 -10000 0 0
KALRN 0.02 0.004 -10000 0 -10000 0 0
Intersectin/N-WASP 0.025 0.013 -10000 0 -10000 0 0
neuron projection morphogenesis 0.023 0.11 0.31 82 -0.2 2 84
MAP2K1 0.011 0.027 -10000 0 -0.15 7 7
WASL 0.017 0.008 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.047 0.025 -10000 0 -0.12 5 5
cell migration 0.006 0.045 0.17 6 -0.28 2 8
NRAS 0.019 0.007 -10000 0 -10000 0 0
SYNJ1 -0.014 0.03 0.17 14 -10000 0 14
PXN 0.021 0.002 -10000 0 -10000 0 0
TF -0.017 0.028 0.16 12 -0.2 1 13
HRAS/GTP 0.031 0.029 -10000 0 -0.11 13 13
Ephrin B1/EPHB1-2 0.035 0.021 -10000 0 -0.12 5 5
cell adhesion mediated by integrin 0.009 0.028 0.11 7 -0.14 16 23
RAC1 0.018 0.008 -10000 0 -10000 0 0
mol:GTP 0.035 0.029 -10000 0 -0.11 14 14
RAC1-CDC42/GTP -0.023 0.018 -10000 0 -0.11 9 9
RASA1 0.021 0.002 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.022 0.057 0.21 38 -0.16 2 40
ruffle organization 0.036 0.13 0.26 153 -10000 0 153
NCK1 0.021 0.005 0.12 1 -10000 0 1
receptor internalization -0.01 0.028 0.16 5 -0.19 9 14
Ephrin B/EPHB2/KALRN 0.048 0.037 -10000 0 -0.12 20 20
ROCK1 -0.012 0.006 0.057 2 -10000 0 2
RAS family/GDP -0.021 0.02 -10000 0 -0.14 8 8
Rac1/GTP -0.02 0.018 -10000 0 -0.11 8 8
Ephrin B/EPHB1/Src/Paxillin 0.014 0.026 -10000 0 -0.16 13 13
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.042 0.024 -10000 0 -0.11 3 3
ER alpha/Gai/GDP/Gbeta gamma -0.018 0.1 -10000 0 -0.39 16 16
AKT1 -0.008 0.14 -10000 0 -0.62 31 31
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.005 0.14 -10000 0 -0.63 31 31
mol:Ca2+ 0.002 0.015 -10000 0 -0.29 1 1
IGF1R 0.021 0.003 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.025 0.018 -10000 0 -0.13 8 8
SHC1 0.023 0.016 0.12 16 -10000 0 16
apoptosis 0.007 0.13 0.59 31 -10000 0 31
RhoA/GTP -0.017 0.008 -10000 0 -0.11 1 1
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.003 0.095 0.19 1 -0.33 15 16
regulation of stress fiber formation 0.008 0.046 -10000 0 -0.15 52 52
E2/ERA-ERB (dimer) 0.028 0.014 0.096 15 -0.13 1 16
KRAS 0.02 0.004 -10000 0 -10000 0 0
G13/GTP 0.025 0.009 -10000 0 -0.11 1 1
pseudopodium formation -0.008 0.046 0.15 52 -10000 0 52
E2/ER alpha (dimer)/PELP1 0.027 0.009 -10000 0 -0.13 1 1
GRB2 0.02 0.004 -10000 0 -10000 0 0
GNG2 0.02 0.004 -10000 0 -10000 0 0
GNAO1 0.021 0.003 -10000 0 -10000 0 0
HRAS 0.02 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.003 0.1 0.23 2 -0.37 25 27
E2/ER beta (dimer) 0.017 0.012 0.089 15 -10000 0 15
mol:GDP 0.005 0.037 0.15 1 -0.16 23 24
mol:NADP 0.003 0.1 0.23 2 -0.37 25 27
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
mol:IP3 0.002 0.016 -10000 0 -0.3 1 1
IGF-1R heterotetramer 0.021 0.003 -10000 0 -10000 0 0
PLCB1 0.008 0.012 -10000 0 -10000 0 0
PLCB2 0.008 0.012 -10000 0 -10000 0 0
IGF1 0.021 0.005 0.12 1 -10000 0 1
mol:L-citrulline 0.003 0.1 0.23 2 -0.37 25 27
RHOA 0.021 0.003 -10000 0 -10000 0 0
Gai/GDP 0.003 0.11 -10000 0 -0.55 22 22
JNK cascade 0.017 0.012 0.089 15 -10000 0 15
BCAR1 0.021 0.003 -10000 0 -10000 0 0
ESR2 0.023 0.016 0.12 15 -10000 0 15
GNAQ 0.021 0.003 -10000 0 -10000 0 0
ESR1 0.02 0.005 -10000 0 -10000 0 0
Gq family/GDP/Gbeta gamma -0.003 0.092 -10000 0 -0.44 11 11
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.023 0.054 -10000 0 -1.1 1 1
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.005 0.095 0.19 1 -0.33 15 16
GNAZ 0.02 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer) 0.015 0.007 -10000 0 -0.15 1 1
STRN 0.021 0.003 -10000 0 -10000 0 0
GNAL 0.016 0.009 -10000 0 -10000 0 0
PELP1 0.021 0.002 -10000 0 -10000 0 0
MAPK11 -0.008 0.007 -10000 0 -10000 0 0
GNAI2 0.021 0.003 -10000 0 -10000 0 0
GNAI3 0.019 0.008 0.12 1 -10000 0 1
GNAI1 0.017 0.008 -10000 0 -10000 0 0
HBEGF 0 0.12 0.33 29 -0.37 14 43
cAMP biosynthetic process -0.006 0.053 -10000 0 -0.1 154 154
SRC -0.022 0.095 -10000 0 -0.36 17 17
PI3K 0.03 0.006 -10000 0 -10000 0 0
GNB1 0.019 0.007 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.026 0.04 -10000 0 -0.14 22 22
SOS1 0.021 0.001 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.015 0.072 -10000 0 -0.27 17 17
Gs family/GTP -0.002 0.056 -10000 0 -0.1 154 154
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.033 0.016 -10000 0 -10000 0 0
vasodilation 0.004 0.1 0.23 2 -0.35 25 27
mol:DAG 0.002 0.016 -10000 0 -0.3 1 1
Gs family/GDP/Gbeta gamma -0.013 0.059 -10000 0 -0.18 30 30
MSN -0.009 0.048 0.15 52 -10000 0 52
Gq family/GTP 0.017 0.013 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.004 0.14 -10000 0 -0.61 31 31
NRAS 0.019 0.007 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.004 0.1 0.35 25 -0.23 2 27
GRB2/SOS1 0.03 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.043 0.16 1 -0.16 25 26
NOS3 0.003 0.11 0.23 2 -0.39 25 27
GNA11 0.02 0.004 -10000 0 -10000 0 0
MAPKKK cascade 0.001 0.11 -10000 0 -0.4 33 33
E2/ER alpha (dimer)/PELP1/Src 0.006 0.1 0.24 16 -0.34 15 31
ruffle organization -0.008 0.046 0.15 52 -10000 0 52
ROCK2 -0.006 0.051 0.16 53 -10000 0 53
GNA14 0.021 0.003 -10000 0 -10000 0 0
GNA15 0.021 0.006 0.12 1 -10000 0 1
GNA13 0.02 0.004 -10000 0 -10000 0 0
MMP9 -0.013 0.1 0.36 6 -0.37 14 20
MMP2 -0.01 0.11 0.24 21 -0.37 14 35
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.014 0.013 -10000 0 -0.081 12 12
TRAF2/ASK1 0.027 0.007 -10000 0 -10000 0 0
ATM 0.021 0.003 -10000 0 -10000 0 0
MAP2K3 0.002 0.058 0.2 3 -0.3 6 9
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.004 0.069 0.2 4 -0.27 14 18
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.051 0.048 0.12 196 -10000 0 196
TXN 0.004 0.001 -10000 0 -10000 0 0
CALM1 0.02 0.005 -10000 0 -10000 0 0
GADD45A 0.026 0.028 0.12 46 -10000 0 46
GADD45B 0.022 0.014 0.12 12 -10000 0 12
MAP3K1 0.024 0.018 0.12 21 -10000 0 21
MAP3K6 0.019 0.006 -10000 0 -10000 0 0
MAP3K7 0.02 0.004 -10000 0 -10000 0 0
MAP3K4 0.02 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.027 0.011 -10000 0 -10000 0 0
TAK1/TAB family -0.002 0.016 0.11 1 -0.13 3 4
RAC1/OSM/MEKK3 0.033 0.016 -10000 0 -10000 0 0
TRAF2 0.021 0.003 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.002 0.047 -10000 0 -0.27 4 4
TRAF6 0.004 0.001 -10000 0 -10000 0 0
RAC1 0.018 0.008 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.012 0.01 -10000 0 -10000 0 0
CCM2 0.018 0.008 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.016 0.065 -10000 0 -0.13 166 166
MAPK11 0.02 0.004 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.006 0.065 -10000 0 -0.12 165 165
OSM/MEKK3 0.025 0.012 -10000 0 -10000 0 0
TAOK1 0.004 0.03 -10000 0 -0.21 13 13
TAOK2 0.009 0.001 -10000 0 -10000 0 0
TAOK3 0.009 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.021 0.002 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.02 0.005 -10000 0 -10000 0 0
MAP3K10 0.019 0.007 -10000 0 -10000 0 0
MAP3K3 0.021 0.003 -10000 0 -10000 0 0
TRX/ASK1 0.017 0.009 -10000 0 -0.099 3 3
GADD45/MTK1/MTK1 0.058 0.041 0.18 14 -10000 0 14
Endothelins

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
AKT1 0.02 0.032 0.13 1 -0.17 6 7
PTK2B 0.021 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.016 0.14 -10000 0 -0.49 31 31
EDN1 0.033 0.03 0.14 12 -0.13 6 18
EDN3 0.02 0.01 0.12 4 -10000 0 4
EDN2 0.023 0.027 0.12 40 -10000 0 40
HRAS/GDP -0.009 0.075 0.22 9 -0.35 8 17
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.019 0.041 -10000 0 -0.28 4 4
ADCY4 -0.019 0.049 0.19 9 -0.2 3 12
ADCY5 -0.026 0.061 0.19 8 -0.18 46 54
ADCY6 -0.02 0.049 0.18 8 -0.2 3 11
ADCY7 -0.02 0.05 0.19 9 -0.2 3 12
ADCY1 -0.018 0.055 0.19 5 -0.19 42 47
ADCY2 -0.021 0.052 0.19 9 -0.19 11 20
ADCY3 -0.02 0.049 0.19 8 -0.2 3 11
ADCY8 -0.019 0.05 0.21 7 -0.2 2 9
ADCY9 -0.019 0.05 0.19 9 -0.2 3 12
arachidonic acid secretion -0.011 0.084 0.25 12 -0.35 18 30
ETB receptor/Endothelin-1/Gq/GTP 0.021 0.028 -10000 0 -0.4 1 1
GNAO1 0.021 0.003 -10000 0 -10000 0 0
HRAS 0.02 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.054 0.049 0.19 7 -0.15 5 12
ETA receptor/Endothelin-1/Gs/GTP 0.021 0.073 0.18 7 -0.17 7 14
mol:GTP 0 0.002 -10000 0 -10000 0 0
COL3A1 0.043 0.057 0.18 11 -0.35 2 13
EDNRB 0.034 0.031 0.13 65 -10000 0 65
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 0.02 0.039 0.18 2 -0.31 4 6
CYSLTR1 0.022 0.036 0.17 4 -0.26 2 6
SLC9A1 0.018 0.021 -10000 0 -10000 0 0
mol:GDP -0.014 0.075 0.22 9 -0.36 9 18
SLC9A3 0.008 0.14 -10000 0 -0.58 21 21
RAF1 -0.018 0.077 0.23 10 -0.35 14 24
JUN -0.019 0.14 -10000 0 -0.48 35 35
JAK2 0.02 0.031 0.13 1 -0.17 6 7
mol:IP3 0.017 0.042 -10000 0 -0.46 2 2
ETA receptor/Endothelin-1 0.064 0.055 0.23 6 -0.2 6 12
PLCB1 0.019 0.006 -10000 0 -0.017 6 6
PLCB2 0.021 0.008 0.12 2 -0.021 7 9
ETA receptor/Endothelin-3 0.037 0.044 0.15 6 -0.14 16 22
FOS -0.017 0.11 0.31 10 -0.7 10 20
Gai/GDP -0.001 0.12 -10000 0 -0.62 22 22
CRK 0.021 0.002 -10000 0 -10000 0 0
mol:Ca ++ 0.018 0.043 0.18 1 -0.32 3 4
BCAR1 0.021 0.003 -10000 0 -10000 0 0
PRKCB1 0.015 0.042 -10000 0 -0.36 3 3
GNAQ 0.021 0.006 -10000 0 -0.023 10 10
GNAZ 0.02 0.004 -10000 0 -10000 0 0
GNAL 0.016 0.009 -10000 0 -10000 0 0
Gs family/GDP -0.031 0.081 -10000 0 -0.31 18 18
ETA receptor/Endothelin-1/Gq/GTP 0.025 0.036 -10000 0 -0.32 2 2
MAPK14 0.011 0.029 0.17 1 -0.19 2 3
TRPC6 -0.017 0.15 -10000 0 -0.52 30 30
GNAI2 0.021 0.003 -10000 0 -10000 0 0
GNAI3 0.019 0.008 0.12 1 -10000 0 1
GNAI1 0.017 0.008 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.017 0.037 -10000 0 -0.3 3 3
ETB receptor/Endothelin-2 0.039 0.032 0.12 23 -10000 0 23
ETB receptor/Endothelin-3 0.035 0.037 0.12 4 -0.15 15 19
ETB receptor/Endothelin-1 0.052 0.038 0.18 5 -10000 0 5
MAPK3 -0.016 0.1 0.31 11 -0.6 11 22
MAPK1 -0.018 0.11 0.31 11 -0.6 12 23
Rac1/GDP -0.008 0.065 0.24 3 -0.36 6 9
cAMP biosynthetic process -0.043 0.093 0.19 7 -0.25 59 66
MAPK8 -0.023 0.16 -10000 0 -0.5 62 62
SRC 0.02 0.004 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.006 0.04 -10000 0 -0.22 8 8
p130Cas/CRK/Src/PYK2 -0.021 0.084 0.3 8 -0.42 9 17
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.008 0.064 0.24 3 -0.36 6 9
COL1A2 0.028 0.043 0.19 2 -10000 0 2
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.043 0.039 0.16 13 -10000 0 13
mol:DAG 0.017 0.042 -10000 0 -0.46 2 2
MAP2K2 -0.016 0.096 0.31 18 -0.45 13 31
MAP2K1 -0.02 0.085 0.24 9 -0.45 13 22
EDNRA 0.04 0.041 0.14 68 -0.12 6 74
positive regulation of muscle contraction 0.03 0.079 0.22 85 -0.15 5 90
Gq family/GDP -0.012 0.071 -10000 0 -0.31 9 9
HRAS/GTP -0.017 0.072 0.22 9 -0.34 11 20
PRKCH 0.011 0.041 0.2 1 -0.34 3 4
RAC1 0.018 0.008 -10000 0 -10000 0 0
PRKCA 0.015 0.051 0.2 14 -0.34 4 18
PRKCB -0.005 0.055 0.2 1 -0.34 5 6
PRKCE 0.011 0.041 0.22 1 -0.27 3 4
PRKCD 0.012 0.044 0.21 3 -0.36 3 6
PRKCG -0.022 0.054 -10000 0 -0.29 7 7
regulation of vascular smooth muscle contraction -0.02 0.13 0.34 10 -0.95 8 18
PRKCQ 0.016 0.049 0.2 17 -0.37 3 20
PLA2G4A -0.012 0.089 0.25 11 -0.38 18 29
GNA14 0.021 0.006 -10000 0 -0.023 10 10
GNA15 0.02 0.008 0.12 1 -0.02 10 11
GNA12 0.018 0.008 -10000 0 -10000 0 0
GNA11 0.02 0.006 -10000 0 -0.027 3 3
Rac1/GTP 0.055 0.048 0.21 3 -0.15 5 8
MMP1 -0.009 0.045 0.36 3 -10000 0 3
Paxillin-dependent events mediated by a4b1

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
CRKL 0.021 0.005 0.12 1 -10000 0 1
Rac1/GDP 0.018 0.01 -10000 0 -0.017 7 7
DOCK1 0.018 0.007 -10000 0 -10000 0 0
ITGA4 0.036 0.036 0.12 95 -10000 0 95
RAC1 0.018 0.008 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.042 0.029 0.18 4 -10000 0 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.021 0.002 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.047 0.031 0.18 10 -10000 0 10
alpha4/beta7 Integrin/Paxillin 0.042 0.029 0.18 7 -10000 0 7
lamellipodium assembly 0.011 0.042 0.25 1 -0.4 4 5
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
PI3K 0.03 0.006 -10000 0 -10000 0 0
ARF6 0.02 0.004 -10000 0 -10000 0 0
TLN1 0.02 0.005 -10000 0 -10000 0 0
PXN -0.012 0.003 -10000 0 -10000 0 0
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
ARF6/GTP 0.044 0.027 0.14 10 -10000 0 10
cell adhesion 0.045 0.03 0.17 10 -10000 0 10
CRKL/CBL 0.03 0.007 0.11 1 -10000 0 1
alpha4/beta1 Integrin/Paxillin 0.038 0.029 0.17 10 -10000 0 10
ITGB1 0.021 0.016 0.12 12 -10000 0 12
ITGB7 0.022 0.012 0.12 8 -10000 0 8
ARF6/GDP 0.02 0.008 -10000 0 -0.017 8 8
alpha4/beta1 Integrin/Paxillin/VCAM1 0.061 0.051 0.18 45 -10000 0 45
p130Cas/Crk/Dock1 0.037 0.015 -10000 0 -10000 0 0
VCAM1 0.054 0.051 0.12 226 -10000 0 226
alpha4/beta1 Integrin/Paxillin/Talin 0.047 0.031 0.17 10 -10000 0 10
alpha4/beta1 Integrin/Paxillin/GIT1 0.048 0.031 0.17 10 -10000 0 10
BCAR1 0.021 0.003 -10000 0 -10000 0 0
mol:GDP -0.046 0.03 -10000 0 -0.17 10 10
CBL 0.021 0.003 -10000 0 -10000 0 0
PRKACA 0.02 0.004 -10000 0 -10000 0 0
GIT1 0.021 0.002 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.047 0.031 0.17 10 -10000 0 10
Rac1/GTP 0.012 0.046 0.26 1 -0.44 4 5
Calcium signaling in the CD4+ TCR 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
NFATC1 0.001 0.016 -10000 0 -10000 0 0
NFATC2 0.003 0.02 0.07 24 -10000 0 24
NFATC3 0.001 0.016 -10000 0 -10000 0 0
CD40LG -0.012 0.074 0.2 21 -0.22 4 25
PTGS2 -0.026 0.098 0.2 15 -0.26 79 94
JUNB 0.021 0.006 0.12 1 -10000 0 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.012 0.014 -10000 0 -10000 0 0
CaM/Ca2+ 0.012 0.014 -10000 0 -10000 0 0
CALM1 0.015 0.015 -10000 0 -0.026 3 3
JUN 0.015 0.014 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.012 0.007 -10000 0 -10000 0 0
FOSL1 0.04 0.041 0.12 126 -10000 0 126
CREM 0.019 0.007 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.024 0.058 0.17 7 -0.17 1 8
FOS 0.017 0.019 0.13 8 -10000 0 8
IFNG -0.014 0.069 0.18 24 -0.22 4 28
AP-1/NFAT1-c-4 0.032 0.092 0.25 14 -0.24 4 18
FASLG -0.013 0.073 0.22 13 -0.22 4 17
NFAT1-c-4/ICER1 0.014 0.037 -10000 0 -10000 0 0
IL2RA -0.002 0.078 0.23 16 -0.22 4 20
FKBP12/FK506 0.015 0.003 -10000 0 -10000 0 0
CSF2 -0.015 0.069 0.24 8 -0.22 4 12
JunB/Fra1/NFAT1-c-4 0.035 0.057 0.19 17 -0.15 1 18
IL4 -0.015 0.069 0.24 8 -0.22 4 12
IL2 -0.002 0.11 -10000 0 -0.86 11 11
IL3 0.015 0.049 -10000 0 -0.59 4 4
FKBP1A 0.02 0.004 -10000 0 -10000 0 0
BATF3 0.022 0.013 0.12 10 -10000 0 10
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.021 0.007 0.12 3 -10000 0 3
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.004 0.075 -10000 0 -0.32 33 33
KLHL20 0.014 0.046 0.15 8 -0.18 7 15
CYFIP2 0.021 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.004 0.052 0.23 5 -0.21 21 26
ENAH -0.004 0.075 -10000 0 -0.32 33 33
AP1M1 0.02 0.004 -10000 0 -10000 0 0
RAP1B 0.021 0.009 0.12 4 -10000 0 4
RAP1A 0.019 0.007 -10000 0 -10000 0 0
CTNNB1 0.021 0.002 -10000 0 -10000 0 0
CDC42/GTP 0.008 0.03 -10000 0 -0.13 10 10
ABI1/Sra1/Nap1 -0.008 0.02 -10000 0 -0.12 8 8
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.047 0.037 -10000 0 -0.12 24 24
RAPGEF1 -0.007 0.071 0.16 22 -0.3 29 51
CTNND1 0.021 0.002 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.003 0.079 -10000 0 -0.33 34 34
CRK -0.008 0.069 -10000 0 -0.31 30 30
E-cadherin/gamma catenin/alpha catenin 0.036 0.034 -10000 0 -0.13 24 24
alphaE/beta7 Integrin 0.032 0.011 -10000 0 -10000 0 0
IQGAP1 0.022 0.01 0.12 6 -10000 0 6
NCKAP1 0.021 0.001 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.033 0.017 -10000 0 -10000 0 0
DLG1 -0.004 0.074 -10000 0 -0.33 32 32
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.02 0.018 -10000 0 -0.1 19 19
MLLT4 0.02 0.005 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.038 0.011 -10000 0 -10000 0 0
PI3K -0.024 0.022 -10000 0 -0.13 15 15
ARF6 0.02 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.025 0.036 -10000 0 -0.16 24 24
TIAM1 0.02 0.004 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.043 0.033 -10000 0 -0.11 24 24
AKT1 -0.012 0.028 0.079 41 -10000 0 41
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
CDH1 0.022 0.013 0.12 9 -10000 0 9
RhoA/GDP 0.008 0.061 0.22 8 -0.21 24 32
actin cytoskeleton organization 0.015 0.042 0.14 28 -0.13 7 35
CDC42/GDP 0.009 0.06 0.23 7 -0.2 24 31
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.007 0.032 -10000 0 -0.16 24 24
ITGB7 0.022 0.012 0.12 8 -10000 0 8
RAC1 0.018 0.008 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.046 0.036 -10000 0 -0.12 24 24
E-cadherin/Ca2+/beta catenin/alpha catenin 0.032 0.029 -10000 0 -0.11 24 24
mol:GDP -0.002 0.066 0.23 8 -0.23 24 32
CDC42/GTP/IQGAP1 0.026 0.011 -10000 0 -10000 0 0
JUP 0.021 0.006 0.12 2 -10000 0 2
p120 catenin/RhoA/GDP 0.014 0.061 0.22 5 -0.21 24 29
RAC1/GTP/IQGAP1 0.024 0.012 0.096 5 -10000 0 5
PIP5K1C/AP1M1 0.03 0.01 -10000 0 -0.16 1 1
RHOA 0.021 0.003 -10000 0 -10000 0 0
CDC42 0.019 0.006 -10000 0 -10000 0 0
CTNNA1 0.021 0.003 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.016 0.036 0.12 36 -0.097 2 38
NME1 0.021 0.006 0.12 2 -10000 0 2
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.003 0.075 -10000 0 -0.33 32 32
regulation of cell-cell adhesion -0.018 0.021 -10000 0 -0.11 12 12
WASF2 0.002 0.02 0.056 21 -0.075 3 24
Rap1/GTP 0.013 0.044 0.16 27 -10000 0 27
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.055 0.038 -10000 0 -0.12 24 24
CCND1 0.018 0.04 0.13 34 -0.12 2 36
VAV2 0.005 0.1 -10000 0 -0.57 10 10
RAP1/GDP 0.014 0.051 0.17 22 -0.17 11 33
adherens junction assembly -0.003 0.073 -10000 0 -0.32 32 32
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.019 0.007 -10000 0 -10000 0 0
PIP5K1C 0.02 0.004 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.039 0.036 0.17 7 -0.12 24 31
E-cadherin/beta catenin 0 0.046 -10000 0 -0.23 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.003 0.074 -10000 0 -0.33 31 31
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.003 0.049 -10000 0 -0.27 8 8
E-cadherin/beta catenin/alpha catenin 0.036 0.035 -10000 0 -0.13 24 24
ITGAE 0.021 0.007 0.12 3 -10000 0 3
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.003 0.08 -10000 0 -0.34 34 34
Regulation of Telomerase

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
Telomerase catalytic core complex 0.064 0.083 -10000 0 -0.42 1 1
RAD9A 0.021 0.003 -10000 0 -10000 0 0
AP1 0.028 0.024 0.11 2 -0.15 7 9
IFNAR2 0.024 0.006 -10000 0 -10000 0 0
AKT1 0.016 0.01 -10000 0 -10000 0 0
ER alpha/Oestrogen 0.017 0.008 -10000 0 -0.15 1 1
NFX1/SIN3/HDAC complex -0.001 0.065 -10000 0 -0.23 22 22
EGF 0.026 0.019 0.13 22 -10000 0 22
SMG5 0.021 0.003 -10000 0 -10000 0 0
SMG6 0.021 0.002 -10000 0 -10000 0 0
SP3/HDAC2 0.036 0.01 -10000 0 -10000 0 0
TERT/c-Abl 0.067 0.078 -10000 0 -0.42 1 1
SAP18 0.021 0.005 -10000 0 -10000 0 0
MRN complex 0.04 0.012 -10000 0 -10000 0 0
WT1 0.033 0.034 0.13 71 -10000 0 71
WRN 0.021 0.003 -10000 0 -10000 0 0
SP1 0.025 0.006 -10000 0 -10000 0 0
SP3 0.023 0.002 -10000 0 -10000 0 0
TERF2IP 0.021 0.003 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.07 0.07 -10000 0 -0.37 1 1
Mad/Max 0.034 0.009 -10000 0 -10000 0 0
TERT 0.065 0.084 -10000 0 -0.43 1 1
CCND1 0.063 0.082 -10000 0 -10000 0 0
MAX 0.022 0.005 -10000 0 -10000 0 0
RBBP7 0.022 0.002 -10000 0 -10000 0 0
RBBP4 0.019 0.007 -10000 0 -10000 0 0
TERF2 0.017 0.004 0.067 1 -10000 0 1
PTGES3 0.021 0.003 -10000 0 -10000 0 0
SIN3A 0.021 0.003 -10000 0 -10000 0 0
Telomerase/911 0.04 0.044 0.2 1 -0.27 3 4
CDKN1B 0.001 0.017 -10000 0 -10000 0 0
RAD1 0.021 0.002 -10000 0 -10000 0 0
XRCC5 0.021 0.001 -10000 0 -10000 0 0
XRCC6 0.02 0.004 -10000 0 -10000 0 0
SAP30 0.021 0.006 0.13 1 -10000 0 1
TRF2/PARP2 0.028 0.007 -10000 0 -10000 0 0
UBE3A 0.022 0.003 -10000 0 -10000 0 0
JUN 0.02 0.007 -10000 0 -10000 0 0
E6 0.001 0.002 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.019 0.004 -10000 0 -10000 0 0
FOS 0.022 0.013 0.12 8 -10000 0 8
IFN-gamma/IRF1 0.039 0.022 0.17 3 -10000 0 3
PARP2 0.02 0.004 -10000 0 -10000 0 0
BLM 0.03 0.03 0.12 61 -10000 0 61
Telomerase 0.021 0.059 0.19 2 -0.28 9 11
IRF1 0.03 0.025 0.13 41 -10000 0 41
ESR1 0.021 0.005 -10000 0 -10000 0 0
KU/TER 0.03 0.006 -10000 0 -10000 0 0
ATM/TRF2 0.03 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.005 0.06 -10000 0 -0.25 14 14
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.005 0.061 -10000 0 -0.25 14 14
HDAC1 0.019 0.007 -10000 0 -10000 0 0
HDAC2 0.024 0.007 -10000 0 -10000 0 0
ATM 0.009 0.005 -10000 0 -10000 0 0
SMAD3 -0.013 0.006 0.047 1 -10000 0 1
ABL1 0.021 0.003 -10000 0 -10000 0 0
MXD1 0.023 0.002 -10000 0 -10000 0 0
MRE11A 0.021 0.003 -10000 0 -10000 0 0
HUS1 0.017 0.008 -10000 0 -10000 0 0
RPS6KB1 0.02 0.004 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.071 0.084 -10000 0 -10000 0 0
NR2F2 0.006 0.018 -10000 0 -0.017 251 251
MAPK3 -0.004 0.012 -10000 0 -10000 0 0
MAPK1 -0.004 0.012 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.018 0.008 0.12 1 -10000 0 1
NFKB1 0.021 0.002 -10000 0 -10000 0 0
HNRNPC 0.02 0.004 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.009 0.005 -10000 0 -10000 0 0
NBN 0.02 0.005 -10000 0 -10000 0 0
EGFR 0.053 0.054 0.12 235 -10000 0 235
mol:Oestrogen 0.001 0.001 -10000 0 -10000 0 0
EGF/EGFR 0.052 0.045 0.11 237 -10000 0 237
MYC 0.049 0.048 0.13 180 -10000 0 180
IL2 0.02 0.006 -10000 0 -10000 0 0
KU 0.03 0.006 -10000 0 -10000 0 0
RAD50 0.021 0.002 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
TGFB1 0.018 0.008 0.12 1 -10000 0 1
TRF2/BLM 0.035 0.021 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.076 0.08 -10000 0 -10000 0 0
SP1/HDAC2 0.038 0.014 -10000 0 -10000 0 0
PINX1 0.021 0.003 -10000 0 -10000 0 0
Telomerase/EST1A 0.071 0.07 -10000 0 -0.37 1 1
Smad3/Myc 0.026 0.042 0.096 158 -10000 0 158
911 complex 0.035 0.017 -10000 0 -10000 0 0
IFNG 0.02 0.01 0.13 5 -10000 0 5
Telomerase/PinX1 0.068 0.07 -10000 0 -0.37 1 1
Telomerase/AKT1/mTOR/p70S6K 0.021 0.08 -10000 0 -0.38 12 12
SIN3B 0.021 0.004 -10000 0 -10000 0 0
YWHAE 0.021 0.002 -10000 0 -10000 0 0
Telomerase/EST1B 0.069 0.07 -10000 0 -0.38 1 1
response to DNA damage stimulus 0.004 0.006 -10000 0 -0.1 1 1
MRN complex/TRF2/Rap1 0.054 0.018 -10000 0 -10000 0 0
TRF2/WRN 0.028 0.006 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.07 0.069 -10000 0 -0.38 1 1
E2F1 0.024 0.013 0.13 7 -10000 0 7
ZNFX1 0.021 0.004 -10000 0 -10000 0 0
PIF1 0.036 0.037 0.12 101 -10000 0 101
NCL 0.021 0.002 -10000 0 -10000 0 0
DKC1 0.021 0.002 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.024 0.021 0.12 27 -10000 0 27
GNB1/GNG2 0.029 0.053 -10000 0 -0.23 7 7
mol:DAG 0.008 0.048 0.18 9 -0.23 6 15
PLCG1 0.008 0.049 0.19 9 -0.24 6 15
YES1 -0.002 0.037 -10000 0 -0.18 14 14
FZD3 0.021 0.003 -10000 0 -10000 0 0
FZD6 0.021 0.012 0.12 7 -10000 0 7
G protein 0.03 0.058 0.18 28 -0.24 6 34
MAP3K7 -0.016 0.05 0.18 3 -0.17 51 54
mol:Ca2+ 0.008 0.047 0.18 9 -0.22 6 15
mol:IP3 0.008 0.048 0.18 9 -0.23 6 15
NLK 0.001 0.046 -10000 0 -0.82 2 2
GNB1 0.019 0.007 -10000 0 -10000 0 0
CAMK2A -0.009 0.043 0.19 3 -0.22 18 21
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD 0.013 0.035 -10000 0 -0.19 16 16
CSNK1A1 0.021 0.003 -10000 0 -10000 0 0
GNAS -0.002 0.038 -10000 0 -0.18 14 14
GO:0007205 0.001 0.048 0.18 9 -0.22 7 16
WNT6 0.022 0.009 0.12 5 -10000 0 5
WNT4 0.019 0.009 0.12 2 -10000 0 2
NFAT1/CK1 alpha 0.026 0.056 0.21 9 -0.22 6 15
GNG2 0.02 0.004 -10000 0 -10000 0 0
WNT5A 0.028 0.026 0.12 45 -10000 0 45
WNT11 0.022 0.01 0.12 6 -10000 0 6
CDC42 -0.002 0.026 0.14 5 -0.16 9 14
PDGFR-beta 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
S1P1/Sphingosine-1-phosphate 0.032 0.054 0.26 16 -0.24 6 22
PDGFB-D/PDGFRB/SLAP 0.031 0.014 0.11 13 -10000 0 13
PDGFB-D/PDGFRB/APS/CBL 0.036 0.023 -10000 0 -10000 0 0
AKT1 -0.005 0.064 0.18 66 -10000 0 66
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.037 0.062 0.24 26 -0.27 6 32
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
FGR -0.019 0.11 0.21 1 -0.35 63 64
mol:Ca2+ 0.027 0.062 0.23 24 -0.28 6 30
MYC 0.083 0.11 0.32 85 -0.32 1 86
SHC1 0.023 0.016 0.12 16 -10000 0 16
HRAS/GDP 0.017 0.012 -10000 0 -10000 0 0
LRP1/PDGFRB/PDGFB 0.041 0.013 -10000 0 -10000 0 0
GRB10 0.017 0.008 -10000 0 -10000 0 0
PTPN11 0.021 0.003 -10000 0 -10000 0 0
GO:0007205 0.027 0.062 0.23 24 -0.29 6 30
PTEN 0.018 0.007 -10000 0 -10000 0 0
GRB2 0.02 0.004 -10000 0 -10000 0 0
GRB7 0.02 0.009 0.12 4 -10000 0 4
PDGFB-D/PDGFRB/SHP2 0.032 0.008 0.11 3 -10000 0 3
PDGFB-D/PDGFRB/GRB10 0.027 0.013 0.11 1 -10000 0 1
cell cycle arrest 0.031 0.014 0.11 13 -10000 0 13
HRAS 0.02 0.005 -10000 0 -10000 0 0
HIF1A -0.008 0.058 0.16 63 -10000 0 63
GAB1 0.033 0.07 0.25 21 -0.29 10 31
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.033 0.074 0.25 40 -0.25 7 47
PDGFB-D/PDGFRB 0.046 0.016 0.14 1 -10000 0 1
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.032 0.008 0.11 2 -10000 0 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.035 0.041 0.19 13 -0.21 4 17
positive regulation of MAPKKK cascade 0.032 0.008 0.11 3 -10000 0 3
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
mol:IP3 0.027 0.062 0.23 24 -0.29 6 30
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.018 0.009 -10000 0 -0.02 30 30
PDGFB-D/PDGFRB/GRB7 0.032 0.01 0.11 7 -10000 0 7
SHB 0.02 0.004 -10000 0 -10000 0 0
BLK 0.019 0.039 0.25 1 -0.34 4 5
PTPN2 0.022 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.032 0.008 0.11 3 -10000 0 3
BCAR1 0.021 0.003 -10000 0 -10000 0 0
VAV2 0.041 0.074 0.25 29 -0.28 10 39
CBL 0.021 0.003 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.032 0.008 0.11 3 -10000 0 3
LCK -0.009 0.12 0.24 6 -0.35 63 69
PDGFRB 0.023 0.009 0.13 4 -0.021 1 5
ACP1 0.021 0.003 -10000 0 -10000 0 0
HCK 0.014 0.02 -10000 0 -10000 0 0
ABL1 0.027 0.071 0.23 28 -0.3 9 37
PDGFB-D/PDGFRB/CBL 0.035 0.072 0.26 15 -0.32 12 27
PTPN1 0.021 0.005 -10000 0 -0.018 1 1
SNX15 0.021 0.003 -10000 0 -10000 0 0
STAT3 0.021 0.002 -10000 0 -10000 0 0
STAT1 0.022 0.011 0.12 7 -10000 0 7
cell proliferation 0.082 0.11 0.31 86 -0.3 1 87
SLA 0.021 0.015 0.12 11 -10000 0 11
actin cytoskeleton reorganization -0.01 0.046 0.18 32 -10000 0 32
SRC 0.013 0.018 -10000 0 -10000 0 0
PI3K -0.022 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.044 0.016 0.18 2 -10000 0 2
SH2B2 0.02 0.02 0.12 20 -10000 0 20
PLCgamma1/SPHK1 0.037 0.063 0.25 25 -0.27 6 31
LYN 0.014 0.027 -10000 0 -0.34 2 2
LRP1 0.02 0.004 -10000 0 -10000 0 0
SOS1 0.021 0.001 -10000 0 -10000 0 0
STAT5B 0.021 0.002 -10000 0 -10000 0 0
STAT5A 0.021 0.002 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.063 0.023 -10000 0 -10000 0 0
SPHK1 0.022 0.011 0.12 6 -10000 0 6
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.027 0.062 0.23 24 -0.29 6 30
PLCG1 0.027 0.063 0.24 24 -0.3 6 30
NHERF/PDGFRB 0.042 0.011 -10000 0 -10000 0 0
YES1 0.005 0.071 0.18 1 -0.49 12 13
cell migration 0.042 0.011 -10000 0 -10000 0 0
SHC/Grb2/SOS1 0.062 0.026 0.18 1 -10000 0 1
SLC9A3R2 0.021 0.002 -10000 0 -10000 0 0
SLC9A3R1 0.021 0.003 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.047 0.021 -10000 0 -10000 0 0
FYN 0.001 0.076 -10000 0 -0.37 24 24
DOK1 -0.012 0.013 0.1 4 -10000 0 4
HRAS/GTP 0.015 0.003 -10000 0 -10000 0 0
PDGFB 0.02 0.004 -10000 0 -10000 0 0
RAC1 0.07 0.1 0.28 81 -0.3 5 86
PRKCD -0.008 0.015 0.2 1 -10000 0 1
FER -0.009 0.015 0.2 1 -10000 0 1
MAPKKK cascade -0.003 0.057 0.18 58 -10000 0 58
RASA1 -0.009 0.015 0.2 1 -10000 0 1
NCK1 0.021 0.005 0.12 1 -10000 0 1
NCK2 0.021 0.001 -10000 0 -10000 0 0
p62DOK/Csk 0.006 0.03 0.16 15 -10000 0 15
PDGFB-D/PDGFRB/SHB 0.031 0.009 0.11 3 -10000 0 3
chemotaxis 0.027 0.07 0.23 29 -0.29 9 38
STAT1-3-5/STAT1-3-5 0.051 0.018 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.017 0.007 0.09 4 -10000 0 4
PTPRJ 0.021 0.003 -10000 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.036 0.034 -10000 0 -0.13 24 24
E-cadherin/beta catenin 0.025 0.037 0.11 9 -0.16 24 33
CTNNB1 0.021 0.002 -10000 0 -10000 0 0
JUP 0.021 0.006 0.12 2 -10000 0 2
CDH1 0.022 0.013 0.12 9 -10000 0 9
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.038 0.026 0.18 1 -10000 0 1
alphaV beta3 Integrin 0.054 0.028 -10000 0 -10000 0 0
PTK2 0.018 0.067 0.24 18 -0.38 2 20
IGF1R 0.021 0.003 -10000 0 -10000 0 0
PI4KB 0.021 0.002 -10000 0 -10000 0 0
MFGE8 0.021 0.006 0.12 2 -10000 0 2
SRC 0.02 0.004 -10000 0 -10000 0 0
CDKN1B 0.017 0.014 -10000 0 -0.31 1 1
VEGFA 0.033 0.034 0.12 79 -10000 0 79
ILK 0.016 0.019 -10000 0 -0.31 2 2
ROCK1 0.021 0.005 0.12 1 -10000 0 1
AKT1 0.007 0.017 -10000 0 -0.29 2 2
PTK2B -0.001 0.045 0.18 31 -10000 0 31
alphaV/beta3 Integrin/JAM-A 0.056 0.03 0.17 4 -0.11 2 6
CBL 0.021 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.048 0.031 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.05 0.021 -10000 0 -0.12 7 7
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.018 0.03 0.13 9 -0.2 1 10
alphaV/beta3 Integrin/Syndecan-1 0.058 0.037 0.18 32 -0.13 1 33
PI4KA 0.02 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.056 0.033 -10000 0 -0.11 7 7
PI4 Kinase 0.029 0.017 -10000 0 -0.16 5 5
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.064 0.045 0.18 58 -0.13 3 61
RPS6KB1 -0.019 0.031 0.18 10 -10000 0 10
TLN1 0.02 0.005 -10000 0 -10000 0 0
MAPK3 0.011 0.042 -10000 0 -0.27 10 10
GPR124 0.021 0.003 -10000 0 -10000 0 0
MAPK1 0.012 0.038 -10000 0 -0.27 8 8
PXN 0.021 0.002 -10000 0 -10000 0 0
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.057 0.036 0.18 5 -0.12 7 12
cell adhesion 0.039 0.036 -10000 0 -10000 0 0
ANGPTL3 0.016 0.007 0.12 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.045 0.025 0.18 1 -10000 0 1
IGF-1R heterotetramer 0.021 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.013 0.006 -10000 0 -10000 0 0
TGFBR2 0.021 0.007 0.12 3 -10000 0 3
ITGB3 0.04 0.04 0.12 124 -10000 0 124
IGF1 0.021 0.005 0.12 1 -10000 0 1
RAC1 0.018 0.008 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.053 0.027 -10000 0 -10000 0 0
apoptosis 0.021 0.001 -10000 0 -10000 0 0
CD47 0.021 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.054 0.027 -10000 0 -10000 0 0
VCL 0.02 0.01 0.12 4 -10000 0 4
alphaV/beta3 Integrin/Del1 0.03 0.068 -10000 0 -0.13 89 89
CSF1 0.02 0.015 0.12 10 -10000 0 10
PIK3C2A 0.017 0.019 -10000 0 -0.31 2 2
PI4 Kinase/Pyk2 0.032 0.024 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.069 0.043 0.18 56 -10000 0 56
FAK1/Vinculin 0.022 0.053 0.22 13 -0.3 2 15
alphaV beta3/Integrin/ppsTEM5 0.054 0.028 -10000 0 -10000 0 0
RHOA 0.021 0.003 -10000 0 -10000 0 0
VTN 0.021 0.006 0.12 2 -10000 0 2
BCAR1 0.021 0.003 -10000 0 -10000 0 0
FGF2 0.021 0.005 0.12 1 -10000 0 1
F11R -0.012 0.006 0.051 5 -10000 0 5
alphaV/beta3 Integrin/Lactadherin 0.054 0.028 0.18 1 -10000 0 1
alphaV/beta3 Integrin/TGFBR2 0.055 0.028 0.18 2 -10000 0 2
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.047 0.022 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.049 0.027 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.036 0.036 0.12 94 -10000 0 94
alphaV/beta3 Integrin/Pyk2 0.048 0.04 0.14 62 -0.12 1 63
SDC1 0.027 0.024 0.12 38 -10000 0 38
VAV3 -0.01 0.03 0.17 14 -10000 0 14
PTPN11 0.021 0.003 -10000 0 -10000 0 0
IRS1 0.021 0.001 -10000 0 -10000 0 0
FAK1/Paxillin 0.026 0.061 0.23 19 -0.31 2 21
cell migration 0.014 0.05 0.19 17 -0.28 2 19
ITGAV 0.021 0.001 -10000 0 -10000 0 0
PI3K 0.06 0.028 0.18 2 -0.1 2 4
SPP1 0.036 0.037 0.12 96 -10000 0 96
KDR 0.021 0.012 0.12 8 -10000 0 8
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.021 0.001 -10000 0 -10000 0 0
COL4A3 0.027 0.025 0.12 41 -10000 0 41
angiogenesis 0.014 0.044 0.22 3 -0.28 8 11
Rac1/GTP -0.016 0.038 0.16 14 -10000 0 14
EDIL3 0.018 0.008 -10000 0 -10000 0 0
cell proliferation 0.054 0.028 0.18 2 -10000 0 2
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.045 0.029 -10000 0 -10000 0 0
AKT1 0.019 0.057 0.29 5 -0.3 1 6
PTK2B -0.001 0.047 0.19 31 -10000 0 31
VEGFR2 homodimer/Frs2 0.022 0.009 -10000 0 -10000 0 0
CAV1 0.028 0.035 0.12 73 -10000 0 73
CALM1 0.02 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.043 0.029 0.21 7 -10000 0 7
endothelial cell proliferation 0.005 0.069 0.26 12 -0.31 4 16
mol:Ca2+ 0.001 0.039 0.18 22 -10000 0 22
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.044 0.03 0.21 3 -10000 0 3
RP11-342D11.1 -0.002 0.025 0.19 8 -10000 0 8
CDH5 0.022 0.01 0.12 6 -10000 0 6
VEGFA homodimer 0.057 0.025 0.18 1 -10000 0 1
SHC1 0.023 0.016 0.12 16 -10000 0 16
SHC2 0.02 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.038 0.022 -10000 0 -10000 0 0
SH2D2A 0.021 0.01 0.12 5 -10000 0 5
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.05 0.053 0.25 9 -0.37 1 10
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.041 0.039 0.21 8 -10000 0 8
VEGFR1 homodimer 0.02 0.005 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.066 0.036 0.22 2 -10000 0 2
GRB10 -0.001 0.032 0.18 14 -10000 0 14
PTPN11 0.021 0.003 -10000 0 -10000 0 0
GRB2 0.02 0.004 -10000 0 -10000 0 0
PAK1 0.015 0.009 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.061 0.033 0.22 9 -10000 0 9
HRAS 0.02 0.005 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.019 0.035 0.17 6 -0.33 1 7
HIF1A 0.021 0.008 0.12 3 -10000 0 3
FRS2 0.02 0.004 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.043 0.029 0.21 3 -10000 0 3
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.025 0.021 0.12 29 -10000 0 29
Nck/Pak -0.018 0.082 -10000 0 -0.16 170 170
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.042 0.03 0.21 8 -10000 0 8
mol:GDP 0.051 0.028 0.18 2 -10000 0 2
mol:NADP 0.026 0.052 0.25 10 -0.37 1 11
eNOS/Hsp90 0.036 0.047 0.27 6 -0.35 1 7
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
mol:IP3 0.001 0.039 0.18 22 -10000 0 22
HIF1A/ARNT 0.03 0.009 -10000 0 -10000 0 0
SHB 0.02 0.004 -10000 0 -10000 0 0
VEGFA 0.034 0.034 0.12 79 -10000 0 79
VEGFC 0.022 0.012 0.12 8 -10000 0 8
FAK1/Vinculin 0.027 0.047 0.23 6 -0.49 1 7
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.021 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.067 0.048 0.26 9 -10000 0 9
PTPN6 0.021 0.009 0.12 4 -10000 0 4
EPAS1 0.025 0.005 -10000 0 -10000 0 0
mol:L-citrulline 0.026 0.052 0.25 10 -0.37 1 11
ITGAV 0.021 0.001 -10000 0 -10000 0 0
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.051 0.031 0.21 7 -10000 0 7
VEGFR2 homodimer/VEGFA homodimer 0.054 0.037 0.21 8 -10000 0 8
VEGFR2/3 heterodimer 0.026 0.021 0.18 5 -10000 0 5
VEGFB 0.021 0.003 -10000 0 -10000 0 0
MAPK11 0 0.046 0.2 23 -10000 0 23
VEGFR2 homodimer 0.01 0.01 -10000 0 -10000 0 0
FLT1 0.02 0.005 -10000 0 -10000 0 0
NEDD4 0.034 0.034 0.12 81 -10000 0 81
MAPK3 -0.018 0.045 0.19 14 -10000 0 14
MAPK1 -0.018 0.045 0.19 12 -10000 0 12
VEGFA145/NRP2 0.041 0.026 0.18 2 -10000 0 2
VEGFR1/2 heterodimer 0.022 0.01 -10000 0 -10000 0 0
KDR 0.01 0.01 -10000 0 -10000 0 0
VEGFA165/NRP1/VEGFR2 homodimer 0.049 0.032 0.2 10 -10000 0 10
SRC 0.02 0.004 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.013 0.053 0.21 14 -10000 0 14
PI3K 0.028 0.037 0.19 5 -10000 0 5
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.044 0.029 0.21 7 -10000 0 7
FES 0.001 0.039 0.18 22 -10000 0 22
GAB1 0.019 0.042 0.19 6 -10000 0 6
VEGFR2 homodimer/VEGFA homodimer/Src 0.042 0.03 0.21 8 -10000 0 8
CTNNB1 0.021 0.002 -10000 0 -10000 0 0
SOS1 0.021 0.001 -10000 0 -10000 0 0
ARNT 0.021 0.002 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.029 0.046 0.25 7 -0.35 1 8
VEGFR2 homodimer/VEGFA homodimer/Yes 0.043 0.031 0.21 8 -10000 0 8
PI3K/GAB1 0.03 0.05 0.25 3 -10000 0 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.017 0.079 0.21 5 -10000 0 5
PRKACA 0.02 0.004 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.037 0.023 0.21 2 -10000 0 2
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
CDC42 0.002 0.039 0.19 22 -10000 0 22
actin cytoskeleton reorganization 0.04 0.039 0.21 8 -10000 0 8
PTK2 0.018 0.043 0.22 9 -10000 0 9
EDG1 -0.002 0.025 0.19 8 -10000 0 8
mol:DAG 0.001 0.039 0.18 22 -10000 0 22
CaM/Ca2+ 0 0.039 0.17 21 -10000 0 21
MAP2K3 -0.007 0.04 0.18 27 -10000 0 27
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.073 0.072 0.23 96 -10000 0 96
PLCG1 0.001 0.039 0.18 22 -10000 0 22
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.051 0.031 0.21 8 -10000 0 8
IQGAP1 0.022 0.01 0.12 6 -10000 0 6
YES1 0.02 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.044 0.03 0.21 8 -10000 0 8
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.043 0.031 0.21 7 -10000 0 7
cell migration 0.031 0.056 0.24 12 -0.48 1 13
mol:PI-3-4-5-P3 0.027 0.036 0.19 5 -10000 0 5
FYN 0.02 0.004 -10000 0 -10000 0 0
VEGFB/NRP1 0.002 0.038 0.17 23 -10000 0 23
mol:NO 0.026 0.052 0.25 10 -0.37 1 11
PXN 0.021 0.002 -10000 0 -10000 0 0
HRAS/GTP -0.008 0.026 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.038 0.042 0.2 28 -10000 0 28
VHL 0.021 0.003 -10000 0 -10000 0 0
ITGB3 0.04 0.04 0.12 124 -10000 0 124
NOS3 0.026 0.054 0.28 7 -0.41 1 8
VEGFR2 homodimer/VEGFA homodimer/Sck 0.042 0.029 0.21 7 -10000 0 7
RAC1 0.018 0.008 -10000 0 -10000 0 0
PRKCA -0.007 0.041 0.18 27 -10000 0 27
PRKCB -0.007 0.029 0.18 13 -10000 0 13
VCL 0.02 0.01 0.12 4 -10000 0 4
VEGFA165/NRP1 0.032 0.039 0.2 23 -10000 0 23
VEGFR1/2 heterodimer/VEGFA homodimer 0.041 0.029 0.21 6 -10000 0 6
VEGFA165/NRP2 0.041 0.026 0.18 2 -10000 0 2
MAPKKK cascade 0.008 0.061 0.18 52 -10000 0 52
NRP2 0.022 0.01 0.12 6 -10000 0 6
VEGFC homodimer 0.022 0.012 0.12 8 -10000 0 8
NCK1 0.021 0.005 0.12 1 -10000 0 1
ROCK1 0.021 0.005 0.12 1 -10000 0 1
FAK1/Paxillin 0.034 0.054 0.23 13 -0.5 1 14
MAP3K13 0 0.038 0.18 21 -10000 0 21
PDPK1 0.003 0.039 0.18 6 -10000 0 6
S1P4 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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.021 0.003 -10000 0 -10000 0 0
CDC42/GTP 0.019 0.047 -10000 0 -0.23 5 5
PLCG1 0.004 0.043 -10000 0 -0.18 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.021 0.003 -10000 0 -10000 0 0
GNAI3 0.019 0.008 0.12 1 -10000 0 1
G12/G13 0.026 0.012 -10000 0 -10000 0 0
cell migration 0.018 0.046 -10000 0 -0.23 5 5
S1PR5 0.017 0.008 -10000 0 -10000 0 0
S1PR4 0.021 0.011 0.12 6 -10000 0 6
MAPK3 0.005 0.044 -10000 0 -0.18 9 9
MAPK1 0.006 0.043 -10000 0 -0.18 9 9
S1P/S1P5/Gi -0.016 0.064 -10000 0 -0.18 72 72
GNAI1 0.017 0.008 -10000 0 -10000 0 0
CDC42/GDP 0.014 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.006 0.048 -10000 0 -0.13 73 73
RHOA 0.023 0.084 0.19 123 -0.11 1 124
S1P/S1P4/Gi 0 0.037 -10000 0 -0.18 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.02 0.004 -10000 0 -10000 0 0
S1P/S1P4/G12/G13 0.033 0.018 -10000 0 -0.12 1 1
GNA12 0.018 0.008 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
CDC42 0.019 0.006 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.008 0.14 -10000 0 -0.57 12 12
PCK1 0.006 0.13 -10000 0 -0.84 8 8
HNF4A -0.025 0.19 -10000 0 -0.68 33 33
KCNJ11 -0.006 0.18 -10000 0 -0.68 21 21
AKT1 0.011 0.11 -10000 0 -0.35 14 14
response to starvation 0.001 0.002 -10000 0 -10000 0 0
DLK1 0.002 0.16 -10000 0 -0.64 9 9
NKX2-1 -0.005 0.095 0.27 2 -0.31 20 22
ACADM -0.006 0.14 -10000 0 -0.57 11 11
TAT 0.022 0.1 -10000 0 -0.5 1 1
CEBPB 0.022 0.008 0.12 2 -10000 0 2
CEBPA 0.021 0.012 0.13 4 -10000 0 4
TTR 0.001 0.17 0.44 13 -0.7 12 25
PKLR -0.009 0.15 -10000 0 -0.7 10 10
APOA1 -0.015 0.19 -10000 0 -0.8 11 11
CPT1C -0.006 0.14 -10000 0 -0.58 12 12
ALAS1 0.017 0.097 -10000 0 -0.52 1 1
TFRC 0.012 0.14 -10000 0 -0.68 8 8
FOXF1 0.022 0.009 0.12 5 -10000 0 5
NF1 0.023 0.003 -10000 0 -10000 0 0
HNF1A (dimer) 0.024 0.008 -10000 0 -10000 0 0
CPT1A -0.006 0.14 -10000 0 -0.57 12 12
HMGCS1 -0.008 0.14 -10000 0 -0.6 9 9
NR3C1 0.04 0.019 -10000 0 -10000 0 0
CPT1B -0.008 0.14 -10000 0 -0.58 13 13
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.023 0.008 -10000 0 -10000 0 0
GCK -0.006 0.19 0.34 9 -0.69 31 40
CREB1 0.023 0.019 -10000 0 -0.19 5 5
IGFBP1 0.037 0.086 -10000 0 -10000 0 0
PDX1 0.013 0.096 -10000 0 -10000 0 0
UCP2 -0.004 0.14 -10000 0 -0.57 12 12
ALDOB -0.004 0.16 -10000 0 -0.65 15 15
AFP 0.021 0.039 -10000 0 -0.26 3 3
BDH1 -0.022 0.19 -10000 0 -0.7 31 31
HADH -0.002 0.16 -10000 0 -0.6 13 13
F2 -0.018 0.2 -10000 0 -0.82 10 10
HNF1A 0.024 0.008 -10000 0 -10000 0 0
G6PC 0.021 0.031 -10000 0 -10000 0 0
SLC2A2 0.011 0.11 -10000 0 -0.57 2 2
INS -0.027 0.017 0.12 1 -10000 0 1
FOXA1 0.032 0.04 0.17 14 -0.24 5 19
FOXA3 0.047 0.055 0.18 21 -0.2 10 31
FOXA2 0.009 0.19 -10000 0 -0.63 24 24
ABCC8 -0.032 0.23 -10000 0 -0.72 55 55
ALB 0.015 0.074 -10000 0 -0.72 6 6
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.012 0.003 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.029 0.011 -10000 0 -10000 0 0
CDKN1B 0.002 0.065 0.19 12 -0.29 25 37
CDKN1A 0.002 0.058 0.19 1 -0.29 22 23
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.021 0.003 -10000 0 -10000 0 0
FOXO3 0.003 0.048 0.19 1 -0.29 15 16
AKT1 -0.003 0.062 -10000 0 -0.3 27 27
BAD 0.021 0.003 -10000 0 -10000 0 0
AKT3 0.009 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.001 0.063 0.19 3 -0.3 26 29
AKT1/ASK1 0.014 0.063 -10000 0 -0.28 26 26
BAD/YWHAZ 0.038 0.013 -10000 0 -10000 0 0
RICTOR 0.021 0.002 -10000 0 -10000 0 0
RAF1 0.021 0.003 -10000 0 -10000 0 0
JNK cascade -0.014 0.061 0.27 26 -10000 0 26
TSC1 -0.001 0.061 0.19 2 -0.29 25 27
YWHAZ 0.02 0.005 -10000 0 -10000 0 0
AKT1/RAF1 0.016 0.066 0.22 1 -0.29 27 28
EP300 0.02 0.004 -10000 0 -10000 0 0
mol:GDP -0.003 0.062 -10000 0 -0.3 27 27
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.003 0.062 0.19 1 -0.29 27 28
YWHAQ 0.021 0.002 -10000 0 -10000 0 0
TBC1D4 -0.003 0.001 -10000 0 -10000 0 0
MAP3K5 0.02 0.005 -10000 0 -10000 0 0
MAPKAP1 0.021 0.003 -10000 0 -10000 0 0
negative regulation of cell cycle -0.017 0.057 0.38 3 -0.15 3 6
YWHAH 0.02 0.005 -10000 0 -10000 0 0
AKT1S1 0.003 0.048 0.19 5 -0.29 14 19
CASP9 0 0.058 0.19 2 -0.29 22 24
YWHAB 0.02 0.004 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.016 0.07 0.24 4 -0.28 27 31
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.039 0.013 -10000 0 -10000 0 0
YWHAE 0.021 0.002 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
AKT2/p21CIP1 -0.001 0.053 0.21 2 -0.26 25 27
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.005 0.02 -10000 0 -10000 0 0
CHUK -0.001 0.053 -10000 0 -0.29 20 20
BAD/BCL-XL 0.015 0.063 -10000 0 -0.28 27 27
mTORC2 0.026 0.005 -10000 0 -10000 0 0
AKT2 0.008 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.01 0.072 0.21 1 -0.32 12 13
PDPK1 0.021 0.002 -10000 0 -10000 0 0
MDM2 0.003 0.065 0.19 15 -0.29 24 39
MAPKKK cascade -0.016 0.065 0.28 27 -0.21 1 28
MDM2/Cbp/p300 0.026 0.068 0.24 3 -0.28 25 28
TSC1/TSC2 -0.003 0.066 0.22 11 -0.29 27 38
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.066 0.23 3 -0.27 25 28
glucose import -0.008 0.016 -10000 0 -0.11 15 15
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.008 0.044 0.18 11 -0.17 17 28
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.006 0.003 -10000 0 -10000 0 0
GSK3A 0.003 0.05 0.19 6 -0.29 15 21
FOXO1 -0.002 0.06 0.19 1 -0.29 25 26
GSK3B -0.001 0.061 0.19 1 -0.29 25 26
SFN 0.022 0.02 0.12 23 -10000 0 23
G1/S transition of mitotic cell cycle -0.001 0.068 0.22 16 -0.28 26 42
p27Kip1/14-3-3 family 0.024 0.053 -10000 0 -0.6 2 2
PRKACA 0.02 0.004 -10000 0 -10000 0 0
KPNA1 0.021 0.003 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
YWHAG 0.017 0.008 -10000 0 -10000 0 0
RHEB 0.017 0.009 -10000 0 -10000 0 0
CREBBP 0.021 0.002 -10000 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB 0.021 0.008 0.12 4 -10000 0 4
alphaV beta3 Integrin 0.045 0.029 -10000 0 -10000 0 0
PTK2 0.013 0.063 -10000 0 -0.26 9 9
positive regulation of JNK cascade -0.004 0.081 -10000 0 -0.28 19 19
CDC42/GDP 0.006 0.11 -10000 0 -0.34 30 30
Rac1/GDP 0.005 0.096 -10000 0 -0.34 21 21
RAP1B 0.021 0.009 0.12 4 -10000 0 4
RAP1A 0.019 0.007 -10000 0 -10000 0 0
CTNNB1 0.021 0.002 -10000 0 -10000 0 0
CDC42/GTP 0 0.1 -10000 0 -0.34 19 19
nectin-3/I-afadin 0.028 0.018 -10000 0 -0.15 5 5
RAPGEF1 -0.007 0.098 0.24 1 -0.33 35 36
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.011 0.1 -10000 0 -0.36 34 34
PDGFB-D/PDGFRB 0.021 0.008 0.12 4 -10000 0 4
TLN1 -0.007 0.007 -10000 0 -0.1 3 3
Rap1/GTP -0.004 0.073 -10000 0 -0.25 35 35
IQGAP1 0.022 0.01 0.12 6 -10000 0 6
Rap1/GTP/I-afadin 0.033 0.017 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.028 0.018 -10000 0 -0.15 5 5
PVR 0.019 0.007 -10000 0 -10000 0 0
Necl-5(dimer) 0.019 0.007 -10000 0 -10000 0 0
mol:GDP -0.005 0.12 -10000 0 -0.41 30 30
MLLT4 0.02 0.005 -10000 0 -10000 0 0
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
PI3K 0.055 0.025 -10000 0 -0.12 5 5
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.027 0.02 -10000 0 -0.16 6 6
positive regulation of lamellipodium assembly 0 0.075 -10000 0 -0.28 16 16
PVRL1 0.02 0.004 -10000 0 -10000 0 0
PVRL3 0.021 0.003 -10000 0 -10000 0 0
PVRL2 0.019 0.007 -10000 0 -10000 0 0
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
CDH1 0.022 0.013 0.12 9 -10000 0 9
CLDN1 0.02 0.004 -10000 0 -10000 0 0
JAM-A/CLDN1 0.046 0.03 -10000 0 -0.12 14 14
SRC -0.011 0.11 -10000 0 -0.39 36 36
ITGB3 0.04 0.04 0.12 124 -10000 0 124
nectin-1(dimer)/I-afadin/I-afadin 0.027 0.02 -10000 0 -0.16 6 6
FARP2 -0.006 0.13 -10000 0 -0.45 25 25
RAC1 0.018 0.008 -10000 0 -10000 0 0
CTNNA1 0.021 0.003 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.034 0.022 -10000 0 -0.13 5 5
nectin-1/I-afadin 0.027 0.02 -10000 0 -0.16 6 6
nectin-2/I-afadin 0.026 0.011 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.024 0.012 0.096 5 -10000 0 5
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.036 0.025 -10000 0 -0.13 11 11
CDC42/GTP/IQGAP1/filamentous actin 0.026 0.011 -10000 0 -10000 0 0
F11R 0.022 0.008 0.12 4 -10000 0 4
positive regulation of filopodium formation -0.004 0.081 -10000 0 -0.28 19 19
alphaV/beta3 Integrin/Talin 0.036 0.051 0.2 28 -0.13 7 35
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.026 0.011 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.026 0.011 -10000 0 -10000 0 0
PIP5K1C -0.004 0.008 -10000 0 -0.1 4 4
VAV2 -0.003 0.13 -10000 0 -0.5 17 17
RAP1/GDP 0.008 0.099 -10000 0 -0.31 34 34
ITGAV 0.021 0.001 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.034 0.022 -10000 0 -0.13 5 5
nectin-3(dimer)/I-afadin/I-afadin 0.028 0.018 -10000 0 -0.15 5 5
Rac1/GTP 0.002 0.09 -10000 0 -0.34 16 16
PTPRM 0.007 0.011 -10000 0 -0.11 5 5
E-cadherin/beta catenin/alpha catenin 0.043 0.043 -10000 0 -0.12 27 27
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.019 0.006 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.02 0.004 -10000 0 -10000 0 0
HDAC4 0.021 0.003 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.013 0.01 -10000 0 -0.05 3 3
CDKN1A 0 0.026 -10000 0 -10000 0 0
KAT2B 0.021 0.005 0.12 1 -10000 0 1
BAX 0.019 0.007 -10000 0 -10000 0 0
FOXO3 -0.001 0.005 -10000 0 -10000 0 0
FOXO1 0.02 0.004 -10000 0 -10000 0 0
FOXO4 0.008 0.008 -10000 0 -0.19 1 1
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.02 0.004 -10000 0 -10000 0 0
TAT 0.034 0.035 0.12 85 -10000 0 85
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.01 0.031 0.051 240 -10000 0 240
PPARGC1A 0.021 0.003 -10000 0 -10000 0 0
FHL2 0.02 0.005 -10000 0 -10000 0 0
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.019 0.021 -10000 0 -10000 0 0
HIST2H4A -0.013 0.01 0.05 3 -10000 0 3
SIRT1/FOXO3a 0.007 0.022 -10000 0 -0.18 3 3
SIRT1 0.01 0.021 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.027 0.027 -10000 0 -0.15 1 1
SIRT1/Histone H1b 0.013 0.025 -10000 0 -0.21 2 2
apoptosis -0.025 0.026 -10000 0 -10000 0 0
SIRT1/PGC1A 0.017 0.021 -10000 0 -0.13 3 3
p53/SIRT1 0.019 0.034 -10000 0 -10000 0 0
SIRT1/FOXO4 0.014 0.021 -10000 0 -0.18 1 1
FOXO1/FHL2/SIRT1 0.022 0.041 -10000 0 -0.12 45 45
HIST1H1E 0.008 0.004 -10000 0 -10000 0 0
SIRT1/p300 0.019 0.021 -10000 0 -10000 0 0
muscle cell differentiation -0.022 0.024 -10000 0 -0.23 3 3
TP53 0.022 0.039 0.12 67 -10000 0 67
KU70/SIRT1/BAX 0.025 0.026 -10000 0 -10000 0 0
CREBBP 0.021 0.002 -10000 0 -10000 0 0
MEF2D 0.021 0.003 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.028 0.032 -10000 0 -10000 0 0
ACSS2 -0.014 0.008 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.022 0.025 0.24 3 -10000 0 3
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.021 0.007 0.12 3 -10000 0 3
positive regulation of NF-kappaB transcription factor activity 0.031 0.011 0.1 10 -10000 0 10
MAP2K4 0.012 0.02 -10000 0 -0.2 1 1
IKBKB 0.021 0.003 -10000 0 -10000 0 0
TNFRSF10B 0.025 0.021 0.12 28 -10000 0 28
TNFRSF10A 0.021 0.005 0.12 1 -10000 0 1
SMPD1 0.009 0.005 -10000 0 -10000 0 0
IKBKG 0.021 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.022 0.011 0.12 7 -10000 0 7
TRAIL/TRAILR2 0.034 0.018 0.11 28 -10000 0 28
TRAIL/TRAILR3 0.044 0.03 0.11 118 -10000 0 118
TRAIL/TRAILR1 0.03 0.013 -10000 0 -0.16 2 2
TRAIL/TRAILR4 0.031 0.011 0.11 10 -10000 0 10
TRAIL/TRAILR1/DAP3/GTP 0.039 0.013 -10000 0 -0.12 2 2
IKK complex -0.002 0.062 -10000 0 -0.2 56 56
RIPK1 0.021 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.015 0.002 -10000 0 -10000 0 0
MAPK3 -0.012 0.005 0.051 3 -10000 0 3
MAP3K1 0.019 0.016 -10000 0 -0.21 1 1
TRAILR4 (trimer) 0.022 0.011 0.12 7 -10000 0 7
TRADD 0.021 0.002 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.021 0.005 0.12 1 -10000 0 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.017 0.012 -10000 0 -0.16 2 2
CFLAR 0.021 0.001 -10000 0 -10000 0 0
MAPK1 -0.012 0.005 0.051 3 -10000 0 3
TRAIL/TRAILR1/FADD/TRADD/RIP 0.059 0.018 -10000 0 -0.12 1 1
mol:ceramide 0.009 0.005 -10000 0 -10000 0 0
FADD 0.021 0.003 -10000 0 -10000 0 0
MAPK8 0.007 0.023 0.19 1 -10000 0 1
TRAF2 0.021 0.003 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.039 0.04 0.12 118 -10000 0 118
CHUK 0.019 0.006 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.041 0.013 -10000 0 -0.13 1 1
DAP3 0.021 0.003 -10000 0 -10000 0 0
CASP10 -0.008 0.007 -10000 0 -10000 0 0
JNK cascade 0.031 0.011 0.1 10 -10000 0 10
TRAIL (trimer) 0.021 0.007 0.12 3 -10000 0 3
TNFRSF10C 0.039 0.04 0.12 118 -10000 0 118
TRAIL/TRAILR1/DAP3/GTP/FADD 0.047 0.015 -10000 0 -0.11 1 1
TRAIL/TRAILR2/FADD 0.044 0.018 0.18 2 -10000 0 2
cell death 0.009 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.019 0.011 -10000 0 -0.17 1 1
TRAILR2 (trimer) 0.025 0.021 0.12 28 -10000 0 28
CASP8 0.012 0.021 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.061 0.022 0.18 2 -10000 0 2
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.001 0.068 -10000 0 -0.37 10 10
BAG4 0.02 0.004 -10000 0 -10000 0 0
BAD -0.001 0.035 0.18 9 -0.14 6 15
NFKBIA 0.021 0.008 0.12 3 -10000 0 3
BIRC3 0.023 0.017 0.12 16 -10000 0 16
BAX 0.002 0.036 0.18 15 -0.14 6 21
EnzymeConsortium:3.1.4.12 0.001 0.019 0.068 2 -0.084 11 13
IKBKB 0.001 0.072 0.2 13 -0.36 10 23
MAP2K2 -0.004 0.042 0.16 23 -0.13 3 26
MAP2K1 -0.007 0.036 0.17 10 -0.15 4 14
SMPD1 0 0.025 0.092 5 -0.1 15 20
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.005 0.074 0.25 6 -0.38 10 16
MAP2K4 -0.005 0.031 0.22 3 -0.15 3 6
protein ubiquitination -0.001 0.069 0.2 1 -0.38 9 10
EnzymeConsortium:2.7.1.37 -0.008 0.041 0.17 10 -0.16 4 14
response to UV 0 0 0.002 11 -0.002 3 14
RAF1 -0.005 0.035 0.16 9 -0.14 7 16
CRADD 0.021 0.002 -10000 0 -10000 0 0
mol:ceramide 0.001 0.029 0.09 5 -0.12 12 17
I-kappa-B-alpha/RELA/p50/ubiquitin 0.027 0.008 0.096 3 -10000 0 3
MADD 0.02 0.004 -10000 0 -10000 0 0
MAP3K1 -0.002 0.03 0.16 4 -0.13 7 11
TRADD 0.021 0.002 -10000 0 -10000 0 0
RELA/p50 0.021 0.003 -10000 0 -10000 0 0
MAPK3 -0.003 0.04 0.14 24 -0.18 3 27
MAPK1 -0.005 0.042 0.14 24 -0.2 4 28
p50/RELA/I-kappa-B-alpha 0.03 0.009 -10000 0 -10000 0 0
FADD 0.003 0.069 0.24 4 -0.38 9 13
KSR1 -0.002 0.031 0.13 6 -0.13 9 15
MAPK8 -0.008 0.03 0.19 5 -0.19 1 6
TRAF2 0.021 0.003 -10000 0 -10000 0 0
response to radiation 0 0 0.002 2 -10000 0 2
CHUK -0.002 0.062 -10000 0 -0.37 8 8
TNF R/SODD 0.027 0.022 -10000 0 -0.16 7 7
TNF 0.021 0.015 0.12 11 -10000 0 11
CYCS 0.01 0.045 0.15 27 -0.16 3 30
IKBKG -0.001 0.067 0.19 5 -0.37 9 14
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.006 0.071 -10000 0 -0.4 9 9
RELA 0.021 0.003 -10000 0 -10000 0 0
RIPK1 0.021 0.003 -10000 0 -10000 0 0
AIFM1 0 0.035 0.14 18 -0.15 3 21
TNF/TNF R/SODD 0.028 0.049 -10000 0 -0.14 49 49
TNFRSF1A 0.021 0.01 0.12 5 -10000 0 5
response to heat 0 0 0.002 2 -10000 0 2
CASP8 0.023 0.069 -10000 0 -0.88 3 3
NSMAF 0.002 0.069 0.23 5 -0.37 10 15
response to hydrogen peroxide 0 0 0.002 11 -0.002 3 14
BCL2 0.021 0.003 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC 0.011 0.04 -10000 0 -10000 0 0
PLK1 0.047 0.068 0.38 1 -10000 0 1
CDKN1B 0.026 0.12 0.33 5 -0.32 24 29
FOXO3 0.049 0.044 -10000 0 -10000 0 0
KAT2B 0.028 0.008 0.13 1 -10000 0 1
FOXO1/SIRT1 0.02 0.031 -10000 0 -10000 0 0
CAT 0.04 0.061 -10000 0 -10000 0 0
CTNNB1 0.021 0.002 -10000 0 -10000 0 0
AKT1 0.028 0.009 -10000 0 -10000 0 0
FOXO1 0.014 0.038 -10000 0 -10000 0 0
MAPK10 0.04 0.063 0.19 104 -10000 0 104
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.036 0.06 0.23 17 -10000 0 17
response to oxidative stress 0.009 0.007 0.035 3 -10000 0 3
FOXO3A/SIRT1 0.047 0.059 -10000 0 -0.42 1 1
XPO1 0.021 0.001 -10000 0 -10000 0 0
EP300 0.021 0.005 -10000 0 -10000 0 0
BCL2L11 0.027 0.041 -10000 0 -0.93 1 1
FOXO1/SKP2 0.024 0.036 -10000 0 -10000 0 0
mol:GDP 0.009 0.007 0.035 3 -10000 0 3
RAN 0.021 0.002 -10000 0 -10000 0 0
GADD45A -0.023 0.19 -10000 0 -0.5 72 72
YWHAQ 0.021 0.002 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.024 0.064 0.18 1 -0.49 3 4
MST1 0.04 0.033 0.13 78 -10000 0 78
CSNK1D 0.02 0.004 -10000 0 -10000 0 0
CSNK1E 0.02 0.004 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.003 0.076 -10000 0 -0.5 6 6
YWHAB 0.02 0.004 -10000 0 -10000 0 0
MAPK8 0.027 0.05 0.19 60 -10000 0 60
MAPK9 0.04 0.063 0.19 104 -10000 0 104
YWHAG 0.017 0.008 -10000 0 -10000 0 0
YWHAE 0.021 0.002 -10000 0 -10000 0 0
YWHAZ 0.02 0.005 -10000 0 -10000 0 0
SIRT1 0.017 0.01 -10000 0 -0.031 1 1
SOD2 0.044 0.091 0.37 1 -0.43 3 4
RBL2 0.051 0.064 -10000 0 -0.56 2 2
RAL/GDP 0.03 0.014 -10000 0 -10000 0 0
CHUK 0.024 0.01 -10000 0 -10000 0 0
Ran/GTP 0.017 0.002 -10000 0 -10000 0 0
CSNK1G2 0.02 0.004 -10000 0 -10000 0 0
RAL/GTP 0.03 0.014 -10000 0 -10000 0 0
CSNK1G1 0.021 0.003 -10000 0 -10000 0 0
FASLG 0.028 0.02 -10000 0 -10000 0 0
SKP2 0.021 0.006 0.12 2 -10000 0 2
USP7 0.021 0.002 -10000 0 -10000 0 0
IKBKB 0.028 0.008 -10000 0 -10000 0 0
CCNB1 0.042 0.069 0.39 3 -10000 0 3
FOXO1-3a-4/beta catenin 0.065 0.071 0.26 24 -10000 0 24
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.036 -10000 0 -10000 0 0
CSNK1A1 0.021 0.003 -10000 0 -10000 0 0
SGK1 0.027 0.009 -10000 0 -10000 0 0
CSNK1G3 0.021 0.002 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.03 0.004 -10000 0 -10000 0 0
ZFAND5 0.033 0.058 0.3 2 -10000 0 2
SFN 0.022 0.02 0.12 23 -10000 0 23
CDK2 0.053 0.048 0.12 198 -10000 0 198
FOXO3A/14-3-3 0.011 0.072 -10000 0 -0.48 5 5
CREBBP 0.022 0.004 -10000 0 -10000 0 0
FBXO32 0.055 0.086 0.51 3 -10000 0 3
BCL6 0.043 0.097 -10000 0 -0.62 9 9
RALB 0.021 0.001 -10000 0 -10000 0 0
RALA 0.018 0.008 -10000 0 -10000 0 0
YWHAH 0.02 0.005 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD 0.013 0.035 -10000 0 -0.19 16 16
FZD6 0.021 0.012 0.12 7 -10000 0 7
WNT6 0.022 0.009 0.12 5 -10000 0 5
WNT4 0.019 0.009 0.12 2 -10000 0 2
FZD3 0.021 0.003 -10000 0 -10000 0 0
WNT5A 0.028 0.026 0.12 45 -10000 0 45
WNT11 0.022 0.01 0.12 6 -10000 0 6
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.021 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.024 0.049 0.19 5 -0.25 3 8
ERC1 0.02 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.047 0.033 0.11 155 -10000 0 155
NFKBIA -0.012 0.025 0.2 8 -10000 0 8
BIRC2 0.021 0.003 -10000 0 -10000 0 0
IKBKB 0.021 0.003 -10000 0 -10000 0 0
RIPK2 0.02 0.007 0.12 2 -10000 0 2
IKBKG 0.015 0.031 -10000 0 -0.32 3 3
IKK complex/A20 0.041 0.052 0.22 1 -0.3 3 4
NEMO/A20/RIP2 0.02 0.007 0.12 2 -10000 0 2
XPO1 0.021 0.001 -10000 0 -10000 0 0
NEMO/ATM 0.03 0.039 -10000 0 -0.31 3 3
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.021 0.002 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.028 0.003 -10000 0 -10000 0 0
IKK complex/ELKS 0.032 0.039 -10000 0 -0.29 3 3
BCL10/MALT1/TRAF6 0.036 0.016 -10000 0 -10000 0 0
NOD2 0.046 0.044 0.12 159 -10000 0 159
NFKB1 0.021 0.003 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
MALT1 0.02 0.004 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.03 0.006 -10000 0 -10000 0 0
ATM 0.021 0.003 -10000 0 -10000 0 0
TNF/TNFR1A 0.019 0.049 -10000 0 -0.16 44 44
TRAF6 0.021 0.003 -10000 0 -10000 0 0
PRKCA 0.02 0.004 -10000 0 -10000 0 0
CHUK 0.019 0.006 -10000 0 -10000 0 0
UBE2D3 0.021 0.002 -10000 0 -10000 0 0
TNF 0.021 0.015 0.12 11 -10000 0 11
NF kappa B1 p50/RelA 0.044 0.01 -10000 0 -10000 0 0
BCL10 0.019 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.012 0.025 0.2 8 -10000 0 8
beta TrCP1/SCF ubiquitin ligase complex 0.021 0.003 -10000 0 -10000 0 0
TNFRSF1A 0.021 0.01 0.12 5 -10000 0 5
IKK complex 0.036 0.043 0.22 1 -0.3 3 4
CYLD 0.021 0.002 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.045 0.041 0.22 1 -0.3 3 4
Arf6 trafficking events

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
SLC2A4 0.02 0.004 -10000 0 -10000 0 0
CLTC 0.011 0.06 -10000 0 -0.32 18 18
calcium ion-dependent exocytosis 0.014 0.034 -10000 0 -0.16 5 5
Dynamin 2/GTP 0.017 0.005 -10000 0 -10000 0 0
EXOC4 0.017 0.009 -10000 0 -10000 0 0
CD59 0.007 0.051 -10000 0 -0.26 19 19
CPE -0.009 0.002 -10000 0 -10000 0 0
CTNNB1 0.021 0.002 -10000 0 -10000 0 0
membrane fusion 0.004 0.011 -10000 0 -0.19 1 1
CTNND1 -0.013 0.021 0.18 8 -10000 0 8
DNM2 0.02 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.009 0.036 0.13 5 -0.18 8 13
TSHR 0.031 0.036 0.063 370 -10000 0 370
INS -0.005 0.092 -10000 0 -0.45 26 26
BIN1 0.021 0.001 -10000 0 -10000 0 0
mol:Choline 0.004 0.011 -10000 0 -0.19 1 1
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP -0.009 0.004 0.063 2 -10000 0 2
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.02 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.017 0.005 -10000 0 -10000 0 0
JUP 0.007 0.052 -10000 0 -0.26 20 20
ASAP2/amphiphysin II 0.039 0.008 -10000 0 -10000 0 0
ARF6/GTP 0.015 0.003 -10000 0 -10000 0 0
CDH1 0.003 0.057 -10000 0 -0.27 20 20
clathrin-independent pinocytosis 0.015 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.021 0.003 -10000 0 -10000 0 0
positive regulation of endocytosis 0.015 0.003 -10000 0 -10000 0 0
EXOC2 0.021 0.003 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.005 0.033 -10000 0 -0.21 8 8
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.021 0.002 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.02 0.054 0.25 18 -10000 0 18
positive regulation of phagocytosis -0.009 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.026 0.016 -10000 0 -0.13 6 6
ACAP1 0.02 0.035 0.12 1 -0.15 5 6
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.03 0.067 -10000 0 -0.35 10 10
clathrin heavy chain/ACAP1 0.015 0.054 0.18 11 -0.22 18 29
JIP4/KLC1 0.038 0.01 -10000 0 -10000 0 0
EXOC1 0.02 0.004 -10000 0 -10000 0 0
exocyst 0.005 0.033 -10000 0 -0.21 8 8
RALA/GTP 0.013 0.006 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.027 0.006 -10000 0 -10000 0 0
receptor recycling 0.015 0.003 -10000 0 -10000 0 0
CTNNA1 -0.013 0.02 0.18 7 -10000 0 7
NME1 -0.009 0.005 0.063 2 -10000 0 2
clathrin coat assembly 0.011 0.061 -10000 0 -0.31 19 19
IL2RA 0.009 0.049 -10000 0 -0.3 13 13
VAMP3 -0.009 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.019 0.051 -10000 0 -0.26 11 11
EXOC6 0.019 0.006 -10000 0 -10000 0 0
PLD1 0.004 0.023 -10000 0 -0.21 7 7
PLD2 0.006 0.007 -10000 0 -10000 0 0
EXOC5 0.02 0.004 -10000 0 -10000 0 0
PIP5K1C 0.009 0.033 -10000 0 -0.19 8 8
SDC1 0.008 0.052 -10000 0 -0.26 20 20
ARF6/GDP 0.018 0.004 -10000 0 -10000 0 0
EXOC7 0.02 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.022 0.055 -10000 0 -0.25 18 18
mol:Phosphatidic acid 0.004 0.011 -10000 0 -0.19 1 1
endocytosis -0.038 0.008 -10000 0 -10000 0 0
SCAMP2 0.021 0.003 -10000 0 -10000 0 0
ADRB2 0.008 0.063 0.25 4 -0.3 20 24
EXOC3 0.021 0.003 -10000 0 -10000 0 0
ASAP2 0.021 0.002 -10000 0 -10000 0 0
Dynamin 2/GDP 0.02 0.006 -10000 0 -10000 0 0
KLC1 0.02 0.004 -10000 0 -10000 0 0
AVPR2 0.009 0.063 0.2 7 -0.3 19 26
RALA 0.018 0.008 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.015 0.053 -10000 0 -0.24 18 18
Insulin Pathway

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
CBL/APS/CAP 0.032 0.022 -10000 0 -10000 0 0
TC10/GTP 0.031 0.02 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.049 0.017 -10000 0 -10000 0 0
HRAS 0.02 0.005 -10000 0 -10000 0 0
APS homodimer 0.02 0.02 0.12 20 -10000 0 20
GRB14 0.016 0.009 -10000 0 -10000 0 0
FOXO3 -0.018 0.14 -10000 0 -0.64 32 32
AKT1 -0.03 0.064 0.19 28 -10000 0 28
INSR 0.022 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.037 0.015 0.18 2 -10000 0 2
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.017 0.008 -10000 0 -10000 0 0
SORBS1 0.019 0.006 -10000 0 -10000 0 0
CRK 0.021 0.002 -10000 0 -10000 0 0
PTPN1 -0.007 0.026 0.16 15 -10000 0 15
CAV1 -0.001 0.034 0.18 9 -10000 0 9
CBL/APS/CAP/Crk-II/C3G 0.048 0.03 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 0.049 0.016 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.039 0.015 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.017 0.019 -10000 0 -0.39 1 1
RPS6KB1 -0.031 0.06 0.16 35 -10000 0 35
PARD6A 0.021 0.002 -10000 0 -10000 0 0
CBL 0.021 0.003 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.014 0.022 -10000 0 -0.51 1 1
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.04 0.045 0.13 14 -10000 0 14
HRAS/GTP -0.021 0.015 -10000 0 -10000 0 0
Insulin Receptor 0.022 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.056 0.024 -10000 0 -10000 0 0
PRKCI 0.016 0.021 -10000 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.007 0.057 -10000 0 -0.11 138 138
SHC1 0.023 0.016 0.12 16 -10000 0 16
negative regulation of MAPKKK cascade 0.028 0.033 -10000 0 -0.42 1 1
PI3K 0.048 0.018 -10000 0 -10000 0 0
NCK2 0.021 0.001 -10000 0 -10000 0 0
RHOQ 0.021 0.001 -10000 0 -10000 0 0
mol:H2O2 -0.001 0.003 0.033 1 -10000 0 1
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
AKT2 -0.031 0.055 0.18 21 -10000 0 21
PRKCZ -0.061 0.16 -10000 0 -0.37 131 131
SH2B2 0.02 0.02 0.12 20 -10000 0 20
SHC/SHIP -0.007 0.039 0.17 21 -10000 0 21
F2RL2 0.04 0.041 0.12 125 -10000 0 125
TRIP10 0.023 0.016 0.12 15 -10000 0 15
Insulin Receptor/Insulin/Shc 0.038 0.017 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.029 0.011 0.096 15 -10000 0 15
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.056 0.024 -10000 0 -10000 0 0
RAPGEF1 0.021 0.003 -10000 0 -10000 0 0
RASA1 0.021 0.002 -10000 0 -10000 0 0
NCK1 0.021 0.005 0.12 1 -10000 0 1
CBL/APS/CAP/Crk-II 0.043 0.027 -10000 0 -10000 0 0
TC10/GDP 0.016 0.001 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.042 0.025 -10000 0 -10000 0 0
INPP5D -0.007 0.035 0.17 22 -10000 0 22
SOS1 0.021 0.001 -10000 0 -10000 0 0
SGK1 -0.023 0.15 -10000 0 -0.67 32 32
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.021 0.003 -10000 0 -10000 0 0
IRS1 0.021 0.001 -10000 0 -10000 0 0
p62DOK/RasGAP 0.029 0.033 -10000 0 -0.42 1 1
INS 0.018 0.01 0.08 9 -10000 0 9
mol:PI-3-4-P2 -0.007 0.035 0.16 22 -10000 0 22
GRB2 0.02 0.004 -10000 0 -10000 0 0
EIF4EBP1 -0.027 0.063 0.18 33 -10000 0 33
PTPRA 0.021 0.005 -10000 0 -10000 0 0
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.029 0.011 0.096 15 -10000 0 15
PDPK1 0.021 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.014 0.021 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.037 0.013 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0.028 0.013 -10000 0 -10000 0 0
Par3/Par6 0.059 0.028 0.17 6 -0.09 1 7
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 -0.011 0.005 -10000 0 -10000 0 0
SMARCC1 0.007 0.009 -10000 0 -10000 0 0
REL 0.021 0.006 0.12 1 -0.015 3 4
HDAC7 -0.01 0.028 0.16 8 -10000 0 8
JUN 0.018 0.008 -10000 0 -0.016 11 11
EP300 0.02 0.004 -10000 0 -10000 0 0
KAT2B 0.021 0.005 0.12 1 -10000 0 1
KAT5 0.021 0.003 -10000 0 -10000 0 0
MAPK14 -0.009 0.009 -10000 0 -10000 0 0
FOXO1 0.02 0.004 -10000 0 -10000 0 0
T-DHT/AR 0.028 0.033 0.19 9 -10000 0 9
MAP2K6 0.021 0.004 -10000 0 -10000 0 0
BRM/BAF57 0.028 0.013 -10000 0 -10000 0 0
MAP2K4 0.021 0.002 -10000 0 -10000 0 0
SMARCA2 0.019 0.009 -10000 0 -0.032 11 11
PDE9A 0.02 0.029 -10000 0 -0.46 2 2
NCOA2 0.02 0.005 -10000 0 -10000 0 0
CEBPA 0.019 0.011 0.12 4 -10000 0 4
EHMT2 0.02 0.005 -10000 0 -0.018 11 11
cell proliferation 0.012 0.07 0.25 23 -0.38 2 25
NR0B1 0.028 0.029 0.12 54 -10000 0 54
EGR1 0.02 0.01 0.12 2 -0.027 12 14
RXRs/9cRA 0.029 0.039 -10000 0 -0.12 40 40
AR/RACK1/Src 0.003 0.047 0.16 38 -10000 0 38
AR/GR 0.025 0.034 0.18 3 -0.19 2 5
GNB2L1 0.023 0.016 0.12 15 -10000 0 15
PKN1 0.02 0.004 -10000 0 -10000 0 0
RCHY1 0.021 0.003 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -10000 0 0
MAPK8 -0.008 0.01 0.028 1 -10000 0 1
T-DHT/AR/TIF2/CARM1 0.023 0.042 0.18 22 -0.22 5 27
SRC -0.017 0.012 -10000 0 -0.12 5 5
NR3C1 0.021 0.002 -10000 0 -10000 0 0
KLK3 -0.048 0.16 -10000 0 -1.1 12 12
APPBP2 0.021 0.004 -10000 0 -10000 0 0
TRIM24 0.016 0.01 -10000 0 -0.03 10 10
T-DHT/AR/TIP60 0.004 0.038 0.18 21 -10000 0 21
TMPRSS2 0.023 0.041 -10000 0 -0.47 3 3
RXRG 0.019 0.008 0.12 1 -0.018 10 11
mol:9cRA 0 0.001 -10000 0 -10000 0 0
RXRA 0.02 0.006 -10000 0 -0.018 10 10
RXRB 0.02 0.005 -10000 0 -0.018 10 10
CARM1 0.02 0.004 -10000 0 -10000 0 0
NR2C2 0.021 0.002 -10000 0 -10000 0 0
KLK2 0.009 0.044 0.25 3 -0.24 5 8
AR 0.016 0.03 0.16 18 -10000 0 18
SENP1 0.02 0.006 -10000 0 -0.018 9 9
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
MDM2 0.019 0.009 -10000 0 -0.018 22 22
SRY 0 0.004 0.03 12 -10000 0 12
GATA2 0.021 0.008 0.12 4 -10000 0 4
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 0.042 0.047 0.12 152 -0.044 12 164
T-DHT/AR/RACK1/Src 0.004 0.052 0.17 47 -10000 0 47
positive regulation of transcription 0.021 0.008 0.12 4 -10000 0 4
DNAJA1 0.021 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.004 -10000 0 -10000 0 0
NCOA1 0.021 0.013 0.13 1 -10000 0 1
SPDEF 0.018 0.009 -10000 0 -0.032 9 9
T-DHT/AR/TIF2 0.002 0.055 0.18 2 -0.22 16 18
T-DHT/AR/Hsp90 0.004 0.036 0.18 19 -10000 0 19
GSK3B 0.021 0.003 -10000 0 -10000 0 0
NR2C1 0.021 0.003 -10000 0 -10000 0 0
mol:T-DHT -0.014 0.011 -10000 0 -0.12 3 3
SIRT1 0.019 0.006 -10000 0 -10000 0 0
ZMIZ2 0.017 0.011 -10000 0 -0.018 2 2
POU2F1 0.028 0.013 0.14 3 -10000 0 3
T-DHT/AR/DAX-1 0.011 0.045 0.19 24 -10000 0 24
CREBBP 0.021 0.002 -10000 0 -10000 0 0
SMARCE1 0.02 0.007 -10000 0 -0.032 12 12
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.02 0.037 -10000 0 -10000 0 0
epithelial cell differentiation -0.008 0.053 -10000 0 -10000 0 0
ITCH 0.018 0.015 -10000 0 -10000 0 0
WWP1 0.009 0.043 -10000 0 -10000 0 0
FYN 0.02 0.004 -10000 0 -10000 0 0
EGFR 0.053 0.054 0.12 235 -10000 0 235
PRL 0.017 0.009 0.12 4 -10000 0 4
neuron projection morphogenesis -0.02 0.067 0.26 15 -10000 0 15
PTPRZ1 0.028 0.034 0.12 70 -10000 0 70
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.014 0.063 -10000 0 -10000 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.004 0.032 -10000 0 -10000 0 0
ADAM17 0.018 0.015 -10000 0 -10000 0 0
ErbB4/ErbB4 0.006 0.031 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.015 0.045 -10000 0 -0.24 1 1
NCOR1 0.021 0.002 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.002 0.053 -10000 0 -10000 0 0
GRIN2B -0.032 0.073 0.22 6 -0.24 7 13
ErbB4/ErbB2/betacellulin 0.024 0.032 -10000 0 -10000 0 0
STAT1 0.022 0.011 0.12 7 -10000 0 7
HBEGF 0.021 0.003 -10000 0 -10000 0 0
PRLR 0.021 0.008 0.12 3 -10000 0 3
E4ICDs/ETO2 0.017 0.043 -10000 0 -0.24 1 1
axon guidance -0.018 0.045 -10000 0 -10000 0 0
NEDD4 0.034 0.036 0.13 81 -10000 0 81
Prolactin receptor/Prolactin receptor/Prolactin 0.025 0.023 0.11 4 -0.16 9 13
CBFA2T3 0.02 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/HBEGF 0.022 0.028 -10000 0 -10000 0 0
MAPK3 -0.019 0.062 0.22 12 -10000 0 12
STAT1 (dimer) 0.021 0.038 -10000 0 -10000 0 0
MAPK1 -0.018 0.061 0.22 12 -10000 0 12
JAK2 0.02 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.012 0.049 -10000 0 -10000 0 0
NRG1 -0.009 0.01 -10000 0 -10000 0 0
NRG3 0.017 0.008 -10000 0 -10000 0 0
NRG2 0.021 0.003 -10000 0 -10000 0 0
NRG4 0.018 0.007 -10000 0 -10000 0 0
heart development -0.018 0.045 -10000 0 -10000 0 0
neural crest cell migration -0.012 0.048 -10000 0 -10000 0 0
ERBB2 -0.01 0.012 0.05 8 -10000 0 8
WWOX/E4ICDs 0.02 0.037 -10000 0 -10000 0 0
SHC1 0.023 0.016 0.12 16 -10000 0 16
ErbB4/EGFR/neuregulin 4 0.035 0.063 -10000 0 -10000 0 0
apoptosis 0.005 0.093 0.3 53 -10000 0 53
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.02 0.038 -10000 0 -0.24 1 1
ErbB4/ErbB2/epiregulin 0.022 0.03 -10000 0 -10000 0 0
ErbB4/ErbB4/betacellulin/betacellulin 0.022 0.04 -10000 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.043 0.045 -10000 0 -10000 0 0
MDM2 0.006 0.046 0.24 16 -10000 0 16
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.005 0.05 -10000 0 -10000 0 0
STAT5A -0.022 0.048 0.24 1 -10000 0 1
ErbB4/EGFR/neuregulin 1 beta 0.018 0.062 0.22 1 -10000 0 1
DLG4 0.021 0.002 -10000 0 -10000 0 0
GRB2/SHC 0.031 0.013 0.11 14 -10000 0 14
E4ICDs/TAB2/NCoR1 0.018 0.034 -10000 0 -10000 0 0
STAT5A (dimer) 0.001 0.061 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.012 0.057 0.28 1 -10000 0 1
LRIG1 0.021 0.005 0.12 1 -10000 0 1
EREG 0.023 0.018 0.12 19 -10000 0 19
BTC 0.024 0.022 0.12 30 -10000 0 30
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.018 0.045 -10000 0 -10000 0 0
ERBB4 0.006 0.031 -10000 0 -10000 0 0
STAT5B 0.021 0.002 -10000 0 -10000 0 0
YAP1 0.013 0.01 -10000 0 -10000 0 0
GRB2 0.02 0.004 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.018 0.032 -10000 0 -10000 0 0
glial cell differentiation -0.018 0.034 -10000 0 -10000 0 0
WWOX 0.021 0.003 -10000 0 -10000 0 0
cell proliferation -0.029 0.068 0.31 2 -0.29 1 3
Arf6 downstream pathway

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
PLAUR 0.015 0.027 -10000 0 -10000 0 0
regulation of axonogenesis -0.001 0.043 0.25 19 -10000 0 19
myoblast fusion -0.011 0.029 0.34 1 -10000 0 1
mol:GTP 0.016 0.03 -10000 0 -0.16 16 16
regulation of calcium-dependent cell-cell adhesion -0.034 0.03 0.11 6 -10000 0 6
ARF1/GTP 0.028 0.028 -10000 0 -0.12 21 21
mol:GM1 0.005 0.022 -10000 0 -0.12 18 18
mol:Choline -0.006 0.019 -10000 0 -0.1 18 18
lamellipodium assembly 0.003 0.048 -10000 0 -0.38 8 8
MAPK3 0.016 0.023 -10000 0 -0.12 1 1
ARF6/GTP/NME1/Tiam1 0.034 0.031 -10000 0 -0.11 6 6
ARF1 0.021 0.002 -10000 0 -10000 0 0
ARF6/GDP 0.011 0.03 -10000 0 -0.34 1 1
ARF1/GDP 0.009 0.05 -10000 0 -0.23 17 17
ARF6 0.028 0.007 -10000 0 -10000 0 0
RAB11A 0.021 0.003 -10000 0 -10000 0 0
TIAM1 0.017 0.012 -10000 0 -0.031 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.016 0.022 -10000 0 -0.12 1 1
actin filament bundle formation -0.013 0.049 0.23 16 -10000 0 16
KALRN 0.008 0.016 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0.031 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.013 0.049 -10000 0 -0.23 16 16
NME1 0.018 0.014 0.13 2 -10000 0 2
Rac1/GDP 0.013 0.042 -10000 0 -0.25 9 9
substrate adhesion-dependent cell spreading 0.016 0.03 -10000 0 -0.16 16 16
cortical actin cytoskeleton organization 0.003 0.049 -10000 0 -0.38 8 8
RAC1 0.018 0.008 -10000 0 -10000 0 0
liver development 0.016 0.03 -10000 0 -0.16 16 16
ARF6/GTP 0.016 0.03 -10000 0 -0.16 16 16
RhoA/GTP 0.028 0.027 -10000 0 -0.12 18 18
mol:GDP 0.004 0.044 -10000 0 -0.25 16 16
ARF6/GTP/RAB11FIP3/RAB11A 0.039 0.028 -10000 0 -0.11 19 19
RHOA 0.021 0.003 -10000 0 -10000 0 0
PLD1 0.011 0.024 -10000 0 -0.12 19 19
RAB11FIP3 0.021 0.002 -10000 0 -10000 0 0
tube morphogenesis 0.003 0.048 -10000 0 -0.38 8 8
ruffle organization 0.001 0.043 -10000 0 -0.25 19 19
regulation of epithelial cell migration 0.016 0.03 -10000 0 -0.16 16 16
PLD2 0.011 0.024 -10000 0 -0.12 20 20
PIP5K1A 0.001 0.043 -10000 0 -0.25 19 19
mol:Phosphatidic acid -0.006 0.019 -10000 0 -0.1 18 18
Rac1/GTP 0.003 0.049 -10000 0 -0.39 8 8
IL27-mediated signaling events

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
TGFB1 0.019 0.008 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.016 0.055 0.33 2 -10000 0 2
IL27/IL27R/JAK1 -0.039 0.061 -10000 0 -10000 0 0
TBX21 -0.084 0.086 0.33 3 -0.31 1 4
IL12B 0.017 0.007 0.13 2 -10000 0 2
IL12A -0.005 0.007 0.05 11 -10000 0 11
IL6ST 0 0.019 -10000 0 -10000 0 0
IL27RA/JAK1 -0.006 0.04 -10000 0 -10000 0 0
IL27 0.005 0.032 0.12 33 -10000 0 33
TYK2 0.019 0.004 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.006 0.11 0.38 1 -0.47 1 2
T-helper 2 cell differentiation 0.016 0.055 0.33 2 -10000 0 2
T cell proliferation during immune response 0.016 0.055 0.33 2 -10000 0 2
MAPKKK cascade -0.016 0.055 -10000 0 -0.33 2 2
STAT3 0.021 0.002 -10000 0 -10000 0 0
STAT2 0.021 0.003 -10000 0 -10000 0 0
STAT1 0.012 0.019 0.12 7 -0.02 136 143
IL12RB1 0.021 0.006 0.12 1 -10000 0 1
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.15 0.12 -10000 0 -0.34 10 10
IL27/IL27R/JAK2/TYK2 -0.016 0.056 -10000 0 -0.34 2 2
positive regulation of T cell mediated cytotoxicity -0.016 0.055 -10000 0 -0.33 2 2
STAT1 (dimer) -0.093 0.1 -10000 0 -10000 0 0
JAK2 0.019 0.005 -10000 0 -10000 0 0
JAK1 0.008 0.016 -10000 0 -0.02 142 142
STAT2 (dimer) -0.013 0.058 -10000 0 -0.32 2 2
T cell proliferation -0.019 0.052 -10000 0 -0.33 1 1
IL12/IL12R/TYK2/JAK2 0.006 0.097 -10000 0 -0.8 9 9
IL17A -0.006 0.11 -10000 0 -10000 0 0
mast cell activation 0.016 0.055 0.33 2 -10000 0 2
IFNG -0.001 0.02 -10000 0 -0.1 11 11
T cell differentiation -0.004 0.003 -10000 0 -0.014 7 7
STAT3 (dimer) -0.013 0.059 -10000 0 -0.32 2 2
STAT5A (dimer) -0.013 0.059 -10000 0 -0.32 2 2
STAT4 (dimer) -0.018 0.075 -10000 0 -0.33 8 8
STAT4 0.009 0.01 -10000 0 -10000 0 0
T cell activation -0.002 0.003 -10000 0 -0.041 1 1
IL27R/JAK2/TYK2 -0.01 0.045 -10000 0 -10000 0 0
GATA3 0.034 0.12 0.66 22 -10000 0 22
IL18 -0.004 0.011 0.05 29 -10000 0 29
positive regulation of mast cell cytokine production -0.013 0.058 -10000 0 -0.31 2 2
IL27/EBI3 0.007 0.034 0.18 1 -10000 0 1
IL27RA -0.003 0.028 -10000 0 -10000 0 0
IL6 0.017 0.019 -10000 0 -10000 0 0
STAT5A 0.021 0.002 -10000 0 -10000 0 0
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.006 0.02 -10000 0 -10000 0 0
IL1B -0.005 0.005 0.05 4 -10000 0 4
EBI3 0.001 0.022 0.12 5 -10000 0 5
TNF -0.005 0.007 0.05 11 -10000 0 11
Angiopoietin receptor Tie2-mediated signaling

Figure S113.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S113.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.037 0.09 -10000 0 -0.74 5 5
NCK1/PAK1/Dok-R -0.017 0.044 -10000 0 -0.39 5 5
NCK1/Dok-R 0.029 0.092 -10000 0 -0.82 5 5
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
mol:beta2-estradiol -0.003 0.018 0.24 3 -10000 0 3
RELA 0.021 0.003 -10000 0 -10000 0 0
SHC1 0.024 0.016 0.13 16 -10000 0 16
Rac/GDP 0.013 0.006 -10000 0 -10000 0 0
F2 -0.011 0.026 0.17 4 -0.067 1 5
TNIP2 0.021 0.009 0.12 5 -10000 0 5
NF kappa B/RelA 0.034 0.09 -10000 0 -0.78 5 5
FN1 0.036 0.036 0.12 94 -10000 0 94
PLD2 0.008 0.082 -10000 0 -0.84 5 5
PTPN11 0.021 0.003 -10000 0 -10000 0 0
GRB14 0.016 0.009 -10000 0 -10000 0 0
ELK1 0.002 0.081 -10000 0 -0.79 5 5
GRB7 0.02 0.009 0.12 4 -10000 0 4
PAK1 0.015 0.009 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.046 0.1 -10000 0 -0.77 5 5
CDKN1A 0.051 0.084 -10000 0 -0.53 5 5
ITGA5 0.034 0.036 0.12 89 -10000 0 89
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.029 0.092 -10000 0 -0.82 5 5
CRK 0.021 0.002 -10000 0 -10000 0 0
mol:NO 0.068 0.11 0.34 11 -0.55 5 16
PLG 0.007 0.082 -10000 0 -0.84 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.033 0.083 -10000 0 -0.68 5 5
GRB2 0.02 0.004 -10000 0 -10000 0 0
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
ANGPT2 0.051 0.069 -10000 0 -0.48 1 1
BMX 0.007 0.083 -10000 0 -0.84 5 5
ANGPT1 0.005 0.073 -10000 0 -1.1 2 2
tube development 0.04 0.082 -10000 0 -0.59 5 5
ANGPT4 0.036 0.037 0.13 92 -10000 0 92
response to hypoxia 0 0.007 0.037 3 -0.059 5 8
Tie2/Ang1/GRB14 0.007 0.094 -10000 0 -0.86 5 5
alpha5/beta1 Integrin 0.037 0.031 0.18 10 -10000 0 10
FGF2 0.019 0.006 0.12 1 -0.016 8 9
STAT5A (dimer) 0.06 0.095 -10000 0 -0.65 5 5
mol:L-citrulline 0.068 0.11 0.34 11 -0.55 5 16
AGTR1 0.029 0.025 0.13 37 -10000 0 37
MAPK14 0.027 0.098 -10000 0 -0.85 6 6
Tie2/SHP2 -0.001 0.11 -10000 0 -0.76 6 6
TEK -0.001 0.11 -10000 0 -0.82 6 6
RPS6KB1 0.038 0.091 -10000 0 -0.72 5 5
Angiotensin II/AT1 0.027 0.021 0.1 37 -10000 0 37
Tie2/Ang1/GRB2 0.017 0.09 -10000 0 -0.86 5 5
MAPK3 0.002 0.078 -10000 0 -0.79 5 5
MAPK1 0.003 0.078 -10000 0 -0.79 5 5
Tie2/Ang1/GRB7 0.016 0.091 -10000 0 -0.86 5 5
NFKB1 0.021 0.002 -10000 0 -10000 0 0
MAPK8 0.006 0.083 -10000 0 -0.84 5 5
PI3K 0.039 0.094 -10000 0 -0.82 5 5
FES 0.025 0.098 -10000 0 -0.89 5 5
Crk/Dok-R 0.029 0.092 -10000 0 -0.82 5 5
Tie2/Ang1/ABIN2 0.018 0.091 -10000 0 -0.85 5 5
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.039 0.085 -10000 0 -0.67 5 5
STAT5A 0.021 0.002 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.045 0.099 0.38 3 -0.69 5 8
Tie2/Ang2 0.046 0.095 -10000 0 -0.75 5 5
Tie2/Ang1 0.014 0.087 -10000 0 -0.88 5 5
FOXO1 0.04 0.086 0.37 1 -0.67 5 6
ELF1 0.025 0.012 -10000 0 -0.11 2 2
ELF2 0.011 0.081 -10000 0 -0.82 5 5
mol:Choline 0.008 0.08 -10000 0 -0.81 5 5
cell migration -0.003 0.031 0.092 2 -0.21 5 7
FYN 0.04 0.086 -10000 0 -0.66 5 5
DOK2 0.026 0.024 0.12 36 -10000 0 36
negative regulation of cell cycle 0.05 0.081 -10000 0 -0.49 5 5
ETS1 0.026 0.028 0.13 22 -0.25 3 25
PXN 0.043 0.093 0.4 4 -0.59 5 9
ITGB1 0.021 0.016 0.12 12 -10000 0 12
NOS3 0.065 0.11 0.36 9 -0.61 5 14
RAC1 0.018 0.008 -10000 0 -10000 0 0
TNF 0.024 0.028 0.13 11 -0.31 3 14
MAPKKK cascade 0.008 0.08 -10000 0 -0.81 5 5
RASA1 0.021 0.002 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.02 0.09 -10000 0 -0.82 5 5
NCK1 0.021 0.005 0.12 1 -10000 0 1
vasculogenesis 0.068 0.1 0.3 24 -0.49 5 29
mol:Phosphatidic acid 0.008 0.08 -10000 0 -0.81 5 5
mol:Angiotensin II 0.003 0.003 -10000 0 -10000 0 0
mol:NADP 0.068 0.11 0.34 11 -0.55 5 16
Rac1/GTP 0.036 0.08 -10000 0 -0.65 5 5
MMP2 0.009 0.084 -10000 0 -0.84 5 5
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.019 0.006 -10000 0 -10000 0 0
mol:PIP3 -0.006 0.013 -10000 0 -0.17 2 2
FRAP1 0.022 0.047 0.24 6 -0.31 1 7
AKT1 0.009 0.048 0.16 56 -0.16 2 58
INSR 0.021 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.023 0.007 0.096 1 -10000 0 1
mol:GTP 0.028 0.046 0.16 42 -10000 0 42
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.009 0.016 -10000 0 -0.18 1 1
TSC2 0.021 0.002 -10000 0 -10000 0 0
RHEB/GDP 0.01 0.02 -10000 0 -0.12 1 1
TSC1 0.021 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.019 0.013 -10000 0 -0.19 2 2
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.018 0.022 -10000 0 -0.2 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.019 0.007 -10000 0 -10000 0 0
RPS6KB1 0.026 0.058 0.22 21 -0.33 1 22
MAP3K5 -0.006 0.041 0.17 2 -0.19 31 33
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
apoptosis -0.006 0.041 0.17 2 -0.19 31 33
mol:LY294002 0 0 -10000 0 -0.001 2 2
EIF4B 0.022 0.058 0.22 25 -0.3 1 26
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.027 0.034 0.18 3 -0.27 1 4
eIF4E/eIF4G1/eIF4A1 0.013 0.019 -10000 0 -0.21 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.033 0.016 0.13 1 -0.18 2 3
mTOR/RHEB/GTP/Raptor/GBL 0 0.029 0.12 26 -10000 0 26
FKBP1A 0.02 0.004 -10000 0 -10000 0 0
RHEB/GTP 0.019 0.029 0.14 4 -10000 0 4
mol:Amino Acids 0 0 -10000 0 -0.001 2 2
FKBP12/Rapamycin 0.015 0.004 -10000 0 -10000 0 0
PDPK1 -0.009 0.016 0.18 2 -0.16 2 4
EIF4E 0.021 0.002 -10000 0 -10000 0 0
ASK1/PP5C 0.006 0.12 -10000 0 -0.53 32 32
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.005 0.03 -10000 0 -0.24 9 9
TSC1/TSC2 0.032 0.053 0.18 45 -10000 0 45
tumor necrosis factor receptor activity 0 0 0.001 2 -10000 0 2
RPS6 0.021 0.015 0.12 11 -10000 0 11
PPP5C 0.019 0.007 -10000 0 -10000 0 0
EIF4G1 0.021 0.003 -10000 0 -10000 0 0
IRS1 0.006 0.013 -10000 0 -0.21 2 2
INS 0.015 0.005 0.12 1 -10000 0 1
PTEN 0.018 0.007 -10000 0 -10000 0 0
PDK2 -0.009 0.015 0.18 2 -0.16 1 3
EIF4EBP1 0.047 0.095 -10000 0 -1 4 4
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
PPP2R5D 0.018 0.046 0.22 8 -0.29 1 9
peptide biosynthetic process -0.013 0.004 -10000 0 -10000 0 0
RHEB 0.017 0.009 -10000 0 -10000 0 0
EIF4A1 0.021 0.002 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.002 61 -10000 0 61
EEF2 -0.013 0.004 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.047 0.084 -10000 0 -0.93 4 4
Atypical NF-kappaB 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
BCL3/RelA 0.03 0.019 -10000 0 -10000 0 0
FBXW11 0.021 0.003 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.019 0.011 0.094 1 -0.13 3 4
NF kappa B1 p50/RelA/I kappa B alpha 0.017 0.047 0.17 1 -0.18 10 11
NFKBIA 0.01 0.014 0.13 5 -10000 0 5
MAPK14 0.021 0.002 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.02 0.004 -10000 0 -10000 0 0
ARRB2 0.009 0.001 -10000 0 -10000 0 0
REL 0.021 0.005 0.12 1 -10000 0 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.021 0.019 0.099 29 -10000 0 29
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.02 0.004 -10000 0 -10000 0 0
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.013 0.003 -10000 0 -10000 0 0
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
NFKB1 -0.012 0.002 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.009 0.04 0.12 1 -0.19 2 3
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.018 0.047 0.17 1 -0.18 11 12
SRC 0.02 0.004 -10000 0 -10000 0 0
PI3K 0.03 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.006 0.037 0.12 1 -0.18 1 2
IKBKB 0.021 0.003 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.021 0.003 -10000 0 -10000 0 0
SYK 0.022 0.013 0.12 10 -10000 0 10
I kappa B alpha/PIK3R1 0.015 0.047 0.18 1 -0.18 11 12
cell death 0.017 0.046 0.16 1 -0.18 11 12
NF kappa B1 p105/c-Rel 0.019 0.011 0.094 1 -0.13 3 4
LCK 0.039 0.042 0.12 129 -10000 0 129
BCL3 0.023 0.023 0.12 29 -10000 0 29
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 0.02 0.004 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.024 0.048 0.21 1 -0.22 2 3
NEF 0.001 0.004 -10000 0 -10000 0 0
NFKBIA 0.02 0.016 0.13 3 -0.073 13 16
BIRC3 -0.017 0.041 0.098 15 -0.28 13 28
CYCS 0.002 0.026 0.18 10 -10000 0 10
RIPK1 0.021 0.003 -10000 0 -10000 0 0
CD247 0.022 0.005 -10000 0 -10000 0 0
MAP2K7 0.013 0.077 -10000 0 -0.54 5 5
protein ubiquitination 0.011 0.053 0.2 9 -0.38 2 11
CRADD 0.021 0.002 -10000 0 -10000 0 0
DAXX 0.021 0.002 -10000 0 -10000 0 0
FAS 0.023 0.021 0.12 25 -10000 0 25
BID 0.008 0.02 0.17 5 -10000 0 5
NF-kappa-B/RelA/I kappa B alpha 0.04 0.033 0.17 1 -0.17 13 14
TRADD 0.021 0.002 -10000 0 -10000 0 0
MAP3K5 0.02 0.005 -10000 0 -10000 0 0
CFLAR 0.021 0.001 -10000 0 -10000 0 0
FADD 0.021 0.003 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.041 0.033 0.17 1 -0.17 13 14
MAPK8 0.013 0.068 -10000 0 -0.48 5 5
APAF1 0.021 0.002 -10000 0 -10000 0 0
TRAF1 0.021 0.003 -10000 0 -10000 0 0
TRAF2 0.021 0.003 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.013 0.016 0.22 1 -10000 0 1
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.005 0.049 -10000 0 -0.48 2 2
CHUK 0.011 0.055 0.2 9 -0.41 2 11
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.058 0.03 0.18 7 -10000 0 7
TCRz/NEF 0.016 0.021 -10000 0 -0.15 9 9
TNF 0.021 0.015 0.12 11 -10000 0 11
FASLG 0.005 0.024 -10000 0 -0.13 7 7
NFKB1 0.02 0.013 -10000 0 -0.074 11 11
TNFR1A/BAG4/TNF-alpha 0.028 0.049 -10000 0 -0.14 49 49
CASP6 0.025 0.077 -10000 0 -0.45 10 10
CASP7 -0.004 0.083 0.26 6 -0.32 23 29
RELA 0.02 0.013 -10000 0 -0.073 13 13
CASP2 0.017 0.009 -10000 0 -10000 0 0
CASP3 0 0.074 0.26 6 -0.37 15 21
TNFRSF1A 0.021 0.01 0.12 5 -10000 0 5
TNFR1A/BAG4 0.027 0.022 -10000 0 -0.16 7 7
CASP8 0.025 0.019 0.12 23 -10000 0 23
CASP9 0.019 0.008 0.12 1 -10000 0 1
MAP3K14 0.013 0.055 -10000 0 -0.37 3 3
APAF-1/Caspase 9 0.003 0.043 0.14 8 -0.2 11 19
BCL2 0.006 0.067 0.24 1 -0.46 4 5
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.019 0.007 -10000 0 -10000 0 0
SPHK1 0.021 0.011 0.12 6 -10000 0 6
GNAI2 0.021 0.003 -10000 0 -10000 0 0
mol:S1P 0.008 0.004 -10000 0 -10000 0 0
GNAO1 0.021 0.003 -10000 0 -10000 0 0
mol:Sphinganine-1-P -0.01 0.007 0.051 6 -10000 0 6
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.027 0.043 -10000 0 -0.19 2 2
GNAI3 0.019 0.008 0.12 1 -10000 0 1
G12/G13 0.026 0.012 -10000 0 -10000 0 0
S1PR3 0.04 0.04 0.12 122 -10000 0 122
S1PR2 0.024 0.019 0.12 21 -10000 0 21
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P -0.004 0.033 -10000 0 -0.24 2 2
S1PR5 0.017 0.008 -10000 0 -10000 0 0
S1PR4 0.021 0.011 0.12 6 -10000 0 6
GNAI1 0.017 0.008 -10000 0 -10000 0 0
S1P/S1P5/G12 0.004 0.057 -10000 0 -0.19 15 15
S1P/S1P3/Gq 0.017 0.049 -10000 0 -0.35 8 8
S1P/S1P4/Gi 0.007 0.065 0.14 1 -0.28 8 9
GNAQ 0.021 0.003 -10000 0 -10000 0 0
GNAZ 0.02 0.004 -10000 0 -10000 0 0
GNA14 0.021 0.003 -10000 0 -10000 0 0
GNA15 0.021 0.006 0.12 1 -10000 0 1
GNA12 0.018 0.008 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
GNA11 0.02 0.004 -10000 0 -10000 0 0
ABCC1 0.021 0.004 0.12 1 -10000 0 1
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.019 0.006 -10000 0 -10000 0 0
HDAC2 0.02 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.036 0.031 -10000 0 -0.12 1 1
forebrain development 0.034 0.082 0.32 5 -0.42 4 9
GNAO1 0.021 0.003 -10000 0 -10000 0 0
SMO/beta Arrestin2 0.032 0.027 0.11 63 -10000 0 63
SMO 0.027 0.033 0.12 64 -10000 0 64
ARRB2 0.021 0.002 -10000 0 -10000 0 0
GLI3/SPOP 0.007 0.061 -10000 0 -0.34 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
GSK3B 0.021 0.003 -10000 0 -10000 0 0
GNAI2 0.021 0.003 -10000 0 -10000 0 0
SIN3/HDAC complex 0.048 0.017 -10000 0 -10000 0 0
GNAI1 0.017 0.008 -10000 0 -10000 0 0
XPO1 0.022 0.002 -10000 0 -10000 0 0
GLI1/Su(fu) 0.021 0.052 -10000 0 -0.75 1 1
SAP30 0.02 0.006 0.12 1 -10000 0 1
mol:GDP 0.027 0.033 0.12 64 -10000 0 64
MIM/GLI2A 0.019 0.007 0.12 1 -10000 0 1
IFT88 0.02 0.005 -10000 0 -10000 0 0
GNAI3 0.019 0.008 0.12 1 -10000 0 1
GLI2 0.016 0.035 0.18 6 -0.24 1 7
GLI3 -0.001 0.06 -10000 0 -0.36 6 6
CSNK1D 0.02 0.004 -10000 0 -10000 0 0
CSNK1E 0.02 0.004 -10000 0 -10000 0 0
SAP18 0.02 0.005 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.02 0.005 -10000 0 -10000 0 0
GNG2 0.02 0.004 -10000 0 -10000 0 0
Gi family/GTP 0.004 0.04 -10000 0 -0.21 7 7
SIN3B 0.02 0.004 -10000 0 -10000 0 0
SIN3A 0.021 0.003 -10000 0 -10000 0 0
GLI3/Su(fu) 0.008 0.056 -10000 0 -0.41 6 6
GLI2/Su(fu) 0.016 0.04 -10000 0 -0.38 3 3
FOXA2 0.016 0.058 -10000 0 -0.61 3 3
neural tube patterning 0.034 0.082 0.32 5 -0.42 4 9
SPOP 0.021 0.002 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.031 0.04 -10000 0 -0.16 1 1
GNB1 0.019 0.007 -10000 0 -10000 0 0
CSNK1G2 0.02 0.004 -10000 0 -10000 0 0
CSNK1G3 0.021 0.002 -10000 0 -10000 0 0
MTSS1 0.019 0.007 0.12 1 -10000 0 1
embryonic limb morphogenesis 0.034 0.082 0.32 5 -0.42 4 9
SUFU 0.014 0.01 -10000 0 -10000 0 0
LGALS3 0.028 0.028 0.12 49 -10000 0 49
catabolic process 0.025 0.065 0.23 2 -0.47 4 6
GLI3A/CBP 0.017 0.05 0.12 2 -0.27 19 21
KIF3A 0.021 0.003 -10000 0 -10000 0 0
GLI1 0.034 0.083 0.34 4 -0.44 4 8
RAB23 0.021 0.002 -10000 0 -10000 0 0
CSNK1A1 0.021 0.003 -10000 0 -10000 0 0
IFT172 0.021 0.002 -10000 0 -10000 0 0
RBBP7 0.021 0.002 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.036 0.044 0.17 13 -0.16 1 14
GNAZ 0.021 0.004 -10000 0 -10000 0 0
RBBP4 0.019 0.006 -10000 0 -10000 0 0
CSNK1G1 0.021 0.003 -10000 0 -10000 0 0
PIAS1 0.021 0.003 -10000 0 -10000 0 0
PRKACA 0.02 0.004 -10000 0 -10000 0 0
GLI2/SPOP 0.025 0.041 0.19 2 -0.4 2 4
STK36 0.022 0.006 0.12 2 -10000 0 2
Gi family/GNB1/GNG2/GDP -0.003 0.055 -10000 0 -0.42 2 2
PTCH1 0.032 0.079 0.35 1 -0.64 1 2
MIM/GLI1 0.039 0.079 0.32 2 -0.69 1 3
CREBBP 0.017 0.05 0.12 2 -0.27 19 21
Su(fu)/SIN3/HDAC complex -0.009 0.09 0.16 1 -0.27 60 61
HIF-2-alpha transcription factor network

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
MMP14 0.035 0.12 -10000 0 -0.53 25 25
oxygen homeostasis 0.004 0.003 -10000 0 -10000 0 0
TCEB2 0.021 0.002 -10000 0 -10000 0 0
TCEB1 0.02 0.004 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.037 0.053 0.18 2 -10000 0 2
EPO 0.048 0.067 0.26 16 -10000 0 16
FIH (dimer) 0.022 0.01 -10000 0 -10000 0 0
APEX1 0.026 0.01 -10000 0 -10000 0 0
SERPINE1 0.045 0.072 0.25 18 -0.31 3 21
FLT1 0.014 0.12 -10000 0 -0.52 23 23
ADORA2A 0.038 0.057 0.27 6 -10000 0 6
germ cell development 0.05 0.062 0.27 5 -10000 0 5
SLC11A2 0.049 0.062 0.27 5 -10000 0 5
BHLHE40 0.049 0.069 0.27 5 -0.32 6 11
HIF1AN 0.022 0.01 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.051 0.061 0.2 18 -10000 0 18
ETS1 0.028 0.02 0.13 22 -10000 0 22
CITED2 0.008 0.11 -10000 0 -0.5 25 25
KDR 0.032 0.065 -10000 0 -0.53 7 7
PGK1 0.05 0.063 0.27 5 -10000 0 5
SIRT1 0.019 0.006 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.1 0.091 0.31 27 -10000 0 27
EPAS1 0.021 0.022 0.11 1 -10000 0 1
SP1 0.031 0.015 -10000 0 -10000 0 0
ABCG2 0.051 0.062 0.28 5 -10000 0 5
EFNA1 0.049 0.061 0.23 3 -10000 0 3
FXN 0.038 0.056 0.27 6 -10000 0 6
POU5F1 0.051 0.063 0.27 5 -10000 0 5
neuron apoptosis -0.099 0.089 -10000 0 -0.3 30 30
EP300 0.02 0.004 -10000 0 -10000 0 0
EGLN3 0.023 0.008 -10000 0 -10000 0 0
EGLN2 0.022 0.01 -10000 0 -10000 0 0
EGLN1 0.024 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.04 0.01 -10000 0 -10000 0 0
VHL 0.021 0.003 -10000 0 -10000 0 0
ARNT 0.026 0.009 -10000 0 -10000 0 0
SLC2A1 0.04 0.052 0.24 6 -10000 0 6
TWIST1 0.03 0.055 0.29 5 -0.29 2 7
ELK1 0.023 0.001 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.058 0.062 0.21 2 -10000 0 2
VEGFA 0.055 0.071 0.24 24 -10000 0 24
CREBBP 0.021 0.002 -10000 0 -10000 0 0
IGF1 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
NCK2 0.021 0.001 -10000 0 -10000 0 0
PTK2 0.019 0.006 -10000 0 -10000 0 0
CRKL -0.012 0.012 -10000 0 -0.13 6 6
GRB2/SOS1/SHC 0.042 0.014 -10000 0 -10000 0 0
HRAS 0.02 0.005 -10000 0 -10000 0 0
IRS1/Crk 0.016 0.018 -10000 0 -0.13 7 7
IGF-1R heterotetramer/IGF1/PTP1B 0.037 0.02 0.16 1 -0.12 6 7
AKT1 -0.015 0.033 0.14 22 -0.12 6 28
BAD -0.018 0.031 0.13 22 -0.12 6 28
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.013 0.013 -10000 0 -0.13 7 7
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.022 0.019 0.2 2 -0.13 7 9
RAF1 -0.002 0.044 0.26 1 -0.42 4 5
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.045 0.024 -10000 0 -0.13 6 6
YWHAZ 0.02 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.025 0.018 -10000 0 -0.14 7 7
PIK3CA 0.021 0.003 -10000 0 -10000 0 0
RPS6KB1 -0.016 0.032 0.14 21 -0.12 5 26
GNB2L1 0.023 0.016 0.12 15 -10000 0 15
positive regulation of MAPKKK cascade -0.008 0.042 0.23 2 -0.35 3 5
PXN 0.021 0.002 -10000 0 -10000 0 0
PIK3R1 0.021 0.003 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.03 0.006 -10000 0 -10000 0 0
HRAS/GTP 0.023 0.019 -10000 0 -0.12 6 6
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.057 0.027 -10000 0 -0.11 6 6
IGF-1R heterotetramer 0.021 0.009 -10000 0 -0.042 11 11
IGF-1R heterotetramer/IGF1/IRS/Nck 0.036 0.022 -10000 0 -0.13 7 7
Crk/p130 Cas/Paxillin 0.041 0.023 0.2 1 -0.13 7 8
IGF1R 0.021 0.009 -10000 0 -0.042 11 11
IGF1 0.022 0.008 0.16 1 -10000 0 1
IRS2/Crk 0.013 0.015 -10000 0 -0.13 7 7
PI3K 0.045 0.023 -10000 0 -0.13 6 6
apoptosis 0.017 0.034 -10000 0 -0.14 22 22
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
PRKCD 0.003 0.032 -10000 0 -0.24 9 9
RAF1/14-3-3 E 0.012 0.046 0.25 1 -0.37 4 5
BAD/14-3-3 -0.017 0.035 0.15 22 -10000 0 22
PRKCZ -0.013 0.029 0.13 18 -0.15 4 22
Crk/p130 Cas/Paxillin/FAK1 -0.026 0.024 0.12 10 -10000 0 10
PTPN1 0.02 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.008 0.036 -10000 0 -0.24 10 10
BCAR1 0.021 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.042 0.028 -10000 0 -0.12 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.021 0.001 -10000 0 -10000 0 0
IRS1/NCK2 0.022 0.021 0.12 8 -0.13 7 15
GRB10 0.017 0.008 -10000 0 -10000 0 0
PTPN11 -0.013 0.013 0.075 1 -0.13 7 8
IRS1 0.008 0.018 0.12 1 -0.14 7 8
IRS2 -0.012 0.014 0.075 1 -0.13 7 8
IGF-1R heterotetramer/IGF1 0.028 0.023 0.17 1 -0.18 7 8
GRB2 0.02 0.004 -10000 0 -10000 0 0
PDPK1 -0.014 0.031 0.17 14 -0.13 6 20
YWHAE 0.021 0.002 -10000 0 -10000 0 0
PRKD1 0.002 0.035 -10000 0 -0.23 11 11
SHC1 0.023 0.016 0.12 16 -10000 0 16
S1P3 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
PDGFRB 0.021 0.008 0.12 4 -10000 0 4
mol:S1P 0 0 -10000 0 -10000 0 0
S1P1/S1P/Gi 0.007 0.026 -10000 0 -0.19 8 8
GNAO1 0.021 0.004 -10000 0 -10000 0 0
S1P/S1P3/G12/G13 0.042 0.03 -10000 0 -10000 0 0
AKT1 0.012 0.071 -10000 0 -0.36 20 20
AKT3 0.02 0.056 -10000 0 -0.61 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.021 0.008 0.12 4 -10000 0 4
GNAI2 0.021 0.003 -10000 0 -10000 0 0
GNAI3 0.019 0.008 0.12 1 -10000 0 1
GNAI1 0.017 0.008 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.04 0.04 0.12 122 -10000 0 122
S1PR2 0.024 0.019 0.12 21 -10000 0 21
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.009 0.045 -10000 0 -0.21 4 4
MAPK3 0.011 0.048 -10000 0 -0.18 7 7
MAPK1 0.012 0.047 -10000 0 -0.2 4 4
JAK2 0.01 0.055 0.18 9 -0.24 9 18
CXCR4 0.014 0.049 -10000 0 -0.2 4 4
FLT1 0.021 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.013 0.006 -10000 0 -10000 0 0
SRC 0.009 0.046 -10000 0 -0.2 4 4
S1P/S1P3/Gi 0.009 0.046 -10000 0 -0.21 4 4
RAC1 0.018 0.008 -10000 0 -10000 0 0
RhoA/GTP 0.024 0.053 -10000 0 -0.31 2 2
VEGFA 0.034 0.034 0.12 79 -10000 0 79
S1P/S1P2/Gi 0.002 0.038 -10000 0 -0.18 9 9
VEGFR1 homodimer/VEGFA homodimer 0.039 0.025 -10000 0 -10000 0 0
RHOA 0.021 0.003 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.02 0.017 -10000 0 -0.16 3 3
GNAQ 0.021 0.003 -10000 0 -10000 0 0
GNAZ 0.021 0.004 -10000 0 -10000 0 0
G12/G13 0.026 0.012 -10000 0 -10000 0 0
GNA14 0.021 0.003 -10000 0 -10000 0 0
GNA15 0.021 0.006 0.12 1 -10000 0 1
GNA12 0.018 0.008 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
GNA11 0.02 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.015 0.047 -10000 0 -0.31 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 0.032 0.065 -10000 0 -0.18 43 43
Ran/GTP/Exportin 1/HDAC1 -0.013 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.011 0.069 -10000 0 -0.21 44 44
SUMO1 0.021 0.001 -10000 0 -10000 0 0
ZFPM1 0.021 0.002 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.008 0.002 -10000 0 -10000 0 0
FKBP3 0.02 0.004 -10000 0 -10000 0 0
Histones 0.035 0.046 -10000 0 -0.16 3 3
YY1/LSF 0.016 0.036 -10000 0 -0.21 5 5
SMG5 0.021 0.003 -10000 0 -10000 0 0
RAN 0.021 0.002 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.005 0.042 -10000 0 -0.15 43 43
I kappa B alpha/HDAC1 0.015 0.045 -10000 0 -0.15 24 24
SAP18 0.02 0.005 -10000 0 -10000 0 0
RELA 0.008 0.046 0.13 3 -0.32 1 4
HDAC1/Smad7 0.03 0.02 -10000 0 -10000 0 0
RANGAP1 0.02 0.004 -10000 0 -10000 0 0
HDAC3/TR2 0.019 0.041 -10000 0 -0.15 7 7
NuRD/MBD3 Complex 0.009 0.03 -10000 0 -0.48 1 1
NF kappa B1 p50/RelA 0.015 0.058 0.17 3 -0.3 5 8
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.021 0.008 0.12 4 -10000 0 4
GATA1 0.02 0.008 0.12 3 -10000 0 3
Mad/Max 0.03 0.007 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.002 0.053 -10000 0 -0.39 1 1
RBBP7 0.021 0.002 -10000 0 -10000 0 0
NPC 0.012 0.001 -10000 0 -10000 0 0
RBBP4 0.019 0.006 -10000 0 -10000 0 0
MAX 0.02 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.021 0.003 -10000 0 -10000 0 0
NFKBIA 0.006 0.031 -10000 0 -0.11 42 42
KAT2B 0.021 0.005 0.12 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.006 0.03 -10000 0 -10000 0 0
SIN3 complex 0.048 0.018 -10000 0 -10000 0 0
SMURF1 0.017 0.009 -10000 0 -10000 0 0
CHD3 0.021 0.003 -10000 0 -10000 0 0
SAP30 0.021 0.006 0.12 1 -10000 0 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.021 0.002 -10000 0 -10000 0 0
YY1/HDAC3 0.006 0.04 -10000 0 -0.18 9 9
YY1/HDAC2 0.017 0.033 -10000 0 -0.2 5 5
YY1/HDAC1 0.014 0.036 -10000 0 -0.22 5 5
NuRD/MBD2 Complex (MeCP1) 0.008 0.031 -10000 0 -0.29 3 3
PPARG 0.001 0.053 0.15 3 -0.19 44 47
HDAC8/hEST1B 0.04 0.01 -10000 0 -10000 0 0
UBE2I 0.021 0.002 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.021 0.003 -10000 0 -10000 0 0
TNFRSF1A 0.021 0.01 0.12 5 -10000 0 5
HDAC3/SMRT (N-CoR2) 0.018 0.041 -10000 0 -0.15 8 8
MBD3L2 0.015 0.003 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.03 0.019 -10000 0 -10000 0 0
CREBBP 0.021 0.002 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.006 0.052 -10000 0 -10000 0 0
HDAC1 0.019 0.006 -10000 0 -10000 0 0
HDAC3 0.006 0.032 -10000 0 -10000 0 0
HDAC2 0.02 0.004 -10000 0 -10000 0 0
YY1 0.01 0.004 -10000 0 -10000 0 0
HDAC8 0.021 0.002 -10000 0 -10000 0 0
SMAD7 0.021 0.003 -10000 0 -10000 0 0
NCOR2 0.021 0.002 -10000 0 -10000 0 0
MXD1 0.021 0.001 -10000 0 -10000 0 0
STAT3 0.013 0.003 -10000 0 -10000 0 0
NFKB1 0.021 0.002 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.021 0.001 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.024 0.037 -10000 0 -0.19 5 5
YY1/SAP30/HDAC1 0.024 0.037 -10000 0 -0.2 5 5
EP300 0.02 0.004 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.013 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.031 -10000 0 -0.11 42 42
histone deacetylation 0.008 0.031 -10000 0 -0.29 3 3
STAT3 (dimer non-phopshorylated)/HDAC3 0.009 0.034 -10000 0 -0.17 1 1
nuclear export -0.04 0.01 -10000 0 -10000 0 0
PRKACA 0.02 0.004 -10000 0 -10000 0 0
GATAD2B 0.021 0.002 -10000 0 -10000 0 0
GATAD2A 0.02 0.004 -10000 0 -10000 0 0
GATA2/HDAC3 0.02 0.041 0.17 1 -0.15 7 8
GATA1/HDAC1 0.027 0.011 -10000 0 -10000 0 0
GATA1/HDAC3 0.016 0.04 -10000 0 -0.16 7 7
CHD4 0.02 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.019 0.049 -10000 0 -0.16 44 44
SIN3/HDAC complex/Mad/Max 0.002 0.048 -10000 0 -0.26 11 11
NuRD Complex 0.006 0.056 -10000 0 -0.24 6 6
positive regulation of chromatin silencing 0.033 0.044 -10000 0 -0.16 3 3
SIN3B 0.02 0.004 -10000 0 -10000 0 0
MTA2 0.021 0.003 -10000 0 -10000 0 0
SIN3A 0.021 0.003 -10000 0 -10000 0 0
XPO1 0.021 0.001 -10000 0 -10000 0 0
SUMO1/HDAC1 0.025 0.025 -10000 0 -0.24 1 1
HDAC complex 0.046 0.02 -10000 0 -10000 0 0
GATA1/Fog1 0.03 0.007 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.036 0.016 -10000 0 -10000 0 0
TNF 0.021 0.015 0.12 11 -10000 0 11
negative regulation of cell growth 0.002 0.047 -10000 0 -0.26 11 11
NuRD/MBD2/PRMT5 Complex 0.008 0.031 -10000 0 -0.29 3 3
Ran/GTP/Exportin 1 0.029 0.023 -10000 0 -0.23 1 1
NF kappa B/RelA/I kappa B alpha 0.001 0.06 -10000 0 -0.22 42 42
SIN3/HDAC complex/NCoR1 -0.001 0.057 -10000 0 -0.26 7 7
TFCP2 0.021 0.003 -10000 0 -10000 0 0
NR2C1 0.021 0.002 -10000 0 -10000 0 0
MBD3 0.02 0.004 -10000 0 -10000 0 0
MBD2 0.021 0.003 -10000 0 -10000 0 0
LPA4-mediated signaling events

Figure S123.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S123.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.009 0.003 -10000 0 -10000 0 0
ADCY5 -0.009 0.003 -10000 0 -10000 0 0
ADCY6 -0.009 0.002 -10000 0 -10000 0 0
ADCY7 -0.01 0.002 -10000 0 -10000 0 0
ADCY1 -0.006 0.005 -10000 0 -10000 0 0
ADCY2 -0.009 0.003 -10000 0 -10000 0 0
ADCY3 -0.01 0.002 -10000 0 -10000 0 0
ADCY8 -0.008 0.005 0.023 12 -10000 0 12
PRKCE -0.006 0.001 -10000 0 -10000 0 0
ADCY9 -0.01 0.002 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.007 0.065 0.17 24 -0.24 21 45
Regulation of cytoplasmic and nuclear SMAD2/3 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
SMAD4 0.021 0.003 -10000 0 -10000 0 0
SMAD2 -0.007 0.038 0.15 1 -0.17 17 18
SMAD3 0.014 0.026 0.12 12 -10000 0 12
SMAD3/SMAD4 0.022 0.048 -10000 0 -0.41 6 6
SMAD4/Ubc9/PIASy 0.04 0.01 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.031 0.048 -10000 0 -0.2 6 6
PPM1A 0.02 0.004 -10000 0 -10000 0 0
CALM1 0.02 0.005 -10000 0 -10000 0 0
SMAD2/SMAD4 0.004 0.041 -10000 0 -0.17 19 19
MAP3K1 0.024 0.018 0.12 21 -10000 0 21
TRAP-1/SMAD4 0.029 0.017 -10000 0 -0.16 5 5
MAPK3 0.021 0.002 -10000 0 -10000 0 0
MAPK1 0.021 0.003 -10000 0 -10000 0 0
NUP214 0.021 0.003 -10000 0 -10000 0 0
CTDSP1 0.021 0.004 0.12 1 -10000 0 1
CTDSP2 0.019 0.006 -10000 0 -10000 0 0
CTDSPL 0.021 0.002 -10000 0 -10000 0 0
KPNB1 0.021 0.002 -10000 0 -10000 0 0
TGFBRAP1 0.021 0.002 -10000 0 -10000 0 0
UBE2I 0.021 0.002 -10000 0 -10000 0 0
NUP153 0.021 0.003 -10000 0 -10000 0 0
KPNA2 0.021 0.003 -10000 0 -10000 0 0
PIAS4 0.02 0.004 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.046 0.021 -10000 0 -0.11 2 2
HDAC3 0.021 0.002 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.014 0.003 -10000 0 -10000 0 0
GATA1/HDAC4 0.029 0.007 -10000 0 -10000 0 0
GATA1/HDAC5 0.03 0.006 -10000 0 -10000 0 0
GATA2/HDAC5 0.031 0.007 0.11 4 -10000 0 4
HDAC5/BCL6/BCoR 0.041 0.008 -10000 0 -10000 0 0
HDAC9 0.018 0.008 -10000 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.04 0.01 -10000 0 -10000 0 0
HDAC4/ANKRA2 0.03 0.006 -10000 0 -10000 0 0
HDAC5/YWHAB 0.03 0.007 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.008 0.002 -10000 0 -10000 0 0
GATA2 0.021 0.008 0.12 4 -10000 0 4
HDAC4/RFXANK 0.03 0.01 -10000 0 -10000 0 0
BCOR 0.021 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.02 0.004 -10000 0 -10000 0 0
HDAC5 0.021 0.002 -10000 0 -10000 0 0
GNB1/GNG2 0.027 0.015 -10000 0 -0.16 2 2
Histones 0.021 0.035 -10000 0 -0.39 1 1
ADRBK1 0.021 0.003 -10000 0 -10000 0 0
HDAC4 0.021 0.003 -10000 0 -10000 0 0
XPO1 0.021 0.001 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.031 0.004 -10000 0 -10000 0 0
HDAC4/Ubc9 0.03 0.006 -10000 0 -10000 0 0
HDAC7 0.02 0.004 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.031 0.004 -10000 0 -10000 0 0
TUBA1B 0.02 0.004 -10000 0 -10000 0 0
HDAC6 0.021 0.001 -10000 0 -10000 0 0
HDAC5/RFXANK 0.031 0.009 0.11 5 -10000 0 5
CAMK4 0.015 0.01 -10000 0 -10000 0 0
Tubulin/HDAC6 0.041 0.011 -10000 0 -0.13 1 1
SUMO1 0.021 0.001 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.02 0.004 -10000 0 -10000 0 0
GATA1 0.02 0.008 0.12 3 -10000 0 3
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.021 0.002 -10000 0 -10000 0 0
NR3C1 0.021 0.002 -10000 0 -10000 0 0
SUMO1/HDAC4 0.028 0.024 -10000 0 -0.23 1 1
SRF 0.021 0.002 -10000 0 -10000 0 0
HDAC4/YWHAB 0.029 0.008 -10000 0 -10000 0 0
Tubulin 0.03 0.01 -10000 0 -0.16 1 1
HDAC4/14-3-3 E 0.03 0.006 -10000 0 -10000 0 0
GNB1 0.019 0.007 -10000 0 -10000 0 0
RANGAP1 0.02 0.004 -10000 0 -10000 0 0
BCL6/BCoR 0.03 0.006 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.041 0.009 -10000 0 -10000 0 0
HDAC4/SRF -0.006 0.077 -10000 0 -0.13 180 180
HDAC4/ER alpha 0.029 0.011 -10000 0 -0.16 1 1
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.021 0.035 -10000 0 -0.39 1 1
cell motility 0.04 0.011 -10000 0 -0.13 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.021 0.002 -10000 0 -10000 0 0
HDAC7/HDAC3 0.03 0.006 -10000 0 -10000 0 0
BCL6 0.021 0.003 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.02 0.003 -10000 0 -10000 0 0
Hsp90/HDAC6 0.03 0.007 -10000 0 -10000 0 0
ESR1 0.02 0.005 -10000 0 -10000 0 0
HDAC6/HDAC11 0.031 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.029 0.023 -10000 0 -0.23 1 1
NPC 0.012 0.001 -10000 0 -10000 0 0
MEF2C 0.02 0.004 -10000 0 -10000 0 0
RAN 0.021 0.002 -10000 0 -10000 0 0
HDAC4/MEF2C 0.056 0.029 -10000 0 -0.12 13 13
GNG2 0.02 0.004 -10000 0 -10000 0 0
NCOR2 0.021 0.002 -10000 0 -10000 0 0
TUBB2A 0.021 0.003 -10000 0 -10000 0 0
HDAC11 0.021 0.002 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
RANBP2 0.021 0.001 -10000 0 -10000 0 0
ANKRA2 0.021 0.002 -10000 0 -10000 0 0
RFXANK 0.021 0.01 0.12 5 -10000 0 5
nuclear import -0.024 0.007 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.006 0.025 0.14 24 -10000 0 24
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.001 0.028 0.12 3 -0.15 4 7
AP2 0.027 0.011 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.02 0.017 -10000 0 -10000 0 0
CLTB 0.021 0.002 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.01 0.006 -10000 0 -10000 0 0
CD4 0.022 0.014 0.12 11 -10000 0 11
CLTA 0.02 0.004 -10000 0 -10000 0 0
mol:GTP -0.003 0.002 -10000 0 -10000 0 0
ARFGAP1 -0.006 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.008 -10000 0 -10000 0 0
ARF1/GTP 0.023 0.011 -10000 0 -0.068 2 2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.003 0.008 -10000 0 -10000 0 0
mol:Choline 0 0.008 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.018 0.012 -10000 0 -0.019 62 62
DDEF1 0 0.013 -10000 0 -10000 0 0
ARF1/GDP 0.001 0.016 -10000 0 -0.086 19 19
AP2M1 0.021 0.003 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.008 0.006 -10000 0 -10000 0 0
Rac/GTP 0.011 0.009 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.023 0.016 -10000 0 -10000 0 0
ARFIP2 0.019 0.008 -10000 0 -0.035 3 3
COPA 0.021 0.002 -10000 0 -10000 0 0
RAC1 0.018 0.008 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.004 0.025 -10000 0 -0.14 14 14
ARF1/GTP/ARHGAP10 0.012 0.009 -10000 0 -10000 0 0
GGA3 0.02 0.004 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.015 0.016 -10000 0 -0.17 1 1
AP2A1 0.019 0.007 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.007 0.015 -10000 0 -0.18 4 4
ARF1/GDP/Membrin 0.017 0.016 -10000 0 -0.22 1 1
Arfaptin 2/Rac/GDP 0.023 0.012 -10000 0 -10000 0 0
CYTH2 0.019 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.023 0.015 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.013 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 0.002 0.037 -10000 0 -0.18 10 10
PLD2 0 0.008 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE -0.006 0.001 -10000 0 -10000 0 0
PIP5K1A 0 0.009 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.007 0.024 -10000 0 -0.13 2 2
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0 0.008 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 -0.006 0.001 -10000 0 -10000 0 0
GOSR2 0.008 0.007 -10000 0 -10000 0 0
USO1 0.004 0.035 -10000 0 -0.33 7 7
GBF1 -0.015 0.082 -10000 0 -0.31 46 46
ARF1/GTP/Arfaptin 2 0.024 0.017 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.036 0.019 -10000 0 -10000 0 0
Circadian rhythm pathway

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
chromatin modification 0.044 0.045 -10000 0 -10000 0 0
CLOCK 0.021 0.006 -10000 0 -10000 0 0
TIMELESS/CRY2 0.029 0.037 -10000 0 -10000 0 0
DEC1/BMAL1 0.027 0.006 -10000 0 -10000 0 0
ATR 0.021 0.003 -10000 0 -10000 0 0
NR1D1 0.015 0.022 -10000 0 -10000 0 0
ARNTL 0.022 0.005 -10000 0 -10000 0 0
TIMELESS 0.02 0.033 -10000 0 -10000 0 0
NPAS2 0.023 0.003 -10000 0 -10000 0 0
CRY2 0.02 0.004 -10000 0 -10000 0 0
mol:CO -0.007 0.01 -10000 0 -10000 0 0
CHEK1 0.029 0.028 0.12 52 -10000 0 52
mol:HEME 0.007 0.01 -10000 0 -10000 0 0
PER1 0.021 0.002 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.044 0.029 -10000 0 -0.13 12 12
BMAL1/CLOCK 0.018 0.05 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.044 0.045 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.044 0.046 -10000 0 -10000 0 0
mol:NADPH 0.007 0.01 -10000 0 -10000 0 0
PER1/TIMELESS 0.03 0.038 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.015 0.002 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.014 0.004 -10000 0 -10000 0 0
SNTA1 0.02 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.013 0.005 0.02 1 -10000 0 1
MAPK12 -0.007 0.002 -10000 0 -10000 0 0
CCND1 0.008 0.014 0.16 1 -10000 0 1
p38 gamma/SNTA1 -0.003 0.035 0.18 19 -10000 0 19
MAP2K3 0.021 0.004 0.12 1 -10000 0 1
PKN1 0.02 0.004 -10000 0 -10000 0 0
G2/M transition checkpoint -0.007 0.002 -10000 0 -10000 0 0
MAP2K6 -0.004 0.001 -10000 0 -10000 0 0
MAPT -0.002 0.039 0.16 8 -0.22 5 13
MAPK13 -0.012 0.004 0.051 1 -10000 0 1
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.004 0.001 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.021 0.005 -10000 0 -0.12 1 1
PI3K Class IB/PDE3B 0.021 0.005 0.12 1 -10000 0 1
PDE3B 0.021 0.005 0.12 1 -10000 0 1
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.019 0.006 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.014 0.006 -9999 0 -10000 0 0
MDM2/SUMO1 0.028 0.023 -9999 0 -0.24 1 1
HDAC4 0.021 0.003 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.013 0.007 -9999 0 -10000 0 0
SUMO1 0.021 0.001 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.007 0.011 -9999 0 -0.27 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0 0.015 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.021 0.002 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.021 0.001 -9999 0 -10000 0 0
SUMO1/HDAC4 0.028 0.024 -9999 0 -0.23 1 1
SUMO1/HDAC1 0.025 0.025 -9999 0 -0.24 1 1
RANGAP1 0.02 0.004 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.05 0.015 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.008 0.002 -9999 0 -10000 0 0
Ran/GTP 0.018 0.022 -9999 0 -0.25 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.02 0.004 -9999 0 -10000 0 0
UBE2I 0.021 0.002 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.014 0.021 -9999 0 -0.23 1 1
NPC 0.012 0.001 -9999 0 -10000 0 0
PIAS2 0.021 0.003 -9999 0 -10000 0 0
PIAS1 0.021 0.003 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.028 0.01 -9999 0 -9999 0 0
FBXW11 0.021 0.003 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.021 0.003 -9999 0 -9999 0 0
CHUK 0.019 0.006 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.05 0.025 -9999 0 -9999 0 0
NFKB1 0.021 0.002 -9999 0 -9999 0 0
MAP3K14 0.021 0.002 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.027 0.01 -9999 0 -9999 0 0
RELB 0.019 0.007 -9999 0 -9999 0 0
NFKB2 0.019 0.006 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.023 0.011 -9999 0 -9999 0 0
regulation of B cell activation 0.023 0.011 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 660 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.WY.A85E TCGA.WY.A85D TCGA.WY.A85C TCGA.WY.A85B
109_MAP3K5 0.014 -0.16 -0.13 -0.16
47_PPARGC1A 0.021 0.021 0.021 0.021
105_BMP4 0.021 0.021 0.021 0.021
105_BMP6 0.021 0.021 0.021 0.021
105_BMP7 0.021 0.021 0.021 0.021
105_BMP2 0.12 0.12 0.12 0.12
131_RELN/VLDLR 0.054 0.054 0.054 0.054
30_TGFB1/TGF beta receptor Type II 0.021 0.021 0.02 0.021
84_STAT5B 0.019 0.019 0.055 0.026
84_STAT5A 0.019 0.019 0.055 0.026
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/GBMLGG-TP/22312676/GBMLGG-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/GBMLGG-TP/22506578/GDAC_Gistic2Report_22534360/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 © 2016 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle